#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_Annotation_Transcript	i_CCLE_ONCOMAP_overlapping_mutations	i_CCLE_ONCOMAP_total_mutations_in_gene	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_Mutation_Type	i_CGC_Name	i_CGC_Other Germline Mut	i_CGC_Other_Diseases	i_CGC_Tissue Type	i_CGC_Translocation_Partner	i_CGC_Tumor_Types_Germline	i_CGC_Tumor_Types_Somatic	i_COSMIC_fusion_genes	i_COSMIC_n_overlapping_mutations	i_COSMIC_overlapping_mutation_descriptions	i_COSMIC_overlapping_mutations	i_COSMIC_overlapping_primary_sites	i_COSMIC_tissue_types_affected	i_COSMIC_total_alterations_in_gene	i_ClinVar_ASSEMBLY	i_ClinVar_HGMD_ID	i_ClinVar_SYM	i_ClinVar_TYPE	i_ClinVar_rs	i_Codon_Change	i_DNARepairGenes_Role	i_Description	i_DrugBank	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_FamilialCancerDatabase_Syndromes	i_Familial_Cancer_Genes_Reference	i_Familial_Cancer_Genes_Synonym	i_GO_Biological_Process	i_GO_Cellular_Component	i_GO_Molecular_Function	i_Genome_Change	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_MUTSIG_Published_Results	i_OREGANNO_ID	i_OREGANNO_Values	i_ORegAnno_bin	i_Other_Transcripts	i_Protein_Change	i_Refseq_mRNA_Id	i_Refseq_prot_Id	i_SwissProt_acc_Id	i_SwissProt_entry_Id	i_TCGAscape_Amplification_Peaks	i_TCGAscape_Deletion_Peaks	i_Transcript_Exon	i_Transcript_Position	i_Transcript_Strand	i_Tumorscape_Amplification_Peaks	i_Tumorscape_Deletion_Peaks	i_UniProt_AApos	i_UniProt_Experimental_Info	i_UniProt_Natural_Variations	i_UniProt_Region	i_UniProt_Site	i_UniProt_alt_uniprot_accessions	i_Variant_Classification	i_Variant_Type	i_annotation_transcript	i_build	i_cDNA_Change	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	isArtifactMode	oxoGCut	pox	pox_cutoff	qox	t_alt_count	t_ref_count	validation_alt_allele	validation_method	validation_status	validation_tumor_sample
PRDM14	63978	broad.mit.edu	37	8	70978498	70978498	+	Silent	SNP	C	C	T			TCGA-DU-7018-01A-11D-2024-08	TCGA-DU-7018-10A-01D-2024-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	29c55a80-cd55-4297-b433-00d0e2b1e08d	453998d9-d9f9-479d-86c0-d889a58b836d	g.chr8:70978498C>T	ENST00000276594.2	-	5	1356	c.1155G>A	c.(1153-1155)ccG>ccA	p.P385P		NM_024504.3	NP_078780.1	Q9GZV8	PRD14_HUMAN	PR domain containing 14	385					cell fate specification (GO:0001708)|cell morphogenesis (GO:0000902)|fertilization (GO:0009566)|germ cell development (GO:0007281)|germ-line stem cell maintenance (GO:0030718)|histone H3-R26 methylation (GO:0034972)|homeostasis of number of cells within a tissue (GO:0048873)|inner cell mass cell fate commitment (GO:0001827)|negative regulation of fibroblast growth factor receptor signaling pathway (GO:0040037)|regulation of DNA methylation (GO:0044030)|regulation of gene expression, epigenetic (GO:0040029)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|methyltransferase activity (GO:0008168)			NS(1)|endometrium(4)|kidney(4)|large_intestine(3)|lung(13)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	32	Breast(64;0.193)		Epithelial(68;0.00508)|all cancers(69;0.0259)|OV - Ovarian serous cystadenocarcinoma(28;0.0405)			GCTGCTTCCCCGGCTCTGTGA	0.537																																					NSCLC(129;99 1813 5906 40656 46114)	ENST00000276594.2																			0				NS(1)|endometrium(4)|kidney(4)|large_intestine(3)|lung(13)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	32						c.(1153-1155)ccG>ccA		PR domain containing 14							63.0	66.0	65.0					8																	70978498		2203	4300	6503	SO:0001819	synonymous_variant	63978				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding	g.chr8:70978498C>T	AF319458	CCDS6206.1	8q13.3	2013-01-08			ENSG00000147596	ENSG00000147596		"""Zinc fingers, C2H2-type"""	14001	protein-coding gene	gene with protein product		611781					Standard	NM_024504		Approved		uc003xym.3	Q9GZV8	OTTHUMG00000150495	ENST00000276594.2:c.1155G>A	8.37:g.70978498C>T							p.P385P	NM_024504.3	NP_078780.1	Q9GZV8	PRD14_HUMAN	Epithelial(68;0.00508)|all cancers(69;0.0259)|OV - Ovarian serous cystadenocarcinoma(28;0.0405)		5	1356	-	Breast(64;0.193)		385					Q86UX9	Silent	SNP	ENST00000276594.2	37	c.1155G>A	CCDS6206.1																																																																																				0.537	PRDM14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318505.1			8	76	0	0	0	0.047766	0	8	76				
PPP1R3A	5506	broad.mit.edu	37	7	113517991	113517991	+	Silent	SNP	A	A	G			TCGA-DU-7018-01A-11D-2024-08	TCGA-DU-7018-10A-01D-2024-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	29c55a80-cd55-4297-b433-00d0e2b1e08d	453998d9-d9f9-479d-86c0-d889a58b836d	g.chr7:113517991A>G	ENST00000284601.3	-	4	3224	c.3156T>C	c.(3154-3156)acT>acC	p.T1052T		NM_002711.3	NP_002702.2	Q16821	PPR3A_HUMAN	protein phosphatase 1, regulatory subunit 3A	1052					glycogen metabolic process (GO:0005977)	integral component of membrane (GO:0016021)				NS(2)|breast(8)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(14)|liver(1)|lung(43)|ovary(10)|pancreas(7)|prostate(3)|skin(15)|stomach(1)|upper_aerodigestive_tract(2)	121						CAGGAAGACTAGTAGAAGCAG	0.368																																						ENST00000284601.3																			0				NS(2)|breast(8)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(14)|liver(1)|lung(43)|ovary(10)|pancreas(7)|prostate(3)|skin(15)|stomach(1)|upper_aerodigestive_tract(2)	121						c.(3154-3156)acT>acC		protein phosphatase 1, regulatory subunit 3A							179.0	178.0	178.0					7																	113517991		2203	4299	6502	SO:0001819	synonymous_variant	5506				glycogen metabolic process	integral to membrane		g.chr7:113517991A>G	AF024578	CCDS5759.1	7q31.1	2012-04-17	2011-10-04	2001-07-02	ENSG00000154415	ENSG00000154415	3.1.3.16	"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	9291	protein-coding gene	gene with protein product	"""glycogen-associated regulatory subunit of protein phosphatase-1"", ""protein phosphatase 1 regulatory subunit GM"""	600917	"""protein phosphatase 1, regulatory (inhibitor) subunit 3A (glycogen and sarcoplasmic reticulum binding subunit, skeletal muscle)"", ""protein phosphatase 1, regulatory (inhibitor) subunit 3A"""	PPP1R3		7926294	Standard	NM_002711		Approved	GM	uc010ljy.1	Q16821	OTTHUMG00000156944	ENST00000284601.3:c.3156T>C	7.37:g.113517991A>G							p.T1052T	NM_002711.3	NP_002702.2	Q16821	PPR3A_HUMAN			4	3224	-			1052					A0AVQ2|A4D0T6|O43476|Q75LN8|Q7KYM8|Q86UI6	Silent	SNP	ENST00000284601.3	37	c.3156T>C	CCDS5759.1																																																																																				0.368	PPP1R3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346724.1	NM_002711		99	124	0	0	0	0.048971	0	99	124				
CLRN3	119467	broad.mit.edu	37	10	129690850	129690850	+	Missense_Mutation	SNP	C	C	T			TCGA-DU-7018-01A-11D-2024-08	TCGA-DU-7018-10A-01D-2024-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	29c55a80-cd55-4297-b433-00d0e2b1e08d	453998d9-d9f9-479d-86c0-d889a58b836d	g.chr10:129690850C>T	ENST00000368671.3	-	1	361	c.199G>A	c.(199-201)Gga>Aga	p.G67R		NM_152311.3	NP_689524.1	Q8NCR9	CLRN3_HUMAN	clarin 3	67						extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				endometrium(1)|large_intestine(1)|lung(2)|skin(1)|upper_aerodigestive_tract(1)	6		all_epithelial(44;0.00168)|all_lung(145;0.0586)|Lung NSC(174;0.0765)|all_neural(114;0.201)|Glioma(114;0.222)|Colorectal(57;0.235)				TCTGCAAGTCCGTGACTCAAT	0.368																																						ENST00000368671.3																			0				endometrium(1)|large_intestine(1)|lung(2)|skin(1)|upper_aerodigestive_tract(1)	6						c.(199-201)Gga>Aga		clarin 3							101.0	96.0	98.0					10																	129690850		2203	4300	6503	SO:0001583	missense	119467					integral to membrane		g.chr10:129690850C>T	BC029478	CCDS7656.1	10q26.2	2006-11-24	2006-11-23	2006-11-23	ENSG00000180745	ENSG00000180745			20795	protein-coding gene	gene with protein product			"""transmembrane protein 12"""	TMEM12		12145752, 12080385	Standard	NM_152311		Approved	MGC32871, USH3AL1	uc001lka.1	Q8NCR9	OTTHUMG00000019253	ENST00000368671.3:c.199G>A	10.37:g.129690850C>T	ENSP00000357660:p.Gly67Arg						p.G67R	NM_152311.3	NP_689524.1	Q8NCR9	CLRN3_HUMAN			1	361	-		all_epithelial(44;0.00168)|all_lung(145;0.0586)|Lung NSC(174;0.0765)|all_neural(114;0.201)|Glioma(114;0.222)|Colorectal(57;0.235)	67					Q6MZX8	Missense_Mutation	SNP	ENST00000368671.3	37	c.199G>A	CCDS7656.1	.	.	.	.	.	.	.	.	.	.	C	20.1	3.937389	0.73557	.	.	ENSG00000180745	ENST00000368671	T	0.80738	-1.41	5.52	5.52	0.82312	.	0.153488	0.45867	D	0.000327	D	0.88840	0.6546	M	0.72894	2.215	0.54753	D	0.999984	D	0.89917	1.0	D	0.97110	1.0	D	0.88137	0.2842	10	0.49607	T	0.09	.	16.4802	0.84156	0.0:1.0:0.0:0.0	.	67	Q8NCR9	CLRN3_HUMAN	R	67	ENSP00000357660:G67R	ENSP00000357660:G67R	G	-	1	0	CLRN3	129580840	0.929000	0.31497	0.641000	0.29422	0.035000	0.12851	2.681000	0.46926	2.880000	0.98712	0.655000	0.94253	GGA		0.368	CLRN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050987.1	NM_152311		4	78	0	0	0	0.009096	0	4	78				
HS3ST6	64711	broad.mit.edu	37	16	1962181	1962181	+	Missense_Mutation	SNP	C	C	T			TCGA-DU-7018-01A-11D-2024-08	TCGA-DU-7018-10A-01D-2024-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	29c55a80-cd55-4297-b433-00d0e2b1e08d	453998d9-d9f9-479d-86c0-d889a58b836d	g.chr16:1962181C>T	ENST00000293937.3	-	2	438	c.439G>A	c.(439-441)Ggg>Agg	p.G147R	HS3ST6_ENST00000443547.1_Missense_Mutation_p.G116R|HS3ST6_ENST00000454677.2_Missense_Mutation_p.G164R			Q96QI5	HS3S6_HUMAN	heparan sulfate (glucosamine) 3-O-sulfotransferase 6	147					carbohydrate metabolic process (GO:0005975)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan metabolic process (GO:0030203)|small molecule metabolic process (GO:0044281)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	[heparan sulfate]-glucosamine 3-sulfotransferase 1 activity (GO:0008467)			endometrium(2)|lung(2)	4						GTGATCTGCCCATCCAGGGTT	0.687																																						ENST00000454677.2																			0				endometrium(2)|lung(2)	4						c.(490-492)Ggg>Agg		heparan sulfate (glucosamine) 3-O-sulfotransferase 6							15.0	17.0	16.0					16																	1962181		2193	4297	6490	SO:0001583	missense	64711							g.chr16:1962181C>T			16p13.3	2008-10-30	2003-06-11	2003-06-13	ENSG00000162040	ENSG00000162040		"""Sulfotransferases, membrane-bound"""	14178	protein-coding gene	gene with protein product			"""heparan sulfate (glucosamine) 3-O-sulfotransferase 5"""	HS3ST5		11157797	Standard	NM_001009606		Approved		uc002cnf.3	Q96QI5	OTTHUMG00000047860	ENST00000293937.3:c.439G>A	16.37:g.1962181C>T	ENSP00000293937:p.Gly147Arg					HS3ST6_ENST00000443547.1_Missense_Mutation_p.G116R|HS3ST6_ENST00000293937.3_Missense_Mutation_p.G147R	p.G164R			C9JH64	C9JH64_HUMAN			2	555	-			116					Q96RX7	Missense_Mutation	SNP	ENST00000293937.3	37	c.490G>A		.	.	.	.	.	.	.	.	.	.	C	23.4	4.412930	0.83449	.	.	ENSG00000162040	ENST00000293937;ENST00000443547;ENST00000454677	T;T	0.55930	0.49;0.49	4.84	4.84	0.62591	Sulfotransferase domain (1);	0.000000	0.85682	D	0.000000	T	0.65344	0.2682	M	0.77486	2.375	0.80722	D	1	P	0.41008	0.735	P	0.47915	0.561	T	0.71517	-0.4569	10	0.72032	D	0.01	.	16.9861	0.86340	0.0:1.0:0.0:0.0	.	147	Q96QI5	HS3S6_HUMAN	R	147;116;186	ENSP00000293937:G147R;ENSP00000390354:G116R	ENSP00000293937:G147R	G	-	1	0	HS3ST6	1902182	1.000000	0.71417	0.967000	0.41034	0.713000	0.41058	5.827000	0.69300	2.252000	0.74401	0.505000	0.49811	GGG		0.687	HS3ST6-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_001009606		6	12	0	0	0	0.021553	0	6	12				
KRT71	112802	broad.mit.edu	37	12	52946764	52946764	+	Missense_Mutation	SNP	C	C	T	rs375403204		TCGA-DU-7018-01A-11D-2024-08	TCGA-DU-7018-10A-01D-2024-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	29c55a80-cd55-4297-b433-00d0e2b1e08d	453998d9-d9f9-479d-86c0-d889a58b836d	g.chr12:52946764C>T	ENST00000267119.5	-	1	167	c.98G>A	c.(97-99)cGg>cAg	p.R33Q		NM_033448.2	NP_258259.1	Q3SY84	K2C71_HUMAN	keratin 71	33	Gly-rich.|Head.				hair follicle morphogenesis (GO:0031069)|intermediate filament organization (GO:0045109)	extracellular vesicular exosome (GO:0070062)|keratin filament (GO:0045095)	structural molecule activity (GO:0005198)			breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(9)|ovary(1)|skin(1)|urinary_tract(1)	22				BRCA - Breast invasive adenocarcinoma(357;0.194)		GCTCCCTGCCCGGAAGGAGGA	0.652													C|||	1	0.000199681	0.0008	0.0	5008	,	,		16151	0.0		0.0	False		,,,				2504	0.0					ENST00000267119.5																			0				breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(9)|ovary(1)|skin(1)|urinary_tract(1)	22						c.(97-99)cGg>cAg		keratin 71		C	GLN/ARG	0,4406		0,0,2203	57.0	67.0	64.0		98	4.3	1.0	12		64	1,8599	1.2+/-3.3	0,1,4299	no	missense	KRT71	NM_033448.2	43	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	possibly-damaging	33/524	52946764	1,13005	2203	4300	6503	SO:0001583	missense	112802						structural molecule activity	g.chr12:52946764C>T	AJ308600	CCDS8831.1	12q13.13	2013-01-16			ENSG00000139648	ENSG00000139648		"""-"", ""Intermediate filaments type II, keratins (basic)"""	28927	protein-coding gene	gene with protein product		608245				11982755, 12648212, 16831889	Standard	NM_033448		Approved	KRT6IRS, KRT6IRS1, K6IRS1	uc001sao.3	Q3SY84	OTTHUMG00000167831	ENST00000267119.5:c.98G>A	12.37:g.52946764C>T	ENSP00000267119:p.Arg33Gln						p.R33Q	NM_033448.2	NP_258259.1	Q3SY84	K2C71_HUMAN		BRCA - Breast invasive adenocarcinoma(357;0.194)	1	167	-			33			Gly-rich.|Head.		B3KVC1|Q3SY85|Q96DU2	Missense_Mutation	SNP	ENST00000267119.5	37	c.98G>A	CCDS8831.1	.	.	.	.	.	.	.	.	.	.	C	15.21	2.765223	0.49574	0.0	1.16E-4	ENSG00000139648	ENST00000267119	D	0.82619	-1.63	5.24	4.33	0.51752	.	0.165052	0.26796	N	0.022443	T	0.73001	0.3531	M	0.62266	1.93	0.28359	N	0.920553	P	0.35401	0.499	B	0.15484	0.013	T	0.65861	-0.6065	10	0.27082	T	0.32	.	7.6086	0.28115	0.0:0.8199:0.0:0.1801	.	33	Q3SY84	K2C71_HUMAN	Q	33	ENSP00000267119:R33Q	ENSP00000267119:R33Q	R	-	2	0	KRT71	51233031	0.000000	0.05858	1.000000	0.80357	0.958000	0.62258	0.298000	0.19120	2.609000	0.88269	0.655000	0.94253	CGG		0.652	KRT71-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396487.1	NM_033448		19	150	0	0	0	0.043863	0	19	150				
RNF130	55819	broad.mit.edu	37	5	179393937	179393937	+	Missense_Mutation	SNP	C	C	A			TCGA-DU-7018-01A-11D-2024-08	TCGA-DU-7018-10A-01D-2024-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	29c55a80-cd55-4297-b433-00d0e2b1e08d	453998d9-d9f9-479d-86c0-d889a58b836d	g.chr5:179393937C>A	ENST00000261947.4	-	7	1417	c.1019G>T	c.(1018-1020)aGa>aTa	p.R340I	RNF130_ENST00000522208.2_Missense_Mutation_p.R340I|CTC-563A5.2_ENST00000510240.1_RNA|RNF130_ENST00000521389.1_Missense_Mutation_p.R340I	NM_001280801.1	NP_001267730.1			ring finger protein 130											breast(2)|kidney(1)|large_intestine(5)|lung(6)|ovary(1)|upper_aerodigestive_tract(2)	17	all_cancers(89;5.49e-05)|all_epithelial(37;1.94e-05)|Renal(175;0.000159)|Lung NSC(126;0.00118)|all_lung(126;0.00212)	all_cancers(40;0.0294)|Medulloblastoma(196;0.00498)|all_neural(177;0.0138)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			GAGGGCTGATCTTCGGTTAAC	0.517																																					GBM(24;432 554 38471 39699 51728)	ENST00000522208.2																			0				breast(2)|kidney(1)|large_intestine(5)|lung(6)|ovary(1)|upper_aerodigestive_tract(2)	17						c.(1018-1020)aGa>aTa		ring finger protein 130							120.0	112.0	115.0					5																	179393937		2203	4300	6503	SO:0001583	missense	55819				apoptosis	cytoplasm|integral to membrane|nucleus	ubiquitin-protein ligase activity|zinc ion binding	g.chr5:179393937C>A	AF155650	CCDS4451.1, CCDS64340.1	5q35.3	2013-01-09			ENSG00000113269	ENSG00000113269		"""RING-type (C3HC4) zinc fingers"""	18280	protein-coding gene	gene with protein product						10806348	Standard	NM_018434		Approved	GP, G1RZFP, GOLIATH	uc003mll.1	Q86XS8	OTTHUMG00000130909	ENST00000261947.4:c.1019G>T	5.37:g.179393937C>A	ENSP00000261947:p.Arg340Ile					RNF130_ENST00000261947.4_Missense_Mutation_p.R340I|RNF130_ENST00000521389.1_Missense_Mutation_p.R340I	p.R340I			Q86XS8	GOLI_HUMAN	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)		7	1037	-	all_cancers(89;5.49e-05)|all_epithelial(37;1.94e-05)|Renal(175;0.000159)|Lung NSC(126;0.00118)|all_lung(126;0.00212)	all_cancers(40;0.0294)|Medulloblastoma(196;0.00498)|all_neural(177;0.0138)	340						Missense_Mutation	SNP	ENST00000261947.4	37	c.1019G>T		.	.	.	.	.	.	.	.	.	.	C	13.03	2.115469	0.37339	.	.	ENSG00000113269	ENST00000522208;ENST00000521389;ENST00000261947	T;T;T	0.05025	3.51;3.51;3.55	5.26	5.26	0.73747	.	0.299562	0.31685	N	0.007232	T	0.06005	0.0156	N	0.17082	0.46	0.80722	D	1	B;B	0.17667	0.023;0.023	B;B	0.14578	0.011;0.011	T	0.44513	-0.9323	10	0.33141	T	0.24	.	18.8618	0.92275	0.0:1.0:0.0:0.0	.	357;340	Q59EL1;Q86XS8	.;GOLI_HUMAN	I	340	ENSP00000429509:R340I;ENSP00000430237:R340I;ENSP00000261947:R340I	ENSP00000261947:R340I	R	-	2	0	RNF130	179326543	1.000000	0.71417	0.996000	0.52242	0.097000	0.18754	6.344000	0.72991	2.435000	0.82474	0.491000	0.48974	AGA		0.517	RNF130-003	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000374205.1	NM_018434		5	91	1	0	3.59834e-05	0.021553	3.76969e-05	5	91				
SOAT1	6646	broad.mit.edu	37	1	179320474	179320474	+	Silent	SNP	T	T	C			TCGA-DU-7018-01A-11D-2024-08	TCGA-DU-7018-10A-01D-2024-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	29c55a80-cd55-4297-b433-00d0e2b1e08d	453998d9-d9f9-479d-86c0-d889a58b836d	g.chr1:179320474T>C	ENST00000367619.3	+	15	1616	c.1473T>C	c.(1471-1473)aaT>aaC	p.N491N	SOAT1_ENST00000540564.1_Silent_p.N433N|SOAT1_ENST00000539888.1_Silent_p.N426N|SOAT1_ENST00000535686.1_Silent_p.N227N	NM_003101.5	NP_003092.4	P35610	SOAT1_HUMAN	sterol O-acyltransferase 1	491					cholesterol efflux (GO:0033344)|cholesterol esterification (GO:0034435)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|cholesterol storage (GO:0010878)|macrophage derived foam cell differentiation (GO:0010742)|positive regulation of amyloid precursor protein biosynthetic process (GO:0042986)|very-low-density lipoprotein particle assembly (GO:0034379)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	cholesterol binding (GO:0015485)|cholesterol O-acyltransferase activity (GO:0034736)|fatty-acyl-CoA binding (GO:0000062)|sterol O-acyltransferase activity (GO:0004772)			central_nervous_system(1)|endometrium(3)|large_intestine(1)|lung(10)|prostate(1)|skin(3)|stomach(1)	20					Ezetimibe(DB00973)|Hesperetin(DB01094)	TCATTGTCAATGATAGTCGGA	0.408																																						ENST00000367619.3																			0				central_nervous_system(1)|endometrium(3)|large_intestine(1)|lung(10)|prostate(1)|skin(3)|stomach(1)	20						c.(1471-1473)aaT>aaC		sterol O-acyltransferase 1	Ezetimibe(DB00973)|Hesperetin(DB01094)						209.0	200.0	203.0					1																	179320474		2203	4300	6503	SO:0001819	synonymous_variant	6646				cholesterol efflux|cholesterol esterification|cholesterol homeostasis|cholesterol metabolic process|cholesterol storage|macrophage derived foam cell differentiation|positive regulation of amyloid precursor protein biosynthetic process|very-low-density lipoprotein particle assembly	endoplasmic reticulum membrane|integral to membrane|microsome	cholesterol binding|cholesterol O-acyltransferase activity|fatty-acyl-CoA binding	g.chr1:179320474T>C	L21934	CCDS1330.1, CCDS58047.1, CCDS58048.1	1q25	2008-08-26	2008-08-26		ENSG00000057252	ENSG00000057252	2.3.1.26		11177	protein-coding gene	gene with protein product	"""acyl-Coenzyme A: cholesterol acyltransferase"""	102642	"""sterol O-acyltransferase (acyl-Coenzyme A: cholesterol acyltransferase) 1"""	SOAT, STAT		8407899	Standard	NM_003101		Approved	ACAT	uc001gml.3	P35610	OTTHUMG00000035253	ENST00000367619.3:c.1473T>C	1.37:g.179320474T>C						SOAT1_ENST00000540564.1_Silent_p.N433N|SOAT1_ENST00000535686.1_Silent_p.N227N|SOAT1_ENST00000539888.1_Silent_p.N426N	p.N491N	NM_003101.5	NP_003092.4	P35610	SOAT1_HUMAN			15	1616	+			491					A6NC40|A8K3P4|A9Z1V7|B4DU95|Q5T0X4|Q8N1E4	Silent	SNP	ENST00000367619.3	37	c.1473T>C	CCDS1330.1																																																																																				0.408	SOAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085286.2	NM_003101		19	183	0	0	0	0.062417	0	19	183				
