#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
OR4A15	81328	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	11	55136122	55136122	+	Missense_Mutation	SNP	A	A	T			TCGA-HW-7490-01A-11D-2024-08	TCGA-HW-7490-10A-01D-2024-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ca68843d-1087-4efa-b5f8-0acd8982fb3b	855988d0-f042-466d-86a8-1ac1cb1bc7a1	g.chr11:55136122A>T	ENST00000314706.3	+	1	763	c.763A>T	c.(763-765)Act>Tct	p.T255S		NM_001005275.1	NP_001005275.1	Q8NGL6	O4A15_HUMAN	olfactory receptor, family 4, subfamily A, member 15	255						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(2)|breast(2)|endometrium(2)|kidney(2)|large_intestine(7)|lung(48)|ovary(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	71						CTCTCTTAAGACTCAGAGTTT	0.438																																																0													160.0	141.0	147.0					11																	55136122		2201	4296	6497	SO:0001583	missense	81328			AB065776	CCDS31500.1	11q11	2012-08-09			ENSG00000181958	ENSG00000181958		"""GPCR / Class A : Olfactory receptors"""	15152	protein-coding gene	gene with protein product							Standard	NM_001005275		Approved		uc010rif.2	Q8NGL6	OTTHUMG00000166711	ENST00000314706.3:c.763A>T	11.37:g.55136122A>T	ENSP00000325065:p.Thr255Ser		Q6IFL4|Q96R65	Missense_Mutation	SNP	ENST00000314706.3	37	CCDS31500.1	.	.	.	.	.	.	.	.	.	.	-	10.96	1.499961	0.26861	.	.	ENSG00000181958	ENST00000314706	T	0.00123	8.7	3.65	-2.34	0.06704	GPCR, rhodopsin-like superfamily (1);	1.952780	0.02747	N	0.116995	T	0.00073	0.0002	N	0.04335	-0.225	0.09310	N	1	B	0.13594	0.008	B	0.21360	0.034	T	0.11518	-1.0584	10	0.15952	T	0.53	.	2.8404	0.05527	0.4809:0.0:0.2032:0.3159	.	255	Q8NGL6	O4A15_HUMAN	S	255	ENSP00000325065:T255S	ENSP00000325065:T255S	T	+	1	0	OR4A15	54892698	0.000000	0.05858	0.000000	0.03702	0.560000	0.35617	-0.696000	0.05104	-0.233000	0.09797	-0.510000	0.04470	ACT		0.438	OR4A15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391161.1	NM_001005275		64	78	64	78
OR5D16	390144	hgsc.bcm.edu;broad.mit.edu	37	11	55606760	55606760	+	Missense_Mutation	SNP	A	A	G			TCGA-HW-7490-01A-11D-2024-08	TCGA-HW-7490-10A-01D-2024-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ca68843d-1087-4efa-b5f8-0acd8982fb3b	855988d0-f042-466d-86a8-1ac1cb1bc7a1	g.chr11:55606760A>G	ENST00000378396.1	+	1	533	c.533A>G	c.(532-534)cAt>cGt	p.H178R		NM_001005496.1	NP_001005496.1	Q8NGK9	OR5DG_HUMAN	olfactory receptor, family 5, subfamily D, member 16	178						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			cervix(1)|endometrium(2)|large_intestine(4)|lung(26)|ovary(5)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	44		all_epithelial(135;0.208)				ACAATCAATCATTTCTTCTGT	0.423																																																0													183.0	162.0	169.0					11																	55606760		2201	4296	6497	SO:0001583	missense	390144			AB065783	CCDS31512.1	11q11	2012-08-09			ENSG00000205029	ENSG00000205029		"""GPCR / Class A : Olfactory receptors"""	15283	protein-coding gene	gene with protein product							Standard	NM_001005496		Approved		uc010rio.2	Q8NGK9	OTTHUMG00000154233	ENST00000378396.1:c.533A>G	11.37:g.55606760A>G	ENSP00000367649:p.His178Arg		Q6IF65|Q96RB4	Missense_Mutation	SNP	ENST00000378396.1	37	CCDS31512.1	.	.	.	.	.	.	.	.	.	.	.	18.09	3.547145	0.65311	.	.	ENSG00000205029	ENST00000378396	T	0.00174	8.62	3.86	3.86	0.44501	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.00695	0.0023	M	0.92691	3.335	0.31042	N	0.716242	D	0.61080	0.989	D	0.67382	0.951	T	0.03761	-1.1006	9	0.87932	D	0	-35.1331	11.9415	0.52903	1.0:0.0:0.0:0.0	.	178	Q8NGK9	OR5DG_HUMAN	R	178	ENSP00000367649:H178R	ENSP00000367649:H178R	H	+	2	0	OR5D16	55363336	0.707000	0.27866	0.581000	0.28614	0.790000	0.44656	4.644000	0.61397	1.556000	0.49512	0.433000	0.28618	CAT		0.423	OR5D16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334506.1	NM_001005496		5	55	5	55
NPAS4	266743	hgsc.bcm.edu;broad.mit.edu	37	11	66192121	66192121	+	Missense_Mutation	SNP	C	C	T	rs142965018	byFrequency	TCGA-HW-7490-01A-11D-2024-08	TCGA-HW-7490-10A-01D-2024-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ca68843d-1087-4efa-b5f8-0acd8982fb3b	855988d0-f042-466d-86a8-1ac1cb1bc7a1	g.chr11:66192121C>T	ENST00000311034.2	+	7	1936	c.1760C>T	c.(1759-1761)aCg>aTg	p.T587M		NM_178864.3	NP_849195.2	Q8IUM7	NPAS4_HUMAN	neuronal PAS domain protein 4	587					positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|signal transducer activity (GO:0004871)			breast(4)|endometrium(2)|kidney(3)|large_intestine(11)|liver(2)|lung(20)|ovary(1)|prostate(3)|skin(3)	49						GGGGACTGCACGCTCTTGGCC	0.607													C|||	10	0.00199681	0.0068	0.0014	5008	,	,		18611	0.0		0.0	False		,,,				2504	0.0															0								C	MET/THR	42,4358	45.3+/-79.5	0,42,2158	79.0	87.0	84.0		1760	4.7	1.0	11	dbSNP_134	84	2,8588	2.2+/-6.3	0,2,4293	yes	missense	NPAS4	NM_178864.3	81	0,44,6451	TT,TC,CC		0.0233,0.9545,0.3387	probably-damaging	587/803	66192121	44,12946	2200	4295	6495	SO:0001583	missense	266743			AB049469	CCDS8138.1	11q13.2	2013-05-21			ENSG00000174576	ENSG00000174576		"""Basic helix-loop-helix proteins"""	18983	protein-coding gene	gene with protein product		608554				14701734	Standard	NM_178864		Approved	PASD10, NXF, Le-PAS, bHLHe79	uc001ohx.1	Q8IUM7	OTTHUMG00000167045	ENST00000311034.2:c.1760C>T	11.37:g.66192121C>T	ENSP00000311196:p.Thr587Met		B7ZL81|Q8N8S5|Q8N9Q9	Missense_Mutation	SNP	ENST00000311034.2	37	CCDS8138.1	7	0.003205128205128205	7	0.014227642276422764	0	0.0	0	0.0	0	0.0	C	16.34	3.096845	0.56075	0.009545	2.33E-4	ENSG00000174576	ENST00000311034	T	0.56611	0.45	4.69	4.69	0.59074	.	0.000000	0.56097	D	0.000022	T	0.50956	0.1646	N	0.24115	0.695	0.50039	D	0.999849	D	0.89917	1.0	D	0.80764	0.994	T	0.60826	-0.7186	10	0.59425	D	0.04	-6.0706	15.1587	0.72764	0.0:1.0:0.0:0.0	.	587	Q8IUM7	NPAS4_HUMAN	M	587	ENSP00000311196:T587M	ENSP00000311196:T587M	T	+	2	0	NPAS4	65948697	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	6.516000	0.73755	2.443000	0.82685	0.655000	0.94253	ACG		0.607	NPAS4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392634.1	NM_178864		17	183	17	183
MMP1	4312	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	11	102666337	102666337	+	Splice_Site	SNP	C	C	T			TCGA-HW-7490-01A-11D-2024-08	TCGA-HW-7490-10A-01D-2024-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ca68843d-1087-4efa-b5f8-0acd8982fb3b	855988d0-f042-466d-86a8-1ac1cb1bc7a1	g.chr11:102666337C>T	ENST00000315274.6	-	5	694	c.627G>A	c.(625-627)gaG>gaA	p.E209E	WTAPP1_ENST00000525739.2_RNA	NM_001145938.1|NM_002421.3	NP_001139410.1|NP_002412.1	P03956	MMP1_HUMAN	matrix metallopeptidase 1 (interstitial collagenase)	209	Metalloprotease.				blood coagulation (GO:0007596)|cellular protein metabolic process (GO:0044267)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|leukocyte migration (GO:0050900)|proteolysis (GO:0006508)|viral process (GO:0016032)	extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			breast(2)|endometrium(1)|large_intestine(2)|lung(18)|ovary(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	30	all_epithelial(12;0.0127)	all_neural(303;0.000318)|all_hematologic(158;0.00092)|Acute lymphoblastic leukemia(157;0.000967)	Epithelial(9;0.072)|Lung(13;0.0828)|LUSC - Lung squamous cell carcinoma(19;0.151)|all cancers(10;0.233)	OV - Ovarian serous cystadenocarcinoma(223;1.82e-07)|Epithelial(105;1.51e-06)|BRCA - Breast invasive adenocarcinoma(274;0.014)	Marimastat(DB00786)	GTAAGTTGTACTCTAAAAAGG	0.368																																																0													49.0	44.0	46.0					11																	102666337		2203	4299	6502	SO:0001630	splice_region_variant	4312			X54925	CCDS8322.1	11q21-q22	2014-01-30	2005-08-08		ENSG00000196611	ENSG00000196611	3.4.24.7	"""Endogenous ligands"""	7155	protein-coding gene	gene with protein product		120353	"""matrix metalloproteinase 1 (interstitial collagenase)"""	CLG			Standard	NM_002421		Approved		uc001phi.2	P03956	OTTHUMG00000048192	ENST00000315274.6:c.626-1G>A	11.37:g.102666337C>T			P08156	Splice_Site	SNP	ENST00000315274.6	37	CCDS8322.1																																																																																				0.368	MMP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109632.1	NM_002421	Silent	11	29	11	29
GRIN2B	2904	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	12	13716801	13716801	+	Missense_Mutation	SNP	C	C	T			TCGA-HW-7490-01A-11D-2024-08	TCGA-HW-7490-10A-01D-2024-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ca68843d-1087-4efa-b5f8-0acd8982fb3b	855988d0-f042-466d-86a8-1ac1cb1bc7a1	g.chr12:13716801C>T	ENST00000609686.1	-	13	3580	c.3371G>A	c.(3370-3372)aGg>aAg	p.R1124K		NM_000834.3	NP_000825.2	Q13224	NMDE2_HUMAN	glutamate receptor, ionotropic, N-methyl D-aspartate 2B	1124					behavioral fear response (GO:0001662)|behavioral response to pain (GO:0048266)|detection of mechanical stimulus involved in sensory perception of pain (GO:0050966)|glutamate receptor signaling pathway (GO:0007215)|in utero embryonic development (GO:0001701)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|learning (GO:0007612)|learning or memory (GO:0007611)|memory (GO:0007613)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of synaptic plasticity (GO:0048167)|response to ethanol (GO:0045471)|sensory organ development (GO:0007423)|startle response (GO:0001964)|suckling behavior (GO:0001967)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transport (GO:0006810)	cell junction (GO:0030054)|cell surface (GO:0009986)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|N-methyl-D-aspartate selective glutamate receptor complex (GO:0017146)|neuron projection (GO:0043005)|neuronal postsynaptic density (GO:0097481)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|synaptic vesicle (GO:0008021)	calcium channel activity (GO:0005262)|extracellular-glutamate-gated ion channel activity (GO:0005234)|glycine binding (GO:0016594)|N-methyl-D-aspartate selective glutamate receptor activity (GO:0004972)|zinc ion binding (GO:0008270)			NS(1)|breast(3)|central_nervous_system(5)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(3)|kidney(12)|large_intestine(12)|liver(1)|lung(70)|ovary(4)|prostate(6)|skin(10)|upper_aerodigestive_tract(5)|urinary_tract(1)	143					Acamprosate(DB00659)|Acetylcysteine(DB06151)|Atomoxetine(DB00289)|Felbamate(DB00949)|Gabapentin(DB00996)|Haloperidol(DB00502)|Ketobemidone(DB06738)|Memantine(DB01043)|Milnacipran(DB04896)|Pentobarbital(DB00312)|Pethidine(DB00454)|Phenobarbital(DB01174)|Secobarbital(DB00418)	TTCCTTGTCCCTGAAGTAGCG	0.617																																																0													84.0	79.0	80.0					12																	13716801		2203	4300	6503	SO:0001583	missense	2904				CCDS8662.1	12p13.1	2014-07-16			ENSG00000273079			"""Ligand-gated ion channels / Glutamate receptors, ionotropic"", ""Glutamate receptors"""	4586	protein-coding gene	gene with protein product		138252		NMDAR2B		1350383	Standard	NM_000834		Approved	GluN2B	uc001rbt.2	Q13224	OTTHUMG00000137373	ENST00000609686.1:c.3371G>A	12.37:g.13716801C>T	ENSP00000477455:p.Arg1124Lys		Q12919|Q13220|Q13225|Q14CU4|Q9UM56	Missense_Mutation	SNP	ENST00000609686.1	37	CCDS8662.1	.	.	.	.	.	.	.	.	.	.	C	7.600	0.672512	0.14776	.	.	ENSG00000150086	ENST00000279593	T	0.12465	2.68	5.34	5.34	0.76211	Glutamate [NMDA] receptor, epsilon subunit, C-terminal (1);	0.000000	0.85682	D	0.000000	T	0.10294	0.0252	N	0.21448	0.665	0.58432	D	0.999998	B	0.14012	0.009	B	0.21360	0.034	T	0.07597	-1.0764	10	0.02654	T	1	.	19.0724	0.93145	0.0:1.0:0.0:0.0	.	1124	Q13224	NMDE2_HUMAN	K	1124	ENSP00000279593:R1124K	ENSP00000279593:R1124K	R	-	2	0	GRIN2B	13608068	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.672000	0.68102	2.492000	0.84095	0.655000	0.94253	AGG		0.617	GRIN2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268014.2			20	29	20	29
KRT84	3890	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	12	52777394	52777394	+	Silent	SNP	G	G	A			TCGA-HW-7490-01A-11D-2024-08	TCGA-HW-7490-10A-01D-2024-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ca68843d-1087-4efa-b5f8-0acd8982fb3b	855988d0-f042-466d-86a8-1ac1cb1bc7a1	g.chr12:52777394G>A	ENST00000257951.3	-	2	801	c.735C>T	c.(733-735)gtC>gtT	p.V245V	RP3-416H24.4_ENST00000547174.1_RNA	NM_033045.3	NP_149034.2	Q9NSB2	KRT84_HUMAN	keratin 84	245	Coil 1B.|Rod.				hair follicle development (GO:0001942)|nail development (GO:0035878)|regulation of keratinocyte differentiation (GO:0045616)	extracellular vesicular exosome (GO:0070062)|keratin filament (GO:0045095)	structural constituent of cytoskeleton (GO:0005200)|structural constituent of epidermis (GO:0030280)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|liver(1)|lung(10)|skin(3)	27	all_hematologic(5;0.12)			BRCA - Breast invasive adenocarcinoma(357;0.189)		AGCCCTCTAGGACATCCTGCA	0.577																																																0													58.0	55.0	56.0					12																	52777394		2203	4300	6503	SO:0001819	synonymous_variant	3890			Y19209	CCDS8825.1	12q13	2013-06-25	2006-07-17	2006-07-17	ENSG00000161849	ENSG00000161849		"""-"", ""Intermediate filaments type II, keratins (basic)"""	6461	protein-coding gene	gene with protein product	"""hard keratin type II 4"""	602766	"""keratin, hair, basic, 4"""	KRTHB4		2431943, 16831889	Standard	NM_033045		Approved	Hb-4	uc001sah.1	Q9NSB2	OTTHUMG00000169634	ENST00000257951.3:c.735C>T	12.37:g.52777394G>A			B2RA43|Q6ISB0|Q701L6	Silent	SNP	ENST00000257951.3	37	CCDS8825.1																																																																																				0.577	KRT84-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405187.1	NM_033045		18	18	18	18
