#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
RBP3	5949	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	10	48390167	48390167	+	Silent	SNP	G	G	A			TCGA-DB-5276-01A-01D-1468-08	TCGA-DB-5276-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fc6b7655-9307-4c8b-b1f6-f29a4dabd72c	289ad150-2e4f-4d98-9ebc-af05a0b95e7f	g.chr10:48390167G>A	ENST00000224600.4	-	1	824	c.711C>T	c.(709-711)ggC>ggT	p.G237G	AL731561.2_ENST00000581861.1_RNA	NM_002900.2	NP_002891.1	P10745	RET3_HUMAN	retinol binding protein 3, interstitial	237	4 X approximate tandem repeats.				lipid metabolic process (GO:0006629)|phototransduction, visible light (GO:0007603)|retinoid metabolic process (GO:0001523)|transport (GO:0006810)|visual perception (GO:0007601)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|interphotoreceptor matrix (GO:0033165)|vesicle (GO:0031982)	retinal binding (GO:0016918)|retinoid binding (GO:0005501)|retinol binding (GO:0019841)|serine-type peptidase activity (GO:0008236)	p.G237G(1)		central_nervous_system(3)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(8)|lung(30)|ovary(1)|prostate(7)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	59					Vitamin A(DB00162)	CCTCGGCCACGCCCCTGGTCT	0.657																																																1	Substitution - coding silent(1)	large_intestine(1)											72.0	63.0	67.0					10																	48390167		2203	4300	6503	SO:0001819	synonymous_variant	5949			M22453	CCDS73119.1	10q11.2	2014-05-06	2001-11-28		ENSG00000107618	ENSG00000265203			9921	protein-coding gene	gene with protein product		180290	"""retinol-binding protein 3, interstitial"""				Standard	NM_002900		Approved	D10S64, D10S65, D10S66, RP66	uc001jez.3	P10745	OTTHUMG00000188321	ENST00000224600.4:c.711C>T	10.37:g.48390167G>A			Q0QD34|Q5VSR0|Q8IXN0	Silent	SNP	ENST00000224600.4	37	CCDS7218.1																																																																																				0.657	RBP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047888.1	NM_002900		25	64	25	64
OR51V1	283111	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	11	5221701	5221701	+	Missense_Mutation	SNP	A	A	G			TCGA-DB-5276-01A-01D-1468-08	TCGA-DB-5276-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fc6b7655-9307-4c8b-b1f6-f29a4dabd72c	289ad150-2e4f-4d98-9ebc-af05a0b95e7f	g.chr11:5221701A>G	ENST00000321255.1	-	1	229	c.230T>C	c.(229-231)cTc>cCc	p.L77P		NM_001004760.2	NP_001004760.2	Q9H2C8	O51V1_HUMAN	olfactory receptor, family 51, subfamily V, member 1	77					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)			endometrium(1)|kidney(2)|large_intestine(13)|lung(19)|skin(2)|upper_aerodigestive_tract(2)	39		Medulloblastoma(188;0.00225)|Breast(177;0.0155)|all_neural(188;0.0212)		Epithelial(150;2.83e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		CAGGTCAGTGAGGGCCAGCAT	0.537																																																0													101.0	84.0	90.0					11																	5221701		2201	4298	6499	SO:0001583	missense	283111			BK004432	CCDS31375.1	11p15.4	2012-08-09			ENSG00000176742	ENSG00000176742		"""GPCR / Class A : Olfactory receptors"""	19597	protein-coding gene	gene with protein product				OR51A12			Standard	NM_001004760		Approved		uc010qyz.2	Q9H2C8	OTTHUMG00000066671	ENST00000321255.1:c.230T>C	11.37:g.5221701A>G	ENSP00000321729:p.Leu77Pro			Missense_Mutation	SNP	ENST00000321255.1	37	CCDS31375.1	.	.	.	.	.	.	.	.	.	.	A	11.87	1.769091	0.31320	.	.	ENSG00000176742	ENST00000321255	T	0.00558	6.61	5.33	5.33	0.75918	GPCR, rhodopsin-like superfamily (1);	1.366140	0.05158	N	0.497283	T	0.03608	0.0103	M	0.93375	3.41	0.42816	D	0.993971	D	0.60160	0.987	P	0.62885	0.908	T	0.06588	-1.0818	10	0.72032	D	0.01	.	9.427	0.38586	0.9171:0.0:0.0829:0.0	.	77	Q9H2C8	O51V1_HUMAN	P	77	ENSP00000321729:L77P	ENSP00000321729:L77P	L	-	2	0	OR51V1	5178277	0.025000	0.19082	0.985000	0.45067	0.100000	0.18952	3.084000	0.50143	2.235000	0.73313	0.528000	0.53228	CTC		0.537	OR51V1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142965.1	NM_001004760		6	76	6	76