PSMC3	5702	broad.mit.edu	37	11	47444498	47444498	+	Missense_Mutation	SNP	C	C	T			TCGA-DU-7018-01A-11D-2024-08	TCGA-DU-7018-10A-01D-2024-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	29c55a80-cd55-4297-b433-00d0e2b1e08d	453998d9-d9f9-479d-86c0-d889a58b836d	g.chr11:47444498C>T	ENST00000298852.3	-	7	775	c.618G>A	c.(616-618)atG>atA	p.M206I	PSMC3_ENST00000602866.1_Missense_Mutation_p.M190I|PSMC3_ENST00000530912.1_Missense_Mutation_p.M164I	NM_002804.4	NP_002795.2	P17980	PRS6A_HUMAN	proteasome (prosome, macropain) 26S subunit, ATPase, 3	206					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|ATP catabolic process (GO:0006200)|cellular nitrogen compound metabolic process (GO:0034641)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of RNA biosynthetic process (GO:2001141)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)	cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|proteasome accessory complex (GO:0022624)|proteasome complex (GO:0000502)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)			breast(1)|central_nervous_system(1)|kidney(1)|large_intestine(4)|lung(5)|ovary(4)|urinary_tract(1)	17				Lung(87;0.0932)|BRCA - Breast invasive adenocarcinoma(625;0.13)		CCTTGTGGTTCATTGGCAAGA	0.592																																						ENST00000298852.3																			0				breast(1)|central_nervous_system(1)|kidney(1)|large_intestine(4)|lung(5)|ovary(4)|urinary_tract(1)	17						c.(616-618)atG>atA		proteasome (prosome, macropain) 26S subunit, ATPase, 3							102.0	103.0	102.0					11																	47444498		2201	4298	6499	SO:0001583	missense	5702				anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|G1/S transition of mitotic cell cycle|interspecies interaction between organisms|M/G1 transition of mitotic cell cycle|mRNA metabolic process|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|regulation of apoptosis|regulation of cellular amino acid metabolic process|S phase of mitotic cell cycle|viral reproduction	cytoplasm|nucleus|proteasome complex	ATP binding|nucleoside-triphosphatase activity|protein binding|transcription coactivator activity|transcription corepressor activity	g.chr11:47444498C>T	M34079	CCDS7935.1	11p11.2	2010-04-21			ENSG00000165916	ENSG00000165916		"""Proteasome (prosome, macropain) subunits"", ""ATPases / AAA-type"""	9549	protein-coding gene	gene with protein product		186852				9048938, 9473509	Standard	NM_002804		Approved	TBP1, TBP-1	uc001nfh.2	P17980	OTTHUMG00000167692	ENST00000298852.3:c.618G>A	11.37:g.47444498C>T	ENSP00000298852:p.Met206Ile					PSMC3_ENST00000602866.1_Missense_Mutation_p.M190I|PSMC3_ENST00000530912.1_Missense_Mutation_p.M164I	p.M206I	NM_002804.4	NP_002795.2	P17980	PRS6A_HUMAN		Lung(87;0.0932)|BRCA - Breast invasive adenocarcinoma(625;0.13)	7	775	-			206					B2R8V1|Q3B757|Q3B865|Q53HU5|Q6GPG8|Q6IBS1|Q96HD3	Missense_Mutation	SNP	ENST00000298852.3	37	c.618G>A	CCDS7935.1	.	.	.	.	.	.	.	.	.	.	C	16.60	3.167487	0.57476	.	.	ENSG00000165916	ENST00000298852;ENST00000530912;ENST00000524447;ENST00000531051;ENST00000530887;ENST00000530651;ENST00000527906	D;D	0.94330	-3.4;-3.4	5.24	5.24	0.73138	.	0.000000	0.85682	D	0.000000	D	0.86351	0.5912	N	0.04805	-0.155	0.80722	D	1	B;B	0.14012	0.002;0.009	B;B	0.11329	0.005;0.006	T	0.81066	-0.1101	10	0.39692	T	0.17	-47.1287	18.8565	0.92254	0.0:1.0:0.0:0.0	.	164;206	E9PM69;P17980	.;PRS6A_HUMAN	I	206;164;150;150;171;171;171	ENSP00000298852:M206I;ENSP00000433097:M164I	ENSP00000298852:M206I	M	-	3	0	PSMC3	47401074	1.000000	0.71417	1.000000	0.80357	0.920000	0.55202	6.022000	0.70839	2.445000	0.82738	0.655000	0.94253	ATG		0.592	PSMC3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395660.2	NM_002804		18	214	0	0	0	0.049695	0	18	214				
AZGP1P1	646282	broad.mit.edu	37	7	99578411	99578411	+	RNA	SNP	T	T	C	rs62484970		TCGA-DU-7018-01A-11D-2024-08	TCGA-DU-7018-10A-01D-2024-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	29c55a80-cd55-4297-b433-00d0e2b1e08d	453998d9-d9f9-479d-86c0-d889a58b836d	g.chr7:99578411T>C	ENST00000425474.1	+	0	27					NR_036679.1				alpha-2-glycoprotein 1, zinc-binding pseudogene 1																		AAGAATGGTGTCTGTCCTGCT	0.582																																						ENST00000425474.1																			0																																																			0							g.chr7:99578411T>C	AW995302		7q22.1	2010-04-16	2006-11-07		ENSG00000214313	ENSG00000214313			911	pseudogene	pseudogene			"""alpha-2-glycoprotein 1, zinc pseudogene 1"""			8241150, 8307568	Standard	NR_036679		Approved		uc003usi.2		OTTHUMG00000156513		7.37:g.99578411T>C								NR_036679.1						0	27	+									RNA	SNP	ENST00000425474.1	37																																																																																						0.582	AZGP1P1-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000344467.1			5	135	0	0	0	0.029380	0	5	135				
SMARCA4	6597	broad.mit.edu	37	19	11144121	11144121	+	Missense_Mutation	SNP	C	C	G			TCGA-DU-7018-01A-11D-2024-08	TCGA-DU-7018-10A-01D-2024-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	29c55a80-cd55-4297-b433-00d0e2b1e08d	453998d9-d9f9-479d-86c0-d889a58b836d	g.chr19:11144121C>G	ENST00000429416.3	+	27	3983	c.3702C>G	c.(3700-3702)ttC>ttG	p.F1234L	SMARCA4_ENST00000444061.3_Missense_Mutation_p.F1234L|SMARCA4_ENST00000541122.2_Missense_Mutation_p.F1234L|SMARCA4_ENST00000538456.3_3'UTR|SMARCA4_ENST00000590574.1_Missense_Mutation_p.F1234L|SMARCA4_ENST00000358026.2_Missense_Mutation_p.F1234L|SMARCA4_ENST00000589677.1_Missense_Mutation_p.F1234L|SMARCA4_ENST00000413806.3_Missense_Mutation_p.F1234L|SMARCA4_ENST00000450717.3_Missense_Mutation_p.F1234L|SMARCA4_ENST00000344626.4_Missense_Mutation_p.F1234L	NM_001128844.1	NP_001122316.1	P51532	SMCA4_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4	1234	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.F1234L(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)				CCGGCATGTTCGACCAGAAGT	0.637			"""F, N, Mis"""		NSCLC																																	ENST00000358026.2				Rec	yes		19	19p13.2	6597	"""F, N, Mis"""	"""SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4"""			E			NSCLC		2	Substitution - Missense(1)|Unknown(1)	p.F1234L(1)|p.?(1)	upper_aerodigestive_tract(1)|lung(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						c.(3700-3702)ttC>ttG		SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4							109.0	105.0	107.0					19																	11144121		2203	4300	6503	SO:0001583	missense	6597				chromatin remodeling|negative regulation of androgen receptor signaling pathway|negative regulation of cell growth|negative regulation of S phase of mitotic cell cycle|negative regulation of transcription from RNA polymerase II promoter|nervous system development|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	nBAF complex|npBAF complex|nuclear chromatin|SWI/SNF complex|WINAC complex	androgen receptor binding|ATP binding|DNA binding|DNA-dependent ATPase activity|helicase activity|histone acetyl-lysine binding|identical protein binding|p53 binding|protein N-terminus binding|transcription corepressor activity	g.chr19:11144121C>G	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.3702C>G	19.37:g.11144121C>G	ENSP00000395654:p.Phe1234Leu					SMARCA4_ENST00000541122.2_Missense_Mutation_p.F1234L|SMARCA4_ENST00000589677.1_Missense_Mutation_p.F1234L|SMARCA4_ENST00000590574.1_Missense_Mutation_p.F1234L|SMARCA4_ENST00000344626.4_Missense_Mutation_p.F1234L|SMARCA4_ENST00000450717.3_Missense_Mutation_p.F1234L|SMARCA4_ENST00000444061.3_Missense_Mutation_p.F1234L|SMARCA4_ENST00000413806.3_Missense_Mutation_p.F1234L|SMARCA4_ENST00000429416.3_Missense_Mutation_p.F1234L	p.F1234L	NM_001128849.1	NP_001122321.1	P51532	SMCA4_HUMAN			26	3986	+		all_lung(6;0.0512)|Lung NSC(9;0.0568)	1234			Helicase C-terminal.		B1A8Z4|B1A8Z5|B1A8Z6|B1A8Z7|E9PBR8|O95052|Q9HBD3	Missense_Mutation	SNP	ENST00000429416.3	37	c.3702C>G	CCDS12253.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	18.10|18.10	3.547597|3.547597	0.65311|0.65311	.|.	.|.	ENSG00000127616|ENSG00000127616	ENST00000429416;ENST00000358026;ENST00000421844;ENST00000344626;ENST00000541122;ENST00000444061;ENST00000450717;ENST00000413806|ENST00000538456	T;T;T;D;D;D;D|.	0.94862|.	-0.8;-0.8;-0.8;-3.54;-3.54;-3.54;-3.54|.	4.74|4.74	-7.13|-7.13	0.01532|0.01532	Helicase, C-terminal (1);|.	0.116713|.	0.64402|.	D|.	0.000017|.	T|T	0.65417|0.65417	0.2689|0.2689	M|M	0.67517|0.67517	2.055|2.055	0.44234|0.44234	D|D	0.997073|0.997073	D;D;D;P;D;D;P|.	0.89917|.	0.999;1.0;1.0;0.694;0.999;1.0;0.694|.	D;D;D;P;D;D;P|.	0.85130|.	0.991;0.997;0.997;0.639;0.973;0.991;0.708|.	T|T	0.71251|0.71251	-0.4648|-0.4648	10|5	0.87932|.	D|.	0|.	-21.6265|-21.6265	13.9487|13.9487	0.64101|0.64101	0.0:0.4136:0.0:0.5864|0.0:0.4136:0.0:0.5864	.|.	1234;1234;1234;1234;1234;454;1234|.	B1A8Z6;B1A8Z4;B1A8Z7;Q9HBD4;B1A8Z5;B4E0F1;P51532|.	.;.;.;.;.;.;SMCA4_HUMAN|.	L|G	1234;1234;1298;1234;1234;1234;1234;1234|4	ENSP00000395654:F1234L;ENSP00000350720:F1234L;ENSP00000343896:F1234L;ENSP00000445036:F1234L;ENSP00000392837:F1234L;ENSP00000397783:F1234L;ENSP00000414727:F1234L|.	ENSP00000343896:F1234L|.	F|R	+|+	3|1	2|2	SMARCA4|SMARCA4	11005121|11005121	0.000000|0.000000	0.05858|0.05858	0.919000|0.919000	0.36401|0.36401	0.969000|0.969000	0.65631|0.65631	-2.606000|-2.606000	0.00888|0.00888	-1.009000|-1.009000	0.03400|0.03400	-1.030000|-1.030000	0.02411|0.02411	TTC|CGA		0.637	SMARCA4-007	KNOWN	alternative_5_UTR|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000452638.2	NM_003072		24	69	0	0	0	0.099896	0	24	69				
PDE8A	5151	broad.mit.edu	37	15	85681058	85681058	+	Missense_Mutation	SNP	A	A	G			TCGA-DU-7018-01A-11D-2024-08	TCGA-DU-7018-10A-01D-2024-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	29c55a80-cd55-4297-b433-00d0e2b1e08d	453998d9-d9f9-479d-86c0-d889a58b836d	g.chr15:85681058A>G	ENST00000310298.4	+	23	2666	c.2414A>G	c.(2413-2415)cAt>cGt	p.H805R	PDE8A_ENST00000339708.5_Missense_Mutation_p.H759R|PDE8A_ENST00000394553.1_Missense_Mutation_p.H805R|PDE8A_ENST00000557957.1_Missense_Mutation_p.H733R			O60658	PDE8A_HUMAN	phosphodiesterase 8A	805	Catalytic. {ECO:0000250}.				cAMP catabolic process (GO:0006198)|cyclic nucleotide metabolic process (GO:0009187)|phosphorelay signal transduction system (GO:0000160)|regulation of transcription, DNA-templated (GO:0006355)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	3',5'-cyclic-AMP phosphodiesterase activity (GO:0004115)|3',5'-cyclic-nucleotide phosphodiesterase activity (GO:0004114)|metal ion binding (GO:0046872)|signal transducer activity (GO:0004871)			NS(1)|central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(4)|lung(8)|ovary(2)|pancreas(1)|prostate(1)|skin(2)	25	Colorectal(223;0.227)		BRCA - Breast invasive adenocarcinoma(143;0.0608)		Caffeine(DB00201)|Ketotifen(DB00920)	TTAATGCAGCATCTTGACAAC	0.463																																						ENST00000310298.4																			0				NS(1)|central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(4)|lung(8)|ovary(2)|pancreas(1)|prostate(1)|skin(2)	25						c.(2413-2415)cAt>cGt		phosphodiesterase 8A							97.0	83.0	87.0					15																	85681058		2203	4299	6502	SO:0001583	missense	5151				cyclic nucleotide metabolic process|regulation of transcription, DNA-dependent	cytosol	3',5'-cyclic-AMP phosphodiesterase activity|metal ion binding|two-component response regulator activity	g.chr15:85681058A>G	AF056490	CCDS10336.1, CCDS10337.1, CCDS58397.1	15q25.3	2008-05-14			ENSG00000073417	ENSG00000073417	3.1.4.17	"""Phosphodiesterases"""	8793	protein-coding gene	gene with protein product		602972				9618252	Standard	NM_001243137		Approved	HsT19550	uc002blh.3	O60658	OTTHUMG00000148670	ENST00000310298.4:c.2414A>G	15.37:g.85681058A>G	ENSP00000311453:p.His805Arg					PDE8A_ENST00000339708.5_Missense_Mutation_p.H759R|PDE8A_ENST00000557957.1_Missense_Mutation_p.H733R|PDE8A_ENST00000394553.1_Missense_Mutation_p.H805R	p.H805R			O60658	PDE8A_HUMAN	BRCA - Breast invasive adenocarcinoma(143;0.0608)		23	2666	+	Colorectal(223;0.227)		805			Catalytic (By similarity).		B3KXE6|H0YMZ7|Q6P9H3|Q969I1|Q96PC9|Q96PD0|Q96PD1|Q96T71|Q9UMB7|Q9UMC3	Missense_Mutation	SNP	ENST00000310298.4	37	c.2414A>G	CCDS10336.1	.	.	.	.	.	.	.	.	.	.	A	17.11	3.305222	0.60305	.	.	ENSG00000073417	ENST00000310298;ENST00000394553;ENST00000339708	T;T;T	0.75938	-0.98;-0.98;-0.98	5.49	5.49	0.81192	5&apos (2);-cyclic nucleotide phosphodiesterase, catalytic domain (2);3&apos (2);	0.000000	0.85682	D	0.000000	T	0.81772	0.4893	L	0.61036	1.89	0.80722	D	1	D;D	0.65815	0.995;0.991	P;P	0.59424	0.857;0.772	D	0.83659	0.0160	10	0.72032	D	0.01	.	13.5962	0.61991	1.0:0.0:0.0:0.0	.	759;805	O60658-2;O60658	.;PDE8A_HUMAN	R	805;805;759	ENSP00000311453:H805R;ENSP00000378056:H805R;ENSP00000340679:H759R	ENSP00000311453:H805R	H	+	2	0	PDE8A	83482062	1.000000	0.71417	0.993000	0.49108	0.117000	0.20001	8.695000	0.91298	2.311000	0.77944	0.533000	0.62120	CAT		0.463	PDE8A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000309018.1	NM_002605		10	37	0	0	0	0.058154	0	10	37				
NKAPL	222698	broad.mit.edu	37	6	28228259	28228259	+	Silent	SNP	A	A	G			TCGA-DU-7018-01A-11D-2024-08	TCGA-DU-7018-10A-01D-2024-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	29c55a80-cd55-4297-b433-00d0e2b1e08d	453998d9-d9f9-479d-86c0-d889a58b836d	g.chr6:28228259A>G	ENST00000343684.3	+	1	1162	c.1110A>G	c.(1108-1110)gcA>gcG	p.A370A	ZKSCAN4_ENST00000423974.2_5'Flank	NM_001007531.1	NP_001007532.1	Q5M9Q1	NKAPL_HUMAN	NFKB activating protein-like	370										breast(2)|endometrium(2)|kidney(1)|large_intestine(8)|lung(8)|ovary(2)|prostate(4)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	31						GAGCTCTTGCATCCTTTAACC	0.443																																						ENST00000343684.3																			0				breast(2)|endometrium(2)|kidney(1)|large_intestine(8)|lung(8)|ovary(2)|prostate(4)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	31						c.(1108-1110)gcA>gcG		NFKB activating protein-like							144.0	134.0	137.0					6																	28228259		2203	4300	6503	SO:0001819	synonymous_variant	222698							g.chr6:28228259A>G	BC038240	CCDS34353.1	6p21.33	2008-02-05	2007-08-16	2007-08-16	ENSG00000189134	ENSG00000189134			21584	protein-coding gene	gene with protein product			"""chromosome 6 open reading frame 194"""	C6orf194			Standard	NM_001007531		Approved	bA424I5.1	uc003nkt.4	Q5M9Q1	OTTHUMG00000014517	ENST00000343684.3:c.1110A>G	6.37:g.28228259A>G							p.A370A	NM_001007531.1	NP_001007532.1	Q5M9Q1	NKAPL_HUMAN			1	1162	+			370					Q3MIV1|Q9H4Q7	Silent	SNP	ENST00000343684.3	37	c.1110A>G	CCDS34353.1																																																																																				0.443	NKAPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040185.1			45	53	0	0	0	0.045515	0	45	53				
MYOM2	9172	broad.mit.edu	37	8	2021511	2021511	+	Missense_Mutation	SNP	G	G	T			TCGA-DU-7018-01A-11D-2024-08	TCGA-DU-7018-10A-01D-2024-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	29c55a80-cd55-4297-b433-00d0e2b1e08d	453998d9-d9f9-479d-86c0-d889a58b836d	g.chr8:2021511G>T	ENST00000262113.4	+	10	1192	c.1051G>T	c.(1051-1053)Ggc>Tgc	p.G351C	MYOM2_ENST00000523438.1_Intron	NM_003970.2	NP_003961.2	P54296	MYOM2_HUMAN	myomesin 2	351	Ig-like C2-type 2.				muscle contraction (GO:0006936)	M band (GO:0031430)|mitochondrion (GO:0005739)|myosin filament (GO:0032982)	structural constituent of muscle (GO:0008307)			autonomic_ganglia(2)|breast(4)|central_nervous_system(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(11)|kidney(2)|large_intestine(17)|lung(39)|ovary(5)|prostate(1)|skin(10)|upper_aerodigestive_tract(3)	104		Ovarian(12;0.0572)|Colorectal(14;0.0844)|Hepatocellular(245;0.217)		BRCA - Breast invasive adenocarcinoma(11;1.85e-05)|Colorectal(4;0.0101)|READ - Rectum adenocarcinoma(4;0.148)|COAD - Colon adenocarcinoma(4;0.179)		GGACGACGAGGGCCTGTACAC	0.602																																						ENST00000262113.4																			0				autonomic_ganglia(2)|breast(4)|central_nervous_system(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(11)|kidney(2)|large_intestine(17)|lung(39)|ovary(5)|prostate(1)|skin(10)|upper_aerodigestive_tract(3)	104						c.(1051-1053)Ggc>Tgc		myomesin 2							78.0	65.0	69.0					8																	2021511		2203	4300	6503	SO:0001583	missense	9172				muscle contraction	myosin filament	structural constituent of muscle	g.chr8:2021511G>T		CCDS5957.1	8p23.3	2014-06-06	2012-10-17		ENSG00000036448	ENSG00000036448		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	7614	protein-coding gene	gene with protein product		603509	"""myomesin (M-protein) 2 (165kD)"", ""myomesin (M-protein) 2, 165kDa"""				Standard	XM_006716237		Approved		uc003wpx.4	P54296	OTTHUMG00000129175	ENST00000262113.4:c.1051G>T	8.37:g.2021511G>T	ENSP00000262113:p.Gly351Cys					MYOM2_ENST00000523438.1_Intron	p.G351C	NM_003970.2	NP_003961.2	P54296	MYOM2_HUMAN		BRCA - Breast invasive adenocarcinoma(11;1.85e-05)|Colorectal(4;0.0101)|READ - Rectum adenocarcinoma(4;0.148)|COAD - Colon adenocarcinoma(4;0.179)	10	1192	+		Ovarian(12;0.0572)|Colorectal(14;0.0844)|Hepatocellular(245;0.217)	351			Ig-like C2-type 2.		Q7Z3Y2	Missense_Mutation	SNP	ENST00000262113.4	37	c.1051G>T	CCDS5957.1	.	.	.	.	.	.	.	.	.	.	G	25.2	4.617408	0.87359	.	.	ENSG00000036448	ENST00000262113	T	0.77750	-1.12	4.9	4.9	0.64082	Immunoglobulin subtype (1);Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	D	0.89361	0.6693	M	0.87971	2.92	0.80722	D	1	D	0.65815	0.995	D	0.69142	0.962	D	0.91172	0.4969	10	0.62326	D	0.03	.	18.0821	0.89444	0.0:0.0:1.0:0.0	.	351	P54296	MYOM2_HUMAN	C	351	ENSP00000262113:G351C	ENSP00000262113:G351C	G	+	1	0	MYOM2	2008918	1.000000	0.71417	0.965000	0.40720	0.756000	0.42949	9.433000	0.97501	2.237000	0.73441	0.655000	0.94253	GGC		0.602	MYOM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251249.1	NM_003970		12	44	1	0	4.3838e-07	0.105934	4.74313e-07	12	44				
PCNXL3	399909	broad.mit.edu	37	11	65393163	65393163	+	Missense_Mutation	SNP	T	T	G			TCGA-DU-7018-01A-11D-2024-08	TCGA-DU-7018-10A-01D-2024-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	29c55a80-cd55-4297-b433-00d0e2b1e08d	453998d9-d9f9-479d-86c0-d889a58b836d	g.chr11:65393163T>G	ENST00000355703.3	+	19	3715	c.3176T>G	c.(3175-3177)aTc>aGc	p.I1059S		NM_032223.2	NP_115599.2	Q9H6A9	PCX3_HUMAN	pecanex-like 3 (Drosophila)	1059						integral component of membrane (GO:0016021)				breast(1)|endometrium(2)|kidney(2)|large_intestine(1)|lung(6)|prostate(1)	13						TGTGTGGTGATCGCCGTGCTC	0.627											OREG0021084	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																										ENST00000355703.3																			0				breast(1)|endometrium(2)|kidney(2)|large_intestine(1)|lung(6)|prostate(1)	13						c.(3175-3177)aTc>aGc		pecanex-like 3 (Drosophila)							75.0	70.0	72.0					11																	65393163		2195	4275	6470	SO:0001583	missense	399909					integral to membrane		g.chr11:65393163T>G	BX640978	CCDS44650.1	11q12.1	2008-07-21			ENSG00000197136	ENSG00000197136			18760	protein-coding gene	gene with protein product						15146197	Standard	NM_032223		Approved	FLJ22427	uc001oey.2	Q9H6A9	OTTHUMG00000166539	ENST00000355703.3:c.3176T>G	11.37:g.65393163T>G	ENSP00000347931:p.Ile1059Ser		OREG0021084	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	1083		p.I1059S	NM_032223.2	NP_115599.2	Q9H6A9	PCX3_HUMAN			19	3715	+			1059					Q6MZN8	Missense_Mutation	SNP	ENST00000355703.3	37	c.3176T>G	CCDS44650.1	.	.	.	.	.	.	.	.	.	.	T	21.1	4.102684	0.76983	.	.	ENSG00000197136	ENST00000355703	T	0.09073	3.02	5.34	5.34	0.76211	.	.	.	.	.	T	0.12732	0.0309	M	0.77103	2.36	0.49483	D	0.999799	P	0.43477	0.808	B	0.36464	0.225	T	0.02491	-1.1151	9	0.49607	T	0.09	.	13.2755	0.60184	0.0:0.0:0.0:1.0	.	1059	Q9H6A9	PCX3_HUMAN	S	1059	ENSP00000347931:I1059S	ENSP00000347931:I1059S	I	+	2	0	PCNXL3	65149739	1.000000	0.71417	0.907000	0.35723	0.914000	0.54420	5.810000	0.69179	2.040000	0.60383	0.533000	0.62120	ATC		0.627	PCNXL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390321.1	NM_032223		11	17	0	0	0	0.093190	0	11	17				