ACAD10	80724	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	12	112193513	112193513	+	Silent	SNP	G	G	A			TCGA-HW-7490-01A-11D-2024-08	TCGA-HW-7490-10A-01D-2024-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ca68843d-1087-4efa-b5f8-0acd8982fb3b	855988d0-f042-466d-86a8-1ac1cb1bc7a1	g.chr12:112193513G>A	ENST00000313698.4	+	20	3158	c.3003G>A	c.(3001-3003)ccG>ccA	p.P1001P	RP11-162P23.2_ENST00000546840.2_Missense_Mutation_p.R23H|ACAD10_ENST00000455480.2_Silent_p.P1032P	NM_025247.5	NP_079523.3	Q6JQN1	ACD10_HUMAN	acyl-CoA dehydrogenase family, member 10	1001						mitochondrion (GO:0005739)	acyl-CoA dehydrogenase activity (GO:0003995)|flavin adenine dinucleotide binding (GO:0050660)|hydrolase activity (GO:0016787)|transferase activity, transferring phosphorus-containing groups (GO:0016772)			NS(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(5)|liver(1)|lung(17)|ovary(4)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(5)	47						TGGTCGCCCCGTCCATGGCCT	0.517																																																0													128.0	125.0	126.0					12																	112193513		2203	4300	6503	SO:0001819	synonymous_variant	0			AY323912	CCDS31903.1, CCDS44973.1	12q24.12	2012-10-02	2010-04-30		ENSG00000111271	ENSG00000111271			21597	protein-coding gene	gene with protein product		611181	"""acyl-Coenzyme A dehydrogenase family, member 10"""			15560374	Standard	NM_025247		Approved	MGC5601	uc009zvx.3	Q6JQN1	OTTHUMG00000169602	ENST00000313698.4:c.3003G>A	12.37:g.112193513G>A			G3XAJ0|Q8N828|Q8NAP2|Q96BX5	Missense_Mutation	SNP	ENST00000313698.4	37	CCDS31903.1																																																																																				0.517	ACAD10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368307.1	NM_025247		19	130	19	130
RAB27A	5873	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	15	55497820	55497820	+	Missense_Mutation	SNP	C	C	T	rs141362723		TCGA-HW-7490-01A-11D-2024-08	TCGA-HW-7490-10A-01D-2024-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ca68843d-1087-4efa-b5f8-0acd8982fb3b	855988d0-f042-466d-86a8-1ac1cb1bc7a1	g.chr15:55497820C>T	ENST00000396307.2	-	6	802	c.551G>A	c.(550-552)cGa>cAa	p.R184Q	RAB27A_ENST00000564609.1_Missense_Mutation_p.R184Q|RAB27A_ENST00000569493.1_Missense_Mutation_p.R184Q|RAB27A_ENST00000336787.1_Missense_Mutation_p.R184Q	NM_004580.4	NP_004571.2	P51159	RB27A_HUMAN	RAB27A, member RAS oncogene family	184					antigen processing and presentation (GO:0019882)|blood coagulation (GO:0007596)|cellular protein metabolic process (GO:0044267)|cytotoxic T cell degranulation (GO:0043316)|exocytosis (GO:0006887)|exosomal secretion (GO:1990182)|melanocyte differentiation (GO:0030318)|melanosome transport (GO:0032402)|multivesicular body organization (GO:0036257)|multivesicular body sorting pathway (GO:0071985)|natural killer cell degranulation (GO:0043320)|positive regulation of exocytosis (GO:0045921)|positive regulation of gene expression (GO:0010628)|protein targeting (GO:0006605)|small GTPase mediated signal transduction (GO:0007264)|synaptic vesicle transport (GO:0048489)	apical plasma membrane (GO:0016324)|dendrite (GO:0030425)|exocytic vesicle (GO:0070382)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|late endosome (GO:0005770)|lysosome (GO:0005764)|melanosome (GO:0042470)|multivesicular body membrane (GO:0032585)|photoreceptor outer segment (GO:0001750)|secretory granule membrane (GO:0030667)	GDP binding (GO:0019003)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)			endometrium(1)|large_intestine(2)|liver(1)|lung(3)|ovary(1)|skin(1)	9				all cancers(107;0.0273)|GBM - Glioblastoma multiforme(80;0.0993)		CCGTTCCATTCGCTTCATTAT	0.463													C|||	1	0.000199681	0.0	0.0	5008	,	,		19080	0.0		0.001	False		,,,				2504	0.0															0								C	GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG	0,4386		0,0,2193	342.0	273.0	296.0		551,551,551,551	5.5	1.0	15	dbSNP_134	296	2,8582	2.2+/-6.3	0,2,4290	no	missense,missense,missense,missense	RAB27A	NM_004580.4,NM_183234.2,NM_183235.2,NM_183236.2	43,43,43,43	0,2,6483	TT,TC,CC		0.0233,0.0,0.0154	probably-damaging,probably-damaging,probably-damaging,probably-damaging	184/222,184/222,184/222,184/222	55497820	2,12968	2193	4292	6485	SO:0001583	missense	5873			U38654	CCDS10153.1	15q15-q21.1	2014-09-17			ENSG00000069974	ENSG00000069974		"""RAB, member RAS oncogene"""	9766	protein-coding gene	gene with protein product		603868				7592656	Standard	NM_183235		Approved	RAB27, RAM, GS2, HsT18676	uc002acq.3	P51159	OTTHUMG00000131959	ENST00000396307.2:c.551G>A	15.37:g.55497820C>T	ENSP00000379601:p.Arg184Gln		O00195|Q6FI40|Q9UIR9|Q9Y5U3	Missense_Mutation	SNP	ENST00000396307.2	37	CCDS10153.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	C	27.7	4.855189	0.91355	0.0	2.33E-4	ENSG00000069974	ENST00000396307;ENST00000396304;ENST00000336787	T;T	0.74106	-0.81;-0.81	5.49	5.49	0.81192	.	0.000000	0.85682	D	0.000000	T	0.52289	0.1725	N	0.08118	0	0.80722	D	1	D	0.53151	0.958	B	0.31101	0.124	T	0.66424	-0.5927	10	0.87932	D	0	-2.7882	18.3593	0.90370	0.0:1.0:0.0:0.0	.	184	P51159	RB27A_HUMAN	Q	184;176;184	ENSP00000379601:R184Q;ENSP00000337761:R184Q	ENSP00000337761:R184Q	R	-	2	0	RAB27A	53285112	1.000000	0.71417	0.987000	0.45799	0.998000	0.95712	7.726000	0.84824	2.585000	0.87301	0.655000	0.94253	CGA		0.463	RAB27A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254918.1	NM_004580, NM_183236		65	84	65	84
HSDL1	83693	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	16	84163854	84163854	+	Missense_Mutation	SNP	G	G	A			TCGA-HW-7490-01A-11D-2024-08	TCGA-HW-7490-10A-01D-2024-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ca68843d-1087-4efa-b5f8-0acd8982fb3b	855988d0-f042-466d-86a8-1ac1cb1bc7a1	g.chr16:84163854G>A	ENST00000219439.4	-	4	579	c.403C>T	c.(403-405)Cca>Tca	p.P135S	HSDL1_ENST00000434463.3_Intron	NM_001146051.1|NM_031463.4	NP_001139523.1|NP_113651.4	Q3SXM5	HSDL1_HUMAN	hydroxysteroid dehydrogenase like 1	135						mitochondrion (GO:0005739)	oxidoreductase activity (GO:0016491)			endometrium(1)|kidney(1)|large_intestine(2)|lung(2)|upper_aerodigestive_tract(1)	7						TCTCGAATTGGAAGGTAGATC	0.473																																																0													147.0	134.0	138.0					16																	84163854		2200	4300	6500	SO:0001583	missense	83693			AF237684	CCDS10942.1, CCDS54046.1	16q24	2011-09-20			ENSG00000103160	ENSG00000103160		"""Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 3"""	16475	protein-coding gene	gene with protein product	"""short chain dehydrogenase/reductase family 12C, member 3"""					12153137, 19027726	Standard	NM_031463		Approved	SDR12C3	uc002fhk.2	Q3SXM5	OTTHUMG00000137635	ENST00000219439.4:c.403C>T	16.37:g.84163854G>A	ENSP00000219439:p.Pro135Ser		B4DSL2|D3DUL4|Q3SXM4|Q8NC98|Q9BY22	Missense_Mutation	SNP	ENST00000219439.4	37	CCDS10942.1	.	.	.	.	.	.	.	.	.	.	G	6.722	0.501902	0.12822	.	.	ENSG00000103160	ENST00000219439	D	0.87103	-2.21	5.25	4.28	0.50868	NAD(P)-binding domain (1);	0.305548	0.41097	D	0.000951	T	0.73369	0.3578	N	0.17838	0.53	0.26225	N	0.979109	B	0.09022	0.002	B	0.16722	0.016	T	0.55854	-0.8075	10	0.11485	T	0.65	.	6.162	0.20370	0.0752:0.1448:0.6473:0.1328	.	135	Q3SXM5	HSDL1_HUMAN	S	135	ENSP00000219439:P135S	ENSP00000219439:P135S	P	-	1	0	HSDL1	82721355	0.977000	0.34250	0.009000	0.14445	0.136000	0.21042	2.001000	0.40825	1.322000	0.45245	0.655000	0.94253	CCA		0.473	HSDL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269076.3	NM_031463		16	165	16	165
TP53	7157	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	17	7577120	7577120	+	Missense_Mutation	SNP	C	C	T	rs28934576		TCGA-HW-7490-01A-11D-2024-08	TCGA-HW-7490-10A-01D-2024-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ca68843d-1087-4efa-b5f8-0acd8982fb3b	855988d0-f042-466d-86a8-1ac1cb1bc7a1	g.chr17:7577120C>T	ENST00000269305.4	-	8	1007	c.818G>A	c.(817-819)cGt>cAt	p.R273H	TP53_ENST00000445888.2_Missense_Mutation_p.R273H|TP53_ENST00000359597.4_Missense_Mutation_p.R273H|TP53_ENST00000574684.1_5'Flank|TP53_ENST00000413465.2_Intron|TP53_ENST00000420246.2_Missense_Mutation_p.R273H|TP53_ENST00000455263.2_Missense_Mutation_p.R273H	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	273	Interaction with AXIN1. {ECO:0000250}.|Interaction with DNA.|Interaction with E4F1.|Interaction with HIPK1. {ECO:0000250}.|Required for interaction with ZNF385A.		R -> C (in LFS; germline mutation and in sporadic cancers; somatic mutation). {ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:17224074, ECO:0000269|PubMed:7887414, ECO:0000269|PubMed:9450901}.|R -> G (in LFS; germline mutation and in sporadic cancers; somatic mutation).|R -> H (in LFS; germline mutation and in sporadic cancers; somatic mutation; abolishes sequence-specific DNA binding; does not induce SNAI1 degradation; dbSNP:rs28934576). {ECO:0000269|PubMed:1394225, ECO:0000269|PubMed:1565144, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:1699228, ECO:0000269|PubMed:1868473, ECO:0000269|PubMed:7682763, ECO:0000269|Ref.14}.|R -> L (in LFS; germline mutation and in sporadic cancers; somatic mutation). {ECO:0000269|PubMed:16959974}.|R -> N (in a sporadic cancer; somatic mutation; requires 2 nucleotide substitutions).|R -> P (in sporadic cancers; somatic mutation).|R -> Q (in sporadic cancers; somatic mutation).|R -> S (in a familial cancer not matching LFS; germline mutation and in sporadic cancers; somatic mutation).|R -> Y (in a sporadic cancer; somatic mutation; requires 2 nucleotide substitutions).		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|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)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.R273H(521)|p.R273L(93)|p.R273P(32)|p.0?(8)|p.?(2)|p.R273fs*32(2)|p.R273_C275delRVC(1)|p.L265_K305del41(1)|p.S269fs*21(1)|p.R273S(1)|p.E258fs*71(1)|p.R273fs*72(1)|p.R273fs*71(1)|p.F270_D281del12(1)|p.R273fs*33(1)|p.E271_R273delEVR(1)|p.V272_K292del21(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	GGCACAAACACGCACCTCAAA	0.542	R273H(EN_ENDOMETRIUM)|R273H(HEC59_ENDOMETRIUM)|R273H(HEC6_ENDOMETRIUM)|R273H(HT29_LARGE_INTESTINE)|R273H(HT_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R273H(MDAMB468_BREAST)|R273H(MOLT13_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R273H(NCIH1155_LUNG)|R273H(NCIH1793_LUNG)|R273H(NCIH1975_LUNG)|R273H(NCIH2405_LUNG)|R273H(NCIH508_LARGE_INTESTINE)|R273H(OC314_OVARY)|R273H(PANC1_PANCREAS)|R273H(PF382_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R273H(SKMEL30_SKIN)|R273H(SNB19_CENTRAL_NERVOUS_SYSTEM)|R273H(SUDHL1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R273H(SUIT2_PANCREAS)|R273H(SUPT1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R273H(SW1783_CENTRAL_NERVOUS_SYSTEM)|R273H(SW480_LARGE_INTESTINE)|R273H(SW620_LARGE_INTESTINE)|R273H(U251MG_CENTRAL_NERVOUS_SYSTEM)	111	"""Mis, N, F"""		"""breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"""	"""breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"""		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)			C|||	1	0.000199681	0.0	0.0	5008	,	,		18620	0.0		0.001	False		,,,				2504	0.0				Pancreas(47;798 1329 9957 10801)	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"""L, E, M, O"""	669	Substitution - Missense(647)|Whole gene deletion(8)|Deletion - Frameshift(6)|Deletion - In frame(5)|Unknown(2)|Insertion - Frameshift(1)	large_intestine(136)|lung(99)|breast(74)|ovary(59)|upper_aerodigestive_tract(55)|central_nervous_system(46)|oesophagus(35)|haematopoietic_and_lymphoid_tissue(30)|stomach(26)|urinary_tract(25)|pancreas(15)|endometrium(13)|liver(12)|skin(11)|bone(9)|biliary_tract(7)|penis(4)|cervix(2)|genital_tract(2)|NS(2)|soft_tissue(2)|vulva(1)|thyroid(1)|fallopian_tube(1)|prostate(1)|thymus(1)	GRCh37	CM004342|CM010472|CM920677	TP53	M	rs28934576						67.0	58.0	61.0					17																	7577120		2203	4300	6503	SO:0001583	missense	7157	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"""Li-Fraumeni syndrome"""	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.818G>A	17.37:g.7577120C>T	ENSP00000269305:p.Arg273His		Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Missense_Mutation	SNP	ENST00000269305.4	37	CCDS11118.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	C	18.03	3.532510	0.64972	.	.	ENSG00000141510	ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000509690	D;D;D;D;D;D	0.99868	-7.32;-7.32;-7.32;-7.32;-7.32;-7.32	4.92	4.92	0.64577	p53, DNA-binding domain (1);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1);	0.000000	0.85682	D	0.000000	D	0.99822	0.9921	M	0.79475	2.455	0.80722	A	1	P;D;P;P	0.89917	0.631;1.0;0.831;0.48	B;D;P;B	0.77004	0.274;0.989;0.516;0.242	D	0.96531	0.9393	9	0.72032	D	0.01	-11.9995	15.662	0.77193	0.0:1.0:0.0:0.0	rs28934576	273;273;273;273	P04637-2;P04637-3;P04637;Q1MSW8	.;.;P53_HUMAN;.	H	273;273;273;273;273;262;141	ENSP00000352610:R273H;ENSP00000269305:R273H;ENSP00000398846:R273H;ENSP00000391127:R273H;ENSP00000391478:R273H;ENSP00000425104:R141H	ENSP00000269305:R273H	R	-	2	0	TP53	7517845	1.000000	0.71417	0.068000	0.19968	0.665000	0.39181	7.587000	0.82613	2.556000	0.86216	0.462000	0.41574	CGT		0.542	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		29	3	29	3
