#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
TNFRSF4	7293	broad.mit.edu	37	1	1147004	1147004	+	Splice_Site	SNP	C	C	T			TCGA-76-4929-01A-01D-1486-08	TCGA-76-4929-10A-01D-1486-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	af4f8b89-837a-48b7-b0e7-12aec23fc285	3e0712a1-b66a-42e7-94a3-07edee7dce2b	g.chr1:1147004C>T	ENST00000379236.3	-	7	769	c.765G>A	c.(763-765)ggG>ggA	p.G255G	TNFRSF4_ENST00000453580.1_5'Flank	NM_003327.3	NP_003318.1	P43489	TNR4_HUMAN	tumor necrosis factor receptor superfamily, member 4	255					cellular defense response (GO:0006968)|immune response (GO:0006955)|inflammatory response (GO:0006954)|negative regulation of cytokine secretion (GO:0050710)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of immunoglobulin secretion (GO:0051024)|regulation of apoptotic process (GO:0042981)|regulation of protein kinase activity (GO:0045859)|T cell proliferation (GO:0042098)	cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)	tumor necrosis factor-activated receptor activity (GO:0005031)			large_intestine(1)|lung(2)|urinary_tract(1)	4	all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;8.75e-19)|all_lung(118;2.3e-08)|Lung NSC(185;2.38e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Lung SC(97;0.128)		Epithelial(90;3.73e-36)|OV - Ovarian serous cystadenocarcinoma(86;1.01e-21)|Colorectal(212;3.94e-05)|COAD - Colon adenocarcinoma(227;4.22e-05)|Kidney(185;0.00227)|BRCA - Breast invasive adenocarcinoma(365;0.0025)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0339)|Lung(427;0.199)		AACTGCCTCCCCCTGGGGAGG	0.677																																						uc001adf.3																			0				large_intestine(1)|lung(2)|urinary_tract(1)	4						c.(853-855)ggG>ggA		Homo sapiens tumor necrosis factor receptor superfamily, member 4 (TNFRSF4), mRNA.							27.0	33.0	31.0					1																	1147004		2201	4298	6499	SO:0001630	splice_region_variant	7293				immune response|negative regulation of sequence-specific DNA binding transcription factor activity|negative regulation of transcription, DNA-dependent|positive regulation of B cell proliferation|positive regulation of immunoglobulin secretion|T cell proliferation	integral to plasma membrane	tumor necrosis factor receptor activity	g.chr1:1147004C>T	X75962	CCDS11.1	1p36	2008-02-05			ENSG00000186827	ENSG00000186827		"""Tumor necrosis factor receptor superfamily"", ""CD molecules"""	11918	protein-coding gene	gene with protein product		600315		TXGP1L		7510240, 2828930	Standard	NM_003327		Approved	ACT35, OX40, CD134	uc001ade.3	P43489	OTTHUMG00000001415	ENST00000379236.3:c.764-1G>A	1.37:g.1147004C>T						TNFRSF4_uc001ade.3_Splice_Site_p.G255_splice	p.G285G			P43489	TNR4_HUMAN		Epithelial(90;3.73e-36)|OV - Ovarian serous cystadenocarcinoma(86;1.01e-21)|Colorectal(212;3.94e-05)|COAD - Colon adenocarcinoma(227;4.22e-05)|Kidney(185;0.00227)|BRCA - Breast invasive adenocarcinoma(365;0.0025)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0339)|Lung(427;0.199)	4	1453	-	all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;8.75e-19)|all_lung(118;2.3e-08)|Lung NSC(185;2.38e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Lung SC(97;0.128)	255					Q13663|Q2M312|Q5T7M0	Silent	SNP	ENST00000379236.3	37	c.855G>A	CCDS11.1																																																																																				0.677	TNFRSF4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000004086.1		Silent
PABPC4	8761	broad.mit.edu	37	1	40030160	40030160	+	Missense_Mutation	SNP	C	C	T	rs139185037		TCGA-76-4929-01A-01D-1486-08	TCGA-76-4929-10A-01D-1486-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	af4f8b89-837a-48b7-b0e7-12aec23fc285	3e0712a1-b66a-42e7-94a3-07edee7dce2b	g.chr1:40030160C>T	ENST00000372857.3	-	10	2180	c.1388G>A	c.(1387-1389)cGc>cAc	p.R463H	PABPC4_ENST00000372858.3_Missense_Mutation_p.R463H|PABPC4_ENST00000372862.3_Missense_Mutation_p.R463H|SNORA55_ENST00000364587.1_RNA|PABPC4_ENST00000372856.3_Missense_Mutation_p.R463H|RP11-69E11.8_ENST00000415255.1_RNA	NM_003819.3	NP_003810.1	Q13310	PABP4_HUMAN	poly(A) binding protein, cytoplasmic 4 (inducible form)	463					blood coagulation (GO:0007596)|RNA catabolic process (GO:0006401)|RNA processing (GO:0006396)|translation (GO:0006412)	cytoplasm (GO:0005737)|cytoplasmic stress granule (GO:0010494)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	nucleotide binding (GO:0000166)|poly(A) binding (GO:0008143)|poly(A) RNA binding (GO:0044822)|poly(U) RNA binding (GO:0008266)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(5)|liver(1)|lung(6)|prostate(1)|skin(3)	21	Lung NSC(20;1.55e-06)|Ovarian(52;0.00769)|all_hematologic(146;0.0501)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;2.89e-18)|Epithelial(16;6.17e-17)|all cancers(16;1.18e-15)|LUSC - Lung squamous cell carcinoma(16;0.000261)|Lung(16;0.000457)			AGCCAGATGGCGAAGAGTTGG	0.542																																						uc001cdl.2																			0				NS(1)|breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(5)|liver(1)|lung(6)|prostate(1)|skin(3)	21						c.(1387-1389)cGc>cAc		Homo sapiens poly(A) binding protein, cytoplasmic 4 (inducible form) (PABPC4), transcript variant 1, mRNA.		C	HIS/ARG,HIS/ARG,HIS/ARG	1,4405	2.1+/-5.4	0,1,2202	119.0	113.0	115.0		1388,1388,1388	3.1	1.0	1	dbSNP_134	115	0,8600		0,0,4300	no	missense,missense,missense	PABPC4	NM_001135653.1,NM_001135654.1,NM_003819.3	29,29,29	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	probably-damaging,probably-damaging,probably-damaging	463/661,463/632,463/645	40030160	1,13005	2203	4300	6503	SO:0001583	missense	8761				blood coagulation|RNA catabolic process|RNA processing|translation	cytoplasm|ribonucleoprotein complex	nucleotide binding|poly(A) RNA binding|poly(U) RNA binding|protein binding	g.chr1:40030160C>T	U33818	CCDS438.1, CCDS44114.1, CCDS44115.1	1p34.2	2013-02-12	2001-11-28		ENSG00000090621	ENSG00000090621		"""RNA binding motif (RRM) containing"""	8557	protein-coding gene	gene with protein product		603407	"""poly(A)-binding protein, cytoplasmic 4 (inducible form)"""			10543404	Standard	NM_001135653		Approved	iPABP, APP-1	uc001cdl.2	Q13310	OTTHUMG00000009097	ENST00000372857.3:c.1388G>A	1.37:g.40030160C>T	ENSP00000361948:p.Arg463His					PABPC4_uc010oiv.1_Missense_Mutation_p.R463H|PABPC4_uc001cdm.2_Missense_Mutation_p.R463H	p.R463H	NM_001135653	NP_001129125	Q13310	PABP4_HUMAN	OV - Ovarian serous cystadenocarcinoma(33;2.89e-18)|Epithelial(16;6.17e-17)|all cancers(16;1.18e-15)|LUSC - Lung squamous cell carcinoma(16;0.000261)|Lung(16;0.000457)		9	2286	-	Lung NSC(20;1.55e-06)|Ovarian(52;0.00769)|all_hematologic(146;0.0501)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	463					B1ANQ8|Q4VC03|Q6P0N3	Missense_Mutation	SNP	ENST00000372857.3	37	c.1388G>A	CCDS438.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	24.1|24.1	4.495380|4.495380	0.85069|0.85069	2.27E-4|2.27E-4	0.0|0.0	ENSG00000090621|ENSG00000090621	ENST00000437136;ENST00000421687;ENST00000527718|ENST00000372862;ENST00000372858;ENST00000372857;ENST00000372856	.|T;T;T;T	.|0.52983	.|0.64;0.64;0.64;0.64	5.94|5.94	3.06|3.06	0.35304|0.35304	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.44705|0.44705	0.1306|0.1306	L|L	0.55481|0.55481	1.735|1.735	0.49389|0.49389	D|D	0.999784|0.999784	.|P;B;B	.|0.46220	.|0.874;0.011;0.003	.|B;B;B	.|0.43194	.|0.411;0.008;0.006	T|T	0.44050|0.44050	-0.9353|-0.9353	5|10	.|0.51188	.|T	.|0.08	.|.	11.7534|11.7534	0.51862|0.51862	0.0:0.8069:0.0:0.1931|0.0:0.8069:0.0:0.1931	.|.	.|463;463;463	.|Q13310;Q13310-2;Q4VC03	.|PABP4_HUMAN;.;.	T|H	2;365;185|463	.|ENSP00000361953:R463H;ENSP00000361949:R463H;ENSP00000361948:R463H;ENSP00000361947:R463H	.|ENSP00000361947:R463H	A|R	-|-	1|2	0|0	PABPC4|PABPC4	39802747|39802747	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.994000|0.994000	0.84299|0.84299	4.301000|4.301000	0.59086|0.59086	0.866000|0.866000	0.35629|0.35629	0.561000|0.561000	0.74099|0.74099	GCC|CGC		0.542	PABPC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000025220.1	NM_001135653	
CASQ1	844	broad.mit.edu	37	1	160162639	160162639	+	Silent	SNP	A	A	T			TCGA-76-4929-01A-01D-1486-08	TCGA-76-4929-10A-01D-1486-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	af4f8b89-837a-48b7-b0e7-12aec23fc285	3e0712a1-b66a-42e7-94a3-07edee7dce2b	g.chr1:160162639A>T	ENST00000368078.3	+	2	523	c.327A>T	c.(325-327)gtA>gtT	p.V109V	CASQ1_ENST00000368079.3_Silent_p.V103V			P31415	CASQ1_HUMAN	calsequestrin 1 (fast-twitch, skeletal muscle)	109					endoplasmic reticulum organization (GO:0007029)|ion transmembrane transport (GO:0034220)|protein polymerization (GO:0051258)|regulation of sequestering of calcium ion (GO:0051282)|regulation of skeletal muscle contraction by regulation of release of sequestered calcium ion (GO:0014809)|response to denervation involved in regulation of muscle adaptation (GO:0014894)|response to heat (GO:0009408)|response to organic substance (GO:0010033)|sarcomere organization (GO:0045214)|skeletal muscle tissue development (GO:0007519)|transmembrane transport (GO:0055085)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum lumen (GO:0033018)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|T-tubule (GO:0030315)|terminal cisterna lumen (GO:0014804)	calcium ion binding (GO:0005509)			breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(9)|ovary(1)|skin(1)	21	all_cancers(52;2.56e-18)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.111)			TCGGGCTGGTAGACTCTGAGA	0.522											OREG0013927	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																										uc010pja.2																			0				breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(9)|ovary(1)|skin(1)	21						c.(325-327)gtA>gtT		Homo sapiens calsequestrin 1 (fast-twitch, skeletal muscle) (CASQ1), nuclear gene encoding mitochondrial protein, mRNA.							121.0	126.0	124.0					1																	160162639		2203	4300	6503	SO:0001819	synonymous_variant	844					mitochondrial matrix|sarcoplasmic reticulum lumen|smooth endoplasmic reticulum	calcium ion binding	g.chr1:160162639A>T	S73775	CCDS1198.1, CCDS1198.2	1q21	2011-10-19			ENSG00000143318	ENSG00000143318		"""Protein disulfide isomerases"""	1512	protein-coding gene	gene with protein product	"""calsequestrin 1, fast-twitch, skeletal muscle"", ""calmitine"""	114250		CASQ		8406504, 2321095	Standard	NM_001231		Approved	PDIB1	uc010pja.2	P31415	OTTHUMG00000031607	ENST00000368078.3:c.327A>T	1.37:g.160162639A>T			OREG0013927	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	1806		p.V109V	NM_001231	NP_001222	P31415	CASQ1_HUMAN	BRCA - Breast invasive adenocarcinoma(70;0.111)		1	584	+	all_cancers(52;2.56e-18)|all_hematologic(112;0.093)		109					B1AKZ2|B2R863|Q8TBW7	Silent	SNP	ENST00000368078.3	37	c.327A>T	CCDS1198.2																																																																																				0.522	CASQ1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077412.1	NM_001231	
TNFSF18	8995	broad.mit.edu	37	1	173010533	173010533	+	Silent	SNP	G	G	A	rs545086841		TCGA-76-4929-01A-01D-1486-08	TCGA-76-4929-10A-01D-1486-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	af4f8b89-837a-48b7-b0e7-12aec23fc285	3e0712a1-b66a-42e7-94a3-07edee7dce2b	g.chr1:173010533G>A	ENST00000404377.3	-	3	574	c.574C>T	c.(574-576)Cta>Tta	p.L192L	RP1-15D23.2_ENST00000432694.2_lincRNA|TNFSF18_ENST00000239468.2_Silent_p.L170L	NM_005092.3	NP_005083.2	Q9UNG2	TNF18_HUMAN	tumor necrosis factor (ligand) superfamily, member 18	192					cell-cell signaling (GO:0007267)|negative regulation of apoptotic process (GO:0043066)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|regulation of T cell proliferation (GO:0042129)|signal transduction (GO:0007165)|T cell proliferation involved in immune response (GO:0002309)|tumor necrosis factor-mediated signaling pathway (GO:0033209)	cell surface (GO:0009986)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	receptor binding (GO:0005102)|tumor necrosis factor receptor superfamily binding (GO:0032813)			breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(3)|skin(1)	9						GGATTTGCTAGTAAAATGATA	0.418													G|||	1	0.000199681	0.0	0.0	5008	,	,		18557	0.0		0.0	False		,,,				2504	0.001					uc001giu.2																			0				breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(3)|skin(1)	9						c.(574-576)Cta>Tta		Homo sapiens tumor necrosis factor (ligand) superfamily, member 18 (TNFSF18), mRNA.							89.0	86.0	87.0					1																	173010533		2203	4300	6503	SO:0001819	synonymous_variant	8995				anti-apoptosis|cell-cell signaling|immune response|signal transduction	extracellular space|integral to membrane	cytokine activity|tumor necrosis factor receptor binding	g.chr1:173010533G>A	AF117713	CCDS1305.2	1q23	2008-02-05			ENSG00000120337	ENSG00000120337		"""Tumor necrosis factor (ligand) superfamily"""	11932	protein-coding gene	gene with protein product		603898				10037686, 10074428	Standard	NM_005092		Approved	AITRL, TL6, hGITRL	uc001giu.2	Q9UNG2	OTTHUMG00000034835	ENST00000404377.3:c.574C>T	1.37:g.173010533G>A							p.L192L	NM_005092	NP_005083	Q9UNG2	TNF18_HUMAN			2	575	-			192					A9IQG8|O95852|Q6ISV1	Silent	SNP	ENST00000404377.3	37	c.574C>T	CCDS1305.2																																																																																				0.418	TNFSF18-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000084268.2	NM_005092	
LHX9	56956	broad.mit.edu	37	1	197887088	197887088	+	Silent	SNP	C	C	T			TCGA-76-4929-01A-01D-1486-08	TCGA-76-4929-10A-01D-1486-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	af4f8b89-837a-48b7-b0e7-12aec23fc285	3e0712a1-b66a-42e7-94a3-07edee7dce2b	g.chr1:197887088C>T	ENST00000367387.4	+	1	560	c.135C>T	c.(133-135)gcC>gcT	p.A45A	LHX9_ENST00000367390.3_Silent_p.A36A|LHX9_ENST00000337020.2_Silent_p.A45A|LHX9_ENST00000561173.1_Silent_p.A51A|LHX9_ENST00000606127.1_3'UTR|LHX9_ENST00000367391.1_Silent_p.A36A	NM_020204.2	NP_064589.2	Q9NQ69	LHX9_HUMAN	LIM homeobox 9	45					cell proliferation (GO:0008283)|female gonad development (GO:0008585)|gonad morphogenesis (GO:0035262)|male gonad development (GO:0008584)|motor neuron axon guidance (GO:0008045)|negative regulation of transcription, DNA-templated (GO:0045892)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)			endometrium(8)|kidney(1)|large_intestine(6)|liver(2)|lung(14)|ovary(2)|skin(1)|stomach(1)	35						AGACTGAGGCCCGTCTGGCCA	0.662																																						uc001guk.1																			0				endometrium(8)|kidney(1)|large_intestine(6)|liver(2)|lung(14)|ovary(2)|skin(1)|stomach(1)	35						c.(133-135)gcC>gcT		Homo sapiens LIM homeobox 9 (LHX9), transcript variant 1, mRNA.							72.0	75.0	74.0					1																	197887088		2203	4300	6503	SO:0001819	synonymous_variant	56956				motor axon guidance|negative regulation of transcription, DNA-dependent	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription corepressor activity|zinc ion binding	g.chr1:197887088C>T	AJ277915	CCDS1393.1, CCDS30962.1	1q31.1	2011-06-20			ENSG00000143355	ENSG00000143355		"""Homeoboxes / LIM class"""	14222	protein-coding gene	gene with protein product		606066					Standard	NM_020204		Approved		uc001guk.1	Q9NQ69	OTTHUMG00000035656	ENST00000367387.4:c.135C>T	1.37:g.197887088C>T						LHX9_uc009wzc.1_Non-coding_Transcript|LHX9_uc001gui.1_Silent_p.A36A	p.A45A	NM_020204	NP_064589	Q9NQ69	LHX9_HUMAN			0	572	+			45					Q5VUE2|Q5VUE3|Q5VUE6|Q86UH2|Q9BYU6|Q9NQ70	Silent	SNP	ENST00000367387.4	37	c.135C>T	CCDS1393.1																																																																																				0.662	LHX9-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086547.2	NM_020204	
NEBL	10529	broad.mit.edu	37	10	21112168	21112168	+	Missense_Mutation	SNP	C	C	T			TCGA-76-4929-01A-01D-1486-08	TCGA-76-4929-10A-01D-1486-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	af4f8b89-837a-48b7-b0e7-12aec23fc285	3e0712a1-b66a-42e7-94a3-07edee7dce2b	g.chr10:21112168C>T	ENST00000377122.4	-	19	2327	c.1931G>A	c.(1930-1932)aGa>aAa	p.R644K	NEBL_ENST00000417816.2_Intron|NEBL_ENST00000377159.4_Intron	NM_006393.2	NP_006384.1	O76041	NEBL_HUMAN	nebulette	644					cardiac muscle thin filament assembly (GO:0071691)	extracellular vesicular exosome (GO:0070062)|I band (GO:0031674)|stress fiber (GO:0001725)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|cytoskeletal protein binding (GO:0008092)|filamin binding (GO:0031005)|structural constituent of muscle (GO:0008307)|tropomyosin binding (GO:0005523)			NS(2)|breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(14)|lung(22)|ovary(2)|pancreas(1)|prostate(2)|skin(8)|stomach(5)|upper_aerodigestive_tract(1)|urinary_tract(2)	70						TTCTTTAACTCTCTTTAGTTC	0.284																																						uc001iqi.3																			0				NS(2)|breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(14)|lung(22)|ovary(2)|pancreas(1)|prostate(2)|skin(8)|stomach(5)|upper_aerodigestive_tract(1)|urinary_tract(2)	70						c.(1930-1932)aGa>aAa		Homo sapiens nebulette (NEBL), transcript variant 1, mRNA.							116.0	110.0	112.0					10																	21112168		2203	4300	6503	SO:0001583	missense	10529				regulation of actin filament length		actin binding|structural constituent of muscle	g.chr10:21112168C>T	Y16241	CCDS7133.1, CCDS7134.1	10p12	2014-09-17			ENSG00000078114	ENSG00000078114			16932	protein-coding gene	gene with protein product		605491				9733644, 10470015	Standard	NM_213569		Approved		uc001iqi.3	O76041	OTTHUMG00000017788	ENST00000377122.4:c.1931G>A	10.37:g.21112168C>T	ENSP00000366326:p.Arg644Lys					NEBL_uc001iqj.3_Non-coding_Transcript|NEBL_uc001iqk.3_Intron|NEBL_uc021pnu.1_Intron	p.R644K	NM_006393	NP_006384	O76041	NEBL_HUMAN			18	2328	-			644					B0YJ45|Q2TBD0|Q70I54|Q9UIC4	Missense_Mutation	SNP	ENST00000377122.4	37	c.1931G>A	CCDS7134.1	.	.	.	.	.	.	.	.	.	.	C	17.67	3.447746	0.63178	.	.	ENSG00000078114	ENST00000377122	T	0.53423	0.62	5.42	4.52	0.55395	.	0.188549	0.42420	N	0.000713	T	0.59487	0.2197	M	0.92923	3.36	0.80722	D	1	P	0.37122	0.583	B	0.39068	0.289	T	0.65615	-0.6125	10	0.40728	T	0.16	.	12.9583	0.58442	0.0:0.9214:0.0:0.0786	.	644	O76041	NEBL_HUMAN	K	644	ENSP00000366326:R644K	ENSP00000366326:R644K	R	-	2	0	NEBL	21152174	1.000000	0.71417	0.734000	0.30879	0.716000	0.41182	4.721000	0.61951	1.428000	0.47296	0.655000	0.94253	AGA		0.284	NEBL-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000047113.1	NM_006393	
RBP3	5949	broad.mit.edu	37	10	48390589	48390589	+	Missense_Mutation	SNP	C	C	T			TCGA-76-4929-01A-01D-1486-08	TCGA-76-4929-10A-01D-1486-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	af4f8b89-837a-48b7-b0e7-12aec23fc285	3e0712a1-b66a-42e7-94a3-07edee7dce2b	g.chr10:48390589C>T	ENST00000224600.4	-	1	402	c.289G>A	c.(289-291)Gag>Aag	p.E97K	AL731561.2_ENST00000581861.1_RNA	NM_002900.2	NP_002891.1	P10745	RET3_HUMAN	retinol binding protein 3, interstitial	97	4 X approximate tandem repeats.				lipid metabolic process (GO:0006629)|phototransduction, visible light (GO:0007603)|retinoid metabolic process (GO:0001523)|transport (GO:0006810)|visual perception (GO:0007601)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|interphotoreceptor matrix (GO:0033165)|vesicle (GO:0031982)	retinal binding (GO:0016918)|retinoid binding (GO:0005501)|retinol binding (GO:0019841)|serine-type peptidase activity (GO:0008236)			central_nervous_system(3)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(8)|lung(30)|ovary(1)|prostate(7)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	59					Vitamin A(DB00162)	GGGGGAGGCTCGGGGGTGCTG	0.627																																						uc001jez.3																			0				central_nervous_system(3)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(8)|lung(30)|ovary(1)|prostate(7)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	59						c.(289-291)Gag>Aag		Homo sapiens retinol binding protein 3, interstitial (RBP3), mRNA.	Vitamin A(DB00162)						53.0	63.0	60.0					10																	48390589		2203	4300	6503	SO:0001583	missense	5949				lipid metabolic process|proteolysis|transport|visual perception	interphotoreceptor matrix	retinal binding|serine-type peptidase activity	g.chr10:48390589C>T	M22453	CCDS73119.1	10q11.2	2014-05-06	2001-11-28		ENSG00000107618	ENSG00000265203			9921	protein-coding gene	gene with protein product		180290	"""retinol-binding protein 3, interstitial"""				Standard	NM_002900		Approved	D10S64, D10S65, D10S66, RP66	uc001jez.3	P10745	OTTHUMG00000188321	ENST00000224600.4:c.289G>A	10.37:g.48390589C>T	ENSP00000224600:p.Glu97Lys						p.E97K	NM_002900	NP_002891	P10745	RET3_HUMAN			0	403	-			97			4 X approximate tandem repeats.		Q0QD34|Q5VSR0|Q8IXN0	Missense_Mutation	SNP	ENST00000224600.4	37	c.289G>A	CCDS7218.1	.	.	.	.	.	.	.	.	.	.	C	9.856	1.195105	0.22037	.	.	ENSG00000107618	ENST00000224600	T	0.63744	-0.06	5.56	4.66	0.58398	Interphotoreceptor retinol-binding, N-terminal (1);	0.249596	0.39834	N	0.001249	T	0.65101	0.2659	M	0.84585	2.705	0.09310	N	1	P	0.39665	0.682	B	0.39904	0.313	T	0.65203	-0.6225	10	0.72032	D	0.01	-19.2325	8.4361	0.32789	0.1524:0.7683:0.0:0.0793	.	97	P10745	RET3_HUMAN	K	97	ENSP00000224600:E97K	ENSP00000224600:E97K	E	-	1	0	RBP3	48010595	0.170000	0.23016	0.087000	0.20705	0.047000	0.14425	1.557000	0.36299	1.358000	0.45922	0.650000	0.86243	GAG		0.627	RBP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047888.1	NM_002900	
ADO	84890	broad.mit.edu	37	10	64564912	64564912	+	Silent	SNP	C	C	T			TCGA-76-4929-01A-01D-1486-08	TCGA-76-4929-10A-01D-1486-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	af4f8b89-837a-48b7-b0e7-12aec23fc285	3e0712a1-b66a-42e7-94a3-07edee7dce2b	g.chr10:64564912C>T	ENST00000373783.1	+	1	397	c.93C>T	c.(91-93)tcC>tcT	p.S31S	RP11-436D10.3_ENST00000425290.1_RNA	NM_032804.5	NP_116193.2	Q96SZ5	AEDO_HUMAN	2-aminoethanethiol (cysteamine) dioxygenase	31						mitochondrion (GO:0005739)	cysteamine dioxygenase activity (GO:0047800)|metal ion binding (GO:0046872)			lung(2)	2	Prostate(12;0.0297)|all_hematologic(501;0.228)					GCGGCGCTTCCGATCGCGACG	0.711																																						uc001jmg.3																			0				lung(2)	2						c.(91-93)tcC>tcT		Homo sapiens 2-aminoethanethiol (cysteamine) dioxygenase (ADO), mRNA.							8.0	10.0	10.0					10																	64564912		2171	4260	6431	SO:0001819	synonymous_variant	84890						cysteamine dioxygenase activity|metal ion binding	g.chr10:64564912C>T	BC028589	CCDS7266.2	10q21.3	2007-08-28	2007-08-28	2007-08-28	ENSG00000181915	ENSG00000181915	1.13.11.19		23506	protein-coding gene	gene with protein product	"""cysteamine dioxygenase"""	611392	"""chromosome 10 open reading frame 22"""	C10orf22		17581819	Standard	NM_032804		Approved	FLJ14547	uc001jmg.3	Q96SZ5	OTTHUMG00000018306	ENST00000373783.1:c.93C>T	10.37:g.64564912C>T							p.S31S	NM_032804	NP_116193	Q96SZ5	AEDO_HUMAN			0	397	+	Prostate(12;0.0297)|all_hematologic(501;0.228)		31					B1AL29	Silent	SNP	ENST00000373783.1	37	c.93C>T	CCDS7266.2																																																																																				0.711	ADO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048243.2	NM_032804	
NT5C2	22978	broad.mit.edu	37	10	104934623	104934623	+	Silent	SNP	G	G	A			TCGA-76-4929-01A-01D-1486-08	TCGA-76-4929-10A-01D-1486-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	af4f8b89-837a-48b7-b0e7-12aec23fc285	3e0712a1-b66a-42e7-94a3-07edee7dce2b	g.chr10:104934623G>A	ENST00000404739.3	-	1	116	c.93C>T	c.(91-93)gcC>gcT	p.A31A	NT5C2_ENST00000343289.5_Silent_p.A31A|NT5C2_ENST00000369857.4_Intron|NT5C2_ENST00000470299.1_Silent_p.A31A			P49902	5NTC_HUMAN	5'-nucleotidase, cytosolic II	31					cell death (GO:0008219)|dephosphorylation (GO:0016311)|drug metabolic process (GO:0017144)|nucleobase-containing small molecule metabolic process (GO:0055086)|phosphorylation (GO:0016310)|purine nucleobase metabolic process (GO:0006144)|purine nucleotide catabolic process (GO:0006195)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	5'-nucleotidase activity (GO:0008253)|metal ion binding (GO:0046872)|nucleoside phosphotransferase activity (GO:0050146)|nucleotide binding (GO:0000166)			cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(6)|urinary_tract(1)	16		all_hematologic(284;0.176)|Colorectal(252;0.178)		Epithelial(162;1.33e-08)|all cancers(201;1.04e-07)|BRCA - Breast invasive adenocarcinoma(275;0.159)	Adenosine triphosphate(DB00171)|Ribavirin(DB00811)	ACCGATGATAGGCTTCTCGAC	0.383																																						uc001kwo.3																			0				cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(6)|urinary_tract(1)	16						c.(91-93)gcC>gcT		Homo sapiens 5'-nucleotidase, cytosolic II (NT5C2), transcript variant 1, mRNA.	Adenosine triphosphate(DB00171)|Ribavirin(DB00811)						221.0	204.0	209.0					10																	104934623		2203	4300	6503	SO:0001819	synonymous_variant	22978				purine base metabolic process|purine nucleotide catabolic process	cytosol	5'-nucleotidase activity|metal ion binding|nucleotide binding|protein binding	g.chr10:104934623G>A	D38524	CCDS7544.1	10q24.32	2014-03-03	2002-04-18	2002-04-19	ENSG00000076685	ENSG00000076685			8022	protein-coding gene	gene with protein product	"""purine 5' nucleotidase"""	600417	"""5'-nucleotidase (purine), cytosolic type B"""	NT5B		7999131, 24482476	Standard	NM_012229		Approved	PNT5, GMP, cN-II, SPG65	uc001kwq.3	P49902	OTTHUMG00000018981	ENST00000404739.3:c.93C>T	10.37:g.104934623G>A						NT5C2_uc001kwq.3_Silent_p.A31A|NT5C2_uc001kwp.3_Intron	p.A31A	NM_012229	NP_036361	P49902	5NTC_HUMAN		Epithelial(162;1.33e-08)|all cancers(201;1.04e-07)|BRCA - Breast invasive adenocarcinoma(275;0.159)	2	286	-		all_hematologic(284;0.176)|Colorectal(252;0.178)	31					B7Z382|D3DR91|Q5JUV5	Silent	SNP	ENST00000404739.3	37	c.93C>T	CCDS7544.1																																																																																				0.383	NT5C2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050121.1	NM_012229	
SLC22A25	387601	broad.mit.edu	37	11	62931319	62931319	+	Missense_Mutation	SNP	G	G	C			TCGA-76-4929-01A-01D-1486-08	TCGA-76-4929-10A-01D-1486-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	af4f8b89-837a-48b7-b0e7-12aec23fc285	3e0712a1-b66a-42e7-94a3-07edee7dce2b	g.chr11:62931319G>C	ENST00000306494.6	-	9	1620	c.1621C>G	c.(1621-1623)Cct>Gct	p.P541A	SLC22A10_ENST00000535888.1_Intron|SLC22A10_ENST00000525620.1_Intron	NM_199352.3	NP_955384.3			solute carrier family 22, member 25											NS(2)|breast(2)|endometrium(4)|kidney(2)|large_intestine(7)|lung(7)|ovary(3)|skin(7)	34						CTCCTCTGAGGGGCAGCTAGG	0.507																																						uc001nwr.1																			0				NS(2)|breast(2)|endometrium(4)|kidney(2)|large_intestine(7)|lung(7)|ovary(3)|skin(7)	34						c.(1621-1623)Cct>Gct		Homo sapiens solute carrier family 22, member 25 (SLC22A25), mRNA.							130.0	125.0	127.0					11																	62931319		2201	4298	6499	SO:0001583	missense	387601				transmembrane transport	integral to membrane		g.chr11:62931319G>C	AY437532	CCDS31592.1	11q12.3	2014-05-20			ENSG00000196600	ENSG00000196600		"""Solute carriers"""	32935	protein-coding gene	gene with protein product		610792	"""MGI:2442751, MGI:2385316, MGI:3042283, MGI:3645714, MGI:3605624, MGI:2442750"""			17714910	Standard	NM_199352		Approved	UST6, HIMTP, MGC120420	uc001nwr.1	Q6T423	OTTHUMG00000165340	ENST00000306494.6:c.1621C>G	11.37:g.62931319G>C	ENSP00000307443:p.Pro541Ala					SLC22A10_uc010rmo.1_Intron|SLC22A25_uc009yoq.1_Non-coding_Transcript|SLC22A25_uc001nws.1_Non-coding_Transcript	p.P541A	NM_199352	NP_955384	Q6T423	S22AP_HUMAN			8	1621	-			541						Missense_Mutation	SNP	ENST00000306494.6	37	c.1621C>G	CCDS31592.1	.	.	.	.	.	.	.	.	.	.	G	1.644	-0.515799	0.04200	.	.	ENSG00000196600	ENST00000306494	T	0.63580	-0.05	4.1	-0.32	0.12721	.	51.435300	0.00166	U	0.000011	T	0.49081	0.1536	L	0.29908	0.895	0.09310	N	1	B	0.09022	0.002	B	0.01281	0.0	T	0.30707	-0.9969	10	0.52906	T	0.07	.	3.7318	0.08496	0.198:0.0:0.471:0.331	.	541	Q6T423	S22AP_HUMAN	A	541	ENSP00000307443:P541A	ENSP00000307443:P541A	P	-	1	0	SLC22A25	62687895	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-0.356000	0.07661	-0.150000	0.11195	0.586000	0.80456	CCT		0.507	SLC22A25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383519.3	NM_199352	
LRRC32	2615	broad.mit.edu	37	11	76371933	76371933	+	Missense_Mutation	SNP	G	G	A	rs147861179		TCGA-76-4929-01A-01D-1486-08	TCGA-76-4929-10A-01D-1486-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	af4f8b89-837a-48b7-b0e7-12aec23fc285	3e0712a1-b66a-42e7-94a3-07edee7dce2b	g.chr11:76371933G>A	ENST00000407242.2	-	3	946	c.704C>T	c.(703-705)aCg>aTg	p.T235M	LRRC32_ENST00000404995.1_Missense_Mutation_p.T235M|LRRC32_ENST00000260061.5_Missense_Mutation_p.T235M|AP001189.4_ENST00000447519.1_RNA|LRRC32_ENST00000464145.1_Intron	NM_005512.2	NP_005503.1	Q14392	LRC32_HUMAN	leucine rich repeat containing 32	235					negative regulation of activated T cell proliferation (GO:0046007)|negative regulation of cytokine secretion (GO:0050710)|positive regulation of gene expression (GO:0010628)	integral component of plasma membrane (GO:0005887)				endometrium(1)|large_intestine(3)|lung(26)|upper_aerodigestive_tract(1)	31						CTGGGAGGCCGTCTGAAAGGC	0.617																																						uc001oxq.4																			0				endometrium(1)|large_intestine(3)|lung(26)|upper_aerodigestive_tract(1)	31						c.(703-705)aCg>aTg		Homo sapiens leucine rich repeat containing 32 (LRRC32), transcript variant 1, mRNA.		G	MET/THR,MET/THR	1,4399	2.1+/-5.4	0,1,2199	43.0	47.0	45.0		704,704	1.5	0.4	11	dbSNP_134	45	0,8584		0,0,4292	yes	missense,missense	LRRC32	NM_001128922.1,NM_005512.2	81,81	0,1,6491	AA,AG,GG		0.0,0.0227,0.0077	probably-damaging,probably-damaging	235/663,235/663	76371933	1,12983	2200	4292	6492	SO:0001583	missense	2615					integral to plasma membrane		g.chr11:76371933G>A	Z24680	CCDS8245.1	11q13.5-q14	2008-02-05	2005-02-25	2005-02-25	ENSG00000137507	ENSG00000137507			4161	protein-coding gene	gene with protein product		137207	"""glycoprotein A repetitions predominant"""	D11S833E, GARP		8180135, 1543912	Standard	NM_005512		Approved		uc001oxq.4	Q14392	OTTHUMG00000133687	ENST00000407242.2:c.704C>T	11.37:g.76371933G>A	ENSP00000384126:p.Thr235Met					LRRC32_uc001oxr.4_Missense_Mutation_p.T235M|LRRC32_uc010rsf.2_Missense_Mutation_p.T235M	p.T235M	NM_005512	NP_005503	Q14392	LRC32_HUMAN			2	947	-			235					Q86V06	Missense_Mutation	SNP	ENST00000407242.2	37	c.704C>T	CCDS8245.1	.	.	.	.	.	.	.	.	.	.	G	7.617	0.676027	0.14841	2.27E-4	0.0	ENSG00000137507	ENST00000260061;ENST00000407242;ENST00000404995	T;T;T	0.79653	-1.29;-1.29;-1.29	4.43	1.55	0.23275	.	0.330320	0.34828	N	0.003650	T	0.64505	0.2604	L	0.35723	1.085	0.43238	D	0.995142	P	0.36144	0.539	B	0.19391	0.025	T	0.57791	-0.7750	10	0.42905	T	0.14	.	9.2819	0.37733	0.2353:0.0:0.7647:0.0	.	235	Q14392	LRC32_HUMAN	M	235	ENSP00000260061:T235M;ENSP00000384126:T235M;ENSP00000385766:T235M	ENSP00000260061:T235M	T	-	2	0	LRRC32	76049581	0.150000	0.22732	0.420000	0.26596	0.552000	0.35366	0.182000	0.16900	0.159000	0.19401	0.462000	0.41574	ACG		0.617	LRRC32-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257926.2	NM_005512	