PRDM11	56981	hgsc.bcm.edu;broad.mit.edu	37	11	45245878	45245878	+	Missense_Mutation	SNP	C	C	T	rs554343280		TCGA-DB-5276-01A-01D-1468-08	TCGA-DB-5276-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fc6b7655-9307-4c8b-b1f6-f29a4dabd72c	289ad150-2e4f-4d98-9ebc-af05a0b95e7f	g.chr11:45245878C>T	ENST00000530656.1	+	7	955	c.955C>T	c.(955-957)Cgt>Tgt	p.R319C	CTD-2560E9.3_ENST00000527450.1_RNA|PRDM11_ENST00000424263.2_Missense_Mutation_p.R285C|PRDM11_ENST00000528980.1_Intron|PRDM11_ENST00000263765.4_Missense_Mutation_p.R319C			Q9NQV5	PRD11_HUMAN	PR domain containing 11	319							methyltransferase activity (GO:0008168)			endometrium(3)|kidney(3)|large_intestine(5)|lung(10)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	26						TCCCTACAAGCGTGGCTTTGA	0.507																																					NSCLC(118;1511 1736 6472 36603 43224)											0													132.0	142.0	138.0					11																	45245878		2203	4299	6502	SO:0001583	missense	56981			AF275818	CCDS58130.1, CCDS73277.1	11p11	2008-07-21			ENSG00000019485	ENSG00000019485			13996	protein-coding gene	gene with protein product	"""PR-domain containing protein 11"""						Standard	NM_001256695		Approved	PFM8	uc031qab.1	Q9NQV5	OTTHUMG00000166478	ENST00000530656.1:c.955C>T	11.37:g.45245878C>T	ENSP00000435976:p.Arg319Cys		Q8N9F1	Missense_Mutation	SNP	ENST00000530656.1	37		.	.	.	.	.	.	.	.	.	.	C	20.3	3.961348	0.74016	.	.	ENSG00000019485	ENST00000263765;ENST00000530656;ENST00000424263	T;T;T	0.52983	0.64;0.64;0.64	5.54	5.54	0.83059	.	0.000000	0.64402	D	0.000011	T	0.54382	0.1855	N	0.24115	0.695	0.48632	D	0.999681	D	0.89917	1.0	D	0.70016	0.967	T	0.58278	-0.7664	10	0.87932	D	0	-15.4774	14.4063	0.67083	0.1475:0.8524:0.0:0.0	.	319	Q9NQV5	PRD11_HUMAN	C	319;319;285	ENSP00000263765:R319C;ENSP00000435976:R319C;ENSP00000394314:R285C	ENSP00000263765:R319C	R	+	1	0	PRDM11	45202454	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	5.103000	0.64578	2.637000	0.89404	0.650000	0.86243	CGT		0.507	PRDM11-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000389928.1	NM_020229		18	291	18	291
AURKC	6795	hgsc.bcm.edu;broad.mit.edu	37	19	57744018	57744018	+	Silent	SNP	C	C	T	rs141028635		TCGA-DB-5276-01A-01D-1468-08	TCGA-DB-5276-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fc6b7655-9307-4c8b-b1f6-f29a4dabd72c	289ad150-2e4f-4d98-9ebc-af05a0b95e7f	g.chr19:57744018C>T	ENST00000302804.7	+	4	591	c.405C>T	c.(403-405)agC>agT	p.S135S	AURKC_ENST00000599062.1_Silent_p.S132S|AURKC_ENST00000598785.1_Silent_p.S101S|AURKC_ENST00000415300.2_Silent_p.S116S|AURKC_ENST00000448930.1_Silent_p.S101S	NM_001015878.1	NP_001015878.1	Q9UQB9	AURKC_HUMAN	aurora kinase C	135	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				attachment of spindle microtubules to kinetochore (GO:0008608)|cytokinesis (GO:0000910)|histone modification (GO:0016570)|meiotic nuclear division (GO:0007126)|positive regulation of cytokinesis (GO:0032467)|protein phosphorylation (GO:0006468)|spindle midzone assembly involved in mitosis (GO:0051256)	chromosome passenger complex (GO:0032133)|chromosome, centromeric region (GO:0000775)|condensed chromosome (GO:0000793)|cytoplasm (GO:0005737)|midbody (GO:0030496)|nucleus (GO:0005634)|spindle (GO:0005819)|spindle midzone (GO:0051233)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)			breast(1)|endometrium(1)|large_intestine(9)|lung(9)|ovary(3)|prostate(1)|stomach(1)	25		Colorectal(82;5.46e-05)|all_neural(62;0.0218)|Ovarian(87;0.0822)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0122)		TGCAGAAAAGCGAGAAATTAG	0.537																																																0								C	,,	1,4405	2.1+/-5.4	0,1,2202	80.0	76.0	78.0		405,348,303	-2.5	0.0	19	dbSNP_134	78	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous,coding-synonymous	AURKC	NM_001015878.1,NM_001015879.1,NM_003160.2	,,	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	,,	135/310,116/291,101/276	