ARHGEF10L	55160	hgsc.bcm.edu;broad.mit.edu	37	1	17961457	17961457	+	Missense_Mutation	SNP	G	G	C			TCGA-HW-7490-01A-11D-2024-08	TCGA-HW-7490-10A-01D-2024-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ca68843d-1087-4efa-b5f8-0acd8982fb3b	855988d0-f042-466d-86a8-1ac1cb1bc7a1	g.chr1:17961457G>C	ENST00000361221.3	+	18	2032	c.1873G>C	c.(1873-1875)Gtg>Ctg	p.V625L	ARHGEF10L_ENST00000167825.4_Missense_Mutation_p.V328L|ARHGEF10L_ENST00000452522.1_Missense_Mutation_p.V586L|ARHGEF10L_ENST00000434513.1_Missense_Mutation_p.V620L|ARHGEF10L_ENST00000375420.3_Missense_Mutation_p.V383L|ARHGEF10L_ENST00000469726.1_3'UTR|ARHGEF10L_ENST00000375408.3_Missense_Mutation_p.V398L|ARHGEF10L_ENST00000375415.1_Missense_Mutation_p.V586L	NM_018125.3	NP_060595	Q9HCE6	ARGAL_HUMAN	Rho guanine nucleotide exchange factor (GEF) 10-like	625						cytoplasm (GO:0005737)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|liver(2)|lung(16)|ovary(4)|pancreas(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	43		Colorectal(325;3.46e-05)|Breast(348;0.000162)|all_lung(284;0.000337)|Lung NSC(340;0.000419)|Renal(390;0.000518)|Ovarian(437;0.00409)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00598)|COAD - Colon adenocarcinoma(227;1.62e-05)|BRCA - Breast invasive adenocarcinoma(304;1.68e-05)|Kidney(64;0.000269)|KIRC - Kidney renal clear cell carcinoma(64;0.00361)|STAD - Stomach adenocarcinoma(196;0.00656)|READ - Rectum adenocarcinoma(331;0.0718)|Lung(427;0.204)		CAAGGACAATGTGCTCATCCA	0.642																																																0													75.0	70.0	72.0					1																	17961457		2203	4300	6503	SO:0001583	missense	55160			AB046846	CCDS182.1, CCDS30617.1	1p36.13	2011-11-16			ENSG00000074964	ENSG00000074964		"""Rho guanine nucleotide exchange factors"""	25540	protein-coding gene	gene with protein product	"""GrinchGEF"""	612494				10997877, 16112081	Standard	XM_005245923		Approved	FLJ10521, KIAA1626	uc001ban.3	Q9HCE6	OTTHUMG00000002514	ENST00000361221.3:c.1873G>C	1.37:g.17961457G>C	ENSP00000355060:p.Val625Leu		B7ZKS1|Q17RW1|Q3YFJ4|Q5VXI5|Q5VXI6|Q66K51|Q6P0L7|Q8NAV5|Q9NVT3	Missense_Mutation	SNP	ENST00000361221.3	37	CCDS182.1	.	.	.	.	.	.	.	.	.	.	G	0.347	-0.947075	0.02304	.	.	ENSG00000074964	ENST00000361221;ENST00000452522;ENST00000434513;ENST00000375415;ENST00000375420;ENST00000375408;ENST00000457829;ENST00000167825	T;T;T;T;T;T;T	0.59906	0.57;0.59;0.37;0.59;0.23;0.29;2.57	4.65	2.67	0.31697	.	0.817856	0.10784	N	0.634532	T	0.32041	0.0816	N	0.04880	-0.145	0.22656	N	0.998884	B;B;B;B;B;B;B;B	0.02656	0.0;0.0;0.0;0.0;0.0;0.0;0.0;0.0	B;B;B;B;B;B;B;B	0.04013	0.001;0.001;0.001;0.001;0.0;0.001;0.001;0.0	T	0.19484	-1.0304	10	0.10902	T	0.67	-7.3736	9.0371	0.36293	0.0842:0.1479:0.7679:0.0	.	398;383;620;328;386;581;586;625	Q5VXI4;B4DTE2;Q9HCE6-5;Q9HCE6-4;B3KX74;Q9HCE6-3;Q9HCE6-2;Q9HCE6	.;.;.;.;.;.;.;ARGAL_HUMAN	L	625;586;620;586;383;398;398;328	ENSP00000355060:V625L;ENSP00000399401:V586L;ENSP00000394621:V620L;ENSP00000364564:V586L;ENSP00000364569:V383L;ENSP00000364557:V398L;ENSP00000167825:V328L	ENSP00000167825:V328L	V	+	1	0	ARHGEF10L	17834044	0.235000	0.23794	0.951000	0.38953	0.013000	0.08279	1.085000	0.30840	0.450000	0.26774	0.655000	0.94253	GTG		0.642	ARHGEF10L-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000007147.1	NM_018125		3	46	3	46
ELMOD3	84173	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	2	85617291	85617291	+	Silent	SNP	C	C	T			TCGA-HW-7490-01A-11D-2024-08	TCGA-HW-7490-10A-01D-2024-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ca68843d-1087-4efa-b5f8-0acd8982fb3b	855988d0-f042-466d-86a8-1ac1cb1bc7a1	g.chr2:85617291C>T	ENST00000409890.2	+	13	1513	c.846C>T	c.(844-846)ccC>ccT	p.P282P	ELMOD3_ENST00000409013.3_Silent_p.P282P|ELMOD3_ENST00000315658.7_Silent_p.P282P|ELMOD3_ENST00000490508.1_3'UTR|ELMOD3_ENST00000393852.4_Silent_p.P282P|ELMOD3_ENST00000409344.3_Silent_p.P282P			Q96FG2	ELMD3_HUMAN	ELMO/CED-12 domain containing 3	282	ELMO. {ECO:0000255|PROSITE- ProRule:PRU00664}.				phagocytosis (GO:0006909)	cilium (GO:0005929)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)				endometrium(1)|kidney(1)|large_intestine(3)|lung(4)|ovary(2)|prostate(1)	12						AGGTCATCCCCGTGGTGAACA	0.567																																																0													104.0	84.0	91.0					2																	85617291		2203	4300	6503	SO:0001819	synonymous_variant	84173			AF258573	CCDS1973.1, CCDS46352.1	2p11.2	2014-01-28	2008-08-14	2008-08-14	ENSG00000115459	ENSG00000115459		"""RNA binding motif (RRM) containing"""	26158	protein-coding gene	gene with protein product		615427	"""RNA binding motif protein 29"", ""RNA binding motif and ELMO/CED-12 domain 1"", ""deafness, autosomal recessive 88"""	RBM29, RBED1, DFNB88		24039609	Standard	NM_032213		Approved	FLJ21977	uc010ysn.2	Q96FG2	OTTHUMG00000130170	ENST00000409890.2:c.846C>T	2.37:g.85617291C>T			B8ZZD6|D6W5K4|Q2M1K3|Q2XSU3|Q2XSU4|Q8NAC1|Q8TCK4|Q8WV70|Q8WY75|Q9H6Q8	Silent	SNP	ENST00000409890.2	37	CCDS46352.1																																																																																				0.567	ELMOD3-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329124.1	NM_032213		23	46	23	46
GPR39	2863	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	2	133175296	133175296	+	Silent	SNP	C	C	T			TCGA-HW-7490-01A-11D-2024-08	TCGA-HW-7490-10A-01D-2024-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ca68843d-1087-4efa-b5f8-0acd8982fb3b	855988d0-f042-466d-86a8-1ac1cb1bc7a1	g.chr2:133175296C>T	ENST00000329321.3	+	1	1150	c.681C>T	c.(679-681)gcC>gcT	p.A227A		NM_001508.2	NP_001499.1	O43194	GPR39_HUMAN	G protein-coupled receptor 39	227					G-protein coupled receptor signaling pathway (GO:0007186)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|metal ion binding (GO:0046872)			breast(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(8)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	22						TCTTCGGCGCCTTCGTGGTCT	0.612																																																0													86.0	79.0	81.0					2																	133175296		2203	4300	6503	SO:0001819	synonymous_variant	2863			AF034633	CCDS2170.1	2q21-q22	2012-08-21			ENSG00000183840	ENSG00000183840		"""GPCR / Class A : Orphans"""	4496	protein-coding gene	gene with protein product		602886				9441746	Standard	NM_001508		Approved		uc002ttl.3	O43194	OTTHUMG00000131679	ENST00000329321.3:c.681C>T	2.37:g.133175296C>T			B2RC12|B6V9G4|Q08AS2|Q53R01	Silent	SNP	ENST00000329321.3	37	CCDS2170.1																																																																																				0.612	GPR39-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254582.1			30	50	30	50
TANK	10010	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	2	162087893	162087893	+	Missense_Mutation	SNP	C	C	T			TCGA-HW-7490-01A-11D-2024-08	TCGA-HW-7490-10A-01D-2024-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ca68843d-1087-4efa-b5f8-0acd8982fb3b	855988d0-f042-466d-86a8-1ac1cb1bc7a1	g.chr2:162087893C>T	ENST00000392749.2	+	7	1171	c.932C>T	c.(931-933)cCc>cTc	p.P311L	TANK_ENST00000259075.2_Missense_Mutation_p.P311L|TANK_ENST00000406287.1_Intron|AC009299.2_ENST00000445372.1_RNA|AC009299.2_ENST00000421122.2_RNA|TANK_ENST00000402568.1_Intron|TANK_ENST00000405852.1_Missense_Mutation_p.P311L	NM_001199135.1	NP_001186064.1	Q92844	TANK_HUMAN	TRAF family member-associated NFKB activator	311					I-kappaB kinase/NF-kappaB signaling (GO:0007249)|innate immune response (GO:0045087)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytosol (GO:0005829)	metal ion binding (GO:0046872)|ubiquitin protein ligase binding (GO:0031625)			breast(1)|endometrium(3)|kidney(2)|large_intestine(6)|lung(7)|ovary(1)|prostate(1)	21						AAAACAAAGCCCTCAAATCTC	0.383																																																0													94.0	94.0	94.0					2																	162087893		2203	4300	6503	SO:0001583	missense	10010			U59863	CCDS2215.1, CCDS46436.1	2q24-q31	2008-02-05			ENSG00000136560	ENSG00000136560			11562	protein-coding gene	gene with protein product		603893		TRAF2		8710854, 8855313	Standard	NM_004180		Approved	I-TRAF	uc002ubr.2	Q92844	OTTHUMG00000132037	ENST00000392749.2:c.932C>T	2.37:g.162087893C>T	ENSP00000376505:p.Pro311Leu		D3DPB5|Q7Z4J6|Q92885	Missense_Mutation	SNP	ENST00000392749.2	37	CCDS2215.1	.	.	.	.	.	.	.	.	.	.	C	8.925	0.962139	0.18583	.	.	ENSG00000136560	ENST00000259075;ENST00000392749;ENST00000405852;ENST00000437623;ENST00000439442	T;T;T;T;T	0.33216	1.89;1.89;1.42;1.43;1.84	5.58	3.73	0.42828	.	0.180894	0.39834	N	0.001256	T	0.27063	0.0663	L	0.59436	1.845	0.80722	D	1	B	0.09022	0.002	B	0.06405	0.002	T	0.07829	-1.0752	10	0.33940	T	0.23	-0.0016	7.9209	0.29846	0.0:0.7245:0.1388:0.1368	.	311	Q92844	TANK_HUMAN	L	311;311;311;202;66	ENSP00000259075:P311L;ENSP00000376505:P311L;ENSP00000385487:P311L;ENSP00000412556:P202L;ENSP00000387439:P66L	ENSP00000259075:P311L	P	+	2	0	TANK	161796139	0.980000	0.34600	0.973000	0.42090	0.659000	0.38960	1.898000	0.39809	1.456000	0.47831	0.591000	0.81541	CCC		0.383	TANK-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324232.1	NM_133484		10	126	10	126
IDH1	3417	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	2	209113112	209113112	+	Missense_Mutation	SNP	C	C	T	rs121913500		TCGA-HW-7490-01A-11D-2024-08	TCGA-HW-7490-10A-01D-2024-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ca68843d-1087-4efa-b5f8-0acd8982fb3b	855988d0-f042-466d-86a8-1ac1cb1bc7a1	g.chr2:209113112C>T	ENST00000415913.1	-	4	776	c.395G>A	c.(394-396)cGt>cAt	p.R132H	IDH1_ENST00000345146.2_Missense_Mutation_p.R132H|IDH1_ENST00000446179.1_Missense_Mutation_p.R132H	NM_001282387.1	NP_001269316.1	O75874	IDHC_HUMAN	isocitrate dehydrogenase 1 (NADP+), soluble	132			R -> C (in colorectal cancer and glioma samples; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha- ketoglutarate but instead alpha- ketoglutarate is converted to R(-)-2- hydroxyglutarate). {ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:19117336}.|R -> G (in a glioma sample; glioblastoma multiforme; somatic mutation). {ECO:0000269|PubMed:19117336}.|R -> H (in a glioma sample; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha-ketoglutarate but instead alpha-ketoglutarate is converted to R(-)-2-hydroxyglutarate). {ECO:0000269|PubMed:18772396}.|R -> L (in a glioma sample; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha-ketoglutarate but instead alpha-ketoglutarate is converted to R(-)-2-hydroxyglutarate). {ECO:0000269|PubMed:19117336}.|R -> S (in a glioma sample; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha-ketoglutarate but instead alpha-ketoglutarate is converted to R(-)-2-hydroxyglutarate). {ECO:0000269|PubMed:18772396}.		2-oxoglutarate metabolic process (GO:0006103)|cellular lipid metabolic process (GO:0044255)|female gonad development (GO:0008585)|glutathione metabolic process (GO:0006749)|glyoxylate cycle (GO:0006097)|isocitrate metabolic process (GO:0006102)|NADPH regeneration (GO:0006740)|response to oxidative stress (GO:0006979)|response to steroid hormone (GO:0048545)|small molecule metabolic process (GO:0044281)|tricarboxylic acid cycle (GO:0006099)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|peroxisomal matrix (GO:0005782)|peroxisome (GO:0005777)	isocitrate dehydrogenase (NADP+) activity (GO:0004450)|magnesium ion binding (GO:0000287)|NAD binding (GO:0051287)|NADP binding (GO:0050661)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)	p.R132H(2774)|p.R132L(59)|p.R132V(1)|p.G131_R132>VL(1)		NS(1)|autonomic_ganglia(2)|biliary_tract(24)|bone(237)|central_nervous_system(3764)|endometrium(3)|haematopoietic_and_lymphoid_tissue(794)|kidney(2)|large_intestine(7)|lung(7)|prostate(6)|skin(5)|soft_tissue(12)|thyroid(22)|urinary_tract(1)	4887				Epithelial(149;0.0322)|LUSC - Lung squamous cell carcinoma(261;0.0711)|Lung(261;0.136)		ATAAGCATGACGACCTATGAT	0.393			Mis		gliobastoma																																Pancreas(158;264 1958 3300 35450 36047)		Dom	yes		2	2q33.3	3417	"""isocitrate dehydrogenase 1 (NADP+), soluble"""		O	2835	Substitution - Missense(2834)|Complex - compound substitution(1)	central_nervous_system(2579)|haematopoietic_and_lymphoid_tissue(205)|bone(43)|prostate(4)|biliary_tract(2)|urinary_tract(1)|skin(1)											79.0	73.0	75.0					2																	209113112		2203	4300	6503	SO:0001583	missense	3417				CCDS2381.1	2q34	2014-09-17			ENSG00000138413	ENSG00000138413	1.1.1.42		5382	protein-coding gene	gene with protein product		147700					Standard	NM_005896		Approved		uc002vcu.3	O75874	OTTHUMG00000132943	ENST00000415913.1:c.395G>A	2.37:g.209113112C>T	ENSP00000390265:p.Arg132His		Q567U4|Q6FHQ6|Q7Z3V0|Q93090|Q9NTJ9|Q9UKW8	Missense_Mutation	SNP	ENST00000415913.1	37	CCDS2381.1	.	.	.	.	.	.	.	.	.	.	C	25.6	4.657324	0.88154	.	.	ENSG00000138413	ENST00000345146;ENST00000446179;ENST00000415913;ENST00000415282	D;D;D;D	0.86956	-2.19;-2.19;-2.19;-2.19	5.57	4.69	0.59074	Isopropylmalate dehydrogenase-like domain (2);	0.000000	0.85682	D	0.000000	D	0.93145	0.7817	H	0.99379	4.54	0.80722	D	1	B	0.25486	0.127	B	0.25405	0.06	D	0.92324	0.5868	10	0.87932	D	0	-20.0399	14.3783	0.66895	0.0:0.9288:0.0:0.0712	.	132	O75874	IDHC_HUMAN	H	132	ENSP00000260985:R132H;ENSP00000410513:R132H;ENSP00000390265:R132H;ENSP00000391075:R132H	ENSP00000260985:R132H	R	-	2	0	IDH1	208821357	1.000000	0.71417	0.997000	0.53966	0.992000	0.81027	6.088000	0.71371	1.356000	0.45884	0.555000	0.69702	CGT		0.393	IDH1-006	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336672.1			24	64	24	64
