#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
RAG2	5897	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	11	36614246	36614246	+	Silent	SNP	G	G	A			TCGA-CS-6667-01A-12D-2024-08	TCGA-CS-6667-10A-01D-2024-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0c14ddc3-acf0-4f96-bdb6-eb517d1da522	49ca5323-38a1-4786-b6aa-66de49b053a1	g.chr11:36614246G>A	ENST00000311485.3	-	2	1634	c.1473C>T	c.(1471-1473)ccC>ccT	p.P491P	C11orf74_ENST00000534635.1_5'Flank|RAG2_ENST00000528428.1_5'Flank|C11orf74_ENST00000334307.5_5'Flank|C11orf74_ENST00000446510.2_5'Flank|C11orf74_ENST00000347206.4_5'Flank	NM_000536.3|NM_001243785.1|NM_001243786.1	NP_000527.2|NP_001230714.1|NP_001230715.1	P55895	RAG2_HUMAN	recombination activating gene 2	491					B cell differentiation (GO:0030183)|chromatin modification (GO:0016568)|pre-B cell allelic exclusion (GO:0002331)|T cell differentiation in thymus (GO:0033077)|V(D)J recombination (GO:0033151)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|methylated histone binding (GO:0035064)|phosphatidylinositol binding (GO:0035091)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|phosphatidylinositol-3,4-bisphosphate binding (GO:0043325)|phosphatidylinositol-3,5-bisphosphate binding (GO:0080025)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|zinc ion binding (GO:0008270)			breast(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(18)|ovary(1)|pancreas(2)|prostate(1)|skin(4)	32	all_lung(20;0.226)	all_hematologic(20;0.00756)				GGACTCTTTGGGGAGTGTGTA	0.448									Familial Hemophagocytic Lymphohistiocytosis																																							0													91.0	91.0	91.0					11																	36614246		2202	4298	6500	SO:0001819	synonymous_variant	5897	Familial Cancer Database	FHLH, FHL, Familial Hemophagocytic Reticulosis, FHR	AF080577	CCDS7903.1	11p13	2014-09-17				ENSG00000175097			9832	protein-coding gene	gene with protein product		179616				1283330	Standard	NM_000536		Approved		uc001mwv.4	P55895		ENST00000311485.3:c.1473C>T	11.37:g.36614246G>A			A8K9E9|Q8TBL4	Silent	SNP	ENST00000311485.3	37	CCDS7903.1																																																																																				0.448	RAG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389536.1	NM_000536		32	59	32	59
FREM2	341640	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	13	39454427	39454427	+	Missense_Mutation	SNP	C	C	G	rs148812741		TCGA-CS-6667-01A-12D-2024-08	TCGA-CS-6667-10A-01D-2024-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0c14ddc3-acf0-4f96-bdb6-eb517d1da522	49ca5323-38a1-4786-b6aa-66de49b053a1	g.chr13:39454427C>G	ENST00000280481.7	+	24	9229	c.9013C>G	c.(9013-9015)Cta>Gta	p.L3005V		NM_207361.4	NP_997244.3	Q5SZK8	FREM2_HUMAN	FRAS1 related extracellular matrix protein 2	3005					cell communication (GO:0007154)|homophilic cell adhesion (GO:0007156)|inner ear development (GO:0048839)|morphogenesis of an epithelium (GO:0002009)	basement membrane (GO:0005604)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(14)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(35)|lung(39)|ovary(9)|pancreas(2)|prostate(12)|skin(11)|upper_aerodigestive_tract(7)|urinary_tract(2)	148		Lung NSC(96;1.04e-07)|Prostate(109;0.00384)|Breast(139;0.00396)|Lung SC(185;0.0565)|Hepatocellular(188;0.114)		all cancers(112;3.32e-07)|Epithelial(112;1.66e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00154)|BRCA - Breast invasive adenocarcinoma(63;0.00631)|GBM - Glioblastoma multiforme(144;0.0312)		CTAGGTCGCTCTAGGCCGAGA	0.388																																																0								C	VAL/LEU	0,4406		0,0,2203	75.0	77.0	76.0		9013	3.0	0.5	13	dbSNP_134	76	1,8599	1.2+/-3.3	0,1,4299	no	missense	FREM2	NM_207361.4	32	0,1,6502	GG,GC,CC		0.0116,0.0,0.0077	benign	3005/3170	39454427	1,13005	2203	4300	6503	SO:0001583	missense	341640			BX538150	CCDS31960.1	13q13.3	2004-12-15			ENSG00000150893	ENSG00000150893			25396	protein-coding gene	gene with protein product		608945				15345741	Standard	NM_207361		Approved	DKFZp686J0811	uc001uwv.3	Q5SZK8	OTTHUMG00000016759	ENST00000280481.7:c.9013C>G	13.37:g.39454427C>G	ENSP00000280481:p.Leu3005Val		Q4QQG1|Q5H9N8|Q5T6Q1|Q6N057|Q6ZSB4|Q7Z305|Q7Z341	Missense_Mutation	SNP	ENST00000280481.7	37	CCDS31960.1	.	.	.	.	.	.	.	.	.	.	C	7.075	0.569062	0.13560	0.0	1.16E-4	ENSG00000150893	ENST00000280481	T	0.62232	0.04	5.89	3.05	0.35203	.	0.315686	0.31123	N	0.008206	T	0.38719	0.1051	N	0.16743	0.435	0.09310	N	0.999999	B	0.09022	0.002	B	0.04013	0.001	T	0.12889	-1.0530	10	0.30078	T	0.28	.	4.4229	0.11490	0.0:0.3952:0.2821:0.3227	.	3005	Q5SZK8	FREM2_HUMAN	V	3005	ENSP00000280481:L3005V	ENSP00000280481:L3005V	L	+	1	2	FREM2	38352427	0.418000	0.25440	0.546000	0.28166	0.712000	0.41017	1.236000	0.32683	0.809000	0.34255	0.563000	0.77884	CTA		0.388	FREM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044599.2	NM_207361		20	37	20	37
TMX1	81542	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	14	51713855	51713855	+	Missense_Mutation	SNP	G	G	C	rs560514277		TCGA-CS-6667-01A-12D-2024-08	TCGA-CS-6667-10A-01D-2024-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0c14ddc3-acf0-4f96-bdb6-eb517d1da522	49ca5323-38a1-4786-b6aa-66de49b053a1	g.chr14:51713855G>C	ENST00000457354.2	+	4	485	c.360G>C	c.(358-360)aaG>aaC	p.K120N	SNORA70_ENST00000364506.1_RNA	NM_030755.4	NP_110382.3	Q9H3N1	TMX1_HUMAN	thioredoxin-related transmembrane protein 1	120	Thioredoxin. {ECO:0000255|PROSITE- ProRule:PRU00691}.				cell redox homeostasis (GO:0045454)|protein folding (GO:0006457)|response to endoplasmic reticulum stress (GO:0034976)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|nucleolus (GO:0005730)	disulfide oxidoreductase activity (GO:0015036)|protein disulfide isomerase activity (GO:0003756)			endometrium(2)|large_intestine(2)|urinary_tract(1)	5						CAAGGACTAAGAAGGACTTCA	0.353																																																0													133.0	127.0	129.0					14																	51713855		1820	4089	5909	SO:0001583	missense	81542			AB048246	CCDS41953.1	14q22.1	2011-10-19	2009-02-23	2009-02-23				"""Protein disulfide isomerases"""	15487	protein-coding gene	gene with protein product	"""thioredoxin-related transmembrane protein"", ""protein disulfide isomerase family A, member 11"""	610527	"""thioredoxin domain-containing"", ""thioredoxin domain containing"", ""thioredoxin domain containing 1"""	TXNDC, TXNDC1		11152479	Standard	NM_030755		Approved	TMX, PDIA11	uc001wza.4	Q9H3N1		ENST00000457354.2:c.360G>C	14.37:g.51713855G>C	ENSP00000393316:p.Lys120Asn		B2R7A4|Q8N487|Q8NBN5|Q9Y4T6	Missense_Mutation	SNP	ENST00000457354.2	37	CCDS41953.1	.	.	.	.	.	.	.	.	.	.	G	16.15	3.040881	0.55003	.	.	ENSG00000139921	ENST00000457354	T	0.70631	-0.5	5.68	2.84	0.33178	Thioredoxin domain (1);Thioredoxin-like fold (3);	0.090894	0.85682	D	0.000000	T	0.81692	0.4876	M	0.90425	3.115	0.53688	D	0.99997	D;D	0.76494	0.999;0.974	D;D	0.69479	0.964;0.946	T	0.79448	-0.1799	10	0.32370	T	0.25	-22.7487	4.8037	0.13310	0.2666:0.1653:0.5681:0.0	.	36;120	B4DZX7;Q9H3N1	.;TMX1_HUMAN	N	120	ENSP00000393316:K120N	ENSP00000393316:K120N	K	+	3	2	TMX1	50783605	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	2.016000	0.40971	1.393000	0.46605	0.563000	0.77884	AAG		0.353	TMX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411206.1	NM_030755		42	57	42	57
