#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
CHD5	26038	genome.wustl.edu	37	1	6209365	6209365	+	Missense_Mutation	SNP	C	C	T			TCGA-DX-A48N-01A-11D-A307-09	TCGA-DX-A48N-10A-01D-A307-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	93d25a05-5221-452e-a4b8-f1504d48e89c	a1a1386f-c8ff-4c7c-b1ee-19a86bd40af2	g.chr1:6209365C>T	ENST00000262450.3	-	8	1201	c.1102G>A	c.(1102-1104)Gta>Ata	p.V368I	CHD5_ENST00000378021.1_5'UTR	NM_015557.2	NP_056372.1	O00258	WRB_HUMAN	chromodomain helicase DNA binding protein 5	0					tail-anchored membrane protein insertion into ER membrane (GO:0071816)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)				breast(3)|central_nervous_system(3)|liver(1)|lung(1)|ovary(4)|pancreas(1)|skin(1)|upper_aerodigestive_tract(2)	16	Ovarian(185;0.0634)	all_cancers(23;5.36e-32)|all_epithelial(116;2.32e-17)|all_neural(13;3.68e-06)|all_lung(118;3.94e-06)|all_hematologic(16;2.39e-05)|Lung NSC(185;5.33e-05)|Acute lymphoblastic leukemia(12;0.000372)|Glioma(11;0.00127)|Renal(390;0.00188)|Colorectal(325;0.00342)|Breast(487;0.00373)|Hepatocellular(190;0.0218)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.15)		Epithelial(90;3.08e-37)|GBM - Glioblastoma multiforme(13;1.36e-31)|OV - Ovarian serous cystadenocarcinoma(86;7.7e-19)|Colorectal(212;9.97e-08)|COAD - Colon adenocarcinoma(227;1.07e-05)|Kidney(185;6.16e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.00109)|BRCA - Breast invasive adenocarcinoma(365;0.0012)|STAD - Stomach adenocarcinoma(132;0.00346)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.193)		TCCAGGCATACGAGATGGTAG	0.652													ENSG00000116254																																					0													67.0	54.0	58.0					1																	6209365		2203	4300	6503	SO:0001583	missense	0			-	AF425231	CCDS57.1	1p36.3	2013-01-28			ENSG00000116254	ENSG00000116254		"""Zinc fingers, PHD-type"""	16816	protein-coding gene	gene with protein product		610771				11889561, 12592387	Standard	NM_015557		Approved		uc001amb.2	Q8TDI0	OTTHUMG00000000952	ENST00000262450.3:c.1102G>A	1.37:g.6209365C>T	ENSP00000262450:p.Val368Ile		A8KAP8|A8MQ44|D3DSH9|O60740	Missense_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_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.V368I	ENST00000262450.3	37	c.1102	CCDS57.1	1	.	.	.	.	.	.	.	.	.	.	C	27.9	4.874795	0.91664	.	.	ENSG00000116254	ENST00000262450	D	0.84589	-1.87	4.03	4.03	0.46877	Zinc finger, PHD-finger (2);Zinc finger, RING/FYVE/PHD-type (1);Zinc finger, PHD-type, conserved site (1);Zinc finger, RING-type (1);Zinc finger, PHD-type (1);Zinc finger, FYVE/PHD-type (1);	0.000000	0.64402	U	0.000014	D	0.89494	0.6731	L	0.48642	1.525	0.80722	D	1	D	0.76494	0.999	D	0.74674	0.984	D	0.90845	0.4726	10	0.66056	D	0.02	-30.1727	16.5458	0.84445	0.0:1.0:0.0:0.0	.	368	Q8TDI0	CHD5_HUMAN	I	368	ENSP00000262450:V368I	ENSP00000262450:V368I	V	-	1	0	CHD5	6131952	1.000000	0.71417	0.970000	0.41538	0.750000	0.42670	5.995000	0.70631	1.995000	0.58328	0.313000	0.20887	GTA	-	CHD5	-	pfam_Znf_PHD-finger,superfamily_Znf_FYVE_PHD,smart_Znf_PHD,pfscan_Znf_PHD-finger		0.652	CHD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	CHD5	HGNC	protein_coding	OTTHUMT00000002823.2	0	0	0	30	30	32	0.00	0.00	C	NM_015557		6209365	-1	24	14	29	24	tier1	no_errors	ENST00000262450	ensembl	human	known	74_37	missense	45.28	36.84	SNP	1.000	T	24	29
BTN2A1	11120	genome.wustl.edu	37	6	26466202	26466202	+	Splice_Site	SNP	G	G	A	rs145303049	byFrequency	TCGA-DX-A48N-01A-11D-A307-09	TCGA-DX-A48N-10A-01D-A307-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	93d25a05-5221-452e-a4b8-f1504d48e89c	a1a1386f-c8ff-4c7c-b1ee-19a86bd40af2	g.chr6:26466202G>A	ENST00000312541.5	+	6	1203		c.e6+1		BTN2A1_ENST00000541522.1_Splice_Site|BTN2A1_ENST00000429381.1_Splice_Site|BTN2A1_ENST00000469185.1_Splice_Site	NM_007049.3|NM_078476.2	NP_008980.1|NP_510961.1	Q7KYR7	BT2A1_HUMAN	butyrophilin, subfamily 2, member A1						lipid metabolic process (GO:0006629)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)				breast(3)|central_nervous_system(1)|cervix(1)|endometrium(2)|large_intestine(2)|lung(9)|ovary(2)|prostate(1)|skin(3)|urinary_tract(3)	27						GAAGAATTGCGTAAGTTTAGC	0.373													ENSG00000112763	G|||	2	0.000399361	0.0	0.0	5008	,	,		25161	0.0		0.001	False		,,,				2504	0.001																0								G	,,,	0,4406		0,0,2203	210.0	188.0	196.0		,,,	3.8	1.0	6	dbSNP_134	196	3,8597	3.0+/-9.4	0,3,4297	yes	splice-5,splice-5,splice-5,splice-5	BTN2A1	NM_001197233.1,NM_001197234.1,NM_007049.3,NM_078476.2	,,,	0,3,6500	AA,AG,GG		0.0349,0.0,0.0231	,,,	,,,	26466202	3,13003	2203	4300	6503	SO:0001630	splice_region_variant	0			GMAF=0.0005	U90543	CCDS4613.1, CCDS47390.1, CCDS56404.1, CCDS56405.1	6p22.1	2014-01-14			ENSG00000112763	ENSG00000112763		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Butyrophilins"""	1136	protein-coding gene	gene with protein product		613590				9382921, 9149941	Standard	NM_007049		Approved	BT2.1, BTF1, BTN2.1	uc003nib.2	Q7KYR7	OTTHUMG00000014457	ENST00000312541.5:c.955+1G>A	6.37:g.26466202G>A			B4DLP9|E9PGR4|O00475|P78408|Q59EN4|Q7KYQ7|Q7Z386|Q96AV7|Q9NU62	Splice_Site	SNP	-	e5+1	ENST00000312541.5	37	c.955+1	CCDS4613.1	6	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	G	8.125	0.781811	0.16120	0.0	3.49E-4	ENSG00000112763	ENST00000312541;ENST00000541522;ENST00000429381;ENST00000265424;ENST00000469185;ENST00000480218	.	.	.	3.84	3.84	0.44239	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	11.9579	0.52991	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	BTN2A1	26574181	1.000000	0.71417	0.980000	0.43619	0.026000	0.11368	5.107000	0.64603	2.057000	0.61298	0.491000	0.48974	.	rs145303049	BTN2A1	-	-		0.373	BTN2A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	BTN2A1	HGNC	protein_coding	OTTHUMT00000040122.2	0	0	0	81	81	49	0.00	0.00	G	NM_007049	Intron	26466202	+1	50	15	56	47	tier1	no_errors	ENST00000312541	ensembl	human	known	74_37	splice_site	47.17	24.19	SNP	0.995	A	50	56
NDNF	79625	genome.wustl.edu	37	4	121958270	121958270	+	Missense_Mutation	SNP	C	C	T			TCGA-DX-A48N-01A-11D-A307-09	TCGA-DX-A48N-10A-01D-A307-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	93d25a05-5221-452e-a4b8-f1504d48e89c	a1a1386f-c8ff-4c7c-b1ee-19a86bd40af2	g.chr4:121958270C>T	ENST00000379692.4	-	4	1382	c.856G>A	c.(856-858)Gtt>Att	p.V286I	NDNF_ENST00000506900.1_5'UTR	NM_024574.3	NP_078850.3	Q8TB73	NDNF_HUMAN	neuron-derived neurotrophic factor	286	Fibronectin type-III 1.				cell growth (GO:0016049)|extracellular matrix organization (GO:0030198)|negative regulation of neuron apoptotic process (GO:0043524)|neuron migration (GO:0001764)|peptide cross-linking via chondroitin 4-sulfate glycosaminoglycan (GO:0019800)|positive regulation of cell-substrate adhesion (GO:0010811)|positive regulation of neuron projection development (GO:0010976)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)	glycosaminoglycan binding (GO:0005539)|heparin binding (GO:0008201)			breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(10)|prostate(3)|skin(1)|urinary_tract(1)	29						TGAATATCAACCTTGGGCCTG	0.443													ENSG00000173376																																					0													98.0	98.0	98.0					4																	121958270		2203	4300	6503	SO:0001583	missense	0			-	BC019351	CCDS3717.2	4q27	2011-07-05	2011-07-05	2011-07-05	ENSG00000173376	ENSG00000173376			26256	protein-coding gene	gene with protein product			"""chromosome 4 open reading frame 31"""	C4orf31		12975309, 20969804	Standard	NM_024574		Approved	FLJ23191	uc003idq.1	Q8TB73	OTTHUMG00000132973	ENST00000379692.4:c.856G>A	4.37:g.121958270C>T	ENSP00000369014:p.Val286Ile		A8K0Q0|Q6UWE5|Q9H5P7	Missense_Mutation	SNP	pfam_DUF2369,superfamily_Fibronectin_type3,smart_Fibronectin_type3	p.V286I	ENST00000379692.4	37	c.856	CCDS3717.2	4	.	.	.	.	.	.	.	.	.	.	C	11.14	1.550249	0.27652	.	.	ENSG00000173376	ENST00000379692	.	.	.	5.77	4.03	0.46877	.	0.637137	0.16890	N	0.195350	T	0.57975	0.2090	L	0.54323	1.7	0.47123	D	0.999323	B	0.14012	0.009	B	0.22152	0.038	T	0.53718	-0.8399	9	0.51188	T	0.08	-3.8459	11.3249	0.49442	0.0:0.8042:0.1276:0.0682	.	286	Q8TB73	NDNF_HUMAN	I	286	.	ENSP00000369014:V286I	V	-	1	0	NDNF	122177720	0.986000	0.35501	0.608000	0.28969	0.979000	0.70002	2.595000	0.46197	0.764000	0.33197	0.655000	0.94253	GTT	-	NDNF	-	superfamily_Fibronectin_type3,smart_Fibronectin_type3		0.443	NDNF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NDNF	HGNC	protein_coding	OTTHUMT00000256532.2	0	0	0	18	18	92	0.00	0.00	C	NM_024574		121958270	-1	5	23	24	81	tier1	no_errors	ENST00000379692	ensembl	human	known	74_37	missense	17.24	22.12	SNP	0.956	T	5	24
PIK3AP1	118788	genome.wustl.edu	37	10	98363808	98363808	+	Splice_Site	SNP	T	T	A			TCGA-DX-A48N-01A-11D-A307-09	TCGA-DX-A48N-10A-01D-A307-09	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	93d25a05-5221-452e-a4b8-f1504d48e89c	a1a1386f-c8ff-4c7c-b1ee-19a86bd40af2	g.chr10:98363808T>A	ENST00000339364.5	-	15	2290		c.e15-2		PIK3AP1_ENST00000371110.2_Splice_Site|PIK3AP1_ENST00000371109.3_Splice_Site	NM_152309.2	NP_689522.2	Q6ZUJ8	BCAP_HUMAN	phosphoinositide-3-kinase adaptor protein 1						negative regulation of toll-like receptor signaling pathway (GO:0034122)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of toll-like receptor signaling pathway (GO:0034123)|regulation of inflammatory response (GO:0050727)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 7 signaling pathway (GO:0034154)|toll-like receptor 9 signaling pathway (GO:0034162)	cytosol (GO:0005829)|membrane (GO:0016020)|plasma membrane (GO:0005886)	phosphatidylinositol 3-kinase regulatory subunit binding (GO:0036312)			NS(1)|autonomic_ganglia(1)|breast(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(27)|ovary(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(4)	52		Colorectal(252;0.0442)		Epithelial(162;6.29e-08)|all cancers(201;3.18e-06)		TTGTGCTACCTAAAGGGTAGA	0.448													ENSG00000155629																																					0													38.0	37.0	38.0					10																	98363808		2202	4300	6502	SO:0001630	splice_region_variant	0			-	AK092883	CCDS31259.1	10q24.2	2008-10-23			ENSG00000155629	ENSG00000155629			30034	protein-coding gene	gene with protein product		607942				1251844, 11163197	Standard	NM_152309		Approved	BCAP, FLJ35564	uc001kmq.3	Q6ZUJ8	OTTHUMG00000018838	ENST00000339364.5:c.2171-2A>T	10.37:g.98363808T>A			Q5TB56|Q5VXJ9|Q8N6J6|Q8NAC8	Splice_Site	SNP	-	e15-2	ENST00000339364.5	37	c.2171-2	CCDS31259.1	10	.	.	.	.	.	.	.	.	.	.	T	11.26	1.585164	0.28268	.	.	ENSG00000155629	ENST00000339364;ENST00000371110;ENST00000371109	.	.	.	5.2	5.2	0.72013	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	11.4539	0.50169	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	PIK3AP1	98353798	1.000000	0.71417	0.896000	0.35187	0.127000	0.20565	4.803000	0.62546	1.956000	0.56807	0.379000	0.24179	.	-	PIK3AP1	-	-		0.448	PIK3AP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	PIK3AP1	HGNC	protein_coding	OTTHUMT00000049619.2	0	0	0	16	16	81	0.00	0.00	T	NM_152309	Intron	98363808	-1	14	12	44	78	tier1	no_errors	ENST00000339364	ensembl	human	known	74_37	splice_site	24.14	13.33	SNP	0.955	A	14	44
SERPINA6	866	genome.wustl.edu	37	14	94772438	94772438	+	Silent	SNP	G	G	A			TCGA-DX-A48N-01A-11D-A307-09	TCGA-DX-A48N-10A-01D-A307-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	93d25a05-5221-452e-a4b8-f1504d48e89c	a1a1386f-c8ff-4c7c-b1ee-19a86bd40af2	g.chr14:94772438G>A	ENST00000341584.3	-	4	1148	c.1002C>T	c.(1000-1002)atC>atT	p.I334I		NM_001756.3	NP_001747	P08185	CBG_HUMAN	serpin peptidase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 6	334					glucocorticoid metabolic process (GO:0008211)|negative regulation of endopeptidase activity (GO:0010951)|regulation of proteolysis (GO:0030162)|transport (GO:0006810)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	serine-type endopeptidase inhibitor activity (GO:0004867)|steroid binding (GO:0005496)			central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(11)|ovary(1)|skin(4)|upper_aerodigestive_tract(1)	26		all_cancers(154;0.0482)|all_epithelial(191;0.166)		COAD - Colon adenocarcinoma(157;0.211)	Alclometasone(DB00240)|Beclomethasone(DB00394)|Ciclesonide(DB01410)|Flumethasone Pivalate(DB00663)|Flunisolide(DB00180)|Fluocinolone Acetonide(DB00591)|Fluocinonide(DB01047)|Fluorometholone(DB00324)|Flurandrenolide(DB00846)|Fluticasone Propionate(DB00588)|Halobetasol Propionate(DB00596)|Medrysone(DB00253)|Mitotane(DB00648)|Paramethasone(DB01384)|Prednisolone(DB00860)|Rimexolone(DB00896)|Triamcinolone(DB00620)	CGTCCTGGGTGATGCGTGAGA	0.458													ENSG00000170099																																					0													144.0	127.0	133.0					14																	94772438		2203	4300	6503	SO:0001819	synonymous_variant	0			-	J02943	CCDS9924.1	14q32.13	2014-02-18	2005-08-18		ENSG00000170099	ENSG00000170099		"""Serine (or cysteine) peptidase inhibitors"""	1540	protein-coding gene	gene with protein product	"""corticosteroid binding globulin"", ""transcortin"""	122500	"""serine (or cysteine) proteinase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 6"""	CBG		3299377, 7912884, 24172014	Standard	NM_001756		Approved		uc001ycv.3	P08185	OTTHUMG00000171346	ENST00000341584.3:c.1002C>T	14.37:g.94772438G>A			A8K456|Q7Z2Q9	Silent	SNP	pfam_Serpin_dom,superfamily_Serpin_dom,smart_Serpin_dom	p.I334	ENST00000341584.3	37	c.1002	CCDS9924.1	14																																																																																			-	SERPI6	-	pfam_Serpin_dom,superfamily_Serpin_dom,smart_Serpin_dom		0.458	SERPINA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	SERPI6	HGNC	protein_coding	OTTHUMT00000413065.1	0	0	0	46	46	105	0.00	0.00	G	NM_001756		94772438	-1	28	61	47	100	tier1	no_errors	ENST00000341584	ensembl	human	known	74_37	silent	37.33	37.89	SNP	0.036	A	28	47
LINC00700	282980	genome.wustl.edu	37	10	2055669	2055669	+	lincRNA	SNP	T	T	C			TCGA-DX-A48N-01A-11D-A307-09	TCGA-DX-A48N-10A-01D-A307-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	93d25a05-5221-452e-a4b8-f1504d48e89c	a1a1386f-c8ff-4c7c-b1ee-19a86bd40af2	g.chr10:2055669T>C	ENST00000413603.1	-	0	214					NR_040253.1				long intergenic non-protein coding RNA 700																		ACAATGAAGATGATTTTGCCA	0.358													ENSG00000234962																																					0																																												0			-	AK097474		10p15.3	2012-12-03			ENSG00000234962	ENSG00000234962		"""Long non-coding RNAs"""	27422	non-coding RNA	RNA, long non-coding							Standard	NR_040253		Approved		uc001igo.2		OTTHUMG00000017547		10.37:g.2055669T>C				R	SNP	-	NULL	ENST00000413603.1	37	NULL		10																																																																																			-	LINC00700	-	-		0.358	LINC00700-003	KNOWN	basic	lincRNA	LINC00700	HGNC	lincRNA	OTTHUMT00000046440.1	0	0	0	63	63	76	0.00	0.00	T	NR_040253		2055669	-1	27	38	32	57	tier1	no_errors	ENST00000438372	ensembl	human	known	74_37	rna	45.76	40.00	SNP	0.721	C	27	32