57744018	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	6795				CCDS33128.1, CCDS46205.1, CCDS46206.1	19q13.43	2013-09-19	2003-07-21	2003-07-23	ENSG00000105146	ENSG00000105146			11391	protein-coding gene	gene with protein product		603495	"""serine/threonine kinase 13 (aurora/IPL1-like)"""	STK13		9799611	Standard	XR_430209		Approved	AurC, ARK3	uc002qoe.3	Q9UQB9	OTTHUMG00000183106	ENST00000302804.7:c.405C>T	19.37:g.57744018C>T			O60681|O75442|Q6AZY8|Q6DLZ0|Q9UPK5	Silent	SNP	ENST00000302804.7	37	CCDS33128.1																																																																																				0.537	AURKC-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000465089.1	NM_003160		7	89	7	89
WDR3	10885	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	1	118483783	118483783	+	Missense_Mutation	SNP	C	C	T	rs150881258		TCGA-DB-5276-01A-01D-1468-08	TCGA-DB-5276-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fc6b7655-9307-4c8b-b1f6-f29a4dabd72c	289ad150-2e4f-4d98-9ebc-af05a0b95e7f	g.chr1:118483783C>T	ENST00000349139.5	+	8	873	c.826C>T	c.(826-828)Cgg>Tgg	p.R276W	WDR3_ENST00000369441.3_3'UTR	NM_006784.2	NP_006775.1	Q9UNX4	WDR3_HUMAN	WD repeat domain 3	276						nuclear membrane (GO:0031965)|nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)	p.R276W(1)		breast(2)|cervix(2)|endometrium(5)|kidney(4)|large_intestine(9)|liver(2)|lung(22)|prostate(2)|upper_aerodigestive_tract(1)	49	Esophageal squamous(2;0.162)	all_cancers(81;2.72e-05)|Acute lymphoblastic leukemia(138;1e-08)|all_epithelial(167;4.4e-07)|all_lung(203;1.7e-06)|Lung NSC(69;1.98e-05)|Prostate(1639;0.00955)|Breast(1374;0.244)		OV - Ovarian serous cystadenocarcinoma(397;1.39e-08)|Epithelial(280;1.82e-07)|all cancers(265;2.04e-05)|Lung(183;0.0525)|BRCA - Breast invasive adenocarcinoma(282;0.0695)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.185)		TTCCATAATGCGGGAAGGAAG	0.423																																																1	Substitution - Missense(1)	large_intestine(1)						C	TRP/ARG	0,4406		0,0,2203	110.0	104.0	106.0		826	4.8	1.0	1	dbSNP_134	106	2,8598	2.2+/-6.3	0,2,4298	no	missense	WDR3	NM_006784.2	101	0,2,6501	TT,TC,CC		0.0233,0.0,0.0154	probably-damaging	276/944	118483783	2,13004	2203	4300	6503	SO:0001583	missense	10885			AF083217	CCDS898.1	1p12	2013-01-09			ENSG00000065183	ENSG00000065183		"""WD repeat domain containing"""	12755	protein-coding gene	gene with protein product		604737				10395803	Standard	NM_006784		Approved	FLJ12796, UTP12, DIP2	uc010oxe.1	Q9UNX4	OTTHUMG00000012197	ENST00000349139.5:c.826C>T	1.37:g.118483783C>T	ENSP00000308179:p.Arg276Trp			Missense_Mutation	SNP	ENST00000349139.5	37	CCDS898.1	.	.	.	.	.	.	.	.	.	.	C	21.7	4.192338	0.78902	0.0	2.33E-4	ENSG00000065183	ENST00000349139	D	0.81996	-1.56	5.7	4.76	0.60689	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.000000	0.85682	D	0.000000	D	0.89248	0.6661	M	0.82193	2.58	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.91118	0.4927	10	0.87932	D	0	-14.1891	13.5282	0.61607	0.2836:0.7164:0.0:0.0	.	276	Q9UNX4	WDR3_HUMAN	W	276	ENSP00000308179:R276W	ENSP00000308179:R276W	R	+	1	2	WDR3	118285306	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	1.638000	0.37165	1.332000	0.45431	0.655000	0.94253	CGG		0.423	WDR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033720.2	NM_006784		21	102	21	102
ALMS1	7840	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	2	73800143	73800143	+	Missense_Mutation	SNP	G	G	C			TCGA-DB-5276-01A-01D-1468-08	TCGA-DB-5276-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fc6b7655-9307-4c8b-b1f6-f29a4dabd72c	289ad150-2e4f-4d98-9ebc-af05a0b95e7f	g.chr2:73800143G>C	ENST00000264448.6	+	16	11247	c.11136G>C	c.