TP53	7157	hgsc.bcm.edu;ucsc.edu	37	17	7578208	7578208	+	Missense_Mutation	SNP	T	T	C			TCGA-CS-6667-01A-12D-2024-08	TCGA-CS-6667-10A-01D-2024-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0c14ddc3-acf0-4f96-bdb6-eb517d1da522	49ca5323-38a1-4786-b6aa-66de49b053a1	g.chr17:7578208T>C	ENST00000269305.4	-	6	830	c.641A>G	c.(640-642)cAt>cGt	p.H214R	TP53_ENST00000359597.4_Missense_Mutation_p.H214R|TP53_ENST00000445888.2_Missense_Mutation_p.H214R|TP53_ENST00000420246.2_Missense_Mutation_p.H214R|TP53_ENST00000455263.2_Missense_Mutation_p.H214R|TP53_ENST00000574684.1_Intron|TP53_ENST00000413465.2_Missense_Mutation_p.H214R	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	214	Interaction with AXIN1. {ECO:0000250}.|Interaction with HIPK1. {ECO:0000250}.|Required for interaction with FBXO42.|Required for interaction with ZNF385A.		H -> D (in sporadic cancers; somatic mutation).|H -> P (in a sporadic cancer; somatic mutation).|H -> Q (in sporadic cancers; somatic mutation).|H -> R (in sporadic cancers; somatic mutation).|H -> Y (in sporadic cancers; somatic mutation).		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.H214R(61)|p.0?(8)|p.?(5)|p.H82R(4)|p.H214fs*33(4)|p.H121R(4)|p.H214fs*5(2)|p.D208fs*1(1)|p.H82fs*>9(1)|p.T211fs*28(1)|p.R213_S215>X(1)|p.D207_V216del10(1)|p.R213fs*32(1)|p.H121fs*33(1)|p.T211_S215delTFRHS(1)|p.R209fs*6(1)|p.D208_V216delDRNTFRHSV(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)	CACCACACTATGTCGAAAAGT	0.542		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)																											Pancreas(47;798 1329 9957 10801)	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"""L, E, M, O"""	98	Substitution - Missense(69)|Deletion - Frameshift(12)|Whole gene deletion(8)|Unknown(5)|Deletion - In frame(3)|Complex - deletion inframe(1)	lung(27)|liver(12)|ovary(8)|biliary_tract(6)|oesophagus(6)|upper_aerodigestive_tract(5)|central_nervous_system(5)|large_intestine(5)|urinary_tract(5)|prostate(4)|bone(4)|stomach(3)|breast(3)|haematopoietic_and_lymphoid_tissue(2)|soft_tissue(1)|skin(1)|pancreas(1)											127.0	114.0	119.0					17																	7578208		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.641A>G	17.37:g.7578208T>C	ENSP00000269305:p.His214Arg		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	.	.	.	.	.	.	.	.	.	.	T	35	5.548167	0.96488	.	.	ENSG00000141510	ENST00000413465;ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000545858;ENST00000509690;ENST00000514944;ENST00000414315	D;D;D;D;D;D;D;D	0.99755	-6.64;-6.64;-6.64;-6.64;-6.64;-6.64;-6.64;-6.64	5.28	5.28	0.74379	p53, DNA-binding domain (1);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1);	0.052737	0.85682	D	0.000000	D	0.99664	0.9875	M	0.75615	2.305	0.80722	D	1	D;D;P;D;D;D;D	0.76494	0.999;0.992;0.733;0.999;0.994;0.994;0.999	D;D;B;D;D;D;D	0.74674	0.984;0.947;0.376;0.982;0.95;0.968;0.962	D	0.97475	1.0043	10	0.72032	D	0.01	-26.1151	13.4753	0.61306	0.0:0.0:0.0:1.0	.	175;214;214;121;214;214;214	B4E095;P04637-2;P04637-3;E9PFT5;P04637;Q1MSW8;E7EQX7	.;.;.;.;P53_HUMAN;.;.	R	214;214;214;214;214;214;203;121;82;121;82	ENSP00000410739:H214R;ENSP00000352610:H214R;ENSP00000269305:H214R;ENSP00000398846:H214R;ENSP00000391127:H214R;ENSP00000391478:H214R;ENSP00000425104:H82R;ENSP00000423862:H121R	ENSP00000269305:H214R	H	-	2	0	TP53	7518933	1.000000	0.71417	0.283000	0.24790	0.961000	0.63080	7.996000	0.88334	2.128000	0.65567	0.460000	0.39030	CAT		0.542	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		13	38	13	38
TP53	7157	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	17	7578550	7578550	+	Missense_Mutation	SNP	G	G	A			TCGA-CS-6667-01A-12D-2024-08	TCGA-CS-6667-10A-01D-2024-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0c14ddc3-acf0-4f96-bdb6-eb517d1da522	49ca5323-38a1-4786-b6aa-66de49b053a1	g.chr17:7578550G>A	ENST00000269305.4	-	5	569	c.380C>T	c.(379-381)tCc>tTc	p.S127F	TP53_ENST00000359597.4_Missense_Mutation_p.S127F|TP53_ENST00000445888.2_Missense_Mutation_p.S127F|TP53_ENST00000420246.2_Missense_Mutation_p.S127F|TP53_ENST00000455263.2_Missense_Mutation_p.S127F|TP53_ENST00000574684.1_5'Flank|TP53_ENST00000413465.2_Missense_Mutation_p.S127F	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	127	Interaction with AXIN1. {ECO:0000250}.|Interaction with HIPK1. {ECO:0000250}.|Required for interaction with FBXO42.|Required for interaction with ZNF385A.		S -> C (in a sporadic cancer; somatic mutation).|S -> F (in sporadic cancers; somatic mutation).|S -> P (in sporadic cancers; somatic mutation).|S -> T (in sporadic cancers; somatic mutation).|S -> Y (in sporadic cancers; somatic mutation).		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.S127F(23)|p.0?(8)|p.S127Y(8)|p.S127C(7)|p.Y126_K132delYSPALNK(6)|p.A129fs*20(3)|p.Y126_N131delYSPALN(3)|p.S34C(2)|p.P128fs*42(2)|p.V73fs*9(1)|p.S127fs*36(1)|p.P128fs*18(1)|p.Y126fs*11(1)|p.S127_Q136del10(1)|p.P13fs*18(1)|p.?(1)|p.S34F(1)|p.A36fs*20(1)|p.S127fs*42(1)|p.Y126fs*18(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)	GAGGGCAGGGGAGTACTGTAG	0.552		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)																											Pancreas(47;798 1329 9957 10801)	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"""L, E, M, O"""	73	Substitution - Missense(41)|Deletion - In frame(10)|Deletion - Frameshift(9)|Whole gene deletion(8)|Insertion - Frameshift(4)|Unknown(1)	lung(13)|ovary(8)|upper_aerodigestive_tract(7)|large_intestine(6)|central_nervous_system(6)|skin(5)|NS(4)|prostate(4)|bone(4)|urinary_tract(3)|breast(3)|stomach(2)|haematopoietic_and_lymphoid_tissue(2)|liver(2)|oesophagus(2)|biliary_tract(1)|pancreas(1)											44.0	44.0	44.0					17																	7578550		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.380C>T	17.37:g.7578550G>A	ENSP00000269305:p.Ser127Phe		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	.	.	.	.	.	.	.	.	.	.	G	22.8	4.338648	0.81911	.	.	ENSG00000141510	ENST00000413465;ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000545858;ENST00000514944;ENST00000508793;ENST00000503591	D;D;D;D;D;D;D;D;D	0.99940	-8.4;-8.4;-8.4;-8.4;-8.4;-8.4;-8.4;-8.4;-8.4	5.48	4.51	0.55191	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	0.99933	0.9970	M	0.91038	3.17	0.80722	D	1	D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D;D	0.97110	1.0;1.0;1.0;0.995;1.0;1.0;1.0	D	0.95614	0.8675	10	0.87932	D	0	-30.2503	12.2742	0.54724	0.0828:0.0:0.9172:0.0	.	88;127;127;34;127;127;127	B4E095;P04637-2;P04637-3;E9PFT5;P04637;Q1MSW8;E7EQX7	.;.;.;.;P53_HUMAN;.;.	F	127;127;127;127;127;127;116;34;34;127;127	ENSP00000410739:S127F;ENSP00000352610:S127F;ENSP00000269305:S127F;ENSP00000398846:S127F;ENSP00000391127:S127F;ENSP00000391478:S127F;ENSP00000423862:S34F;ENSP00000424104:S127F;ENSP00000426252:S127F	ENSP00000269305:S127F	S	-	2	0	TP53	7519275	1.000000	0.71417	0.890000	0.34922	0.931000	0.56810	9.763000	0.98947	1.448000	0.47680	0.655000	0.94253	TCC		0.552	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		15	22	15	22
CASP14	23581	hgsc.bcm.edu;broad.mit.edu	37	19	15166067	15166067	+	Missense_Mutation	SNP	G	G	A	rs148526551		TCGA-CS-6667-01A-12D-2024-08	TCGA-CS-6667-10A-01D-2024-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0c14ddc3-acf0-4f96-bdb6-eb517d1da522	49ca5323-38a1-4786-b6aa-66de49b053a1	g.chr19:15166067G>A	ENST00000427043.3	+	5	810	c.502G>A	c.(502-504)Gtt>Att	p.V168I	AC004699.1_ENST00000411269.1_RNA|CASP14_ENST00000221740.1_Missense_Mutation_p.V168I	NM_012114.2	NP_036246.1	P31944	CASPE_HUMAN	caspase 14, apoptosis-related cysteine peptidase	168					cornification (GO:0070268)|epidermis development (GO:0008544)|extrinsic apoptotic signaling pathway in absence of ligand (GO:0097192)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|keratinization (GO:0031424)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|keratin filament (GO:0045095)|nucleus (GO:0005634)	cysteine-type endopeptidase activity (GO:0004197)			NS(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(8)|ovary(1)|prostate(1)|skin(3)	26						TGCCTTGCACGTTTATTCCAC	0.547													G|||	1	0.000199681	0.0	0.0	5008	,	,		17516	0.0		0.001	False		,,,				2504	0.0															0								G	ILE/VAL	0,4406		0,0,2203	121.0	109.0	114.0		502	-2.0	0.0	19	dbSNP_134	114	2,8598	2.2+/-6.3	0,2,4298	yes	missense	CASP14	NM_012114.2	29	0,2,6501	AA,AG,GG		0.0233,0.0,0.0154	benign	168/243	15166067	2,13004	2203	4300	6503	SO:0001583	missense	23581				CCDS12323.1	19p13.1	2008-07-16	2005-08-17			ENSG00000105141			1502	protein-coding gene	gene with protein product	"""apoptosis-related cysteine protease"""	605848	"""caspase 14, apoptosis-related cysteine protease"""			10203698, 9792675	Standard	NM_012114		Approved	MICE, MGC119078, MGC119079	uc010dzv.2	P31944		ENST00000427043.3:c.502G>A	19.37:g.15166067G>A	ENSP00000393417:p.Val168Ile		O95823|Q3SYC9	Missense_Mutation	SNP	ENST00000427043.3	37	CCDS12323.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	g	0.013	-1.646683	0.00792	0.0	2.33E-4	ENSG00000105141	ENST00000427043;ENST00000221740	T;T	0.18960	2.18;2.18	4.32	-2.02	0.07388	Peptidase C14, caspase catalytic (1);Peptidase C14, caspase non-catalytic subunit p10 (1);Peptidase C14, caspase precursor p45, core (1);	0.788814	0.11704	N	0.537616	T	0.08626	0.0214	N	0.16037	0.36	0.09310	N	1	B	0.18863	0.031	B	0.17979	0.02	T	0.40515	-0.9559	10	0.05620	T	0.96	.	7.7189	0.28721	0.5243:0.0:0.4757:0.0	.	168	P31944	CASPE_HUMAN	I	168	ENSP00000393417:V168I;ENSP00000221740:V168I	ENSP00000221740:V168I	V	+	1	0	CASP14	15027067	0.001000	0.12720	0.018000	0.16275	0.009000	0.06853	-0.597000	0.05713	-0.508000	0.06540	0.455000	0.32223	GTT		0.547	CASP14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465663.1	NM_012114		4	50	4	50