GPR143	4935	genome.wustl.edu	37	X	9711638	9711638	+	Missense_Mutation	SNP	C	C	T			TCGA-DX-A48N-01A-11D-A307-09	TCGA-DX-A48N-10A-01D-A307-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	93d25a05-5221-452e-a4b8-f1504d48e89c	a1a1386f-c8ff-4c7c-b1ee-19a86bd40af2	g.chrX:9711638C>T	ENST00000467482.1	-	6	880	c.734G>A	c.(733-735)cGa>cAa	p.R245Q	GPR143_ENST00000380929.2_Missense_Mutation_p.R265Q			P51810	GP143_HUMAN	G protein-coupled receptor 143	245					calcium-mediated signaling using intracellular calcium source (GO:0035584)|eye pigment biosynthetic process (GO:0006726)|G-protein coupled receptor signaling pathway (GO:0007186)|melanosome localization (GO:0032400)|melanosome organization (GO:0032438)|melanosome transport (GO:0032402)|neuropeptide signaling pathway (GO:0007218)|phosphatidylinositol-mediated signaling (GO:0048015)|regulation of calcium-mediated signaling (GO:0050848)|signal transduction (GO:0007165)|visual perception (GO:0007601)	apical plasma membrane (GO:0016324)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|melanosome (GO:0042470)|melanosome membrane (GO:0033162)|membrane (GO:0016020)|plasma membrane (GO:0005886)	dopamine binding (GO:0035240)|G-protein coupled receptor activity (GO:0004930)|L-DOPA binding (GO:0072544)|L-DOPA receptor activity (GO:0035643)|tyrosine binding (GO:0072545)			endometrium(2)|large_intestine(4)|lung(6)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	15		Hepatocellular(5;0.000888)				TTTGAAAAATCGGATCTTGAT	0.398													ENSG00000101850																																					0													154.0	133.0	140.0					X																	9711638		2203	4300	6503	SO:0001583	missense	0			-	Z48804	CCDS14134.1, CCDS14134.2	Xp22.3	2013-09-27	2003-12-01		ENSG00000101850	ENSG00000101850		"""GPCR / Unclassified : 7TM orphan receptors"""	20145	protein-coding gene	gene with protein product	"""ocular albinism 1"""	300808	"""ocular albinism 1 (Nettleship-Falls)"""	OA1		7647783, 10471510	Standard	NM_000273		Approved		uc004cst.2	P51810	OTTHUMG00000021118	ENST00000467482.1:c.734G>A	X.37:g.9711638C>T	ENSP00000417161:p.Arg245Gln		Q6NTI7	Missense_Mutation	SNP	pfam_Ocular_alb1,pfam_GPCR_2_secretin-like,prints_Ocular_alb1	p.R265Q	ENST00000467482.1	37	c.794	CCDS14134.2	X	.	.	.	.	.	.	.	.	.	.	C	25.8	4.676327	0.88445	.	.	ENSG00000101850	ENST00000467482;ENST00000380929;ENST00000431126	D;D;D	0.99405	-5.84;-5.84;-5.84	5.15	5.15	0.70609	.	0.000000	0.85682	D	0.000000	D	0.99399	0.9788	M	0.75777	2.31	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.99908	1.1188	10	0.30078	T	0.28	-8.3958	16.3904	0.83533	0.0:1.0:0.0:0.0	.	245	P51810	GP143_HUMAN	Q	245;265;161	ENSP00000417161:R245Q;ENSP00000370316:R265Q;ENSP00000406138:R161Q	ENSP00000370316:R265Q	R	-	2	0	GPR143	9671638	1.000000	0.71417	0.844000	0.33320	0.568000	0.35870	6.601000	0.74136	2.124000	0.65301	0.513000	0.50165	CGA	-	GPR143	-	pfam_Ocular_alb1,pfam_GPCR_2_secretin-like,prints_Ocular_alb1		0.398	GPR143-001	KNOWN	basic|appris_principal|CCDS	protein_coding	GPR143	HGNC	protein_coding	OTTHUMT00000055714.2	0	0	0	20	20	37	0.00	0.00	C	NM_000273		9711638	-1	23	30	24	33	tier1	no_errors	ENST00000380929	ensembl	human	known	74_37	missense	48.94	47.62	SNP	1.000	T	23	24
ACLY	47	genome.wustl.edu	37	17	40065259	40065259	+	Missense_Mutation	SNP	A	A	C			TCGA-DX-A48N-01A-11D-A307-09	TCGA-DX-A48N-10A-01D-A307-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	93d25a05-5221-452e-a4b8-f1504d48e89c	a1a1386f-c8ff-4c7c-b1ee-19a86bd40af2	g.chr17:40065259A>C	ENST00000352035.2	-	6	729	c.599T>G	c.(598-600)cTc>cGc	p.L200R	ACLY_ENST00000537919.1_Intron|ACLY_ENST00000353196.1_Missense_Mutation_p.L200R|ACLY_ENST00000590151.1_Missense_Mutation_p.L200R|ACLY_ENST00000393896.2_Missense_Mutation_p.L200R	NM_001096.2	NP_001087.2	P53396	ACLY_HUMAN	ATP citrate lyase	200	ATP-grasp.				ATP catabolic process (GO:0006200)|cellular carbohydrate metabolic process (GO:0044262)|cellular lipid metabolic process (GO:0044255)|citrate metabolic process (GO:0006101)|coenzyme A metabolic process (GO:0015936)|energy reserve metabolic process (GO:0006112)|lipid biosynthetic process (GO:0008610)|long-chain fatty-acyl-CoA biosynthetic process (GO:0035338)|positive regulation of cellular metabolic process (GO:0031325)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)	citrate lyase complex (GO:0009346)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATP citrate synthase activity (GO:0003878)|cofactor binding (GO:0048037)|metal ion binding (GO:0046872)|succinate-CoA ligase (ADP-forming) activity (GO:0004775)		NTN1/ACLY(2)	breast(2)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(5)|lung(4)|ovary(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	28		Breast(137;0.000143)				ATTGATCTCGAGGTAGGTGAA	0.537													ENSG00000131473																									Colon(64;807 1396 15971 30971)												0													70.0	71.0	71.0					17																	40065259		2203	4300	6503	SO:0001583	missense	0			-	X64330	CCDS11412.1, CCDS11413.1	17q21.2	2010-04-27			ENSG00000131473	ENSG00000131473	2.3.3.8		115	protein-coding gene	gene with protein product	"""ATP citrate synthase"""	108728				1371749, 8088842	Standard	NM_001096		Approved	ATPCL, CLATP, ACL	uc002hyg.3	P53396	OTTHUMG00000133507	ENST00000352035.2:c.599T>G	17.37:g.40065259A>C	ENSP00000253792:p.Leu200Arg		B4DIM0|B4E3P0|Q13037|Q9BRL0	Missense_Mutation	SNP	pfam_Citrate_synthase-like,pfam_CoA_ligase,pfam_CoA-bd,pfam_ATP-grasp_succ-CoA_synth-type,superfamily_Citrate_synthase-like_core,superfamily_Succinyl-CoA_synth-like,smart_CoA-bd,pirsf_ATP-citrate_synthase	p.L200R	ENST00000352035.2	37	c.599	CCDS11412.1	17	.	.	.	.	.	.	.	.	.	.	A	27.2	4.813515	0.90790	.	.	ENSG00000131473	ENST00000352035;ENST00000401700;ENST00000353196;ENST00000393896	T;T;T	0.66460	-0.21;-0.21;-0.21	5.73	5.73	0.89815	ATP-grasp fold, subdomain 2 (1);ATP-grasp fold, succinyl-CoA synthetase-type (1);	0.000000	0.85682	D	0.000000	D	0.84529	0.5492	M	0.88450	2.955	0.80722	D	1	D;D;D;D	0.89917	0.999;0.993;1.0;0.988	D;P;D;P	0.77004	0.958;0.803;0.989;0.777	D	0.87646	0.2525	10	0.87932	D	0	.	16.0069	0.80370	1.0:0.0:0.0:0.0	.	254;254;200;200	B4DIM0;E7ENH9;G3XAI4;P53396	.;.;.;ACLY_HUMAN	R	200;254;200;200	ENSP00000253792:L200R;ENSP00000345398:L200R;ENSP00000377474:L200R	ENSP00000253792:L200R	L	-	2	0	ACLY	37318785	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	9.336000	0.96533	2.180000	0.69256	0.460000	0.39030	CTC	-	ACLY	-	pfam_ATP-grasp_succ-CoA_synth-type,pirsf_ATP-citrate_synthase		0.537	ACLY-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	ACLY	HGNC	protein_coding	OTTHUMT00000257465.1	0	0	0	32	32	75	0.00	0.00	A	NM_001096		40065259	-1	10	14	52	91	tier1	no_errors	ENST00000352035	ensembl	human	known	74_37	missense	16.13	13.33	SNP	1.000	C	10	52
TMTC4	84899	genome.wustl.edu	37	13	101264682	101264682	+	Silent	SNP	T	T	C			TCGA-DX-A48N-01A-11D-A307-09	TCGA-DX-A48N-10A-01D-A307-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	93d25a05-5221-452e-a4b8-f1504d48e89c	a1a1386f-c8ff-4c7c-b1ee-19a86bd40af2	g.chr13:101264682T>C	ENST00000376234.3	-	16	2166	c.1977A>G	c.(1975-1977)gcA>gcG	p.A659A	TMTC4_ENST00000328767.5_Silent_p.A548A|TMTC4_ENST00000342624.5_Silent_p.A678A	NM_001079669.1	NP_001073137.1	Q5T4D3	TMTC4_HUMAN	transmembrane and tetratricopeptide repeat containing 4	659						integral component of membrane (GO:0016021)				breast(3)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(5)|liver(1)|lung(14)|ovary(2)|prostate(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	34	all_neural(89;0.0837)|Medulloblastoma(90;0.18)|Lung SC(71;0.184)					CCAGCACGTTTGCCAACGAGA	0.458													ENSG00000125247																																					0													141.0	131.0	135.0					13																	101264682		2203	4300	6503	SO:0001819	synonymous_variant	0			-		CCDS9497.2, CCDS41904.1, CCDS66575.1	13q32.3	2013-01-10	2006-01-06		ENSG00000125247	ENSG00000125247		"""Tetratricopeptide (TTC) repeat domain containing"""	25904	protein-coding gene	gene with protein product							Standard	XM_005254082		Approved	FLJ14624, FLJ22153	uc001vot.3	Q5T4D3	OTTHUMG00000017289	ENST00000376234.3:c.1977A>G	13.37:g.101264682T>C			A6NLI7|B7Z666|Q5T4D4|Q5T4D5|Q5T4D6|Q8WV63|Q96SU8	Silent	SNP	pfam_TPR_1,pfam_DUF1736,pfam_TPR_2,smart_TPR_repeat,pfscan_TPR_repeat,pfscan_TPR-contain_dom	p.A678	ENST00000376234.3	37	c.2034	CCDS41904.1	13																																																																																			-	TMTC4	-	smart_TPR_repeat,pfscan_TPR-contain_dom		0.458	TMTC4-004	KNOWN	basic|appris_principal|CCDS	protein_coding	TMTC4	HGNC	protein_coding	OTTHUMT00000045649.2	0	0	0	36	36	80	0.00	0.00	T	NM_032813		101264682	-1	44	41	31	29	tier1	no_errors	ENST00000342624	ensembl	human	known	74_37	silent	58.67	58.57	SNP	0.984	C	44	31
CASZ1	54897	genome.wustl.edu	37	1	10719966	10719966	+	Missense_Mutation	SNP	A	A	T			TCGA-DX-A48N-01A-11D-A307-09	TCGA-DX-A48N-10A-01D-A307-09	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	93d25a05-5221-452e-a4b8-f1504d48e89c	a1a1386f-c8ff-4c7c-b1ee-19a86bd40af2	g.chr1:10719966A>T	ENST00000377022.3	-	6	1450	c.1133T>A	c.(1132-1134)gTc>gAc	p.V378D	CASZ1_ENST00000344008.5_Missense_Mutation_p.V378D|CASZ1_ENST00000478728.2_5'Flank	NM_001079843.2	NP_001073312.1	Q86V15	CASZ1_HUMAN	castor zinc finger 1	378					multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(9)|large_intestine(13)|lung(18)|ovary(2)|prostate(5)|skin(2)|urinary_tract(1)	54	Ovarian(185;0.203)|all_lung(157;0.204)	Lung NSC(185;4.96e-06)|all_lung(284;1.22e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00212)|Hepatocellular(190;0.00913)|Ovarian(437;0.0229)|Myeloproliferative disorder(586;0.0255)	STAD - Stomach adenocarcinoma(5;0.0224)	UCEC - Uterine corpus endometrioid carcinoma (279;0.0265)|Colorectal(212;3.54e-08)|COAD - Colon adenocarcinoma(227;9.56e-06)|BRCA - Breast invasive adenocarcinoma(304;0.000219)|Kidney(185;0.00142)|KIRC - Kidney renal clear cell carcinoma(229;0.00381)|READ - Rectum adenocarcinoma(331;0.0419)|STAD - Stomach adenocarcinoma(132;0.0623)		GATGCCCCGGACGTCGTACTT	0.716													ENSG00000130940																																					0													29.0	33.0	31.0					1																	10719966		2203	4298	6501	SO:0001583	missense	0			-	AK000328	CCDS120.2, CCDS41246.1	1p36.22	2013-01-07	2007-02-02		ENSG00000130940	ENSG00000130940		"""Zinc fingers, C2H2-type"""	26002	protein-coding gene	gene with protein product	"""zinc finger protein 693"", ""survival related gene"""	609895	"""castor homolog 1, zinc finger (Drosophila)"""			16631614, 21252912	Standard	NM_001079843		Approved	FLJ20321, ZNF693, castor, cst, SRG	uc001aro.4	Q86V15	OTTHUMG00000002035	ENST00000377022.3:c.1133T>A	1.37:g.10719966A>T	ENSP00000366221:p.Val378Asp		Q078S9|Q2EN02|Q5T9S1|Q6ZNM8|Q8WX49|Q8WX50|Q9BT16|Q9NXC6	Missense_Mutation	SNP	smart_Znf_C2H2-like,pfscan_Znf_C2H2	p.V378D	ENST00000377022.3	37	c.1133	CCDS41246.1	1	.	.	.	.	.	.	.	.	.	.	a	23.3	4.400881	0.83120	.	.	ENSG00000130940	ENST00000377022;ENST00000344008	.	.	.	4.63	4.63	0.57726	.	0.061020	0.64402	D	0.000004	T	0.63165	0.2488	L	0.27053	0.805	0.58432	D	0.999994	D;D;D;D	0.76494	0.998;0.998;0.998;0.999	D;D;D;D	0.67548	0.952;0.937;0.937;0.919	T	0.68322	-0.5439	9	0.87932	D	0	-37.3562	14.3665	0.66810	1.0:0.0:0.0:0.0	.	402;378;378;378	B7Z1S3;B3KRV8;Q86V15-2;Q86V15	.;.;.;CASZ1_HUMAN	D	378	.	ENSP00000339445:V378D	V	-	2	0	CASZ1	10642553	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	8.589000	0.90817	1.874000	0.54306	0.398000	0.26397	GTC	-	CASZ1	-	NULL		0.716	CASZ1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	CASZ1	HGNC	protein_coding	OTTHUMT00000005673.2	0	0	0	68	68	34	0.00	0.00	A	NM_017766		10719966	-1	36	6	42	13	tier1	no_errors	ENST00000377022	ensembl	human	known	74_37	missense	46.15	31.58	SNP	1.000	T	36	42
CCL23	6368	genome.wustl.edu	37	17	34344871	34344871	+	Missense_Mutation	SNP	G	G	A			TCGA-DX-A48N-01A-11D-A307-09	TCGA-DX-A48N-10A-01D-A307-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	93d25a05-5221-452e-a4b8-f1504d48e89c	a1a1386f-c8ff-4c7c-b1ee-19a86bd40af2	g.chr17:34344871G>A	ENST00000591423.1	-	1	128	c.64C>T	c.(64-66)Cgg>Tgg	p.R22W	CCL23_ENST00000293280.2_Missense_Mutation_p.R22W	NM_145898.1	NP_665905.1	P55773	CCL23_HUMAN	chemokine (C-C motif) ligand 23	22				MLVTALGSQARVTKDAETEFMMSKLPLENPVLL -> HAFL LPLVPGPGHKRCRDRVHECQSFHWKIQYFW (in Ref. 1). {ECO:0000305}.	cell-cell signaling (GO:0007267)|cellular calcium ion homeostasis (GO:0006874)|chemotaxis (GO:0006935)|G-protein coupled receptor signaling pathway (GO:0007186)|immune response (GO:0006955)|inflammatory response (GO:0006954)|monocyte chemotaxis (GO:0002548)|negative regulation of C-C chemokine binding (GO:2001264)|negative regulation of cell proliferation (GO:0008285)|signal transduction (GO:0007165)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	CCR1 chemokine receptor binding (GO:0031726)|chemokine activity (GO:0008009)|heparin binding (GO:0008201)			large_intestine(2)|liver(1)|lung(2)|prostate(1)	6		Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0182)		TTTGTGACCCGGGCCTGGGAT	0.577													ENSG00000167236																																					0													72.0	63.0	66.0					17																	34344871		2203	4300	6503	SO:0001583	missense	0			-	U58913	CCDS11305.1, CCDS59282.1	17q11.2	2014-05-06	2002-08-22	2002-08-23	ENSG00000167236	ENSG00000274736		"""Chemokine ligands"", ""Endogenous ligands"""	10622	protein-coding gene	gene with protein product		602494	"""small inducible cytokine subfamily A (Cys-Cys), member 23"""	SCYA23		9104803, 10409433	Standard	XR_429910		Approved	Ckb-8, MPIF-1, MIP-3, CKb8	uc002hks.1	P55773	OTTHUMG00000188409	ENST00000591423.1:c.64C>T	17.37:g.34344871G>A	ENSP00000465954:p.Arg22Trp		B7ZKQ3|O00174|O75950|Q52LD4	Missense_Mutation	SNP	pfam_Chemokine_IL8-like_dom,superfamily_Chemokine_IL8-like_dom,smart_Chemokine_IL8-like_dom	p.R22W	ENST00000591423.1	37	c.64	CCDS59282.1	17	.	.	.	.	.	.	.	.	.	.	G	11.32	1.603347	0.28534	.	.	ENSG00000167236	ENST00000293280	T	0.04119	3.7	4.43	-4.09	0.03951	.	26.135200	0.00166	N	0.000000	T	0.03348	0.0097	N	0.22421	0.69	0.09310	N	1	B;B	0.13145	0.001;0.007	B;B	0.04013	0.0;0.001	T	0.43097	-0.9412	10	0.72032	D	0.01	.	0.3225	0.00305	0.3607:0.1421:0.225:0.2722	.	22;22	P55773;P55773-2	CCL23_HUMAN;.	W	22	ENSP00000293280:R22W	ENSP00000293280:R22W	R	-	1	2	CCL23	31368984	0.000000	0.05858	0.000000	0.03702	0.430000	0.31655	-0.037000	0.12164	-0.571000	0.06014	-0.741000	0.03529	CGG	-	CCL23	-	NULL		0.577	CCL23-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	CCL23	HGNC	protein_coding	OTTHUMT00000450228.1	0	0	0	35	35	35	0.00	0.00	G	NM_005064, NM_145898		34344871	-1	9	5	53	39	tier1	no_errors	ENST00000293280	ensembl	human	known	74_37	missense	14.52	11.36	SNP	0.000	A	9	53
