#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_AAChange	i_ACHILLES_Lineage_Results_Top_Genes	i_BAM_File	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_Codon	i_COSMIC_Gene	i_COSMIC_Gene_Freq	i_COSMIC_n_overlapping_mutations	i_COSMIC_overlapping_mutation_descriptions	i_COSMIC_overlapping_primary_sites	i_ChromChange	i_ClinVar_ASSEMBLY	i_ClinVar_HGMD_ID	i_ClinVar_SYM	i_ClinVar_TYPE	i_ClinVar_rs	i_Drug_Target	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_Exon	i_Familial_Cancer_Genes_Reference	i_Familial_Cancer_Genes_Synonym	i_Genome_Plus_Minus_10_Bp	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_NTotCov	i_NVarCov	i_ORegAnno_bin	i_TTotCov	i_TVarCov	i_TranscriptID	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_dbSNPPopFreq	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
ACTR1B	10120	ucsc.edu;bcgsc.ca	37	2	98274501	98274501	+	Missense_Mutation	SNP	T	T	C			TCGA-FV-A3R3-01A-11D-A22F-10	TCGA-FV-A3R3-10A-01D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.		Illumina HiSeq	c285c2fa-24b4-47a1-874d-86e74b002b05	64edddfd-f366-4d51-a8b4-a357b2c68e6c	g.chr2:98274501T>C	ENST00000289228.5	-	8	1046	c.830A>G	c.(829-831)gAg>gGg	p.E277G		NM_005735.3	NP_005726.1	P42025	ACTY_HUMAN	ARP1 actin-related protein 1 homolog B, centractin beta (yeast)	277					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dynactin complex (GO:0005869)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	ATP binding (GO:0005524)			endometrium(1)|large_intestine(5)|lung(7)|ovary(1)|skin(1)	15						GGCCACCACCTCATGGAGCCC	0.597																																					p.E277G		.											.	ACTR1B	91	0			c.A830G						.						73.0	70.0	71.0					2																	98274501		2203	4300	6503	SO:0001583	missense	10120	exon8			ACCACCTCATGGA	X82207	CCDS2033.1	2q11.1-q11.2	2008-05-20	2001-11-28		ENSG00000115073	ENSG00000115073			168	protein-coding gene	gene with protein product		605144	"""ARP1 (actin-related protein 1, yeast) homolog B (centractin beta)"""	CTRN2		7696711, 10343100	Standard	NM_005735		Approved		uc002syb.2	P42025	OTTHUMG00000130549	ENST00000289228.5:c.830A>G	2.37:g.98274501T>C	ENSP00000289228:p.Glu277Gly	42.0	0.0		38.0	5.0	NM_005735	D3DVH2|Q53SK5|Q9BRB7	Missense_Mutation	SNP	ENST00000289228.5	37	CCDS2033.1	.	.	.	.	.	.	.	.	.	.	.	20.4	3.982098	0.74474	.	.	ENSG00000115073	ENST00000289228	D	0.95307	-3.67	4.72	4.72	0.59763	.	0.125962	0.52532	D	0.000078	D	0.96405	0.8827	M	0.92649	3.33	0.80722	D	1	B	0.28439	0.212	B	0.41174	0.349	D	0.96657	0.9486	10	0.87932	D	0	.	12.1972	0.54305	0.0:0.0:0.0:1.0	.	277	P42025	ACTY_HUMAN	G	277	ENSP00000289228:E277G	ENSP00000289228:E277G	E	-	2	0	ACTR1B	97640933	1.000000	0.71417	0.998000	0.56505	0.934000	0.57294	7.844000	0.86867	1.986000	0.57962	0.533000	0.62120	GAG	.		0.597	ACTR1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252973.1	NM_005735	
AKAP13	11214	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	15	86265519	86265519	+	Missense_Mutation	SNP	T	T	G			TCGA-FV-A3R3-01A-11D-A22F-10	TCGA-FV-A3R3-10A-01D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c285c2fa-24b4-47a1-874d-86e74b002b05	64edddfd-f366-4d51-a8b4-a357b2c68e6c	g.chr15:86265519T>G	ENST00000394518.2	+	25	6532	c.6437T>G	c.(6436-6438)gTa>gGa	p.V2146G	AKAP13_ENST00000394510.2_Missense_Mutation_p.V391G|AKAP13_ENST00000560579.1_3'UTR|AKAP13_ENST00000361243.2_Missense_Mutation_p.V2150G	NM_001270546.1|NM_007200.4	NP_001257475.1|NP_009131.2	Q12802	AKP13_HUMAN	A kinase (PRKA) anchor protein 13	2146	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.|Interaction with ESR1.				apoptotic signaling pathway (GO:0097190)|neurotrophin TRK receptor signaling pathway (GO:0048011)|nuclear export (GO:0051168)|positive regulation of apoptotic process (GO:0043065)|protein phosphorylation (GO:0006468)|regulation of cardiac muscle hypertrophy (GO:0010611)|regulation of glucocorticoid mediated signaling pathway (GO:1900169)|regulation of protein kinase activity (GO:0045859)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	cAMP-dependent protein kinase activity (GO:0004691)|metal ion binding (GO:0046872)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|signal transducer activity (GO:0004871)			NS(1)|breast(2)|central_nervous_system(4)|endometrium(12)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(13)|liver(1)|lung(43)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	98						ATATTGCTTGTAACTCAGCGG	0.413																																					p.V2150G	Melanoma(94;603 1453 3280 32295 32951)	.											.	AKAP13	258	0			c.T6449G						.						237.0	226.0	230.0					15																	86265519		2202	4299	6501	SO:0001583	missense	11214	exon25			TGCTTGTAACTCA	M90360	CCDS32319.1, CCDS32320.1, CCDS73778.1	15q24-q25	2013-01-10	2002-06-13			ENSG00000170776		"""A-kinase anchor proteins"", ""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	371	protein-coding gene	gene with protein product		604686	"""lymphoid blast crisis oncogene"""	LBC		9627117, 1860836	Standard	NM_007200		Approved	Ht31, BRX, AKAP-Lbc, c-lbc, PROTO-LB, HA-3, ARHGEF13	uc002blu.2	Q12802		ENST00000394518.2:c.6437T>G	15.37:g.86265519T>G	ENSP00000378026:p.Val2146Gly	136.0	0.0		138.0	14.0	NM_006738	Q14572|Q59FP6|Q86W90|Q8WXQ6|Q96JP6|Q96P79|Q9Y5T0|Q9Y5T6	Missense_Mutation	SNP	ENST00000394518.2	37	CCDS32319.1	.	.	.	.	.	.	.	.	.	.	T	27.4	4.824186	0.90955	.	.	ENSG00000170776	ENST00000426424;ENST00000361243;ENST00000394518;ENST00000394516;ENST00000458540;ENST00000394510	T;T;T	0.68765	-0.35;-0.35;-0.35	5.69	5.69	0.88448	Dbl homology (DH) domain (5);	.	.	.	.	T	0.79747	0.4499	L	0.61218	1.895	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.999;0.999	T	0.81276	-0.1006	9	0.62326	D	0.03	.	15.117	0.72410	0.0:0.0:0.0:1.0	.	2126;2146;2150	Q12802-4;Q12802;Q12802-2	.;AKP13_HUMAN;.	G	226;2150;2146;2149;2125;391	ENSP00000354718:V2150G;ENSP00000378026:V2146G;ENSP00000378018:V391G	ENSP00000354718:V2150G	V	+	2	0	AKAP13	84066523	1.000000	0.71417	0.994000	0.49952	0.986000	0.74619	7.698000	0.84413	2.150000	0.67090	0.533000	0.62120	GTA	.		0.413	AKAP13-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000417318.1	NM_007200	
