#version 2.4
## 
## Oncotator v1.8.0.0 | Flat File Reference hg19 | GENCODE v19 EFFECT | UniProt_AAxform 2014_12 | ClinVar 12.03.20 | ESP 6500SI-V2 | ORegAnno UCSC Track | dbSNP build 142 | CCLE_By_GP 09292010 | COSMIC v62_291112 | 1000gp3 20130502 | UniProt_AA 2014_12 | dbNSFP v2.4 | ESP 6500SI-V2 | COSMIC_FusionGenes v62_291112 | gencode_xref_refseq metadata_v19 | CCLE_By_Gene 09292010 | ACHILLES_Lineage_Results 110303 | CGC full_2012-03-15 | UniProt 2014_12 | HumanDNARepairGenes 20110905 | HGNC Sept172014 | COSMIC_Tissue 291112 | Familial_Cancer_Genes 20110905 | TUMORScape 20100104 | Ensembl ICGC MUCOPA | TCGAScape 110405 | MutSig Published Results 20110905 
Hugo_Symbol	Entrez_Gene_Id	Center	NCBI_Build	Chromosome	Start_position	End_position	Strand	Variant_Classification	Variant_Type	Reference_Allele	Tumor_Seq_Allele1	Tumor_Seq_Allele2	dbSNP_RS	dbSNP_Val_Status	Tumor_Sample_Barcode	Matched_Norm_Sample_Barcode	Match_Norm_Seq_Allele1	Match_Norm_Seq_Allele2	Tumor_Validation_Allele1	Tumor_Validation_Allele2	Match_Norm_Validation_Allele1	Match_Norm_Validation_Allele2	Verification_Status	Validation_Status	Mutation_Status	Sequencing_Phase	Sequence_Source	Validation_Method	Score	BAM_file	Sequencer	Tumor_Sample_UUID	Matched_Norm_Sample_UUID	Genome_Change	Annotation_Transcript	Transcript_Strand	Transcript_Exon	Transcript_Position	cDNA_Change	Codon_Change	Protein_Change	Other_Transcripts	Refseq_mRNA_Id	Refseq_prot_Id	SwissProt_acc_Id	SwissProt_entry_Id	Description	UniProt_AApos	UniProt_Region	UniProt_Site	UniProt_Natural_Variations	UniProt_Experimental_Info	GO_Biological_Process	GO_Cellular_Component	GO_Molecular_Function	COSMIC_overlapping_mutations	COSMIC_fusion_genes	COSMIC_tissue_types_affected	COSMIC_total_alterations_in_gene	Tumorscape_Amplification_Peaks	Tumorscape_Deletion_Peaks	TCGAscape_Amplification_Peaks	TCGAscape_Deletion_Peaks	DrugBank	ref_context	gc_content	CCLE_ONCOMAP_overlapping_mutations	CCLE_ONCOMAP_total_mutations_in_gene	CGC_Mutation_Type	CGC_Translocation_Partner	CGC_Tumor_Types_Somatic	CGC_Tumor_Types_Germline	CGC_Other_Diseases	DNARepairGenes_Role	FamilialCancerDatabase_Syndromes	MUTSIG_Published_Results	OREGANNO_ID	OREGANNO_Values	i_1000gp3_AA	i_1000gp3_AC	i_1000gp3_AF	i_1000gp3_AFR_AF	i_1000gp3_AMR_AF	i_1000gp3_AN	i_1000gp3_CIEND	i_1000gp3_CIPOS	i_1000gp3_CS	i_1000gp3_DP	i_1000gp3_EAS_AF	i_1000gp3_END	i_1000gp3_EUR_AF	i_1000gp3_IMPRECISE	i_1000gp3_MC	i_1000gp3_MEINFO	i_1000gp3_MEND	i_1000gp3_MLEN	i_1000gp3_MSTART	i_1000gp3_NS	i_1000gp3_SAS_AF	i_1000gp3_SVLEN	i_1000gp3_SVTYPE	i_1000gp3_TSD	i_ACHILLES_Lineage_Results_Top_Genes	i_CGC_Cancer Germline Mut	i_CGC_Cancer Molecular Genetics	i_CGC_Cancer Somatic Mut	i_CGC_Cancer Syndrome	i_CGC_Chr	i_CGC_Chr Band	i_CGC_GeneID	i_CGC_Name	i_CGC_Other Germline Mut	i_CGC_Tissue Type	i_COSMIC_n_overlapping_mutations	i_COSMIC_overlapping_mutation_descriptions	i_COSMIC_overlapping_primary_sites	i_ClinVar_ASSEMBLY	i_ClinVar_HGMD_ID	i_ClinVar_SYM	i_ClinVar_TYPE	i_ClinVar_rs	i_ESP_AA	i_ESP_AAC	i_ESP_AA_AC	i_ESP_AA_AGE	i_ESP_AA_GTC	i_ESP_AvgAAsampleReadDepth	i_ESP_AvgEAsampleReadDepth	i_ESP_AvgSampleReadDepth	i_ESP_CA	i_ESP_CDP	i_ESP_CG	i_ESP_CP	i_ESP_Chromosome	i_ESP_DBSNP	i_ESP_DP	i_ESP_EA_AC	i_ESP_EA_AGE	i_ESP_EA_GTC	i_ESP_EXOME_CHIP	i_ESP_FG	i_ESP_GL	i_ESP_GM	i_ESP_GS	i_ESP_GTC	i_ESP_GTS	i_ESP_GWAS_PUBMED	i_ESP_MAF	i_ESP_PH	i_ESP_PP	i_ESP_Position	i_ESP_TAC	i_ESP_TotalAAsamplesCovered	i_ESP_TotalEAsamplesCovered	i_ESP_TotalSamplesCovered	i_Ensembl_so_accession	i_Ensembl_so_term	i_Entrez_Gene_Id	i_Familial_Cancer_Genes_Reference	i_Familial_Cancer_Genes_Synonym	i_HGNC_Accession Numbers	i_HGNC_CCDS IDs	i_HGNC_Chromosome	i_HGNC_Date Modified	i_HGNC_Date Name Changed	i_HGNC_Date Symbol Changed	i_HGNC_Ensembl Gene ID	i_HGNC_Ensembl ID(supplied by Ensembl)	i_HGNC_Enzyme IDs	i_HGNC_Gene family description	i_HGNC_HGNC ID	i_HGNC_Locus Group	i_HGNC_Locus Type	i_HGNC_Name Synonyms	i_HGNC_OMIM ID(supplied by NCBI)	i_HGNC_Previous Names	i_HGNC_Previous Symbols	i_HGNC_Primary IDs	i_HGNC_Pubmed IDs	i_HGNC_Record Type	i_HGNC_RefSeq(supplied by NCBI)	i_HGNC_Secondary IDs	i_HGNC_Status	i_HGNC_Synonyms	i_HGNC_UCSC ID(supplied by UCSC)	i_HGNC_UniProt ID(supplied by UniProt)	i_HGNC_VEGA IDs	i_HGVS_coding_DNA_change	i_HGVS_genomic_change	i_HGVS_protein_change	i_ORegAnno_bin	i_UniProt_alt_uniprot_accessions	i_Variant_Classification	i_Variant_Type	i_annotation_transcript	i_build	i_ccds_id	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_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_type	i_havana_transcript	i_refseq_mrna_id	i_secondary_variant_classification	i_t_alt_count_full	i_t_ref_count_full	t_alt_count	t_ref_count
OR6Q1	219952	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	11	57799000	57799000	+	Silent	SNP	G	G	A	rs528605468		TCGA-HW-7491-01A-11D-2024-08	TCGA-HW-7491-10A-01D-2024-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1c29c663-c1ec-468e-9e86-74a2b70da59e	0ba3d269-712a-4990-a51b-7288d4f2adbb	g.chr11:57799000G>A	ENST00000302622.3	+	1	599	c.576G>A	c.(574-576)tcG>tcA	p.S192S	OR9Q1_ENST00000335397.3_Intron	NM_001005186.2	NP_001005186.2	Q8NGQ2	OR6Q1_HUMAN	olfactory receptor, family 6, subfamily Q, member 1	192						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			biliary_tract(1)|central_nervous_system(1)|kidney(1)|large_intestine(3)|lung(11)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	21		Breast(21;0.0707)|all_epithelial(135;0.142)				TAGCCTTGTCGTGCTCAGATG	0.498													G|||	1	0.000199681	0.0	0.0	5008	,	,		24556	0.0		0.0	False		,,,				2504	0.001															0													253.0	223.0	233.0					11																	57799000		2201	4296	6497	SO:0001819	synonymous_variant	219952			AB065737	CCDS31541.1	11q12.1	2012-08-09			ENSG00000172381	ENSG00000172381		"""GPCR / Class A : Olfactory receptors"""	15302	protein-coding gene	gene with protein product							Standard	NM_001005186		Approved		uc010rjz.2	Q8NGQ2	OTTHUMG00000168831	ENST00000302622.3:c.576G>A	11.37:g.57799000G>A			B9EKW1|Q6IFH1|Q96R34	Silent	SNP	ENST00000302622.3	37	CCDS31541.1																																																																																				0.498	OR6Q1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401257.1	NM_001005186		70	65	70	65