ANO7	50636	genome.wustl.edu	37	2	242146995	242146995	+	Silent	SNP	A	A	G			TCGA-DX-A48N-01A-11D-A307-09	TCGA-DX-A48N-10A-01D-A307-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	93d25a05-5221-452e-a4b8-f1504d48e89c	a1a1386f-c8ff-4c7c-b1ee-19a86bd40af2	g.chr2:242146995A>G	ENST00000274979.8	+	11	1252	c.1149A>G	c.(1147-1149)gaA>gaG	p.E383E	ANO7_ENST00000402430.3_Silent_p.E382E	NM_001001891.3	NP_001001891.2	Q6IWH7	ANO7_HUMAN	anoctamin 7	383					calcium activated galactosylceramide scrambling (GO:0061591)|calcium activated phosphatidylcholine scrambling (GO:0061590)|calcium activated phosphatidylserine scrambling (GO:0061589)|chloride transport (GO:0006821)|ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	cell junction (GO:0030054)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|intracellular (GO:0005622)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	intracellular calcium activated chloride channel activity (GO:0005229)|phospholipid scramblase activity (GO:0017128)			NS(1)|central_nervous_system(1)|endometrium(3)|large_intestine(5)|lung(14)|pancreas(2)|prostate(1)|skin(3)|urinary_tract(2)	32						GCAGGCAGGAACTGTGTGGCA	0.642													ENSG00000146205																																					0													103.0	98.0	99.0					2																	242146995		2203	4300	6503	SO:0001819	synonymous_variant	0			-	AY617079	CCDS33423.1, CCDS46563.1	2q37.3	2014-04-09	2008-08-28	2008-08-28	ENSG00000146205	ENSG00000146205		"""Ion channels / Chloride channels : Calcium activated : Anoctamins"""	31677	protein-coding gene	gene with protein product		605096	"""transmembrane protein 16G"""	PCANAP5, TMEM16G		14981236, 15375614, 24692353	Standard	NM_001001891		Approved	NGEP, PCANAP5L, IPCA-5	uc002wax.2	Q6IWH7	OTTHUMG00000151702	ENST00000274979.8:c.1149A>G	2.37:g.242146995A>G			Q6IWH6	Silent	SNP	pfam_Anoctamin	p.E383	ENST00000274979.8	37	c.1149	CCDS33423.1	2																																																																																			-	ANO7	-	pfam_Anoctamin		0.642	ANO7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	ANO7	HGNC	protein_coding	OTTHUMT00000323509.1	0	0	0	69	69	50	0.00	0.00	A	NM_001001891		242146995	+1	33	16	57	35	tier1	no_errors	ENST00000274979	ensembl	human	known	74_37	silent	36.67	31.37	SNP	1.000	G	33	57
METTL25	84190	genome.wustl.edu	37	12	82872802	82872802	+	Nonstop_Mutation	SNP	G	G	C			TCGA-DX-A48N-01A-11D-A307-09	TCGA-DX-A48N-10A-01D-A307-09	G	G	G	C	G	G	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	93d25a05-5221-452e-a4b8-f1504d48e89c	a1a1386f-c8ff-4c7c-b1ee-19a86bd40af2	g.chr12:82872802G>C	ENST00000248306.3	+	12	1880	c.1811G>C	c.(1810-1812)tGa>tCa	p.*604S	RP11-263K4.5_ENST00000552532.1_lincRNA	NM_032230.2	NP_115606.2	Q8N6Q8	MET25_HUMAN	methyltransferase like 25	0							methyltransferase activity (GO:0008168)										AAGCAGCAGTGATTTCCATTG	0.348													ENSG00000127720																																					0													162.0	143.0	150.0					12																	82872802		2203	4300	6503	SO:0001578	stop_lost	0			-	BC029120	CCDS9024.1	12q21.31	2012-08-13	2012-08-13	2012-08-13	ENSG00000127720	ENSG00000127720			26228	protein-coding gene	gene with protein product			"""chromosome 12 open reading frame 26"""	C12orf26			Standard	NM_032230		Approved	FLJ22789	uc001szq.3	Q8N6Q8	OTTHUMG00000170252	ENST00000248306.3:c.1811G>C	12.37:g.82872802G>C	ENSP00000248306:p.*604Serext*13		Q9H5Y3	Nonstop_Mutation	SNP	NULL	p.*604S	ENST00000248306.3	37	c.1811	CCDS9024.1	12	.	.	.	.	.	.	.	.	.	.	G	13.04	2.118207	0.37339	.	.	ENSG00000127720	ENST00000248306	.	.	.	5.33	5.33	0.75918	.	.	.	.	.	.	.	.	.	.	.	0.09310	N	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	11.5405	0.50663	0.0817:0.0:0.9183:0.0	.	.	.	.	S	604	.	.	X	+	2	2	C12orf26	81396933	1.000000	0.71417	0.984000	0.44739	0.711000	0.40976	2.519000	0.45546	2.492000	0.84095	0.650000	0.86243	TGA	-	METTL25	-	NULL		0.348	METTL25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	METTL25	HGNC	protein_coding	OTTHUMT00000408192.1	0	0	0	39	39	46	0.00	0.00	G	NM_032230		82872802	+1	211	249	338	477	tier1	no_errors	ENST00000248306	ensembl	human	known	74_37	nonstop	38.36	34.25	SNP	0.686	C	211	338
HRH3	11255	genome.wustl.edu	37	20	60791718	60791718	+	Missense_Mutation	SNP	G	G	A			TCGA-DX-A48N-01A-11D-A307-09	TCGA-DX-A48N-10A-01D-A307-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	93d25a05-5221-452e-a4b8-f1504d48e89c	a1a1386f-c8ff-4c7c-b1ee-19a86bd40af2	g.chr20:60791718G>A	ENST00000340177.5	-	3	966	c.682C>T	c.(682-684)Cgc>Tgc	p.R228C	HRH3_ENST00000317393.6_Missense_Mutation_p.R228C	NM_007232.2	NP_009163.2	Q9Y5N1	HRH3_HUMAN	histamine receptor H3	228					brain development (GO:0007420)|drinking behavior (GO:0042756)|eating behavior (GO:0042755)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|learning (GO:0007612)|memory (GO:0007613)|negative regulation of adenylate cyclase activity (GO:0007194)|negative regulation of blood pressure (GO:0045776)|negative regulation of gamma-aminobutyric acid secretion (GO:0014053)|negative regulation of glutamate secretion (GO:0014050)|negative regulation of serotonin secretion (GO:0014063)|neurotransmitter secretion (GO:0007269)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of epithelial cell proliferation (GO:0050679)|regulation of norepinephrine secretion (GO:0014061)|response to organic cyclic compound (GO:0014070)	integral component of plasma membrane (GO:0005887)|myelin sheath (GO:0043209)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)	drug binding (GO:0008144)|histamine receptor activity (GO:0004969)			breast(1)|endometrium(1)|lung(4)|skin(2)|upper_aerodigestive_tract(1)	9	Breast(26;7.76e-09)		BRCA - Breast invasive adenocarcinoma(19;7.08e-07)		Betahistine(DB06698)|Histamine Phosphate(DB00667)|Mirtazapine(DB00370)	AGGCGGGTGCGCCTCTGGATG	0.657													ENSG00000101180																																					0													45.0	41.0	42.0					20																	60791718		2202	4300	6502	SO:0001583	missense	0			-	AF140538	CCDS13493.1	20q13.33	2013-09-19			ENSG00000101180	ENSG00000101180		"""GPCR / Class A : Histamine receptors"""	5184	protein-coding gene	gene with protein product		604525				10347254	Standard	NM_007232		Approved	GPCR97	uc002ycf.2	Q9Y5N1	OTTHUMG00000032899	ENST00000340177.5:c.682C>T	20.37:g.60791718G>A	ENSP00000342560:p.Arg228Cys		Q4QRI7|Q9GZX2|Q9H4K8	Missense_Mutation	SNP	pfam_GPCR_Rhodpsn,pfscan_GPCR_Rhodpsn_7TM,prints_Histamine_H3_rcpt,prints_GPCR_Rhodpsn,prints_Musac_Ach_rcpt	p.R228C	ENST00000340177.5	37	c.682	CCDS13493.1	20	.	.	.	.	.	.	.	.	.	.	G	21.2	4.112382	0.77210	.	.	ENSG00000101180	ENST00000340177;ENST00000317393;ENST00000370797	T;T	0.38887	1.11;1.11	4.52	4.52	0.55395	GPCR, rhodopsin-like superfamily (1);	0.000000	0.85682	D	0.000000	T	0.71500	0.3347	M	0.90145	3.09	0.58432	D	0.999995	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.91635	0.973;0.999;0.997;0.999	T	0.79825	-0.1640	10	0.87932	D	0	-44.2605	17.5911	0.87997	0.0:0.0:1.0:0.0	.	228;228;228;228	Q9Y5N1-2;E7EWA7;Q8WXZ9;Q9Y5N1	.;.;.;HRH3_HUMAN	C	228	ENSP00000342560:R228C;ENSP00000321482:R228C	ENSP00000321482:R228C	R	-	1	0	HRH3	60225113	1.000000	0.71417	1.000000	0.80357	0.810000	0.45777	5.255000	0.65462	2.209000	0.71365	0.205000	0.17691	CGC	-	HRH3	-	pfam_GPCR_Rhodpsn,pfscan_GPCR_Rhodpsn_7TM		0.657	HRH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	HRH3	HGNC	protein_coding	OTTHUMT00000079994.1	0	0	0	25	25	39	0.00	0.00	G	NM_007232		60791718	-1	22	22	50	42	tier1	no_errors	ENST00000317393	ensembl	human	known	74_37	missense	30.14	34.38	SNP	1.000	A	22	50
DYSF	8291	genome.wustl.edu	37	2	71797272	71797272	+	Intron	SNP	G	G	A			TCGA-DX-A48N-01A-11D-A307-09	TCGA-DX-A48N-10A-01D-A307-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	93d25a05-5221-452e-a4b8-f1504d48e89c	a1a1386f-c8ff-4c7c-b1ee-19a86bd40af2	g.chr2:71797272G>A	ENST00000258104.3	+	28	3202				DYSF_ENST00000410041.1_Intron|DYSF_ENST00000413539.2_Intron|DYSF_ENST00000409366.1_Intron|DYSF_ENST00000394120.2_Intron|DYSF_ENST00000429174.2_Intron|DYSF_ENST00000409744.1_Intron|DYSF_ENST00000409651.1_Intron|DYSF_ENST00000410020.3_Intron|DYSF_ENST00000409762.1_Intron|DYSF_ENST00000409582.3_Intron	NM_001130976.1|NM_003494.3	NP_001124448.1|NP_003485.1	O75923	DYSF_HUMAN	dysferlin						plasma membrane repair (GO:0001778)|vesicle fusion (GO:0006906)	cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)	calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)|phospholipid binding (GO:0005543)			autonomic_ganglia(2)|breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(22)|lung(57)|ovary(3)|pancreas(1)|prostate(2)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(2)	111						CTTGGAGGACGTATGTTGTCA	0.522													ENSG00000135636																																					0																																										SO:0001627	intron_variant	0			-	AF075575	CCDS1918.1, CCDS46323.1, CCDS46324.1, CCDS46325.1, CCDS46326.1, CCDS46327.1, CCDS46328.1, CCDS46329.1, CCDS46330.1, CCDS46331.1, CCDS46332.1	2p13.3	2014-09-17	2013-09-12		ENSG00000135636	ENSG00000135636			3097	protein-coding gene	gene with protein product	"""fer-1-like family member 1"""	603009	"""limb girdle muscular dystrophy 2B (autosomal recessive)"""	LGMD2B		8320700	Standard	NM_003494		Approved	FER1L1	uc010fen.3	O75923	OTTHUMG00000129757	ENST00000258104.3:c.2926-87G>A	2.37:g.71797272G>A			A0FK00|B1PZ70|B1PZ71|B1PZ72|B1PZ73|B1PZ74|B1PZ75|B1PZ76|B1PZ77|B1PZ78|B1PZ79|B1PZ80|B1PZ81|B3KQB9|O75696|Q09EX5|Q0H395|Q53QY3|Q53TD2|Q8TEL8|Q9UEN7	R	SNP	-	NULL	ENST00000258104.3	37	NULL	CCDS1918.1	2																																																																																			-	DYSF	-	-		0.522	DYSF-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	DYSF	HGNC	protein_coding	OTTHUMT00000251970.3	0	0	0	58	58	71	0.00	0.00	G	NM_003494		71797272	+1	26	24	57	77	tier1	no_errors	ENST00000461565	ensembl	human	known	74_37	rna	31.33	23.76	SNP	0.000	A	26	57
LIPI	149998	genome.wustl.edu	37	21	15481348	15481348	+	Missense_Mutation	SNP	A	A	G			TCGA-DX-A48N-01A-11D-A307-09	TCGA-DX-A48N-10A-01D-A307-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	93d25a05-5221-452e-a4b8-f1504d48e89c	a1a1386f-c8ff-4c7c-b1ee-19a86bd40af2	g.chr21:15481348A>G	ENST00000536861.1	-	10	1348	c.1349T>C	c.(1348-1350)cTt>cCt	p.L450P	LIPI_ENST00000344577.2_Missense_Mutation_p.L471P|AP001347.6_ENST00000432621.1_RNA|AP001347.6_ENST00000428809.1_RNA			Q6XZB0	LIPI_HUMAN	lipase, member I	450					lipid catabolic process (GO:0016042)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|membrane (GO:0016020)|plasma membrane (GO:0005886)	heparin binding (GO:0008201)|phospholipase activity (GO:0004620)			endometrium(1)|kidney(13)|large_intestine(9)|liver(3)|lung(24)|ovary(3)|urinary_tract(1)	54				Epithelial(23;0.000155)|COAD - Colon adenocarcinoma(22;0.0015)|Colorectal(24;0.00693)|Lung(58;0.166)		GTTTGGATTAAGAAACACTTC	0.333													ENSG00000188992																																					0													176.0	179.0	178.0					21																	15481348		2203	4299	6502	SO:0001583	missense	0			-	BC028732	CCDS13564.1	21q11.2	2012-07-31			ENSG00000188992	ENSG00000188992			18821	protein-coding gene	gene with protein product	"""membrane-associated phospholipase A1 beta"", ""cancer/testis antigen 17"""	609252				12719377	Standard	XM_005260924		Approved	PRED5, LPDL, CT17, mPA-PLA1beta, PLA1C	uc002yjm.3	Q6XZB0	OTTHUMG00000074258	ENST00000536861.1:c.1349T>C	21.37:g.15481348A>G	ENSP00000440381:p.Leu450Pro		G1JSG3|G1JSG4|G1JSG5|G1JSG6|G1JSG7|G1JSG8|G1JSG9	Missense_Mutation	SNP	pfam_Lipase_N,pirsf_Lipoprotein_lipase_LIPH,prints_Lipase	p.L471P	ENST00000536861.1	37	c.1412		21	.	.	.	.	.	.	.	.	.	.	a	11.47	1.648969	0.29336	.	.	ENSG00000188992	ENST00000344577;ENST00000536861	D;D	0.90385	-2.66;-2.64	3.7	3.7	0.42460	.	0.153654	0.49916	D	0.000138	D	0.91637	0.7357	L	0.46157	1.445	0.28944	N	0.890781	D	0.58970	0.984	D	0.64506	0.926	D	0.86107	0.1560	10	0.66056	D	0.02	.	9.056	0.36405	1.0:0.0:0.0:0.0	.	471	Q6XZB0-2	.	P	471;450	ENSP00000343331:L471P;ENSP00000440381:L450P	ENSP00000343331:L471P	L	-	2	0	LIPI	14403219	0.933000	0.31639	0.302000	0.25058	0.113000	0.19764	2.716000	0.47219	1.909000	0.55274	0.533000	0.62120	CTT	-	LIPI	-	pirsf_Lipoprotein_lipase_LIPH		0.333	LIPI-201	KNOWN	basic|appris_candidate	protein_coding	LIPI	HGNC	protein_coding		0	0	0	48	48	107	0.00	0.00	A	NM_198996		15481348	-1	33	37	44	57	tier1	no_errors	ENST00000344577	ensembl	human	known	74_37	missense	42.86	39.36	SNP	0.460	G	33	44
APBA2	321	genome.wustl.edu	37	15	29346408	29346408	+	Silent	SNP	C	C	T	rs369962967		TCGA-DX-A48N-01A-11D-A307-09	TCGA-DX-A48N-10A-01D-A307-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	93d25a05-5221-452e-a4b8-f1504d48e89c	a1a1386f-c8ff-4c7c-b1ee-19a86bd40af2	g.chr15:29346408C>T	ENST00000558402.1	+	5	920	c.321C>T	c.(319-321)gaC>gaT	p.D107D	APBA2_ENST00000411764.1_Silent_p.D107D|APBA2_ENST00000561069.1_Silent_p.D107D|APBA2_ENST00000558330.1_Silent_p.D107D|APBA2_ENST00000558259.1_Silent_p.D107D			Q99767	APBA2_HUMAN	amyloid beta (A4) precursor protein-binding, family A, member 2	107					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)		GCCCTGAGGACGACAGCTACC	0.602													ENSG00000034053																																					0								C	,	1,4405	2.1+/-5.4	0,1,2202	144.0	120.0	129.0		321,321	-2.8	1.0	15		129	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	APBA2	NM_001130414.1,NM_005503.3	,	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	,	107/738,107/750	29346408	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	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.321C>T	15.37:g.29346408C>T			E9PGI4|O60571|Q5XKC0	Silent	SNP	pfam_PTB/PI_dom,pfam_PDZ,superfamily_PDZ,smart_PTB/PI_dom,smart_PDZ,pfscan_PDZ,pfscan_PTB/PI_dom	p.D107	ENST00000558402.1	37	c.321	CCDS10022.1	15																																																																																			-	APBA2	-	NULL		0.602	APBA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	APBA2	HGNC	protein_coding	OTTHUMT00000251362.3	0	0	0	31	31	30	0.00	0.00	C	NM_005503		29346408	+1	32	20	36	17	tier1	no_errors	ENST00000558259	ensembl	human	known	74_37	silent	47.06	54.05	SNP	0.995	T	32	36