WDR62	284403	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	19	36572456	36572456	+	Missense_Mutation	SNP	A	A	T			TCGA-CS-6667-01A-12D-2024-08	TCGA-CS-6667-10A-01D-2024-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0c14ddc3-acf0-4f96-bdb6-eb517d1da522	49ca5323-38a1-4786-b6aa-66de49b053a1	g.chr19:36572456A>T	ENST00000270301.7	+	10	1355	c.1355A>T	c.(1354-1356)aAa>aTa	p.K452I	WDR62_ENST00000401500.2_Missense_Mutation_p.K452I|WDR62_ENST00000388999.3_Missense_Mutation_p.K452I			O43379	WDR62_HUMAN	WD repeat domain 62	452					cerebral cortex development (GO:0021987)|neurogenesis (GO:0022008)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|spindle pole (GO:0000922)				cervix(1)|endometrium(8)|kidney(2)|large_intestine(8)|lung(15)|prostate(4)|stomach(2)|urinary_tract(3)	43	Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.06)			CACTGGCAGAAAAACATCTTC	0.473																																																0													142.0	125.0	131.0					19																	36572456		2203	4300	6503	SO:0001583	missense	284403			BX647726	CCDS33001.1, CCDS46059.1	19q13.12	2013-01-09	2005-05-09	2005-05-09	ENSG00000075702	ENSG00000075702		"""WD repeat domain containing"""	24502	protein-coding gene	gene with protein product		613583	"""chromosome 19 open reading frame 14"", ""microcephaly, primary autosomal recessive 2"""	C19orf14, MCPH2		19910486, 20729831, 20890278, 21496009	Standard	NM_001083961		Approved	DKFZP434J046, FLJ33298	uc002odd.2	O43379	OTTHUMG00000048139	ENST00000270301.7:c.1355A>T	19.37:g.36572456A>T	ENSP00000270301:p.Lys452Ile		Q63HP9|Q659D7|Q8NBF7|Q96AD9	Missense_Mutation	SNP	ENST00000270301.7	37	CCDS33001.1	.	.	.	.	.	.	.	.	.	.	A	21.9	4.209783	0.79240	.	.	ENSG00000075702	ENST00000401500;ENST00000388999;ENST00000270301	T;T;T	0.63417	0.79;0.33;-0.04	5.23	4.22	0.49857	WD40/YVTN repeat-like-containing domain (1);	0.335659	0.32703	N	0.005741	T	0.62502	0.2433	L	0.27053	0.805	0.38772	D	0.954572	D;D	0.89917	1.0;0.998	D;D	0.76575	0.988;0.952	T	0.64854	-0.6309	10	0.45353	T	0.12	-10.0693	5.8745	0.18822	0.8129:0.0:0.1871:0.0	.	452;452	O43379-4;O43379	.;WDR62_HUMAN	I	452	ENSP00000384792:K452I;ENSP00000373651:K452I;ENSP00000270301:K452I	ENSP00000270301:K452I	K	+	2	0	WDR62	41264296	0.030000	0.19436	0.994000	0.49952	0.983000	0.72400	0.558000	0.23469	1.993000	0.58246	0.533000	0.62120	AAA		0.473	WDR62-006	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000457436.1	NM_015671		19	90	19	90
WARS2	10352	hgsc.bcm.edu;ucsc.edu	37	1	119575933	119575933	+	Silent	SNP	C	C	T	rs77497675	byFrequency	TCGA-CS-6667-01A-12D-2024-08	TCGA-CS-6667-10A-01D-2024-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0c14ddc3-acf0-4f96-bdb6-eb517d1da522	49ca5323-38a1-4786-b6aa-66de49b053a1	g.chr1:119575933C>T	ENST00000235521.4	-	6	710	c.684G>A	c.(682-684)tcG>tcA	p.S228S	WARS2_ENST00000537870.1_Silent_p.S134S|WARS2_ENST00000369426.5_3'UTR	NM_015836.3|NM_201263.2	NP_056651.1|NP_957715.1	Q9UGM6	SYWM_HUMAN	tryptophanyl tRNA synthetase 2, mitochondrial	228					gene expression (GO:0010467)|tRNA aminoacylation for protein translation (GO:0006418)|tryptophanyl-tRNA aminoacylation (GO:0006436)|vasculogenesis (GO:0001570)	mitochondrial matrix (GO:0005759)	ATP binding (GO:0005524)|tryptophan-tRNA ligase activity (GO:0004830)			breast(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(7)|prostate(2)	15	all_neural(166;0.187)	all_lung(203;2.48e-06)|Lung NSC(69;1.74e-05)|all_epithelial(167;0.000564)		Lung(183;0.0629)	L-Tryptophan(DB00150)	GGTCTGATTTCGACATTTTGG	0.458													C|||	14	0.00279553	0.0106	0.0	5008	,	,		16607	0.0		0.0	False		,,,				2504	0.0															0								C	,	35,4371	39.2+/-71.8	0,35,2168	190.0	183.0	186.0		684,	-11.7	0.0	1	dbSNP_131	186	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,utr-3	WARS2	NM_015836.3,NM_201263.2	,	0,36,6467	TT,TC,CC		0.0116,0.7944,0.2768	,	228/361,	119575933	36,12970	2203	4300	6503	SO:0001819	synonymous_variant	10352			BC021722	CCDS900.1, CCDS30817.1	1p12	2011-07-01	2007-02-23		ENSG00000116874	ENSG00000116874	6.1.1.2	"""Aminoacyl tRNA synthetases / Class I"""	12730	protein-coding gene	gene with protein product	"""tryptophan tRNA ligase 2, mitochondrial"""	604733				10072595, 10828066	Standard	NM_201263		Approved	TrpRS	uc001ehn.3	Q9UGM6	OTTHUMG00000012335	ENST00000235521.4:c.684G>A	1.37:g.119575933C>T			B1ALR1|B2R9D4|Q53FT4|Q5VUD2|Q86TQ0	Silent	SNP	ENST00000235521.4	37	CCDS900.1																																																																																				0.458	WARS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034362.1	NM_015836		45	129	45	129
IDH1	3417	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	2	209113112	209113112	+	Missense_Mutation	SNP	C	C	T	rs121913500		TCGA-CS-6667-01A-12D-2024-08	TCGA-CS-6667-10A-01D-2024-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0c14ddc3-acf0-4f96-bdb6-eb517d1da522	49ca5323-38a1-4786-b6aa-66de49b053a1	g.chr2:209113112C>T	ENST00000415913.1	-	4	776	c.395G>A	c.(394-396)cGt>cAt	p.R132H	IDH1_ENST00000446179.1_Missense_Mutation_p.R132H|IDH1_ENST00000345146.2_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			33	53	33	53
ABCA12	26154	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	2	215823176	215823176	+	Missense_Mutation	SNP	A	A	G			TCGA-CS-6667-01A-12D-2024-08	TCGA-CS-6667-10A-01D-2024-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0c14ddc3-acf0-4f96-bdb6-eb517d1da522	49ca5323-38a1-4786-b6aa-66de49b053a1	g.chr2:215823176A>G	ENST00000272895.7	-	41	6161	c.5942T>C	c.(5941-5943)aTc>aCc	p.I1981T	AC072062.1_ENST00000420134.1_RNA|AC072062.1_ENST00000607412.1_RNA|ABCA12_ENST00000389661.4_Missense_Mutation_p.I1663T	NM_173076.2	NP_775099.2	Q86UK0	ABCAC_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 12	1981					cellular homeostasis (GO:0019725)|ceramide transport (GO:0035627)|establishment of skin barrier (GO:0061436)|keratinization (GO:0031424)|lipid homeostasis (GO:0055088)|lipid transport (GO:0006869)|lung alveolus development (GO:0048286)|phospholipid efflux (GO:0033700)|positive regulation of cholesterol efflux (GO:0010875)|positive regulation of protein localization to cell surface (GO:2000010)|protein localization to plasma membrane (GO:0072659)|regulated secretory pathway (GO:0045055)|secretion by cell (GO:0032940)|surfactant homeostasis (GO:0043129)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|epidermal lamellar body (GO:0097209)|integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|plasma membrane (GO:0005886)	apolipoprotein A-I receptor binding (GO:0034191)|ATP binding (GO:0005524)|lipid transporter activity (GO:0005319)|lipid-transporting ATPase activity (GO:0034040)|receptor binding (GO:0005102)			NS(3)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(45)|lung(44)|ovary(8)|pancreas(2)|prostate(4)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	139		Renal(323;0.127)		Epithelial(149;1.01e-05)|all cancers(144;0.00112)|LUSC - Lung squamous cell carcinoma(224;0.00829)|Lung(261;0.011)		TAAACTGCTGATTCTAGAGTG	0.388																																					Ovarian(66;664 1488 5121 34295)											0													93.0	77.0	82.0					2																	215823176		2203	4300	6503	SO:0001583	missense	26154			AF418105	CCDS33372.1, CCDS33373.1	2q34	2012-03-14			ENSG00000144452	ENSG00000144452		"""ATP binding cassette transporters / subfamily A"""	14637	protein-coding gene	gene with protein product		607800	"""ichthyosis congenita II, lamellar ichthyosis B"""	ICR2B		11435397, 12915478, 8845852, 10094194	Standard	NM_015657		Approved	DKFZP434G232, LI2	uc002vew.3	Q86UK0	OTTHUMG00000154801	ENST00000272895.7:c.5942T>C	2.37:g.215823176A>G	ENSP00000272895:p.Ile1981Thr		Q53QE2|Q53S55|Q8IZW6|Q96JT3|Q9Y4M5	Missense_Mutation	SNP	ENST00000272895.7	37	CCDS33372.1	.	.	.	.	.	.	.	.	.	.	A	12.68	2.012090	0.35511	.	.	ENSG00000144452	ENST00000272895;ENST00000389661	D;D	0.82526	-1.62;-1.62	5.52	5.52	0.82312	.	0.162995	0.43579	D	0.000549	T	0.72495	0.3467	N	0.24115	0.695	0.80722	D	1	B;B	0.15473	0.013;0.003	B;B	0.16289	0.012;0.015	T	0.70026	-0.4985	10	0.87932	D	0	.	10.3258	0.43792	0.9265:0.0:0.0735:0.0	.	1981;1663	Q86UK0;Q86UK0-2	ABCAC_HUMAN;.	T	1981;1663	ENSP00000272895:I1981T;ENSP00000374312:I1663T	ENSP00000272895:I1981T	I	-	2	0	ABCA12	215531421	1.000000	0.71417	1.000000	0.80357	0.973000	0.67179	6.916000	0.75776	2.232000	0.73038	0.528000	0.53228	ATC		0.388	ABCA12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337111.1	NM_173076		25	25	25	25