PIK3C2G	5288	broad.mit.edu	37	12	18544153	18544153	+	Missense_Mutation	SNP	T	T	C			TCGA-76-4929-01A-01D-1486-08	TCGA-76-4929-10A-01D-1486-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	af4f8b89-837a-48b7-b0e7-12aec23fc285	3e0712a1-b66a-42e7-94a3-07edee7dce2b	g.chr12:18544153T>C	ENST00000266497.5	+	13	2008	c.1970T>C	c.(1969-1971)aTt>aCt	p.I657T	PIK3C2G_ENST00000538779.1_Missense_Mutation_p.I698T|PIK3C2G_ENST00000433979.1_Missense_Mutation_p.I657T			O75747	P3C2G_HUMAN	phosphatidylinositol-4-phosphate 3-kinase, catalytic subunit type 2 gamma	657	PIK helical. {ECO:0000255|PROSITE- ProRule:PRU00878}.				chemotaxis (GO:0006935)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|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)|phosphatidylinositol binding (GO:0035091)|phosphatidylinositol phosphate kinase activity (GO:0016307)			breast(5)|central_nervous_system(6)|endometrium(2)|kidney(4)|large_intestine(8)|lung(31)|ovary(2)|prostate(1)|skin(2)|stomach(4)|upper_aerodigestive_tract(1)	66		Hepatocellular(102;0.194)				ATAAAACATATTGCCAGACTT	0.383																																						uc001rdt.3																			0				breast(5)|central_nervous_system(6)|endometrium(2)|kidney(4)|large_intestine(8)|lung(31)|ovary(2)|prostate(1)|skin(2)|stomach(4)|upper_aerodigestive_tract(1)	66						c.(1969-1971)aTt>aCt		Homo sapiens phosphoinositide-3-kinase, class 2, gamma polypeptide (PIK3C2G), mRNA.							89.0	83.0	85.0					12																	18544153		1842	4091	5933	SO:0001583	missense	5288				cell communication|phosphatidylinositol-mediated signaling	membrane|phosphatidylinositol 3-kinase complex	1-phosphatidylinositol-3-kinase activity|ATP binding|phosphatidylinositol binding|phosphatidylinositol-4-phosphate 3-kinase activity	g.chr12:18544153T>C	AJ000008	CCDS44839.1, CCDS73452.1	12p12	2012-07-13	2012-07-13		ENSG00000139144	ENSG00000139144	2.7.1.154		8973	protein-coding gene	gene with protein product		609001	"""phosphoinositide-3-kinase, class 2, gamma polypeptide"""			9878262	Standard	XM_005253393		Approved		uc001rdt.3	O75747	OTTHUMG00000168841	ENST00000266497.5:c.1970T>C	12.37:g.18544153T>C	ENSP00000266497:p.Ile657Thr					PIK3C2G_uc010sia.2_Non-coding_Transcript|PIK3C2G_uc010sib.2_Missense_Mutation_p.I698T|PIK3C2G_uc010sic.2_Missense_Mutation_p.I476T	p.I657T	NM_004570	NP_004561	O75747	P3C2G_HUMAN			13	2086	+		Hepatocellular(102;0.194)	657					A1L3U0	Missense_Mutation	SNP	ENST00000266497.5	37	c.1970T>C	CCDS44839.1	.	.	.	.	.	.	.	.	.	.	T	14.89	2.671051	0.47781	.	.	ENSG00000139144	ENST00000433979;ENST00000266497;ENST00000538779	T;T;T	0.67171	-0.25;-0.25;-0.25	5.03	5.03	0.67393	Phosphoinositide 3-kinase, accessory (PIK) domain (2);Armadillo-type fold (1);	0.077706	0.49305	D	0.000145	T	0.79209	0.4407	M	0.71206	2.165	0.45390	D	0.998377	D;D;D	0.76494	0.999;0.998;0.999	D;D;D	0.71414	0.973;0.954;0.973	T	0.80926	-0.1164	10	0.59425	D	0.04	-19.1021	12.9215	0.58234	0.0:0.0:0.0:1.0	.	697;698;657	B7ZLY6;F5H369;O75747	.;.;P3C2G_HUMAN	T	657;657;698	ENSP00000404845:I657T;ENSP00000266497:I657T;ENSP00000445381:I698T	ENSP00000266497:I657T	I	+	2	0	PIK3C2G	18435420	0.986000	0.35501	1.000000	0.80357	0.839000	0.47603	4.552000	0.60747	2.237000	0.73441	0.528000	0.53228	ATT		0.383	PIK3C2G-002	KNOWN	NAGNAG_splice_site|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401316.1	NM_004570	
KSR2	283455	broad.mit.edu	37	12	117962680	117962680	+	Silent	SNP	C	C	T	rs140960062	byFrequency	TCGA-76-4929-01A-01D-1486-08	TCGA-76-4929-10A-01D-1486-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	af4f8b89-837a-48b7-b0e7-12aec23fc285	3e0712a1-b66a-42e7-94a3-07edee7dce2b	g.chr12:117962680C>T	ENST00000339824.5	-	14	2923	c.2196G>A	c.(2194-2196)ccG>ccA	p.P732P	KSR2_ENST00000302438.5_Silent_p.P429P|KSR2_ENST00000545002.1_5'UTR|KSR2_ENST00000425217.1_Silent_p.P703P			Q6VAB6	KSR2_HUMAN	kinase suppressor of ras 2	732	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				intracellular signal transduction (GO:0035556)	cytoplasm (GO:0005737)|membrane (GO:0016020)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(3)|central_nervous_system(2)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(25)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	67	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)					CCAGGTGAGGCGGGCTCATGC	0.557													C|||	3	0.000599042	0.0	0.0	5008	,	,		18539	0.002		0.001	False		,,,				2504	0.0					uc001two.2																			0				NS(1)|breast(3)|central_nervous_system(2)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(25)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	67						c.(2107-2109)ccG>ccA		Homo sapiens kinase suppressor of ras 2 (KSR2), mRNA.							46.0	47.0	47.0					12																	117962680		2065	4182	6247	SO:0001819	synonymous_variant	283455				intracellular signal transduction	cytoplasm|membrane	ATP binding|metal ion binding|protein serine/threonine kinase activity	g.chr12:117962680C>T	AY345972	CCDS61250.1	12q24.22-q24.23	2014-08-12			ENSG00000171435	ENSG00000171435			18610	protein-coding gene	gene with protein product		610737				12471243	Standard	NM_173598		Approved	FLJ25965	uc001two.2	Q6VAB6	OTTHUMG00000169020	ENST00000339824.5:c.2196G>A	12.37:g.117962680C>T							p.P703P	NM_173598	NP_775869	Q6VAB6	KSR2_HUMAN			13	2164	-	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)		732			Protein kinase.		A0PJT2|Q3B828|Q8N775	Silent	SNP	ENST00000339824.5	37	c.2109G>A																																																																																					0.557	KSR2-001	KNOWN	non_canonical_conserved|not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000401987.2	NM_173598	
TMEM132D	121256	broad.mit.edu	37	12	130184667	130184667	+	Missense_Mutation	SNP	G	G	A	rs146143180		TCGA-76-4929-01A-01D-1486-08	TCGA-76-4929-10A-01D-1486-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	af4f8b89-837a-48b7-b0e7-12aec23fc285	3e0712a1-b66a-42e7-94a3-07edee7dce2b	g.chr12:130184667G>A	ENST00000422113.2	-	2	982	c.656C>T	c.(655-657)cCg>cTg	p.P219L	RP11-174M13.2_ENST00000544036.1_lincRNA	NM_133448.2	NP_597705.2	Q14C87	T132D_HUMAN	transmembrane protein 132D	219					negative regulation of phosphatase activity (GO:0010923)	integral component of membrane (GO:0016021)		p.P219L(2)		NS(1)|breast(6)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(33)|liver(1)|lung(69)|ovary(10)|pancreas(2)|prostate(2)|skin(7)|upper_aerodigestive_tract(5)|urinary_tract(2)	152	all_neural(191;0.101)|Medulloblastoma(191;0.163)	all_epithelial(31;0.0934)|Breast(359;0.133)		OV - Ovarian serous cystadenocarcinoma(86;0.000288)|Epithelial(86;0.0116)|all cancers(50;0.0246)		GGTCCCCTCCGGCTGGTCCAC	0.682																																						uc009zyl.1																			2	Substitution - Missense(2)	p.P219L(4)|p.P219P(1)|p.P219T(1)|p.Q218H(1)	ovary(1)|prostate(1)	NS(1)|breast(6)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(33)|liver(1)|lung(69)|ovary(10)|pancreas(2)|prostate(2)|skin(7)|upper_aerodigestive_tract(5)|urinary_tract(2)	152						c.(655-657)cCg>cTg		Homo sapiens transmembrane protein 132D (TMEM132D), mRNA.		G	LEU/PRO	0,4406		0,0,2203	38.0	40.0	39.0		656	2.5	0.0	12	dbSNP_134	39	3,8597	3.0+/-9.4	0,3,4297	no	missense	TMEM132D	NM_133448.2	98	0,3,6500	AA,AG,GG		0.0349,0.0,0.0231	benign	219/1100	130184667	3,13003	2203	4300	6503	SO:0001583	missense	121256					integral to membrane		g.chr12:130184667G>A	AB061814	CCDS9266.1	12q24.32-q24.33	2014-06-13			ENSG00000151952	ENSG00000151952			29411	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 153"""	611257				11853319, 12966072	Standard	NM_133448		Approved	KIAA1944, MOLT, PPP1R153	uc009zyl.1	Q14C87	OTTHUMG00000168400	ENST00000422113.2:c.656C>T	12.37:g.130184667G>A	ENSP00000408581:p.Pro219Leu						p.P219L	NM_133448	NP_597705	Q14C87	T132D_HUMAN		OV - Ovarian serous cystadenocarcinoma(86;0.000288)|Epithelial(86;0.0116)|all cancers(50;0.0246)	1	984	-	all_neural(191;0.101)|Medulloblastoma(191;0.163)	all_epithelial(31;0.0934)|Breast(359;0.133)	219					Q14C96|Q76M59|Q8N1W9|Q8N3Q5|Q8TF57	Missense_Mutation	SNP	ENST00000422113.2	37	c.656C>T	CCDS9266.1	.	.	.	.	.	.	.	.	.	.	G	1.196	-0.633920	0.03584	0.0	3.49E-4	ENSG00000151952	ENST00000422113	T	0.10860	2.83	5.35	2.46	0.29980	.	0.521615	0.18832	N	0.129936	T	0.08714	0.0216	L	0.40543	1.245	0.09310	N	0.999999	B	0.12630	0.006	B	0.06405	0.002	T	0.34576	-0.9823	9	.	.	.	-7.5313	9.0373	0.36296	0.069:0.0:0.6664:0.2646	.	219	Q14C87	T132D_HUMAN	L	219	ENSP00000408581:P219L	.	P	-	2	0	TMEM132D	128750620	0.002000	0.14202	0.000000	0.03702	0.022000	0.10575	1.224000	0.32539	0.212000	0.20703	-0.175000	0.13238	CCG		0.682	TMEM132D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399592.1	NM_133448	
SFSWAP	6433	broad.mit.edu	37	12	132249171	132249171	+	Missense_Mutation	SNP	T	T	A			TCGA-76-4929-01A-01D-1486-08	TCGA-76-4929-10A-01D-1486-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	af4f8b89-837a-48b7-b0e7-12aec23fc285	3e0712a1-b66a-42e7-94a3-07edee7dce2b	g.chr12:132249171T>A	ENST00000261674.4	+	12	2032	c.1891T>A	c.(1891-1893)Tgt>Agt	p.C631S	SFSWAP_ENST00000541286.1_Missense_Mutation_p.C631S	NM_004592.3	NP_004583.2	Q12872	SFSWA_HUMAN	splicing factor, suppressor of white-apricot family	631					mRNA processing (GO:0006397)|mRNA splice site selection (GO:0006376)|negative regulation of mRNA splicing, via spliceosome (GO:0048025)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	RNA binding (GO:0003723)			endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(9)|lung(8)|ovary(1)|skin(2)	25						TGCCCCACCCTGTGTAGTTGT	0.423																																						uc001uja.1																			0				endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(9)|lung(8)|ovary(1)|skin(2)	25						c.(1891-1893)Tgt>Agt		Homo sapiens splicing factor, suppressor of white-apricot homolog (Drosophila) (SFSWAP), mRNA.							81.0	69.0	73.0					12																	132249171		2203	4300	6503	SO:0001583	missense	6433				mRNA splice site selection|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	protein binding|RNA binding	g.chr12:132249171T>A	U08377	CCDS9273.1, CCDS58290.1	12q24.33	2014-04-14	2014-04-14	2010-09-15	ENSG00000061936	ENSG00000061936			10790	protein-coding gene	gene with protein product		601945	"""splicing factor, arginine/serine-rich 8 (suppressor-of-white-apricot, Drosophila homolog)"", ""splicing factor, arginine/serine-rich 8 (suppressor-of-white-apricot homolog, Drosophila)"", ""splicing factor, suppressor of white-apricot homolog (Drosophila)"""	SFRS8		8940107	Standard	NM_004592		Approved	SWAP	uc010tbn.2	Q12872	OTTHUMG00000168319	ENST00000261674.4:c.1891T>A	12.37:g.132249171T>A	ENSP00000261674:p.Cys631Ser					SFSWAP_uc010tbn.1_Missense_Mutation_p.C631S|SFSWAP_uc001ujb.1_Missense_Mutation_p.C424S	p.C631S	NM_004592	NP_004583	Q12872	SFSWA_HUMAN			11	2031	+			631					B2RN45|B7ZM97|F5H6B8|Q6PJF7	Missense_Mutation	SNP	ENST00000261674.4	37	c.1891T>A	CCDS9273.1	.	.	.	.	.	.	.	.	.	.	T	1.943	-0.443031	0.04604	.	.	ENSG00000061936	ENST00000261674;ENST00000535236;ENST00000541286	T;T;T	0.19938	3.12;2.11;3.1	5.09	3.94	0.45596	.	0.529435	0.22602	N	0.057954	T	0.08313	0.0207	N	0.08118	0	0.24024	N	0.996132	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.38001	-0.9681	10	0.07482	T	0.82	-5.1053	6.7346	0.23403	0.1357:0.075:0.0:0.7893	.	631;631	F5H6B8;Q12872	.;SFSWA_HUMAN	S	631;424;631	ENSP00000261674:C631S;ENSP00000443045:C424S;ENSP00000437738:C631S	ENSP00000261674:C631S	C	+	1	0	SFSWAP	130815124	1.000000	0.71417	0.210000	0.23637	0.981000	0.71138	2.122000	0.41987	0.887000	0.36136	0.402000	0.26972	TGT		0.423	SFSWAP-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000399276.1	NM_004592	
LRFN5	145581	broad.mit.edu	37	14	42356720	42356720	+	Missense_Mutation	SNP	G	G	T			TCGA-76-4929-01A-01D-1486-08	TCGA-76-4929-10A-01D-1486-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	af4f8b89-837a-48b7-b0e7-12aec23fc285	3e0712a1-b66a-42e7-94a3-07edee7dce2b	g.chr14:42356720G>T	ENST00000298119.4	+	3	2081	c.892G>T	c.(892-894)Gtc>Ttc	p.V298F	LRFN5_ENST00000554120.1_Missense_Mutation_p.V298F|LRFN5_ENST00000554171.1_Missense_Mutation_p.V298F	NM_152447.3	NP_689660.2	Q96NI6	LRFN5_HUMAN	leucine rich repeat and fibronectin type III domain containing 5	298	Ig-like.					integral component of membrane (GO:0016021)				breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(12)|liver(1)|lung(67)|ovary(5)|pancreas(3)|prostate(1)|skin(9)|stomach(1)|upper_aerodigestive_tract(9)|urinary_tract(2)	120			LUAD - Lung adenocarcinoma(50;0.0223)|Lung(238;0.0728)	GBM - Glioblastoma multiforme(112;0.00847)		TGAGATGAGAGTCCTGGAGGG	0.478										HNSCC(30;0.082)																												uc001wvm.3																			0				breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(12)|liver(1)|lung(67)|ovary(5)|pancreas(3)|prostate(1)|skin(9)|stomach(1)|upper_aerodigestive_tract(9)|urinary_tract(2)	120						c.(892-894)Gtc>Ttc		Homo sapiens leucine rich repeat and fibronectin type III domain containing 5 (LRFN5), mRNA.							109.0	104.0	106.0					14																	42356720		2203	4300	6503	SO:0001583	missense	145581					integral to membrane		g.chr14:42356720G>T	AK055365	CCDS9678.1	14q21.1	2013-02-11	2004-02-02	2004-02-04	ENSG00000165379	ENSG00000165379		"""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	20360	protein-coding gene	gene with protein product	"""fibronectin type III, immunoglobulin and leucine rich repeat domains 8"""	612811	"""chromosome 14 open reading frame 146"""	C14orf146		16828986	Standard	NM_152447		Approved	FIGLER8, SALM5	uc001wvm.3	Q96NI6	OTTHUMG00000140261	ENST00000298119.4:c.892G>T	14.37:g.42356720G>T	ENSP00000298119:p.Val298Phe	HNSCC(30;0.082)				LRFN5_uc010ana.3_Missense_Mutation_p.V298F	p.V298F	NM_152447	NP_689660	Q96NI6	LRFN5_HUMAN	LUAD - Lung adenocarcinoma(50;0.0223)|Lung(238;0.0728)	GBM - Glioblastoma multiforme(112;0.00847)	2	2090	+			298			Ig-like.		B3KU78|Q86XL2	Missense_Mutation	SNP	ENST00000298119.4	37	c.892G>T	CCDS9678.1	.	.	.	.	.	.	.	.	.	.	G	18.65	3.669904	0.67814	.	.	ENSG00000165379	ENST00000298119;ENST00000554120;ENST00000554171	T;T;T	0.72167	-0.63;-0.63;-0.63	5.4	5.4	0.78164	Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.50627	D	0.000104	D	0.88876	0.6556	H	0.95816	3.725	0.80722	D	1	D;D	0.71674	0.97;0.998	D;D	0.79784	0.955;0.993	D	0.91716	0.5385	10	0.72032	D	0.01	.	17.0338	0.86468	0.0:0.0:1.0:0.0	.	298;298	G3V364;Q96NI6	.;LRFN5_HUMAN	F	298	ENSP00000298119:V298F;ENSP00000451897:V298F;ENSP00000451067:V298F	ENSP00000298119:V298F	V	+	1	0	LRFN5	41426470	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.813000	0.99286	2.680000	0.91292	0.563000	0.77884	GTC		0.478	LRFN5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276786.1	NM_152447	
MOAP1	64112	broad.mit.edu	37	14	93650454	93650454	+	Missense_Mutation	SNP	G	G	A			TCGA-76-4929-01A-01D-1486-08	TCGA-76-4929-10A-01D-1486-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	af4f8b89-837a-48b7-b0e7-12aec23fc285	3e0712a1-b66a-42e7-94a3-07edee7dce2b	g.chr14:93650454G>A	ENST00000556883.1	-	2	618	c.134C>T	c.(133-135)cCc>cTc	p.P45L	RP11-371E8.4_ENST00000557574.1_5'Flank|TMEM251_ENST00000283534.4_5'Flank|MOAP1_ENST00000298894.4_Missense_Mutation_p.P45L|TMEM251_ENST00000415050.2_5'Flank			Q96BY2	MOAP1_HUMAN	modulator of apoptosis 1	45					apoptotic signaling pathway (GO:0097190)|extrinsic apoptotic signaling pathway in absence of ligand (GO:0097192)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|positive regulation of apoptotic process (GO:0043065)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:0001844)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)	ubiquitin protein ligase binding (GO:0031625)			central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(4)|ovary(1)|skin(2)	13		all_cancers(154;0.00528)|Acute lymphoblastic leukemia(33;0.0497)|all_epithelial(191;0.125)|all_neural(303;0.13)		Epithelial(152;0.178)|all cancers(159;0.2)|COAD - Colon adenocarcinoma(157;0.204)		ctcccccaagggagctaaacc	0.557																																						uc021saw.1																			0				central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(4)|ovary(1)|skin(2)	13						c.(133-135)cCc>cTc		Homo sapiens modulator of apoptosis 1 (MOAP1), mRNA.							118.0	129.0	126.0					14																	93650454		2203	4300	6503	SO:0001583	missense	64112				activation of caspase activity|apoptotic nuclear change	cytoplasm	protein homodimerization activity	g.chr14:93650454G>A	BC015044	CCDS9908.1	14q32.12	2012-02-09			ENSG00000165943	ENSG00000165943		"""Paraneoplastic Ma antigens"""	16658	protein-coding gene	gene with protein product	"""paraneoplastic Ma antigen family member 4"""	609485				11060313	Standard	NM_022151		Approved	MAP-1, PNMA4	uc001ybj.3	Q96BY2	OTTHUMG00000169184	ENST00000556883.1:c.134C>T	14.37:g.93650454G>A	ENSP00000451594:p.Pro45Leu					MOAP1_uc001ybj.3_Missense_Mutation_p.P45L|C14orf109_uc001ybk.4_5'Flank|C14orf109_uc010auo.3_5'Flank|C14orf109_uc021sax.1_5'Flank	p.P45L	NM_022151	NP_071434	Q96BY2	MOAP1_HUMAN		Epithelial(152;0.178)|all cancers(159;0.2)|COAD - Colon adenocarcinoma(157;0.204)	0	134	-		all_cancers(154;0.00528)|Acute lymphoblastic leukemia(33;0.0497)|all_epithelial(191;0.125)|all_neural(303;0.13)	45					B2RDF6|Q9H833|Q9HAS1	Missense_Mutation	SNP	ENST00000556883.1	37	c.134C>T	CCDS9908.1	.	.	.	.	.	.	.	.	.	.	G	13.71	2.319179	0.41096	.	.	ENSG00000165943	ENST00000298894;ENST00000556883	T;T	0.18960	2.18;2.18	3.46	1.51	0.23008	.	.	.	.	.	T	0.36963	0.0986	M	0.71036	2.16	0.09310	N	1	D	0.59357	0.985	P	0.61397	0.888	T	0.11012	-1.0605	9	0.87932	D	0	-1.522	6.0068	0.19551	0.0:0.2135:0.5662:0.2204	.	45	Q96BY2	MOAP1_HUMAN	L	45	ENSP00000298894:P45L;ENSP00000451594:P45L	ENSP00000298894:P45L	P	-	2	0	MOAP1	92720207	0.007000	0.16637	0.004000	0.12327	0.530000	0.34684	0.596000	0.24044	0.428000	0.26173	0.650000	0.86243	CCC		0.557	MOAP1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412685.1		
RBBP6	5930	broad.mit.edu	37	16	24581488	24581489	+	Frame_Shift_Del	DEL	TT	TT	-			TCGA-76-4929-01A-01D-1486-08	TCGA-76-4929-10A-01D-1486-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	af4f8b89-837a-48b7-b0e7-12aec23fc285	3e0712a1-b66a-42e7-94a3-07edee7dce2b	g.chr16:24581488_24581489delTT	ENST00000319715.4	+	17	3909_3910	c.3477_3478delTT	c.(3475-3480)gattttfs	p.F1160fs	RBBP6_ENST00000348022.2_Frame_Shift_Del_p.F1126fs|RBBP6_ENST00000381039.3_Intron	NM_006910.4	NP_008841.2	Q7Z6E9	RBBP6_HUMAN	retinoblastoma binding protein 6	1160					embryonic organ development (GO:0048568)|in utero embryonic development (GO:0001701)|multicellular organism growth (GO:0035264)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|somite development (GO:0061053)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	ligase activity (GO:0016874)|poly(A) RNA binding (GO:0044822)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(10)|lung(17)|ovary(4)|pancreas(1)|prostate(2)|urinary_tract(1)	46				GBM - Glioblastoma multiforme(48;0.0518)		TAGATAAAGATTTTGAGTCTTC	0.342																																						uc002dmh.3																			0				NS(1)|breast(3)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(10)|lung(17)|ovary(4)|pancreas(1)|prostate(2)|urinary_tract(1)	46						c.(3475-3480)gattttfs		Homo sapiens retinoblastoma binding protein 6 (RBBP6), transcript variant 1, mRNA.																																				SO:0001589	frameshift_variant	5930				protein ubiquitination involved in ubiquitin-dependent protein catabolic process	chromosome|nucleolus|ubiquitin ligase complex	nucleic acid binding|protein binding|ubiquitin-protein ligase activity|zinc ion binding	g.chr16:24581488_24581489delTT		CCDS10621.1, CCDS10622.1, CCDS45444.1	16p12.2	2008-08-04	2001-11-28		ENSG00000122257	ENSG00000122257			9889	protein-coding gene	gene with protein product	"""proliferation potential-related protein"""	600938	"""retinoblastoma-binding protein 6"""			8595913, 16396680	Standard	NM_006910		Approved	P2P-R, PACT, SNAMA	uc002dmh.3	Q7Z6E9	OTTHUMG00000096991	ENST00000319715.4:c.3477_3478delTT	16.37:g.24581490_24581491delTT	ENSP00000317872:p.Phe1160fs					RBBP6_uc010vcb.1_Frame_Shift_Del_p.D1026fs|RBBP6_uc002dmi.3_Frame_Shift_Del_p.D1125fs|RBBP6_uc010bxr.3_Intron|RBBP6_uc002dmk.3_Frame_Shift_Del_p.D992fs	p.D1159fs	NM_006910	NP_008841	Q7Z6E9	RBBP6_HUMAN		GBM - Glioblastoma multiforme(48;0.0518)	16	4517_4518	+			1159					Q147T5|Q15290|Q6DKH4|Q6P4C2|Q6YNC9|Q7Z6E8|Q8N0V2|Q96PH3|Q9H3I8|Q9H5M5|Q9NPX4	Frame_Shift_Del	DEL	ENST00000319715.4	37	c.3477_3478delTT	CCDS10621.1																																																																																				0.342	RBBP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214067.2	NM_006910	
IRX5	10265	broad.mit.edu	37	16	54967470	54967470	+	Silent	SNP	C	C	T			TCGA-76-4929-01A-01D-1486-08	TCGA-76-4929-10A-01D-1486-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	af4f8b89-837a-48b7-b0e7-12aec23fc285	3e0712a1-b66a-42e7-94a3-07edee7dce2b	g.chr16:54967470C>T	ENST00000394636.4	+	3	1474	c.1137C>T	c.(1135-1137)gcC>gcT	p.A379A	IRX5_ENST00000558597.1_Silent_p.A313A|IRX5_ENST00000560154.1_Silent_p.A159A|IRX5_ENST00000320990.5_Silent_p.A378A|CTD-3032H12.2_ENST00000560487.1_lincRNA			P78411	IRX5_HUMAN	iroquois homeobox 5	379					embryonic cranial skeleton morphogenesis (GO:0048701)|gonad development (GO:0008406)|neuron maturation (GO:0042551)|regulation of heart rate (GO:0002027)|regulation of transcription, DNA-templated (GO:0006355)|response to stimulus (GO:0050896)|retinal bipolar neuron differentiation (GO:0060040)|transcription, DNA-templated (GO:0006351)|visual perception (GO:0007601)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|vitamin D binding (GO:0005499)			kidney(3)|large_intestine(6)|lung(4)|prostate(1)	14						CGTCGCCGGCCCCGGCGCCGT	0.721																																						uc002ehv.3																			0				kidney(3)|large_intestine(6)|lung(4)|prostate(1)	14						c.(1135-1137)gcC>gcT		Homo sapiens iroquois homeobox 5 (IRX5), transcript variant 1, mRNA.							9.0	11.0	11.0					16																	54967470		2163	4236	6399	SO:0001819	synonymous_variant	10265				response to stimulus|visual perception	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|vitamin D binding	g.chr16:54967470C>T	U90309	CCDS10751.1, CCDS58462.1	16q12.2	2011-06-20	2007-07-13		ENSG00000176842	ENSG00000176842		"""Homeoboxes / TALE class"""	14361	protein-coding gene	gene with protein product		606195					Standard	NM_005853		Approved	IRX-2a	uc002ehv.3	P78411	OTTHUMG00000133201	ENST00000394636.4:c.1137C>T	16.37:g.54967470C>T						IRX5_uc021tin.1_Silent_p.A378A|IRX5_uc002ehw.3_Silent_p.A313A	p.A379A	NM_005853	NP_005844	P78411	IRX5_HUMAN			2	1137	+			379					H0YMS7|P78416|Q7Z2E1	Silent	SNP	ENST00000394636.4	37	c.1137C>T	CCDS10751.1																																																																																				0.721	IRX5-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256911.2		
CLEC3A	10143	broad.mit.edu	37	16	78064624	78064624	+	Silent	SNP	C	C	T	rs371337987		TCGA-76-4929-01A-01D-1486-08	TCGA-76-4929-10A-01D-1486-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	af4f8b89-837a-48b7-b0e7-12aec23fc285	3e0712a1-b66a-42e7-94a3-07edee7dce2b	g.chr16:78064624C>T	ENST00000575655.1	+	3	561	c.480C>T	c.(478-480)aaC>aaT	p.N160N	CLEC3A_ENST00000565808.1_3'UTR|CLEC3A_ENST00000299642.4_Silent_p.N169N|RP11-281J9.2_ENST00000563114.1_RNA	NM_005752.4	NP_005743.4	O75596	CLC3A_HUMAN	C-type lectin domain family 3, member A	160	C-type lectin. {ECO:0000255|PROSITE- ProRule:PRU00040}.				skeletal system development (GO:0001501)	extracellular region (GO:0005576)	carbohydrate binding (GO:0030246)			NS(1)|endometrium(2)|large_intestine(1)|lung(11)|ovary(1)|upper_aerodigestive_tract(2)	18						CACAGCCTAACGGTGGCAAGC	0.522																																						uc002ffh.4																			0				NS(1)|endometrium(2)|large_intestine(1)|lung(11)|ovary(1)|upper_aerodigestive_tract(2)	18						c.(478-480)aaC>aaT		Homo sapiens C-type lectin domain family 3, member A (CLEC3A), transcript variant 1, mRNA.		C		0,4396		0,0,2198	132.0	119.0	123.0		480	-4.2	0.1	16		123	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	CLEC3A	NM_005752.4		0,1,6497	TT,TC,CC		0.0116,0.0,0.0077		160/198	78064624	1,12995	2198	4300	6498	SO:0001819	synonymous_variant	10143				skeletal system development	extracellular region	sugar binding	g.chr16:78064624C>T	AF077345	CCDS10927.1, CCDS10927.2	16q23	2008-02-05	2005-02-09	2005-02-11	ENSG00000166509	ENSG00000166509		"""C-type lectin domain containing"""	2052	protein-coding gene	gene with protein product		613588	"""C-type (calcium dependent, carbohydrate-recognition domain) lectin, superfamily member 1 (cartilage-derived)"""	CLECSF1		10524194	Standard	NM_001244755		Approved		uc002ffh.5	O75596	OTTHUMG00000137620	ENST00000575655.1:c.480C>T	16.37:g.78064624C>T						CLEC3A_uc021tlr.1_Silent_p.N108N	p.N160N	NM_005752	NP_005743	O75596	CLC3A_HUMAN			2	561	+			160			C-type lectin.		B2R8C4|Q3SX91|Q6UXF5	Silent	SNP	ENST00000575655.1	37	c.480C>T																																																																																					0.522	CLEC3A-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_005752	
ACAP1	9744	broad.mit.edu	37	17	7253543	7253543	+	Missense_Mutation	SNP	G	G	A			TCGA-76-4929-01A-01D-1486-08	TCGA-76-4929-10A-01D-1486-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	af4f8b89-837a-48b7-b0e7-12aec23fc285	3e0712a1-b66a-42e7-94a3-07edee7dce2b	g.chr17:7253543G>A	ENST00000158762.3	+	20	2265	c.2059G>A	c.(2059-2061)Gac>Aac	p.D687N	RP11-542C16.1_ENST00000572417.1_RNA|KCTD11_ENST00000333751.3_5'Flank|ACAP1_ENST00000575415.1_5'Flank|ACAP1_ENST00000571471.1_5'Flank|ACAP1_ENST00000570504.1_5'Flank|ACAP1_ENST00000574499.1_5'Flank	NM_014716.3	NP_055531.1	Q15027	ACAP1_HUMAN	ArfGAP with coiled-coil, ankyrin repeat and PH domains 1	687	Required for interaction with GULP1.				protein transport (GO:0015031)|regulation of ARF GTPase activity (GO:0032312)	endosome (GO:0005768)|membrane (GO:0016020)	ARF GTPase activator activity (GO:0008060)|zinc ion binding (GO:0008270)			NS(1)|breast(5)|cervix(3)|endometrium(4)|kidney(1)|large_intestine(7)|liver(1)|lung(6)|prostate(3)|skin(1)|urinary_tract(1)	33						AGCCAACGCTGACATCGTCAC	0.682																																						uc002ggd.2																			0				NS(1)|breast(5)|cervix(3)|endometrium(4)|kidney(1)|large_intestine(7)|liver(1)|lung(6)|prostate(3)|skin(1)|urinary_tract(1)	33						c.(2059-2061)Gac>Aac		Homo sapiens ArfGAP with coiled-coil, ankyrin repeat and PH domains 1 (ACAP1), mRNA.							66.0	66.0	66.0					17																	7253543		2203	4300	6503	SO:0001583	missense	9744				intracellular signal transduction|lipid metabolic process|protein transport|regulation of ARF GTPase activity		ARF GTPase activator activity|phospholipase C activity|protein binding|zinc ion binding	g.chr17:7253543G>A	D30758	CCDS11101.1	17p13.1	2013-01-11	2008-09-22	2008-09-22	ENSG00000072818	ENSG00000072818		"""ADP-ribosylation factor GTPase activating proteins"", ""Pleckstrin homology (PH) domain containing"", ""Ankyrin repeat domain containing"""	16467	protein-coding gene	gene with protein product		607763	"""centaurin, beta 1"""	CENTB1		11050434, 11062263	Standard	NM_014716		Approved	KIAA0050	uc002ggd.2	Q15027	OTTHUMG00000102199	ENST00000158762.3:c.2059G>A	17.37:g.7253543G>A	ENSP00000158762:p.Asp687Asn					KCTD11_uc002gge.4_5'Flank	p.D687N	NM_014716	NP_055531	Q15027	ACAP1_HUMAN			19	2265	+			687			Required for interaction with GULP1.		Q53XN9	Missense_Mutation	SNP	ENST00000158762.3	37	c.2059G>A	CCDS11101.1	.	.	.	.	.	.	.	.	.	.	G	35	5.540630	0.96474	.	.	ENSG00000072818	ENST00000158762	T	0.36340	1.26	5.16	5.16	0.70880	Ankyrin repeat-containing domain (3);	0.104708	0.64402	D	0.000005	T	0.64735	0.2625	M	0.85462	2.755	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	T	0.69266	-0.5190	10	0.62326	D	0.03	.	16.1815	0.81909	0.0:0.0:1.0:0.0	.	687	Q15027	ACAP1_HUMAN	N	687	ENSP00000158762:D687N	ENSP00000158762:D687N	D	+	1	0	ACAP1	7194267	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	8.664000	0.91139	2.681000	0.91329	0.448000	0.29417	GAC		0.682	ACAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000220049.4	NM_014716	