AKNA	80709	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	9	117122236	117122236	+	Frame_Shift_Del	DEL	A	A	-			TCGA-FV-A3R3-01A-11D-A22F-10	TCGA-FV-A3R3-10A-01D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c285c2fa-24b4-47a1-874d-86e74b002b05	64edddfd-f366-4d51-a8b4-a357b2c68e6c	g.chr9:117122236delA	ENST00000307564.4	-	10	2392	c.2231delT	c.(2230-2232)ctgfs	p.L744fs	AKNA_ENST00000312033.3_Frame_Shift_Del_p.L744fs|AKNA_ENST00000223791.3_Frame_Shift_Del_p.L204fs|AKNA_ENST00000374088.3_Frame_Shift_Del_p.L744fs|AKNA_ENST00000374075.5_Frame_Shift_Del_p.L663fs	NM_030767.4	NP_110394.3	Q7Z591	AKNA_HUMAN	AT-hook transcription factor	744					positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	membrane (GO:0016020)|nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			breast(3)|central_nervous_system(4)|cervix(1)|endometrium(2)|kidney(4)|large_intestine(7)|liver(2)|lung(22)|ovary(4)|stomach(2)	51						GAGTCGGGCCAGGGGGTCCTG	0.632																																					p.L744fs		.											.	AKNA	94	0			c.2231delT						.						92.0	73.0	80.0					9																	117122236		2203	4300	6503	SO:0001589	frameshift_variant	80709	exon10			CGGGCCAGGGGGT	AK024431	CCDS6805.1	9q32	2008-02-05			ENSG00000106948	ENSG00000106948			24108	protein-coding gene	gene with protein product		605729				11268217, 11853319	Standard	NM_030767		Approved	KIAA1968	uc004bis.3	Q7Z591	OTTHUMG00000020538	ENST00000307564.4:c.2231delT	9.37:g.117122236delA	ENSP00000303769:p.Leu744fs	76.0	0.0		49.0	11.0	NM_030767	Q05BK5|Q5T535|Q5T536|Q5T537|Q64FX6|Q64FX7|Q64FX8|Q64FY2|Q6ZMK0|Q6ZNL2|Q6ZTX0|Q8TET1|Q8TF33|Q96RR9|Q9H7P7	Frame_Shift_Del	DEL	ENST00000307564.4	37	CCDS6805.1																																																																																			.		0.632	AKNA-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053767.2	NM_030767	
AMMECR1	9949	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	X	109444278	109444278	+	Splice_Site	SNP	C	C	T			TCGA-FV-A3R3-01A-11D-A22F-10	TCGA-FV-A3R3-10A-01D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c285c2fa-24b4-47a1-874d-86e74b002b05	64edddfd-f366-4d51-a8b4-a357b2c68e6c	g.chrX:109444278C>T	ENST00000262844.5	-	5	958	c.791G>A	c.(790-792)gGa>gAa	p.G264E	AMMECR1_ENST00000372059.2_Splice_Site_p.G227E|AMMECR1_ENST00000372057.1_Splice_Site_p.G141E	NM_015365.2	NP_056180.1	Q9Y4X0	AMMR1_HUMAN	Alport syndrome, mental retardation, midface hypoplasia and elliptocytosis chromosomal region gene 1	264	AMMECR1. {ECO:0000255|PROSITE- ProRule:PRU00467}.									large_intestine(1)|lung(4)|ovary(1)|stomach(1)	7						ATGGTCCCATCCTGTAGAGAG	0.383																																					p.G264E		.											.	AMMECR1	130	0			c.G791A						.						171.0	148.0	156.0					X																	109444278		2203	4300	6503	SO:0001630	splice_region_variant	9949	exon5			TCCCATCCTGTAG	AJ007014	CCDS14551.1, CCDS35368.1, CCDS55476.1	Xq22.3	2014-06-17	2008-09-12		ENSG00000101935	ENSG00000101935			467	protein-coding gene	gene with protein product		300195				10049589, 9480748	Standard	NM_001171689		Approved		uc004eoo.3	Q9Y4X0	OTTHUMG00000022197	ENST00000262844.5:c.791-1G>A	X.37:g.109444278C>T		97.0	0.0		72.0	10.0	NM_015365	Q5JYV9|Q6P9D8|Q8WX22|Q9UIQ8	Missense_Mutation	SNP	ENST00000262844.5	37	CCDS14551.1	.	.	.	.	.	.	.	.	.	.	C	18.32	3.597226	0.66332	.	.	ENSG00000101935	ENST00000262844;ENST00000372059;ENST00000372057	.	.	.	5.8	4.94	0.65067	AMMECR1 domain (2);	0.000000	0.85682	D	0.000000	T	0.73353	0.3576	M	0.75884	2.315	0.80722	D	1	P;P	0.49696	0.911;0.927	P;P	0.54706	0.55;0.759	T	0.75470	-0.3306	9	0.52906	T	0.07	.	13.9424	0.64064	0.0:0.9255:0.0:0.0745	.	227;264	Q9Y4X0-3;Q9Y4X0	.;AMER1_HUMAN	E	264;227;141	.	ENSP00000262844:G264E	G	-	2	0	AMMECR1	109330934	1.000000	0.71417	1.000000	0.80357	0.969000	0.65631	7.487000	0.81328	1.206000	0.43276	0.600000	0.82982	GGA	.		0.383	AMMECR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057907.1		Missense_Mutation
ARHGAP24	83478	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	4	86643102	86643102	+	Missense_Mutation	SNP	A	A	T			TCGA-FV-A3R3-01A-11D-A22F-10	TCGA-FV-A3R3-10A-01D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c285c2fa-24b4-47a1-874d-86e74b002b05	64edddfd-f366-4d51-a8b4-a357b2c68e6c	g.chr4:86643102A>T	ENST00000395184.1	+	3	711	c.245A>T	c.(244-246)aAg>aTg	p.K82M	ARHGAP24_ENST00000503995.1_Missense_Mutation_p.K82M|MIR4451_ENST00000580577.1_RNA|ARHGAP24_ENST00000506421.1_3'UTR	NM_001025616.2	NP_001020787.2	Q8N264	RHG24_HUMAN	Rho GTPase activating protein 24	82	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				activation of Rac GTPase activity (GO:0032863)|angiogenesis (GO:0001525)|cell differentiation (GO:0030154)|negative regulation of Rac protein signal transduction (GO:0035021)|negative regulation of ruffle assembly (GO:1900028)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|wound healing, spreading of epidermal cells (GO:0035313)	cell projection (GO:0042995)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|focal adhesion (GO:0005925)	Rac GTPase activator activity (GO:0030675)	p.K82T(1)		breast(3)|cervix(1)|endometrium(3)|large_intestine(4)|lung(10)|skin(1)|stomach(1)|urinary_tract(1)	24		Hepatocellular(203;0.114)|all_hematologic(202;0.21)|Acute lymphoblastic leukemia(40;0.242)		OV - Ovarian serous cystadenocarcinoma(123;0.000571)		AACCCAGGGAAGTTCCTTTTT	0.383																																					p.K82M		.											.	ARHGAP24	227	1	Substitution - Missense(1)	prostate(1)	c.A245T						.						