(11134-11136)caG>caC	p.Q3712H	ALMS1_ENST00000409009.1_Missense_Mutation_p.Q3670H	NM_015120.4	NP_055935	Q8TCU4	ALMS1_HUMAN	Alstrom syndrome 1	3712					endosomal transport (GO:0016197)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|regulation of stress fiber assembly (GO:0051492)	centrosome (GO:0005813)|cilium (GO:0005929)|cytoplasm (GO:0005737)|cytosol (GO:0005829)				breast(4)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(31)|lung(68)|ovary(4)|pancreas(4)|prostate(3)|skin(8)|upper_aerodigestive_tract(1)|urinary_tract(2)	147						AAATTGAACAGATTAAATTTG	0.373																																																0													39.0	39.0	39.0					2																	73800143		1807	4063	5870	SO:0001583	missense	7840			AB002326	CCDS42697.1	2p13.1	2014-09-17			ENSG00000116127	ENSG00000116127			428	protein-coding gene	gene with protein product		606844				9063741	Standard	NM_015120		Approved	KIAA0328	uc002sje.1	Q8TCU4	OTTHUMG00000152812	ENST00000264448.6:c.11136G>C	2.37:g.73800143G>C	ENSP00000264448:p.Gln3712His		Q53S05|Q580Q8|Q86VP9|Q9Y4G4	Missense_Mutation	SNP	ENST00000264448.6	37	CCDS42697.1	.	.	.	.	.	.	.	.	.	.	G	11.96	1.793273	0.31685	.	.	ENSG00000116127	ENST00000409009;ENST00000264448	T;T	0.07567	3.18;3.18	4.63	2.77	0.32553	.	0.334537	0.22019	N	0.065754	T	0.08758	0.0217	L	0.46157	1.445	0.80722	D	1	B;B;B	0.27679	0.05;0.05;0.185	B;B;B	0.29716	0.038;0.038;0.106	T	0.11916	-1.0568	10	0.72032	D	0.01	.	7.6971	0.28600	0.0886:0.0:0.7491:0.1623	.	3712;3670;3712	Q8TCU4-3;B8ZZJ3;Q8TCU4	.;.;ALMS1_HUMAN	H	3670;3712	ENSP00000386627:Q3670H;ENSP00000264448:Q3712H	ENSP00000264448:Q3712H	Q	+	3	2	ALMS1	73653651	0.995000	0.38212	0.998000	0.56505	0.993000	0.82548	1.497000	0.35649	0.656000	0.30886	0.655000	0.94253	CAG		0.373	ALMS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000327776.1	NM_015120		16	83	16	83
XIRP2	129446	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	2	168110545	168110545	+	Missense_Mutation	SNP	C	C	G			TCGA-DB-5276-01A-01D-1468-08	TCGA-DB-5276-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fc6b7655-9307-4c8b-b1f6-f29a4dabd72c	289ad150-2e4f-4d98-9ebc-af05a0b95e7f	g.chr2:168110545C>G	ENST00000409728.1	+	10	1368	c.1279C>G	c.(1279-1281)Ctg>Gtg	p.L427V	XIRP2_ENST00000409605.1_Missense_Mutation_p.L172V|XIRP2_ENST00000420519.1_Missense_Mutation_p.L427V|XIRP2_ENST00000409043.1_Missense_Mutation_p.L394V|XIRP2_ENST00000409273.1_Missense_Mutation_p.A3298G|XIRP2_ENST00000409195.1_Missense_Mutation_p.A3520G|XIRP2_ENST00000295237.9_Missense_Mutation_p.A3520G|XIRP2_ENST00000409756.2_Missense_Mutation_p.L394V	NM_001199143.1	NP_001186072.1	A4UGR9	XIRP2_HUMAN	xin actin-binding repeat containing 2	0					actin cytoskeleton organization (GO:0030036)|cardiac muscle tissue morphogenesis (GO:0055008)|cell-cell junction organization (GO:0045216)|ventricular septum development (GO:0003281)	cell junction (GO:0030054)|Z disc (GO:0030018)				NS(3)|biliary_tract(2)|breast(5)|cervix(3)|endometrium(16)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(51)|lung(160)|ovary(7)|pancreas(3)|prostate(11)|skin(14)|stomach(5)|upper_aerodigestive_tract(8)|urinary_tract(7)	315						TTTTTAGAAGCTGCTGCTCCA	0.343																																																0													67.0	64.0	65.0					2																	168110545		1820	4086	5906	SO:0001583	missense	129446			AK056582	CCDS42768.1, CCDS42769.1, CCDS56143.1, CCDS56144.1, CCDS56145.1	2q31.1	2013-10-25	2007-06-27	2007-06-27	ENSG00000163092	ENSG00000163092			14303	protein-coding gene	gene with protein product	"""myomaxin"""	609778	"""cardiomyopathy associated 3"""	CMYA3		17046827, 12203715, 15454575	Standard	NM_001079810		Approved		uc002udx.3	A4UGR9	OTTHUMG00000154027	ENST00000409728.1:c.1279C>G	2.37:g.168110545C>G	ENSP00000386619:p.Leu427Val		A0PJ94|B2BBS0|B2BBS1|B2BBS4|B3KVH0|J3KNB1|Q53R52|Q5MJ67|Q702N7|Q86T36|Q86T38|Q86T46|Q86T51|Q86T53|Q86T55|Q86T79|Q86TB6|Q8N1M9|Q8N3R5|Q8TBV6	Missense_Mutation	SNP	ENST00000409728.1	37	CCDS56143.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	11.67|11.67	1.707085|1.707085	0.30232|0.30232	.|.	.|.	ENSG00000163092|ENSG00000163092	ENST00000409195;ENST00000295237;ENST00000409273;ENST00000413534|ENST00000409043;ENST00000409728;ENST00000409756;ENST00000420519;ENST00000409605	T;T;T|T;T;T;T;T	0.02656|0.77489	4.21;4.21;4.21|-1.09;-1.09;-1.09;-1.09;-1.1	5.69|5.69	4.79|4.79	0.61399|0.61399	.