SLC6A11	6538	hgsc.bcm.edu;broad.mit.edu	37	3	10885932	10885932	+	Missense_Mutation	SNP	G	G	C			TCGA-HW-7490-01A-11D-2024-08	TCGA-HW-7490-10A-01D-2024-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ca68843d-1087-4efa-b5f8-0acd8982fb3b	855988d0-f042-466d-86a8-1ac1cb1bc7a1	g.chr3:10885932G>C	ENST00000254488.2	+	5	723	c.657G>C	c.(655-657)gaG>gaC	p.E219D		NM_014229.1	NP_055044.1	P48066	S6A11_HUMAN	solute carrier family 6 (neurotransmitter transporter), member 11	219					brain development (GO:0007420)|neurotransmitter secretion (GO:0007269)|response to drug (GO:0042493)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	gamma-aminobutyric acid:sodium symporter activity (GO:0005332)|neurotransmitter binding (GO:0042165)|neurotransmitter:sodium symporter activity (GO:0005328)			breast(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(13)|lung(13)|ovary(1)|skin(4)	35				OV - Ovarian serous cystadenocarcinoma(96;0.229)	Clobazam(DB00349)	ACGGGATCGAGCACATCGGGA	0.587																																																0													127.0	108.0	114.0					3																	10885932		2203	4300	6503	SO:0001583	missense	6538			S75989	CCDS2602.1	3p25.3	2013-07-19	2013-07-19		ENSG00000132164	ENSG00000132164		"""Solute carriers"""	11044	protein-coding gene	gene with protein product	"""GABA transporter 3"""	607952	"""solute carrier family 6 (neurotransmitter transporter, GABA), member 11"""			7874447	Standard	NM_014229		Approved	GAT3	uc003bvz.3	P48066	OTTHUMG00000129718	ENST00000254488.2:c.657G>C	3.37:g.10885932G>C	ENSP00000254488:p.Glu219Asp		B2R6U6|Q8IYC9	Missense_Mutation	SNP	ENST00000254488.2	37	CCDS2602.1	.	.	.	.	.	.	.	.	.	.	G	9.836	1.189734	0.21954	.	.	ENSG00000132164	ENST00000254488	T	0.74842	-0.88	5.73	1.86	0.25419	.	0.098518	0.64402	N	0.000002	T	0.48114	0.1482	N	0.12569	0.235	0.80722	D	1	B	0.02656	0.0	B	0.12156	0.007	T	0.17776	-1.0358	10	0.08837	T	0.75	.	6.1777	0.20453	0.3388:0.1296:0.5316:0.0	.	219	P48066	S6A11_HUMAN	D	219	ENSP00000254488:E219D	ENSP00000254488:E219D	E	+	3	2	SLC6A11	10860932	0.995000	0.38212	1.000000	0.80357	0.984000	0.73092	0.324000	0.19610	0.322000	0.23283	-0.219000	0.12488	GAG		0.587	SLC6A11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251927.1	NM_014229		3	44	3	44
MAN2B2	23324	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	4	6612960	6612960	+	Silent	SNP	C	C	T			TCGA-HW-7490-01A-11D-2024-08	TCGA-HW-7490-10A-01D-2024-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ca68843d-1087-4efa-b5f8-0acd8982fb3b	855988d0-f042-466d-86a8-1ac1cb1bc7a1	g.chr4:6612960C>T	ENST00000285599.3	+	15	2554	c.2518C>T	c.(2518-2520)Ctg>Ttg	p.L840L	MAN2B2_ENST00000504248.1_Silent_p.L789L	NM_015274.1	NP_056089.1	Q9Y2E5	MA2B2_HUMAN	mannosidase, alpha, class 2B, member 2	840					mannose metabolic process (GO:0006013)	extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)	alpha-mannosidase activity (GO:0004559)|carbohydrate binding (GO:0030246)|zinc ion binding (GO:0008270)			breast(2)|cervix(2)|endometrium(4)|kidney(1)|large_intestine(3)|lung(9)|ovary(4)|prostate(2)|skin(2)|urinary_tract(1)	30						GAGGAGCGCACTGGCGCTGCA	0.627																																																0													45.0	44.0	44.0					4																	6612960		2203	4300	6503	SO:0001819	synonymous_variant	23324			BC033307	CCDS33951.1	4p16.2	2005-11-09			ENSG00000013288	ENSG00000013288			29623	protein-coding gene	gene with protein product	"""core-specific lysosomal alpha-1,6-Mannosidase"""					10231032, 16115860	Standard	XR_241647		Approved	KIAA0935	uc003gjf.1	Q9Y2E5	OTTHUMG00000160073	ENST00000285599.3:c.2518C>T	4.37:g.6612960C>T			Q66MP2|Q86T67	Silent	SNP	ENST00000285599.3	37	CCDS33951.1																																																																																				0.627	MAN2B2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359106.2	NM_015274		15	21	15	21
COL25A1	84570	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	4	109805344	109805344	+	Missense_Mutation	SNP	G	G	A			TCGA-HW-7490-01A-11D-2024-08	TCGA-HW-7490-10A-01D-2024-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ca68843d-1087-4efa-b5f8-0acd8982fb3b	855988d0-f042-466d-86a8-1ac1cb1bc7a1	g.chr4:109805344G>A	ENST00000399132.1	-	19	1540	c.1010C>T	c.(1009-1011)cCg>cTg	p.P337L	COL25A1_ENST00000399126.1_Missense_Mutation_p.P337L|COL25A1_ENST00000399127.1_Missense_Mutation_p.P333L	NM_198721.2	NP_942014.1			collagen, type XXV, alpha 1											NS(3)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(8)|lung(19)|ovary(2)|pancreas(1)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	49		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;0.000173)		CTTTATCCCCGGAAGTCCAGG	0.413																																																0													73.0	69.0	70.0					4																	109805344		1843	4080	5923	SO:0001583	missense	84570			AF293340	CCDS43258.1, CCDS43259.1, CCDS58922.1	4q25	2013-01-16			ENSG00000188517	ENSG00000188517		"""Collagens"""	18603	protein-coding gene	gene with protein product		610004				11927537	Standard	NM_001256074		Approved		uc003hze.2	Q9BXS0	OTTHUMG00000150039	ENST00000399132.1:c.1010C>T	4.37:g.109805344G>A	ENSP00000382083:p.Pro337Leu			Missense_Mutation	SNP	ENST00000399132.1	37	CCDS43258.1	.	.	.	.	.	.	.	.	.	.	G	17.60	3.430938	0.62844	.	.	ENSG00000188517	ENST00000399132;ENST00000333642;ENST00000399127;ENST00000399126;ENST00000443653	T;T;T	0.32753	1.44;1.44;1.44	5.49	5.49	0.81192	.	0.236919	0.42821	D	0.000660	T	0.60894	0.2304	M	0.84156	2.68	0.58432	D	0.999998	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.995	T	0.63528	-0.6617	9	.	.	.	-4.114	18.3662	0.90391	0.0:0.0:1.0:0.0	.	337;337	Q9BXS0-2;Q9BXS0	.;COPA1_HUMAN	L	337;339;333;337;267	ENSP00000382083:P337L;ENSP00000382078:P333L;ENSP00000382077:P337L	.	P	-	2	0	COL25A1	110024793	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.511000	0.81718	2.566000	0.86566	0.557000	0.71058	CCG		0.413	COL25A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315938.2	NM_032518		25	47	25	47
ZBED9	114821	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	6	28540794	28540794	+	Missense_Mutation	SNP	A	A	G			TCGA-HW-7490-01A-11D-2024-08	TCGA-HW-7490-10A-01D-2024-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ca68843d-1087-4efa-b5f8-0acd8982fb3b	855988d0-f042-466d-86a8-1ac1cb1bc7a1	g.chr6:28540794A>G	ENST00000452236.2	-	4	3489	c.2872T>C	c.(2872-2874)Tgt>Cgt	p.C958R	SCAND3_ENST00000530247.1_5'Flank	NM_052923.1	NP_443155.1														NS(3)|autonomic_ganglia(1)|breast(5)|central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(14)|liver(1)|lung(29)|ovary(2)|prostate(1)|skin(6)|upper_aerodigestive_tract(3)	71						tccaaaccacatttgttaaca	0.353																																																0													43.0	43.0	43.0					6																	28540794		2202	4299	6501	SO:0001583	missense	114821																														ENST00000452236.2:c.2872T>C	6.37:g.28540794A>G	ENSP00000395259:p.Cys958Arg			Missense_Mutation	SNP	ENST00000452236.2	37	CCDS34355.1	.	.	.	.	.	.	.	.	.	.	A	9.615	1.132184	0.21041	.	.	ENSG00000232040	ENST00000452236	T	0.21361	2.01	2.14	2.14	0.27477	Ribonuclease H-like (1);	.	.	.	.	T	0.10551	0.0258	N	0.08118	0	0.47476	D	0.999438	D	0.55800	0.973	D	0.77557	0.99	T	0.11690	-1.0577	9	0.26408	T	0.33	.	6.2738	0.20969	1.0:0.0:0.0:0.0	.	958	Q6R2W3	SCND3_HUMAN	R	958	ENSP00000395259:C958R	ENSP00000395259:C958R	C	-	1	0	SCAND3	28648773	1.000000	0.71417	0.995000	0.50966	0.986000	0.74619	2.200000	0.42724	1.237000	0.43756	0.459000	0.35465	TGT		0.353	SCAND3-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000043551.3			9	45	9	45
PTCHD4	442213	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	6	47976601	47976601	+	Missense_Mutation	SNP	A	A	T			TCGA-HW-7490-01A-11D-2024-08	TCGA-HW-7490-10A-01D-2024-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ca68843d-1087-4efa-b5f8-0acd8982fb3b	855988d0-f042-466d-86a8-1ac1cb1bc7a1	g.chr6:47976601A>T	ENST00000339488.4	-	2	709	c.676T>A	c.(676-678)Ttt>Att	p.F226I	PTCHD4_ENST00000543600.1_Missense_Mutation_p.F209I	NM_001013732.3	NP_001013754.3	Q6ZW05	PTHD4_HUMAN	patched domain containing 4	226						integral component of membrane (GO:0016021)	hedgehog receptor activity (GO:0008158)										GTCTTATGAAAGTCCCTCCAG	0.527																																																0													72.0	72.0	72.0					6																	47976601		1975	4181	6156	SO:0001583	missense	442213				CCDS34473.2	6p12.3	2012-02-06	2012-02-06	2012-02-06	ENSG00000244694	ENSG00000244694			21345	protein-coding gene	gene with protein product			"""chromosome 6 open reading frame 138"""	C6orf138			Standard	NM_001013732		Approved	dJ402H5.2, FLJ41841	uc011dwm.2	Q6ZW05	OTTHUMG00000150404	ENST00000339488.4:c.676T>A	6.37:g.47976601A>T	ENSP00000341914:p.Phe226Ile		B0QZ29|B4DRK3|Q5T884	Missense_Mutation	SNP	ENST00000339488.4	37	CCDS34473.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	24.9|24.9	4.582380|4.582380	0.86748|0.86748	.|.	.|.	ENSG00000244694|ENSG00000244694	ENST00000339488;ENST00000543600|ENST00000398738	D;D|.	0.83837|.	-1.77;-1.77|.	6.16|6.16	6.16|6.16	0.99307|0.99307	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.68869|0.68869	0.3048|0.3048	M|M	0.72118|0.72118	2.19|2.19	0.80722|0.80722	D|D	1|1	B;D|.	0.69078|.	0.302;0.997|.	B;D|.	0.80764|.	0.205;0.994|.	T|T	0.68981|0.68981	-0.5266|-0.5266	10|5	0.27082|.	T|.	0.32|.	.|.	16.8061|16.8061	0.85666|0.85666	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	226;209|.	Q6ZW05;B0QZ29|.	CF138_HUMAN;.|.	I|H	226;209|225	ENSP00000341914:F226I;ENSP00000439864:F209I|.	ENSP00000341914:F226I|.	F|L	-|-	1|2	0|0	C6orf138|C6orf138	48084560|48084560	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.997000|0.997000	0.91878|0.91878	8.962000|8.962000	0.93254|0.93254	2.367000|2.367000	0.80283|0.80283	0.528000|0.528000	0.53228|0.53228	TTT|CTT		0.527	PTCHD4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317987.2	NM_001013732		18	38	18	38
CDK14	5218	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	7	90613505	90613505	+	Silent	SNP	T	T	A			TCGA-HW-7490-01A-11D-2024-08	TCGA-HW-7490-10A-01D-2024-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ca68843d-1087-4efa-b5f8-0acd8982fb3b	855988d0-f042-466d-86a8-1ac1cb1bc7a1	g.chr7:90613505T>A	ENST00000380050.3	+	10	1121	c.990T>A	c.(988-990)gcT>gcA	p.A330A	CDK14_ENST00000406263.1_Silent_p.A284A|CDK14_ENST00000436577.2_Silent_p.A201A|CDK14_ENST00000265741.3_Silent_p.A312A			O94921	CDK14_HUMAN	cyclin-dependent kinase 14	330	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cell division (GO:0051301)|G2/M transition of mitotic cell cycle (GO:0000086)|regulation of canonical Wnt signaling pathway (GO:0060828)|regulation of cell cycle (GO:0051726)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|cytoplasmic cyclin-dependent protein kinase holoenzyme complex (GO:0000308)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cyclin binding (GO:0030332)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)			breast(2)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(6)|liver(1)|lung(12)|ovary(1)|skin(4)	32						AAGGAGTTGCTGCTTTTCCAG	0.348																																					GBM(83;1228 1256 8311 16577 31299)											0													171.0	168.0	169.0					7																	90613505		2203	4300	6503	SO:0001819	synonymous_variant	5218				CCDS5619.1, CCDS75626.1, CCDS75627.1, CCDS75628.1	7q21-q22	2011-11-08	2009-12-16	2009-12-16	ENSG00000058091	ENSG00000058091		"""Cyclin-dependent kinases"""	8883	protein-coding gene	gene with protein product		610679	"""PFTAIRE protein kinase 1"""	PFTK1		9202329, 11313143, 19884882	Standard	XM_005250436		Approved	PFTAIRE1	uc003ukz.1	O94921	OTTHUMG00000023649	ENST00000380050.3:c.990T>A	7.37:g.90613505T>A			A4D1E6|A6NK51|A8WFP6|B4DHG5|B4DNM2|Q75N06|Q75N22|Q8N764|Q9H3D7|Q9UDR0	Silent	SNP	ENST00000380050.3	37																																																																																					0.348	CDK14-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000059970.5	NM_012395		42	115	42	115