CMKLR1	1240	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	12	108685742	108685742	+	Missense_Mutation	SNP	C	C	T	rs201296420		TCGA-HW-7491-01A-11D-2024-08	TCGA-HW-7491-10A-01D-2024-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1c29c663-c1ec-468e-9e86-74a2b70da59e	0ba3d269-712a-4990-a51b-7288d4f2adbb	g.chr12:108685742C>T	ENST00000312143.7	-	3	1361	c.998G>A	c.(997-999)cGc>cAc	p.R333H	CMKLR1_ENST00000397688.2_Missense_Mutation_p.R331H|CMKLR1_ENST00000552995.1_Missense_Mutation_p.R331H|CMKLR1_ENST00000550402.1_Missense_Mutation_p.R333H|CMKLR1_ENST00000412676.1_Missense_Mutation_p.R333H	NM_001142344.1|NM_004072.2	NP_001135816.1|NP_004063.1	Q99788	CML1_HUMAN	chemokine-like receptor 1	333					chemokine-mediated signaling pathway (GO:0070098)|chemotaxis (GO:0006935)|G-protein coupled receptor signaling pathway (GO:0007186)|immune response (GO:0006955)|negative regulation of interleukin-12 production (GO:0032695)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|positive regulation of fat cell differentiation (GO:0045600)|positive regulation of macrophage chemotaxis (GO:0010759)|regulation of calcium-mediated signaling (GO:0050848)|skeletal system development (GO:0001501)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	chemokine receptor activity (GO:0004950)|G-protein coupled receptor activity (GO:0004930)|receptor activity (GO:0004872)			endometrium(5)|large_intestine(3)|lung(20)|ovary(1)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)	37						ATTGACCAGGCGAGAGAAGAG	0.483																																																0													94.0	95.0	94.0					12																	108685742		1951	4139	6090	SO:0001583	missense	1240			U79526	CCDS41829.1, CCDS44965.1	12q23.3	2013-07-29			ENSG00000174600	ENSG00000174600		"""GPCR / Class A : Resolvin receptors"""	2121	protein-coding gene	gene with protein product	"""resolvin E1 receptor"", ""chemerin receptor"""	602351					Standard	NM_004072		Approved	RVER1	uc009zuw.3	Q99788	OTTHUMG00000169576	ENST00000312143.7:c.998G>A	12.37:g.108685742C>T	ENSP00000311733:p.Arg333His		A8K6Y5|O75748|Q3KP37|Q5U0H0|Q99789	Missense_Mutation	SNP	ENST00000312143.7	37	CCDS44965.1	.	.	.	.	.	.	.	.	.	.	c	16.14	3.038798	0.55003	.	.	ENSG00000174600	ENST00000312143;ENST00000412676;ENST00000397688;ENST00000552995;ENST00000550402	T;T;T;T;T	0.39592	1.07;1.07;1.07;1.07;1.07	5.36	5.36	0.76844	.	0.745739	0.12476	N	0.465606	T	0.51719	0.1691	L	0.29908	0.895	0.36742	D	0.882304	D	0.76494	0.999	D	0.66351	0.943	T	0.44112	-0.9349	10	0.15499	T	0.54	.	18.0847	0.89454	0.0:1.0:0.0:0.0	.	333	Q99788	CML1_HUMAN	H	333;333;331;331;333	ENSP00000311733:R333H;ENSP00000401293:R333H;ENSP00000380803:R331H;ENSP00000447579:R331H;ENSP00000449716:R333H	ENSP00000311733:R333H	R	-	2	0	CMKLR1	107209872	1.000000	0.71417	1.000000	0.80357	0.568000	0.35870	2.729000	0.47327	2.499000	0.84300	0.556000	0.70494	CGC		0.483	CMKLR1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000404867.1			29	55	29	55
SLITRK6	84189	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	13	86370348	86370348	+	Missense_Mutation	SNP	T	T	C			TCGA-HW-7491-01A-11D-2024-08	TCGA-HW-7491-10A-01D-2024-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1c29c663-c1ec-468e-9e86-74a2b70da59e	0ba3d269-712a-4990-a51b-7288d4f2adbb	g.chr13:86370348T>C	ENST00000400286.2	-	2	894	c.296A>G	c.(295-297)aAt>aGt	p.N99S		NM_032229.2	NP_115605.2	Q9H5Y7	SLIK6_HUMAN	SLIT and NTRK-like family, member 6	99					adult locomotory behavior (GO:0008344)|auditory behavior (GO:0031223)|auditory receptor cell morphogenesis (GO:0002093)|axonogenesis (GO:0007409)|cochlea development (GO:0090102)|innervation (GO:0060384)|lens development in camera-type eye (GO:0002088)|linear vestibuloocular reflex (GO:0060007)|multicellular organism growth (GO:0035264)|sensory perception of sound (GO:0007605)|startle response (GO:0001964)|synapse assembly (GO:0007416)|vestibulocochlear nerve development (GO:0021562)|visual perception (GO:0007601)	cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)				breast(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(13)|lung(18)|ovary(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_neural(89;0.117)|Medulloblastoma(90;0.163)			GBM - Glioblastoma multiforme(99;0.0456)		ATCTGCAATATTGTTAAATCC	0.353																																																0													160.0	150.0	153.0					13																	86370348		1862	4095	5957	SO:0001583	missense	84189			AK026427	CCDS41903.1	13q31.1	2006-04-12			ENSG00000184564	ENSG00000184564			23503	protein-coding gene	gene with protein product		609681				14557068	Standard	NM_032229		Approved	FLJ22774	uc001vll.1	Q9H5Y7	OTTHUMG00000017157	ENST00000400286.2:c.296A>G	13.37:g.86370348T>C	ENSP00000383143:p.Asn99Ser		A8K9S8|Q495Q0|Q6AW93|Q9HAA8|Q9NT60	Missense_Mutation	SNP	ENST00000400286.2	37	CCDS41903.1	.	.	.	.	.	.	.	.	.	.	T	4.390	0.072031	0.08436	.	.	ENSG00000184564	ENST00000400286	T	0.52526	0.66	6.17	5.01	0.66863	.	0.046027	0.85682	D	0.000000	T	0.31606	0.0802	L	0.31664	0.95	0.43719	D	0.996198	B	0.09022	0.002	B	0.06405	0.002	T	0.10823	-1.0613	10	0.09590	T	0.72	-23.2043	10.8158	0.46575	0.0:0.0735:0.0:0.9265	.	99	Q9H5Y7	SLIK6_HUMAN	S	99	ENSP00000383143:N99S	ENSP00000383143:N99S	N	-	2	0	SLITRK6	85268349	1.000000	0.71417	0.999000	0.59377	0.998000	0.95712	4.959000	0.63666	2.371000	0.80710	0.533000	0.62120	AAT		0.353	SLITRK6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045404.2	NM_032229		80	22	80	22