129.0	128.0	128.0					4																	86643102		2203	4300	6503	SO:0001583	missense	83478	exon3			CAGGGAAGTTCCT	AK091196	CCDS3611.1, CCDS34025.1, CCDS43246.1	4q22.1	2013-01-10			ENSG00000138639	ENSG00000138639		"""Rho GTPase activating proteins"", ""Pleckstrin homology (PH) domain containing"""	25361	protein-coding gene	gene with protein product		610586				11230166, 15254788	Standard	NM_001042669		Approved	DKFZP564B1162, FLJ33877, FilGAP	uc003hpk.3	Q8N264	OTTHUMG00000130427	ENST00000395184.1:c.245A>T	4.37:g.86643102A>T	ENSP00000378611:p.Lys82Met	207.0	0.0		172.0	22.0	NM_001025616	Q4KMG1|Q6ZNV3|Q86TI5|Q86WE4|Q9H0T6	Missense_Mutation	SNP	ENST00000395184.1	37	CCDS34025.1	.	.	.	.	.	.	.	.	.	.	A	16.28	3.079527	0.55753	.	.	ENSG00000138639	ENST00000395184;ENST00000503995	T;T	0.14516	2.5;2.5	4.97	4.97	0.65823	Pleckstrin homology-type (1);Pleckstrin homology domain (3);	0.000000	0.85682	D	0.000000	T	0.40979	0.1139	M	0.88181	2.935	0.80722	D	1	P;B;D	0.69078	0.955;0.018;0.997	P;B;D	0.63192	0.768;0.074;0.912	T	0.50709	-0.8796	10	0.87932	D	0	.	13.9319	0.64001	1.0:0.0:0.0:0.0	.	82;82;227	Q8N264;Q8N264-4;Q8N264-5	RHG24_HUMAN;.;.	M	82	ENSP00000378611:K82M;ENSP00000423206:K82M	ENSP00000378611:K82M	K	+	2	0	ARHGAP24	86862126	1.000000	0.71417	0.985000	0.45067	0.939000	0.58152	6.030000	0.70903	1.998000	0.58463	0.528000	0.53228	AAG	.		0.383	ARHGAP24-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252815.2	NM_031305	
ARSI	340075	ucsc.edu;bcgsc.ca	37	5	149681722	149681722	+	Missense_Mutation	SNP	G	G	T			TCGA-FV-A3R3-01A-11D-A22F-10	TCGA-FV-A3R3-10A-01D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.		Illumina HiSeq	c285c2fa-24b4-47a1-874d-86e74b002b05	64edddfd-f366-4d51-a8b4-a357b2c68e6c	g.chr5:149681722G>T	ENST00000328668.7	-	1	794	c.215C>A	c.(214-216)cCt>cAt	p.P72H		NM_001012301.2	NP_001012301.1	Q5FYB1	ARSI_HUMAN	arylsulfatase family, member I	72					cellular protein metabolic process (GO:0044267)|glycosphingolipid metabolic process (GO:0006687)|post-translational protein modification (GO:0043687)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)	arylsulfatase activity (GO:0004065)|metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(11)|ovary(1)|pancreas(1)|skin(1)|urinary_tract(1)	23			KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			GTCCAGCGTAGGGGTCTCGAT	0.617																																					p.P72H		.											.	ARSI	92	0			c.C215A						.						53.0	46.0	48.0					5																	149681722		2203	4300	6503	SO:0001583	missense	340075	exon1			AGCGTAGGGGTCT	AY875937	CCDS34275.1	5q32	2014-03-03	2006-03-07			ENSG00000183876		"""Arylsulfatase family"""	32521	protein-coding gene	gene with protein product		610009	"""arylsulfatase I"""			16174644, 24482476	Standard	NM_001012301		Approved	FLJ16069, SPG66	uc003lrv.2	Q5FYB1		ENST00000328668.7:c.215C>A	5.37:g.149681722G>T	ENSP00000333395:p.Pro72His	37.0	0.0		21.0	4.0	NM_001012301	A1L3B0|B3KV22|B7XD03	Missense_Mutation	SNP	ENST00000328668.7	37	CCDS34275.1	.	.	.	.	.	.	.	.	.	.	G	20.8	4.053526	0.75960	.	.	ENSG00000183876	ENST00000328668	D	0.99748	-6.62	5.1	3.28	0.37604	Alkaline phosphatase-like, alpha/beta/alpha (1);Sulfatase (1);Alkaline-phosphatase-like, core domain (1);	0.052821	0.85682	D	0.000000	D	0.99851	0.9931	H	0.99642	4.675	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.97162	0.9838	10	0.87932	D	0	.	10.4014	0.44231	0.0731:0.1349:0.792:0.0	.	72	Q5FYB1	ARSI_HUMAN	H	72	ENSP00000333395:P72H	ENSP00000333395:P72H	P	-	2	0	ARSI	149661915	1.000000	0.71417	0.932000	0.37286	0.973000	0.67179	9.616000	0.98359	0.698000	0.31739	0.561000	0.74099	CCT	.		0.617	ARSI-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373681.1	NM_001012301	
ASXL1	171023	bcgsc.ca;mdanderson.org	37	20	31017824	31017824	+	Missense_Mutation	SNP	C	C	A	rs576523117		TCGA-FV-A3R3-01A-11D-A22F-10	TCGA-FV-A3R3-10A-01D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.		Illumina HiSeq	c285c2fa-24b4-47a1-874d-86e74b002b05	64edddfd-f366-4d51-a8b4-a357b2c68e6c	g.chr20:31017824C>A	ENST00000375687.4	+	8	1110	c.686C>A	c.(685-687)cCg>cAg	p.P229Q	ASXL1_ENST00000306058.5_Missense_Mutation_p.P224Q	NM_015338.5	NP_056153	Q8IXJ9	ASXL1_HUMAN	additional sex combs like transcriptional regulator 1	229	Interaction with KDM1A. {ECO:0000250}.				bone development (GO:0060348)|monoubiquitinated histone H2A deubiquitination (GO:0035522)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of peroxisome proliferator activated receptor signaling pathway (GO:0035359)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of retinoic acid receptor signaling pathway (GO:0048386)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|response to retinoic acid (GO:0032526)|transcription, DNA-templated (GO:0006351)	extracellular vesicular exosome (GO:0070062)|nuclear chromatin (GO:0000790)|PR-DUB complex (GO:0035517)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|peroxisome proliferator activated receptor binding (GO:0042975)|retinoic acid receptor binding (GO:0042974)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)			NS(1)|breast(2)|central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(655)|kidney(5)|large_intestine(18)|liver(1)|lung(27)|ovary(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	722						GACCCTGCCCCGCTCCTGAGA	0.657			"""F, N, Mis"""		"""MDS, CMML"""																																p.P229Q		.		Rec	yes		20	20q11.1	171023	additional sex combs like 1		L	.	ASXL1	2057	0			c.C686A						.						17.0	21.0	20.0					20																	31017824		2143	4187	6330	SO:0001583	missense	171023	exon7			CTGCCCCGCTCCT	AJ438952	CCDS13201.1	20q11	2014-09-17	2014-06-17		ENSG00000171456	ENSG00000171456			18318	protein-coding gene	gene with protein product		612990	"""additional sex combs like 1 (Drosophila)"""			12657473	Standard	NM_015338		Approved	KIAA0978	uc002wxs.3	Q8IXJ9	OTTHUMG00000032218	ENST00000375687.4:c.686C>A	20.37:g.31017824C>A	ENSP00000364839:p.Pro229Gln	24.0	0.0		15.0	3.0	NM_015338	B2RP59|Q5JWS9|Q8IYY7|Q9H466|Q9NQF8|Q9UFJ0|Q9UFP8|Q9Y2I4	Missense_Mutation	SNP	ENST00000375687.4	37	CCDS13201.1	.	.	.	.	.	.	.	.	.	.	C	14.77	2.635759	0.47049	.	.	ENSG00000171456	ENST00000358956;ENST00000375687;ENST00000421155;ENST00000306058	T;T	0.13901	2.56;2.55	4.89	3.88	0.44766	.	0.099749	0.44902	D	0.000419	T	0.10895	0.0266	N	0.08118	0	0.52501	D	0.999953	D	0.57257	0.979	P	0.57057	0.812	T	0.14392	-1.0474	10	0.08381	T	0.77	-13.2083	10.425	0.44373	0.2746:0.7254:0.0:0.0	.	229	Q8IXJ9	ASXL1_HUMAN	Q	229;229;229;224	ENSP00000364839:P229Q;ENSP00000305119:P224Q	ENSP00000305119:P224Q	P	+	2	0	ASXL1	30481485	1.000000	0.71417	1.000000	0.80357	1.000000	0.99986	2.263000	0.43293	2.715000	0.92844	0.655000	0.94253	CCG	.		0.657	ASXL1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000078624.2	NM_015338	