XKR9	389668	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	8	71646066	71646066	+	Missense_Mutation	SNP	T	T	C			TCGA-HW-7490-01A-11D-2024-08	TCGA-HW-7490-10A-01D-2024-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ca68843d-1087-4efa-b5f8-0acd8982fb3b	855988d0-f042-466d-86a8-1ac1cb1bc7a1	g.chr8:71646066T>C	ENST00000408926.3	+	5	1063	c.529T>C	c.(529-531)Tgg>Cgg	p.W177R	XKR9_ENST00000520273.1_Intron|XKR9_ENST00000520030.1_Missense_Mutation_p.W177R	NM_001011720.1	NP_001011720.1	Q5GH70	XKR9_HUMAN	XK, Kell blood group complex subunit-related family, member 9	177						integral component of membrane (GO:0016021)				breast(1)|endometrium(1)|kidney(1)|large_intestine(5)|liver(2)|lung(4)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	19	Breast(64;0.0716)		Epithelial(68;0.00301)|all cancers(69;0.0165)|OV - Ovarian serous cystadenocarcinoma(28;0.0524)|BRCA - Breast invasive adenocarcinoma(89;0.166)			TGCTATTTCTTGGTCAACTGT	0.299																																																0													68.0	61.0	64.0					8																	71646066		2203	4299	6502	SO:0001583	missense	389668			AY534247	CCDS34905.1	8q13.3	2006-01-12	2006-01-12			ENSG00000221947			20937	protein-coding gene	gene with protein product			"""X Kell blood group precursor-related family, member 9"""				Standard	NM_001287258		Approved		uc003xyq.3	Q5GH70		ENST00000408926.3:c.529T>C	8.37:g.71646066T>C	ENSP00000386141:p.Trp177Arg		B2RNS9|B9EH74	Missense_Mutation	SNP	ENST00000408926.3	37	CCDS34905.1	.	.	.	.	.	.	.	.	.	.	T	16.20	3.056377	0.55325	.	.	ENSG00000221947	ENST00000408926;ENST00000520030	T;T	0.72835	-0.69;-0.69	4.69	2.14	0.27477	.	0.813151	0.11881	N	0.520537	T	0.80341	0.4605	M	0.77486	2.375	0.53688	D	0.999978	D	0.55172	0.97	P	0.57620	0.824	T	0.77991	-0.2379	10	0.62326	D	0.03	8.6529	11.4241	0.50001	0.0:0.0:0.2876:0.7124	.	177	Q5GH70	XKR9_HUMAN	R	177	ENSP00000386141:W177R;ENSP00000431088:W177R	ENSP00000386141:W177R	W	+	1	0	XKR9	71808620	1.000000	0.71417	0.978000	0.43139	0.972000	0.66771	2.461000	0.45040	0.339000	0.23719	0.460000	0.39030	TGG		0.299	XKR9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378752.1	NM_001011720		6	50	6	50
CDH17	1015	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	8	95182644	95182644	+	Silent	SNP	G	G	A			TCGA-HW-7490-01A-11D-2024-08	TCGA-HW-7490-10A-01D-2024-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ca68843d-1087-4efa-b5f8-0acd8982fb3b	855988d0-f042-466d-86a8-1ac1cb1bc7a1	g.chr8:95182644G>A	ENST00000027335.3	-	9	1171	c.1047C>T	c.(1045-1047)gtC>gtT	p.V349V	CDH17_ENST00000441892.2_Intron|CDH17_ENST00000450165.2_Silent_p.V349V	NM_004063.3	NP_004054.3	Q12864	CAD17_HUMAN	cadherin 17, LI cadherin (liver-intestine)	349	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|oligopeptide transmembrane transport (GO:0035672)|oligopeptide transport (GO:0006857)|transport (GO:0006810)	basolateral plasma membrane (GO:0016323)|integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)|proton-dependent oligopeptide secondary active transmembrane transporter activity (GO:0005427)|transporter activity (GO:0005215)			NS(1)|endometrium(5)|kidney(3)|large_intestine(10)|lung(18)|ovary(6)|prostate(3)|skin(4)|stomach(2)	52	Breast(36;4.65e-06)		BRCA - Breast invasive adenocarcinoma(8;0.00691)			CATTCTCCTGGACCTCAAATA	0.438																																																0													156.0	144.0	148.0					8																	95182644		2203	4300	6503	SO:0001819	synonymous_variant	1015			X83228	CCDS6260.1	8q22.1	2010-01-26			ENSG00000079112	ENSG00000079112		"""Cadherins / Major cadherins"""	1756	protein-coding gene	gene with protein product		603017				9615235, 10191097	Standard	NM_004063		Approved	HPT-1, cadherin	uc003ygh.2	Q12864	OTTHUMG00000164391	ENST00000027335.3:c.1047C>T	8.37:g.95182644G>A			Q15336|Q2M2E0	Silent	SNP	ENST00000027335.3	37	CCDS6260.1																																																																																				0.438	CDH17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378560.1	NM_004063		64	101	64	101
FAM78A	286336	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	9	134136482	134136482	+	Silent	SNP	C	C	T			TCGA-HW-7490-01A-11D-2024-08	TCGA-HW-7490-10A-01D-2024-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ca68843d-1087-4efa-b5f8-0acd8982fb3b	855988d0-f042-466d-86a8-1ac1cb1bc7a1	g.chr9:134136482C>T	ENST00000372271.3	-	2	946	c.579G>A	c.(577-579)ctG>ctA	p.L193L	FAM78A_ENST00000372269.3_Silent_p.L190L|FAM78A_ENST00000247295.4_5'UTR	NM_033387.3	NP_203745.2	Q5JUQ0	FA78A_HUMAN	family with sequence similarity 78, member A	193										NS(1)|endometrium(1)|large_intestine(2)|lung(3)|ovary(1)|skin(1)	9	all_hematologic(7;0.0028)	Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;2.15e-05)|Epithelial(140;0.000267)		TGGTGGCCACCAGCCAGGTGG	0.617																																																0													102.0	92.0	95.0					9																	134136482		2203	4300	6503	SO:0001819	synonymous_variant	286336			AK095423	CCDS6941.2	9q34	2008-02-05	2005-07-18	2005-07-18	ENSG00000126882	ENSG00000126882			25465	protein-coding gene	gene with protein product			"""chromosome 9 open reading frame 59"""	C9orf59		11214971	Standard	NM_033387		Approved	FLJ00024	uc004cak.3	Q5JUQ0	OTTHUMG00000020821	ENST00000372271.3:c.579G>A	9.37:g.134136482C>T			Q86VQ9|Q9H7P4	Silent	SNP	ENST00000372271.3	37	CCDS6941.2																																																																																				0.617	FAM78A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054720.1	NM_033387		28	48	28	48
FRMD7	90167	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	X	131214037	131214037	+	Silent	SNP	T	T	C			TCGA-HW-7490-01A-11D-2024-08	TCGA-HW-7490-10A-01D-2024-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ca68843d-1087-4efa-b5f8-0acd8982fb3b	855988d0-f042-466d-86a8-1ac1cb1bc7a1	g.chrX:131214037T>C	ENST00000298542.4	-	11	1222	c.1047A>G	c.(1045-1047)aaA>aaG	p.K349K	FRMD7_ENST00000370879.1_Silent_p.K229K|FRMD7_ENST00000464296.1_Silent_p.K334K	NM_194277.2	NP_919253.1	Q6ZUT3	FRMD7_HUMAN	FERM domain containing 7	349					regulation of neuron projection development (GO:0010975)	cytoskeleton (GO:0005856)|extracellular space (GO:0005615)|growth cone (GO:0030426)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)				breast(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(12)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	24	Acute lymphoblastic leukemia(192;0.000127)					ACCTTACTTGTTTTGACACAT	0.398																																																0													143.0	140.0	141.0					X																	131214037		2203	4300	6503	SO:0001819	synonymous_variant	90167			AL161984	CCDS35397.1	Xq26.2	2014-09-17	2006-09-01	2006-09-01	ENSG00000165694	ENSG00000165694			8079	protein-coding gene	gene with protein product		300628	"""nystagmus 1, congenital"""	NYS, NYS1		2063919, 17013395	Standard	NM_194277		Approved	FLJ43346	uc004ewn.3	Q6ZUT3	OTTHUMG00000022421	ENST00000298542.4:c.1047A>G	X.37:g.131214037T>C			C0LLJ3|Q5JX99	Silent	SNP	ENST00000298542.4	37	CCDS35397.1																																																																																				0.398	FRMD7-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000355031.1	NM_194277		85	34	85	34
RPS4Y2	140032	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	Y	22930744	22930744	+	Missense_Mutation	SNP	C	C	A			TCGA-HW-7490-01A-11D-2024-08	TCGA-HW-7490-10A-01D-2024-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ca68843d-1087-4efa-b5f8-0acd8982fb3b	855988d0-f042-466d-86a8-1ac1cb1bc7a1	g.chrY:22930744C>A	ENST00000288666.5	+	5	414	c.414C>A	c.(412-414)caC>caA	p.H138Q		NM_001039567.2	NP_001034656.1	Q8TD47	RS4Y2_HUMAN	ribosomal protein S4, Y-linked 2	138					translation (GO:0006412)	ribosome (GO:0005840)	rRNA binding (GO:0019843)|structural constituent of ribosome (GO:0003735)			lung(2)	2						GAATTCCACACCTGGTGACTC	0.438																																																0																																										SO:0001583	missense	140032			AF497481	CCDS44028.1	Yq11.223	2006-02-22	2006-02-22	2006-02-22	ENSG00000157828	ENSG00000157828		"""S ribosomal proteins"""	18501	protein-coding gene	gene with protein product		400030	"""ribosomal protein S4, Y-linked 2 pseudogene"""	RPS4Y2P		12815422	Standard	NM_001039567		Approved		uc011nbb.2	Q8TD47	OTTHUMG00000036540	ENST00000288666.5:c.414C>A	Y.37:g.22930744C>A	ENSP00000288666:p.His138Gln		A6NIR6	Missense_Mutation	SNP	ENST00000288666.5	37	CCDS44028.1	.	.	.	.	.	.	.	.	.	.	.	2.830	-0.242748	0.05906	.	.	ENSG00000157828	ENST00000288666	D	0.87729	-2.29	1.47	-1.91	0.07641	Ribosomal protein S4e, central (2);	0.000000	0.64402	U	0.000001	T	0.63105	0.2483	L	0.45744	1.44	0.30355	N	0.7843720000000001	B	0.06786	0.001	B	0.17979	0.02	T	0.35649	-0.9780	7	.	.	.	.	.	.	.	.	138	Q8TD47	RS4Y2_HUMAN	Q	138	ENSP00000288666:H138Q	.	H	+	3	2	RPS4Y2	21340132	1.000000	0.71417	0.977000	0.42913	0.138000	0.21146	1.016000	0.29976	-0.618000	0.05656	0.163000	0.16589	CAC		0.438	RPS4Y2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088873.1			22	29	22	29
PALD1	27143	broad.mit.edu;ucsc.edu	37	10	72307126	72307126	+	Missense_Mutation	SNP	C	C	T	rs192719429		TCGA-HW-7490-01A-11D-2024-08	TCGA-HW-7490-10A-01D-2024-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ca68843d-1087-4efa-b5f8-0acd8982fb3b	855988d0-f042-466d-86a8-1ac1cb1bc7a1	g.chr10:72307126C>T	ENST00000263563.6	+	18	2454	c.2186C>T	c.(2185-2187)gCg>gTg	p.A729V		NM_014431.2	NP_055246.2	Q9ULE6	PALD_HUMAN	phosphatase domain containing, paladin 1	729						cytosol (GO:0005829)											GTGGACGCAGCGCTGGACACT	0.617																																																0													170.0	135.0	147.0					10																	72307126		2203	4300	6503	SO:0001583	missense	27143			AB033100	CCDS31215.1	10q22.2	2012-07-17	2012-07-17	2012-07-17	ENSG00000107719	ENSG00000107719			23530	protein-coding gene	gene with protein product		614656	"""paladin"", ""KIAA1274"""	PALD, KIAA1274			Standard	NM_014431		Approved		uc001jrd.4	Q9ULE6	OTTHUMG00000018411	ENST00000263563.6:c.2186C>T	10.37:g.72307126C>T	ENSP00000263563:p.Ala729Val		B2RMS1|B9EGC6|Q5JTK7|Q5JTK8	Missense_Mutation	SNP	ENST00000263563.6	37	CCDS31215.1	.	.	.	.	.	.	.	.	.	.	C	14.31	2.496632	0.44352	.	.	ENSG00000107719	ENST00000263563;ENST00000373214	T	0.24723	1.84	4.03	4.03	0.46877	.	0.000000	0.85682	D	0.000000	T	0.27419	0.0673	M	0.70595	2.14	0.80722	D	1	B	0.29115	0.233	B	0.21917	0.037	T	0.10590	-1.0623	10	0.16896	T	0.51	-30.019	15.9605	0.79928	0.0:1.0:0.0:0.0	.	729	Q9ULE6	PALD_HUMAN	V	729;705	ENSP00000263563:A729V	ENSP00000263563:A729V	A	+	2	0	KIAA1274	71977132	1.000000	0.71417	0.135000	0.22099	0.561000	0.35649	7.511000	0.81718	2.100000	0.63781	0.551000	0.68910	GCG		0.617	PALD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048515.2	NM_014431		29	58	29	58
GPX2	2877	broad.mit.edu;ucsc.edu	37	14	65406296	65406296	+	Silent	SNP	C	C	T	rs17885748	byFrequency	TCGA-HW-7490-01A-11D-2024-08	TCGA-HW-7490-10A-01D-2024-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ca68843d-1087-4efa-b5f8-0acd8982fb3b	855988d0-f042-466d-86a8-1ac1cb1bc7a1	g.chr14:65406296C>T	ENST00000389614.5	-	2	569	c.483G>A	c.(481-483)ccG>ccA	p.P161P	FNTB_ENST00000542227.1_Intron|FNTB_ENST00000447296.2_Intron|CHURC1-FNTB_ENST00000549987.1_Intron	NM_002083.3	NP_002074.2	P18283	GPX2_HUMAN	glutathione peroxidase 2 (gastrointestinal)	161					interaction with symbiont (GO:0051702)|negative regulation of inflammatory response to antigenic stimulus (GO:0002862)|response to oxidative stress (GO:0006979)|response to symbiotic bacterium (GO:0009609)|temperature homeostasis (GO:0001659)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	electron carrier activity (GO:0009055)|glutathione peroxidase activity (GO:0004602)			large_intestine(2)|ovary(1)|skin(1)	4				all cancers(60;0.00117)|OV - Ovarian serous cystadenocarcinoma(108;0.00557)|BRCA - Breast invasive adenocarcinoma(234;0.00971)	Glutathione(DB00143)	GCTCTCCCTCCGGCCCTATGA	0.537													C|||	8	0.00159744	0.0023	0.0014	5008	,	,		19882	0.0		0.0	False		,,,				2504	0.0041															0								C	,,	15,3925		0,15,1955	115.0	113.0	114.0		,,483	-12.1	0.1	14	dbSNP_124	114	1,8309		0,1,4154	no	intron,intron,coding-synonymous	GPX2,CHURC1-FNTB	NM_001202558.1,NM_001202559.1,NM_002083.2	,,	0,16,6109	TT,TC,CC		0.012,0.3807,0.1306	,,	,,161/191	65406296	16,12234	1970	4155	6125	SO:0001819	synonymous_variant	2877				CCDS41964.1	14q23.3	2012-05-22			ENSG00000176153	ENSG00000176153	1.11.1.9		4554	protein-coding gene	gene with protein product		138319				8428933, 8287691	Standard	NM_002083		Approved	GSHPX-GI	uc021ruq.2	P18283	OTTHUMG00000171677	ENST00000389614.5:c.483G>A	14.37:g.65406296C>T			Q6PJ52|Q8WWI7|Q9NRP9	Silent	SNP	ENST00000389614.5	37	CCDS41964.1																																																																																				0.537	GPX2-001	KNOWN	basic|appris_principal|CCDS|seleno	protein_coding	protein_coding	OTTHUMT00000414708.1			20	105	20	105