TP53	7157	broad.mit.edu	37	17	7574003	7574003	+	Nonsense_Mutation	SNP	G	G	A			TCGA-76-4929-01A-01D-1486-08	TCGA-76-4929-10A-01D-1486-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	af4f8b89-837a-48b7-b0e7-12aec23fc285	3e0712a1-b66a-42e7-94a3-07edee7dce2b	g.chr17:7574003G>A	ENST00000269305.4	-	10	1213	c.1024C>T	c.(1024-1026)Cga>Tga	p.R342*	TP53_ENST00000455263.2_3'UTR|TP53_ENST00000420246.2_3'UTR|TP53_ENST00000413465.2_Intron|TP53_ENST00000359597.4_Intron|TP53_ENST00000445888.2_Nonsense_Mutation_p.R342*	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	342	Interaction with CARM1.|Interaction with HIPK1. {ECO:0000250}.|Interaction with HIPK2.|Oligomerization.		R -> L (in a sporadic cancer; somatic mutation).|R -> P (in sporadic cancers; somatic mutation).|R -> Q (in sporadic cancers; somatic mutation).		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.R342*(70)|p.0?(8)|p.R342fs*3(8)|p.?(1)|p.R342_N345delRELN(1)|p.I332fs*5(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	TTCAGCTCTCGGAACATCTCG	0.557		111	"""Mis, N, F"""		"""breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"""	"""breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"""		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											Pancreas(47;798 1329 9957 10801)	uc002gim.2		111	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	"""Mis, N, F"""	tumor protein p53			"""L, E, M, O"""		"""breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"""	"""breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"""		89	Substitution - Nonsense(70)|Whole gene deletion(8)|Deletion - Frameshift(7)|Insertion - Frameshift(2)|Deletion - In frame(1)|Unknown(1)	p.R342*(132)|p.R342fs*3(17)|p.0?(8)|p.R342P(3)|p.R342_N345delRELN(2)|p.R342Q(2)|p.?(1)|p.F341fs*4(1)|p.F341C(1)|p.I332fs*5(1)	breast(16)|upper_aerodigestive_tract(11)|large_intestine(9)|central_nervous_system(9)|ovary(7)|lung(6)|skin(5)|liver(5)|haematopoietic_and_lymphoid_tissue(4)|pancreas(4)|bone(4)|stomach(2)|urinary_tract(2)|oesophagus(2)|kidney(1)|peritoneum(1)|endometrium(1)	NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185	GRCh37	CM004908	TP53	M		c.(1024-1026)Cga>Tga	Other conserved DNA damage response genes	Homo sapiens tumor protein p53 (TP53), transcript variant 2, mRNA.							62.0	48.0	53.0					17																	7574003		2203	4300	6503	SO:0001587	stop_gained	7157	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	activation of caspase activity by cytochrome c|base-excision repair|blood coagulation|cell cycle arrest|cell differentiation|cell proliferation|cellular protein localization|cellular response to drug|cellular response to glucose starvation|cellular response to hypoxia|cellular response to ionizing radiation|cellular response to UV|determination of adult lifespan|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator|ER overload response|interspecies interaction between organisms|negative regulation of apoptosis|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of helicase activity|negative regulation of transcription from RNA polymerase II promoter|nucleotide-excision repair|oxidative stress-induced premature senescence|positive regulation of histone deacetylation|positive regulation of neuron apoptosis|positive regulation of peptidyl-tyrosine phosphorylation|positive regulation of reactive oxygen species metabolic process|positive regulation of thymocyte apoptosis|positive regulation of transcription from RNA polymerase II promoter|protein localization|protein tetramerization|Ras protein signal transduction|regulation of mitochondrial membrane permeability|replicative senescence|response to antibiotic|response to gamma radiation|response to X-ray	cytoplasm|cytosol|endoplasmic reticulum|insoluble fraction|mitochondrion|nuclear chromatin|nuclear matrix|nucleolus|nucleus|PML body|protein complex|replication fork	ATP binding|chaperone binding|chromatin binding|copper ion binding|damaged DNA binding|DNA strand annealing activity|histone acetyltransferase binding|p53 binding|protease binding|protein binding|protein heterodimerization activity|protein kinase binding|protein N-terminus binding|protein phosphatase 2A binding|RNA polymerase II transcription factor binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding|transcription repressor activity|ubiquitin protein ligase binding|zinc ion binding	g.chr17:7574003G>A	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"""Li-Fraumeni syndrome"""	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.1024C>T	17.37:g.7574003G>A	ENSP00000269305:p.Arg342*	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)				TP53_uc002gig.1_Intron|TP53_uc002gih.3_Intron|TP53_uc010cne.1_Intron|TP53_uc010cng.1_3'UTR|TP53_uc010cnf.1_3'UTR|TP53_uc002gii.1_Nonsense_Mutation_p.R210*|TP53_uc010cni.1_3'UTR|TP53_uc010cnh.1_3'UTR|TP53_uc002gij.2_Nonsense_Mutation_p.R342*|DL476313_uc021tpe.1_5'Flank	p.R342*	NM_001126112	NP_001119587	P04637	P53_HUMAN		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	9	1218	-		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)	342		R -> L (in a sporadic cancer; somatic mutation).|R -> P (in sporadic cancers; somatic mutation).|R -> Q (in sporadic cancers; somatic mutation).	Interaction with CARM1.|Interaction with HIPK1 (By similarity).|Interaction with HIPK2.|Oligomerization.		Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Nonsense_Mutation	SNP	ENST00000269305.4	37	c.1024C>T	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	G	37	6.061927	0.97246	.	.	ENSG00000141510	ENST00000269305;ENST00000445888;ENST00000396473	.	.	.	5.43	3.43	0.39272	.	0.217683	0.37906	N	0.001893	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.09338	T	0.73	-0.3792	6.4477	0.21885	0.0845:0.0:0.5925:0.323	.	.	.	.	X	342;342;331	.	ENSP00000269305:R342X	R	-	1	2	TP53	7514728	0.820000	0.29190	0.702000	0.30337	0.859000	0.49053	2.169000	0.42434	0.657000	0.30906	0.561000	0.74099	CGA		0.557	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546	
TP53	7157	broad.mit.edu	37	17	7578476	7578476	+	Missense_Mutation	SNP	G	G	A	rs137852790|rs137852791		TCGA-76-4929-01A-01D-1486-08	TCGA-76-4929-10A-01D-1486-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	af4f8b89-837a-48b7-b0e7-12aec23fc285	3e0712a1-b66a-42e7-94a3-07edee7dce2b	g.chr17:7578476G>A	ENST00000269305.4	-	5	643	c.454C>T	c.(454-456)Ccg>Tcg	p.P152S	TP53_ENST00000455263.2_Missense_Mutation_p.P152S|TP53_ENST00000420246.2_Missense_Mutation_p.P152S|TP53_ENST00000574684.1_5'Flank|TP53_ENST00000413465.2_Missense_Mutation_p.P152S|TP53_ENST00000359597.4_Missense_Mutation_p.P152S|TP53_ENST00000445888.2_Missense_Mutation_p.P152S	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	152	Interaction with AXIN1. {ECO:0000250}.|Interaction with HIPK1. {ECO:0000250}.|Required for interaction with FBXO42.|Required for interaction with ZNF385A.		P -> A (in sporadic cancers; somatic mutation).|P -> L (in LFS; germline mutation and in sporadic cancers; somatic mutation). {ECO:0000269|PubMed:1868473}.|P -> Q (in sporadic cancers; somatic mutation).|P -> R (in sporadic cancers; somatic mutation).|P -> S (in sporadic cancers; somatic mutation). {ECO:0000269|PubMed:9450901}.|P -> T (in sporadic cancers; somatic mutation).		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.P152S(22)|p.0?(8)|p.P152T(7)|p.T150fs*16(6)|p.P152fs*29(5)|p.?(5)|p.P152fs*14(5)|p.P152A(2)|p.P152fs*18(2)|p.P153fs*16(1)|p.P151_V173del23(1)|p.P152_P153del(1)|p.P152L(1)|p.P152fs*28(1)|p.T57fs*16(1)|p.D148_T155delDSTPPPGT(1)|p.T150_P153delTPPP(1)|p.D148fs*23(1)|p.P152del(1)|p.S149fs*72(1)|p.S149fs*17(1)|p.Q144_G154del11(1)|p.Q144fs*16(1)|p.T18fs*16(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	GTGCCGGGCGGGGGTGTGGAA	0.607		111	"""Mis, N, F"""		"""breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"""	"""breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"""		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											Pancreas(47;798 1329 9957 10801)	uc002gim.2		111	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	"""Mis, N, F"""	tumor protein p53			"""L, E, M, O"""		"""breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"""	"""breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"""		77	Substitution - Missense(32)|Deletion - Frameshift(21)|Whole gene deletion(8)|Deletion - In frame(6)|Insertion - Frameshift(5)|Unknown(5)	p.P151S(66)|p.P152L(64)|p.P152S(44)|p.P151H(27)|p.P152fs*18(20)|p.P152T(14)|p.P151T(14)|p.P151P(12)|p.P152fs*29(10)|p.P152fs*14(10)|p.P151A(9)|p.0?(8)|p.P151L(7)|p.P151fs*30(7)|p.P151R(7)|p.P152R(6)|p.T150fs*16(6)|p.P152P(5)|p.?(5)|p.P152A(4)|p.P152fs*28(4)|p.P152Q(4)|p.P151_V173del23(2)|p.P152_P153del(2)|p.D148_T155delDSTPPPGT(2)|p.T150_P153delTPPP(2)|p.P152del(2)|p.Q144_G154del11(2)|p.P153fs*16(1)|p.P151del(1)|p.T57fs*16(1)|p.D148fs*23(1)|p.S149fs*72(1)|p.S149fs*17(1)|p.P152fs*27(1)|p.P152_P153insXXX(1)|p.Q144fs*16(1)|p.T18fs*16(1)|p.T150_P151delTP(1)	skin(17)|large_intestine(8)|lung(7)|ovary(7)|central_nervous_system(6)|upper_aerodigestive_tract(5)|haematopoietic_and_lymphoid_tissue(5)|breast(5)|bone(4)|stomach(3)|urinary_tract(3)|oesophagus(3)|liver(2)|soft_tissue(1)|pancreas(1)	NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185						c.(454-456)Ccg>Tcg	Other conserved DNA damage response genes	Homo sapiens tumor protein p53 (TP53), transcript variant 2, mRNA.							52.0	53.0	53.0					17																	7578476		2203	4300	6503	SO:0001583	missense	7157	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	activation of caspase activity by cytochrome c|base-excision repair|blood coagulation|cell cycle arrest|cell differentiation|cell proliferation|cellular protein localization|cellular response to drug|cellular response to glucose starvation|cellular response to hypoxia|cellular response to ionizing radiation|cellular response to UV|determination of adult lifespan|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator|ER overload response|interspecies interaction between organisms|negative regulation of apoptosis|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of helicase activity|negative regulation of transcription from RNA polymerase II promoter|nucleotide-excision repair|oxidative stress-induced premature senescence|positive regulation of histone deacetylation|positive regulation of neuron apoptosis|positive regulation of peptidyl-tyrosine phosphorylation|positive regulation of reactive oxygen species metabolic process|positive regulation of thymocyte apoptosis|positive regulation of transcription from RNA polymerase II promoter|protein localization|protein tetramerization|Ras protein signal transduction|regulation of mitochondrial membrane permeability|replicative senescence|response to antibiotic|response to gamma radiation|response to X-ray	cytoplasm|cytosol|endoplasmic reticulum|insoluble fraction|mitochondrion|nuclear chromatin|nuclear matrix|nucleolus|nucleus|PML body|protein complex|replication fork	ATP binding|chaperone binding|chromatin binding|copper ion binding|damaged DNA binding|DNA strand annealing activity|histone acetyltransferase binding|p53 binding|protease binding|protein binding|protein heterodimerization activity|protein kinase binding|protein N-terminus binding|protein phosphatase 2A binding|RNA polymerase II transcription factor binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding|transcription repressor activity|ubiquitin protein ligase binding|zinc ion binding	g.chr17:7578476G>A	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"""Li-Fraumeni syndrome"""	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.454C>T	17.37:g.7578476G>A	ENSP00000269305:p.Pro152Ser	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)				TP53_uc002gig.1_Missense_Mutation_p.P152S|TP53_uc002gih.3_Missense_Mutation_p.P152S|TP53_uc010cne.1_5'Flank|TP53_uc010cng.1_Missense_Mutation_p.P20S|TP53_uc010cnf.1_Missense_Mutation_p.P20S|TP53_uc002gii.1_Missense_Mutation_p.P20S|TP53_uc010cni.1_Missense_Mutation_p.P152S|TP53_uc010cnh.1_Missense_Mutation_p.P152S|TP53_uc002gij.2_Missense_Mutation_p.P152S|TP53_uc010cnj.1_Non-coding_Transcript|TP53_uc002gin.2_Missense_Mutation_p.P59S|TP53_uc002gio.2_Missense_Mutation_p.P20S|TP53_uc010vug.2_Missense_Mutation_p.P113S	p.P152S	NM_001126112	NP_001119587	P04637	P53_HUMAN		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	4	648	-		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)	152		P -> A (in sporadic cancers; somatic mutation).|P -> L (in LFS; germline mutation and in sporadic cancers; somatic mutation).|P -> Q (in sporadic cancers; somatic mutation).|P -> R (in sporadic cancers; somatic mutation).|P -> S (in sporadic cancers; somatic mutation).|P -> T (in sporadic cancers; somatic mutation).	Interaction with AXIN1 (By similarity).|Interaction with HIPK1 (By similarity).|Required for interaction with FBXO42.		Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Missense_Mutation	SNP	ENST00000269305.4	37	c.454C>T	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	G	19.19	3.779594	0.70107	.	.	ENSG00000141510	ENST00000413465;ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000545858;ENST00000509690;ENST00000514944;ENST00000414315;ENST00000508793	D;D;D;D;D;D;D;D;D	0.99881	-7.47;-7.47;-7.47;-7.47;-7.47;-7.47;-7.47;-7.47;-7.47	5.59	5.59	0.84812	p53, DNA-binding domain (1);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1);	0.000000	0.85682	D	0.000000	D	0.99906	0.9955	M	0.91768	3.24	0.80722	D	1	D;D;D;D;D;D;D	0.89917	1.0;0.997;1.0;1.0;1.0;0.998;1.0	D;D;D;D;D;D;D	0.91635	0.987;0.986;0.999;0.973;0.995;0.989;0.966	D	0.96400	0.9296	10	0.87932	D	0	-5.4688	17.4784	0.87667	0.0:0.0:1.0:0.0	.	113;152;152;59;152;152;152	B4E095;P04637-2;P04637-3;E9PFT5;P04637;Q1MSW8;E7EQX7	.;.;.;.;P53_HUMAN;.;.	S	152;152;152;152;152;152;141;59;20;59;20;152	ENSP00000410739:P152S;ENSP00000352610:P152S;ENSP00000269305:P152S;ENSP00000398846:P152S;ENSP00000391127:P152S;ENSP00000391478:P152S;ENSP00000425104:P20S;ENSP00000423862:P59S;ENSP00000424104:P152S	ENSP00000269305:P152S	P	-	1	0	TP53	7519201	1.000000	0.71417	0.969000	0.41365	0.035000	0.12851	9.813000	0.99286	2.804000	0.96469	0.655000	0.94253	CCG		0.607	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546	
PFAS	5198	broad.mit.edu	37	17	8170745	8170745	+	Silent	SNP	G	G	A			TCGA-76-4929-01A-01D-1486-08	TCGA-76-4929-10A-01D-1486-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	af4f8b89-837a-48b7-b0e7-12aec23fc285	3e0712a1-b66a-42e7-94a3-07edee7dce2b	g.chr17:8170745G>A	ENST00000314666.6	+	25	3364	c.3231G>A	c.(3229-3231)cgG>cgA	p.R1077R	PFAS_ENST00000545834.1_Silent_p.R653R	NM_012393.2	NP_036525.1	O15067	PUR4_HUMAN	phosphoribosylformylglycinamidine synthase	1077	Glutamine amidotransferase type-1.				'de novo' IMP biosynthetic process (GO:0006189)|glutamine metabolic process (GO:0006541)|nucleobase-containing small molecule metabolic process (GO:0055086)|purine nucleobase metabolic process (GO:0006144)|purine ribonucleoside monophosphate biosynthetic process (GO:0009168)|response to drug (GO:0042493)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|phosphoribosylformylglycinamidine synthase activity (GO:0004642)			central_nervous_system(3)|endometrium(8)|kidney(2)|large_intestine(2)|lung(9)|ovary(3)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(3)	35					L-Glutamine(DB00130)	ATGGAGACCGGGAGATGGCCG	0.612																																						uc002gkr.3																			0				central_nervous_system(3)|endometrium(8)|kidney(2)|large_intestine(2)|lung(9)|ovary(3)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(3)	35						c.(3229-3231)cgG>cgA		Homo sapiens phosphoribosylformylglycinamidine synthase (PFAS), mRNA.	L-Glutamic Acid(DB00142)|L-Glutamine(DB00130)						89.0	96.0	94.0					17																	8170745		2203	4300	6503	SO:0001819	synonymous_variant	5198				'de novo' IMP biosynthetic process|glutamine metabolic process|purine base metabolic process	cytosol	ATP binding|phosphoribosylformylglycinamidine synthase activity|protein binding	g.chr17:8170745G>A	AB002359	CCDS11136.1	17p13.1	2008-07-31	2008-07-31		ENSG00000178921	ENSG00000178921	6.3.5.3		8863	protein-coding gene	gene with protein product	"""FGAR amidotransferase"""	602133				8110788	Standard	NM_012393		Approved	PURL, FGARAT, KIAA0361	uc002gkr.3	O15067	OTTHUMG00000108188	ENST00000314666.6:c.3231G>A	17.37:g.8170745G>A						PFAS_uc010vuv.2_Silent_p.R653R|PFAS_uc002gks.3_Silent_p.R156R	p.R1077R	NM_012393	NP_036525	O15067	PUR4_HUMAN			24	3372	+			1077			Glutamine amidotransferase type-1.		A6H8V8	Silent	SNP	ENST00000314666.6	37	c.3231G>A	CCDS11136.1																																																																																				0.612	PFAS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226994.2		
KRT13	3860	broad.mit.edu	37	17	39661389	39661389	+	Silent	SNP	G	G	A			TCGA-76-4929-01A-01D-1486-08	TCGA-76-4929-10A-01D-1486-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	af4f8b89-837a-48b7-b0e7-12aec23fc285	3e0712a1-b66a-42e7-94a3-07edee7dce2b	g.chr17:39661389G>A	ENST00000246635.3	-	1	460	c.414C>T	c.(412-414)gaC>gaT	p.D138D	KRT13_ENST00000587544.1_Silent_p.D138D|AC019349.5_ENST00000411759.1_RNA|KRT13_ENST00000336861.3_Silent_p.D138D|KRT13_ENST00000587118.1_5'Flank	NM_153490.2	NP_705694	P13646	K1C13_HUMAN	keratin 13	138	Coil 1A.|Rod.				cellular response to retinoic acid (GO:0071300)|cytoskeleton organization (GO:0007010)|response to radiation (GO:0009314)|tongue morphogenesis (GO:0043587)	extracellular vesicular exosome (GO:0070062)|intermediate filament cytoskeleton (GO:0045111)|keratin filament (GO:0045095)|nucleus (GO:0005634)	structural molecule activity (GO:0005198)			NS(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(10)|ovary(2)|pancreas(1)|prostate(2)|skin(4)|urinary_tract(1)	33		Breast(137;0.000286)				TCAGGTGCCAGTCACGGATCT	0.602																																						uc002hwu.1																			0		p.R137H(1)		NS(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(10)|ovary(2)|pancreas(1)|prostate(2)|skin(4)|urinary_tract(1)	33						c.(412-414)gaC>gaT		Homo sapiens keratin 13 (KRT13), transcript variant 1, mRNA.							124.0	115.0	118.0					17																	39661389		2203	4300	6503	SO:0001819	synonymous_variant	3860				epidermis development	intermediate filament	structural molecule activity	g.chr17:39661389G>A		CCDS11396.1, CCDS11397.1	17q21.2	2013-06-20			ENSG00000171401	ENSG00000171401		"""-"", ""Intermediate filaments type I, keratins (acidic)"""	6415	protein-coding gene	gene with protein product	"""keratin, type I cytoskeletal 13"", ""cytokeratin 13"""	148065				16831889	Standard	NM_153490		Approved	K13, CK13, MGC3781, MGC161462	uc002hwu.1	P13646	OTTHUMG00000133434	ENST00000246635.3:c.414C>T	17.37:g.39661389G>A						KRT13_uc002hwv.1_Silent_p.D138D|KRT13_uc010wfr.2_Silent_p.D31D|KRT13_uc010cxo.3_Silent_p.D138D|KRT13_uc021txk.1_Silent_p.D31D	p.D138D	NM_153490	NP_705694	P13646	K1C13_HUMAN			0	477	-		Breast(137;0.000286)	138			Coil 1A.|Rod.		Q53G54|Q6AZK5|Q8N240	Silent	SNP	ENST00000246635.3	37	c.414C>T	CCDS11396.1																																																																																				0.602	KRT13-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257297.1	NM_153490	
FMNL1	752	broad.mit.edu	37	17	43320637	43320637	+	Silent	SNP	C	C	T			TCGA-76-4929-01A-01D-1486-08	TCGA-76-4929-10A-01D-1486-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	af4f8b89-837a-48b7-b0e7-12aec23fc285	3e0712a1-b66a-42e7-94a3-07edee7dce2b	g.chr17:43320637C>T	ENST00000331495.3	+	17	2499	c.2163C>T	c.(2161-2163)acC>acT	p.T721T	CTD-2020K17.3_ENST00000393507.2_RNA|FMNL1_ENST00000587489.1_Silent_p.T299T|CTD-2020K17.4_ENST00000420431.2_RNA|FMNL1_ENST00000328118.3_Silent_p.T721T|CTD-2020K17.3_ENST00000587534.1_RNA	NM_005892.3	NP_005883	O95466	FMNL_HUMAN	formin-like 1	721	FH2. {ECO:0000255|PROSITE- ProRule:PRU00774}.				actin filament severing (GO:0051014)|cortical actin cytoskeleton organization (GO:0030866)|regulation of cell shape (GO:0008360)|substrate-dependent cell migration (GO:0006929)	cell projection (GO:0042995)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|phagocytic vesicle (GO:0045335)|plasma membrane (GO:0005886)	actin filament binding (GO:0051015)|GTPase activating protein binding (GO:0032794)|Rac GTPase binding (GO:0048365)			biliary_tract(1)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(8)|lung(12)|pancreas(1)|skin(1)|urinary_tract(2)	33						TGGCCATCACCCTGCGGAAGG	0.642																																					GBM(164;1247 1997 8702 11086 51972)	uc002iin.3																			0				biliary_tract(1)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(8)|lung(12)|pancreas(1)|skin(1)|urinary_tract(2)	33						c.(2161-2163)acC>acT		Homo sapiens formin-like 1 (FMNL1), mRNA.							60.0	55.0	56.0					17																	43320637		2203	4300	6503	SO:0001819	synonymous_variant	752				actin cytoskeleton organization		actin binding|Rho GTPase binding	g.chr17:43320637C>T	AJ008112	CCDS11497.1	17q21.31	2008-05-14	2003-12-02	2003-12-03		ENSG00000184922			1212	protein-coding gene	gene with protein product		604656	"""formin-like"""	C17orf1B, FMNL		9799091	Standard	NM_005892		Approved	C17orf1	uc002iin.3	O95466		ENST00000331495.3:c.2163C>T	17.37:g.43320637C>T						FMNL1_uc002iiq.3_Silent_p.T299T|FMNL1_uc010dag.3_Non-coding_Transcript|FMNL1_uc021tyj.1_Silent_p.T48T	p.T721T	NM_005892	NP_005883	O95466	FMNL_HUMAN			16	2363	+			721			FH2.		D2DGW2|Q6DKG5|Q6IBP3|Q86UH1|Q8N671|Q8TDH1|Q96H10	Silent	SNP	ENST00000331495.3	37	c.2163C>T	CCDS11497.1																																																																																				0.642	FMNL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450198.1	NM_005892	
RGS9	8787	broad.mit.edu	37	17	63193312	63193312	+	Missense_Mutation	SNP	C	C	T			TCGA-76-4929-01A-01D-1486-08	TCGA-76-4929-10A-01D-1486-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	af4f8b89-837a-48b7-b0e7-12aec23fc285	3e0712a1-b66a-42e7-94a3-07edee7dce2b	g.chr17:63193312C>T	ENST00000262406.9	+	13	996	c.929C>T	c.(928-930)cCc>cTc	p.P310L	RGS9_ENST00000443584.3_Missense_Mutation_p.P307L|RGS9_ENST00000449996.3_Missense_Mutation_p.P307L	NM_003835.3	NP_003826.2	O75916	RGS9_HUMAN	regulator of G-protein signaling 9	310	RGS. {ECO:0000255|PROSITE- ProRule:PRU00171}.				dopamine receptor signaling pathway (GO:0007212)|intracellular signal transduction (GO:0035556)|nervous system development (GO:0007399)|phototransduction, visible light (GO:0007603)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|response to estrogen (GO:0043627)|rhodopsin mediated signaling pathway (GO:0016056)|termination of G-protein coupled receptor signaling pathway (GO:0038032)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|heterotrimeric G-protein complex (GO:0005834)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	GTPase activator activity (GO:0005096)|signal transducer activity (GO:0004871)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(5)|kidney(2)|large_intestine(8)|liver(2)|lung(12)|ovary(2)|prostate(3)|skin(3)	41						ATCCGAGACCCCAAAGGTCGA	0.423																																						uc002jfe.3																			0				NS(1)|breast(1)|central_nervous_system(2)|endometrium(5)|kidney(2)|large_intestine(8)|liver(2)|lung(12)|ovary(2)|prostate(3)|skin(3)	41						c.(928-930)cCc>cTc		Homo sapiens regulator of G-protein signaling 9 (RGS9), transcript variant 1, mRNA.							60.0	59.0	59.0					17																	63193312		1877	4108	5985	SO:0001583	missense	8787				intracellular signal transduction|negative regulation of signal transduction|regulation of G-protein coupled receptor protein signaling pathway|visual perception	cytoplasm|heterotrimeric G-protein complex	GTPase activator activity|signal transducer activity	g.chr17:63193312C>T	AF071476	CCDS42373.1, CCDS45764.1	17q24	2008-07-18	2007-08-14			ENSG00000108370		"""Regulators of G-protein signaling"""	10004	protein-coding gene	gene with protein product	"""regulator of G protein signalling 9"", ""regulator of G protein signalling 9L"", ""regulator of G-protein signaling 9L"""	604067	"""regulator of G-protein signalling 9"""			9765512	Standard	NM_003835		Approved	PERRS, RGS9L, MGC26458, MGC111763	uc002jfe.3	O75916		ENST00000262406.9:c.929C>T	17.37:g.63193312C>T	ENSP00000262406:p.Pro310Leu					RGS9_uc021ubw.1_Missense_Mutation_p.P307L|RGS9_uc010dem.3_Missense_Mutation_p.P307L|RGS9_uc002jfd.3_Missense_Mutation_p.P307L|RGS9_uc002jfg.3_Missense_Mutation_p.P81L	p.P310L	NM_003835	NP_003826	O75916	RGS9_HUMAN			12	1132	+			310			RGS.		A8K3C0|O75573|Q696R2|Q8TD64|Q8TD65|Q9HC32|Q9HC33	Missense_Mutation	SNP	ENST00000262406.9	37	c.929C>T	CCDS42373.1	.	.	.	.	.	.	.	.	.	.	C	12.15	1.852122	0.32699	.	.	ENSG00000108370	ENST00000262406;ENST00000449996;ENST00000443584	T;T	0.37411	1.2;1.2	5.27	5.27	0.74061	Regulator of G protein signalling (4);Regulator of G protein signalling superfamily (1);Regulator of G-protein signaling, domain 1 (1);	0.115218	0.64402	D	0.000011	T	0.62816	0.2459	M	0.76574	2.34	0.80722	D	1	D;P;P	0.89917	1.0;0.923;0.906	D;P;P	0.97110	1.0;0.678;0.55	T	0.66160	-0.5993	10	0.66056	D	0.02	.	18.9073	0.92467	0.0:1.0:0.0:0.0	.	310;310;307	A8K1G1;O75916;O75916-5	.;RGS9_HUMAN;.	L	310;307;310	ENSP00000262406:P310L;ENSP00000396329:P307L	ENSP00000262406:P310L	P	+	2	0	RGS9	60623774	0.998000	0.40836	1.000000	0.80357	0.835000	0.47333	3.762000	0.55250	2.468000	0.83385	0.563000	0.77884	CCC		0.423	RGS9-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000445885.1	NM_003835	
ICAM5	7087	broad.mit.edu	37	19	10405102	10405102	+	Silent	SNP	C	C	A			TCGA-76-4929-01A-01D-1486-08	TCGA-76-4929-10A-01D-1486-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	af4f8b89-837a-48b7-b0e7-12aec23fc285	3e0712a1-b66a-42e7-94a3-07edee7dce2b	g.chr19:10405102C>A	ENST00000221980.4	+	9	2079	c.2016C>A	c.(2014-2016)acC>acA	p.T672T		NM_003259.3	NP_003250.3	Q9UMF0	ICAM5_HUMAN	intercellular adhesion molecule 5, telencephalin	672	Ig-like C2-type 8.				phagocytosis (GO:0006909)|single organismal cell-cell adhesion (GO:0016337)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)				breast(3)|endometrium(2)|kidney(1)|large_intestine(4)|lung(8)|prostate(2)|upper_aerodigestive_tract(1)	21			OV - Ovarian serous cystadenocarcinoma(20;2.64e-09)|Epithelial(33;4.31e-06)|all cancers(31;9.75e-06)			ATGAATCTACCTGCCCAAGTC	0.692																																						uc002mnu.4																			0				breast(3)|endometrium(2)|kidney(1)|large_intestine(4)|lung(8)|prostate(2)|upper_aerodigestive_tract(1)	21						c.(2014-2016)acC>acA		Homo sapiens intercellular adhesion molecule 5, telencephalin (ICAM5), mRNA.							36.0	41.0	39.0					19																	10405102		2203	4300	6503	SO:0001819	synonymous_variant	7087				cell-cell adhesion	integral to plasma membrane		g.chr19:10405102C>A	U72671	CCDS12233.1	19p13.2	2013-01-14				ENSG00000105376		"""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	5348	protein-coding gene	gene with protein product	"""telencephalin"""	601852		TLCN		8995416, 9828136	Standard	NM_003259		Approved	TLN	uc002mnu.4	Q9UMF0		ENST00000221980.4:c.2016C>A	19.37:g.10405102C>A						ICAM5_uc002mnv.4_Silent_p.T547T	p.T672T	NM_003259	NP_003250	Q9UMF0	ICAM5_HUMAN	OV - Ovarian serous cystadenocarcinoma(20;2.64e-09)|Epithelial(33;4.31e-06)|all cancers(31;9.75e-06)		8	2081	+			672			Ig-like C2-type 8.		Q9Y6F3	Silent	SNP	ENST00000221980.4	37	c.2016C>A	CCDS12233.1																																																																																				0.692	ICAM5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451217.1	NM_003259	
HADHA	3030	broad.mit.edu	37	2	26457099	26457099	+	Missense_Mutation	SNP	C	C	T			TCGA-76-4929-01A-01D-1486-08	TCGA-76-4929-10A-01D-1486-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	af4f8b89-837a-48b7-b0e7-12aec23fc285	3e0712a1-b66a-42e7-94a3-07edee7dce2b	g.chr2:26457099C>T	ENST00000380649.3	-	5	568	c.439G>A	c.(439-441)Gga>Aga	p.G147R	HADHA_ENST00000461025.1_5'UTR|HADHA_ENST00000457468.2_Missense_Mutation_p.G60R	NM_000182.4	NP_000173.2	P40939	ECHA_HUMAN	hydroxyacyl-CoA dehydrogenase/3-ketoacyl-CoA thiolase/enoyl-CoA hydratase (trifunctional protein), alpha subunit	147					cardiolipin acyl-chain remodeling (GO:0035965)|cellular lipid metabolic process (GO:0044255)|fatty acid beta-oxidation (GO:0006635)|glycerophospholipid biosynthetic process (GO:0046474)|phospholipid metabolic process (GO:0006644)|response to drug (GO:0042493)|response to insulin (GO:0032868)|small molecule metabolic process (GO:0044281)	mitochondrial fatty acid beta-oxidation multienzyme complex (GO:0016507)|mitochondrial inner membrane (GO:0005743)|mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)	3-hydroxyacyl-CoA dehydrogenase activity (GO:0003857)|acetyl-CoA C-acetyltransferase activity (GO:0003985)|enoyl-CoA hydratase activity (GO:0004300)|fatty-acyl-CoA binding (GO:0000062)|long-chain-3-hydroxyacyl-CoA dehydrogenase activity (GO:0016509)|long-chain-enoyl-CoA hydratase activity (GO:0016508)|NAD binding (GO:0051287)			autonomic_ganglia(1)|breast(1)|endometrium(5)|kidney(1)|large_intestine(6)|lung(10)|ovary(1)|prostate(4)|skin(1)	30	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					AGTCCTCCTCCCAGGCAGGAT	0.433																																						uc002rgy.3																			0				autonomic_ganglia(1)|breast(1)|endometrium(5)|kidney(1)|large_intestine(6)|lung(10)|ovary(1)|prostate(4)|skin(1)	30						c.(439-441)Gga>Aga		Homo sapiens hydroxyacyl-CoA dehydrogenase/3-ketoacyl-CoA thiolase/enoyl-CoA hydratase (trifunctional protein), alpha subunit (HADHA), nuclear gene encoding mitochondrial protein, mRNA.	NADH(DB00157)						103.0	96.0	98.0					2																	26457099		2203	4300	6503	SO:0001583	missense	3030				fatty acid beta-oxidation	fatty acid beta-oxidation multienzyme complex|mitochondrial nucleoid|nucleolus	3-hydroxyacyl-CoA dehydrogenase activity|acetyl-CoA C-acetyltransferase activity|coenzyme binding|enoyl-CoA hydratase activity|long-chain-3-hydroxyacyl-CoA dehydrogenase activity|protein binding	g.chr2:26457099C>T	D16480	CCDS1721.1	2p23	2014-09-17	2010-04-30		ENSG00000084754	ENSG00000084754	1.1.1.211, 4.2.1.17		4801	protein-coding gene	gene with protein product	"""gastrin-binding protein"", ""long-chain-3-hydroxyacyl-CoA dehydrogenase"", ""long-chain 2-enoyl-CoA hydratase"", ""mitochondrial trifunctional protein, alpha subunit"""	600890	"""hydroxyacyl-Coenzyme A dehydrogenase/3-ketoacyl-Coenzyme A thiolase/enoyl-Coenzyme A hydratase (trifunctional protein), alpha subunit"""			9605857, 7918661	Standard	NM_000182		Approved	GBP, LCEH, LCHAD, MTPA	uc002rgy.3	P40939	OTTHUMG00000096979	ENST00000380649.3:c.439G>A	2.37:g.26457099C>T	ENSP00000370023:p.Gly147Arg					HADHA_uc010yks.2_Missense_Mutation_p.G60R|HADHA_uc010ykt.1_Missense_Mutation_p.G60R	p.G147R	NM_000182	NP_000173	P40939	ECHA_HUMAN			4	569	-	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)		147					B2R7L4|B4DYP2|Q16679|Q53T69|Q53TA2|Q96GT7|Q9UQC5	Missense_Mutation	SNP	ENST00000380649.3	37	c.439G>A	CCDS1721.1	.	.	.	.	.	.	.	.	.	.	C	32	5.129356	0.94473	.	.	ENSG00000084754	ENST00000380649;ENST00000457468	D;D	0.89196	-2.48;-2.48	5.71	5.71	0.89125	Enoyl-CoA hydratase/isomerase, conserved site (1);Crotonase, core (1);	0.000000	0.85682	D	0.000000	D	0.97399	0.9149	H	0.99764	4.76	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.998;0.998	D	0.98979	1.0804	10	0.87932	D	0	-37.1727	17.3612	0.87350	0.0:1.0:0.0:0.0	.	60;147;147	B4DYP2;E9KL44;P40939	.;.;ECHA_HUMAN	R	147;60	ENSP00000370023:G147R;ENSP00000405344:G60R	ENSP00000370023:G147R	G	-	1	0	HADHA	26310603	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	7.095000	0.76952	2.709000	0.92574	0.655000	0.94253	GGA		0.433	HADHA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214051.1	NM_000182	
AMER3	205147	broad.mit.edu	37	2	131520666	131520666	+	Missense_Mutation	SNP	C	C	T	rs555251292	byFrequency	TCGA-76-4929-01A-01D-1486-08	TCGA-76-4929-10A-01D-1486-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	af4f8b89-837a-48b7-b0e7-12aec23fc285	3e0712a1-b66a-42e7-94a3-07edee7dce2b	g.chr2:131520666C>T	ENST00000423981.1	+	2	1131	c.1021C>T	c.(1021-1023)Cgg>Tgg	p.R341W	AMER3_ENST00000321420.4_Missense_Mutation_p.R341W	NM_001105193.1|NM_001105194.1|NM_001105195.1|NM_152698.2	NP_001098663.1|NP_001098664.1|NP_001098665.1|NP_689911.2	Q8N944	AMER3_HUMAN	APC membrane recruitment protein 3	341					Wnt signaling pathway (GO:0016055)	plasma membrane (GO:0005886)	lipid binding (GO:0008289)	p.R341W(1)									GGACCAATCCCGGCTGGACAC	0.667													C|||	3	0.000599042	0.0	0.0	5008	,	,		15805	0.003		0.0	False		,,,				2504	0.0					uc021voy.1																			1	Substitution - Missense(1)	p.R341W(2)	lung(1)	breast(1)|endometrium(4)|kidney(3)|large_intestine(5)|lung(43)|ovary(2)|pancreas(4)|prostate(3)|skin(8)	73						c.(1021-1023)Cgg>Tgg		Homo sapiens family with sequence similarity 123C (FAM123C), transcript variant 1, mRNA.							31.0	35.0	34.0					2																	131520666		2203	4300	6503	SO:0001583	missense	205147							g.chr2:131520666C>T	AK095696	CCDS2164.1	2q21.1	2012-12-03	2012-12-03	2012-12-03	ENSG00000178171	ENSG00000178171		"""-"""	26771	protein-coding gene	gene with protein product			"""family with sequence similarity 123C"""	FAM123C		20843316	Standard	NM_001105195		Approved	FLJ38377	uc002trw.2	Q8N944	OTTHUMG00000131637	ENST00000423981.1:c.1021C>T	2.37:g.131520666C>T	ENSP00000392700:p.Arg341Trp					FAM123C_uc002trw.2_Missense_Mutation_p.R341W|FAM123C_uc010fmv.2_Missense_Mutation_p.R341W|FAM123C_uc010fms.1_Missense_Mutation_p.R341W|FAM123C_uc010fmt.1_Missense_Mutation_p.R341W|FAM123C_uc010fmu.1_Missense_Mutation_p.R341W	p.R341W	NM_152698	NP_689911	Q8N944	F123C_HUMAN		BRCA - Breast invasive adenocarcinoma(221;0.13)	0	1021	+	Colorectal(110;0.1)		341					B7ZLH6	Missense_Mutation	SNP	ENST00000423981.1	37	c.1021C>T	CCDS2164.1	.	.	.	.	.	.	.	.	.	.	C	10.42	1.345446	0.24426	.	.	ENSG00000178171	ENST00000321420;ENST00000423981	T;T	0.18960	2.18;2.18	5.0	-0.621	0.11564	.	0.843641	0.10363	N	0.683786	T	0.37265	0.0997	M	0.62723	1.935	0.09310	N	1	D	0.76494	0.999	D	0.69654	0.965	T	0.21075	-1.0256	10	0.72032	D	0.01	-9.2446	7.5197	0.27620	0.4961:0.4253:0.0786:0.0	.	341	Q8N944	F123C_HUMAN	W	341	ENSP00000314914:R341W;ENSP00000392700:R341W	ENSP00000314914:R341W	R	+	1	2	FAM123C	131237136	0.008000	0.16893	0.007000	0.13788	0.039000	0.13416	0.530000	0.23036	-0.248000	0.09583	-0.410000	0.06199	CGG		0.667	AMER3-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254531.3	NM_152698	
