#version 2.4
## 
## Oncotator v1.8.0.0 | Flat File Reference hg19 | GENCODE v19 EFFECT | UniProt_AAxform 2014_12 | ClinVar 12.03.20 | ESP 6500SI-V2 | ORegAnno UCSC Track | dbSNP build 142 | CCLE_By_GP 09292010 | COSMIC v62_291112 | 1000gp3 20130502 | UniProt_AA 2014_12 | dbNSFP v2.4 | ESP 6500SI-V2 | COSMIC_FusionGenes v62_291112 | gencode_xref_refseq metadata_v19 | CCLE_By_Gene 09292010 | ACHILLES_Lineage_Results 110303 | CGC full_2012-03-15 | UniProt 2014_12 | HumanDNARepairGenes 20110905 | HGNC Sept172014 | COSMIC_Tissue 291112 | Familial_Cancer_Genes 20110905 | TUMORScape 20100104 | Ensembl ICGC MUCOPA | TCGAScape 110405 | MutSig Published Results 20110905 
Hugo_Symbol	Entrez_Gene_Id	Center	NCBI_Build	Chromosome	Start_position	End_position	Strand	Variant_Classification	Variant_Type	Reference_Allele	Tumor_Seq_Allele1	Tumor_Seq_Allele2	dbSNP_RS	dbSNP_Val_Status	Tumor_Sample_Barcode	Matched_Norm_Sample_Barcode	Match_Norm_Seq_Allele1	Match_Norm_Seq_Allele2	Tumor_Validation_Allele1	Tumor_Validation_Allele2	Match_Norm_Validation_Allele1	Match_Norm_Validation_Allele2	Verification_Status	Validation_Status	Mutation_Status	Sequencing_Phase	Sequence_Source	Validation_Method	Score	BAM_file	Sequencer	Tumor_Sample_UUID	Matched_Norm_Sample_UUID	Genome_Change	Annotation_Transcript	Transcript_Strand	Transcript_Exon	Transcript_Position	cDNA_Change	Codon_Change	Protein_Change	Other_Transcripts	Refseq_mRNA_Id	Refseq_prot_Id	SwissProt_acc_Id	SwissProt_entry_Id	Description	UniProt_AApos	UniProt_Region	UniProt_Site	UniProt_Natural_Variations	UniProt_Experimental_Info	GO_Biological_Process	GO_Cellular_Component	GO_Molecular_Function	COSMIC_overlapping_mutations	COSMIC_fusion_genes	COSMIC_tissue_types_affected	COSMIC_total_alterations_in_gene	Tumorscape_Amplification_Peaks	Tumorscape_Deletion_Peaks	TCGAscape_Amplification_Peaks	TCGAscape_Deletion_Peaks	DrugBank	ref_context	gc_content	CCLE_ONCOMAP_overlapping_mutations	CCLE_ONCOMAP_total_mutations_in_gene	CGC_Mutation_Type	CGC_Translocation_Partner	CGC_Tumor_Types_Somatic	CGC_Tumor_Types_Germline	CGC_Other_Diseases	DNARepairGenes_Role	FamilialCancerDatabase_Syndromes	MUTSIG_Published_Results	OREGANNO_ID	OREGANNO_Values	i_1000gp3_AA	i_1000gp3_AC	i_1000gp3_AF	i_1000gp3_AFR_AF	i_1000gp3_AMR_AF	i_1000gp3_AN	i_1000gp3_CIEND	i_1000gp3_CIPOS	i_1000gp3_CS	i_1000gp3_DP	i_1000gp3_EAS_AF	i_1000gp3_END	i_1000gp3_EUR_AF	i_1000gp3_IMPRECISE	i_1000gp3_MC	i_1000gp3_MEINFO	i_1000gp3_MEND	i_1000gp3_MLEN	i_1000gp3_MSTART	i_1000gp3_NS	i_1000gp3_SAS_AF	i_1000gp3_SVLEN	i_1000gp3_SVTYPE	i_1000gp3_TSD	i_ACHILLES_Lineage_Results_Top_Genes	i_CGC_Cancer Germline Mut	i_CGC_Cancer Molecular Genetics	i_CGC_Cancer Somatic Mut	i_CGC_Cancer Syndrome	i_CGC_Chr	i_CGC_Chr Band	i_CGC_GeneID	i_CGC_Name	i_CGC_Other Germline Mut	i_CGC_Tissue Type	i_COSMIC_n_overlapping_mutations	i_COSMIC_overlapping_mutation_descriptions	i_COSMIC_overlapping_primary_sites	i_ClinVar_ASSEMBLY	i_ClinVar_HGMD_ID	i_ClinVar_SYM	i_ClinVar_TYPE	i_ClinVar_rs	i_ESP_AA	i_ESP_AAC	i_ESP_AA_AC	i_ESP_AA_AGE	i_ESP_AA_GTC	i_ESP_AvgAAsampleReadDepth	i_ESP_AvgEAsampleReadDepth	i_ESP_AvgSampleReadDepth	i_ESP_CA	i_ESP_CDP	i_ESP_CG	i_ESP_CP	i_ESP_Chromosome	i_ESP_DBSNP	i_ESP_DP	i_ESP_EA_AC	i_ESP_EA_AGE	i_ESP_EA_GTC	i_ESP_EXOME_CHIP	i_ESP_FG	i_ESP_GL	i_ESP_GM	i_ESP_GS	i_ESP_GTC	i_ESP_GTS	i_ESP_GWAS_PUBMED	i_ESP_MAF	i_ESP_PH	i_ESP_PP	i_ESP_Position	i_ESP_TAC	i_ESP_TotalAAsamplesCovered	i_ESP_TotalEAsamplesCovered	i_ESP_TotalSamplesCovered	i_Ensembl_so_accession	i_Ensembl_so_term	i_Entrez_Gene_Id	i_Familial_Cancer_Genes_Reference	i_Familial_Cancer_Genes_Synonym	i_HGNC_Accession Numbers	i_HGNC_CCDS IDs	i_HGNC_Chromosome	i_HGNC_Date Modified	i_HGNC_Date Name Changed	i_HGNC_Date Symbol Changed	i_HGNC_Ensembl Gene ID	i_HGNC_Ensembl ID(supplied by Ensembl)	i_HGNC_Enzyme IDs	i_HGNC_Gene family description	i_HGNC_HGNC ID	i_HGNC_Locus Group	i_HGNC_Locus Type	i_HGNC_Name Synonyms	i_HGNC_OMIM ID(supplied by NCBI)	i_HGNC_Previous Names	i_HGNC_Previous Symbols	i_HGNC_Primary IDs	i_HGNC_Pubmed IDs	i_HGNC_Record Type	i_HGNC_RefSeq(supplied by NCBI)	i_HGNC_Secondary IDs	i_HGNC_Status	i_HGNC_Synonyms	i_HGNC_UCSC ID(supplied by UCSC)	i_HGNC_UniProt ID(supplied by UniProt)	i_HGNC_VEGA IDs	i_HGVS_coding_DNA_change	i_HGVS_genomic_change	i_HGVS_protein_change	i_ORegAnno_bin	i_UniProt_alt_uniprot_accessions	i_Variant_Classification	i_Variant_Type	i_annotation_transcript	i_build	i_ccds_id	i_dbNSFP_1000Gp1_AC	i_dbNSFP_1000Gp1_AF	i_dbNSFP_1000Gp1_AFR_AC	i_dbNSFP_1000Gp1_AFR_AF	i_dbNSFP_1000Gp1_AMR_AC	i_dbNSFP_1000Gp1_AMR_AF	i_dbNSFP_1000Gp1_ASN_AC	i_dbNSFP_1000Gp1_ASN_AF	i_dbNSFP_1000Gp1_EUR_AC	i_dbNSFP_1000Gp1_EUR_AF	i_dbNSFP_Ancestral_allele	i_dbNSFP_CADD_phred	i_dbNSFP_CADD_raw	i_dbNSFP_CADD_raw_rankscore	i_dbNSFP_ESP6500_AA_AF	i_dbNSFP_ESP6500_EA_AF	i_dbNSFP_Ensembl_geneid	i_dbNSFP_Ensembl_transcriptid	i_dbNSFP_FATHMM_pred	i_dbNSFP_FATHMM_rankscore	i_dbNSFP_FATHMM_score	i_dbNSFP_GERP++_NR	i_dbNSFP_GERP++_RS	i_dbNSFP_GERP++_RS_rankscore	i_dbNSFP_Interpro_domain	i_dbNSFP_LRT_Omega	i_dbNSFP_LRT_converted_rankscore	i_dbNSFP_LRT_pred	i_dbNSFP_LRT_score	i_dbNSFP_LR_pred	i_dbNSFP_LR_rankscore	i_dbNSFP_LR_score	i_dbNSFP_MutationAssessor_pred	i_dbNSFP_MutationAssessor_rankscore	i_dbNSFP_MutationAssessor_score	i_dbNSFP_MutationTaster_converted_rankscore	i_dbNSFP_MutationTaster_pred	i_dbNSFP_MutationTaster_score	i_dbNSFP_Polyphen2_HDIV_pred	i_dbNSFP_Polyphen2_HDIV_rankscore	i_dbNSFP_Polyphen2_HDIV_score	i_dbNSFP_Polyphen2_HVAR_pred	i_dbNSFP_Polyphen2_HVAR_rankscore	i_dbNSFP_Polyphen2_HVAR_score	i_dbNSFP_RadialSVM_pred	i_dbNSFP_RadialSVM_rankscore	i_dbNSFP_RadialSVM_score	i_dbNSFP_Reliability_index	i_dbNSFP_SIFT_converted_rankscore	i_dbNSFP_SIFT_pred	i_dbNSFP_SIFT_score	i_dbNSFP_SLR_test_statistic	i_dbNSFP_SiPhy_29way_logOdds	i_dbNSFP_SiPhy_29way_logOdds_rankscore	i_dbNSFP_SiPhy_29way_pi	i_dbNSFP_UniSNP_ids	i_dbNSFP_Uniprot_aapos	i_dbNSFP_Uniprot_acc	i_dbNSFP_Uniprot_id	i_dbNSFP_aaalt	i_dbNSFP_aapos	i_dbNSFP_aapos_FATHMM	i_dbNSFP_aapos_SIFT	i_dbNSFP_aaref	i_dbNSFP_cds_strand	i_dbNSFP_codonpos	i_dbNSFP_fold-degenerate	i_dbNSFP_genename	i_dbNSFP_hg18_pos(1-coor)	i_dbNSFP_phastCons100way_vertebrate	i_dbNSFP_phastCons100way_vertebrate_rankscore	i_dbNSFP_phastCons46way_placental	i_dbNSFP_phastCons46way_placental_rankscore	i_dbNSFP_phastCons46way_primate	i_dbNSFP_phastCons46way_primate_rankscore	i_dbNSFP_phyloP100way_vertebrate	i_dbNSFP_phyloP100way_vertebrate_rankscore	i_dbNSFP_phyloP46way_placental	i_dbNSFP_phyloP46way_placental_rankscore	i_dbNSFP_phyloP46way_primate	i_dbNSFP_phyloP46way_primate_rankscore	i_dbNSFP_refcodon	i_entrez_gene_id	i_gc_content_full	i_gencode_transcript_name	i_gencode_transcript_status	i_gencode_transcript_tags	i_gencode_transcript_type	i_gene_type	i_havana_transcript	i_refseq_mrna_id	i_secondary_variant_classification	i_t_alt_count_full	i_t_ref_count_full	t_alt_count	t_ref_count
CDC42BPG	55561	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	11	64603009	64603009	+	Missense_Mutation	SNP	C	C	T	rs200332352		TCGA-HT-7611-01A-11D-2395-08	TCGA-HT-7611-10B-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b60b581b-2e7d-4c89-af6f-2de8cf79bcd7	cbdff4de-7729-4d99-b9be-f4807a99630f	g.chr11:64603009C>T	ENST00000342711.5	-	15	1842	c.1843G>A	c.(1843-1845)Gcc>Acc	p.A615T		NM_017525.2	NP_059995.2			CDC42 binding protein kinase gamma (DMPK-like)											central_nervous_system(1)|lung(3)	4						TCTCGCAGGGCGGCCACCTCC	0.692																																																0													40.0	46.0	44.0					11																	64603009		2200	4297	6497	SO:0001583	missense	55561			AY648038	CCDS31601.1	11q13	2013-01-10			ENSG00000171219	ENSG00000171219		"""Pleckstrin homology (PH) domain containing"""	29829	protein-coding gene	gene with protein product		613991				9341881, 15194684	Standard	NM_017525		Approved	HSMDPKIN, MRCKgamma, DMPK2, kappa-200	uc001obs.4	Q6DT37	OTTHUMG00000045365	ENST00000342711.5:c.1843G>A	11.37:g.64603009C>T	ENSP00000345133:p.Ala615Thr			Missense_Mutation	SNP	ENST00000342711.5	37	CCDS31601.1	.	.	.	.	.	.	.	.	.	.	C	5.581	0.292037	0.10567	.	.	ENSG00000171219	ENST00000342711	T	0.21734	1.99	3.87	1.92	0.25849	.	0.483380	0.17268	N	0.180503	T	0.11367	0.0277	N	0.20986	0.625	0.09310	N	1	B	0.11235	0.004	B	0.04013	0.001	T	0.28522	-1.0041	10	0.25106	T	0.35	.	5.2973	0.15758	0.1997:0.6878:0.0:0.1125	.	615	Q6DT37	MRCKG_HUMAN	T	615	ENSP00000345133:A615T	ENSP00000345133:A615T	A	-	1	0	CDC42BPG	64359585	0.000000	0.05858	0.008000	0.14137	0.867000	0.49689	-0.802000	0.04545	0.353000	0.24079	-0.448000	0.05591	GCC		0.692	CDC42BPG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000105352.4	XM_290516		14	132	14	132
STOML3	161003	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	13	39564828	39564828	+	Nonsense_Mutation	SNP	G	G	A	rs147878470		TCGA-HT-7611-01A-11D-2395-08	TCGA-HT-7611-10B-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b60b581b-2e7d-4c89-af6f-2de8cf79bcd7	cbdff4de-7729-4d99-b9be-f4807a99630f	g.chr13:39564828G>A	ENST00000379631.4	-	1	375	c.31C>T	c.(31-33)Caa>Taa	p.Q11*	STOML3_ENST00000423210.1_5'UTR	NM_145286.2	NP_660329.1	Q8TAV4	STML3_HUMAN	stomatin (EPB72)-like 3	11					signal transduction (GO:0007165)	cilium (GO:0005929)|integral component of membrane (GO:0016021)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)				breast(1)|large_intestine(2)|lung(5)|ovary(1)|prostate(1)|skin(1)	11		Lung NSC(96;1.42e-05)|Prostate(109;0.00851)|Breast(139;0.0199)|Lung SC(185;0.0743)		all cancers(112;2.93e-08)|Epithelial(112;3.64e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.00107)|BRCA - Breast invasive adenocarcinoma(63;0.00349)|GBM - Glioblastoma multiforme(144;0.0137)		TCTTTATCTTGCTTCTCAGGT	0.388																																																0													140.0	134.0	136.0					13																	39564828		2203	4300	6503	SO:0001587	stop_gained	161003			BC025760	CCDS9367.1, CCDS45040.1	13q13.2	2004-03-05			ENSG00000133115	ENSG00000133115			19420	protein-coding gene	gene with protein product		608327				12122055	Standard	NM_145286		Approved	SRO, Epb7.2l	uc001uwx.3	Q8TAV4	OTTHUMG00000016763	ENST00000379631.4:c.31C>T	13.37:g.39564828G>A	ENSP00000368952:p.Gln11*		B4E285|Q5JS35	Nonsense_Mutation	SNP	ENST00000379631.4	37	CCDS9367.1	.	.	.	.	.	.	.	.	.	.	G	36	5.765598	0.96906	.	.	ENSG00000133115	ENST00000379631	.	.	.	5.27	5.27	0.74061	.	1.407170	0.04221	N	0.333600	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.11182	T	0.66	-0.5535	11.524	0.50569	0.0:0.0:0.8213:0.1787	.	.	.	.	X	11	.	ENSP00000368952:Q11X	Q	-	1	0	STOML3	38462828	0.842000	0.29525	0.598000	0.28837	0.212000	0.24457	2.998000	0.49465	2.456000	0.83038	0.650000	0.86243	CAA		0.388	STOML3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000044604.2			20	87	20	87