SDHAP1	255812	genome.wustl.edu	37	3	195713419	195713419	+	RNA	SNP	C	C	T			TCGA-DX-A48N-01A-11D-A307-09	TCGA-DX-A48N-10A-01D-A307-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	93d25a05-5221-452e-a4b8-f1504d48e89c	a1a1386f-c8ff-4c7c-b1ee-19a86bd40af2	g.chr3:195713419C>T	ENST00000427841.1	-	0	146					NR_003264.2				succinate dehydrogenase complex, subunit A, flavoprotein pseudogene 1																		GATGCCCTCTCGTTCCTTCAA	0.438													ENSG00000185485																									Ovarian(67;1158 1227 12109 20189 43170)												0																																												0			-	BC071730		3q29	2009-12-02	2006-11-21	2009-12-02	ENSG00000185485	ENSG00000185485			32455	pseudogene	pseudogene			"""succinate dehydrogenase complex, subunit A, flavoprotein-like 1"""	SDHAL1, SDHALP1			Standard	NR_003264		Approved		uc003fvy.3		OTTHUMG00000155716		3.37:g.195713419C>T				R	SNP	-	NULL	ENST00000427841.1	37	NULL		3																																																																																			-	SDHAP1	-	-		0.438	SDHAP1-002	KNOWN	basic	processed_transcript	SDHAP1	HGNC	pseudogene	OTTHUMT00000341367.1	0	0	0	94	94	18	0.00	0.00	C			195713419	-1	29	2	139	13	tier1	no_errors	ENST00000413474	ensembl	human	known	74_37	rna	17.26	13.33	SNP	0.031	T	29	139
RIN1	9610	genome.wustl.edu	37	11	66101439	66101439	+	Silent	SNP	C	C	A			TCGA-DX-A48N-01A-11D-A307-09	TCGA-DX-A48N-10A-01D-A307-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	93d25a05-5221-452e-a4b8-f1504d48e89c	a1a1386f-c8ff-4c7c-b1ee-19a86bd40af2	g.chr11:66101439C>A	ENST00000311320.4	-	7	1668	c.1542G>T	c.(1540-1542)cgG>cgT	p.R514R	RIN1_ENST00000530056.1_Silent_p.R348R|RP11-867G23.12_ENST00000526655.1_RNA|RIN1_ENST00000424433.2_Silent_p.R409R|RIN1_ENST00000524804.1_5'Flank	NM_004292.2	NP_004283.2	Q13671	RIN1_HUMAN	Ras and Rab interactor 1	514	Ras and 14-3-3 protein binding region.|VPS9. {ECO:0000255|PROSITE- ProRule:PRU00550}.				associative learning (GO:0008306)|endocytosis (GO:0006897)|memory (GO:0007613)|negative regulation of synaptic plasticity (GO:0031914)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|dendrite (GO:0030425)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	GTPase activator activity (GO:0005096)			breast(1)|central_nervous_system(3)|haematopoietic_and_lymphoid_tissue(1)|lung(8)|ovary(1)	14						CCTGCAGGAGCCGCTTGACCT	0.652													ENSG00000174791																																					0													17.0	11.0	13.0					11																	66101439		2156	4238	6394	SO:0001819	synonymous_variant	0			-	L36463	CCDS31614.1	11q13.2	2005-09-18				ENSG00000174791			18749	protein-coding gene	gene with protein product		605965				9144171, 1849280	Standard	NM_004292		Approved		uc001ohn.1	Q13671		ENST00000311320.4:c.1542G>T	11.37:g.66101439C>A			O15010|Q00427|Q96CC8	Silent	SNP	pfam_VPS9,pfam_Ras-assoc,smart_SH2,smart_VPS9_subgr,smart_Ras-assoc,pfscan_Ras-assoc,pfscan_SH2,pfscan_VPS9	p.R514	ENST00000311320.4	37	c.1542	CCDS31614.1	11																																																																																			-	RIN1	-	pfam_VPS9,smart_VPS9_subgr,pfscan_VPS9		0.652	RIN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	RIN1	HGNC	protein_coding	OTTHUMT00000392980.2	0	0	0	82	82	18	0.00	0.00	C	NM_004292		66101439	-1	41	11	60	13	tier1	no_errors	ENST00000311320	ensembl	human	known	74_37	silent	40.20	45.83	SNP	0.342	A	41	60
GPR98	84059	genome.wustl.edu	37	5	90055265	90055265	+	Missense_Mutation	SNP	G	G	C	rs267600732		TCGA-DX-A48N-01A-11D-A307-09	TCGA-DX-A48N-10A-01D-A307-09	G	G	G	C	G	G	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	93d25a05-5221-452e-a4b8-f1504d48e89c	a1a1386f-c8ff-4c7c-b1ee-19a86bd40af2	g.chr5:90055265G>C	ENST00000405460.2	+	58	12076	c.11980G>C	c.(11980-11982)Gaa>Caa	p.E3994Q		NM_032119.3	NP_115495.3	Q8WXG9	GPR98_HUMAN	G protein-coupled receptor 98	3994	Calx-beta 26. {ECO:0000255}.				detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|G-protein coupled receptor signaling pathway (GO:0007186)|inner ear receptor stereocilium organization (GO:0060122)|maintenance of organ identity (GO:0048496)|nervous system development (GO:0007399)|neurological system process (GO:0050877)|neuropeptide signaling pathway (GO:0007218)|photoreceptor cell maintenance (GO:0045494)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|single organismal cell-cell adhesion (GO:0016337)|visual perception (GO:0007601)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|stereocilia ankle link complex (GO:0002142)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)			NS(4)|breast(7)|central_nervous_system(6)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(3)|kidney(18)|large_intestine(46)|liver(2)|lung(80)|ovary(12)|pancreas(5)|prostate(1)|skin(50)|stomach(7)|upper_aerodigestive_tract(8)|urinary_tract(6)	269		all_cancers(142;1.05e-09)|all_epithelial(76;1.81e-12)|all_lung(232;5.41e-06)|Lung NSC(167;1.72e-05)|Ovarian(174;0.00948)|Colorectal(57;0.133)|Breast(839;0.192)		OV - Ovarian serous cystadenocarcinoma(54;7.01e-30)|Epithelial(54;6.79e-25)|all cancers(79;1.88e-20)		TGATGATGCTGAATTTGAATT	0.393													ENSG00000164199																																					0													149.0	138.0	142.0					5																	90055265		2000	4180	6180	SO:0001583	missense	0			-	AB014586	CCDS47246.1	5q13	2014-08-08	2006-05-26	2006-05-26	ENSG00000164199	ENSG00000164199		"""-"", ""GPCR / Class B : Orphans"""	17416	protein-coding gene	gene with protein product		602851	"""monogenic, audiogenic seizure susceptibility 1 homolog (mouse)"""	USH2C, MASS1		10976914, 14740321	Standard	NM_032119		Approved	DKFZp761P0710, KIAA0686, FEB4, VLGR1b	uc003kju.3	Q8WXG9	OTTHUMG00000162668	ENST00000405460.2:c.11980G>C	5.37:g.90055265G>C	ENSP00000384582:p.Glu3994Gln		O75171|Q8TF58|Q9H0X5|Q9UL61	Missense_Mutation	SNP	pfam_Calx_beta,pfam_EPTP,pfam_GPCR_2_secretin-like,pfam_GPS_dom,superfamily_ConA-like_lec_gl_sf,superfamily_Gal_Oxase/kelch_b-propeller,smart_Calx_beta,pfscan_EAR,pfscan_GPS_dom,pfscan_GPCR_2-like	p.E3994Q	ENST00000405460.2	37	c.11980	CCDS47246.1	5	.	.	.	.	.	.	.	.	.	.	G	9.332	1.060726	0.19987	.	.	ENSG00000164199	ENST00000405460;ENST00000296619	T	0.29917	1.55	4.99	4.12	0.48240	Na-Ca exchanger/integrin-beta4 (2);	0.683831	0.15609	N	0.253496	T	0.36496	0.0969	M	0.87971	2.92	0.09310	N	1	B;B	0.30634	0.202;0.288	B;B	0.34038	0.173;0.174	T	0.33523	-0.9865	10	0.22706	T	0.39	.	5.7766	0.18283	0.1602:0.0:0.6832:0.1566	.	3994;3994	E7ETI5;Q8WXG9	.;GPR98_HUMAN	Q	3994	ENSP00000384582:E3994Q	ENSP00000296619:E3994Q	E	+	1	0	GPR98	90091021	0.064000	0.20934	0.969000	0.41365	0.738000	0.42128	1.691000	0.37721	1.241000	0.43820	0.563000	0.77884	GAA	-	GPR98	-	pfam_Calx_beta,smart_Calx_beta		0.393	GPR98-001	KNOWN	basic|appris_principal|CCDS	protein_coding	GPR98	HGNC	protein_coding	OTTHUMT00000369993.2	0	0	0	95	95	63	0.00	0.00	G	NM_032119		90055265	+1	40	27	65	49	tier1	no_errors	ENST00000405460	ensembl	human	known	74_37	missense	38.10	35.53	SNP	0.000	C	40	65
NTRK1	4914	genome.wustl.edu	37	1	156837972	156837972	+	Missense_Mutation	SNP	G	G	A	rs367836863	byFrequency	TCGA-DX-A48N-01A-11D-A307-09	TCGA-DX-A48N-10A-01D-A307-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	93d25a05-5221-452e-a4b8-f1504d48e89c	a1a1386f-c8ff-4c7c-b1ee-19a86bd40af2	g.chr1:156837972G>A	ENST00000524377.1	+	5	546	c.505G>A	c.(505-507)Gga>Aga	p.G169R	NTRK1_ENST00000392302.2_Missense_Mutation_p.G139R|NTRK1_ENST00000368196.3_Missense_Mutation_p.G169R|NTRK1_ENST00000358660.3_Missense_Mutation_p.G169R	NM_002529.3	NP_002520.2	P04629	NTRK1_HUMAN	neurotrophic tyrosine kinase, receptor, type 1	169	LRRCT.				activation of adenylate cyclase activity (GO:0007190)|activation of MAPKK activity (GO:0000186)|activation of phospholipase C activity (GO:0007202)|aging (GO:0007568)|axon guidance (GO:0007411)|axonogenesis involved in innervation (GO:0060385)|B cell differentiation (GO:0030183)|cellular response to nerve growth factor stimulus (GO:1990090)|cellular response to nicotine (GO:0071316)|circadian rhythm (GO:0007623)|detection of mechanical stimulus involved in sensory perception of pain (GO:0050966)|detection of temperature stimulus involved in sensory perception of pain (GO:0050965)|developmental programmed cell death (GO:0010623)|learning or memory (GO:0007611)|mechanoreceptor differentiation (GO:0042490)|negative regulation of cell proliferation (GO:0008285)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|olfactory nerve development (GO:0021553)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of angiogenesis (GO:0045766)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of neuron projection development (GO:0010976)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of programmed cell death (GO:0043068)|positive regulation of Ras GTPase activity (GO:0032320)|positive regulation of Ras protein signal transduction (GO:0046579)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|Ras protein signal transduction (GO:0007265)|response to activity (GO:0014823)|response to axon injury (GO:0048678)|response to drug (GO:0042493)|response to electrical stimulus (GO:0051602)|response to ethanol (GO:0045471)|response to hydrostatic pressure (GO:0051599)|response to nutrient levels (GO:0031667)|response to radiation (GO:0009314)|Sertoli cell development (GO:0060009)|small GTPase mediated signal transduction (GO:0007264)|sympathetic nervous system development (GO:0048485)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	axon (GO:0030424)|cell surface (GO:0009986)|cytoplasmic vesicle (GO:0031410)|dendrite (GO:0030425)|early endosome (GO:0005769)|endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)|late endosome (GO:0005770)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|nerve growth factor binding (GO:0048406)|nerve growth factor receptor activity (GO:0010465)|neurotrophin binding (GO:0043121)|protein homodimerization activity (GO:0042803)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			breast(3)|central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(7)|lung(35)|ovary(8)|prostate(2)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	74	all_hematologic(923;0.0839)|Hepatocellular(266;0.158)				Amitriptyline(DB00321)|Imatinib(DB00619)|Regorafenib(DB08896)	GGGACTGGGCGGAGTGCCTGA	0.657			T	"""TPM3, TPR, TFG"""	papillary thyroid					TSP Lung(10;0.080)			ENSG00000198400	G|||	3	0.000599042	0.0	0.0	5008	,	,		17479	0.0		0.0	False		,,,				2504	0.0031							Dom	yes		1	1q21-q22	4914	"""neurotrophic tyrosine kinase, receptor, type 1"""		E	0								G	ARG/GLY,ARG/GLY,ARG/GLY	1,4405	2.1+/-5.4	0,1,2202	59.0	60.0	60.0		415,505,505	1.4	0.0	1		60	2,8598	2.2+/-6.3	0,2,4298	no	missense,missense,missense	NTRK1	NM_001007792.1,NM_001012331.1,NM_002529.3	125,125,125	0,3,6500	AA,AG,GG		0.0233,0.0227,0.0231	possibly-damaging,possibly-damaging,possibly-damaging	139/761,169/791,169/797	156837972	3,13003	2203	4300	6503	SO:0001583	missense	0			-	Y09028	CCDS1161.1, CCDS30890.1, CCDS30891.1	1q21-q22	2014-09-17			ENSG00000198400	ENSG00000198400	2.7.10.1	"""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	8031	protein-coding gene	gene with protein product	"""high affinity nerve growth factor receptor"""	191315				2869410	Standard	NM_001007792		Approved	TRK, TRKA, MTC	uc001fqh.1	P04629	OTTHUMG00000041304	ENST00000524377.1:c.505G>A	1.37:g.156837972G>A	ENSP00000431418:p.Gly169Arg		B2R6T5|B7ZM34|P08119|Q15655|Q15656|Q5D056|Q5VZS2|Q7Z5C3|Q9UIU7	Missense_Mutation	SNP	pfam_Ser-Thr/Tyr_kinase_cat_dom,pfam_Prot_kinase_dom,superfamily_Kinase-like_dom,smart_Cys-rich_flank_reg_C,smart_Ser/Thr_dual-sp_kinase_dom,smart_Tyr_kinase_cat_dom,pfscan_Prot_kinase_dom,pfscan_Ig-like_dom,prints_Ser-Thr/Tyr_kinase_cat_dom,prints_Tyr_kinase_neurotrophic_rcpt_1,prints_Tyr_kinase_NGF_rcpt	p.G169R	ENST00000524377.1	37	c.505	CCDS1161.1	1	.	.	.	.	.	.	.	.	.	.	G	14.58	2.577689	0.45902	2.27E-4	2.33E-4	ENSG00000198400	ENST00000392302;ENST00000368196;ENST00000524377;ENST00000358660	D;D;D;D	0.90069	-2.61;-2.61;-2.61;-2.61	4.48	1.43	0.22495	Cysteine-rich flanking region, C-terminal (1);	0.562320	0.15956	N	0.236498	T	0.69088	0.3072	L	0.40543	1.245	0.09310	N	1	B;B;B;B	0.23316	0.008;0.046;0.083;0.067	B;B;B;B	0.19148	0.003;0.009;0.024;0.006	T	0.60193	-0.7311	10	0.40728	T	0.16	.	7.6135	0.28144	0.3738:0.0:0.6262:0.0	.	169;169;169;139	A8K3Z4;P04629-2;P04629;A6NF12	.;.;NTRK1_HUMAN;.	R	139;169;169;169	ENSP00000376120:G139R;ENSP00000357179:G169R;ENSP00000431418:G169R;ENSP00000351486:G169R	ENSP00000351486:G169R	G	+	1	0	NTRK1	155104596	0.003000	0.15002	0.003000	0.11579	0.847000	0.48162	-0.015000	0.12634	0.180000	0.19960	0.462000	0.41574	GGA	-	NTRK1	-	smart_Cys-rich_flank_reg_C		0.657	NTRK1-007	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NTRK1	HGNC	protein_coding	OTTHUMT00000392279.1	0	0	0	38	38	40	0.00	0.00	G	NM_002529		156837972	+1	15	13	64	39	tier1	no_errors	ENST00000524377	ensembl	human	known	74_37	missense	18.99	25.00	SNP	0.001	A	15	64
