#version 2.4
## 
## Oncotator v1.8.0.0 | Flat File Reference hg19 | GENCODE v19 EFFECT | UniProt_AAxform 2014_12 | ClinVar 12.03.20 | ESP 6500SI-V2 | ORegAnno UCSC Track | dbSNP build 142 | CCLE_By_GP 09292010 | COSMIC v62_291112 | 1000gp3 20130502 | UniProt_AA 2014_12 | dbNSFP v2.4 | ESP 6500SI-V2 | COSMIC_FusionGenes v62_291112 | gencode_xref_refseq metadata_v19 | CCLE_By_Gene 09292010 | ACHILLES_Lineage_Results 110303 | CGC full_2012-03-15 | UniProt 2014_12 | HumanDNARepairGenes 20110905 | HGNC Sept172014 | COSMIC_Tissue 291112 | Familial_Cancer_Genes 20110905 | TUMORScape 20100104 | Ensembl ICGC MUCOPA | TCGAScape 110405 | MutSig Published Results 20110905 
Hugo_Symbol	Entrez_Gene_Id	Center	NCBI_Build	Chromosome	Start_position	End_position	Strand	Variant_Classification	Variant_Type	Reference_Allele	Tumor_Seq_Allele1	Tumor_Seq_Allele2	dbSNP_RS	dbSNP_Val_Status	Tumor_Sample_Barcode	Matched_Norm_Sample_Barcode	Match_Norm_Seq_Allele1	Match_Norm_Seq_Allele2	Tumor_Validation_Allele1	Tumor_Validation_Allele2	Match_Norm_Validation_Allele1	Match_Norm_Validation_Allele2	Verification_Status	Validation_Status	Mutation_Status	Sequencing_Phase	Sequence_Source	Validation_Method	Score	BAM_file	Sequencer	Tumor_Sample_UUID	Matched_Norm_Sample_UUID	Genome_Change	Annotation_Transcript	Transcript_Strand	Transcript_Exon	Transcript_Position	cDNA_Change	Codon_Change	Protein_Change	Other_Transcripts	Refseq_mRNA_Id	Refseq_prot_Id	SwissProt_acc_Id	SwissProt_entry_Id	Description	UniProt_AApos	UniProt_Region	UniProt_Site	UniProt_Natural_Variations	UniProt_Experimental_Info	GO_Biological_Process	GO_Cellular_Component	GO_Molecular_Function	COSMIC_overlapping_mutations	COSMIC_fusion_genes	COSMIC_tissue_types_affected	COSMIC_total_alterations_in_gene	Tumorscape_Amplification_Peaks	Tumorscape_Deletion_Peaks	TCGAscape_Amplification_Peaks	TCGAscape_Deletion_Peaks	DrugBank	ref_context	gc_content	CCLE_ONCOMAP_overlapping_mutations	CCLE_ONCOMAP_total_mutations_in_gene	CGC_Mutation_Type	CGC_Translocation_Partner	CGC_Tumor_Types_Somatic	CGC_Tumor_Types_Germline	CGC_Other_Diseases	DNARepairGenes_Role	FamilialCancerDatabase_Syndromes	MUTSIG_Published_Results	OREGANNO_ID	OREGANNO_Values	i_1000gp3_AA	i_1000gp3_AC	i_1000gp3_AF	i_1000gp3_AFR_AF	i_1000gp3_AMR_AF	i_1000gp3_AN	i_1000gp3_CIEND	i_1000gp3_CIPOS	i_1000gp3_CS	i_1000gp3_DP	i_1000gp3_EAS_AF	i_1000gp3_END	i_1000gp3_EUR_AF	i_1000gp3_IMPRECISE	i_1000gp3_MC	i_1000gp3_MEINFO	i_1000gp3_MEND	i_1000gp3_MLEN	i_1000gp3_MSTART	i_1000gp3_NS	i_1000gp3_SAS_AF	i_1000gp3_SVLEN	i_1000gp3_SVTYPE	i_1000gp3_TSD	i_ACHILLES_Lineage_Results_Top_Genes	i_Annotation_Transcript	i_CCLE_ONCOMAP_overlapping_mutations	i_CCLE_ONCOMAP_total_mutations_in_gene	i_CGC_Cancer Germline Mut	i_CGC_Cancer Molecular Genetics	i_CGC_Cancer Somatic Mut	i_CGC_Cancer Syndrome	i_CGC_Chr	i_CGC_Chr Band	i_CGC_GeneID	i_CGC_Mutation_Type	i_CGC_Name	i_CGC_Other Germline Mut	i_CGC_Other_Diseases	i_CGC_Tissue Type	i_CGC_Translocation_Partner	i_CGC_Tumor_Types_Germline	i_CGC_Tumor_Types_Somatic	i_COSMIC_fusion_genes	i_COSMIC_n_overlapping_mutations	i_COSMIC_overlapping_mutation_descriptions	i_COSMIC_overlapping_mutations	i_COSMIC_overlapping_primary_sites	i_COSMIC_tissue_types_affected	i_COSMIC_total_alterations_in_gene	i_ClinVar_ASSEMBLY	i_ClinVar_HGMD_ID	i_ClinVar_SYM	i_ClinVar_TYPE	i_ClinVar_rs	i_Codon_Change	i_DNARepairGenes_Role	i_Description	i_DrugBank	i_ESP_AA	i_ESP_AAC	i_ESP_AA_AC	i_ESP_AA_AGE	i_ESP_AA_GTC	i_ESP_AvgAAsampleReadDepth	i_ESP_AvgEAsampleReadDepth	i_ESP_AvgSampleReadDepth	i_ESP_CA	i_ESP_CDP	i_ESP_CG	i_ESP_CP	i_ESP_Chromosome	i_ESP_DBSNP	i_ESP_DP	i_ESP_EA_AC	i_ESP_EA_AGE	i_ESP_EA_GTC	i_ESP_EXOME_CHIP	i_ESP_FG	i_ESP_GL	i_ESP_GM	i_ESP_GS	i_ESP_GTC	i_ESP_GTS	i_ESP_GWAS_PUBMED	i_ESP_MAF	i_ESP_PH	i_ESP_PP	i_ESP_Position	i_ESP_TAC	i_ESP_TotalAAsamplesCovered	i_ESP_TotalEAsamplesCovered	i_ESP_TotalSamplesCovered	i_Ensembl_so_accession	i_Ensembl_so_term	i_Entrez_Gene_Id	i_FamilialCancerDatabase_Syndromes	i_Familial_Cancer_Genes_Reference	i_Familial_Cancer_Genes_Synonym	i_GO_Biological_Process	i_GO_Cellular_Component	i_GO_Molecular_Function	i_Genome_Change	i_HGNC_Accession Numbers	i_HGNC_CCDS IDs	i_HGNC_Chromosome	i_HGNC_Date Modified	i_HGNC_Date Name Changed	i_HGNC_Date Symbol Changed	i_HGNC_Ensembl Gene ID	i_HGNC_Ensembl ID(supplied by Ensembl)	i_HGNC_Enzyme IDs	i_HGNC_Gene family description	i_HGNC_HGNC ID	i_HGNC_Locus Group	i_HGNC_Locus Type	i_HGNC_Name Synonyms	i_HGNC_OMIM ID(supplied by NCBI)	i_HGNC_Previous Names	i_HGNC_Previous Symbols	i_HGNC_Primary IDs	i_HGNC_Pubmed IDs	i_HGNC_Record Type	i_HGNC_RefSeq(supplied by NCBI)	i_HGNC_Secondary IDs	i_HGNC_Status	i_HGNC_Synonyms	i_HGNC_UCSC ID(supplied by UCSC)	i_HGNC_UniProt ID(supplied by UniProt)	i_HGNC_VEGA IDs	i_HGVS_coding_DNA_change	i_HGVS_genomic_change	i_HGVS_protein_change	i_MUTSIG_Published_Results	i_OREGANNO_ID	i_OREGANNO_Values	i_ORegAnno_bin	i_Other_Transcripts	i_Protein_Change	i_Refseq_mRNA_Id	i_Refseq_prot_Id	i_SwissProt_acc_Id	i_SwissProt_entry_Id	i_TCGAscape_Amplification_Peaks	i_TCGAscape_Deletion_Peaks	i_Transcript_Exon	i_Transcript_Position	i_Transcript_Strand	i_Tumorscape_Amplification_Peaks	i_Tumorscape_Deletion_Peaks	i_UniProt_AApos	i_UniProt_Experimental_Info	i_UniProt_Natural_Variations	i_UniProt_Region	i_UniProt_Site	i_UniProt_alt_uniprot_accessions	i_Variant_Classification	i_Variant_Type	i_annotation_transcript	i_build	i_cDNA_Change	i_ccds_id	i_dbNSFP_1000Gp1_AC	i_dbNSFP_1000Gp1_AF	i_dbNSFP_1000Gp1_AFR_AC	i_dbNSFP_1000Gp1_AFR_AF	i_dbNSFP_1000Gp1_AMR_AC	i_dbNSFP_1000Gp1_AMR_AF	i_dbNSFP_1000Gp1_ASN_AC	i_dbNSFP_1000Gp1_ASN_AF	i_dbNSFP_1000Gp1_EUR_AC	i_dbNSFP_1000Gp1_EUR_AF	i_dbNSFP_Ancestral_allele	i_dbNSFP_CADD_phred	i_dbNSFP_CADD_raw	i_dbNSFP_CADD_raw_rankscore	i_dbNSFP_ESP6500_AA_AF	i_dbNSFP_ESP6500_EA_AF	i_dbNSFP_Ensembl_geneid	i_dbNSFP_Ensembl_transcriptid	i_dbNSFP_FATHMM_pred	i_dbNSFP_FATHMM_rankscore	i_dbNSFP_FATHMM_score	i_dbNSFP_GERP++_NR	i_dbNSFP_GERP++_RS	i_dbNSFP_GERP++_RS_rankscore	i_dbNSFP_Interpro_domain	i_dbNSFP_LRT_Omega	i_dbNSFP_LRT_converted_rankscore	i_dbNSFP_LRT_pred	i_dbNSFP_LRT_score	i_dbNSFP_LR_pred	i_dbNSFP_LR_rankscore	i_dbNSFP_LR_score	i_dbNSFP_MutationAssessor_pred	i_dbNSFP_MutationAssessor_rankscore	i_dbNSFP_MutationAssessor_score	i_dbNSFP_MutationTaster_converted_rankscore	i_dbNSFP_MutationTaster_pred	i_dbNSFP_MutationTaster_score	i_dbNSFP_Polyphen2_HDIV_pred	i_dbNSFP_Polyphen2_HDIV_rankscore	i_dbNSFP_Polyphen2_HDIV_score	i_dbNSFP_Polyphen2_HVAR_pred	i_dbNSFP_Polyphen2_HVAR_rankscore	i_dbNSFP_Polyphen2_HVAR_score	i_dbNSFP_RadialSVM_pred	i_dbNSFP_RadialSVM_rankscore	i_dbNSFP_RadialSVM_score	i_dbNSFP_Reliability_index	i_dbNSFP_SIFT_converted_rankscore	i_dbNSFP_SIFT_pred	i_dbNSFP_SIFT_score	i_dbNSFP_SLR_test_statistic	i_dbNSFP_SiPhy_29way_logOdds	i_dbNSFP_SiPhy_29way_logOdds_rankscore	i_dbNSFP_SiPhy_29way_pi	i_dbNSFP_UniSNP_ids	i_dbNSFP_Uniprot_aapos	i_dbNSFP_Uniprot_acc	i_dbNSFP_Uniprot_id	i_dbNSFP_aaalt	i_dbNSFP_aapos	i_dbNSFP_aapos_FATHMM	i_dbNSFP_aapos_SIFT	i_dbNSFP_aaref	i_dbNSFP_cds_strand	i_dbNSFP_codonpos	i_dbNSFP_fold-degenerate	i_dbNSFP_genename	i_dbNSFP_hg18_pos(1-coor)	i_dbNSFP_phastCons100way_vertebrate	i_dbNSFP_phastCons100way_vertebrate_rankscore	i_dbNSFP_phastCons46way_placental	i_dbNSFP_phastCons46way_placental_rankscore	i_dbNSFP_phastCons46way_primate	i_dbNSFP_phastCons46way_primate_rankscore	i_dbNSFP_phyloP100way_vertebrate	i_dbNSFP_phyloP100way_vertebrate_rankscore	i_dbNSFP_phyloP46way_placental	i_dbNSFP_phyloP46way_placental_rankscore	i_dbNSFP_phyloP46way_primate	i_dbNSFP_phyloP46way_primate_rankscore	i_dbNSFP_refcodon	i_entrez_gene_id	i_gc_content_full	i_gencode_transcript_name	i_gencode_transcript_status	i_gencode_transcript_tags	i_gencode_transcript_type	i_gene_type	i_havana_transcript	i_refseq_mrna_id	i_secondary_variant_classification	i_t_alt_count_full	i_t_ref_count_full	isArtifactMode	oxoGCut	pox	pox_cutoff	qox	t_alt_count	t_ref_count	validation_alt_allele	validation_method	validation_status	validation_tumor_sample
CALCRL	10203	broad.mit.edu	37	2	188225389	188225389	+	Silent	SNP	T	T	G			TCGA-CS-4943-01A-01D-1468-08	TCGA-CS-4943-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	14627ffd-642c-42b5-9d95-ad436c9b1d35	0d4a92bf-0624-4dfa-9d95-8f91a693ea3f	g.chr2:188225389T>G	ENST00000409998.1	-	11	1498	c.717A>C	c.(715-717)acA>acC	p.T239T	CALCRL_ENST00000392370.3_Silent_p.T239T|CALCRL_ENST00000410068.1_Silent_p.T239T|AC007319.1_ENST00000412276.1_RNA|AC007319.1_ENST00000453517.1_RNA			Q16602	CALRL_HUMAN	calcitonin receptor-like	239					adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|angiogenesis (GO:0001525)|calcium ion transport (GO:0006816)|cAMP biosynthetic process (GO:0006171)|cellular response to sucrose stimulus (GO:0071329)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|heart development (GO:0007507)|negative regulation of inflammatory response (GO:0050728)|positive regulation of cAMP biosynthetic process (GO:0030819)|positive regulation of smooth muscle cell proliferation (GO:0048661)|protein transport (GO:0015031)|receptor internalization (GO:0031623)|regulation of muscle contraction (GO:0006937)	endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)|lysosome (GO:0005764)|plasma membrane (GO:0005886)	adrenomedullin receptor activity (GO:0001605)|calcitonin gene-related polypeptide receptor activity (GO:0001635)|calcitonin receptor activity (GO:0004948)|G-protein coupled receptor activity (GO:0004930)|protein transporter activity (GO:0008565)			endometrium(1)|large_intestine(7)|lung(21)|ovary(1)|prostate(1)|skin(1)	32			OV - Ovarian serous cystadenocarcinoma(117;0.0554)|Epithelial(96;0.227)			CCACAATGAGTGTGTGTAGGT	0.403																																						ENST00000409998.1																			0				endometrium(1)|large_intestine(7)|lung(21)|ovary(1)|prostate(1)|skin(1)	32						c.(715-717)acA>acC		calcitonin receptor-like							96.0	85.0	88.0					2																	188225389		2203	4300	6503	SO:0001819	synonymous_variant	10203					integral to plasma membrane		g.chr2:188225389T>G	U17473	CCDS2293.1	2q21.1-q21.3	2012-08-10			ENSG00000064989	ENSG00000064989		"""GPCR / Class B : Calcitonin receptors"""	16709	protein-coding gene	gene with protein product		114190				7818539, 8626685	Standard	NM_005795		Approved	CGRPR, CRLR	uc010frt.4	Q16602	OTTHUMG00000132636	ENST00000409998.1:c.717A>C	2.37:g.188225389T>G						AC007319.1_ENST00000453517.1_RNA|CALCRL_ENST00000392370.3_Silent_p.T239T|CALCRL_ENST00000410068.1_Silent_p.T239T|AC007319.1_ENST00000412276.1_RNA	p.T239T			Q16602	CALRL_HUMAN	OV - Ovarian serous cystadenocarcinoma(117;0.0554)|Epithelial(96;0.227)		11	1498	-			239					A8K6G5|A8KAD3|Q53S02|Q53TS5	Silent	SNP	ENST00000409998.1	37	c.717A>C	CCDS2293.1																																																																																				0.403	CALCRL-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334648.1	NM_005795		36	42	0	0	0	0.796494	0	36	42				
RYR1	6261	broad.mit.edu	37	19	39070725	39070725	+	Missense_Mutation	SNP	C	C	T	rs148540135		TCGA-CS-4943-01A-01D-1468-08	TCGA-CS-4943-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	14627ffd-642c-42b5-9d95-ad436c9b1d35	0d4a92bf-0624-4dfa-9d95-8f91a693ea3f	g.chr19:39070725C>T	ENST00000359596.3	+	100	14468	c.14468C>T	c.(14467-14469)aCg>aTg	p.T4823M	RYR1_ENST00000360985.3_Missense_Mutation_p.T4818M|RYR1_ENST00000355481.4_Missense_Mutation_p.T4818M			P21817	RYR1_HUMAN	ryanodine receptor 1 (skeletal)	4823					calcium ion transport (GO:0006816)|cellular response to caffeine (GO:0071313)|cytosolic calcium ion homeostasis (GO:0051480)|ion transmembrane transport (GO:0034220)|muscle contraction (GO:0006936)|ossification involved in bone maturation (GO:0043931)|outflow tract morphogenesis (GO:0003151)|release of sequestered calcium ion into cytosol (GO:0051209)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|skeletal muscle fiber development (GO:0048741)|skin development (GO:0043588)|transmembrane transport (GO:0055085)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|I band (GO:0031674)|integral component of plasma membrane (GO:0005887)|junctional membrane complex (GO:0030314)|junctional sarcoplasmic reticulum membrane (GO:0014701)|plasma membrane (GO:0005886)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|T-tubule (GO:0030315)|terminal cisterna (GO:0014802)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-release channel activity (GO:0015278)|calmodulin binding (GO:0005516)|ryanodine-sensitive calcium-release channel activity (GO:0005219)|voltage-gated calcium channel activity (GO:0005245)			NS(4)|autonomic_ganglia(2)|breast(3)|central_nervous_system(5)|endometrium(26)|haematopoietic_and_lymphoid_tissue(3)|kidney(34)|large_intestine(42)|liver(1)|lung(106)|ovary(11)|pancreas(5)|prostate(9)|skin(12)|stomach(11)|upper_aerodigestive_tract(4)|urinary_tract(7)	285	all_cancers(60;7.91e-06)		Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272)		Caffeine(DB00201)|Dantrolene(DB01219)|Suramin(DB04786)	GGGGTCAAGACGCTGCGCACC	0.597																																						ENST00000355481.4																			0				NS(4)|autonomic_ganglia(2)|breast(3)|central_nervous_system(5)|endometrium(26)|haematopoietic_and_lymphoid_tissue(3)|kidney(34)|large_intestine(42)|liver(1)|lung(106)|ovary(11)|pancreas(5)|prostate(9)|skin(12)|stomach(11)|upper_aerodigestive_tract(4)|urinary_tract(7)	285	GRCh37	CM083554	RYR1	M	rs148540135	c.(14452-14454)aCg>aTg		ryanodine receptor 1 (skeletal)	Dantrolene(DB01219)	C	MET/THR,MET/THR	1,4405	2.1+/-5.4	0,1,2202	122.0	85.0	98.0		14468,14453	4.6	1.0	19	dbSNP_134	98	0,8600		0,0,4300	no	missense,missense	RYR1	NM_000540.2,NM_001042723.1	81,81	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	probably-damaging,probably-damaging	4823/5039,4818/5034	39070725	1,13005	2203	4300	6503	SO:0001583	missense	6261				muscle contraction|release of sequestered calcium ion into cytosol|response to caffeine|response to hypoxia	cell cortex|cytosol|I band|integral to plasma membrane|junctional sarcoplasmic reticulum membrane|smooth endoplasmic reticulum|terminal cisterna	calcium ion binding|calmodulin binding|receptor activity|ryanodine-sensitive calcium-release channel activity	g.chr19:39070725C>T	J05200	CCDS33011.1, CCDS42563.1	19q13.1	2014-09-17				ENSG00000196218		"""Ion channels / Ryanodine receptors"""	10483	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 137"""	180901	"""central core disease of muscle"""	MHS, MHS1, CCO		1862346, 16621918	Standard	NM_000540		Approved	RYR, PPP1R137	uc002oit.3	P21817		ENST00000359596.3:c.14468C>T	19.37:g.39070725C>T	ENSP00000352608:p.Thr4823Met					RYR1_ENST00000360985.3_Missense_Mutation_p.T4818M|RYR1_ENST00000359596.3_Missense_Mutation_p.T4823M	p.T4818M	NM_000540.2|NM_001042723.1	NP_000531.2|NP_001036188.1	P21817	RYR1_HUMAN	Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272)		99	14584	+	all_cancers(60;7.91e-06)		4823					Q16314|Q16368|Q9NPK1|Q9P1U4	Missense_Mutation	SNP	ENST00000359596.3	37	c.14453C>T	CCDS33011.1	.	.	.	.	.	.	.	.	.	.	C	15.15	2.746556	0.49257	2.27E-4	0.0	ENSG00000196218	ENST00000359596;ENST00000355481;ENST00000360985	D;D;D	0.98617	-5.03;-5.03;-5.03	4.57	4.57	0.56435	Ion transport (1);	0.000000	0.64402	U	0.000001	D	0.99026	0.9667	M	0.80422	2.495	0.58432	D	0.999999	D;D	0.89917	1.0;1.0	D;D	0.91635	0.998;0.999	D	0.99342	1.0912	10	0.36615	T	0.2	.	17.129	0.86722	0.0:1.0:0.0:0.0	.	4818;4823	P21817-2;P21817	.;RYR1_HUMAN	M	4823;4818;4818	ENSP00000352608:T4823M;ENSP00000347667:T4818M;ENSP00000354254:T4818M	ENSP00000347667:T4818M	T	+	2	0	RYR1	43762565	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	7.617000	0.83032	2.357000	0.79964	0.462000	0.41574	ACG		0.597	RYR1-010	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000462137.1			43	52	0	0	0	0.859065	0	43	52				
MT-ND5	4540	broad.mit.edu	37	M	13133	13133	+	Missense_Mutation	SNP	T	T	C			TCGA-CS-4943-01A-01D-1468-08	TCGA-CS-4943-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	14627ffd-642c-42b5-9d95-ad436c9b1d35	0d4a92bf-0624-4dfa-9d95-8f91a693ea3f	g.chrM:13133T>C	ENST00000361567.2	+	1	797	c.797T>C	c.(796-798)cTa>cCa	p.L266P	MT-TH_ENST00000387441.1_RNA|MT-TP_ENST00000387461.2_RNA|MT-TL2_ENST00000387456.1_RNA|MT-TS2_ENST00000387449.1_RNA|MT-TE_ENST00000387459.1_RNA|MT-TR_ENST00000387439.1_RNA|MT-TT_ENST00000387460.2_RNA|MT-CYB_ENST00000361789.2_5'Flank			P03915	NU5M_HUMAN	mitochondrially encoded NADH dehydrogenase 5	266					cellular metabolic process (GO:0044237)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex I (GO:0005747)	NADH dehydrogenase (ubiquinone) activity (GO:0008137)			breast(4)|endometrium(29)|kidney(33)|pancreas(1)|prostate(7)	74						CTTCCACCCCCTAGCAGAAAA	0.502																																						ENST00000361567.2																			0				breast(4)|endometrium(29)|kidney(33)|pancreas(1)|prostate(7)	74						c.(796-798)cTa>cCa		mitochondrially encoded NADH dehydrogenase 5	NADH(DB00157)																																			SO:0001583	missense	4540				mitochondrial electron transport, NADH to ubiquinone|transport	integral to membrane|mitochondrial respiratory chain complex I	NADH dehydrogenase (ubiquinone) activity	g.chrM:13133T>C			mitochondria	2011-07-04	2005-02-15	2005-02-16	ENSG00000198786	ENSG00000198786	1.6.5.3	"""Mitochondrial respiratory chain complex / Complex I"""	7461	protein-coding gene	gene with protein product	"""complex I ND5 subunit"", ""NADH-ubiquinone oxidoreductase chain 5"""	516005	"""NADH dehydrogenase 5"""	MTND5			Standard			Approved	ND5, NAD5		P03915		ENST00000361567.2:c.797T>C	M.37:g.13133T>C	ENSP00000354813:p.Leu266Pro						p.L266P			P03915	NU5M_HUMAN			1	797	+			266					Q34773|Q8WCY3	Missense_Mutation	SNP	ENST00000361567.2	37	c.797T>C																																																																																					0.502	MT-ND5-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		YP_003024036		7	186	0	0	0	0.248553	0	7	186				
RSPH14	27156	broad.mit.edu	37	22	23404005	23404005	+	Missense_Mutation	SNP	C	C	T			TCGA-CS-4943-01A-01D-1468-08	TCGA-CS-4943-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	14627ffd-642c-42b5-9d95-ad436c9b1d35	0d4a92bf-0624-4dfa-9d95-8f91a693ea3f	g.chr22:23404005C>T	ENST00000216036.4	-	6	968	c.772G>A	c.(772-774)Gcc>Acc	p.A258T		NM_014433.2	NP_055248.1	Q9UHP6	RTDR1_HUMAN		258										breast(1)|endometrium(3)|large_intestine(4)|lung(6)|ovary(1)|prostate(1)|stomach(1)|urinary_tract(1)	18	all_hematologic(9;0.0197)|Acute lymphoblastic leukemia(84;0.181)			READ - Rectum adenocarcinoma(21;0.175)		ATCACTGTGGCGAACATCAGG	0.587																																						ENST00000216036.4																			0				breast(1)|endometrium(3)|large_intestine(4)|lung(6)|ovary(1)|prostate(1)|stomach(1)|urinary_tract(1)	18						c.(772-774)Gcc>Acc		rhabdoid tumor deletion region gene 1							89.0	68.0	75.0					22																	23404005		2203	4300	6503	SO:0001583	missense	27156						binding	g.chr22:23404005C>T																												ENST00000216036.4:c.772G>A	22.37:g.23404005C>T	ENSP00000216036:p.Ala258Thr						p.A258T	NM_014433.2	NP_055248.1	Q9UHP6	RTDR1_HUMAN		READ - Rectum adenocarcinoma(21;0.175)	6	968	-	all_hematologic(9;0.0197)|Acute lymphoblastic leukemia(84;0.181)		258						Missense_Mutation	SNP	ENST00000216036.4	37	c.772G>A	CCDS13803.1	.	.	.	.	.	.	.	.	.	.	C	3.695	-0.062667	0.07273	.	.	ENSG00000100218	ENST00000216036	T	0.48836	0.8	4.77	3.72	0.42706	Armadillo-like helical (1);Armadillo-type fold (1);	0.444604	0.22403	N	0.060514	T	0.34454	0.0898	L	0.59436	1.845	0.21147	N	0.999775	P	0.43578	0.811	B	0.28849	0.095	T	0.30475	-0.9977	10	0.40728	T	0.16	-12.2163	7.9737	0.30143	0.0:0.8749:0.0:0.1251	.	258	Q9UHP6	RTDR1_HUMAN	T	258	ENSP00000216036:A258T	ENSP00000216036:A258T	A	-	1	0	RTDR1	21734005	0.945000	0.32115	0.014000	0.15608	0.007000	0.05969	2.613000	0.46351	1.076000	0.40961	0.462000	0.41574	GCC		0.587	RTDR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319049.1			12	24	0	0	0	0.435327	0	12	24				