PHOSPHO2	493911	broad.mit.edu	37	2	170558142	170558142	+	Missense_Mutation	SNP	T	T	C			TCGA-76-4929-01A-01D-1486-08	TCGA-76-4929-10A-01D-1486-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	af4f8b89-837a-48b7-b0e7-12aec23fc285	3e0712a1-b66a-42e7-94a3-07edee7dce2b	g.chr2:170558142T>C	ENST00000359744.3	+	4	1049	c.661T>C	c.(661-663)Tct>Cct	p.S221P	KLHL23_ENST00000272797.4_Intron|KLHL23_ENST00000602521.1_Intron	NM_001008489.3|NM_001199285.1|NM_001199286.1|NM_001199288.1	NP_001008489.1|NP_001186214.1|NP_001186215.1|NP_001186217.1	Q8TCD6	PHOP2_HUMAN	phosphatase, orphan 2	221							metal ion binding (GO:0046872)|pyridoxal phosphatase activity (GO:0033883)			breast(1)|large_intestine(1)|lung(6)|skin(2)	10						TATGGAATATTCTGTTGTAGT	0.328																																						uc021vsh.1																			0				breast(1)|large_intestine(1)|lung(6)|skin(2)	10						c.(661-663)Tct>Cct		Homo sapiens phosphatase, orphan 2 (PHOSPHO2), transcript variant 5, mRNA.							57.0	57.0	57.0					2																	170558142		2203	4298	6501	SO:0001583	missense	493911						metal ion binding|pyridoxal phosphatase activity	g.chr2:170558142T>C	BC022324	CCDS33319.1	2q31.1	2008-02-05			ENSG00000144362	ENSG00000144362			28316	protein-coding gene	gene with protein product						16054448	Standard	NM_001199285		Approved	MGC22679	uc021vsh.1	Q8TCD6	OTTHUMG00000153981	ENST00000359744.3:c.661T>C	2.37:g.170558142T>C	ENSP00000352782:p.Ser221Pro					PHOSPHO2_uc021vsi.1_Missense_Mutation_p.S221P|PHOSPHO2_uc021vsj.1_Missense_Mutation_p.S221P|PHOSPHO2_uc021vsg.1_Missense_Mutation_p.S221P|PHOSPHO2_uc002ufg.3_Missense_Mutation_p.S221P|KLHL23_uc002ufh.2_Intron|PHOSPHO2_uc021vsk.1_Missense_Mutation_p.S221P	p.S221P	NM_001199288	NP_001186217	Q8TCD6	PHOP2_HUMAN			3	979	+			221					B2RC30|D3DPC7	Missense_Mutation	SNP	ENST00000359744.3	37	c.661T>C	CCDS33319.1	.	.	.	.	.	.	.	.	.	.	T	14.54	2.565556	0.45694	.	.	ENSG00000144362	ENST00000359744	T	0.38240	1.15	5.59	4.41	0.53225	HAD-like domain (1);	0.387872	0.23791	U	0.044521	T	0.44603	0.1301	M	0.78049	2.395	0.28426	N	0.917504	P	0.41978	0.767	P	0.46419	0.516	T	0.42999	-0.9418	10	0.41790	T	0.15	.	7.9664	0.30102	0.1361:0.0:0.1425:0.7214	.	221	Q8TCD6	PHOP2_HUMAN	P	221	ENSP00000352782:S221P	ENSP00000352782:S221P	S	+	1	0	PHOSPHO2	170266388	0.996000	0.38824	0.999000	0.59377	0.964000	0.63967	1.325000	0.33724	0.921000	0.36994	0.533000	0.62120	TCT		0.328	PHOSPHO2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333304.1	NM_001008489	
MYO1B	4430	broad.mit.edu	37	2	192248067	192248067	+	Splice_Site	SNP	A	A	T			TCGA-76-4929-01A-01D-1486-08	TCGA-76-4929-10A-01D-1486-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	af4f8b89-837a-48b7-b0e7-12aec23fc285	3e0712a1-b66a-42e7-94a3-07edee7dce2b	g.chr2:192248067A>T	ENST00000392318.3	+	15	1599	c.1352A>T	c.(1351-1353)aAt>aTt	p.N451I	MYO1B_ENST00000339514.4_Splice_Site_p.N451I|MYO1B_ENST00000304164.4_Splice_Site_p.N451I|MYO1B_ENST00000392316.1_Splice_Site_p.N451I	NM_001130158.1	NP_001123630.1	O43795	MYO1B_HUMAN	myosin IB	451	Myosin motor.				actin filament bundle assembly (GO:0051017)|actin filament organization (GO:0007015)|actin filament-based movement (GO:0030048)|metabolic process (GO:0008152)|post-Golgi vesicle-mediated transport (GO:0006892)	actin filament (GO:0005884)|brush border (GO:0005903)|cell periphery (GO:0071944)|cytoplasm (GO:0005737)|early endosome (GO:0005769)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|myosin complex (GO:0016459)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	actin filament binding (GO:0051015)|ATP binding (GO:0005524)|microfilament motor activity (GO:0000146)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)			NS(1)|central_nervous_system(6)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(22)|lung(19)|ovary(1)	55			OV - Ovarian serous cystadenocarcinoma(117;0.0112)|Epithelial(96;0.104)|all cancers(119;0.236)			CTAATAGAAAATGTGAGTACT	0.313																																						uc010fsg.2																			0				NS(1)|central_nervous_system(6)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(22)|lung(19)|ovary(1)	55						c.e15+1		Homo sapiens myosin IB (MYO1B), transcript variant 1, mRNA.							107.0	103.0	104.0					2																	192248067		2202	4300	6502	SO:0001630	splice_region_variant	4430					myosin complex	actin binding|ATP binding|calmodulin binding|motor activity	g.chr2:192248067A>T	L29138	CCDS2311.1, CCDS46477.1	2q12-q34	2011-09-27			ENSG00000128641	ENSG00000128641		"""Myosins / Myosin superfamily : Class I"""	7596	protein-coding gene	gene with protein product		606537				8022818, 8449985	Standard	NM_012223		Approved	myr1	uc010fsg.2	O43795	OTTHUMG00000132718	ENST00000392318.3:c.1353+1A>T	2.37:g.192248067A>T						MYO1B_uc002usq.2_Splice_Site_p.N451_splice|MYO1B_uc002usr.2_Splice_Site_p.N451_splice|MYO1B_uc002ust.1_Splice_Site_p.N89_splice	p.N451_splice	NM_001130158	NP_001155291	O43795	MYO1B_HUMAN	OV - Ovarian serous cystadenocarcinoma(117;0.0112)|Epithelial(96;0.104)|all cancers(119;0.236)		15	1608	+			451			Myosin head-like.		O43794|Q7Z6L5	Missense_Mutation	SNP	ENST00000392318.3	37	c.1353_splice	CCDS46477.1	.	.	.	.	.	.	.	.	.	.	A	23.8	4.459412	0.84317	.	.	ENSG00000128641	ENST00000339514;ENST00000392318;ENST00000304164;ENST00000392316	T;T;T;T	0.72051	-0.62;-0.62;-0.62;-0.62	6.15	6.15	0.99193	Myosin head, motor domain (3);	0.000000	0.85682	D	0.000000	T	0.70369	0.3216	L	0.28649	0.875	0.80722	D	1	P;P;P	0.42203	0.773;0.773;0.713	P;P;P	0.49451	0.611;0.611;0.477	T	0.70706	-0.4798	10	0.45353	T	0.12	.	16.7886	0.85580	1.0:0.0:0.0:0.0	.	451;451;451	B0I1S9;O43795;O43795-2	.;MYO1B_HUMAN;.	I	451	ENSP00000341903:N451I;ENSP00000376132:N451I;ENSP00000306382:N451I;ENSP00000376130:N451I	ENSP00000306382:N451I	N	+	2	0	MYO1B	191956312	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.339000	0.96797	2.363000	0.80096	0.523000	0.50628	AAT		0.313	MYO1B-010	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334774.1	NM_012223	Missense_Mutation
ALS2	57679	broad.mit.edu	37	2	202609022	202609022	+	Missense_Mutation	SNP	C	C	G			TCGA-76-4929-01A-01D-1486-08	TCGA-76-4929-10A-01D-1486-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	af4f8b89-837a-48b7-b0e7-12aec23fc285	3e0712a1-b66a-42e7-94a3-07edee7dce2b	g.chr2:202609022C>G	ENST00000264276.6	-	10	2501	c.2129G>C	c.(2128-2130)aGt>aCt	p.S710T	ALS2_ENST00000457679.2_Missense_Mutation_p.S22T	NM_020919.3	NP_065970.2	Q96Q42	ALS2_HUMAN	amyotrophic lateral sclerosis 2 (juvenile)	710	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.				behavioral fear response (GO:0001662)|cell death (GO:0008219)|endosomal transport (GO:0016197)|endosome organization (GO:0007032)|locomotory behavior (GO:0007626)|neuromuscular junction development (GO:0007528)|neuron projection morphogenesis (GO:0048812)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|positive regulation of Rab GTPase activity (GO:0032851)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of Rac protein signal transduction (GO:0035022)|positive regulation of Ran GTPase activity (GO:0032853)|protein localization (GO:0008104)|receptor recycling (GO:0001881)|regulation of endosome size (GO:0051036)|response to oxidative stress (GO:0006979)|synaptic transmission, glutamatergic (GO:0035249)|vesicle organization (GO:0016050)	centrosome (GO:0005813)|cytosol (GO:0005829)|dendrite (GO:0030425)|dendritic spine (GO:0043197)|early endosome (GO:0005769)|growth cone (GO:0030426)|lamellipodium (GO:0030027)|postsynaptic density (GO:0014069)|protein complex (GO:0043234)|ruffle (GO:0001726)|vesicle (GO:0031982)	protein homodimerization activity (GO:0042803)|protein serine/threonine kinase activator activity (GO:0043539)|Rab GTPase binding (GO:0017137)|Rab guanyl-nucleotide exchange factor activity (GO:0017112)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)|Ran guanyl-nucleotide exchange factor activity (GO:0005087)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|lung(22)|ovary(1)|prostate(4)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)	72						TTTGATATCACTTAGTTTTGA	0.398																																						uc002uyo.3																			0				NS(1)|breast(1)|central_nervous_system(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|lung(22)|ovary(1)|prostate(4)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)	72						c.(2128-2130)aGt>aCt		Homo sapiens amyotrophic lateral sclerosis 2 (juvenile) (ALS2), transcript variant 1, mRNA.							143.0	138.0	140.0					2																	202609022		1865	4113	5978	SO:0001583	missense	57679				cell death|endosome organization|positive regulation of Rac GTPase activity|regulation of endosome size	centrosome|cytosol|early endosome|growth cone|lamellipodium|protein complex|ruffle	protein homodimerization activity|protein serine/threonine kinase activator activity|Rab GTPase binding|Rab guanyl-nucleotide exchange factor activity|Rac guanyl-nucleotide exchange factor activity|Ran guanyl-nucleotide exchange factor activity	g.chr2:202609022C>G	AB053305	CCDS42800.1, CCDS46492.1	2q33-q35	2014-09-17	2004-06-23		ENSG00000003393	ENSG00000003393		"""Rho guanine nucleotide exchange factors"""	443	protein-coding gene	gene with protein product	"""alsin"""	606352	"""amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 6"""	ALS2CR6		11586298	Standard	NM_020919		Approved		uc002uyo.3	Q96Q42	OTTHUMG00000154507	ENST00000264276.6:c.2129G>C	2.37:g.202609022C>G	ENSP00000264276:p.Ser710Thr					ALS2_uc002uyp.4_Missense_Mutation_p.S710T|ALS2_uc002uyq.3_Missense_Mutation_p.S710T|ALS2_uc010ftl.3_Non-coding_Transcript	p.S710T	NM_020919	NP_065970	Q96Q42	ALS2_HUMAN			9	2485	-			710			DH.		Q53TT1|Q53TV2|Q8N1E0|Q96PC4|Q96Q41|Q9H973|Q9HCK9	Missense_Mutation	SNP	ENST00000264276.6	37	c.2129G>C	CCDS42800.1	.	.	.	.	.	.	.	.	.	.	C	18.62	3.663564	0.67700	.	.	ENSG00000003393	ENST00000264276;ENST00000457679	T;T	0.63744	-0.06;-0.06	5.95	5.95	0.96441	Dbl homology (DH) domain (4);	0.043781	0.85682	D	0.000000	T	0.70798	0.3265	L	0.29908	0.895	0.80722	D	1	D;D;P	0.76494	0.998;0.999;0.47	D;D;B	0.75484	0.986;0.97;0.42	T	0.64774	-0.6328	10	0.25751	T	0.34	.	20.3932	0.98965	0.0:1.0:0.0:0.0	.	710;710;710	Q96Q42-3;Q6IQ41;Q96Q42	.;.;ALS2_HUMAN	T	710;22	ENSP00000264276:S710T;ENSP00000394823:S22T	ENSP00000264276:S710T	S	-	2	0	ALS2	202317267	1.000000	0.71417	1.000000	0.80357	0.869000	0.49853	5.177000	0.65032	2.824000	0.97209	0.655000	0.94253	AGT		0.398	ALS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335562.3	NM_020919	
SLC11A1	6556	broad.mit.edu	37	2	219254613	219254613	+	Silent	SNP	C	C	T			TCGA-76-4929-01A-01D-1486-08	TCGA-76-4929-10A-01D-1486-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	af4f8b89-837a-48b7-b0e7-12aec23fc285	3e0712a1-b66a-42e7-94a3-07edee7dce2b	g.chr2:219254613C>T	ENST00000233202.6	+	9	1156	c.816C>T	c.(814-816)gcC>gcT	p.A272A	SLC11A1_ENST00000539932.1_Silent_p.A154A	NM_000578.3	NP_000569.3	P49279	NRAM1_HUMAN	solute carrier family 11 (proton-coupled divalent metal ion transporter), member 1	272					activation of protein kinase activity (GO:0032147)|antigen processing and presentation of peptide antigen (GO:0048002)|cadmium ion transmembrane transport (GO:0070574)|cellular cadmium ion homeostasis (GO:0006876)|cellular iron ion homeostasis (GO:0006879)|defense response to bacterium (GO:0042742)|defense response to Gram-negative bacterium (GO:0050829)|defense response to protozoan (GO:0042832)|divalent metal ion export (GO:0070839)|inflammatory response (GO:0006954)|interaction with host (GO:0051701)|interleukin-2 production (GO:0032623)|interleukin-3 production (GO:0032632)|iron ion homeostasis (GO:0055072)|iron ion transport (GO:0006826)|L-arginine import (GO:0043091)|macrophage activation (GO:0042116)|manganese ion transport (GO:0006828)|MHC class II biosynthetic process (GO:0045342)|mRNA stabilization (GO:0048255)|multicellular organismal iron ion homeostasis (GO:0060586)|negative regulation of cytokine production (GO:0001818)|nitrite transport (GO:0015707)|phagocytosis (GO:0006909)|phagosome maturation (GO:0090382)|positive regulation of cytokine production (GO:0001819)|positive regulation of dendritic cell antigen processing and presentation (GO:0002606)|positive regulation of gene expression (GO:0010628)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of phagocytosis (GO:0050766)|positive regulation of T-helper 1 type immune response (GO:0002827)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein import into nucleus, translocation (GO:0000060)|respiratory burst (GO:0045730)|response to bacterium (GO:0009617)|response to interferon-gamma (GO:0034341)|response to lipopolysaccharide (GO:0032496)|T cell cytokine production (GO:0002369)|T cell proliferation involved in immune response (GO:0002309)|transmembrane transport (GO:0055085)|vacuolar acidification (GO:0007035)|wound healing (GO:0042060)	cell outer membrane (GO:0009279)|integral component of plasma membrane (GO:0005887)|late endosome (GO:0005770)|late endosome membrane (GO:0031902)|lysosome (GO:0005764)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)|tertiary granule membrane (GO:0070821)	manganese ion transmembrane transporter activity (GO:0005384)|metal ion:proton antiporter activity (GO:0051139)|protein homodimerization activity (GO:0042803)|transition metal ion transmembrane transporter activity (GO:0046915)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(3)|ovary(3)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)	19		Renal(207;0.0474)		Epithelial(149;1.16e-06)|all cancers(144;0.000195)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		TAGACCGGGCCCGCCGAGCAG	0.537																																						uc002vhv.3																			0				NS(1)|breast(2)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(3)|ovary(3)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)	19						c.(814-816)gcC>gcT		Homo sapiens solute carrier family 11 (proton-coupled divalent metal ion transporters), member 1 (SLC11A1), mRNA.							118.0	93.0	101.0					2																	219254613		2203	4300	6503	SO:0001819	synonymous_variant	6556				activation of protein kinase activity|antigen processing and presentation of peptide antigen|cadmium ion transmembrane transport|cellular cadmium ion homeostasis|cellular iron ion homeostasis|defense response to Gram-negative bacterium|defense response to protozoan|divalent metal ion export|inflammatory response|interleukin-2 production|interleukin-3 production|iron ion transport|L-arginine import|macrophage activation|MHC class II biosynthetic process|mRNA stabilization|multicellular organismal iron ion homeostasis|negative regulation of cytokine production|nitrite transport|phagocytosis|positive regulation of dendritic cell antigen processing and presentation|positive regulation of interferon-gamma production|positive regulation of phagocytosis|positive regulation of T-helper 1 type immune response|positive regulation of transcription from RNA polymerase II promoter|respiratory burst|response to interferon-gamma|response to lipopolysaccharide|T cell cytokine production|T cell proliferation involved in immune response|vacuolar acidification|wound healing	integral to plasma membrane|late endosome membrane|lysosome|phagocytic vesicle membrane|tertiary granule membrane	manganese ion transmembrane transporter activity|metal ion:hydrogen antiporter activity|protein homodimerization activity	g.chr2:219254613C>T	D38171	CCDS2415.1	2q35	2013-07-18	2013-07-18		ENSG00000018280	ENSG00000018280		"""Solute carriers"""	10907	protein-coding gene	gene with protein product	"""natural resistance-associated macrophage protein 1"""	600266		LSH, NRAMP, NRAMP1		7964458, 7980580	Standard	NM_000578		Approved		uc002vhv.3	P49279	OTTHUMG00000086747	ENST00000233202.6:c.816C>T	2.37:g.219254613C>T						SLC11A1_uc010fvp.1_Silent_p.A272A|SLC11A1_uc010fvq.1_Silent_p.A205A|SLC11A1_uc010zkc.1_Silent_p.A205A|SLC11A1_uc002vhu.1_Silent_p.A67A|SLC11A1_uc002vhw.3_Silent_p.A154A|SLC11A1_uc010fvr.3_Silent_p.A67A	p.A272A	NM_000578	NP_000569	P49279	NRAM1_HUMAN		Epithelial(149;1.16e-06)|all cancers(144;0.000195)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)	8	1156	+		Renal(207;0.0474)	272					C0H5Y3	Silent	SNP	ENST00000233202.6	37	c.816C>T	CCDS2415.1																																																																																				0.537	SLC11A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195076.2	NM_000578	
NANP	140838	broad.mit.edu	37	20	25597030	25597030	+	Missense_Mutation	SNP	G	G	C			TCGA-76-4929-01A-01D-1486-08	TCGA-76-4929-10A-01D-1486-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	af4f8b89-837a-48b7-b0e7-12aec23fc285	3e0712a1-b66a-42e7-94a3-07edee7dce2b	g.chr20:25597030G>C	ENST00000304788.3	-	2	504	c.278C>G	c.(277-279)gCt>gGt	p.A93G		NM_152667.2	NP_689880.1	Q8TBE9	NANP_HUMAN	N-acetylneuraminic acid phosphatase	93					carbohydrate metabolic process (GO:0005975)|dephosphorylation (GO:0016311)|N-acetylglucosamine biosynthetic process (GO:0006045)|N-acetylneuraminate biosynthetic process (GO:0046380)		N-acylneuraminate-9-phosphatase activity (GO:0050124)			endometrium(2)|lung(2)|prostate(1)	5						ACATTCTTCAGCCAATTTTCT	0.403																																						uc002wuy.3																			0				endometrium(2)|lung(2)|prostate(1)	5						c.(277-279)gCt>gGt		Homo sapiens N-acetylneuraminic acid phosphatase (NANP), mRNA.							72.0	74.0	73.0					20																	25597030		2203	4300	6503	SO:0001583	missense	140838				N-acetylneuraminate biosynthetic process		N-acylneuraminate-9-phosphatase activity|phosphoglycolate phosphatase activity	g.chr20:25597030G>C	AL031673	CCDS13173.1	20p11.1	2006-10-24	2006-01-24	2006-01-24	ENSG00000170191	ENSG00000170191			16140	protein-coding gene	gene with protein product		610763	"""chromosome 20 open reading frame 147"", ""haloacid dehalogenase-like hydrolase domain containing 4"""	C20orf147, HDHD4		16237198	Standard	NM_152667		Approved	dJ694B14.3, MGC26833	uc002wuy.3	Q8TBE9	OTTHUMG00000032132	ENST00000304788.3:c.278C>G	20.37:g.25597030G>C	ENSP00000302441:p.Ala93Gly						p.A93G	NM_152667	NP_689880	Q8TBE9	NANP_HUMAN			1	342	-			93					B3KP12|Q5JYN8|Q8TE97|Q9Y3N0	Missense_Mutation	SNP	ENST00000304788.3	37	c.278C>G	CCDS13173.1	.	.	.	.	.	.	.	.	.	.	G	23.3	4.402572	0.83230	.	.	ENSG00000170191	ENST00000304788	T	0.05996	3.36	5.28	5.28	0.74379	Haloacid dehalogenase-like hydrolase (1);HAD-like domain (2);	0.049618	0.85682	D	0.000000	T	0.16811	0.0404	L	0.48877	1.53	0.80722	D	1	D	0.58268	0.982	D	0.63957	0.92	T	0.03043	-1.1079	10	0.23891	T	0.37	-20.2061	16.4739	0.84127	0.0:0.0:1.0:0.0	.	93	Q8TBE9	NANP_HUMAN	G	93	ENSP00000302441:A93G	ENSP00000302441:A93G	A	-	2	0	NANP	25545030	1.000000	0.71417	0.989000	0.46669	0.911000	0.54048	8.461000	0.90372	2.469000	0.83416	0.485000	0.47835	GCT		0.403	NANP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078457.2	NM_152667	
CDH4	1002	broad.mit.edu	37	20	60509217	60509217	+	Missense_Mutation	SNP	C	C	T			TCGA-76-4929-01A-01D-1486-08	TCGA-76-4929-10A-01D-1486-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	af4f8b89-837a-48b7-b0e7-12aec23fc285	3e0712a1-b66a-42e7-94a3-07edee7dce2b	g.chr20:60509217C>T	ENST00000360469.5	+	15	2571	c.2483C>T	c.(2482-2484)cCc>cTc	p.P828L	CDH4_ENST00000543233.1_Missense_Mutation_p.P754L	NM_001794.3	NP_001785.2	P55283	CADH4_HUMAN	cadherin 4, type 1, R-cadherin (retinal)	828					adherens junction organization (GO:0034332)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(2)|breast(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(17)|liver(2)|lung(25)|ovary(2)|prostate(1)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	74			BRCA - Breast invasive adenocarcinoma(19;2.36e-08)			GGCGCTGAGCCCCAGTACCCG	0.677																																						uc002ybn.2																			0				NS(2)|breast(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(17)|liver(2)|lung(25)|ovary(2)|prostate(1)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	74						c.(2482-2484)cCc>cTc		Homo sapiens cadherin 4, type 1, R-cadherin (retinal) (CDH4), transcript variant 1, mRNA.							28.0	32.0	31.0					20																	60509217		2202	4295	6497	SO:0001583	missense	1002				adherens junction organization|cell junction assembly		calcium ion binding	g.chr20:60509217C>T	L34059	CCDS13488.1, CCDS58784.1	20q13.3	2010-01-26			ENSG00000179242	ENSG00000179242		"""Cadherins / Major cadherins"""	1763	protein-coding gene	gene with protein product	"""R-Cadherin"""	603006				10191097, 10516427	Standard	NM_001794		Approved		uc002ybn.2	P55283	OTTHUMG00000032890	ENST00000360469.5:c.2483C>T	20.37:g.60509217C>T	ENSP00000353656:p.Pro828Leu					CDH4_uc002ybr.2_Missense_Mutation_p.P791L|CDH4_uc002ybp.2_Missense_Mutation_p.P754L	p.P828L	NM_001794	NP_001785	P55283	CADH4_HUMAN	BRCA - Breast invasive adenocarcinoma(19;2.36e-08)		14	2571	+			828					B3KWB8|G3V1P8|Q2M208|Q5VZ44|Q9BZ05	Missense_Mutation	SNP	ENST00000360469.5	37	c.2483C>T	CCDS13488.1	.	.	.	.	.	.	.	.	.	.	C	26.1	4.708151	0.89018	.	.	ENSG00000179242	ENST00000360469;ENST00000536643;ENST00000543233	T;T	0.74947	-0.89;-0.89	4.52	4.52	0.55395	Cadherin, cytoplasmic domain (1);	0.057469	0.64402	D	0.000001	T	0.77458	0.4133	L	0.39898	1.24	0.80722	D	1	P	0.45634	0.863	P	0.54856	0.762	T	0.76072	-0.3093	9	.	.	.	.	17.2442	0.87022	0.0:1.0:0.0:0.0	.	828	P55283	CADH4_HUMAN	L	828;736;754	ENSP00000353656:P828L;ENSP00000443301:P754L	.	P	+	2	0	CDH4	59942612	1.000000	0.71417	1.000000	0.80357	0.547000	0.35210	5.677000	0.68142	2.054000	0.61138	0.491000	0.48974	CCC		0.677	CDH4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079965.2	NM_001794	
NTSR1	4923	broad.mit.edu	37	20	61341151	61341151	+	Missense_Mutation	SNP	C	C	A			TCGA-76-4929-01A-01D-1486-08	TCGA-76-4929-10A-01D-1486-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	af4f8b89-837a-48b7-b0e7-12aec23fc285	3e0712a1-b66a-42e7-94a3-07edee7dce2b	g.chr20:61341151C>A	ENST00000370501.3	+	1	963	c.592C>A	c.(592-594)Ctg>Atg	p.L198M		NM_002531.2	NP_002522.2	P30989	NTR1_HUMAN	neurotensin receptor 1 (high affinity)	198					adult locomotory behavior (GO:0008344)|G-protein coupled receptor signaling pathway (GO:0007186)|negative regulation of apoptotic process (GO:0043066)|neuropeptide signaling pathway (GO:0007218)|synaptic transmission (GO:0007268)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)	G-protein coupled neurotensin receptor activity (GO:0016492)|G-protein coupled receptor activity (GO:0004930)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(16)|prostate(1)|skin(3)	27	Breast(26;3.65e-08)		BRCA - Breast invasive adenocarcinoma(19;3.63e-06)			CGCCTCGGCCCTGCTGGCGGT	0.672																																					GBM(37;400 780 6403 19663 35669)	uc002ydf.3																			0				breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(16)|prostate(1)|skin(3)	27						c.(592-594)Ctg>Atg		Homo sapiens neurotensin receptor 1 (high affinity) (NTSR1), mRNA.							62.0	51.0	55.0					20																	61341151		2203	4300	6503	SO:0001583	missense	4923					endoplasmic reticulum|Golgi apparatus|integral to plasma membrane	neurotensin receptor activity, G-protein coupled	g.chr20:61341151C>A		CCDS13502.1	20q13	2012-08-08			ENSG00000101188	ENSG00000101188		"""GPCR / Class A : Neurotensin receptors"""	8039	protein-coding gene	gene with protein product		162651				8075503	Standard	NM_002531		Approved	NTR	uc002ydf.3	P30989	OTTHUMG00000032932	ENST00000370501.3:c.592C>A	20.37:g.61341151C>A	ENSP00000359532:p.Leu198Met						p.L198M	NM_002531	NP_002522	P30989	NTR1_HUMAN	BRCA - Breast invasive adenocarcinoma(19;3.63e-06)		0	963	+	Breast(26;3.65e-08)		198					Q9H4H1|Q9H4T5	Missense_Mutation	SNP	ENST00000370501.3	37	c.592C>A	CCDS13502.1	.	.	.	.	.	.	.	.	.	.	C	16.50	3.140219	0.56936	.	.	ENSG00000101188	ENST00000370501	T	0.48522	0.81	5.15	4.2	0.49525	GPCR, rhodopsin-like superfamily (1);	0.253598	0.34507	N	0.003917	T	0.49677	0.1571	M	0.76938	2.355	0.30798	N	0.740198	P	0.40144	0.704	B	0.40864	0.342	T	0.57195	-0.7853	10	0.37606	T	0.19	-19.995	10.4968	0.44783	0.1506:0.7043:0.1451:0.0	.	198	P30989	NTR1_HUMAN	M	198	ENSP00000359532:L198M	ENSP00000359532:L198M	L	+	1	2	NTSR1	60811596	1.000000	0.71417	0.922000	0.36590	0.994000	0.84299	2.464000	0.45067	1.153000	0.42468	0.561000	0.74099	CTG		0.672	NTSR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080061.1		
GAB4	128954	broad.mit.edu	37	22	17450832	17450832	+	Splice_Site	SNP	C	C	T			TCGA-76-4929-01A-01D-1486-08	TCGA-76-4929-10A-01D-1486-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	af4f8b89-837a-48b7-b0e7-12aec23fc285	3e0712a1-b66a-42e7-94a3-07edee7dce2b	g.chr22:17450832C>T	ENST00000400588.1	-	4	1045		c.e4+1		GAB4_ENST00000523144.1_Intron	NM_001037814.1	NP_001032903.1	Q2WGN9	GAB4_HUMAN	GRB2-associated binding protein family, member 4											breast(2)|endometrium(2)|kidney(2)|large_intestine(6)|lung(24)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	44		all_epithelial(15;0.112)|Lung NSC(13;0.248)				GGGGTACACACCCTCATTATC	0.597																																						uc002zlw.3																			0				breast(2)|endometrium(2)|kidney(2)|large_intestine(6)|lung(24)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	44						c.e4+1		Homo sapiens GRB2-associated binding protein family, member 4 (GAB4), mRNA.							81.0	87.0	85.0					22																	17450832		2159	4283	6442	SO:0001630	splice_region_variant	128954							g.chr22:17450832C>T	AK057252	CCDS42976.1	22q11.2	2013-01-10			ENSG00000215568	ENSG00000215568		"""Pleckstrin homology (PH) domain containing"""	18325	protein-coding gene	gene with protein product							Standard	NM_001037814		Approved		uc002zlw.3	Q2WGN9	OTTHUMG00000149992	ENST00000400588.1:c.937+1G>A	22.37:g.17450832C>T						GAB4_uc010gqs.1_Intron	p.A313_splice	NM_001037814	NP_001032903	Q2WGN9	GAB4_HUMAN			4	1045	-		all_epithelial(15;0.112)|Lung NSC(13;0.248)	313						Splice_Site	SNP	ENST00000400588.1	37	c.937_splice	CCDS42976.1	.	.	.	.	.	.	.	.	.	.	C	7.527	0.657951	0.14645	.	.	ENSG00000215568	ENST00000400588	.	.	.	1.97	0.804	0.18697	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	4.7253	0.12938	0.0:0.2311:0.0:0.7689	.	.	.	.	.	-1	.	.	.	-	.	.	GAB4	15830832	1.000000	0.71417	0.998000	0.56505	0.282000	0.26991	5.264000	0.65513	0.155000	0.19261	0.411000	0.27672	.		0.597	GAB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315426.1	XM_372882	Intron
DEPDC5	9681	broad.mit.edu	37	22	32234828	32234828	+	Nonsense_Mutation	SNP	C	C	T			TCGA-76-4929-01A-01D-1486-08	TCGA-76-4929-10A-01D-1486-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	af4f8b89-837a-48b7-b0e7-12aec23fc285	3e0712a1-b66a-42e7-94a3-07edee7dce2b	g.chr22:32234828C>T	ENST00000382112.3	+	26	2555	c.2485C>T	c.(2485-2487)Cga>Tga	p.R829*	RNU6-201P_ENST00000517100.1_RNA|DEPDC5_ENST00000400246.1_Nonsense_Mutation_p.R838*|DEPDC5_ENST00000382105.2_Nonsense_Mutation_p.R760*|DEPDC5_ENST00000400248.2_Nonsense_Mutation_p.R829*|DEPDC5_ENST00000266091.3_Nonsense_Mutation_p.R838*|DEPDC5_ENST00000400249.2_Nonsense_Mutation_p.R829*|DEPDC5_ENST00000382111.2_Nonsense_Mutation_p.R838*|DEPDC5_ENST00000535622.1_Nonsense_Mutation_p.R760*	NM_001136029.2|NM_001242896.1	NP_001129501.1|NP_001229825.1	O75140	DEPD5_HUMAN	DEP domain containing 5	838					intracellular signal transduction (GO:0035556)	cytosol (GO:0005829)|lysosomal membrane (GO:0005765)|perinuclear region of cytoplasm (GO:0048471)	GTPase activator activity (GO:0005096)			breast(1)|central_nervous_system(5)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|lung(24)|ovary(5)|pancreas(2)|prostate(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	63						ACTCTATAGCCGAGGTGAGTT	0.458																																						uc011alu.2																			0				breast(1)|central_nervous_system(5)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|lung(24)|ovary(5)|pancreas(2)|prostate(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	63						c.(2512-2514)Cga>Tga		Homo sapiens DEP domain containing 5 (DEPDC5), transcript variant 4, mRNA.							94.0	93.0	94.0					22																	32234828		1858	4101	5959	SO:0001587	stop_gained	9681				intracellular signal transduction			g.chr22:32234828C>T	AB014545	CCDS43006.1, CCDS43007.1, CCDS46692.1, CCDS56229.1, CCDS74849.1	22q12.3	2013-04-29			ENSG00000100150	ENSG00000100150			18423	protein-coding gene	gene with protein product		614191				23542697, 23542701	Standard	NM_001242896		Approved	KIAA0645, DEP.5	uc011alu.2	O75140	OTTHUMG00000030926	ENST00000382112.3:c.2485C>T	22.37:g.32234828C>T	ENSP00000371546:p.Arg829*					DEPDC5_uc011als.2_Nonsense_Mutation_p.R760*|DEPDC5_uc003als.3_Nonsense_Mutation_p.R829*|DEPDC5_uc011alv.2_Non-coding_Transcript|DEPDC5_uc003alt.3_Nonsense_Mutation_p.R829*|DEPDC5_uc003alv.3_Non-coding_Transcript|DEPDC5_uc003alu.3_Nonsense_Mutation_p.R278*|DEPDC5_uc011alw.1_Nonsense_Mutation_p.R159*|DEPDC5_uc003alw.3_Nonsense_Mutation_p.R127*|DEPDC5_uc011alx.2_Intron	p.R838*	NM_001242896	NP_001229825	O75140	DEPD5_HUMAN			26	2714	+			829					A6H8V6|A8MPX9|B4DH93|B9EGN9|Q5K3V5|Q5THY9|Q5THZ0|Q5THZ1|Q5THZ3|Q68DR1|Q6MZX3|Q6PEZ1|Q9UGV8|Q9UH13	Nonsense_Mutation	SNP	ENST00000382112.3	37	c.2512C>T	CCDS46692.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	40|40	7.938622|7.938622	0.98571|0.98571	.|.	.|.	ENSG00000100150|ENSG00000100150	ENST00000433147|ENST00000535622;ENST00000266091;ENST00000400249;ENST00000382109;ENST00000400246;ENST00000382105;ENST00000382112;ENST00000382111;ENST00000400248	.|.	.|.	.|.	5.65|5.65	2.13|2.13	0.27403|0.27403	.|.	.|0.064498	.|0.64402	.|D	.|0.000012	T|.	0.33673|.	0.0871|.	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|.	0.07121|.	-1.0789|.	4|.	.|0.06625	.|T	.|0.88	.|.	10.0115|10.0115	0.41990|0.41990	0.4579:0.4291:0.113:0.0|0.4579:0.4291:0.113:0.0	.|.	.|.	.|.	.|.	L|X	235|760;838;829;760;838;760;829;838;829	.|.	.|ENSP00000266091:R838X	P|R	+|+	2|1	0|2	DEPDC5|DEPDC5	30564828|30564828	0.867000|0.867000	0.29959|0.29959	0.999000|0.999000	0.59377|0.59377	0.999000|0.999000	0.98932|0.98932	0.486000|0.486000	0.22340|0.22340	0.677000|0.677000	0.31305|0.31305	0.655000|0.655000	0.94253|0.94253	CCG|CGA		0.458	DEPDC5-006	NOVEL	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000129087.1	NM_014662	