METTL13	51603	genome.wustl.edu	37	1	171763629	171763629	+	Missense_Mutation	SNP	C	C	G			TCGA-DX-A48N-01A-11D-A307-09	TCGA-DX-A48N-10A-01D-A307-09	C	C	C	G	C	C	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	93d25a05-5221-452e-a4b8-f1504d48e89c	a1a1386f-c8ff-4c7c-b1ee-19a86bd40af2	g.chr1:171763629C>G	ENST00000361735.3	+	7	2053	c.1787C>G	c.(1786-1788)tCt>tGt	p.S596C	METTL13_ENST00000458517.1_Missense_Mutation_p.S595C|METTL13_ENST00000466643.1_3'UTR|METTL13_ENST00000367737.5_Missense_Mutation_p.S440C|METTL13_ENST00000362019.3_Missense_Mutation_p.S510C	NM_015935.4	NP_057019.3	Q8N6R0	MET13_HUMAN	methyltransferase like 13	596							methyltransferase activity (GO:0008168)			breast(3)|cervix(1)|endometrium(4)|kidney(5)|large_intestine(8)|lung(17)|stomach(3)	41						GTGGAGCAATCTTTTCTACAG	0.448													ENSG00000010165																																					0													80.0	72.0	75.0					1																	171763629		2203	4300	6503	SO:0001583	missense	0			-	AF132936	CCDS1299.1, CCDS1300.1, CCDS30936.1	1q24-q25.3	2009-02-23	2009-02-23	2009-02-23	ENSG00000010165	ENSG00000010165			24248	protein-coding gene	gene with protein product			"""KIAA0859"""	KIAA0859		10810093, 10048485	Standard	NM_001007239		Approved	CGI-01	uc001ghz.3	Q8N6R0	OTTHUMG00000034912	ENST00000361735.3:c.1787C>G	1.37:g.171763629C>G	ENSP00000354920:p.Ser596Cys		A6NFK0|A8K6S5|O94940|Q53EZ6|Q5TGP9|Q5TGQ0|Q8N2P8|Q96J11|Q96SQ0|Q9Y2Z1|Q9Y3M6	Missense_Mutation	SNP	pfam_Methyltransf_11,pfam_Spermidine/spermine_synthase	p.S596C	ENST00000361735.3	37	c.1787	CCDS1299.1	1	.	.	.	.	.	.	.	.	.	.	C	12.59	1.985074	0.35036	.	.	ENSG00000010165	ENST00000458517;ENST00000362019;ENST00000367737;ENST00000361735;ENST00000367736;ENST00000341850	T;T;T;T;T	0.77877	-1.13;-1.13;-1.13;-1.13;-1.13	5.84	0.257	0.15574	.	1.243330	0.05024	N	0.473287	T	0.59569	0.2203	L	0.41824	1.3	0.09310	N	1	P;B;B	0.37352	0.591;0.352;0.405	P;B;B	0.45829	0.494;0.361;0.421	T	0.57481	-0.7804	10	0.62326	D	0.03	-35.223	4.2153	0.10531	0.2298:0.4891:0.0:0.2811	.	595;440;596	B4E2X3;Q8N6R0-1;Q8N6R0	.;.;MTL13_HUMAN	C	595;510;440;596;296;293	ENSP00000401955:S595C;ENSP00000355393:S510C;ENSP00000356711:S440C;ENSP00000354920:S596C;ENSP00000356710:S296C	ENSP00000341732:S293C	S	+	2	0	METTL13	170030252	0.000000	0.05858	0.128000	0.21923	0.681000	0.39784	0.306000	0.19279	0.375000	0.24679	0.655000	0.94253	TCT	-	METTL13	-	pfam_Spermidine/spermine_synthase		0.448	METTL13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	METTL13	HGNC	protein_coding	OTTHUMT00000084528.5	0	0	0	52	52	94	0.00	0.00	C	NM_014955		171763629	+1	16	50	184	314	tier1	no_errors	ENST00000361735	ensembl	human	known	74_37	missense	8.00	13.74	SNP	0.002	G	16	184
HMMR	3161	genome.wustl.edu	37	5	162891728	162891728	+	Splice_Site	SNP	G	G	C			TCGA-DX-A48N-01A-11D-A307-09	TCGA-DX-A48N-10A-01D-A307-09	G	G	G	C	G	G	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	93d25a05-5221-452e-a4b8-f1504d48e89c	a1a1386f-c8ff-4c7c-b1ee-19a86bd40af2	g.chr5:162891728G>C	ENST00000358715.3	+	3	181		c.e3-1		HMMR_ENST00000393915.4_Splice_Site|HMMR_ENST00000432118.2_Intron|HMMR_ENST00000353866.3_Splice_Site			O75330	HMMR_HUMAN	hyaluronan-mediated motility receptor (RHAMM)						carbohydrate metabolic process (GO:0005975)|glycosaminoglycan metabolic process (GO:0030203)|hyaluronan catabolic process (GO:0030214)|hyaluronan metabolic process (GO:0030212)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|membrane (GO:0016020)|plasma membrane (GO:0005886)	hyaluronic acid binding (GO:0005540)			cervix(1)|kidney(3)|large_intestine(6)|lung(9)|pancreas(1)|prostate(1)|skin(1)|stomach(1)	23	Renal(175;0.000281)	Medulloblastoma(196;0.00853)|all_neural(177;0.0408)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	all cancers(165;0.0296)|OV - Ovarian serous cystadenocarcinoma(192;0.0423)|Epithelial(171;0.0848)	Hyaluronan(DB08818)	TTTTTCCGCAGAATCTAAACA	0.333													ENSG00000072571																																					0													111.0	109.0	110.0					5																	162891728		2203	4300	6503	SO:0001630	splice_region_variant	0			-	U29343	CCDS4362.1, CCDS4363.1, CCDS47334.1, CCDS47335.1	5q34	2013-09-19			ENSG00000072571	ENSG00000072571		"""CD molecules"""	5012	protein-coding gene	gene with protein product		600936					Standard	NM_001142556		Approved	RHAMM, CD168	uc003lzh.3	O75330	OTTHUMG00000130381	ENST00000358715.3:c.146-1G>C	5.37:g.162891728G>C			A8K3G2|B4E114|D3DQK9|D3DQL0|E9PCS0|Q32N02|Q92767	Splice_Site	SNP	-	e3-1	ENST00000358715.3	37	c.146-1	CCDS4362.1	5	.	.	.	.	.	.	.	.	.	.	G	8.386	0.838534	0.16891	.	.	ENSG00000072571	ENST00000353866;ENST00000434157;ENST00000393915;ENST00000426586;ENST00000358715	.	.	.	4.87	4.87	0.63330	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.8992	0.63792	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	HMMR	162824306	1.000000	0.71417	0.992000	0.48379	0.023000	0.10783	4.198000	0.58419	2.432000	0.82394	0.563000	0.77884	.	-	HMMR	-	-		0.333	HMMR-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	HMMR	HGNC	protein_coding	OTTHUMT00000252752.1	0	0	0	47	47	73	0.00	0.00	G	NM_012484	Intron	162891728	+1	13	21	73	93	tier1	no_errors	ENST00000393915	ensembl	human	known	74_37	splice_site	15.12	18.42	SNP	0.992	C	13	73
ZNF611	81856	genome.wustl.edu	37	19	53208629	53208629	+	Missense_Mutation	SNP	T	T	G			TCGA-DX-A48N-01A-11D-A307-09	TCGA-DX-A48N-10A-01D-A307-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	93d25a05-5221-452e-a4b8-f1504d48e89c	a1a1386f-c8ff-4c7c-b1ee-19a86bd40af2	g.chr19:53208629T>G	ENST00000319783.1	-	7	1995	c.1679A>C	c.(1678-1680)cAt>cCt	p.H560P	ZNF611_ENST00000595798.1_Missense_Mutation_p.H491P|ZNF611_ENST00000602046.1_5'Flank|ZNF611_ENST00000602162.1_Missense_Mutation_p.H491P|ZNF611_ENST00000453741.2_Missense_Mutation_p.H491P|ZNF611_ENST00000540744.1_Missense_Mutation_p.H560P|ZNF611_ENST00000543227.1_Missense_Mutation_p.H560P	NM_030972.3	NP_112234.3	Q8N823	ZN611_HUMAN	zinc finger protein 611	560					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(4)|kidney(4)|large_intestine(10)|lung(12)|ovary(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	36				OV - Ovarian serous cystadenocarcinoma(262;0.0233)|GBM - Glioblastoma multiforme(134;0.04)		CTCTCCACTATGAATTCTAGT	0.403													ENSG00000213020																																					0													200.0	195.0	196.0					19																	53208629		2203	4297	6500	SO:0001583	missense	0			-	AK091389	CCDS12855.1, CCDS54312.1	19q13.42	2013-01-08			ENSG00000213020	ENSG00000213020		"""Zinc fingers, C2H2-type"", ""-"""	28766	protein-coding gene	gene with protein product						12477932	Standard	NM_030972		Approved	MGC5384	uc010ydq.2	Q8N823	OTTHUMG00000154908	ENST00000319783.1:c.1679A>C	19.37:g.53208629T>G	ENSP00000322427:p.His560Pro		B3KRD5|Q69YG9	Missense_Mutation	SNP	pfam_Znf_C2H2,pfam_Krueppel-associated_box,superfamily_Krueppel-associated_box,smart_Krueppel-associated_box,smart_Znf_C2H2-like,pfscan_Znf_C2H2,pfscan_Krueppel-associated_box	p.H560P	ENST00000319783.1	37	c.1679	CCDS12855.1	19	.	.	.	.	.	.	.	.	.	.	.	10.52	1.374590	0.24857	.	.	ENSG00000213020	ENST00000543227;ENST00000540744;ENST00000453741;ENST00000319783	T;T;T;T	0.67698	-0.28;-0.28;-0.28;-0.28	1.47	1.47	0.22746	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	D	0.85839	0.5790	H	0.97611	4.04	0.27605	N	0.948834	D	0.89917	1.0	D	0.97110	1.0	T	0.74797	-0.3543	9	0.87932	D	0	.	7.8147	0.29252	0.0:0.0:0.0:1.0	.	560	Q8N823	ZN611_HUMAN	P	560;560;491;560	ENSP00000437616:H560P;ENSP00000439211:H560P;ENSP00000443505:H491P;ENSP00000322427:H560P	ENSP00000322427:H560P	H	-	2	0	ZNF611	57900441	0.999000	0.42202	0.491000	0.27477	0.246000	0.25737	3.441000	0.52893	0.656000	0.30886	0.163000	0.16589	CAT	-	ZNF611	-	smart_Znf_C2H2-like,pfscan_Znf_C2H2		0.403	ZNF611-001	KNOWN	basic|appris_principal|CCDS	protein_coding	ZNF611	HGNC	protein_coding	OTTHUMT00000337612.1	0	0	0	71	71	29	0.00	0.00	T	NM_030972		53208629	-1	67	21	71	16	tier1	no_errors	ENST00000319783	ensembl	human	known	74_37	missense	48.55	55.26	SNP	1.000	G	67	71
LACE1	246269	genome.wustl.edu	37	6	108616232	108616232	+	5'UTR	SNP	C	C	G	rs559248641		TCGA-DX-A48N-01A-11D-A307-09	TCGA-DX-A48N-10A-01D-A307-09	C	C	C	G	C	C	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	93d25a05-5221-452e-a4b8-f1504d48e89c	a1a1386f-c8ff-4c7c-b1ee-19a86bd40af2	g.chr6:108616232C>G	ENST00000368977.4	+	0	135				RNU6-1144P_ENST00000384247.1_RNA	NM_145315.3	NP_660358.2	Q8WV93	LACE1_HUMAN	lactation elevated 1							mitochondrion (GO:0005739)	ATP binding (GO:0005524)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(6)|lung(4)|upper_aerodigestive_tract(1)	15		all_cancers(87;1.5e-07)|Acute lymphoblastic leukemia(125;2.66e-08)|all_hematologic(75;1.13e-06)|all_epithelial(87;6.79e-05)|Colorectal(196;0.0294)|all_lung(197;0.0486)|Lung SC(18;0.152)		BRCA - Breast invasive adenocarcinoma(108;0.00179)|Epithelial(106;0.0024)|all cancers(137;0.00379)|OV - Ovarian serous cystadenocarcinoma(136;0.0118)		CACCGTCTCTCTTCTGGGTTC	0.567													ENSG00000135537																																					0													28.0	25.0	26.0					6																	108616232		870	1991	2861	SO:0001623	5_prime_UTR_variant	0			-	AF520418	CCDS5067.1	6q22.1	2006-11-10			ENSG00000135537	ENSG00000135537			16411	protein-coding gene	gene with protein product	"""ATPase family gene 1 homolog (S. cerevisiae)"""					12079282	Standard	XM_005266885		Approved	AFG1	uc003psj.3	Q8WV93	OTTHUMG00000015324	ENST00000368977.4:c.-52C>G	6.37:g.108616232C>G			Q8N6A3	R	SNP	-	NULL	ENST00000368977.4	37	NULL	CCDS5067.1	6																																																																																			-	LACE1	-	-		0.567	LACE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	LACE1	HGNC	protein_coding	OTTHUMT00000041719.4	0	0	0	32	32	41	0.00	0.00	C	NM_145315		108616232	+1	24	6	52	40	tier1	no_errors	ENST00000430458	ensembl	human	known	74_37	rna	31.58	13.04	SNP	0.000	G	24	52
TGFB1	7040	genome.wustl.edu	37	19	41850691	41850691	+	Missense_Mutation	SNP	C	C	G			TCGA-DX-A48N-01A-11D-A307-09	TCGA-DX-A48N-10A-01D-A307-09	C	C	C	G	C	C	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	93d25a05-5221-452e-a4b8-f1504d48e89c	a1a1386f-c8ff-4c7c-b1ee-19a86bd40af2	g.chr19:41850691C>G	ENST00000221930.5	-	3	1461	c.595G>C	c.(595-597)Gat>Cat	p.D199H		NM_000660.4	NP_000651.3	P01137	TGFB1_HUMAN	transforming growth factor, beta 1	199	Arm domain. {ECO:0000250}.				active induction of host immune response by virus (GO:0046732)|adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains (GO:0002460)|aging (GO:0007568)|ATP biosynthetic process (GO:0006754)|blood coagulation (GO:0007596)|branch elongation involved in mammary gland duct branching (GO:0060751)|cell cycle arrest (GO:0007050)|cell growth (GO:0016049)|cell-cell junction organization (GO:0045216)|cellular calcium ion homeostasis (GO:0006874)|cellular response to dexamethasone stimulus (GO:0071549)|cellular response to organic cyclic compound (GO:0071407)|cellular response to transforming growth factor beta stimulus (GO:0071560)|chondrocyte differentiation (GO:0002062)|common-partner SMAD protein phosphorylation (GO:0007182)|connective tissue replacement involved in inflammatory response wound healing (GO:0002248)|defense response to fungus, incompatible interaction (GO:0009817)|digestive tract development (GO:0048565)|embryo development (GO:0009790)|endoderm development (GO:0007492)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial to mesenchymal transition (GO:0001837)|evasion or tolerance of host defenses by virus (GO:0019049)|extracellular matrix assembly (GO:0085029)|extracellular matrix organization (GO:0030198)|extrinsic apoptotic signaling pathway (GO:0097191)|face morphogenesis (GO:0060325)|female pregnancy (GO:0007565)|frontal suture morphogenesis (GO:0060364)|germ cell migration (GO:0008354)|hematopoietic progenitor cell differentiation (GO:0002244)|hyaluronan catabolic process (GO:0030214)|inflammatory response (GO:0006954)|inner ear development (GO:0048839)|lens fiber cell differentiation (GO:0070306)|lipopolysaccharide-mediated signaling pathway (GO:0031663)|lymph node development (GO:0048535)|macrophage derived foam cell differentiation (GO:0010742)|mammary gland branching involved in thelarche (GO:0060744)|MAPK cascade (GO:0000165)|mitotic cell cycle checkpoint (GO:0007093)|modulation by virus of host morphology or physiology (GO:0019048)|mononuclear cell proliferation (GO:0032943)|myelination (GO:0042552)|myeloid dendritic cell differentiation (GO:0043011)|negative regulation of blood vessel endothelial cell migration (GO:0043537)|negative regulation of cell cycle (GO:0045786)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of DNA replication (GO:0008156)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of extracellular matrix disassembly (GO:0010716)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of gene expression (GO:0010629)|negative regulation of hyaluronan biosynthetic process (GO:1900126)|negative regulation of immune response (GO:0050777)|negative regulation of macrophage cytokine production (GO:0010936)|negative regulation of mitotic cell cycle (GO:0045930)|negative regulation of myoblast differentiation (GO:0045662)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of ossification (GO:0030279)|negative regulation of phagocytosis (GO:0050765)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of release of sequestered calcium ion into cytosol (GO:0051280)|negative regulation of skeletal muscle tissue development (GO:0048642)|negative regulation of T cell proliferation (GO:0042130)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|organ regeneration (GO:0031100)|ossification involved in bone remodeling (GO:0043932)|pathway-restricted SMAD protein phosphorylation (GO:0060389)|phosphate-containing compound metabolic process (GO:0006796)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of apoptotic process (GO:0043065)|positive regulation of blood vessel endothelial cell migration (GO:0043536)|positive regulation of bone mineralization (GO:0030501)|positive regulation of branching involved in ureteric bud morphogenesis (GO:0090190)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cellular protein metabolic process (GO:0032270)|positive regulation of chemotaxis (GO:0050921)|positive regulation of collagen biosynthetic process (GO:0032967)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of exit from mitosis (GO:0031536)|positive regulation of extracellular matrix assembly (GO:1901203)|positive regulation of fibroblast migration (GO:0010763)|positive regulation of gene expression (GO:0010628)|positive regulation of histone acetylation (GO:0035066)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of interleukin-17 production (GO:0032740)|positive regulation of isotype switching to IgA isotypes (GO:0048298)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of NAD+ ADP-ribosyltransferase activity (GO:1901666)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of odontogenesis (GO:0042482)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of protein complex assembly (GO:0031334)|positive regulation of protein dephosphorylation (GO:0035307)|positive regulation of protein import into nucleus (GO:0042307)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein localization to nucleus (GO:1900182)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of protein secretion (GO:0050714)|positive regulation of SMAD protein import into nucleus (GO:0060391)|positive regulation of smooth muscle cell differentiation (GO:0051152)|positive regulation of superoxide anion generation (GO:0032930)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription regulatory region DNA binding (GO:2000679)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation vascular endothelial growth factor production (GO:0010575)|protein export from nucleus (GO:0006611)|protein import into nucleus, translocation (GO:0000060)|protein kinase B signaling (GO:0043491)|protein phosphorylation (GO:0006468)|receptor catabolic process (GO:0032801)|regulation of actin cytoskeleton reorganization (GO:2000249)|regulation of binding (GO:0051098)|regulation of blood vessel remodeling (GO:0060312)|regulation of branching involved in mammary gland duct morphogenesis (GO:0060762)|regulation of cartilage development (GO:0061035)|regulation of cell migration (GO:0030334)|regulation of DNA binding (GO:0051101)|regulation of miRNA metabolic process (GO:2000628)|regulation of protein import into nucleus (GO:0042306)|regulation of sodium ion transport (GO:0002028)|regulation of striated muscle tissue development (GO:0016202)|regulation of transforming growth factor beta receptor signaling pathway (GO:0017015)|regulatory T cell differentiation (GO:0045066)|response to cholesterol (GO:0070723)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to glucose (GO:0009749)|response to hypoxia (GO:0001666)|response to laminar fluid shear stress (GO:0034616)|response to progesterone (GO:0032570)|response to radiation (GO:0009314)|response to vitamin D (GO:0033280)|response to wounding (GO:0009611)|salivary gland morphogenesis (GO:0007435)|SMAD protein complex assembly (GO:0007183)|SMAD protein import into nucleus (GO:0007184)|T cell homeostasis (GO:0043029)|tolerance induction to self antigen (GO:0002513)|transforming growth factor beta receptor signaling pathway (GO:0007179)|ureteric bud development (GO:0001657)|viral life cycle (GO:0019058)	axon (GO:0030424)|blood microparticle (GO:0072562)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi lumen (GO:0005796)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|platelet alpha granule lumen (GO:0031093)|proteinaceous extracellular matrix (GO:0005578)	antigen binding (GO:0003823)|cytokine activity (GO:0005125)|enzyme binding (GO:0019899)|glycoprotein binding (GO:0001948)|type II transforming growth factor beta receptor binding (GO:0005114)			endometrium(1)|large_intestine(2)|lung(4)|skin(1)	8					Hyaluronidase(DB00070)	CCGGTGACATCAAAAGATAAC	0.552													ENSG00000105329																																					0													110.0	76.0	88.0					19																	41850691		2203	4300	6503	SO:0001583	missense	0			-	X02812	CCDS33031.1	19q13.1	2014-01-30	2007-02-16			ENSG00000105329		"""Endogenous ligands"""	11766	protein-coding gene	gene with protein product	"""Camurati-Engelmann disease"", ""prepro-transforming growth factor beta-1"""	190180		TGFB, DPD1		10631145, 10843814	Standard	NM_000660		Approved	CED, TGFbeta	uc002oqh.2	P01137		ENST00000221930.5:c.595G>C	19.37:g.41850691C>G	ENSP00000221930:p.Asp199His		A8K792|Q9UCG4	Missense_Mutation	SNP	pfam_TGF-b_N,pfam_TGF-b_C,smart_TGF-b_C,pirsf_TGF-beta,prints_TGFb1,prints_TGF-beta	p.D199H	ENST00000221930.5	37	c.595	CCDS33031.1	19	.	.	.	.	.	.	.	.	.	.	C	25.3	4.621717	0.87460	.	.	ENSG00000105329	ENST00000221930	T	0.77750	-1.12	5.44	5.44	0.79542	Transforming growth factor-beta, N-terminal (1);	0.101665	0.64402	D	0.000004	D	0.88262	0.6389	M	0.84433	2.695	0.80722	D	1	D	0.89917	1.0	D	0.67900	0.954	D	0.89474	0.3745	10	0.87932	D	0	-1.9476	14.6416	0.68729	0.0:1.0:0.0:0.0	.	199	P01137	TGFB1_HUMAN	H	199	ENSP00000221930:D199H	ENSP00000221930:D199H	D	-	1	0	TGFB1	46542531	1.000000	0.71417	0.988000	0.46212	0.980000	0.70556	5.309000	0.65774	2.837000	0.97791	0.655000	0.94253	GAT	-	TGFB1	-	pfam_TGF-b_N,pirsf_TGF-beta,prints_TGF-beta		0.552	TGFB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	TGFB1	HGNC	protein_coding	OTTHUMT00000463500.2	0	0	0	41	41	81	0.00	0.00	C			41850691	-1	15	15	68	71	tier1	no_errors	ENST00000221930	ensembl	human	known	74_37	missense	18.07	17.44	SNP	1.000	G	15	68
GABRG1	2565	genome.wustl.edu	37	4	46067556	46067556	+	Frame_Shift_Del	DEL	G	G	-	rs267600168		TCGA-DX-A48N-01A-11D-A307-09	TCGA-DX-A48N-10A-01D-A307-09	G	G	G	-	G	G	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	93d25a05-5221-452e-a4b8-f1504d48e89c	a1a1386f-c8ff-4c7c-b1ee-19a86bd40af2	g.chr4:46067556delG	ENST00000295452.4	-	4	534	c.367delC	c.(367-369)cgtfs	p.R123fs		NM_173536.3	NP_775807.2	Q8N1C3	GBRG1_HUMAN	gamma-aminobutyric acid (GABA) A receptor, gamma 1	123					gamma-aminobutyric acid signaling pathway (GO:0007214)|synaptic transmission (GO:0007268)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|postsynaptic membrane (GO:0045211)|receptor complex (GO:0043235)	chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)			breast(2)|central_nervous_system(5)|endometrium(3)|kidney(4)|large_intestine(11)|liver(1)|lung(37)|ovary(2)|prostate(5)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	76				Lung(65;0.106)|LUSC - Lung squamous cell carcinoma(721;0.23)	Acamprosate(DB00659)|Adinazolam(DB00546)|Alprazolam(DB00404)|Amoxapine(DB00543)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Chlordiazepoxide(DB00475)|Cinolazepam(DB01594)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Clotiazepam(DB01559)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Fludiazepam(DB01567)|Flumazenil(DB01205)|Flurazepam(DB00690)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Isoflurane(DB00753)|Ketazolam(DB01587)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Topiramate(DB00273)|Triazolam(DB00897)	AATTTTAAACGACTGTCAAAC	0.289													ENSG00000163285																																					0													49.0	49.0	49.0					4																	46067556		2203	4300	6503	SO:0001589	frameshift_variant	0				BC031087	CCDS3470.1	4p12	2012-06-22			ENSG00000163285	ENSG00000163285		"""GABA receptors"", ""Ligand-gated ion channels / GABA(A) receptors"""	4086	protein-coding gene	gene with protein product	"""GABA(A) receptor, gamma"""	137166				1321425	Standard	NM_173536		Approved		uc003gxb.3	Q8N1C3	OTTHUMG00000128609	ENST00000295452.4:c.367delC	4.37:g.46067556delG	ENSP00000295452:p.Arg123fs		Q5H9T8	Frame_Shift_Del	DEL	pfam_Neur_chan_lig-bd,pfam_Neurotrans-gated_channel_TM,superfamily_Neur_chan_lig-bd,superfamily_Neurotrans-gated_channel_TM,prints_GABBAg_rcpt,prints_GABAA_rcpt,prints_GABBAg1_rcpt,prints_GABAAa_rcpt,prints_Neur_channel,tigrfam_Neur_channel	p.R123fs	ENST00000295452.4	37	c.367	CCDS3470.1	4																																																																																				GABRG1	-	pfam_Neur_chan_lig-bd,superfamily_Neur_chan_lig-bd,prints_Neur_channel,tigrfam_Neur_channel		0.289	GABRG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	GABRG1	HGNC	protein_coding	OTTHUMT00000250470.1	0	0	0	31	31	90	0.00	0.00	G	NM_173536		46067556	-1	22	36	30	57	tier1	no_errors	ENST00000295452	ensembl	human	known	74_37	frame_shift_del	42.31	38.71	DEL	1.000	-	22	30
SLC11A1	6556	genome.wustl.edu	37	2	219251373	219251376	+	Frame_Shift_Del	DEL	CTCT	CTCT	-			TCGA-DX-A48N-01A-11D-A307-09	TCGA-DX-A48N-10A-01D-A307-09	CTCT	CTCT	CTCT	-	CTCT	CTCT	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	93d25a05-5221-452e-a4b8-f1504d48e89c	a1a1386f-c8ff-4c7c-b1ee-19a86bd40af2	g.chr2:219251373_219251376delCTCT	ENST00000233202.6	+	5	749_752	c.409_412delCTCT	c.(409-414)ctctggfs	p.LW137fs	SLC11A1_ENST00000473367.1_3'UTR|SLC11A1_ENST00000539932.1_Frame_Shift_Del_p.LW19fs	NM_000578.3	NP_000569.3	P49279	NRAM1_HUMAN	solute carrier family 11 (proton-coupled divalent metal ion transporter), member 1	137					activation of protein kinase activity (GO:0032147)|antigen processing and presentation of peptide antigen (GO:0048002)|cadmium ion transmembrane transport (GO:0070574)|cellular cadmium ion homeostasis (GO:0006876)|cellular iron ion homeostasis (GO:0006879)|defense response to bacterium (GO:0042742)|defense response to Gram-negative bacterium (GO:0050829)|defense response to protozoan (GO:0042832)|divalent metal ion export (GO:0070839)|inflammatory response (GO:0006954)|interaction with host (GO:0051701)|interleukin-2 production (GO:0032623)|interleukin-3 production (GO:0032632)|iron ion homeostasis (GO:0055072)|iron ion transport (GO:0006826)|L-arginine import (GO:0043091)|macrophage activation (GO:0042116)|manganese ion transport (GO:0006828)|MHC class II biosynthetic process (GO:0045342)|mRNA stabilization (GO:0048255)|multicellular organismal iron ion homeostasis (GO:0060586)|negative regulation of cytokine production (GO:0001818)|nitrite transport (GO:0015707)|phagocytosis (GO:0006909)|phagosome maturation (GO:0090382)|positive regulation of cytokine production (GO:0001819)|positive regulation of dendritic cell antigen processing and presentation (GO:0002606)|positive regulation of gene expression (GO:0010628)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of phagocytosis (GO:0050766)|positive regulation of T-helper 1 type immune response (GO:0002827)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein import into nucleus, translocation (GO:0000060)|respiratory burst (GO:0045730)|response to bacterium (GO:0009617)|response to interferon-gamma (GO:0034341)|response to lipopolysaccharide (GO:0032496)|T cell cytokine production (GO:0002369)|T cell proliferation involved in immune response (GO:0002309)|transmembrane transport (GO:0055085)|vacuolar acidification (GO:0007035)|wound healing (GO:0042060)	cell outer membrane (GO:0009279)|integral component of plasma membrane (GO:0005887)|late endosome (GO:0005770)|late endosome membrane (GO:0031902)|lysosome (GO:0005764)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)|tertiary granule membrane (GO:0070821)	manganese ion transmembrane transporter activity (GO:0005384)|metal ion:proton antiporter activity (GO:0051139)|protein homodimerization activity (GO:0042803)|transition metal ion transmembrane transporter activity (GO:0046915)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(3)|ovary(3)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)	19		Renal(207;0.0474)		Epithelial(149;1.16e-06)|all cancers(144;0.000195)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		CCGCACCGTCCTCTGGCTGACCAT	0.564													ENSG00000018280																																					0																																										SO:0001589	frameshift_variant	0				D38171	CCDS2415.1	2q35	2013-07-18	2013-07-18		ENSG00000018280	ENSG00000018280		"""Solute carriers"""	10907	protein-coding gene	gene with protein product	"""natural resistance-associated macrophage protein 1"""	600266		LSH, NRAMP, NRAMP1		7964458, 7980580	Standard	NM_000578		Approved		uc002vhv.3	P49279	OTTHUMG00000086747	ENST00000233202.6:c.409_412delCTCT	2.37:g.219251373_219251376delCTCT	ENSP00000233202:p.Leu137fs		C0H5Y3	Frame_Shift_Del	DEL	pfam_NRAMP-like,prints_NRAMP-like,tigrfam_NRAMP-like	p.L137fs	ENST00000233202.6	37	c.409_412	CCDS2415.1	2																																																																																				SLC11A1	-	pfam_NRAMP-like,prints_NRAMP-like,tigrfam_NRAMP-like		0.564	SLC11A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	SLC11A1	HGNC	protein_coding	OTTHUMT00000195076.2	0	0	0	20	20	51	0.00	0.00	CTCT	NM_000578		219251376	+1	5	21	22	36	tier1	no_errors	ENST00000233202	ensembl	human	known	74_37	frame_shift_del	18.52	36.84	DEL	1.000:1.000:0.998:1.000	-	5	22
PPP1R3E	90673	genome.wustl.edu	37	14	23764732	23764733	+	IGR	INS	-	-	A			TCGA-DX-A48N-01A-11D-A307-09	TCGA-DX-A48N-10A-01D-A307-09	-	-	-	A	-	-	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	93d25a05-5221-452e-a4b8-f1504d48e89c	a1a1386f-c8ff-4c7c-b1ee-19a86bd40af2	g.chr14:23764732_23764733insA	ENST00000452015.4	-	0	4773				HOMEZ_ENST00000561013.1_Intron|RP11-124D2.7_ENST00000604456.1_RNA|HOMEZ_ENST00000431326.2_5'Flank|PPP1R3E_ENST00000561426.1_5'Flank	NM_001276318.1	NP_001263247.1	Q9H7J1	PPR3E_HUMAN	protein phosphatase 1, regulatory subunit 3E						glycogen metabolic process (GO:0005977)												ACTTCATTCTTAAAAAAAAAAA	0.406													ENSG00000270433																																					0																																										SO:0001628	intergenic_variant	0				AK024489	CCDS61403.1	14q11.2	2013-01-29	2011-10-04		ENSG00000235194	ENSG00000235194		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	14943	protein-coding gene	gene with protein product			"""protein phosphatase 1, regulatory (inhibitor) subunit 3E"""			11948623, 15752363	Standard	NM_001276318		Approved	FLJ00089	uc031qns.1	Q9H7J1	OTTHUMG00000172116		14.37:g.23764743_23764743dupA			D3DS47	R	INS	-	NULL	ENST00000452015.4	37	NULL		14																																																																																				RP11-124D2.7	-	-		0.406	PPP1R3E-001	KNOWN	NMD_exception|basic|appris_principal|readthrough_transcript	protein_coding	ENSG00000270433	Clone_based_vega_gene	protein_coding	OTTHUMT00000416883.2	0	0	0	15	15	9	0.00	0.00	-			23764733	+1	6	2	34	8	tier1	no_errors	ENST00000604456	ensembl	human	known	74_37	rna	15.00	20.00	INS	0.820:0.835	A	6	34