CCDC108	255101	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	2	219895549	219895549	+	Silent	SNP	G	G	A	rs375597036		TCGA-CS-6667-01A-12D-2024-08	TCGA-CS-6667-10A-01D-2024-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0c14ddc3-acf0-4f96-bdb6-eb517d1da522	49ca5323-38a1-4786-b6aa-66de49b053a1	g.chr2:219895549G>A	ENST00000341552.5	-	9	1106	c.1023C>T	c.(1021-1023)tgC>tgT	p.C341C	CCDC108_ENST00000441968.1_Silent_p.C341C|CCDC108_ENST00000409865.3_Silent_p.C330C|CCDC108_ENST00000410037.1_Silent_p.C276C|CCDC108_ENST00000453220.1_Silent_p.C341C	NM_194302.2	NP_919278.2	Q6ZU64	CC108_HUMAN	coiled-coil domain containing 108	341						integral component of membrane (GO:0016021)	poly(A) RNA binding (GO:0044822)|structural molecule activity (GO:0005198)			autonomic_ganglia(1)|breast(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(18)|liver(1)|lung(34)|ovary(2)|pancreas(1)|prostate(6)|skin(5)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	80		Renal(207;0.0915)		Epithelial(149;1.12e-06)|all cancers(144;0.000196)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		GCAGCTGGGCGCACTTGGCTG	0.637																																																0								G		1,4405	2.1+/-5.4	0,1,2202	36.0	38.0	37.0		1023	-4.6	0.8	2		37	0,8600		0,0,4300	no	coding-synonymous	CCDC108	NM_194302.2		0,1,6502	AA,AG,GG		0.0,0.0227,0.0077		341/1926	219895549	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	255101			NM_194302, AL833882, AK127189	CCDS2430.2, CCDS2431.2, CCDS63125.1, CCDS63126.1	2q35	2008-02-05			ENSG00000181378	ENSG00000181378			25325	protein-coding gene	gene with protein product		614270				12477932	Standard	NM_194302		Approved	DKFZp434O0527, MGC35338	uc002vjl.2	Q6ZU64	OTTHUMG00000133013	ENST00000341552.5:c.1023C>T	2.37:g.219895549G>A			A2BDD8|E9PCR1|E9PG25|E9PG72|Q6ZSR8|Q8N0T4|Q8NDJ3	Silent	SNP	ENST00000341552.5	37	CCDS2430.2																																																																																				0.637	CCDC108-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256598.4	NM_194302		9	30	9	30
FAM208A	23272	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	3	56694986	56694986	+	Missense_Mutation	SNP	G	G	A			TCGA-CS-6667-01A-12D-2024-08	TCGA-CS-6667-10A-01D-2024-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0c14ddc3-acf0-4f96-bdb6-eb517d1da522	49ca5323-38a1-4786-b6aa-66de49b053a1	g.chr3:56694986G>A	ENST00000493960.2	-	10	1230	c.1220C>T	c.(1219-1221)cCt>cTt	p.P407L	FAM208A_ENST00000355628.5_Missense_Mutation_p.P407L|FAM208A_ENST00000431842.2_Missense_Mutation_p.P11L	NM_001112736.1	NP_001106207.1	Q9UK61	F208A_HUMAN	family with sequence similarity 208, member A	407							poly(A) RNA binding (GO:0044822)			NS(1)|breast(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(4)|lung(11)|prostate(3)|skin(1)	32						CAGTGCTGGAGGGATTTTCTG	0.299																																																0													113.0	113.0	113.0					3																	56694986		2202	4299	6501	SO:0001583	missense	23272			AF180425	CCDS2877.1, CCDS46853.1	3p14.3	2011-09-14	2011-09-14	2011-09-14	ENSG00000163946	ENSG00000163946			30314	protein-coding gene	gene with protein product			"""chromosome 3 open reading frame 63"""	C3orf63		10470851, 11149944	Standard	NM_015224		Approved	se89-1, RAP140, KIAA1105	uc003die.4	Q9UK61	OTTHUMG00000158827	ENST00000493960.2:c.1220C>T	3.37:g.56694986G>A	ENSP00000417509:p.Pro407Leu		A1L3A4|B5ME28|Q9H2F7|Q9UPP7	Missense_Mutation	SNP	ENST00000493960.2	37	CCDS46853.1	.	.	.	.	.	.	.	.	.	.	G	27.0	4.788611	0.90367	.	.	ENSG00000163946	ENST00000431842;ENST00000493960;ENST00000355628	T;T;T	0.29397	1.57;1.61;1.68	5.8	5.8	0.92144	.	0.102567	0.44097	D	0.000481	T	0.57021	0.2025	M	0.66939	2.045	0.80722	D	1	D;D;D	0.89917	1.0;0.996;0.998	D;P;D	0.74674	0.984;0.866;0.923	T	0.57189	-0.7854	10	0.87932	D	0	-14.2646	20.062	0.97678	0.0:0.0:1.0:0.0	.	407;407;11	Q9UK61-3;Q9UK61-4;Q9UK61-2	.;.;.	L	11;407;407	ENSP00000399410:P11L;ENSP00000417509:P407L;ENSP00000347845:P407L	ENSP00000347845:P407L	P	-	2	0	C3orf63	56670026	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.263000	0.89864	2.730000	0.93505	0.563000	0.77884	CCT		0.299	FAM208A-004	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352352.2	NM_015224		16	54	16	54
EPHA5	2044	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	4	66201659	66201659	+	Missense_Mutation	SNP	G	G	A			TCGA-CS-6667-01A-12D-2024-08	TCGA-CS-6667-10A-01D-2024-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0c14ddc3-acf0-4f96-bdb6-eb517d1da522	49ca5323-38a1-4786-b6aa-66de49b053a1	g.chr4:66201659G>A	ENST00000273854.3	-	16	3443	c.2843C>T	c.(2842-2844)gCa>gTa	p.A948V	EPHA5_ENST00000432638.2_Missense_Mutation_p.A785V|EPHA5_ENST00000354839.4_Missense_Mutation_p.A926V|EPHA5_ENST00000511294.1_Missense_Mutation_p.A949V	NM_001281765.1|NM_004439.5	NP_001268694.1|NP_004430.4	P54756	EPHA5_HUMAN	EPH receptor A5	948					axon guidance (GO:0007411)|cAMP-mediated signaling (GO:0019933)|ephrin receptor signaling pathway (GO:0048013)|hippocampus development (GO:0021766)|negative regulation of synapse assembly (GO:0051964)|neuron development (GO:0048666)|positive regulation of CREB transcription factor activity (GO:0032793)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0061178)|regulation of Rac GTPase activity (GO:0032314)	dendrite (GO:0030425)|external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|neuronal cell body (GO:0043025)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|rough endoplasmic reticulum (GO:0005791)	ATP binding (GO:0005524)|ephrin receptor activity (GO:0005003)|GPI-linked ephrin receptor activity (GO:0005004)|transmembrane-ephrin receptor activity (GO:0005005)			autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(25)|liver(1)|lung(76)|ovary(3)|pancreas(1)|prostate(1)|skin(3)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(3)	142						CCTGCAGGATGCATTAACCAG	0.403										TSP Lung(17;0.13)																																						0													169.0	154.0	159.0					4																	66201659		2203	4300	6503	SO:0001583	missense	2044			L36644	CCDS3513.1, CCDS3514.1, CCDS75131.1, CCDS75132.1, CCDS75133.1	4q13.1	2013-02-11	2004-10-28		ENSG00000145242	ENSG00000145242		"""EPH receptors"", ""Sterile alpha motif (SAM) domain containing"", ""Fibronectin type III domain containing"""	3389	protein-coding gene	gene with protein product		600004	"""EphA5"""			9267020, 7528718	Standard	NM_004439		Approved	Hek7, TYRO4, CEK7, EHK1	uc003hcy.3	P54756	OTTHUMG00000129273	ENST00000273854.3:c.2843C>T	4.37:g.66201659G>A	ENSP00000273854:p.Ala948Val		Q7Z3F2	Missense_Mutation	SNP	ENST00000273854.3	37	CCDS3513.1	.	.	.	.	.	.	.	.	.	.	G	12.06	1.824378	0.32237	.	.	ENSG00000145242	ENST00000273854;ENST00000432638;ENST00000354839;ENST00000511294	T;T;T;T	0.61742	0.08;0.08;0.08;0.08	6.17	6.17	0.99709	Protein kinase-like domain (1);	0.000000	0.64402	D	0.000009	T	0.44787	0.1310	N	0.16903	0.455	0.46701	D	0.999169	B;B;B;B	0.30455	0.184;0.212;0.28;0.212	B;B;B;B	0.26770	0.033;0.014;0.073;0.009	T	0.26395	-1.0104	10	0.25106	T	0.35	.	20.8794	0.99867	0.0:0.0:1.0:0.0	.	927;949;926;948	B7ZKW7;B7ZKJ3;P54756-2;P54756	.;.;.;EPHA5_HUMAN	V	948;785;926;949	ENSP00000273854:A948V;ENSP00000389208:A785V;ENSP00000346899:A926V;ENSP00000427638:A949V	ENSP00000273854:A948V	A	-	2	0	EPHA5	65884254	1.000000	0.71417	1.000000	0.80357	0.234000	0.25298	7.859000	0.86982	2.941000	0.99782	0.655000	0.94253	GCA		0.403	EPHA5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251388.2	NM_004439		45	85	45	85