SULF2	55959	broad.mit.edu	37	20	46291893	46291893	+	Missense_Mutation	SNP	T	T	C	rs145371797		TCGA-CS-4943-01A-01D-1468-08	TCGA-CS-4943-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	14627ffd-642c-42b5-9d95-ad436c9b1d35	0d4a92bf-0624-4dfa-9d95-8f91a693ea3f	g.chr20:46291893T>C	ENST00000359930.4	-	17	3142	c.2291A>G	c.(2290-2292)aAt>aGt	p.N764S	SULF2_ENST00000361612.4_Missense_Mutation_p.N764S|SULF2_ENST00000467815.1_Missense_Mutation_p.N764S|SULF2_ENST00000484875.1_Missense_Mutation_p.N764S	NM_018837.3	NP_061325.1	Q8IWU5	SULF2_HUMAN	sulfatase 2	764					bone development (GO:0060348)|cartilage development (GO:0051216)|chondrocyte development (GO:0002063)|embryonic skeletal system development (GO:0048706)|esophagus smooth muscle contraction (GO:0014846)|glial cell-derived neurotrophic factor receptor signaling pathway (GO:0035860)|glomerular basement membrane development (GO:0032836)|glomerular filtration (GO:0003094)|heparan sulfate proteoglycan metabolic process (GO:0030201)|innervation (GO:0060384)|kidney development (GO:0001822)|negative regulation of fibroblast growth factor receptor signaling pathway (GO:0040037)|positive regulation of Wnt signaling pathway (GO:0030177)|positive regulation vascular endothelial growth factor production (GO:0010575)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)	arylsulfatase activity (GO:0004065)|calcium ion binding (GO:0005509)|N-acetylglucosamine-6-sulfatase activity (GO:0008449)			breast(2)|endometrium(4)|kidney(1)|large_intestine(7)|lung(22)|ovary(4)|pancreas(1)|prostate(5)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	54						GTGAGTCTCATTGATGGTCCT	0.517											OREG0026005	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																										ENST00000359930.4																			0				breast(2)|endometrium(4)|kidney(1)|large_intestine(7)|lung(22)|ovary(4)|pancreas(1)|prostate(5)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	54						c.(2290-2292)aAt>aGt		sulfatase 2		T	SER/ASN,SER/ASN,SER/ASN	0,4406		0,0,2203	184.0	163.0	170.0		2291,2291,2291	5.7	1.0	20	dbSNP_134	170	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense,missense	SULF2	NM_001161841.1,NM_018837.3,NM_198596.2	46,46,46	0,1,6502	CC,CT,TT		0.0116,0.0,0.0077	possibly-damaging,possibly-damaging,possibly-damaging	764/871,764/871,764/868	46291893	1,13005	2203	4300	6503	SO:0001583	missense	55959				bone development|heparan sulfate proteoglycan metabolic process|kidney development|negative regulation of fibroblast growth factor receptor signaling pathway	cell surface|endoplasmic reticulum|extracellular space|Golgi stack	arylsulfatase activity|calcium ion binding	g.chr20:46291893T>C	AY101176	CCDS13408.1, CCDS13409.1, CCDS13409.2	20q13.12-q13.13	2008-05-14			ENSG00000196562	ENSG00000196562			20392	protein-coding gene	gene with protein product		610013				12368295	Standard	NM_018837		Approved	KIAA1247, HSULF-2, SULF-2	uc002xto.3	Q8IWU5	OTTHUMG00000032675	ENST00000359930.4:c.2291A>G	20.37:g.46291893T>C	ENSP00000353007:p.Asn764Ser		OREG0026005	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	938	SULF2_ENST00000467815.1_Missense_Mutation_p.N764S|SULF2_ENST00000361612.4_Missense_Mutation_p.N764S|SULF2_ENST00000484875.1_Missense_Mutation_p.N764S	p.N764S	NM_018837.3	NP_061325.1	Q8IWU5	SULF2_HUMAN			17	3142	-			764					E1P5U6|Q5JYE1|Q6UX86|Q96SG2|Q9H1H0|Q9UJR3|Q9ULH3	Missense_Mutation	SNP	ENST00000359930.4	37	c.2291A>G	CCDS13408.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	28.4|28.4	4.915498|4.915498	0.92178|0.92178	0.0|0.0	1.16E-4|1.16E-4	ENSG00000196562|ENSG00000196562	ENST00000495544|ENST00000359930;ENST00000484875;ENST00000361612;ENST00000371978;ENST00000467815	.|T;T;T;T	.|0.26223	.|1.75;1.75;1.75;1.75	5.69|5.69	5.69|5.69	0.88448|0.88448	.|Alkaline-phosphatase-like, core domain (1);	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.44159|0.44159	0.1280|0.1280	L|L	0.43701|0.43701	1.375|1.375	0.58432|0.58432	D|D	0.999992|0.999992	.|D;D	.|0.89917	.|1.0;0.998	.|D;D	.|0.87578	.|0.998;0.99	T|T	0.22173|0.22173	-1.0224|-1.0224	5|10	.|0.45353	.|T	.|0.12	-22.3956|-22.3956	15.9538|15.9538	0.79865|0.79865	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	.|764;764	.|Q8IWU5-2;Q8IWU5	.|.;SULF2_HUMAN	V|S	119|764;764;764;183;764	.|ENSP00000353007:N764S;ENSP00000418290:N764S;ENSP00000354662:N764S;ENSP00000418442:N764S	.|ENSP00000353007:N764S	M|N	-|-	1|2	0|0	SULF2|SULF2	45725300|45725300	1.000000|1.000000	0.71417|0.71417	0.999000|0.999000	0.59377|0.59377	0.982000|0.982000	0.71751|0.71751	8.040000|8.040000	0.89188|0.89188	2.185000|2.185000	0.69588|0.69588	0.454000|0.454000	0.30748|0.30748	ATG|AAT		0.517	SULF2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079606.1	NM_018837		5	102	0	0	0	0.184627	0	5	102				
CDKN2A	1029	broad.mit.edu	37	9	21974684	21974684	+	Missense_Mutation	SNP	G	G	C			TCGA-CS-4943-01A-01D-1468-08	TCGA-CS-4943-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	14627ffd-642c-42b5-9d95-ad436c9b1d35	0d4a92bf-0624-4dfa-9d95-8f91a693ea3f	g.chr9:21974684G>C	ENST00000304494.5	-	1	413	c.143C>G	c.(142-144)cCg>cGg	p.P48R	CDKN2A_ENST00000446177.1_Missense_Mutation_p.P48R|CDKN2A_ENST00000494262.1_Intron|CDKN2A_ENST00000579122.1_Missense_Mutation_p.P48R|CDKN2A_ENST00000498124.1_Missense_Mutation_p.P48R|CDKN2A_ENST00000530628.2_Intron|CDKN2A_ENST00000361570.3_Intron|CDKN2A_ENST00000579755.1_Intron|RP11-145E5.5_ENST00000404796.2_Intron|CDKN2A_ENST00000498628.2_Intron	NM_000077.4	NP_000068.1	P42771	CD2A1_HUMAN	cyclin-dependent kinase inhibitor 2A	48			P -> L (in CMM2 and a head and neck tumor; somatic mutation). {ECO:0000269|PubMed:10651484}.		cell cycle arrest (GO:0007050)|cell cycle checkpoint (GO:0000075)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of phosphorylation (GO:0042326)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of cellular senescence (GO:2000774)|positive regulation of macrophage apoptotic process (GO:2000111)|positive regulation of smooth muscle cell apoptotic process (GO:0034393)|Ras protein signal transduction (GO:0007265)|replicative senescence (GO:0090399)|senescence-associated heterochromatin focus assembly (GO:0035986)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|senescence-associated heterochromatin focus (GO:0035985)	cyclin-dependent protein serine/threonine kinase inhibitor activity (GO:0004861)|NF-kappaB binding (GO:0051059)|poly(A) RNA binding (GO:0044822)|protein kinase binding (GO:0019901)	p.0?(1315)|p.?(25)|p.P48L(8)|p.P48R(1)|p.0(1)|p.V28_V51del(1)		NS(28)|adrenal_gland(6)|autonomic_ganglia(11)|biliary_tract(74)|bone(84)|breast(46)|central_nervous_system(522)|cervix(23)|endometrium(14)|eye(4)|genital_tract(15)|haematopoietic_and_lymphoid_tissue(698)|kidney(39)|large_intestine(11)|liver(92)|lung(365)|meninges(18)|oesophagus(239)|ovary(98)|pancreas(263)|pleura(94)|prostate(13)|salivary_gland(10)|skin(541)|small_intestine(1)|soft_tissue(93)|stomach(48)|thymus(4)|thyroid(24)|upper_aerodigestive_tract(436)|urinary_tract(283)|vulva(2)	4199		all_cancers(5;0)|Acute lymphoblastic leukemia(3;0)|all_hematologic(3;0)|all_epithelial(2;2.37e-290)|Lung NSC(2;1.26e-139)|all_lung(2;4.48e-131)|Glioma(2;3.26e-60)|all_neural(2;2.1e-52)|Renal(3;1.07e-46)|Esophageal squamous(3;3.83e-46)|Melanoma(2;2.74e-34)|Breast(3;1.14e-11)|Ovarian(3;0.000128)|Hepatocellular(5;0.00162)|Colorectal(97;0.172)		all cancers(2;0)|GBM - Glioblastoma multiforme(3;0)|Lung(2;4.07e-74)|Epithelial(2;1.08e-61)|LUSC - Lung squamous cell carcinoma(2;3.82e-48)|LUAD - Lung adenocarcinoma(2;4.56e-26)|OV - Ovarian serous cystadenocarcinoma(39;7.64e-10)|BRCA - Breast invasive adenocarcinoma(2;5.01e-09)|STAD - Stomach adenocarcinoma(4;4.63e-07)|Kidney(2;5.79e-07)|KIRC - Kidney renal clear cell carcinoma(2;7.27e-07)|COAD - Colon adenocarcinoma(8;5.15e-05)		CACCTGGATCGGCCTCCGACC	0.677		17								HNSCC(2;<9.43e_08)|TSP Lung(5;3.83e-07)																												ENST00000304494.5		17																	1351	Whole gene deletion(1316)|Unknown(25)|Substitution - Missense(9)|Deletion - In frame(1)	p.0?(1315)|p.?(25)|p.P48L(8)|p.P48R(1)|p.0(1)|p.V28_V51del(1)	haematopoietic_and_lymphoid_tissue(278)|skin(173)|central_nervous_system(163)|lung(148)|urinary_tract(90)|bone(73)|soft_tissue(57)|pleura(52)|oesophagus(50)|upper_aerodigestive_tract(49)|ovary(35)|kidney(31)|breast(30)|pancreas(29)|thyroid(14)|biliary_tract(14)|NS(12)|stomach(12)|large_intestine(7)|autonomic_ganglia(7)|meninges(7)|liver(6)|salivary_gland(4)|thymus(4)|vulva(2)|endometrium(2)|prostate(2)	NS(28)|adrenal_gland(6)|autonomic_ganglia(11)|biliary_tract(74)|bone(84)|breast(46)|central_nervous_system(522)|cervix(23)|endometrium(14)|eye(4)|genital_tract(15)|haematopoietic_and_lymphoid_tissue(698)|kidney(39)|large_intestine(11)|liver(92)|lung(365)|meninges(18)|oesophagus(239)|ovary(98)|pancreas(263)|pleura(94)|prostate(13)|salivary_gland(10)|skin(541)|small_intestine(1)|soft_tissue(93)|stomach(48)|thymus(4)|thyroid(24)|upper_aerodigestive_tract(436)|urinary_tract(283)|vulva(2)	4199	GRCh37	CM970251	CDKN2A	M		c.(142-144)cCg>cGg		cyclin-dependent kinase inhibitor 2A							76.0	90.0	85.0					9																	21974684		2203	4300	6503	SO:0001583	missense	1029				cell cycle arrest|cell cycle checkpoint|G1 phase of mitotic cell cycle|G1/S transition of mitotic cell cycle|induction of apoptosis|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of cell-matrix adhesion|negative regulation of cyclin-dependent protein kinase activity|negative regulation of NF-kappaB transcription factor activity|positive regulation of macrophage apoptosis|positive regulation of smooth muscle cell apoptosis|Ras protein signal transduction|replicative senescence	cytosol|nucleus	cyclin-dependent protein kinase inhibitor activity|NF-kappaB binding|protein binding|protein kinase binding	g.chr9:21974684G>C	L27211	CCDS6510.1, CCDS6511.1, CCDS6511.2, CCDS56565.1	9p21	2014-09-17	2012-03-08		ENSG00000147889	ENSG00000147889			1787	protein-coding gene	gene with protein product		600160	"""cyclin-dependent kinase inhibitor 2A (melanoma, p16, inhibits CDK4)"""	CDKN2, MLM		8152487, 7606716	Standard	NM_058195		Approved	CDK4I, p16, INK4a, MTS1, CMM2, ARF, p19, p14, INK4, p16INK4a, p19Arf	uc003zpk.3	P42771	OTTHUMG00000019686	ENST00000304494.5:c.143C>G	9.37:g.21974684G>C	ENSP00000307101:p.Pro48Arg	HNSCC(2;<9.43e_08)|TSP Lung(5;3.83e-07)				CDKN2A_ENST00000498124.1_Missense_Mutation_p.P48R|RP11-145E5.5_ENST00000404796.2_Intron|CDKN2A_ENST00000579755.1_Intron|CDKN2A_ENST00000530628.2_Intron|CDKN2A_ENST00000579122.1_Missense_Mutation_p.P48R|CDKN2A_ENST00000498628.2_Intron|CDKN2A_ENST00000361570.3_Intron|CDKN2A_ENST00000446177.1_Missense_Mutation_p.P48R|CDKN2A_ENST00000494262.1_Intron	p.P48R	NM_000077.4	NP_000068.1	P42771	CD2A1_HUMAN		all cancers(2;0)|GBM - Glioblastoma multiforme(3;0)|Lung(2;4.07e-74)|Epithelial(2;1.08e-61)|LUSC - Lung squamous cell carcinoma(2;3.82e-48)|LUAD - Lung adenocarcinoma(2;4.56e-26)|OV - Ovarian serous cystadenocarcinoma(39;7.64e-10)|BRCA - Breast invasive adenocarcinoma(2;5.01e-09)|STAD - Stomach adenocarcinoma(4;4.63e-07)|Kidney(2;5.79e-07)|KIRC - Kidney renal clear cell carcinoma(2;7.27e-07)|COAD - Colon adenocarcinoma(8;5.15e-05)	1	413	-		all_cancers(5;0)|Acute lymphoblastic leukemia(3;0)|all_hematologic(3;0)|all_epithelial(2;2.37e-290)|Lung NSC(2;1.26e-139)|all_lung(2;4.48e-131)|Glioma(2;3.26e-60)|all_neural(2;2.1e-52)|Renal(3;1.07e-46)|Esophageal squamous(3;3.83e-46)|Melanoma(2;2.74e-34)|Breast(3;1.14e-11)|Ovarian(3;0.000128)|Hepatocellular(5;0.00162)|Colorectal(97;0.172)	48		P -> L (in CMM2 and a head and neck tumor; somatic mutation).			A5X2G7|D3DRK1|O95440|Q15191|Q5VVJ5|Q96B52|Q9NP05	Missense_Mutation	SNP	ENST00000304494.5	37	c.143C>G	CCDS6510.1	.	.	.	.	.	.	.	.	.	.	G	16.08	3.022727	0.54683	.	.	ENSG00000147889	ENST00000304494;ENST00000446177	D;D	0.94576	-3.46;-3.46	4.89	4.89	0.63831	Ankyrin repeat-containing domain (3);	.	.	.	.	D	0.96861	0.8975	M	0.86268	2.805	0.80722	D	1	D;D	0.76494	0.999;0.99	D;P	0.63877	0.919;0.842	D	0.96994	0.9724	9	0.87932	D	0	.	13.1018	0.59224	0.0:0.1617:0.8383:0.0	.	48;48	P42771;G3XAG3	CD2A1_HUMAN;.	R	48	ENSP00000307101:P48R;ENSP00000394932:P48R	ENSP00000307101:P48R	P	-	2	0	CDKN2A	21964684	0.979000	0.34478	0.971000	0.41717	0.119000	0.20118	4.091000	0.57700	2.681000	0.91329	0.655000	0.94253	CCG		0.677	CDKN2A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000051915.1	NM_000077		10	21	0	0	0	0.387290	0	10	21				
TBC1D4	9882	broad.mit.edu	37	13	75873512	75873512	+	Missense_Mutation	SNP	T	T	A			TCGA-CS-4943-01A-01D-1468-08	TCGA-CS-4943-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	14627ffd-642c-42b5-9d95-ad436c9b1d35	0d4a92bf-0624-4dfa-9d95-8f91a693ea3f	g.chr13:75873512T>A	ENST00000377636.3	-	17	3456	c.3110A>T	c.(3109-3111)gAc>gTc	p.D1037V	TBC1D4_ENST00000377625.2_Missense_Mutation_p.D974V|TBC1D4_ENST00000431480.2_Missense_Mutation_p.D1029V|TBC1D4_ENST00000478591.1_5'UTR|TBC1D4_ENST00000425511.1_Missense_Mutation_p.D201V	NM_014832.2	NP_055647.2	O60343	TBCD4_HUMAN	TBC1 domain family, member 4	1037	Rab-GAP TBC. {ECO:0000255|PROSITE- ProRule:PRU00163}.				cellular response to insulin stimulus (GO:0032869)|membrane organization (GO:0061024)|negative regulation of vesicle fusion (GO:0031339)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|extracellular vesicular exosome (GO:0070062)	Rab GTPase activator activity (GO:0005097)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(12)|lung(18)|ovary(4)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	50		Prostate(6;0.014)|Breast(118;0.0982)		GBM - Glioblastoma multiforme(99;0.0116)		GAAGCCGAGGTCATACATGAG	0.512																																						ENST00000377636.3																			0				breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(12)|lung(18)|ovary(4)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	50						c.(3109-3111)gAc>gTc		TBC1 domain family, member 4							67.0	75.0	73.0					13																	75873512		2024	4180	6204	SO:0001583	missense	9882					cytoplasm	Rab GTPase activator activity	g.chr13:75873512T>A	AB011175	CCDS41901.1, CCDS66563.1, CCDS66564.1	13q22.2	2013-07-09			ENSG00000136111	ENSG00000136111			19165	protein-coding gene	gene with protein product	"""Akt substrate of 160 kDa"""	612465				11829485, 11994271, 15304337	Standard	XM_005266603		Approved	KIAA0603, AS160, DKFZp779C0666	uc001vjl.1	O60343	OTTHUMG00000017088	ENST00000377636.3:c.3110A>T	13.37:g.75873512T>A	ENSP00000366863:p.Asp1037Val					TBC1D4_ENST00000478591.1_5'UTR|TBC1D4_ENST00000377625.2_Missense_Mutation_p.D974V|TBC1D4_ENST00000425511.1_Missense_Mutation_p.D201V|TBC1D4_ENST00000431480.2_Missense_Mutation_p.D1029V	p.D1037V	NM_014832.2	NP_055647.2	O60343	TBCD4_HUMAN		GBM - Glioblastoma multiforme(99;0.0116)	17	3456	-		Prostate(6;0.014)|Breast(118;0.0982)	1037			Rab-GAP TBC.		A7E2X8|B4DU25|B4E235|B6ETN8|B6ETN9|Q5W0B9|Q68D14	Missense_Mutation	SNP	ENST00000377636.3	37	c.3110A>T	CCDS41901.1	.	.	.	.	.	.	.	.	.	.	T	23.6	4.441196	0.83993	.	.	ENSG00000136111	ENST00000377636;ENST00000431480;ENST00000377625;ENST00000425511	T;T;T;T	0.11712	2.75;2.75;2.75;2.75	5.63	5.63	0.86233	Rab-GAP/TBC domain (4);	0.000000	0.64402	D	0.000001	T	0.36524	0.0970	M	0.81497	2.545	0.80722	D	1	P;P;D;D	0.89917	0.504;0.825;0.957;1.0	B;B;P;D	0.87578	0.226;0.353;0.838;0.998	T	0.17349	-1.0372	10	0.62326	D	0.03	-30.0041	15.8391	0.78831	0.0:0.0:0.0:1.0	.	201;974;1029;1037	O60343-4;O60343-2;O60343-3;O60343	.;.;.;TBCD4_HUMAN	V	1037;1029;974;201	ENSP00000366863:D1037V;ENSP00000395986:D1029V;ENSP00000366852:D974V;ENSP00000390654:D201V	ENSP00000366852:D974V	D	-	2	0	TBC1D4	74771513	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	7.698000	0.84413	2.134000	0.65973	0.482000	0.46254	GAC		0.512	TBC1D4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045283.1	NM_014832		3	43	0	0	0	0.150653	0	3	43				
NBPF10	100132406	broad.mit.edu	37	1	145367739	145367739	+	Silent	SNP	A	A	G			TCGA-CS-4943-01A-01D-1468-08	TCGA-CS-4943-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	14627ffd-642c-42b5-9d95-ad436c9b1d35	0d4a92bf-0624-4dfa-9d95-8f91a693ea3f	g.chr1:145367739A>G	ENST00000342960.5	+	83	10370	c.10335A>G	c.(10333-10335)aaA>aaG	p.K3445K	NBPF10_ENST00000369339.3_Intron|NBPF10_ENST00000369338.1_Intron	NM_001039703.4	NP_001034792.4	Q6P3W6	NBPFA_HUMAN	neuroblastoma breakpoint family, member 10	750						cytoplasm (GO:0005737)	poly(A) RNA binding (GO:0044822)	p.K3445K(4)		NS(3)|breast(1)|central_nervous_system(3)|endometrium(12)|kidney(23)|lung(15)|ovary(1)|prostate(7)|skin(6)|urinary_tract(2)	73	all_hematologic(923;0.032)			Colorectal(1306;1.36e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.00258)		ggaaggggaaaaaaagaaggg	0.413																																						ENST00000342960.5																			4	Substitution - coding silent(4)	p.K3445K(4)	prostate(3)|kidney(1)	NS(3)|breast(1)|central_nervous_system(3)|endometrium(12)|kidney(23)|lung(15)|ovary(1)|prostate(7)|skin(6)|urinary_tract(2)	73						c.(10333-10335)aaA>aaG		neuroblastoma breakpoint family, member 10																																				SO:0001819	synonymous_variant	100132406							g.chr1:145367739A>G	BC021111		1q21.1	2013-01-17			ENSG00000163386	ENSG00000271425		"""neuroblastoma breakpoint family"""	31992	protein-coding gene	gene with protein product		614000				16079250	Standard	NM_001039703		Approved	AG1		Q6P3W6	OTTHUMG00000013757	ENST00000342960.5:c.10335A>G	1.37:g.145367739A>G						NBPF10_ENST00000369338.1_Intron|NBPF10_ENST00000369339.2_Intron	p.K3445K	NM_001039703.4	NP_001034792.4	A6NDV3	A6NDV3_HUMAN		Colorectal(1306;1.36e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.00258)	83	10370	+	all_hematologic(923;0.032)		3445					Q5RHC0|Q9NWN6	Silent	SNP	ENST00000342960.5	37	c.10335A>G	CCDS53355.1																																																																																				0.413	NBPF10-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001039703		5	125	0	0	0	0.184627	0	5	125				
GFPT2	9945	broad.mit.edu	37	5	179740844	179740844	+	Missense_Mutation	SNP	A	A	T			TCGA-CS-4943-01A-01D-1468-08	TCGA-CS-4943-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	14627ffd-642c-42b5-9d95-ad436c9b1d35	0d4a92bf-0624-4dfa-9d95-8f91a693ea3f	g.chr5:179740844A>T	ENST00000253778.8	-	14	1563	c.1394T>A	c.(1393-1395)aTc>aAc	p.I465N	GFPT2_ENST00000520165.1_5'Flank	NM_005110.2	NP_005101.1	O94808	GFPT2_HUMAN	glutamine-fructose-6-phosphate transaminase 2	465	SIS 1. {ECO:0000255|PROSITE- ProRule:PRU00797}.				carbohydrate biosynthetic process (GO:0016051)|cellular protein metabolic process (GO:0044267)|dolichol-linked oligosaccharide biosynthetic process (GO:0006488)|energy reserve metabolic process (GO:0006112)|fructose 6-phosphate metabolic process (GO:0006002)|glutamine metabolic process (GO:0006541)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|UDP-N-acetylglucosamine biosynthetic process (GO:0006048)	cytosol (GO:0005829)	carbohydrate binding (GO:0030246)|glutamine-fructose-6-phosphate transaminase (isomerizing) activity (GO:0004360)			breast(1)|central_nervous_system(2)|kidney(2)|large_intestine(9)|lung(12)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	34	all_cancers(89;4.97e-05)|all_epithelial(37;1.22e-05)|Renal(175;0.000269)|Lung NSC(126;0.00199)|all_lung(126;0.00351)|Breast(19;0.137)	Medulloblastoma(196;0.0392)|all_neural(177;0.0529)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)		L-Glutamine(DB00130)	CCCTGCGTTGATGTGGACGCC	0.701																																						ENST00000253778.8																			0				breast(1)|central_nervous_system(2)|kidney(2)|large_intestine(9)|lung(12)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	34						c.(1393-1395)aTc>aAc		glutamine-fructose-6-phosphate transaminase 2	L-Glutamine(DB00130)						14.0	19.0	17.0					5																	179740844		2190	4286	6476	SO:0001583	missense	9945				dolichol-linked oligosaccharide biosynthetic process|energy reserve metabolic process|fructose 6-phosphate metabolic process|glutamine metabolic process|post-translational protein modification|protein N-linked glycosylation via asparagine|UDP-N-acetylglucosamine biosynthetic process	cytosol	glutamine-fructose-6-phosphate transaminase (isomerizing) activity|sugar binding	g.chr5:179740844A>T	AB016789	CCDS43411.1	5q	2008-07-18			ENSG00000131459	ENSG00000131459			4242	protein-coding gene	gene with protein product	"""glutamine: fructose-6-phosphate aminotransferase 2"""	603865				10198162	Standard	NM_005110		Approved	GFAT2	uc003mlw.1	O94808	OTTHUMG00000163442	ENST00000253778.8:c.1394T>A	5.37:g.179740844A>T	ENSP00000253778:p.Ile465Asn						p.I465N	NM_005110.2	NP_005101.1	O94808	GFPT2_HUMAN	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)		14	1563	-	all_cancers(89;4.97e-05)|all_epithelial(37;1.22e-05)|Renal(175;0.000269)|Lung NSC(126;0.00199)|all_lung(126;0.00351)|Breast(19;0.137)	Medulloblastoma(196;0.0392)|all_neural(177;0.0529)	465			SIS 1.		Q53XM2|Q9BWS4	Missense_Mutation	SNP	ENST00000253778.8	37	c.1394T>A	CCDS43411.1	.	.	.	.	.	.	.	.	.	.	A	33	5.212863	0.95069	.	.	ENSG00000131459	ENST00000253778	T	0.68025	-0.3	5.8	5.8	0.92144	Sugar isomerase (SIS) (2);	0.048654	0.85682	D	0.000000	D	0.85948	0.5816	M	0.92833	3.35	0.80722	D	1	D	0.89917	1.0	D	0.81914	0.995	D	0.89397	0.3693	9	.	.	.	-34.1873	16.1537	0.81640	1.0:0.0:0.0:0.0	.	465	O94808	GFPT2_HUMAN	N	465	ENSP00000253778:I465N	.	I	-	2	0	GFPT2	179673450	1.000000	0.71417	1.000000	0.80357	0.823000	0.46562	8.932000	0.92897	2.213000	0.71641	0.528000	0.53228	ATC		0.701	GFPT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373444.4	NM_005110		6	10	0	0	0	0.335167	0	6	10				
NKAIN2	154215	broad.mit.edu	37	6	124979504	124979504	+	Missense_Mutation	SNP	C	C	T			TCGA-CS-4943-01A-01D-1468-08	TCGA-CS-4943-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	14627ffd-642c-42b5-9d95-ad436c9b1d35	0d4a92bf-0624-4dfa-9d95-8f91a693ea3f	g.chr6:124979504C>T	ENST00000368417.1	+	4	506	c.446C>T	c.(445-447)gCt>gTt	p.A149V	NKAIN2_ENST00000546092.1_Intron|NKAIN2_ENST00000368416.1_Missense_Mutation_p.A149V|NKAIN2_ENST00000545433.1_Missense_Mutation_p.A134V	NM_001040214.1	NP_001035304.1	Q5VXU1	NKAI2_HUMAN	Na+/K+ transporting ATPase interacting 2	149						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				cervix(1)|endometrium(1)|large_intestine(3)|lung(12)|skin(2)	19				GBM - Glioblastoma multiforme(226;0.104)		ATAGAAGTGGCTCATAGTTCC	0.542																																						ENST00000368417.1																			0				cervix(1)|endometrium(1)|large_intestine(3)|lung(12)|skin(2)	19						c.(445-447)gCt>gTt		Na+/K+ transporting ATPase interacting 2							161.0	113.0	130.0					6																	124979504		2203	4300	6503	SO:0001583	missense	154215					integral to membrane|plasma membrane		g.chr6:124979504C>T	AB070452	CCDS34526.1	6q21	2008-02-05	2007-10-04	2007-10-04	ENSG00000188580	ENSG00000188580		"""Na+/K+ transporting ATPase interacting"""	16443	protein-coding gene	gene with protein product		609758	"""T-cell lymphoma breakpoint associated target 1"""	TCBA1		17606467	Standard	XM_005266833		Approved	FAM77B	uc003pzo.3	Q5VXU1	OTTHUMG00000015500	ENST00000368417.1:c.446C>T	6.37:g.124979504C>T	ENSP00000357402:p.Ala149Val					NKAIN2_ENST00000545433.1_Missense_Mutation_p.A134V|NKAIN2_ENST00000368416.1_Missense_Mutation_p.A149V|NKAIN2_ENST00000546092.1_Intron	p.A149V	NM_001040214.1	NP_001035304.1	Q5VXU1	NKAI2_HUMAN		GBM - Glioblastoma multiforme(226;0.104)	4	506	+			149					Q8IYR4|Q8TF67	Missense_Mutation	SNP	ENST00000368417.1	37	c.446C>T	CCDS34526.1	.	.	.	.	.	.	.	.	.	.	C	24.7	4.564238	0.86335	.	.	ENSG00000188580	ENST00000368416;ENST00000368417;ENST00000539866;ENST00000545433	T;T;T	0.13196	2.61;2.61;2.61	5.72	4.85	0.62838	.	0.105591	0.64402	D	0.000004	T	0.08891	0.0220	N	0.22421	0.69	0.45899	D	0.998749	P;B;P;B	0.51240	0.943;0.004;0.943;0.095	P;B;P;B	0.53912	0.737;0.007;0.737;0.058	T	0.29212	-1.0019	10	0.24483	T	0.36	-2.9332	14.6114	0.68519	0.0:0.9303:0.0:0.0697	.	134;148;149;149	B3KNZ0;Q5VXU1-3;Q5VXU1;Q5VXU1-2	.;.;NKAI2_HUMAN;.	V	149;149;148;134	ENSP00000357401:A149V;ENSP00000357402:A149V;ENSP00000437798:A134V	ENSP00000357401:A149V	A	+	2	0	NKAIN2	125021203	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.433000	0.80362	1.433000	0.47394	0.650000	0.86243	GCT		0.542	NKAIN2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042057.1	NM_001040214		38	50	0	0	0	0.819951	0	38	50				