CHRM5	1133	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	15	34356257	34356257	+	Missense_Mutation	SNP	A	A	G	rs373677487		TCGA-HT-7611-01A-11D-2395-08	TCGA-HT-7611-10B-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b60b581b-2e7d-4c89-af6f-2de8cf79bcd7	cbdff4de-7729-4d99-b9be-f4807a99630f	g.chr15:34356257A>G	ENST00000383263.5	+	3	2009	c.1339A>G	c.(1339-1341)Att>Gtt	p.I447V	CHRM5_ENST00000557872.1_Missense_Mutation_p.I447V	NM_012125.3	NP_036257.1	P08912	ACM5_HUMAN	cholinergic receptor, muscarinic 5	447					adenylate cyclase-inhibiting G-protein coupled acetylcholine receptor signaling pathway (GO:0007197)|cell proliferation (GO:0008283)|dopamine transport (GO:0015872)|G-protein coupled acetylcholine receptor signaling pathway (GO:0007213)|gastric acid secretion (GO:0001696)|metabolic process (GO:0008152)|regulation of phosphatidylinositol dephosphorylation (GO:0060304)|transmission of nerve impulse (GO:0019226)	cell junction (GO:0030054)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	G-protein coupled acetylcholine receptor activity (GO:0016907)|phosphatidylinositol phospholipase C activity (GO:0004435)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(10)|ovary(1)|skin(1)	20		all_lung(180;1.76e-08)		all cancers(64;4.82e-17)|GBM - Glioblastoma multiforme(113;2.58e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0262)	Aclidinium(DB08897)|Amitriptyline(DB00321)|Amoxapine(DB00543)|Aripiprazole(DB01238)|Atropine(DB00572)|Brompheniramine(DB00835)|Chlorprothixene(DB01239)|Cinnarizine(DB00568)|Clozapine(DB00363)|Cryptenamine(DB00785)|Darifenacin(DB00496)|Desipramine(DB01151)|Doxepin(DB01142)|Fesoterodine(DB06702)|Homatropine Methylbromide(DB00725)|Imipramine(DB00458)|Ketamine(DB01221)|Loxapine(DB00408)|Maprotiline(DB00934)|Methotrimeprazine(DB01403)|Metixene(DB00340)|Nicardipine(DB00622)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Paroxetine(DB00715)|Pethidine(DB00454)|Promazine(DB00420)|Promethazine(DB01069)|Propiomazine(DB00777)|Quetiapine(DB01224)|Scopolamine(DB00747)|Solifenacin(DB01591)|Tolterodine(DB01036)|Trihexyphenidyl(DB00376)|Trimipramine(DB00726)|Ziprasidone(DB00246)	ACTGAGTGCCATTCTCCTGGC	0.512																																																0								A	VAL/ILE	1,4401	2.1+/-5.4	0,1,2200	186.0	141.0	156.0		1339	5.4	1.0	15		156	0,8596		0,0,4298	no	missense	CHRM5	NM_012125.3	29	0,1,6498	GG,GA,AA		0.0,0.0227,0.0077	probably-damaging	447/533	34356257	1,12997	2201	4298	6499	SO:0001583	missense	1133				CCDS10031.1	15q26	2012-08-08			ENSG00000184984	ENSG00000184984		"""Cholinergic receptors"", ""GPCR / Class A : Cholinergic receptors, muscarinic"""	1954	protein-coding gene	gene with protein product	"""acetylcholine receptor, muscarinic 5"""	118496					Standard	NM_012125		Approved		uc001zhk.1	P08912	OTTHUMG00000129369	ENST00000383263.5:c.1339A>G	15.37:g.34356257A>G	ENSP00000372750:p.Ile447Val		Q96RG7	Missense_Mutation	SNP	ENST00000383263.5	37	CCDS10031.1	.	.	.	.	.	.	.	.	.	.	A	18.81	3.702671	0.68501	2.27E-4	0.0	ENSG00000184984	ENST00000383263	T	0.34072	1.38	5.45	5.45	0.79879	GPCR, rhodopsin-like superfamily (1);	0.050075	0.85682	D	0.000000	T	0.60274	0.2256	M	0.70842	2.15	0.80722	D	1	D	0.67145	0.996	D	0.87578	0.998	T	0.64183	-0.6467	10	0.87932	D	0	-16.4242	15.6958	0.77494	1.0:0.0:0.0:0.0	.	447	P08912	ACM5_HUMAN	V	447	ENSP00000372750:I447V	ENSP00000372750:I447V	I	+	1	0	CHRM5	32143549	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.139000	0.94554	2.288000	0.76882	0.528000	0.53228	ATT		0.512	CHRM5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251521.2			35	67	35	67
CASC5	57082	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	15	40915064	40915064	+	Missense_Mutation	SNP	G	G	A			TCGA-HT-7611-01A-11D-2395-08	TCGA-HT-7611-10B-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b60b581b-2e7d-4c89-af6f-2de8cf79bcd7	cbdff4de-7729-4d99-b9be-f4807a99630f	g.chr15:40915064G>A	ENST00000346991.5	+	11	3070	c.2680G>A	c.(2680-2682)Gat>Aat	p.D894N	CASC5_ENST00000399668.2_Missense_Mutation_p.D868N|CASC5_ENST00000527044.1_3'UTR			Q8NG31	CASC5_HUMAN	cancer susceptibility candidate 5	894	2 X 104 AA approximate repeats.				acrosome assembly (GO:0001675)|attachment of spindle microtubules to kinetochore (GO:0008608)|CENP-A containing nucleosome assembly (GO:0034080)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of phosphatase activity (GO:0010923)|nucleosome assembly (GO:0006334)|protein localization to kinetochore (GO:0034501)|spindle assembly checkpoint (GO:0071173)	acrosomal vesicle (GO:0001669)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|kinetochore (GO:0000776)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)				NS(1)|breast(7)|central_nervous_system(1)|endometrium(6)|kidney(4)|large_intestine(13)|lung(16)|skin(3)|stomach(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	57		all_cancers(109;2.03e-18)|all_epithelial(112;4.26e-15)|Lung NSC(122;1.12e-10)|all_lung(180;2.59e-09)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.0946)		GBM - Glioblastoma multiforme(113;4.99e-05)|BRCA - Breast invasive adenocarcinoma(123;0.0861)|COAD - Colon adenocarcinoma(120;0.211)		TTCAGAAGACGATAAGAATGA	0.333																																																0													71.0	69.0	70.0					15																	40915064		1827	4074	5901	SO:0001583	missense	57082			AF173994	CCDS42023.1, CCDS42024.1	15q14	2013-07-03			ENSG00000137812	ENSG00000137812		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	24054	protein-coding gene	gene with protein product	"""cancer/testis antigen 29"", ""kinetochore null 1 homolog (C. elegans)"", ""blinkin, bub-linking kinetochore protein"", ""protein phosphatase 1, regulatory subunit 55"""	609173				10980622, 10780384, 18045986	Standard	NM_170589		Approved	D40, AF15Q14, CT29, hKNL-1, KNL1, hSpc105, PPP1R55, Spc7	uc010bbt.1	Q8NG31	OTTHUMG00000166532	ENST00000346991.5:c.2680G>A	15.37:g.40915064G>A	ENSP00000335463:p.Asp894Asn		Q8NHE1|Q8WXA6|Q9HCK2|Q9NR92	Missense_Mutation	SNP	ENST00000346991.5	37	CCDS42023.1	.	.	.	.	.	.	.	.	.	.	G	9.144	1.014587	0.19355	.	.	ENSG00000137812	ENST00000346991;ENST00000260369;ENST00000399668	T;T	0.35236	1.32;1.32	5.03	2.09	0.27110	.	0.698644	0.12945	N	0.426301	T	0.24122	0.0584	L	0.41236	1.265	0.09310	N	1	B;B;B	0.22983	0.003;0.003;0.078	B;B;B	0.20384	0.003;0.003;0.029	T	0.31641	-0.9936	10	0.06365	T	0.9	.	8.882	0.35380	0.25:0.0:0.75:0.0	.	868;894;868	Q8NG31-2;Q8NG31;Q8NG31-4	.;CASC5_HUMAN;.	N	894;868;868	ENSP00000335463:D894N;ENSP00000382576:D868N	ENSP00000260369:D868N	D	+	1	0	CASC5	38702356	0.000000	0.05858	0.016000	0.15963	0.493000	0.33554	-0.019000	0.12546	0.157000	0.19338	0.508000	0.49915	GAT		0.333	CASC5-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000390224.2	NM_144508		10	92	10	92
GPRC5B	51704	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	16	19883181	19883181	+	Silent	SNP	G	G	C			TCGA-HT-7611-01A-11D-2395-08	TCGA-HT-7611-10B-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b60b581b-2e7d-4c89-af6f-2de8cf79bcd7	cbdff4de-7729-4d99-b9be-f4807a99630f	g.chr16:19883181G>C	ENST00000300571.2	-	2	1178	c.987C>G	c.(985-987)gcC>gcG	p.A329A	GPRC5B_ENST00000535671.1_Silent_p.A329A|GPRC5B_ENST00000537135.1_Silent_p.A355A|GPRC5B_ENST00000569479.1_Silent_p.A329A|GPRC5B_ENST00000569847.1_Silent_p.A329A	NM_016235.1	NP_057319.1	Q9NZH0	GPC5B_HUMAN	G protein-coupled receptor, class C, group 5, member B	329					glucose homeostasis (GO:0042593)|locomotory behavior (GO:0007626)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of inflammatory response (GO:0050729)|positive regulation of macrophage cytokine production (GO:0060907)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of neuron projection development (GO:0010976)|positive regulation of protein tyrosine kinase activity (GO:0061098)	cell surface (GO:0009986)|cytoplasmic vesicle (GO:0031410)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|membrane raft (GO:0045121)|nucleolus (GO:0005730)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|G-protein coupled receptor binding (GO:0001664)|protein kinase activator activity (GO:0030295)|protein kinase binding (GO:0019901)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(5)|lung(11)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	25						TCTCCATATAGGCCCGCGGCA	0.597																																																0													81.0	78.0	79.0					16																	19883181		2197	4300	6497	SO:0001819	synonymous_variant	51704			AF202640	CCDS10581.1	16p12	2014-01-30	2014-01-30		ENSG00000167191	ENSG00000167191		"""GPCR / Class C : Orphans"""	13308	protein-coding gene	gene with protein product		605948	"""G protein-coupled receptor, family C, group 1, member B"", ""G protein-coupled receptor, family C, group 5, member B"""			10493829, 10783259	Standard	XM_005255357		Approved	RAIG-2	uc002dgt.3	Q9NZH0	OTTHUMG00000131460	ENST00000300571.2:c.987C>G	16.37:g.19883181G>C			D2DFB0|O75205|Q8NBZ8	Silent	SNP	ENST00000300571.2	37	CCDS10581.1																																																																																				0.597	GPRC5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254285.1			9	87	9	87
GPRC5B	51704	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	16	19883826	19883826	+	Silent	SNP	G	G	T			TCGA-HT-7611-01A-11D-2395-08	TCGA-HT-7611-10B-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b60b581b-2e7d-4c89-af6f-2de8cf79bcd7	cbdff4de-7729-4d99-b9be-f4807a99630f	g.chr16:19883826G>T	ENST00000300571.2	-	2	533	c.342C>A	c.(340-342)atC>atA	p.I114I	GPRC5B_ENST00000535671.1_Silent_p.I114I|GPRC5B_ENST00000537135.1_Silent_p.I140I|GPRC5B_ENST00000569479.1_Silent_p.I114I|GPRC5B_ENST00000569847.1_Silent_p.I114I	NM_016235.1	NP_057319.1	Q9NZH0	GPC5B_HUMAN	G protein-coupled receptor, class C, group 5, member B	114					glucose homeostasis (GO:0042593)|locomotory behavior (GO:0007626)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of inflammatory response (GO:0050729)|positive regulation of macrophage cytokine production (GO:0060907)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of neuron projection development (GO:0010976)|positive regulation of protein tyrosine kinase activity (GO:0061098)	cell surface (GO:0009986)|cytoplasmic vesicle (GO:0031410)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|membrane raft (GO:0045121)|nucleolus (GO:0005730)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|G-protein coupled receptor binding (GO:0001664)|protein kinase activator activity (GO:0030295)|protein kinase binding (GO:0019901)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(5)|lung(11)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	25						CCTCCTGGATGATGAAGGCAA	0.612																																																0													31.0	29.0	29.0					16																	19883826		2197	4300	6497	SO:0001819	synonymous_variant	51704			AF202640	CCDS10581.1	16p12	2014-01-30	2014-01-30		ENSG00000167191	ENSG00000167191		"""GPCR / Class C : Orphans"""	13308	protein-coding gene	gene with protein product		605948	"""G protein-coupled receptor, family C, group 1, member B"", ""G protein-coupled receptor, family C, group 5, member B"""			10493829, 10783259	Standard	XM_005255357		Approved	RAIG-2	uc002dgt.3	Q9NZH0	OTTHUMG00000131460	ENST00000300571.2:c.342C>A	16.37:g.19883826G>T			D2DFB0|O75205|Q8NBZ8	Silent	SNP	ENST00000300571.2	37	CCDS10581.1																																																																																				0.612	GPRC5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254285.1			5	27	5	27