TRIM9	114088	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	14	51448645	51448645	+	Missense_Mutation	SNP	G	G	C			TCGA-HW-7491-01A-11D-2024-08	TCGA-HW-7491-10A-01D-2024-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1c29c663-c1ec-468e-9e86-74a2b70da59e	0ba3d269-712a-4990-a51b-7288d4f2adbb	g.chr14:51448645G>C	ENST00000298355.3	-	8	2901	c.1780C>G	c.(1780-1782)Cct>Gct	p.P594A	TRIM9_ENST00000338969.5_Missense_Mutation_p.P675A|TRIM9_ENST00000557456.1_5'Flank	NM_015163.5	NP_055978.4	Q9C026	TRIM9_HUMAN	tripartite motif containing 9	594	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.				negative regulation of calcium ion-dependent exocytosis (GO:0045955)|negative regulation of SNARE complex assembly (GO:0035544)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|synaptic vesicle exocytosis (GO:0016079)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|dendrite (GO:0030425)|synaptic vesicle (GO:0008021)	ligase activity (GO:0016874)|protein homodimerization activity (GO:0042803)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|endometrium(4)|kidney(2)|large_intestine(7)|liver(1)|lung(11)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	31	all_epithelial(31;0.00418)|Breast(41;0.148)					CCAAAGGCAGGATCAGGGTGG	0.517																																																0													204.0	165.0	178.0					14																	51448645		2203	4300	6503	SO:0001583	missense	114088			AF220036	CCDS9703.1, CCDS45105.1	14q21.3	2013-02-11	2011-01-25		ENSG00000100505	ENSG00000100505		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"", ""Fibronectin type III domain containing"""	16288	protein-coding gene	gene with protein product		606555	"""tripartite motif-containing 9"""			11331580, 11524423	Standard	NM_015163		Approved	SPRING, RNF91	uc001wyx.4	Q9C026	OTTHUMG00000140291	ENST00000298355.3:c.1780C>G	14.37:g.51448645G>C	ENSP00000298355:p.Pro594Ala		D3DSB7|D3DSB8|Q92557|Q96D24|Q96NI4|Q9C025|Q9C027	Missense_Mutation	SNP	ENST00000298355.3	37	CCDS9703.1	.	.	.	.	.	.	.	.	.	.	G	13.54	2.267968	0.40095	.	.	ENSG00000100505	ENST00000298355;ENST00000338969	T;T	0.67523	-0.27;-0.27	6.08	5.18	0.71444	Concanavalin A-like lectin/glucanase (1);B30.2/SPRY domain (1);SPla/RYanodine receptor SPRY (1);	0.050087	0.85682	D	0.000000	T	0.76877	0.4049	L	0.49640	1.575	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.992	T	0.73668	-0.3910	10	0.23891	T	0.37	.	16.4654	0.84077	0.0:0.1312:0.8688:0.0	.	675;594	Q9C026-4;Q9C026	.;TRIM9_HUMAN	A	594;675	ENSP00000298355:P594A;ENSP00000342970:P675A	ENSP00000298355:P594A	P	-	1	0	TRIM9	50518395	1.000000	0.71417	0.991000	0.47740	0.022000	0.10575	9.869000	0.99810	1.560000	0.49568	-0.282000	0.10007	CCT		0.517	TRIM9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276874.1	NM_015163		43	58	43	58
IDH2	3418	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	15	90631838	90631838	+	Missense_Mutation	SNP	C	C	T	rs121913503		TCGA-HW-7491-01A-11D-2024-08	TCGA-HW-7491-10A-01D-2024-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1c29c663-c1ec-468e-9e86-74a2b70da59e	0ba3d269-712a-4990-a51b-7288d4f2adbb	g.chr15:90631838C>T	ENST00000330062.3	-	4	628	c.515G>A	c.(514-516)aGg>aAg	p.R172K	IDH2_ENST00000559482.1_Intron|IDH2_ENST00000540499.2_Missense_Mutation_p.R120K|IDH2_ENST00000539790.1_Missense_Mutation_p.R42K	NM_002168.2	NP_002159.2	P48735	IDHP_HUMAN	isocitrate dehydrogenase 2 (NADP+), mitochondrial	172					2-oxoglutarate metabolic process (GO:0006103)|carbohydrate metabolic process (GO:0005975)|cellular metabolic process (GO:0044237)|glyoxylate cycle (GO:0006097)|isocitrate metabolic process (GO:0006102)|small molecule metabolic process (GO:0044281)|tricarboxylic acid cycle (GO:0006099)	extracellular vesicular exosome (GO:0070062)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	isocitrate dehydrogenase (NADP+) activity (GO:0004450)|magnesium ion binding (GO:0000287)|NAD binding (GO:0051287)	p.R172K(116)|p.R172M(21)|p.R172N(1)		biliary_tract(11)|bone(19)|central_nervous_system(107)|endometrium(1)|haematopoietic_and_lymphoid_tissue(953)|large_intestine(8)|lung(5)|skin(5)	1109	Melanoma(11;0.00551)|Lung NSC(78;0.0196)|all_lung(78;0.04)		BRCA - Breast invasive adenocarcinoma(143;0.0146)|KIRC - Kidney renal clear cell carcinoma(17;0.0286)|Kidney(142;0.0514)|STAD - Stomach adenocarcinoma(125;0.106)			ATGGGCGTGCCTGCCAATGGT	0.632			M		GBM																																		Dom	yes		15	15q26.1	3418	"""socitrate dehydrogenase 2 (NADP+), mitochondrial """		M	138	Substitution - Missense(138)	haematopoietic_and_lymphoid_tissue(67)|central_nervous_system(65)|biliary_tract(6)											85.0	81.0	82.0					15																	90631838		2200	4298	6498	SO:0001583	missense	3418				CCDS10359.1	15q26.1	2014-09-17			ENSG00000182054	ENSG00000182054	1.1.1.42		5383	protein-coding gene	gene with protein product		147650					Standard	NM_001289910		Approved		uc002box.3	P48735	OTTHUMG00000149815	ENST00000330062.3:c.515G>A	15.37:g.90631838C>T	ENSP00000331897:p.Arg172Lys		B2R6L6|B4DFL2|Q96GT3	Missense_Mutation	SNP	ENST00000330062.3	37	CCDS10359.1	.	.	.	.	.	.	.	.	.	.	C	15.86	2.957149	0.53293	.	.	ENSG00000182054	ENST00000330062;ENST00000539790;ENST00000540499	D;D;D	0.86432	-2.12;-2.12;-2.12	5.93	4.07	0.47477	Isopropylmalate dehydrogenase-like domain (2);	0.000000	0.85682	D	0.000000	D	0.95217	0.8449	H	0.96889	3.9	0.49687	D	0.999812	D	0.89917	1.0	D	0.91635	0.999	D	0.95096	0.8226	10	0.87932	D	0	.	10.781	0.46377	0.0:0.8464:0.0:0.1536	.	172	P48735	IDHP_HUMAN	K	172;42;120	ENSP00000331897:R172K;ENSP00000438457:R42K;ENSP00000446147:R120K	ENSP00000331897:R172K	R	-	2	0	IDH2	88432842	1.000000	0.71417	0.025000	0.17156	0.001000	0.01503	7.797000	0.85911	0.862000	0.35528	-0.258000	0.10820	AGG		0.632	IDH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313426.1			36	32	36	32