AC008132.13	0	broad.mit.edu	37	22	18842988	18842988	+	Intron	SNP	G	G	T			TCGA-CS-4943-01A-01D-1468-08	TCGA-CS-4943-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	14627ffd-642c-42b5-9d95-ad436c9b1d35	0d4a92bf-0624-4dfa-9d95-8f91a693ea3f	g.chr22:18842988G>T	ENST00000412938.1	+	4	2208																											TCCCATCCATGCAAACCTAGG	0.602																																						ENST00000412938.1																			0																																																	SO:0001627	intron_variant	0							g.chr22:18842988G>T																												ENST00000412938.1:c.2209-315G>T	22.37:g.18842988G>T														0	2208	+									RNA	SNP	ENST00000412938.1	37																																																																																						0.602	AC008132.13-002	KNOWN	basic	processed_transcript	protein_coding	OTTHUMT00000471615.1			3	9	1	0	0.00024832	0.150653	0.000265155	3	9				
TPM3P9	147804	broad.mit.edu	37	19	53945909	53945909	+	RNA	SNP	T	T	C	rs28727441	byFrequency	TCGA-CS-4943-01A-01D-1468-08	TCGA-CS-4943-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	14627ffd-642c-42b5-9d95-ad436c9b1d35	0d4a92bf-0624-4dfa-9d95-8f91a693ea3f	g.chr19:53945909T>C	ENST00000424846.3	+	0	906				ZNF761_ENST00000454407.1_RNA	NR_003148.3				tropomyosin 3 pseudogene 9																		ACCCTGACTCTGCCTGAGGCC	0.562													N|||	2656	0.530351	0.5348	0.5533	5008	,	,		11317	0.2728		0.6402	False		,,,				2504	0.6605					ENST00000454407.1																			0				endometrium(1)|kidney(2)|large_intestine(5)|lung(13)|ovary(1)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	30								zinc finger protein 761																																						388561				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding	g.chr19:53945909T>C			19q13.42	2012-07-04			ENSG00000241015	ENSG00000241015			44142	pseudogene	pseudogene							Standard	NR_003148		Approved				OTTHUMG00000157312		19.37:g.53945909T>C						TPM3P9_ENST00000424846.3_RNA				Q86XN6	ZN761_HUMAN		GBM - Glioblastoma multiforme(134;0.00786)	0	55	+									RNA	SNP	ENST00000424846.3	37																																																																																						0.562	TPM3P9-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000347070.1	NR_003148		3	47	0	0	0	0.184627	0	3	47				
SDHAP1	255812	broad.mit.edu	37	3	195692347	195692347	+	RNA	SNP	G	G	A	rs62282794		TCGA-CS-4943-01A-01D-1468-08	TCGA-CS-4943-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	14627ffd-642c-42b5-9d95-ad436c9b1d35	0d4a92bf-0624-4dfa-9d95-8f91a693ea3f	g.chr3:195692347G>A	ENST00000427841.1	-	0	2155					NR_003264.2				succinate dehydrogenase complex, subunit A, flavoprotein pseudogene 1																		TTCCTCCAGTGCTCCTCAAAG	0.572																																					Ovarian(67;1158 1227 12109 20189 43170)	ENST00000427841.1																			0																																																			0							g.chr3:195692347G>A	BC071730		3q29	2009-12-02	2006-11-21	2009-12-02	ENSG00000185485	ENSG00000185485			32455	pseudogene	pseudogene			"""succinate dehydrogenase complex, subunit A, flavoprotein-like 1"""	SDHAL1, SDHALP1			Standard	NR_003264		Approved		uc003fvy.3		OTTHUMG00000155716		3.37:g.195692347G>A								NR_003264.2						0	2155	-									RNA	SNP	ENST00000427841.1	37																																																																																						0.572	SDHAP1-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000341367.1			5	26	0	0	0	0.278610	0	5	26				
EIF3B	8662	broad.mit.edu	37	7	2404028	2404028	+	Missense_Mutation	SNP	C	C	T	rs368514580		TCGA-CS-4943-01A-01D-1468-08	TCGA-CS-4943-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	14627ffd-642c-42b5-9d95-ad436c9b1d35	0d4a92bf-0624-4dfa-9d95-8f91a693ea3f	g.chr7:2404028C>T	ENST00000360876.4	+	6	1077	c.1021C>T	c.(1021-1023)Cgt>Tgt	p.R341C	EIF3B_ENST00000397011.2_Missense_Mutation_p.R341C	NM_001037283.1	NP_001032360.1			eukaryotic translation initiation factor 3, subunit B											breast(2)|endometrium(4)|kidney(2)|large_intestine(3)|lung(11)|ovary(1)|skin(1)	24		Ovarian(82;0.0253)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0833)|OV - Ovarian serous cystadenocarcinoma(56;7.76e-14)		GACGTATGTGCGTTGGTCTCC	0.458																																						ENST00000360876.4																			0				breast(2)|endometrium(4)|kidney(2)|large_intestine(3)|lung(11)|ovary(1)|skin(1)	24						c.(1021-1023)Cgt>Tgt		eukaryotic translation initiation factor 3, subunit B		C	CYS/ARG,CYS/ARG	0,4406		0,0,2203	135.0	138.0	137.0		1021,1021	5.9	1.0	7		137	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	EIF3B	NM_001037283.1,NM_003751.3	180,180	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging,probably-damaging	341/815,341/815	2404028	1,13005	2203	4300	6503	SO:0001583	missense	8662				regulation of translational initiation	cytosol|eukaryotic translation initiation factor 3 complex	nucleotide binding|protein complex scaffold|translation initiation factor activity	g.chr7:2404028C>T	U62583	CCDS5332.1	7p22	2013-02-12	2007-07-27	2007-07-27	ENSG00000106263	ENSG00000106263		"""RNA binding motif (RRM) containing"""	3280	protein-coding gene	gene with protein product		603917	"""eukaryotic translation initiation factor 3, subunit 9 eta, 116kDa"""	EIF3S9		8995410	Standard	NM_001037283		Approved	PRT1, eIF3b	uc003sly.3	P55884	OTTHUMG00000022839	ENST00000360876.4:c.1021C>T	7.37:g.2404028C>T	ENSP00000354125:p.Arg341Cys					EIF3B_ENST00000397011.2_Missense_Mutation_p.R341C	p.R341C	NM_001037283.1	NP_001032360.1	P55884	EIF3B_HUMAN		UCEC - Uterine corpus endometrioid carcinoma (27;0.0833)|OV - Ovarian serous cystadenocarcinoma(56;7.76e-14)	6	1077	+		Ovarian(82;0.0253)	341			Sufficient for interaction with EIF3E.			Missense_Mutation	SNP	ENST00000360876.4	37	c.1021C>T	CCDS5332.1	.	.	.	.	.	.	.	.	.	.	C	35	5.581538	0.96565	0.0	1.16E-4	ENSG00000106263	ENST00000431643;ENST00000314800;ENST00000360876;ENST00000413917;ENST00000397011;ENST00000489558	T;T;T;T	0.57595	0.91;0.91;0.39;0.91	5.93	5.93	0.95920	WD40/YVTN repeat-like-containing domain (1);	0.000000	0.85682	D	0.000000	T	0.63094	0.2482	L	0.52266	1.64	0.80722	D	1	D;D	0.76494	0.997;0.999	P;P	0.53146	0.676;0.719	T	0.64390	-0.6419	10	0.87932	D	0	-25.5779	20.3437	0.98782	0.0:1.0:0.0:0.0	.	302;341	A4D210;P55884	.;EIF3B_HUMAN	C	69;341;341;302;341;265	ENSP00000408062:R69C;ENSP00000354125:R341C;ENSP00000407785:R302C;ENSP00000380206:R341C	ENSP00000316638:R341C	R	+	1	0	EIF3B	2370554	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.381000	0.79718	2.815000	0.96918	0.561000	0.74099	CGT		0.458	EIF3B-002	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207006.1			88	107	0	0	0	0.870114	0	88	107				
NUP214	8021	broad.mit.edu	37	9	134073213	134073213	+	Silent	SNP	A	A	G			TCGA-CS-4943-01A-01D-1468-08	TCGA-CS-4943-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	14627ffd-642c-42b5-9d95-ad436c9b1d35	0d4a92bf-0624-4dfa-9d95-8f91a693ea3f	g.chr9:134073213A>G	ENST00000359428.5	+	29	4476	c.4332A>G	c.(4330-4332)caA>caG	p.Q1444Q	NUP214_ENST00000451030.1_Silent_p.Q1445Q|NUP214_ENST00000483497.2_Silent_p.Q270Q|NUP214_ENST00000411637.2_Silent_p.Q1434Q|NUP214_ENST00000465486.2_3'UTR			P35658	NU214_HUMAN	nucleoporin 214kDa	1444	11 X 3 AA approximate repeats.|11 X 5 AA approximate repeats.|18 X 4 AA approximate repeats.|Pro/Ser/Thr-rich.				carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|gene expression (GO:0010467)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA export from nucleus (GO:0006406)|mRNA metabolic process (GO:0016071)|protein export from nucleus (GO:0006611)|protein import into nucleus (GO:0006606)|regulation of cell cycle (GO:0051726)|regulation of glucose transport (GO:0010827)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytosol (GO:0005829)|focal adhesion (GO:0005925)|intracellular membrane-bounded organelle (GO:0043231)|nuclear pore (GO:0005643)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	nucleocytoplasmic transporter activity (GO:0005487)|transporter activity (GO:0005215)			NS(1)|breast(9)|central_nervous_system(3)|endometrium(13)|kidney(2)|large_intestine(9)|liver(2)|lung(29)|ovary(2)|prostate(3)|skin(7)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	86	all_hematologic(7;0.0028)	Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;3.42e-05)|Epithelial(140;0.000256)		TTGGAAGCCAACAGACCAATA	0.522			T	"""DEK, SET, ABL1"""	"""AML, T-ALL"""																																Pancreas(4;24 48 25510 30394 32571)	ENST00000359428.5				Dom	yes		9	9q34.1	8021	T	nucleoporin 214kDa (CAN)			L	"""DEK, SET, ABL1"""		"""AML, T-ALL"""		0				NS(1)|breast(9)|central_nervous_system(3)|endometrium(13)|kidney(2)|large_intestine(9)|liver(2)|lung(29)|ovary(2)|prostate(3)|skin(7)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	86						c.(4330-4332)caA>caG		nucleoporin 214kDa							129.0	119.0	122.0					9																	134073213		2203	4300	6503	SO:0001819	synonymous_variant	8021				carbohydrate metabolic process|glucose transport|mRNA metabolic process|protein export from nucleus|regulation of glucose transport|transmembrane transport|viral reproduction	cytosol|nuclear pore|nucleoplasm	protein binding	g.chr9:134073213A>G	X64228	CCDS6940.1	9q34	2008-07-21	2002-08-29		ENSG00000126883	ENSG00000126883			8064	protein-coding gene	gene with protein product	"""nuclear pore complex protein Nup214"", ""CAN protein, putative oncogene"""	114350	"""nucleoporin 214kD (CAIN)"""			8108440, 2370860	Standard	NM_005085		Approved	CAIN, CAN, D9S46E, N214	uc004cag.3	P35658	OTTHUMG00000020816	ENST00000359428.5:c.4332A>G	9.37:g.134073213A>G						NUP214_ENST00000465486.2_3'UTR|NUP214_ENST00000451030.1_Silent_p.Q1445Q|NUP214_ENST00000411637.2_Silent_p.Q1434Q|NUP214_ENST00000483497.2_Silent_p.Q270Q	p.Q1444Q			P35658	NU214_HUMAN		OV - Ovarian serous cystadenocarcinoma(145;3.42e-05)|Epithelial(140;0.000256)	29	4476	+	all_hematologic(7;0.0028)	Myeloproliferative disorder(178;0.204)	1444			11 X 3 AA approximate repeats.|11 X 5 AA approximate repeats.|18 X 4 AA approximate repeats.|Pro/Ser/Thr-rich.		A6NFQ0|Q15010|Q3KQZ0|Q5JUP7|Q75R47|Q86XD3	Silent	SNP	ENST00000359428.5	37	c.4332A>G	CCDS6940.1																																																																																				0.522	NUP214-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000054694.2	NM_005085		20	98	0	0	0	0.592651	0	20	98				
PCDH11Y	83259	broad.mit.edu	37	Y	5369105	5369105	+	Missense_Mutation	SNP	G	G	T			TCGA-CS-4943-01A-01D-1468-08	TCGA-CS-4943-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	14627ffd-642c-42b5-9d95-ad436c9b1d35	0d4a92bf-0624-4dfa-9d95-8f91a693ea3f	g.chrY:5369105G>T	ENST00000215473.6	+	3	3137	c.3137G>T	c.(3136-3138)cGg>cTg	p.R1046L				Q9BZA8	PC11Y_HUMAN	protocadherin 11 Y-linked	1046					homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			autonomic_ganglia(1)|kidney(2)|large_intestine(7)|lung(14)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	27						CAGTCCCAGCGGCGTGTCACA	0.473																																						ENST00000215473.6																			0				autonomic_ganglia(1)|kidney(2)|large_intestine(7)|lung(14)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	27						c.(3136-3138)cGg>cTg		protocadherin 11 Y-linked							29.0	28.0	28.0					Y																	5369105		830	2279	3109	SO:0001583	missense	83259				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding	g.chrY:5369105G>T	AF332217	CCDS14776.1, CCDS14777.1, CCDS76066.1	Yp11.2	2010-01-26	2002-05-22	2002-05-24	ENSG00000099715	ENSG00000099715		"""Cadherins / Protocadherins : Non-clustered"""	15813	protein-coding gene	gene with protein product		400022	"""protocadherin 22"""	PCDH22		10644456, 11003707	Standard	NM_032971		Approved	PCDHY	uc004fqo.3	Q9BZA8	OTTHUMG00000035105	ENST00000215473.6:c.3137G>T	Y.37:g.5369105G>T	ENSP00000215473:p.Arg1046Leu						p.R1046L			Q9BZA8	PC11Y_HUMAN			3	3137	+			1046					Q70LR6|Q70LR8|Q70LS0|Q70LS1|Q70LS2|Q70LS3|Q70LS4|Q70LS5|Q8WY34|Q9BZA9|Q9H4E1	Missense_Mutation	SNP	ENST00000215473.6	37	c.3137G>T																																																																																					0.473	PCDH11Y-201	KNOWN	basic	protein_coding	protein_coding		NM_032973		3	59	1	0	0.00909568	0.150653	0.00955046	3	59				
PKD1L1	168507	broad.mit.edu	37	7	47876598	47876598	+	Missense_Mutation	SNP	G	G	A	rs202116763		TCGA-CS-4943-01A-01D-1468-08	TCGA-CS-4943-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	14627ffd-642c-42b5-9d95-ad436c9b1d35	0d4a92bf-0624-4dfa-9d95-8f91a693ea3f	g.chr7:47876598G>A	ENST00000289672.2	-	37	5914	c.5864C>T	c.(5863-5865)cCg>cTg	p.P1955L		NM_138295.3	NP_612152.1	Q8TDX9	PK1L1_HUMAN	polycystic kidney disease 1 like 1	1955					detection of mechanical stimulus (GO:0050982)|detection of nodal flow (GO:0003127)|left/right axis specification (GO:0070986)|single organismal cell-cell adhesion (GO:0016337)	calcium channel complex (GO:0034704)|cilium (GO:0005929)|membrane (GO:0016020)|nonmotile primary cilium (GO:0031513)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)		BBS9/PKD1L1(2)	NS(1)|breast(9)|central_nervous_system(1)|cervix(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(27)|lung(44)|ovary(12)|prostate(5)|skin(8)|stomach(4)|upper_aerodigestive_tract(5)	142						GGTGAGGCGCGGCGTGTGCAG	0.582													G|||	1	0.000199681	0.0	0.0	5008	,	,		18705	0.0		0.001	False		,,,				2504	0.0					ENST00000289672.2																		BBS9/PKD1L1(2)	0				NS(1)|breast(9)|central_nervous_system(1)|cervix(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(27)|lung(44)|ovary(12)|prostate(5)|skin(8)|stomach(4)|upper_aerodigestive_tract(5)	142						c.(5863-5865)cCg>cTg		polycystic kidney disease 1 like 1							63.0	56.0	58.0					7																	47876598		2203	4300	6503	SO:0001583	missense	168507				cell-cell adhesion	integral to membrane		g.chr7:47876598G>A	AB061683	CCDS34633.1	7p12.3	2008-07-18			ENSG00000158683	ENSG00000158683			18053	protein-coding gene	gene with protein product	"""polycystin-1L1"""	609721				11863367	Standard	NM_138295		Approved	PRO19563	uc003tny.2	Q8TDX9	OTTHUMG00000155649	ENST00000289672.2:c.5864C>T	7.37:g.47876598G>A	ENSP00000289672:p.Pro1955Leu						p.P1955L	NM_138295.3	NP_612152.1	Q8TDX9	PK1L1_HUMAN			37	5914	-			1955					Q6UWK1	Missense_Mutation	SNP	ENST00000289672.2	37	c.5864C>T	CCDS34633.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	G	10.59	1.393548	0.25205	.	.	ENSG00000158683	ENST00000289672	T	0.18502	2.21	5.1	-5.36	0.02689	.	0.593958	0.14878	N	0.293123	T	0.08044	0.0201	N	0.22421	0.69	0.09310	N	1	P	0.51351	0.944	B	0.31290	0.127	T	0.17018	-1.0383	10	0.42905	T	0.14	-7.5679	16.6748	0.85276	0.0:0.0:0.1795:0.8205	.	1955	Q8TDX9	PK1L1_HUMAN	L	1955	ENSP00000289672:P1955L	ENSP00000289672:P1955L	P	-	2	0	PKD1L1	47843123	0.483000	0.25956	0.000000	0.03702	0.301000	0.27625	0.966000	0.29331	-0.676000	0.05238	0.655000	0.94253	CCG		0.582	PKD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340974.1	NM_138295		3	41	0	0	0	0.150653	0	3	41				
DDX5	1655	broad.mit.edu	37	17	62498302	62498302	+	Missense_Mutation	SNP	T	T	G	rs372537624		TCGA-CS-4943-01A-01D-1468-08	TCGA-CS-4943-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	14627ffd-642c-42b5-9d95-ad436c9b1d35	0d4a92bf-0624-4dfa-9d95-8f91a693ea3f	g.chr17:62498302T>G	ENST00000225792.5	-	10	1535	c.1134A>C	c.(1132-1134)caA>caC	p.Q378H	DDX5_ENST00000580026.1_5'Flank|MIR3064_ENST00000581130.1_RNA|DDX5_ENST00000578804.1_Missense_Mutation_p.Q378H|DDX5_ENST00000450599.2_Missense_Mutation_p.Q299H|MIR5047_ENST00000579212.1_RNA	NM_004396.3	NP_004387.1	P17844	DDX5_HUMAN	DEAD (Asp-Glu-Ala-Asp) box helicase 5	378	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.				cell growth (GO:0016049)|circadian rhythm (GO:0007623)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|mRNA splicing, via spliceosome (GO:0000398)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043517)|positive regulation of intracellular estrogen receptor signaling pathway (GO:0033148)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|regulation of androgen receptor signaling pathway (GO:0060765)|regulation of osteoblast differentiation (GO:0045667)|regulation of skeletal muscle cell differentiation (GO:2001014)|regulation of viral genome replication (GO:0045069)|transcription, DNA-templated (GO:0006351)	catalytic step 2 spliceosome (GO:0071013)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	androgen receptor binding (GO:0050681)|ATP binding (GO:0005524)|ATP-dependent RNA helicase activity (GO:0004004)|estrogen receptor binding (GO:0030331)|poly(A) RNA binding (GO:0044822)|pre-mRNA binding (GO:0036002)|RNA helicase activity (GO:0003724)|transcription coactivator activity (GO:0003713)			breast(3)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(2)|lung(5)|ovary(2)	19	Breast(5;2.15e-14)		BRCA - Breast invasive adenocarcinoma(8;8.6e-12)			AGTCACGCTCTTGTTGACTCT	0.378			T	ETV4	prostate																																NSCLC(22;406 813 4871 19580 40307)	ENST00000225792.5				Dom	yes		17	17q21	1655	T	DEAD (Asp-Glu-Ala-Asp) box polypeptide 5			E	ETV4		prostate		0				breast(3)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(2)|lung(5)|ovary(2)	19						c.(1132-1134)caA>caC		DEAD (Asp-Glu-Ala-Asp) box helicase 5							62.0	58.0	60.0					17																	62498302		2203	4300	6503	SO:0001583	missense	1655				cell growth|regulation of alternative nuclear mRNA splicing, via spliceosome	catalytic step 2 spliceosome|nucleolus	ATP binding|ATP-dependent helicase activity|mRNA binding|protein binding|RNA helicase activity|transcription cofactor activity	g.chr17:62498302T>G	AF015812	CCDS11659.1	17q21	2012-07-27	2012-02-23		ENSG00000108654	ENSG00000108654		"""DEAD-boxes"""	2746	protein-coding gene	gene with protein product		180630	"""DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 5 (RNA helicase, 68kD)"", ""DEAD (Asp-Glu-Ala-Asp) box polypeptide 5"""	HLR1, G17P1		22156369, 18698352	Standard	NM_004396		Approved	p68	uc002jek.2	P17844	OTTHUMG00000178936	ENST00000225792.5:c.1134A>C	17.37:g.62498302T>G	ENSP00000225792:p.Gln378His					DDX5_ENST00000578804.1_Missense_Mutation_p.Q378H|DDX5_ENST00000450599.2_Missense_Mutation_p.Q299H	p.Q378H	NM_004396.3	NP_004387.1	P17844	DDX5_HUMAN	BRCA - Breast invasive adenocarcinoma(8;8.6e-12)		10	1535	-	Breast(5;2.15e-14)		378			Helicase C-terminal.		B4DLW8|B5BU21|D3DU32|E7ETL9|O75681|Q53Y61	Missense_Mutation	SNP	ENST00000225792.5	37	c.1134A>C	CCDS11659.1	.	.	.	.	.	.	.	.	.	.	T	13.81	2.347019	0.41599	.	.	ENSG00000108654	ENST00000540698;ENST00000450599;ENST00000225792	.	.	.	6.17	4.2	0.49525	Helicase, C-terminal (3);	0.000000	0.85682	D	0.000000	T	0.51736	0.1692	L	0.38649	1.16	0.80722	D	1	B;B;B	0.30664	0.126;0.159;0.289	B;B;B	0.37304	0.246;0.159;0.159	T	0.52419	-0.8578	9	0.56958	D	0.05	-7.3255	12.3973	0.55393	0.0:0.8631:0.0:0.1369	.	299;378;378	B4DLW8;B5BUE6;P17844	.;.;DDX5_HUMAN	H	378;308;367	.	ENSP00000225792:Q367H	Q	-	3	2	DDX5	59928764	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	1.478000	0.35442	0.926000	0.37118	-0.242000	0.12053	CAA		0.378	DDX5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444030.1	NM_004396		10	51	0	0	0	0.435327	0	10	51				
GBP1	2633	broad.mit.edu	37	1	89520410	89520410	+	Silent	SNP	G	G	C			TCGA-CS-4943-01A-01D-1468-08	TCGA-CS-4943-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	14627ffd-642c-42b5-9d95-ad436c9b1d35	0d4a92bf-0624-4dfa-9d95-8f91a693ea3f	g.chr1:89520410G>C	ENST00000370473.4	-	10	1839	c.1620C>G	c.(1618-1620)gtC>gtG	p.V540V	GBP1_ENST00000484970.1_5'UTR	NM_002053.2	NP_002044.2	P32455	GBP1_HUMAN	guanylate binding protein 1, interferon-inducible	540					cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|interferon-gamma-mediated signaling pathway (GO:0060333)	cytosol (GO:0005829)|extracellular region (GO:0005576)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|identical protein binding (GO:0042802)			endometrium(7)|kidney(4)|large_intestine(8)|lung(6)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	30		Lung NSC(277;0.123)		all cancers(265;0.0156)|Epithelial(280;0.0291)		TCAGCAACTGGACCCTGTCGT	0.433																																						ENST00000370473.4																			0				endometrium(7)|kidney(4)|large_intestine(8)|lung(6)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	30						c.(1618-1620)gtC>gtG		guanylate binding protein 1, interferon-inducible							271.0	272.0	272.0					1																	89520410		2203	4300	6503	SO:0001819	synonymous_variant	2633				interferon-gamma-mediated signaling pathway	plasma membrane	GTP binding|GTPase activity	g.chr1:89520410G>C	BC002666	CCDS718.1	1p22.2	2011-03-09	2011-03-09		ENSG00000117228	ENSG00000117228			4182	protein-coding gene	gene with protein product		600411	"""guanylate binding protein 1, interferon-inducible, 67kDa"""			7518790	Standard	NM_002053		Approved		uc001dmx.2	P32455	OTTHUMG00000010614	ENST00000370473.4:c.1620C>G	1.37:g.89520410G>C						GBP1_ENST00000484970.1_5'UTR	p.V540V	NM_002053.2	NP_002044.2	P32455	GBP1_HUMAN		all cancers(265;0.0156)|Epithelial(280;0.0291)	10	1839	-		Lung NSC(277;0.123)	540					D3DT26|Q5T8M1	Silent	SNP	ENST00000370473.4	37	c.1620C>G	CCDS718.1																																																																																				0.433	GBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029289.3	NM_002053		86	281	0	0	0	0.870114	0	86	281				