CHD9	80205	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	16	53348818	53348818	+	Missense_Mutation	SNP	T	T	A			TCGA-HT-7611-01A-11D-2395-08	TCGA-HT-7611-10B-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b60b581b-2e7d-4c89-af6f-2de8cf79bcd7	cbdff4de-7729-4d99-b9be-f4807a99630f	g.chr16:53348818T>A	ENST00000398510.3	+	35	7533	c.7446T>A	c.(7444-7446)gaT>gaA	p.D2482E	CHD9_ENST00000447540.1_Missense_Mutation_p.D2467E|CHD9_ENST00000564845.1_Missense_Mutation_p.D2466E|CHD9_ENST00000566029.1_Missense_Mutation_p.D2466E			Q3L8U1	CHD9_HUMAN	chromodomain helicase DNA binding protein 9	2482					cellular lipid metabolic process (GO:0044255)|chromatin modification (GO:0016568)|regulation of transcription, DNA-templated (GO:0006355)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(5)|kidney(6)|large_intestine(21)|lung(32)|ovary(2)|prostate(2)|skin(2)|stomach(1)|urinary_tract(1)	78		all_cancers(37;0.0212)				GAATTCCTGATACAGAAAGTC	0.398																																																0													113.0	106.0	108.0					16																	53348818		1821	4087	5908	SO:0001583	missense	80205			AK022240	CCDS45485.1	16q12.2	2006-04-12				ENSG00000177200			25701	protein-coding gene	gene with protein product						9205841	Standard	XM_005256168		Approved	FLJ12178, KIAA0308, BC022889	uc002egy.3	Q3L8U1		ENST00000398510.3:c.7446T>A	16.37:g.53348818T>A	ENSP00000381522:p.Asp2482Glu		B2RTU2|B9ZVQ0|O15025|Q1WF12|Q6DTK9|Q9H9V7|Q9UHM2	Missense_Mutation	SNP	ENST00000398510.3	37		.	.	.	.	.	.	.	.	.	.	T	19.12	3.765826	0.69878	.	.	ENSG00000177200	ENST00000447540;ENST00000398510;ENST00000450543	T	0.42131	0.98	5.82	0.893	0.19236	BRK domain (2);	0.000000	0.64402	D	0.000010	T	0.50480	0.1618	L	0.40543	1.245	0.39808	D	0.972666	D;D;D;D	0.71674	0.998;0.986;0.998;0.996	D;P;D;D	0.83275	0.996;0.648;0.996;0.99	T	0.49881	-0.8892	10	0.72032	D	0.01	-21.418	10.0956	0.42473	0.0:0.2574:0.0:0.7426	.	548;2467;2482;2466	C9JR69;Q3L8U1-3;Q3L8U1;Q3L8U1-2	.;.;CHD9_HUMAN;.	E	2467;2466;548	ENSP00000396345:D2467E	ENSP00000381522:D2466E	D	+	3	2	CHD9	51906319	0.694000	0.27738	0.783000	0.31826	0.932000	0.56968	1.051000	0.30417	0.112000	0.17975	0.533000	0.62120	GAT		0.398	CHD9-020	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000422345.1	NM_025134		14	87	14	87
TP53	7157	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	17	7577081	7577081	+	Missense_Mutation	SNP	T	T	C			TCGA-HT-7611-01A-11D-2395-08	TCGA-HT-7611-10B-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b60b581b-2e7d-4c89-af6f-2de8cf79bcd7	cbdff4de-7729-4d99-b9be-f4807a99630f	g.chr17:7577081T>C	ENST00000269305.4	-	8	1046	c.857A>G	c.(856-858)gAa>gGa	p.E286G	TP53_ENST00000574684.1_5'Flank|TP53_ENST00000445888.2_Missense_Mutation_p.E286G|TP53_ENST00000420246.2_Missense_Mutation_p.E286G|TP53_ENST00000413465.2_Intron|TP53_ENST00000455263.2_Missense_Mutation_p.E286G|TP53_ENST00000359597.4_Missense_Mutation_p.E286G	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	286	Interaction with AXIN1. {ECO:0000250}.|Interaction with E4F1.|Interaction with HIPK1. {ECO:0000250}.|Required for interaction with ZNF385A.		E -> A (in LFS; germline mutation and in sporadic cancers; somatic mutation).|E -> D (in sporadic cancers; somatic mutation).|E -> G (in sporadic cancers; somatic mutation).|E -> K (in sporadic cancers; somatic mutation). {ECO:0000269|PubMed:11023613, ECO:0000269|PubMed:8316628}.|E -> L (in a sporadic cancer; somatic mutation; requires 2 nucleotide substitutions).|E -> Q (in sporadic cancers; somatic mutation). {ECO:0000269|PubMed:8829627}.|E -> V (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.E286G(18)|p.E286V(9)|p.0?(8)|p.?(2)|p.E286fs*17(2)|p.R283fs*16(2)|p.R282_E287delRRTEEE(1)|p.L265_K305del41(1)|p.T284fs*57(1)|p.T284_G293del10(1)|p.E285_L289delEEENL(1)|p.E286A(1)|p.R283fs*56(1)|p.E285fs*13(1)|p.V272_K292del21(1)|p.E285_N288delEEEN(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)	GAGATTCTCTTCCTCTGTGCG	0.562		111	"""Mis, N, F"""		"""breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"""	"""breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"""		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											Pancreas(47;798 1329 9957 10801)	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"""L, E, M, O"""	51	Substitution - Missense(28)|Whole gene deletion(8)|Deletion - Frameshift(7)|Deletion - In frame(6)|Unknown(2)	large_intestine(9)|liver(6)|haematopoietic_and_lymphoid_tissue(5)|upper_aerodigestive_tract(4)|lung(4)|breast(4)|bone(4)|stomach(3)|central_nervous_system(3)|urinary_tract(3)|oesophagus(2)|ovary(2)|soft_tissue(1)|skin(1)	GRCh37	CM920679	TP53	M							95.0	81.0	86.0					17																	7577081		2203	4300	6503	SO:0001583	missense	7157	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"""Li-Fraumeni syndrome"""	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.857A>G	17.37:g.7577081T>C	ENSP00000269305:p.Glu286Gly		Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Missense_Mutation	SNP	ENST00000269305.4	37	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	T	17.60	3.431106	0.62844	.	.	ENSG00000141510	ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000509690	D;D;D;D;D;D	0.99859	-7.24;-7.24;-7.24;-7.24;-7.24;-7.24	5.12	4.04	0.47022	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	0.99857	0.9933	M	0.92077	3.27	0.58432	D	0.999999	D;D;D;D	0.89917	0.999;1.0;1.0;1.0	D;D;D;D	0.81914	0.992;0.989;0.992;0.995	D	0.97429	1.0014	10	0.87932	D	0	-23.2961	9.0226	0.36209	0.0:0.0873:0.0:0.9127	.	286;286;286;286	P04637-2;P04637-3;P04637;Q1MSW8	.;.;P53_HUMAN;.	G	286;286;286;286;286;275;154	ENSP00000352610:E286G;ENSP00000269305:E286G;ENSP00000398846:E286G;ENSP00000391127:E286G;ENSP00000391478:E286G;ENSP00000425104:E154G	ENSP00000269305:E286G	E	-	2	0	TP53	7517806	1.000000	0.71417	0.970000	0.41538	0.305000	0.27757	7.447000	0.80620	0.965000	0.38133	-0.379000	0.06801	GAA		0.562	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		49	22	49	22
TP53	7157	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	17	7578266	7578266	+	Missense_Mutation	SNP	T	T	A			TCGA-HT-7611-01A-11D-2395-08	TCGA-HT-7611-10B-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b60b581b-2e7d-4c89-af6f-2de8cf79bcd7	cbdff4de-7729-4d99-b9be-f4807a99630f	g.chr17:7578266T>A	ENST00000269305.4	-	6	772	c.583A>T	c.(583-585)Atc>Ttc	p.I195F	TP53_ENST00000574684.1_Intron|TP53_ENST00000445888.2_Missense_Mutation_p.I195F|TP53_ENST00000420246.2_Missense_Mutation_p.I195F|TP53_ENST00000413465.2_Missense_Mutation_p.I195F|TP53_ENST00000455263.2_Missense_Mutation_p.I195F|TP53_ENST00000359597.4_Missense_Mutation_p.I195F	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	195	Interaction with AXIN1. {ECO:0000250}.|Interaction with HIPK1. {ECO:0000250}.|Required for interaction with FBXO42.|Required for interaction with ZNF385A.		I -> F (in sporadic cancers; somatic mutation).|I -> L (in a sporadic cancer; somatic mutation).|I -> N (in sporadic cancers; somatic mutation).|I -> S (in sporadic cancers; somatic mutation).|I -> T (in sporadic cancers; somatic mutation). {ECO:0000269|PubMed:17224074, ECO:0000269|PubMed:9450901}.|I -> V (in a sporadic cancer; somatic mutation).|I -> Y (in a sporadic cancer; somatic mutation; requires 2 nucleotide substitutions).		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.I195F(20)|p.0?(8)|p.?(6)|p.I195fs*14(4)|p.A189_V197delAPPQHLIRV(4)|p.P191_E198>Q(3)|p.I102F(1)|p.I195fs*52(1)|p.L194fs*52(1)|p.I63fs*14(1)|p.I195fs*50(1)|p.I102fs*14(1)|p.P191fs*6(1)|p.I195_G199delIRVEG(1)|p.I195L(1)|p.P98_E105>Q(1)|p.I63F(1)|p.H193_I195delHLI(1)|p.P59_E66>Q(1)|p.H193_I195>AP(1)|p.I195fs*12(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)	TCCACTCGGATAAGATGCTGA	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)	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"""L, E, M, O"""	60	Substitution - Missense(23)|Whole gene deletion(8)|Deletion - In frame(6)|Insertion - Frameshift(6)|Complex - deletion inframe(6)|Unknown(6)|Deletion - Frameshift(4)|Complex - frameshift(1)	upper_aerodigestive_tract(8)|breast(8)|large_intestine(6)|biliary_tract(5)|skin(5)|lung(5)|oesophagus(4)|bone(4)|central_nervous_system(3)|haematopoietic_and_lymphoid_tissue(3)|ovary(3)|urinary_tract(2)|liver(2)|stomach(1)|soft_tissue(1)											99.0	89.0	92.0					17																	7578266		2203	4300	6503	SO:0001583	missense	7157	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"""Li-Fraumeni syndrome"""	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.583A>T	17.37:g.7578266T>A	ENSP00000269305:p.Ile195Phe		Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Missense_Mutation	SNP	ENST00000269305.4	37	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	T	17.86	3.493726	0.64186	.	.	ENSG00000141510	ENST00000413465;ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000545858;ENST00000509690;ENST00000514944;ENST00000414315	D;D;D;D;D;D;D;D	0.99824	-6.96;-6.96;-6.96;-6.96;-6.96;-6.96;-6.96;-6.96	5.41	5.41	0.78517	p53, DNA-binding domain (1);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1);	0.103171	0.64402	D	0.000004	D	0.99802	0.9915	M	0.85099	2.735	0.58432	D	0.999999	D;D;D;D;D;D;D	0.89917	1.0;0.999;0.998;0.998;0.997;0.998;1.0	D;D;D;D;D;D;D	0.91635	0.999;0.989;0.955;0.972;0.988;0.99;0.992	D	0.96806	0.9593	10	0.87932	D	0	-18.4587	13.709	0.62656	0.0:0.0:0.0:1.0	.	156;195;195;102;195;195;195	B4E095;P04637-2;P04637-3;E9PFT5;P04637;Q1MSW8;E7EQX7	.;.;.;.;P53_HUMAN;.;.	F	195;195;195;195;195;195;184;102;63;102;63	ENSP00000410739:I195F;ENSP00000352610:I195F;ENSP00000269305:I195F;ENSP00000398846:I195F;ENSP00000391127:I195F;ENSP00000391478:I195F;ENSP00000425104:I63F;ENSP00000423862:I102F	ENSP00000269305:I195F	I	-	1	0	TP53	7518991	1.000000	0.71417	0.895000	0.35142	0.030000	0.12068	6.159000	0.71856	2.183000	0.69458	0.533000	0.62120	ATC		0.557	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		4	47	4	47