RNF123	63891	broad.mit.edu	37	3	49737157	49737157	+	Silent	SNP	C	C	T			TCGA-76-4929-01A-01D-1486-08	TCGA-76-4929-10A-01D-1486-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	af4f8b89-837a-48b7-b0e7-12aec23fc285	3e0712a1-b66a-42e7-94a3-07edee7dce2b	g.chr3:49737157C>T	ENST00000327697.6	+	12	1080	c.936C>T	c.(934-936)acC>acT	p.T312T	RNF123_ENST00000432042.1_Silent_p.T166T	NM_022064.3	NP_071347.2	Q5XPI4	RN123_HUMAN	ring finger protein 123	312					protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)	ligase activity (GO:0016874)|zinc ion binding (GO:0008270)			NS(1)|breast(4)|cervix(2)|endometrium(4)|kidney(4)|large_intestine(6)|lung(11)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	38				BRCA - Breast invasive adenocarcinoma(193;4.71e-05)|Kidney(197;0.00227)|KIRC - Kidney renal clear cell carcinoma(197;0.00255)		GCCAGCCCACCGTCCTCCTCA	0.647																																						uc003cxh.3																			0				NS(1)|breast(4)|cervix(2)|endometrium(4)|kidney(4)|large_intestine(6)|lung(11)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	38						c.(934-936)acC>acT		Homo sapiens ring finger protein 123 (RNF123), mRNA.							61.0	64.0	63.0					3																	49737157		2203	4300	6503	SO:0001819	synonymous_variant	63891					cytoplasm	ligase activity|protein binding|zinc ion binding	g.chr3:49737157C>T	AK022627	CCDS33758.1	3p24.3	2008-02-05			ENSG00000164068	ENSG00000164068		"""RING-type (C3HC4) zinc fingers"""	21148	protein-coding gene	gene with protein product		614472					Standard	NM_022064		Approved	FLJ12565	uc003cxh.4	Q5XPI4	OTTHUMG00000156891	ENST00000327697.6:c.936C>T	3.37:g.49737157C>T						RNF123_uc010hky.1_5'UTR|RNF123_uc003cxi.3_Non-coding_Transcript	p.T312T	NM_022064	NP_071347	Q5XPI4	RN123_HUMAN		BRCA - Breast invasive adenocarcinoma(193;4.71e-05)|Kidney(197;0.00227)|KIRC - Kidney renal clear cell carcinoma(197;0.00255)	11	1022	+			312					A1L4Q3|A6NLS5|Q5I022|Q6PFW4|Q71RH0|Q8IW18|Q9H0M8|Q9H5L8|Q9H9T2	Silent	SNP	ENST00000327697.6	37	c.936C>T	CCDS33758.1																																																																																				0.647	RNF123-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346475.2	NM_022064	
ALG3	10195	broad.mit.edu	37	3	183962404	183962404	+	Silent	SNP	G	G	A			TCGA-76-4929-01A-01D-1486-08	TCGA-76-4929-10A-01D-1486-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	af4f8b89-837a-48b7-b0e7-12aec23fc285	3e0712a1-b66a-42e7-94a3-07edee7dce2b	g.chr3:183962404G>A	ENST00000397676.3	-	5	741	c.711C>T	c.(709-711)atC>atT	p.I237I	EIF2B5_ENST00000444495.1_Intron|ALG3_ENST00000445626.2_Silent_p.I189I|ALG3_ENST00000463495.1_5'Flank|ALG3_ENST00000455059.1_Silent_p.I197I|ALG3_ENST00000418734.2_Silent_p.I181I	NM_005787.5	NP_005778.1	Q92685	ALG3_HUMAN	ALG3, alpha-1,3- mannosyltransferase	237					cellular protein metabolic process (GO:0044267)|dolichol-linked oligosaccharide biosynthetic process (GO:0006488)|mannosylation (GO:0097502)|post-translational protein modification (GO:0043687)|protein glycosylation (GO:0006486)|protein N-linked glycosylation via asparagine (GO:0018279)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	alpha-1,3-mannosyltransferase activity (GO:0000033)|dol-P-Man:Man(5)GlcNAc(2)-PP-Dol alpha-1,3-mannosyltransferase activity (GO:0052925)			kidney(1)|large_intestine(1)|lung(6)|upper_aerodigestive_tract(1)	9	all_cancers(143;1.39e-10)|Ovarian(172;0.0339)		Epithelial(37;8.28e-34)|OV - Ovarian serous cystadenocarcinoma(80;2.72e-22)			GGCCAGCACAGATTCCCAGCT	0.537																																						uc003fne.2																			0				kidney(1)|large_intestine(1)|lung(6)|upper_aerodigestive_tract(1)	9						c.(709-711)atC>atT		Homo sapiens asparagine-linked glycosylation 3, alpha-1,3- mannosyltransferase homolog (S. cerevisiae) (ALG3), transcript variant 1, mRNA.							37.0	40.0	39.0					3																	183962404		1949	4125	6074	SO:0001819	synonymous_variant	10195				dolichol-linked oligosaccharide biosynthetic process|post-translational protein modification|protein N-linked glycosylation via asparagine	endoplasmic reticulum membrane|integral to membrane	alpha-1,3-mannosyltransferase activity	g.chr3:183962404G>A	BC002839	CCDS46967.1, CCDS46968.1	3q27.3	2013-02-26	2013-02-26		ENSG00000214160	ENSG00000214160	2.4.1.258	"""Dolichyl D-mannosyl phosphate dependent mannosyltransferases"""	23056	protein-coding gene	gene with protein product	"""carbohydrate deficient glycoprotein syndrome type IV"", ""dol-P-Man:Man(5)GlcNAc(2)-PP-Dol alpha-1,3-mannosyltransferase"", ""dol-P-Man dependent alpha-1,3- mannosyltransferase"""	608750	"""asparagine-linked glycosylation 3 homolog (yeast, alpha-1,3-mannosyltransferase)"", ""asparagine-linked glycosylation 3, alpha-1,3- mannosyltransferase homolog (S. cerevisiae)"""			1058125	Standard	NM_005787		Approved	NOT56L, Not56, CDGS4, D16Ertd36e	uc003fne.2	Q92685	OTTHUMG00000156823	ENST00000397676.3:c.711C>T	3.37:g.183962404G>A						ALG3_uc011brc.1_Silent_p.I202I|ALG3_uc011brd.1_Silent_p.I181I|ALG3_uc011bre.1_Silent_p.I189I	p.I237I	NM_005787	NP_005778	Q92685	ALG3_HUMAN	Epithelial(37;8.28e-34)|OV - Ovarian serous cystadenocarcinoma(80;2.72e-22)		4	742	-	all_cancers(143;1.39e-10)|Ovarian(172;0.0339)		237					A8JZZ6|Q9BT71	Silent	SNP	ENST00000397676.3	37	c.711C>T	CCDS46968.1																																																																																				0.537	ALG3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346033.1	NM_005787	
PDGFRA	5156	broad.mit.edu	37	4	55131090	55131090	+	Silent	SNP	A	A	G			TCGA-76-4929-01A-01D-1486-08	TCGA-76-4929-10A-01D-1486-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	af4f8b89-837a-48b7-b0e7-12aec23fc285	3e0712a1-b66a-42e7-94a3-07edee7dce2b	g.chr4:55131090A>G	ENST00000257290.5	+	5	964	c.633A>G	c.(631-633)acA>acG	p.T211T	FIP1L1_ENST00000507166.1_Intron|PDGFRA_ENST00000508170.1_3'UTR	NM_006206.4	NP_006197.1	P16234	PGFRA_HUMAN	platelet-derived growth factor receptor, alpha polypeptide	211	Ig-like C2-type 3.				adrenal gland development (GO:0030325)|cardiac myofibril assembly (GO:0055003)|cell activation (GO:0001775)|cell chemotaxis (GO:0060326)|cellular response to amino acid stimulus (GO:0071230)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic skeletal system morphogenesis (GO:0048704)|epidermal growth factor receptor signaling pathway (GO:0007173)|estrogen metabolic process (GO:0008210)|extracellular matrix organization (GO:0030198)|face morphogenesis (GO:0060325)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|hematopoietic progenitor cell differentiation (GO:0002244)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|Leydig cell differentiation (GO:0033327)|lung development (GO:0030324)|luteinization (GO:0001553)|male genitalia development (GO:0030539)|metanephric glomerular capillary formation (GO:0072277)|negative regulation of platelet activation (GO:0010544)|neurotrophin TRK receptor signaling pathway (GO:0048011)|odontogenesis of dentin-containing tooth (GO:0042475)|palate development (GO:0060021)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|platelet aggregation (GO:0070527)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|platelet-derived growth factor receptor-alpha signaling pathway (GO:0035790)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell proliferation by VEGF-activated platelet derived growth factor receptor signaling pathway (GO:0038091)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of DNA replication (GO:0045740)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of phospholipase C activity (GO:0010863)|protein autophosphorylation (GO:0046777)|regulation of actin cytoskeleton reorganization (GO:2000249)|regulation of chemotaxis (GO:0050920)|regulation of mesenchymal stem cell differentiation (GO:2000739)|retina vasculature development in camera-type eye (GO:0061298)|signal transduction involved in regulation of gene expression (GO:0023019)|viral process (GO:0016032)|wound healing (GO:0042060)	cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|intrinsic component of plasma membrane (GO:0031226)|membrane (GO:0016020)|microvillus (GO:0005902)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|platelet-derived growth factor alpha-receptor activity (GO:0005018)|platelet-derived growth factor binding (GO:0048407)|platelet-derived growth factor receptor binding (GO:0005161)|protein homodimerization activity (GO:0042803)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|vascular endothelial growth factor binding (GO:0038085)|vascular endothelial growth factor-activated receptor activity (GO:0005021)			NS(1)|autonomic_ganglia(1)|bone(1)|breast(4)|central_nervous_system(17)|cervix(1)|endometrium(4)|eye(1)|gastrointestinal_tract_(site_indeterminate)(1)|haematopoietic_and_lymphoid_tissue(22)|kidney(6)|large_intestine(26)|liver(4)|lung(48)|ovary(4)|prostate(6)|skin(11)|small_intestine(49)|soft_tissue(727)|stomach(32)|urinary_tract(1)	967	all_cancers(7;0.000425)|all_lung(4;0.000343)|Lung NSC(11;0.000467)|all_epithelial(27;0.0131)|all_neural(26;0.0209)|Glioma(25;0.08)		GBM - Glioblastoma multiforme(1;4.18e-71)|all cancers(1;4.76e-45)|LUSC - Lung squamous cell carcinoma(32;0.00256)		Becaplermin(DB00102)|Imatinib(DB00619)|Pazopanib(DB06589)|Ponatinib(DB08901)|Regorafenib(DB08896)|Sunitinib(DB01268)	TTATAGCAACATCAGAGCTGG	0.373			"""Mis, O, T"""	FIP1L1	"""GIST, idiopathic hypereosinophilic syndrome, paediatric GBM"""				Gastrointestinal Stromal Tumors, Sporadic Multiple Primary;Familial Intestinal Neurofibromatosis	TSP Lung(21;0.16)																											Pancreas(151;208 1913 7310 23853 37092)	uc003han.4				Dom	yes		4	4q11-q13	5156	"""Mis, O, T"""	"""platelet-derived growth factor, alpha-receptor"""			"""L, M, O"""	FIP1L1		"""GIST, idiopathic hypereosinophilic syndrome, paediatric GBM"""		0		p.A210V(1)|p.A210fs*7(1)		NS(1)|autonomic_ganglia(1)|bone(1)|breast(4)|central_nervous_system(17)|cervix(1)|endometrium(4)|eye(1)|gastrointestinal_tract_(site_indeterminate)(1)|haematopoietic_and_lymphoid_tissue(22)|kidney(6)|large_intestine(26)|liver(4)|lung(48)|ovary(4)|prostate(6)|skin(11)|small_intestine(49)|soft_tissue(727)|stomach(32)|urinary_tract(1)	967						c.(631-633)acA>acG		Homo sapiens platelet-derived growth factor receptor, alpha polypeptide (PDGFRA), mRNA.	Becaplermin(DB00102)|Imatinib(DB00619)|Sunitinib(DB01268)						126.0	127.0	126.0					4																	55131090		2203	4300	6503	SO:0001819	synonymous_variant	5156	Gastrointestinal Stromal Tumors, Sporadic Multiple Primary;Familial Intestinal Neurofibromatosis	Familial Cancer Database	Sporadic Multiple GIST;Familial Intestinal Stromal Tumors, NF3B, subset of Familial GIST,	cardiac myofibril assembly|cell activation|luteinization|metanephric glomerular capillary formation|peptidyl-tyrosine phosphorylation|positive regulation of cell migration|positive regulation of DNA replication|positive regulation of fibroblast proliferation|protein autophosphorylation|retina vasculature development in camera-type eye	cytoplasm|integral to plasma membrane|nucleus	ATP binding|platelet-derived growth factor alpha-receptor activity|platelet-derived growth factor binding|platelet-derived growth factor receptor binding|protein homodimerization activity|vascular endothelial growth factor receptor activity	g.chr4:55131090A>G	D50001	CCDS3495.1	4q12	2014-09-17			ENSG00000134853	ENSG00000134853		"""CD molecules"", ""Immunoglobulin superfamily / I-set domain containing"""	8803	protein-coding gene	gene with protein product		173490					Standard	NM_006206		Approved	CD140a, PDGFR2	uc003han.4	P16234	OTTHUMG00000128699	ENST00000257290.5:c.633A>G	4.37:g.55131090A>G		TSP Lung(21;0.16)				PDGFRA_uc003haa.3_Intron|PDGFRA_uc003hal.3_3'UTR|PDGFRA_uc010igq.1_Silent_p.T105T|PDGFRA_uc003ham.2_Non-coding_Transcript	p.T211T	NM_006206	NP_006197	P16234	PGFRA_HUMAN	GBM - Glioblastoma multiforme(1;4.18e-71)|all cancers(1;4.76e-45)|LUSC - Lung squamous cell carcinoma(32;0.00256)		4	964	+	all_cancers(7;0.000425)|all_lung(4;0.000343)|Lung NSC(11;0.000467)|all_epithelial(27;0.0131)|all_neural(26;0.0209)|Glioma(25;0.08)		211			Ig-like C2-type 3.		B2RE69|E9PBH0|Q6P4H5|Q96KZ7|Q9UD28	Silent	SNP	ENST00000257290.5	37	c.633A>G	CCDS3495.1																																																																																				0.373	PDGFRA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250598.2	NM_006206	
LPHN3	23284	broad.mit.edu	37	4	62363023	62363023	+	Silent	SNP	G	G	A	rs371504666		TCGA-76-4929-01A-01D-1486-08	TCGA-76-4929-10A-01D-1486-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	af4f8b89-837a-48b7-b0e7-12aec23fc285	3e0712a1-b66a-42e7-94a3-07edee7dce2b	g.chr4:62363023G>A	ENST00000514591.1	+	3	341	c.12G>A	c.(10-12)tcG>tcA	p.S4S	LPHN3_ENST00000508946.1_Silent_p.S4S|LPHN3_ENST00000545650.1_Silent_p.S4S|LPHN3_ENST00000514157.1_Silent_p.S4S|LPHN3_ENST00000504896.1_Silent_p.S4S|LPHN3_ENST00000506746.1_Silent_p.S4S|LPHN3_ENST00000507625.1_Silent_p.S4S|LPHN3_ENST00000514996.1_Silent_p.S4S|LPHN3_ENST00000509896.1_Silent_p.S4S|LPHN3_ENST00000511324.1_Silent_p.S4S|LPHN3_ENST00000508693.1_Silent_p.S4S|LPHN3_ENST00000512091.2_Silent_p.S4S|LPHN3_ENST00000506700.1_Silent_p.S4S|LPHN3_ENST00000506720.1_Silent_p.S4S|LPHN3_ENST00000507164.1_Silent_p.S4S			Q9HAR2	LPHN3_HUMAN	latrophilin 3	4					G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)|G-protein coupled receptor activity (GO:0004930)			breast(5)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(5)|kidney(4)|large_intestine(21)|lung(73)|ovary(1)|pancreas(1)|prostate(6)|upper_aerodigestive_tract(1)	125						TGTGGCCATCGCAGCTACTAA	0.348													G|||	1	0.000199681	0.0008	0.0	5008	,	,		14428	0.0		0.0	False		,,,				2504	0.0					uc010ihh.3																			0				breast(5)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(5)|kidney(4)|large_intestine(21)|lung(73)|ovary(1)|pancreas(1)|prostate(6)|upper_aerodigestive_tract(1)	125						c.(10-12)tcG>tcA		Homo sapiens latrophilin 3 (LPHN3), mRNA.		G		2,3726		0,2,1862	153.0	144.0	147.0		12	-1.0	0.9	4		147	0,8224		0,0,4112	no	coding-synonymous	LPHN3	NM_015236.4		0,2,5974	AA,AG,GG		0.0,0.0536,0.0167		4/1470	62363023	2,11950	1864	4112	5976	SO:0001819	synonymous_variant	23284				neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity|sugar binding	g.chr4:62363023G>A	AB018311	CCDS54768.1	4q13.1	2014-08-08				ENSG00000150471		"""-"", ""GPCR / Class B : Orphans"""	20974	protein-coding gene	gene with protein product						10994649	Standard	NM_015236		Approved	KIAA0768, LEC3	uc010ihh.3	Q9HAR2		ENST00000514591.1:c.12G>A	4.37:g.62363023G>A						LPHN3_uc003hcq.4_Silent_p.S4S|LPHN3_uc010ihg.1_Silent_p.S4S	p.S4S	NM_015236	NP_056051	Q9HAR2	LPHN3_HUMAN			0	185	+			4					E9PE04|O94867|Q9NWK5	Silent	SNP	ENST00000514591.1	37	c.12G>A	CCDS54768.1																																																																																				0.348	LPHN3-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000361765.1		
DCK	1633	broad.mit.edu	37	4	71888254	71888254	+	Missense_Mutation	SNP	T	T	G			TCGA-76-4929-01A-01D-1486-08	TCGA-76-4929-10A-01D-1486-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	af4f8b89-837a-48b7-b0e7-12aec23fc285	3e0712a1-b66a-42e7-94a3-07edee7dce2b	g.chr4:71888254T>G	ENST00000286648.5	+	3	775	c.378T>G	c.(376-378)ttT>ttG	p.F126L	DCK_ENST00000504730.1_Missense_Mutation_p.F126L|DCK_ENST00000504952.1_Missense_Mutation_p.F126L	NM_000788.2	NP_000779.1	P27707	DCK_HUMAN	deoxycytidine kinase	126					deoxyribonucleoside monophosphate biosynthetic process (GO:0009157)|nucleobase-containing small molecule metabolic process (GO:0055086)|nucleotide biosynthetic process (GO:0009165)|purine nucleobase metabolic process (GO:0006144)|purine-containing compound salvage (GO:0043101)|pyrimidine nucleobase metabolic process (GO:0006206)|pyrimidine nucleoside salvage (GO:0043097)|pyrimidine nucleotide metabolic process (GO:0006220)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|deoxycytidine kinase activity (GO:0004137)|drug binding (GO:0008144)|nucleoside kinase activity (GO:0019206)|protein homodimerization activity (GO:0042803)			endometrium(2)|large_intestine(3)|lung(3)|ovary(1)	9			Lung(101;0.235)		Cladribine(DB00242)|Clofarabine(DB00631)|Cytarabine(DB00987)|Decitabine(DB01262)|Emtricitabine(DB00879)|Fludarabine(DB01073)|Gemcitabine(DB00441)|Lamivudine(DB00709)|Nelarabine(DB01280)|Pemetrexed(DB00642)|Zalcitabine(DB00943)	TATTATTTTTTGAACGATCTG	0.358																																						uc003hfx.3																			0				endometrium(2)|large_intestine(3)|lung(3)|ovary(1)	9						c.(376-378)ttT>ttG		Homo sapiens deoxycytidine kinase (DCK), mRNA.	Cladribine(DB00242)|Clofarabine(DB00631)|Decitabine(DB01262)|Fludarabine(DB01073)|Gemcitabine(DB00441)|Pemetrexed(DB00642)|Zalcitabine(DB00943)						105.0	107.0	106.0					4																	71888254		2203	4300	6503	SO:0001583	missense	1633				purine base metabolic process|purine-containing compound salvage|pyrimidine base metabolic process|pyrimidine nucleoside salvage|pyrimidine nucleotide metabolic process	cytosol|nucleus	ATP binding|deoxycytidine kinase activity|drug binding|phosphotransferase activity, alcohol group as acceptor|protein homodimerization activity	g.chr4:71888254T>G	M60527	CCDS3548.1	4q13.3-q21.1	2008-02-05			ENSG00000156136	ENSG00000156136	2.7.1.74		2704	protein-coding gene	gene with protein product		125450				8406512	Standard	NM_000788		Approved		uc003hfx.3	P27707	OTTHUMG00000129908	ENST00000286648.5:c.378T>G	4.37:g.71888254T>G	ENSP00000286648:p.Phe126Leu					DCK_uc011cbb.2_Missense_Mutation_p.F54L	p.F126L	NM_000788	NP_000779	P27707	DCK_HUMAN	Lung(101;0.235)		2	666	+			126					B2R8V6|Q5TZY7|Q6FI11	Missense_Mutation	SNP	ENST00000286648.5	37	c.378T>G	CCDS3548.1	.	.	.	.	.	.	.	.	.	.	T	25.2	4.617426	0.87359	.	.	ENSG00000156136	ENST00000286648;ENST00000504730;ENST00000504952	D;D;D	0.93859	-3.3;-3.3;-3.3	5.83	2.19	0.27852	.	0.044381	0.85682	D	0.000000	D	0.92776	0.7703	L	0.41961	1.31	0.58432	D	0.999991	D	0.59767	0.986	P	0.59703	0.862	D	0.89846	0.4006	9	.	.	.	.	9.5337	0.39209	0.0:0.2685:0.0:0.7315	.	126	P27707	DCK_HUMAN	L	126	ENSP00000286648:F126L;ENSP00000425578:F126L;ENSP00000421508:F126L	.	F	+	3	2	DCK	72107118	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	0.579000	0.23788	0.485000	0.27652	0.460000	0.39030	TTT		0.358	DCK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252159.2		
ANXA3	306	broad.mit.edu	37	4	79507428	79507428	+	Silent	SNP	C	C	T	rs144437584		TCGA-76-4929-01A-01D-1486-08	TCGA-76-4929-10A-01D-1486-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	af4f8b89-837a-48b7-b0e7-12aec23fc285	3e0712a1-b66a-42e7-94a3-07edee7dce2b	g.chr4:79507428C>T	ENST00000264908.6	+	6	706	c.327C>T	c.(325-327)aaC>aaT	p.N109N	ANXA3_ENST00000503570.2_Silent_p.N70N|ANXA3_ENST00000512884.1_Silent_p.N70N	NM_005139.2	NP_005130.1	P12429	ANXA3_HUMAN	annexin A3	109					defense response to bacterium (GO:0042742)|neutrophil degranulation (GO:0043312)|phagocytosis (GO:0006909)|positive regulation of angiogenesis (GO:0045766)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)|specific granule (GO:0042581)	calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)|calcium-dependent protein binding (GO:0048306)|phospholipase A2 inhibitor activity (GO:0019834)			NS(1)|breast(1)|kidney(1)|large_intestine(1)|lung(7)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	15						CGGGAACAAACGAAGATGCCT	0.343																																					GBM(2;126 157 27790 28920 42492)	uc003hld.3																			0				NS(1)|breast(1)|kidney(1)|large_intestine(1)|lung(7)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	15						c.(325-327)aaC>aaT		Homo sapiens annexin A3 (ANXA3), mRNA.		C		0,4406		0,0,2203	124.0	122.0	123.0		327	-1.4	1.0	4	dbSNP_134	123	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	ANXA3	NM_005139.2		0,1,6502	TT,TC,CC		0.0116,0.0,0.0077		109/324	79507428	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	306				defense response to bacterium|neutrophil degranulation|phagocytosis|positive regulation of angiogenesis|positive regulation of endothelial cell migration|positive regulation of sequence-specific DNA binding transcription factor activity	phagocytic vesicle membrane|plasma membrane|specific granule	calcium ion binding|calcium-dependent phospholipid binding|phospholipase A2 inhibitor activity	g.chr4:79507428C>T	M63310	CCDS3584.1	4q21.21	2009-07-10			ENSG00000138772	ENSG00000138772	3.1.4.43	"""Annexins"""	541	protein-coding gene	gene with protein product		106490		ANX3		1830024	Standard	XM_005262973		Approved		uc003hld.3	P12429	OTTHUMG00000130198	ENST00000264908.6:c.327C>T	4.37:g.79507428C>T							p.N109N	NM_005139	NP_005130	P12429	ANXA3_HUMAN			5	637	+			109					B2R9W6|Q6LET2	Silent	SNP	ENST00000264908.6	37	c.327C>T	CCDS3584.1																																																																																				0.343	ANXA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252516.3	NM_005139	
FGG	2266	broad.mit.edu	37	4	155529787	155529787	+	Missense_Mutation	SNP	C	C	T			TCGA-76-4929-01A-01D-1486-08	TCGA-76-4929-10A-01D-1486-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	af4f8b89-837a-48b7-b0e7-12aec23fc285	3e0712a1-b66a-42e7-94a3-07edee7dce2b	g.chr4:155529787C>T	ENST00000336098.3	-	7	720	c.682G>A	c.(682-684)Gta>Ata	p.V228I	FGG_ENST00000404648.3_Missense_Mutation_p.V228I|FGG_ENST00000405164.1_Missense_Mutation_p.V236I|FGG_ENST00000407946.1_Missense_Mutation_p.V236I	NM_021870.2	NP_068656.2	P02679	FIBG_HUMAN	fibrinogen gamma chain	228	Fibrinogen C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00739}.				blood coagulation (GO:0007596)|cell-matrix adhesion (GO:0007160)|cellular protein complex assembly (GO:0043623)|extracellular matrix organization (GO:0030198)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|platelet degranulation (GO:0002576)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of exocytosis (GO:0045921)|positive regulation of heterotypic cell-cell adhesion (GO:0034116)|positive regulation of peptide hormone secretion (GO:0090277)|positive regulation of protein secretion (GO:0050714)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|positive regulation of vasoconstriction (GO:0045907)|protein polymerization (GO:0051258)|response to calcium ion (GO:0051592)|signal transduction (GO:0007165)	blood microparticle (GO:0072562)|cell cortex (GO:0005938)|cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|fibrinogen complex (GO:0005577)|plasma membrane (GO:0005886)|platelet alpha granule (GO:0031091)|platelet alpha granule lumen (GO:0031093)	cell adhesion molecule binding (GO:0050839)|metal ion binding (GO:0046872)|receptor binding (GO:0005102)|structural molecule activity (GO:0005198)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(9)|prostate(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	27	all_hematologic(180;0.215)	Renal(120;0.0458)			Sucralfate(DB00364)	TTGAAATCTACACTGCCATCA	0.343																																						uc003ioj.3																			0				breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(9)|prostate(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	27						c.(682-684)Gta>Ata		Homo sapiens fibrinogen gamma chain (FGG), transcript variant gamma-B, mRNA.	Sucralfate(DB00364)						77.0	79.0	78.0					4																	155529787		2203	4299	6502	SO:0001583	missense	2266				platelet activation|platelet degranulation|protein polymerization|response to calcium ion|signal transduction	external side of plasma membrane|fibrinogen complex|platelet alpha granule lumen	eukaryotic cell surface binding|protein binding, bridging|receptor binding	g.chr4:155529787C>T		CCDS3788.1, CCDS47153.1	4q28	2014-09-17			ENSG00000171557	ENSG00000171557		"""Fibrinogen C domain containing"", ""Endogenous ligands"""	3694	protein-coding gene	gene with protein product		134850	"""fibrinogen, gamma polypeptide"""				Standard	NM_000509		Approved		uc003ioj.3	P02679	OTTHUMG00000150329	ENST00000336098.3:c.682G>A	4.37:g.155529787C>T	ENSP00000336829:p.Val228Ile					FGG_uc003iog.3_Missense_Mutation_p.V228I	p.V228I	NM_021870	NP_068656	P02679	FIBG_HUMAN			6	823	-	all_hematologic(180;0.215)	Renal(120;0.0458)	228			Fibrinogen C-terminal.		A8K057|P04469|P04470|Q53Y18|Q96A14|Q96KJ3|Q9UC62|Q9UC63|Q9UCF3	Missense_Mutation	SNP	ENST00000336098.3	37	c.682G>A	CCDS3788.1	.	.	.	.	.	.	.	.	.	.	C	17.52	3.409405	0.62399	.	.	ENSG00000171557	ENST00000404648;ENST00000405164;ENST00000336098;ENST00000407946	D;D;D;D	0.97455	-4.39;-4.39;-4.39;-4.39	6.17	-12.3	0.00002	Fibrinogen, alpha/beta/gamma chain, C-terminal globular (4);Fibrinogen, alpha/beta/gamma chain, C-terminal globular, subdomain 1 (1);	1.021490	0.07785	N	0.953925	D	0.95456	0.8524	M	0.73430	2.235	0.09310	N	0.999998	B;P;P;B;B	0.36974	0.231;0.506;0.576;0.433;0.379	B;B;B;B;B	0.40285	0.093;0.295;0.325;0.205;0.157	D	0.88974	0.3403	10	0.66056	D	0.02	.	15.4059	0.74877	0.5017:0.1474:0.3509:0.0	.	125;236;228;236;228	D3DP16;C9JC84;P02679;C9JEU5;P02679-2	.;.;FIBG_HUMAN;.;.	I	228;236;228;236	ENSP00000384860:V228I;ENSP00000384101:V236I;ENSP00000336829:V228I;ENSP00000384552:V236I	ENSP00000336829:V228I	V	-	1	0	FGG	155749237	0.000000	0.05858	0.006000	0.13384	0.944000	0.59088	-0.233000	0.09041	-2.101000	0.00846	-0.165000	0.13383	GTA		0.343	FGG-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000317581.1	NM_021870	
PLEKHG4B	153478	broad.mit.edu	37	5	181778	181778	+	Missense_Mutation	SNP	G	G	A	rs114040866		TCGA-76-4929-01A-01D-1486-08	TCGA-76-4929-10A-01D-1486-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	af4f8b89-837a-48b7-b0e7-12aec23fc285	3e0712a1-b66a-42e7-94a3-07edee7dce2b	g.chr5:181778G>A	ENST00000283426.6	+	17	3534	c.3484G>A	c.(3484-3486)Gtc>Atc	p.V1162I		NM_052909.3	NP_443141.3	Q96PX9	PKH4B_HUMAN	pleckstrin homology domain containing, family G (with RhoGef domain) member 4B	1162							Rho guanyl-nucleotide exchange factor activity (GO:0005089)			endometrium(1)|large_intestine(2)|lung(2)|prostate(3)|skin(3)	11			all cancers(22;0.0253)|Lung(60;0.113)	Kidney(1;0.119)		CGACAGCATCGTCAAGGGCAC	0.637																																						uc003jak.2																			0				endometrium(1)|large_intestine(2)|lung(2)|prostate(3)|skin(3)	11						c.(3484-3486)Gtc>Atc		Homo sapiens pleckstrin homology domain containing, family G (with RhoGef domain) member 4B (PLEKHG4B), mRNA.							97.0	89.0	92.0					5																	181778		2203	4300	6503	SO:0001583	missense	153478				regulation of Rho protein signal transduction	intracellular	Rho guanyl-nucleotide exchange factor activity	g.chr5:181778G>A	BC008352	CCDS34124.1	5p15.33	2013-01-11			ENSG00000153404	ENSG00000153404		"""Pleckstrin homology (PH) domain containing"""	29399	protein-coding gene	gene with protein product						11572484	Standard	NM_052909		Approved	KIAA1909	uc003jak.2	Q96PX9	OTTHUMG00000161570	ENST00000283426.6:c.3484G>A	5.37:g.181778G>A	ENSP00000283426:p.Val1162Ile						p.V1162I	NM_052909	NP_443141	Q96PX9	PKH4B_HUMAN	all cancers(22;0.0253)|Lung(60;0.113)	Kidney(1;0.119)	16	3534	+			1162						Missense_Mutation	SNP	ENST00000283426.6	37	c.3484G>A	CCDS34124.1	.	.	.	.	.	.	.	.	.	.	G	6.800	0.516575	0.12944	.	.	ENSG00000153404	ENST00000283426	T	0.27720	1.65	2.51	-2.93	0.05598	.	.	.	.	.	T	0.14830	0.0358	N	0.22421	0.69	0.09310	N	0.999996	B	0.10296	0.003	B	0.04013	0.001	T	0.27157	-1.0082	9	0.23302	T	0.38	.	3.2299	0.06745	0.4867:0.2187:0.2946:0.0	.	1162	Q96PX9	PKH4B_HUMAN	I	1162	ENSP00000283426:V1162I	ENSP00000283426:V1162I	V	+	1	0	PLEKHG4B	234778	1.000000	0.71417	0.000000	0.03702	0.006000	0.05464	1.376000	0.34306	-0.660000	0.05352	-0.550000	0.04213	GTC		0.637	PLEKHG4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365359.1	NM_052909	
BASP1	10409	broad.mit.edu	37	5	17275370	17275370	+	Silent	SNP	C	C	T			TCGA-76-4929-01A-01D-1486-08	TCGA-76-4929-10A-01D-1486-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	af4f8b89-837a-48b7-b0e7-12aec23fc285	3e0712a1-b66a-42e7-94a3-07edee7dce2b	g.chr5:17275370C>T	ENST00000322611.3	+	2	305	c.45C>T	c.(43-45)aaC>aaT	p.N15N		NM_001271606.1|NM_006317.3	NP_001258535.1|NP_006308.3	P80723	BASP1_HUMAN	brain abundant, membrane attached signal protein 1	15					diaphragm development (GO:0060539)|glomerular visceral epithelial cell differentiation (GO:0072112)|gonad development (GO:0008406)|mesenchymal to epithelial transition (GO:0060231)|metanephric mesenchyme development (GO:0072075)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of heart growth (GO:0060421)|positive regulation of metanephric ureteric bud development (GO:2001076)|substantia nigra development (GO:0021762)|thorax and anterior abdomen determination (GO:0007356)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|vesicle (GO:0031982)	protein domain specific binding (GO:0019904)|transcription corepressor activity (GO:0003714)|transcription regulatory region DNA binding (GO:0044212)			endometrium(1)|lung(8)	9						ACAATGTGAACGACGAGAAAG	0.567																																						uc003jfx.3																			0				endometrium(1)|lung(8)	9						c.(43-45)aaC>aaT		Homo sapiens brain abundant, membrane attached signal protein 1 (BASP1), mRNA.							44.0	48.0	47.0					5																	17275370		2197	4284	6481	SO:0001819	synonymous_variant	10409				glomerular visceral epithelial cell differentiation|negative regulation of transcription, DNA-dependent	cytoplasm|cytoskeleton|growth cone|nuclear speck|plasma membrane	protein domain specific binding|transcription corepressor activity|transcription regulatory region DNA binding	g.chr5:17275370C>T	AF039656	CCDS3888.1	5p15.1	2010-12-03			ENSG00000176788	ENSG00000176788			957	protein-coding gene	gene with protein product		605940				9310187, 9749536	Standard	NM_001271606		Approved	NAP-22, NAP22, CAP23, CAP-23	uc031siz.1	P80723	OTTHUMG00000131061	ENST00000322611.3:c.45C>T	5.37:g.17275370C>T						BASP1_uc021xws.1_Silent_p.N15N	p.N15N	NM_006317	NP_006308	P80723	BASP1_HUMAN			1	224	+			15					B4DJA8|D3DTD5|O43596|Q5U0S0|Q9BWA5	Silent	SNP	ENST00000322611.3	37	c.45C>T	CCDS3888.1																																																																																				0.567	BASP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253716.2		