HSPG2	3339	genome.wustl.edu	37	1	22204712	22204712	+	Silent	SNP	G	G	A			TCGA-DX-A48N-01A-11D-A307-09	TCGA-DX-A48N-10A-01D-A307-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	93d25a05-5221-452e-a4b8-f1504d48e89c	a1a1386f-c8ff-4c7c-b1ee-19a86bd40af2	g.chr1:22204712G>A	ENST00000374695.3	-	21	2731	c.2652C>T	c.(2650-2652)agC>agT	p.S884S		NM_005529.5	NP_005520.4	P98160	PGBM_HUMAN	heparan sulfate proteoglycan 2	884	Laminin EGF-like 4; truncated. {ECO:0000255|PROSITE-ProRule:PRU00460}.				angiogenesis (GO:0001525)|brain development (GO:0007420)|carbohydrate metabolic process (GO:0005975)|cardiac muscle tissue development (GO:0048738)|cartilage development involved in endochondral bone morphogenesis (GO:0060351)|chondrocyte differentiation (GO:0002062)|chondroitin sulfate metabolic process (GO:0030204)|embryonic skeletal system morphogenesis (GO:0048704)|endochondral ossification (GO:0001958)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|lipoprotein metabolic process (GO:0042157)|phototransduction, visible light (GO:0007603)|protein localization (GO:0008104)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)	basal lamina (GO:0005605)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|protein C-terminus binding (GO:0008022)			breast(6)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(15)|liver(1)|lung(44)|ovary(10)|pancreas(1)|prostate(10)|skin(9)|upper_aerodigestive_tract(3)|urinary_tract(3)	127		Colorectal(325;3.46e-05)|all_lung(284;7.93e-05)|Lung NSC(340;8.71e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0498)|OV - Ovarian serous cystadenocarcinoma(117;1.14e-26)|Colorectal(126;4.18e-07)|COAD - Colon adenocarcinoma(152;1.82e-05)|GBM - Glioblastoma multiforme(114;3.13e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000756)|STAD - Stomach adenocarcinoma(196;0.00656)|KIRC - Kidney renal clear cell carcinoma(1967;0.00942)|READ - Rectum adenocarcinoma(331;0.0721)|Lung(427;0.223)	Palifermin(DB00039)	AGGTCCCCATGCTGCCACGCT	0.632													ENSG00000142798																																					0													34.0	34.0	34.0					1																	22204712		2203	4300	6503	SO:0001819	synonymous_variant	0			-	M85289	CCDS30625.1	1p36.1-p35	2013-01-29	2007-02-16	2007-02-16	ENSG00000142798	ENSG00000142798		"""Proteoglycans / Extracellular Matrix : Other"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	5273	protein-coding gene	gene with protein product	"""perlecan proteoglycan"""	142461	"""Schwartz-Jampel syndrome 1 (chondrodystrophic myotonia)"""	SJS1		1685141, 11941538	Standard	XM_005245863		Approved	perlecan, PRCAN	uc001bfj.3	P98160	OTTHUMG00000002674	ENST00000374695.3:c.2652C>T	1.37:g.22204712G>A			Q16287|Q5SZI3|Q9H3V5	Silent	SNP	pfam_Ig_I-set,pfam_Immunoglobulin,pfam_Laminin_G,pfam_Laminin_B_type_IV,pfam_EGF_laminin,pfam_LDrepeatLR_classA_rpt,pfam_EG-like_dom,superfamily_ConA-like_lec_gl_sf,superfamily_LDrepeatLR_classA_rpt,smart_SEA_dom,smart_LDrepeatLR_classA_rpt,smart_EG-like_dom,smart_Ig_sub,smart_Ig_sub2,smart_Ig_V-set_subgr,smart_Laminin_B_subgr,smart_EGF_laminin,smart_EGF-like_Ca-bd_dom,smart_Laminin_G,pfscan_EG-like_dom,pfscan_Laminin_B_type_IV,pfscan_EGF_laminin,pfscan_Laminin_G,pfscan_LDrepeatLR_classA_rpt,pfscan_SEA_dom,pfscan_Ig-like_dom,prints_LDrepeatLR_classA_rpt	p.S884	ENST00000374695.3	37	c.2652	CCDS30625.1	1																																																																																			-	HSPG2	-	pfam_EGF_laminin,smart_EGF_laminin		0.632	HSPG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	HSPG2	HGNC	protein_coding	OTTHUMT00000007598.1	0	0	0	38	38	10	0.00	0.00	G	NM_005529		22204712	-1	42	4	37	6	tier1	no_errors	ENST00000374695	ensembl	human	known	74_37	silent	53.16	40.00	SNP	0.591	A	42	37
SPTBN5	51332	genome.wustl.edu	37	15	42154053	42154053	+	Silent	SNP	C	C	T			TCGA-DX-A48N-01A-11D-A307-09	TCGA-DX-A48N-10A-01D-A307-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	93d25a05-5221-452e-a4b8-f1504d48e89c	a1a1386f-c8ff-4c7c-b1ee-19a86bd40af2	g.chr15:42154053C>T	ENST00000320955.6	-	45	7844	c.7617G>A	c.(7615-7617)gcG>gcA	p.A2539A		NM_016642.2	NP_057726.4	Q9NRC6	SPTN5_HUMAN	spectrin, beta, non-erythrocytic 5	2539					actin cytoskeleton organization (GO:0030036)|actin filament capping (GO:0051693)|axon guidance (GO:0007411)|Golgi organization (GO:0007030)|lysosomal transport (GO:0007041)|protein homooligomerization (GO:0051260)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|photoreceptor connecting cilium (GO:0032391)|photoreceptor disc membrane (GO:0097381)|spectrin (GO:0008091)	actin binding (GO:0003779)|dynactin binding (GO:0034452)|dynein intermediate chain binding (GO:0045505)|kinesin binding (GO:0019894)|myosin tail binding (GO:0032029)|protein self-association (GO:0043621)|spectrin binding (GO:0030507)			NS(1)|breast(1)|central_nervous_system(3)|endometrium(9)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(6)|lung(18)|ovary(5)|prostate(8)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	62		all_cancers(109;1.84e-17)|all_epithelial(112;1.12e-15)|Lung NSC(122;7.6e-10)|all_lung(180;4.15e-09)|Melanoma(134;0.0179)|Ovarian(310;0.143)|Colorectal(260;0.173)		all cancers(2;4.33e-34)|Epithelial(2;1.72e-25)|OV - Ovarian serous cystadenocarcinoma(18;8.32e-20)|GBM - Glioblastoma multiforme(94;4.69e-07)|Colorectal(2;0.00104)|COAD - Colon adenocarcinoma(120;0.0405)|READ - Rectum adenocarcinoma(92;0.0908)		AGGGGTGCCCCGCTGTGAGCA	0.642													ENSG00000137877																																					0													25.0	29.0	28.0					15																	42154053		2030	4190	6220	SO:0001819	synonymous_variant	0			-	AF233523	CCDS61599.1	15q21	2010-08-17			ENSG00000137877	ENSG00000137877			15680	protein-coding gene	gene with protein product	"""beta V spectrin"""	605916				10764729	Standard	NM_016642		Approved	HUSPECV, BSPECV, HUBSPECV	uc001zos.4	Q9NRC6		ENST00000320955.6:c.7617G>A	15.37:g.42154053C>T				Silent	SNP	pfam_Spectrin_repeat,pfam_CH-domain,superfamily_CH-domain,smart_CH-domain,smart_Spectrin/alpha-actinin,smart_Pleckstrin_homology,pfscan_CH-domain,pfscan_Pleckstrin_homology	p.A2539	ENST00000320955.6	37	c.7617		15																																																																																			-	SPTBN5	-	pfam_Spectrin_repeat,smart_Spectrin/alpha-actinin		0.642	SPTBN5-001	KNOWN	basic|appris_principal	protein_coding	SPTBN5	HGNC	protein_coding	OTTHUMT00000420237.1	0	0	0	35	35	11	0.00	0.00	C	NM_016642		42154053	-1	39	2	38	2	tier1	no_errors	ENST00000320955	ensembl	human	known	74_37	silent	50.65	50.00	SNP	0.000	T	39	38
C20orf166-AS1	253868	genome.wustl.edu	37	20	61143851	61143851	+	RNA	SNP	C	C	T			TCGA-DX-A48N-01A-11D-A307-09	TCGA-DX-A48N-10A-01D-A307-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	93d25a05-5221-452e-a4b8-f1504d48e89c	a1a1386f-c8ff-4c7c-b1ee-19a86bd40af2	g.chr20:61143851C>T	ENST00000475015.1	-	0	487				C20orf166-AS1_ENST00000412495.1_RNA|C20orf166-AS1_ENST00000436101.1_RNA			Q96NR2	C2AS1_HUMAN	C20orf166 antisense RNA 1																		TCTGCATGTGCCTCTACTTAC	0.662													ENSG00000174403																																					0													85.0	77.0	79.0					20																	61143851		2203	4300	6503			0			-	AK054875		20q13.33	2012-10-12	2012-08-15	2011-08-10	ENSG00000174403	ENSG00000174403		"""Long non-coding RNAs"""	26393	non-coding RNA	RNA, long non-coding			"""chromosome 20 open reading frame 200"", ""non-protein coding RNA 335"", ""C20orf166 antisense RNA 1 (non-protein coding)"""	C20orf200, NCRNA00335			Standard	NR_033263		Approved	FLJ30313	uc002ycz.3	Q96NR2	OTTHUMG00000048002		20.37:g.61143851C>T			Q52LN1	R	SNP	-	NULL	ENST00000475015.1	37	NULL		20																																																																																			-	C20orf166-AS1	-	-		0.662	C20orf166-AS1-002	KNOWN	basic	antisense	C20orf166-AS1	HGNC	antisense	OTTHUMT00000109266.2	0	0	0	88	88	19	0.00	0.00	C	NR_033263		61143851	-1	37	8	246	76	tier1	no_errors	ENST00000412495	ensembl	human	known	74_37	rna	13.07	9.52	SNP	0.003	T	37	246
NOS1	4842	genome.wustl.edu	37	12	117723944	117723944	+	Missense_Mutation	SNP	G	G	A			TCGA-DX-A48N-01A-11D-A307-09	TCGA-DX-A48N-10A-01D-A307-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	93d25a05-5221-452e-a4b8-f1504d48e89c	a1a1386f-c8ff-4c7c-b1ee-19a86bd40af2	g.chr12:117723944G>A	ENST00000338101.4	-	5	1259	c.1255C>T	c.(1255-1257)Cgc>Tgc	p.R419C	NOS1_ENST00000317775.6_Missense_Mutation_p.R419C|NOS1_ENST00000344089.3_3'UTR			Q8WY41	NANO1_HUMAN	nitric oxide synthase 1 (neuronal)	0					cell migration (GO:0016477)|epithelial cell migration (GO:0010631)|negative regulation of translation (GO:0017148)	cytoplasm (GO:0005737)|perinuclear region of cytoplasm (GO:0048471)	RNA binding (GO:0003723)|translation repressor activity (GO:0030371)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(3)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(17)|large_intestine(21)|lung(43)|ovary(3)|pancreas(1)|prostate(6)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	117	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)			BRCA - Breast invasive adenocarcinoma(302;0.0561)		CCCACACAGCGCGAGGCATTC	0.557													ENSG00000089250																									Esophageal Squamous(162;1748 2599 51982 52956)												0													130.0	131.0	131.0					12																	117723944		2168	4298	6466	SO:0001583	missense	0			-		CCDS41842.1, CCDS55890.1	12q24.22	2013-09-19			ENSG00000089250	ENSG00000089250	1.14.13.39		7872	protein-coding gene	gene with protein product		163731		NOS		1385308, 7682706	Standard	NM_001204213		Approved	nNOS	uc001twn.2	P29475	OTTHUMG00000137376	ENST00000338101.4:c.1255C>T	12.37:g.117723944G>A	ENSP00000337459:p.Arg419Cys			Missense_Mutation	SNP	pfam_NO_synthase_oxygenase_dom,pfam_FAD-binding_1,pfam_Flavodoxin/NO_synth,pfam_OxRdtase_FAD/D-bd,pfam_PDZ,superfamily_NO_synthase_oxygenase_dom,superfamily_Riboflavin_synthase-like_b-brl,superfamily_PDZ,smart_PDZ,pirsf_NOS_euk,pfscan_PDZ,pfscan_Flavodoxin/NO_synth,prints_Flavoprot_Pyr_Nucl_cyt_Rdtase,prints_Flavdoxin	p.R419C	ENST00000338101.4	37	c.1255	CCDS55890.1	12	.	.	.	.	.	.	.	.	.	.	G	22.6	4.305182	0.81247	.	.	ENSG00000089250	ENST00000397605;ENST00000317775;ENST00000541241;ENST00000338101	T;T	0.56444	0.46;0.46	4.93	4.93	0.64822	Nitric oxide synthase, oxygenase domain (4);	0.000000	0.85682	D	0.000000	T	0.81763	0.4891	H	0.96175	3.78	0.80722	D	1	D	0.89917	1.0	D	0.79784	0.993	D	0.87928	0.2708	10	0.87932	D	0	-26.0352	18.3299	0.90264	0.0:0.0:1.0:0.0	.	419	P29475	NOS1_HUMAN	C	419	ENSP00000320758:R419C;ENSP00000337459:R419C	ENSP00000320758:R419C	R	-	1	0	NOS1	116208327	1.000000	0.71417	1.000000	0.80357	0.955000	0.61496	4.362000	0.59467	2.559000	0.86315	0.591000	0.81541	CGC	-	NOS1	-	pfam_NO_synthase_oxygenase_dom,superfamily_NO_synthase_oxygenase_dom,pirsf_NOS_euk		0.557	NOS1-002	NOVEL	basic|exp_conf|CCDS	protein_coding	NOS1	HGNC	protein_coding	OTTHUMT00000268053.1	0	0	0	35	35	52	0.00	0.00	G			117723944	-1	13	9	122	103	tier1	no_errors	ENST00000317775	ensembl	human	known	74_37	missense	9.63	8.04	SNP	1.000	A	13	122
CHSY3	337876	genome.wustl.edu	37	5	129241142	129241142	+	Missense_Mutation	SNP	C	C	T	rs540643583	byFrequency	TCGA-DX-A48N-01A-11D-A307-09	TCGA-DX-A48N-10A-01D-A307-09	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	93d25a05-5221-452e-a4b8-f1504d48e89c	a1a1386f-c8ff-4c7c-b1ee-19a86bd40af2	g.chr5:129241142C>T	ENST00000305031.4	+	1	978	c.620C>T	c.(619-621)tCc>tTc	p.S207F	CTC-575N7.1_ENST00000503616.1_RNA|CTC-575N7.1_ENST00000515569.1_RNA	NM_175856.4	NP_787052.3	Q70JA7	CHSS3_HUMAN	chondroitin sulfate synthase 3	207					carbohydrate metabolic process (GO:0005975)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate metabolic process (GO:0030204)|glycosaminoglycan metabolic process (GO:0030203)|small molecule metabolic process (GO:0044281)	Golgi cisterna membrane (GO:0032580)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	glucuronosyl-N-acetylgalactosaminyl-proteoglycan 4-beta-N-acetylgalactosaminyltransferase activity (GO:0047238)|metal ion binding (GO:0046872)|N-acetylgalactosaminyl-proteoglycan 3-beta-glucuronosyltransferase activity (GO:0050510)			central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(7)|lung(9)|ovary(2)|pancreas(1)|prostate(2)|stomach(1)|urinary_tract(1)	28		all_cancers(142;0.0227)|Breast(839;0.198)|Prostate(80;0.215)|Lung NSC(810;0.239)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)	OV - Ovarian serous cystadenocarcinoma(64;0.136)		GAGTTCTTTTCCAGCCAGCAG	0.687													ENSG00000198108																																					0													12.0	18.0	16.0					5																	129241142		2177	4260	6437	SO:0001583	missense	0			-	AB086062	CCDS34223.1	5q13	2013-02-19			ENSG00000198108	ENSG00000198108	2.4.1.175, 2.4.1.226	"""Beta 3-glycosyltransferases"", ""Beta 4-glycosyltransferases"""	24293	protein-coding gene	gene with protein product		609963				12907687	Standard	XM_005271982		Approved	CSS3, CHSY-2	uc003kvd.3	Q70JA7	OTTHUMG00000163043	ENST00000305031.4:c.620C>T	5.37:g.129241142C>T	ENSP00000302629:p.Ser207Phe		B2RP97|Q76L22|Q86Y52	Missense_Mutation	SNP	pfam_Chond_Galc,pfam_Fringe-like	p.S207F	ENST00000305031.4	37	c.620	CCDS34223.1	5	.	.	.	.	.	.	.	.	.	.	C	24.3	4.519188	0.85495	.	.	ENSG00000198108	ENST00000305031	T	0.41758	0.99	3.5	3.5	0.40072	.	0.000000	0.35040	U	0.003487	T	0.60196	0.2250	M	0.63843	1.955	0.80722	D	1	D	0.76494	0.999	D	0.74674	0.984	T	0.62469	-0.6848	9	.	.	.	.	16.3289	0.83001	0.0:1.0:0.0:0.0	.	207	Q70JA7	CHSS3_HUMAN	F	207	ENSP00000302629:S207F	.	S	+	2	0	CHSY3	129269041	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	5.749000	0.68704	2.250000	0.74265	0.460000	0.39030	TCC	-	CHSY3	-	pfam_Fringe-like		0.687	CHSY3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	CHSY3	HGNC	protein_coding	OTTHUMT00000371453.1	0	0	0	32	32	10	0.00	0.00	C	NM_175856		129241142	+1	7	1	20	9	tier1	no_errors	ENST00000305031	ensembl	human	known	74_37	missense	25.93	10.00	SNP	1.000	T	7	20
KRTAP5-5	439915	genome.wustl.edu	37	11	1651420	1651420	+	Missense_Mutation	SNP	G	G	T			TCGA-DX-A48N-01A-11D-A307-09	TCGA-DX-A48N-10A-01D-A307-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	93d25a05-5221-452e-a4b8-f1504d48e89c	a1a1386f-c8ff-4c7c-b1ee-19a86bd40af2	g.chr11:1651420G>T	ENST00000399676.2	+	1	388	c.350G>T	c.(349-351)gGg>gTg	p.G117V		NM_001001480.2	NP_001001480.2	Q701N2	KRA55_HUMAN	keratin associated protein 5-5	117	8 X 4 AA repeats of C-C-X-P.			Missing (in Ref. 1; BAD20201 and 2; CAF31639). {ECO:0000305}.		keratin filament (GO:0045095)				endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(17)|ovary(2)|prostate(5)|urinary_tract(1)	33		all_epithelial(84;0.00018)|Ovarian(85;0.0014)|Breast(177;0.00147)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.000614)|Lung(200;0.0681)|LUSC - Lung squamous cell carcinoma(625;0.082)		GGGTCCAAGGGGGGCTGTGGC	0.701													ENSG00000185940																																					0													16.0	25.0	22.0					11																	1651420		1979	3985	5964	SO:0001583	missense	0			-	AB125074	CCDS41592.1	11p15.5	2008-10-30			ENSG00000185940	ENSG00000185940		"""Keratin associated proteins"""	23601	protein-coding gene	gene with protein product						15144888	Standard	NM_001001480		Approved	KRTAP5.5, KRTAP5-11	uc001lty.3	Q701N2	OTTHUMG00000057554	ENST00000399676.2:c.350G>T	11.37:g.1651420G>T	ENSP00000382584:p.Gly117Val		A8MWN2	Missense_Mutation	SNP	NULL	p.G117V	ENST00000399676.2	37	c.350	CCDS41592.1	11	.	.	.	.	.	.	.	.	.	.	G	4.255	0.046386	0.08243	.	.	ENSG00000185940	ENST00000399676;ENST00000422553	T	0.01126	5.3	2.98	2.98	0.34508	.	.	.	.	.	T	0.04815	0.0130	M	0.84948	2.725	0.36925	D	0.891601	D	0.65815	0.995	P	0.56163	0.793	T	0.19549	-1.0302	9	0.72032	D	0.01	.	9.443	0.38679	0.0:0.0:1.0:0.0	.	117	Q701N2	KRA55_HUMAN	V	117;88	ENSP00000382584:G117V	ENSP00000382584:G117V	G	+	2	0	KRTAP5-5	1607996	0.651000	0.27340	0.990000	0.47175	0.029000	0.11900	0.903000	0.28475	1.240000	0.43803	0.418000	0.28097	GGG	-	KRTAP5-5	-	NULL		0.701	KRTAP5-5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	KRTAP5-5	HGNC	protein_coding	OTTHUMT00000127919.1	0	0	0	53	53	6	0.00	0.00	G			1651420	+1	21	0	25	2	tier1	no_errors	ENST00000399676	ensembl	human	known	74_37	missense	45.65	0.00	SNP	0.998	T	21	25