POTEG	404785	broad.mit.edu	37	14	19553818	19553818	+	Silent	SNP	C	C	T	rs545468513		TCGA-DU-7018-01A-11D-2024-08	TCGA-DU-7018-10A-01D-2024-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	29c55a80-cd55-4297-b433-00d0e2b1e08d	453998d9-d9f9-479d-86c0-d889a58b836d	g.chr14:19553818C>T	ENST00000409832.3	+	1	454	c.402C>T	c.(400-402)caC>caT	p.H134H		NM_001005356.2	NP_001005356.1	Q6S5H5	POTEG_HUMAN	POTE ankyrin domain family, member G	134										cervix(1)|endometrium(4)|kidney(3)|large_intestine(4)|lung(31)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	47						CGAGGTACCACGTCCGTCGAG	0.587													C|||	1	0.000199681	0.0	0.0	5008	,	,		51605	0.001		0.0	False		,,,				2504	0.0					ENST00000409832.3																			0				cervix(1)|endometrium(4)|kidney(3)|large_intestine(4)|lung(31)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	47						c.(400-402)caC>caT		POTE ankyrin domain family, member G							125.0	137.0	133.0					14																	19553818		1848	3844	5692	SO:0001819	synonymous_variant	404785							g.chr14:19553818C>T		CCDS73610.1	14q11.2	2013-01-10	2008-11-26	2008-11-26	ENSG00000222036	ENSG00000222036		"""POTE ankyrin domain containing"", ""Ankyrin repeat domain containing"""	33896	protein-coding gene	gene with protein product	"""cancer/testis antigen family 104, member 4"""	608916	"""ANKRD26-like family C, member 2"""	A26C2			Standard	NR_027480		Approved	POTE14, POTE-14, POTE14alpha, CT104.4	uc001vuz.1	Q6S5H5	OTTHUMG00000170340	ENST00000409832.3:c.402C>T	14.37:g.19553818C>T							p.H134H	NM_001005356.2	NP_001005356.1	Q6S5H5	POTEG_HUMAN			1	454	+			134					A1L153|A6NMI9|Q6S5H6|Q6S8J2	Silent	SNP	ENST00000409832.3	37	c.402C>T	CCDS32018.1																																																																																				0.587	POTEG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408579.1	NM_001005356		30	348	0	0	0	0.045515	0	30	348				
DAB2	1601	broad.mit.edu	37	5	39381673	39381673	+	Missense_Mutation	SNP	C	C	T	rs374766869		TCGA-DU-7018-01A-11D-2024-08	TCGA-DU-7018-10A-01D-2024-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	29c55a80-cd55-4297-b433-00d0e2b1e08d	453998d9-d9f9-479d-86c0-d889a58b836d	g.chr5:39381673C>T	ENST00000320816.6	-	11	1854	c.1387G>A	c.(1387-1389)Gtc>Atc	p.V463I	DAB2_ENST00000545653.1_Missense_Mutation_p.V442I|DAB2_ENST00000339788.6_Missense_Mutation_p.V245I|DAB2_ENST00000509337.1_Missense_Mutation_p.V442I	NM_001343.3	NP_001334.2	P98082	DAB2_HUMAN	Dab, mitogen-responsive phosphoprotein, homolog 2 (Drosophila)	463					activation of JUN kinase activity (GO:0007257)|apoptotic process (GO:0006915)|cell morphogenesis involved in differentiation (GO:0000904)|cell proliferation (GO:0008283)|cellular response to transforming growth factor beta stimulus (GO:0071560)|clathrin coat assembly (GO:0048268)|endoderm development (GO:0007492)|excretion (GO:0007588)|in utero embryonic development (GO:0001701)|leading edge cell differentiation (GO:0035026)|membrane organization (GO:0061024)|myeloid cell differentiation (GO:0030099)|negative regulation of androgen receptor signaling pathway (GO:0060766)|negative regulation of apoptotic process (GO:0043066)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of protein binding (GO:0032091)|negative regulation of protein localization to plasma membrane (GO:1903077)|negative regulation of transcription, DNA-templated (GO:0045892)|pinocytosis (GO:0006907)|positive regulation of cell migration (GO:0030335)|positive regulation of clathrin-mediated endocytosis (GO:2000370)|positive regulation of early endosome to late endosome transport (GO:2000643)|positive regulation of endocytosis (GO:0045807)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of integrin-mediated signaling pathway (GO:2001046)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of receptor recycling (GO:0001921)|positive regulation of SMAD protein import into nucleus (GO:0060391)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|positive regulation of transcription elongation from RNA polymerase II promoter (GO:0032968)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|positive regulation of Wnt signaling pathway, planar cell polarity pathway (GO:2000096)|protein transport (GO:0015031)|receptor-mediated endocytosis (GO:0006898)|Wnt signaling pathway (GO:0016055)	apical plasma membrane (GO:0016324)|clathrin coat of coated pit (GO:0030132)|clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|intracellular membrane-bounded organelle (GO:0043231)|lysosomal membrane (GO:0005765)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)	cargo receptor activity (GO:0038024)|clathrin adaptor activity (GO:0035615)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|protein C-terminus binding (GO:0008022)|SMAD binding (GO:0046332)			autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|endometrium(1)|kidney(5)|large_intestine(9)|lung(19)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)	47	all_lung(31;0.000197)		Epithelial(62;0.137)			GGTTCTGAGACGGGAGGAGCA	0.542																																						ENST00000545653.1																			0				autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|endometrium(1)|kidney(5)|large_intestine(9)|lung(19)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)	47						c.(1324-1326)Gtc>Atc		Dab, mitogen-responsive phosphoprotein, homolog 2 (Drosophila)		C	ILE/VAL	1,4405	2.1+/-5.4	0,1,2202	123.0	119.0	120.0		1387	-2.2	0.0	5		120	0,8600		0,0,4300	no	missense	DAB2	NM_001343.3	29	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	benign	463/771	39381673	1,13005	2203	4300	6503	SO:0001583	missense	1601				cell proliferation|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of protein binding|negative regulation of transcription, DNA-dependent|positive regulation of proteasomal ubiquitin-dependent protein catabolic process|positive regulation of protein phosphorylation|positive regulation of transcription, DNA-dependent|positive regulation of Wnt receptor signaling pathway, planar cell polarity pathway	clathrin coated vesicle membrane|coated pit	protein C-terminus binding	g.chr5:39381673C>T	U53446	CCDS34149.1, CCDS58946.1	5p13.1	2013-10-03	2013-03-08		ENSG00000153071	ENSG00000153071			2662	protein-coding gene	gene with protein product		601236	"""disabled (Drosophila) homolog 2 (mitogen-responsive phosphoprotein)"", ""disabled homolog 2, mitogen-responsive phosphoprotein (Drosophila)"""			8660969, 9620555	Standard	NM_001343		Approved	DOC-2	uc003jlx.3	P98082	OTTHUMG00000162043	ENST00000320816.6:c.1387G>A	5.37:g.39381673C>T	ENSP00000313391:p.Val463Ile					DAB2_ENST00000339788.6_Missense_Mutation_p.V245I|DAB2_ENST00000509337.1_Missense_Mutation_p.V442I|DAB2_ENST00000320816.6_Missense_Mutation_p.V463I	p.V442I	NM_001244871.1	NP_001231800.1	P98082	DAB2_HUMAN	Epithelial(62;0.137)		10	1854	-	all_lung(31;0.000197)		463					A6NES5|Q13598|Q9BTY0|Q9UK04	Missense_Mutation	SNP	ENST00000320816.6	37	c.1324G>A	CCDS34149.1	.	.	.	.	.	.	.	.	.	.	C	6.926	0.540582	0.13250	2.27E-4	0.0	ENSG00000153071	ENST00000320816;ENST00000339788;ENST00000545653;ENST00000509337	T;T;T;T	0.36520	1.28;1.25;1.25;1.25	5.8	-2.25	0.06888	.	1.104930	0.06675	N	0.766898	T	0.23649	0.0572	N	0.22421	0.69	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.30446	-0.9978	10	0.16896	T	0.51	0.7637	12.3456	0.55119	0.0:0.3412:0.0:0.6588	.	463;442	P98082;P98082-3	DAB2_HUMAN;.	I	463;245;442;442	ENSP00000313391:V463I;ENSP00000345508:V245I;ENSP00000439919:V442I;ENSP00000426245:V442I	ENSP00000313391:V463I	V	-	1	0	DAB2	39417430	0.000000	0.05858	0.003000	0.11579	0.977000	0.68977	-1.132000	0.03235	-0.321000	0.08627	-0.794000	0.03295	GTC		0.542	DAB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367014.1	NM_001343		21	98	0	0	0	0.069288	0	21	98				
EDEM2	55741	broad.mit.edu	37	20	33722668	33722668	+	Missense_Mutation	SNP	G	G	A			TCGA-DU-7018-01A-11D-2024-08	TCGA-DU-7018-10A-01D-2024-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	29c55a80-cd55-4297-b433-00d0e2b1e08d	453998d9-d9f9-479d-86c0-d889a58b836d	g.chr20:33722668G>A	ENST00000374492.3	-	6	680	c.575C>T	c.(574-576)aCg>aTg	p.T192M	EDEM2_ENST00000374491.3_Missense_Mutation_p.T155M|EDEM2_ENST00000542871.1_Intron|EDEM2_ENST00000541621.1_De_novo_Start_InFrame|EDEM2_ENST00000540582.1_Missense_Mutation_p.T151M	NM_018217.2	NP_060687.2	Q9BV94	EDEM2_HUMAN	ER degradation enhancer, mannosidase alpha-like 2	192					cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)|protein folding (GO:0006457)|protein N-linked glycosylation via asparagine (GO:0018279)|response to unfolded protein (GO:0006986)	endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)	calcium ion binding (GO:0005509)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(10)|prostate(1)|stomach(1)|upper_aerodigestive_tract(2)	22			BRCA - Breast invasive adenocarcinoma(18;0.00936)			AATCCCTGCCGTACAGGTGAC	0.542																																					Esophageal Squamous(51;906 1021 24535 36410 39145)	ENST00000540582.1																			0				breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(10)|prostate(1)|stomach(1)|upper_aerodigestive_tract(2)	22						c.(451-453)aCg>aTg		ER degradation enhancer, mannosidase alpha-like 2							101.0	85.0	91.0					20																	33722668		2203	4300	6503	SO:0001583	missense	55741				post-translational protein modification|protein folding|protein N-linked glycosylation via asparagine|response to unfolded protein	endoplasmic reticulum lumen|endoplasmic reticulum membrane|extracellular region	calcium ion binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity|misfolded protein binding	g.chr20:33722668G>A	AK001645	CCDS13247.1, CCDS46592.1	20q11.22	2006-03-31	2006-03-31	2006-03-31	ENSG00000088298	ENSG00000088298			15877	protein-coding gene	gene with protein product		610302	"""chromosome 20 open reading frame 31"""	C20orf49, C20orf31		15537790, 15579471	Standard	NM_018217		Approved	FLJ10783, bA4204.1	uc002xbo.2	Q9BV94	OTTHUMG00000032322	ENST00000374492.3:c.575C>T	20.37:g.33722668G>A	ENSP00000363616:p.Thr192Met					EDEM2_ENST00000374491.2_Missense_Mutation_p.T155M|EDEM2_ENST00000374492.3_Missense_Mutation_p.T192M|EDEM2_ENST00000542871.1_Intron|EDEM2_ENST00000541621.1_De_novo_Start_InFrame	p.T151M			Q9BV94	EDEM2_HUMAN	BRCA - Breast invasive adenocarcinoma(18;0.00936)		10	1173	-			192					B4DTG9|Q6GU33|Q6IA89|Q6UWZ4|Q9H4U0|Q9H886|Q9NTL9|Q9NVE6	Missense_Mutation	SNP	ENST00000374492.3	37	c.452C>T	CCDS13247.1	.	.	.	.	.	.	.	.	.	.	G	32	5.173862	0.94807	.	.	ENSG00000088298	ENST00000374491;ENST00000374492;ENST00000540582	T;T;T	0.48201	0.82;0.82;0.82	5.87	5.87	0.94306	.	0.000000	0.85682	D	0.000000	T	0.75369	0.3840	M	0.87269	2.87	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.983;0.998;0.999	T	0.77811	-0.2449	10	0.87932	D	0	-13.2531	20.5827	0.99408	0.0:0.0:1.0:0.0	.	151;155;192	F5GZ44;Q9BV94-2;Q9BV94	.;.;EDEM2_HUMAN	M	155;192;151	ENSP00000363615:T155M;ENSP00000363616:T192M;ENSP00000441548:T151M	ENSP00000363615:T155M	T	-	2	0	EDEM2	33186329	1.000000	0.71417	0.993000	0.49108	0.999000	0.98932	9.568000	0.98166	2.941000	0.99782	0.655000	0.94253	ACG		0.542	EDEM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078842.2	NM_018217		8	58	0	0	0	0.058154	0	8	58				
SMYD1	150572	broad.mit.edu	37	2	88393054	88393054	+	Silent	SNP	C	C	G			TCGA-DU-7018-01A-11D-2024-08	TCGA-DU-7018-10A-01D-2024-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	29c55a80-cd55-4297-b433-00d0e2b1e08d	453998d9-d9f9-479d-86c0-d889a58b836d	g.chr2:88393054C>G	ENST00000419482.2	+	5	763	c.678C>G	c.(676-678)tcC>tcG	p.S226S	SMYD1_ENST00000438570.1_Intron|SMYD1_ENST00000444564.2_Intron	NM_198274.3	NP_938015.1	Q8NB12	SMYD1_HUMAN	SET and MYND domain containing 1	226	SET. {ECO:0000255|PROSITE- ProRule:PRU00190}.				chromatin remodeling (GO:0006338)|heart development (GO:0007507)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of myoblast differentiation (GO:0045663)|positive regulation of myotube differentiation (GO:0010831)|skeletal muscle cell differentiation (GO:0035914)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|metal ion binding (GO:0046872)|transcription corepressor activity (GO:0003714)			NS(1)|breast(4)|central_nervous_system(1)|large_intestine(6)|lung(19)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	41						CAGTGAAATCCATGTTTCATA	0.493																																						ENST00000419482.2																			0				NS(1)|breast(4)|central_nervous_system(1)|large_intestine(6)|lung(19)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	41						c.(676-678)tcC>tcG		SET and MYND domain containing 1							239.0	203.0	215.0					2																	88393054		2203	4300	6503	SO:0001819	synonymous_variant	150572				regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	DNA binding|zinc ion binding	g.chr2:88393054C>G	AF086123	CCDS33240.1	2p11.1	2011-07-01			ENSG00000115593	ENSG00000115593		"""Zinc fingers, MYND-type"", ""Chromatin-modifying enzymes / K-methyltransferases"""	20986	protein-coding gene	gene with protein product		606846				11923873	Standard	NM_198274		Approved	BOP, ZMYND22, KMT3D	uc002ssr.3	Q8NB12	OTTHUMG00000155045	ENST00000419482.2:c.678C>G	2.37:g.88393054C>G						SMYD1_ENST00000438570.1_Intron|SMYD1_ENST00000444564.2_Intron	p.S226S	NM_198274.3	NP_938015.1	Q8NB12	SMYD1_HUMAN			5	763	+			226			SET.		A0AV30|A6NE13	Silent	SNP	ENST00000419482.2	37	c.678C>G	CCDS33240.1																																																																																				0.493	SMYD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338229.2	XM_097915		14	69	0	0	0	0.033300	0	14	69				
OTUD5	55593	broad.mit.edu	37	X	48791845	48791845	+	Silent	SNP	G	G	A			TCGA-DU-7018-01A-11D-2024-08	TCGA-DU-7018-10A-01D-2024-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	29c55a80-cd55-4297-b433-00d0e2b1e08d	453998d9-d9f9-479d-86c0-d889a58b836d	g.chrX:48791845G>A	ENST00000156084.4	-	5	1026	c.966C>T	c.(964-966)gaC>gaT	p.D322D	OTUD5_ENST00000484499.1_5'UTR|OTUD5_ENST00000376488.3_Silent_p.D317D|OTUD5_ENST00000396743.3_Silent_p.D317D|OTUD5_ENST00000428668.2_Silent_p.D100D	NM_017602.3	NP_060072.1	Q96G74	OTUD5_HUMAN	OTU deubiquitinase 5	322	OTU. {ECO:0000255|PROSITE- ProRule:PRU00139}.				innate immune response (GO:0045087)|negative regulation of type I interferon production (GO:0032480)|protein K48-linked deubiquitination (GO:0071108)|protein K63-linked deubiquitination (GO:0070536)|response to lipopolysaccharide (GO:0032496)	cytosol (GO:0005829)	ubiquitin-specific protease activity (GO:0004843)			endometrium(2)|large_intestine(3)|lung(6)|pancreas(2)	13						GAATGGGTTCGTCCTCGTTTT	0.507																																						ENST00000156084.4																			0				endometrium(2)|large_intestine(3)|lung(6)|pancreas(2)	13						c.(964-966)gaC>gaT		OTU domain containing 5							188.0	127.0	148.0					X																	48791845		2203	4300	6503	SO:0001819	synonymous_variant	55593				negative regulation of type I interferon production		cysteine-type peptidase activity	g.chrX:48791845G>A		CCDS14313.1, CCDS48104.1, CCDS48105.1	Xp11.23	2014-06-09	2014-02-24		ENSG00000068308	ENSG00000068308		"""OTU domain containing"""	25402	protein-coding gene	gene with protein product		300713	"""OTU domain containing 5"""			24143256	Standard	NM_001136157		Approved	DKFZp761A052, DUBA	uc004dlu.3	Q96G74	OTTHUMG00000024130	ENST00000156084.4:c.966C>T	X.37:g.48791845G>A						OTUD5_ENST00000396743.3_Silent_p.D317D|OTUD5_ENST00000428668.2_Silent_p.D100D|OTUD5_ENST00000376488.3_Silent_p.D317D|OTUD5_ENST00000484499.1_5'UTR	p.D322D	NM_017602.3	NP_060072.1	Q96G74	OTUD5_HUMAN			5	1026	-			322			OTU.		B4DGG7|G5E9D7|Q4KMN9|Q8N6T5|Q9H650|Q9H9U0|Q9NT65	Silent	SNP	ENST00000156084.4	37	c.966C>T	CCDS14313.1																																																																																				0.507	OTUD5-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000060799.1	NM_017602		13	120	0	0	0	0.105934	0	13	120				
KRTCAP3	200634	broad.mit.edu	37	2	27666916	27666916	+	Nonsense_Mutation	SNP	G	G	A			TCGA-DU-7018-01A-11D-2024-08	TCGA-DU-7018-10A-01D-2024-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	29c55a80-cd55-4297-b433-00d0e2b1e08d	453998d9-d9f9-479d-86c0-d889a58b836d	g.chr2:27666916G>A	ENST00000543753.1	+	6	763	c.716G>A	c.(715-717)tGg>tAg	p.W239*	KRTCAP3_ENST00000288873.3_Nonsense_Mutation_p.W239*|KRTCAP3_ENST00000407293.1_Nonsense_Mutation_p.W221*	NM_001168364.1	NP_001161836.1	Q53RY4	KCP3_HUMAN	keratinocyte associated protein 3	239						integral component of membrane (GO:0016021)				large_intestine(1)|lung(2)	3	Acute lymphoblastic leukemia(172;0.155)					CAGAGAAGTTGGGTTTAGGAC	0.483																																						ENST00000543753.1																			0				large_intestine(1)|lung(2)	3						c.(715-717)tGg>tAg		keratinocyte associated protein 3							57.0	60.0	59.0					2																	27666916		2203	4300	6503	SO:0001587	stop_gained	200634					integral to membrane		g.chr2:27666916G>A	AY157576	CCDS1754.1	2p23.3	2008-02-05			ENSG00000157992	ENSG00000157992			28943	protein-coding gene	gene with protein product							Standard	NM_173853		Approved	KCP3	uc002rks.3	Q53RY4	OTTHUMG00000097782	ENST00000543753.1:c.716G>A	2.37:g.27666916G>A	ENSP00000442400:p.Trp239*					KRTCAP3_ENST00000288873.3_Nonsense_Mutation_p.W239*|KRTCAP3_ENST00000407293.1_Nonsense_Mutation_p.W221*	p.W239*	NM_001168364.1	NP_001161836.1	Q53RY4	KCP3_HUMAN			6	763	+	Acute lymphoblastic leukemia(172;0.155)		239					B7ZL49|Q6UW42|Q8IWS5	Nonsense_Mutation	SNP	ENST00000543753.1	37	c.716G>A	CCDS1754.1	.	.	.	.	.	.	.	.	.	.	G	18.16	3.562647	0.65538	.	.	ENSG00000157992	ENST00000543753;ENST00000288873;ENST00000407293;ENST00000452499	.	.	.	5.82	5.82	0.92795	.	0.000000	0.53938	D	0.000051	.	.	.	.	.	.	0.27106	N	0.962501	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-35.9685	15.5865	0.76489	0.0:0.0:1.0:0.0	.	.	.	.	X	239;239;221;61	.	ENSP00000288873:W239X	W	+	2	0	KRTCAP3	27520420	1.000000	0.71417	1.000000	0.80357	0.536000	0.34869	2.965000	0.49200	2.758000	0.94735	0.555000	0.69702	TGG		0.483	KRTCAP3-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215025.1	NM_173853		4	21	0	0	0	0.009096	0	4	21				
GPR83	10888	broad.mit.edu	37	11	94113592	94113592	+	Missense_Mutation	SNP	C	C	A			TCGA-DU-7018-01A-11D-2024-08	TCGA-DU-7018-10A-01D-2024-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	29c55a80-cd55-4297-b433-00d0e2b1e08d	453998d9-d9f9-479d-86c0-d889a58b836d	g.chr11:94113592C>A	ENST00000243673.2	-	4	1166	c.995G>T	c.(994-996)tGg>tTg	p.W332L	GPR83_ENST00000539203.2_Missense_Mutation_p.W290L	NM_016540.3	NP_057624.3	Q9NYM4	GPR83_HUMAN	G protein-coupled receptor 83	332					response to glucocorticoid (GO:0051384)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|neuropeptide Y receptor activity (GO:0004983)			NS(1)|breast(1)|central_nervous_system(2)|kidney(2)|large_intestine(2)|lung(9)|ovary(1)|prostate(1)	19		Acute lymphoblastic leukemia(157;2.26e-05)|all_hematologic(158;0.0123)				CATGGCAAACCAGTGGAAGGC	0.517																																						ENST00000243673.2																			0				NS(1)|breast(1)|central_nervous_system(2)|kidney(2)|large_intestine(2)|lung(9)|ovary(1)|prostate(1)	19						c.(994-996)tGg>tTg		G protein-coupled receptor 83							163.0	140.0	147.0					11																	94113592		2201	4298	6499	SO:0001583	missense	10888					integral to membrane|plasma membrane	neuropeptide Y receptor activity	g.chr11:94113592C>A	AF236081	CCDS8297.1	11q21	2012-08-21	2003-07-30	2003-08-01	ENSG00000123901	ENSG00000123901		"""GPCR / Class A : Orphans"""	4523	protein-coding gene	gene with protein product		605569	"""G protein-coupled receptor 72"""	GPR72		10760605, 11060465	Standard	NM_016540		Approved		uc001pet.2	Q9NYM4	OTTHUMG00000167779	ENST00000243673.2:c.995G>T	11.37:g.94113592C>A	ENSP00000243673:p.Trp332Leu					GPR83_ENST00000539203.2_Missense_Mutation_p.W290L	p.W332L	NM_016540.3	NP_057624.3	Q9NYM4	GPR83_HUMAN			4	1166	-		Acute lymphoblastic leukemia(157;2.26e-05)|all_hematologic(158;0.0123)	332					B0M0K5|Q6NWR4|Q9P1Y8	Missense_Mutation	SNP	ENST00000243673.2	37	c.995G>T	CCDS8297.1	.	.	.	.	.	.	.	.	.	.	C	24.0	4.486591	0.84854	.	.	ENSG00000123901	ENST00000243673;ENST00000539203	T;T	0.73897	-0.79;-0.79	5.75	5.75	0.90469	GPCR, rhodopsin-like superfamily (1);	0.000000	0.85682	D	0.000000	D	0.83876	0.5349	L	0.55103	1.725	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.82100	-0.0624	10	0.40728	T	0.16	.	18.5085	0.90907	0.0:1.0:0.0:0.0	.	332	Q9NYM4	GPR83_HUMAN	L	332;290	ENSP00000243673:W332L;ENSP00000441550:W290L	ENSP00000243673:W332L	W	-	2	0	GPR83	93753240	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.602000	0.82796	2.719000	0.93026	0.655000	0.94253	TGG		0.517	GPR83-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396232.1	NM_016540		68	150	1	0	5.26073e-25	0.048971	6.09137e-25	68	150				