DVL2	1856	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	17	7132713	7132713	+	Silent	SNP	T	T	C			TCGA-HW-7491-01A-11D-2024-08	TCGA-HW-7491-10A-01D-2024-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1c29c663-c1ec-468e-9e86-74a2b70da59e	0ba3d269-712a-4990-a51b-7288d4f2adbb	g.chr17:7132713T>C	ENST00000005340.5	-	7	1083	c.801A>G	c.(799-801)acA>acG	p.T267T	DVL2_ENST00000574642.1_5'UTR|DVL2_ENST00000575458.1_Silent_p.T261T	NM_004422.2	NP_004413.1	O14641	DVL2_HUMAN	dishevelled segment polarity protein 2	267	PDZ. {ECO:0000255|PROSITE- ProRule:PRU00143}.				canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in regulation of cell proliferation (GO:0044340)|cell migration in hindbrain (GO:0021535)|cellular protein localization (GO:0034613)|cochlea morphogenesis (GO:0090103)|convergent extension (GO:0060026)|convergent extension involved in neural plate elongation (GO:0022007)|heart development (GO:0007507)|heart morphogenesis (GO:0003007)|hippo signaling (GO:0035329)|neural tube closure (GO:0001843)|non-canonical Wnt signaling pathway (GO:0035567)|outflow tract morphogenesis (GO:0003151)|planar cell polarity pathway involved in neural tube closure (GO:0090179)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of protein tyrosine kinase activity (GO:0061098)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription, DNA-templated (GO:0045893)|segment specification (GO:0007379)|transcription from RNA polymerase II promoter (GO:0006366)|Wnt signaling pathway (GO:0016055)|Wnt signaling pathway, planar cell polarity pathway (GO:0060071)	apical part of cell (GO:0045177)|cell cortex (GO:0005938)|clathrin-coated endocytic vesicle (GO:0045334)|clathrin-coated vesicle (GO:0030136)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	frizzled binding (GO:0005109)|identical protein binding (GO:0042802)			breast(2)|endometrium(3)|kidney(1)|large_intestine(11)|lung(7)|skin(1)	25						TTAGCGTGACTGTGATGATAT	0.567																																																0													149.0	141.0	144.0					17																	7132713		2203	4300	6503	SO:0001819	synonymous_variant	1856			BC014844	CCDS11091.1	17p13.1	2013-05-22	2013-05-22		ENSG00000004975	ENSG00000004975		"""Dishevelled homologs"""	3086	protein-coding gene	gene with protein product		602151	"""dishevelled 2 (homologous to Drosophila dsh)"", ""dishevelled, dsh homolog 2 (Drosophila)"""			8662242	Standard	NM_004422		Approved		uc002gez.1	O14641	OTTHUMG00000102155	ENST00000005340.5:c.801A>G	17.37:g.7132713T>C			D3DTN3|Q53XM0	Silent	SNP	ENST00000005340.5	37	CCDS11091.1																																																																																				0.567	DVL2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000219999.2	NM_004422		41	62	41	62
CIC	23152	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	19	42791757	42791757	+	Missense_Mutation	SNP	C	C	T			TCGA-HW-7491-01A-11D-2024-08	TCGA-HW-7491-10A-01D-2024-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1c29c663-c1ec-468e-9e86-74a2b70da59e	0ba3d269-712a-4990-a51b-7288d4f2adbb	g.chr19:42791757C>T	ENST00000575354.2	+	5	683	c.643C>T	c.(643-645)Cgg>Tgg	p.R215W	CIC_ENST00000160740.3_Missense_Mutation_p.R215W|CIC_ENST00000572681.2_Missense_Mutation_p.R1124W	NM_015125.3	NP_055940.3	Q96RK0	CIC_HUMAN	capicua transcriptional repressor	215					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)	p.R215W(4)		autonomic_ganglia(1)|breast(5)|central_nervous_system(32)|endometrium(10)|kidney(2)|large_intestine(7)|lung(9)|ovary(7)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	82		Prostate(69;0.00682)				CAAGCGGCACCGGGCCCTGGT	0.612			"""Mis, F, S"""		oligodendroglioma																																		Rec	yes		19	19q13.2	23152	capicua homolog		O	4	Substitution - Missense(4)	central_nervous_system(4)											64.0	64.0	64.0					19																	42791757		2203	4300	6503	SO:0001583	missense	23152			AB002304	CCDS12601.1	19q13.2	2013-03-15	2013-03-15		ENSG00000079432	ENSG00000079432			14214	protein-coding gene	gene with protein product		612082	"""capicua (Drosophila) homolog"", ""capicua homolog (Drosophila)"""			12393275, 15981098	Standard	NM_015125		Approved	KIAA0306	uc002otf.1	Q96RK0		ENST00000575354.2:c.643C>T	19.37:g.42791757C>T	ENSP00000458663:p.Arg215Trp		Q7LGI1|Q9UEG5|Q9Y6T1	Missense_Mutation	SNP	ENST00000575354.2	37	CCDS12601.1	.	.	.	.	.	.	.	.	.	.	C	16.71	3.199892	0.58126	.	.	ENSG00000079432	ENST00000160740	.	.	.	4.39	4.39	0.52855	High mobility group, superfamily (1);High mobility group, HMG1/HMG2 (4);	.	.	.	.	T	0.82033	0.4949	M	0.93241	3.395	0.58432	D	0.999999	D	0.89917	1.0	D	0.91635	0.999	D	0.85234	0.1034	8	0.87932	D	0	-14.3323	9.6958	0.40156	0.2069:0.7931:0.0:0.0	.	215	Q96RK0	CIC_HUMAN	W	215	.	ENSP00000160740:R215W	R	+	1	2	CIC	47483597	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.293000	0.59037	2.284000	0.76573	0.555000	0.69702	CGG		0.612	CIC-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000438532.2			37	10	37	10