ASCL1	429	genome.wustl.edu	37	12	103352171	103352172	+	In_Frame_Ins	INS	-	-	GCAGCA	rs71438488|rs3832799|rs369257660		TCGA-DX-A48N-01A-11D-A307-09	TCGA-DX-A48N-10A-01D-A307-09	-	-					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	93d25a05-5221-452e-a4b8-f1504d48e89c	a1a1386f-c8ff-4c7c-b1ee-19a86bd40af2	g.chr12:103352171_103352172insGCAGCA	ENST00000266744.3	+	1	708_709	c.149_150insGCAGCA	c.(148-153)gcgcag>gcGCAGCAgcag	p.61_62insQQ		NM_004316.3	NP_004307.2	P50553	ASCL1_HUMAN	achaete-scute family bHLH transcription factor 1	61	Poly-Gln.			Q -> QQQ (in Ref. 1; AAA58376). {ECO:0000305}.	adrenal chromaffin cell differentiation (GO:0061104)|carotid body glomus cell differentiation (GO:0061103)|cell maturation (GO:0048469)|cellular response to magnetism (GO:0071259)|central nervous system neuron development (GO:0021954)|cerebral cortex development (GO:0021987)|cerebral cortex GABAergic interneuron differentiation (GO:0021892)|commitment of neuronal cell to specific neuron type in forebrain (GO:0021902)|lung epithelial cell differentiation (GO:0060487)|lung neuroendocrine cell differentiation (GO:0061100)|musculoskeletal movement, spinal reflex action (GO:0050883)|negative regulation of apoptotic process (GO:0043066)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of transcription, DNA-templated (GO:0045892)|neuroblast fate determination (GO:0007400)|neuroblast proliferation (GO:0007405)|neurogenesis (GO:0022008)|neuron fate specification (GO:0048665)|neuron migration (GO:0001764)|noradrenergic neuron development (GO:0003358)|noradrenergic neuron fate commitment (GO:0003359)|Notch signaling pathway (GO:0007219)|olfactory pit development (GO:0060166)|oligodendrocyte development (GO:0014003)|positive regulation of cell cycle (GO:0045787)|positive regulation of neural precursor cell proliferation (GO:2000179)|positive regulation of neurogenesis (GO:0050769)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of Notch signaling pathway (GO:0045747)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of epithelial cell differentiation (GO:0030856)|regulation of gene expression (GO:0010468)|regulation of mitotic cell cycle (GO:0007346)|regulation of timing of subpallium neuron differentiation (GO:0060165)|response to epidermal growth factor (GO:0070849)|response to folic acid (GO:0051593)|response to lithium ion (GO:0010226)|response to retinoic acid (GO:0032526)|spinal cord association neuron differentiation (GO:0021527)|spinal cord oligodendrocyte cell fate specification (GO:0021530)|stomach neuroendocrine cell differentiation (GO:0061102)|subpallium neuron fate commitment (GO:0060163)|sympathetic ganglion development (GO:0061549)|sympathetic nervous system development (GO:0048485)|transcription, DNA-templated (GO:0006351)|ventral spinal cord interneuron fate commitment (GO:0060579)|vestibular nucleus development (GO:0021750)	neuronal cell body (GO:0043025)|nucleus (GO:0005634)	bHLH transcription factor binding (GO:0043425)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|double-stranded DNA binding (GO:0003690)|E-box binding (GO:0070888)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding transcription factor activity (GO:0000989)			NS(3)|large_intestine(1)|lung(1)	5						gcgcagagcgcgcagcagcagc	0.757													ENSG00000139352																																					0																																										SO:0001652	inframe_insertion	0				L08424	CCDS31886.1	12q22-q23	2013-10-17	2013-10-17			ENSG00000139352		"""Basic helix-loop-helix proteins"""	738	protein-coding gene	gene with protein product		100790	"""achaete-scute complex (Drosophila) homolog-like 1"", ""achaete-scute complex-like 1 (Drosophila)"", ""achaete-scute complex homolog 1 (Drosophila)"""			8390674	Standard	NM_004316		Approved	ASH1, HASH1, bHLHa46	uc001tjr.4	P50553		ENST00000266744.3:c.180_185dupGCAGCA	12.37:g.103352172_103352177dupGCAGCA	ENSP00000266744:p.Gln60_Gln61dup		A8K3C4|Q9BQ30	In_Frame_Ins	INS	pfam_bHLH_dom,superfamily_bHLH_dom,smart_bHLH_dom,pfscan_bHLH_dom	p.54in_frame_insQQ	ENST00000266744.3	37	c.149_150	CCDS31886.1	12																																																																																				ASCL1	-	NULL		0.757	ASCL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	ASCL1	HGNC	protein_coding	OTTHUMT00000406707.1	0	0	0	0	0	0	0.00	0.00	-			103352172	+1	0	0	1	1	tier1	no_errors	ENST00000266744	ensembl	human	known	74_37	in_frame_ins	0.00	0.00	INS	0.997:0.997	GCAGCA	0	1
AC118282.1	0	genome.wustl.edu	37	4	49200283	49200283	+	RNA	SNP	T	T	A			TCGA-DX-A48N-01A-11D-A307-09	TCGA-DX-A48N-10A-01D-A307-09	T	T					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	93d25a05-5221-452e-a4b8-f1504d48e89c	a1a1386f-c8ff-4c7c-b1ee-19a86bd40af2	g.chr4:49200283T>A	ENST00000408488.1	+	0	60				AC118282.3_ENST00000410505.1_RNA|AC118282.2_ENST00000408820.1_RNA																							ctcatagcagtgttctggaat	0.458													ENSG00000221415																																					0																																												0			-																													4.37:g.49200283T>A				R	SNP	-	NULL	ENST00000408488.1	37	NULL		4																																																																																			-	AC118282.1	-	-		0.458	AC118282.1-201	NOVEL	basic	miRNA	ENSG00000221415	Clone_based_ensembl_gene	miRNA		0	0	0	10	10	0	0.00	0.00	T			49200283	+1	8	0	19	0	tier1	no_errors	ENST00000408488	ensembl	human	novel	74_37	rna	29.63	0.00	SNP	0.005	A	8	19
PDE6B	5158	genome.wustl.edu	37	4	619722	619722	+	Missense_Mutation	SNP	G	G	A			TCGA-DX-A48N-01A-11D-A307-09	TCGA-DX-A48N-10A-01D-A307-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	93d25a05-5221-452e-a4b8-f1504d48e89c	a1a1386f-c8ff-4c7c-b1ee-19a86bd40af2	g.chr4:619722G>A	ENST00000496514.1	+	1	328	c.307G>A	c.(307-309)Gtg>Atg	p.V103M	PDE6B_ENST00000255622.6_Missense_Mutation_p.V103M			P35913	PDE6B_HUMAN	phosphodiesterase 6B, cGMP-specific, rod, beta	103	GAF 1.				cytosolic calcium ion homeostasis (GO:0051480)|GMP metabolic process (GO:0046037)|phototransduction, visible light (GO:0007603)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|retina development in camera-type eye (GO:0060041)|rhodopsin mediated signaling pathway (GO:0016056)|visual perception (GO:0007601)	photoreceptor disc membrane (GO:0097381)|plasma membrane (GO:0005886)	3',5'-cyclic-GMP phosphodiesterase activity (GO:0047555)|metal ion binding (GO:0046872)			NS(1)|breast(3)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(5)|lung(11)|ovary(2)|prostate(2)|urinary_tract(1)	30					Caffeine(DB00201)	GCGCAACGGCGTGGCCGAGCT	0.662													ENSG00000133256																									GBM(71;463 1194 9848 25922 46834)												0													14.0	12.0	13.0					4																	619722		2195	4294	6489	SO:0001583	missense	0			-	BC000249	CCDS33932.1, CCDS46993.1, CCDS54703.1	4p16.3	2014-01-28	2008-07-31		ENSG00000133256	ENSG00000133256	3.1.4.17	"""Phosphodiesterases"""	8786	protein-coding gene	gene with protein product	"""congenital stationary night blindness 3, autosomal dominant"""	180072		PDEB		1313787	Standard	NM_001145292		Approved	CSNB3, rd1, RP40, CSNBAD2	uc003gap.3	P35913	OTTHUMG00000159909	ENST00000496514.1:c.307G>A	4.37:g.619722G>A	ENSP00000420295:p.Val103Met		B7Z9T9|E7ETT3|Q53XN5|Q9BWH5|Q9UD49	Missense_Mutation	SNP	pfam_PDEase_catalytic_dom,pfam_GAF,smart_GAF,smart_HD/PDEase_dom,prints_PDEase	p.V103M	ENST00000496514.1	37	c.307	CCDS33932.1	4	.	.	.	.	.	.	.	.	.	.	G	12.49	1.954748	0.34471	.	.	ENSG00000133256	ENST00000255622;ENST00000496514	T;T	0.68331	-0.32;-0.32	4.98	2.23	0.28157	GAF (2);	0.329570	0.30028	N	0.010582	T	0.60637	0.2284	L	0.34521	1.04	0.09310	N	1	P;P	0.38863	0.65;0.597	P;B	0.48166	0.569;0.433	T	0.52268	-0.8598	10	0.46703	T	0.11	.	7.786	0.29093	0.3535:0.0:0.6465:0.0	.	103;103	P35913;P35913-2	PDE6B_HUMAN;.	M	103	ENSP00000255622:V103M;ENSP00000420295:V103M	ENSP00000255622:V103M	V	+	1	0	PDE6B	609722	0.000000	0.05858	0.961000	0.40146	0.644000	0.38419	0.445000	0.21677	0.499000	0.27970	0.561000	0.74099	GTG	-	PDE6B	-	pfam_GAF,smart_GAF		0.662	PDE6B-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	PDE6B	HGNC	protein_coding	OTTHUMT00000358109.1	0	0	0	47	47	1	0.00	0.00	G	NM_000283		619722	+1	17	0	32	9	tier1	no_errors	ENST00000496514	ensembl	human	known	74_37	missense	34.69	0.00	SNP	0.012	A	17	32
MAML3	55534	genome.wustl.edu	37	4	140811111	140811111	+	Silent	SNP	C	C	T	rs62344937		TCGA-DX-A48N-01A-11D-A307-09	TCGA-DX-A48N-10A-01D-A307-09	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	93d25a05-5221-452e-a4b8-f1504d48e89c	a1a1386f-c8ff-4c7c-b1ee-19a86bd40af2	g.chr4:140811111C>T	ENST00000509479.2	-	2	2335	c.1479G>A	c.(1477-1479)caG>caA	p.Q493Q	MAML3_ENST00000398940.1_Silent_p.Q32Q|MAML3_ENST00000327122.5_Silent_p.Q337Q	NM_018717.4	NP_061187			mastermind-like 3 (Drosophila)											breast(1)|endometrium(7)|kidney(2)|large_intestine(1)|lung(9)|ovary(1)|prostate(2)|urinary_tract(2)	25	all_hematologic(180;0.162)					gctgctgctgctgctgctgct	0.542													ENSG00000196782																																					0													15.0	19.0	17.0					4																	140811111		2180	4283	6463	SO:0001819	synonymous_variant	0			-	AB058719	CCDS54805.1	4q31.1	2014-08-12	2003-09-24		ENSG00000196782	ENSG00000196782			16272	protein-coding gene	gene with protein product	"""mastermind (drosophila)-like 3"""	608991	"""trinucleotide repeat containing 3"""	TNRC3		12370315, 12386158	Standard	NM_018717		Approved	KIAA1816, MAM2, CAGH3, GDN	uc021xsg.1	Q96JK9	OTTHUMG00000161441	ENST00000509479.2:c.1479G>A	4.37:g.140811111C>T				Silent	SNP	pfam_Neuroggenic_mastermind-like_N	p.Q493	ENST00000509479.2	37	c.1479	CCDS54805.1	4																																																																																			rs62344937	MAML3	-	NULL		0.542	MAML3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	MAML3	HGNC	protein_coding	OTTHUMT00000364934.2	0	0	0	45	45	0	0.00	0.00	C			140811111	-1	6	0	27	0	tier1	no_errors	ENST00000509479	ensembl	human	known	74_37	silent	18.18	0.00	SNP	1.000	T	6	27
TTC3	7267	genome.wustl.edu	37	21	38463868	38463869	+	Intron	INS	-	-	TTATTTAT	rs138290419|rs56149628|rs147677870	byFrequency	TCGA-DX-A48N-01A-11D-A307-09	TCGA-DX-A48N-10A-01D-A307-09	-	-					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	93d25a05-5221-452e-a4b8-f1504d48e89c	a1a1386f-c8ff-4c7c-b1ee-19a86bd40af2	g.chr21:38463868_38463869insTTATTTAT	ENST00000399017.2	+	7	3348				TTC3_ENST00000540756.1_Intron|TTC3_ENST00000479930.1_Intron|TTC3_ENST00000399010.1_Intron|TTC3_ENST00000355666.1_Intron|TTC3_ENST00000354749.2_Intron	NM_003316.3	NP_003307.3	P53804	TTC3_HUMAN	tetratricopeptide repeat domain 3						negative regulation of cell morphogenesis involved in differentiation (GO:0010771)|negative regulation of neuron differentiation (GO:0045665)|protein K48-linked ubiquitination (GO:0070936)|ubiquitin-dependent protein catabolic process (GO:0006511)	mitochondrion (GO:0005739)|nucleus (GO:0005634)|vacuole (GO:0005773)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(5)|endometrium(7)|kidney(5)|large_intestine(17)|liver(1)|lung(18)|ovary(4)|prostate(2)|skin(9)|upper_aerodigestive_tract(2)|urinary_tract(5)	75		Myeloproliferative disorder(46;0.0412)				tcttttttttattatttattta	0.302													ENSG00000182670																									Ovarian(38;194 1649 35661)												0																																										SO:0001627	intron_variant	0				D84296	CCDS13651.1	21q22.2	2013-01-11			ENSG00000182670	ENSG00000182670		"""RING-type (C3HC4) zinc fingers"", ""Tetratricopeptide (TTC) repeat domain containing"""	12393	protein-coding gene	gene with protein product		602259				8947847	Standard	NM_003316		Approved	TPRD, TPRDI, DCRR1, TPRDII, TPRDIII, RNF105	uc002yvz.3	P53804	OTTHUMG00000086654	ENST00000399017.2:c.601+155->TTATTTAT	21.37:g.38463869_38463876dupTTATTTAT			A8K7H7|B2RPA7|D3DSG9|D3DSH2|D3DSH3|O60767|P78476|P78477|Q569I2|Q6P578|Q9UEK4	R	INS	-	NULL	ENST00000399017.2	37	NULL	CCDS13651.1	21																																																																																				TTC3	-	-		0.302	TTC3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	TTC3	HGNC	protein_coding	OTTHUMT00000194776.1	0	0	0	0	0	0	0.00	0.00	-			38463869	+1	0	0	0	0	tier1	no_errors	ENST00000484047	ensembl	human	known	74_37	rna	0.00	0.00	INS	0.001:0.000	TTATTTAT	0	0
MTMR9	66036	genome.wustl.edu	37	8	11177525	11177526	+	Intron	INS	-	-	T	rs113060213		TCGA-DX-A48N-01A-11D-A307-09	TCGA-DX-A48N-10A-01D-A307-09	-	-					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	93d25a05-5221-452e-a4b8-f1504d48e89c	a1a1386f-c8ff-4c7c-b1ee-19a86bd40af2	g.chr8:11177525_11177526insT	ENST00000221086.3	+	9	1959				AF131216.6_ENST00000498997.2_RNA|MTMR9_ENST00000526292.1_Intron	NM_015458.3	NP_056273.2	Q96QG7	MTMR9_HUMAN	myotubularin related protein 9							cytoplasm (GO:0005737)	enzyme regulator activity (GO:0030234)|phosphatase activity (GO:0016791)			cervix(1)|endometrium(3)|kidney(2)|large_intestine(2)|lung(4)|ovary(1)|skin(1)|urinary_tract(2)	16			STAD - Stomach adenocarcinoma(15;0.215)	COAD - Colon adenocarcinoma(149;0.0678)		TCTAGCCACACTTTTTTTTTTT	0.361													ENSG00000246477																																					0																																										SO:0001627	intron_variant	0				AJ297823	CCDS5979.1	8p23-p22	2011-06-09	2002-09-05	2002-09-06	ENSG00000104643	ENSG00000104643		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Myotubularins"""	14596	protein-coding gene	gene with protein product		606260	"""myotubularin related protein 8"""	C8orf9, MTMR8		11472061, 11896452, 12890864	Standard	NM_015458		Approved	DKFZp434K171, LIP-STYX	uc003wtm.3	Q96QG7	OTTHUMG00000090647	ENST00000221086.3:c.1486+178->T	8.37:g.11177536_11177536dupT			B7Z291|Q52LU3|Q8WW11|Q96QG6|Q9NX50	R	INS	-	NULL	ENST00000221086.3	37	NULL	CCDS5979.1	8																																																																																				AF131216.6	-	-		0.361	MTMR9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	LOC101929290	Clone_based_vega_gene	protein_coding	OTTHUMT00000207307.2	0	0	0	19	19	30	0.00	0.00	-	NM_015458		11177526	-1	4	3	16	32	tier1	no_errors	ENST00000498997	ensembl	human	known	74_37	rna	20.00	8.57	INS	0.004:0.005	T	4	16