SNCAIP	9627	broad.mit.edu	37	5	121786734	121786734	+	Missense_Mutation	SNP	G	G	A	rs146515227	byFrequency	TCGA-DU-7018-01A-11D-2024-08	TCGA-DU-7018-10A-01D-2024-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	29c55a80-cd55-4297-b433-00d0e2b1e08d	453998d9-d9f9-479d-86c0-d889a58b836d	g.chr5:121786734G>A	ENST00000261368.8	+	10	2454	c.2192G>A	c.(2191-2193)cGc>cAc	p.R731H	SNCAIP_ENST00000504884.2_3'UTR|CTC-210G5.1_ENST00000503529.1_RNA|SNCAIP_ENST00000261367.7_Missense_Mutation_p.R778H|SNCAIP_ENST00000379533.2_Missense_Mutation_p.R778H|CTC-210G5.1_ENST00000506053.1_RNA|CTC-210G5.1_ENST00000505546.1_RNA|CTC-210G5.1_ENST00000509993.1_RNA|CTC-210G5.1_ENST00000510972.1_RNA|SNCAIP_ENST00000379538.3_Missense_Mutation_p.R365H|SNCAIP_ENST00000414317.2_Missense_Mutation_p.R333H|SNCAIP_ENST00000379536.2_Missense_Mutation_p.R671H|SNCAIP_ENST00000503116.2_3'UTR|SNCAIP_ENST00000542191.1_Missense_Mutation_p.R289H	NM_005460.2	NP_005451.2	Q9Y6H5	SNCAP_HUMAN	synuclein, alpha interacting protein	731					cell death (GO:0008219)|dopamine metabolic process (GO:0042417)|regulation of inclusion body assembly (GO:0090083)|regulation of neurotransmitter secretion (GO:0046928)	cytoplasm (GO:0005737)|neuronal cell body (GO:0043025)|presynaptic membrane (GO:0042734)|synaptic vesicle (GO:0008021)	identical protein binding (GO:0042802)|ubiquitin protein ligase binding (GO:0031625)			NS(3)|breast(2)|endometrium(4)|kidney(1)|large_intestine(5)|lung(9)|ovary(2)|pancreas(1)|prostate(4)|skin(7)|urinary_tract(1)	39		all_cancers(142;0.00787)|Prostate(80;0.0327)	KIRC - Kidney renal clear cell carcinoma(527;0.206)	OV - Ovarian serous cystadenocarcinoma(64;0.000625)|Epithelial(69;0.00216)|all cancers(49;0.0232)		TCAGGGGGACGCAGGTTTCCT	0.542													G|||	3	0.000599042	0.0	0.0014	5008	,	,		19623	0.001		0.001	False		,,,				2504	0.0					ENST00000261367.7																			0				NS(3)|breast(2)|endometrium(4)|kidney(1)|large_intestine(5)|lung(9)|ovary(2)|pancreas(1)|prostate(4)|skin(7)|urinary_tract(1)	39						c.(2332-2334)cGc>cAc		synuclein, alpha interacting protein		G	HIS/ARG	0,4406		0,0,2203	88.0	90.0	89.0		2192	6.1	1.0	5	dbSNP_134	89	3,8597	3.0+/-9.4	0,3,4297	yes	missense	SNCAIP	NM_005460.2	29	0,3,6500	AA,AG,GG		0.0349,0.0,0.0231	probably-damaging	731/920	121786734	3,13003	2203	4300	6503	SO:0001583	missense	9627				cell death|dopamine metabolic process|regulation of inclusion body assembly|regulation of neurotransmitter secretion	cytoplasm|neuronal cell body|nucleolus|presynaptic membrane	ubiquitin protein ligase binding	g.chr5:121786734G>A	AF167306	CCDS4131.1, CCDS58964.1	5q23.2	2013-01-10	2008-07-31		ENSG00000064692	ENSG00000064692		"""Ankyrin repeat domain containing"""	11139	protein-coding gene	gene with protein product	"""synphilin"""	603779				10319874	Standard	NM_001242935		Approved	SYPH1	uc003ksw.1	Q9Y6H5	OTTHUMG00000128915	ENST00000261368.8:c.2192G>A	5.37:g.121786734G>A	ENSP00000261368:p.Arg731His					SNCAIP_ENST00000379538.3_Missense_Mutation_p.R365H|CTC-210G5.1_ENST00000510972.1_RNA|SNCAIP_ENST00000379536.2_Missense_Mutation_p.R671H|SNCAIP_ENST00000504884.2_3'UTR|SNCAIP_ENST00000379533.2_Missense_Mutation_p.R778H|CTC-210G5.1_ENST00000503529.1_RNA|CTC-210G5.1_ENST00000505546.1_RNA|SNCAIP_ENST00000542191.1_Missense_Mutation_p.R289H|CTC-210G5.1_ENST00000509993.1_RNA|CTC-210G5.1_ENST00000506053.1_RNA|SNCAIP_ENST00000261368.8_Missense_Mutation_p.R731H|SNCAIP_ENST00000503116.2_3'UTR|SNCAIP_ENST00000414317.2_Missense_Mutation_p.R333H	p.R778H			Q9Y6H5	SNCAP_HUMAN	KIRC - Kidney renal clear cell carcinoma(527;0.206)	OV - Ovarian serous cystadenocarcinoma(64;0.000625)|Epithelial(69;0.00216)|all cancers(49;0.0232)	12	3761	+		all_cancers(142;0.00787)|Prostate(80;0.0327)	731					D3DSZ1|Q05BS1|Q1PSC2|Q49AC6|Q504U9|Q6L984|Q6L985|Q6L986|Q9HC59	Missense_Mutation	SNP	ENST00000261368.8	37	c.2333G>A	CCDS4131.1	2	9.157509157509158E-4	0	0.0	1	0.0027624309392265192	0	0.0	1	0.0013192612137203166	G	16.25	3.070337	0.55539	0.0	3.49E-4	ENSG00000064692	ENST00000542191;ENST00000509154;ENST00000261368;ENST00000379533;ENST00000379536;ENST00000379538;ENST00000261367;ENST00000414317	T;T;T;T;T;T;T;T	0.19806	3.99;4.56;2.21;2.12;4.56;4.44;2.12;4.2	6.06	6.06	0.98353	.	0.052234	0.64402	D	0.000001	T	0.51839	0.1698	M	0.77313	2.365	0.46131	D	0.99888	D;D;D;D;D;D;D;D	0.89917	0.998;0.999;0.999;0.997;0.999;0.997;1.0;0.996	D;D;D;P;D;P;D;P	0.79784	0.953;0.915;0.931;0.862;0.979;0.862;0.993;0.732	T	0.50092	-0.8868	10	0.87932	D	0	-22.0882	20.6208	0.99490	0.0:0.0:1.0:0.0	.	671;359;333;671;365;365;778;731	D6R9G8;Q9NVG1;B7Z995;Q9Y6H5-4;Q9Y6H5-5;Q9Y6H5-2;Q9Y6H5-3;Q9Y6H5	.;.;.;.;.;.;.;SNCAP_HUMAN	H	289;671;731;778;671;365;778;333	ENSP00000441681:R289H;ENSP00000422106:R671H;ENSP00000261368:R731H;ENSP00000368848:R778H;ENSP00000368851:R671H;ENSP00000368854:R365H;ENSP00000261367:R778H;ENSP00000394392:R333H	ENSP00000261367:R778H	R	+	2	0	SNCAIP	121814633	1.000000	0.71417	1.000000	0.80357	0.274000	0.26718	6.182000	0.71995	2.882000	0.98803	0.655000	0.94253	CGC		0.542	SNCAIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250888.1			5	62	0	0	0	0.014758	0	5	62				
SASH3	54440	broad.mit.edu	37	X	128914084	128914084	+	Missense_Mutation	SNP	G	G	A			TCGA-DU-7018-01A-11D-2024-08	TCGA-DU-7018-10A-01D-2024-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	29c55a80-cd55-4297-b433-00d0e2b1e08d	453998d9-d9f9-479d-86c0-d889a58b836d	g.chrX:128914084G>A	ENST00000356892.3	+	1	125	c.11G>A	c.(10-12)cGc>cAc	p.R4H	SASH3_ENST00000476532.1_3'UTR	NM_018990.3	NP_061863.1	O75995	SASH3_HUMAN	SAM and SH3 domain containing 3	4					homeostasis of number of cells within a tissue (GO:0048873)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of CD4-positive, alpha-beta T cell differentiation (GO:0043372)|positive regulation of immunoglobulin production (GO:0002639)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interleukin-10 production (GO:0032733)|positive regulation of interleukin-2 production (GO:0032743)|positive regulation of interleukin-4 production (GO:0032753)|positive regulation of organ growth (GO:0046622)|positive regulation of T cell cytokine production (GO:0002726)|positive regulation of T cell proliferation (GO:0042102)|positive regulation of tumor necrosis factor production (GO:0032760)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				breast(2)|endometrium(2)|large_intestine(1)|lung(3)|ovary(2)|pancreas(1)|upper_aerodigestive_tract(1)	12						ATGCTGCGCCGCAAGCCCTCC	0.577																																						ENST00000356892.3																			0				breast(2)|endometrium(2)|large_intestine(1)|lung(3)|ovary(2)|pancreas(1)|upper_aerodigestive_tract(1)	12						c.(10-12)cGc>cAc		SAM and SH3 domain containing 3							90.0	79.0	83.0					X																	128914084		2203	4300	6503	SO:0001583	missense	54440							g.chrX:128914084G>A	BC051881	CCDS14614.1	Xq26	2013-01-10	2008-02-18	2008-02-18	ENSG00000122122	ENSG00000122122		"""SAM and SH3 domain containing"", ""Sterile alpha motif (SAM) domain containing"""	15975	protein-coding gene	gene with protein product		300441	"""chromosome X open reading frame 9"""	CXorf9		11470164	Standard	NM_018990		Approved	SLY, 753P9, SH3D6C, HACS2	uc004euu.3	O75995	OTTHUMG00000022372	ENST00000356892.3:c.11G>A	X.37:g.128914084G>A	ENSP00000349359:p.Arg4His					SASH3_ENST00000476532.1_3'UTR	p.R4H	NM_018990.3	NP_061863.1	O75995	SASH3_HUMAN			1	125	+			4					A6NCH1|A8K7K8|Q5JZ38	Missense_Mutation	SNP	ENST00000356892.3	37	c.11G>A	CCDS14614.1	.	.	.	.	.	.	.	.	.	.	G	18.67	3.672773	0.67928	.	.	ENSG00000122122	ENST00000443760;ENST00000356892	T	0.56941	0.43	5.31	5.31	0.75309	.	0.115953	0.64402	D	0.000012	T	0.67869	0.2939	L	0.56199	1.76	0.58432	D	0.999999	D	0.76494	0.999	D	0.73380	0.98	T	0.71087	-0.4694	10	0.87932	D	0	-10.4509	15.2979	0.73925	0.0:0.0:1.0:0.0	.	4	O75995	SASH3_HUMAN	H	4	ENSP00000349359:R4H	ENSP00000349359:R4H	R	+	2	0	SASH3	128741765	1.000000	0.71417	0.995000	0.50966	0.956000	0.61745	7.660000	0.83776	2.203000	0.70933	0.513000	0.50165	CGC		0.577	SASH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058208.1	NM_018990		10	24	0	0	0	0.080935	0	10	24				
ZNF91	7644	broad.mit.edu	37	19	23543197	23543197	+	Missense_Mutation	SNP	C	C	T			TCGA-DU-7018-01A-11D-2024-08	TCGA-DU-7018-10A-01D-2024-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	29c55a80-cd55-4297-b433-00d0e2b1e08d	453998d9-d9f9-479d-86c0-d889a58b836d	g.chr19:23543197C>T	ENST00000300619.7	-	4	2789	c.2584G>A	c.(2584-2586)Gct>Act	p.A862T	ZNF91_ENST00000599743.1_Intron|ZNF91_ENST00000596528.1_5'Flank|ZNF91_ENST00000397082.2_Missense_Mutation_p.A830T	NM_003430.2	NP_003421.2	Q05481	ZNF91_HUMAN	zinc finger protein 91	862					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)						all_lung(12;0.0349)|Lung NSC(12;0.0538)|all_epithelial(12;0.0611)				TGATTAAAAGCTTTGCCACAT	0.358																																						ENST00000300619.7																			0											c.(2584-2586)Gct>Act		zinc finger protein 91							69.0	75.0	73.0					19																	23543197		2128	4274	6402	SO:0001583	missense	7644					nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding	g.chr19:23543197C>T	M61871	CCDS42541.1, CCDS74322.1	19p12	2014-02-04	2006-05-12		ENSG00000167232	ENSG00000167232		"""Zinc fingers, C2H2-type"", ""-"""	13166	protein-coding gene	gene with protein product		603971	"""zinc finger protein 91 (HPF7, HTF10)"""			2023909, 2505992	Standard	XR_430154		Approved	HPF7, HTF10	uc002nre.3	Q05481	OTTHUMG00000183268	ENST00000300619.7:c.2584G>A	19.37:g.23543197C>T	ENSP00000300619:p.Ala862Thr					ZNF91_ENST00000599743.1_Intron|ZNF91_ENST00000397082.2_Missense_Mutation_p.A830T	p.A862T	NM_003430.2	NP_003421.2	Q05481	ZNF91_HUMAN			4	2789	-		all_lung(12;0.0349)|Lung NSC(12;0.0538)|all_epithelial(12;0.0611)	862					A8K5E1|B7Z6G6	Missense_Mutation	SNP	ENST00000300619.7	37	c.2584G>A	CCDS42541.1	.	.	.	.	.	.	.	.	.	.	C	7.575	0.667518	0.14710	.	.	ENSG00000167232	ENST00000300619;ENST00000397082	T;T	0.48836	0.8;0.8	1.41	-1.89	0.07689	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.36991	0.0987	N	0.05177	-0.1	0.18873	N	0.999983	P;D	0.76494	0.812;0.999	P;D	0.71870	0.482;0.975	T	0.21621	-1.0240	9	0.32370	T	0.25	.	3.6528	0.08210	0.5645:0.2743:0.0:0.1611	.	830;862	Q05481-2;Q05481	.;ZNF91_HUMAN	T	862;830	ENSP00000300619:A862T;ENSP00000380272:A830T	ENSP00000300619:A862T	A	-	1	0	ZNF91	23335037	0.000000	0.05858	0.003000	0.11579	0.013000	0.08279	-1.955000	0.01523	-0.688000	0.05155	-0.678000	0.03780	GCT		0.358	ZNF91-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000465891.1	NM_003430		5	38	0	0	0	0.021553	0	5	38				
PCDHGA11	56105	broad.mit.edu	37	5	140801469	140801469	+	Silent	SNP	C	C	T			TCGA-DU-7018-01A-11D-2024-08	TCGA-DU-7018-10A-01D-2024-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	29c55a80-cd55-4297-b433-00d0e2b1e08d	453998d9-d9f9-479d-86c0-d889a58b836d	g.chr5:140801469C>T	ENST00000398587.2	+	1	708	c.675C>T	c.(673-675)ggC>ggT	p.G225G	PCDHGB2_ENST00000522605.1_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGA11_ENST00000518882.1_Silent_p.G225G|PCDHGA8_ENST00000398604.2_Intron|PCDHGB7_ENST00000398594.2_Intron|PCDHGA7_ENST00000518325.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGA10_ENST00000398610.2_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA9_ENST00000573521.1_Intron|PCDHGB6_ENST00000520790.1_Intron|PCDHGB4_ENST00000519479.1_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGB3_ENST00000576222.1_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGA6_ENST00000517434.1_Intron	NM_018914.2|NM_032092.1	NP_061737.1|NP_114481.1	Q9Y5H2	PCDGB_HUMAN	protocadherin gamma subfamily A, 11	225	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.G225G(1)		breast(3)|endometrium(8)|kidney(3)|large_intestine(9)|lung(22)|ovary(2)|pancreas(1)|upper_aerodigestive_tract(1)	49			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TCCGAAAGGGCGCAGTTCCCA	0.527																																						ENST00000398587.2																			1	Substitution - coding silent(1)	p.G225G(1)	endometrium(1)	breast(3)|endometrium(8)|kidney(3)|large_intestine(9)|lung(22)|ovary(2)|pancreas(1)|upper_aerodigestive_tract(1)	49						c.(673-675)ggC>ggT									65.0	70.0	68.0					5																	140801469		2049	4211	6260	SO:0001819	synonymous_variant	0							g.chr5:140801469C>T	AF152505	CCDS47294.1, CCDS54930.1, CCDS75345.1	5q31	2010-01-26			ENSG00000253873	ENSG00000253873		"""Cadherins / Protocadherins : Clustered"""	8698	other	protocadherin		606298				10380929	Standard	NM_018914		Approved	PCDH-GAMMA-A11		Q9Y5H2	OTTHUMG00000164055	ENST00000398587.2:c.675C>T	5.37:g.140801469C>T						PCDHGB3_ENST00000576222.1_Intron|PCDHGB4_ENST00000519479.1_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGA7_ENST00000518325.1_Intron|PCDHGA10_ENST00000398610.2_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGA8_ENST00000398604.2_Intron|PCDHGB7_ENST00000398594.2_Intron|PCDHGA9_ENST00000573521.1_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGA11_ENST00000518882.1_Silent_p.G225G|PCDHGA6_ENST00000517434.1_Intron|PCDHGB6_ENST00000520790.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGA4_ENST00000571252.1_Intron	p.G225G	NM_018914.2|NM_032092.1	NP_061737.1|NP_114481.1			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)		1	708	+								B7ZVY8|Q9Y5D8|Q9Y5D9	Silent	SNP	ENST00000398587.2	37	c.675C>T	CCDS47294.1																																																																																				0.527	PCDHGA11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376974.1	NM_018914		5	66	0	0	0	0.014758	0	5	66				
CPEB4	80315	broad.mit.edu	37	5	173317440	173317440	+	Missense_Mutation	SNP	A	A	T			TCGA-DU-7018-01A-11D-2024-08	TCGA-DU-7018-10A-01D-2024-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	29c55a80-cd55-4297-b433-00d0e2b1e08d	453998d9-d9f9-479d-86c0-d889a58b836d	g.chr5:173317440A>T	ENST00000265085.5	+	1	2158	c.704A>T	c.(703-705)cAt>cTt	p.H235L	CPEB4_ENST00000520867.1_Missense_Mutation_p.H235L|CPEB4_ENST00000334035.5_Missense_Mutation_p.H235L|CPEB4_ENST00000517880.1_5'Flank|CPEB4_ENST00000519835.1_Missense_Mutation_p.H235L|CPEB4_ENST00000522336.1_5'Flank	NM_030627.2	NP_085130.2	Q17RY0	CPEB4_HUMAN	cytoplasmic polyadenylation element binding protein 4	235	His-rich.				cellular response to amino acid stimulus (GO:0071230)|cellular response to decreased oxygen levels (GO:0036294)|cellular response to glucose starvation (GO:0042149)|ionotropic glutamate receptor signaling pathway (GO:0035235)|negative regulation of neuron apoptotic process (GO:0043524)|response to ischemia (GO:0002931)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)|postsynaptic density (GO:0014069)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			NS(1)|endometrium(4)|kidney(2)|large_intestine(4)|lung(5)|prostate(1)|stomach(1)|upper_aerodigestive_tract(2)	20	Renal(175;0.000159)|Lung NSC(126;0.0128)|all_lung(126;0.0202)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;3.85e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000183)			CACCACCCACATCACCCTCAT	0.537																																						ENST00000265085.5																			0				NS(1)|endometrium(4)|kidney(2)|large_intestine(4)|lung(5)|prostate(1)|stomach(1)|upper_aerodigestive_tract(2)	20						c.(703-705)cAt>cTt		cytoplasmic polyadenylation element binding protein 4							129.0	139.0	136.0					5																	173317440		2203	4300	6503	SO:0001583	missense	80315						nucleotide binding|RNA binding	g.chr5:173317440A>T	BX538213	CCDS4390.1	5q21	2013-02-12			ENSG00000113742	ENSG00000113742		"""RNA binding motif (RRM) containing"""	21747	protein-coding gene	gene with protein product		610607				11214970, 12672660	Standard	NM_030627		Approved	KIAA1673	uc003mcs.4	Q17RY0	OTTHUMG00000130541	ENST00000265085.5:c.704A>T	5.37:g.173317440A>T	ENSP00000265085:p.His235Leu					CPEB4_ENST00000520867.1_Missense_Mutation_p.H235L|CPEB4_ENST00000519835.1_Missense_Mutation_p.H235L|CPEB4_ENST00000334035.5_Missense_Mutation_p.H235L	p.H235L	NM_030627.2	NP_085130.2	Q17RY0	CPEB4_HUMAN	Kidney(164;3.85e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000183)		1	2158	+	Renal(175;0.000159)|Lung NSC(126;0.0128)|all_lung(126;0.0202)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	235			His-rich.		B7ZLQ7|Q7Z310|Q8N405|Q9C0J0	Missense_Mutation	SNP	ENST00000265085.5	37	c.704A>T	CCDS4390.1	.	.	.	.	.	.	.	.	.	.	A	12.19	1.865004	0.32977	.	.	ENSG00000113742	ENST00000265085;ENST00000520867;ENST00000334035;ENST00000519835	T;T;T;T	0.42900	0.98;0.97;0.98;0.96	5.34	5.34	0.76211	.	0.050107	0.85682	D	0.000000	T	0.28300	0.0699	N	0.08118	0	0.80722	D	1	P;P;P;B	0.42735	0.565;0.692;0.788;0.145	B;B;B;B	0.42522	0.218;0.39;0.201;0.041	T	0.14364	-1.0475	10	0.38643	T	0.18	-19.0867	14.9846	0.71336	1.0:0.0:0.0:0.0	.	235;235;235;235	B7ZLQ8;Q17RY0-2;E5RJM0;Q17RY0	.;.;.;CPEB4_HUMAN	L	235	ENSP00000265085:H235L;ENSP00000429092:H235L;ENSP00000334533:H235L;ENSP00000429048:H235L	ENSP00000265085:H235L	H	+	2	0	CPEB4	173250046	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	6.426000	0.73374	2.023000	0.59567	0.460000	0.39030	CAT		0.537	CPEB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252964.2	NM_030627		18	104	0	0	0	0.033300	0	18	104				
LOC150776	150776	broad.mit.edu	37	2	132256505	132256505	+	RNA	SNP	A	A	C	rs3817572	byFrequency	TCGA-DU-7018-01A-11D-2024-08	TCGA-DU-7018-10A-01D-2024-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	29c55a80-cd55-4297-b433-00d0e2b1e08d	453998d9-d9f9-479d-86c0-d889a58b836d	g.chr2:132256505A>C	ENST00000438378.2	+	0	478					NR_026922.1																						TGATTAAAGTAATTGAGGATT	0.388													.|||	2568	0.51278	0.6256	0.5331	5008	,	,		20535	0.6845		0.3231	False		,,,				2504	0.364					ENST00000438378.2																			0																																																			0							g.chr2:132256505A>C																													2.37:g.132256505A>C								NR_026922.1						0	478	+									RNA	SNP	ENST00000438378.2	37																																																																																						0.388	AC093838.4-001	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000331819.7			4	87	0	0	0	0.021553	0	4	87				
IDH1	3417	broad.mit.edu	37	2	209113112	209113112	+	Missense_Mutation	SNP	C	C	T	rs121913500		TCGA-DU-7018-01A-11D-2024-08	TCGA-DU-7018-10A-01D-2024-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	29c55a80-cd55-4297-b433-00d0e2b1e08d	453998d9-d9f9-479d-86c0-d889a58b836d	g.chr2:209113112C>T	ENST00000415913.1	-	4	776	c.395G>A	c.(394-396)cGt>cAt	p.R132H	IDH1_ENST00000345146.2_Missense_Mutation_p.R132H|IDH1_ENST00000446179.1_Missense_Mutation_p.R132H	NM_001282387.1	NP_001269316.1	O75874	IDHC_HUMAN	isocitrate dehydrogenase 1 (NADP+), soluble	132			R -> C (in colorectal cancer and glioma samples; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha- ketoglutarate but instead alpha- ketoglutarate is converted to R(-)-2- hydroxyglutarate). {ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:19117336}.|R -> G (in a glioma sample; glioblastoma multiforme; somatic mutation). {ECO:0000269|PubMed:19117336}.|R -> H (in a glioma sample; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha-ketoglutarate but instead alpha-ketoglutarate is converted to R(-)-2-hydroxyglutarate). {ECO:0000269|PubMed:18772396}.|R -> L (in a glioma sample; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha-ketoglutarate but instead alpha-ketoglutarate is converted to R(-)-2-hydroxyglutarate). {ECO:0000269|PubMed:19117336}.|R -> S (in a glioma sample; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha-ketoglutarate but instead alpha-ketoglutarate is converted to R(-)-2-hydroxyglutarate). {ECO:0000269|PubMed:18772396}.		2-oxoglutarate metabolic process (GO:0006103)|cellular lipid metabolic process (GO:0044255)|female gonad development (GO:0008585)|glutathione metabolic process (GO:0006749)|glyoxylate cycle (GO:0006097)|isocitrate metabolic process (GO:0006102)|NADPH regeneration (GO:0006740)|response to oxidative stress (GO:0006979)|response to steroid hormone (GO:0048545)|small molecule metabolic process (GO:0044281)|tricarboxylic acid cycle (GO:0006099)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|peroxisomal matrix (GO:0005782)|peroxisome (GO:0005777)	isocitrate dehydrogenase (NADP+) activity (GO:0004450)|magnesium ion binding (GO:0000287)|NAD binding (GO:0051287)|NADP binding (GO:0050661)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)	p.R132H(2774)|p.R132L(59)|p.R132V(1)|p.G131_R132>VL(1)		NS(1)|autonomic_ganglia(2)|biliary_tract(24)|bone(237)|central_nervous_system(3764)|endometrium(3)|haematopoietic_and_lymphoid_tissue(794)|kidney(2)|large_intestine(7)|lung(7)|prostate(6)|skin(5)|soft_tissue(12)|thyroid(22)|urinary_tract(1)	4887				Epithelial(149;0.0322)|LUSC - Lung squamous cell carcinoma(261;0.0711)|Lung(261;0.136)		ATAAGCATGACGACCTATGAT	0.393			Mis		gliobastoma																																Pancreas(158;264 1958 3300 35450 36047)	ENST00000415913.1				Dom	yes		2	2q33.3	3417	Mis	"""isocitrate dehydrogenase 1 (NADP+), soluble"""			O			gliobastoma		2835	Substitution - Missense(2834)|Complex - compound substitution(1)	p.R132H(2774)|p.R132L(59)|p.R132V(1)|p.G131_R132>VL(1)	central_nervous_system(2579)|haematopoietic_and_lymphoid_tissue(205)|bone(43)|prostate(4)|biliary_tract(2)|urinary_tract(1)|skin(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						c.(394-396)cGt>cAt		isocitrate dehydrogenase 1 (NADP+), soluble							79.0	73.0	75.0					2																	209113112		2203	4300	6503	SO:0001583	missense	3417				2-oxoglutarate metabolic process|cellular lipid metabolic process|glyoxylate cycle|isocitrate metabolic process|NADPH regeneration|tricarboxylic acid cycle	cytosol|peroxisomal matrix	isocitrate dehydrogenase (NADP+) activity|magnesium ion binding|NAD binding|protein homodimerization activity	g.chr2:209113112C>T		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					IDH1_ENST00000446179.1_Missense_Mutation_p.R132H|IDH1_ENST00000345146.2_Missense_Mutation_p.R132H	p.R132H			O75874	IDHC_HUMAN		Epithelial(149;0.0322)|LUSC - Lung squamous cell carcinoma(261;0.0711)|Lung(261;0.136)	4	776	-			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).|R -> G (in a glioma sample; glioblastoma multiforme; somatic mutation).|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).|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).|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).			Q567U4|Q6FHQ6|Q7Z3V0|Q93090|Q9NTJ9|Q9UKW8	Missense_Mutation	SNP	ENST00000415913.1	37	c.395G>A	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			41	44	0	0	0	0.045515	0	41	44				