ATAD2	29028	broad.mit.edu;bcgsc.ca	37	8	124382254	124382254	+	Silent	SNP	T	T	C			TCGA-FV-A3R3-01A-11D-A22F-10	TCGA-FV-A3R3-10A-01D-A22F-10	T	T	.	.	.	.	.	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c285c2fa-24b4-47a1-874d-86e74b002b05	64edddfd-f366-4d51-a8b4-a357b2c68e6c	g.chr8:124382254T>C	ENST00000287394.5	-	7	845	c.738A>G	c.(736-738)gaA>gaG	p.E246E	ATAD2_ENST00000521903.1_5'UTR|ATAD2_ENST00000534257.1_5'Flank	NM_014109.3	NP_054828.2	Q6PL18	ATAD2_HUMAN	ATPase family, AAA domain containing 2	246					ATP catabolic process (GO:0006200)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(12)|lung(16)|ovary(3)|prostate(3)|skin(1)|urinary_tract(2)	48	Lung NSC(37;1.25e-09)|Ovarian(258;0.00838)		STAD - Stomach adenocarcinoma(47;0.00288)			CTTCACCCTCTTCAGATGACT	0.373																																					p.E246E		.											.	ATAD2	92	0			c.A738G						.						133.0	114.0	121.0					8																	124382254		2203	4300	6503	SO:0001819	synonymous_variant	29028	exon7			ACCCTCTTCAGAT	BC019909	CCDS6343.1	8q24.13	2014-01-21		2007-02-08	ENSG00000156802	ENSG00000156802		"""ATPases / AAA-type"""	30123	protein-coding gene	gene with protein product		611941				12477932	Standard	NM_014109		Approved	PRO2000, DKFZp667N1320, MGC5254, MGC29843, CT137	uc003yqh.4	Q6PL18	OTTHUMG00000165090	ENST00000287394.5:c.738A>G	8.37:g.124382254T>C		118.0	0.0		89.0	5.0	NM_014109	Q14CR1|Q658P2|Q68CQ0|Q6PJV6|Q8N890|Q9UHS5	Silent	SNP	ENST00000287394.5	37	CCDS6343.1																																																																																			.		0.373	ATAD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381766.2	NM_014109	
BAZ1A	11177	broad.mit.edu;ucsc.edu;bcgsc.ca	37	14	35231121	35231121	+	Missense_Mutation	SNP	T	T	C			TCGA-FV-A3R3-01A-11D-A22F-10	TCGA-FV-A3R3-10A-01D-A22F-10	T	T	.	.	.	.	.	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c285c2fa-24b4-47a1-874d-86e74b002b05	64edddfd-f366-4d51-a8b4-a357b2c68e6c	g.chr14:35231121T>C	ENST00000382422.2	-	23	4412	c.4085A>G	c.(4084-4086)aAa>aGa	p.K1362R	BAZ1A_ENST00000360310.1_Missense_Mutation_p.K1362R|BAZ1A_ENST00000358716.4_Missense_Mutation_p.K1330R			Q9NRL2	BAZ1A_HUMAN	bromodomain adjacent to zinc finger domain, 1A	1362					chromatin remodeling (GO:0006338)|DNA-dependent DNA replication (GO:0006261)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	ACF complex (GO:0016590)|CHRAC (GO:0008623)|nuclear chromosome (GO:0000228)	zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(2)|cervix(2)|endometrium(6)|kidney(2)|large_intestine(7)|lung(19)|ovary(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	48	Breast(36;0.0388)|Hepatocellular(127;0.158)		LUAD - Lung adenocarcinoma(48;7.23e-05)|Lung(238;0.00019)|Epithelial(34;0.0793)|all cancers(34;0.175)	GBM - Glioblastoma multiforme(112;0.0659)		ATTAGCACTTTTCCTGCCTCT	0.423																																					p.K1362R		.											.	BAZ1A	291	0			c.A4085G						.						204.0	197.0	200.0					14																	35231121		2203	4300	6503	SO:0001583	missense	11177	exon24			GCACTTTTCCTGC	AB032252	CCDS9651.1, CCDS41943.1	14q13.2	2013-01-28			ENSG00000198604	ENSG00000198604		"""Zinc fingers, PHD-type"""	960	protein-coding gene	gene with protein product		605680				10662543	Standard	NM_013448		Approved	hACF1, ACF1, WALp1, WCRF180	uc001wsk.3	Q9NRL2	OTTHUMG00000140216	ENST00000382422.2:c.4085A>G	14.37:g.35231121T>C	ENSP00000371859:p.Lys1362Arg	365.0	1.0		328.0	36.0	NM_013448	Q9NZ15|Q9P065|Q9UIG1|Q9Y3V3	Missense_Mutation	SNP	ENST00000382422.2	37	CCDS9651.1	.	.	.	.	.	.	.	.	.	.	.	11.48	1.650362	0.29336	.	.	ENSG00000198604	ENST00000358716;ENST00000382422;ENST00000360310;ENST00000543083	T;T;T	0.53206	0.63;0.63;0.63	6.04	-0.5	0.12012	.	0.372715	0.31092	N	0.008279	T	0.31544	0.0800	L	0.36672	1.1	0.42862	D	0.994114	B;B	0.10296	0.003;0.001	B;B	0.10450	0.005;0.002	T	0.03981	-1.0987	10	0.41790	T	0.15	.	6.6965	0.23201	0.0:0.2426:0.1131:0.6443	.	1330;1362	Q9NRL2-2;Q9NRL2	.;BAZ1A_HUMAN	R	1330;1362;1362;1014	ENSP00000351555:K1330R;ENSP00000371859:K1362R;ENSP00000353458:K1362R	ENSP00000351555:K1330R	K	-	2	0	BAZ1A	34300872	0.990000	0.36364	0.903000	0.35520	0.576000	0.36127	0.602000	0.24134	-0.308000	0.08792	-1.098000	0.02139	AAA	.		0.423	BAZ1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276646.1		