IDH1	3417	broad.mit.edu	37	2	209113112	209113112	+	Missense_Mutation	SNP	C	C	T	rs121913500		TCGA-CS-4943-01A-01D-1468-08	TCGA-CS-4943-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	14627ffd-642c-42b5-9d95-ad436c9b1d35	0d4a92bf-0624-4dfa-9d95-8f91a693ea3f	g.chr2:209113112C>T	ENST00000415913.1	-	4	776	c.395G>A	c.(394-396)cGt>cAt	p.R132H	IDH1_ENST00000446179.1_Missense_Mutation_p.R132H|IDH1_ENST00000345146.2_Missense_Mutation_p.R132H	NM_001282387.1	NP_001269316.1	O75874	IDHC_HUMAN	isocitrate dehydrogenase 1 (NADP+), soluble	132			R -> C (in colorectal cancer and glioma samples; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha- ketoglutarate but instead alpha- ketoglutarate is converted to R(-)-2- hydroxyglutarate). {ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:19117336}.|R -> G (in a glioma sample; glioblastoma multiforme; somatic mutation). {ECO:0000269|PubMed:19117336}.|R -> H (in a glioma sample; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha-ketoglutarate but instead alpha-ketoglutarate is converted to R(-)-2-hydroxyglutarate). {ECO:0000269|PubMed:18772396}.|R -> L (in a glioma sample; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha-ketoglutarate but instead alpha-ketoglutarate is converted to R(-)-2-hydroxyglutarate). {ECO:0000269|PubMed:19117336}.|R -> S (in a glioma sample; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha-ketoglutarate but instead alpha-ketoglutarate is converted to R(-)-2-hydroxyglutarate). {ECO:0000269|PubMed:18772396}.		2-oxoglutarate metabolic process (GO:0006103)|cellular lipid metabolic process (GO:0044255)|female gonad development (GO:0008585)|glutathione metabolic process (GO:0006749)|glyoxylate cycle (GO:0006097)|isocitrate metabolic process (GO:0006102)|NADPH regeneration (GO:0006740)|response to oxidative stress (GO:0006979)|response to steroid hormone (GO:0048545)|small molecule metabolic process (GO:0044281)|tricarboxylic acid cycle (GO:0006099)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|peroxisomal matrix (GO:0005782)|peroxisome (GO:0005777)	isocitrate dehydrogenase (NADP+) activity (GO:0004450)|magnesium ion binding (GO:0000287)|NAD binding (GO:0051287)|NADP binding (GO:0050661)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)	p.R132H(2774)|p.R132L(59)|p.R132V(1)|p.G131_R132>VL(1)		NS(1)|autonomic_ganglia(2)|biliary_tract(24)|bone(237)|central_nervous_system(3764)|endometrium(3)|haematopoietic_and_lymphoid_tissue(794)|kidney(2)|large_intestine(7)|lung(7)|prostate(6)|skin(5)|soft_tissue(12)|thyroid(22)|urinary_tract(1)	4887				Epithelial(149;0.0322)|LUSC - Lung squamous cell carcinoma(261;0.0711)|Lung(261;0.136)		ATAAGCATGACGACCTATGAT	0.393			Mis		gliobastoma																																Pancreas(158;264 1958 3300 35450 36047)	ENST00000415913.1				Dom	yes		2	2q33.3	3417	Mis	"""isocitrate dehydrogenase 1 (NADP+), soluble"""			O			gliobastoma		2835	Substitution - Missense(2834)|Complex - compound substitution(1)	p.R132H(2774)|p.R132L(59)|p.R132V(1)|p.G131_R132>VL(1)	central_nervous_system(2579)|haematopoietic_and_lymphoid_tissue(205)|bone(43)|prostate(4)|biliary_tract(2)|urinary_tract(1)|skin(1)	NS(1)|autonomic_ganglia(2)|biliary_tract(24)|bone(237)|central_nervous_system(3764)|endometrium(3)|haematopoietic_and_lymphoid_tissue(794)|kidney(2)|large_intestine(7)|lung(7)|prostate(6)|skin(5)|soft_tissue(12)|thyroid(22)|urinary_tract(1)	4887						c.(394-396)cGt>cAt		isocitrate dehydrogenase 1 (NADP+), soluble							79.0	73.0	75.0					2																	209113112		2203	4300	6503	SO:0001583	missense	3417				2-oxoglutarate metabolic process|cellular lipid metabolic process|glyoxylate cycle|isocitrate metabolic process|NADPH regeneration|tricarboxylic acid cycle	cytosol|peroxisomal matrix	isocitrate dehydrogenase (NADP+) activity|magnesium ion binding|NAD binding|protein homodimerization activity	g.chr2:209113112C>T		CCDS2381.1	2q34	2014-09-17			ENSG00000138413	ENSG00000138413	1.1.1.42		5382	protein-coding gene	gene with protein product		147700					Standard	NM_005896		Approved		uc002vcu.3	O75874	OTTHUMG00000132943	ENST00000415913.1:c.395G>A	2.37:g.209113112C>T	ENSP00000390265:p.Arg132His					IDH1_ENST00000446179.1_Missense_Mutation_p.R132H|IDH1_ENST00000345146.2_Missense_Mutation_p.R132H	p.R132H			O75874	IDHC_HUMAN		Epithelial(149;0.0322)|LUSC - Lung squamous cell carcinoma(261;0.0711)|Lung(261;0.136)	4	776	-			132		R -> C (in colorectal cancer and glioma samples; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha- ketoglutarate but instead alpha- ketoglutarate is converted to R(-)-2- hydroxyglutarate).|R -> G (in a glioma sample; glioblastoma multiforme; somatic mutation).|R -> H (in a glioma sample; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha-ketoglutarate but instead alpha-ketoglutarate is converted to R(-)-2-hydroxyglutarate).|R -> L (in a glioma sample; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha-ketoglutarate but instead alpha-ketoglutarate is converted to R(-)-2-hydroxyglutarate).|R -> S (in a glioma sample; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha-ketoglutarate but instead alpha-ketoglutarate is converted to R(-)-2-hydroxyglutarate).			Q567U4|Q6FHQ6|Q7Z3V0|Q93090|Q9NTJ9|Q9UKW8	Missense_Mutation	SNP	ENST00000415913.1	37	c.395G>A	CCDS2381.1	.	.	.	.	.	.	.	.	.	.	C	25.6	4.657324	0.88154	.	.	ENSG00000138413	ENST00000345146;ENST00000446179;ENST00000415913;ENST00000415282	D;D;D;D	0.86956	-2.19;-2.19;-2.19;-2.19	5.57	4.69	0.59074	Isopropylmalate dehydrogenase-like domain (2);	0.000000	0.85682	D	0.000000	D	0.93145	0.7817	H	0.99379	4.54	0.80722	D	1	B	0.25486	0.127	B	0.25405	0.06	D	0.92324	0.5868	10	0.87932	D	0	-20.0399	14.3783	0.66895	0.0:0.9288:0.0:0.0712	.	132	O75874	IDHC_HUMAN	H	132	ENSP00000260985:R132H;ENSP00000410513:R132H;ENSP00000390265:R132H;ENSP00000391075:R132H	ENSP00000260985:R132H	R	-	2	0	IDH1	208821357	1.000000	0.71417	0.997000	0.53966	0.992000	0.81027	6.088000	0.71371	1.356000	0.45884	0.555000	0.69702	CGT		0.393	IDH1-006	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336672.1			41	48	0	0	0	0.840704	0	41	48				
SIRPA	140885	broad.mit.edu	37	20	1902301	1902301	+	Missense_Mutation	SNP	G	G	A	rs199733185		TCGA-CS-4943-01A-01D-1468-08	TCGA-CS-4943-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	14627ffd-642c-42b5-9d95-ad436c9b1d35	0d4a92bf-0624-4dfa-9d95-8f91a693ea3f	g.chr20:1902301G>A	ENST00000358771.4	+	3	849	c.697G>A	c.(697-699)Gtc>Atc	p.V233I	SIRPA_ENST00000400068.3_Missense_Mutation_p.V233I|SIRPA_ENST00000356025.3_Missense_Mutation_p.V233I	NM_001040023.1	NP_001035112.1	P78324	SHPS1_HUMAN	signal-regulatory protein alpha	233	Ig-like C1-type 1.				blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|leukocyte migration (GO:0050900)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)		p.V233I(1)		cervix(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(13)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)	21				Colorectal(46;0.018)|READ - Rectum adenocarcinoma(1;0.0556)		GGTGGCCCACGTCACCTTGCA	0.617																																					GBM(155;1668 1920 5945 42733 48121)	ENST00000358771.4																			1	Substitution - Missense(1)	p.V233I(1)	lung(1)	cervix(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(13)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)	21						c.(697-699)Gtc>Atc		signal-regulatory protein alpha							67.0	60.0	62.0					20																	1902301		2203	4296	6499	SO:0001583	missense	140885				blood coagulation|cell adhesion|cell junction assembly|leukocyte migration	integral to membrane|plasma membrane	SH3 domain binding	g.chr20:1902301G>A	D86043	CCDS13022.1	20p13	2013-01-11	2006-03-29	2006-03-29	ENSG00000198053	ENSG00000198053		"""Signal-regulatory proteins"", ""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C1-set domain containing"""	9662	protein-coding gene	gene with protein product		602461	"""protein tyrosine phosphatase, non-receptor type substrate 1"""	PTPNS1		9070220, 9062191, 16339511	Standard	XM_005260669		Approved	SHPS1, SIRP, MYD-1, BIT, P84, SHPS-1, SIRPalpha, CD172a, SIRPalpha2, MFR, SIRP-ALPHA-1	uc002wfr.3	P78324	OTTHUMG00000031682	ENST00000358771.4:c.697G>A	20.37:g.1902301G>A	ENSP00000351621:p.Val233Ile					SIRPA_ENST00000356025.3_Missense_Mutation_p.V233I|SIRPA_ENST00000400068.3_Missense_Mutation_p.V233I	p.V233I	NM_001040023.1	NP_001035112.1	P78324	SHPS1_HUMAN		Colorectal(46;0.018)|READ - Rectum adenocarcinoma(1;0.0556)	3	849	+			233			Ig-like C1-type 1.		A2A2E1|A8K411|B2R6C3|O00683|O43799|Q8N517|Q8TAL8|Q9H0Z2|Q9UDX2|Q9UIJ6|Q9Y4U9	Missense_Mutation	SNP	ENST00000358771.4	37	c.697G>A	CCDS13022.1	.	.	.	.	.	.	.	.	.	.	G	10.55	1.382458	0.24944	.	.	ENSG00000198053	ENST00000400068;ENST00000356025;ENST00000358771	T;T;T	0.02863	4.13;4.13;4.13	4.86	-7.7	0.01259	Immunoglobulin-like (1);Immunoglobulin C1-set (2);Immunoglobulin-like fold (1);	2.216010	0.01765	N	0.030825	T	0.02727	0.0082	L	0.27053	0.805	0.09310	N	1	B;B;B	0.14805	0.002;0.011;0.008	B;B;B	0.12156	0.002;0.007;0.006	T	0.30765	-0.9967	10	0.20519	T	0.43	.	13.8982	0.63785	0.7446:0.0:0.2554:0.0	.	213;233;233	B4DP97;P78324-2;P78324	.;.;SHPS1_HUMAN	I	233	ENSP00000382941:V233I;ENSP00000348307:V233I;ENSP00000351621:V233I	ENSP00000348307:V233I	V	+	1	0	SIRPA	1850301	0.000000	0.05858	0.000000	0.03702	0.766000	0.43426	-2.041000	0.01415	-1.573000	0.01659	-0.355000	0.07637	GTC		0.617	SIRPA-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000077568.2	NM_080792		5	120	0	0	0	0.184627	0	5	120				
LVRN	206338	broad.mit.edu	37	5	115351039	115351039	+	Silent	SNP	T	T	C			TCGA-CS-4943-01A-01D-1468-08	TCGA-CS-4943-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	14627ffd-642c-42b5-9d95-ad436c9b1d35	0d4a92bf-0624-4dfa-9d95-8f91a693ea3f	g.chr5:115351039T>C	ENST00000357872.4	+	17	2665	c.2541T>C	c.(2539-2541)acT>acC	p.T847T	AQPEP_ENST00000515454.1_3'UTR	NM_173800.4	NP_776161.3	Q6Q4G3	AMPQ_HUMAN		847						integral component of membrane (GO:0016021)	metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)										ATACTTACACTAATACAACAA	0.348																																						ENST00000357872.4																			0											c.(2539-2541)acT>acC									107.0	107.0	107.0					5																	115351039		2202	4300	6502	SO:0001819	synonymous_variant	0				proteolysis	integral to membrane	metallopeptidase activity|zinc ion binding	g.chr5:115351039T>C																												ENST00000357872.4:c.2541T>C	5.37:g.115351039T>C						AQPEP_ENST00000515454.1_3'UTR	p.T847T	NM_173800.4	NP_776161.3	Q6Q4G3	AMPQ_HUMAN			17	2665	+			847					A8K6J0|C9JGD2|Q32MR1|Q4G0I9|Q4G0V2|Q86XA3|Q8NBZ2	Silent	SNP	ENST00000357872.4	37	c.2541T>C	CCDS4124.1																																																																																				0.348	AQPEP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250852.1			6	86	0	0	0	0.217242	0	6	86				
PLCG2	5336	broad.mit.edu	37	16	81969947	81969947	+	Missense_Mutation	SNP	G	G	A			TCGA-CS-4943-01A-01D-1468-08	TCGA-CS-4943-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	14627ffd-642c-42b5-9d95-ad436c9b1d35	0d4a92bf-0624-4dfa-9d95-8f91a693ea3f	g.chr16:81969947G>A	ENST00000359376.3	+	27	3230	c.3016G>A	c.(3016-3018)Ggt>Agt	p.G1006S		NM_002661.3	NP_002652.2	P16885	PLCG2_HUMAN	phospholipase C, gamma 2 (phosphatidylinositol-specific)	1006	PI-PLC Y-box. {ECO:0000255|PROSITE- ProRule:PRU00271}.				B cell differentiation (GO:0030183)|B cell receptor signaling pathway (GO:0050853)|blood coagulation (GO:0007596)|calcium-mediated signaling (GO:0019722)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|inositol phosphate metabolic process (GO:0043647)|phosphatidylinositol biosynthetic process (GO:0006661)|phospholipid catabolic process (GO:0009395)|platelet activation (GO:0030168)|release of sequestered calcium ion into cytosol (GO:0051209)|small molecule metabolic process (GO:0044281)|T cell receptor signaling pathway (GO:0050852)|Wnt signaling pathway (GO:0016055)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	phosphatidylinositol phospholipase C activity (GO:0004435)|phospholipase C activity (GO:0004629)|signal transducer activity (GO:0004871)			NS(1)|breast(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(18)|lung(21)|ovary(1)|prostate(2)|skin(2)|urinary_tract(1)	58						CTGGCTGTGCGGTTCTCAGAT	0.572																																						ENST00000359376.3																			0				NS(1)|breast(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(18)|lung(21)|ovary(1)|prostate(2)|skin(2)|urinary_tract(1)	58						c.(3016-3018)Ggt>Agt		phospholipase C, gamma 2 (phosphatidylinositol-specific)							68.0	73.0	72.0					16																	81969947		2086	4212	6298	SO:0001583	missense	5336				intracellular signal transduction|phospholipid catabolic process|platelet activation	plasma membrane	phosphatidylinositol phospholipase C activity|protein binding|signal transducer activity	g.chr16:81969947G>A		CCDS42204.1	16q24.1	2014-09-17				ENSG00000197943	3.1.4.11	"""SH2 domain containing"""	9066	protein-coding gene	gene with protein product		600220				7835906	Standard	XR_248240		Approved		uc002fgt.3	P16885		ENST00000359376.3:c.3016G>A	16.37:g.81969947G>A	ENSP00000352336:p.Gly1006Ser						p.G1006S	NM_002661.3	NP_002652.2	P16885	PLCG2_HUMAN			27	3230	+			1006			PI-PLC Y-box.		D3DUL3|Q3ZTS2|Q59H45|Q969T5	Missense_Mutation	SNP	ENST00000359376.3	37	c.3016G>A	CCDS42204.1	.	.	.	.	.	.	.	.	.	.	G	34	5.408118	0.96051	.	.	ENSG00000197943	ENST00000359376	D	0.87103	-2.21	4.79	4.79	0.61399	PLC-like phosphodiesterase, TIM beta/alpha-barrel domain (2);Phospholipase C, phosphatidylinositol-specific, Y domain (3);	0.000000	0.85682	D	0.000000	D	0.95626	0.8578	H	0.95645	3.7	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.97195	0.9860	10	0.87932	D	0	.	17.8393	0.88710	0.0:0.0:1.0:0.0	.	1006	P16885	PLCG2_HUMAN	S	1006	ENSP00000352336:G1006S	ENSP00000352336:G1006S	G	+	1	0	PLCG2	80527448	1.000000	0.71417	0.944000	0.38274	0.878000	0.50629	9.869000	0.99810	2.208000	0.71279	0.561000	0.74099	GGT		0.572	PLCG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432429.1			51	55	0	0	0	0.870114	0	51	55				
RSBN1	54665	broad.mit.edu	37	1	114310931	114310931	+	Missense_Mutation	SNP	C	C	G			TCGA-CS-4943-01A-01D-1468-08	TCGA-CS-4943-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	14627ffd-642c-42b5-9d95-ad436c9b1d35	0d4a92bf-0624-4dfa-9d95-8f91a693ea3f	g.chr1:114310931C>G	ENST00000261441.5	-	5	1802	c.1739G>C	c.(1738-1740)aGa>aCa	p.R580T	RSBN1_ENST00000369581.2_5'Flank	NM_018364.3	NP_060834.2	Q5VWQ0	RSBN1_HUMAN	round spermatid basic protein 1	580						nucleus (GO:0005634)				breast(1)|endometrium(2)|large_intestine(4)|lung(16)|ovary(1)|prostate(3)|urinary_tract(2)	29	Lung SC(450;0.184)	all_cancers(81;3.78e-08)|all_epithelial(167;5.56e-08)|all_lung(203;6.97e-06)|Lung NSC(69;1.18e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|all cancers(265;0.0792)|Epithelial(280;0.0866)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)		AGCATGAGCTCTAGTCCTATC	0.433																																						ENST00000261441.5																			0				breast(1)|endometrium(2)|large_intestine(4)|lung(16)|ovary(1)|prostate(3)|urinary_tract(2)	29						c.(1738-1740)aGa>aCa		round spermatid basic protein 1							130.0	124.0	126.0					1																	114310931		2203	4300	6503	SO:0001583	missense	54665					nucleus		g.chr1:114310931C>G	AK002082	CCDS862.1	1p13.1	2008-02-05			ENSG00000081019	ENSG00000081019			25642	protein-coding gene	gene with protein product		615858				12477932	Standard	NM_018364		Approved	FLJ11220, ROSBIN	uc001edq.3	Q5VWQ0	OTTHUMG00000011938	ENST00000261441.5:c.1739G>C	1.37:g.114310931C>G	ENSP00000261441:p.Arg580Thr						p.R580T	NM_018364.3	NP_060834.2	Q5VWQ0	RSBN1_HUMAN		Lung(183;0.0234)|Colorectal(144;0.0686)|all cancers(265;0.0792)|Epithelial(280;0.0866)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)	5	1802	-	Lung SC(450;0.184)	all_cancers(81;3.78e-08)|all_epithelial(167;5.56e-08)|all_lung(203;6.97e-06)|Lung NSC(69;1.18e-05)	580					A8K937|Q6AI21|Q8TC33|Q9HA80|Q9NUP6	Missense_Mutation	SNP	ENST00000261441.5	37	c.1739G>C	CCDS862.1	.	.	.	.	.	.	.	.	.	.	C	33	5.199348	0.94997	.	.	ENSG00000081019	ENST00000261441	.	.	.	5.7	5.7	0.88788	.	0.044125	0.85682	D	0.000000	T	0.72598	0.3480	L	0.54323	1.7	0.80722	D	1	D	0.61080	0.989	D	0.75020	0.985	T	0.73107	-0.4087	9	0.62326	D	0.03	-9.9448	19.8336	0.96646	0.0:1.0:0.0:0.0	.	580	Q5VWQ0	RSBN1_HUMAN	T	580	.	ENSP00000261441:R580T	R	-	2	0	RSBN1	114112454	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	6.073000	0.71245	2.692000	0.91855	0.655000	0.94253	AGA		0.433	RSBN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033022.2	NM_018364		45	67	0	0	0	0.859065	0	45	67				
TP53	7157	broad.mit.edu	37	17	7578190	7578190	+	Missense_Mutation	SNP	T	T	C	rs121912666		TCGA-CS-4943-01A-01D-1468-08	TCGA-CS-4943-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	14627ffd-642c-42b5-9d95-ad436c9b1d35	0d4a92bf-0624-4dfa-9d95-8f91a693ea3f	g.chr17:7578190T>C	ENST00000269305.4	-	6	848	c.659A>G	c.(658-660)tAt>tGt	p.Y220C	TP53_ENST00000420246.2_Missense_Mutation_p.Y220C|TP53_ENST00000413465.2_Missense_Mutation_p.Y220C|TP53_ENST00000574684.1_Intron|TP53_ENST00000445888.2_Missense_Mutation_p.Y220C|TP53_ENST00000359597.4_Missense_Mutation_p.Y220C|TP53_ENST00000455263.2_Missense_Mutation_p.Y220C	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	220	Interaction with AXIN1. {ECO:0000250}.|Interaction with HIPK1. {ECO:0000250}.|Required for interaction with FBXO42.|Required for interaction with ZNF385A.		Y -> C (in LFS; germline mutation and in sporadic cancers; somatic mutation). {ECO:0000269|PubMed:7682763, ECO:0000269|PubMed:9450901}.|Y -> D (in sporadic cancers; somatic mutation).|Y -> F (in a sporadic cancer; somatic mutation).|Y -> H (in sporadic cancers; somatic mutation).|Y -> N (in sporadic cancers; somatic mutation).|Y -> S (in a brain tumor with no family history; germline mutation and 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.Y220C(278)|p.Y127C(24)|p.Y220S(12)|p.?(11)|p.0?(8)|p.D208fs*1(1)|p.Y220_P223delYEPP(1)|p.V218_E224delVPYEPPE(1)|p.V218_E221delVPYE(1)|p.Y127S(1)|p.V218_Y220delVPY(1)|p.Y220fs*25(1)|p.V216_Y220delVVVPY(1)|p.Y220fs*2(1)|p.V218fs*26(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)	AGGCGGCTCATAGGGCACCAC	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)	ENST00000420246.2		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"""		343	Substitution - Missense(315)|Unknown(11)|Whole gene deletion(8)|Deletion - In frame(5)|Deletion - Frameshift(3)|Insertion - Frameshift(1)	p.Y220C(278)|p.Y127C(24)|p.Y220S(12)|p.?(11)|p.0?(8)|p.D208fs*1(1)|p.Y220_P223delYEPP(1)|p.V218_E224delVPYEPPE(1)|p.V218_E221delVPYE(1)|p.Y127S(1)|p.V218_Y220delVPY(1)|p.Y220fs*25(1)|p.V216_Y220delVVVPY(1)|p.Y220fs*2(1)|p.V218fs*26(1)	ovary(55)|breast(54)|lung(37)|upper_aerodigestive_tract(35)|urinary_tract(19)|oesophagus(19)|large_intestine(17)|liver(17)|central_nervous_system(16)|stomach(15)|haematopoietic_and_lymphoid_tissue(15)|endometrium(14)|soft_tissue(8)|biliary_tract(6)|bone(5)|pancreas(4)|prostate(4)|peritoneum(2)|small_intestine(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	CM015378|CM951227	TP53	M	rs121912666	c.(658-660)tAt>tGt	Other conserved DNA damage response genes	tumor protein p53							102.0	94.0	97.0					17																	7578190		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.chr17:7578190T>C	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.659A>G	17.37:g.7578190T>C	ENSP00000269305:p.Tyr220Cys	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_ENST00000269305.4_Missense_Mutation_p.Y220C|TP53_ENST00000359597.4_Missense_Mutation_p.Y220C|TP53_ENST00000574684.1_Intron|TP53_ENST00000413465.2_Missense_Mutation_p.Y220C|TP53_ENST00000445888.2_Missense_Mutation_p.Y220C|TP53_ENST00000455263.2_Missense_Mutation_p.Y220C	p.Y220C	NM_001126114.2|NM_001276696.1	NP_001119586.1|NP_001263625.1	P04637	P53_HUMAN		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	6	791	-		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)	220		Y -> C (in LFS; germline mutation and in sporadic cancers; somatic mutation).|Y -> D (in sporadic cancers; somatic mutation).|Y -> F (in a sporadic cancer; somatic mutation).|Y -> H (in sporadic cancers; somatic mutation).|Y -> N (in sporadic cancers; somatic mutation).|Y -> S (in a brain tumor with no family history; germline mutation and 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.659A>G	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	T	22.1	4.248510	0.80024	.	.	ENSG00000141510	ENST00000413465;ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000545858;ENST00000509690;ENST00000514944	D;D;D;D;D;D;D;D	0.99840	-7.08;-7.08;-7.08;-7.08;-7.08;-7.08;-7.08;-7.08	5.28	5.28	0.74379	p53, DNA-binding domain (1);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1);	0.000000	0.85682	D	0.000000	D	0.99822	0.9921	M	0.89287	3.02	0.80722	D	1	D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D;D	0.97110	1.0;0.998;0.996;1.0;0.999;0.998;1.0	D	0.96735	0.9542	10	0.87932	D	0	-1.87	13.4753	0.61306	0.0:0.0:0.0:1.0	.	181;220;220;127;220;220;220	B4E095;P04637-2;P04637-3;E9PFT5;P04637;Q1MSW8;E7EQX7	.;.;.;.;P53_HUMAN;.;.	C	220;220;220;220;220;220;209;127;88;127	ENSP00000410739:Y220C;ENSP00000352610:Y220C;ENSP00000269305:Y220C;ENSP00000398846:Y220C;ENSP00000391127:Y220C;ENSP00000391478:Y220C;ENSP00000425104:Y88C;ENSP00000423862:Y127C	ENSP00000269305:Y220C	Y	-	2	0	TP53	7518915	1.000000	0.71417	0.585000	0.28666	0.993000	0.82548	6.232000	0.72313	2.128000	0.65567	0.460000	0.39030	TAT		0.557	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		45	8	0	0	0	0.870114	0	45	8				