ESX1	80712	broad.mit.edu	37	X	103499230	103499230	+	Missense_Mutation	SNP	C	C	A			TCGA-DU-7018-01A-11D-2024-08	TCGA-DU-7018-10A-01D-2024-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	29c55a80-cd55-4297-b433-00d0e2b1e08d	453998d9-d9f9-479d-86c0-d889a58b836d	g.chrX:103499230C>A	ENST00000372588.4	-	2	194	c.111G>T	c.(109-111)atG>atT	p.M37I		NM_153448.3	NP_703149.1	Q8N693	ESX1_HUMAN	ESX homeobox 1	37					labyrinthine layer blood vessel development (GO:0060716)|labyrinthine layer morphogenesis (GO:0060713)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|regulation of cell cycle (GO:0051726)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001227)|sequence-specific DNA binding (GO:0043565)			endometrium(2)|large_intestine(10)|lung(12)|ovary(1)|skin(2)	27						CTCCCCTTGCCATCAGCGAGG	0.602																																					Pancreas(200;1705 2227 25194 28471 45274)	ENST00000372588.4																			0				endometrium(2)|large_intestine(10)|lung(12)|ovary(1)|skin(2)	27						c.(109-111)atG>atT		ESX homeobox 1							161.0	146.0	151.0					X																	103499230		2203	4300	6503	SO:0001583	missense	80712				negative regulation of transcription, DNA-dependent|regulation of cell cycle	cytoplasm|nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity	g.chrX:103499230C>A	AL049631	CCDS14516.1	Xq22.2	2011-06-20	2007-07-11	2006-02-08	ENSG00000123576	ENSG00000123576		"""Homeoboxes / PRD class"""	14865	protein-coding gene	gene with protein product		300154	"""extraembryonic, spermatogenesis, homeobox 1 homolog (mouse)"""	ESX1L		11374906, 17242862	Standard	NM_153448		Approved	ESXR1	uc004ely.3	Q8N693	OTTHUMG00000022125	ENST00000372588.4:c.111G>T	X.37:g.103499230C>A	ENSP00000361669:p.Met37Ile						p.M37I	NM_153448.3	NP_703149.1	Q8N693	ESX1_HUMAN			2	194	-			37					B0QYU3|Q7Z6K7	Missense_Mutation	SNP	ENST00000372588.4	37	c.111G>T	CCDS14516.1	.	.	.	.	.	.	.	.	.	.	c	10.04	1.240786	0.22711	.	.	ENSG00000123576	ENST00000372588	D	0.90197	-2.63	3.9	-4.12	0.03916	.	.	.	.	.	T	0.75715	0.3887	N	0.14661	0.345	0.09310	N	1	B	0.10296	0.003	B	0.04013	0.001	T	0.60078	-0.7333	9	0.27082	T	0.32	1.296	1.7636	0.02997	0.2303:0.4195:0.2089:0.1414	.	37	Q8N693	ESX1_HUMAN	I	37	ENSP00000361669:M37I	ENSP00000361669:M37I	M	-	3	0	ESX1	103385886	0.000000	0.05858	0.000000	0.03702	0.018000	0.09664	-0.225000	0.09151	-1.033000	0.03299	-0.467000	0.05162	ATG		0.602	ESX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057763.2	NM_153448		25	198	1	0	1.1804e-14	0.091800	1.32044e-14	25	198				
LOC101927209	101927209	broad.mit.edu	37	1	142713407	142713407	+	lincRNA	SNP	C	C	T	rs200984414		TCGA-DU-7018-01A-11D-2024-08	TCGA-DU-7018-10A-01D-2024-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	29c55a80-cd55-4297-b433-00d0e2b1e08d	453998d9-d9f9-479d-86c0-d889a58b836d	g.chr1:142713407C>T	ENST00000610091.1	-	0	2251																											CAGTAAGAAACTCATTCTTAT	0.318																																						ENST00000369381.2																			0																																																			0							g.chr1:142713407C>T																													1.37:g.142713407C>T														0	1198	-									RNA	SNP	ENST00000610091.1	37																																																																																						0.318	RP11-417J8.6-001	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000037265.2			4	11	0	0	0	0.014758	0	4	11				
APOBEC3B	9582	broad.mit.edu	37	22	39387537	39387537	+	Silent	SNP	C	C	T	rs144471703		TCGA-DU-7018-01A-11D-2024-08	TCGA-DU-7018-10A-01D-2024-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	29c55a80-cd55-4297-b433-00d0e2b1e08d	453998d9-d9f9-479d-86c0-d889a58b836d	g.chr22:39387537C>T	ENST00000333467.3	+	6	969	c.924C>T	c.(922-924)ttC>ttT	p.F308F	APOBEC3B-AS1_ENST00000513758.2_RNA|APOBEC3B_ENST00000407298.3_Silent_p.F283F|APOBEC3B_ENST00000402182.3_Silent_p.F308F	NM_001270411.1|NM_004900.4	NP_001257340.1|NP_004891	Q9UH17	ABC3B_HUMAN	apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like 3B	308					defense response to virus (GO:0051607)|innate immune response (GO:0045087)|metabolic process (GO:0008152)|negative regulation of transposition (GO:0010529)	nucleus (GO:0005634)	deoxycytidine deaminase activity (GO:0047844)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			cervix(2)|endometrium(2)|kidney(3)|large_intestine(1)|lung(3)|ovary(1)|skin(1)	13	Melanoma(58;0.04)					TGCGCATCTTCGCTGCCCGCA	0.572																																						ENST00000402182.3																			0				cervix(2)|endometrium(2)|kidney(3)|large_intestine(1)|lung(3)|ovary(1)|skin(1)	13						c.(922-924)ttC>ttT		apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like 3B		C		1,4397		0,1,2198	135.0	134.0	134.0		924	-4.0	0.0	22	dbSNP_134	134	0,8564		0,0,4282	no	coding-synonymous	APOBEC3B	NM_004900.3		0,1,6480	TT,TC,CC		0.0,0.0227,0.0077		308/383	39387537	1,12961	2199	4282	6481	SO:0001819	synonymous_variant	9582				negative regulation of transposition		hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amidines|RNA binding|zinc ion binding	g.chr22:39387537C>T	AK024854	CCDS13982.1, CCDS58807.1	22q13.1-q13.2	2008-05-15			ENSG00000179750	ENSG00000179750		"""Apolipoprotein B mRNA editing enzymes"""	17352	protein-coding gene	gene with protein product	"""phorbolin 3"""	607110				11863358, 10469298	Standard	NM_004900		Approved	PHRBNL, FLJ21201	uc003awo.2	Q9UH17	OTTHUMG00000151085	ENST00000333467.3:c.924C>T	22.37:g.39387537C>T						APOBEC3B_ENST00000407298.3_Silent_p.F283F|APOBEC3B_ENST00000333467.3_Silent_p.F308F	p.F308F			Q9UH17	ABC3B_HUMAN			6	979	+	Melanoma(58;0.04)		308					B0QYD2|O95618|Q20WL1|Q5IFJ4|Q7Z2N3|Q7Z6D6|Q9UE74	Silent	SNP	ENST00000333467.3	37	c.924C>T	CCDS13982.1																																																																																				0.572	APOBEC3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321233.1	NM_004900		35	194	0	0	0	0.059317	0	35	194				
RBM22	55696	broad.mit.edu	37	5	150073655	150073655	+	Silent	SNP	C	C	T			TCGA-DU-7018-01A-11D-2024-08	TCGA-DU-7018-10A-01D-2024-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	29c55a80-cd55-4297-b433-00d0e2b1e08d	453998d9-d9f9-479d-86c0-d889a58b836d	g.chr5:150073655C>T	ENST00000199814.4	-	8	1015	c.894G>A	c.(892-894)ctG>ctA	p.L298L	RBM22_ENST00000540000.1_Silent_p.L249L|RBM22_ENST00000447771.2_Silent_p.L249L	NM_018047.2	NP_060517.1	Q9NW64	RBM22_HUMAN	RNA binding motif protein 22	298	RRM. {ECO:0000255|PROSITE- ProRule:PRU00176}.				cellular response to drug (GO:0035690)|mRNA cis splicing, via spliceosome (GO:0045292)|mRNA splicing, via spliceosome (GO:0000398)|positive regulation of intracellular protein transport (GO:0090316)|positive regulation of RNA splicing (GO:0033120)|protein import into nucleus, translocation (GO:0000060)	catalytic step 2 spliceosome (GO:0071013)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	calcium-dependent protein binding (GO:0048306)|metal ion binding (GO:0046872)|nucleocytoplasmic transporter activity (GO:0005487)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|pre-mRNA binding (GO:0036002)|snRNA binding (GO:0017069)			breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(4)|ovary(1)	17		Medulloblastoma(196;0.167)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			ATTTCACATTCAGTCTGCGGC	0.398																																						ENST00000199814.4																			0				breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(4)|ovary(1)	17						c.(892-894)ctG>ctA		RNA binding motif protein 22							102.0	101.0	101.0					5																	150073655		2203	4300	6503	SO:0001819	synonymous_variant	55696				protein import into nucleus, translocation	catalytic step 2 spliceosome|cytoplasm	calcium-dependent protein binding|nucleotide binding|RNA binding|zinc ion binding	g.chr5:150073655C>T	AL136933	CCDS34278.1	5q33.1	2013-02-12			ENSG00000086589	ENSG00000086589		"""Zinc fingers, CCCH-type domain containing"", ""RNA binding motif (RRM) containing"""	25503	protein-coding gene	gene with protein product	"""functional spliceosome-associated protein 47"""	612430				20013661, 19133299	Standard	NM_018047		Approved	FLJ10290, ZC3H16, fSAP47, Cwc2	uc031slu.1	Q9NW64	OTTHUMG00000163589	ENST00000199814.4:c.894G>A	5.37:g.150073655C>T						RBM22_ENST00000447771.2_Silent_p.L249L|RBM22_ENST00000540000.1_Silent_p.L249L	p.L298L	NM_018047.2	NP_060517.1	Q9NW64	RBM22_HUMAN	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)		8	1015	-		Medulloblastoma(196;0.167)	298			RRM.		A6NDM5|B4DLI9|O95607	Silent	SNP	ENST00000199814.4	37	c.894G>A	CCDS34278.1																																																																																				0.398	RBM22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374431.2	NM_018047		5	129	0	0	0	0.014758	0	5	129				
VPS13B	157680	broad.mit.edu	37	8	100589785	100589785	+	Missense_Mutation	SNP	T	T	C	rs180177362		TCGA-DU-7018-01A-11D-2024-08	TCGA-DU-7018-10A-01D-2024-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	29c55a80-cd55-4297-b433-00d0e2b1e08d	453998d9-d9f9-479d-86c0-d889a58b836d	g.chr8:100589785T>C	ENST00000358544.2	+	33	5330	c.5219T>C	c.(5218-5220)gTg>gCg	p.V1740A	VPS13B_ENST00000395996.1_3'UTR|VPS13B_ENST00000357162.2_Missense_Mutation_p.V1715A	NM_017890.4	NP_060360.3	Q7Z7G8	VP13B_HUMAN	vacuolar protein sorting 13 homolog B (yeast)	1740			Missing (in COH1).		protein transport (GO:0015031)					NS(1)|autonomic_ganglia(1)|breast(6)|central_nervous_system(4)|cervix(3)|endometrium(11)|haematopoietic_and_lymphoid_tissue(4)|kidney(10)|large_intestine(37)|lung(78)|ovary(8)|pancreas(3)|prostate(5)|skin(9)|upper_aerodigestive_tract(4)|urinary_tract(9)	193	Breast(36;3.73e-07)		OV - Ovarian serous cystadenocarcinoma(57;0.00636)			TTCCTAAGTGTGGCTCAAGTT	0.388																																					Colon(161;2205 2542 7338 31318)	ENST00000358544.2																			0				NS(1)|autonomic_ganglia(1)|breast(6)|central_nervous_system(4)|cervix(3)|endometrium(11)|haematopoietic_and_lymphoid_tissue(4)|kidney(10)|large_intestine(37)|lung(78)|ovary(8)|pancreas(3)|prostate(5)|skin(9)|upper_aerodigestive_tract(4)|urinary_tract(9)	193						c.(5218-5220)gTg>gCg		vacuolar protein sorting 13 homolog B (yeast)							141.0	131.0	135.0					8																	100589785		2203	4300	6503	SO:0001583	missense	157680				protein transport			g.chr8:100589785T>C	AJ608772	CCDS6280.1, CCDS6281.1, CCDS6283.1, CCDS47903.1	8q22-q23	2014-09-17	2006-12-19	2005-04-08	ENSG00000132549	ENSG00000132549			2183	protein-coding gene	gene with protein product		607817	"""Cohen syndrome 1"""	CHS1, COH1		7920642, 15498460	Standard	NM_181661		Approved		uc003yiv.4	Q7Z7G8	OTTHUMG00000140383	ENST00000358544.2:c.5219T>C	8.37:g.100589785T>C	ENSP00000351346:p.Val1740Ala					VPS13B_ENST00000395996.1_3'UTR|VPS13B_ENST00000357162.2_Missense_Mutation_p.V1715A	p.V1740A	NM_017890.4	NP_060360.3	Q7Z7G8	VP13B_HUMAN	OV - Ovarian serous cystadenocarcinoma(57;0.00636)		33	5330	+	Breast(36;3.73e-07)		1740		Missing (in COH1).			C9JD30|Q709C6|Q709C7|Q7Z7G4|Q7Z7G5|Q7Z7G6|Q7Z7G7|Q8NB77|Q9NWV1|Q9Y4E7	Missense_Mutation	SNP	ENST00000358544.2	37	c.5219T>C	CCDS6280.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	24.6|24.6	4.546176|4.546176	0.86022|0.86022	.|.	.|.	ENSG00000132549|ENSG00000132549	ENST00000357162;ENST00000358544|ENST00000521559	T;T|.	0.70164|.	-0.45;-0.46|.	5.84|5.84	5.84|5.84	0.93424|0.93424	.|.	0.000000|.	0.64402|.	D|.	0.000001|.	T|T	0.51550|0.51550	0.1681|0.1681	N|N	0.19112|0.19112	0.55|0.55	0.80722|0.80722	D|D	1|1	D;D|.	0.71674|.	0.998;0.997|.	D;D|.	0.77557|.	0.99;0.978|.	T|T	0.48736|0.48736	-0.9009|-0.9009	10|5	0.66056|.	D|.	0.02|.	.|.	15.867|15.867	0.79071|0.79071	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	1715;1740|.	Q7Z7G8-2;Q7Z7G8|.	.;VP13B_HUMAN|.	A|R	1715;1740|103	ENSP00000349685:V1715A;ENSP00000351346:V1740A|.	ENSP00000349685:V1715A|.	V|W	+|+	2|1	0|0	VPS13B|VPS13B	100658961|100658961	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	5.675000|5.675000	0.68123|0.68123	2.226000|2.226000	0.72624|0.72624	0.482000|0.482000	0.46254|0.46254	GTG|TGG		0.388	VPS13B-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000277138.1	NM_184042		10	87	0	0	0	0.069234	0	10	87				
OR1A1	8383	broad.mit.edu	37	17	3119139	3119139	+	Silent	SNP	G	G	A	rs113780617		TCGA-DU-7018-01A-11D-2024-08	TCGA-DU-7018-10A-01D-2024-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	29c55a80-cd55-4297-b433-00d0e2b1e08d	453998d9-d9f9-479d-86c0-d889a58b836d	g.chr17:3119139G>A	ENST00000304094.1	+	1	225	c.225G>A	c.(223-225)tcG>tcA	p.S75S		NM_014565.2	NP_055380.2	Q9P1Q5	OR1A1_HUMAN	olfactory receptor, family 1, subfamily A, member 1	75						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(7)|ovary(1)|pancreas(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	23						TCTTCTCATCGGTAACCATCC	0.483																																						ENST00000304094.1																			0				NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(7)|ovary(1)|pancreas(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	23						c.(223-225)tcG>tcA		olfactory receptor, family 1, subfamily A, member 1							220.0	183.0	195.0					17																	3119139		2203	4300	6503	SO:0001819	synonymous_variant	8383				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity	g.chr17:3119139G>A	AF087918	CCDS11022.1	17p13.3	2012-08-09			ENSG00000172146	ENSG00000172146		"""GPCR / Class A : Olfactory receptors"""	8179	protein-coding gene	gene with protein product						10673334	Standard	NM_014565		Approved	OR17-7	uc010vrc.2	Q9P1Q5	OTTHUMG00000090637	ENST00000304094.1:c.225G>A	17.37:g.3119139G>A							p.S75S	NM_014565.2	NP_055380.2	Q9P1Q5	OR1A1_HUMAN			1	225	+			75					A5D914|Q6IFM1|Q6NTA9|Q96R87	Silent	SNP	ENST00000304094.1	37	c.225G>A	CCDS11022.1																																																																																				0.483	OR1A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207292.1	NM_014565		20	179	0	0	0	0.049695	0	20	179				
ITPRIPL1	150771	broad.mit.edu	37	2	96993753	96993753	+	Missense_Mutation	SNP	C	C	T			TCGA-DU-7018-01A-11D-2024-08	TCGA-DU-7018-10A-01D-2024-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	29c55a80-cd55-4297-b433-00d0e2b1e08d	453998d9-d9f9-479d-86c0-d889a58b836d	g.chr2:96993753C>T	ENST00000439118.2	+	3	1635	c.1384C>T	c.(1384-1386)Ctc>Ttc	p.L462F	ITPRIPL1_ENST00000361124.4_Missense_Mutation_p.L470F|ITPRIPL1_ENST00000542887.1_Missense_Mutation_p.L454F|ITPRIPL1_ENST00000536814.1_Missense_Mutation_p.L454F	NM_001008949.2	NP_001008949.1	Q6GPH6	IPIL1_HUMAN	inositol 1,4,5-trisphosphate receptor interacting protein-like 1	462						integral component of membrane (GO:0016021)|membrane (GO:0016020)				breast(1)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|lung(7)|ovary(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	27						ACGGCTGCCCCTCACGGACTG	0.567																																						ENST00000361124.4																			0				breast(1)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|lung(7)|ovary(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	27						c.(1408-1410)Ctc>Ttc		inositol 1,4,5-trisphosphate receptor interacting protein-like 1							94.0	93.0	93.0					2																	96993753		2203	4300	6503	SO:0001583	missense	150771					integral to membrane		g.chr2:96993753C>T		CCDS33250.1, CCDS46360.1, CCDS54378.1	2q11.2	2011-04-28	2011-04-28	2008-08-11	ENSG00000198885	ENSG00000198885			29371	protein-coding gene	gene with protein product			"""KIAA1754-like"", ""inositol 1,4,5-triphosphate receptor interacting protein-like 1"""	KIAA1754L		12477932	Standard	NM_178495		Approved		uc010yul.2	Q6GPH6	OTTHUMG00000155230	ENST00000439118.2:c.1384C>T	2.37:g.96993753C>T	ENSP00000389308:p.Leu462Phe					ITPRIPL1_ENST00000542887.1_Missense_Mutation_p.L454F|ITPRIPL1_ENST00000439118.2_Missense_Mutation_p.L462F|ITPRIPL1_ENST00000536814.1_Missense_Mutation_p.L454F	p.L470F	NM_178495.5	NP_848590.3	Q6GPH6	IPIL1_HUMAN			1	1819	+			462					F5H1L8|Q8NE61	Missense_Mutation	SNP	ENST00000439118.2	37	c.1408C>T	CCDS46360.1	.	.	.	.	.	.	.	.	.	.	C	11.72	1.721875	0.30503	.	.	ENSG00000198885	ENST00000536814;ENST00000439118;ENST00000361124;ENST00000542887	T;T;T;T	0.07908	3.15;3.15;3.15;3.15	5.5	4.63	0.57726	.	0.000000	0.36002	N	0.002857	T	0.11324	0.0276	L	0.27053	0.805	0.32809	D	0.50119	D;D	0.57899	0.976;0.981	P;P	0.57101	0.715;0.813	T	0.15925	-1.0420	10	0.22706	T	0.39	-19.6597	9.7148	0.40268	0.0:0.8414:0.0:0.1586	.	470;462	Q6GPH6-2;Q6GPH6	.;IPIL1_HUMAN	F	454;462;470;454	ENSP00000439566:L454F;ENSP00000389308:L462F;ENSP00000355121:L470F;ENSP00000438212:L454F	ENSP00000355121:L470F	L	+	1	0	ITPRIPL1	96357480	0.818000	0.29161	0.968000	0.41197	0.926000	0.56050	1.627000	0.37050	1.561000	0.49584	0.655000	0.94253	CTC		0.567	ITPRIPL1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000338896.1	NM_178495		17	83	0	0	0	0.028581	0	17	83				