CDH18	1016	broad.mit.edu	37	5	19721516	19721516	+	Missense_Mutation	SNP	C	C	T			TCGA-76-4929-01A-01D-1486-08	TCGA-76-4929-10A-01D-1486-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	af4f8b89-837a-48b7-b0e7-12aec23fc285	3e0712a1-b66a-42e7-94a3-07edee7dce2b	g.chr5:19721516C>T	ENST00000507958.1	-	7	1573	c.583G>A	c.(583-585)Gct>Act	p.A195T	CDH18_ENST00000511273.1_Missense_Mutation_p.A195T|CDH18_ENST00000502796.1_Missense_Mutation_p.A195T|CDH18_ENST00000506372.1_Missense_Mutation_p.A195T|CDH18_ENST00000274170.4_Missense_Mutation_p.A195T|CDH18_ENST00000382275.1_Missense_Mutation_p.A195T			Q13634	CAD18_HUMAN	cadherin 18, type 2	195	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				adherens junction organization (GO:0034332)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.A195T(1)		breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(24)|lung(76)|ovary(5)|prostate(4)|skin(6)|upper_aerodigestive_tract(1)	138	Lung NSC(1;0.00734)|all_lung(1;0.0197)					ACCACCCGAGCGCTGTTTCCA	0.463																																						uc003jgd.3																			1	Substitution - Missense(1)	p.A195T(2)|p.S194R(1)	ovary(1)	breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(24)|lung(76)|ovary(5)|prostate(4)|skin(6)|upper_aerodigestive_tract(1)	138						c.(583-585)Gct>Act		Homo sapiens cadherin 18, type 2 (CDH18), transcript variant 1, mRNA.							153.0	136.0	142.0					5																	19721516		2203	4300	6503	SO:0001583	missense	1016				adherens junction organization|cell junction assembly|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding	g.chr5:19721516C>T	U59325	CCDS3889.1, CCDS54835.1, CCDS75229.1	5p14.3	2010-01-26			ENSG00000145526	ENSG00000145526		"""Cadherins / Major cadherins"""	1757	protein-coding gene	gene with protein product		603019				9030594, 10191097	Standard	NM_004934		Approved	CDH14, EY-CADHERIN	uc003jgd.3	Q13634	OTTHUMG00000090578	ENST00000507958.1:c.583G>A	5.37:g.19721516C>T	ENSP00000425093:p.Ala195Thr					CDH18_uc011cnm.2_Missense_Mutation_p.A195T|CDH18_uc003jgc.3_Missense_Mutation_p.A195T|CDH18_uc021xwu.1_Missense_Mutation_p.A195T	p.A195T	NM_004934	NP_004925	Q13634	CAD18_HUMAN			4	1117	-	Lung NSC(1;0.00734)|all_lung(1;0.0197)		195			Cadherin 2.		A8K0I2|B4DHG6|Q8N5Z2	Missense_Mutation	SNP	ENST00000507958.1	37	c.583G>A	CCDS3889.1	.	.	.	.	.	.	.	.	.	.	C	36	5.694576	0.96793	.	.	ENSG00000145526	ENST00000382275;ENST00000507958;ENST00000542864;ENST00000274170;ENST00000506372;ENST00000502796;ENST00000515257;ENST00000511273	T;T;T;T;T;T;T	0.60797	0.16;0.16;0.16;0.16;0.16;0.16;0.16	5.5	5.5	0.81552	Cadherin (4);Cadherin-like (1);	0.000000	0.85682	D	0.000000	T	0.77942	0.4206	M	0.80847	2.515	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.999;1.0	T	0.78863	-0.2036	9	.	.	.	.	17.9639	0.89094	0.0:1.0:0.0:0.0	.	195;195	B4DHG6;Q13634	.;CAD18_HUMAN	T	195;195;195;195;195;195;141;195	ENSP00000371710:A195T;ENSP00000425093:A195T;ENSP00000274170:A195T;ENSP00000424931:A195T;ENSP00000422138:A195T;ENSP00000427383:A141T;ENSP00000425854:A195T	.	A	-	1	0	CDH18	19757273	1.000000	0.71417	0.900000	0.35374	0.910000	0.53928	7.764000	0.85297	2.571000	0.86741	0.650000	0.86243	GCT		0.463	CDH18-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366747.1	NM_004934	
PIK3R1	5295	broad.mit.edu	37	5	67575468	67575468	+	Frame_Shift_Del	DEL	G	G	-	rs143572224		TCGA-76-4929-01A-01D-1486-08	TCGA-76-4929-10A-01D-1486-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	af4f8b89-837a-48b7-b0e7-12aec23fc285	3e0712a1-b66a-42e7-94a3-07edee7dce2b	g.chr5:67575468delG	ENST00000521381.1	+	5	1157	c.541delG	c.(541-543)gttfs	p.V181fs	PIK3R1_ENST00000396611.1_Frame_Shift_Del_p.V181fs|PIK3R1_ENST00000274335.5_Frame_Shift_Del_p.V181fs|PIK3R1_ENST00000521657.1_Frame_Shift_Del_p.V181fs	NM_181523.2	NP_852664.1	P27986	P85A_HUMAN	phosphoinositide-3-kinase, regulatory subunit 1 (alpha)	181	Rho-GAP. {ECO:0000255|PROSITE- ProRule:PRU00172}.				B cell differentiation (GO:0030183)|blood coagulation (GO:0007596)|cellular response to UV (GO:0034644)|epidermal growth factor receptor signaling pathway (GO:0007173)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|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)|growth hormone receptor signaling pathway (GO:0060396)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|insulin-like growth factor receptor signaling pathway (GO:0048009)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|leukocyte migration (GO:0050900)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of osteoclast differentiation (GO:0045671)|neurotrophin TRK receptor signaling pathway (GO:0048011)|NFAT protein import into nucleus (GO:0051531)|phosphatidylinositol 3-kinase signaling (GO:0014065)|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 cell migration (GO:0030335)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of glucose import (GO:0046326)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tumor necrosis factor production (GO:0032760)|protein phosphorylation (GO:0006468)|regulation of phosphatidylinositol 3-kinase activity (GO:0043551)|small molecule metabolic process (GO:0044281)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|viral process (GO:0016032)	1-phosphatidylinositol-4-phosphate 3-kinase, class IA complex (GO:0005943)|cell-cell junction (GO:0005911)|cytosol (GO:0005829)|membrane (GO:0016020)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	ErbB-3 class receptor binding (GO:0043125)|insulin binding (GO:0043559)|insulin receptor binding (GO:0005158)|insulin receptor substrate binding (GO:0043560)|insulin-like growth factor receptor binding (GO:0005159)|neurotrophin TRKA receptor binding (GO:0005168)|phosphatidylinositol 3-kinase binding (GO:0043548)|phosphatidylinositol 3-kinase regulator activity (GO:0035014)|protein phosphatase binding (GO:0019903)|transmembrane receptor protein tyrosine kinase adaptor activity (GO:0005068)	p.0?(1)|p.?(1)		breast(12)|central_nervous_system(31)|cervix(1)|endometrium(68)|haematopoietic_and_lymphoid_tissue(5)|kidney(1)|large_intestine(32)|lung(10)|ovary(9)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	178		Lung NSC(167;1.99e-05)|Prostate(74;0.00308)|Ovarian(174;0.00473)|Colorectal(97;0.0176)		OV - Ovarian serous cystadenocarcinoma(47;3.76e-51)|Lung(70;0.0211)	Isoprenaline(DB01064)	CGATGTGCACGTTTTGGCTGA	0.393			"""Mis, F, O"""		"""gliobastoma, ovarian, colorectal"""					TCGA GBM(4;<1E-08)																												uc003jva.3				Rec	yes		5	5q13.1	5295	"""Mis, F, O"""	"""phosphoinositide-3-kinase, regulatory subunit 1 (alpha)"""			"""E, O"""			"""gliobastoma, ovarian, colorectal"""		2	Whole gene deletion(1)|Unknown(1)	p.0?(1)|p.?(1)	large_intestine(1)|lung(1)	breast(12)|central_nervous_system(31)|cervix(1)|endometrium(68)|haematopoietic_and_lymphoid_tissue(5)|kidney(1)|large_intestine(32)|lung(10)|ovary(9)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	178						c.(541-543)gttfs		Homo sapiens phosphoinositide-3-kinase, regulatory subunit 1 (alpha) (PIK3R1), transcript variant 1, mRNA.	Isoproterenol(DB01064)						149.0	137.0	141.0					5																	67575468		2203	4300	6503	SO:0001589	frameshift_variant	5295				epidermal growth factor receptor signaling pathway|fibroblast growth factor receptor signaling pathway|growth hormone receptor signaling pathway|insulin receptor signaling pathway|insulin-like growth factor receptor signaling pathway|interspecies interaction between organisms|leukocyte migration|nerve growth factor receptor signaling pathway|phosphatidylinositol 3-kinase cascade|phosphatidylinositol phosphorylation|phosphatidylinositol-mediated signaling|platelet activation|positive regulation of establishment of protein localization in plasma membrane|positive regulation of glucose import|T cell costimulation|T cell receptor signaling pathway	1-phosphatidylinositol-4-phosphate 3-kinase, class IA complex	1-phosphatidylinositol binding|ErbB-3 class receptor binding|insulin binding|insulin receptor binding|insulin receptor substrate binding|insulin-like growth factor receptor binding|phosphatidylinositol 3-kinase regulator activity|protein phosphatase binding	g.chr5:67575468delG	M61906	CCDS3993.1, CCDS3994.1, CCDS3995.1, CCDS56374.1	5q13.1	2014-09-17	2008-02-04		ENSG00000145675	ENSG00000145675		"""SH2 domain containing"""	8979	protein-coding gene	gene with protein product		171833				1314371, 18387942	Standard	NM_181524		Approved	GRB1, p85-ALPHA, p85	uc003jva.3	P27986	OTTHUMG00000131251	ENST00000521381.1:c.541delG	5.37:g.67575468delG	ENSP00000428056:p.Val181fs	TCGA GBM(4;<1E-08)					p.V181fs	NM_181523	NP_852664	P27986	P85A_HUMAN		OV - Ovarian serous cystadenocarcinoma(47;3.76e-51)|Lung(70;0.0211)	4	1121	+		Lung NSC(167;1.99e-05)|Prostate(74;0.00308)|Ovarian(174;0.00473)|Colorectal(97;0.0176)	181			Rho-GAP.		B3KT19|D3DWA0|E7EX19|Q15747|Q4VBZ7|Q53EM6|Q8IXA2|Q8N1C5	Frame_Shift_Del	DEL	ENST00000521381.1	37	c.541delG	CCDS3993.1																																																																																				0.393	PIK3R1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254013.2	NM_181504	
POU5F2	134187	broad.mit.edu	37	5	93077142	93077142	+	Missense_Mutation	SNP	C	C	T	rs181777565	byFrequency	TCGA-76-4929-01A-01D-1486-08	TCGA-76-4929-10A-01D-1486-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	af4f8b89-837a-48b7-b0e7-12aec23fc285	3e0712a1-b66a-42e7-94a3-07edee7dce2b	g.chr5:93077142C>T	ENST00000510627.4	-	1	201	c.128G>A	c.(127-129)aGg>aAg	p.R43K	RP11-185E12.2_ENST00000606528.1_RNA|FAM172A_ENST00000509163.1_Intron|FAM172A_ENST00000509739.1_Intron|FAM172A_ENST00000505869.1_Intron|POU5F2_ENST00000606183.1_5'Flank|FAM172A_ENST00000395965.3_Intron	NM_153216.1	NP_694948.1	Q8N7G0	PO5F2_HUMAN	POU domain class 5, transcription factor 2	43					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)						all_cancers(142;3.87e-05)|all_epithelial(76;4.59e-07)|all_lung(232;0.0126)|Lung NSC(167;0.0155)|Ovarian(174;0.0218)|Prostate(281;0.173)|Colorectal(57;0.19)		UCEC - Uterine corpus endometrioid carcinoma (5;0.0415)|all cancers(79;2.03e-19)		GACCATCACCCTGCCAGGGGC	0.687													C|||	8	0.00159744	0.0	0.0	5008	,	,		14499	0.0079		0.0	False		,,,				2504	0.0					uc003kkl.1																			0											c.(127-129)aGg>aAg		Homo sapiens POU domain class 5, transcription factor 2 (POU5F2), mRNA.							18.0	22.0	21.0					5																	93077142		1926	4120	6046	SO:0001583	missense	134187					nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity	g.chr5:93077142C>T		CCDS59489.1	5q15	2011-06-20				ENSG00000248483		"""Homeoboxes / POU class"""	26367	protein-coding gene	gene with protein product						7908264	Standard	NM_153216		Approved	SPRM-1, FLJ25680	uc003kkl.1	Q8N7G0		ENST00000510627.4:c.128G>A	5.37:g.93077142C>T	ENSP00000464890:p.Arg43Lys					FAM172A_uc010jbd.3_Intron|FAM172A_uc011cuf.2_Intron|FAM172A_uc011cug.2_Intron|FAM172A_uc011cuh.2_Intron|FAM172A_uc011cui.2_Intron|FAM172A_uc011cuj.2_Intron	p.R43K	NM_153216	NP_694948	Q8N7G0	PO5F2_HUMAN		UCEC - Uterine corpus endometrioid carcinoma (5;0.0415)|all cancers(79;2.03e-19)	0	168	-		all_cancers(142;3.87e-05)|all_epithelial(76;4.59e-07)|all_lung(232;0.0126)|Lung NSC(167;0.0155)|Ovarian(174;0.0218)|Prostate(281;0.173)|Colorectal(57;0.19)	43					Q15169|Q6MZL7|Q8N748	Missense_Mutation	SNP	ENST00000510627.4	37	c.128G>A	CCDS59489.1																																																																																				0.687	POU5F2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369873.5	NM_153216	
FTMT	94033	broad.mit.edu	37	5	121187720	121187720	+	Missense_Mutation	SNP	C	C	T			TCGA-76-4929-01A-01D-1486-08	TCGA-76-4929-10A-01D-1486-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	af4f8b89-837a-48b7-b0e7-12aec23fc285	3e0712a1-b66a-42e7-94a3-07edee7dce2b	g.chr5:121187720C>T	ENST00000321339.1	+	1	71	c.62C>T	c.(61-63)cCg>cTg	p.P21L		NM_177478.1	NP_803431.1	Q8N4E7	FTMT_HUMAN	ferritin mitochondrial	21					cellular iron ion homeostasis (GO:0006879)|iron ion transport (GO:0006826)|positive regulation of cell proliferation (GO:0008284)|positive regulation of lyase activity (GO:0051349)|positive regulation of oxidoreductase activity (GO:0051353)|positive regulation of transferase activity (GO:0051347)	mitochondrion (GO:0005739)|nucleus (GO:0005634)	ferric iron binding (GO:0008199)|ferroxidase activity (GO:0004322)			NS(1)|breast(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(15)|ovary(1)|skin(4)|upper_aerodigestive_tract(1)	33		all_cancers(142;0.0124)|Prostate(80;0.0322)	KIRC - Kidney renal clear cell carcinoma(527;0.206)	Epithelial(69;0.000171)|OV - Ovarian serous cystadenocarcinoma(64;0.000188)|all cancers(49;0.0027)		TCTCTGCGCCCGGTGCGCTGC	0.736																																						uc003kss.3																			0		p.R20C(1)|p.R20S(1)		NS(1)|breast(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(15)|ovary(1)|skin(4)|upper_aerodigestive_tract(1)	33						c.(61-63)cCg>cTg		Homo sapiens ferritin mitochondrial (FTMT), nuclear gene encoding mitochondrial protein, mRNA.							17.0	20.0	19.0					5																	121187720		2200	4295	6495	SO:0001583	missense	94033				cellular iron ion homeostasis|iron ion transport|positive regulation of cell proliferation|positive regulation of lyase activity|positive regulation of oxidoreductase activity|positive regulation of transferase activity	mitochondrion	ferric iron binding|ferroxidase activity	g.chr5:121187720C>T	BC034419	CCDS4128.1	5q23.1	2008-02-05			ENSG00000181867	ENSG00000181867			17345	protein-coding gene	gene with protein product		608847				11323407	Standard	NM_177478		Approved	MtF	uc003kss.3	Q8N4E7	OTTHUMG00000128912	ENST00000321339.1:c.62C>T	5.37:g.121187720C>T	ENSP00000313691:p.Pro21Leu						p.P21L	NM_177478	NP_803431	Q8N4E7	FTMT_HUMAN	KIRC - Kidney renal clear cell carcinoma(527;0.206)	Epithelial(69;0.000171)|OV - Ovarian serous cystadenocarcinoma(64;0.000188)|all cancers(49;0.0027)	0	71	+		all_cancers(142;0.0124)|Prostate(80;0.0322)	21						Missense_Mutation	SNP	ENST00000321339.1	37	c.62C>T	CCDS4128.1	.	.	.	.	.	.	.	.	.	.	C	9.132	1.011685	0.19277	.	.	ENSG00000181867	ENST00000321339	T	0.62498	0.02	2.95	0.00785	0.14072	.	.	.	.	.	T	0.34164	0.0888	N	0.14661	0.345	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.15263	-1.0443	9	0.13853	T	0.58	.	1.3672	0.02203	0.1376:0.2334:0.4168:0.2122	.	21	Q8N4E7	FTMT_HUMAN	L	21	ENSP00000313691:P21L	ENSP00000313691:P21L	P	+	2	0	FTMT	121215619	0.001000	0.12720	0.000000	0.03702	0.000000	0.00434	0.748000	0.26305	-0.026000	0.13895	-0.171000	0.13296	CCG		0.736	FTMT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250884.1	NM_177478	
SLU7	10569	broad.mit.edu	37	5	159842130	159842130	+	Splice_Site	DEL	A	A	-			TCGA-76-4929-01A-01D-1486-08	TCGA-76-4929-10A-01D-1486-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	af4f8b89-837a-48b7-b0e7-12aec23fc285	3e0712a1-b66a-42e7-94a3-07edee7dce2b	g.chr5:159842130delA	ENST00000297151.4	-	2	558		c.e2+1			NM_006425.4	NP_006416.3	O95391	SLU7_HUMAN	SLU7 splicing factor homolog (S. cerevisiae)						alternative mRNA splicing, via spliceosome (GO:0000380)|cellular response to heat (GO:0034605)|intracellular protein transport (GO:0006886)|mRNA 3'-splice site recognition (GO:0000389)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing, via transesterification reactions (GO:0000375)	catalytic step 2 spliceosome (GO:0071013)|cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|small nuclear ribonucleoprotein complex (GO:0030532)|spliceosomal complex (GO:0005681)	pre-mRNA 3'-splice site binding (GO:0030628)|second spliceosomal transesterification activity (GO:0000386)|zinc ion binding (GO:0008270)			endometrium(4)|kidney(5)|large_intestine(4)|lung(6)|ovary(1)	20	Renal(175;0.00196)	Medulloblastoma(196;0.0354)|all_neural(177;0.116)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			TTAAGTACTTACTTTCCTTCT	0.358																																						uc003lyg.3																			0				endometrium(4)|kidney(5)|large_intestine(4)|lung(6)|ovary(1)	20						c.e2+1		Homo sapiens SLU7 splicing factor homolog (S. cerevisiae) (SLU7), mRNA.							129.0	131.0	130.0					5																	159842130		2203	4300	6503	SO:0001630	splice_region_variant	10569				alternative nuclear mRNA splicing, via spliceosome|nuclear mRNA 3'-splice site recognition	catalytic step 2 spliceosome|cytoplasm|nuclear speck|small nuclear ribonucleoprotein complex	pre-mRNA 3'-splice site binding|second spliceosomal transesterification activity|zinc ion binding	g.chr5:159842130delA	AF101074	CCDS4352.1	5q33.3	2010-04-13			ENSG00000164609	ENSG00000164609			16939	protein-coding gene	gene with protein product	zinc knuckle motif containing	605974				10197984, 15728250	Standard	NM_006425		Approved	9G8	uc003lyg.3	O95391	OTTHUMG00000130324	ENST00000297151.4:c.170+1T>-	5.37:g.159842130delA						SLU7_uc003lyh.1_Splice_Site_p.K57_splice|SLU7_uc003lyi.1_Splice_Site_p.K57_splice	p.K57_splice	NM_006425	NP_006416	O95391	SLU7_HUMAN	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)		2	325	-	Renal(175;0.00196)	Medulloblastoma(196;0.0354)|all_neural(177;0.116)	57					D3DQK2|Q3LUJ0|Q3LUJ1|Q6RXQ5|Q96FM9	Splice_Site	DEL	ENST00000297151.4	37	c.170_splice	CCDS4352.1																																																																																				0.358	SLU7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252673.1	NM_006425	Intron
GABRB2	2561	broad.mit.edu	37	5	160721269	160721269	+	Missense_Mutation	SNP	C	C	T	rs371728438		TCGA-76-4929-01A-01D-1486-08	TCGA-76-4929-10A-01D-1486-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	af4f8b89-837a-48b7-b0e7-12aec23fc285	3e0712a1-b66a-42e7-94a3-07edee7dce2b	g.chr5:160721269C>T	ENST00000393959.1	-	10	1357	c.1358G>A	c.(1357-1359)cGa>cAa	p.R453Q	GABRB2_ENST00000517547.1_Missense_Mutation_p.R255Q|GABRB2_ENST00000520240.1_Missense_Mutation_p.R415Q|GABRB2_ENST00000353437.6_Missense_Mutation_p.R415Q|GABRB2_ENST00000274547.2_Missense_Mutation_p.R453Q|GABRB2_ENST00000517901.1_Missense_Mutation_p.R352Q			P47870	GBRB2_HUMAN	gamma-aminobutyric acid (GABA) A receptor, beta 2	453					cellular response to histamine (GO:0071420)|chloride transmembrane transport (GO:1902476)|cochlea development (GO:0090102)|gamma-aminobutyric acid signaling pathway (GO:0007214)|inner ear receptor cell development (GO:0060119)|innervation (GO:0060384)|ion transmembrane transport (GO:0034220)|negative regulation of neuron apoptotic process (GO:0043524)|sensory perception of sound (GO:0007605)|synaptic transmission (GO:0007268)|synaptic transmission, GABAergic (GO:0051932)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|GABA-A receptor complex (GO:1902711)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	chloride channel activity (GO:0005254)|GABA-A receptor activity (GO:0004890)|inhibitory extracellular ligand-gated ion channel activity (GO:0005237)			breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(6)|liver(1)|lung(9)|soft_tissue(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	26	Renal(175;0.00259)	Medulloblastoma(196;0.021)|all_neural(177;0.0463)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)		Acamprosate(DB00659)|Adinazolam(DB00546)|Alprazolam(DB00404)|Amoxapine(DB00543)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Chlordiazepoxide(DB00475)|Cinolazepam(DB01594)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Clotiazepam(DB01559)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Fludiazepam(DB01567)|Flumazenil(DB01205)|Flurazepam(DB00690)|Fospropofol(DB06716)|Ginkgo biloba(DB01381)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Isoflurane(DB00753)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Topiramate(DB00273)|Triazolam(DB00897)	CAGAGCATTTCGGCCAAAACT	0.532																																						uc003lys.1																			0				breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(6)|liver(1)|lung(9)|soft_tissue(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	26						c.(1357-1359)cGa>cAa		Homo sapiens gamma-aminobutyric acid (GABA) A receptor, beta 2 (GABRB2), transcript variant 1, mRNA.	Ethchlorvynol(DB00189)|Flurazepam(DB00690)|Lorazepam(DB00186)|Midazolam(DB00683)	C	GLN/ARG,GLN/ARG	0,4406		0,0,2203	107.0	95.0	99.0		1244,1358	5.7	1.0	5		99	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	GABRB2	NM_000813.2,NM_021911.2	43,43	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	benign,benign	415/475,453/513	160721269	1,13005	2203	4300	6503	SO:0001583	missense	2561				gamma-aminobutyric acid signaling pathway|synaptic transmission	cell junction|chloride channel complex|integral to plasma membrane|postsynaptic membrane	chloride channel activity|GABA-A receptor activity	g.chr5:160721269C>T		CCDS4354.1, CCDS4355.1	5q34	2012-06-22			ENSG00000145864	ENSG00000145864		"""GABA receptors"", ""Ligand-gated ion channels / GABA(A) receptors"""	4082	protein-coding gene	gene with protein product	"""GABA(A) receptor, beta 2"""	600232				7851879	Standard	NM_000813		Approved		uc003lys.1	P47870	OTTHUMG00000130349	ENST00000393959.1:c.1358G>A	5.37:g.160721269C>T	ENSP00000377531:p.Arg453Gln					GABRB2_uc011deh.1_Missense_Mutation_p.R254Q|GABRB2_uc003lyr.1_Missense_Mutation_p.R415Q|GABRB2_uc003lyt.1_Missense_Mutation_p.R415Q	p.R453Q	NM_021911	NP_068711	P47870	GBRB2_HUMAN	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)		10	1576	-	Renal(175;0.00259)	Medulloblastoma(196;0.021)|all_neural(177;0.0463)	453					A8K115|A8K1A0|D1LYT0|D1LYT1|Q16323|Q4FZB2	Missense_Mutation	SNP	ENST00000393959.1	37	c.1358G>A	CCDS4355.1	.	.	.	.	.	.	.	.	.	.	C	23.4	4.417304	0.83449	0.0	1.16E-4	ENSG00000145864	ENST00000393959;ENST00000274547;ENST00000353437;ENST00000520240;ENST00000517901;ENST00000517547	D;D;D;D;D;D	0.85556	-2.0;-2.0;-1.87;-1.87;-1.87;-1.87	5.74	5.74	0.90152	Neurotransmitter-gated ion-channel transmembrane domain (2);	0.463565	0.23088	N	0.052073	D	0.89118	0.6624	L	0.39898	1.24	0.51767	D	0.999936	B;B;D;B	0.71674	0.373;0.037;0.998;0.05	B;B;D;B	0.67382	0.071;0.009;0.951;0.026	D	0.86345	0.1707	10	0.29301	T	0.29	.	19.9252	0.97100	0.0:1.0:0.0:0.0	.	255;352;453;415	B7Z279;E7EV50;P47870;P47870-1	.;.;GBRB2_HUMAN;.	Q	453;453;415;415;352;255	ENSP00000377531:R453Q;ENSP00000274547:R453Q;ENSP00000274546:R415Q;ENSP00000429320:R415Q;ENSP00000430532:R352Q;ENSP00000429750:R255Q	ENSP00000274547:R453Q	R	-	2	0	GABRB2	160653847	0.942000	0.31987	0.997000	0.53966	0.985000	0.73830	2.100000	0.41777	2.715000	0.92844	0.650000	0.86243	CGA		0.532	GABRB2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252704.1		
FKBPL	63943	broad.mit.edu	37	6	32097113	32097113	+	Missense_Mutation	SNP	C	C	T			TCGA-76-4929-01A-01D-1486-08	TCGA-76-4929-10A-01D-1486-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	af4f8b89-837a-48b7-b0e7-12aec23fc285	3e0712a1-b66a-42e7-94a3-07edee7dce2b	g.chr6:32097113C>T	ENST00000375156.3	-	2	715	c.445G>A	c.(445-447)Ggg>Agg	p.G149R	ATF6B_ENST00000375203.3_5'Flank|ATF6B_ENST00000375201.4_5'Flank|ATF6B_ENST00000468502.1_5'Flank	NM_022110.3	NP_071393.2	Q9UIM3	FKBPL_HUMAN	FK506 binding protein like	149					chaperone-mediated protein folding (GO:0061077)|protein peptidyl-prolyl isomerization (GO:0000413)|response to radiation (GO:0009314)	endoplasmic reticulum membrane (GO:0005789)	FK506 binding (GO:0005528)|peptidyl-prolyl cis-trans isomerase activity (GO:0003755)										CTCCATGGCCCTACGCCCATA	0.582																																						uc003nzr.3																			0											c.(445-447)Ggg>Agg		Homo sapiens FK506 binding protein like (FKBPL), mRNA.							198.0	215.0	209.0					6																	32097113		2203	4300	6503	SO:0001583	missense	63943				response to radiation	membrane|nucleus	FK506 binding|peptidyl-prolyl cis-trans isomerase activity	g.chr6:32097113C>T	AF139374	CCDS4738.1	6p21.3	2013-12-13	2001-11-28		ENSG00000204315	ENSG00000204315		"""Tetratricopeptide (TTC) repeat domain containing"""	13949	protein-coding gene	gene with protein product	"""WAF-1/CIP1 stabilizing protein 39"""		"""FK506-binding protein like"""			9056895	Standard	NM_022110		Approved	DIR1, NG7, WISp39	uc003nzr.3	Q9UIM3	OTTHUMG00000031129	ENST00000375156.3:c.445G>A	6.37:g.32097113C>T	ENSP00000364298:p.Gly149Arg					ATF6B_uc003nzn.3_5'Flank|ATF6B_uc003nzo.3_5'Flank|ATF6B_uc011dpg.2_5'Flank|ATF6B_uc011dph.2_5'Flank|FKBPL_uc021yvh.1_Missense_Mutation_p.G149R	p.G149R	NM_022110	NP_071393	Q9UIM3	FKBPL_HUMAN			1	715	-			149					A8K5V3|B0UYX8|Q9H5G3	Missense_Mutation	SNP	ENST00000375156.3	37	c.445G>A	CCDS4738.1	.	.	.	.	.	.	.	.	.	.	C	17.96	3.516912	0.64634	.	.	ENSG00000204315	ENST00000375156	D	0.91068	-2.78	5.23	5.23	0.72850	.	0.248284	0.33813	N	0.004540	D	0.87819	0.6273	N	0.24115	0.695	0.32524	N	0.535909	D	0.89917	1.0	D	0.66602	0.945	D	0.87969	0.2735	10	0.66056	D	0.02	-13.1764	11.2503	0.49022	0.1822:0.8178:0.0:0.0	.	149	Q9UIM3	FKBPL_HUMAN	R	149	ENSP00000364298:G149R	ENSP00000364298:G149R	G	-	1	0	FKBPL	32205091	0.939000	0.31865	0.143000	0.22291	0.899000	0.52679	3.149000	0.50655	2.728000	0.93425	0.462000	0.41574	GGG		0.582	FKBPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076221.2		
PKHD1	5314	broad.mit.edu	37	6	51890856	51890856	+	Missense_Mutation	SNP	G	G	T			TCGA-76-4929-01A-01D-1486-08	TCGA-76-4929-10A-01D-1486-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	af4f8b89-837a-48b7-b0e7-12aec23fc285	3e0712a1-b66a-42e7-94a3-07edee7dce2b	g.chr6:51890856G>T	ENST00000371117.3	-	32	4027	c.3752C>A	c.(3751-3753)aCc>aAc	p.T1251N	PKHD1_ENST00000340994.4_Missense_Mutation_p.T1251N	NM_138694.3	NP_619639.3	P08F94	PKHD1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)	1251	IPT/TIG 7.				cellular calcium ion homeostasis (GO:0006874)|cilium assembly (GO:0042384)|homeostatic process (GO:0042592)|kidney development (GO:0001822)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cellular component movement (GO:0051271)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of protein kinase B signaling (GO:0051898)|positive regulation of cell proliferation (GO:0008284)|regulation of centrosome duplication (GO:0010824)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of TOR signaling (GO:0032006)|single organismal cell-cell adhesion (GO:0016337)	anchored component of external side of plasma membrane (GO:0031362)|apical plasma membrane (GO:0016324)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|mitotic spindle (GO:0072686)|perinuclear region of cytoplasm (GO:0048471)|primary cilium (GO:0072372)	receptor activity (GO:0004872)			NS(1)|autonomic_ganglia(1)|breast(8)|central_nervous_system(5)|cervix(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(59)|lung(139)|ovary(16)|prostate(8)|skin(20)|soft_tissue(1)|stomach(2)|upper_aerodigestive_tract(7)|urinary_tract(5)	304	Lung NSC(77;0.0605)					GGCTGGCAGGGTTTCACACCA	0.597																																						uc003pah.1																			0				NS(1)|autonomic_ganglia(1)|breast(8)|central_nervous_system(5)|cervix(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(59)|lung(139)|ovary(16)|prostate(8)|skin(20)|soft_tissue(1)|stomach(2)|upper_aerodigestive_tract(7)|urinary_tract(5)	304						c.(3751-3753)aCc>aAc		Homo sapiens polycystic kidney and hepatic disease 1 (autosomal recessive) (PKHD1), transcript variant 1, mRNA.							49.0	51.0	50.0					6																	51890856		2203	4300	6503	SO:0001583	missense	5314				cell-cell adhesion|cilium assembly|homeostatic process|kidney development|negative regulation of cellular component movement	anchored to external side of plasma membrane|apical plasma membrane|integral to membrane|microtubule basal body	protein binding|receptor activity	g.chr6:51890856G>T	AF480064	CCDS4935.1, CCDS4936.1	6p21.2-p12	2012-11-26	2003-04-16		ENSG00000170927	ENSG00000170927			9016	protein-coding gene	gene with protein product	"""tigmin"", ""polyductin"", ""fibrocystin"""	606702	"""TIG multiple domains 1"""	TIGM1		9503014	Standard	NM_138694		Approved	ARPKD, FCYT	uc003pah.1	P08F94	OTTHUMG00000014841	ENST00000371117.3:c.3752C>A	6.37:g.51890856G>T	ENSP00000360158:p.Thr1251Asn					PKHD1_uc003pai.3_Missense_Mutation_p.T1251N	p.T1251N	NM_138694	NP_619639	P08F94	PKHD1_HUMAN			31	4028	-	Lung NSC(77;0.0605)		1251			IPT/TIG 7.		Q5VUA2|Q5VUA3|Q5VWV1|Q86Z26|Q8TCZ9	Missense_Mutation	SNP	ENST00000371117.3	37	c.3752C>A	CCDS4935.1	.	.	.	.	.	.	.	.	.	.	G	14.29	2.490920	0.44249	.	.	ENSG00000170927	ENST00000371117;ENST00000340994;ENST00000393616	T;T	0.79940	-1.32;-1.32	5.87	4.07	0.47477	Cell surface receptor IPT/TIG (2);Immunoglobulin E-set (1);Immunoglobulin-like fold (1);	0.281993	0.35677	N	0.003045	D	0.87669	0.6235	M	0.90705	3.14	0.28283	N	0.923871	D;D	0.89917	1.0;1.0	D;D	0.77557	0.984;0.99	T	0.80139	-0.1507	10	0.56958	D	0.05	.	10.7579	0.46247	0.1313:0.0:0.8687:0.0	.	1251;1251	P08F94-2;P08F94	.;PKHD1_HUMAN	N	1251	ENSP00000360158:T1251N;ENSP00000341097:T1251N	ENSP00000341097:T1251N	T	-	2	0	PKHD1	51998815	0.957000	0.32711	0.949000	0.38748	0.005000	0.04900	1.510000	0.35790	2.780000	0.95670	0.655000	0.94253	ACC		0.597	PKHD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040893.1	NM_138694	
WBSCR17	64409	broad.mit.edu	37	7	70597844	70597844	+	Missense_Mutation	SNP	C	C	T			TCGA-76-4929-01A-01D-1486-08	TCGA-76-4929-10A-01D-1486-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	af4f8b89-837a-48b7-b0e7-12aec23fc285	3e0712a1-b66a-42e7-94a3-07edee7dce2b	g.chr7:70597844C>T	ENST00000333538.5	+	1	690	c.56C>T	c.(55-57)gCc>gTc	p.A19V		NM_022479.1	NP_071924.1	Q6IS24	GLTL3_HUMAN	Williams-Beuren syndrome chromosome region 17	19					protein glycosylation (GO:0006486)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)|polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)			NS(5)|breast(2)|central_nervous_system(1)|endometrium(7)|kidney(7)|large_intestine(22)|lung(45)|ovary(2)|pancreas(2)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)	100		all_cancers(73;0.2)|Lung NSC(55;0.094)|all_lung(88;0.125)				ATCGCGGTAGCCGGCTTCGTG	0.677																																						uc003tvy.3																			0		p.V18L(1)		NS(5)|breast(2)|central_nervous_system(1)|endometrium(7)|kidney(7)|large_intestine(22)|lung(45)|ovary(2)|pancreas(2)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)	100						c.(55-57)gCc>gTc		Homo sapiens Williams-Beuren syndrome chromosome region 17 (WBSCR17), mRNA.							54.0	50.0	51.0					7																	70597844		2201	4299	6500	SO:0001583	missense	64409					Golgi membrane|integral to membrane	polypeptide N-acetylgalactosaminyltransferase activity|sugar binding	g.chr7:70597844C>T	AF410457	CCDS5540.1	7q11.23	2014-03-13			ENSG00000185274	ENSG00000185274		"""Glycosyltransferase family 2 domain containing"""	16347	protein-coding gene	gene with protein product	"""polypeptide N-acetylgalactosaminyltransferase-like 3"", ""polypeptide GalNAc transferase 3"""	615137				12073013, 15744064, 22787146	Standard	NM_022479		Approved	GALNTL3, GalNAc-T5L	uc003tvy.4	Q6IS24	OTTHUMG00000129783	ENST00000333538.5:c.56C>T	7.37:g.70597844C>T	ENSP00000329654:p.Ala19Val						p.A19V	NM_022479	NP_071924	Q6IS24	GLTL3_HUMAN			0	56	+		all_cancers(73;0.2)|Lung NSC(55;0.094)|all_lung(88;0.125)	19					Q8NFV9|Q9NTA8	Missense_Mutation	SNP	ENST00000333538.5	37	c.56C>T	CCDS5540.1	.	.	.	.	.	.	.	.	.	.	C	10.99	1.508337	0.27036	.	.	ENSG00000185274	ENST00000333538	T	0.54279	0.58	4.85	4.85	0.62838	.	0.489617	0.20549	N	0.090146	T	0.28863	0.0716	N	0.04508	-0.205	0.53688	D	0.999978	B	0.14438	0.01	B	0.12837	0.008	T	0.19160	-1.0314	10	0.02654	T	1	.	17.1215	0.86702	0.0:1.0:0.0:0.0	.	19	Q6IS24	GLTL3_HUMAN	V	19	ENSP00000329654:A19V	ENSP00000329654:A19V	A	+	2	0	WBSCR17	70235780	1.000000	0.71417	1.000000	0.80357	0.920000	0.55202	6.056000	0.71111	2.512000	0.84698	0.563000	0.77884	GCC		0.677	WBSCR17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252006.1	NM_022479	