FRY	10129	broad.mit.edu;ucsc.edu	37	13	32852686	32852686	+	Splice_Site	SNP	G	G	C			TCGA-HW-7490-01A-11D-2024-08	TCGA-HW-7490-10A-01D-2024-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ca68843d-1087-4efa-b5f8-0acd8982fb3b	855988d0-f042-466d-86a8-1ac1cb1bc7a1	g.chr13:32852686G>C	ENST00000380250.3	+	58	8965		c.e58+1		FRY_ENST00000542859.1_Splice_Site	NM_023037.2	NP_075463.2	Q5TBA9	FRY_HUMAN	furry homolog (Drosophila)							cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)				NS(3)|breast(4)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(31)|lung(50)|ovary(5)|pancreas(1)|prostate(6)|skin(9)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	132		Lung SC(185;0.0271)		all cancers(112;4.81e-05)|Epithelial(112;0.000656)|OV - Ovarian serous cystadenocarcinoma(117;0.0123)|BRCA - Breast invasive adenocarcinoma(63;0.0295)|GBM - Glioblastoma multiforme(144;0.104)		CGAAGAAAAGGTAATAAAAGC	0.443																																																0													125.0	126.0	126.0					13																	32852686		1845	4094	5939	SO:0001630	splice_region_variant	10129			AL049784	CCDS41875.1	13q13.1	2008-02-05	2005-11-24	2005-11-24	ENSG00000073910	ENSG00000073910			20367	protein-coding gene	gene with protein product		614818	"""chromosome 13 open reading frame 14"""	C13orf14		14702039, 8812419	Standard	NM_023037		Approved	bA37E23.1, 13CDNA73, CG003	uc001utx.3	Q5TBA9	OTTHUMG00000016696	ENST00000380250.3:c.8469+1G>C	13.37:g.32852686G>C			Q9Y3N6	Splice_Site	SNP	ENST00000380250.3	37	CCDS41875.1	.	.	.	.	.	.	.	.	.	.	G	26.6	4.752619	0.89753	.	.	ENSG00000073910	ENST00000380250;ENST00000542859	.	.	.	5.77	5.77	0.91146	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	20.3626	0.98863	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	FRY	31750686	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	9.029000	0.93718	2.885000	0.99019	0.655000	0.94253	.		0.443	FRY-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044405.1	NM_023037	Intron	16	100	16	100
OR2M7	391196	broad.mit.edu;ucsc.edu	37	1	248487368	248487368	+	Missense_Mutation	SNP	T	T	C			TCGA-HW-7490-01A-11D-2024-08	TCGA-HW-7490-10A-01D-2024-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ca68843d-1087-4efa-b5f8-0acd8982fb3b	855988d0-f042-466d-86a8-1ac1cb1bc7a1	g.chr1:248487368T>C	ENST00000317965.2	-	1	531	c.503A>G	c.(502-504)tAc>tGc	p.Y168C		NM_001004691.1	NP_001004691.1	Q8NG81	OR2M7_HUMAN	olfactory receptor, family 2, subfamily M, member 7	168						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|endometrium(6)|large_intestine(3)|lung(29)|skin(3)	42	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0265)			AGACCCACAGTAGGAGAAGGA	0.448																																																0													194.0	196.0	196.0					1																	248487368		2203	4300	6503	SO:0001583	missense	391196			BK004486	CCDS31111.1	1q44	2012-08-09			ENSG00000177186	ENSG00000177186		"""GPCR / Class A : Olfactory receptors"""	19594	protein-coding gene	gene with protein product							Standard	NM_001004691		Approved		uc010pzk.2	Q8NG81	OTTHUMG00000040461	ENST00000317965.2:c.503A>G	1.37:g.248487368T>C	ENSP00000324557:p.Tyr168Cys		B2RNL0|Q6IEX6	Missense_Mutation	SNP	ENST00000317965.2	37	CCDS31111.1	.	.	.	.	.	.	.	.	.	.	T	7.405	0.633458	0.14322	.	.	ENSG00000177186	ENST00000317965	T	0.00107	8.72	1.54	0.269	0.15631	GPCR, rhodopsin-like superfamily (1);	1.011580	0.07977	N	0.984945	T	0.00178	0.0005	M	0.63169	1.94	0.20196	N	0.999921	B	0.17268	0.021	B	0.26416	0.069	T	0.30504	-0.9976	10	0.87932	D	0	.	5.8488	0.18681	0.0:0.1512:0.0:0.8488	.	168	Q8NG81	OR2M7_HUMAN	C	168	ENSP00000324557:Y168C	ENSP00000324557:Y168C	Y	-	2	0	OR2M7	246553991	0.001000	0.12720	0.071000	0.20095	0.061000	0.15899	-0.504000	0.06375	-0.093000	0.12396	0.155000	0.16302	TAC		0.448	OR2M7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097357.1	NM_001004691		108	182	108	182
MYO18A	399687	broad.mit.edu;ucsc.edu	37	17	27430667	27430667	+	Missense_Mutation	SNP	G	G	C			TCGA-HW-7490-01A-11D-2024-08	TCGA-HW-7490-10A-01D-2024-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ca68843d-1087-4efa-b5f8-0acd8982fb3b	855988d0-f042-466d-86a8-1ac1cb1bc7a1	g.chr17:27430667G>C	ENST00000527372.1	-	21	3637	c.3457C>G	c.(3457-3459)Ctg>Gtg	p.L1153V	MYO18A_ENST00000533112.1_Missense_Mutation_p.L1153V|MYO18A_ENST00000354329.4_Missense_Mutation_p.L1153V|MYO18A_ENST00000531253.1_Missense_Mutation_p.L1153V	NM_078471.3	NP_510880.2	Q92614	MY18A_HUMAN	myosin XVIIIA	1153	Myosin motor.				actomyosin structure organization (GO:0031032)|cell migration (GO:0016477)|DNA metabolic process (GO:0006259)|Golgi organization (GO:0007030)|Golgi vesicle budding (GO:0048194)|negative regulation of apoptotic process (GO:0043066)|positive regulation of protein secretion (GO:0050714)	actomyosin (GO:0042641)|Golgi membrane (GO:0000139)|membrane (GO:0016020)|myosin complex (GO:0016459)|trans-Golgi network (GO:0005802)	actin filament binding (GO:0051015)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|DNA binding (GO:0003677)|motor activity (GO:0003774)|poly(A) RNA binding (GO:0044822)			NS(1)|cervix(1)|endometrium(6)|kidney(6)|lung(20)|urinary_tract(2)	36			Epithelial(11;4.97e-05)|BRCA - Breast invasive adenocarcinoma(11;0.000221)|all cancers(11;0.000234)|Colorectal(6;0.0102)|COAD - Colon adenocarcinoma(6;0.031)			AAGCACTCCAGCAGCTCCTCC	0.667																																					Esophageal Squamous(182;472 2015 7001 15270 22562)											0													41.0	46.0	44.0					17																	27430667		2067	4207	6274	SO:0001583	missense	399687			D86970	CCDS45641.1, CCDS45642.1	17q11.2	2011-09-27			ENSG00000196535	ENSG00000196535		"""Myosins / Myosin superfamily : Class XVIII"""	31104	protein-coding gene	gene with protein product		610067				12761286	Standard	NM_078471		Approved	KIAA0216, MysPDZ	uc002hdt.1	Q92614	OTTHUMG00000166360	ENST00000527372.1:c.3457C>G	17.37:g.27430667G>C	ENSP00000437073:p.Leu1153Val		Q5H9U3|Q5W9F9|Q5W9G1|Q8IXP8	Missense_Mutation	SNP	ENST00000527372.1	37	CCDS45642.1	.	.	.	.	.	.	.	.	.	.	G	19.42	3.823792	0.71143	.	.	ENSG00000196535	ENST00000354329;ENST00000359450;ENST00000533112;ENST00000531253;ENST00000527372;ENST00000529799;ENST00000540575;ENST00000458428	D;D;D;D	0.91180	-2.8;-2.8;-2.8;-2.8	5.44	5.44	0.79542	Myosin head, motor domain (2);	0.158193	0.45606	D	0.000353	D	0.91841	0.7418	L	0.58969	1.84	0.40707	D	0.98253	P;P;P;P;D	0.54047	0.918;0.775;0.86;0.86;0.964	P;B;P;B;P	0.55577	0.628;0.266;0.453;0.359;0.779	D	0.92386	0.5917	10	0.87932	D	0	.	10.3036	0.43667	0.0894:0.0:0.9106:0.0	.	822;765;1153;1153;1153	Q92614-2;F8W6Y3;Q92614-3;Q92614-4;Q92614	.;.;.;.;MY18A_HUMAN	V	1153;1153;1153;1153;1153;49;49;765	ENSP00000346291:L1153V;ENSP00000435932:L1153V;ENSP00000434228:L1153V;ENSP00000437073:L1153V	ENSP00000346291:L1153V	L	-	1	2	MYO18A	24454793	1.000000	0.71417	1.000000	0.80357	0.913000	0.54294	3.218000	0.51192	2.541000	0.85698	0.561000	0.74099	CTG		0.667	MYO18A-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000389396.1	NM_078471		3	47	3	47
APRT	353	broad.mit.edu;ucsc.edu	37	16	88876924	88876924	+	Silent	SNP	G	G	A			TCGA-HW-7490-01A-11D-2024-08	TCGA-HW-7490-10A-01D-2024-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ca68843d-1087-4efa-b5f8-0acd8982fb3b	855988d0-f042-466d-86a8-1ac1cb1bc7a1	g.chr16:88876924G>A	ENST00000378364.3	-	3	272	c.228C>T	c.(226-228)gcC>gcT	p.A76A	APRT_ENST00000563655.1_Intron|APRT_ENST00000426324.2_Silent_p.A76A	NM_000485.2	NP_000476.1	P07741	APT_HUMAN	adenine phosphoribosyltransferase	76					adenine salvage (GO:0006168)|AMP salvage (GO:0044209)|cellular response to insulin stimulus (GO:0032869)|grooming behavior (GO:0007625)|lactation (GO:0007595)|nucleobase-containing small molecule metabolic process (GO:0055086)|purine nucleobase metabolic process (GO:0006144)|purine-containing compound salvage (GO:0043101)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	adenine binding (GO:0002055)|adenine phosphoribosyltransferase activity (GO:0003999)|AMP binding (GO:0016208)			cervix(1)|endometrium(1)|liver(1)	3				BRCA - Breast invasive adenocarcinoma(80;0.0477)	Adenine(DB00173)|Adenosine monophosphate(DB00131)	CAAGCTCCTGGGCCAGGGAGG	0.637																																																0													19.0	21.0	21.0					16																	88876924		2195	4293	6488	SO:0001819	synonymous_variant	353				CCDS32511.1, CCDS45546.1	16q24	2012-10-02				ENSG00000198931	2.4.2.7		626	protein-coding gene	gene with protein product		102600					Standard	NM_000485		Approved		uc002flv.3	P07741		ENST00000378364.3:c.228C>T	16.37:g.88876924G>A			G5E9J2|Q3KP55|Q68DF9	Silent	SNP	ENST00000378364.3	37	CCDS32511.1																																																																																				0.637	APRT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000430000.2	NM_000485		2	22	2	22
SDAD1P1	157489	broad.mit.edu;ucsc.edu	37	8	26237249	26237249	+	RNA	SNP	G	G	A			TCGA-HW-7490-01A-11D-2024-08	TCGA-HW-7490-10A-01D-2024-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ca68843d-1087-4efa-b5f8-0acd8982fb3b	855988d0-f042-466d-86a8-1ac1cb1bc7a1	g.chr8:26237249G>A	ENST00000519902.1	-	0	2699									SDA1 domain containing 1 pseudogene 1																		GGGATTTCCCGGGGACAGCGT	0.458																																																0																																												157489					8p21.2	2010-11-24			ENSG00000228451	ENSG00000228451			31403	pseudogene	pseudogene							Standard	NG_006994		Approved				OTTHUMG00000163945		8.37:g.26237249G>A				RNA	SNP	ENST00000519902.1	37																																																																																					0.458	SDAD1P1-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000376512.1	NG_006994		6	45	6	45
PHF23	79142	broad.mit.edu;ucsc.edu	37	17	7139547	7139547	+	Silent	SNP	T	T	C			TCGA-HW-7490-01A-11D-2024-08	TCGA-HW-7490-10A-01D-2024-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ca68843d-1087-4efa-b5f8-0acd8982fb3b	855988d0-f042-466d-86a8-1ac1cb1bc7a1	g.chr17:7139547T>C	ENST00000320316.3	-	4	925	c.699A>G	c.(697-699)ccA>ccG	p.P233P	DVL2_ENST00000005340.5_5'Flank|DVL2_ENST00000575458.1_5'Flank|PHF23_ENST00000454255.2_Silent_p.P229P|PHF23_ENST00000576955.1_Silent_p.P103P|PHF23_ENST00000571362.1_Silent_p.P166P|PHF23_ENST00000570753.1_5'Flank	NM_001284518.1|NM_024297.2	NP_001271447.1|NP_077273.2	Q9BUL5	PHF23_HUMAN	PHD finger protein 23	233							zinc ion binding (GO:0008270)			breast(4)|kidney(2)|large_intestine(6)|lung(3)	15						GCCCAGGAGGTGGGAGTCTAT	0.552																																																0													100.0	113.0	109.0					17																	7139547		1928	4123	6051	SO:0001819	synonymous_variant	79142			AK122791	CCDS42250.1, CCDS67143.1, CCDS67144.1	17p13.1	2014-08-13			ENSG00000040633	ENSG00000040633		"""Zinc fingers, PHD-type"""	28428	protein-coding gene	gene with protein product		612910					Standard	NM_024297		Approved	MGC2941, FLJ16355	uc002gfa.3	Q9BUL5	OTTHUMG00000177972	ENST00000320316.3:c.699A>G	17.37:g.7139547T>C			A1DZ74|B3KVH8|B4DLK6|D3DTN4|Q8IZK0|Q96HG7|Q9H5X0	Silent	SNP	ENST00000320316.3	37	CCDS42250.1																																																																																				0.552	PHF23-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440047.1	NM_024297		41	81	41	81
RUNX1T1	862	broad.mit.edu;ucsc.edu	37	8	93026829	93026829	+	Missense_Mutation	SNP	C	C	T			TCGA-HW-7490-01A-11D-2024-08	TCGA-HW-7490-10A-01D-2024-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ca68843d-1087-4efa-b5f8-0acd8982fb3b	855988d0-f042-466d-86a8-1ac1cb1bc7a1	g.chr8:93026829C>T	ENST00000523629.1	-	4	900	c.446G>A	c.(445-447)cGc>cAc	p.R149H	RUNX1T1_ENST00000422361.2_Missense_Mutation_p.R112H|RUNX1T1_ENST00000522163.1_5'Flank|RUNX1T1_ENST00000360348.2_Missense_Mutation_p.R112H|RUNX1T1_ENST00000396218.1_Missense_Mutation_p.R122H|RUNX1T1_ENST00000436581.2_Missense_Mutation_p.R160H|RUNX1T1_ENST00000521553.1_Missense_Mutation_p.R112H|RUNX1T1_ENST00000518844.1_Missense_Mutation_p.R122H|RUNX1T1_ENST00000520724.1_Missense_Mutation_p.R112H|RUNX1T1_ENST00000265814.3_Missense_Mutation_p.R149H	NM_001198626.1|NM_001198630.1|NM_001198633.1|NM_175634.2	NP_001185555.1|NP_001185559.1|NP_001185562.1|NP_783552.1	Q06455	MTG8_HUMAN	runt-related transcription factor 1; translocated to, 1 (cyclin D-related)	149	TAFH. {ECO:0000255|PROSITE- ProRule:PRU00440}.				fat cell differentiation (GO:0045444)|generation of precursor metabolites and energy (GO:0006091)|regulation of DNA binding (GO:0051101)|transcription, DNA-templated (GO:0006351)	nuclear matrix (GO:0016363)	DNA binding (GO:0003677)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.R160H(1)|p.R112H(1)|p.R149H(1)		NS(1)|breast(3)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(17)|lung(54)|pancreas(1)|skin(3)|upper_aerodigestive_tract(2)	86			BRCA - Breast invasive adenocarcinoma(11;0.0141)			AACGAGGGTGCGAACTCTTTC	0.507																																																3	Substitution - Missense(3)	large_intestine(3)											120.0	112.0	115.0					8																	93026829		2203	4300	6503	SO:0001583	missense	862			D43638	CCDS6256.1, CCDS6257.1, CCDS47891.1, CCDS56544.1, CCDS75766.1, CCDS75767.1	8q22	2007-01-29	2005-01-20	2005-01-22	ENSG00000079102	ENSG00000079102		"""Zinc fingers, MYND-type"""	1535	protein-coding gene	gene with protein product		133435	"""core-binding factor, runt domain, alpha subunit 2; translocated to, 1; cyclin D-related"""	AML1T1, CBFA2T1		1391946, 9790752	Standard	NM_004349		Approved	CDR, ETO, MTG8, ZMYND2	uc011lgi.2	Q06455	OTTHUMG00000164066	ENST00000523629.1:c.446G>A	8.37:g.93026829C>T	ENSP00000428543:p.Arg149His		B7Z4P4|E7EPN4|O14784|Q06456|Q14873|Q16239|Q16346|Q16347|Q6IBL1|Q6NXH1|Q7Z4J5|Q92479|Q9BRZ0	Missense_Mutation	SNP	ENST00000523629.1	37	CCDS6256.1	.	.	.	.	.	.	.	.	.	.	C	28.9	4.957546	0.92726	.	.	ENSG00000079102	ENST00000523629;ENST00000396218;ENST00000265814;ENST00000360348;ENST00000422361;ENST00000520724;ENST00000436581;ENST00000518844;ENST00000521553;ENST00000518992;ENST00000521054;ENST00000519847;ENST00000517792;ENST00000522467	T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.57907	0.37;0.37;0.37;0.37;0.37;0.37;0.37;0.37;0.37;0.37;0.37;0.37;0.37;0.37	6.05	6.05	0.98169	TAFH/NHR1 (3);	0.000000	0.85682	D	0.000000	T	0.73345	0.3575	M	0.70595	2.14	0.80722	D	1	P;D;D;D;D	0.76494	0.93;0.98;0.999;0.98;0.996	P;D;D;D;D	0.69479	0.565;0.949;0.964;0.949;0.917	T	0.73122	-0.4082	10	0.66056	D	0.02	-19.2647	20.6013	0.99457	0.0:1.0:0.0:0.0	.	160;160;122;149;122	E7EPN4;B7Z4P4;B2R6I9;Q06455;Q06455-2	.;.;.;MTG8_HUMAN;.	H	149;122;149;112;112;112;160;122;112;149;112;149;112;149	ENSP00000428543:R149H;ENSP00000379520:R122H;ENSP00000265814:R149H;ENSP00000353504:R112H;ENSP00000390137:R112H;ENSP00000428742:R112H;ENSP00000402257:R160H;ENSP00000430728:R122H;ENSP00000429728:R112H;ENSP00000431094:R149H;ENSP00000427763:R112H;ENSP00000430204:R149H;ENSP00000429940:R112H;ENSP00000429532:R149H	ENSP00000265814:R149H	R	-	2	0	RUNX1T1	93096005	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.783000	0.85696	2.878000	0.98634	0.650000	0.86243	CGC		0.507	RUNX1T1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000377045.3	NM_004349, NM_175635		12	88	12	88