TTC7A	57217	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	2	47220609	47220609	+	Missense_Mutation	SNP	G	G	A			TCGA-HW-7491-01A-11D-2024-08	TCGA-HW-7491-10A-01D-2024-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1c29c663-c1ec-468e-9e86-74a2b70da59e	0ba3d269-712a-4990-a51b-7288d4f2adbb	g.chr2:47220609G>A	ENST00000319190.5	+	6	1153	c.785G>A	c.(784-786)aGa>aAa	p.R262K	TTC7A_ENST00000263737.6_5'UTR|TTC7A_ENST00000461601.1_3'UTR|TTC7A_ENST00000409245.1_Missense_Mutation_p.R228K|TTC7A_ENST00000394850.2_Missense_Mutation_p.R262K	NM_020458.2	NP_065191.2	Q9ULT0	TTC7A_HUMAN	tetratricopeptide repeat domain 7A	262					cellular iron ion homeostasis (GO:0006879)|hemopoiesis (GO:0030097)					breast(4)|endometrium(3)|kidney(2)|large_intestine(4)|lung(8)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	25		all_hematologic(82;0.152)|Acute lymphoblastic leukemia(82;0.18)	Lung(47;0.0792)|LUSC - Lung squamous cell carcinoma(58;0.114)			AAGGGCATGAGAGAGCTCCGG	0.547																																																0													142.0	142.0	142.0					2																	47220609		2203	4300	6503	SO:0001583	missense	57217			AB032966	CCDS33193.1, CCDS74510.1, CCDS74511.1	2p16.3	2013-01-10	2004-06-02	2004-06-02	ENSG00000068724	ENSG00000068724		"""Tetratricopeptide (TTC) repeat domain containing"""	19750	protein-coding gene	gene with protein product		609332	"""tetratricopeptide repeat domain 7"""	TTC7		10574461	Standard	XM_005264439		Approved	KIAA1140	uc002rvo.3	Q9ULT0	OTTHUMG00000153121	ENST00000319190.5:c.785G>A	2.37:g.47220609G>A	ENSP00000316699:p.Arg262Lys		Q6PIX4|Q8ND67|Q9BUS3	Missense_Mutation	SNP	ENST00000319190.5	37	CCDS33193.1	.	.	.	.	.	.	.	.	.	.	G	14.70	2.613205	0.46631	.	.	ENSG00000068724	ENST00000409245;ENST00000319190;ENST00000394850;ENST00000434093	T;T;T	0.29142	2.0;2.01;1.58	5.65	3.85	0.44370	.	0.207551	0.44902	D	0.000415	T	0.14184	0.0343	N	0.16478	0.41	0.80722	D	1	B;B;B;B;B	0.14438	0.0;0.0;0.0;0.01;0.0	B;B;B;B;B	0.10450	0.001;0.001;0.0;0.005;0.003	T	0.09997	-1.0649	10	0.06236	T	0.91	-10.3073	6.4375	0.21831	0.1515:0.0:0.7002:0.1483	.	262;228;262;90;228	Q2T9J9;B3KPK7;Q9ULT0;Q6P0M3;G5E9G4	.;.;TTC7A_HUMAN;.;.	K	228;262;262;89	ENSP00000386307:R228K;ENSP00000316699:R262K;ENSP00000378320:R262K	ENSP00000316699:R262K	R	+	2	0	TTC7A	47074113	0.961000	0.32948	0.994000	0.49952	0.991000	0.79684	1.841000	0.39240	0.731000	0.32448	0.655000	0.94253	AGA		0.547	TTC7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329667.2	XM_372927		50	57	50	57
AGPS	8540	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	2	178386040	178386040	+	Missense_Mutation	SNP	T	T	G			TCGA-HW-7491-01A-11D-2024-08	TCGA-HW-7491-10A-01D-2024-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1c29c663-c1ec-468e-9e86-74a2b70da59e	0ba3d269-712a-4990-a51b-7288d4f2adbb	g.chr2:178386040T>G	ENST00000264167.4	+	18	1887	c.1741T>G	c.(1741-1743)Ttt>Gtt	p.F581V	AGPS_ENST00000409888.1_Intron	NM_003659.3	NP_003650.1	O00116	ADAS_HUMAN	alkylglycerone phosphate synthase	581					cellular lipid metabolic process (GO:0044255)|ether lipid biosynthetic process (GO:0008611)|lipid biosynthetic process (GO:0008610)|small molecule metabolic process (GO:0044281)	intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|peroxisomal matrix (GO:0005782)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)	alkylglycerone-phosphate synthase activity (GO:0008609)|FAD binding (GO:0071949)|UDP-N-acetylmuramate dehydrogenase activity (GO:0008762)			breast(2)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(8)|lung(12)|ovary(2)|skin(1)	32			OV - Ovarian serous cystadenocarcinoma(117;0.0018)|Epithelial(96;0.00919)|all cancers(119;0.0358)			CTACTTCTATTTTGCCTTTAA	0.383																																																0													177.0	166.0	169.0					2																	178386040		2203	4300	6503	SO:0001583	missense	8540			Y09443	CCDS2275.1	2q	2008-02-05			ENSG00000018510	ENSG00000018510	2.5.1.26		327	protein-coding gene	gene with protein product		603051				9187299, 9553082	Standard	NM_003659		Approved	ADHAPS, ADAS, ALDHPSY, ADPS, ADAP-S	uc002ull.2	O00116	OTTHUMG00000132530	ENST00000264167.4:c.1741T>G	2.37:g.178386040T>G	ENSP00000264167:p.Phe581Val		A5D8U9|Q2TU35	Missense_Mutation	SNP	ENST00000264167.4	37	CCDS2275.1	.	.	.	.	.	.	.	.	.	.	T	26.2	4.717678	0.89205	.	.	ENSG00000018510	ENST00000264167	D	0.84298	-1.83	5.83	5.83	0.93111	FAD-linked oxidase-like, C-terminal (1);FAD-linked oxidase, C-terminal (1);	0.000000	0.85682	D	0.000000	D	0.86957	0.6058	M	0.66378	2.025	0.80722	D	1	P	0.41848	0.763	P	0.49421	0.61	D	0.85123	0.0970	10	0.30854	T	0.27	.	11.267	0.49116	0.0:0.0707:0.0:0.9293	.	581	O00116	ADAS_HUMAN	V	581	ENSP00000264167:F581V	ENSP00000264167:F581V	F	+	1	0	AGPS	178094286	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.505000	0.66981	2.236000	0.73375	0.528000	0.53228	TTT		0.383	AGPS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255730.2			38	81	38	81
SCN10A	6336	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	3	38739794	38739794	+	Silent	SNP	G	G	A	rs142804903		TCGA-HW-7491-01A-11D-2024-08	TCGA-HW-7491-10A-01D-2024-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1c29c663-c1ec-468e-9e86-74a2b70da59e	0ba3d269-712a-4990-a51b-7288d4f2adbb	g.chr3:38739794G>A	ENST00000449082.2	-	27	4916	c.4917C>T	c.(4915-4917)gaC>gaT	p.D1639D		NM_006514.2	NP_006505.2	Q9Y5Y9	SCNAA_HUMAN	sodium channel, voltage-gated, type X, alpha subunit	1639					AV node cell to bundle of His cell communication (GO:0086067)|bundle of His cell to Purkinje myocyte communication (GO:0086069)|membrane depolarization during action potential (GO:0086010)|neuronal action potential (GO:0019228)|regulation of atrial cardiac muscle cell membrane depolarization (GO:0060371)|regulation of cardiac muscle contraction (GO:0055117)|regulation of heart rate (GO:0002027)|regulation of ion transmembrane transport (GO:0034765)|sensory perception (GO:0007600)|sensory perception of pain (GO:0019233)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	C-fiber (GO:0044299)|extracellular vesicular exosome (GO:0070062)|voltage-gated sodium channel complex (GO:0001518)	voltage-gated sodium channel activity (GO:0005248)			