|.	0.282739|.	0.25777|.	N|.	0.028368|.	T|T	0.73992|0.73992	0.3658|0.3658	.|.	.|.	.|.	0.28963|0.28963	N|N	0.889722|0.889722	B;B|P;P	0.02656|0.47545	0.0;0.0|0.897;0.897	B;B|B;B	0.04013|0.41440	0.0;0.001|0.357;0.357	T|T	0.71017|0.71017	-0.4714|-0.4714	9|8	0.51188|0.62326	T|D	0.08|0.03	7.6785|7.6785	13.594|13.594	0.61978|0.61978	0.2823:0.7177:0.0:0.0|0.2823:0.7177:0.0:0.0	.|.	3345;3298|394;427	A4UGR9;A4UGR9-2|A4UGR9-4;A4UGR9-6	XIRP2_HUMAN;.|.;.	G|V	3520;3520;3298;934|394;427;394;427;172	ENSP00000386840:A3520G;ENSP00000295237:A3520G;ENSP00000387255:A3298G|ENSP00000386454:L394V;ENSP00000386619:L427V;ENSP00000386724:L394V;ENSP00000415541:L427V;ENSP00000386981:L172V	ENSP00000295237:A3520G|ENSP00000386454:L394V	A|L	+|+	2|1	0|2	XIRP2|XIRP2	167818791|167818791	0.998000|0.998000	0.40836|0.40836	0.671000|0.671000	0.29857|0.29857	0.893000|0.893000	0.52053|0.52053	1.277000|1.277000	0.33167|0.33167	1.368000|1.368000	0.46115|0.46115	0.563000|0.563000	0.77884|0.77884	GCT|CTG		0.343	XIRP2-006	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000333552.1	NM_152381		17	98	17	98
IDH1	3417	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	2	209113113	209113113	+	Missense_Mutation	SNP	G	G	A	rs121913499		TCGA-DB-5276-01A-01D-1468-08	TCGA-DB-5276-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fc6b7655-9307-4c8b-b1f6-f29a4dabd72c	289ad150-2e4f-4d98-9ebc-af05a0b95e7f	g.chr2:209113113G>A	ENST00000415913.1	-	4	775	c.394C>T	c.(394-396)Cgt>Tgt	p.R132C	IDH1_ENST00000345146.2_Missense_Mutation_p.R132C|IDH1_ENST00000446179.1_Missense_Mutation_p.R132C	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>T	2.37:g.209113113G>A	ENSP00000390265:p.Arg132Cys		Q567U4|Q6FHQ6|Q7Z3V0|Q93090|Q9NTJ9|Q9UKW8	Missense_Mutation	SNP	ENST00000415913.1	37	CCDS2381.1	.	.	.	.	.	.	.	.	.	.	G	24.6	4.550898	0.86127	.	.	ENSG00000138413	ENST00000345146;ENST00000446179;ENST00000415913;ENST00000415282	D;D;D;D	0.87029	-2.2;-2.2;-2.2;-2.2	5.57	5.57	0.84162	Isopropylmalate dehydrogenase-like domain (2);	0.000000	0.85682	D	0.000000	D	0.94049	0.8093	H	0.99379	4.54	0.80722	D	1	B	0.29862	0.259	B	0.31245	0.126	D	0.94048	0.7315	10	0.87932	D	0	-20.0399	19.5341	0.95242	0.0:0.0:1.0:0.0	.	132	O75874	IDHC_HUMAN	C	132	ENSP00000260985:R132C;ENSP00000410513:R132C;ENSP00000390265:R132C;ENSP00000391075:R132C	ENSP00000260985:R132C	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			17	68	17	68
CCDC158	339965	hgsc.bcm.edu;broad.mit.edu	37	4	77250102	77250102	+	Silent	SNP	G	G	A	rs138548683	byFrequency	TCGA-DB-5276-01A-01D-1468-08	TCGA-DB-5276-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fc6b7655-9307-4c8b-b1f6-f29a4dabd72c	289ad150-2e4f-4d98-9ebc-af05a0b95e7f	g.chr4:77250102G>A	ENST00000388914.3	-	21	3101	c.2949C>T	c.(2947-2949)caC>caT	p.H983H		NM_001042784.1	NP_001036249.1	Q5M9N0	CD158_HUMAN	coiled-coil domain containing 158	983	Ser-rich.									breast(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|lung(28)|ovary(3)|pancreas(1)|prostate(1)|skin(6)|stomach(1)	56						TGTCTCCTGCGTGTAATGTGA	0.433													G|||	12	0.00239617	0.0015	0.0014	5008	,	,		19858	0.0089		0.0	False		,,,				2504	0.0															0								G		8,3938		0,8,1965	127.0	119.0	121.0		2949	-6.4	0.0	4	dbSNP_134	121	0,8348		0,0,4174	no	coding-synonymous	CCDC158	NM_001042784.1		0,8,6139	AA,AG,GG		0.0,0.2027,0.0651		983/1114	77250102	8,12286	1973	4174	6147	SO:0001819	synonymous_variant	339965			BC035224	CCDS43242.1	4q21.1	2009-04-06			ENSG00000163749	ENSG00000163749			26374	protein-coding gene	gene with protein product						12477932	Standard	NM_001042784		Approved	FLJ25770	uc003hkb.4	Q5M9N0	OTTHUMG00000160916	ENST00000388914.3:c.2949C>T	4.37:g.77250102G>A			Q8IYQ1|Q8N7D4|Q8N7E3	Silent	SNP	ENST00000388914.3	37	CCDS43242.1																																																																																				0.433	CCDC158-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362694.2	NM_001042784		8	79	8	79