FCGBP	8857	hgsc.bcm.edu;broad.mit.edu	37	19	40366226	40366226	+	Missense_Mutation	SNP	C	C	T			TCGA-HT-7611-01A-11D-2395-08	TCGA-HT-7611-10B-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b60b581b-2e7d-4c89-af6f-2de8cf79bcd7	cbdff4de-7729-4d99-b9be-f4807a99630f	g.chr19:40366226C>T	ENST00000221347.6	-	30	14015	c.14008G>A	c.(14008-14010)Gtg>Atg	p.V4670M		NM_003890.2	NP_003881.2	Q9Y6R7	FCGBP_HUMAN	Fc fragment of IgG binding protein	4670	VWFD 11. {ECO:0000255|PROSITE- ProRule:PRU00580}.					extracellular vesicular exosome (GO:0070062)				NS(3)|autonomic_ganglia(1)|breast(7)|central_nervous_system(5)|endometrium(13)|kidney(9)|large_intestine(27)|lung(49)|ovary(8)|pancreas(3)|prostate(13)|skin(9)|stomach(9)|upper_aerodigestive_tract(6)|urinary_tract(3)	165	all_cancers(60;6.03e-06)|all_lung(34;5.58e-08)|Lung NSC(34;6.62e-08)|Ovarian(47;0.06)		Epithelial(26;6.25e-23)|all cancers(26;1.13e-20)			GCGGAGATCACGCCGCAGGCG	0.726																																																0													21.0	31.0	27.0					19																	40366226		2196	4295	6491	SO:0001583	missense	8857			D84239		19q13.2	2013-09-20			ENSG00000090920	ENSG00000275395			13572	protein-coding gene	gene with protein product	"""IgG Fc binding protein"", ""Human Fc gamma BP"""					9182547	Standard	NM_003890		Approved	FC(GAMMA)BP	uc002omp.4	Q9Y6R7	OTTHUMG00000182580	ENST00000221347.6:c.14008G>A	19.37:g.40366226C>T	ENSP00000221347:p.Val4670Met		O95784	Missense_Mutation	SNP	ENST00000221347.6	37	CCDS12546.1	.	.	.	.	.	.	.	.	.	.	C	9.937	1.216347	0.22373	.	.	ENSG00000090920	ENST00000221347	T	0.78126	-1.15	4.32	0.939	0.19506	von Willebrand factor, type D domain (1);Uncharacterised domain, cysteine-rich (2);	0.625388	0.14703	U	0.303402	T	0.74382	0.3709	L	0.46614	1.455	0.09310	N	0.999999	D	0.60575	0.988	P	0.53490	0.727	T	0.62845	-0.6768	10	0.48119	T	0.1	.	4.1735	0.10341	0.0:0.4318:0.1691:0.399	.	4670	Q9Y6R7	FCGBP_HUMAN	M	4670	ENSP00000221347:V4670M	ENSP00000221347:V4670M	V	-	1	0	FCGBP	45058066	0.000000	0.05858	0.238000	0.24106	0.428000	0.31595	-1.149000	0.03182	0.176000	0.19873	0.305000	0.20034	GTG		0.726	FCGBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462507.1	NM_003890		20	74	20	74
ATAD3C	219293	hgsc.bcm.edu;broad.mit.edu	37	1	1396282	1396282	+	Missense_Mutation	SNP	C	C	A			TCGA-HT-7611-01A-11D-2395-08	TCGA-HT-7611-10B-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b60b581b-2e7d-4c89-af6f-2de8cf79bcd7	cbdff4de-7729-4d99-b9be-f4807a99630f	g.chr1:1396282C>A	ENST00000378785.2	+	10	1960	c.965C>A	c.(964-966)gCc>gAc	p.A322D		NM_001039211.2	NP_001034300.2	Q5T2N8	ATD3C_HUMAN	ATPase family, AAA domain containing 3C	322							ATP binding (GO:0005524)			autonomic_ganglia(1)|endometrium(1)|kidney(1)|lung(4)	7	all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;9.48e-15)|all_lung(118;9.67e-07)|Lung NSC(185;5.59e-05)|Renal(390;0.00571)|Breast(487;0.0183)|Hepatocellular(190;0.0268)|Myeloproliferative disorder(586;0.028)|Ovarian(437;0.127)|Lung SC(97;0.217)		Epithelial(90;1.79e-36)|OV - Ovarian serous cystadenocarcinoma(86;3.94e-22)|Colorectal(212;0.000155)|COAD - Colon adenocarcinoma(227;0.000193)|Kidney(185;0.00227)|BRCA - Breast invasive adenocarcinoma(365;0.00461)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0339)|Lung(427;0.145)		CTTAAGCCGGCCACAGAAGGA	0.627																																																0													129.0	108.0	114.0					1																	1396282		692	1591	2283	SO:0001583	missense	219293			AK091918	CCDS44039.1	1p36.33	2010-04-21		2007-02-08	ENSG00000215915	ENSG00000215915		"""ATPases / AAA-type"""	32151	protein-coding gene	gene with protein product							Standard	NM_001039211		Approved	FLJ34599	uc001aft.2	Q5T2N8	OTTHUMG00000000531	ENST00000378785.2:c.965C>A	1.37:g.1396282C>A	ENSP00000368062:p.Ala322Asp		Q8N1Z5	Missense_Mutation	SNP	ENST00000378785.2	37	CCDS44039.1	.	.	.	.	.	.	.	.	.	.	.	10.79	1.449404	0.26074	.	.	ENSG00000215915	ENST00000378785	D	0.94046	-3.34	2.37	2.37	0.29283	.	0.000000	0.85682	D	0.000000	D	0.89462	0.6722	L	0.55017	1.72	0.80722	D	1	B	0.32620	0.378	B	0.27170	0.077	D	0.88078	0.2805	10	0.52906	T	0.07	.	11.6921	0.51521	0.0:1.0:0.0:0.0	.	322	Q5T2N8	ATD3C_HUMAN	D	322	ENSP00000368062:A322D	ENSP00000368062:A322D	A	+	2	0	ATAD3C	1386145	1.000000	0.71417	0.988000	0.46212	0.011000	0.07611	7.417000	0.80156	1.139000	0.42245	0.205000	0.17691	GCC		0.627	ATAD3C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001279.3	NM_001039211		7	40	7	40
RNF19B	127544	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	1	33402666	33402666	+	Missense_Mutation	SNP	C	C	T			TCGA-HT-7611-01A-11D-2395-08	TCGA-HT-7611-10B-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b60b581b-2e7d-4c89-af6f-2de8cf79bcd7	cbdff4de-7729-4d99-b9be-f4807a99630f	g.chr1:33402666C>T	ENST00000373456.7	-	9	1939	c.1940G>A	c.(1939-1941)tGc>tAc	p.C647Y	RNF19B_ENST00000356990.5_3'UTR|RNF19B_ENST00000235150.4_Missense_Mutation_p.C646Y	NM_153341.2	NP_699172.2	Q6ZMZ0	RN19B_HUMAN	ring finger protein 19B	647					interferon-gamma secretion (GO:0072643)|natural killer cell mediated cytotoxicity (GO:0042267)|protein ubiquitination (GO:0016567)	cytolytic granule (GO:0044194)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)	ligase activity (GO:0016874)|zinc ion binding (GO:0008270)			endometrium(4)|kidney(2)|large_intestine(3)|lung(4)	13		Myeloproliferative disorder(586;0.0393)|all_neural(195;0.186)				GCTGGCCAGGCAGTCTTTCTG	0.547																																																0													131.0	118.0	122.0					1																	33402666		2203	4300	6503	SO:0001583	missense	127544			AK074486	CCDS372.2, CCDS44107.1, CCDS72754.1	1p35.1	2010-05-11	2007-08-20	2007-08-20	ENSG00000116514	ENSG00000116514		"""RING-type (C3HC4) zinc fingers"""	26886	protein-coding gene	gene with protein product		610872	"""IBR domain containing 3"""	IBRDC3		12477932	Standard	XM_006710356		Approved	FLJ90005	uc010oho.2	Q6ZMZ0	OTTHUMG00000004013	ENST00000373456.7:c.1940G>A	1.37:g.33402666C>T	ENSP00000362555:p.Cys647Tyr		B7ZLB2|E9PAW6|G3XA82|Q0VG77|Q5TH44|Q5TH45|Q6P6A4|Q8N2S8|Q8WUF3	Missense_Mutation	SNP	ENST00000373456.7	37	CCDS372.2	.	.	.	.	.	.	.	.	.	.	C	18.75	3.691449	0.68271	.	.	ENSG00000116514	ENST00000373456;ENST00000235150	T;T	0.34072	1.38;1.38	4.91	4.91	0.64330	.	0.125552	0.56097	D	0.000034	T	0.42154	0.1190	N	0.19112	0.55	0.50813	D	0.999895	D;D	0.65815	0.995;0.991	P;P	0.61201	0.885;0.77	T	0.31779	-0.9931	10	0.41790	T	0.15	.	16.3028	0.82831	0.0:1.0:0.0:0.0	.	646;647	G3XA82;Q6ZMZ0	.;RN19B_HUMAN	Y	647;646	ENSP00000362555:C647Y;ENSP00000235150:C646Y	ENSP00000235150:C646Y	C	-	2	0	RNF19B	33175253	0.999000	0.42202	1.000000	0.80357	0.995000	0.86356	2.182000	0.42556	2.443000	0.82685	0.537000	0.68136	TGC		0.547	RNF19B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000011465.3	NM_153341		61	88	61	88
LCE3C	353144	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	1	152573380	152573380	+	Missense_Mutation	SNP	G	G	A			TCGA-HT-7611-01A-11D-2395-08	TCGA-HT-7611-10B-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b60b581b-2e7d-4c89-af6f-2de8cf79bcd7	cbdff4de-7729-4d99-b9be-f4807a99630f	g.chr1:152573380G>A	ENST00000333881.3	+	1	243	c.173G>A	c.(172-174)aGg>aAg	p.R58K		NM_178434.2	NP_848521.1	Q5T5A8	LCE3C_HUMAN	late cornified envelope 3C	58					keratinization (GO:0031424)					lung(1)	1	Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.206)	UCEC - Uterine corpus endometrioid carcinoma (5;0.153)|KIRC - Kidney renal clear cell carcinoma(4;0.0313)|Kidney(5;0.0367)		AGCCACCACAGGCACTTCAGG	0.642																																																0													52.0	49.0	50.0					1																	152573380		1810	2702	4512	SO:0001583	missense	353144			BI670516	CCDS1015.1	1q21.3	2008-02-05		2004-10-15	ENSG00000244057	ENSG00000244057		"""Late cornified envelopes"""	16612	protein-coding gene	gene with protein product		612615	"""small proline rich-like (epidermal differentiation complex) 3A"""	SPRL3A		11698679	Standard	NM_178434		Approved	LEP15	uc001fac.2	Q5T5A8	OTTHUMG00000014403	ENST00000333881.3:c.173G>A	1.37:g.152573380G>A	ENSP00000334644:p.Arg58Lys		A1L420	Missense_Mutation	SNP	ENST00000333881.3	37	CCDS1015.1	.	.	.	.	.	.	.	.	.	.	G	3.634	-0.075029	0.07184	.	.	ENSG00000244057	ENST00000333881	T	0.08720	3.06	4.01	2.07	0.26955	.	.	.	.	.	T	0.02193	0.0068	.	.	.	0.09310	N	1	B	0.20671	0.047	B	0.15484	0.013	T	0.43114	-0.9411	8	0.87932	D	0	.	6.4177	0.21725	0.2388:0.0:0.7612:0.0	.	58	Q5T5A8	LCE3C_HUMAN	K	58	ENSP00000334644:R58K	ENSP00000334644:R58K	R	+	2	0	LCE3C	150840004	0.514000	0.26202	0.705000	0.30386	0.060000	0.15804	2.296000	0.43584	0.890000	0.36211	0.313000	0.20887	AGG		0.642	LCE3C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040061.2	NM_178434		74	9	74	9
SNAPIN	23557	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	1	153633756	153633756	+	Silent	SNP	C	C	T			TCGA-HT-7611-01A-11D-2395-08	TCGA-HT-7611-10B-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b60b581b-2e7d-4c89-af6f-2de8cf79bcd7	cbdff4de-7729-4d99-b9be-f4807a99630f	g.chr1:153633756C>T	ENST00000368685.5	+	4	480	c.390C>T	c.(388-390)ccC>ccT	p.P130P	ILF2_ENST00000480213.1_5'Flank|SNAPIN_ENST00000478558.1_3'UTR	NM_012437.5	NP_036569.1	O95295	SNAPN_HUMAN	SNAP-associated protein	130	Interaction with TOR1A.				anterograde axon cargo transport (GO:0008089)|anterograde synaptic vesicle transport (GO:0048490)|endosome to lysosome transport (GO:0008333)|intracellular protein transport (GO:0006886)|melanosome organization (GO:0032438)|negative regulation of neuron projection development (GO:0010977)|neuron projection development (GO:0031175)|neurotransmitter secretion (GO:0007269)|positive regulation of late endosome to lysosome transport (GO:1902824)|regulation of protein binding (GO:0043393)|synaptic vesicle exocytosis (GO:0016079)|synaptic vesicle fusion to presynaptic membrane (GO:0031629)|synaptic vesicle maturation (GO:0016188)|synaptic vesicle transport (GO:0048489)|terminal button organization (GO:0072553)|viral process (GO:0016032)	BLOC-1 complex (GO:0031083)|cell junction (GO:0030054)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|nucleolus (GO:0005730)|perinuclear region of cytoplasm (GO:0048471)|secretory granule (GO:0030141)|synapse (GO:0045202)|synaptic vesicle (GO:0008021)	SNARE binding (GO:0000149)			lung(3)	3	all_lung(78;1.84e-32)|Lung NSC(65;6.67e-31)|Hepatocellular(266;0.0877)|Melanoma(130;0.199)		LUSC - Lung squamous cell carcinoma(543;0.171)			GAATTTACCCCCCTGGCTCCC	0.507																																																0													83.0	81.0	82.0					1																	153633756		2203	4300	6503	SO:0001819	synonymous_variant	23557			AF086837	CCDS1049.1	1q22	2013-09-27		2007-11-14	ENSG00000143553	ENSG00000143553		"""Biogenesis of lysosomal organelles complex-1 subunits"""	17145	protein-coding gene	gene with protein product	"""snapin"", ""SNAP-25-binding protein"", ""biogenesis of lysosomal organelles complex-1, subunit 7"""	607007		SNAPAP		10195194, 12659861	Standard	NM_012437		Approved	BLOC1S7	uc001fcq.4	O95295	OTTHUMG00000037086	ENST00000368685.5:c.390C>T	1.37:g.153633756C>T			D3DV56|Q5SXU8	Silent	SNP	ENST00000368685.5	37	CCDS1049.1																																																																																				0.507	SNAPIN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090036.1	NM_012437		8	38	8	38