FAT4	79633	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	4	126239329	126239329	+	Missense_Mutation	SNP	A	A	G			TCGA-CS-6667-01A-12D-2024-08	TCGA-CS-6667-10A-01D-2024-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0c14ddc3-acf0-4f96-bdb6-eb517d1da522	49ca5323-38a1-4786-b6aa-66de49b053a1	g.chr4:126239329A>G	ENST00000394329.3	+	1	1776	c.1763A>G	c.(1762-1764)tAt>tGt	p.Y588C		NM_024582.4	NP_078858.4	Q6V0I7	FAT4_HUMAN	FAT atypical cadherin 4	588	Cadherin 6. {ECO:0000255|PROSITE- ProRule:PRU00043}.				branching involved in ureteric bud morphogenesis (GO:0001658)|cerebral cortex development (GO:0021987)|digestive tract development (GO:0048565)|heart morphogenesis (GO:0003007)|heterophilic cell-cell adhesion (GO:0007157)|hippo signaling (GO:0035329)|homophilic cell adhesion (GO:0007156)|inner ear receptor stereocilium organization (GO:0060122)|neurogenesis (GO:0022008)|ossification involved in bone maturation (GO:0043931)|plasma membrane organization (GO:0007009)|regulation of metanephric nephron tubule epithelial cell differentiation (GO:0072307)	apical part of cell (GO:0045177)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(6)|autonomic_ganglia(1)|breast(4)|central_nervous_system(3)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(3)|kidney(10)|large_intestine(93)|liver(3)|lung(120)|ovary(9)|pancreas(2)|prostate(21)|skin(31)|stomach(1)|upper_aerodigestive_tract(12)|urinary_tract(6)	355						CCAGAAGGGTATGATGTGTCT	0.532																																																0													75.0	78.0	77.0					4																	126239329		2018	4182	6200	SO:0001583	missense	79633			AY356402	CCDS3732.3	4q28.1	2013-05-31	2013-05-31		ENSG00000196159	ENSG00000196159		"""Cadherins / Cadherin-related"""	23109	protein-coding gene	gene with protein product	"""cadherin-related family member 11"""	612411	"""FAT tumor suppressor homolog 4 (Drosophila)"""			15003449	Standard	NM_024582		Approved	CDHF14, FAT-J, CDHR11	uc003ifj.4	Q6V0I7	OTTHUMG00000133100	ENST00000394329.3:c.1763A>G	4.37:g.126239329A>G	ENSP00000377862:p.Tyr588Cys		A8K5Z6|B5MDG4|Q3LIA6|Q8TCK7|Q9H5T6	Missense_Mutation	SNP	ENST00000394329.3	37	CCDS3732.3	.	.	.	.	.	.	.	.	.	.	A	13.06	2.125084	0.37533	.	.	ENSG00000196159	ENST00000394329	T	0.48836	0.8	4.77	4.77	0.60923	Cadherin (3);Cadherin-like (1);	0.000000	0.31834	U	0.006986	T	0.76241	0.3960	H	0.95079	3.62	0.80722	D	1	D	0.71674	0.998	D	0.67900	0.954	D	0.84343	0.0528	10	0.87932	D	0	.	14.4803	0.67576	1.0:0.0:0.0:0.0	.	588	Q6V0I7	FAT4_HUMAN	C	588	ENSP00000377862:Y588C	ENSP00000377862:Y588C	Y	+	2	0	FAT4	126458779	1.000000	0.71417	0.030000	0.17652	0.936000	0.57629	7.027000	0.76463	2.006000	0.58801	0.459000	0.35465	TAT		0.532	FAT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256765.2	NM_024582		35	54	35	54
GEMIN5	25929	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	5	154270897	154270897	+	Missense_Mutation	SNP	T	T	C			TCGA-CS-6667-01A-12D-2024-08	TCGA-CS-6667-10A-01D-2024-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0c14ddc3-acf0-4f96-bdb6-eb517d1da522	49ca5323-38a1-4786-b6aa-66de49b053a1	g.chr5:154270897T>C	ENST00000285873.7	-	26	4241	c.4166A>G	c.(4165-4167)cAa>cGa	p.Q1389R		NM_001252156.1|NM_015465.4	NP_001239085.1|NP_056280.2	Q8TEQ6	GEMI5_HUMAN	gem (nuclear organelle) associated protein 5	1389					gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|ncRNA metabolic process (GO:0034660)|protein complex assembly (GO:0006461)|RNA metabolic process (GO:0016070)|spliceosomal snRNP assembly (GO:0000387)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nuclear body (GO:0016604)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|SMN complex (GO:0032797)|SMN-Sm protein complex (GO:0034719)	poly(A) RNA binding (GO:0044822)|snRNA binding (GO:0017069)			breast(1)|central_nervous_system(2)|endometrium(5)|kidney(3)|large_intestine(10)|lung(10)|ovary(1)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	38	Renal(175;0.00488)	Medulloblastoma(196;0.0354)|all_neural(177;0.147)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)			TTGACTCTTTTGGTGTTGTCG	0.458																																																0													134.0	130.0	131.0					5																	154270897		2203	4300	6503	SO:0001583	missense	25929			AK022748	CCDS4330.1	5q34	2013-01-10			ENSG00000082516	ENSG00000082516		"""WD repeat domain containing"""	20043	protein-coding gene	gene with protein product		607005				11714716	Standard	NM_015465		Approved		uc003lvx.3	Q8TEQ6	OTTHUMG00000130189	ENST00000285873.7:c.4166A>G	5.37:g.154270897T>C	ENSP00000285873:p.Gln1389Arg		Q14CV0|Q8WWV4|Q969W4|Q9H9K3|Q9UFI5	Missense_Mutation	SNP	ENST00000285873.7	37	CCDS4330.1	.	.	.	.	.	.	.	.	.	.	T	10.57	1.388315	0.25118	.	.	ENSG00000082516	ENST00000285873	T	0.71222	-0.55	6.07	4.92	0.64577	.	0.185119	0.51477	N	0.000097	T	0.68513	0.3009	M	0.67953	2.075	0.33520	D	0.592202	B;B	0.13145	0.007;0.007	B;B	0.10450	0.005;0.005	T	0.73388	-0.3998	10	0.72032	D	0.01	-10.1733	11.9702	0.53060	0.0:0.067:0.0:0.933	.	1388;1389	B7ZLC9;Q8TEQ6	.;GEMI5_HUMAN	R	1389	ENSP00000285873:Q1389R	ENSP00000285873:Q1389R	Q	-	2	0	GEMIN5	154251090	1.000000	0.71417	1.000000	0.80357	0.119000	0.20118	2.840000	0.48215	1.128000	0.42052	0.533000	0.62120	CAA		0.458	GEMIN5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252507.1			36	56	36	56
GRM4	2914	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	6	33996059	33996059	+	Missense_Mutation	SNP	A	A	C			TCGA-CS-6667-01A-12D-2024-08	TCGA-CS-6667-10A-01D-2024-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0c14ddc3-acf0-4f96-bdb6-eb517d1da522	49ca5323-38a1-4786-b6aa-66de49b053a1	g.chr6:33996059A>C	ENST00000538487.2	-	10	2970	c.2527T>G	c.(2527-2529)Tac>Gac	p.Y843D	GRM4_ENST00000535756.1_Missense_Mutation_p.Y710D|GRM4_ENST00000374181.4_Missense_Mutation_p.Y843D|GRM4_ENST00000609222.1_Missense_Mutation_p.Y710D|GRM4_ENST00000455714.2_Missense_Mutation_p.Y703D|GRM4_ENST00000374177.3_Missense_Mutation_p.Y727D|GRM4_ENST00000545715.1_5'UTR|GRM4_ENST00000544773.2_Missense_Mutation_p.Y674D	NM_000841.2|NM_001256811.1	NP_000832.1|NP_001243740.1	Q14833	GRM4_HUMAN	glutamate receptor, metabotropic 4	843					activation of MAPK activity (GO:0000187)|adenylate cyclase-inhibiting G-protein coupled glutamate receptor signaling pathway (GO:0007196)|learning (GO:0007612)|neurotransmitter secretion (GO:0007269)|positive regulation of MAPK cascade (GO:0043410)|regulation of neuron apoptotic process (GO:0043523)|regulation of synaptic transmission, glutamatergic (GO:0051966)|synaptic transmission (GO:0007268)	cytoplasmic vesicle (GO:0031410)|dendritic shaft (GO:0043198)|integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)|plasma membrane (GO:0005886)|presynaptic active zone membrane (GO:0048787)|presynaptic membrane (GO:0042734)|terminal bouton (GO:0043195)	G-protein coupled receptor activity (GO:0004930)|glutamate receptor activity (GO:0008066)|group III metabotropic glutamate receptor activity (GO:0001642)			NS(1)|breast(1)|endometrium(4)|kidney(4)|large_intestine(9)|liver(1)|lung(19)|ovary(1)|prostate(4)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	48						AGGATGATGTAGACTTTGGGC	0.607																																																0													147.0	130.0	136.0					6																	33996059		2203	4300	6503	SO:0001583	missense	2914			U92457	CCDS4787.1, CCDS59010.1, CCDS59011.1, CCDS59012.1, CCDS75432.1	6p21.3	2012-08-29			ENSG00000124493	ENSG00000124493		"""GPCR / Class C : Glutamate receptors, metabotropic"", ""Glutamate receptors"""	4596	protein-coding gene	gene with protein product		604100				8738157, 9473604	Standard	NM_000841		Approved	GPRC1D, mGlu4, MGLUR4	uc010jvh.4	Q14833	OTTHUMG00000014538	ENST00000538487.2:c.2527T>G	6.37:g.33996059A>C	ENSP00000440556:p.Tyr843Asp		B3KVL9|B7Z1T9|B7Z1U6|F5GXM5|Q5SZ84|Q6ZMQ2	Missense_Mutation	SNP	ENST00000538487.2	37	CCDS4787.1	.	.	.	.	.	.	.	.	.	.	A	20.5	4.004825	0.74932	.	.	ENSG00000124493	ENST00000374181;ENST00000374177;ENST00000545715;ENST00000535756;ENST00000544773;ENST00000538487;ENST00000455714	D;D;D;D;D;D;D	0.90504	-2.68;-2.68;-2.68;-2.68;-2.68;-2.68;-2.68	4.18	4.18	0.49190	GPCR, family 3, C-terminal (2);	0.178204	0.37906	N	0.001895	D	0.95326	0.8483	M	0.92219	3.285	0.80722	D	1	D;D;P;P;D	0.62365	0.981;0.991;0.835;0.713;0.972	D;D;B;B;D	0.68943	0.936;0.947;0.429;0.437;0.961	D	0.96272	0.9199	10	0.87932	D	0	.	13.3834	0.60783	1.0:0.0:0.0:0.0	.	796;674;703;843;710	B7ZLU9;B7Z1T9;F5GXM5;Q14833;B3KVL9	.;.;.;GRM4_HUMAN;.	D	843;727;535;710;674;843;703	ENSP00000363296:Y843D;ENSP00000363292:Y727D;ENSP00000445533:Y535D;ENSP00000437925:Y710D;ENSP00000437730:Y674D;ENSP00000440556:Y843D;ENSP00000398456:Y703D	ENSP00000363292:Y727D	Y	-	1	0	GRM4	34104037	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	7.262000	0.78410	1.754000	0.51921	0.391000	0.25812	TAC		0.607	GRM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040213.2			56	80	56	80