TBX22	50945	hgsc.bcm.edu;broad.mit.edu	37	X	79279563	79279563	+	Splice_Site	SNP	C	C	T			TCGA-DB-5276-01A-01D-1468-08	TCGA-DB-5276-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fc6b7655-9307-4c8b-b1f6-f29a4dabd72c	289ad150-2e4f-4d98-9ebc-af05a0b95e7f	g.chrX:79279563C>T	ENST00000373294.5	+	3	386	c.358C>T	c.(358-360)Cgg>Tgg	p.R120W	TBX22_ENST00000373296.3_Splice_Site_p.R120W|TBX22_ENST00000373291.1_5'UTR|TBX22_ENST00000442340.1_5'UTR	NM_016954.2	NP_058650.1	Q9Y458	TBX22_HUMAN	T-box 22	120					multicellular organismal development (GO:0007275)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(2)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(13)|lung(38)|ovary(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	65						TTCTTACAGGCGGATGTTCCC	0.483																																																0			GRCh37	CM054867	TBX22	M							105.0	87.0	93.0					X																	79279563		2203	4300	6503	SO:0001630	splice_region_variant	50945			AL031000	CCDS14445.1, CCDS43975.1	Xq21.1	2011-02-11			ENSG00000122145	ENSG00000122145		"""T-boxes"""	11600	protein-coding gene	gene with protein product		300307	"""cleft palate and/or ankyloglossia"""	CPX, CLPA		11559848, 14729838	Standard	NM_001109878		Approved		uc004edj.1	Q9Y458	OTTHUMG00000021901	ENST00000373294.5:c.357-1C>T	X.37:g.79279563C>T			Q5JZ06|Q96LC0|Q9HBF1	Splice_Site	SNP	ENST00000373294.5	37	CCDS14445.1	.	.	.	.	.	.	.	.	.	.	C	17.07	3.295089	0.60086	.	.	ENSG00000122145	ENST00000373296;ENST00000373294	D;D	0.91351	-2.83;-2.83	4.71	1.66	0.24008	Transcription factor, T-box, conserved site (1);p53-like transcription factor, DNA-binding (1);	0.000000	0.64402	D	0.000001	D	0.96163	0.8749	H	0.95712	3.71	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.95640	0.8697	10	0.87932	D	0	.	11.7981	0.52112	0.7044:0.2956:0.0:0.0	.	120	Q9Y458	TBX22_HUMAN	W	120	ENSP00000362393:R120W;ENSP00000362390:R120W	ENSP00000362390:R120W	R	+	1	2	TBX22	79166219	0.984000	0.35163	0.996000	0.52242	0.798000	0.45092	0.213000	0.17521	0.242000	0.21303	0.594000	0.82650	CGG		0.483	TBX22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057334.1	NM_016954	Missense_Mutation	21	27	21	27
CPEB4	80315	broad.mit.edu;hgsc.bcm.edu	37	5	173316976	173316977	+	Frame_Shift_Del	DEL	AA	AA	-			TCGA-DB-5276-01A-01D-1468-08	TCGA-DB-5276-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fc6b7655-9307-4c8b-b1f6-f29a4dabd72c	289ad150-2e4f-4d98-9ebc-af05a0b95e7f	g.chr5:173316976_173316977delAA	ENST00000265085.5	+	1	1694_1695	c.240_241delAA	c.(238-243)gcaaaafs	p.K81fs	CPEB4_ENST00000520867.1_Frame_Shift_Del_p.K81fs|CPEB4_ENST00000519835.1_Frame_Shift_Del_p.K81fs|CPEB4_ENST00000334035.5_Frame_Shift_Del_p.K81fs	NM_030627.2	NP_085130.2	Q17RY0	CPEB4_HUMAN	cytoplasmic polyadenylation element binding protein 4	81					cellular response to amino acid stimulus (GO:0071230)|cellular response to decreased oxygen levels (GO:0036294)|cellular response to glucose starvation (GO:0042149)|ionotropic glutamate receptor signaling pathway (GO:0035235)|negative regulation of neuron apoptotic process (GO:0043524)|response to ischemia (GO:0002931)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)|postsynaptic density (GO:0014069)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			NS(1)|endometrium(4)|kidney(2)|large_intestine(4)|lung(5)|prostate(1)|stomach(1)|upper_aerodigestive_tract(2)	20	Renal(175;0.000159)|Lung NSC(126;0.0128)|all_lung(126;0.0202)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;3.85e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000183)			CAGAAAAAGCAAAAAGTCAGCA	0.49																																																0																																										SO:0001589	frameshift_variant	80315			BX538213	CCDS4390.1	5q21	2013-02-12			ENSG00000113742	ENSG00000113742		"""RNA binding motif (RRM) containing"""	21747	protein-coding gene	gene with protein product		610607				11214970, 12672660	Standard	NM_030627		Approved	KIAA1673	uc003mcs.4	Q17RY0	OTTHUMG00000130541	ENST00000265085.5:c.240_241delAA	5.37:g.173316978_173316979delAA	ENSP00000265085:p.Lys81fs		B7ZLQ7|Q7Z310|Q8N405|Q9C0J0	Frame_Shift_Del	DEL	ENST00000265085.5	37	CCDS4390.1																																																																																				0.490	CPEB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252964.2	NM_030627		39	163	39	163