PIK3CA	5290	broad.mit.edu	37	3	178936082	178936082	+	Missense_Mutation	SNP	G	G	A	rs121913273		TCGA-DU-7018-01A-11D-2024-08	TCGA-DU-7018-10A-01D-2024-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	29c55a80-cd55-4297-b433-00d0e2b1e08d	453998d9-d9f9-479d-86c0-d889a58b836d	g.chr3:178936082G>A	ENST00000263967.3	+	10	1781	c.1624G>A	c.(1624-1626)Gaa>Aaa	p.E542K		NM_006218.2	NP_006209.2	P42336	PK3CA_HUMAN	phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit alpha	542	PIK helical. {ECO:0000255|PROSITE- ProRule:PRU00878}.		E -> K (in CLOVE, KERSEB, CRC and BC; also found in glioblastoma multiforme and endometrial carcinoma; shows an increase in lipid kinase activity; oncogenic in vivo; occurs in the interface between the PI3K helical domain and the nSH2 (N- terminal SH2) region of the p85 regulatory subunit and may reduce the inhibitory effect of p85; requires interaction with RAS to induce cellular transformation). {ECO:0000269|PubMed:15289301, ECO:0000269|PubMed:15784156, ECO:0000269|PubMed:15924253, ECO:0000269|PubMed:15994075, ECO:0000269|PubMed:16322209, ECO:0000269|PubMed:16353168, ECO:0000269|PubMed:16533766, ECO:0000269|PubMed:17673550, ECO:0000269|PubMed:22658544}.|E -> Q (found in an endometrial carcinoma sample; unknown pathological significance). {ECO:0000269|PubMed:16322209}.|E -> V (in BC; unknown pathological significance). {ECO:0000269|PubMed:16353168}.		angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|endothelial cell migration (GO:0043542)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glucose metabolic process (GO:0006006)|hypomethylation of CpG island (GO:0044029)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|insulin receptor signaling pathway via phosphatidylinositol 3-kinase (GO:0038028)|leukocyte migration (GO:0050900)|negative regulation of anoikis (GO:2000811)|negative regulation of fibroblast apoptotic process (GO:2000270)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|protein kinase B signaling (GO:0043491)|regulation of genetic imprinting (GO:2000653)|regulation of multicellular organism growth (GO:0040014)|small molecule metabolic process (GO:0044281)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|vasculature development (GO:0001944)	1-phosphatidylinositol-4-phosphate 3-kinase, class IA complex (GO:0005943)|cytosol (GO:0005829)|lamellipodium (GO:0030027)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|kinase activity (GO:0016301)|phosphatidylinositol 3-kinase activity (GO:0035004)|phosphatidylinositol-4,5-bisphosphate 3-kinase activity (GO:0046934)|protein kinase activator activity (GO:0030295)|protein serine/threonine kinase activity (GO:0004674)	p.E542K(545)|p.E542Q(10)		NS(16)|autonomic_ganglia(4)|biliary_tract(22)|bone(1)|breast(2150)|central_nervous_system(110)|cervix(33)|endometrium(473)|eye(1)|haematopoietic_and_lymphoid_tissue(35)|kidney(14)|large_intestine(1202)|liver(42)|lung(202)|meninges(1)|oesophagus(28)|ovary(235)|pancreas(17)|penis(8)|pituitary(12)|prostate(10)|skin(155)|small_intestine(1)|soft_tissue(18)|stomach(121)|thyroid(80)|upper_aerodigestive_tract(70)|urinary_tract(208)	5269	all_cancers(143;1.19e-17)|Ovarian(172;0.00769)|Breast(254;0.155)		OV - Ovarian serous cystadenocarcinoma(80;9.59e-28)|GBM - Glioblastoma multiforme(14;0.003)|BRCA - Breast invasive adenocarcinoma(182;0.0282)		Caffeine(DB00201)	TCCTCTCTCTGAAATCACTGA	0.333	E542K(BT483_BREAST)|E542K(CAL51_BREAST)|E542K(HGC27_STOMACH)|E542K(IM95_STOMACH)|E542K(JHUEM1_ENDOMETRIUM)|E542K(NCIH1341_LUNG)|E542K(SW948_LARGE_INTESTINE)|E542K(T84_LARGE_INTESTINE)|E542K(VMCUB1_URINARY_TRACT)	57	Mis		"""colorectal, gastric, gliobastoma, breast"""					HNSCC(19;0.045)|TSP Lung(28;0.18)																											Colon(199;1504 1750 3362 26421 31210 32040)	ENST00000263967.3	E542K(BT483_BREAST)|E542K(CAL51_BREAST)|E542K(HGC27_STOMACH)|E542K(IM95_STOMACH)|E542K(JHUEM1_ENDOMETRIUM)|E542K(NCIH1341_LUNG)|E542K(SW948_LARGE_INTESTINE)|E542K(T84_LARGE_INTESTINE)|E542K(VMCUB1_URINARY_TRACT)	57		Dom	yes		3	3q26.3	5290	Mis	"""phosphoinositide-3-kinase, catalytic, alpha polypeptide"""			"""E, O"""			"""colorectal, gastric, gliobastoma, breast"""		555	Substitution - Missense(555)	p.E542K(545)|p.E542Q(10)	breast(176)|large_intestine(166)|urinary_tract(45)|endometrium(37)|skin(19)|lung(18)|stomach(16)|ovary(16)|thyroid(14)|upper_aerodigestive_tract(9)|central_nervous_system(7)|cervix(6)|liver(6)|oesophagus(5)|penis(4)|kidney(3)|soft_tissue(2)|haematopoietic_and_lymphoid_tissue(2)|prostate(2)|biliary_tract(1)|pituitary(1)	NS(16)|autonomic_ganglia(4)|biliary_tract(22)|bone(1)|breast(2150)|central_nervous_system(110)|cervix(33)|endometrium(473)|eye(1)|haematopoietic_and_lymphoid_tissue(35)|kidney(14)|large_intestine(1202)|liver(42)|lung(202)|meninges(1)|oesophagus(28)|ovary(235)|pancreas(17)|penis(8)|pituitary(12)|prostate(10)|skin(155)|small_intestine(1)|soft_tissue(18)|stomach(121)|thyroid(80)|upper_aerodigestive_tract(70)|urinary_tract(208)	5269						c.(1624-1626)Gaa>Aaa		phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit alpha							56.0	56.0	56.0					3																	178936082		1809	4069	5878	SO:0001583	missense	5290				epidermal growth factor receptor signaling pathway|fibroblast growth factor receptor signaling pathway|insulin receptor signaling pathway|leukocyte migration|nerve growth factor receptor signaling pathway|phosphatidylinositol-mediated signaling|platelet activation|T cell costimulation|T cell receptor signaling pathway		1-phosphatidylinositol-3-kinase activity|ATP binding|phosphatidylinositol-4,5-bisphosphate 3-kinase activity	g.chr3:178936082G>A		CCDS43171.1	3q26.3	2014-09-17	2012-07-13		ENSG00000121879	ENSG00000121879	2.7.1.153		8975	protein-coding gene	gene with protein product		171834	"""phosphoinositide-3-kinase, catalytic, alpha polypeptide"""			1322797	Standard	NM_006218		Approved	PI3K	uc003fjk.3	P42336	OTTHUMG00000157311	ENST00000263967.3:c.1624G>A	3.37:g.178936082G>A	ENSP00000263967:p.Glu542Lys	HNSCC(19;0.045)|TSP Lung(28;0.18)					p.E542K	NM_006218.2	NP_006209.2	P42336	PK3CA_HUMAN	OV - Ovarian serous cystadenocarcinoma(80;9.59e-28)|GBM - Glioblastoma multiforme(14;0.003)|BRCA - Breast invasive adenocarcinoma(182;0.0282)		10	1781	+	all_cancers(143;1.19e-17)|Ovarian(172;0.00769)|Breast(254;0.155)		542		E -> K (in KERSEB; shows an increase in lipid kinase activity; oncogenic in vivo; occurs in the interface between the PI3K helical domain and the nSH2 (N-terminal SH2) region of the p85 regulatory subunit and may reduce the inhibitory effect of p85; requires interaction with RAS to induce cellular transformation).|E -> Q (in cancer).|E -> V (in cancer).	PI3K helical.		Q14CW1|Q99762	Missense_Mutation	SNP	ENST00000263967.3	37	c.1624G>A	CCDS43171.1	.	.	.	.	.	.	.	.	.	.	G	34	5.360420	0.95877	.	.	ENSG00000121879	ENST00000263967	T	0.62105	0.05	5.78	5.78	0.91487	Phosphoinositide 3-kinase, accessory (PIK) domain (3);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.69287	0.3094	L	0.41356	1.27	0.80722	D	1	D	0.65815	0.995	D	0.63192	0.912	T	0.60296	-0.7291	10	0.09843	T	0.71	-23.9623	20.0024	0.97423	0.0:0.0:1.0:0.0	.	542	P42336	PK3CA_HUMAN	K	542	ENSP00000263967:E542K	ENSP00000263967:E542K	E	+	1	0	PIK3CA	180418776	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	9.476000	0.97823	2.722000	0.93159	0.467000	0.42956	GAA		0.333	PIK3CA-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000348409.2			6	39	0	0	0	0.029380	0	6	39				
LOC647323	647323	broad.mit.edu	37	3	193711891	193711891	+	lincRNA	SNP	T	T	C	rs111993093	byFrequency	TCGA-DU-7018-01A-11D-2024-08	TCGA-DU-7018-10A-01D-2024-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	29c55a80-cd55-4297-b433-00d0e2b1e08d	453998d9-d9f9-479d-86c0-d889a58b836d	g.chr3:193711891T>C	ENST00000397645.2	-	0	75				RP11-699L21.2_ENST00000426616.1_lincRNA	NR_033944.1																						CTTGGTTCCATTTGTTCCATA	0.388													T|||	190	0.0379393	0.1036	0.0159	5008	,	,		19460	0.0		0.0278	False		,,,				2504	0.0143					ENST00000397645.2																			0																																																			0							g.chr3:193711891T>C																													3.37:g.193711891T>C						RP11-699L21.2_ENST00000426616.1_lincRNA		NR_033944.1						0	75	-									RNA	SNP	ENST00000397645.2	37																																																																																						0.388	RP11-699L21.1-001	KNOWN	basic|exp_conf	lincRNA	lincRNA	OTTHUMT00000342625.1			3	44	0	0	0	0.014758	0	3	44				
FGD6	55785	broad.mit.edu	37	12	95604123	95604123	+	Missense_Mutation	SNP	G	G	A			TCGA-DU-7018-01A-11D-2024-08	TCGA-DU-7018-10A-01D-2024-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	29c55a80-cd55-4297-b433-00d0e2b1e08d	453998d9-d9f9-479d-86c0-d889a58b836d	g.chr12:95604123G>A	ENST00000343958.4	-	2	1160	c.937C>T	c.(937-939)Cca>Tca	p.P313S	FGD6_ENST00000546711.1_Missense_Mutation_p.P313S|FGD6_ENST00000550368.1_5'Flank|FGD6_ENST00000549499.1_Missense_Mutation_p.P313S	NM_018351.3	NP_060821.3	Q6ZV73	FGD6_HUMAN	FYVE, RhoGEF and PH domain containing 6	313					actin cytoskeleton organization (GO:0030036)|cytoskeleton organization (GO:0007010)|filopodium assembly (GO:0046847)|positive regulation of GTPase activity (GO:0043547)|regulation of Cdc42 GTPase activity (GO:0043088)|regulation of cell shape (GO:0008360)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|lamellipodium (GO:0030027)|ruffle (GO:0001726)	guanyl-nucleotide exchange factor activity (GO:0005085)|metal ion binding (GO:0046872)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|small GTPase binding (GO:0031267)			breast(3)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(14)|liver(1)|lung(12)|ovary(3)|prostate(3)|skin(6)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	56						TTGGGAGTTGGAAATTTTGGG	0.413																																						ENST00000343958.4																			0				breast(3)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(14)|liver(1)|lung(12)|ovary(3)|prostate(3)|skin(6)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	56						c.(937-939)Cca>Tca		FYVE, RhoGEF and PH domain containing 6							96.0	101.0	99.0					12																	95604123		2203	4300	6503	SO:0001583	missense	55785				actin cytoskeleton organization|filopodium assembly|regulation of Cdc42 GTPase activity|regulation of cell shape	cytoskeleton|Golgi apparatus|lamellipodium|ruffle	metal ion binding|Rho guanyl-nucleotide exchange factor activity|small GTPase binding	g.chr12:95604123G>A	AB037783	CCDS31878.1	12q23.1	2013-01-10				ENSG00000180263		"""Zinc fingers, FYVE domain containing"", ""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	21740	protein-coding gene	gene with protein product		613520					Standard	NM_018351		Approved	ZFYVE24, FLJ11183	uc001tdp.4	Q6ZV73	OTTHUMG00000170133	ENST00000343958.4:c.937C>T	12.37:g.95604123G>A	ENSP00000344446:p.Pro313Ser					FGD6_ENST00000549499.1_Missense_Mutation_p.P313S|FGD6_ENST00000546711.1_Missense_Mutation_p.P313S	p.P313S	NM_018351.3	NP_060821.3	Q6ZV73	FGD6_HUMAN			2	1160	-			313					Q6ZR53|Q7Z2Z7|Q96D44|Q9NUR8|Q9P2I5	Missense_Mutation	SNP	ENST00000343958.4	37	c.937C>T	CCDS31878.1	.	.	.	.	.	.	.	.	.	.	G	19.28	3.796802	0.70567	.	.	ENSG00000180263	ENST00000343958;ENST00000546711;ENST00000549499	D;D;D	0.83837	-1.57;-1.69;-1.77	5.51	5.51	0.81932	.	0.000000	0.44688	D	0.000422	D	0.90504	0.7025	M	0.66939	2.045	0.51767	D	0.999934	D	0.89917	1.0	D	0.85130	0.997	D	0.89687	0.3895	10	0.45353	T	0.12	-13.4445	19.4241	0.94734	0.0:0.0:1.0:0.0	.	313	Q6ZV73	FGD6_HUMAN	S	313	ENSP00000344446:P313S;ENSP00000450342:P313S;ENSP00000449005:P313S	ENSP00000344446:P313S	P	-	1	0	FGD6	94128254	1.000000	0.71417	1.000000	0.80357	0.958000	0.62258	6.744000	0.74854	2.578000	0.87016	0.561000	0.74099	CCA		0.413	FGD6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407600.1	NM_018351		12	143	0	0	0	0.080935	0	12	143				
NOTCH1	4851	broad.mit.edu	37	9	139392000	139392000	+	Missense_Mutation	SNP	G	G	A			TCGA-DU-7018-01A-11D-2024-08	TCGA-DU-7018-10A-01D-2024-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	29c55a80-cd55-4297-b433-00d0e2b1e08d	453998d9-d9f9-479d-86c0-d889a58b836d	g.chr9:139392000G>A	ENST00000277541.6	-	34	6266	c.6191C>T	c.(6190-6192)cCc>cTc	p.P2064L		NM_017617.3	NP_060087.3	P46531	NOTC1_HUMAN	notch 1	2064					anagen (GO:0042640)|aortic valve morphogenesis (GO:0003180)|apoptotic process involved in embryonic digit morphogenesis (GO:1902263)|arterial endothelial cell differentiation (GO:0060842)|atrioventricular node development (GO:0003162)|atrioventricular valve morphogenesis (GO:0003181)|auditory receptor cell fate commitment (GO:0009912)|axonogenesis (GO:0007409)|branching morphogenesis of an epithelial tube (GO:0048754)|cardiac atrium morphogenesis (GO:0003209)|cardiac chamber formation (GO:0003207)|cardiac epithelial to mesenchymal transition (GO:0060317)|cardiac left ventricle morphogenesis (GO:0003214)|cardiac muscle cell proliferation (GO:0060038)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac right atrium morphogenesis (GO:0003213)|cardiac right ventricle formation (GO:0003219)|cardiac septum morphogenesis (GO:0060411)|cardiac vascular smooth muscle cell development (GO:0060948)|cardiac ventricle morphogenesis (GO:0003208)|cell fate specification (GO:0001708)|cell migration involved in endocardial cushion formation (GO:0003273)|cellular response to follicle-stimulating hormone stimulus (GO:0071372)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|cilium morphogenesis (GO:0060271)|collecting duct development (GO:0072044)|compartment pattern specification (GO:0007386)|coronary artery morphogenesis (GO:0060982)|coronary vein morphogenesis (GO:0003169)|determination of left/right symmetry (GO:0007368)|distal tubule development (GO:0072017)|embryonic hindlimb morphogenesis (GO:0035116)|endocardial cell differentiation (GO:0060956)|endocardial cushion morphogenesis (GO:0003203)|endocardium development (GO:0003157)|endocardium morphogenesis (GO:0003160)|endoderm development (GO:0007492)|epithelial to mesenchymal transition (GO:0001837)|epithelial to mesenchymal transition involved in endocardial cushion formation (GO:0003198)|forebrain development (GO:0030900)|foregut morphogenesis (GO:0007440)|gene expression (GO:0010467)|glial cell differentiation (GO:0010001)|glomerular mesangial cell development (GO:0072144)|growth involved in heart morphogenesis (GO:0003241)|hair follicle morphogenesis (GO:0031069)|heart development (GO:0007507)|heart looping (GO:0001947)|heart trabecula morphogenesis (GO:0061384)|humoral immune response (GO:0006959)|immune response (GO:0006955)|in utero embryonic development (GO:0001701)|inflammatory response to antigenic stimulus (GO:0002437)|interleukin-4 secretion (GO:0072602)|keratinocyte differentiation (GO:0030216)|left/right axis specification (GO:0070986)|liver development (GO:0001889)|lung development (GO:0030324)|mesenchymal cell development (GO:0014031)|mitral valve formation (GO:0003192)|negative regulation of anoikis (GO:2000811)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of calcium ion-dependent exocytosis (GO:0045955)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of catalytic activity (GO:0043086)|negative regulation of cell migration involved in sprouting angiogenesis (GO:0090051)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell-substrate adhesion (GO:0010812)|negative regulation of endothelial cell chemotaxis (GO:2001027)|negative regulation of glial cell proliferation (GO:0060253)|negative regulation of myoblast differentiation (GO:0045662)|negative regulation of myotube differentiation (GO:0010832)|negative regulation of neurogenesis (GO:0050768)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of ossification (GO:0030279)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of photoreceptor cell differentiation (GO:0046533)|negative regulation of pro-B cell differentiation (GO:2000974)|negative regulation of stem cell differentiation (GO:2000737)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|neural tube development (GO:0021915)|neuronal stem cell maintenance (GO:0097150)|Notch receptor processing (GO:0007220)|Notch signaling involved in heart development (GO:0061314)|Notch signaling pathway (GO:0007219)|Notch signaling pathway involved in regulation of secondary heart field cardioblast proliferation (GO:0003270)|pericardium morphogenesis (GO:0003344)|positive regulation of apoptotic process (GO:0043065)|positive regulation of astrocyte differentiation (GO:0048711)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of JAK-STAT cascade (GO:0046427)|positive regulation of keratinocyte differentiation (GO:0045618)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061419)|positive regulation of transcription of Notch receptor target (GO:0007221)|positive regulation of transcription, DNA-templated (GO:0045893)|prostate gland epithelium morphogenesis (GO:0060740)|pulmonary valve morphogenesis (GO:0003184)|regulation of epithelial cell proliferation involved in prostate gland development (GO:0060768)|regulation of extracellular matrix assembly (GO:1901201)|regulation of somitogenesis (GO:0014807)|regulation of transcription from RNA polymerase II promoter involved in myocardial precursor cell differentiation (GO:0003256)|regulation of transcription, DNA-templated (GO:0006355)|response to muramyl dipeptide (GO:0032495)|secretory columnal luminar epithelial cell differentiation involved in prostate glandular acinus development (GO:0060528)|skeletal muscle cell differentiation (GO:0035914)|somatic stem cell division (GO:0048103)|sprouting angiogenesis (GO:0002040)|transcription initiation from RNA polymerase II promoter (GO:0006367)|tube formation (GO:0035148)|vasculogenesis involved in coronary vascular morphogenesis (GO:0060979)|venous endothelial cell differentiation (GO:0060843)|ventricular septum morphogenesis (GO:0060412)|ventricular trabecula myocardium morphogenesis (GO:0003222)	cell surface (GO:0009986)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|MAML1-RBP-Jkappa- ICN1 complex (GO:0002193)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)|chromatin DNA binding (GO:0031490)|core promoter binding (GO:0001047)|enzyme binding (GO:0019899)|enzyme inhibitor activity (GO:0004857)|receptor activity (GO:0004872)|RNA polymerase II transcription factor binding transcription factor activity involved in positive regulation of transcription (GO:0001190)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(16)|central_nervous_system(17)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1183)|kidney(4)|large_intestine(1)|lung(57)|oesophagus(2)|ovary(3)|pancreas(1)|prostate(3)|skin(21)|upper_aerodigestive_tract(39)|urinary_tract(3)	1359	all_cancers(76;0.223)	Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;5.34e-06)|Epithelial(140;7.77e-06)		CAGAAACAGGGGTGTCTCCTC	0.677			"""T, Mis, O"""	TRB@	T-ALL					HNSCC(8;0.001)																												ENST00000277541.6				Dom	yes		9	9q34.3	4851	"""T, Mis, O"""	"""Notch homolog 1, translocation-associated (Drosophila) (TAN1)"""			L	TRB@		T-ALL		0				breast(16)|central_nervous_system(17)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1183)|kidney(4)|large_intestine(1)|lung(57)|oesophagus(2)|ovary(3)|pancreas(1)|prostate(3)|skin(21)|upper_aerodigestive_tract(39)|urinary_tract(3)	1359						c.(6190-6192)cCc>cTc		notch 1							12.0	14.0	13.0					9																	139392000		1977	4165	6142	SO:0001583	missense	4851				aortic valve morphogenesis|immune response|negative regulation of BMP signaling pathway|negative regulation of cell-substrate adhesion|negative regulation of myoblast differentiation|negative regulation of osteoblast differentiation|negative regulation of transcription, DNA-dependent|Notch receptor processing	cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to membrane|nucleoplasm|plasma membrane	calcium ion binding|protein binding|receptor activity	g.chr9:139392000G>A	AF308602	CCDS43905.1	9q34.3	2013-01-10	2010-06-24		ENSG00000148400	ENSG00000148400		"""Ankyrin repeat domain containing"""	7881	protein-coding gene	gene with protein product		190198	"""Notch (Drosophila) homolog 1 (translocation-associated)"", ""Notch homolog 1, translocation-associated (Drosophila)"""	TAN1		1831692	Standard	NM_017617		Approved		uc004chz.3	P46531	OTTHUMG00000020935	ENST00000277541.6:c.6191C>T	9.37:g.139392000G>A	ENSP00000277541:p.Pro2064Leu	HNSCC(8;0.001)					p.P2064L	NM_017617.3	NP_060087.3	P46531	NOTC1_HUMAN		OV - Ovarian serous cystadenocarcinoma(145;5.34e-06)|Epithelial(140;7.77e-06)	34	6266	-	all_cancers(76;0.223)	Myeloproliferative disorder(178;0.0511)	2064					Q59ED8|Q5SXM3	Missense_Mutation	SNP	ENST00000277541.6	37	c.6191C>T	CCDS43905.1	.	.	.	.	.	.	.	.	.	.	G	21.1	4.097509	0.76870	.	.	ENSG00000148400	ENST00000277541	T	0.70516	-0.49	5.42	5.42	0.78866	Ankyrin repeat-containing domain (4);	0.115829	0.64402	D	0.000011	D	0.87317	0.6147	M	0.91038	3.17	0.80722	D	1	D	0.69078	0.997	D	0.66847	0.947	D	0.89790	0.3967	10	0.87932	D	0	.	18.5525	0.91071	0.0:0.0:1.0:0.0	.	2064	P46531	NOTC1_HUMAN	L	2064	ENSP00000277541:P2064L	ENSP00000277541:P2064L	P	-	2	0	NOTCH1	138511821	1.000000	0.71417	0.343000	0.25615	0.859000	0.49053	9.598000	0.98277	2.703000	0.92315	0.561000	0.74099	CCC		0.677	NOTCH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055087.1	NM_017617		3	20	0	0	0	0.009096	0	3	20				
MIR509-1	574514	broad.mit.edu	37	X	146342130	146342130	+	RNA	SNP	C	C	A			TCGA-DU-7018-01A-11D-2024-08	TCGA-DU-7018-10A-01D-2024-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	29c55a80-cd55-4297-b433-00d0e2b1e08d	453998d9-d9f9-479d-86c0-d889a58b836d	g.chrX:146342130C>A	ENST00000385265.1	-	0	13				MIR509-2_ENST00000390724.1_RNA|MIR509-3_ENST00000390725.1_RNA	NR_030236.1|NR_030586.1				microRNA 509-1																		CAGTAGGGTACCACACACAGC	0.438																																						ENST00000385265.1																			0																				131.0	114.0	120.0					X																	146342130		1568	3579	5147			0							g.chrX:146342130C>A			Xq27.3	2011-09-12	2007-10-23	2008-12-18	ENSG00000208000	ENSG00000208000		"""ncRNAs / Micro RNAs"""	32146	non-coding RNA	RNA, micro		300875	"""microRNA 509"""	MIRN509, MIRN509-1			Standard	NR_030236		Approved	hsa-mir-509, hsa-mir-509-1	uc022cfy.1				X.37:g.146342130C>A								NR_030236.1|NR_030586.1						0	13	-									RNA	SNP	ENST00000385265.1	37																																																																																						0.438	MIR509-1-201	KNOWN	basic	miRNA	miRNA		NR_030236		27	165	1	0	4.4194e-11	0.054565	4.86134e-11	27	165				