RARRES2	5919	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	7	150037192	150037192	+	Silent	SNP	A	A	G			TCGA-CS-6667-01A-12D-2024-08	TCGA-CS-6667-10A-01D-2024-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0c14ddc3-acf0-4f96-bdb6-eb517d1da522	49ca5323-38a1-4786-b6aa-66de49b053a1	g.chr7:150037192A>G	ENST00000466675.1	-	2	1309	c.276T>C	c.(274-276)aaT>aaC	p.N92N	RARRES2_ENST00000482669.1_Silent_p.N92N|RARRES2_ENST00000223271.3_Silent_p.N92N|RP4-584D14.7_ENST00000563946.1_RNA			Q99969	RARR2_HUMAN	retinoic acid receptor responder (tazarotene induced) 2	92					brown fat cell differentiation (GO:0050873)|chemotaxis (GO:0006935)|embryonic digestive tract development (GO:0048566)|in utero embryonic development (GO:0001701)|inflammatory response (GO:0006954)|positive regulation of chemotaxis (GO:0050921)|positive regulation of fat cell differentiation (GO:0045600)|positive regulation of glucose import in response to insulin stimulus (GO:2001275)|positive regulation of macrophage chemotaxis (GO:0010759)|positive regulation of protein phosphorylation (GO:0001934)|regulation of lipid catabolic process (GO:0050994)|retinoid metabolic process (GO:0001523)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	receptor binding (GO:0005102)			endometrium(1)|large_intestine(1)|lung(1)|pancreas(1)|skin(1)	5			OV - Ovarian serous cystadenocarcinoma(82;0.011)			CACTCACCCCATTGGGCCTGA	0.567																																																0													411.0	422.0	418.0					7																	150037192		2203	4300	6503	SO:0001819	synonymous_variant	5919			U77594	CCDS5902.1	7q36.1	2013-02-25			ENSG00000106538	ENSG00000106538		"""Endogenous ligands"""	9868	protein-coding gene	gene with protein product	"""chemerin"""	601973				9270552, 17767914	Standard	NM_002889		Approved	TIG2, HP10433	uc003wha.3	Q99969	OTTHUMG00000158325	ENST00000466675.1:c.276T>C	7.37:g.150037192A>G			Q7LE02	Silent	SNP	ENST00000466675.1	37	CCDS5902.1																																																																																				0.567	RARRES2-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350693.1			237	389	237	389
KCNU1	157855	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	8	36694322	36694322	+	Silent	SNP	A	A	G			TCGA-CS-6667-01A-12D-2024-08	TCGA-CS-6667-10A-01D-2024-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0c14ddc3-acf0-4f96-bdb6-eb517d1da522	49ca5323-38a1-4786-b6aa-66de49b053a1	g.chr8:36694322A>G	ENST00000399881.3	+	14	1414	c.1377A>G	c.(1375-1377)ccA>ccG	p.P459P		NM_001031836.2	NP_001027006.2	A8MYU2	KCNU1_HUMAN	potassium channel, subfamily U, member 1	459	RCK N-terminal.				multicellular organism reproduction (GO:0032504)|potassium ion transmembrane transport (GO:0071805)|single fertilization (GO:0007338)|sperm-egg recognition (GO:0035036)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	large conductance calcium-activated potassium channel activity (GO:0060072)|potassium channel activity (GO:0005267)|voltage-gated potassium channel activity (GO:0005249)			breast(4)|central_nervous_system(1)|cervix(1)|endometrium(8)|kidney(1)|large_intestine(9)|lung(31)|ovary(1)|urinary_tract(1)	57				KIRC - Kidney renal clear cell carcinoma(67;0.0504)|Kidney(114;0.0634)		TTTATCTGCCAAAGATTCCCA	0.423																																																0													102.0	102.0	102.0					8																	36694322		1856	4120	5976	SO:0001819	synonymous_variant	157855			BC028701	CCDS55220.1	8p11.2	2012-07-05				ENSG00000215262		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels, calcium-activated"""	18867	protein-coding gene	gene with protein product		615215				16382103	Standard	NM_001031836		Approved	KCa5.1, Slo3, KCNMC1, Kcnma3	uc010lvw.3	A8MYU2		ENST00000399881.3:c.1377A>G	8.37:g.36694322A>G				Silent	SNP	ENST00000399881.3	37	CCDS55220.1																																																																																				0.423	KCNU1-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376631.1	NM_001031836		16	41	16	41
WWC3	55841	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	X	10106879	10106879	+	Missense_Mutation	SNP	G	G	A			TCGA-CS-6667-01A-12D-2024-08	TCGA-CS-6667-10A-01D-2024-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0c14ddc3-acf0-4f96-bdb6-eb517d1da522	49ca5323-38a1-4786-b6aa-66de49b053a1	g.chrX:10106879G>A	ENST00000380861.4	+	21	3378	c.2987G>A	c.(2986-2988)cGg>cAg	p.R996Q	WWC3_ENST00000454666.1_Missense_Mutation_p.R996Q	NM_015691.3	NP_056506.2	Q9ULE0	WWC3_HUMAN	WWC family member 3	996					negative regulation of hippo signaling (GO:0035331)|negative regulation of organ growth (GO:0046621)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)	cytosol (GO:0005829)	kinase binding (GO:0019900)|protein complex scaffold (GO:0032947)			NS(1)|breast(3)|endometrium(10)|kidney(1)|large_intestine(11)|lung(17)|ovary(5)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	52						CTGCGGCAGCGGTTGGAGGAC	0.701																																																0													27.0	24.0	25.0					X																	10106879		2203	4294	6497	SO:0001583	missense	55841			AK091936	CCDS14136.1	Xp22.32	2008-02-05			ENSG00000047644	ENSG00000047644		"""WW, C2 and coiled-coil domain containing"""	29237	protein-coding gene	gene with protein product						10574462	Standard	NM_015691		Approved	KIAA1280, BM042	uc004csx.4	Q9ULE0	OTTHUMG00000021123	ENST00000380861.4:c.2987G>A	X.37:g.10106879G>A	ENSP00000370242:p.Arg996Gln		A8KA96|Q659C1|Q9BTQ1	Missense_Mutation	SNP	ENST00000380861.4	37	CCDS14136.1	.	.	.	.	.	.	.	.	.	.	G	14.63	2.592130	0.46214	.	.	ENSG00000047644	ENST00000380861;ENST00000454666;ENST00000543412	T;T	0.39997	1.05;1.05	5.2	4.32	0.51571	.	0.051598	0.85682	N	0.000000	T	0.38719	0.1051	L	0.43152	1.355	0.48762	D	0.999709	P	0.49862	0.929	B	0.43701	0.428	T	0.12785	-1.0534	9	.	.	.	-12.6578	14.495	0.67680	0.0:0.0:0.8518:0.1482	.	996	Q9ULE0	WWC3_HUMAN	Q	996;996;491	ENSP00000370242:R996Q;ENSP00000399584:R996Q	.	R	+	2	0	WWC3	10066879	1.000000	0.71417	0.419000	0.26584	0.435000	0.31806	9.495000	0.97964	1.064000	0.40671	0.436000	0.28706	CGG		0.701	WWC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055725.1	NM_015691		12	20	12	20
POLA1	5422	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	X	24753561	24753561	+	Missense_Mutation	SNP	T	T	A			TCGA-CS-6667-01A-12D-2024-08	TCGA-CS-6667-10A-01D-2024-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0c14ddc3-acf0-4f96-bdb6-eb517d1da522	49ca5323-38a1-4786-b6aa-66de49b053a1	g.chrX:24753561T>A	ENST00000379059.3	+	18	1876	c.1861T>A	c.(1861-1863)Ttt>Att	p.F621I	POLA1_ENST00000379068.3_Missense_Mutation_p.F627I	NM_016937.3	NP_058633.2	P09884	DPOLA_HUMAN	polymerase (DNA directed), alpha 1, catalytic subunit	621					cell proliferation (GO:0008283)|DNA replication (GO:0006260)|DNA replication initiation (GO:0006270)|DNA replication, synthesis of RNA primer (GO:0006269)|DNA strand elongation involved in DNA replication (GO:0006271)|double-strand break repair via nonhomologous end joining (GO:0006303)|G1/S transition of mitotic cell cycle (GO:0000082)|lagging strand elongation (GO:0006273)|leading strand elongation (GO:0006272)|mitotic cell cycle (GO:0000278)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)|telomere maintenance (GO:0000723)|telomere maintenance via recombination (GO:0000722)|telomere maintenance via semi-conservative replication (GO:0032201)|translesion synthesis (GO:0019985)|viral process (GO:0016032)	alpha DNA polymerase:primase complex (GO:0005658)|cytoplasm (GO:0005737)|nuclear envelope (GO:0005635)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	3'-5' exonuclease activity (GO:0008408)|4 iron, 4 sulfur cluster binding (GO:0051539)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA-directed DNA polymerase activity (GO:0003887)|metal ion binding (GO:0046872)|nucleoside binding (GO:0001882)|nucleotide binding (GO:0000166)|protein kinase binding (GO:0019901)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|ovary(2)|skin(2)	11					Cladribine(DB00242)|Clofarabine(DB00631)|Fludarabine(DB01073)|Nelarabine(DB01280)	ACTGCTAGGTTTTTTCCTTGC	0.393																																																0													168.0	149.0	155.0					X																	24753561		2203	4300	6503	SO:0001583	missense	5422				CCDS14214.1	Xp22.1-p21.3	2014-01-30	2008-08-07	2006-09-26	ENSG00000101868	ENSG00000101868	2.7.7.7	"""DNA polymerases"""	9173	protein-coding gene	gene with protein product		312040	"""polymerase (DNA directed), alpha"", ""polymerase (DNA directed), alpha 1"", ""N syndrome (mental retardation, malformations, chromosome breakage)"""	POLA, NSX		1689958	Standard	NM_016937		Approved	p180	uc004dbl.3	P09884	OTTHUMG00000021277	ENST00000379059.3:c.1861T>A	X.37:g.24753561T>A	ENSP00000368349:p.Phe621Ile		Q86UQ7	Missense_Mutation	SNP	ENST00000379059.3	37	CCDS14214.1	.	.	.	.	.	.	.	.	.	.	T	28.7	4.939503	0.92526	.	.	ENSG00000101868	ENST00000379068;ENST00000379059	T;T	0.42131	0.98;0.98	4.76	4.76	0.60689	DNA-directed DNA polymerase, family B, exonuclease domain (1);Ribonuclease H-like (1);	0.000000	0.85682	D	0.000000	T	0.60932	0.2307	M	0.79475	2.455	0.80722	D	1	D	0.63880	0.993	D	0.65874	0.939	T	0.60209	-0.7308	10	0.22109	T	0.4	-12.8592	13.608	0.62058	0.0:0.0:0.0:1.0	.	621	P09884	DPOLA_HUMAN	I	627;621	ENSP00000368358:F627I;ENSP00000368349:F621I	ENSP00000368349:F621I	F	+	1	0	POLA1	24663482	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	7.201000	0.77847	1.855000	0.53841	0.417000	0.27973	TTT		0.393	POLA1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000056111.1	NM_016937		33	66	33	66