BMP5	653	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca;mdanderson.org	37	6	55620459	55620459	+	Missense_Mutation	SNP	G	G	C			TCGA-FV-A3R3-01A-11D-A22F-10	TCGA-FV-A3R3-10A-01D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c285c2fa-24b4-47a1-874d-86e74b002b05	64edddfd-f366-4d51-a8b4-a357b2c68e6c	g.chr6:55620459G>C	ENST00000370830.3	-	7	1935	c.1237C>G	c.(1237-1239)Cac>Gac	p.H413D	BMP5_ENST00000446683.2_Missense_Mutation_p.H376D	NM_021073.2	NP_066551.1	P22003	BMP5_HUMAN	bone morphogenetic protein 5	413					cartilage development (GO:0051216)|growth (GO:0040007)|male genitalia development (GO:0030539)|negative regulation of aldosterone biosynthetic process (GO:0032348)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cortisol biosynthetic process (GO:2000065)|negative regulation of epithelial to mesenchymal transition (GO:0010719)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|negative regulation of insulin-like growth factor receptor signaling pathway (GO:0043569)|negative regulation of mononuclear cell migration (GO:0071676)|negative regulation of steroid biosynthetic process (GO:0010894)|ossification (GO:0001503)|pattern specification process (GO:0007389)|positive regulation of dendrite development (GO:1900006)|positive regulation of DNA-dependent DNA replication (GO:2000105)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|skeletal system development (GO:0001501)|type B pancreatic cell development (GO:0003323)	extracellular space (GO:0005615)|membrane-bounded vesicle (GO:0031988)	BMP receptor binding (GO:0070700)			cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(6)|lung(19)|ovary(2)|prostate(1)|skin(7)|upper_aerodigestive_tract(1)	45	Lung NSC(77;0.0462)		LUSC - Lung squamous cell carcinoma(124;0.181)			TTTGGTACGTGGTCAGGAAAC	0.308																																					p.H413D		.											.	BMP5	516	0			c.C1237G						.						105.0	104.0	104.0					6																	55620459		2203	4299	6502	SO:0001583	missense	653	exon7			GTACGTGGTCAGG		CCDS4958.1	6p12.1	2014-01-30			ENSG00000112175	ENSG00000112175		"""Bone morphogenetic proteins"", ""Endogenous ligands"""	1072	protein-coding gene	gene with protein product		112265				1427904, 11580864	Standard	NM_021073		Approved		uc003pcq.3	P22003	OTTHUMG00000014903	ENST00000370830.3:c.1237C>G	6.37:g.55620459G>C	ENSP00000359866:p.His413Asp	242.0	0.0		266.0	20.0	NM_021073	B4E0Y4|Q9H547|Q9NTM5	Missense_Mutation	SNP	ENST00000370830.3	37	CCDS4958.1	.	.	.	.	.	.	.	.	.	.	G	9.080	0.998956	0.19121	.	.	ENSG00000112175	ENST00000370830;ENST00000446683	D;D	0.83335	-1.71;-1.71	5.73	5.73	0.89815	Transforming growth factor-beta, C-terminal (3);	0.045134	0.85682	D	0.000000	T	0.66376	0.2783	N	0.12182	0.205	0.48762	D	0.999708	B;B	0.29805	0.131;0.257	B;B	0.36030	0.145;0.216	T	0.65405	-0.6176	10	0.28530	T	0.3	.	20.2699	0.98469	0.0:0.0:1.0:0.0	.	376;413	B4E0Y4;P22003	.;BMP5_HUMAN	D	413;376	ENSP00000359866:H413D;ENSP00000391818:H376D	ENSP00000359866:H413D	H	-	1	0	BMP5	55728418	1.000000	0.71417	0.998000	0.56505	0.979000	0.70002	4.582000	0.60957	2.854000	0.98071	0.655000	0.94253	CAC	.		0.308	BMP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041000.1		
C9orf57	138240	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	9	74667237	74667237	+	Missense_Mutation	SNP	C	C	A			TCGA-FV-A3R3-01A-11D-A22F-10	TCGA-FV-A3R3-10A-01D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c285c2fa-24b4-47a1-874d-86e74b002b05	64edddfd-f366-4d51-a8b4-a357b2c68e6c	g.chr9:74667237C>A	ENST00000377024.3	-	5	556	c.461G>T	c.(460-462)tGc>tTc	p.C154F	C9orf57_ENST00000424431.2_Missense_Mutation_p.C120F	NM_001128618.1	NP_001122090.1	Q5W0N0	CI057_HUMAN	chromosome 9 open reading frame 57	154						integral component of membrane (GO:0016021)				endometrium(1)	1						AGAATGATTGCAGCAGTGAGT	0.428																																					p.C154F		.											.	.	.	0			c.G461T						.						223.0	190.0	200.0					9																	74667237		692	1591	2283	SO:0001583	missense	138240	exon5			TGATTGCAGCAGT	BC036255	CCDS47980.1	9q21.2	2012-03-15			ENSG00000204669	ENSG00000204669			27037	protein-coding gene	gene with protein product						12477932	Standard	NM_001128618		Approved		uc004aip.3	Q5W0N0	OTTHUMG00000020003	ENST00000377024.3:c.461G>T	9.37:g.74667237C>A	ENSP00000366223:p.Cys154Phe	86.0	0.0		79.0	13.0	NM_001128618	A1L456	Missense_Mutation	SNP	ENST00000377024.3	37	CCDS47980.1	.	.	.	.	.	.	.	.	.	.	C	12.54	1.968291	0.34754	.	.	ENSG00000204669	ENST00000377024;ENST00000424431	D;D	0.99158	-5.5;-5.5	4.66	4.66	0.58398	.	0.000000	0.37530	U	0.002041	D	0.98317	0.9442	N	0.24115	0.695	0.37319	D	0.909478	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	D	0.99871	1.1096	10	0.87932	D	0	-10.9597	13.226	0.59914	0.0:1.0:0.0:0.0	.	120;154	A1L456;Q5W0N0	.;CI057_HUMAN	F	154;120	ENSP00000366223:C154F;ENSP00000412956:C120F	ENSP00000366223:C154F	C	-	2	0	C9orf57	73857057	0.999000	0.42202	0.993000	0.49108	0.019000	0.09904	3.137000	0.50562	2.584000	0.87258	0.453000	0.30009	TGC	.		0.428	C9orf57-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052631.1	NM_001128618	
C9orf84	158401	broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	9	114462240	114462240	+	Silent	SNP	A	A	G			TCGA-FV-A3R3-01A-11D-A22F-10	TCGA-FV-A3R3-10A-01D-A22F-10	A	A	.	.	.	.	.	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c285c2fa-24b4-47a1-874d-86e74b002b05	64edddfd-f366-4d51-a8b4-a357b2c68e6c	g.chr9:114462240A>G	ENST00000318737.4	-	22	3113	c.2985T>C	c.(2983-2985)gaT>gaC	p.D995D	C9orf84_ENST00000394777.4_Silent_p.D921D|C9orf84_ENST00000374287.3_Silent_p.D995D|C9orf84_ENST00000394779.3_Silent_p.D956D	NM_173521.3	NP_775792.3	Q5VXU9	CI084_HUMAN	chromosome 9 open reading frame 84	995										breast(1)|cervix(1)|endometrium(3)|kidney(7)|large_intestine(10)|liver(1)|lung(7)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	35						ATACCTTTACATCCAGTTCTT	0.323																																					p.D995D		.											.	C9orf84	92	0			c.T2985C						.						101.0	105.0	104.0					9																	114462240		2203	4300	6503	SO:0001819	synonymous_variant	158401	exon22			CTTTACATCCAGT	AL833535	CCDS6781.3, CCDS43863.1	9q32	2012-03-16			ENSG00000165181	ENSG00000165181			26535	protein-coding gene	gene with protein product							Standard	XM_005251738		Approved	FLJ32779	uc004bfr.3	Q5VXU9	OTTHUMG00000020495	ENST00000318737.4:c.2985T>C	9.37:g.114462240A>G		61.0	0.0		48.0	13.0	NM_173521	A2A2V3|Q2M1H8|Q96M73	Silent	SNP	ENST00000318737.4	37	CCDS6781.3																																																																																			.		0.323	C9orf84-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000053656.2	NM_173521	