CLIP2	7461	broad.mit.edu	37	7	73791076	73791076	+	Missense_Mutation	SNP	G	G	A			TCGA-76-4929-01A-01D-1486-08	TCGA-76-4929-10A-01D-1486-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	af4f8b89-837a-48b7-b0e7-12aec23fc285	3e0712a1-b66a-42e7-94a3-07edee7dce2b	g.chr7:73791076G>A	ENST00000395060.1	+	9	2345	c.2345G>A	c.(2344-2346)aGt>aAt	p.S782N	CLIP2_ENST00000223398.6_Missense_Mutation_p.S782N|CLIP2_ENST00000361545.5_Missense_Mutation_p.S747N			Q9UDT6	CLIP2_HUMAN	CAP-GLY domain containing linker protein 2	782						cytoplasmic microtubule (GO:0005881)|microtubule associated complex (GO:0005875)|microtubule plus-end (GO:0035371)				breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(13)|pancreas(1)|prostate(2)|skin(3)	30						GAGGTCGAGAGTTTGCGGGAG	0.632																																						uc003uam.3																			0				breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(13)|pancreas(1)|prostate(2)|skin(3)	30						c.(2344-2346)aGt>aAt		Homo sapiens CAP-GLY domain containing linker protein 2 (CLIP2), transcript variant 1, mRNA.							23.0	25.0	24.0					7																	73791076		2202	4300	6502	SO:0001583	missense	7461					microtubule associated complex		g.chr7:73791076G>A	AB006629	CCDS5569.1, CCDS5570.1	7q11.23	2008-06-12	2007-01-04	2007-01-04	ENSG00000106665	ENSG00000106665			2586	protein-coding gene	gene with protein product		603432	"""cytoplasmic linker 2"", ""Williams-Beuren syndrome chromosome region 3"""	WBSCR4, CYLN2, WBSCR3		8812460, 9799601	Standard	NM_003388		Approved	CLIP-115, KIAA0291, WSCR4, CLIP, WSCR3	uc003uam.3	Q9UDT6	OTTHUMG00000022980	ENST00000395060.1:c.2345G>A	7.37:g.73791076G>A	ENSP00000378500:p.Ser782Asn					CLIP2_uc003uan.3_Missense_Mutation_p.S747N|CLIP2_uc003uao.3_Missense_Mutation_p.S176N	p.S782N	NM_003388	NP_003379	Q9UDT6	CLIP2_HUMAN			9	2672	+			782					O14527|O43611	Missense_Mutation	SNP	ENST00000395060.1	37	c.2345G>A	CCDS5569.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	7.616|7.616	0.675756|0.675756	0.14841|0.14841	.|.	.|.	ENSG00000106665|ENSG00000106665	ENST00000539676;ENST00000223398;ENST00000361545;ENST00000395060|ENST00000493166	T;T;T|.	0.60171|.	0.24;0.21;0.24|.	4.92|4.92	4.92|4.92	0.64577|0.64577	.|.	0.760515|.	0.12655|.	N|.	0.450155|.	T|T	0.36608|0.36608	0.0973|0.0973	N|N	0.19112|0.19112	0.55|0.55	0.21220|0.21220	N|N	0.99975|0.99975	B;B;B|.	0.14012|.	0.009;0.006;0.003|.	B;B;B|.	0.15870|.	0.01;0.014;0.006|.	T|T	0.26815|0.26815	-1.0092|-1.0092	10|5	0.18710|.	T|.	0.47|.	-13.1756|-13.1756	16.7413|16.7413	0.85460|0.85460	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	747;747;782|.	A7E2F7;Q9UDT6-2;Q9UDT6|.	.;.;CLIP2_HUMAN|.	N|I	782;782;747;782|18	ENSP00000223398:S782N;ENSP00000355151:S747N;ENSP00000378500:S782N|.	ENSP00000223398:S782N|.	S|V	+|+	2|1	0|0	CLIP2|CLIP2	73429012|73429012	0.971000|0.971000	0.33674|0.33674	0.998000|0.998000	0.56505|0.56505	0.381000|0.381000	0.30169|0.30169	2.100000|2.100000	0.41777|0.41777	2.286000|2.286000	0.76751|0.76751	0.549000|0.549000	0.68633|0.68633	AGT|GTT		0.632	CLIP2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252556.1	NM_003388	
AKAP9	10142	broad.mit.edu	37	7	91711915	91711915	+	Frame_Shift_Del	DEL	C	C	-			TCGA-76-4929-01A-01D-1486-08	TCGA-76-4929-10A-01D-1486-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	af4f8b89-837a-48b7-b0e7-12aec23fc285	3e0712a1-b66a-42e7-94a3-07edee7dce2b	g.chr7:91711915delC	ENST00000359028.2	+	33	8360	c.8135delC	c.(8134-8136)gctfs	p.A2712fs	AKAP9_ENST00000358100.2_Frame_Shift_Del_p.A2712fs|AKAP9_ENST00000356239.3_Frame_Shift_Del_p.A2700fs			Q99996	AKAP9_HUMAN	A kinase (PRKA) anchor protein 9	2712	Glu-rich.				G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|Sertoli cell development (GO:0060009)|signal transduction (GO:0007165)|spermatogenesis (GO:0007283)|synaptic transmission (GO:0007268)|transport (GO:0006810)	centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|pericentriolar material (GO:0000242)|voltage-gated potassium channel complex (GO:0008076)	ion channel binding (GO:0044325)|protein complex scaffold (GO:0032947)|receptor binding (GO:0005102)			NS(1)|autonomic_ganglia(2)|breast(14)|central_nervous_system(3)|cervix(1)|endometrium(13)|kidney(12)|large_intestine(35)|lung(49)|ovary(8)|prostate(6)|skin(8)|stomach(1)|urinary_tract(2)	155	all_cancers(62;2.46e-09)|all_epithelial(64;4.42e-08)|Breast(17;0.00206)|all_lung(186;0.185)|all_hematologic(106;0.215)|Lung NSC(181;0.249)		STAD - Stomach adenocarcinoma(171;6.16e-05)|Lung(22;0.123)|LUSC - Lung squamous cell carcinoma(200;0.225)			GAATCAGTGGCTACCAAAGCA	0.373			T	BRAF	papillary thyroid																																	uc003ulg.3				Dom	yes		7	7q21-q22	10142	T	A kinase (PRKA) anchor protein (yotiao) 9			E	BRAF		papillary thyroid		0				NS(1)|autonomic_ganglia(2)|breast(14)|central_nervous_system(3)|cervix(1)|endometrium(13)|kidney(12)|large_intestine(35)|lung(49)|ovary(8)|prostate(6)|skin(8)|stomach(1)|urinary_tract(2)	155						c.(8098-8100)gctfs		Homo sapiens A kinase (PRKA) anchor protein (yotiao) 9 (AKAP9), transcript variant 2, mRNA.							65.0	67.0	66.0					7																	91711915		2203	4299	6502	SO:0001589	frameshift_variant	10142				G2/M transition of mitotic cell cycle|signal transduction|synaptic transmission|transport	centrosome|cytosol|Golgi apparatus	receptor binding	g.chr7:91711915delC	AF091711	CCDS5622.1	7q21-q22	2014-09-17	2013-09-25		ENSG00000127914	ENSG00000127914		"""A-kinase anchor proteins"", ""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	379	protein-coding gene	gene with protein product	"""A-kinase anchoring protein 450"", ""AKAP9-BRAF fusion protein"", ""AKAP120-like protein"", ""centrosome- and golgi-localized protein kinase N-associated protein"", ""protein kinase A anchoring protein 9"", ""A-kinase anchor protein, 350kDa"", ""protein phosphatase 1, regulatory subunit 45"", ""yotiao"""	604001				9482789, 10390370, 24475373	Standard	NM_147185		Approved	KIAA0803, AKAP350, AKAP450, CG-NAP, YOTIAO, HYPERION, PRKA9, MU-RMS-40.16A, PPP1R45, LQT11	uc003ulg.3	Q99996	OTTHUMG00000131127	ENST00000359028.2:c.8135delC	7.37:g.91711915delC	ENSP00000351922:p.Ala2712fs					AKAP9_uc003ulf.3_Frame_Shift_Del_p.A2692fs|AKAP9_uc003uli.3_Frame_Shift_Del_p.A2323fs|AKAP9_uc003ulj.3_Frame_Shift_Del_p.A470fs|AKAP9_uc003ulk.3_5'Flank	p.A2700fs	NM_005751	NP_005742	Q99996	AKAP9_HUMAN	STAD - Stomach adenocarcinoma(171;6.16e-05)|Lung(22;0.123)|LUSC - Lung squamous cell carcinoma(200;0.225)		31	8324	+	all_cancers(62;2.46e-09)|all_epithelial(64;4.42e-08)|Breast(17;0.00206)|all_lung(186;0.185)|all_hematologic(106;0.215)|Lung NSC(181;0.249)		2712			Glu-rich.		A4D1F0|A4D1F2|A4D1F4|O14869|O43355|O94895|Q75N20|Q9UQH3|Q9UQQ4|Q9Y6B8|Q9Y6Y2	Frame_Shift_Del	DEL	ENST00000359028.2	37	c.8099delC																																																																																					0.373	AKAP9-202	KNOWN	basic	protein_coding	protein_coding		NM_005751	
KDM7A	80853	broad.mit.edu	37	7	139824534	139824534	+	Missense_Mutation	SNP	C	C	T	rs369398521		TCGA-76-4929-01A-01D-1486-08	TCGA-76-4929-10A-01D-1486-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	af4f8b89-837a-48b7-b0e7-12aec23fc285	3e0712a1-b66a-42e7-94a3-07edee7dce2b	g.chr7:139824534C>T	ENST00000397560.2	-	7	1035	c.938G>A	c.(937-939)cGt>cAt	p.R313H	JHDM1D_ENST00000006967.5_Missense_Mutation_p.R313H	NM_030647.1	NP_085150.1	Q6ZMT4	KDM7A_HUMAN		313	JmjC. {ECO:0000255|PROSITE- ProRule:PRU00538}.				histone H3-K27 demethylation (GO:0071557)|histone H3-K36 demethylation (GO:0070544)|histone H3-K9 demethylation (GO:0033169)|histone H4-K20 demethylation (GO:0035574)|midbrain development (GO:0030901)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	nucleolus (GO:0005730)|nucleus (GO:0005634)	histone demethylase activity (H3-K27 specific) (GO:0071558)|histone demethylase activity (H3-K36 specific) (GO:0051864)|histone demethylase activity (H3-K9 specific) (GO:0032454)|histone demethylase activity (H4-K20 specific) (GO:0035575)|iron ion binding (GO:0005506)|methylated histone binding (GO:0035064)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors (GO:0016706)|zinc ion binding (GO:0008270)			central_nervous_system(2)|endometrium(4)|kidney(1)|large_intestine(1)|lung(10)|ovary(1)|prostate(1)|skin(1)|stomach(1)	22	Melanoma(164;0.0142)					AGATTCATAACGTGCCAAATT	0.358																																						uc003vvm.3																			0				central_nervous_system(2)|endometrium(4)|kidney(1)|large_intestine(1)|lung(10)|ovary(1)|prostate(1)|skin(1)|stomach(1)	22						c.(937-939)cGt>cAt		Homo sapiens jumonji C domain containing histone demethylase 1 homolog D (S. cerevisiae) (JHDM1D), mRNA.		C	HIS/ARG	0,3682		0,0,1841	95.0	86.0	89.0		938	4.3	1.0	7		89	3,8177		0,3,4087	no	missense	JHDM1D	NM_030647.1	29	0,3,5928	TT,TC,CC		0.0367,0.0,0.0253	benign	313/942	139824534	3,11859	1841	4090	5931	SO:0001583	missense	80853				midbrain development|transcription, DNA-dependent	nucleolus	histone demethylase activity (H3-K27 specific)|histone demethylase activity (H3-K36 specific)|histone demethylase activity (H3-K9 specific)|histone demethylase activity (H4-K20 specific)|iron ion binding|methylated histone residue binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|zinc ion binding	g.chr7:139824534C>T																												ENST00000397560.2:c.938G>A	7.37:g.139824534C>T	ENSP00000380692:p.Arg313His						p.R313H	NM_030647	NP_085150	Q6ZMT4	KDM7_HUMAN			6	942	-	Melanoma(164;0.0142)		313			JmjC.		A4D1S9|C9JJH9|C9JQU2|Q6MZL8|Q9C0E5	Missense_Mutation	SNP	ENST00000397560.2	37	c.938G>A	CCDS43658.1	.	.	.	.	.	.	.	.	.	.	C	18.23	3.577367	0.65878	0.0	3.67E-4	ENSG00000006459	ENST00000397560;ENST00000006967	T;T	0.71817	-0.6;-0.6	5.49	4.34	0.51931	Transcription factor jumonji/aspartyl beta-hydroxylase (2);Transcription factor jumonji (1);	0.060735	0.64402	D	0.000002	T	0.52435	0.1734	N	0.16656	0.425	0.35337	D	0.786138	B	0.30686	0.29	B	0.13407	0.009	T	0.62296	-0.6884	10	0.87932	D	0	-3.5299	12.7856	0.57502	0.8568:0.1432:0.0:0.0	.	313	Q6ZMT4	KDM7_HUMAN	H	313	ENSP00000380692:R313H;ENSP00000006967:R313H	ENSP00000006967:R313H	R	-	2	0	JHDM1D	139471003	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	5.085000	0.64468	1.021000	0.39600	-0.262000	0.10625	CGT		0.358	JHDM1D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348460.1		
MGAM	8972	broad.mit.edu	37	7	141765179	141765179	+	Missense_Mutation	SNP	G	G	A			TCGA-76-4929-01A-01D-1486-08	TCGA-76-4929-10A-01D-1486-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	af4f8b89-837a-48b7-b0e7-12aec23fc285	3e0712a1-b66a-42e7-94a3-07edee7dce2b	g.chr7:141765179G>A	ENST00000549489.2	+	38	4624	c.4529G>A	c.(4528-4530)cGc>cAc	p.R1510H	MGAM_ENST00000475668.2_Missense_Mutation_p.R1510H	NM_004668.2	NP_004659.2	O43451	MGA_HUMAN	maltase-glucoamylase (alpha-glucosidase)	1510	Glucoamylase.				carbohydrate metabolic process (GO:0005975)|polysaccharide digestion (GO:0044245)|small molecule metabolic process (GO:0044281)|starch catabolic process (GO:0005983)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	alpha-1,4-glucosidase activity (GO:0004558)|amylase activity (GO:0016160)|carbohydrate binding (GO:0030246)|catalytic activity (GO:0003824)|glucan 1,4-alpha-glucosidase activity (GO:0004339)|maltose alpha-glucosidase activity (GO:0032450)			cervix(1)|endometrium(1)|large_intestine(4)|lung(3)|ovary(2)|skin(2)	13	Melanoma(164;0.0272)				Acarbose(DB00284)|Miglitol(DB00491)|Voglibose(DB04878)	GTCATCACCCGCTCCACATTT	0.597																																						uc003vwy.3																			0				cervix(1)|endometrium(1)|large_intestine(4)|lung(3)|ovary(2)|skin(2)	13						c.(4528-4530)cGc>cAc		Homo sapiens maltase-glucoamylase (alpha-glucosidase) (MGAM), mRNA.	Acarbose(DB00284)|Miglitol(DB00491)|Voglibose(DB04878)						50.0	55.0	53.0					7																	141765179		2037	4183	6220	SO:0001583	missense	8972				polysaccharide digestion|starch catabolic process	apical plasma membrane|integral to membrane	carbohydrate binding|glucan 1,4-alpha-glucosidase activity|maltose alpha-glucosidase activity	g.chr7:141765179G>A	AF016833	CCDS47727.1	7q34	2012-10-03			ENSG00000257335	ENSG00000257335			7043	protein-coding gene	gene with protein product		154360				9446624	Standard	NM_004668		Approved	MGA	uc003vwy.3	O43451	OTTHUMG00000158395	ENST00000549489.2:c.4529G>A	7.37:g.141765179G>A	ENSP00000447378:p.Arg1510His						p.R1510H	NM_004668	NP_004659	O43451	MGA_HUMAN			37	4583	+	Melanoma(164;0.0272)		1510			Glucoamylase.		Q0VAX6|Q75ME7|Q86UM5	Missense_Mutation	SNP	ENST00000549489.2	37	c.4529G>A	CCDS47727.1	.	.	.	.	.	.	.	.	.	.	G	27.6	4.847132	0.91277	.	.	ENSG00000257335	ENST00000549489;ENST00000475668;ENST00000548812	D	0.97016	-4.21	3.97	3.97	0.46021	Glycoside hydrolase, superfamily (1);	.	.	.	.	D	0.99096	0.9689	H	0.99789	4.78	0.44221	D	0.997054	D	0.89917	1.0	D	0.97110	1.0	D	0.98472	1.0601	9	0.87932	D	0	.	14.8747	0.70485	0.0:0.0:1.0:0.0	.	1510	O43451	MGA_HUMAN	H	1510;1510;1387	ENSP00000447378:R1510H	ENSP00000316431:R1387H	R	+	2	0	MGAM	141411648	1.000000	0.71417	0.998000	0.56505	0.935000	0.57460	9.718000	0.98758	1.759000	0.51996	0.306000	0.20318	CGC		0.597	MGAM-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000351244.3		
KEL	3792	broad.mit.edu	37	7	142658027	142658027	+	Missense_Mutation	SNP	G	G	A	rs184131044	byFrequency	TCGA-76-4929-01A-01D-1486-08	TCGA-76-4929-10A-01D-1486-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	af4f8b89-837a-48b7-b0e7-12aec23fc285	3e0712a1-b66a-42e7-94a3-07edee7dce2b	g.chr7:142658027G>A	ENST00000355265.2	-	4	862	c.388C>T	c.(388-390)Cgg>Tgg	p.R130W	KEL_ENST00000479768.2_5'UTR	NM_000420.2	NP_000411.1	P23276	KELL_HUMAN	Kell blood group, metallo-endopeptidase	130					vasoconstriction (GO:0042310)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)			central_nervous_system(1)|endometrium(3)|kidney(5)|large_intestine(11)|lung(34)|ovary(3)|prostate(2)|skin(1)	60	Melanoma(164;0.059)					AGTATTCTCCGAAGTCGGTTT	0.502													G|||	4	0.000798722	0.0	0.0	5008	,	,		19594	0.002		0.0	False		,,,				2504	0.002					uc003wcb.3																			0				central_nervous_system(1)|endometrium(3)|kidney(5)|large_intestine(11)|lung(34)|ovary(3)|prostate(2)|skin(1)	60	GRCh37	CM973369	KEL	M	rs184131044	c.(388-390)Cgg>Tgg		Homo sapiens Kell blood group, metallo-endopeptidase (KEL), mRNA.							185.0	189.0	188.0					7																	142658027		2203	4300	6503	SO:0001583	missense	3792				proteolysis|vasoconstriction	integral to membrane|plasma membrane	metal ion binding|metalloendopeptidase activity|protein binding	g.chr7:142658027G>A	BC003135	CCDS34766.1	7q33	2014-07-19	2006-10-10		ENSG00000197993	ENSG00000197993		"""CD molecules"", ""Blood group antigens"""	6308	protein-coding gene	gene with protein product		613883	"""Kell blood group"", ""Kell blood group, metalloendopeptidase"""			1712490, 7683930	Standard	NM_000420		Approved	ECE3, CD238	uc003wcb.3	P23276	OTTHUMG00000157159	ENST00000355265.2:c.388C>T	7.37:g.142658027G>A	ENSP00000347409:p.Arg130Trp						p.R130W	NM_000420	NP_000411	P23276	KELL_HUMAN			3	598	-	Melanoma(164;0.059)		130					B2RBV4|Q96RS8|Q99885	Missense_Mutation	SNP	ENST00000355265.2	37	c.388C>T	CCDS34766.1	3|3	0.0013736263736263737|0.0013736263736263737	0|0	0.0|0.0	0|0	0.0|0.0	2|2	0.0034965034965034965|0.0034965034965034965	1|1	0.0013192612137203166|0.0013192612137203166	G|G	5.875|5.875	0.345548|0.345548	0.11126|0.11126	.|.	.|.	ENSG00000197993|ENSG00000197993	ENST00000355265;ENST00000476829;ENST00000467543|ENST00000460479	T;T;T|.	0.77229|.	-1.08;-1.08;-1.08|.	5.84|5.84	1.87|1.87	0.25490|0.25490	Peptidase M13 (1);|.	0.616178|.	0.14380|.	N|.	0.323161|.	T|T	0.36166|0.36166	0.0957|0.0957	L|L	0.43152|0.43152	1.355|1.355	0.09310|0.09310	N|N	1|1	B|.	0.30236|.	0.274|.	B|.	0.28465|.	0.09|.	T|T	0.24440|0.24440	-1.0160|-1.0160	10|5	0.62326|.	D|.	0.03|.	-17.8298|-17.8298	6.7327|6.7327	0.23393|0.23393	0.0825:0.0:0.4634:0.4541|0.0825:0.0:0.4634:0.4541	.|.	130|.	P23276|.	KELL_HUMAN|.	W|L	130;130;111|140	ENSP00000347409:R130W;ENSP00000419889:R130W;ENSP00000420011:R111W|.	ENSP00000347409:R130W|.	R|S	-|-	1|2	2|0	KEL|KEL	142368149|142368149	0.004000|0.004000	0.15560|0.15560	0.003000|0.003000	0.11579|0.11579	0.050000|0.050000	0.14768|0.14768	0.366000|0.366000	0.20365|0.20365	0.056000|0.056000	0.16144|0.16144	0.655000|0.655000	0.94253|0.94253	CGG|TCG		0.502	KEL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347671.2	NM_000420	
NEFL	4747	broad.mit.edu	37	8	24813390	24813390	+	RNA	SNP	C	C	T			TCGA-76-4929-01A-01D-1486-08	TCGA-76-4929-10A-01D-1486-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	af4f8b89-837a-48b7-b0e7-12aec23fc285	3e0712a1-b66a-42e7-94a3-07edee7dce2b	g.chr8:24813390C>T	ENST00000221169.5	-	0	1234				CTD-2168K21.2_ENST00000607735.1_RNA			P07196	NFL_HUMAN	neurofilament, light polypeptide						anterograde axon cargo transport (GO:0008089)|axon transport of mitochondrion (GO:0019896)|cell death (GO:0008219)|intermediate filament organization (GO:0045109)|locomotion (GO:0040011)|microtubule cytoskeleton organization (GO:0000226)|negative regulation of neuron apoptotic process (GO:0043524)|neurofilament bundle assembly (GO:0033693)|neuromuscular process controlling balance (GO:0050885)|neuron projection morphogenesis (GO:0048812)|peripheral nervous system axon regeneration (GO:0014012)|positive regulation of axonogenesis (GO:0050772)|protein polymerization (GO:0051258)|regulation of axon diameter (GO:0031133)|response to corticosterone (GO:0051412)|response to peptide hormone (GO:0043434)|response to toxic substance (GO:0009636)|retrograde axon cargo transport (GO:0008090)|synaptic transmission (GO:0007268)	axon (GO:0030424)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|growth cone (GO:0030426)|neurofilament (GO:0005883)	identical protein binding (GO:0042802)|protein binding, bridging (GO:0030674)|protein C-terminus binding (GO:0008022)|structural constituent of cytoskeleton (GO:0005200)			central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(5)|ovary(1)|prostate(1)|skin(2)	21		Ovarian(32;0.00965)|Prostate(55;0.157)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0197)|Epithelial(17;2.44e-10)|Colorectal(74;0.0108)|COAD - Colon adenocarcinoma(73;0.0375)		ATCAAGCTGTCGATGCGCTTC	0.632																																						uc003xee.3																			0				central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(5)|ovary(1)|prostate(1)|skin(2)	21						c.(640-642)Gac>Aac		Homo sapiens neurofilament, light polypeptide (NEFL), mRNA.							28.0	30.0	30.0					8																	24813390		1970	4146	6116			4747				anterograde axon cargo transport|axon transport of mitochondrion|neurofilament bundle assembly|retrograde axon cargo transport|synaptic transmission	cytosol|neurofilament	identical protein binding|protein C-terminus binding|structural constituent of cytoskeleton	g.chr8:24813390C>T		CCDS75712.1	8p21.2	2014-09-17	2008-09-19		ENSG00000104725	ENSG00000277586		"""Intermediate filaments type IV"""	7739	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 110"""	162280	"""neurofilament, light polypeptide 68kDa"""			17620486, 3145240	Standard	NM_006158		Approved	NFL, CMT1F, CMT2E, NF68, PPP1R110	uc003xee.4	P07196	OTTHUMG00000134284		8.37:g.24813390C>T							p.D214N	NM_006158	NP_006149	P07196	NFL_HUMAN		UCEC - Uterine corpus endometrioid carcinoma (27;0.0197)|Epithelial(17;2.44e-10)|Colorectal(74;0.0108)|COAD - Colon adenocarcinoma(73;0.0375)	0	742	-		Ovarian(32;0.00965)|Prostate(55;0.157)	214			Coil 1B.|Rod.		B9ZVN2|Q16154|Q8IU72	Missense_Mutation	SNP	ENST00000221169.5	37	c.640G>A																																																																																					0.632	NEFL-001	KNOWN	sequence_error|basic	processed_transcript	processed_transcript	OTTHUMT00000258943.4	NM_006158	
INSL6	11172	broad.mit.edu	37	9	5185459	5185459	+	Silent	SNP	G	G	A			TCGA-76-4929-01A-01D-1486-08	TCGA-76-4929-10A-01D-1486-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	af4f8b89-837a-48b7-b0e7-12aec23fc285	3e0712a1-b66a-42e7-94a3-07edee7dce2b	g.chr9:5185459G>A	ENST00000381641.3	-	1	209	c.144C>T	c.(142-144)gcC>gcT	p.A48A		NM_007179.2	NP_009110.2	Q9Y581	INSL6_HUMAN	insulin-like 6	48					fertilization (GO:0009566)|male gonad development (GO:0008584)|negative regulation of apoptotic process (GO:0043066)|sperm motility (GO:0030317)|spermatid development (GO:0007286)	extracellular region (GO:0005576)	hormone activity (GO:0005179)			breast(2)|endometrium(3)|kidney(1)|large_intestine(7)|lung(2)	15	all_hematologic(13;0.137)	Breast(48;0.147)|Acute lymphoblastic leukemia(23;0.158)		GBM - Glioblastoma multiforme(50;0.0128)|Lung(218;0.145)		GGCTCCAGTTGGCATGGCCGC	0.532																																						uc003zix.3																			0				breast(2)|endometrium(3)|kidney(1)|large_intestine(7)|lung(2)	15						c.(142-144)gcC>gcT		Homo sapiens insulin-like 6 (INSL6), mRNA.							85.0	80.0	81.0					9																	5185459		2203	4300	6503	SO:0001819	synonymous_variant	11172					extracellular region	hormone activity	g.chr9:5185459G>A	AF156094	CCDS6458.1	9p24	2008-07-21			ENSG00000120210	ENSG00000120210			6089	protein-coding gene	gene with protein product	"""relaxin/insulin-like factor 1"""	606414				10819760	Standard	NM_007179		Approved	RIF1	uc003zix.3	Q9Y581	OTTHUMG00000019489	ENST00000381641.3:c.144C>T	9.37:g.5185459G>A							p.A48A	NM_007179	NP_009110	Q9Y581	INSL6_HUMAN		GBM - Glioblastoma multiforme(50;0.0128)|Lung(218;0.145)	0	160	-	all_hematologic(13;0.137)	Breast(48;0.147)|Acute lymphoblastic leukemia(23;0.158)	48					A0AVS0|Q9NS16	Silent	SNP	ENST00000381641.3	37	c.144C>T	CCDS6458.1																																																																																				0.532	INSL6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051608.3	NM_007179	
NUDT2	318	broad.mit.edu	37	9	34343182	34343182	+	Missense_Mutation	SNP	C	C	T			TCGA-76-4929-01A-01D-1486-08	TCGA-76-4929-10A-01D-1486-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	af4f8b89-837a-48b7-b0e7-12aec23fc285	3e0712a1-b66a-42e7-94a3-07edee7dce2b	g.chr9:34343182C>T	ENST00000379158.2	+	5	546	c.188C>T	c.(187-189)gCa>gTa	p.A63V	NUDT2_ENST00000379155.5_Missense_Mutation_p.A63V|NUDT2_ENST00000346365.4_Missense_Mutation_p.A63V	NM_001161.4	NP_001152.1	P50583	AP4A_HUMAN	nudix (nucleoside diphosphate linked moiety X)-type motif 2	63	Nudix hydrolase. {ECO:0000255|PROSITE- ProRule:PRU00794}.				apoptotic process (GO:0006915)|nucleobase-containing compound metabolic process (GO:0006139)	mitochondrion (GO:0005739)	bis(5'-nucleosyl)-tetraphosphatase (asymmetrical) activity (GO:0004081)|bis(5'-nucleosyl)-tetraphosphatase (symmetrical) activity (GO:0008803)|GTP binding (GO:0005525)			lung(3)	3			LUSC - Lung squamous cell carcinoma(29;0.0107)	GBM - Glioblastoma multiforme(74;0.126)		CAAGAGGAAGCAGGCATAGAA	0.493																																					Melanoma(95;1683 1957 4276 39813)	uc003zuc.3																			0				lung(3)	3						c.(187-189)gCa>gTa		Homo sapiens nudix (nucleoside diphosphate linked moiety X)-type motif 2 (NUDT2), transcript variant 2, mRNA.							145.0	135.0	138.0					9																	34343182		2203	4300	6503	SO:0001583	missense	318				induction of apoptosis|nucleobase, nucleoside, nucleotide and nucleic acid metabolic process		bis(5'-nucleosyl)-tetraphosphatase (asymmetrical) activity|bis(5'-nucleosyl)-tetraphosphatase (symmetrical) activity|GTP binding	g.chr9:34343182C>T	U30313	CCDS6552.1	9p13	2008-07-21			ENSG00000164978	ENSG00000164978		"""Nudix motif containing"""	8049	protein-coding gene	gene with protein product	"""Ap4A hydrolase 1"", ""Ap4Aase"", ""bis(5'-nucleosyl)-tetraphosphatase (asymmetrical)"", ""diadenosine tetraphosphatase"", ""diadenosine 5',5''-P1,P4-tetraphosphate pyrophosphohydrolase"""	602852		APAH1		7487923, 9479504	Standard	NM_001161		Approved		uc022bga.1	P50583	OTTHUMG00000019817	ENST00000379158.2:c.188C>T	9.37:g.34343182C>T	ENSP00000368455:p.Ala63Val					NUDT2_uc003zub.3_Missense_Mutation_p.A63V|NUDT2_uc003zud.3_Missense_Mutation_p.A63V|NUDT2_uc022bga.1_Missense_Mutation_p.A63V	p.A63V	NM_147172	NP_671701	P50583	AP4A_HUMAN	LUSC - Lung squamous cell carcinoma(29;0.0107)	GBM - Glioblastoma multiforme(74;0.126)	4	475	+			63			Nudix hydrolase.		D3DRM0|Q5T589	Missense_Mutation	SNP	ENST00000379158.2	37	c.188C>T	CCDS6552.1	.	.	.	.	.	.	.	.	.	.	C	21.5	4.153136	0.78001	.	.	ENSG00000164978	ENST00000337747;ENST00000379154;ENST00000379155;ENST00000346365;ENST00000379158	T;T;T	0.07021	3.23;3.23;3.23	5.88	4.99	0.66335	NUDIX hydrolase domain (3);NUDIX hydrolase, conserved site (1);NUDIX hydrolase domain-like (1);	0.134136	0.64402	N	0.000002	T	0.14830	0.0358	L	0.39566	1.225	0.80722	D	1	P	0.46621	0.881	P	0.51866	0.682	T	0.01596	-1.1316	10	0.40728	T	0.16	-1.4721	15.2069	0.73186	0.0:0.9325:0.0:0.0675	.	63	P50583	AP4A_HUMAN	V	63	ENSP00000368452:A63V;ENSP00000344187:A63V;ENSP00000368455:A63V	ENSP00000338397:A63V	A	+	2	0	NUDT2	34333182	1.000000	0.71417	0.958000	0.39756	0.376000	0.30014	5.893000	0.69798	1.504000	0.48704	-0.291000	0.09656	GCA		0.493	NUDT2-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052160.2	NM_001161	
NAA35	60560	broad.mit.edu	37	9	88633637	88633637	+	Silent	SNP	T	T	C			TCGA-76-4929-01A-01D-1486-08	TCGA-76-4929-10A-01D-1486-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	af4f8b89-837a-48b7-b0e7-12aec23fc285	3e0712a1-b66a-42e7-94a3-07edee7dce2b	g.chr9:88633637T>C	ENST00000361671.5	+	21	2071	c.1938T>C	c.(1936-1938)taT>taC	p.Y646Y		NM_024635.3	NP_078911.3	Q5VZE5	NAA35_HUMAN	N(alpha)-acetyltransferase 35, NatC auxiliary subunit	646					negative regulation of apoptotic process (GO:0043066)|smooth muscle cell proliferation (GO:0048659)	cytoplasm (GO:0005737)|NatC complex (GO:0031417)				central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(4)|lung(9)|ovary(2)|skin(2)|urinary_tract(1)	25						TCAATAAATATAGCCCTCCTC	0.363																																						uc004aoi.4																			0				central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(4)|lung(9)|ovary(2)|skin(2)|urinary_tract(1)	25						c.(1936-1938)taT>taC		Homo sapiens N(alpha)-acetyltransferase 35, NatC auxiliary subunit (NAA35), mRNA.							115.0	119.0	118.0					9																	88633637		2203	4300	6503	SO:0001819	synonymous_variant	60560				smooth muscle cell proliferation	cytoplasm|nucleus|plasma membrane		g.chr9:88633637T>C	AK025266	CCDS6673.1	9q22.1	2010-01-14	2010-01-14	2010-01-14	ENSG00000135040	ENSG00000135040		"""N(alpha)-acetyltransferase subunits"""	24340	protein-coding gene	gene with protein product			"""MAK10 homolog, amino-acid N-acetyltransferase subunit (S. cerevisiae)"""	MAK10		14702039, 19660095	Standard	NM_024635		Approved	FLJ21613, FLJ22643, bA379P1.1	uc004aoi.4	Q5VZE5	OTTHUMG00000020131	ENST00000361671.5:c.1938T>C	9.37:g.88633637T>C						NAA35_uc004aoj.4_Silent_p.Y646Y	p.Y646Y	NM_024635	NP_078911	Q5VZE5	NAA35_HUMAN			20	2075	+			646					Q5VZE6|Q9H631|Q9H703	Silent	SNP	ENST00000361671.5	37	c.1938T>C	CCDS6673.1																																																																																				0.363	NAA35-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052906.1	NM_024635	
PTPN3	5774	broad.mit.edu	37	9	112189356	112189356	+	Missense_Mutation	SNP	C	C	T	rs374370776		TCGA-76-4929-01A-01D-1486-08	TCGA-76-4929-10A-01D-1486-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	af4f8b89-837a-48b7-b0e7-12aec23fc285	3e0712a1-b66a-42e7-94a3-07edee7dce2b	g.chr9:112189356C>T	ENST00000374541.2	-	12	979	c.875G>A	c.(874-876)cGa>cAa	p.R292Q	PTPN3_ENST00000412145.1_Missense_Mutation_p.R161Q|PTPN3_ENST00000262539.3_Missense_Mutation_p.R183Q|PTPN3_ENST00000446349.1_Missense_Mutation_p.R161Q	NM_001145368.1|NM_002829.3	NP_001138840.1|NP_002820.3	P26045	PTN3_HUMAN	protein tyrosine phosphatase, non-receptor type 3	292	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.				negative regulation of membrane protein ectodomain proteolysis (GO:0051045)|negative regulation of mitotic cell cycle (GO:0045930)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|regulation of membrane depolarization during action potential (GO:0098902)|regulation of sodium ion transmembrane transporter activity (GO:2000649)	cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytoskeleton (GO:0005856)	ATPase binding (GO:0051117)|phosphotyrosine binding (GO:0001784)|protein tyrosine phosphatase activity (GO:0004725)|sodium channel regulator activity (GO:0017080)			breast(1)|endometrium(2)|kidney(2)|large_intestine(8)|liver(1)|lung(14)|ovary(4)|prostate(3)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	41						TTTGCAAGATCGGTAATTCAG	0.448																																						uc004bed.2																			0				breast(1)|endometrium(2)|kidney(2)|large_intestine(8)|liver(1)|lung(14)|ovary(4)|prostate(3)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	41						c.(874-876)cGa>cAa		Homo sapiens protein tyrosine phosphatase, non-receptor type 3 (PTPN3), transcript variant 1, mRNA.		C	GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG	0,4406		0,0,2203	148.0	132.0	137.0		875,482,482,14,14,875	5.8	1.0	9		137	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense,missense,missense,missense,missense	PTPN3	NM_001145368.1,NM_001145369.1,NM_001145370.1,NM_001145371.1,NM_001145372.1,NM_002829.3	43,43,43,43,43,43	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging	292/869,161/783,161/738,5/627,5/582,292/914	112189356	1,13005	2203	4300	6503	SO:0001583	missense	5774				negative regulation of membrane protein ectodomain proteolysis|negative regulation of mitotic cell cycle	cytoplasm|cytoskeleton|internal side of plasma membrane	ATPase binding|cytoskeletal protein binding|phosphotyrosine binding|protein tyrosine phosphatase activity	g.chr9:112189356C>T		CCDS6776.1, CCDS48000.1, CCDS48001.1	9q31	2011-06-09			ENSG00000070159	ENSG00000070159		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"""	9655	protein-coding gene	gene with protein product		176877				1648725	Standard	NM_002829		Approved	PTPH1	uc004bed.2	P26045	OTTHUMG00000020475	ENST00000374541.2:c.875G>A	9.37:g.112189356C>T	ENSP00000363667:p.Arg292Gln					PTPN3_uc004beb.2_Missense_Mutation_p.R161Q|PTPN3_uc004bec.2_Missense_Mutation_p.R161Q|PTPN3_uc010mtu.2_Non-coding_Transcript|PTPN3_uc011lwg.1_Missense_Mutation_p.R292Q|PTPN3_uc011lwh.1_Missense_Mutation_p.R183Q|PTPN3_uc011lwe.1_Missense_Mutation_p.R5Q|PTPN3_uc011lwf.1_Missense_Mutation_p.R5Q	p.R292Q	NM_002829	NP_001138843	P26045	PTN3_HUMAN			11	987	-			292			FERM.		A0AUW9|E7EN99|E9PGU7	Missense_Mutation	SNP	ENST00000374541.2	37	c.875G>A	CCDS6776.1	.	.	.	.	.	.	.	.	.	.	C	35	5.547613	0.96488	0.0	1.16E-4	ENSG00000070159	ENST00000394831;ENST00000412145;ENST00000446349;ENST00000374541;ENST00000262539	D;D;D;D	0.87809	-2.3;-2.3;-2.3;-2.3	5.76	5.76	0.90799	FERM, C-terminal PH-like domain (1);FERM domain (1);Pleckstrin homology-type (1);	0.057506	0.64402	D	0.000007	D	0.93739	0.7999	M	0.79614	2.46	0.80722	D	1	D;D;D	0.89917	1.0;0.999;1.0	D;D;D	0.74674	0.97;0.971;0.984	D	0.93755	0.7062	10	0.72032	D	0.01	.	19.976	0.97309	0.0:1.0:0.0:0.0	.	183;292;292	B7Z3H5;B7Z9V1;P26045	.;.;PTN3_HUMAN	Q	292;161;161;292;183	ENSP00000416654:R161Q;ENSP00000395384:R161Q;ENSP00000363667:R292Q;ENSP00000262539:R183Q	ENSP00000262539:R183Q	R	-	2	0	PTPN3	111229177	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	4.172000	0.58243	2.713000	0.92767	0.655000	0.94253	CGA		0.448	PTPN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053598.4		