DCAF8L1	139425	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	X	27999088	27999088	+	Nonsense_Mutation	SNP	G	G	A			TCGA-CS-6667-01A-12D-2024-08	TCGA-CS-6667-10A-01D-2024-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0c14ddc3-acf0-4f96-bdb6-eb517d1da522	49ca5323-38a1-4786-b6aa-66de49b053a1	g.chrX:27999088G>A	ENST00000441525.1	-	1	478	c.364C>T	c.(364-366)Cga>Tga	p.R122*		NM_001017930.1	NP_001017930.1	A6NGE4	DC8L1_HUMAN	DDB1 and CUL4 associated factor 8-like 1	122										NS(1)|breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(10)|lung(24)|ovary(3)|prostate(1)|skin(4)|stomach(1)|urinary_tract(1)	56						CCACCGCATCGTGGACACATC	0.547																																																0													152.0	81.0	105.0					X																	27999088		2202	4300	6502	SO:0001587	stop_gained	139425				CCDS35222.1	Xp22.11	2013-01-09	2009-07-17	2009-07-17	ENSG00000226372	ENSG00000226372		"""WD repeat domain containing"""	31810	protein-coding gene	gene with protein product			"""WD repeat domain 42B"""	WDR42B			Standard	NM_001017930		Approved		uc004dbx.1	A6NGE4	OTTHUMG00000021312	ENST00000441525.1:c.364C>T	X.37:g.27999088G>A	ENSP00000405222:p.Arg122*		B3KXX1	Nonsense_Mutation	SNP	ENST00000441525.1	37	CCDS35222.1	.	.	.	.	.	.	.	.	.	.	G	17.00	3.277700	0.59758	.	.	ENSG00000226372	ENST00000441525	.	.	.	0.842	-0.524	0.11920	.	0.757589	0.12065	N	0.502793	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.40728	T	0.16	-3.1887	5.985	0.19430	0.0:0.3252:0.6748:0.0	.	.	.	.	X	122	.	ENSP00000405222:R122X	R	-	1	2	DCAF8L1	27909009	0.980000	0.34600	0.001000	0.08648	0.049000	0.14656	3.345000	0.52182	-0.217000	0.10033	0.284000	0.19432	CGA		0.547	DCAF8L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056150.2	XM_066690		14	28	14	28
ZNF157	7712	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	X	47272249	47272249	+	Silent	SNP	A	A	C			TCGA-CS-6667-01A-12D-2024-08	TCGA-CS-6667-10A-01D-2024-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0c14ddc3-acf0-4f96-bdb6-eb517d1da522	49ca5323-38a1-4786-b6aa-66de49b053a1	g.chrX:47272249A>C	ENST00000377073.3	+	4	863	c.777A>C	c.(775-777)gcA>gcC	p.A259A		NM_003446.3	NP_003437.2	P51786	ZN157_HUMAN	zinc finger protein 157	259					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|endometrium(2)|large_intestine(2)|lung(5)|upper_aerodigestive_tract(1)	11						CTGAGAAGGCAACCCTCACGA	0.438																																																0													59.0	51.0	54.0					X																	47272249		2203	4300	6503	SO:0001819	synonymous_variant	7712			U28687	CCDS14278.1	Xp11.2	2013-01-08	2006-08-22		ENSG00000147117	ENSG00000147117		"""Zinc fingers, C2H2-type"", ""-"""	12942	protein-coding gene	gene with protein product		300024	"""zinc finger protein 157 (HZF22)"""			8586441	Standard	NM_003446		Approved	HZF22	uc004dhr.1	P51786	OTTHUMG00000021443	ENST00000377073.3:c.777A>C	X.37:g.47272249A>C			Q96LE9	Silent	SNP	ENST00000377073.3	37	CCDS14278.1																																																																																				0.438	ZNF157-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056415.1	NM_003446		7	27	7	27
KCND1	3750	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	X	48826090	48826090	+	Missense_Mutation	SNP	C	C	T			TCGA-CS-6667-01A-12D-2024-08	TCGA-CS-6667-10A-01D-2024-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0c14ddc3-acf0-4f96-bdb6-eb517d1da522	49ca5323-38a1-4786-b6aa-66de49b053a1	g.chrX:48826090C>T	ENST00000218176.3	-	1	1886	c.589G>A	c.(589-591)Gcc>Acc	p.A197T	KCND1_ENST00000376477.1_5'Flank	NM_004979.4	NP_004970.3	Q9NSA2	KCND1_HUMAN	potassium voltage-gated channel, Shal-related subfamily, member 1	197					protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)	cell projection (GO:0042995)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|metal ion binding (GO:0046872)			endometrium(3)|large_intestine(7)|lung(7)|ovary(2)|prostate(1)|skin(1)|soft_tissue(1)|upper_aerodigestive_tract(2)	24					Dalfampridine(DB06637)	ACCGACACGGCGATGAAGAAG	0.642													c|||	1	0.000264901	0.0008	0.0	3775	,	,		13183	0.0		0.0	False		,,,				2504	0.0															0													17.0	16.0	16.0					X																	48826090		2199	4297	6496	SO:0001583	missense	3750			AF166003	CCDS14314.1	Xp11.23	2012-07-05			ENSG00000102057	ENSG00000102057		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	6237	protein-coding gene	gene with protein product		300281				10729221, 16382104	Standard	NM_004979		Approved	Kv4.1	uc004dlx.1	Q9NSA2	OTTHUMG00000024127	ENST00000218176.3:c.589G>A	X.37:g.48826090C>T	ENSP00000218176:p.Ala197Thr		A6NEF1|B2RCG0|O75671	Missense_Mutation	SNP	ENST00000218176.3	37	CCDS14314.1	.	.	.	.	.	.	.	.	.	.	C	21.5	4.152276	0.78001	.	.	ENSG00000102057	ENST00000218176	D	0.97505	-4.41	5.45	5.45	0.79879	.	0.056253	0.64402	D	0.000001	D	0.95105	0.8414	L	0.60904	1.88	0.80722	D	1	P	0.47677	0.899	B	0.36808	0.233	D	0.95200	0.8316	10	0.49607	T	0.09	.	17.0203	0.86432	0.0:1.0:0.0:0.0	.	197	Q9NSA2	KCND1_HUMAN	T	197	ENSP00000218176:A197T	ENSP00000218176:A197T	A	-	1	0	KCND1	48711034	1.000000	0.71417	0.751000	0.31187	0.929000	0.56500	5.999000	0.70665	2.282000	0.76494	0.594000	0.82650	GCC		0.642	KCND1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060774.1	NM_004979		11	8	11	8
OPCML	4978	broad.mit.edu;ucsc.edu	37	11	132527046	132527046	+	Silent	SNP	C	C	T	rs369569350		TCGA-CS-6667-01A-12D-2024-08	TCGA-CS-6667-10A-01D-2024-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0c14ddc3-acf0-4f96-bdb6-eb517d1da522	49ca5323-38a1-4786-b6aa-66de49b053a1	g.chr11:132527046C>T	ENST00000331898.7	-	2	914	c.336G>A	c.(334-336)ccG>ccA	p.P112P	OPCML_ENST00000529038.1_5'UTR|OPCML_ENST00000524381.1_Silent_p.P105P|OPCML_ENST00000541867.1_Silent_p.P112P|OPCML_ENST00000374778.4_Silent_p.P71P	NM_002545.3	NP_002536.1	Q14982	OPCM_HUMAN	opioid binding protein/cell adhesion molecule-like	112	Ig-like C2-type 1.				cell adhesion (GO:0007155)|neuron recognition (GO:0008038)|opioid receptor signaling pathway (GO:0038003)	anchored component of membrane (GO:0031225)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	opioid receptor activity (GO:0004985)			endometrium(5)|kidney(1)|large_intestine(12)|lung(17)|ovary(2)|skin(2)|urinary_tract(8)	47	all_hematologic(175;0.019)	all_cancers(12;5.86e-24)|all_epithelial(12;2.65e-17)|all_lung(97;2.89e-05)|Lung NSC(97;6.16e-05)|Breast(109;0.000126)|Medulloblastoma(222;0.0269)|all_neural(223;0.0326)|Esophageal squamous(93;0.129)		all cancers(11;4.61e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.012)		AGCAGGTGTACGGACCTTCGT	0.502																																																0								C	,	0,4402		0,0,2201	252.0	197.0	216.0		315,336	-11.7	0.0	11		216	1,8593	1.2+/-3.3	0,1,4296	no	coding-synonymous,coding-synonymous	OPCML	NM_001012393.1,NM_002545.3	,	0,1,6497	TT,TC,CC		0.0116,0.0,0.0077	,	105/339,112/346	132527046	1,12995	2201	4297	6498	SO:0001819	synonymous_variant	4978			BX537377	CCDS8492.1, CCDS31722.1	11q25	2013-01-11	2001-11-28		ENSG00000183715	ENSG00000183715		"""Immunoglobulin superfamily / I-set domain containing"""	8143	protein-coding gene	gene with protein product	"""IgLON family member 1"""	600632	"""opioid-binding protein/cell adhesion molecule-like"""			8244387	Standard	XM_005271578		Approved	OPCM, OBCAM, IGLON1	uc001qgs.3	Q14982	OTTHUMG00000163658	ENST00000331898.7:c.336G>A	11.37:g.132527046C>T			B2CZX2|B7ZLQ1|Q17RN7|Q7Z3W6	Silent	SNP	ENST00000331898.7	37	CCDS8492.1																																																																																				0.502	OPCML-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374689.3	NM_001012393		20	61	20	61