NS(5)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(14)|kidney(5)|large_intestine(33)|lung(54)|ovary(5)|pancreas(1)|prostate(5)|skin(13)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(1)	150				KIRC - Kidney renal clear cell carcinoma(284;0.0769)|Kidney(284;0.0945)	Benzocaine(DB01086)|Bupivacaine(DB00297)|Chloroprocaine(DB01161)|Cinchocaine(DB00527)|Cocaine(DB00907)|Dyclonine(DB00645)|Hexylcaine(DB00473)|Lacosamide(DB06218)|Levobupivacaine(DB01002)|Lidocaine(DB00281)|Mepivacaine(DB00961)|Orphenadrine(DB01173)|Oxybuprocaine(DB00892)|Procaine(DB00721)|Proparacaine(DB00807)|Ropivacaine(DB00296)|Valproic Acid(DB00313)	TGAACATGTCGTCGATGCCAG	0.547													G|||	1	0.000199681	0.0008	0.0	5008	,	,		21167	0.0		0.0	False		,,,				2504	0.0															0								G		1,4405	2.1+/-5.4	0,1,2202	174.0	163.0	167.0		4917	-10.1	0.1	3	dbSNP_134	167	0,8600		0,0,4300	no	coding-synonymous	SCN10A	NM_006514.2		0,1,6502	AA,AG,GG		0.0,0.0227,0.0077		1639/1957	38739794	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	6336			AF117907	CCDS33736.1	3p22.2	2012-02-26	2007-01-23		ENSG00000185313	ENSG00000185313		"""Sodium channels"", ""Voltage-gated ion channels / Sodium channels"""	10582	protein-coding gene	gene with protein product		604427	"""sodium channel, voltage-gated, type X, alpha polypeptide"""			9839820, 10198179, 16382098	Standard	NM_006514		Approved	Nav1.8, hPN3, SNS, PN3	uc003ciq.3	Q9Y5Y9	OTTHUMG00000048245	ENST00000449082.2:c.4917C>T	3.37:g.38739794G>A			A6NDQ1	Silent	SNP	ENST00000449082.2	37	CCDS33736.1																																																																																				0.547	SCN10A-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109745.3	NM_006514		78	77	78	77
TINAG	27283	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	6	54191662	54191662	+	Missense_Mutation	SNP	G	G	A	rs368916966		TCGA-HW-7491-01A-11D-2024-08	TCGA-HW-7491-10A-01D-2024-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1c29c663-c1ec-468e-9e86-74a2b70da59e	0ba3d269-712a-4990-a51b-7288d4f2adbb	g.chr6:54191662G>A	ENST00000259782.4	+	4	668	c.572G>A	c.(571-573)cGc>cAc	p.R191H	TINAG_ENST00000370864.3_Missense_Mutation_p.R173H|TINAG_ENST00000370869.3_Missense_Mutation_p.R187H	NM_014464.3	NP_055279.3	Q9UJW2	TINAG_HUMAN	tubulointerstitial nephritis antigen	191					cell adhesion (GO:0007155)|immune response (GO:0006955)	basement membrane (GO:0005604)	cysteine-type endopeptidase activity (GO:0004197)|nucleotide binding (GO:0000166)|polysaccharide binding (GO:0030247)|scavenger receptor activity (GO:0005044)	p.R191H(1)|p.R191L(1)		NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(11)|ovary(4)|skin(1)	34	Lung NSC(77;0.0518)		LUSC - Lung squamous cell carcinoma(124;0.246)			TTTAAATTTCGCCTTGGCACT	0.373																																																2	Substitution - Missense(2)	haematopoietic_and_lymphoid_tissue(1)|endometrium(1)						G	HIS/ARG	1,4405	2.1+/-5.4	0,1,2202	139.0	127.0	131.0		572	4.0	1.0	6		131	0,8600		0,0,4300	no	missense	TINAG	NM_014464.3	29	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	probably-damaging	191/477	54191662	1,13005	2203	4300	6503	SO:0001583	missense	27283			AB022277	CCDS4955.1	6p12.1	2008-05-15			ENSG00000137251	ENSG00000137251			14599	protein-coding gene	gene with protein product		606749				10652240	Standard	NM_014464		Approved		uc003pcj.2	Q9UJW2	OTTHUMG00000014893	ENST00000259782.4:c.572G>A	6.37:g.54191662G>A	ENSP00000259782:p.Arg191His		Q5T467|Q9UJW1|Q9ULZ4	Missense_Mutation	SNP	ENST00000259782.4	37	CCDS4955.1	.	.	.	.	.	.	.	.	.	.	G	14.32	2.501658	0.44455	2.27E-4	0.0	ENSG00000137251	ENST00000370869;ENST00000339741;ENST00000259782;ENST00000370864	T;T;T	0.77750	-1.12;-1.12;-1.12	5.82	4.01	0.46588	.	0.349950	0.28544	N	0.014979	T	0.53077	0.1774	M	0.67517	2.055	0.45822	D	0.99869	P	0.44659	0.84	B	0.26517	0.07	T	0.62798	-0.6778	10	0.59425	D	0.04	.	6.5973	0.22681	0.0884:0.0:0.7325:0.1791	.	191	Q9UJW2	TINAG_HUMAN	H	187;141;191;173	ENSP00000359906:R187H;ENSP00000259782:R191H;ENSP00000359901:R173H	ENSP00000259782:R191H	R	+	2	0	TINAG	54299621	1.000000	0.71417	0.994000	0.49952	0.709000	0.40893	2.893000	0.48633	1.420000	0.47138	0.643000	0.83706	CGC		0.373	TINAG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040984.1	NM_014464		32	65	32	65
LAMB4	22798	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	7	107748127	107748127	+	Missense_Mutation	SNP	G	G	T			TCGA-HW-7491-01A-11D-2024-08	TCGA-HW-7491-10A-01D-2024-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1c29c663-c1ec-468e-9e86-74a2b70da59e	0ba3d269-712a-4990-a51b-7288d4f2adbb	g.chr7:107748127G>T	ENST00000388781.3	-	6	623	c.540C>A	c.(538-540)gaC>gaA	p.D180E	LAMB4_ENST00000205386.4_Missense_Mutation_p.D180E|LAMB4_ENST00000418464.1_Missense_Mutation_p.D180E|LAMB4_ENST00000388780.3_Missense_Mutation_p.D180E|LAMB4_ENST00000414450.2_Missense_Mutation_p.D180E	NM_007356.2	NP_031382.2	A4D0S4	LAMB4_HUMAN	laminin, beta 4	180	Laminin N-terminal. {ECO:0000255|PROSITE- ProRule:PRU00466}.				cell adhesion (GO:0007155)	basement membrane (GO:0005604)				NS(1)|breast(5)|endometrium(8)|haematopoietic_and_lymphoid_tissue(3)|kidney(5)|large_intestine(22)|lung(40)|ovary(4)|prostate(5)|skin(4)	97						CACAAACAATGTCTCCCACTC	0.398																																																0													109.0	107.0	107.0					7																	107748127		2203	4300	6503	SO:0001583	missense	22798			AF028816	CCDS34732.1	7q31	2013-03-01			ENSG00000091128	ENSG00000091128		"""Laminins"""	6491	protein-coding gene	gene with protein product							Standard	NM_007356		Approved		uc010ljo.1	A4D0S4	OTTHUMG00000154874	ENST00000388781.3:c.540C>A	7.37:g.107748127G>T	ENSP00000373433:p.Asp180Glu		A5PKU6|B2RTT3|B5MEB9|Q86TP7|Q86XN2|Q8NBX5	Missense_Mutation	SNP	ENST00000388781.3	37	CCDS34732.1	.	.	.	.	.	.	.	.	.	.	G	14.50	2.553236	0.45487	.	.	ENSG00000091128	ENST00000205386;ENST00000388781;ENST00000388780;ENST00000418464;ENST00000414450	T;T;T;T;T	0.75050	-0.9;-0.9;-0.9;-0.9;-0.9	5.86	4.02	0.46733	Laminin, N-terminal (3);	0.000000	0.56097	D	0.000039	T	0.64778	0.2629	L	0.35723	1.085	0.58432	D	0.999996	P	0.46784	0.884	P	0.45138	0.471	T	0.66040	-0.6022	10	0.62326	D	0.03	.	5.6274	0.17490	0.2204:0.1627:0.6169:0.0	.	180	A4D0S4	LAMB4_HUMAN	E	180	ENSP00000205386:D180E;ENSP00000373433:D180E;ENSP00000373432:D180E;ENSP00000402353:D180E;ENSP00000402265:D180E	ENSP00000205386:D180E	D	-	3	2	LAMB4	107535363	0.064000	0.20934	0.977000	0.42913	0.347000	0.29111	-0.105000	0.10907	1.438000	0.47492	0.655000	0.94253	GAC		0.398	LAMB4-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337442.1	XM_209857		31	45	31	45