C12orf40	283461	broad.mit.edu;hgsc.bcm.edu	37	12	40114882	40114885	+	Frame_Shift_Del	DEL	ACAA	ACAA	-			TCGA-DB-5276-01A-01D-1468-08	TCGA-DB-5276-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fc6b7655-9307-4c8b-b1f6-f29a4dabd72c	289ad150-2e4f-4d98-9ebc-af05a0b95e7f	g.chr12:40114882_40114885delACAA	ENST00000324616.5	+	13	1942_1945	c.1788_1791delACAA	c.(1786-1791)atacaafs	p.IQ596fs		NM_001031748.2	NP_001026918.2	Q86WS4	CL040_HUMAN	chromosome 12 open reading frame 40	596										breast(4)|central_nervous_system(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(14)|ovary(6)|prostate(1)|skin(2)	38						ATGCAGGGATACAAACAGAGAGTG	0.402																																																0																																										SO:0001589	frameshift_variant	0			AK097445	CCDS41770.1	12q12	2008-08-04			ENSG00000180116	ENSG00000180116			26846	protein-coding gene	gene with protein product						12477932	Standard	XM_005268806		Approved	FLJ40126	uc001rmc.3	Q86WS4	OTTHUMG00000133567	ENST00000324616.5:c.1788_1791delACAA	12.37:g.40114882_40114885delACAA	ENSP00000317671:p.Ile596fs		B7WNU1|Q8IXY6|Q8N818|V9HW02	Frame_Shift_Del	DEL	ENST00000324616.5	37	CCDS41770.1																																																																																				0.402	C12orf40-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257664.2	NM_173599		23	109	23	109
BAIAP3	8938	broad.mit.edu;hgsc.bcm.edu	37	16	1397309	1397310	+	Frame_Shift_Ins	INS	-	-	T			TCGA-DB-5276-01A-01D-1468-08	TCGA-DB-5276-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fc6b7655-9307-4c8b-b1f6-f29a4dabd72c	289ad150-2e4f-4d98-9ebc-af05a0b95e7f	g.chr16:1397309_1397310insT	ENST00000324385.5	+	29	3025_3026	c.2867_2868insT	c.(2866-2871)agttttfs	p.SF956fs	BAIAP3_ENST00000568887.1_Frame_Shift_Ins_p.SF893fs|BAIAP3_ENST00000562208.1_Frame_Shift_Ins_p.SF898fs|BAIAP3_ENST00000564213.1_3'UTR|BAIAP3_ENST00000397489.1_Frame_Shift_Ins_p.SF938fs|BAIAP3_ENST00000421665.2_Frame_Shift_Ins_p.SF885fs|BAIAP3_ENST00000426824.3_Frame_Shift_Ins_p.SF921fs|BAIAP3_ENST00000397488.2_Frame_Shift_Ins_p.SF938fs	NM_003933.4	NP_003924.2	O94812	BAIP3_HUMAN	BAI1-associated protein 3	956	MHD2. {ECO:0000255|PROSITE- ProRule:PRU00588}.				G-protein coupled receptor signaling pathway (GO:0007186)|neurotransmitter secretion (GO:0007269)		protein C-terminus binding (GO:0008022)			breast(2)|central_nervous_system(2)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(1)|lung(25)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	42		Hepatocellular(780;0.0893)				GCCCTGGTCAGTTTTTTCCACG	0.639																																																0																																										SO:0001589	frameshift_variant	8938			AB017111	CCDS10434.1, CCDS55978.1, CCDS55979.1, CCDS58402.1, CCDS58403.1, CCDS66894.1	16p13.3	2008-07-04			ENSG00000007516	ENSG00000007516			948	protein-coding gene	gene with protein product		604009				9790924	Standard	NM_003933		Approved	BAP3, KIAA0734	uc002clk.2	O94812	OTTHUMG00000047833	ENST00000324385.5:c.2873dupT	16.37:g.1397315_1397315dupT	ENSP00000324510:p.Ser956fs		A2A2B2|B2RCD7|B4DGS5|B4DIK3|B4DRK9|B4DRP1|E7EUB9|H3BUH8|H3BVI3|H7C2Q1|O94839|Q2M226|Q658J2|Q76N05|Q96RZ3|Q9UJK1	Frame_Shift_Ins	INS	ENST00000324385.5	37	CCDS10434.1																																																																																				0.639	BAIAP3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000109056.3			12	60	12	60