TTN	7273	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	2	179417788	179417788	+	Nonsense_Mutation	SNP	G	G	A			TCGA-HT-7611-01A-11D-2395-08	TCGA-HT-7611-10B-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b60b581b-2e7d-4c89-af6f-2de8cf79bcd7	cbdff4de-7729-4d99-b9be-f4807a99630f	g.chr2:179417788G>A	ENST00000591111.1	-	285	85140	c.84916C>T	c.(84916-84918)Cga>Tga	p.R28306*	TTN_ENST00000460472.2_Nonsense_Mutation_p.R20882*|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN_ENST00000342175.6_Nonsense_Mutation_p.R21074*|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000586831.1_RNA|TTN_ENST00000589042.1_Nonsense_Mutation_p.R29947*|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000590932.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000586707.1_RNA|TTN-AS1_ENST00000438095.1_RNA|RP11-65L3.2_ENST00000603415.1_RNA|TTN_ENST00000359218.5_Nonsense_Mutation_p.R21007*|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN_ENST00000342992.6_Nonsense_Mutation_p.R27379*|TTN-AS1_ENST00000592689.1_RNA			Q8WZ42	TITIN_HUMAN	titin	28306	Fibronectin type-III 106. {ECO:0000255|PROSITE-ProRule:PRU00316}.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			ACTGTGCCTCGAGAAACATGT	0.423																																																0													79.0	76.0	77.0					2																	179417788		1906	4113	6019	SO:0001587	stop_gained	7273			X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	12403	protein-coding gene	gene with protein product		188840	"""cardiomyopathy, dilated 1G (autosomal dominant)"""	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.84916C>T	2.37:g.179417788G>A	ENSP00000465570:p.Arg28306*		A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Nonsense_Mutation	SNP	ENST00000591111.1	37		.	.	.	.	.	.	.	.	.	.	G	66	95.207490	0.99997	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	.	.	.	5.49	4.58	0.56647	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	15.9738	0.80044	0.0:0.0:0.8558:0.1442	.	.	.	.	X	27379;20882;21074;21007;20879	.	ENSP00000340554:R21074X	R	-	1	2	TTN	179126034	0.942000	0.31987	0.933000	0.37362	0.978000	0.69477	2.471000	0.45127	1.367000	0.46095	0.655000	0.94253	CGA		0.423	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		8	43	8	43
IDH1	3417	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	2	209113113	209113113	+	Missense_Mutation	SNP	G	G	C	rs121913499		TCGA-HT-7611-01A-11D-2395-08	TCGA-HT-7611-10B-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b60b581b-2e7d-4c89-af6f-2de8cf79bcd7	cbdff4de-7729-4d99-b9be-f4807a99630f	g.chr2:209113113G>C	ENST00000415913.1	-	4	775	c.394C>G	c.(394-396)Cgt>Ggt	p.R132G	IDH1_ENST00000446179.1_Missense_Mutation_p.R132G|IDH1_ENST00000345146.2_Missense_Mutation_p.R132G	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.R132C(446)|p.R132G(125)|p.R132S(106)|p.G131_R132>VL(1)|p.R132V(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)		TAAGCATGACGACCTATGATG	0.398			Mis		gliobastoma																																Pancreas(158;264 1958 3300 35450 36047)		Dom	yes		2	2q33.3	3417	"""isocitrate dehydrogenase 1 (NADP+), soluble"""		O	679	Substitution - Missense(678)|Complex - compound substitution(1)	haematopoietic_and_lymphoid_tissue(280)|central_nervous_system(181)|bone(177)|biliary_tract(21)|soft_tissue(12)|large_intestine(2)|skin(2)|autonomic_ganglia(1)|endometrium(1)|NS(1)|prostate(1)											81.0	74.0	76.0					2																	209113113		2203	4300	6503	SO:0001583	missense	3417				CCDS2381.1	2q34	2014-09-17			ENSG00000138413	ENSG00000138413	1.1.1.42		5382	protein-coding gene	gene with protein product		147700					Standard	NM_005896		Approved		uc002vcu.3	O75874	OTTHUMG00000132943	ENST00000415913.1:c.394C>G	2.37:g.209113113G>C	ENSP00000390265:p.Arg132Gly		Q567U4|Q6FHQ6|Q7Z3V0|Q93090|Q9NTJ9|Q9UKW8	Missense_Mutation	SNP	ENST00000415913.1	37	CCDS2381.1	.	.	.	.	.	.	.	.	.	.	G	22.4	4.286370	0.80803	.	.	ENSG00000138413	ENST00000345146;ENST00000446179;ENST00000415913;ENST00000415282	D;D;D;D	0.86956	-2.19;-2.19;-2.19;-2.19	5.57	5.57	0.84162	Isopropylmalate dehydrogenase-like domain (2);	0.000000	0.85682	D	0.000000	D	0.96636	0.8902	H	0.99379	4.54	0.80722	D	1	D	0.57899	0.981	P	0.62813	0.907	D	0.98312	1.0524	10	0.87932	D	0	-20.0399	19.5341	0.95242	0.0:0.0:1.0:0.0	.	132	O75874	IDHC_HUMAN	G	132	ENSP00000260985:R132G;ENSP00000410513:R132G;ENSP00000390265:R132G;ENSP00000391075:R132G	ENSP00000260985:R132G	R	-	1	0	IDH1	208821358	1.000000	0.71417	0.999000	0.59377	0.994000	0.84299	7.074000	0.76791	2.616000	0.88540	0.555000	0.69702	CGT		0.398	IDH1-006	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336672.1			26	54	26	54
AGAP1	116987	hgsc.bcm.edu;broad.mit.edu	37	2	236626276	236626277	+	Missense_Mutation	DNP	GA	GA	TC			TCGA-HT-7611-01A-11D-2395-08	TCGA-HT-7611-10B-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b60b581b-2e7d-4c89-af6f-2de8cf79bcd7	cbdff4de-7729-4d99-b9be-f4807a99630f	g.chr2:236626276_236626277GA>TC	ENST00000304032.8	+	3	878_879	c.298_299GA>TC	c.(298-300)GAg>TCg	p.E100S	AGAP1_ENST00000336665.5_Missense_Mutation_p.E100S|AGAP1_ENST00000409538.1_Missense_Mutation_p.E365S|AGAP1_ENST00000409457.1_Missense_Mutation_p.E100S	NM_001037131.2	NP_001032208.1	Q9UPQ3	AGAP1_HUMAN	ArfGAP with GTPase domain, ankyrin repeat and PH domain 1	100	Small GTPase-like.				protein transport (GO:0015031)|regulation of ARF GTPase activity (GO:0032312)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)	ARF GTPase activator activity (GO:0008060)|GTP binding (GO:0005525)|phospholipid binding (GO:0005543)|zinc ion binding (GO:0008270)			breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(12)|lung(11)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	41						TGTCCAGGAGGAGTCTCCGGAA	0.446																																																0																																										SO:0001583	missense	116987			AF413078	CCDS2514.1, CCDS33408.1, CCDS58756.1	2q37	2013-01-10	2008-09-22	2008-09-22	ENSG00000157985	ENSG00000157985		"""ADP-ribosylation factor GTPase activating proteins"", ""Pleckstrin homology (PH) domain containing"", ""Ankyrin repeat domain containing"""	16922	protein-coding gene	gene with protein product		608651	"""centaurin, gamma 2"""	CENTG2			Standard	NM_001037131		Approved	KIAA1099, GGAP1	uc002vvs.3	Q9UPQ3	OTTHUMG00000133293	Exception_encountered	2.37:g.236626276_236626277delinsTC	ENSP00000307634:p.Glu100Ser		B2RTX7|Q541S5|Q6P9D7|Q9NV93	Nonsense_Mutation|Missense_Mutation	SNP	ENST00000304032.8	37	CCDS33408.1																																																																																				0.446	AGAP1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000257076.2	NM_014914		16	57	16	57
PLEKHG4B	153478	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	5	161918	161918	+	Silent	SNP	A	A	G			TCGA-HT-7611-01A-11D-2395-08	TCGA-HT-7611-10B-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b60b581b-2e7d-4c89-af6f-2de8cf79bcd7	cbdff4de-7729-4d99-b9be-f4807a99630f	g.chr5:161918A>G	ENST00000283426.6	+	10	1490	c.1440A>G	c.(1438-1440)ctA>ctG	p.L480L		NM_052909.3	NP_443141.3	Q96PX9	PKH4B_HUMAN	pleckstrin homology domain containing, family G (with RhoGef domain) member 4B	480							Rho guanyl-nucleotide exchange factor activity (GO:0005089)			endometrium(1)|large_intestine(2)|lung(2)|prostate(3)|skin(3)	11			all cancers(22;0.0253)|Lung(60;0.113)	Kidney(1;0.119)		AGAAAGGACTACAGCTGGCGA	0.582																																																0													84.0	80.0	81.0					5																	161918		2203	4300	6503	SO:0001819	synonymous_variant	153478			BC008352	CCDS34124.1	5p15.33	2013-01-11			ENSG00000153404	ENSG00000153404		"""Pleckstrin homology (PH) domain containing"""	29399	protein-coding gene	gene with protein product						11572484	Standard	NM_052909		Approved	KIAA1909	uc003jak.2	Q96PX9	OTTHUMG00000161570	ENST00000283426.6:c.1440A>G	5.37:g.161918A>G				Silent	SNP	ENST00000283426.6	37	CCDS34124.1																																																																																				0.582	PLEKHG4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365359.1	NM_052909		11	46	11	46
KIAA0319	9856	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	6	24566850	24566850	+	Missense_Mutation	SNP	C	C	A			TCGA-HT-7611-01A-11D-2395-08	TCGA-HT-7611-10B-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b60b581b-2e7d-4c89-af6f-2de8cf79bcd7	cbdff4de-7729-4d99-b9be-f4807a99630f	g.chr6:24566850C>A	ENST00000378214.3	-	14	2791	c.2267G>T	c.(2266-2268)cGg>cTg	p.R756L	KIAA0319_ENST00000537886.1_Missense_Mutation_p.R756L|KIAA0319_ENST00000430948.2_Missense_Mutation_p.R711L|KIAA0319_ENST00000543707.1_Missense_Mutation_p.R756L|KIAA0319_ENST00000535378.1_Missense_Mutation_p.R747L	NM_001168375.1|NM_014809.3	NP_001161847.1|NP_055624.2	Q5VV43	K0319_HUMAN	KIAA0319	756	PKD 5. {ECO:0000255|PROSITE- ProRule:PRU00151}.				negative regulation of dendrite development (GO:2000171)|neuron migration (GO:0001764)	early endosome (GO:0005769)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(3)|endometrium(6)|kidney(3)|large_intestine(11)|lung(19)|ovary(1)|prostate(3)|skin(6)|upper_aerodigestive_tract(1)	53						CTGGCCATCCCGGATCCACAG	0.463																																																0													99.0	96.0	97.0					6																	24566850		2203	4300	6503	SO:0001583	missense	9856			AB002317	CCDS34348.1, CCDS54969.1, CCDS54970.1, CCDS54971.1, CCDS75409.1	6p22.3	2013-12-13			ENSG00000137261	ENSG00000137261			21580	protein-coding gene	gene with protein product	"""neuronal migration"""	609269				9205841, 15514892	Standard	NM_014809		Approved	NMIG	uc003neh.1	Q5VV43	OTTHUMG00000014358	ENST00000378214.3:c.2267G>T	6.37:g.24566850C>A	ENSP00000367459:p.Arg756Leu		A7MD37|B2RTU7|B4DHA7|B4DK75|B7ZML3|F5H123|Q9UJC8|Q9Y4G7	Missense_Mutation	SNP	ENST00000378214.3	37	CCDS34348.1	.	.	.	.	.	.	.	.	.	.	C	24.5	4.534720	0.85812	.	.	ENSG00000137261	ENST00000537886;ENST00000535378;ENST00000430948;ENST00000378214;ENST00000543707	T;T;T;T;T	0.12147	2.71;2.71;2.71;2.71;2.71	4.01	4.01	0.46588	PKD/Chitinase domain (1);Fibronectin, type III (1);PKD domain (2);	0.000000	0.64402	D	0.000005	T	0.20495	0.0493	L	0.39514	1.22	0.58432	D	0.999999	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.998;0.999	T	0.03112	-1.1071	10	0.72032	D	0.01	-18.6805	16.3188	0.82938	0.0:1.0:0.0:0.0	.	756;747;756	F5H123;Q5VV43-2;Q5VV43	.;.;K0319_HUMAN	L	756;747;711;756;756	ENSP00000439700:R756L;ENSP00000442403:R747L;ENSP00000401086:R711L;ENSP00000367459:R756L;ENSP00000437656:R756L	ENSP00000367459:R756L	R	-	2	0	KIAA0319	24674829	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.679000	0.61649	2.055000	0.61198	0.591000	0.81541	CGG		0.463	KIAA0319-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040009.1	NM_014809		39	64	39	64