SLC37A3	84255	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	7	140058508	140058508	+	Silent	SNP	G	G	A	rs142313913		TCGA-HW-7491-01A-11D-2024-08	TCGA-HW-7491-10A-01D-2024-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1c29c663-c1ec-468e-9e86-74a2b70da59e	0ba3d269-712a-4990-a51b-7288d4f2adbb	g.chr7:140058508G>A	ENST00000326232.9	-	6	656	c.453C>T	c.(451-453)aaC>aaT	p.N151N	SLC37A3_ENST00000461089.1_5'UTR|SLC37A3_ENST00000447932.2_Silent_p.N151N|SLC37A3_ENST00000340308.3_Silent_p.N151N|SLC37A3_ENST00000429996.2_Intron	NM_207113.1	NP_996996.1	Q8NCC5	SPX3_HUMAN	solute carrier family 37, member 3	151					carbohydrate transport (GO:0008643)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)	transporter activity (GO:0005215)			endometrium(4)|kidney(1)|large_intestine(5)|lung(7)|ovary(3)|prostate(1)|stomach(3)	24	Melanoma(164;0.0142)					GCAGCAGGCCGTTCACAATCC	0.512													G|||	1	0.000199681	0.0008	0.0	5008	,	,		19595	0.0		0.0	False		,,,				2504	0.0				Esophageal Squamous(133;211 1716 4665 11387 37873)											0								G	,	6,4400	11.4+/-27.6	0,6,2197	159.0	154.0	155.0		453,453	-6.5	0.7	7	dbSNP_134	155	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	SLC37A3	NM_032295.2,NM_207113.1	,	0,6,6497	AA,AG,GG		0.0,0.1362,0.0461	,	151/444,151/495	140058508	6,13000	2203	4300	6503	SO:0001819	synonymous_variant	84255			AK074823	CCDS5858.1, CCDS5859.1, CCDS75669.1	7q34	2013-07-17	2013-07-17		ENSG00000157800	ENSG00000157800		"""Solute carriers"""	20651	protein-coding gene	gene with protein product							Standard	NM_001287498		Approved	DKFZp761N0624	uc003vvo.3	Q8NCC5	OTTHUMG00000157343	ENST00000326232.9:c.453C>T	7.37:g.140058508G>A			Q6PIU7|Q86SS4|Q9BQG7	Silent	SNP	ENST00000326232.9	37	CCDS5859.1	.	.	.	.	.	.	.	.	.	.	G	10.36	1.329628	0.24167	0.001362	0.0	ENSG00000157800	ENST00000485861	.	.	.	5.58	-6.48	0.01896	.	.	.	.	.	T	0.66607	0.2806	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.68977	-0.5267	4	.	.	.	-27.0721	18.7155	0.91673	0.7421:0.0:0.2579:0.0	.	.	.	.	M	76	.	.	T	-	2	0	SLC37A3	139704977	0.591000	0.26824	0.662000	0.29724	0.987000	0.75469	-0.069000	0.11542	-1.477000	0.01872	-0.793000	0.03317	ACG		0.512	SLC37A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348492.1	NM_032295		63	99	63	99
VPS13A	23230	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	9	79936584	79936584	+	Missense_Mutation	SNP	G	G	A			TCGA-HW-7491-01A-11D-2024-08	TCGA-HW-7491-10A-01D-2024-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1c29c663-c1ec-468e-9e86-74a2b70da59e	0ba3d269-712a-4990-a51b-7288d4f2adbb	g.chr9:79936584G>A	ENST00000360280.3	+	44	6012	c.5752G>A	c.(5752-5754)Gat>Aat	p.D1918N	VPS13A_ENST00000376636.3_Missense_Mutation_p.D1879N|VPS13A_ENST00000376634.4_Missense_Mutation_p.D1918N|VPS13A_ENST00000357409.5_Missense_Mutation_p.D1918N	NM_033305.2	NP_150648.2	Q96RL7	VP13A_HUMAN	vacuolar protein sorting 13 homolog A (S. cerevisiae)	1918					cell death (GO:0008219)|Golgi to endosome transport (GO:0006895)|locomotory behavior (GO:0007626)|nervous system development (GO:0007399)|protein localization (GO:0008104)|protein transport (GO:0015031)|social behavior (GO:0035176)	dense core granule (GO:0031045)|intracellular (GO:0005622)				breast(4)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(28)|liver(1)|lung(42)|ovary(3)|pancreas(3)|prostate(3)|skin(9)|upper_aerodigestive_tract(1)|urinary_tract(1)	104						TTTAAGTATGGATTATATCCG	0.338																																																0													86.0	83.0	84.0					9																	79936584		2203	4299	6502	SO:0001583	missense	23230			AB023203	CCDS6655.1, CCDS6656.1, CCDS47983.1, CCDS55321.1	9q21	2014-01-30	2006-04-04	2004-02-11	ENSG00000197969	ENSG00000197969			1908	protein-coding gene	gene with protein product	"""chorein"""	605978	"""chorea acanthocytosis"", ""vacuolar protein sorting 13A (yeast)"""	CHAC		9382101, 11381253	Standard	NM_001018038		Approved	KIAA0986	uc004akr.3	Q96RL7	OTTHUMG00000020055	ENST00000360280.3:c.5752G>A	9.37:g.79936584G>A	ENSP00000353422:p.Asp1918Asn		Q5JSX9|Q5JSY0|Q5VYR5|Q702P4|Q709D0|Q86YF8|Q96S61|Q9H995|Q9Y2J1	Missense_Mutation	SNP	ENST00000360280.3	37	CCDS6655.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	18.83|18.83	3.707763|3.707763	0.68615|0.68615	.|.	.|.	ENSG00000197969|ENSG00000197969	ENST00000376634;ENST00000376636;ENST00000360280;ENST00000357409|ENST00000419472	T;T;T;T|.	0.47869|.	1.0;0.83;0.92;1.0|.	5.8|5.8	5.8|5.8	0.92144|0.92144	.|.	0.054540|.	0.64402|.	D|.	0.000001|.	T|.	0.75838|.	0.3904|.	M|M	0.66939|0.66939	2.045|2.045	0.80722|0.80722	D|D	1|1	D;P;D;D;D|.	0.89917|.	1.0;0.57;0.999;0.997;0.997|.	D;B;P;D;D|.	0.70227|.	0.968;0.295;0.859;0.933;0.933|.	T|.	0.72839|.	-0.4171|.	10|.	0.26408|.	T|.	0.33|.	.|.	20.064|20.064	0.97700|0.97700	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	170;1879;1918;1918;1918|.	B1ALW4;Q96RL7-3;Q96RL7;Q96RL7-2;Q96RL7-4|.	.;.;VP13A_HUMAN;.;.|.	N|X	1918;1879;1918;1918|170	ENSP00000365821:D1918N;ENSP00000365823:D1879N;ENSP00000353422:D1918N;ENSP00000349985:D1918N|.	ENSP00000349985:D1918N|.	D|W	+|+	1|3	0|0	VPS13A|VPS13A	79126404|79126404	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.916000|0.916000	0.54674|0.54674	7.325000|7.325000	0.79124|0.79124	2.739000|2.739000	0.93911|0.93911	0.467000|0.467000	0.42956|0.42956	GAT|TGG		0.338	VPS13A-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000052753.2	NM_015186		25	37	25	37