ALS2	57679	broad.mit.edu	37	2	202609063	202609063	+	Silent	SNP	G	G	A			TCGA-CS-4943-01A-01D-1468-08	TCGA-CS-4943-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	14627ffd-642c-42b5-9d95-ad436c9b1d35	0d4a92bf-0624-4dfa-9d95-8f91a693ea3f	g.chr2:202609063G>A	ENST00000264276.6	-	10	2460	c.2088C>T	c.(2086-2088)caC>caT	p.H696H	ALS2_ENST00000457679.2_Silent_p.H8H	NM_020919.3	NP_065970.2	Q96Q42	ALS2_HUMAN	amyotrophic lateral sclerosis 2 (juvenile)	696	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						TAGCTAACTCGTGGAGACTGG	0.398																																						ENST00000264276.6																			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.(2086-2088)caC>caT		amyotrophic lateral sclerosis 2 (juvenile)							138.0	129.0	132.0					2																	202609063		1865	4114	5979	SO:0001819	synonymous_variant	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.chr2:202609063G>A	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.2088C>T	2.37:g.202609063G>A						ALS2_ENST00000457679.2_Silent_p.H8H	p.H696H	NM_020919.3	NP_065970.2	Q96Q42	ALS2_HUMAN			10	2460	-			696			DH.		Q53TT1|Q53TV2|Q8N1E0|Q96PC4|Q96Q41|Q9H973|Q9HCK9	Silent	SNP	ENST00000264276.6	37	c.2088C>T	CCDS42800.1																																																																																				0.398	ALS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335562.3	NM_020919		31	35	0	0	0	0.740014	0	31	35				
MCM2	4171	broad.mit.edu	37	3	127337890	127337890	+	Silent	SNP	C	C	T			TCGA-CS-4943-01A-01D-1468-08	TCGA-CS-4943-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	14627ffd-642c-42b5-9d95-ad436c9b1d35	0d4a92bf-0624-4dfa-9d95-8f91a693ea3f	g.chr3:127337890C>T	ENST00000265056.7	+	13	2278	c.2034C>T	c.(2032-2034)ttC>ttT	p.F678F	MCM2_ENST00000468414.1_3'UTR	NM_004526.2	NP_004517.2	P49736	MCM2_HUMAN	minichromosome maintenance complex component 2	678	MCM.				cell cycle (GO:0007049)|cellular response to interleukin-4 (GO:0071353)|DNA replication (GO:0006260)|DNA replication initiation (GO:0006270)|DNA strand elongation involved in DNA replication (GO:0006271)|DNA unwinding involved in DNA replication (GO:0006268)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)|nucleosome assembly (GO:0006334)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|MCM complex (GO:0042555)|microtubule cytoskeleton (GO:0015630)|nuclear origin of replication recognition complex (GO:0005664)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)|DNA replication origin binding (GO:0003688)|metal ion binding (GO:0046872)			ovary(3)|skin(2)|stomach(1)	6						TGGCCCGCTTCGTGGTGGGCA	0.632																																						ENST00000265056.7																			0				ovary(3)|skin(2)|stomach(1)	6						c.(2032-2034)ttC>ttT		minichromosome maintenance complex component 2							27.0	28.0	27.0					3																	127337890		2201	4300	6501	SO:0001819	synonymous_variant	4171				cell cycle checkpoint|DNA strand elongation involved in DNA replication|DNA-dependent DNA replication initiation|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|S phase of mitotic cell cycle	chromatin|MCM complex	ATP binding|helicase activity|metal ion binding	g.chr3:127337890C>T	X67334	CCDS3043.1	3q21	2007-04-04	2007-04-04		ENSG00000073111	ENSG00000073111			6944	protein-coding gene	gene with protein product	"""mitotin"""	116945	"""minichromosome maintenance deficient (S. cerevisiae) 2 (mitotin)"", ""MCM2 minichromosome maintenance deficient 2, mitotin (S. cerevisiae)"""	CCNL1, CDCL1		1710453, 8258304	Standard	NM_004526		Approved	D3S3194, KIAA0030, BM28, cdc19	uc003ejp.4	P49736	OTTHUMG00000159637	ENST00000265056.7:c.2034C>T	3.37:g.127337890C>T						MCM2_ENST00000468414.1_3'UTR	p.F678F	NM_004526.2	NP_004517.2	P49736	MCM2_HUMAN			13	2278	+			678			MCM.		Q14577|Q15023|Q8N2V1|Q969W7|Q96AE1|Q9BRM7	Silent	SNP	ENST00000265056.7	37	c.2034C>T	CCDS3043.1	.	.	.	.	.	.	.	.	.	.	C	9.983	1.228693	0.22542	.	.	ENSG00000073111	ENST00000491422	.	.	.	5.61	-2.21	0.06973	.	.	.	.	.	T	0.62804	0.2458	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.60372	-0.7276	4	.	.	.	-14.8965	12.7755	0.57445	0.0:0.4717:0.0:0.5282	.	.	.	.	L	610	.	.	S	+	2	0	MCM2	128820580	0.088000	0.21588	0.991000	0.47740	0.959000	0.62525	-0.639000	0.05446	-0.386000	0.07821	-0.469000	0.05056	TCG		0.632	MCM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356612.1			5	24	0	0	0	0.217242	0	5	24				
CP	1356	broad.mit.edu	37	3	148930358	148930358	+	Missense_Mutation	SNP	A	A	G			TCGA-CS-4943-01A-01D-1468-08	TCGA-CS-4943-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	14627ffd-642c-42b5-9d95-ad436c9b1d35	0d4a92bf-0624-4dfa-9d95-8f91a693ea3f	g.chr3:148930358A>G	ENST00000264613.6	-	2	536	c.274T>C	c.(274-276)Ttt>Ctt	p.F92L		NM_000096.3	NP_000087	P00450	CERU_HUMAN	ceruloplasmin (ferroxidase)	92	F5/8 type A 1.|Plastocyanin-like 1.				cellular iron ion homeostasis (GO:0006879)|copper ion transport (GO:0006825)|transmembrane transport (GO:0055085)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|lysosomal membrane (GO:0005765)	chaperone binding (GO:0051087)|copper ion binding (GO:0005507)|ferroxidase activity (GO:0004322)			breast(6)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(14)|ovary(1)|prostate(1)|soft_tissue(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	44		Prostate(884;0.00217)|Hepatocellular(537;0.00826)|Myeloproliferative disorder(1037;0.0122)|all_neural(597;0.0189)|Melanoma(1037;0.152)	LUSC - Lung squamous cell carcinoma(72;0.0473)|Lung(72;0.0607)		Drotrecogin alfa(DB00055)	GGGCCTAAAAACCCAAGCCAG	0.398																																						ENST00000264613.6																			0				breast(6)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(14)|ovary(1)|prostate(1)|soft_tissue(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	44						c.(274-276)Ttt>Ctt		ceruloplasmin (ferroxidase)	Drotrecogin alfa(DB00055)						104.0	103.0	103.0					3																	148930358		2203	4300	6503	SO:0001583	missense	1356				cellular iron ion homeostasis|copper ion transport|transmembrane transport	extracellular space	chaperone binding|ferroxidase activity	g.chr3:148930358A>G	M13536	CCDS3141.1	3q23-q25	2010-07-01			ENSG00000047457	ENSG00000047457	1.16.3.1		2295	protein-coding gene	gene with protein product		117700					Standard	NM_000096		Approved		uc003ewy.4	P00450	OTTHUMG00000159563	ENST00000264613.6:c.274T>C	3.37:g.148930358A>G	ENSP00000264613:p.Phe92Leu						p.F92L	NM_000096.3	NP_000087.1	P00450	CERU_HUMAN	LUSC - Lung squamous cell carcinoma(72;0.0473)|Lung(72;0.0607)		2	536	-		Prostate(884;0.00217)|Hepatocellular(537;0.00826)|Myeloproliferative disorder(1037;0.0122)|all_neural(597;0.0189)|Melanoma(1037;0.152)	92			F5/8 type A 1.|Plastocyanin-like 1.		Q14063|Q2PP18|Q9UKS4	Missense_Mutation	SNP	ENST00000264613.6	37	c.274T>C	CCDS3141.1	.	.	.	.	.	.	.	.	.	.	A	14.77	2.633539	0.47049	.	.	ENSG00000047457	ENST00000264613;ENST00000455472	D;D	0.99462	-5.94;-5.94	5.42	2.99	0.34606	Cupredoxin (2);Multicopper oxidase, type 3 (1);	0.174928	0.52532	N	0.000065	D	0.97427	0.9158	L	0.42245	1.32	0.35600	D	0.807809	B;B	0.19583	0.037;0.037	B;B	0.25405	0.04;0.06	D	0.95640	0.8697	10	0.09338	T	0.73	-14.7078	8.2842	0.31920	0.7108:0.0:0.2892:0.0	.	92;92	A8K5A4;P00450	.;CERU_HUMAN	L	92;132	ENSP00000264613:F92L;ENSP00000426888:F132L	ENSP00000264613:F92L	F	-	1	0	CP	150413048	0.994000	0.37717	0.980000	0.43619	0.689000	0.40095	3.486000	0.53215	0.478000	0.27488	0.460000	0.39030	TTT		0.398	CP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317498.1	NM_000096		6	88	0	0	0	0.217242	0	6	88				
XPA	7507	broad.mit.edu	37	9	100459509	100459509	+	Silent	SNP	G	G	A			TCGA-CS-4943-01A-01D-1468-08	TCGA-CS-4943-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	14627ffd-642c-42b5-9d95-ad436c9b1d35	0d4a92bf-0624-4dfa-9d95-8f91a693ea3f	g.chr9:100459509G>A	ENST00000375128.4	-	1	130	c.66C>T	c.(64-66)gcC>gcT	p.A22A		NM_000380.3	NP_000371.1	P23025	XPA_HUMAN	xeroderma pigmentosum, complementation group A	22	Interaction with CEP164 and required for UV resistance.				DNA repair (GO:0006281)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|multicellular organism growth (GO:0035264)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA damage removal (GO:0000718)|response to oxidative stress (GO:0006979)|response to toxic substance (GO:0009636)|response to UV (GO:0009411)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|intercellular bridge (GO:0045171)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	damaged DNA binding (GO:0003684)|metal ion binding (GO:0046872)|protein domain specific binding (GO:0019904)|protein homodimerization activity (GO:0042803)			breast(1)|endometrium(4)|large_intestine(1)|lung(4)|prostate(1)	11		Acute lymphoblastic leukemia(62;0.158)				CCCGCACCGAGGCAGGCAGCT	0.736			"""Mis, N, F, S"""			"""skin basal cell, skin squamous cell, melanoma"""		Nucleotide excision repair (NER)	Xeroderma Pigmentosum																													ENST00000375128.4			yes	Rec		Xeroderma pigmentosum (A)	9	9q22.3	7507	"""Mis, N, F, S"""	"""xeroderma pigmentosum, complementation group A"""			E		"""skin basal cell, skin squamous cell, melanoma"""			0				breast(1)|endometrium(4)|large_intestine(1)|lung(4)|prostate(1)	11						c.(64-66)gcC>gcT	Nucleotide excision repair (NER)	xeroderma pigmentosum, complementation group A							9.0	13.0	12.0					9																	100459509		1987	3991	5978	SO:0001819	synonymous_variant	7507	Xeroderma Pigmentosum	Familial Cancer Database	incl. XPA, XPB, XPC, XPD, XPE, XPF, XPG, XP Variant, XPV	nucleotide-excision repair, DNA damage removal	nucleoplasm	damaged DNA binding|metal ion binding|nucleotide binding|protein domain specific binding|protein homodimerization activity	g.chr9:100459509G>A	D14533	CCDS6729.1	9q22.3	2014-09-17			ENSG00000136936	ENSG00000136936			12814	protein-coding gene	gene with protein product		611153					Standard	NM_000380		Approved	XPAC, XP1	uc004axr.4	P23025	OTTHUMG00000020330	ENST00000375128.4:c.66C>T	9.37:g.100459509G>A							p.A22A	NM_000380.3	NP_000371.1	P23025	XPA_HUMAN			1	130	-		Acute lymphoblastic leukemia(62;0.158)	22			Interaction with CEP164 and required for UV resistance.		Q5T1U9|Q6LCW7|Q6LD02	Silent	SNP	ENST00000375128.4	37	c.66C>T	CCDS6729.1																																																																																				0.736	XPA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053332.1	NM_000380		4	12	0	0	0	0.184627	0	4	12				
SNHG24	101929369	broad.mit.edu	37	14	101438447	101438447	+	lincRNA	SNP	A	A	G			TCGA-CS-4943-01A-01D-1468-08	TCGA-CS-4943-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	14627ffd-642c-42b5-9d95-ad436c9b1d35	0d4a92bf-0624-4dfa-9d95-8f91a693ea3f	g.chr14:101438447A>G	ENST00000554693.2	+	0	299				SNORD114-14_ENST00000362723.1_RNA|SNORD114-15_ENST00000364687.1_RNA|SNORD114-13_ENST00000364377.1_RNA|SNORD114-16_ENST00000363044.1_RNA|SNORD114-17_ENST00000364699.1_RNA																							TCCTGGACCAATGATGACAAC	0.373																																						ENST00000554693.2																			0																				89.0	90.0	90.0					14																	101438447		876	1991	2867			0							g.chr14:101438447A>G																													14.37:g.101438447A>G						SNORD114-14_ENST00000362723.1_RNA								0	299	+									RNA	SNP	ENST00000554693.2	37																																																																																						0.373	RP11-909M7.3-001	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000468646.1			15	26	0	0	0	0.500413	0	15	26				
WNK2	65268	broad.mit.edu	37	9	96080327	96080327	+	3'UTR	SNP	G	G	A			TCGA-CS-4943-01A-01D-1468-08	TCGA-CS-4943-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	14627ffd-642c-42b5-9d95-ad436c9b1d35	0d4a92bf-0624-4dfa-9d95-8f91a693ea3f	g.chr9:96080327G>A	ENST00000297954.4	+	0	6912				WNK2_ENST00000395475.2_Intron|WNK2_ENST00000427277.2_Missense_Mutation_p.A1828T|WNK2_ENST00000356055.3_Intron|WNK2_ENST00000471076.1_Intron|WNK2_ENST00000349097.3_Intron|WNK2_ENST00000395477.2_Intron	NM_001282394.1	NP_001269323.1	Q9Y3S1	WNK2_HUMAN	WNK lysine deficient protein kinase 2						intracellular signal transduction (GO:0035556)|negative regulation of cell proliferation (GO:0008285)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|positive regulation of sodium ion transmembrane transporter activity (GO:2000651)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of ion homeostasis (GO:2000021)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|central_nervous_system(1)|endometrium(11)|kidney(4)|large_intestine(5)|lung(17)|ovary(2)|prostate(3)|skin(4)|stomach(3)|upper_aerodigestive_tract(2)	54						TGGTCCACGCGCCGTCTCCAC	0.582																																						ENST00000427277.2																			0				breast(2)|central_nervous_system(1)|endometrium(11)|kidney(4)|large_intestine(5)|lung(17)|ovary(2)|prostate(3)|skin(4)|stomach(3)|upper_aerodigestive_tract(2)	54						c.(5482-5484)Gcc>Acc		WNK lysine deficient protein kinase 2							122.0	112.0	115.0					9																	96080327		876	1991	2867	SO:0001624	3_prime_UTR_variant	65268				intracellular protein kinase cascade		ATP binding|protein binding|protein serine/threonine kinase activity	g.chr9:96080327G>A	AJ242724	CCDS75858.1	9q22.3	2008-02-05	2003-06-23	2005-01-22	ENSG00000165238	ENSG00000165238			14542	protein-coding gene	gene with protein product		606249	"""serologically defined colon cancer antigen 43"""	SDCCAG43, PRKWNK2		9610721, 11571656	Standard	NM_006648		Approved	NY-CO-43, KIAA1760	uc004atj.3	Q9Y3S1	OTTHUMG00000020247	ENST00000297954.4:c.*18G>A	9.37:g.96080327G>A						WNK2_ENST00000395475.2_Intron|WNK2_ENST00000297954.4_3'UTR|WNK2_ENST00000395477.2_Intron|WNK2_ENST00000471076.1_Intron|WNK2_ENST00000356055.3_Intron|WNK2_ENST00000349097.3_Intron	p.A1828T			Q9Y3S1	WNK2_HUMAN			29	6646	+			118					Q5VWF1|Q5VWF2|Q8IY36|Q9C0A3|Q9H3P4	Missense_Mutation	SNP	ENST00000297954.4	37	c.5482G>A		.	.	.	.	.	.	.	.	.	.	G	16.36	3.101685	0.56183	.	.	ENSG00000165238	ENST00000427277	T	0.59772	0.24	4.63	-3.61	0.04556	.	.	.	.	.	T	0.26048	0.0635	.	.	.	0.09310	N	1	B	0.28584	0.216	B	0.21546	0.035	T	0.19353	-1.0308	8	0.11485	T	0.65	.	1.953	0.03370	0.3421:0.1198:0.4153:0.1228	.	2216	Q9Y3S1-2	.	T	1828	ENSP00000411181:A1828T	ENSP00000411181:A1828T	A	+	1	0	WNK2	95120148	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	0.046000	0.14035	-1.131000	0.02910	-1.113000	0.02065	GCC		0.582	WNK2-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000317359.1	NM_006648		7	104	0	0	0	0.387290	0	7	104				
ROS1	6098	broad.mit.edu	37	6	117609712	117609712	+	Silent	SNP	A	A	G	rs375228224		TCGA-CS-4943-01A-01D-1468-08	TCGA-CS-4943-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	14627ffd-642c-42b5-9d95-ad436c9b1d35	0d4a92bf-0624-4dfa-9d95-8f91a693ea3f	g.chr6:117609712A>G	ENST00000368508.3	-	43	7185	c.6987T>C	c.(6985-6987)ccT>ccC	p.P2329P	ROS1_ENST00000368507.3_Silent_p.P2323P	NM_002944.2	NP_002935.2	P08922	ROS1_HUMAN	ROS proto-oncogene 1 , receptor tyrosine kinase	2329					cell differentiation (GO:0030154)|cell growth (GO:0016049)|cell proliferation (GO:0008283)|columnar/cuboidal epithelial cell development (GO:0002066)|negative regulation of gene expression (GO:0010629)|peptidyl-tyrosine phosphorylation (GO:0018108)|protein phosphorylation (GO:0006468)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of phosphate transport (GO:0010966)|regulation of TOR signaling (GO:0032006)|spermatogenesis (GO:0007283)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|protein phosphatase binding (GO:0019903)|protein tyrosine kinase activity (GO:0004713)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)		TPM3_ENST00000368530/ROS1(4)|LRIG3/ROS1(2)|CD74_ENST00000009530/ROS1(32)|SLC34A2/ROS1(14)|EZR/ROS1(4)|GOPC/ROS1(14)|SDC4/ROS1(7)	NS(2)|breast(7)|central_nervous_system(5)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(28)|lung(56)|ovary(8)|prostate(5)|skin(19)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(3)	162		all_cancers(87;0.00846)|all_epithelial(87;0.0242)		GBM - Glioblastoma multiforme(226;0.0387)|OV - Ovarian serous cystadenocarcinoma(136;0.0954)|all cancers(137;0.137)		TCAGGCCTTCAGGCTTGCCAG	0.438			T	"""GOPC, SDC4, SLC34A2, EZR, LRIG3"""	"""glioblastoma, NSCLC"""																																	ENST00000368508.3				Dom	yes		6	6q22	6098	T	v-ros UR2 sarcoma virus oncogene homolog 1 (avian)			"""O, E"""	"""GOPC, SDC4, SLC34A2, EZR, LRIG3"""		"""glioblastoma, NSCLC"""	TPM3_ENST00000368530/ROS1(4)|LRIG3/ROS1(2)|CD74_ENST00000009530/ROS1(32)|SLC34A2/ROS1(14)|EZR/ROS1(4)|GOPC/ROS1(14)|SDC4/ROS1(7)	0				NS(2)|breast(7)|central_nervous_system(5)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(28)|lung(56)|ovary(8)|prostate(5)|skin(19)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(3)	162						c.(6985-6987)ccT>ccC		c-ros oncogene 1 , receptor tyrosine kinase							109.0	104.0	106.0					6																	117609712		2203	4300	6503	SO:0001819	synonymous_variant	6098				transmembrane receptor protein tyrosine kinase signaling pathway	membrane fraction|sodium:potassium-exchanging ATPase complex	ATP binding|transmembrane receptor protein tyrosine kinase activity	g.chr6:117609712A>G	M13599	CCDS5116.1	6q21-q22	2014-06-26	2014-06-26		ENSG00000047936	ENSG00000047936		"""Fibronectin type III domain containing"""	10261	protein-coding gene	gene with protein product		165020	"""v-ros avian UR2 sarcoma virus oncogene homolog 1"", ""v-ros UR2 sarcoma virus oncogene homolog 1 (avian)"", ""c-ros oncogene 1 , receptor tyrosine kinase"""			1611909	Standard	NM_002944		Approved	MCF3, ROS, c-ros-1	uc003pxp.1	P08922	OTTHUMG00000016188	ENST00000368508.3:c.6987T>C	6.37:g.117609712A>G						ROS1_ENST00000368507.3_Silent_p.P2323P	p.P2329P	NM_002944.2	NP_002935.2	P08922	ROS_HUMAN		GBM - Glioblastoma multiforme(226;0.0387)|OV - Ovarian serous cystadenocarcinoma(136;0.0954)|all cancers(137;0.137)	43	7185	-		all_cancers(87;0.00846)|all_epithelial(87;0.0242)	2329					Q15368|Q5TDB5	Silent	SNP	ENST00000368508.3	37	c.6987T>C	CCDS5116.1																																																																																				0.438	ROS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000043464.1			43	69	0	0	0	0.853193	0	43	69				
TP53	7157	broad.mit.edu	37	17	7577548	7577548	+	Missense_Mutation	SNP	C	C	T	rs28934575|rs397516437		TCGA-CS-4943-01A-01D-1468-08	TCGA-CS-4943-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	14627ffd-642c-42b5-9d95-ad436c9b1d35	0d4a92bf-0624-4dfa-9d95-8f91a693ea3f	g.chr17:7577548C>T	ENST00000269305.4	-	7	922	c.733G>A	c.(733-735)Ggc>Agc	p.G245S	TP53_ENST00000420246.2_Missense_Mutation_p.G245S|TP53_ENST00000413465.2_Missense_Mutation_p.G245S|TP53_ENST00000574684.1_5'Flank|TP53_ENST00000445888.2_Missense_Mutation_p.G245S|TP53_ENST00000359597.4_Missense_Mutation_p.G245S|TP53_ENST00000455263.2_Missense_Mutation_p.G245S	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	245	Interaction with AXIN1. {ECO:0000250}.|Interaction with HIPK1. {ECO:0000250}.|Interacts with the 53BP2 SH3 domain.|Required for interaction with ZNF385A.		G -> A (in sporadic cancers; somatic mutation).|G -> C (in LFS; germline mutation and in sporadic cancers; somatic mutation). {ECO:0000269|PubMed:1394225, ECO:0000269|PubMed:1978757}.|G -> D (in LFS; germline mutation and in sporadic cancers; somatic mutation). {ECO:0000269|PubMed:2259385}.|G -> E (in a sporadic cancer; somatic mutation).|G -> F (in sporadic cancers; somatic mutation; requires 2 nucleotide substitutions).|G -> H (in a sporadic cancer; somatic mutation; requires 2 nucleotide substitutions).|G -> L (in sporadic cancers; somatic mutation; requires 2 nucleotide substitutions).|G -> N (in sporadic cancers; somatic mutation; requires 2 nucleotide substitutions).|G -> R (in sporadic cancers; somatic mutation).|G -> S (in LFS; germline mutation and in sporadic cancers; somatic mutation; dbSNP:rs28934575). {ECO:0000269|PubMed:8829627}.|G -> V (in LFS; germline mutation and in sporadic cancers; somatic mutation). {ECO:0000269|PubMed:2263646}.		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.G245S(304)|p.G245C(59)|p.G245R(10)|p.G152S(8)|p.0?(8)|p.?(5)|p.G152C(4)|p.G244_M246>V(3)|p.G245N(2)|p.G245fs*2(2)|p.G245H(1)|p.G245L(1)|p.G244fs*17(1)|p.G245F(1)|p.C242_M246>L(1)|p.C238_M246delCNSSCMGGM(1)|p.G245fs*22(1)|p.S241_G245delSCMGG(1)|p.C242fs*98(1)|p.M243fs*18(1)|p.G151_M153>V(1)|p.G245del(1)|p.G245fs*14(1)|p.G245fs*17(1)|p.G245fs*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)	CGGTTCATGCCGCCCATGCAG	0.577	G245S(LS1034_LARGE_INTESTINE)|G245S(NUGC2_STOMACH)|G245S(PANC0403_PANCREAS)|G245S(SKLMS1_SOFT_TISSUE)|G245S(SKMEL2_SKIN)	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)	ENST00000420246.2	G245S(LS1034_LARGE_INTESTINE)|G245S(NUGC2_STOMACH)|G245S(PANC0403_PANCREAS)|G245S(SKLMS1_SOFT_TISSUE)|G245S(SKMEL2_SKIN)	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"""		420	Substitution - Missense(390)|Deletion - Frameshift(8)|Whole gene deletion(8)|Complex - deletion inframe(5)|Unknown(5)|Deletion - In frame(3)|Insertion - Frameshift(1)	p.G245S(304)|p.G245C(59)|p.G245R(10)|p.G152S(8)|p.0?(8)|p.?(5)|p.G152C(4)|p.G244_M246>V(3)|p.G245N(2)|p.G245fs*2(2)|p.G245H(1)|p.G245L(1)|p.G244fs*17(1)|p.G245F(1)|p.C242_M246>L(1)|p.C238_M246delCNSSCMGGM(1)|p.G245fs*22(1)|p.S241_G245delSCMGG(1)|p.C242fs*98(1)|p.M243fs*18(1)|p.G151_M153>V(1)|p.G245del(1)|p.G245fs*14(1)|p.G245fs*17(1)|p.G245fs*16(1)	large_intestine(119)|lung(51)|breast(38)|ovary(29)|central_nervous_system(27)|upper_aerodigestive_tract(25)|stomach(25)|haematopoietic_and_lymphoid_tissue(23)|oesophagus(22)|urinary_tract(14)|skin(9)|liver(7)|prostate(7)|biliary_tract(5)|bone(5)|pancreas(4)|soft_tissue(3)|vulva(2)|endometrium(2)|kidney(1)|cervix(1)|salivary_gland(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	CM010463|CM900210|CM920674	TP53	M	rs28934575	c.