RGS3	5998	broad.mit.edu	37	9	116268773	116268773	+	Splice_Site	SNP	G	G	A			TCGA-76-4929-01A-01D-1486-08	TCGA-76-4929-10A-01D-1486-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	af4f8b89-837a-48b7-b0e7-12aec23fc285	3e0712a1-b66a-42e7-94a3-07edee7dce2b	g.chr9:116268773G>A	ENST00000374140.2	+	13	1294	c.1085G>A	c.(1084-1086)cGg>cAg	p.R362Q	RGS3_ENST00000374136.1_5'UTR|RGS3_ENST00000317613.6_Splice_Site_p.R250Q|RGS3_ENST00000394646.3_Splice_Site_p.R81Q|RGS3_ENST00000350696.5_Splice_Site_p.R362Q|RGS3_ENST00000343817.5_Splice_Site_p.R81Q	NM_001282923.1|NM_144488.4	NP_001269852.1|NP_652759.3	P49796	RGS3_HUMAN	regulator of G-protein signaling 3	362	PDZ. {ECO:0000255|PROSITE- ProRule:PRU00143}.				inactivation of MAPK activity (GO:0000188)|positive regulation of GTPase activity (GO:0043547)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	GTPase activator activity (GO:0005096)			cervix(1)|endometrium(3)|kidney(5)|large_intestine(11)|lung(22)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	48						CACGAGATCCGGTGACAGGGG	0.677																																						uc004bhq.3																			0				cervix(1)|endometrium(3)|kidney(5)|large_intestine(11)|lung(22)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	48						c.e13+1		Homo sapiens regulator of G-protein signaling 3 (RGS3), transcript variant 6, mRNA.							28.0	24.0	25.0					9																	116268773		2200	4295	6495	SO:0001630	splice_region_variant	5998				inactivation of MAPK activity|regulation of G-protein coupled receptor protein signaling pathway	cytosol|nucleus|plasma membrane	GTPase activator activity|signal transducer activity	g.chr9:116268773G>A	AF006610	CCDS6797.1, CCDS6798.1, CCDS35113.1, CCDS35114.1, CCDS43869.1, CCDS65111.1	9q32	2008-02-05	2007-08-14		ENSG00000138835	ENSG00000138835		"""Regulators of G-protein signaling"""	9999	protein-coding gene	gene with protein product		602189	"""regulator of G-protein signalling 3"""			8602223, 11034339	Standard	NM_001276260		Approved	C2PA, FLJ20370, PDZ-RGS3	uc004bhq.4	P49796	OTTHUMG00000021048	ENST00000374140.2:c.1085+1G>A	9.37:g.116268773G>A						RGS3_uc004bhr.3_Splice_Site_p.R250_splice|RGS3_uc004bhs.3_Splice_Site_p.R252_splice|RGS3_uc004bht.3_Splice_Site_p.R81_splice|RGS3_uc010muy.3_Splice_Site_p.R81_splice|RGS3_uc004bhu.3_Splice_Site	p.R362_splice	NM_144488	NP_652759	P49796	RGS3_HUMAN			13	1294	+			362			PDZ.		A6NHA0|A8K0V1|B3KUB2|Q5VXB8|Q5VXC1|Q5VZ05|Q5VZ06|Q6ZRM5|Q8IUQ1|Q8NC47|Q8NFN4|Q8NFN5|Q8NFN6|Q8TD59|Q8TD68|Q8WV02|Q8WXA0	Missense_Mutation	SNP	ENST00000374140.2	37	c.1085_splice	CCDS43869.1	.	.	.	.	.	.	.	.	.	.	G	33	5.207995	0.95033	.	.	ENSG00000138835	ENST00000374140;ENST00000350696;ENST00000317613;ENST00000343817;ENST00000394646	T;T;T;T;T	0.29142	1.58;1.58;1.58;1.58;1.58	5.27	4.38	0.52667	PDZ/DHR/GLGF (4);	0.049643	0.85682	N	0.000000	T	0.45518	0.1346	L	0.42008	1.315	0.80722	D	1	B;D;D;D;D	0.89917	0.12;1.0;1.0;1.0;1.0	B;D;D;D;D	0.97110	0.019;1.0;0.999;0.997;0.998	T	0.39057	-0.9632	10	0.56958	D	0.05	.	11.5002	0.50433	0.082:0.0:0.918:0.0	.	81;81;252;250;362	B3KUB2;P49796-4;B3KWG8;P49796-5;P49796	.;.;.;.;RGS3_HUMAN	Q	362;362;250;81;81	ENSP00000363255:R362Q;ENSP00000259406:R362Q;ENSP00000312844:R250Q;ENSP00000340284:R81Q;ENSP00000378141:R81Q	ENSP00000312844:R250Q	R	+	2	0	RGS3	115308594	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.774000	0.91767	1.454000	0.47793	0.655000	0.94253	CGG		0.677	RGS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055561.3	NM_017790	Missense_Mutation
GYG2	8908	broad.mit.edu	37	X	2799206	2799206	+	Silent	SNP	G	G	A			TCGA-76-4929-01A-01D-1486-08	TCGA-76-4929-10A-01D-1486-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	af4f8b89-837a-48b7-b0e7-12aec23fc285	3e0712a1-b66a-42e7-94a3-07edee7dce2b	g.chrX:2799206G>A	ENST00000381163.3	+	12	1740	c.1458G>A	c.(1456-1458)aaG>aaA	p.K486K	GYG2_ENST00000338623.5_Silent_p.K450K|GYG2_ENST00000542787.1_Silent_p.K415K|GYG2_ENST00000381161.1_3'UTR|GYG2_ENST00000398806.3_Silent_p.K455K	NM_001079855.1|NM_001184702.1|NM_003918.2	NP_001073324.1|NP_001171631.1|NP_003909.2	O15488	GLYG2_HUMAN	glycogenin 2	486					carbohydrate metabolic process (GO:0005975)|glucose metabolic process (GO:0006006)|glycogen biosynthetic process (GO:0005978)|glycogen catabolic process (GO:0005980)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	glycogenin glucosyltransferase activity (GO:0008466)			endometrium(1)|kidney(1)|large_intestine(5)|lung(5)|ovary(1)	13		all_cancers(21;4.28e-07)|all_epithelial(21;2.07e-08)|all_lung(23;2.81e-05)|Lung NSC(23;0.000693)|Lung SC(21;0.122)				ACATGGGGAAGGACGCGTTTG	0.552																																						uc004cqs.1																			0				endometrium(1)|kidney(1)|large_intestine(5)|lung(5)|ovary(1)	13						c.(1456-1458)aaG>aaA		Homo sapiens glycogenin 2 (GYG2), transcript variant 2, mRNA.							149.0	89.0	109.0					X																	2799206		2203	4298	6501	SO:0001819	synonymous_variant	8908				glucose metabolic process|glycogen biosynthetic process|glycogen catabolic process	cytosol|soluble fraction	glycogenin glucosyltransferase activity	g.chrX:2799206G>A	U94361	CCDS14121.1, CCDS48074.1	Xp22.3	2013-02-22			ENSG00000056998	ENSG00000056998	2.4.1.186	"""Glycosyltransferase family 8 domain containing"""	4700	protein-coding gene	gene with protein product	"""glycogenin glucosyltransferase"""	300198				9857012	Standard	NM_001079855		Approved	GN-2	uc004cqs.1	O15488	OTTHUMG00000021079	ENST00000381163.3:c.1458G>A	X.37:g.2799206G>A						GYG2_uc004cqu.1_Silent_p.K454K|GYG2_uc004cqx.2_Silent_p.K415K|GYG2_uc004cqt.1_Silent_p.K455K|GYG2_uc004cqv.1_Silent_p.K229K|GYG2_uc004cqw.1_Silent_p.K446K|GYG2_uc010ndc.1_Silent_p.K264K	p.K486K	NM_003918	NP_003909	O15488	GLYG2_HUMAN			11	1740	+		all_cancers(21;4.28e-07)|all_epithelial(21;2.07e-08)|all_lung(23;2.81e-05)|Lung NSC(23;0.000693)|Lung SC(21;0.122)	486					B7WNN6|O15485|O15486|O15487|O15489|O15490	Silent	SNP	ENST00000381163.3	37	c.1458G>A	CCDS14121.1																																																																																				0.552	GYG2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000055645.1	NM_003918	
MXRA5	25878	broad.mit.edu	37	X	3229254	3229254	+	Silent	SNP	G	G	A	rs369770483		TCGA-76-4929-01A-01D-1486-08	TCGA-76-4929-10A-01D-1486-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	af4f8b89-837a-48b7-b0e7-12aec23fc285	3e0712a1-b66a-42e7-94a3-07edee7dce2b	g.chrX:3229254G>A	ENST00000217939.6	-	7	7144	c.6990C>T	c.(6988-6990)gtC>gtT	p.V2330V		NM_015419.3	NP_056234.2	Q9NR99	MXRA5_HUMAN	matrix-remodelling associated 5	2330	Ig-like C2-type 7.					extracellular vesicular exosome (GO:0070062)				NS(1)|biliary_tract(1)|breast(4)|central_nervous_system(3)|cervix(2)|endometrium(8)|kidney(2)|large_intestine(32)|lung(81)|ovary(6)|prostate(3)|skin(9)|stomach(3)|urinary_tract(2)	157		all_lung(23;0.00031)|Lung NSC(23;0.000946)				CGTCCTTCCCGACCTGATTTT	0.542																																						uc004crg.4																			0				NS(1)|biliary_tract(1)|breast(4)|central_nervous_system(3)|cervix(2)|endometrium(8)|kidney(2)|large_intestine(32)|lung(81)|ovary(6)|prostate(3)|skin(9)|stomach(3)|urinary_tract(2)	157						c.(6988-6990)gtC>gtT		Homo sapiens matrix-remodelling associated 5 (MXRA5), mRNA.		G		1,3834		0,1,1631,571	206.0	170.0	182.0		6990	-8.3	0.0	X		182	0,6728		0,0,2428,1872	no	coding-synonymous	MXRA5	NM_015419.3		0,1,4059,2443	AA,AG,GG,G		0.0,0.0261,0.0095		2330/2829	3229254	1,10562	2203	4300	6503	SO:0001819	synonymous_variant	25878					extracellular region		g.chrX:3229254G>A	AF245505	CCDS14124.1	Xp22.33	2013-01-29			ENSG00000101825	ENSG00000101825		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	7539	protein-coding gene	gene with protein product	"""adlican"""					12101425	Standard	NM_015419		Approved	DKFZp564I1922	uc004crg.4	Q9NR99	OTTHUMG00000021083	ENST00000217939.6:c.6990C>T	X.37:g.3229254G>A							p.V2330V	NM_015419	NP_056234	Q9NR99	MXRA5_HUMAN			6	7147	-		all_lung(23;0.00031)|Lung NSC(23;0.000946)	2330			Ig-like C2-type 7.		Q6P1M7|Q9Y3Y8	Silent	SNP	ENST00000217939.6	37	c.6990C>T	CCDS14124.1																																																																																				0.542	MXRA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055655.2	NM_015419	
ARHGAP6	395	broad.mit.edu	37	X	11272748	11272748	+	Missense_Mutation	SNP	T	T	C			TCGA-76-4929-01A-01D-1486-08	TCGA-76-4929-10A-01D-1486-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	af4f8b89-837a-48b7-b0e7-12aec23fc285	3e0712a1-b66a-42e7-94a3-07edee7dce2b	g.chrX:11272748T>C	ENST00000337414.4	-	2	1540	c.668A>G	c.(667-669)gAg>gGg	p.E223G	ARHGAP6_ENST00000380732.3_Missense_Mutation_p.E255G|ARHGAP6_ENST00000380718.1_Missense_Mutation_p.E223G|ARHGAP6_ENST00000303025.6_Missense_Mutation_p.E20G|ARHGAP6_ENST00000413512.3_Missense_Mutation_p.E32G|ARHGAP6_ENST00000534860.1_Missense_Mutation_p.E48G|ARHGAP6_ENST00000380736.1_Missense_Mutation_p.E20G	NM_013427.2	NP_038286.2	O43182	RHG06_HUMAN	Rho GTPase activating protein 6	223					actin filament polymerization (GO:0030041)|activation of phospholipase C activity (GO:0007202)|focal adhesion assembly (GO:0048041)|negative regulation of focal adhesion assembly (GO:0051895)|negative regulation of stress fiber assembly (GO:0051497)|positive regulation of phospholipase activity (GO:0010518)|positive regulation of signal transduction (GO:0009967)|regulation of GTPase activity (GO:0043087)|regulation of small GTPase mediated signal transduction (GO:0051056)|Rho protein signal transduction (GO:0007266)|small GTPase mediated signal transduction (GO:0007264)	actin cytoskeleton (GO:0015629)|actin filament (GO:0005884)|cytoplasm (GO:0005737)|cytosol (GO:0005829)	phospholipase activator activity (GO:0016004)|phospholipase binding (GO:0043274)|Rho GTPase activator activity (GO:0005100)|SH3/SH2 adaptor activity (GO:0005070)			cervix(1)|endometrium(5)|kidney(1)|large_intestine(5)|lung(19)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	38						CCGGGCCCTCTCCAGCTCTGA	0.522																																						uc004cup.1																			0				cervix(1)|endometrium(5)|kidney(1)|large_intestine(5)|lung(19)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	38						c.(667-669)gAg>gGg		Homo sapiens Rho GTPase activating protein 6 (ARHGAP6), transcript variant 1, mRNA.							63.0	60.0	61.0					X																	11272748		2203	4300	6503	SO:0001583	missense	395				actin filament polymerization|activation of phospholipase C activity|negative regulation of focal adhesion assembly|negative regulation of stress fiber assembly|Rho protein signal transduction	actin filament|cytosol	phospholipase activator activity|phospholipase binding|Rho GTPase activator activity|SH3 domain binding|SH3/SH2 adaptor activity	g.chrX:11272748T>C	AF012272	CCDS14140.1, CCDS14141.1, CCDS14142.1	Xp22.3	2008-02-05			ENSG00000047648	ENSG00000047648		"""Rho GTPase activating proteins"""	676	protein-coding gene	gene with protein product		300118				9417914	Standard	XM_005274507		Approved	rhoGAPX-1	uc004cup.1	O43182	OTTHUMG00000021134	ENST00000337414.4:c.668A>G	X.37:g.11272748T>C	ENSP00000338967:p.Glu223Gly					ARHGAP6_uc004cuo.1_Non-coding_Transcript|ARHGAP6_uc004cur.1_Missense_Mutation_p.E223G|ARHGAP6_uc004cum.1_Missense_Mutation_p.E20G|ARHGAP6_uc004cun.1_Missense_Mutation_p.E43G|ARHGAP6_uc010neb.1_Missense_Mutation_p.E45G|ARHGAP6_uc011mif.1_Missense_Mutation_p.E20G	p.E223G	NM_013427	NP_038286	O43182	RHG06_HUMAN			1	1541	-			223					B2RWQ0|O43437|Q9P1B3|Q9UK81|Q9UK82	Missense_Mutation	SNP	ENST00000337414.4	37	c.668A>G	CCDS14140.1	.	.	.	.	.	.	.	.	.	.	T	27.4	4.828276	0.90955	.	.	ENSG00000047648	ENST00000534860;ENST00000380736;ENST00000303025;ENST00000337414;ENST00000380717;ENST00000380718;ENST00000413512;ENST00000380732	T;T;T;T;T;T;T;T	0.70986	-0.43;0.1;0.1;-0.49;-0.43;-0.53;0.0;0.51	4.94	4.94	0.65067	.	0.000000	0.52532	D	0.000074	T	0.81621	0.4861	L	0.61218	1.895	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.91635	0.996;0.999;0.999;0.999;0.999	D	0.83701	0.0182	10	0.87932	D	0	.	13.8014	0.63202	0.0:0.0:0.0:1.0	.	32;20;223;223;223	B7Z8H7;O43182-5;O43182-2;O43182;A8KAL3	.;.;.;RHG06_HUMAN;.	G	48;20;20;223;59;223;32;255	ENSP00000438135:E48G;ENSP00000370112:E20G;ENSP00000302312:E20G;ENSP00000338967:E223G;ENSP00000370093:E59G;ENSP00000370094:E223G;ENSP00000389394:E32G;ENSP00000370108:E255G	ENSP00000302312:E20G	E	-	2	0	ARHGAP6	11182669	1.000000	0.71417	0.993000	0.49108	0.992000	0.81027	7.538000	0.82048	1.634000	0.50500	0.486000	0.48141	GAG		0.522	ARHGAP6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000055760.2	NM_013427	
CDKL5	6792	broad.mit.edu	37	X	18627018	18627018	+	Missense_Mutation	SNP	C	C	T			TCGA-76-4929-01A-01D-1486-08	TCGA-76-4929-10A-01D-1486-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	af4f8b89-837a-48b7-b0e7-12aec23fc285	3e0712a1-b66a-42e7-94a3-07edee7dce2b	g.chrX:18627018C>T	ENST00000379989.3	+	14	2317	c.2032C>T	c.(2032-2034)Cgc>Tgc	p.R678C	CDKL5_ENST00000379996.3_Missense_Mutation_p.R678C|CDKL5_ENST00000463994.1_3'UTR	NM_001037343.1	NP_001032420.1	O76039	CDKL5_HUMAN	cyclin-dependent kinase-like 5	678					neuron migration (GO:0001764)|positive regulation of axon extension (GO:0045773)|positive regulation of dendrite morphogenesis (GO:0050775)|positive regulation of Rac GTPase activity (GO:0032855)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of dendrite development (GO:0050773)	cytoplasm (GO:0005737)|dendrite cytoplasm (GO:0032839)|dendritic growth cone (GO:0044294)|nucleus (GO:0005634)|ruffle membrane (GO:0032587)	ATP binding (GO:0005524)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)|kinase activity (GO:0016301)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|Rac GTPase binding (GO:0048365)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|lung(12)|ovary(4)|skin(5)|stomach(1)	44	Hepatocellular(33;0.183)					CTTCCATACACGCCAGAAGTC	0.433																																						uc004cym.3																			0				NS(2)|breast(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|lung(12)|ovary(4)|skin(5)|stomach(1)	44						c.(2032-2034)Cgc>Tgc		Homo sapiens cyclin-dependent kinase-like 5 (CDKL5), transcript variant I, mRNA.							68.0	57.0	61.0					X																	18627018		2203	4300	6503	SO:0001583	missense	6792				neuron migration|positive regulation of axon extension|positive regulation of dendrite morphogenesis|positive regulation of Rac GTPase activity|protein autophosphorylation	dendrite cytoplasm|dendritic growth cone|nucleus	ATP binding|cyclin-dependent protein kinase activity|Rac GTPase binding	g.chrX:18627018C>T	Y15057	CCDS14186.1	Xp22	2011-11-04	2002-11-26	2002-11-29	ENSG00000008086	ENSG00000008086		"""Cyclin-dependent kinases"""	11411	protein-coding gene	gene with protein product		300203	"""serine/threonine kinase 9"""	STK9		9721213, 16935860	Standard	XM_005274584		Approved	EIEE2	uc004cym.3	O76039	OTTHUMG00000021214	ENST00000379989.3:c.2032C>T	X.37:g.18627018C>T	ENSP00000369325:p.Arg678Cys					CDKL5_uc004cyn.3_Missense_Mutation_p.R678C|CDKL5_uc022btn.1_Missense_Mutation_p.R669C	p.R678C	NM_003159	NP_003150	O76039	CDKL5_HUMAN			12	2285	+	Hepatocellular(33;0.183)		678					G9B9X4|Q14198|Q5H985|Q8IYC7|Q9UJL6	Missense_Mutation	SNP	ENST00000379989.3	37	c.2032C>T	CCDS14186.1	.	.	.	.	.	.	.	.	.	.	c	15.33	2.802395	0.50315	.	.	ENSG00000008086	ENST00000379996;ENST00000379989	T;T	0.75477	-0.94;-0.94	5.81	3.99	0.46301	.	0.099352	0.64402	D	0.000001	T	0.67515	0.2901	L	0.32530	0.975	0.39267	D	0.964324	D	0.61697	0.99	P	0.46885	0.53	T	0.70149	-0.4951	10	0.87932	D	0	-9.8963	10.7377	0.46135	0.1557:0.7103:0.134:0.0	.	678	O76039	CDKL5_HUMAN	C	678	ENSP00000369332:R678C;ENSP00000369325:R678C	ENSP00000369325:R678C	R	+	1	0	CDKL5	18536939	0.527000	0.26306	0.190000	0.23270	0.296000	0.27459	1.064000	0.30579	0.568000	0.29311	0.519000	0.50382	CGC		0.433	CDKL5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055945.2	NM_003159	
IL1RAPL1	11141	broad.mit.edu	37	X	29972739	29972739	+	Silent	SNP	A	A	G			TCGA-76-4929-01A-01D-1486-08	TCGA-76-4929-10A-01D-1486-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	af4f8b89-837a-48b7-b0e7-12aec23fc285	3e0712a1-b66a-42e7-94a3-07edee7dce2b	g.chrX:29972739A>G	ENST00000378993.1	+	10	1975	c.1302A>G	c.(1300-1302)ctA>ctG	p.L434L	IL1RAPL1_ENST00000302196.4_Silent_p.L434L	NM_014271.3	NP_055086.1	Q9NZN1	IRPL1_HUMAN	interleukin 1 receptor accessory protein-like 1	434	TIR. {ECO:0000255|PROSITE- ProRule:PRU00204}.				calcium ion transmembrane transport (GO:0070588)|heterophilic cell-cell adhesion (GO:0007157)|negative regulation of exocytosis (GO:0045920)|neuron differentiation (GO:0030182)|positive regulation of dendrite morphogenesis (GO:0050775)|presynaptic membrane assembly (GO:0097105)|regulation of neuron projection development (GO:0010975)|signal transduction (GO:0007165)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	receptor binding (GO:0005102)|voltage-gated calcium channel activity (GO:0005245)			biliary_tract(1)|breast(1)|endometrium(5)|large_intestine(9)|lung(38)|ovary(3)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	62						TTGAAATCCTACCTGATATGC	0.363																																						uc004dby.2																			0				biliary_tract(1)|breast(1)|endometrium(5)|large_intestine(9)|lung(38)|ovary(3)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	62						c.(1300-1302)ctA>ctG		Homo sapiens interleukin 1 receptor accessory protein-like 1 (IL1RAPL1), mRNA.							101.0	87.0	91.0					X																	29972739		2202	4300	6502	SO:0001819	synonymous_variant	11141				innate immune response|negative regulation of calcium ion transport via voltage-gated calcium channel activity|negative regulation of exocytosis|regulation of neuron projection development	cytoplasm|integral to membrane|plasma membrane	protein binding|transmembrane receptor activity	g.chrX:29972739A>G	AJ243874	CCDS14218.1	Xp22.1-p21.3	2013-01-29	2004-02-13		ENSG00000169306	ENSG00000169306		"""Interleukins and interleukin receptors"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	5996	protein-coding gene	gene with protein product		300206	"""mental retardation, X-linked 34"", ""mental retardation, X-linked 21"", ""mental retardation, X-linked 10"""	IL1RAPL, MRX34, MRX21, MRX10		10471494, 10757639	Standard	NM_014271		Approved	OPHN4, TIGIRR-2, IL1R8	uc004dby.2	Q9NZN1	OTTHUMG00000021317	ENST00000378993.1:c.1302A>G	X.37:g.29972739A>G							p.L434L	NM_014271	NP_055086	Q9NZN1	IRPL1_HUMAN			9	1810	+			434			TIR.		A0AVG4|Q9UJ53	Silent	SNP	ENST00000378993.1	37	c.1302A>G	CCDS14218.1																																																																																				0.363	IL1RAPL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056155.1	NM_014271	
GRIPAP1	56850	broad.mit.edu	37	X	48831638	48831638	+	Missense_Mutation	SNP	G	G	A			TCGA-76-4929-01A-01D-1486-08	TCGA-76-4929-10A-01D-1486-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	af4f8b89-837a-48b7-b0e7-12aec23fc285	3e0712a1-b66a-42e7-94a3-07edee7dce2b	g.chrX:48831638G>A	ENST00000376441.1	-	25	2396	c.2362C>T	c.(2362-2364)Ctt>Ttt	p.L788F	GRIPAP1_ENST00000376425.3_Missense_Mutation_p.L757F|GRIPAP1_ENST00000473581.1_5'Flank|GRIPAP1_ENST00000376444.3_Missense_Mutation_p.L743F	NM_020137.3	NP_064522.3	Q4V328	GRAP1_HUMAN	GRIP1 associated protein 1	788						blood microparticle (GO:0072562)|endosome (GO:0005768)				breast(2)|endometrium(1)|kidney(1)|large_intestine(4)|lung(2)	10						ATCTCCCGAAGGTTCTCGTCG	0.592																																						uc004dly.1																			0				breast(2)|endometrium(1)|kidney(1)|large_intestine(4)|lung(2)	10						c.(2362-2364)Ctt>Ttt		Homo sapiens GRIP1 associated protein 1 (GRIPAP1), transcript variant 1, mRNA.							66.0	50.0	56.0					X																	48831638		2203	4300	6503	SO:0001583	missense	56850					early endosome		g.chrX:48831638G>A	AB032993	CCDS35248.1	Xp11.23	2008-02-05			ENSG00000068400	ENSG00000068400			18706	protein-coding gene	gene with protein product		300408				10896157	Standard	NM_020137		Approved	GRASP-1, GRASP1, KIAA1167, MPMGp800B12492Q3, DKFZp434P0630	uc004dly.1	Q4V328	OTTHUMG00000033192	ENST00000376441.1:c.2362C>T	X.37:g.48831638G>A	ENSP00000365624:p.Leu788Phe						p.L788F	NM_020137	NP_064522	Q4V328	GRAP1_HUMAN			24	2397	-			788					A6NL78|Q3MJ75|Q4V327|Q4V330|Q5HYG1|Q6N046|Q96DH8|Q9NQ43|Q9ULQ3	Missense_Mutation	SNP	ENST00000376441.1	37	c.2362C>T	CCDS35248.1	.	.	.	.	.	.	.	.	.	.	g	18.53	3.642911	0.67244	.	.	ENSG00000068400	ENST00000376425;ENST00000376444;ENST00000376441;ENST00000537291	.	.	.	3.66	3.66	0.41972	.	0.000000	0.64402	U	0.000017	T	0.75953	0.3920	M	0.77820	2.39	0.80722	D	1	D	0.71674	0.998	D	0.68943	0.961	T	0.77552	-0.2545	9	0.48119	T	0.1	-3.4351	11.6458	0.51261	0.0:0.0:1.0:0.0	.	788	Q4V328	GRAP1_HUMAN	F	757;743;788;757	.	ENSP00000365608:L757F	L	-	1	0	GRIPAP1	48716582	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	6.693000	0.74582	1.674000	0.50907	0.488000	0.48403	CTT		0.592	GRIPAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080970.2	NM_207672	
NOX1	27035	broad.mit.edu	37	X	100117739	100117739	+	Silent	SNP	G	G	A			TCGA-76-4929-01A-01D-1486-08	TCGA-76-4929-10A-01D-1486-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	af4f8b89-837a-48b7-b0e7-12aec23fc285	3e0712a1-b66a-42e7-94a3-07edee7dce2b	g.chrX:100117739G>A	ENST00000372966.3	-	5	613	c.408C>T	c.(406-408)tcC>tcT	p.S136S	NOX1_ENST00000372964.1_Silent_p.S136S|NOX1_ENST00000217885.5_Silent_p.S136S|NOX1_ENST00000372960.4_Silent_p.S99S	NM_007052.4|NM_013955.2	NP_008983.2|NP_039249.1	Q9Y5S8	NOX1_HUMAN	NADPH oxidase 1	136	Ferric oxidoreductase.				angiogenesis (GO:0001525)|cell migration (GO:0016477)|cellular response to hyperoxia (GO:0071455)|cellular stress response to acidic pH (GO:1990451)|extracellular matrix organization (GO:0030198)|hydrogen peroxide metabolic process (GO:0042743)|inflammatory response (GO:0006954)|intracellular pH elevation (GO:0051454)|NADP metabolic process (GO:0006739)|oxidation-reduction process (GO:0055114)|oxygen metabolic process (GO:0072592)|positive regulation of cell proliferation (GO:0008284)|positive regulation of integrin biosynthetic process (GO:0045726)|positive regulation of JNK cascade (GO:0046330)|positive regulation of oxidative stress-induced intrinsic apoptotic signaling pathway (GO:1902177)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation vascular endothelial growth factor production (GO:0010575)|proton transport (GO:0015992)|regulation of blood pressure (GO:0008217)|regulation of systemic arterial blood pressure by renin-angiotensin (GO:0003081)|respiratory burst (GO:0045730)|signal transduction (GO:0007165)|superoxide anion generation (GO:0042554)|superoxide metabolic process (GO:0006801)	cell junction (GO:0030054)|early endosome (GO:0005769)|integral component of membrane (GO:0016021)|invadopodium membrane (GO:0071438)|NADPH oxidase complex (GO:0043020)	metal ion binding (GO:0046872)|NADP binding (GO:0050661)|Rac GTPase binding (GO:0048365)|superoxide-generating NADPH oxidase activity (GO:0016175)|voltage-gated proton channel activity (GO:0030171)			cervix(1)|lung(3)|ovary(1)|skin(2)	7						TGGAGGCAAGGGAGCCATCTG	0.453																																						uc004egj.3																			0				cervix(1)|lung(3)|ovary(1)|skin(2)	7						c.(406-408)tcC>tcT		Homo sapiens NADPH oxidase 1 (NOX1), transcript variant NOH-1L, mRNA.							156.0	155.0	155.0					X																	100117739		2203	4299	6502	SO:0001819	synonymous_variant	27035				angiogenesis|cell migration|electron transport chain|FADH2 metabolic process|hydrogen peroxide metabolic process|inflammatory response|intracellular pH elevation|positive regulation of integrin biosynthetic process|positive regulation of smooth muscle cell proliferation|positive regulation vascular endothelial growth factor production|respiratory burst|response to pH|signal transduction|superoxide anion generation	cell junction|early endosome|invadopodium membrane|NADPH oxidase complex	electron carrier activity|flavin adenine dinucleotide binding|iron ion binding|Rac GTPase binding|superoxide-generating NADPH oxidase activity|voltage-gated proton channel activity	g.chrX:100117739G>A	AF127763	CCDS14474.1, CCDS14475.1, CCDS65298.1	Xq22	2008-08-01			ENSG00000007952	ENSG00000007952			7889	protein-coding gene	gene with protein product	"""mitogenic oxidase (pyridine nucleotide-dependent superoxide-generating)"", ""NADPH oxidase homolog-1"", ""NADPH oxidase 1 variant NOH-1L"""	300225				10485709, 10615049	Standard	NM_007052		Approved	NOH1, NOH-1, MOX1, GP91-2	uc004egj.3	Q9Y5S8	OTTHUMG00000022007	ENST00000372966.3:c.408C>T	X.37:g.100117739G>A						NOX1_uc004egl.4_Silent_p.S136S|NOX1_uc010nne.3_Silent_p.S99S	p.S136S	NM_007052	NP_008983	Q9Y5S8	NOX1_HUMAN			4	614	-			136			Ferric oxidoreductase.		A8K836|O95691|Q2PP02	Silent	SNP	ENST00000372966.3	37	c.408C>T	CCDS14474.1																																																																																				0.453	NOX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057495.1	NM_007052	
BHLHB9	80823	broad.mit.edu	37	X	102004877	102004877	+	Silent	SNP	C	C	T			TCGA-76-4929-01A-01D-1486-08	TCGA-76-4929-10A-01D-1486-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	af4f8b89-837a-48b7-b0e7-12aec23fc285	3e0712a1-b66a-42e7-94a3-07edee7dce2b	g.chrX:102004877C>T	ENST00000372735.1	+	4	1539	c.954C>T	c.(952-954)tgC>tgT	p.C318C	BHLHB9_ENST00000361229.4_Silent_p.C318C|BHLHB9_ENST00000447531.1_Silent_p.C318C|BHLHB9_ENST00000457056.1_Silent_p.C318C|BHLHB9_ENST00000448867.1_Silent_p.C318C			Q6PI77	BHLH9_HUMAN	basic helix-loop-helix domain containing, class B, 9	318			C -> R (in dbSNP:rs4514179).		learning or memory (GO:0007611)|negative regulation of neuron apoptotic process (GO:0043524)|positive regulation of dendritic spine morphogenesis (GO:0061003)|positive regulation of neurogenesis (GO:0050769)|positive regulation of synapse assembly (GO:0051965)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	protein homodimerization activity (GO:0042803)			cervix(1)|endometrium(6)|kidney(3)|large_intestine(1)|lung(8)|ovary(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	26						AAATGGAATGCTATATGGATT	0.398																																						uc022cbi.1																			0				cervix(1)|endometrium(6)|kidney(3)|large_intestine(1)|lung(8)|ovary(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	26						c.(952-954)tgC>tgT		Homo sapiens basic helix-loop-helix domain containing, class B, 9 (BHLHB9), transcript variant 2, mRNA.							85.0	80.0	82.0					X																	102004877		2203	4300	6503	SO:0001819	synonymous_variant	80823					cytoplasm|nucleus	binding	g.chrX:102004877C>T	AB051488	CCDS14502.1	Xq23	2014-03-21			ENSG00000198908	ENSG00000198908		"""Basic helix-loop-helix proteins"", ""Armadillo repeat containing"""	29353	protein-coding gene	gene with protein product		300921				11214970, 15034937, 16221301	Standard	NM_030639		Approved	p60TRP, KIAA1701, GASP3	uc011mrv.2	Q6PI77	OTTHUMG00000022060	ENST00000372735.1:c.954C>T	X.37:g.102004877C>T						BHLHB9_uc010nog.3_Silent_p.C318C|BHLHB9_uc011mrq.2_Silent_p.C318C|BHLHB9_uc011mrr.2_Silent_p.C318C|BHLHB9_uc011mrs.2_Silent_p.C318C|BHLHB9_uc011mrt.2_Silent_p.C318C|BHLHB9_uc004ejo.3_Silent_p.C318C|BHLHB9_uc011mru.2_Silent_p.C318C|BHLHB9_uc011mrv.2_Silent_p.C318C	p.C318C	NM_030639	NP_085142	Q6PI77	BHLH9_HUMAN			0	954	+			318		C -> R (in dbSNP:rs4514179).			Q9C0G2	Silent	SNP	ENST00000372735.1	37	c.954C>T	CCDS14502.1																																																																																				0.398	BHLHB9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057630.1	NM_030639	
MAGEA4	4103	broad.mit.edu	37	X	151093031	151093031	+	Missense_Mutation	SNP	C	C	T			TCGA-76-4929-01A-01D-1486-08	TCGA-76-4929-10A-01D-1486-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	af4f8b89-837a-48b7-b0e7-12aec23fc285	3e0712a1-b66a-42e7-94a3-07edee7dce2b	g.chrX:151093031C>T	ENST00000360243.2	+	3	1162	c.895C>T	c.(895-897)Cgc>Tgc	p.R299C	MAGEA4_ENST00000370337.4_Missense_Mutation_p.R299C|MAGEA4_ENST00000370340.3_Missense_Mutation_p.R299C|MAGEA4_ENST00000393921.1_Missense_Mutation_p.R299C|MAGEA4_ENST00000276344.2_Missense_Mutation_p.R299C|MAGEA4_ENST00000393920.1_Missense_Mutation_p.R299C|MAGEA4_ENST00000370335.1_Missense_Mutation_p.R299C	NM_001011550.1	NP_001011550.1	P43358	MAGA4_HUMAN	melanoma antigen family A, 4	299	MAGE. {ECO:0000255|PROSITE- ProRule:PRU00127}.									breast(2)|central_nervous_system(4)|endometrium(1)|kidney(1)|large_intestine(3)|lung(14)|ovary(2)	27	Acute lymphoblastic leukemia(192;6.56e-05)					TGCAAGAGTTCGCATTGCCTA	0.567																																						uc022cgv.1																			0				breast(2)|central_nervous_system(4)|endometrium(1)|kidney(1)|large_intestine(3)|lung(14)|ovary(2)	27						c.(895-897)Cgc>Tgc		Homo sapiens melanoma antigen family A, 4 (MAGEA4), transcript variant 2, mRNA.							118.0	111.0	114.0					X																	151093031		2203	4300	6503	SO:0001583	missense	4103						protein binding	g.chrX:151093031C>T		CCDS14702.1	Xq28	2009-03-13			ENSG00000147381	ENSG00000147381			6802	protein-coding gene	gene with protein product	"""melanoma-associated antigen 4"", ""cancer/testis antigen family 1, member 4"""	300175		MAGE4		8575766	Standard	XM_005274677		Approved	MAGE4A, MAGE4B, MAGE-41, MAGE-X2, MGC21336, CT1.4	uc004ffa.3	P43358	OTTHUMG00000024174	ENST00000360243.2:c.895C>T	X.37:g.151093031C>T	ENSP00000353379:p.Arg299Cys					MAGEA4_uc004fez.3_Missense_Mutation_p.R299C|MAGEA4_uc004ffa.3_Missense_Mutation_p.R299C|MAGEA4_uc004ffb.3_Missense_Mutation_p.R299C|MAGEA4_uc022cgu.1_Missense_Mutation_p.R327C|MAGEA4_uc004ffc.3_Missense_Mutation_p.R299C|MAGEA4_uc004ffd.3_Missense_Mutation_p.R299C	p.R299C	NM_002362	NP_002353	P43358	MAGA4_HUMAN			0	895	+	Acute lymphoblastic leukemia(192;6.56e-05)		299			MAGE.		Q14798	Missense_Mutation	SNP	ENST00000360243.2	37	c.895C>T	CCDS14702.1	.	.	.	.	.	.	.	.	.	.	C	13.89	2.371334	0.42003	.	.	ENSG00000147381	ENST00000276344;ENST00000393921;ENST00000370337;ENST00000393920;ENST00000370340;ENST00000370335;ENST00000360243	T;T;T;T;T;T;T	0.01599	4.74;4.74;4.74;4.74;4.74;4.74;4.74	2.55	2.55	0.30701	.	0.240065	0.42964	D	0.000630	T	0.03390	0.0098	M	0.68317	2.08	0.09310	N	1	D	0.76494	0.999	P	0.47645	0.553	T	0.36890	-0.9729	9	.	.	.	.	7.8294	0.29334	0.0:1.0:0.0:0.0	.	299	P43358	MAGA4_HUMAN	C	299	ENSP00000276344:R299C;ENSP00000377498:R299C;ENSP00000359362:R299C;ENSP00000377497:R299C;ENSP00000359365:R299C;ENSP00000359360:R299C;ENSP00000353379:R299C	.	R	+	1	0	MAGEA4	150843687	0.001000	0.12720	0.002000	0.10522	0.017000	0.09413	0.673000	0.25203	1.554000	0.49487	0.292000	0.19580	CGC		0.567	MAGEA4-010	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060898.1	NM_002362	