CCDC132	55610	broad.mit.edu;bcgsc.ca	37	7	92935295	92935295	+	Silent	SNP	A	A	G			TCGA-FV-A3R3-01A-11D-A22F-10	TCGA-FV-A3R3-10A-01D-A22F-10	A	A	.	.	.	.	.	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c285c2fa-24b4-47a1-874d-86e74b002b05	64edddfd-f366-4d51-a8b4-a357b2c68e6c	g.chr7:92935295A>G	ENST00000305866.5	+	18	1736	c.1608A>G	c.(1606-1608)gaA>gaG	p.E536E	CCDC132_ENST00000535481.1_Silent_p.E256E|CCDC132_ENST00000544910.1_Silent_p.E506E|CCDC132_ENST00000317751.6_Silent_p.E267E|CCDC132_ENST00000541136.1_Silent_p.E347E	NM_017667.3	NP_060137.2	Q96JG6	CC132_HUMAN	coiled-coil domain containing 132	536						extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)				endometrium(1)|large_intestine(2)|lung(5)	8	all_cancers(62;2.64e-11)|all_epithelial(64;1.4e-10)|Breast(17;0.000675)|Lung NSC(181;0.0618)|all_lung(186;0.0837)		STAD - Stomach adenocarcinoma(171;0.000302)			AAGAAACAGAAGATGTCTTAG	0.368																																					p.E536E		.											.	CCDC132	90	0			c.A1608G						.						135.0	124.0	127.0					7																	92935295		1872	4115	5987	SO:0001819	synonymous_variant	55610	exon18			AACAGAAGATGTC	AL833112, AK055965, AL832393	CCDS5630.1, CCDS43617.1, CCDS59065.1	7q21.3	2007-07-23			ENSG00000004766	ENSG00000004766			25956	protein-coding gene	gene with protein product						11347906	Standard	NM_024553		Approved	KIAA1861, FLJ20097, DKFZp313I2429	uc003umo.4	Q96JG6	OTTHUMG00000131733	ENST00000305866.5:c.1608A>G	7.37:g.92935295A>G		83.0	0.0		71.0	4.0	NM_017667	B3KX22|D1MQ00|F5H5U7|Q75N07|Q8WVK3|Q9H5C6	Silent	SNP	ENST00000305866.5	37	CCDS43617.1	.	.	.	.	.	.	.	.	.	.	A	8.923	0.961439	0.18583	.	.	ENSG00000004766	ENST00000458707	.	.	.	5.6	3.22	0.36961	.	.	.	.	.	T	0.57257	0.2041	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.50311	-0.8843	4	.	.	.	0.1222	7.8583	0.29495	0.7617:0.0:0.2383:0.0	.	.	.	.	R	323	.	.	K	+	2	0	CCDC132	92773231	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	1.126000	0.31344	0.490000	0.27771	0.528000	0.53228	AAG	.		0.368	CCDC132-019	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341687.1	NM_017667	
CFB	629	broad.mit.edu;bcgsc.ca	37	6	31917266	31917266	+	Missense_Mutation	SNP	A	A	G			TCGA-FV-A3R3-01A-11D-A22F-10	TCGA-FV-A3R3-10A-01D-A22F-10	A	A	.	.	.	.	.	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c285c2fa-24b4-47a1-874d-86e74b002b05	64edddfd-f366-4d51-a8b4-a357b2c68e6c	g.chr6:31917266A>G	ENST00000425368.2	+	10	1853	c.1340A>G	c.(1339-1341)gAc>gGc	p.D447G	CFB_ENST00000477310.1_Missense_Mutation_p.D798G|CFB_ENST00000556679.1_Missense_Mutation_p.D949G|CFB_ENST00000456570.1_Missense_Mutation_p.D949G|CFB_ENST00000497841.1_3'UTR	NM_001710.5	NP_001701.2	P00751	CFAB_HUMAN	complement factor B	447	VWFA. {ECO:0000255|PROSITE- ProRule:PRU00219}.				complement activation (GO:0006956)|complement activation, alternative pathway (GO:0006957)|innate immune response (GO:0045087)|regulation of complement activation (GO:0030449)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	complement binding (GO:0001848)|serine-type endopeptidase activity (GO:0004252)			NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(10)|pancreas(1)|skin(1)|urinary_tract(1)	21						TCCAAGAAAGACAATGAGCAA	0.428																																					p.D447G		.											.	CFB	91	0			c.A1340G						.						78.0	78.0	78.0					6																	31917266		1511	2709	4220	SO:0001583	missense	629	exon10			AGAAAGACAATGA	L15702	CCDS4729.1	6p21.33	2014-09-17	2006-02-10	2006-02-10	ENSG00000243649	ENSG00000243649	3.4.21.47	"""Complement system"""	1037	protein-coding gene	gene with protein product		138470	"""B-factor, properdin"""	BFD, BF			Standard	NM_001710		Approved	H2-Bf	uc011dor.2	P00751	OTTHUMG00000031198	ENST00000425368.2:c.1340A>G	6.37:g.31917266A>G	ENSP00000416561:p.Asp447Gly	101.0	0.0		75.0	5.0	NM_001710	B0QZQ6|O15006|Q29944|Q53F89|Q5JP67|Q5ST50|Q96HX6|Q9BTF5|Q9BX92	Missense_Mutation	SNP	ENST00000425368.2	37	CCDS4729.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	22.9|22.9	4.354959|4.354959	0.82243|0.82243	.|.	.|.	ENSG00000243649;ENSG00000243649;ENSG00000244255;ENSG00000244255|ENSG00000243649	ENST00000556679;ENST00000425368;ENST00000456570;ENST00000477310|ENST00000483004	D;D;D;D|.	0.83914|.	-1.78;-1.78;-1.78;-1.78|.	5.95|5.95	4.81|4.81	0.61882|0.61882	von Willebrand factor, type A (3);|.	0.325836|.	0.26658|.	N|.	0.023168|.	T|T	0.44350|0.44350	0.1289|0.1289	L|L	0.60455|0.60455	1.87|1.87	0.35605|0.35605	D|D	0.808214|0.808214	D;B;P|.	0.56968|.	0.978;0.297;0.833|.	P;B;P|.	0.57548|.	0.823;0.371;0.452|.	T|T	0.49771|0.49771	-0.8904|-0.8904	10|5	0.46703|.	T|.	0.11|.	-13.9122|-13.9122	7.9868|7.9868	0.30216|0.30216	0.9114:0.0:0.0886:0.0|0.9114:0.0:0.0886:0.0	.|.	949;447;447|.	B4E1Z4;P00751;P00751-2|.	.;CFAB_HUMAN;.|.	G|A	949;447;949;798|60	ENSP00000451848:D949G;ENSP00000416561:D447G;ENSP00000410815:D949G;ENSP00000418996:D798G|.	ENSP00000416561:D447G|.	D|T	+|+	2|1	0|0	CFB;XXbac-BPG116M5.17|CFB	32025245|32025245	0.659000|0.659000	0.27411|0.27411	0.797000|0.797000	0.32132|0.32132	0.991000|0.991000	0.79684|0.79684	1.878000|1.878000	0.39608|0.39608	2.279000|2.279000	0.76181|0.76181	0.533000|0.533000	0.62120|0.62120	GAC|ACA	.		0.428	CFB-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000076395.3	NM_001710	