ICT1	3396	broad.mit.edu;hgsc.bcm.edu	37	17	73016725	73016727	+	In_Frame_Del	DEL	AAG	AAG	-			TCGA-DB-5276-01A-01D-1468-08	TCGA-DB-5276-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fc6b7655-9307-4c8b-b1f6-f29a4dabd72c	289ad150-2e4f-4d98-9ebc-af05a0b95e7f	g.chr17:73016725_73016727delAAG	ENST00000301585.5	+	5	522_524	c.509_511delAAG	c.(508-513)aaagaa>aaa	p.E171del		NM_001545.1	NP_001536.1	Q14197	ICT1_HUMAN	immature colon carcinoma transcript 1	171					mitochondrial translational termination (GO:0070126)	mitochondrial large ribosomal subunit (GO:0005762)|mitochondrion (GO:0005739)	aminoacyl-tRNA hydrolase activity (GO:0004045)|translation release factor activity, codon nonspecific (GO:0016150)			NS(1)|central_nervous_system(1)|lung(2)|ovary(1)|urinary_tract(1)	6	all_lung(278;0.226)					GAGCCAACAAAAGAAGATGTTAA	0.473																																																0																																										SO:0001651	inframe_deletion	3396			X81788	CCDS11711.1	17q25	2014-02-12				ENSG00000167862			5359	protein-coding gene	gene with protein product		603000				8575443, 20186120	Standard	NM_001545		Approved	DS-1	uc002jmm.3	Q14197		ENST00000301585.5:c.509_511delAAG	17.37:g.73016728_73016730delAAG	ENSP00000301585:p.Glu171del		B2RAD1|Q53HM7|Q53Y11	In_Frame_Del	DEL	ENST00000301585.5	37	CCDS11711.1																																																																																				0.473	ICT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445314.1	NM_001545		18	59	18	59
BCOR	54880	broad.mit.edu;hgsc.bcm.edu	37	X	39922031	39922032	+	Frame_Shift_Del	DEL	CT	CT	-			TCGA-DB-5276-01A-01D-1468-08	TCGA-DB-5276-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fc6b7655-9307-4c8b-b1f6-f29a4dabd72c	289ad150-2e4f-4d98-9ebc-af05a0b95e7f	g.chrX:39922031_39922032delCT	ENST00000378444.4	-	9	4368_4369	c.4140_4141delAG	c.(4138-4143)acagggfs	p.G1381fs	BCOR_ENST00000378463.1_Frame_Shift_Del_p.G224fs|BCOR_ENST00000342274.4_Frame_Shift_Del_p.G1347fs|BCOR_ENST00000397354.3_Frame_Shift_Del_p.G1347fs|BCOR_ENST00000378455.4_Frame_Shift_Del_p.G1329fs	NM_001123385.1	NP_001116857.1	Q6W2J9	BCOR_HUMAN	BCL6 corepressor	1381					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						TAGTATTCCCCTGTCAGTGGCA	0.579			"""F, N, S, T"""	RARA	"""retinoblastoma, AML, APL(translocation)"""		oculo-facio-cardio-dental genetic																																Rec	yes		X	Xp11.4	54880	BCL6 corepressor	yes		0			GRCh37	CD041157	BCOR	D																																				SO:0001589	frameshift_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.4140_4141delAG	X.37:g.39922031_39922032delCT	ENSP00000367705:p.Gly1381fs		D3DWB3|D3DWB4|Q29RF6|Q6P4B6|Q7Z2K7|Q8TEB4|Q96DB3|Q9H232|Q9H233|Q9HCJ7|Q9NXF2	Frame_Shift_Del	DEL	ENST00000378444.4	37	CCDS48093.1																																																																																				0.579	BCOR-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000060666.2	NM_017745		14	26	14	26
ATRX	546	broad.mit.edu;hgsc.bcm.edu	37	X	76939181	76939184	+	Frame_Shift_Del	DEL	AGGA	AGGA	-	rs374670846		TCGA-DB-5276-01A-01D-1468-08	TCGA-DB-5276-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fc6b7655-9307-4c8b-b1f6-f29a4dabd72c	289ad150-2e4f-4d98-9ebc-af05a0b95e7f	g.chrX:76939181_76939184delAGGA	ENST00000373344.5	-	9	1778_1781	c.1564_1567delTCCT	c.(1564-1569)tcctcafs	p.SS522fs	ATRX_ENST00000480283.1_5'UTR|ATRX_ENST00000395603.3_Frame_Shift_Del_p.SS484fs	NM_000489.3	NP_000480.3	P46100	ATRX_HUMAN	alpha thalassemia/mental retardation syndrome X-linked	522					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						TCTGGAACTGAGGAAGGAACAGAC	0.407			"""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.1564_1567delTCCT	X.37:g.76939185_76939188delAGGA	ENSP00000362441:p.Ser522fs		D3DTE2|P51068|Q15886|Q59FB5|Q59H31|Q5H9A2|Q5JWI4|Q7Z2J1|Q9H0Z1|Q9NTS3	Frame_Shift_Del	DEL	ENST00000373344.5	37	CCDS14434.1																																																																																				0.407	ATRX-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058860.2	NM_000489		72	202	72	202