EPHB6	2051	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	7	142568143	142568143	+	Silent	SNP	C	C	T			TCGA-HT-7611-01A-11D-2395-08	TCGA-HT-7611-10B-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b60b581b-2e7d-4c89-af6f-2de8cf79bcd7	cbdff4de-7729-4d99-b9be-f4807a99630f	g.chr7:142568143C>T	ENST00000392957.2	+	18	3571	c.2784C>T	c.(2782-2784)ggC>ggT	p.G928G	EPHB6_ENST00000442129.1_Silent_p.G928G|EPHB6_ENST00000476059.1_3'UTR|EPHB6_ENST00000411471.2_Silent_p.G651G	NM_004445.3	NP_004436.3	O15197	EPHB6_HUMAN	EPH receptor B6	928						extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|ephrin receptor activity (GO:0005003)|receptor activity (GO:0004872)			NS(1)|breast(1)|central_nervous_system(4)|cervix(1)|endometrium(5)|kidney(4)|large_intestine(9)|lung(46)|ovary(2)|pancreas(2)|prostate(1)|skin(9)|stomach(1)|upper_aerodigestive_tract(1)	87	Melanoma(164;0.059)					TGCAGGCTGGCGGGGACCCAG	0.582																																																0													46.0	57.0	53.0					7																	142568143		2203	4300	6503	SO:0001819	synonymous_variant	2051			D83492	CCDS5873.2, CCDS75672.1	7q33-q35	2013-02-11	2004-10-28		ENSG00000106123	ENSG00000106123		"""EPH receptors"", ""Sterile alpha motif (SAM) domain containing"", ""Fibronectin type III domain containing"""	3396	protein-coding gene	gene with protein product		602757	"""EphB6"""				Standard	XM_006715881		Approved	HEP	uc011kst.2	O15197	OTTHUMG00000155707	ENST00000392957.2:c.2784C>T	7.37:g.142568143C>T			A4D2I7|A8CDT5|D3DXD3|Q2TB23|Q2TB24	Silent	SNP	ENST00000392957.2	37	CCDS5873.2																																																																																				0.582	EPHB6-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341329.1			28	112	28	112
AOC1	26	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	7	150556078	150556078	+	Missense_Mutation	SNP	A	A	G			TCGA-HT-7611-01A-11D-2395-08	TCGA-HT-7611-10B-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b60b581b-2e7d-4c89-af6f-2de8cf79bcd7	cbdff4de-7729-4d99-b9be-f4807a99630f	g.chr7:150556078A>G	ENST00000493429.1	+	5	2382	c.1798A>G	c.(1798-1800)Atg>Gtg	p.M600V	AOC1_ENST00000480582.1_3'UTR|AOC1_ENST00000360937.4_Missense_Mutation_p.M600V|AOC1_ENST00000416793.2_Missense_Mutation_p.M600V|AOC1_ENST00000467291.1_Missense_Mutation_p.M600V			P19801	AOC1_HUMAN	amine oxidase, copper containing 1	600					amine metabolic process (GO:0009308)|cellular response to azide (GO:0097185)|cellular response to copper ion (GO:0071280)|cellular response to copper ion starvation (GO:0035874)|cellular response to heparin (GO:0071504)|cellular response to histamine (GO:0071420)|oxidation-reduction process (GO:0055114)|response to antibiotic (GO:0046677)|response to drug (GO:0042493)|sodium ion transmembrane transport (GO:0035725)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|peroxisome (GO:0005777)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	calcium ion binding (GO:0005509)|cation channel activity (GO:0005261)|copper ion binding (GO:0005507)|diamine oxidase activity (GO:0052597)|drug binding (GO:0008144)|heparin binding (GO:0008201)|histamine oxidase activity (GO:0052598)|methylputrescine oxidase activity (GO:0052599)|primary amine oxidase activity (GO:0008131)|propane-1,3-diamine oxidase activity (GO:0052600)|protein complex binding (GO:0032403)|protein homodimerization activity (GO:0042803)|quinone binding (GO:0048038)|receptor activity (GO:0004872)|sodium channel activity (GO:0005272)|zinc ion binding (GO:0008270)									Amiloride(DB00594)	GATCCACTCCATGGCCGACCA	0.647																																																0													12.0	14.0	13.0					7																	150556078		1906	4110	6016	SO:0001583	missense	26			AK092514	CCDS43679.1, CCDS64797.1	7q36.1	2013-06-19	2013-06-19	2013-06-19	ENSG00000002726	ENSG00000002726	1.4.3.22		80	protein-coding gene	gene with protein product	"""diamine oxidase"""	104610	"""amiloride binding protein 1 (amine oxidase (copper-containing))"""	ABP1		8182053	Standard	NM_001091		Approved	DAO	uc003wia.2	P19801	OTTHUMG00000158306	ENST00000493429.1:c.1798A>G	7.37:g.150556078A>G	ENSP00000418614:p.Met600Val		C9J690|Q16683|Q16684|Q56II4|Q6GU42	Missense_Mutation	SNP	ENST00000493429.1	37	CCDS43679.1	.	.	.	.	.	.	.	.	.	.	A	10.99	1.508521	0.27036	.	.	ENSG00000002726	ENST00000493429;ENST00000467291;ENST00000360937;ENST00000487631;ENST00000416793;ENST00000437714	T;T;T;T	0.03413	3.94;3.94;3.94;3.94	5.57	3.19	0.36642	Copper amine oxidase, C-terminal (3);	0.208217	0.53938	D	0.000056	T	0.03520	0.0101	L	0.53729	1.69	0.27327	N	0.956876	B;B	0.15719	0.014;0.008	B;B	0.21151	0.033;0.011	T	0.41052	-0.9530	10	0.16420	T	0.52	-33.1521	1.9961	0.03457	0.578:0.1714:0.0865:0.1641	.	600;600	C9J690;P19801	.;ABP1_HUMAN	V	600;600;600;126;600;476	ENSP00000418614:M600V;ENSP00000418328:M600V;ENSP00000354193:M600V;ENSP00000411613:M600V	ENSP00000354193:M600V	M	+	1	0	ABP1	150187011	0.001000	0.12720	1.000000	0.80357	0.996000	0.88848	0.671000	0.25172	0.918000	0.36919	0.459000	0.35465	ATG		0.647	AOC1-009	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350628.1	NM_001091		6	14	6	14
TRPM6	140803	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	9	77377091	77377091	+	Missense_Mutation	SNP	A	A	G			TCGA-HT-7611-01A-11D-2395-08	TCGA-HT-7611-10B-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b60b581b-2e7d-4c89-af6f-2de8cf79bcd7	cbdff4de-7729-4d99-b9be-f4807a99630f	g.chr9:77377091A>G	ENST00000360774.1	-	26	4733	c.4496T>C	c.(4495-4497)cTa>cCa	p.L1499P	TRPM6_ENST00000376872.3_Intron|TRPM6_ENST00000451710.3_Missense_Mutation_p.L1499P|TRPM6_ENST00000361255.3_Missense_Mutation_p.L1494P|TRPM6_ENST00000449912.2_Missense_Mutation_p.L1494P|TRPM6_ENST00000376871.3_Intron|TRPM6_ENST00000376864.4_Missense_Mutation_p.L1499P	NM_017662.4	NP_060132.3	Q9BX84	TRPM6_HUMAN	transient receptor potential cation channel, subfamily M, member 6	1499					calcium ion transmembrane transport (GO:0070588)|ion transmembrane transport (GO:0034220)|response to toxic substance (GO:0009636)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium channel activity (GO:0005262)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)			NS(2)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(22)|liver(1)|lung(53)|ovary(1)|prostate(7)|skin(12)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	126						GTTATCAGATAGGGAGCTGTC	0.507																																																0													134.0	119.0	124.0					9																	77377091		2203	4300	6503	SO:0001583	missense	140803			AK026281	CCDS6647.1, CCDS55318.1, CCDS55319.1	9q21.13	2011-12-14	2003-12-02		ENSG00000119121	ENSG00000119121		"""Voltage-gated ion channels / Transient receptor potential cation channels"""	17995	protein-coding gene	gene with protein product		607009	"""hypomagnesemia, secondary hypocalcemia"""	HOMG, HSH		10021370, 12032570, 16382100	Standard	NM_017662		Approved	CHAK2, FLJ22628	uc004ajk.1	Q9BX84	OTTHUMG00000020027	ENST00000360774.1:c.4496T>C	9.37:g.77377091A>G	ENSP00000354006:p.Leu1499Pro		Q6VPR8|Q6VPR9|Q6VPS0|Q6VPS1|Q6VPS2	Missense_Mutation	SNP	ENST00000360774.1	37	CCDS6647.1	.	.	.	.	.	.	.	.	.	.	A	15.59	2.877787	0.51801	.	.	ENSG00000119121	ENST00000360774;ENST00000451710;ENST00000449912;ENST00000361255;ENST00000376864	T;T;T;T;T	0.56444	0.56;0.56;0.56;0.56;0.46	5.05	3.89	0.44902	.	1.328000	0.05220	N	0.508462	T	0.58850	0.2151	L	0.51422	1.61	0.09310	N	0.999997	D;D;D	0.59767	0.976;0.969;0.986	P;P;P	0.51016	0.454;0.656;0.564	T	0.41980	-0.9478	10	0.28530	T	0.3	.	10.9734	0.47452	0.8368:0.1632:0.0:0.0	.	1499;1494;1494	Q9BX84;Q9BX84-3;Q9BX84-2	TRPM6_HUMAN;.;.	P	1499;1499;1494;1494;1499	ENSP00000354006:L1499P;ENSP00000407341:L1499P;ENSP00000396672:L1494P;ENSP00000354962:L1494P;ENSP00000366060:L1499P	ENSP00000354006:L1499P	L	-	2	0	TRPM6	76566911	0.015000	0.18098	0.001000	0.08648	0.004000	0.04260	2.758000	0.47565	0.753000	0.32945	0.533000	0.62120	CTA		0.507	TRPM6-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000052693.1	NM_017662		17	127	17	127
OR1Q1	158131	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	9	125377695	125377695	+	Missense_Mutation	SNP	C	C	T	rs544593447		TCGA-HT-7611-01A-11D-2395-08	TCGA-HT-7611-10B-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b60b581b-2e7d-4c89-af6f-2de8cf79bcd7	cbdff4de-7729-4d99-b9be-f4807a99630f	g.chr9:125377695C>T	ENST00000297913.2	+	1	748	c.679C>T	c.(679-681)Cgg>Tgg	p.R227W	RP11-64P14.7_ENST00000431442.1_RNA	NM_012364.1	NP_036496.1	Q15612	OR1Q1_HUMAN	olfactory receptor, family 1, subfamily Q, member 1	227					detection of chemical stimulus involved in sensory perception of smell (GO:0050911)|sensory perception of smell (GO:0007608)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(9)|ovary(1)|prostate(1)|skin(2)	17						GGTGGTCCTCCGGATCCCCTC	0.537													C|||	1	0.000199681	0.0	0.0	5008	,	,		20910	0.0		0.0	False		,,,				2504	0.001															0													119.0	116.0	117.0					9																	125377695		2203	4300	6503	SO:0001583	missense	158131				CCDS35125.1	9q33.2	2013-09-20			ENSG00000165202	ENSG00000165202		"""GPCR / Class A : Olfactory receptors"""	8223	protein-coding gene	gene with protein product				OR1Q2, OR1Q3			Standard	NM_012364		Approved	OST226, OR9-A, HSTPCR106, OST226OR9-A, TPCR106	uc011lyy.2	Q15612	OTTHUMG00000020615	ENST00000297913.2:c.679C>T	9.37:g.125377695C>T	ENSP00000297913:p.Arg227Trp		Q6IFN4|Q8NGR7|Q96R82	Missense_Mutation	SNP	ENST00000297913.2	37	CCDS35125.1	.	.	.	.	.	.	.	.	.	.	C	10.94	1.492667	0.26774	.	.	ENSG00000165202	ENST00000297913	T	0.00269	8.37	5.57	-1.51	0.08664	GPCR, rhodopsin-like superfamily (1);	1.273640	0.05577	N	0.572082	T	0.00384	0.0012	H	0.94658	3.565	0.09310	N	1	B	0.27140	0.169	B	0.23419	0.046	T	0.46162	-0.9211	10	0.87932	D	0	-4.7971	10.9065	0.47084	0.7161:0.2116:0.0:0.0723	.	227	Q15612	OR1Q1_HUMAN	W	227	ENSP00000297913:R227W	ENSP00000297913:R227W	R	+	1	2	OR1Q1	124417516	0.000000	0.05858	0.000000	0.03702	0.376000	0.30014	-0.929000	0.03976	-0.081000	0.12662	0.650000	0.86243	CGG		0.537	OR1Q1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053946.1			34	130	34	130