ASPM	259266	broad.mit.edu;hgsc.bcm.edu	37	1	197070598	197070599	+	Frame_Shift_Del	DEL	TC	TC	-	rs587783270|rs199422173|rs144088344		TCGA-HW-7490-01A-11D-2024-08	TCGA-HW-7490-10A-01D-2024-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ca68843d-1087-4efa-b5f8-0acd8982fb3b	855988d0-f042-466d-86a8-1ac1cb1bc7a1	g.chr1:197070598_197070599delTC	ENST00000367409.4	-	18	8038_8039	c.7782_7783delGA	c.(7780-7785)cagaaafs	p.K2595fs	ASPM_ENST00000367408.1_Intron|ASPM_ENST00000294732.7_Intron	NM_018136.4	NP_060606.3	Q8IZT6	ASPM_HUMAN	asp (abnormal spindle) homolog, microcephaly associated (Drosophila)	2595					developmental growth (GO:0048589)|forebrain neuroblast division (GO:0021873)|maintenance of centrosome location (GO:0051661)|mitotic nuclear division (GO:0007067)|negative regulation of asymmetric cell division (GO:0045769)|negative regulation of neuron differentiation (GO:0045665)|neuron migration (GO:0001764)|oogenesis (GO:0048477)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of neuroblast proliferation (GO:0002052)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|midbody (GO:0030496)|nucleus (GO:0005634)|spindle pole (GO:0000922)		p.Q2594Q(1)		breast(6)|central_nervous_system(2)|cervix(2)|endometrium(10)|kidney(9)|large_intestine(28)|liver(1)|lung(87)|ovary(5)|pancreas(2)|prostate(6)|skin(4)|urinary_tract(3)	165						TGAAATACTTTCTGTTTCTTTT	0.356																																																1	Substitution - coding silent(1)	urinary_tract(1)							,	5,4261		2,1,2130					,	2.7	0.0			52	3,8251		0,3,4124	no	frameshift,intron	ASPM	NM_018136.4,NM_001206846.1	,	2,4,6254	A1A1,A1R,RR		0.0363,0.1172,0.0639	,	,		8,12512				SO:0001589	frameshift_variant	259266			AY367065	CCDS1389.1, CCDS55672.1	1q31	2008-02-05	2006-09-12		ENSG00000066279	ENSG00000066279			19048	protein-coding gene	gene with protein product		605481	"""microcephaly, primary autosomal recessive 5"", ""asp (abnormal spindle)-like, microcephaly associated (Drosophila)"""	MCPH5		11078481	Standard	NM_018136		Approved	Calmbp1, ASP, FLJ10517, FLJ10549	uc001gtu.3	Q8IZT6	OTTHUMG00000036277	ENST00000367409.4:c.7782_7783delGA	1.37:g.197070598_197070599delTC	ENSP00000356379:p.Lys2595fs		Q4G1H1|Q5VYL3|Q86UX4|Q8IUL2|Q8IZJ7|Q8IZJ8|Q8IZJ9|Q8N4D1|Q9NVS1|Q9NVT6	Frame_Shift_Del	DEL	ENST00000367409.4	37	CCDS1389.1																																																																																				0.356	ASPM-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000088256.1	NM_018136		12	32	12	32
AMOTL2	51421	broad.mit.edu;hgsc.bcm.edu	37	3	134078153	134078155	+	In_Frame_Del	DEL	TGT	TGT	-			TCGA-HW-7490-01A-11D-2024-08	TCGA-HW-7490-10A-01D-2024-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ca68843d-1087-4efa-b5f8-0acd8982fb3b	855988d0-f042-466d-86a8-1ac1cb1bc7a1	g.chr3:134078153_134078155delTGT	ENST00000422605.2	-	8	2240_2242	c.2074_2076delACA	c.(2074-2076)acadel	p.T692del	AMOTL2_ENST00000514516.1_In_Frame_Del_p.T750del|AMOTL2_ENST00000249883.5_In_Frame_Del_p.T692del|RPL39P5_ENST00000273411.2_RNA|AMOTL2_ENST00000513145.1_In_Frame_Del_p.T690del			Q9Y2J4	AMOL2_HUMAN	angiomotin like 2	692					hippo signaling (GO:0035329)|Wnt signaling pathway (GO:0016055)	apical plasma membrane (GO:0016324)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|endosome (GO:0005768)|tight junction (GO:0005923)				endometrium(8)|kidney(1)|large_intestine(2)|lung(4)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	19						GGGCGTCTGCTGTTTGTCGCTCA	0.596																																																0																																										SO:0001651	inframe_deletion	51421			AF175966	CCDS33860.1, CCDS63783.1, CCDS63784.1	3q21-q22	2008-07-18			ENSG00000114019	ENSG00000114019			17812	protein-coding gene	gene with protein product	"""Leman coiled-coil protein"", ""angiomotin-like protein 2"""	614658					Standard	NM_016201		Approved	LCCP	uc003eqg.1	Q9Y2J4	OTTHUMG00000159777	ENST00000422605.2:c.2074_2076delACA	3.37:g.134078153_134078155delTGT	ENSP00000409999:p.Thr692del		A8K6F1|B7Z5Q1|E9PHW3|Q53EP1|Q96F99|Q9UKB4	In_Frame_Del	DEL	ENST00000422605.2	37																																																																																					0.596	AMOTL2-014	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000358149.1	NM_016201		21	66	21	66
CYP3A7	1551	broad.mit.edu;hgsc.bcm.edu	37	7	99312223	99312224	+	Frame_Shift_Del	DEL	TT	TT	-			TCGA-HW-7490-01A-11D-2024-08	TCGA-HW-7490-10A-01D-2024-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ca68843d-1087-4efa-b5f8-0acd8982fb3b	855988d0-f042-466d-86a8-1ac1cb1bc7a1	g.chr7:99312223_99312224delTT	ENST00000336374.2	-	8	754_755	c.752_753delAA	c.(751-753)aaafs	p.K251fs	AC069294.1_ENST00000408560.1_RNA	NM_000765.3	NP_000756.2	P24462	CP3A7_HUMAN	cytochrome P450, family 3, subfamily A, polypeptide 7	251					small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)	aromatase activity (GO:0070330)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|monooxygenase activity (GO:0004497)|oxygen binding (GO:0019825)			autonomic_ganglia(1)|breast(3)|endometrium(2)|kidney(1)|large_intestine(9)|lung(10)|ovary(1)|skin(4)|upper_aerodigestive_tract(1)	32	Lung NSC(181;0.0144)|Esophageal squamous(72;0.0166)|all_lung(186;0.0228)				Alfentanil(DB00802)|Alprazolam(DB00404)|Aminophenazone(DB01424)|Amiodarone(DB01118)|Amlodipine(DB00381)|Aprepitant(DB00673)|Aripiprazole(DB01238)|Astemizole(DB00637)|Atorvastatin(DB01076)|Buprenorphine(DB00921)|Buspirone(DB00490)|Caffeine(DB00201)|Carbamazepine(DB00564)|Chloramphenicol(DB00446)|Chlorphenamine(DB01114)|Cilostazol(DB01166)|Cimetidine(DB00501)|Ciprofloxacin(DB00537)|Cisapride(DB00604)|Clarithromycin(DB01211)|Clotrimazole(DB00257)|Cocaine(DB00907)|Codeine(DB00318)|Cyclophosphamide(DB00531)|Cyclosporine(DB00091)|Dapsone(DB00250)|Delavirdine(DB00705)|Dexamethasone(DB01234)|Dextromethorphan(DB00514)|Dextropropoxyphene(DB00647)|Diazepam(DB00829)|Diltiazem(DB00343)|Docetaxel(DB01248)|Dolutegravir(DB08930)|Domperidone(DB01184)|Eplerenone(DB00700)|Erythromycin(DB00199)|Estradiol(DB00783)|Ethosuximide(DB00593)|Ethylmorphine(DB01466)|Felodipine(DB01023)|Fentanyl(DB00813)|Finasteride(DB01216)|Fluconazole(DB00196)|Fluticasone Propionate(DB00588)|Fluvoxamine(DB00176)|Gestodene(DB06730)|Haloperidol(DB00502)|Hydrocortisone(DB00741)|Ifosfamide(DB01181)|Iloperidone(DB04946)|Imatinib(DB00619)|Imipramine(DB00458)|Indinavir(DB00224)|Irinotecan(DB00762)|Itraconazole(DB01167)|Ketoconazole(DB01026)|Lercanidipine(DB00528)|Levomethadyl Acetate(DB01227)|Lidocaine(DB00281)|Lovastatin(DB00227)|Methadone(DB00333)|Midazolam(DB00683)|Mifepristone(DB00834)|Nateglinide(DB00731)|Nefazodone(DB01149)|Nelfinavir(DB00220)|Nifedipine(DB01115)|Nisoldipine(DB00401)|Nitrendipine(DB01054)|Norethindrone(DB00717)|Norfloxacin(DB01059)|Ondansetron(DB00904)|Oxazepam(DB00842)|Oxycodone(DB00497)|Paclitaxel(DB01229)|Phenelzine(DB00780)|Phenobarbital(DB01174)|Phenytoin(DB00252)|Pimozide(DB01100)|Praziquantel(DB01058)|Progesterone(DB00396)|Propranolol(DB00571)|Quetiapine(DB01224)|Quinidine(DB00908)|Quinine(DB00468)|Rifampicin(DB01045)|Rifapentine(DB01201)|Risperidone(DB00734)|Ritonavir(DB00503)|Salmeterol(DB00938)|Saquinavir(DB01232)|Sildenafil(DB00203)|Simvastatin(DB00641)|Sirolimus(DB00877)|Sorafenib(DB00398)|Sunitinib(DB01268)|Tacrolimus(DB00864)|Tamoxifen(DB00675)|Telithromycin(DB00976)|Temsirolimus(DB06287)|Testosterone(DB00624)|Trazodone(DB00656)|Tretinoin(DB00755)|Triazolam(DB00897)|Verapamil(DB00661)|Vincristine(DB00541)|Voriconazole(DB00582)|Zalcitabine(DB00943)|Zaleplon(DB00962)|Ziprasidone(DB00246)|Zolpidem(DB00425)	GTTTTACAGATTTTGTTAGAAA	0.312																																																0																																										SO:0001589	frameshift_variant	1551			AF315325	CCDS5673.1	7q21-q22.1	2007-12-14	2003-01-14		ENSG00000160870	ENSG00000160870		"""Cytochrome P450s"""	2640	protein-coding gene	gene with protein product		605340	"""cytochrome P450, subfamily IIIA, polypeptide 7"""			2722762	Standard	NM_000765		Approved	CP37, P450-HFLA		P24462	OTTHUMG00000156726	ENST00000336374.2:c.752_753delAA	7.37:g.99312225_99312226delTT	ENSP00000337450:p.Lys251fs		A4D288|Q9H241	Frame_Shift_Del	DEL	ENST00000336374.2	37	CCDS5673.1																																																																																				0.312	CYP3A7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345484.1			19	89	19	89
RANBP6	26953	broad.mit.edu;hgsc.bcm.edu	37	9	6013101	6013102	+	Frame_Shift_Del	DEL	AG	AG	-	rs201088423		TCGA-HW-7490-01A-11D-2024-08	TCGA-HW-7490-10A-01D-2024-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ca68843d-1087-4efa-b5f8-0acd8982fb3b	855988d0-f042-466d-86a8-1ac1cb1bc7a1	g.chr9:6013101_6013102delAG	ENST00000259569.5	-	1	2516_2517	c.2506_2507delCT	c.(2506-2508)ctgfs	p.L836fs	RANBP6_ENST00000485372.1_5'Flank	NM_001243202.1|NM_001243203.1|NM_012416.3	NP_001230131.1|NP_001230132.1|NP_036548.1	O60518	RNBP6_HUMAN	RAN binding protein 6	836					protein transport (GO:0015031)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				NS(1)|breast(4)|central_nervous_system(1)|endometrium(8)|kidney(5)|large_intestine(8)|lung(9)|ovary(7)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	51		Acute lymphoblastic leukemia(23;0.158)		GBM - Glioblastoma multiforme(50;0.00522)|Lung(218;0.101)		CTCATCTTGCAGAGACATCTCA	0.337																																																0																																										SO:0001589	frameshift_variant	26953			AF039023	CCDS6467.1	9p24.1	2008-03-26			ENSG00000137040	ENSG00000137040			9851	protein-coding gene	gene with protein product							Standard	NM_001243202		Approved		uc003zjr.3	O60518	OTTHUMG00000019512	ENST00000259569.5:c.2506_2507delCT	9.37:g.6013103_6013104delAG	ENSP00000259569:p.Leu836fs		Q5T7X4|Q7Z3V2|Q96E78	Frame_Shift_Del	DEL	ENST00000259569.5	37	CCDS6467.1																																																																																				0.337	RANBP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051650.1	NM_012416		24	97	24	97
UHRF2	115426	broad.mit.edu;hgsc.bcm.edu	37	9	6497275	6497278	+	Frame_Shift_Del	DEL	CAGT	CAGT	-			TCGA-HW-7490-01A-11D-2024-08	TCGA-HW-7490-10A-01D-2024-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ca68843d-1087-4efa-b5f8-0acd8982fb3b	855988d0-f042-466d-86a8-1ac1cb1bc7a1	g.chr9:6497275_6497278delCAGT	ENST00000276893.5	+	11	1850_1853	c.1682_1685delCAGT	c.(1681-1686)ccagtcfs	p.PV561fs	UHRF2_ENST00000485617.2_3'UTR	NM_152896.2	NP_690856.1	Q96PU4	UHRF2_HUMAN	ubiquitin-like with PHD and ring finger domains 2, E3 ubiquitin protein ligase	561	Methyl-CpG binding and interaction with HDAC1.|YDG. {ECO:0000255|PROSITE- ProRule:PRU00358}.				cell cycle (GO:0007049)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|positive regulation of cell cycle arrest (GO:0071158)|protein autoubiquitination (GO:0051865)|protein ubiquitination (GO:0016567)|regulation of cell cycle (GO:0051726)|ubiquitin-dependent protein catabolic process (GO:0006511)	nuclear heterochromatin (GO:0005720)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone binding (GO:0042393)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			cervix(2)|endometrium(2)|kidney(3)|large_intestine(4)|lung(5)|ovary(1)	17		Acute lymphoblastic leukemia(23;0.158)		GBM - Glioblastoma multiforme(50;0.0392)|Lung(218;0.129)		GCTGGTAAGCCAGTCAGAGTGATA	0.426																																																0																																										SO:0001589	frameshift_variant	115426			AF274049	CCDS6469.1	9p24.1	2013-01-28	2012-02-23		ENSG00000147854	ENSG00000147854		"""RING-type (C3HC4) zinc fingers"", ""Zinc fingers, PHD-type"""	12557	protein-coding gene	gene with protein product	"""Np95-like ring finger protein"""	615211	"""ubiquitin-like with PHD and ring finger domains 2"""			12176013	Standard	NM_152896		Approved	RNF107, NIRF, URF2, MGC33463	uc003zjy.3	Q96PU4	OTTHUMG00000019521	ENST00000276893.5:c.1682_1685delCAGT	9.37:g.6497275_6497278delCAGT	ENSP00000276893:p.Pro561fs		Q5VYR1|Q5VYR3|Q659C8|Q8TAG7	Frame_Shift_Del	DEL	ENST00000276893.5	37	CCDS6469.1																																																																																				0.426	UHRF2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051665.3	NM_152306		16	40	16	40