CHL1	10752	broad.mit.edu;bcgsc.ca	37	3	425546	425546	+	Missense_Mutation	SNP	A	A	G			TCGA-FV-A3R3-01A-11D-A22F-10	TCGA-FV-A3R3-10A-01D-A22F-10	A	A	.	.	.	.	.	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c285c2fa-24b4-47a1-874d-86e74b002b05	64edddfd-f366-4d51-a8b4-a357b2c68e6c	g.chr3:425546A>G	ENST00000256509.2	+	19	2866	c.2224A>G	c.(2224-2226)Aag>Gag	p.K742E	CHL1-AS1_ENST00000417612.1_RNA|CHL1_ENST00000397491.2_Missense_Mutation_p.K726E	NM_001253387.1|NM_001253388.1|NM_006614.3	NP_001240316.1|NP_001240317.1|NP_006605.2	Q96FC9	DDX11_HUMAN	cell adhesion molecule L1-like	0					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|ATP catabolic process (GO:0006200)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|sister chromatid cohesion (GO:0007062)|viral process (GO:0016032)	midbody (GO:0030496)|nuclear chromatin (GO:0000790)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle pole (GO:0000922)	4 iron, 4 sulfur cluster binding (GO:0051539)|ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|DNA-dependent ATPase activity (GO:0008094)|double-stranded DNA binding (GO:0003690)|helicase activity (GO:0004386)|metal ion binding (GO:0046872)|RNA binding (GO:0003723)|single-stranded DNA binding (GO:0003697)			NS(1)|central_nervous_system(5)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(25)|lung(31)|ovary(1)|prostate(4)|skin(10)|stomach(1)	93		all_cancers(2;1.14e-06)|all_epithelial(2;0.00367)|all_lung(1;0.061)|Lung NSC(2;0.201)		Epithelial(13;5.36e-06)|all cancers(10;1.4e-05)|OV - Ovarian serous cystadenocarcinoma(96;0.00323)|COAD - Colon adenocarcinoma(1;0.00925)|Colorectal(20;0.0198)		CTCTCAACCCAAGGAAATGAT	0.343																																					p.K742E		.											.	CHL1	583	0			c.A2224G						.						149.0	149.0	149.0					3																	425546		2203	4299	6502	SO:0001583	missense	10752	exon17			CAACCCAAGGAAA	AF002246	CCDS2556.1, CCDS58812.1, CCDS74887.1	3p26	2013-05-01	2013-05-01		ENSG00000134121	ENSG00000134121		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	1939	protein-coding gene	gene with protein product	"""neural cell adhesion molecule"", ""close homolog of L1"""	607416	"""cell adhesion molecule with homology to L1CAM (close homologue of L1)"", ""cell adhesion molecule with homology to L1CAM (close homolog of L1)"""			9799093	Standard	NM_006614		Approved	CALL, L1CAM2, FLJ44930, MGC132578	uc003bot.3	O00533	OTTHUMG00000090601	ENST00000256509.2:c.2224A>G	3.37:g.425546A>G	ENSP00000256509:p.Lys742Glu	133.0	0.0		97.0	9.0	NM_001253388	Q13333|Q86VQ4|Q86W62|Q92498|Q92770|Q92998|Q92999	Missense_Mutation	SNP	ENST00000256509.2	37	CCDS2556.1	.	.	.	.	.	.	.	.	.	.	A	11.09	1.537280	0.27475	.	.	ENSG00000134121	ENST00000256509;ENST00000397491	T;T	0.56776	0.44;0.44	4.67	4.67	0.58626	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.187320	0.46758	D	0.000278	T	0.42675	0.1213	N	0.14661	0.345	0.30987	N	0.721862	B;B;B	0.33637	0.032;0.032;0.42	B;B;B	0.43052	0.058;0.058;0.406	T	0.54669	-0.8259	10	0.72032	D	0.01	.	10.3306	0.43820	0.6944:0.3056:0.0:0.0	.	726;726;742	B3KX75;O00533;O00533-2	.;CHL1_HUMAN;.	E	742;726	ENSP00000256509:K742E;ENSP00000380628:K726E	ENSP00000256509:K742E	K	+	1	0	CHL1	400546	1.000000	0.71417	1.000000	0.80357	0.525000	0.34531	2.525000	0.45598	1.862000	0.54008	0.454000	0.30748	AAG	.		0.343	CHL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207155.2	NM_006614	
CLGN	1047	broad.mit.edu;bcgsc.ca	37	4	141313503	141313503	+	Silent	SNP	T	T	C			TCGA-FV-A3R3-01A-11D-A22F-10	TCGA-FV-A3R3-10A-01D-A22F-10	T	T	.	.	.	.	.	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c285c2fa-24b4-47a1-874d-86e74b002b05	64edddfd-f366-4d51-a8b4-a357b2c68e6c	g.chr4:141313503T>C	ENST00000325617.5	-	13	1961	c.1521A>G	c.(1519-1521)aaA>aaG	p.K507K	CLGN_ENST00000414773.1_Silent_p.K507K|CLGN_ENST00000537281.1_Silent_p.K507K	NM_004362.2	NP_004353.1	O14967	CLGN_HUMAN	calmegin	507					binding of sperm to zona pellucida (GO:0007339)|protein complex assembly (GO:0006461)|protein folding (GO:0006457)|single fertilization (GO:0007338)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|nuclear envelope (GO:0005635)	calcium ion binding (GO:0005509)|unfolded protein binding (GO:0051082)			breast(2)|endometrium(3)|kidney(1)|large_intestine(2)|liver(2)|lung(5)|ovary(2)|prostate(3)|skin(4)|urinary_tract(1)	25	all_hematologic(180;0.162)					ATATGTCGGTTTTTTTATACT	0.328																																					p.K507K		.											.	CLGN	93	0			c.A1521G						.						125.0	119.0	121.0					4																	141313503		2203	4300	6503	SO:0001819	synonymous_variant	1047	exon14			GTCGGTTTTTTTA	D86322	CCDS3751.1	4q28.3-q31.1	2008-02-05			ENSG00000153132	ENSG00000153132			2060	protein-coding gene	gene with protein product		601858					Standard	NM_004362		Approved		uc003iii.3	O14967	OTTHUMG00000133414	ENST00000325617.5:c.1521A>G	4.37:g.141313503T>C		264.0	1.0		243.0	12.0	NM_001130675	B3KS90|B4DXV8|D3DNY8	Silent	SNP	ENST00000325617.5	37	CCDS3751.1																																																																																			.		0.328	CLGN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257272.2	NM_004362	
COL5A1	1289	broad.mit.edu;bcgsc.ca	37	9	137674544	137674544	+	Missense_Mutation	SNP	A	A	G			TCGA-FV-A3R3-01A-11D-A22F-10	TCGA-FV-A3R3-10A-01D-A22F-10	A	A	.	.	.	.	.	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c285c2fa-24b4-47a1-874d-86e74b002b05	64edddfd-f366-4d51-a8b4-a357b2c68e6c	g.chr9:137674544A>G	ENST00000371817.3	+	29	2876	c.2462A>G	c.(2461-2463)gAc>gGc	p.D821G		NM_000093.3|NM_001278074.1	NP_000084.3|NP_001265003.1	P20908	CO5A1_HUMAN	collagen, type V, alpha 1	821	Triple-helical region.				axon guidance (GO:0007411)|blood vessel development (GO:0001568)|cell adhesion (GO:0007155)|cell migration (GO:0016477)|collagen biosynthetic process (GO:0032964)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular fibril organization (GO:0043206)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|eye morphogenesis (GO:0048592)|heart morphogenesis (GO:0003007)|integrin biosynthetic process (GO:0045112)|negative regulation of endodermal cell differentiation (GO:1903225)|regulation of cellular component organization (GO:0051128)|skin development (GO:0043588)|tendon development (GO:0035989)|wound healing, spreading of epidermal cells (GO:0035313)	basement membrane (GO:0005604)|collagen type V trimer (GO:0005588)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	extracellular matrix structural constituent (GO:0005201)|heparin binding (GO:0008201)|integrin binding (GO:0005178)|metal ion binding (GO:0046872)|platelet-derived growth factor binding (GO:0048407)|proteoglycan binding (GO:0043394)			NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(26)|liver(2)|lung(36)|ovary(4)|pancreas(4)|prostate(5)|skin(10)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(4)	115		Myeloproliferative disorder(178;0.0341)		all cancers(34;2.28e-08)|OV - Ovarian serous cystadenocarcinoma(145;6.03e-08)|Epithelial(140;6.4e-08)|GBM - Glioblastoma multiforme(294;0.131)		TTTAAAGGAGACATGGGCATC	0.597																																					p.D821G		.											