(733-735)Ggc>Agc	Other conserved DNA damage response genes	tumor protein p53		C	SER/GLY,SER/GLY,SER/GLY,SER/GLY,SER/GLY,SER/GLY,SER/GLY	0,4406		0,0,2203	149.0	112.0	125.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	733,733,733,733,337,337,337	4.6	1.0	17	dbSNP_125	125	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense,missense,missense,missense,missense,missense	TP53	NM_000546.4,NM_001126112.1,NM_001126113.1,NM_001126114.1,NM_001126115.1,NM_001126116.1,NM_001126117.1	56,56,56,56,56,56,56	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging	245/394,245/394,245/347,245/342,113/262,113/210,113/215	7577548	1,13005	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.chr17:7577548C>T	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.733G>A	17.37:g.7577548C>T	ENSP00000269305:p.Gly245Ser	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_ENST00000269305.4_Missense_Mutation_p.G245S|TP53_ENST00000359597.4_Missense_Mutation_p.G245S|TP53_ENST00000413465.2_Missense_Mutation_p.G245S|TP53_ENST00000445888.2_Missense_Mutation_p.G245S|TP53_ENST00000455263.2_Missense_Mutation_p.G245S	p.G245S	NM_001126114.2|NM_001276696.1	NP_001119586.1|NP_001263625.1	P04637	P53_HUMAN		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	7	865	-		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)	245		G -> A (in sporadic cancers; somatic mutation).|G -> C (in LFS; germline mutation and in sporadic cancers; somatic mutation).|G -> D (in LFS; germline mutation and in sporadic cancers; somatic mutation).|G -> E (in a sporadic cancer; somatic mutation).|G -> F (in sporadic cancers; somatic mutation; requires 2 nucleotide substitutions).|G -> H (in a sporadic cancer; somatic mutation; requires 2 nucleotide substitutions).|G -> L (in sporadic cancers; somatic mutation; requires 2 nucleotide substitutions).|G -> N (in sporadic cancers; somatic mutation; requires 2 nucleotide substitutions).|G -> R (in sporadic cancers; somatic mutation).|G -> S (in LFS; germline mutation and in sporadic cancers; somatic mutation; dbSNP:rs28934575).|G -> V (in LFS; germline mutation and in sporadic cancers; somatic mutation).	Interaction with AXIN1 (By similarity).|Interaction with HIPK1 (By similarity).|Interacts with the 53BP2 SH3 domain.		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.733G>A	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	C	33	5.259904	0.95368	0.0	1.16E-4	ENSG00000141510	ENST00000413465;ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000545858;ENST00000509690;ENST00000514944	D;D;D;D;D;D;D;D	0.99894	-7.58;-7.58;-7.58;-7.58;-7.58;-7.58;-7.58;-7.58	4.62	4.62	0.57501	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	0.99878	0.9942	M	0.84585	2.705	0.80722	D	1	D;D;D;D;D;D	0.89917	1.0;0.999;1.0;1.0;1.0;1.0	D;D;D;D;D;D	0.97110	0.999;0.976;0.992;0.999;0.999;1.0	D	0.96039	0.9023	10	0.87932	D	0	-19.4293	15.3618	0.74483	0.0:1.0:0.0:0.0	rs28934575	245;245;152;245;245;245	P04637-2;P04637-3;E9PFT5;P04637;Q1MSW8;E7EQX7	.;.;.;P53_HUMAN;.;.	S	245;245;245;245;245;245;234;152;113;152	ENSP00000410739:G245S;ENSP00000352610:G245S;ENSP00000269305:G245S;ENSP00000398846:G245S;ENSP00000391127:G245S;ENSP00000391478:G245S;ENSP00000425104:G113S;ENSP00000423862:G152S	ENSP00000269305:G245S	G	-	1	0	TP53	7518273	1.000000	0.71417	0.965000	0.40720	0.974000	0.67602	7.609000	0.82925	2.564000	0.86499	0.462000	0.41574	GGC		0.577	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		4	90	0	0	0	0.150653	0	4	90				
ROCK2	9475	broad.mit.edu	37	2	11355517	11355517	+	Missense_Mutation	SNP	A	A	T			TCGA-CS-4943-01A-01D-1468-08	TCGA-CS-4943-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	14627ffd-642c-42b5-9d95-ad436c9b1d35	0d4a92bf-0624-4dfa-9d95-8f91a693ea3f	g.chr2:11355517A>T	ENST00000315872.6	-	15	2067	c.1619T>A	c.(1618-1620)cTt>cAt	p.L540H	ROCK2_ENST00000401753.1_Missense_Mutation_p.L297H	NM_004850.3	NP_004841.2	O75116	ROCK2_HUMAN	Rho-associated, coiled-coil containing protein kinase 2	540	Interaction with PPP1R12A.				actin cytoskeleton organization (GO:0030036)|axon guidance (GO:0007411)|centrosome duplication (GO:0051298)|cytokinesis (GO:0000910)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|intracellular signal transduction (GO:0035556)|negative regulation of angiogenesis (GO:0016525)|neural tube closure (GO:0001843)|positive regulation of centrosome duplication (GO:0010825)|protein phosphorylation (GO:0006468)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of cell adhesion (GO:0030155)|regulation of cell motility (GO:2000145)|regulation of circadian rhythm (GO:0042752)|regulation of establishment of cell polarity (GO:2000114)|regulation of focal adhesion assembly (GO:0051893)|regulation of keratinocyte differentiation (GO:0045616)|regulation of stress fiber assembly (GO:0051492)|rhythmic process (GO:0048511)|smooth muscle contraction (GO:0006939)	centrosome (GO:0005813)|cytoplasmic ribonucleoprotein granule (GO:0036464)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|spindle pole centrosome (GO:0031616)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|protein serine/threonine kinase activity (GO:0004674)|structural molecule activity (GO:0005198)			breast(2)|central_nervous_system(1)|cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(5)|large_intestine(6)|lung(10)|prostate(1)|skin(4)|stomach(3)|urinary_tract(2)	43	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.137)|OV - Ovarian serous cystadenocarcinoma(76;0.162)		CAAATCTTCAAGTTGATCTTT	0.308																																						ENST00000315872.6																			0				breast(2)|central_nervous_system(1)|cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(5)|large_intestine(6)|lung(10)|prostate(1)|skin(4)|stomach(3)|urinary_tract(2)	43						c.(1618-1620)cTt>cAt		Rho-associated, coiled-coil containing protein kinase 2							109.0	94.0	99.0					2																	11355517		1810	4072	5882	SO:0001583	missense	9475				axon guidance|cytokinesis|intracellular signal transduction	cytosol|plasma membrane	ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity|structural molecule activity	g.chr2:11355517A>T	D87931	CCDS42654.1	2p24	2013-01-10			ENSG00000134318	ENSG00000134318	2.7.11.1	"""Pleckstrin homology (PH) domain containing"""	10252	protein-coding gene	gene with protein product		604002				9933571	Standard	NM_004850		Approved		uc002rbd.1	O75116	OTTHUMG00000149916	ENST00000315872.6:c.1619T>A	2.37:g.11355517A>T	ENSP00000317985:p.Leu540His					ROCK2_ENST00000401753.1_Missense_Mutation_p.L297H	p.L540H	NM_004850.3	NP_004841.2	O75116	ROCK2_HUMAN		Epithelial(75;0.137)|OV - Ovarian serous cystadenocarcinoma(76;0.162)	15	2067	-	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)		540			Interaction with PPP1R12A.		Q53QZ0|Q53SJ7|Q9UQN5	Missense_Mutation	SNP	ENST00000315872.6	37	c.1619T>A	CCDS42654.1	.	.	.	.	.	.	.	.	.	.	A	22.6	4.314831	0.81358	.	.	ENSG00000134318	ENST00000315872;ENST00000401753	D;D	0.85484	-1.99;-1.99	5.17	5.17	0.71159	.	0.000000	0.85682	D	0.000000	D	0.91099	0.7198	M	0.68593	2.085	0.80722	D	1	D	0.89917	1.0	D	0.81914	0.995	D	0.91965	0.5582	10	0.66056	D	0.02	.	15.0145	0.71573	1.0:0.0:0.0:0.0	.	540	O75116	ROCK2_HUMAN	H	540;297	ENSP00000317985:L540H;ENSP00000385509:L297H	ENSP00000317985:L540H	L	-	2	0	ROCK2	11272968	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.486000	0.81215	1.955000	0.56771	0.533000	0.62120	CTT		0.308	ROCK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313886.3			33	40	0	0	0	0.740014	0	33	40				
LINC00854	100874261	broad.mit.edu	37	17	41381938	41381938	+	RNA	SNP	C	C	G	rs4986161	byFrequency	TCGA-CS-4943-01A-01D-1468-08	TCGA-CS-4943-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	14627ffd-642c-42b5-9d95-ad436c9b1d35	0d4a92bf-0624-4dfa-9d95-8f91a693ea3f	g.chr17:41381938C>G	ENST00000433702.2	-	0	14				LINC00854_ENST00000600764.1_RNA|LINC00854_ENST00000608223.1_RNA	NR_047479.1				long intergenic non-protein coding RNA 854																		aagagctgatcttatgcaggg	0.552																																						ENST00000433702.2																			0																																																			0							g.chr17:41381938C>G			17q21.31	2013-02-13	2013-02-13	2013-02-13	ENSG00000236383	ENSG00000236383		"""Long non-coding RNAs"""	43658	non-coding RNA	RNA, long non-coding			"""TMEM106A antisense RNA 1 (non-protein coding)"", ""TMEM106A antisense RNA 1"", ""TMEM106A antisense RNA 1 (tail to tail)"""	TMEM106A-AS1		22196729	Standard	NR_047479		Approved		uc031ras.1		OTTHUMG00000132641		17.37:g.41381938C>G								NR_047479.1						0	14	-									RNA	SNP	ENST00000433702.2	37																																																																																						0.552	LINC00854-001	KNOWN	basic	antisense	processed_transcript	OTTHUMT00000255889.2			4	17	0	0	0	0.184627	0	4	17				
ATRX	546	broad.mit.edu	37	X	76829760	76829760	+	Nonsense_Mutation	SNP	G	G	C			TCGA-CS-4943-01A-01D-1468-08	TCGA-CS-4943-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	14627ffd-642c-42b5-9d95-ad436c9b1d35	0d4a92bf-0624-4dfa-9d95-8f91a693ea3f	g.chrX:76829760G>C	ENST00000373344.5	-	28	6495	c.6281C>G	c.(6280-6282)tCa>tGa	p.S2094*	ATRX_ENST00000480283.1_5'UTR|ATRX_ENST00000395603.3_Nonsense_Mutation_p.S2056*	NM_000489.3	NP_000480.3	P46100	ATRX_HUMAN	alpha thalassemia/mental retardation syndrome X-linked	2094	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.|Interaction with MECP2.				ATP catabolic process (GO:0006200)|cellular response to hydroxyurea (GO:0072711)|chromatin remodeling (GO:0006338)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA duplex unwinding (GO:0032508)|DNA methylation (GO:0006306)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|DNA replication-independent nucleosome assembly (GO:0006336)|forebrain development (GO:0030900)|negative regulation of telomeric RNA transcription from RNA pol II promoter (GO:1901581)|nucleosome assembly (GO:0006334)|positive regulation of nuclear cell cycle DNA replication (GO:0010571)|positive regulation of telomere maintenance (GO:0032206)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|replication fork processing (GO:0031297)|seminiferous tubule development (GO:0072520)|Sertoli cell development (GO:0060009)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nuclear heterochromatin (GO:0005720)|nucleolus (GO:0005730)|nucleus (GO:0005634)|SWI/SNF superfamily-type complex (GO:0070603)|telomeric heterochromatin (GO:0031933)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|chromo shadow domain binding (GO:0070087)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)|DNA translocase activity (GO:0015616)|helicase activity (GO:0004386)|histone binding (GO:0042393)|methylated histone binding (GO:0035064)|zinc ion binding (GO:0008270)	p.?(1)		bone(1)|breast(6)|central_nervous_system(31)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(15)|kidney(14)|large_intestine(1)|liver(1)|lung(40)|ovary(2)|pancreas(13)|prostate(5)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	145						CTTCTTCCTTGACTGTGCAGT	0.313			"""Mis, F, N"""		"""Pancreatic neuroendocrine tumors, paediatric GBM"""		ATR-X (alpha thalassemia/mental retardation) syndrome																															ENST00000373344.5				Rec	yes		X	Xq21.1	546	"""Mis, F, N"""	alpha thalassemia/mental retardation syndrome X-linked	yes	ATR-X (alpha thalassemia/mental retardation) syndrome	E			"""Pancreatic neuroendocrine tumors, paediatric GBM"""		1	Unknown(1)	p.?(1)	bone(1)	bone(1)|breast(6)|central_nervous_system(31)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(15)|kidney(14)|large_intestine(1)|liver(1)|lung(40)|ovary(2)|pancreas(13)|prostate(5)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	145						c.(6280-6282)tCa>tGa		alpha thalassemia/mental retardation syndrome X-linked	Phosphatidylserine(DB00144)						139.0	125.0	130.0					X																	76829760		2203	4296	6499	SO:0001587	stop_gained	546				DNA methylation|DNA recombination|DNA repair|regulation of transcription, DNA-dependent	nuclear heterochromatin	ATP binding|chromo shadow domain binding|DNA binding|DNA helicase activity|zinc ion binding	g.chrX:76829760G>C	U72937	CCDS14434.1, CCDS14435.1	Xq21.1	2014-06-17	2010-06-24		ENSG00000085224	ENSG00000085224			886	protein-coding gene	gene with protein product	"""RAD54 homolog (S. cerevisiae)"""	300032	"""alpha thalassemia/mental retardation syndrome X-linked (RAD54 (S. cerevisiae) homolog)"", ""Juberg-Marsidi syndrome"""	RAD54, JMS		7874112, 1415255, 8503439, 8630485	Standard	NM_000489		Approved	XH2, XNP	uc004ecp.4	P46100	OTTHUMG00000022686	ENST00000373344.5:c.6281C>G	X.37:g.76829760G>C	ENSP00000362441:p.Ser2094*					ATRX_ENST00000395603.3_Nonsense_Mutation_p.S2056*|ATRX_ENST00000480283.1_5'UTR	p.S2094*	NM_000489.3	NP_000480.2	P46100	ATRX_HUMAN			28	6495	-			2094			Helicase C-terminal.		D3DTE2|P51068|Q15886|Q59FB5|Q59H31|Q5H9A2|Q5JWI4|Q7Z2J1|Q9H0Z1|Q9NTS3	Nonsense_Mutation	SNP	ENST00000373344.5	37	c.6281C>G	CCDS14434.1	.	.	.	.	.	.	.	.	.	.	-	49	15.142353	0.99824	.	.	ENSG00000085224	ENST00000373344;ENST00000395603	.	.	.	5.45	5.45	0.79879	.	0.093852	0.45867	U	0.000331	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.42905	T	0.14	-4.7825	18.0086	0.89216	0.0:0.0:1.0:0.0	.	.	.	.	X	2094;2056	.	ENSP00000362441:S2094X	S	-	2	0	ATRX	76716416	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.949000	0.93012	2.288000	0.76882	0.540000	0.68198	TCA		0.313	ATRX-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058860.2	NM_000489		69	12	0	0	0	0.870114	0	69	12				
MT-ND5	4540	broad.mit.edu	37	M	13143	13143	+	Silent	SNP	T	T	C			TCGA-CS-4943-01A-01D-1468-08	TCGA-CS-4943-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	14627ffd-642c-42b5-9d95-ad436c9b1d35	0d4a92bf-0624-4dfa-9d95-8f91a693ea3f	g.chrM:13143T>C	ENST00000361567.2	+	1	807	c.807T>C	c.(805-807)aaT>aaC	p.N269N	MT-TH_ENST00000387441.1_RNA|MT-TP_ENST00000387461.2_RNA|MT-TL2_ENST00000387456.1_RNA|MT-TS2_ENST00000387449.1_RNA|MT-TE_ENST00000387459.1_RNA|MT-TR_ENST00000387439.1_RNA|MT-TT_ENST00000387460.2_RNA|MT-CYB_ENST00000361789.2_5'Flank			P03915	NU5M_HUMAN	mitochondrially encoded NADH dehydrogenase 5	269					cellular metabolic process (GO:0044237)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex I (GO:0005747)	NADH dehydrogenase (ubiquinone) activity (GO:0008137)			breast(4)|endometrium(29)|kidney(33)|pancreas(1)|prostate(7)	74						CTAGCAGAAAATAGCCCACTA	0.483																																						ENST00000361567.2																			0				breast(4)|endometrium(29)|kidney(33)|pancreas(1)|prostate(7)	74						c.(805-807)aaT>aaC		mitochondrially encoded NADH dehydrogenase 5	NADH(DB00157)																																			SO:0001819	synonymous_variant	4540				mitochondrial electron transport, NADH to ubiquinone|transport	integral to membrane|mitochondrial respiratory chain complex I	NADH dehydrogenase (ubiquinone) activity	g.chrM:13143T>C			mitochondria	2011-07-04	2005-02-15	2005-02-16	ENSG00000198786	ENSG00000198786	1.6.5.3	"""Mitochondrial respiratory chain complex / Complex I"""	7461	protein-coding gene	gene with protein product	"""complex I ND5 subunit"", ""NADH-ubiquinone oxidoreductase chain 5"""	516005	"""NADH dehydrogenase 5"""	MTND5			Standard			Approved	ND5, NAD5		P03915		ENST00000361567.2:c.807T>C	M.37:g.13143T>C							p.N269N			P03915	NU5M_HUMAN			1	807	+			269					Q34773|Q8WCY3	Silent	SNP	ENST00000361567.2	37	c.807T>C																																																																																					0.483	MT-ND5-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		YP_003024036		113	85	0	0	0	0.870114	0	113	85				
KCNH8	131096	broad.mit.edu	37	3	19575087	19575087	+	Silent	SNP	C	C	T	rs151258565	byFrequency	TCGA-CS-4943-01A-01D-1468-08	TCGA-CS-4943-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	14627ffd-642c-42b5-9d95-ad436c9b1d35	0d4a92bf-0624-4dfa-9d95-8f91a693ea3f	g.chr3:19575087C>T	ENST00000328405.2	+	16	3086	c.2820C>T	c.(2818-2820)ggC>ggT	p.G940G		NM_144633.2	NP_653234.2	Q96L42	KCNH8_HUMAN	potassium voltage-gated channel, subfamily H (eag-related), member 8	940					potassium ion transmembrane transport (GO:0071805)|regulation of membrane potential (GO:0042391)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	phosphorelay sensor kinase activity (GO:0000155)|voltage-gated potassium channel activity (GO:0005249)			NS(1)|breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|liver(3)|lung(37)|ovary(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	77						TGCAAACAGGCGGGGCTGCTT	0.542													C|||	3	0.000599042	0.0008	0.0014	5008	,	,		18580	0.0		0.001	False		,,,				2504	0.0				NSCLC(124;1625 1765 8018 24930 42026)	ENST00000328405.2																			0				NS(1)|breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|liver(3)|lung(37)|ovary(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	77						c.(2818-2820)ggC>ggT		potassium voltage-gated channel, subfamily H (eag-related), member 8		C		2,4404	4.2+/-10.8	0,2,2201	81.0	79.0	79.0		2820	-7.2	0.0	3	dbSNP_134	79	0,8600		0,0,4300	no	coding-synonymous	KCNH8	NM_144633.2		0,2,6501	TT,TC,CC		0.0,0.0454,0.0154		940/1108	19575087	2,13004	2203	4300	6503	SO:0001819	synonymous_variant	131096					integral to membrane	two-component sensor activity	g.chr3:19575087C>T	AY053503	CCDS2632.1	3p24.3	2012-07-05			ENSG00000183960	ENSG00000183960		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	18864	protein-coding gene	gene with protein product		608260				16382104	Standard	NM_144633		Approved	Kv12.1, elk3	uc003cbk.1	Q96L42	OTTHUMG00000129891	ENST00000328405.2:c.2820C>T	3.37:g.19575087C>T							p.G940G	NM_144633.2	NP_653234.2	Q96L42	KCNH8_HUMAN			16	3086	+			940					B7Z2I7|Q59GQ6	Silent	SNP	ENST00000328405.2	37	c.2820C>T	CCDS2632.1																																																																																				0.542	KCNH8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252139.2	NM_144633		50	76	0	0	0	0.870114	0	50	76				
RYR1	6261	broad.mit.edu	37	19	39071043	39071043	+	Missense_Mutation	SNP	G	G	T	rs118192168		TCGA-CS-4943-01A-01D-1468-08	TCGA-CS-4943-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	14627ffd-642c-42b5-9d95-ad436c9b1d35	0d4a92bf-0624-4dfa-9d95-8f91a693ea3f	g.chr19:39071043G>T	ENST00000359596.3	+	101	14545	c.14545G>T	c.(14545-14547)Gtc>Ttc	p.V4849F	RYR1_ENST00000360985.3_Missense_Mutation_p.V4844F|RYR1_ENST00000355481.4_Missense_Mutation_p.V4844F			P21817	RYR1_HUMAN	ryanodine receptor 1 (skeletal)	4849			V -> I (in MHS1 and CCD; autosomal recessive form). {ECO:0000269|PubMed:12136074, ECO:0000269|PubMed:16163667, ECO:0000269|PubMed:17226826, ECO:0000269|PubMed:18253926}.		calcium ion transport (GO:0006816)|cellular response to caffeine (GO:0071313)|cytosolic calcium ion homeostasis (GO:0051480)|ion transmembrane transport (GO:0034220)|muscle contraction (GO:0006936)|ossification involved in bone maturation (GO:0043931)|outflow tract morphogenesis (GO:0003151)|release of sequestered calcium ion into cytosol (GO:0051209)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|skeletal muscle fiber development (GO:0048741)|skin development (GO:0043588)|transmembrane transport (GO:0055085)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|I band (GO:0031674)|integral component of plasma membrane (GO:0005887)|junctional membrane complex (GO:0030314)|junctional sarcoplasmic reticulum membrane (GO:0014701)|plasma membrane (GO:0005886)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|T-tubule (GO:0030315)|terminal cisterna (GO:0014802)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-release channel activity (GO:0015278)|calmodulin binding (GO:0005516)|ryanodine-sensitive calcium-release channel activity (GO:0005219)|voltage-gated calcium channel activity (GO:0005245)			NS(4)|autonomic_ganglia(2)|breast(3)|central_nervous_system(5)|endometrium(26)|haematopoietic_and_lymphoid_tissue(3)|kidney(34)|large_intestine(42)|liver(1)|lung(106)|ovary(11)|pancreas(5)|prostate(9)|skin(12)|stomach(11)|upper_aerodigestive_tract(4)|urinary_tract(7)	285	all_cancers(60;7.91e-06)		Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272)		Caffeine(DB00201)|Dantrolene(DB01219)|Suramin(DB04786)	GGCGGTGGTCGTCTACCTGTA	0.602																																						ENST00000355481.4																			0				NS(4)|autonomic_ganglia(2)|breast(3)|central_nervous_system(5)|endometrium(26)|haematopoietic_and_lymphoid_tissue(3)|kidney(34)|large_intestine(42)|liver(1)|lung(106)|ovary(11)|pancreas(5)|prostate(9)|skin(12)|stomach(11)|upper_aerodigestive_tract(4)|urinary_tract(7)	285	GRCh37	CM021677	RYR1	M	rs118192168	c.(14530-14532)Gtc>Ttc		ryanodine receptor 1 (skeletal)	Dantrolene(DB01219)						152.0	116.0	128.0					19																	39071043		2203	4300	6503	SO:0001583	missense	6261				muscle contraction|release of sequestered calcium ion into cytosol|response to caffeine|response to hypoxia	cell cortex|cytosol|I band|integral to plasma membrane|junctional sarcoplasmic reticulum membrane|smooth endoplasmic reticulum|terminal cisterna	calcium ion binding|calmodulin binding|receptor activity|ryanodine-sensitive calcium-release channel activity	g.chr19:39071043G>T	J05200	CCDS33011.1, CCDS42563.1	19q13.1	2014-09-17				ENSG00000196218		"""Ion channels / Ryanodine receptors"""	10483	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 137"""	180901	"""central core disease of muscle"""	MHS, MHS1, CCO		1862346, 16621918	Standard	NM_000540		Approved	RYR, PPP1R137	uc002oit.3	P21817		ENST00000359596.3:c.14545G>T	19.37:g.39071043G>T	ENSP00000352608:p.Val4849Phe					RYR1_ENST00000360985.3_Missense_Mutation_p.V4844F|RYR1_ENST00000359596.3_Missense_Mutation_p.V4849F	p.V4844F	NM_000540.2|NM_001042723.1	NP_000531.2|NP_001036188.1	P21817	RYR1_HUMAN	Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272)		100	14661	+	all_cancers(60;7.91e-06)		4849					Q16314|Q16368|Q9NPK1|Q9P1U4	Missense_Mutation	SNP	ENST00000359596.3	37	c.14530G>T	CCDS33011.1	.	.	.	.	.	.	.	.	.	.	G	15.92	2.974553	0.53720	.	.	ENSG00000196218	ENST00000359596;ENST00000355481;ENST00000360985	D;D;D	0.98313	-4.86;-4.86;-4.86	4.57	4.57	0.56435	Ion transport (1);	0.000000	0.64402	U	0.000014	D	0.99013	0.9663	M	0.87097	2.86	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	D	0.99659	1.0993	10	0.87932	D	0	.	17.129	0.86722	0.0:0.0:1.0:0.0	.	4844;4849	P21817-2;P21817	.;RYR1_HUMAN	F	4849;4844;4844	ENSP00000352608:V4849F;ENSP00000347667:V4844F;ENSP00000354254:V4844F	ENSP00000347667:V4844F	V	+	1	0	RYR1	43762883	1.000000	0.71417	1.000000	0.80357	0.950000	0.60333	7.776000	0.85560	2.357000	0.79964	0.462000	0.41574	GTC		0.602	RYR1-010	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000462137.1			22	25	1	0	6.44725e-10	0.624587	7.00305e-10	22	25				