GPBP1L1	60313	broad.mit.edu	37	1	46120875	46120875	+	Silent	SNP	T	T	C			TCGA-DU-7018-01A-11D-2024-08	TCGA-DU-7018-10A-01D-2024-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	29c55a80-cd55-4297-b433-00d0e2b1e08d	453998d9-d9f9-479d-86c0-d889a58b836d	g.chr1:46120875T>C	ENST00000290795.3	-	4	1398	c.177A>G	c.(175-177)ctA>ctG	p.L59L	GPBP1L1_ENST00000355105.3_Silent_p.L59L			Q9HC44	GPBL1_HUMAN	GC-rich promoter binding protein 1-like 1	59					positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)		GPBP1L1/MAST2_ENST00000361297(2)	breast(1)|endometrium(2)|large_intestine(4)|lung(10)|ovary(1)|skin(2)|stomach(1)	21	Acute lymphoblastic leukemia(166;0.155)					CTGCAGTTCGTAGGGGACCAT	0.453																																						ENST00000355105.3																		GPBP1L1/MAST2_ENST00000361297(2)	0				breast(1)|endometrium(2)|large_intestine(4)|lung(10)|ovary(1)|skin(2)|stomach(1)	21						c.(175-177)ctA>ctG		GC-rich promoter binding protein 1-like 1							107.0	109.0	108.0					1																	46120875		2203	4300	6503	SO:0001819	synonymous_variant	60313				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding	g.chr1:46120875T>C		CCDS528.1	1p34.1	2008-02-05			ENSG00000159592	ENSG00000159592			28843	protein-coding gene	gene with protein product						12477932	Standard	NM_021639		Approved	SP192	uc001coq.3	Q9HC44	OTTHUMG00000040990	ENST00000290795.3:c.177A>G	1.37:g.46120875T>C						GPBP1L1_ENST00000290795.3_Silent_p.L59L	p.L59L	NM_021639.4	NP_067652.1	Q9HC44	GPBL1_HUMAN			5	1537	-	Acute lymphoblastic leukemia(166;0.155)		59					D3DQ10|Q9H751	Silent	SNP	ENST00000290795.3	37	c.177A>G	CCDS528.1																																																																																				0.453	GPBP1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098375.1	NM_021639		13	57	0	0	0	0.020292	0	13	57				
SMARCAL1	50485	broad.mit.edu	37	2	217279430	217279430	+	Start_Codon_SNP	SNP	G	G	A			TCGA-DU-7018-01A-11D-2024-08	TCGA-DU-7018-10A-01D-2024-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	29c55a80-cd55-4297-b433-00d0e2b1e08d	453998d9-d9f9-479d-86c0-d889a58b836d	g.chr2:217279430G>A	ENST00000357276.4	+	3	333	c.3G>A	c.(1-3)atG>atA	p.M1I	SMARCAL1_ENST00000358207.5_Start_Codon_SNP_p.M1I|AC098820.2_ENST00000457694.1_RNA	NM_014140.3	NP_054859.2	Q9NZC9	SMAL1_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a-like 1	1					cellular response to DNA damage stimulus (GO:0006974)|chromatin modification (GO:0016568)|DNA metabolic process (GO:0006259)|DNA strand renaturation (GO:0000733)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|replication fork processing (GO:0031297)	nucleus (GO:0005634)|site of double-strand break (GO:0035861)	annealing helicase activity (GO:0036310)|ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA-dependent ATPase activity (GO:0008094)|helicase activity (GO:0004386)			NS(1)|breast(3)|endometrium(4)|kidney(3)|large_intestine(10)|liver(1)|lung(15)|ovary(3)|prostate(1)|skin(1)	42		Renal(323;0.0458)		Epithelial(149;9.48e-06)|all cancers(144;0.000621)|LUSC - Lung squamous cell carcinoma(224;0.00829)|Lung(261;0.0111)		CTGTGAAAATGTCCTTGCCTC	0.413									Schimke Immuno-Osseous Dysplasia																													ENST00000357276.4																			0				NS(1)|breast(3)|endometrium(4)|kidney(3)|large_intestine(10)|liver(1)|lung(15)|ovary(3)|prostate(1)|skin(1)	42						c.(1-3)atG>atA		SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a-like 1							44.0	50.0	48.0					2																	217279430		2201	4300	6501	SO:0001582	initiator_codon_variant	50485	Schimke Immuno-Osseous Dysplasia	Familial Cancer Database	SIOD	chromatin modification|DNA metabolic process|regulation of transcription from RNA polymerase II promoter	nucleus	ATP binding|DNA binding|DNA helicase activity|DNA-dependent ATPase activity	g.chr2:217279430G>A	AF210833	CCDS2403.1	2q35	2014-09-17			ENSG00000138375	ENSG00000138375			11102	protein-coding gene	gene with protein product	"""HepA-related protein"", ""ATP-driven annealing helicase"""	606622				10713074, 10857751, 18974355	Standard	NM_014140		Approved	HHARP, HARP	uc002vgd.4	Q9NZC9	OTTHUMG00000133055	ENST00000357276.4:c.3G>A	2.37:g.217279430G>A	ENSP00000349823:p.Met1Ile					SMARCAL1_ENST00000358207.5_Start_Codon_SNP_p.M1I	p.M1I	NM_014140.3	NP_054859.2	Q9NZC9	SMAL1_HUMAN		Epithelial(149;9.48e-06)|all cancers(144;0.000621)|LUSC - Lung squamous cell carcinoma(224;0.00829)|Lung(261;0.0111)	3	333	+		Renal(323;0.0458)	1					A6NEH0|Q53R00|Q96AY1|Q9NXQ5|Q9UFH3|Q9UI93	Translation_Start_Site	SNP	ENST00000357276.4	37	c.3G>A	CCDS2403.1	.	.	.	.	.	.	.	.	.	.	G	26.1	4.707917	0.89018	.	.	ENSG00000138375	ENST00000430374;ENST00000357276;ENST00000444508;ENST00000425815;ENST00000358207;ENST00000434435	T;D;T;D;D;T	0.92299	0.16;-2.83;0.22;-3.01;-2.83;-0.19	5.45	5.45	0.79879	.	0.096042	0.64402	D	0.000002	D	0.95953	0.8682	.	.	.	0.80722	D	1	D	0.63880	0.993	D	0.66196	0.942	D	0.96325	0.9239	9	0.87932	D	0	-29.1156	17.8589	0.88775	0.0:0.0:1.0:0.0	.	1	Q9NZC9	SMAL1_HUMAN	I	1	ENSP00000405077:M1I;ENSP00000349823:M1I;ENSP00000398969:M1I;ENSP00000394410:M1I;ENSP00000350940:M1I;ENSP00000402967:M1I	ENSP00000349823:M1I	M	+	3	0	SMARCAL1	216987675	1.000000	0.71417	1.000000	0.80357	0.874000	0.50279	6.599000	0.74127	2.556000	0.86216	0.563000	0.77884	ATG		0.413	SMARCAL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256671.2		Missense_Mutation	10	55	0	0	0	0.058154	0	10	55				
PLCD3	113026	broad.mit.edu	37	17	43194022	43194022	+	Missense_Mutation	SNP	G	G	T			TCGA-DU-7018-01A-11D-2024-08	TCGA-DU-7018-10A-01D-2024-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	29c55a80-cd55-4297-b433-00d0e2b1e08d	453998d9-d9f9-479d-86c0-d889a58b836d	g.chr17:43194022G>T	ENST00000322765.5	-	8	1503	c.1390C>A	c.(1390-1392)Ccc>Acc	p.P464T	PLCD3_ENST00000540511.1_5'UTR	NM_133373.3	NP_588614.1	Q8N3E9	PLCD3_HUMAN	phospholipase C, delta 3	464	PI-PLC X-box. {ECO:0000255|PROSITE- ProRule:PRU00270}.				angiogenesis (GO:0001525)|inositol phosphate metabolic process (GO:0043647)|intracellular signal transduction (GO:0035556)|labyrinthine layer blood vessel development (GO:0060716)|lipid catabolic process (GO:0016042)|regulation of cell proliferation (GO:0042127)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|phosphatidylinositol phospholipase C activity (GO:0004435)|signal transducer activity (GO:0004871)			breast(2)|endometrium(2)|large_intestine(3)|lung(5)|prostate(1)|stomach(2)|urinary_tract(2)	17						AGCTCCTCGGGATTTGGGGAG	0.692																																						ENST00000322765.5																			0				breast(2)|endometrium(2)|large_intestine(3)|lung(5)|prostate(1)|stomach(2)|urinary_tract(2)	17						c.(1390-1392)Ccc>Acc		phospholipase C, delta 3	Phosphatidylserine(DB00144)						39.0	45.0	43.0					17																	43194022		2086	4198	6284	SO:0001583	missense	113026				intracellular signal transduction|lipid catabolic process	cleavage furrow|cytoplasm|membrane	calcium ion binding|phosphatidylinositol phospholipase C activity|signal transducer activity	g.chr17:43194022G>T	AC002117	CCDS74077.1	17q21	2012-04-20			ENSG00000161714	ENSG00000161714	3.1.4.11		9061	protein-coding gene	gene with protein product		608795				10702670, 9056492	Standard	NM_133373		Approved		uc002iib.3	Q8N3E9	OTTHUMG00000168029	ENST00000322765.5:c.1390C>A	17.37:g.43194022G>T	ENSP00000313731:p.Pro464Thr					PLCD3_ENST00000540511.1_5'UTR	p.P464T	NM_133373.3	NP_588614.1	Q8N3E9	PLCD3_HUMAN			8	1503	-			464			PI-PLC X-box.		Q8TEC1|Q8TF37|Q96FL6	Missense_Mutation	SNP	ENST00000322765.5	37	c.1390C>A		.	.	.	.	.	.	.	.	.	.	G	13.04	2.116925	0.37339	.	.	ENSG00000161714	ENST00000322765	T	0.61627	0.09	4.36	4.36	0.52297	PLC-like phosphodiesterase, TIM beta/alpha-barrel domain (2);Phospholipase C, phosphatidylinositol-specific , X domain (3);	0.187009	0.46758	D	0.000267	T	0.48768	0.1518	.	.	.	0.09310	N	0.999997	P	0.42785	0.79	P	0.48141	0.568	T	0.34104	-0.9842	9	0.10377	T	0.69	.	11.4264	0.50014	0.0:0.0:0.8193:0.1807	.	464	Q8N3E9	PLCD3_HUMAN	T	464	ENSP00000313731:P464T	ENSP00000313731:P464T	P	-	1	0	PLCD3	40549548	0.999000	0.42202	0.959000	0.39883	0.193000	0.23685	4.342000	0.59341	2.417000	0.82017	0.555000	0.69702	CCC		0.692	PLCD3-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_133373		29	34	1	0	1.61788e-16	0.050027	1.84103e-16	29	34				
IL9	3578	broad.mit.edu	37	5	135231431	135231431	+	Silent	SNP	C	C	T	rs368804746		TCGA-DU-7018-01A-11D-2024-08	TCGA-DU-7018-10A-01D-2024-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	29c55a80-cd55-4297-b433-00d0e2b1e08d	453998d9-d9f9-479d-86c0-d889a58b836d	g.chr5:135231431C>T	ENST00000274520.1	-	1	85	c.75G>A	c.(73-75)gcG>gcA	p.A25A	GS1-39E22.2_ENST00000522973.1_RNA	NM_000590.1	NP_000581.1	P15248	IL9_HUMAN	interleukin 9	25					immune response (GO:0006955)|inflammatory response (GO:0006954)|positive regulation of cell growth (GO:0030307)|positive regulation of cell proliferation (GO:0008284)|positive regulation of interleukin-5 biosynthetic process (GO:0045407)	extracellular space (GO:0005615)				large_intestine(3)|lung(2)|pancreas(1)	6			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)			CCAGGATCCCCGCCAAGGTTG	0.567																																						ENST00000274520.1																			0				large_intestine(3)|lung(2)|pancreas(1)	6						c.(73-75)gcG>gcA		interleukin 9		C		1,4405	2.1+/-5.4	0,1,2202	68.0	72.0	71.0		75	-9.6	0.0	5		71	0,8600		0,0,4300	no	coding-synonymous	IL9	NM_000590.1		0,1,6502	TT,TC,CC		0.0,0.0227,0.0077		25/145	135231431	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	3578				immune response|inflammatory response|positive regulation of cell proliferation|positive regulation of interleukin-5 biosynthetic process	extracellular space	cytokine activity|cytokine receptor binding|growth factor activity	g.chr5:135231431C>T	S63356	CCDS4189.1	5q31-q35	2008-07-18			ENSG00000145839	ENSG00000145839		"""Interleukins and interleukin receptors"""	6029	protein-coding gene	gene with protein product	"""p40 T-cell and mast cell growth factor"", ""T-cell growth factor p40"", ""p40 cytokine"", ""homolog of mouse T cell and mast cell growth factor 40"""	146931				8379467	Standard	NM_000590		Approved	IL-9, HP40, P40	uc003lbb.1	P15248	OTTHUMG00000129147	ENST00000274520.1:c.75G>A	5.37:g.135231431C>T							p.A25A	NM_000590.1	NP_000581.1	P15248	IL9_HUMAN	KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)		1	85	-			25						Silent	SNP	ENST00000274520.1	37	c.75G>A	CCDS4189.1																																																																																				0.567	IL9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251210.1	NM_000590		6	80	0	0	0	0.021553	0	6	80				
LINC00969	440993	broad.mit.edu	37	3	195395399	195395399	+	lincRNA	SNP	G	G	A	rs62287990	byFrequency	TCGA-DU-7018-01A-11D-2024-08	TCGA-DU-7018-10A-01D-2024-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	29c55a80-cd55-4297-b433-00d0e2b1e08d	453998d9-d9f9-479d-86c0-d889a58b836d	g.chr3:195395399G>A	ENST00000445430.1	+	0	806									long intergenic non-protein coding RNA 969																		GGCTACGGGCGCACCTACTTG	0.607																																						ENST00000445430.1																			0																																																			0							g.chr3:195395399G>A	AK128346		3q29	2013-06-07			ENSG00000242086	ENSG00000242086		"""Long non-coding RNAs"""	48729	non-coding RNA	RNA, long non-coding							Standard	XR_427455		Approved				OTTHUMG00000155834		3.37:g.195395399G>A														0	806	+									RNA	SNP	ENST00000445430.1	37																																																																																						0.607	LINC00969-038	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000341951.1			4	73	0	0	0	0.029380	0	4	73				
TACR2	6865	broad.mit.edu	37	10	71164757	71164757	+	Missense_Mutation	SNP	G	G	A	rs149794645		TCGA-DU-7018-01A-11D-2024-08	TCGA-DU-7018-10A-01D-2024-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	29c55a80-cd55-4297-b433-00d0e2b1e08d	453998d9-d9f9-479d-86c0-d889a58b836d	g.chr10:71164757G>A	ENST00000373306.4	-	5	1565	c.1022C>T	c.(1021-1023)aCg>aTg	p.T341M	TACR2_ENST00000373307.1_Missense_Mutation_p.T129M	NM_001057.2	NP_001048.2	P21452	NK2R_HUMAN	tachykinin receptor 2	341					excretion (GO:0007588)|intestine smooth muscle contraction (GO:0014827)|muscle contraction (GO:0006936)|negative regulation of luteinizing hormone secretion (GO:0033685)|operant conditioning (GO:0035106)|positive regulation of acetylcholine secretion, neurotransmission (GO:0014057)|positive regulation of uterine smooth muscle contraction (GO:0070474)|positive regulation of vascular permeability (GO:0043117)|prolactin secretion (GO:0070459)|tachykinin receptor signaling pathway (GO:0007217)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	substance K receptor activity (GO:0016497)|tachykinin receptor activity (GO:0004995)			endometrium(2)|kidney(1)|large_intestine(1)|lung(3)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	11						GAGGGAGGTCGTGGGAGTCAG	0.627													G|||	1	0.000199681	0.0	0.0	5008	,	,		18514	0.001		0.0	False		,,,				2504	0.0					ENST00000373306.4																			0				endometrium(2)|kidney(1)|large_intestine(1)|lung(3)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	11						c.(1021-1023)aCg>aTg		tachykinin receptor 2	Clonidine(DB00575)|Octreotide(DB00104)						155.0	137.0	143.0					10																	71164757		2203	4300	6503	SO:0001583	missense	6865				excretion|muscle contraction	integral to plasma membrane	tachykinin receptor activity	g.chr10:71164757G>A		CCDS7293.1	10q22.1	2012-09-20			ENSG00000075073	ENSG00000075073		"""GPCR / Class A : Tachykinin receptors"""	11527	protein-coding gene	gene with protein product		162321		TAC2R, NKNAR			Standard	NM_001057		Approved	SKR, NK2R	uc001jpn.2	P21452	OTTHUMG00000018377	ENST00000373306.4:c.1022C>T	10.37:g.71164757G>A	ENSP00000362403:p.Thr341Met					TACR2_ENST00000373307.1_Missense_Mutation_p.T129M	p.T341M	NM_001057.2	NP_001048.2	P21452	NK2R_HUMAN			5	1565	-			341					A8K7I1|Q4QRI5|Q8NGQ8|Q9UDE6|Q9UDE7	Missense_Mutation	SNP	ENST00000373306.4	37	c.1022C>T	CCDS7293.1	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	G	10.92	1.485782	0.26686	.	.	ENSG00000075073	ENST00000373307;ENST00000373306	T;T	0.72942	0.02;-0.7	5.72	1.61	0.23674	.	0.304031	0.36002	N	0.002841	T	0.58991	0.2161	L	0.61036	1.89	0.09310	N	1	D	0.54772	0.968	B	0.40285	0.325	T	0.53472	-0.8434	10	0.35671	T	0.21	.	4.6949	0.12799	0.0799:0.1335:0.5392:0.2473	.	341	P21452	NK2R_HUMAN	M	129;341	ENSP00000362404:T129M;ENSP00000362403:T341M	ENSP00000362403:T341M	T	-	2	0	TACR2	70834763	0.073000	0.21202	0.135000	0.22099	0.085000	0.17905	1.769000	0.38522	0.749000	0.32854	-0.150000	0.13652	ACG		0.627	TACR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048411.1			4	84	0	0	0	0.009096	0	4	84				
RUFY4	285180	broad.mit.edu	37	2	218954072	218954072	+	Missense_Mutation	SNP	C	C	T			TCGA-DU-7018-01A-11D-2024-08	TCGA-DU-7018-10A-01D-2024-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	29c55a80-cd55-4297-b433-00d0e2b1e08d	453998d9-d9f9-479d-86c0-d889a58b836d	g.chr2:218954072C>T	ENST00000344321.7	+	12	2118	c.1600C>T	c.(1600-1602)Cgg>Tgg	p.R534W	RUFY4_ENST00000374155.3_Missense_Mutation_p.R554W|RUFY4_ENST00000441828.2_3'UTR	NM_198483.3	NP_940885.2	Q6ZNE9	RUFY4_HUMAN	RUN and FYVE domain containing 4	534							metal ion binding (GO:0046872)			endometrium(2)|kidney(2)|large_intestine(4)|pancreas(1)|upper_aerodigestive_tract(1)	10		Renal(207;0.0915)		Epithelial(149;4.11e-06)|all cancers(144;0.000519)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00948)		ATTTTCTCGGCGGTATCCATG	0.602																																						ENST00000374155.3																			0				endometrium(2)|kidney(2)|large_intestine(4)|pancreas(1)|upper_aerodigestive_tract(1)	10						c.(1660-1662)Cgg>Tgg		RUN and FYVE domain containing 4							57.0	59.0	59.0					2																	218954072		1990	4154	6144	SO:0001583	missense	285180						metal ion binding	g.chr2:218954072C>T	AK128393		2q35	2007-01-29			ENSG00000188282	ENSG00000188282		"""Zinc fingers, FYVE domain containing"""	24804	protein-coding gene	gene with protein product							Standard	NM_198483		Approved	FLJ46536	uc010fvl.2	Q6ZNE9	OTTHUMG00000155235	ENST00000344321.7:c.1600C>T	2.37:g.218954072C>T	ENSP00000345900:p.Arg534Trp					RUFY4_ENST00000344321.7_Missense_Mutation_p.R534W|RUFY4_ENST00000441828.2_3'UTR	p.R554W			Q6ZNE9	RUFY4_HUMAN		Epithelial(149;4.11e-06)|all cancers(144;0.000519)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00948)	11	2070	+		Renal(207;0.0915)	534					Q6ZR96	Missense_Mutation	SNP	ENST00000344321.7	37	c.1660C>T		.	.	.	.	.	.	.	.	.	.	C	18.22	3.575524	0.65878	.	.	ENSG00000188282	ENST00000344321;ENST00000374155	T;T	0.79033	-1.23;0.2	5.08	1.92	0.25849	Zinc finger, RING/FYVE/PHD-type (1);Zinc finger, FYVE-related (1);Zinc finger, FYVE/PHD-type (1);	0.157483	0.29631	N	0.011617	D	0.88518	0.6458	M	0.91872	3.25	0.80722	D	1	D	0.89917	1.0	D	0.81914	0.995	D	0.88797	0.3282	10	0.87932	D	0	-34.34	10.3152	0.43732	0.5572:0.4428:0.0:0.0	.	534	Q6ZNE9	RUFY4_HUMAN	W	534;554	ENSP00000345900:R534W;ENSP00000363270:R554W	ENSP00000345900:R534W	R	+	1	2	RUFY4	218662317	0.998000	0.40836	1.000000	0.80357	0.917000	0.54804	0.106000	0.15354	0.671000	0.31185	0.561000	0.74099	CGG		0.602	RUFY4-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_198483		6	28	0	0	0	0.021553	0	6	28				
OR4D2	124538	broad.mit.edu	37	17	56247641	56247641	+	Missense_Mutation	SNP	G	G	A	rs149114670		TCGA-DU-7018-01A-11D-2024-08	TCGA-DU-7018-10A-01D-2024-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	29c55a80-cd55-4297-b433-00d0e2b1e08d	453998d9-d9f9-479d-86c0-d889a58b836d	g.chr17:56247641G>A	ENST00000545221.1	+	1	625	c.625G>A	c.(625-627)Gtc>Atc	p.V209I		NM_001004707.3	NP_001004707.1	P58180	OR4D2_HUMAN	olfactory receptor, family 4, subfamily D, member 2	209						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.V209I(2)		breast(1)|kidney(1)|large_intestine(1)|lung(19)|ovary(1)|skin(2)|stomach(1)	26						GCTGGATGTCGTCTGGTTCTT	0.527																																						ENST00000545221.1																			2	Substitution - Missense(2)	p.V209I(2)	ovary(1)|kidney(1)	breast(1)|kidney(1)|large_intestine(1)|lung(19)|ovary(1)|skin(2)|stomach(1)	26						c.(625-627)Gtc>Atc		olfactory receptor, family 4, subfamily D, member 2		A	ILE/VAL	2,4404	826.0+/-416.6	0,2,2201	174.0	130.0	145.0		625	4.6	0.9	17	dbSNP_134	145	0,8600		0,0,4300	yes	missense	OR4D2	NM_001004707.3	29	0,2,6501	AA,AG,GG		0.0,0.0454,0.0154	benign	209/308	56247641	2,13004	2203	4300	6503	SO:0001583	missense	124538				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity	g.chr17:56247641G>A		CCDS32688.1	17q22	2013-09-23			ENSG00000255713	ENSG00000255713		"""GPCR / Class A : Olfactory receptors"""	8294	protein-coding gene	gene with protein product							Standard	NM_001004707		Approved		uc010wnp.2	P58180	OTTHUMG00000178801	ENST00000545221.1:c.625G>A	17.37:g.56247641G>A	ENSP00000441354:p.Val209Ile						p.V209I	NM_001004707.3	NP_001004707.1	P58180	OR4D2_HUMAN			1	625	+			209					Q6IFN8|Q96R75	Missense_Mutation	SNP	ENST00000545221.1	37	c.625G>A	CCDS32688.1	.	.	.	.	.	.	.	.	.	.	A	0.012	-1.670560	0.00758	4.54E-4	0.0	ENSG00000255713	ENST00000545221	T	0.35236	1.32	5.71	4.63	0.57726	GPCR, rhodopsin-like superfamily (1);	0.114355	0.39274	N	0.001415	T	0.17492	0.0420	N	0.16130	0.375	0.18873	N	0.999984	B	0.06786	0.001	B	0.09377	0.004	T	0.33574	-0.9863	10	0.02654	T	1	-40.4738	9.1704	0.37076	0.8488:0.0:0.1512:0.0	.	209	P58180	OR4D2_HUMAN	I	209	ENSP00000441354:V209I	ENSP00000441354:V209I	V	+	1	0	OR4D2	53602640	0.000000	0.05858	0.867000	0.34043	0.054000	0.15201	-0.064000	0.11636	0.516000	0.28340	-0.308000	0.09152	GTC		0.527	OR4D2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443366.1			17	72	0	0	0	0.033300	0	17	72				
RP11-13J8.1	0	broad.mit.edu	37	2	201967218	201967218	+	lincRNA	DEL	G	G	-	rs371047928|rs368317583		TCGA-DU-7018-01A-11D-2024-08	TCGA-DU-7018-10A-01D-2024-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	29c55a80-cd55-4297-b433-00d0e2b1e08d	453998d9-d9f9-479d-86c0-d889a58b836d	g.chr2:201967218delG	ENST00000448256.1	+	0	628																											aaaaaaaaaagaaTTTGTTCT	0.463																																						ENST00000448256.1																			0																																																			0							g.chr2:201967218delG																													2.37:g.201967218delG														0	628	+									RNA	DEL	ENST00000448256.1	37																																																																																						0.463	RP11-13J8.1-001	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000347397.1			3	4						3	4	---	---	---	---