AKAP8	10270	broad.mit.edu;hgsc.bcm.edu	37	19	15471767	15471769	+	In_Frame_Del	DEL	GAA	GAA	-			TCGA-HW-7490-01A-11D-2024-08	TCGA-HW-7490-10A-01D-2024-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ca68843d-1087-4efa-b5f8-0acd8982fb3b	855988d0-f042-466d-86a8-1ac1cb1bc7a1	g.chr19:15471767_15471769delGAA	ENST00000269701.2	-	12	1477_1479	c.1417_1419delTTC	c.(1417-1419)ttcdel	p.F473del		NM_005858.3	NP_005849.1	O43823	AKAP8_HUMAN	A kinase (PRKA) anchor protein 8	473					mitotic chromosome condensation (GO:0007076)|mitotic nuclear division (GO:0007067)|signal transduction (GO:0007165)	condensed chromosome (GO:0000793)|female pronucleus (GO:0001939)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nuclear matrix (GO:0016363)|nucleus (GO:0005634)	double-stranded DNA binding (GO:0003690)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			breast(2)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(4)|kidney(1)|large_intestine(5)|lung(6)|ovary(2)	26						CGATCTTCTTGAAGAAGTGCTCC	0.571																																					GBM(190;1671 2163 3274 27186 30476)											0																																										SO:0001651	inframe_deletion	10270			Y11997	CCDS12329.1	19p13.12	2012-05-16			ENSG00000105127	ENSG00000105127		"""A-kinase anchor proteins"""	378	protein-coding gene	gene with protein product	"""A-kinase anchor protein, 95kDa"""	604692				9473338	Standard	NM_005858		Approved	AKAP95, DKFZp586B1222	uc002nav.3	O43823		ENST00000269701.2:c.1417_1419delTTC	19.37:g.15471770_15471772delGAA	ENSP00000269701:p.Phe473del			In_Frame_Del	DEL	ENST00000269701.2	37	CCDS12329.1																																																																																				0.571	AKAP8-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461293.3	NM_005858		10	21	10	21
LENG9	94059	broad.mit.edu;hgsc.bcm.edu	37	19	54973460	54973461	+	Frame_Shift_Del	DEL	TG	TG	-			TCGA-HW-7490-01A-11D-2024-08	TCGA-HW-7490-10A-01D-2024-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ca68843d-1087-4efa-b5f8-0acd8982fb3b	855988d0-f042-466d-86a8-1ac1cb1bc7a1	g.chr19:54973460_54973461delTG	ENST00000333834.4	-	1	1433_1434	c.1315_1316delCA	c.(1315-1317)cagfs	p.Q439fs		NM_198988.1	NP_945339.2	Q96B70	LENG9_HUMAN	leukocyte receptor cluster (LRC) member 9	439							catalytic activity (GO:0003824)|metal ion binding (GO:0046872)			breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(5)	11	Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.134)		CCCTGGAGACTGTAGTGTACTC	0.644																																																0																																										SO:0001589	frameshift_variant	94059			AF211976		19q13.4	2014-05-06			ENSG00000182909	ENSG00000275183			16306	protein-coding gene	gene with protein product						10941842	Standard	NM_198988		Approved		uc010yez.2	Q96B70	OTTHUMG00000188273	ENST00000333834.4:c.1315_1316delCA	19.37:g.54973460_54973461delTG	ENSP00000331647:p.Gln439fs		B2VAM3	Frame_Shift_Del	DEL	ENST00000333834.4	37	CCDS12895.2																																																																																				0.644	LENG9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000140806.3	NM_198988		44	53	44	53
USP9X	8239	broad.mit.edu;hgsc.bcm.edu	37	X	41088882	41088884	+	In_Frame_Del	DEL	AAG	AAG	-			TCGA-HW-7490-01A-11D-2024-08	TCGA-HW-7490-10A-01D-2024-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ca68843d-1087-4efa-b5f8-0acd8982fb3b	855988d0-f042-466d-86a8-1ac1cb1bc7a1	g.chrX:41088882_41088884delAAG	ENST00000324545.8	+	43	7914_7916	c.7281_7283delAAG	c.(7279-7284)gaaaga>gaa	p.R2429del	USP9X_ENST00000378308.2_In_Frame_Del_p.R2429del	NM_001039590.2|NM_001039591.2	NP_001034679.2|NP_001034680.2	Q93008	USP9X_HUMAN	ubiquitin specific peptidase 9, X-linked	2429					axon extension (GO:0048675)|BMP signaling pathway (GO:0030509)|cerebellar cortex structural organization (GO:0021698)|chromosome segregation (GO:0007059)|female gamete generation (GO:0007292)|gene expression (GO:0010467)|hippocampus development (GO:0021766)|in utero embryonic development (GO:0001701)|mitotic nuclear division (GO:0007067)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuron migration (GO:0001764)|post-embryonic development (GO:0009791)|protein deubiquitination (GO:0016579)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|ubiquitin-dependent protein catabolic process (GO:0006511)	apical part of cell (GO:0045177)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|growth cone (GO:0030426)|membrane (GO:0016020)	co-SMAD binding (GO:0070410)|cysteine-type endopeptidase activity (GO:0004197)|cysteine-type peptidase activity (GO:0008234)|ubiquitin thiolesterase activity (GO:0004221)			NS(3)|breast(6)|central_nervous_system(1)|endometrium(14)|haematopoietic_and_lymphoid_tissue(3)|kidney(6)|large_intestine(16)|lung(29)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	87						ATGAACTTGAAAGAAGACCATAT	0.404																																					Ovarian(172;1807 2695 35459 49286)											0																																										SO:0001651	inframe_deletion	8239			X98296	CCDS43930.1, CCDS55403.1	Xp11.4	2010-08-03	2006-02-14		ENSG00000124486	ENSG00000124486		"""Ubiquitin-specific peptidases"""	12632	protein-coding gene	gene with protein product		300072	"""ubiquitin specific protease 9, X chromosome (fat facets-like Drosophila)"", ""ubiquitin specific protease 9, X-linked (fat facets-like, Drosophila)"", ""ubiquitin specific peptidase 9, X-linked (fat facets-like, Drosophila)"""			8922996	Standard	NM_001039590		Approved	DFFRX, FAF	uc004dfb.3	Q93008	OTTHUMG00000021367	ENST00000324545.8:c.7281_7283delAAG	X.37:g.41088885_41088887delAAG	ENSP00000316357:p.Arg2429del		O75550|Q8WWT3|Q8WX12	In_Frame_Del	DEL	ENST00000324545.8	37	CCDS43930.1																																																																																				0.404	USP9X-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000056250.4	NM_004652		15	34	15	34
ATRX	546	broad.mit.edu;hgsc.bcm.edu	37	X	76918976	76918977	+	Frame_Shift_Del	DEL	TA	TA	-			TCGA-HW-7490-01A-11D-2024-08	TCGA-HW-7490-10A-01D-2024-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ca68843d-1087-4efa-b5f8-0acd8982fb3b	855988d0-f042-466d-86a8-1ac1cb1bc7a1	g.chrX:76918976_76918977delTA	ENST00000373344.5	-	12	4228_4229	c.4014_4015delTA	c.(4012-4017)cataggfs	p.HR1338fs	ATRX_ENST00000480283.1_5'UTR|ATRX_ENST00000395603.3_Frame_Shift_Del_p.HR1300fs	NM_000489.3	NP_000480.3	P46100	ATRX_HUMAN	alpha thalassemia/mental retardation syndrome X-linked	1338					ATP catabolic process (GO:0006200)|cellular response to hydroxyurea (GO:0072711)|chromatin remodeling (GO:0006338)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA duplex unwinding (GO:0032508)|DNA methylation (GO:0006306)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|DNA replication-independent nucleosome assembly (GO:0006336)|forebrain development (GO:0030900)|negative regulation of telomeric RNA transcription from RNA pol II promoter (GO:1901581)|nucleosome assembly (GO:0006334)|positive regulation of nuclear cell cycle DNA replication (GO:0010571)|positive regulation of telomere maintenance (GO:0032206)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|replication fork processing (GO:0031297)|seminiferous tubule development (GO:0072520)|Sertoli cell development (GO:0060009)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nuclear heterochromatin (GO:0005720)|nucleolus (GO:0005730)|nucleus (GO:0005634)|SWI/SNF superfamily-type complex (GO:0070603)|telomeric heterochromatin (GO:0031933)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|chromo shadow domain binding (GO:0070087)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)|DNA translocase activity (GO:0015616)|helicase activity (GO:0004386)|histone binding (GO:0042393)|methylated histone binding (GO:0035064)|zinc ion binding (GO:0008270)	p.?(1)		bone(1)|breast(6)|central_nervous_system(31)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(15)|kidney(14)|large_intestine(1)|liver(1)|lung(40)|ovary(2)|pancreas(13)|prostate(5)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	145						CGCAAAAGCCTATGTCTGTATC	0.356			"""Mis, F, N"""		"""Pancreatic neuroendocrine tumors, paediatric GBM"""		ATR-X (alpha thalassemia/mental retardation) syndrome																																Rec	yes		X	Xq21.1	546	alpha thalassemia/mental retardation syndrome X-linked	yes	E	1	Unknown(1)	bone(1)																																								SO:0001589	frameshift_variant	546			U72937	CCDS14434.1, CCDS14435.1	Xq21.1	2014-06-17	2010-06-24		ENSG00000085224	ENSG00000085224			886	protein-coding gene	gene with protein product	"""RAD54 homolog (S. cerevisiae)"""	300032	"""alpha thalassemia/mental retardation syndrome X-linked (RAD54 (S. cerevisiae) homolog)"", ""Juberg-Marsidi syndrome"""	RAD54, JMS		7874112, 1415255, 8503439, 8630485	Standard	NM_000489		Approved	XH2, XNP	uc004ecp.4	P46100	OTTHUMG00000022686	ENST00000373344.5:c.4014_4015delTA	X.37:g.76918976_76918977delTA	ENSP00000362441:p.His1338fs		D3DTE2|P51068|Q15886|Q59FB5|Q59H31|Q5H9A2|Q5JWI4|Q7Z2J1|Q9H0Z1|Q9NTS3	Frame_Shift_Del	DEL	ENST00000373344.5	37	CCDS14434.1																																																																																				0.356	ATRX-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058860.2	NM_000489		21	5	21	5
ARID1A	8289	broad.mit.edu	37	1	27057848	27057848	+	Frame_Shift_Del	DEL	C	C	-			TCGA-HW-7490-01A-11D-2024-08	TCGA-HW-7490-10A-01D-2024-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ca68843d-1087-4efa-b5f8-0acd8982fb3b	855988d0-f042-466d-86a8-1ac1cb1bc7a1	g.chr1:27057848delC	ENST00000324856.7	+	3	1927	c.1556delC	c.(1555-1557)tccfs	p.S519fs	ARID1A_ENST00000374152.2_Frame_Shift_Del_p.S136fs|ARID1A_ENST00000457599.2_Frame_Shift_Del_p.S519fs	NM_006015.4	NP_006006.3	O14497	ARI1A_HUMAN	AT rich interactive domain 1A (SWI-like)	519					androgen receptor signaling pathway (GO:0030521)|ATP-dependent chromatin remodeling (GO:0043044)|cardiac chamber development (GO:0003205)|chromatin remodeling (GO:0006338)|chromatin-mediated maintenance of transcription (GO:0048096)|forebrain development (GO:0030900)|glucocorticoid receptor signaling pathway (GO:0042921)|intracellular estrogen receptor signaling pathway (GO:0030520)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural tube closure (GO:0001843)|nucleosome disassembly (GO:0006337)|nucleosome mobilization (GO:0042766)|optic cup formation involved in camera-type eye development (GO:0003408)|placenta blood vessel development (GO:0060674)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nBAF complex (GO:0071565)|npBAF complex (GO:0071564)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|SWI/SNF complex (GO:0016514)	DNA binding (GO:0003677)|ligand-dependent nuclear receptor binding (GO:0016922)|transcription coactivator activity (GO:0003713)		ARID1A/MAST2_ENST00000361297(2)	NS(1)|autonomic_ganglia(1)|biliary_tract(1)|breast(13)|central_nervous_system(6)|cervix(2)|endometrium(56)|haematopoietic_and_lymphoid_tissue(8)|kidney(10)|large_intestine(41)|liver(31)|lung(34)|ovary(130)|pancreas(18)|prostate(8)|skin(9)|stomach(14)|upper_aerodigestive_tract(4)|urinary_tract(24)	411		all_cancers(24;6.36e-27)|all_epithelial(13;5.93e-24)|Colorectal(325;3.46e-05)|all_lung(284;4.76e-05)|Lung NSC(340;5.83e-05)|Breast(348;9.7e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|all cancers(4;2.61e-56)|Epithelial(14;7.53e-55)|OV - Ovarian serous cystadenocarcinoma(117;4.5e-30)|Colorectal(126;2.07e-09)|COAD - Colon adenocarcinoma(152;4.29e-07)|BRCA - Breast invasive adenocarcinoma(304;4.13e-05)|STAD - Stomach adenocarcinoma(196;0.000279)|KIRC - Kidney renal clear cell carcinoma(1967;0.000794)|GBM - Glioblastoma multiforme(114;0.0132)|READ - Rectum adenocarcinoma(331;0.0469)|Lung(427;0.167)|LUSC - Lung squamous cell carcinoma(448;0.242)		CCTCCATACTCCCAGCAGCCA	0.632			"""Mis, N, F, S, D"""		"""clear cell ovarian carcinoma, RCC"""																																		Rec	yes		1	1p35.3	8289	AT rich interactive domain 1A (SWI-like)		E	0													273.0	255.0	261.0					1																	27057848		2203	4300	6503	SO:0001589	frameshift_variant	8289			AB001895	CCDS285.1, CCDS44091.1	1p36.1-p35	2014-09-17	2006-11-08	2004-01-30	ENSG00000117713	ENSG00000117713		"""-"""	11110	protein-coding gene	gene with protein product		603024	"""SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily f, member 1"", ""AT rich interactive domain 1A (SWI- like)"""	C1orf4, SMARCF1		9630625, 9434167	Standard	NM_139135		Approved	B120, P270, C10rf4, BAF250, BAF250a	uc001bmv.1	O14497	OTTHUMG00000004004	ENST00000324856.7:c.1556delC	1.37:g.27057848delC	ENSP00000320485:p.Ser519fs		D3DPL1|Q53FK9|Q5T0W1|Q5T0W2|Q5T0W3|Q8NFD6|Q96T89|Q9BY33|Q9HBJ5|Q9UPZ1	Frame_Shift_Del	DEL	ENST00000324856.7	37	CCDS285.1																																																																																				0.632	ARID1A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000011437.2	NM_139135		25	245	25	245