CDC45	8318	broad.mit.edu	37	22	19470284	19470284	+	Silent	SNP	C	C	T			TCGA-CS-4943-01A-01D-1468-08	TCGA-CS-4943-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	14627ffd-642c-42b5-9d95-ad436c9b1d35	0d4a92bf-0624-4dfa-9d95-8f91a693ea3f	g.chr22:19470284C>T	ENST00000407835.1	+	5	532	c.276C>T	c.(274-276)gaC>gaT	p.D92D	CDC45_ENST00000263201.1_Silent_p.D92D|CDC45_ENST00000437685.2_Silent_p.D92D|CDC45_ENST00000483431.1_3'UTR|CDC45_ENST00000404724.3_Intron			O75419	CDC45_HUMAN	cell division cycle 45	92					DNA replication (GO:0006260)|DNA replication checkpoint (GO:0000076)|DNA replication initiation (GO:0006270)|DNA strand elongation involved in DNA replication (GO:0006271)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)				breast(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(2)|lung(7)|prostate(2)|skin(1)	19						CTGATGAAGACACTATATTCT	0.363																																						ENST00000407835.1																			0				breast(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(2)|lung(7)|prostate(2)|skin(1)	19						c.(274-276)gaC>gaT		cell division cycle 45							259.0	229.0	239.0					22																	19470284		2203	4300	6503	SO:0001819	synonymous_variant	8318				DNA replication checkpoint|DNA strand elongation involved in DNA replication|DNA-dependent DNA replication initiation|M/G1 transition of mitotic cell cycle|regulation of transcription involved in G1/S phase of mitotic cell cycle|S phase of mitotic cell cycle	centrosome|nucleoplasm	protein binding	g.chr22:19470284C>T	AF053074	CCDS13762.1, CCDS54499.1, CCDS54500.1	22q11.21	2013-01-17	2013-01-17	2010-03-24	ENSG00000093009	ENSG00000093009			1739	protein-coding gene	gene with protein product	"""human CDC45"""	603465	"""CDC45 (cell division cycle 45, S.cerevisiae, homolog)-like"", ""CDC45 cell division cycle 45-like (S. cerevisiae)"", ""cell division cycle 45 homolog (S. cerevisiae)"""	CDC45L2, CDC45L		9660782, 9724329, 17608804	Standard	NM_001178010		Approved		uc011aha.2	O75419	OTTHUMG00000150386	ENST00000407835.1:c.276C>T	22.37:g.19470284C>T						CDC45_ENST00000404724.3_Intron|CDC45_ENST00000483431.1_3'UTR|CDC45_ENST00000437685.2_Silent_p.D92D|CDC45_ENST00000263201.1_Silent_p.D92D	p.D92D			O75419	CDC45_HUMAN			5	532	+			92					B4DDB4|B4DDU3|E9PDH7|O60856|Q20WK8|Q6UW54|Q9UP68	Silent	SNP	ENST00000407835.1	37	c.276C>T	CCDS13762.1																																																																																				0.363	CDC45-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000317903.1	NM_003504		6	288	0	0	0	0.248553	0	6	288				
USP25	29761	broad.mit.edu	37	21	17238647	17238647	+	Missense_Mutation	SNP	A	A	G			TCGA-CS-4943-01A-01D-1468-08	TCGA-CS-4943-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	14627ffd-642c-42b5-9d95-ad436c9b1d35	0d4a92bf-0624-4dfa-9d95-8f91a693ea3f	g.chr21:17238647A>G	ENST00000285679.6	+	20	2948	c.2579A>G	c.(2578-2580)aAc>aGc	p.N860S	USP25_ENST00000351097.5_Intron|USP25_ENST00000400183.2_Missense_Mutation_p.N930S|USP25_ENST00000285681.2_Missense_Mutation_p.N892S	NM_013396.3	NP_037528.3	Q9UHP3	UBP25_HUMAN	ubiquitin specific peptidase 25	860					cellular protein modification process (GO:0006464)|protein K48-linked deubiquitination (GO:0071108)|protein K63-linked deubiquitination (GO:0070536)|proteolysis (GO:0006508)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	peptidase activity (GO:0008233)|SUMO binding (GO:0032183)|ubiquitin-specific protease activity (GO:0004843)			breast(4)|endometrium(6)|kidney(2)|large_intestine(13)|liver(5)|lung(14)|ovary(4)|prostate(1)|skin(1)|urinary_tract(2)	52				Epithelial(23;7.55e-05)|all cancers(11;0.000429)|COAD - Colon adenocarcinoma(22;0.00543)|OV - Ovarian serous cystadenocarcinoma(11;0.00743)|Colorectal(24;0.0116)|Lung(58;0.0853)|LUSC - Lung squamous cell carcinoma(23;0.0889)		GAAGAAGTAAACTTGGAGGAA	0.358																																						ENST00000285681.2																			0				breast(4)|endometrium(6)|kidney(2)|large_intestine(13)|liver(5)|lung(14)|ovary(4)|prostate(1)|skin(1)|urinary_tract(2)	52						c.(2674-2676)aAc>aGc		ubiquitin specific peptidase 25							122.0	127.0	125.0					21																	17238647		2203	4299	6502	SO:0001583	missense	29761				protein modification process|ubiquitin-dependent protein catabolic process	cytoplasm|nucleus	ubiquitin thiolesterase activity|ubiquitin-specific protease activity	g.chr21:17238647A>G	AF170562	CCDS33515.1, CCDS63336.1, CCDS63337.1	21q11.2	2011-02-24	2005-08-08		ENSG00000155313	ENSG00000155313		"""Ubiquitin-specific peptidases"""	12624	protein-coding gene	gene with protein product		604736	"""ubiquitin specific protease 25"""			12838346, 10612803	Standard	NM_013396		Approved	USP21	uc002yjy.1	Q9UHP3	OTTHUMG00000074343	ENST00000285679.6:c.2579A>G	21.37:g.17238647A>G	ENSP00000285679:p.Asn860Ser					USP25_ENST00000285679.6_Missense_Mutation_p.N860S|USP25_ENST00000400183.2_Missense_Mutation_p.N930S|USP25_ENST00000351097.5_Intron	p.N892S			Q9UHP3	UBP25_HUMAN		Epithelial(23;7.55e-05)|all cancers(11;0.000429)|COAD - Colon adenocarcinoma(22;0.00543)|OV - Ovarian serous cystadenocarcinoma(11;0.00743)|Colorectal(24;0.0116)|Lung(58;0.0853)|LUSC - Lung squamous cell carcinoma(23;0.0889)	21	3044	+			860					C0LSZ0|Q6DHZ9|Q9H9W1	Missense_Mutation	SNP	ENST00000285679.6	37	c.2675A>G	CCDS33515.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	15.35|15.35	2.807202|2.807202	0.50421|0.50421	.|.	.|.	ENSG00000155313|ENSG00000155313	ENST00000285681;ENST00000285679;ENST00000400183|ENST00000449491	T;T;T|.	0.25414|.	1.85;1.87;1.8|.	5.93|5.93	5.93|5.93	0.95920|0.95920	.|.	0.163089|.	0.64402|.	D|.	0.000003|.	T|T	0.71290|0.71290	0.3322|0.3322	L|L	0.59436|0.59436	1.845|1.845	0.48571|0.48571	D|D	0.999675|0.999675	P;P;B|.	0.44309|.	0.832;0.534;0.058|.	P;B;B|.	0.49421|.	0.61;0.127;0.022|.	T|T	0.69397|0.69397	-0.5156|-0.5156	10|5	0.62326|.	D|.	0.03|.	.|.	16.3839|16.3839	0.83495|0.83495	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	930;892;860|.	Q9UHP3-3;Q9UHP3-1;Q9UHP3|.	.;.;UBP25_HUMAN|.	S|A	892;860;930|159	ENSP00000285681:N892S;ENSP00000285679:N860S;ENSP00000383044:N930S|.	ENSP00000285679:N860S|.	N|T	+|+	2|1	0|0	USP25|USP25	16160518|16160518	1.000000|1.000000	0.71417|0.71417	0.997000|0.997000	0.53966|0.53966	0.387000|0.387000	0.30353|0.30353	6.822000|6.822000	0.75277|0.75277	2.258000|2.258000	0.74832|0.74832	0.533000|0.533000	0.62120|0.62120	AAC|ACT		0.358	USP25-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157964.1			16	51	0	0	0	0.539581	0	16	51				
FBXO7	25793	broad.mit.edu	37	22	32879927	32879927	+	Missense_Mutation	SNP	A	A	G			TCGA-CS-4943-01A-01D-1468-08	TCGA-CS-4943-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	14627ffd-642c-42b5-9d95-ad436c9b1d35	0d4a92bf-0624-4dfa-9d95-8f91a693ea3f	g.chr22:32879927A>G	ENST00000266087.7	+	3	788	c.461A>G	c.(460-462)aAt>aGt	p.N154S	FBXO7_ENST00000382058.3_Missense_Mutation_p.N75S|FBXO7_ENST00000397426.1_Missense_Mutation_p.N40S	NM_012179.3	NP_036311.3	Q9Y3I1	FBX7_HUMAN	F-box protein 7	154	Important for interaction with CDK6.			N -> S (in Ref. 4; BAG63187). {ECO:0000305}.	cell death (GO:0008219)|mitochondrion degradation (GO:0000422)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of lymphocyte differentiation (GO:0045620)|protein targeting to mitochondrion (GO:0006626)|protein ubiquitination (GO:0016567)|regulation of protein stability (GO:0031647)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytosol (GO:0005829)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|protein complex (GO:0043234)|ubiquitin ligase complex (GO:0000151)	ubiquitin-protein transferase activity (GO:0004842)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(3)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	19						ATTCAAGATAATGCGCATATG	0.383																																						ENST00000266087.7																			0				breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(3)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	19						c.(460-462)aAt>aGt		F-box protein 7							123.0	115.0	117.0					22																	32879927		2203	4300	6503	SO:0001583	missense	25793				cell death|regulation of protein stability|ubiquitin-dependent protein catabolic process	ubiquitin ligase complex	protein binding|ubiquitin-protein ligase activity	g.chr22:32879927A>G	AF129537	CCDS13907.1, CCDS58806.1	22q12.3	2013-09-19	2004-06-15		ENSG00000100225	ENSG00000100225		"""F-boxes /  ""other"""", ""Parkinson disease"""	13586	protein-coding gene	gene with protein product		605648	"""F-box only protein 7"""			10531035, 10531037, 19038853	Standard	NM_001257990		Approved	FBX7, Fbx, PARK15	uc003amq.3	Q9Y3I1	OTTHUMG00000030674	ENST00000266087.7:c.461A>G	22.37:g.32879927A>G	ENSP00000266087:p.Asn154Ser					FBXO7_ENST00000382058.3_Missense_Mutation_p.N75S|FBXO7_ENST00000397426.1_Missense_Mutation_p.N40S	p.N154S	NM_012179.3	NP_036311.3	Q9Y3I1	FBX7_HUMAN			3	788	+			154					B4DNB3|B4DWX5|Q5TGC4|Q5TI86|Q96HM6|Q9UF21|Q9UKT2	Missense_Mutation	SNP	ENST00000266087.7	37	c.461A>G	CCDS13907.1	.	.	.	.	.	.	.	.	.	.	A	0.077	-1.190721	0.01607	.	.	ENSG00000100225	ENST00000266087;ENST00000452138;ENST00000382058;ENST00000397426;ENST00000444207	T;T;T;T;T	0.41065	1.01;1.01;1.01;1.01;1.01	5.45	0.0432	0.14221	.	0.837211	0.10750	N	0.638487	T	0.19805	0.0476	N	0.08118	0	0.09310	N	1	B;B;B	0.06786	0.001;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.17592	-1.0364	10	0.51188	T	0.08	-2.9948	4.3432	0.11120	0.4929:0.2935:0.0:0.2136	.	75;154;40	Q9Y3I1-2;Q9Y3I1;Q5TI86	.;FBX7_HUMAN;.	S	154;75;75;40;40	ENSP00000266087:N154S;ENSP00000388547:N75S;ENSP00000371490:N75S;ENSP00000380571:N40S;ENSP00000404388:N40S	ENSP00000266087:N154S	N	+	2	0	FBXO7	31209927	0.103000	0.21917	0.057000	0.19452	0.147000	0.21601	0.379000	0.20585	0.051000	0.15978	-0.580000	0.04137	AAT		0.383	FBXO7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000129001.1			26	47	0	0	0	0.681144	0	26	47				
HOXC13	3229	broad.mit.edu	37	12	54338833	54338833	+	Silent	SNP	G	G	A			TCGA-CS-4943-01A-01D-1468-08	TCGA-CS-4943-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	14627ffd-642c-42b5-9d95-ad436c9b1d35	0d4a92bf-0624-4dfa-9d95-8f91a693ea3f	g.chr12:54338833G>A	ENST00000243056.3	+	2	942	c.786G>A	c.(784-786)aaG>aaA	p.K262K		NM_017410.2	NP_059106.2	P31276	HXC13_HUMAN	homeobox C13	262					anatomical structure morphogenesis (GO:0009653)|anterior/posterior pattern specification (GO:0009952)|hair follicle development (GO:0001942)|nail development (GO:0035878)|tongue morphogenesis (GO:0043587)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding (GO:0043565)			breast(1)|large_intestine(1)|skin(1)	3						GCGGGCGCAAGAAACGCGTGC	0.612			T	NUP98	AML																																	ENST00000243056.3				Dom	yes		12	12q13.3	3229	T	homeo box C13			L	NUP98		AML		0				breast(1)|large_intestine(1)|skin(1)	3						c.(784-786)aaG>aaA		homeobox C13							75.0	83.0	80.0					12																	54338833		2203	4300	6503	SO:0001819	synonymous_variant	3229					nucleus	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity	g.chr12:54338833G>A		CCDS8865.1	12q13.13	2011-06-20	2005-12-22		ENSG00000123364	ENSG00000123364		"""Homeoboxes / ANTP class : HOXL subclass"""	5125	protein-coding gene	gene with protein product		142976	"""homeo box C13"""	HOX3, HOX3G		1973146, 1358459	Standard	NM_017410		Approved		uc001sei.3	P31276	OTTHUMG00000160008	ENST00000243056.3:c.786G>A	12.37:g.54338833G>A							p.K262K	NM_017410.2	NP_059106.2	P31276	HXC13_HUMAN			2	942	+			262					Q5BL02|Q96J32|Q9NR24|Q9NYD5	Silent	SNP	ENST00000243056.3	37	c.786G>A	CCDS8865.1																																																																																				0.612	HOXC13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358865.2			86	144	0	0	0	0.870114	0	86	144				
C2CD3	26005	broad.mit.edu	37	11	73829328	73829328	+	Missense_Mutation	SNP	C	C	G			TCGA-CS-4943-01A-01D-1468-08	TCGA-CS-4943-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	14627ffd-642c-42b5-9d95-ad436c9b1d35	0d4a92bf-0624-4dfa-9d95-8f91a693ea3f	g.chr11:73829328C>G	ENST00000334126.7	-	9	1691	c.1465G>C	c.(1465-1467)Gtt>Ctt	p.V489L	C2CD3_ENST00000313663.7_Missense_Mutation_p.V489L			Q4AC94	C2CD3_HUMAN	C2 calcium-dependent domain containing 3	489					brain development (GO:0007420)|centriole elongation (GO:0061511)|embryonic digit morphogenesis (GO:0042733)|heart looping (GO:0001947)|in utero embryonic development (GO:0001701)|neural plate axis specification (GO:0021997)|neural tube development (GO:0021915)|nonmotile primary cilium assembly (GO:0035058)|protein localization to centrosome (GO:0071539)|protein processing (GO:0016485)|regulation of proteolysis (GO:0030162)|regulation of smoothened signaling pathway (GO:0008589)	centriolar satellite (GO:0034451)|centriole (GO:0005814)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)				NS(1)|breast(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(16)|lung(26)|ovary(4)|pancreas(2)|prostate(1)|skin(3)	64	Breast(11;4.16e-06)					GACTCCAGAACCTTAGATGAT	0.413																																						ENST00000334126.7																			0				NS(1)|breast(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(16)|lung(26)|ovary(4)|pancreas(2)|prostate(1)|skin(3)	64						c.(1465-1467)Gtt>Ctt		C2 calcium-dependent domain containing 3							115.0	109.0	111.0					11																	73829328		2200	4293	6493	SO:0001583	missense	26005					centrosome		g.chr11:73829328C>G	BC035599	CCDS31636.1, CCDS66167.1	11q13.4	2014-02-12	2007-10-17		ENSG00000168014	ENSG00000168014			24564	protein-coding gene	gene with protein product		615944					Standard	XM_005273897		Approved	DKFZP586P0123	uc001ouu.2	Q4AC94	OTTHUMG00000168110	ENST00000334126.7:c.1465G>C	11.37:g.73829328C>G	ENSP00000334379:p.Val489Leu					C2CD3_ENST00000313663.7_Missense_Mutation_p.V489L	p.V489L			Q4AC94	C2CD3_HUMAN			9	1691	-	Breast(11;4.16e-06)		489					C9JR55|E2QRD1|Q2NLE1|Q3C1U9|Q6ZU92|Q8IYM4|Q8NB87|Q8NDH7|Q9Y4M2	Missense_Mutation	SNP	ENST00000334126.7	37	c.1465G>C		.	.	.	.	.	.	.	.	.	.	C	3.942	-0.013973	0.07681	.	.	ENSG00000168014	ENST00000334126;ENST00000313663;ENST00000313681	T;T	0.09817	2.94;2.95	6.02	3.15	0.36227	.	0.711905	0.14175	N	0.336426	T	0.09468	0.0233	L	0.57536	1.79	0.19300	N	0.999979	B;B	0.09022	0.002;0.001	B;B	0.09377	0.004;0.002	T	0.44982	-0.9292	10	0.10377	T	0.69	0.0823	4.754	0.13075	0.1247:0.6185:0.1207:0.1361	.	489;489	Q4AC94;Q4AC94-1	C2CD3_HUMAN;.	L	489	ENSP00000334379:V489L;ENSP00000323339:V489L	ENSP00000323339:V489L	V	-	1	0	C2CD3	73506976	0.000000	0.05858	0.051000	0.19133	0.529000	0.34654	-0.880000	0.04183	0.428000	0.26173	-0.156000	0.13503	GTT		0.413	C2CD3-201	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_015531		50	75	0	0	0	0.870114	0	50	75				
GLYAT	10249	broad.mit.edu	37	11	58477535	58477535	+	Missense_Mutation	SNP	G	G	A	rs138125182	byFrequency	TCGA-CS-4943-01A-01D-1468-08	TCGA-CS-4943-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	14627ffd-642c-42b5-9d95-ad436c9b1d35	0d4a92bf-0624-4dfa-9d95-8f91a693ea3f	g.chr11:58477535G>A	ENST00000344743.3	-	6	736	c.595C>T	c.(595-597)Cgc>Tgc	p.R199C	GLYAT_ENST00000529732.1_Missense_Mutation_p.R199C	NM_201648.2	NP_964011.2	Q6IB77	GLYAT_HUMAN	glycine-N-acyltransferase	199					acyl-CoA metabolic process (GO:0006637)|glycine metabolic process (GO:0006544)|monocarboxylic acid metabolic process (GO:0032787)|response to toxic substance (GO:0009636)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	extracellular vesicular exosome (GO:0070062)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	glycine N-acyltransferase activity (GO:0047961)|glycine N-benzoyltransferase activity (GO:0047962)|transferase activity, transferring acyl groups (GO:0016746)			NS(1)|autonomic_ganglia(1)|kidney(1)|large_intestine(3)|lung(8)|skin(1)|urinary_tract(1)	16		Breast(21;0.0044)|all_epithelial(135;0.0157)			Glycine(DB00145)	TGAATGCAGCGCTCAATGAAT	0.502													G|||	2	0.000399361	0.0008	0.0	5008	,	,		19262	0.001		0.0	False		,,,				2504	0.0					ENST00000344743.3																			0				NS(1)|autonomic_ganglia(1)|kidney(1)|large_intestine(3)|lung(8)|skin(1)|urinary_tract(1)	16						c.(595-597)Cgc>Tgc		glycine-N-acyltransferase	Glycine(DB00145)	G	CYS/ARG	0,4402		0,0,2201	78.0	79.0	79.0		595	5.2	0.0	11	dbSNP_134	79	2,8588	2.2+/-6.3	0,2,4293	yes	missense	GLYAT	NM_201648.2	180	0,2,6494	AA,AG,GG		0.0233,0.0,0.0154	probably-damaging	199/297	58477535	2,12990	2201	4295	6496	SO:0001583	missense	10249				acyl-CoA metabolic process|response to toxin|xenobiotic metabolic process	mitochondrial matrix	glycine N-acyltransferase activity|glycine N-benzoyltransferase activity	g.chr11:58477535G>A	AF023466	CCDS7970.1, CCDS7971.1	11q12.1	2008-03-11					2.3.1.13		13734	protein-coding gene	gene with protein product		607424					Standard	NM_201648		Approved	GAT, ACGNAT	uc001nnb.3	Q6IB77		ENST00000344743.3:c.595C>T	11.37:g.58477535G>A	ENSP00000340200:p.Arg199Cys					GLYAT_ENST00000529732.1_Missense_Mutation_p.R199C	p.R199C	NM_201648.2	NP_964011.2	Q6IB77	GLYAT_HUMAN			6	736	-		Breast(21;0.0044)|all_epithelial(135;0.0157)	199					O14833|Q96QK7	Missense_Mutation	SNP	ENST00000344743.3	37	c.595C>T	CCDS7970.1	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	G	12.43	1.935409	0.34189	0.0	2.33E-4	ENSG00000149124	ENST00000344743;ENST00000529732	T;T	0.19938	2.11;2.11	6.06	5.16	0.70880	Acyl-CoA N-acyltransferase (2);Glycine N-acyltransferase, N-terminal (1);	0.304112	0.36338	N	0.002658	T	0.52354	0.1729	M	0.91717	3.235	0.22292	N	0.999225	D	0.89917	1.0	D	0.74674	0.984	T	0.55879	-0.8071	10	0.62326	D	0.03	-10.1399	11.4349	0.50062	0.0825:0.0:0.9175:0.0	.	199	Q6IB77	GLYAT_HUMAN	C	199	ENSP00000340200:R199C;ENSP00000431688:R199C	ENSP00000340200:R199C	R	-	1	0	GLYAT	58234111	0.978000	0.34361	0.027000	0.17364	0.054000	0.15201	2.344000	0.44010	1.578000	0.49821	0.650000	0.86243	CGC		0.502	GLYAT-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394593.1			62	78	0	0	0	0.870114	0	62	78				
ST14	6768	broad.mit.edu	37	11	130069892	130069892	+	Silent	SNP	C	C	T			TCGA-CS-4943-01A-01D-1468-08	TCGA-CS-4943-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	14627ffd-642c-42b5-9d95-ad436c9b1d35	0d4a92bf-0624-4dfa-9d95-8f91a693ea3f	g.chr11:130069892C>T	ENST00000278742.5	+	16	2272	c.1854C>T	c.(1852-1854)ggC>ggT	p.G618G		NM_021978.3	NP_068813.1	Q9Y5Y6	ST14_HUMAN	suppression of tumorigenicity 14 (colon carcinoma)	618	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				keratinocyte differentiation (GO:0030216)|proteolysis (GO:0006508)	basolateral plasma membrane (GO:0016323)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|extrinsic component of plasma membrane (GO:0019897)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)			central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(4)|lung(12)|ovary(3)|pancreas(2)|prostate(1)|skin(3)	32	all_hematologic(175;0.0429)	Lung NSC(97;0.000602)|Breast(109;0.000962)|all_lung(97;0.00126)|Medulloblastoma(222;0.0425)|all_neural(223;0.0837)		OV - Ovarian serous cystadenocarcinoma(99;0.0183)|Lung(977;0.228)	Urokinase(DB00013)	TTGTTGGGGGCACGGATGCGG	0.617																																						ENST00000278742.5																			0				central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(4)|lung(12)|ovary(3)|pancreas(2)|prostate(1)|skin(3)	32						c.(1852-1854)ggC>ggT		suppression of tumorigenicity 14 (colon carcinoma)	Urokinase(DB00013)						80.0	73.0	76.0					11																	130069892		2201	4297	6498	SO:0001819	synonymous_variant	6768				proteolysis	integral to plasma membrane	serine-type endopeptidase activity	g.chr11:130069892C>T	AF118224	CCDS8487.1	11q24-q25	2011-08-31	2005-11-19		ENSG00000149418	ENSG00000149418		"""Serine peptidases / Transmembrane"""	11344	protein-coding gene	gene with protein product	"""epithin"", ""matriptase"""	606797		PRSS14		9925927, 10373424	Standard	NM_021978		Approved	SNC19, HAI, MT-SP1, TMPRSS14	uc001qfw.3	Q9Y5Y6	OTTHUMG00000165768	ENST00000278742.5:c.1854C>T	11.37:g.130069892C>T							p.G618G	NM_021978.3	NP_068813.1	Q9Y5Y6	ST14_HUMAN		OV - Ovarian serous cystadenocarcinoma(99;0.0183)|Lung(977;0.228)	16	2272	+	all_hematologic(175;0.0429)	Lung NSC(97;0.000602)|Breast(109;0.000962)|all_lung(97;0.00126)|Medulloblastoma(222;0.0425)|all_neural(223;0.0837)	618			Peptidase S1.		Q9BS01|Q9H3S0|Q9HB36|Q9HCA3	Silent	SNP	ENST00000278742.5	37	c.1854C>T	CCDS8487.1																																																																																				0.617	ST14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386119.1			6	119	0	0	0	0.248553	0	6	119				