IQCJ-SCHIP1	100505385	broad.mit.edu	37	3	159482272	159482274	+	In_Frame_Del	DEL	GCA	GCA	-	rs149416208		TCGA-DU-7018-01A-11D-2024-08	TCGA-DU-7018-10A-01D-2024-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	29c55a80-cd55-4297-b433-00d0e2b1e08d	453998d9-d9f9-479d-86c0-d889a58b836d	g.chr3:159482272_159482274delGCA	ENST00000460298.1	+	2	264_266	c.23_25delGCA	c.(22-27)ggcagc>ggc	p.S14del	IQCJ-SCHIP1-AS1_ENST00000460574.1_RNA|IQCJ-SCHIP1_ENST00000476809.1_In_Frame_Del_p.S90del|IQCJ-SCHIP1_ENST00000412423.2_In_Frame_Del_p.S41del|IQCJ-SCHIP1_ENST00000337808.6_In_Frame_Del_p.S41del|IQCJ-SCHIP1_ENST00000467442.1_3'UTR|IQCJ-SCHIP1_ENST00000485419.1_In_Frame_Del_p.S117del|IQCJ-SCHIP1_ENST00000527095.1_Intron					IQCJ-SCHIP1 readthrough									p.S41delS(1)|p.S117delS(1)		central_nervous_system(1)|cervix(1)|endometrium(1)|large_intestine(2)|lung(7)	12						AGTGACGCCGgcagcagcagcag	0.635																																						ENST00000337808.6																			2	Deletion - In frame(2)	p.S41delS(1)|p.S117delS(1)	central_nervous_system(2)	central_nervous_system(1)|cervix(1)|endometrium(1)|large_intestine(2)|lung(7)	12						c.(103-108)ggc>g					,,,,	305,12,3701		12,0,281,2,8,1706					,,,,	2.5	1.0		dbSNP_134	20	596,2,7224		21,0,554,0,2,3334	no	codingComplex,codingComplex,codingComplex,intron,codingComplex	SCHIP1,IQCJ-SCHIP1	NM_014575.3,NM_001197114.1,NM_001197113.1,NM_001197108.1,NM_001197107.1	,,,,	33,0,835,2,10,5040	A1A1,A1A2,A1R,A2A2,A2R,RR		7.6451,7.8895,7.728	,,,,	,,,,		901,14,10925				SO:0001651	inframe_deletion	0					cytoplasm	identical protein binding|protein binding	g.chr3:159482272_159482274delGCA		CCDS56289.1, CCDS56291.1	3q25.33	2011-03-24			ENSG00000250588	ENSG00000250588			38842	other	readthrough							Standard	NM_001197113		Approved		uc003fcq.2		OTTHUMG00000162426	ENST00000460298.1:c.23_25delGCA	3.37:g.159482281_159482283delGCA	ENSP00000417305:p.Ser14del					IQCJ-SCHIP1_ENST00000412423.2_In_Frame_Del_p.GS35del|IQCJ-SCHIP1_ENST00000460298.1_In_Frame_Del_p.GS8del|IQCJ-SCHIP1_ENST00000467442.1_3'UTR|IQCJ-SCHIP1_ENST00000527095.1_Intron|IQCJ-SCHIP1_ENST00000485419.1_In_Frame_Del_p.GS111del|IQCJ-SCHIP1_ENST00000476809.1_In_Frame_Del_p.GS84del	p.GS35del	NM_001197107.1|NM_014575.3	NP_001184036.1|NP_055390.1	Q9P0W5	SCHI1_HUMAN			2	681_683	+			35			Ser-rich.			In_Frame_Del	DEL	ENST00000460298.1	37	c.104_106delGCA																																																																																					0.635	IQCJ-SCHIP1-011	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000352558.2	NM_001197113		3	5						3	5	---	---	---	---
RNF180	285671	broad.mit.edu	37	5	63509839	63509840	+	Frame_Shift_Del	DEL	AT	AT	-	rs146938584	byFrequency	TCGA-DU-7018-01A-11D-2024-08	TCGA-DU-7018-10A-01D-2024-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	29c55a80-cd55-4297-b433-00d0e2b1e08d	453998d9-d9f9-479d-86c0-d889a58b836d	g.chr5:63509839_63509840delAT	ENST00000389100.4	+	4	758_759	c.686_687delAT	c.(685-687)catfs	p.H229fs	RNF180_ENST00000381081.2_Intron|RNF180_ENST00000296615.6_Frame_Shift_Del_p.H229fs	NM_001113561.1	NP_001107033.1	Q86T96	RN180_HUMAN	ring finger protein 180	229					adult behavior (GO:0030534)|norepinephrine metabolic process (GO:0042415)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein ubiquitination (GO:0031398)|protein polyubiquitination (GO:0000209)|regulation of catalytic activity (GO:0050790)|serotonin metabolic process (GO:0042428)	integral component of membrane (GO:0016021)|intrinsic component of endoplasmic reticulum membrane (GO:0031227)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|kidney(1)|large_intestine(4)|lung(9)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	20		Lung NSC(810;3.55e-06)|Prostate(74;0.0352)|Ovarian(174;0.0545)|Breast(144;0.0848)|Colorectal(97;0.234)		Lung(70;0.114)		AGAAAATCACATAGTTTGGATC	0.386																																						ENST00000389100.4																			0				breast(1)|kidney(1)|large_intestine(4)|lung(9)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	20						c.(685-687)cfs		ring finger protein 180																																				SO:0001589	frameshift_variant	285671					integral to membrane|nuclear envelope	zinc ion binding	g.chr5:63509839_63509840delAT	AK090756	CCDS34169.1, CCDS47219.1	5q12.3	2013-01-09			ENSG00000164197	ENSG00000164197		"""RING-type (C3HC4) zinc fingers"""	27752	protein-coding gene	gene with protein product							Standard	NM_178532		Approved		uc003jti.3	Q86T96	OTTHUMG00000162278	ENST00000389100.4:c.686_687delAT	5.37:g.63509839_63509840delAT	ENSP00000373752:p.His229fs					RNF180_ENST00000296615.6_Frame_Shift_Del_p.H229fs|RNF180_ENST00000381081.2_Intron	p.H229fs	NM_001113561.1	NP_001107033.1	Q86T96	RN180_HUMAN		Lung(70;0.114)	4	758_759	+		Lung NSC(810;3.55e-06)|Prostate(74;0.0352)|Ovarian(174;0.0545)|Breast(144;0.0848)|Colorectal(97;0.234)	229					Q0JSU3|Q495A8|Q8NBD1	Frame_Shift_Del	DEL	ENST00000389100.4	37	c.686_687delAT	CCDS47219.1																																																																																				0.386	RNF180-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368394.1	NM_178532		19	115						19	115	---	---	---	---
STAG3L2	442582	broad.mit.edu	37	7	74300557	74300564	+	RNA	DEL	AGAGCTCC	AGAGCTCC	-	rs367732188		TCGA-DU-7018-01A-11D-2024-08	TCGA-DU-7018-10A-01D-2024-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	29c55a80-cd55-4297-b433-00d0e2b1e08d	453998d9-d9f9-479d-86c0-d889a58b836d	g.chr7:74300557_74300564delAGAGCTCC	ENST00000423186.1	-	0	573_580							P0CL84	ST3L2_HUMAN	stromal antigen 3-like 2 (pseudogene)							nucleus (GO:0005634)		p.E82fs*32(2)		breast(1)|central_nervous_system(1)|large_intestine(1)|lung(1)|pancreas(1)	5						CGGCCAGTGAAGAGCTCCAGGCGTGCGG	0.572																																						ENST00000423186.1																			2	Deletion - Frameshift(2)	p.E82fs*32(2)	large_intestine(1)|central_nervous_system(1)	breast(1)|central_nervous_system(1)|large_intestine(1)|lung(1)|pancreas(1)	5												96,356		38,20,168							0.0			1	208,1036		88,32,502	no	frameshift	STAG3L2	NM_001025202.2		126,52,670	A1A1,A1R,RR		16.7203,21.2389,17.9245				304,1392						0					nucleus	binding	g.chr7:74300557_74300564delAGAGCTCC			7q11.23	2013-06-26	2013-06-26			ENSG00000277072			33886	pseudogene	pseudogene			"""stromal antigen 3-like 2"""				Standard	NR_040584		Approved	MGC131759, STAG3L2P	uc011kfj.2	P0CL84	OTTHUMG00000156216		7.37:g.74300557_74300564delAGAGCTCC										P0CL84	ST3L2_HUMAN			0	573_580	-								A6NMT8|A8K0A1|Q32NE4|Q6NXR2|Q7L5M5|Q7Z5K6	RNA	DEL	ENST00000423186.1	37																																																																																						0.572	STAG3L2-002	KNOWN	basic	retained_intron	pseudogene	OTTHUMT00000343523.2	NM_001025202		6	7						6	7	---	---	---	---
MRPL15	29088	broad.mit.edu	37	8	55049886	55049889	+	Frame_Shift_Del	DEL	GGTC	GGTC	-	rs144260791|rs149600755		TCGA-DU-7018-01A-11D-2024-08	TCGA-DU-7018-10A-01D-2024-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	29c55a80-cd55-4297-b433-00d0e2b1e08d	453998d9-d9f9-479d-86c0-d889a58b836d	g.chr8:55049886_55049889delGGTC	ENST00000260102.4	+	3	396_399	c.322_325delGGTC	c.(322-327)ggtcgtfs	p.GR108fs		NM_014175.3	NP_054894.1	Q9P015	RM15_HUMAN	mitochondrial ribosomal protein L15	108					translation (GO:0006412)	large ribosomal subunit (GO:0015934)|mitochondrion (GO:0005739)	poly(A) RNA binding (GO:0044822)|structural constituent of ribosome (GO:0003735)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(1)|prostate(1)|skin(3)	10		Lung NSC(129;0.109)|all_epithelial(80;0.134)|all_lung(136;0.181)	OV - Ovarian serous cystadenocarcinoma(7;4.3e-07)|Epithelial(17;5.79e-05)|all cancers(17;0.000458)			TATTGATTTGGGTCGTGTTGATCC	0.426																																						ENST00000260102.4																			0				endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(1)|prostate(1)|skin(3)	10						c.(322-327)gtfs		mitochondrial ribosomal protein L15																																				SO:0001589	frameshift_variant	29088				translation	large ribosomal subunit|mitochondrion	structural constituent of ribosome	g.chr8:55049886_55049889delGGTC	AB051619	CCDS6158.1	8q11.2-q13	2012-09-13			ENSG00000137547	ENSG00000137547		"""Mitochondrial ribosomal proteins / large subunits"""	14054	protein-coding gene	gene with protein product		611828				11543634	Standard	NM_014175		Approved	RPML7, MRP-L7, HSPC145, L15mt, MRP-L15	uc003xsa.2	Q9P015	OTTHUMG00000164315	ENST00000260102.4:c.322_325delGGTC	8.37:g.55049886_55049889delGGTC	ENSP00000260102:p.Gly108fs						p.GR108fs	NM_014175.3	NP_054894.1	Q9P015	RM15_HUMAN	OV - Ovarian serous cystadenocarcinoma(7;4.3e-07)|Epithelial(17;5.79e-05)|all cancers(17;0.000458)		3	396_399	+		Lung NSC(129;0.109)|all_epithelial(80;0.134)|all_lung(136;0.181)	108					Q96Q54|Q9H0Y1	Frame_Shift_Del	DEL	ENST00000260102.4	37	c.322_325delGGTC	CCDS6158.1																																																																																				0.426	MRPL15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378254.1	NM_014175		28	60						28	60	---	---	---	---
TCF12	6938	broad.mit.edu	37	15	57555366	57555369	+	Frame_Shift_Del	DEL	AAAG	AAAG	-			TCGA-DU-7018-01A-11D-2024-08	TCGA-DU-7018-10A-01D-2024-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	29c55a80-cd55-4297-b433-00d0e2b1e08d	453998d9-d9f9-479d-86c0-d889a58b836d	g.chr15:57555366_57555369delAAAG	ENST00000267811.5	+	17	1871_1874	c.1567_1570delAAAG	c.(1567-1572)aaagaafs	p.KE523fs	TCF12_ENST00000438423.2_Frame_Shift_Del_p.KE547fs|TCF12_ENST00000452095.2_Frame_Shift_Del_p.KE543fs|TCF12_ENST00000559710.1_Frame_Shift_Del_p.KE157fs|TCF12_ENST00000559703.1_Frame_Shift_Del_p.KE181fs|TCF12_ENST00000543579.1_Frame_Shift_Del_p.KE377fs|TCF12_ENST00000537840.1_Frame_Shift_Del_p.KE287fs|TCF12_ENST00000333725.5_Frame_Shift_Del_p.KE547fs|TCF12_ENST00000557843.1_Frame_Shift_Del_p.KE523fs|TCF12_ENST00000343827.3_Frame_Shift_Del_p.KE353fs	NM_003205.3|NM_207038.1	NP_003196.1|NP_996921.1	Q99081	HTF4_HUMAN	transcription factor 12	523				K -> E (in Ref. 3; CAD89914). {ECO:0000305}.	immune response (GO:0006955)|muscle organ development (GO:0007517)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	bHLH transcription factor binding (GO:0043425)|E-box binding (GO:0070888)|enhancer binding (GO:0035326)|sequence-specific DNA binding transcription factor activity (GO:0003700)|SMAD binding (GO:0046332)|transcription factor binding (GO:0008134)		TCF12/NR4A3(2)	breast(2)|central_nervous_system(5)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(1)|lung(13)|ovary(2)|prostate(1)|skin(2)|urinary_tract(1)	36		Colorectal(260;0.0907)		all cancers(107;0.000313)|GBM - Glioblastoma multiforme(80;0.00878)|STAD - Stomach adenocarcinoma(283;0.239)		GACTGAAAACAAAGAAAAGGATGA	0.382			T	TEC	extraskeletal myxoid chondrosarcoma																																	ENST00000267811.5				Dom	yes		15	15q21	6938	T	"""transcription factor 12 (HTF4, helix-loop-helix transcription factors 4)"""			M	TEC		extraskeletal myxoid chondrosarcoma	TCF12/NR4A3(2)	0				breast(2)|central_nervous_system(5)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(1)|lung(13)|ovary(2)|prostate(1)|skin(2)|urinary_tract(1)	36						c.(1567-1572)aafs		transcription factor 12																																				SO:0001589	frameshift_variant	6938				immune response|muscle organ development|regulation of transcription from RNA polymerase II promoter	nucleus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity	g.chr15:57555366_57555369delAAAG	BC050556	CCDS10159.1, CCDS10160.1, CCDS42042.1	15q21	2013-05-21	2008-07-31		ENSG00000140262	ENSG00000140262		"""Basic helix-loop-helix proteins"""	11623	protein-coding gene	gene with protein product	"""helix-loop-helix transcription factor 4"""	600480				1886779	Standard	NM_003205		Approved	HEB, HTF4, HsT17266, bHLHb20	uc002aeb.3	Q99081	OTTHUMG00000132047	ENST00000267811.5:c.1567_1570delAAAG	15.37:g.57555366_57555369delAAAG	ENSP00000267811:p.Lys523fs					TCF12_ENST00000537840.1_Frame_Shift_Del_p.KE287fs|TCF12_ENST00000543579.1_Frame_Shift_Del_p.KE377fs|TCF12_ENST00000333725.5_Frame_Shift_Del_p.KE547fs|TCF12_ENST00000557843.1_Frame_Shift_Del_p.KE523fs|TCF12_ENST00000452095.2_Frame_Shift_Del_p.KE543fs|TCF12_ENST00000559703.1_Frame_Shift_Del_p.KE181fs|TCF12_ENST00000438423.2_Frame_Shift_Del_p.KE547fs|TCF12_ENST00000343827.3_Frame_Shift_Del_p.KE353fs|TCF12_ENST00000559710.1_Frame_Shift_Del_p.KE157fs	p.KE523fs	NM_003205.3|NM_207038.1	NP_003196.1|NP_996921.1	Q99081	HTF4_HUMAN		all cancers(107;0.000313)|GBM - Glioblastoma multiforme(80;0.00878)|STAD - Stomach adenocarcinoma(283;0.239)	17	1871_1874	+		Colorectal(260;0.0907)	523	K -> E (in Ref. 3; CAD89914).				Q7Z3D9|Q86TC1|Q86VM2	Frame_Shift_Del	DEL	ENST00000267811.5	37	c.1567_1570delAAAG	CCDS10159.1																																																																																				0.382	TCF12-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000255069.3	NM_003205		22	28						22	28	---	---	---	---
IL32	9235	broad.mit.edu	37	16	3119304	3119305	+	Frame_Shift_Ins	INS	-	-	G	rs398100042|rs2981599		TCGA-DU-7018-01A-11D-2024-08	TCGA-DU-7018-10A-01D-2024-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	29c55a80-cd55-4297-b433-00d0e2b1e08d	453998d9-d9f9-479d-86c0-d889a58b836d	g.chr16:3119304_3119305insG	ENST00000534507.1	+	6	864_865	c.653_654insG	c.(652-657)gacaagfs	p.DK218fs	IL32_ENST00000008180.9_Frame_Shift_Ins_p.DK152fs|IL32_ENST00000396890.2_Frame_Shift_Ins_p.DK218fs|IL32_ENST00000548246.1_Frame_Shift_Ins_p.DK132fs|IL32_ENST00000548652.1_Frame_Shift_Ins_p.DK163fs|IL32_ENST00000551122.1_Frame_Shift_Ins_p.DK115fs|IL32_ENST00000529699.1_Frame_Shift_Ins_p.DK152fs|IL32_ENST00000528163.2_Frame_Shift_Ins_p.DK172fs|IL32_ENST00000552664.1_Frame_Shift_Ins_p.DK172fs|IL32_ENST00000552936.1_Frame_Shift_Ins_p.DK196fs|IL32_ENST00000530538.2_Frame_Shift_Ins_p.DK172fs|IL32_ENST00000533097.2_Frame_Shift_Ins_p.DK172fs|IL32_ENST00000440815.3_Frame_Shift_Ins_p.DK172fs|IL32_ENST00000552356.1_Frame_Shift_Ins_p.DK152fs|IL32_ENST00000548476.1_Frame_Shift_Ins_p.DK218fs|RNU1-125P_ENST00000516752.1_RNA|IL32_ENST00000525643.2_Frame_Shift_Ins_p.DK172fs|IL32_ENST00000382213.3_Frame_Shift_Ins_p.DK163fs|IL32_ENST00000325568.5_Frame_Shift_Ins_p.DK172fs|IL32_ENST00000444393.3_Frame_Shift_Ins_p.DK172fs|IL32_ENST00000531965.1_Frame_Shift_Ins_p.DK162fs|IL32_ENST00000530890.1_Frame_Shift_Ins_p.DK152fs|IL32_ENST00000549213.1_Frame_Shift_Ins_p.DK115fs|IL32_ENST00000526464.2_Frame_Shift_Ins_p.DK172fs|IL32_ENST00000396887.3_Frame_Shift_Ins_p.DK115fs|IL32_ENST00000529550.1_Frame_Shift_Ins_p.DK172fs|IL32_ENST00000551513.1_Frame_Shift_Ins_p.DK209fs			P24001	IL32_HUMAN	interleukin 32	218					cell adhesion (GO:0007155)|defense response (GO:0006952)|immune response (GO:0006955)	extracellular space (GO:0005615)|membrane (GO:0016020)				breast(1)|endometrium(1)|large_intestine(3)|lung(6)|ovary(1)|pancreas(1)|skin(1)|urinary_tract(1)	15						CCACGGGGGGACAAGGAGGAGC	0.574																																						ENST00000525643.2																			0				breast(1)|endometrium(1)|large_intestine(3)|lung(6)|ovary(1)|pancreas(1)|skin(1)|urinary_tract(1)	15						c.(514-516)gaafs		interleukin 32																																				SO:0001589	frameshift_variant	9235				cell adhesion|defense response|immune response	extracellular space	cytokine activity	g.chr16:3119304_3119305insG	M59807	CCDS32377.1, CCDS32378.1, CCDS32379.1, CCDS45394.1	16p13.3	2011-07-21			ENSG00000008517	ENSG00000008517		"""Interleukins and interleukin receptors"""	16830	protein-coding gene	gene with protein product	"""natural killer cell transcript 4"""	606001				1729377, 9653642	Standard	XM_005255686		Approved	NK4, TAIF, TAIFb, TAIFd	uc002ctn.3	P24001	OTTHUMG00000167498	Exception_encountered	16.37:g.3119304_3119305insG	ENSP00000431775:p.Asp218fs					IL32_ENST00000533097.2_Frame_Shift_Ins_p.E172fs|IL32_ENST00000396890.2_Frame_Shift_Ins_p.E218fs|IL32_ENST00000548246.1_Frame_Shift_Ins_p.E132fs|IL32_ENST00000529699.1_Frame_Shift_Ins_p.E152fs|IL32_ENST00000530890.1_Frame_Shift_Ins_p.E152fs|IL32_ENST00000551513.1_Frame_Shift_Ins_p.E209fs|IL32_ENST00000008180.9_Frame_Shift_Ins_p.E152fs|IL32_ENST00000551122.1_Frame_Shift_Ins_p.E115fs|IL32_ENST00000444393.3_Frame_Shift_Ins_p.E172fs|IL32_ENST00000549213.1_Frame_Shift_Ins_p.E115fs|IL32_ENST00000325568.5_Frame_Shift_Ins_p.E172fs|IL32_ENST00000548476.1_Frame_Shift_Ins_p.E218fs|IL32_ENST00000396887.3_Frame_Shift_Ins_p.E115fs|IL32_ENST00000440815.3_Frame_Shift_Ins_p.E172fs|IL32_ENST00000530538.2_Frame_Shift_Ins_p.E172fs|IL32_ENST00000529550.1_Frame_Shift_Ins_p.E172fs|IL32_ENST00000548652.1_Frame_Shift_Ins_p.E163fs|IL32_ENST00000552664.1_Frame_Shift_Ins_p.E172fs|IL32_ENST00000552936.1_Frame_Shift_Ins_p.E196fs|IL32_ENST00000382213.3_Frame_Shift_Ins_p.E163fs|IL32_ENST00000534507.1_Frame_Shift_Ins_p.E218fs|IL32_ENST00000528163.2_Frame_Shift_Ins_p.E172fs|IL32_ENST00000526464.2_Frame_Shift_Ins_p.E172fs|IL32_ENST00000531965.1_Frame_Shift_Ins_p.E162fs|IL32_ENST00000552356.1_Frame_Shift_Ins_p.E152fs	p.E172fs			P24001	IL32_HUMAN			7	847_848	+			218					A6NNM0|A8MPX0|B4DJM1|B8Q191|D3DUB0|D3DUB2|Q5VFH7|Q5VFH8|Q8WV38|Q96GK9	Frame_Shift_Ins	INS	ENST00000534507.1	37	c.515_516insG																																																																																					0.574	IL32-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000394812.2	NM_004221		8	250						8	250	---	---	---	---
ROCK1P1	727758	broad.mit.edu	37	18	112402	112405	+	RNA	DEL	AACC	AACC	-	rs113232824|rs111811281|rs11080396		TCGA-DU-7018-01A-11D-2024-08	TCGA-DU-7018-10A-01D-2024-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	29c55a80-cd55-4297-b433-00d0e2b1e08d	453998d9-d9f9-479d-86c0-d889a58b836d	g.chr18:112402_112405delAACC	ENST00000608049.1	+	0	389					NR_033770.1				Rho-associated, coiled-coil containing protein kinase 1 pseudogene 1																		CCCTGCCCCGAACCACCCGACCCC	0.711																																						ENST00000576266.1																			0																																																			0							g.chr18:112402_112405delAACC			18p11.32	2012-10-04			ENSG00000263006	ENSG00000263006			37832	pseudogene	pseudogene							Standard	NR_033770		Approved		uc002kke.3		OTTHUMG00000177913		18.37:g.112402_112405delAACC														0	36_39	+									RNA	DEL	ENST00000608049.1	37																																																																																						0.711	ROCK1P1-003	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000472417.1			3	6						3	6	---	---	---	---
CIC	23152	broad.mit.edu	37	19	42791372	42791373	+	Frame_Shift_Del	DEL	AG	AG	-			TCGA-DU-7018-01A-11D-2024-08	TCGA-DU-7018-10A-01D-2024-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	29c55a80-cd55-4297-b433-00d0e2b1e08d	453998d9-d9f9-479d-86c0-d889a58b836d	g.chr19:42791372_42791373delAG	ENST00000575354.2	+	3	472_473	c.432_433delAG	c.(430-435)acagagfs	p.E145fs	CIC_ENST00000160740.3_Frame_Shift_Del_p.E145fs|CIC_ENST00000572681.2_Frame_Shift_Del_p.E1054fs	NM_015125.3	NP_055940.3	Q96RK0	CIC_HUMAN	capicua transcriptional repressor	145					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)			autonomic_ganglia(1)|breast(5)|central_nervous_system(32)|endometrium(10)|kidney(2)|large_intestine(7)|lung(9)|ovary(7)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	82		Prostate(69;0.00682)				ACAGTGAGACAGAGAGTGACCA	0.663			"""Mis, F, S"""		oligodendroglioma																																	ENST00000572681.2				Rec	yes		19	19q13.2	23152	"""Mis, F, S"""	capicua homolog			O			oligodendroglioma		0				autonomic_ganglia(1)|breast(5)|central_nervous_system(32)|endometrium(10)|kidney(2)|large_intestine(7)|lung(9)|ovary(7)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	82						c.(3157-3162)acagfs		capicua transcriptional repressor																																				SO:0001589	frameshift_variant	23152				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|protein binding	g.chr19:42791372_42791373delAG	AB002304	CCDS12601.1	19q13.2	2013-03-15	2013-03-15		ENSG00000079432	ENSG00000079432			14214	protein-coding gene	gene with protein product		612082	"""capicua (Drosophila) homolog"", ""capicua homolog (Drosophila)"""			12393275, 15981098	Standard	NM_015125		Approved	KIAA0306	uc002otf.1	Q96RK0		ENST00000575354.2:c.432_433delAG	19.37:g.42791376_42791377delAG	ENSP00000458663:p.Glu145fs					CIC_ENST00000160740.3_Frame_Shift_Del_p.TE144fs|CIC_ENST00000575354.2_Frame_Shift_Del_p.TE144fs	p.TE1053fs			Q96RK0	CIC_HUMAN			4	3227_3228	+		Prostate(69;0.00682)	144			Pro-rich.		Q7LGI1|Q9UEG5|Q9Y6T1	Frame_Shift_Del	DEL	ENST00000575354.2	37	c.3159_3160delAG	CCDS12601.1																																																																																				0.663	CIC-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000438532.2			19	8						19	8	---	---	---	---