IL17REL	400935	broad.mit.edu;ucsc.edu	37	22	50435799	50435799	+	Silent	SNP	G	G	A			TCGA-CS-6667-01A-12D-2024-08	TCGA-CS-6667-10A-01D-2024-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0c14ddc3-acf0-4f96-bdb6-eb517d1da522	49ca5323-38a1-4786-b6aa-66de49b053a1	g.chr22:50435799G>A	ENST00000389983.2	-	13	1188	c.924C>T	c.(922-924)agC>agT	p.S308S	IL17REL_ENST00000341280.5_Silent_p.S308S	NM_001001694.2	NP_001001694.2	Q6ZVW7	I17EL_HUMAN	interleukin 17 receptor E-like	308										endometrium(1)|large_intestine(1)|lung(3)|pancreas(1)	6		all_cancers(38;5.53e-07)|all_epithelial(38;3.84e-06)|all_lung(38;0.00208)|Breast(42;0.0104)|Lung NSC(38;0.0199)|Ovarian(80;0.0907)|Lung SC(80;0.236)		BRCA - Breast invasive adenocarcinoma(115;0.2)|LUAD - Lung adenocarcinoma(64;0.247)		CAGGCAGGGAGCTGTGACTTC	0.667																																																0													79.0	69.0	73.0					22																	50435799		2203	4300	6503	SO:0001819	synonymous_variant	400935			AK123987	CCDS33679.1	22q13.33	2009-01-13			ENSG00000188263	ENSG00000188263			33808	protein-coding gene	gene with protein product		613414					Standard	NM_001001694		Approved	FLJ41993	uc003bje.1	Q6ZVW7	OTTHUMG00000150242	ENST00000389983.2:c.924C>T	22.37:g.50435799G>A			A6NCN4|A6PVC1	Silent	SNP	ENST00000389983.2	37	CCDS33679.1																																																																																				0.667	IL17REL-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317011.1	NM_001001694		6	33	6	33
VPS13C	54832	broad.mit.edu;hgsc.bcm.edu	37	15	62302761	62302776	+	Frame_Shift_Del	DEL	CATGTAGAGTTTTGCA	CATGTAGAGTTTTGCA	-	rs199504742|rs566277100		TCGA-CS-6667-01A-12D-2024-08	TCGA-CS-6667-10A-01D-2024-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0c14ddc3-acf0-4f96-bdb6-eb517d1da522	49ca5323-38a1-4786-b6aa-66de49b053a1	g.chr15:62302761_62302776delCATGTAGAGTTTTGCA	ENST00000261517.5	-	13	979_994	c.906_921delTGCAAAACTCTACATG	c.(904-921)tctgcaaaactctacatgfs	p.SAKLYM302fs	VPS13C_ENST00000249837.3_Frame_Shift_Del_p.SAKLYM259fs|VPS13C_ENST00000395896.4_Frame_Shift_Del_p.SAKLYM302fs|VPS13C_ENST00000395898.3_Frame_Shift_Del_p.SAKLYM259fs	NM_020821.2	NP_065872.1			vacuolar protein sorting 13 homolog C (S. cerevisiae)											NS(3)|breast(4)|endometrium(4)|kidney(9)|large_intestine(26)|lung(46)|ovary(5)|prostate(6)|skin(6)|stomach(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	117						CATAAGGATTCATGTAGAGTTTTGCAGAGGCTGATA	0.352																																																0																																										SO:0001589	frameshift_variant	54832			AJ608770	CCDS10180.1, CCDS32257.1, CCDS45272.1, CCDS58367.1	15q21.3	2009-07-09	2006-04-04		ENSG00000129003	ENSG00000129003			23594	protein-coding gene	gene with protein product		608879	"""vacuolar protein sorting 13C (yeast)"""				Standard	NM_018080		Approved	FLJ20136, FLJ10381, KIAA1421	uc002agz.3	Q709C8	OTTHUMG00000132801	ENST00000261517.5:c.906_921delTGCAAAACTCTACATG	15.37:g.62302761_62302776delCATGTAGAGTTTTGCA	ENSP00000261517:p.Ser302fs			Frame_Shift_Del	DEL	ENST00000261517.5	37	CCDS32257.1																																																																																				0.352	VPS13C-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000415997.1	NM_017684		17	58	17	58
SMARCA4	6597	broad.mit.edu	37	19	11143993	11143993	+	Missense_Mutation	SNP	C	C	T			TCGA-CS-6667-01A-12D-2024-08	TCGA-CS-6667-10A-01D-2024-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0c14ddc3-acf0-4f96-bdb6-eb517d1da522	49ca5323-38a1-4786-b6aa-66de49b053a1	g.chr19:11143993C>T	ENST00000429416.3	+	27	3855	c.3574C>T	c.(3574-3576)Cgc>Tgc	p.R1192C	SMARCA4_ENST00000358026.2_Missense_Mutation_p.R1192C|SMARCA4_ENST00000450717.3_Missense_Mutation_p.R1192C|SMARCA4_ENST00000413806.3_Missense_Mutation_p.R1192C|SMARCA4_ENST00000344626.4_Missense_Mutation_p.R1192C|SMARCA4_ENST00000444061.3_Missense_Mutation_p.R1192C|SMARCA4_ENST00000541122.2_Missense_Mutation_p.R1192C|SMARCA4_ENST00000589677.1_Missense_Mutation_p.R1192C|SMARCA4_ENST00000590574.1_Missense_Mutation_p.R1192C	NM_001128844.1	NP_001122316.1	P51532	SMCA4_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4	1192	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.				aortic smooth muscle cell differentiation (GO:0035887)|ATP catabolic process (GO:0006200)|ATP-dependent chromatin remodeling (GO:0043044)|blastocyst growth (GO:0001832)|blastocyst hatching (GO:0001835)|cell morphogenesis (GO:0000902)|chromatin remodeling (GO:0006338)|definitive erythrocyte differentiation (GO:0060318)|DNA methylation on cytosine within a CG sequence (GO:0010424)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic organ morphogenesis (GO:0048562)|epidermis morphogenesis (GO:0048730)|extracellular matrix organization (GO:0030198)|forebrain development (GO:0030900)|glial cell fate determination (GO:0007403)|heart trabecula formation (GO:0060347)|hindbrain development (GO:0030902)|histone H3 acetylation (GO:0043966)|keratinocyte differentiation (GO:0030216)|lens fiber cell development (GO:0070307)|liver development (GO:0001889)|methylation-dependent chromatin silencing (GO:0006346)|negative regulation of androgen receptor signaling pathway (GO:0060766)|negative regulation of cell growth (GO:0030308)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription from RNA polymerase II promoter during mitosis (GO:0007070)|negative regulation of transcription, DNA-templated (GO:0045892)|neural retina development (GO:0003407)|nucleosome disassembly (GO:0006337)|positive regulation by host of viral transcription (GO:0043923)|positive regulation of DNA binding (GO:0043388)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|stem cell maintenance (GO:0019827)|vasculogenesis (GO:0001570)	extracellular space (GO:0005615)|heterochromatin (GO:0000792)|membrane (GO:0016020)|nBAF complex (GO:0071565)|npBAF complex (GO:0071564)|nuclear chromatin (GO:0000790)|nuclear euchromatin (GO:0005719)|nucleolus (GO:0005730)|nucleus (GO:0005634)|perichromatin fibrils (GO:0005726)|protein complex (GO:0043234)|SWI/SNF complex (GO:0016514)	androgen receptor binding (GO:0050681)|ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA-dependent ATPase activity (GO:0008094)|helicase activity (GO:0004386)|lysine-acetylated histone binding (GO:0070577)|p53 binding (GO:0002039)|protein N-terminus binding (GO:0047485)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription coactivator activity (GO:0001105)|Tat protein binding (GO:0030957)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)	p.R1192C(1)|p.?(1)		adrenal_gland(1)|autonomic_ganglia(1)|breast(6)|central_nervous_system(23)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(16)|liver(4)|lung(60)|ovary(10)|pancreas(7)|prostate(3)|skin(8)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	163		all_lung(6;0.0512)|Lung NSC(9;0.0568)				CCGAGCCCACCGCATCGGGCA	0.607			"""F, N, Mis"""		NSCLC																																		Rec	yes		19	19p13.2	6597	"""SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4"""		E	2	Substitution - Missense(1)|Unknown(1)	lung(1)|central_nervous_system(1)											61.0	61.0	61.0					19																	11143993		2203	4300	6503	SO:0001583	missense	6597			D26156	CCDS12253.1, CCDS45972.1, CCDS45973.1, CCDS54217.1, CCDS54218.1	19p13.3	2014-09-17	2006-11-09		ENSG00000127616	ENSG00000127616			11100	protein-coding gene	gene with protein product	"""SNF2-like 4"", ""global transcription activator homologous sequence"", ""sucrose nonfermenting-like 4"", ""mitotic growth and transcription activator"", ""BRM/SWI2-related gene 1"", ""homeotic gene regulator"", ""nuclear protein GRB1"", ""brahma protein-like 1"", ""ATP-dependent helicase SMARCA4"""	603254		SNF2L4		8208605	Standard	NM_003072		Approved	hSNF2b, BRG1, BAF190, SNF2, SWI2, SNF2-BETA, SNF2LB, FLJ39786	uc010dxo.3	P51532	OTTHUMG00000169272	ENST00000429416.3:c.3574C>T	19.37:g.11143993C>T	ENSP00000395654:p.Arg1192Cys		B1A8Z4|B1A8Z5|B1A8Z6|B1A8Z7|E9PBR8|O95052|Q9HBD3	Missense_Mutation	SNP	ENST00000429416.3	37	CCDS12253.1	.	.	.	.	.	.	.	.	.	.	C	24.2	4.507268	0.85282	.	.	ENSG00000127616	ENST00000429416;ENST00000358026;ENST00000421844;ENST00000344626;ENST00000541122;ENST00000444061;ENST00000450717;ENST00000413806	D;D;D;D;D;D;D	0.97888	-4.59;-4.59;-4.59;-4.59;-4.59;-4.59;-4.59	4.74	4.74	0.60224	Helicase, C-terminal (3);	0.000000	0.85682	D	0.000000	D	0.99498	0.9821	H	0.99982	5.21	0.80722	D	1	D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D;D	0.97110	1.0;1.0;1.0;1.0;1.0;1.0;1.0	D	0.97352	0.9964	10	0.87932	D	0	-34.1151	16.7067	0.85374	0.0:1.0:0.0:0.0	.	1192;1192;1192;1192;1192;412;1192	B1A8Z6;B1A8Z4;B1A8Z7;Q9HBD4;B1A8Z5;B4E0F1;P51532	.;.;.;.;.;.;SMCA4_HUMAN	C	1192;1192;1256;1192;1192;1192;1192;1192	ENSP00000395654:R1192C;ENSP00000350720:R1192C;ENSP00000343896:R1192C;ENSP00000445036:R1192C;ENSP00000392837:R1192C;ENSP00000397783:R1192C;ENSP00000414727:R1192C	ENSP00000343896:R1192C	R	+	1	0	SMARCA4	11004993	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	5.675000	0.68123	2.488000	0.83962	0.558000	0.71614	CGC		0.607	SMARCA4-007	KNOWN	alternative_5_UTR|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000452638.2	NM_003072		8	42	8	42