BCOR	54880	hgsc.bcm.edu;broad.mit.edu	37	X	39932880	39932880	+	Silent	SNP	G	G	T			TCGA-HT-7611-01A-11D-2395-08	TCGA-HT-7611-10B-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b60b581b-2e7d-4c89-af6f-2de8cf79bcd7	cbdff4de-7729-4d99-b9be-f4807a99630f	g.chrX:39932880G>T	ENST00000378444.4	-	4	1947	c.1719C>A	c.(1717-1719)gcC>gcA	p.A573A	BCOR_ENST00000342274.4_Silent_p.A573A|BCOR_ENST00000378455.4_Silent_p.A573A|BCOR_ENST00000397354.3_Silent_p.A573A	NM_001123385.1	NP_001116857.1	Q6W2J9	BCOR_HUMAN	BCL6 corepressor	573					heart development (GO:0007507)|histone H2A monoubiquitination (GO:0035518)|negative regulation of bone mineralization (GO:0030502)|negative regulation of histone H3-K36 methylation (GO:0000415)|negative regulation of histone H3-K4 methylation (GO:0051572)|negative regulation of tooth mineralization (GO:0070171)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|odontogenesis (GO:0042476)|palate development (GO:0060021)|specification of axis polarity (GO:0065001)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	heat shock protein binding (GO:0031072)|histone deacetylase binding (GO:0042826)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)			breast(4)|central_nervous_system(11)|cervix(1)|endometrium(24)|eye(6)|haematopoietic_and_lymphoid_tissue(33)|kidney(2)|large_intestine(11)|lung(22)|ovary(2)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	126						TGGCATTGGGGGCGGGTGATG	0.617			"""F, N, S, T"""	RARA	"""retinoblastoma, AML, APL(translocation)"""		oculo-facio-cardio-dental genetic																																Rec	yes		X	Xp11.4	54880	BCL6 corepressor	yes		0													72.0	62.0	65.0					X																	39932880		2202	4300	6502	SO:0001819	synonymous_variant	54880			AF317391	CCDS14250.1, CCDS48092.1, CCDS48093.1	Xp11.4	2014-09-17	2010-06-10		ENSG00000183337	ENSG00000183337		"""Ankyrin repeat domain containing"""	20893	protein-coding gene	gene with protein product		300485	"""BCL6 co-repressor"""			10898795	Standard	NM_017745		Approved	FLJ20285, KIAA1575	uc004den.4	Q6W2J9	OTTHUMG00000024100	ENST00000378444.4:c.1719C>A	X.37:g.39932880G>T			D3DWB3|D3DWB4|Q29RF6|Q6P4B6|Q7Z2K7|Q8TEB4|Q96DB3|Q9H232|Q9H233|Q9HCJ7|Q9NXF2	Silent	SNP	ENST00000378444.4	37	CCDS48093.1																																																																																				0.617	BCOR-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000060666.2	NM_017745		4	48	4	48
RP11-24M17.5	0	broad.mit.edu;ucsc.edu	37	15	76067993	76067993	+	RNA	SNP	G	G	A			TCGA-HT-7611-01A-11D-2395-08	TCGA-HT-7611-10B-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b60b581b-2e7d-4c89-af6f-2de8cf79bcd7	cbdff4de-7729-4d99-b9be-f4807a99630f	g.chr15:76067993G>A	ENST00000395215.3	+	0	100																											ACTCAACAGAGTAAATTGGCA	0.532																																																0																																												0																															15.37:g.76067993G>A				RNA	SNP	ENST00000395215.3	37		.	.	.	.	.	.	.	.	.	.	.	6.323	0.427693	0.11987	.	.	ENSG00000187812	ENST00000395215	.	.	.	0.756	0.756	0.18421	.	.	.	.	.	T	0.18130	0.0435	.	.	.	.	.	.	B	0.10296	0.003	B	0.15052	0.012	T	0.30238	-0.9985	6	0.10636	T	0.68	.	3.1289	0.06417	0.3287:0.0:0.6713:0.0	.	20	B4DZE6	.	N	20	.	ENSP00000378641:S20N	S	+	2	0	AC019294.2	73855048	0.657000	0.27393	0.885000	0.34714	0.027000	0.11550	-0.031000	0.12287	0.706000	0.31912	0.162000	0.16502	AGT		0.532	RP11-24M17.5-001	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000420501.1			6	32	6	32
HIST1H4C	8364	broad.mit.edu;ucsc.edu	37	6	26104327	26104327	+	Missense_Mutation	SNP	T	T	C			TCGA-HT-7611-01A-11D-2395-08	TCGA-HT-7611-10B-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b60b581b-2e7d-4c89-af6f-2de8cf79bcd7	cbdff4de-7729-4d99-b9be-f4807a99630f	g.chr6:26104327T>C	ENST00000377803.2	+	1	224	c.152T>C	c.(151-153)aTc>aCc	p.I51T		NM_003542.3	NP_003533.1	P62805	H4_HUMAN	histone cluster 1, H4c	51					CENP-A containing nucleosome assembly (GO:0034080)|chromatin organization (GO:0006325)|DNA replication-dependent nucleosome assembly (GO:0006335)|DNA replication-independent nucleosome assembly (GO:0006336)|histone H4-K20 demethylation (GO:0035574)|mitotic cell cycle (GO:0000278)|negative regulation of megakaryocyte differentiation (GO:0045653)|nucleosome assembly (GO:0006334)|telomere maintenance (GO:0000723)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nuclear chromosome (GO:0000228)|nucleoplasm (GO:0005654)|nucleosome (GO:0000786)|nucleus (GO:0005634)|protein complex (GO:0043234)	DNA binding (GO:0003677)|histone demethylase activity (H4-K20 specific) (GO:0035575)|poly(A) RNA binding (GO:0044822)			central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(3)|skin(1)	7						TCCGGTCTTATCTATGAGGAG	0.542																																																0													72.0	69.0	70.0					6																	26104327		2203	4300	6503	SO:0001583	missense	8364			X60486	CCDS4583.1	6p22.1	2011-01-27	2006-10-11	2003-02-21	ENSG00000197061	ENSG00000197061		"""Histones / Replication-dependent"""	4787	protein-coding gene	gene with protein product		602827	"""H4 histone family, member G"", ""histone 1, H4c"""	H4FG		9119399, 12408966	Standard	NM_003542		Approved	H4/g, dJ221C16.1	uc003ngi.3	P62805	OTTHUMG00000014429	ENST00000377803.2:c.152T>C	6.37:g.26104327T>C	ENSP00000367034:p.Ile51Thr		A2VCL0|P02304|P02305|Q6DRA9|Q6FGB8|Q6NWP7	Missense_Mutation	SNP	ENST00000377803.2	37	CCDS4583.1	.	.	.	.	.	.	.	.	.	.	.	17.27	3.347592	0.61183	.	.	ENSG00000197061	ENST00000377803	T	0.66099	-0.19	4.57	4.57	0.56435	.	0.000000	0.85682	D	0.000000	T	0.66597	0.2805	.	.	.	0.58432	D	0.999999	.	.	.	.	.	.	T	0.71777	-0.4490	7	0.66056	D	0.02	.	13.5543	0.61751	0.0:0.0:0.0:1.0	.	.	.	.	T	51	ENSP00000367034:I51T	ENSP00000367034:I51T	I	+	2	0	HIST1H4C	26212306	1.000000	0.71417	1.000000	0.80357	0.011000	0.07611	7.868000	0.87116	2.052000	0.61016	0.459000	0.35465	ATC		0.542	HIST1H4C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040092.2	NM_003542		10	51	10	51
ABO	28	broad.mit.edu;ucsc.edu	37	9	136131727	136131727	+	RNA	SNP	T	T	C			TCGA-HT-7611-01A-11D-2395-08	TCGA-HT-7611-10B-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b60b581b-2e7d-4c89-af6f-2de8cf79bcd7	cbdff4de-7729-4d99-b9be-f4807a99630f	g.chr9:136131727T>C	ENST00000453660.2	-	0	401				RP11-430N14.4_ENST00000606717.1_RNA			P16442	BGAT_HUMAN	ABO blood group (transferase A, alpha 1-3-N-acetylgalactosaminyltransferase; transferase B, alpha 1-3-galactosyltransferase)						protein glycosylation (GO:0006486)	extracellular region (GO:0005576)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	fucosylgalactoside 3-alpha-galactosyltransferase activity (GO:0004381)|glycoprotein-fucosylgalactoside alpha-N-acetylgalactosaminyltransferase activity (GO:0004380)|metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(3)|large_intestine(2)|lung(2)|prostate(1)|stomach(2)	11				OV - Ovarian serous cystadenocarcinoma(145;5.82e-06)|Epithelial(140;3.45e-05)		AGGAACAGCTTCAGGAAAGCC	0.701																																																0													38.0	40.0	39.0					9																	136131727		1936	4103	6039			28			AF134415		9q34.2	2014-07-19			ENSG00000175164	ENSG00000175164	2.4.1.40, 2.4.1.37	"""Blood group antigens"", ""Glycosyltransferase family 6 domain containing"""	79	protein-coding gene	gene with protein product		110300				184030	Standard	NM_020469		Approved	A3GALNT, A3GALT1	uc004cda.1	P16442	OTTHUMG00000020872		9.37:g.136131727T>C			B0JDB9|O14758|Q14490|Q53I57|Q6ISD4|Q6KFZ2|Q70V27|Q99484|Q99485|Q9NY01|Q9UQ68|Q9UQ69	RNA	SNP	ENST00000453660.2	37																																																																																					0.701	ABO-001	KNOWN	basic	processed_transcript	processed_transcript	OTTHUMT00000054907.4	NM_020469		36	45	36	45
HAPLN1	1404	broad.mit.edu;ucsc.edu	37	5	82937364	82937364	+	Missense_Mutation	SNP	T	T	A			TCGA-HT-7611-01A-11D-2395-08	TCGA-HT-7611-10B-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b60b581b-2e7d-4c89-af6f-2de8cf79bcd7	cbdff4de-7729-4d99-b9be-f4807a99630f	g.chr5:82937364T>A	ENST00000274341.4	-	5	1866	c.1016A>T	c.(1015-1017)gAt>gTt	p.D339V		NM_001884.3	NP_001875.1	P10915	HPLN1_HUMAN	hyaluronan and proteoglycan link protein 1	339	Link 2. {ECO:0000255|PROSITE- ProRule:PRU00323}.				cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)	extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	hyaluronic acid binding (GO:0005540)			breast(1)|endometrium(1)|kidney(1)|large_intestine(12)|liver(1)|lung(15)|ovary(1)|prostate(1)|skin(1)	34		Lung NSC(167;0.0484)|all_lung(232;0.0522)|Ovarian(174;0.142)		OV - Ovarian serous cystadenocarcinoma(54;7.82e-42)|Epithelial(54;5.88e-35)|all cancers(79;1.14e-29)	Hyaluronan(DB08818)	ATGCTTTTTATCTGGGAAACC	0.517																																																0													130.0	140.0	137.0					5																	82937364		2203	4300	6503	SO:0001583	missense	1404				CCDS4061.1	5q14.3	2013-01-11	2004-03-16	2004-03-17	ENSG00000145681	ENSG00000145681		"""Immunoglobulin superfamily / V-set domain containing"""	2380	protein-coding gene	gene with protein product	"""Cartilage link protein"", ""hyaluronan and proteoglycan link protein 1"""	115435	"""cartilage linking protein 1"""	CRTL1		2286376, 2320422	Standard	NM_001884		Approved		uc003kin.3	P10915	OTTHUMG00000119045	ENST00000274341.4:c.1016A>T	5.37:g.82937364T>A	ENSP00000274341:p.Asp339Val		B2R9A9	Missense_Mutation	SNP	ENST00000274341.4	37	CCDS4061.1	.	.	.	.	.	.	.	.	.	.	T	18.37	3.608916	0.66558	.	.	ENSG00000145681	ENST00000274341	T	0.28895	1.59	5.22	5.22	0.72569	C-type lectin fold (1);Link (3);C-type lectin-like (1);	0.000000	0.85682	D	0.000000	T	0.51702	0.1690	M	0.66378	2.025	0.80722	D	1	D	0.58970	0.984	D	0.64144	0.922	T	0.51888	-0.8648	10	0.48119	T	0.1	.	15.4173	0.74980	0.0:0.0:0.0:1.0	.	339	P10915	HPLN1_HUMAN	V	339	ENSP00000274341:D339V	ENSP00000274341:D339V	D	-	2	0	HAPLN1	82973120	1.000000	0.71417	0.991000	0.47740	0.973000	0.67179	6.097000	0.71452	2.088000	0.63022	0.533000	0.62120	GAT		0.517	HAPLN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239256.2	NM_001884		9	178	9	178
CYP4F8	11283	broad.mit.edu;ucsc.edu	37	19	15734031	15734031	+	RNA	SNP	G	G	A			TCGA-HT-7611-01A-11D-2395-08	TCGA-HT-7611-10B-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b60b581b-2e7d-4c89-af6f-2de8cf79bcd7	cbdff4de-7729-4d99-b9be-f4807a99630f	g.chr19:15734031G>A	ENST00000441682.2	+	0	825							P98187	CP4F8_HUMAN	cytochrome P450, family 4, subfamily F, polypeptide 8						icosanoid metabolic process (GO:0006690)|prostaglandin metabolic process (GO:0006693)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	alkane 1-monooxygenase activity (GO:0018685)|aromatase activity (GO:0070330)|heme binding (GO:0020037)|iron ion binding (GO:0005506)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(14)|skin(1)	26						TGTGGACGGCGCTTCCACAGG	0.562																																																0													76.0	77.0	77.0					19																	15734031		2203	4300	6503			11283			AF133298	CCDS74303.1	19p13.12	2013-11-11	2003-01-14		ENSG00000186526	ENSG00000186526		"""Cytochrome P450s"""	2648	protein-coding gene	gene with protein product		611545	"""cytochrome P450, subfamily IVF, polypeptide 8"""			10405341	Standard	NM_007253		Approved		uc002nbi.3	P98187	OTTHUMG00000182386		19.37:g.15734031G>A				RNA	SNP	ENST00000441682.2	37		.	.	.	.	.	.	.	.	.	.	.	13.33	2.204486	0.38905	.	.	ENSG00000186526	ENST00000441682;ENST00000325723;ENST00000443973	.	.	.	3.2	2.06	0.26882	.	0.192171	0.33110	U	0.005280	T	0.29716	0.0742	.	.	.	0.35221	D	0.776060	B;P	0.44877	0.381;0.845	B;B	0.40940	0.219;0.344	T	0.41484	-0.9506	7	0.66056	D	0.02	.	3.8669	0.09019	0.3281:0.0:0.6719:0.0	.	67;255	B4DU85;P98187	.;CP4F8_HUMAN	H	254;67;104	.	ENSP00000314398:R67H	R	+	2	0	CYP4F8	15595031	0.969000	0.33509	0.915000	0.36163	0.008000	0.06430	3.081000	0.50120	1.607000	0.50170	0.411000	0.27672	CGC		0.562	CYP4F8-201	KNOWN	basic	processed_transcript	processed_transcript		NM_007253		47	50	47	50