CDRT1	374286	broad.mit.edu	37	17	15496762	15496762	+	Missense_Mutation	SNP	C	C	T			TCGA-CS-4943-01A-01D-1468-08	TCGA-CS-4943-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	14627ffd-642c-42b5-9d95-ad436c9b1d35	0d4a92bf-0624-4dfa-9d95-8f91a693ea3f	g.chr17:15496762C>T	ENST00000395906.3	-	11	1894	c.1895G>A	c.(1894-1896)tGt>tAt	p.C632Y	CDRT1_ENST00000354433.3_Missense_Mutation_p.C132Y|CDRT1_ENST00000583965.1_Intron|RP11-385D13.1_ENST00000455584.2_Intron	NM_006382.3	NP_006373.2	O95170	CDRT1_HUMAN	CMT1A duplicated region transcript 1	632										endometrium(2)|kidney(1)|large_intestine(4)|lung(1)|stomach(1)|upper_aerodigestive_tract(1)	10				UCEC - Uterine corpus endometrioid carcinoma (92;0.0822)|READ - Rectum adenocarcinoma(2;1.36e-05)|BRCA - Breast invasive adenocarcinoma(8;0.0541)		GCCATCTGCACAGGCGCTGAT	0.498																																						ENST00000395906.3																			0				endometrium(2)|kidney(1)|large_intestine(4)|lung(1)|stomach(1)|upper_aerodigestive_tract(1)	10						c.(1894-1896)tGt>tAt		CMT1A duplicated region transcript 1							171.0	185.0	181.0					17																	15496762		2203	4300	6503	SO:0001583	missense	374286							g.chr17:15496762C>T	U65652	CCDS45619.1, CCDS73996.1	17p11	2013-01-10			ENSG00000241322	ENSG00000241322		"""F-boxes / WD-40 domains"", ""WD repeat domain containing"""	14379	protein-coding gene	gene with protein product		604596	"""F-box and WD repeat domain containing 10 pseudogene 1"", ""F-box and WD-40 domain protein 10 pseudogene 1"""	FBXW10P1		9787083, 11381029	Standard	NM_006382		Approved	HREP, SM25H2, FBXW10B		O95170	OTTHUMG00000059074	ENST00000395906.3:c.1895G>A	17.37:g.15496762C>T	ENSP00000379242:p.Cys632Tyr					CDRT1_ENST00000583965.1_Intron|RP11-385D13.1_ENST00000455584.2_Intron|CDRT1_ENST00000354433.3_Missense_Mutation_p.C132Y	p.C632Y	NM_006382.3	NP_006373.2	O95170	CDRT1_HUMAN		UCEC - Uterine corpus endometrioid carcinoma (92;0.0822)|READ - Rectum adenocarcinoma(2;1.36e-05)|BRCA - Breast invasive adenocarcinoma(8;0.0541)	11	1894	-			632					O43848|O95611	Missense_Mutation	SNP	ENST00000395906.3	37	c.1895G>A	CCDS45619.1	.	.	.	.	.	.	.	.	.	.	c	18.56	3.650408	0.67472	.	.	ENSG00000241322;ENSG00000251537;ENSG00000251537	ENST00000354433;ENST00000261644;ENST00000395906	T;T	0.17854	2.25;2.25	4.74	3.75	0.43078	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	.	.	.	.	T	0.39279	0.1072	M	0.73962	2.25	0.80722	D	1	D	0.76494	0.999	D	0.81914	0.995	T	0.18618	-1.0331	8	.	.	.	.	12.2743	0.54726	0.0:0.9136:0.0:0.0864	.	632	O95170	CDRT1_HUMAN	Y	132;662;632	ENSP00000346416:C132Y;ENSP00000379242:C632Y	.	C	-	2	0	CDRT1;RP11-385D13.1	15437487	1.000000	0.71417	0.965000	0.40720	0.975000	0.68041	6.372000	0.73123	2.192000	0.70111	0.650000	0.86243	TGT		0.498	CDRT1-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448127.1	NM_006382		15	308	0	0	0	0.500413	0	15	308				
LIMS2	55679	broad.mit.edu	37	2	128399630	128399630	+	Silent	SNP	G	G	A			TCGA-CS-4943-01A-01D-1468-08	TCGA-CS-4943-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	14627ffd-642c-42b5-9d95-ad436c9b1d35	0d4a92bf-0624-4dfa-9d95-8f91a693ea3f	g.chr2:128399630G>A	ENST00000355119.4	-	6	819	c.654C>T	c.(652-654)caC>caT	p.H218H	LIMS2_ENST00000409254.1_Silent_p.H66H|LIMS2_ENST00000409808.2_Silent_p.H213H|LIMS2_ENST00000494613.1_5'Flank|LIMS2_ENST00000324938.5_Silent_p.H242H|LIMS2_ENST00000410011.1_Silent_p.H213H|LIMS2_ENST00000545738.2_Silent_p.H240H|LIMS2_ENST00000409754.1_Silent_p.H66H|LIMS2_ENST00000409286.1_Silent_p.H66H|LIMS2_ENST00000410038.1_Silent_p.H66H|LIMS2_ENST00000409455.1_Silent_p.H213H	NM_001161403.1	NP_001154875.1	Q7Z4I7	LIMS2_HUMAN	LIM and senescent cell antigen-like domains 2	218	LIM zinc-binding 4. {ECO:0000255|PROSITE- ProRule:PRU00125}.				cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|negative regulation of apoptotic process (GO:0043066)|negative regulation of hepatocyte proliferation (GO:2000346)|negative regulation of neural precursor cell proliferation (GO:2000178)|positive regulation of integrin-mediated signaling pathway (GO:2001046)|single organismal cell-cell adhesion (GO:0016337)	cytosol (GO:0005829)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	zinc ion binding (GO:0008270)	p.H242H(1)		endometrium(3)|kidney(1)|large_intestine(2)|lung(5)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	15	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.0681)		TCACCTCCACGTGCCACTGCT	0.677																																						ENST00000409455.1																			1	Substitution - coding silent(1)	p.H242H(1)	endometrium(1)	endometrium(3)|kidney(1)|large_intestine(2)|lung(5)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	15						c.(637-639)caC>caT		LIM and senescent cell antigen-like domains 2							23.0	25.0	24.0					2																	128399630		2202	4298	6500	SO:0001819	synonymous_variant	55679				cell junction assembly	cytosol|focal adhesion|nucleus	zinc ion binding	g.chr2:128399630G>A	AF520987	CCDS2147.1, CCDS54394.1, CCDS54395.1, CCDS54396.1, CCDS58725.1	2q21.1	2008-02-05			ENSG00000072163	ENSG00000072163			16084	protein-coding gene	gene with protein product		607908					Standard	NM_017980		Approved		uc002tox.3	Q7Z4I7	OTTHUMG00000131529	ENST00000355119.4:c.654C>T	2.37:g.128399630G>A						LIMS2_ENST00000409754.1_Silent_p.H66H|LIMS2_ENST00000409286.1_Silent_p.H66H|LIMS2_ENST00000410011.1_Silent_p.H213H|LIMS2_ENST00000409808.2_Silent_p.H213H|LIMS2_ENST00000410038.1_Silent_p.H66H|LIMS2_ENST00000355119.4_Silent_p.H218H|LIMS2_ENST00000545738.2_Silent_p.H240H|LIMS2_ENST00000409254.1_Silent_p.H66H|LIMS2_ENST00000324938.5_Silent_p.H242H	p.H213H			Q7Z4I7	LIMS2_HUMAN		BRCA - Breast invasive adenocarcinoma(221;0.0681)	6	1274	-	Colorectal(110;0.1)		218			LIM zinc-binding 4.		A6NLH0|B4DMV1|F5H6E6|Q7Z4I2|Q7Z4I6|Q7Z4I8|Q8NFE7|Q9HA13	Silent	SNP	ENST00000355119.4	37	c.639C>T	CCDS54395.1	.	.	.	.	.	.	.	.	.	.	g	11.15	1.554027	0.27739	.	.	ENSG00000072163	ENST00000426981	.	.	.	5.27	-7.07	0.01563	.	.	.	.	.	T	0.64394	0.2594	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.68284	-0.5449	4	.	.	.	.	16.6731	0.85271	0.34:0.0:0.66:0.0	.	.	.	.	M	26	.	.	T	-	2	0	LIMS2	128116100	0.616000	0.27035	0.697000	0.30258	0.982000	0.71751	-0.289000	0.08365	-1.855000	0.01162	-0.783000	0.03347	ACG		0.677	LIMS2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000331133.2	NM_017980		15	26	0	0	0	0.539581	0	15	26				
MT-CO1	4512	broad.mit.edu	37	M	6762	6762	+	Missense_Mutation	SNP	G	G	A			TCGA-CS-4943-01A-01D-1468-08	TCGA-CS-4943-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	14627ffd-642c-42b5-9d95-ad436c9b1d35	0d4a92bf-0624-4dfa-9d95-8f91a693ea3f	g.chrM:6762G>A	ENST00000361624.2	+	1	859	c.859G>A	c.(859-861)Gtg>Atg	p.V287M	MT-TC_ENST00000387405.1_RNA|MT-ATP8_ENST00000361851.1_5'Flank|MT-TK_ENST00000387421.1_RNA|MT-TN_ENST00000387400.1_RNA|MT-TQ_ENST00000387372.1_RNA|MT-TI_ENST00000387365.1_RNA|MT-TS1_ENST00000387416.2_RNA|MT-TY_ENST00000387409.1_RNA|MT-TW_ENST00000387382.1_RNA|MT-ATP6_ENST00000361899.2_5'Flank|MT-TA_ENST00000387392.1_RNA|MT-CO3_ENST00000362079.2_5'Flank|MT-TD_ENST00000387419.1_RNA|MT-TM_ENST00000387377.1_RNA|MT-CO2_ENST00000361739.1_5'Flank			P00395	COX1_HUMAN	mitochondrially encoded cytochrome c oxidase I	287					aerobic respiration (GO:0009060)|cellular metabolic process (GO:0044237)|hydrogen ion transmembrane transport (GO:1902600)|oxidative phosphorylation (GO:0006119)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex IV (GO:0005751)|respiratory chain complex IV (GO:0045277)	cytochrome-c oxidase activity (GO:0004129)|heme binding (GO:0020037)|iron ion binding (GO:0005506)			breast(4)|endometrium(25)|kidney(19)|lung(3)|prostate(3)	54						TAGGGTTTATCGTGTGAGCAC	0.418																																						ENST00000361624.2																			0				breast(4)|endometrium(25)|kidney(19)|lung(3)|prostate(3)	54						c.(859-861)Gtg>Atg		mitochondrially encoded cytochrome c oxidase I																																				SO:0001583	missense	4512							g.chrM:6762G>A			mitochondria	2011-07-04	2005-02-15	2005-02-16	ENSG00000198804	ENSG00000198804		"""Mitochondrial respiratory chain complex / Complex IV"""	7419	protein-coding gene	gene with protein product		516030	"""cytochrome c oxidase I"""	MTCO1		7219534	Standard			Approved	COX1, COI		P00395		ENST00000361624.2:c.859G>A	M.37:g.6762G>A	ENSP00000354499:p.Val287Met						p.287_287insM							1	859	+								Q34770	Missense_Mutation	SNP	ENST00000361624.2	37	c.859G>A																																																																																					0.418	MT-CO1-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		YP_003024028		19	37	0	0	0	0.750413	0	19	37				
DOC2A	8448	broad.mit.edu	37	16	30018527	30018529	+	In_Frame_Del	DEL	CTT	CTT	-	rs139431507		TCGA-CS-4943-01A-01D-1468-08	TCGA-CS-4943-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	14627ffd-642c-42b5-9d95-ad436c9b1d35	0d4a92bf-0624-4dfa-9d95-8f91a693ea3f	g.chr16:30018527_30018529delCTT	ENST00000350119.4	-	6	809_811	c.619_621delAAG	c.(619-621)aagdel	p.K207del	DOC2A_ENST00000564944.1_In_Frame_Del_p.K207del|DOC2A_ENST00000564979.1_In_Frame_Del_p.K207del	NM_001282062.1|NM_001282063.1|NM_001282068.1|NM_003586.2	NP_001268991.1|NP_001268992.1|NP_001268997.1|NP_003577.2	Q14183	DOC2A_HUMAN	double C2-like domains, alpha	207					nervous system development (GO:0007399)|regulation of calcium ion-dependent exocytosis (GO:0017158)|synaptic transmission (GO:0007268)|synaptic vesicle exocytosis (GO:0016079)	cell junction (GO:0030054)|lysosome (GO:0005764)|membrane (GO:0016020)|neuron projection (GO:0043005)|synaptic vesicle (GO:0008021)	calcium-dependent phospholipid binding (GO:0005544)|transporter activity (GO:0005215)			central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(2)|ovary(2)	9						TGTTAAAATGCTTCTTCTGCGAA	0.635																																						ENST00000350119.4																			0				central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(2)|ovary(2)	9						c.(619-621)del		double C2-like domains, alpha																																				SO:0001651	inframe_deletion	8448				nervous system development|regulation of calcium ion-dependent exocytosis	cell junction|lysosome|synaptic vesicle membrane|synaptosome	calcium-dependent phospholipid binding|protein binding|transporter activity	g.chr16:30018527_30018529delCTT	D31897	CCDS10666.1	16p11.2	2014-07-02			ENSG00000149927	ENSG00000149927		"""Synaptotagmins"""	2985	protein-coding gene	gene with protein product		604567				7826360, 9736751	Standard	NM_003586		Approved		uc002dvn.3	Q14183	OTTHUMG00000132109	ENST00000350119.4:c.619_621delAAG	16.37:g.30018530_30018532delCTT	ENSP00000340017:p.Lys207del					DOC2A_ENST00000564979.1_In_Frame_Del_p.K207del|DOC2A_ENST00000564944.1_In_Frame_Del_p.K207del	p.K207del	NM_003586.2	NP_003577.2	Q14183	DOC2A_HUMAN			6	809_811	-			207					B4DEJ2|H3BNH6|Q6P4G4|Q7Z5G0|Q8IVX0	In_Frame_Del	DEL	ENST00000350119.4	37	c.619_621delAAG	CCDS10666.1																																																																																				0.635	DOC2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255148.2	NM_003586		45	75						45	75	---	---	---	---
DDX52	11056	broad.mit.edu	37	17	36003613	36003614	+	5'Flank	INS	-	-	T	rs59697282|rs377450634		TCGA-CS-4943-01A-01D-1468-08	TCGA-CS-4943-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	14627ffd-642c-42b5-9d95-ad436c9b1d35	0d4a92bf-0624-4dfa-9d95-8f91a693ea3f	g.chr17:36003613_36003614insT	ENST00000349699.2	-	0	0				RP11-697E22.2_ENST00000586950.1_RNA|RP11-697E22.2_ENST00000586163.1_RNA|DDX52_ENST00000394367.3_5'Flank	NM_007010.3	NP_008941.2	Q9Y2R4	DDX52_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 52							membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|poly(A) RNA binding (GO:0044822)			biliary_tract(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(3)|lung(5)|ovary(1)|skin(3)	17		Breast(25;0.00637)|Ovarian(249;0.15)				CATTAtttatcttttttttttt	0.51																																						ENST00000586163.1																			0																																																	SO:0001631	upstream_gene_variant	0							g.chr17:36003613_36003614insT	AF077033	CCDS11323.1	17q21.1	2014-05-06			ENSG00000141141	ENSG00000278053		"""DEAD-boxes"""	20038	protein-coding gene	gene with protein product		612500				11124703	Standard	XM_006721650		Approved	ROK1	uc002hoi.2	Q9Y2R4	OTTHUMG00000188475		17.37:g.36003624_36003624dupT	Exception_encountered					RP11-697E22.2_ENST00000586950.1_RNA								0	590	+								Q86YG1|Q8N213|Q9NVE0|Q9Y482	RNA	INS	ENST00000349699.2	37		CCDS11323.1																																																																																				0.510	DDX52-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256795.1	NM_152300		4	8						4	8	---	---	---	---
CDC27	996	broad.mit.edu	37	17	45219612	45219612	+	Frame_Shift_Del	DEL	A	A	-			TCGA-CS-4943-01A-01D-1468-08	TCGA-CS-4943-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	14627ffd-642c-42b5-9d95-ad436c9b1d35	0d4a92bf-0624-4dfa-9d95-8f91a693ea3f	g.chr17:45219612delA	ENST00000066544.3	-	11	1454	c.1361delT	c.(1360-1362)ctafs	p.L454fs	CDC27_ENST00000527547.1_Frame_Shift_Del_p.L454fs|CDC27_ENST00000531206.1_Frame_Shift_Del_p.L460fs|CDC27_ENST00000446365.2_Frame_Shift_Del_p.L393fs	NM_001114091.1|NM_001256.3	NP_001107563.1|NP_001247.3	P30260	CDC27_HUMAN	cell division cycle 27	454					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|cell proliferation (GO:0008283)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cell cycle (GO:0000278)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein K11-linked ubiquitination (GO:0070979)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)	anaphase-promoting complex (GO:0005680)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle (GO:0005819)	protein phosphatase binding (GO:0019903)			NS(1)|breast(5)|central_nervous_system(3)|cervix(1)|endometrium(2)|kidney(17)|large_intestine(18)|lung(11)|ovary(5)|pancreas(1)|prostate(19)|skin(5)|upper_aerodigestive_tract(2)	90						TGCTTTTTGTAGATTAAAGGC	0.308																																						ENST00000066544.3																			0				NS(1)|breast(5)|central_nervous_system(3)|cervix(1)|endometrium(2)|kidney(17)|large_intestine(18)|lung(11)|ovary(5)|pancreas(1)|prostate(19)|skin(5)|upper_aerodigestive_tract(2)	90						c.(1360-1362)cafs		cell division cycle 27							30.0	30.0	30.0					17																	45219612		2201	4295	6496	SO:0001589	frameshift_variant	996				anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|cell proliferation|mitotic cell cycle spindle assembly checkpoint|mitotic metaphase/anaphase transition|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|protein K11-linked ubiquitination	anaphase-promoting complex|centrosome|cytosol|nucleoplasm|spindle microtubule	protein phosphatase binding	g.chr17:45219612delA	U00001	CCDS11509.1, CCDS45720.1, CCDS74090.1	17q21.32	2013-01-17	2013-01-17		ENSG00000004897	ENSG00000004897		"""Anaphase promoting complex subunits"", ""Tetratricopeptide (TTC) repeat domain containing"""	1728	protein-coding gene	gene with protein product	"""anaphase promoting complex subunit 3"""	116946	"""cell division cycle 27"", ""cell division cycle 27 homolog (S. cerevisiae)"""	D0S1430E, D17S978E		8234252	Standard	XM_005257892		Approved	APC3, ANAPC3, NUC2	uc002ile.4	P30260	OTTHUMG00000166429	ENST00000066544.3:c.1361delT	17.37:g.45219612delA	ENSP00000066544:p.Leu454fs					CDC27_ENST00000531206.1_Frame_Shift_Del_p.L460fs|CDC27_ENST00000527547.1_Frame_Shift_Del_p.L454fs|CDC27_ENST00000446365.2_Frame_Shift_Del_p.L393fs	p.L454fs	NM_001114091.1|NM_001256.3	NP_001107563.1|NP_001247.3	P30260	CDC27_HUMAN			11	1454	-			454					G3V1C4|Q16349|Q96F35	Frame_Shift_Del	DEL	ENST00000066544.3	37	c.1361delT	CCDS11509.1																																																																																				0.308	CDC27-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000389742.2			8	52						8	52	---	---	---	---
LOC727993	727993	broad.mit.edu	37	20	1933766	1933773	+	RNA	DEL	AAGGAAGG	AAGGAAGG	-	rs147387918|rs372181188		TCGA-CS-4943-01A-01D-1468-08	TCGA-CS-4943-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	14627ffd-642c-42b5-9d95-ad436c9b1d35	0d4a92bf-0624-4dfa-9d95-8f91a693ea3f	g.chr20:1933766_1933773delAAGGAAGG	ENST00000446562.1	+	0	476																											ggaggaaggaaaggaaggaaggaaggaa	0.519																																						ENST00000446562.1																			0																																																			0							g.chr20:1933766_1933773delAAGGAAGG																													20.37:g.1933774_1933781delAAGGAAGG														0	476	+									RNA	DEL	ENST00000446562.1	37																																																																																						0.519	RP4-684O24.5-001	KNOWN	basic	antisense	antisense	OTTHUMT00000251764.1			3	5						3	5	---	---	---	---
MIR646HG	284757	broad.mit.edu	37	20	58889651	58889662	+	lincRNA	DEL	CATTCTCCCATT	CATTCTCCCATT	-	rs374603250|rs111212420|rs117834183		TCGA-CS-4943-01A-01D-1468-08	TCGA-CS-4943-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	14627ffd-642c-42b5-9d95-ad436c9b1d35	0d4a92bf-0624-4dfa-9d95-8f91a693ea3f	g.chr20:58889651_58889662delCATTCTCCCATT	ENST00000432910.1	+	0	332					NR_046099.1																						tccatccatccattctcccattcatccatcct	0.538																																						ENST00000432910.1																			0																																																			0							g.chr20:58889651_58889662delCATTCTCCCATT																													20.37:g.58889651_58889662delCATTCTCCCATT								NR_046099.1						0	332	+									RNA	DEL	ENST00000432910.1	37																																																																																						0.538	RP5-1043L13.1-001	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000079947.1			11	14						11	14	---	---	---	---
ATRX	546	broad.mit.edu	37	X	76938044	76938044	+	Frame_Shift_Del	DEL	T	T	-			TCGA-CS-4943-01A-01D-1468-08	TCGA-CS-4943-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	14627ffd-642c-42b5-9d95-ad436c9b1d35	0d4a92bf-0624-4dfa-9d95-8f91a693ea3f	g.chrX:76938044delT	ENST00000373344.5	-	9	2918	c.2704delA	c.(2704-2706)atgfs	p.M902fs	ATRX_ENST00000480283.1_5'UTR|ATRX_ENST00000395603.3_Frame_Shift_Del_p.M864fs	NM_000489.3	NP_000480.3	P46100	ATRX_HUMAN	alpha thalassemia/mental retardation syndrome X-linked	902					ATP catabolic process (GO:0006200)|cellular response to hydroxyurea (GO:0072711)|chromatin remodeling (GO:0006338)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA duplex unwinding (GO:0032508)|DNA methylation (GO:0006306)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|DNA replication-independent nucleosome assembly (GO:0006336)|forebrain development (GO:0030900)|negative regulation of telomeric RNA transcription from RNA pol II promoter (GO:1901581)|nucleosome assembly (GO:0006334)|positive regulation of nuclear cell cycle DNA replication (GO:0010571)|positive regulation of telomere maintenance (GO:0032206)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|replication fork processing (GO:0031297)|seminiferous tubule development (GO:0072520)|Sertoli cell development (GO:0060009)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nuclear heterochromatin (GO:0005720)|nucleolus (GO:0005730)|nucleus (GO:0005634)|SWI/SNF superfamily-type complex (GO:0070603)|telomeric heterochromatin (GO:0031933)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|chromo shadow domain binding (GO:0070087)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)|DNA translocase activity (GO:0015616)|helicase activity (GO:0004386)|histone binding (GO:0042393)|methylated histone binding (GO:0035064)|zinc ion binding (GO:0008270)	p.?(1)		bone(1)|breast(6)|central_nervous_system(31)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(15)|kidney(14)|large_intestine(1)|liver(1)|lung(40)|ovary(2)|pancreas(13)|prostate(5)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	145						CTTAATTCCATGATGGTCGTG	0.428			"""Mis, F, N"""		"""Pancreatic neuroendocrine tumors, paediatric GBM"""		ATR-X (alpha thalassemia/mental retardation) syndrome																															ENST00000373344.5				Rec	yes		X	Xq21.1	546	"""Mis, F, N"""	alpha thalassemia/mental retardation syndrome X-linked	yes	ATR-X (alpha thalassemia/mental retardation) syndrome	E			"""Pancreatic neuroendocrine tumors, paediatric GBM"""		1	Unknown(1)	p.?(1)	bone(1)	bone(1)|breast(6)|central_nervous_system(31)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(15)|kidney(14)|large_intestine(1)|liver(1)|lung(40)|ovary(2)|pancreas(13)|prostate(5)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	145						c.(2704-2706)tgfs		alpha thalassemia/mental retardation syndrome X-linked	Phosphatidylserine(DB00144)						199.0	185.0	190.0					X																	76938044		2203	4296	6499	SO:0001589	frameshift_variant	546				DNA methylation|DNA recombination|DNA repair|regulation of transcription, DNA-dependent	nuclear heterochromatin	ATP binding|chromo shadow domain binding|DNA binding|DNA helicase activity|zinc ion binding	g.chrX:76938044delT	U72937	CCDS14434.1, CCDS14435.1	Xq21.1	2014-06-17	2010-06-24		ENSG00000085224	ENSG00000085224			886	protein-coding gene	gene with protein product	"""RAD54 homolog (S. cerevisiae)"""	300032	"""alpha thalassemia/mental retardation syndrome X-linked (RAD54 (S. cerevisiae) homolog)"", ""Juberg-Marsidi syndrome"""	RAD54, JMS		7874112, 1415255, 8503439, 8630485	Standard	NM_000489		Approved	XH2, XNP	uc004ecp.4	P46100	OTTHUMG00000022686	ENST00000373344.5:c.2704delA	X.37:g.76938044delT	ENSP00000362441:p.Met902fs					ATRX_ENST00000480283.1_5'UTR|ATRX_ENST00000395603.3_Frame_Shift_Del_p.M864fs	p.M902fs	NM_000489.3	NP_000480.2	P46100	ATRX_HUMAN			9	2918	-			902					D3DTE2|P51068|Q15886|Q59FB5|Q59H31|Q5H9A2|Q5JWI4|Q7Z2J1|Q9H0Z1|Q9NTS3	Frame_Shift_Del	DEL	ENST00000373344.5	37	c.2704delA	CCDS14434.1																																																																																				0.428	ATRX-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058860.2	NM_000489		7	207						7	207	---	---	---	---