PIK3CA	5290	broad.mit.edu;hgsc.bcm.edu	37	3	178916938	178916940	+	In_Frame_Del	DEL	GAA	GAA	-			TCGA-HW-7491-01A-11D-2024-08	TCGA-HW-7491-10A-01D-2024-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1c29c663-c1ec-468e-9e86-74a2b70da59e	0ba3d269-712a-4990-a51b-7288d4f2adbb	g.chr3:178916938_178916940delGAA	ENST00000263967.3	+	2	482_484	c.325_327delGAA	c.(325-327)gaadel	p.E110del		NM_006218.2	NP_006209.2	P42336	PK3CA_HUMAN	phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit alpha	110					angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|endothelial cell migration (GO:0043542)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glucose metabolic process (GO:0006006)|hypomethylation of CpG island (GO:0044029)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|insulin receptor signaling pathway via phosphatidylinositol 3-kinase (GO:0038028)|leukocyte migration (GO:0050900)|negative regulation of anoikis (GO:2000811)|negative regulation of fibroblast apoptotic process (GO:2000270)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|protein kinase B signaling (GO:0043491)|regulation of genetic imprinting (GO:2000653)|regulation of multicellular organism growth (GO:0040014)|small molecule metabolic process (GO:0044281)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|vasculature development (GO:0001944)	1-phosphatidylinositol-4-phosphate 3-kinase, class IA complex (GO:0005943)|cytosol (GO:0005829)|lamellipodium (GO:0030027)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|kinase activity (GO:0016301)|phosphatidylinositol 3-kinase activity (GO:0035004)|phosphatidylinositol-4,5-bisphosphate 3-kinase activity (GO:0046934)|protein kinase activator activity (GO:0030295)|protein serine/threonine kinase activity (GO:0004674)	p.E109del(3)|p.G106_R108del(1)		NS(16)|autonomic_ganglia(4)|biliary_tract(22)|bone(1)|breast(2150)|central_nervous_system(110)|cervix(33)|endometrium(473)|eye(1)|haematopoietic_and_lymphoid_tissue(35)|kidney(14)|large_intestine(1202)|liver(42)|lung(202)|meninges(1)|oesophagus(28)|ovary(235)|pancreas(17)|penis(8)|pituitary(12)|prostate(10)|skin(155)|small_intestine(1)|soft_tissue(18)|stomach(121)|thyroid(80)|upper_aerodigestive_tract(70)|urinary_tract(208)	5269	all_cancers(143;1.19e-17)|Ovarian(172;0.00769)|Breast(254;0.155)		OV - Ovarian serous cystadenocarcinoma(80;9.59e-28)|GBM - Glioblastoma multiforme(14;0.003)|BRCA - Breast invasive adenocarcinoma(182;0.0282)		Caffeine(DB00201)	AGGCAACCGTGAAGAAAAGATCC	0.34		57	Mis		"""colorectal, gastric, gliobastoma, breast"""					HNSCC(19;0.045)|TSP Lung(28;0.18)																											Colon(199;1504 1750 3362 26421 31210 32040)		Dom	yes		3	3q26.3	5290	"""phosphoinositide-3-kinase, catalytic, alpha polypeptide"""		"""E, O"""	4	Deletion - In frame(4)	endometrium(2)|large_intestine(1)|lung(1)																																								SO:0001651	inframe_deletion	5290				CCDS43171.1	3q26.3	2014-09-17	2012-07-13		ENSG00000121879	ENSG00000121879	2.7.1.153		8975	protein-coding gene	gene with protein product		171834	"""phosphoinositide-3-kinase, catalytic, alpha polypeptide"""			1322797	Standard	NM_006218		Approved	PI3K	uc003fjk.3	P42336	OTTHUMG00000157311	ENST00000263967.3:c.325_327delGAA	3.37:g.178916941_178916943delGAA	ENSP00000263967:p.Glu110del		Q14CW1|Q99762	In_Frame_Del	DEL	ENST00000263967.3	37	CCDS43171.1																																																																																				0.340	PIK3CA-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000348409.2			44	54	44	54
FUT5	2527	broad.mit.edu;hgsc.bcm.edu	37	19	5867346	5867347	+	Frame_Shift_Ins	INS	-	-	GG	rs111394159		TCGA-HW-7491-01A-11D-2024-08	TCGA-HW-7491-10A-01D-2024-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1c29c663-c1ec-468e-9e86-74a2b70da59e	0ba3d269-712a-4990-a51b-7288d4f2adbb	g.chr19:5867346_5867347insGG	ENST00000588525.1	-	2	477_478	c.390_391insCC	c.(388-393)cccagtfs	p.S131fs	FUT5_ENST00000252675.5_Frame_Shift_Ins_p.S131fs	NM_002034.2	NP_002025.2	Q11128	FUT5_HUMAN	fucosyltransferase 5 (alpha (1,3) fucosyltransferase)	131					carbohydrate metabolic process (GO:0005975)|fucosylation (GO:0036065)|L-fucose catabolic process (GO:0042355)|protein glycosylation (GO:0006486)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	3-galactosyl-N-acetylglucosaminide 4-alpha-L-fucosyltransferase activity (GO:0017060)|alpha-(1->3)-fucosyltransferase activity (GO:0046920)|fucosyltransferase activity (GO:0008417)			central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(8)|upper_aerodigestive_tract(1)	12						AGGTTGGCACTGGGGTTGTACA	0.663																																																0																																										SO:0001589	frameshift_variant	2527				CCDS12154.1	19p13.3	2013-02-26				ENSG00000130383	2.4.1.65	"""Fucosyltransferases"""	4016	protein-coding gene	gene with protein product		136835				1740457	Standard	NM_002034		Approved	FUC-TV	uc002mdo.4	Q11128	OTTHUMG00000180616	ENST00000588525.1:c.389_390dupCC	19.37:g.5867349_5867350dupGG	ENSP00000466880:p.Ser131fs		A8K4X2	Frame_Shift_Ins	INS	ENST00000588525.1	37	CCDS12154.1																																																																																				0.663	FUT5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452213.1	NM_002034		25	39	25	39