IFI35	3430	broad.mit.edu;ucsc.edu	37	17	41166236	41166236	+	Missense_Mutation	SNP	G	G	A			TCGA-HT-7611-01A-11D-2395-08	TCGA-HT-7611-10B-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b60b581b-2e7d-4c89-af6f-2de8cf79bcd7	cbdff4de-7729-4d99-b9be-f4807a99630f	g.chr17:41166236G>A	ENST00000415816.2	+	7	1004	c.781G>A	c.(781-783)Ggg>Agg	p.G261R	IFI35_ENST00000438323.2_Missense_Mutation_p.G263R	NM_005533.4	NP_005524.2	P80217	IN35_HUMAN	interferon-induced protein 35	261					cytokine-mediated signaling pathway (GO:0019221)|type I interferon signaling pathway (GO:0060337)	cytosol (GO:0005829)|nucleus (GO:0005634)				central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(2)|ovary(1)	8		Breast(137;0.00499)		BRCA - Breast invasive adenocarcinoma(366;0.157)		GCCCACCCGCGGGGGCGGGGA	0.622																																																0													55.0	55.0	55.0					17																	41166236		2203	4300	6503	SO:0001583	missense	3430			BC001356	CCDS11450.1	17q21	2006-04-05			ENSG00000068079	ENSG00000068079			5399	protein-coding gene	gene with protein product		600735					Standard	NM_005533		Approved	IFP35	uc021txx.1	P80217	OTTHUMG00000167720	ENST00000415816.2:c.781G>A	17.37:g.41166236G>A	ENSP00000394579:p.Gly261Arg		C9JGX1|Q92984|Q99537|Q9BV98	Missense_Mutation	SNP	ENST00000415816.2	37		.	.	.	.	.	.	.	.	.	.	G	16.23	3.065723	0.55539	.	.	ENSG00000068079	ENST00000415816;ENST00000438323	T;T	0.67345	-0.26;-0.26	5.8	4.81	0.61882	Nmi/IFP 35 (1);	0.000000	0.85682	D	0.000000	T	0.81187	0.4770	M	0.79258	2.445	0.54753	D	0.999989	D	0.89917	1.0	D	0.97110	1.0	D	0.83606	0.0131	10	0.87932	D	0	.	13.1773	0.59635	0.0:0.0:0.8403:0.1597	.	261	P80217	IN35_HUMAN	R	261;263	ENSP00000394579:G261R;ENSP00000395590:G263R	ENSP00000394579:G261R	G	+	1	0	IFI35	38419762	1.000000	0.71417	0.574000	0.28523	0.143000	0.21401	7.454000	0.80714	1.408000	0.46895	0.462000	0.41574	GGG		0.622	IFI35-002	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000395851.1	NM_005533		39	32	39	32
FOXM1	2305	broad.mit.edu;hgsc.bcm.edu	37	12	2983282	2983283	+	Frame_Shift_Del	DEL	GA	GA	-			TCGA-HT-7611-01A-11D-2395-08	TCGA-HT-7611-10B-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b60b581b-2e7d-4c89-af6f-2de8cf79bcd7	cbdff4de-7729-4d99-b9be-f4807a99630f	g.chr12:2983282_2983283delGA	ENST00000359843.3	-	2	430_431	c.362_363delTC	c.(361-363)ctcfs	p.L121fs	FOXM1_ENST00000537018.1_5'UTR|FOXM1_ENST00000342628.2_Frame_Shift_Del_p.L121fs|FOXM1_ENST00000361953.3_Frame_Shift_Del_p.L121fs	NM_021953.3	NP_068772.2	Q08050	FOXM1_HUMAN	forkhead box M1	121					cell cycle (GO:0007049)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA repair (GO:0006281)|G2/M transition of mitotic cell cycle (GO:0000086)|liver development (GO:0001889)|mitotic cell cycle (GO:0000278)|negative regulation of cell aging (GO:0090344)|negative regulation of stress-activated MAPK cascade (GO:0032873)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of cell proliferation (GO:0008284)|positive regulation of double-strand break repair (GO:2000781)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cell cycle (GO:0051726)|regulation of cell cycle arrest (GO:0071156)|regulation of cell growth (GO:0001558)|regulation of cell proliferation (GO:0042127)|regulation of Ras protein signal transduction (GO:0046578)|regulation of reactive oxygen species metabolic process (GO:2000377)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)|transcription, DNA-templated (GO:0006351)|vasculogenesis (GO:0001570)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|protein kinase binding (GO:0019901)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			breast(1)|central_nervous_system(1)|kidney(1)|large_intestine(7)|lung(9)|prostate(1)|skin(1)|urinary_tract(3)	24			OV - Ovarian serous cystadenocarcinoma(31;0.000622)			TTTGAGGCCGGAGTCCTGGAGG	0.54																																																0																																										SO:0001589	frameshift_variant	2305			Y12773	CCDS8515.1, CCDS8516.1, CCDS8517.1	12p13	2007-09-18			ENSG00000111206	ENSG00000111206		"""Forkhead boxes"""	3818	protein-coding gene	gene with protein product	"""M-phase phosphoprotein 2"""	602341		FKHL16		9032290, 9441747	Standard	NM_202002		Approved	HFH-11, trident, HNF-3, INS-1, MPP2, MPHOSPH2, TGT3	uc001qlf.3	Q08050	OTTHUMG00000168118	ENST00000359843.3:c.362_363delTC	12.37:g.2983282_2983283delGA	ENSP00000352901:p.Leu121fs		O43258|O43259|O43260|Q4ZGG7|Q9BRL2	Frame_Shift_Del	DEL	ENST00000359843.3	37	CCDS8515.1																																																																																				0.540	FOXM1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000398272.1	NM_021953		27	119	27	119
ATRX	546	broad.mit.edu;hgsc.bcm.edu	37	X	76938601	76938605	+	Frame_Shift_Del	DEL	AATTT	AATTT	-			TCGA-HT-7611-01A-11D-2395-08	TCGA-HT-7611-10B-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b60b581b-2e7d-4c89-af6f-2de8cf79bcd7	cbdff4de-7729-4d99-b9be-f4807a99630f	g.chrX:76938601_76938605delAATTT	ENST00000373344.5	-	9	2357_2361	c.2143_2147delAAATT	c.(2143-2148)aaattgfs	p.KL715fs	ATRX_ENST00000480283.1_5'UTR|ATRX_ENST00000395603.3_Frame_Shift_Del_p.KL677fs	NM_000489.3	NP_000480.3	P46100	ATRX_HUMAN	alpha thalassemia/mental retardation syndrome X-linked	715					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						AGATTTTGGCAATTTATTAGGCTTA	0.361			"""Mis, F, N"""		"""Pancreatic neuroendocrine tumors, paediatric GBM"""		ATR-X (alpha thalassemia/mental retardation) syndrome																																Rec	yes		X	Xq21.1	546	alpha thalassemia/mental retardation syndrome X-linked	yes	E	1	Unknown(1)	bone(1)																																								SO:0001589	frameshift_variant	546			U72937	CCDS14434.1, CCDS14435.1	Xq21.1	2014-06-17	2010-06-24		ENSG00000085224	ENSG00000085224			886	protein-coding gene	gene with protein product	"""RAD54 homolog (S. cerevisiae)"""	300032	"""alpha thalassemia/mental retardation syndrome X-linked (RAD54 (S. cerevisiae) homolog)"", ""Juberg-Marsidi syndrome"""	RAD54, JMS		7874112, 1415255, 8503439, 8630485	Standard	NM_000489		Approved	XH2, XNP	uc004ecp.4	P46100	OTTHUMG00000022686	ENST00000373344.5:c.2143_2147delAAATT	X.37:g.76938601_76938605delAATTT	ENSP00000362441:p.Lys715fs		D3DTE2|P51068|Q15886|Q59FB5|Q59H31|Q5H9A2|Q5JWI4|Q7Z2J1|Q9H0Z1|Q9NTS3	Frame_Shift_Del	DEL	ENST00000373344.5	37	CCDS14434.1																																																																																				0.361	ATRX-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058860.2	NM_000489		25	117	25	117
ARID1A	8289	broad.mit.edu	37	1	27056286	27056286	+	Nonsense_Mutation	SNP	C	C	T			TCGA-HT-7611-01A-11D-2395-08	TCGA-HT-7611-10B-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b60b581b-2e7d-4c89-af6f-2de8cf79bcd7	cbdff4de-7729-4d99-b9be-f4807a99630f	g.chr1:27056286C>T	ENST00000324856.7	+	2	1653	c.1282C>T	c.(1282-1284)Cag>Tag	p.Q428*	ARID1A_ENST00000374152.2_Nonsense_Mutation_p.Q45*|ARID1A_ENST00000457599.2_Nonsense_Mutation_p.Q428*	NM_006015.4	NP_006006.3	O14497	ARI1A_HUMAN	AT rich interactive domain 1A (SWI-like)	428					androgen receptor signaling pathway (GO:0030521)|ATP-dependent chromatin remodeling (GO:0043044)|cardiac chamber development (GO:0003205)|chromatin remodeling (GO:0006338)|chromatin-mediated maintenance of transcription (GO:0048096)|forebrain development (GO:0030900)|glucocorticoid receptor signaling pathway (GO:0042921)|intracellular estrogen receptor signaling pathway (GO:0030520)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural tube closure (GO:0001843)|nucleosome disassembly (GO:0006337)|nucleosome mobilization (GO:0042766)|optic cup formation involved in camera-type eye development (GO:0003408)|placenta blood vessel development (GO:0060674)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nBAF complex (GO:0071565)|npBAF complex (GO:0071564)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|SWI/SNF complex (GO:0016514)	DNA binding (GO:0003677)|ligand-dependent nuclear receptor binding (GO:0016922)|transcription coactivator activity (GO:0003713)		ARID1A/MAST2_ENST00000361297(2)	NS(1)|autonomic_ganglia(1)|biliary_tract(1)|breast(13)|central_nervous_system(6)|cervix(2)|endometrium(56)|haematopoietic_and_lymphoid_tissue(8)|kidney(10)|large_intestine(41)|liver(31)|lung(34)|ovary(130)|pancreas(18)|prostate(8)|skin(9)|stomach(14)|upper_aerodigestive_tract(4)|urinary_tract(24)	411		all_cancers(24;6.36e-27)|all_epithelial(13;5.93e-24)|Colorectal(325;3.46e-05)|all_lung(284;4.76e-05)|Lung NSC(340;5.83e-05)|Breast(348;9.7e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|all cancers(4;2.61e-56)|Epithelial(14;7.53e-55)|OV - Ovarian serous cystadenocarcinoma(117;4.5e-30)|Colorectal(126;2.07e-09)|COAD - Colon adenocarcinoma(152;4.29e-07)|BRCA - Breast invasive adenocarcinoma(304;4.13e-05)|STAD - Stomach adenocarcinoma(196;0.000279)|KIRC - Kidney renal clear cell carcinoma(1967;0.000794)|GBM - Glioblastoma multiforme(114;0.0132)|READ - Rectum adenocarcinoma(331;0.0469)|Lung(427;0.167)|LUSC - Lung squamous cell carcinoma(448;0.242)		CCAGACCCCGCAGCGGTACCC	0.607			"""Mis, N, F, S, D"""		"""clear cell ovarian carcinoma, RCC"""																																		Rec	yes		1	1p35.3	8289	AT rich interactive domain 1A (SWI-like)		E	0													45.0	49.0	48.0					1																	27056286		2203	4300	6503	SO:0001587	stop_gained	8289			AB001895	CCDS285.1, CCDS44091.1	1p36.1-p35	2014-09-17	2006-11-08	2004-01-30	ENSG00000117713	ENSG00000117713		"""-"""	11110	protein-coding gene	gene with protein product		603024	"""SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily f, member 1"", ""AT rich interactive domain 1A (SWI- like)"""	C1orf4, SMARCF1		9630625, 9434167	Standard	NM_139135		Approved	B120, P270, C10rf4, BAF250, BAF250a	uc001bmv.1	O14497	OTTHUMG00000004004	ENST00000324856.7:c.1282C>T	1.37:g.27056286C>T	ENSP00000320485:p.Gln428*		D3DPL1|Q53FK9|Q5T0W1|Q5T0W2|Q5T0W3|Q8NFD6|Q96T89|Q9BY33|Q9HBJ5|Q9UPZ1	Nonsense_Mutation	SNP	ENST00000324856.7	37	CCDS285.1	.	.	.	.	.	.	.	.	.	.	C	37	6.356864	0.97502	.	.	ENSG00000117713	ENST00000324856;ENST00000457599;ENST00000524572;ENST00000374152	.	.	.	5.94	5.94	0.96194	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.31617	T	0.26	-7.4111	20.3771	0.98923	0.0:1.0:0.0:0.0	.	.	.	.	X	428;428;45;45	.	ENSP00000320485:Q428X	Q	+	1	0	ARID1A	26928873	1.000000	0.71417	0.993000	0.49108	0.991000	0.79684	7.406000	0.80017	2.824000	0.97209	0.650000	0.86243	CAG		0.607	ARID1A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000011437.2	NM_139135		11	81	11	81