.	COL5A1	524	0			c.A2462G						.						234.0	227.0	230.0					9																	137674544		2203	4300	6503	SO:0001583	missense	1289	exon29			AAGGAGACATGGG	D90279	CCDS6982.1, CCDS75932.1	9q34.2-q34.3	2014-09-17			ENSG00000130635	ENSG00000130635		"""Collagens"""	2209	protein-coding gene	gene with protein product	"""alpha 1 type V collagen"""	120215				1572660	Standard	NM_001278074		Approved		uc031tfl.1	P20908	OTTHUMG00000020891	ENST00000371817.3:c.2462A>G	9.37:g.137674544A>G	ENSP00000360882:p.Asp821Gly	102.0	0.0		78.0	4.0	NM_000093	Q15094|Q5SUX4	Missense_Mutation	SNP	ENST00000371817.3	37	CCDS6982.1	.	.	.	.	.	.	.	.	.	.	A	22.6	4.308577	0.81247	.	.	ENSG00000130635	ENST00000371817	D	0.93426	-3.22	4.18	4.18	0.49190	.	0.000000	0.85682	U	0.000000	D	0.95166	0.8433	L	0.55990	1.75	0.58432	D	0.999999	D	0.69078	0.997	D	0.83275	0.996	D	0.95409	0.8496	10	0.87932	D	0	.	12.522	0.56065	1.0:0.0:0.0:0.0	.	821	P20908	CO5A1_HUMAN	G	821	ENSP00000360882:D821G	ENSP00000360882:D821G	D	+	2	0	COL5A1	136814365	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.887000	0.87295	1.673000	0.50895	0.460000	0.39030	GAC	.		0.597	COL5A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054954.2	NM_000093	
COQ6	51004	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	14	74422552	74422552	+	Missense_Mutation	SNP	T	T	G			TCGA-FV-A3R3-01A-11D-A22F-10	TCGA-FV-A3R3-10A-01D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c285c2fa-24b4-47a1-874d-86e74b002b05	64edddfd-f366-4d51-a8b4-a357b2c68e6c	g.chr14:74422552T>G	ENST00000334571.2	+	4	442	c.402T>G	c.(400-402)gaT>gaG	p.D134E	COQ6_ENST00000238709.4_Missense_Mutation_p.D59E|COQ6_ENST00000394026.4_Missense_Mutation_p.D109E|COQ6_ENST00000555552.1_3'UTR|COQ6_ENST00000554920.1_Missense_Mutation_p.D134E	NM_182476.2	NP_872282.1	Q9Y2Z9	COQ6_HUMAN	coenzyme Q6 monooxygenase	134					small molecule metabolic process (GO:0044281)|ubiquinone biosynthetic process (GO:0006744)	cell projection (GO:0042995)|Golgi apparatus (GO:0005794)|mitochondrion (GO:0005739)	flavin adenine dinucleotide binding (GO:0050660)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen (GO:0016709)			breast(1)|endometrium(6)|kidney(1)|large_intestine(3)|lung(3)|prostate(1)|upper_aerodigestive_tract(1)	16				BRCA - Breast invasive adenocarcinoma(234;0.00337)		TTGATAAGGATAATTTAGATG	0.468																																					p.D134E		.											.	COQ6	90	0			c.T402G						.						185.0	174.0	178.0					14																	74422552		2203	4300	6503	SO:0001583	missense	51004	exon4			TAAGGATAATTTA	AF132944	CCDS9823.1, CCDS9824.1, CCDS9824.2	14q24.1	2013-05-01	2013-05-01		ENSG00000119723	ENSG00000119723			20233	protein-coding gene	gene with protein product		614647	"""coenzyme Q6 homolog (yeast)"", ""coenzyme Q6 homolog, monooxygenase (yeast)"", ""coenzyme Q6 homolog, monooxygenase (S. cerevisiae)"""			21540551	Standard	NM_182476		Approved	CGI-10	uc001xph.3	Q9Y2Z9	OTTHUMG00000171260	ENST00000334571.2:c.402T>G	14.37:g.74422552T>G	ENSP00000333946:p.Asp134Glu	122.0	0.0		91.0	17.0	NM_182476	B7Z3K8|Q53GG6|Q86U30|Q96CA1|Q96CK2	Missense_Mutation	SNP	ENST00000334571.2	37	CCDS9823.1	.	.	.	.	.	.	.	.	.	.	T	15.15	2.747178	0.49257	.	.	ENSG00000119723	ENST00000394026;ENST00000555376;ENST00000238709;ENST00000553462;ENST00000334571;ENST00000556300;ENST00000554153;ENST00000557584;ENST00000554920;ENST00000557205;ENST00000554320;ENST00000555392	T;T;T;T	0.41400	1.0;1.0;1.0;1.0	5.51	-1.29	0.09288	.	0.283457	0.44285	N	0.000467	T	0.17916	0.0430	N	0.12663	0.25	0.45962	D	0.998787	B;B;B;B;B;B;B;B	0.29988	0.264;0.036;0.234;0.012;0.0;0.036;0.019;0.001	B;B;B;B;B;B;B;B	0.28465	0.057;0.086;0.09;0.004;0.002;0.023;0.015;0.002	T	0.06215	-1.0839	10	0.20519	T	0.43	-1.5003	6.1558	0.20335	0.0:0.2834:0.1231:0.5935	.	79;134;79;109;134;59;59;59	B7Z8E9;B7Z357;B7Z262;B7Z3K8;Q9Y2Z9;G3V3A1;G3XA86;Q86U30	.;.;.;.;COQ6_HUMAN;.;.;.	E	109;59;59;59;134;134;79;79;134;79;59;59	ENSP00000377594:D109E;ENSP00000238709:D59E;ENSP00000333946:D134E;ENSP00000451123:D59E	ENSP00000238709:D59E	D	+	3	2	COQ6	73492305	0.360000	0.24964	0.743000	0.31040	0.968000	0.65278	-0.499000	0.06413	-0.346000	0.08312	0.459000	0.35465	GAT	.		0.468	COQ6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412616.1		
COX18	285521	broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	4	73923971	73923971	+	Missense_Mutation	SNP	C	C	A	rs201251329		TCGA-FV-A3R3-01A-11D-A22F-10	TCGA-FV-A3R3-10A-01D-A22F-10	C	C	.	.	.	.	.	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c285c2fa-24b4-47a1-874d-86e74b002b05	64edddfd-f366-4d51-a8b4-a357b2c68e6c	g.chr4:73923971C>A	ENST00000295890.4	-	6	953	c.862G>T	c.(862-864)Gtg>Ttg	p.V288L	COX18_ENST00000507544.2_Missense_Mutation_p.V289L	NM_173827.2	NP_776188.1	Q8N8Q8	COX18_HUMAN	COX18 cytochrome C oxidase assembly factor	288					protein insertion into mitochondrial membrane (GO:0051204)|protein transport (GO:0015031)|respiratory chain complex IV assembly (GO:0008535)	integral component of mitochondrial inner membrane (GO:0031305)	protein transporter activity (GO:0008565)			large_intestine(4)|lung(2)	6	Breast(15;0.00096)		Epithelial(6;1.26e-06)|OV - Ovarian serous cystadenocarcinoma(6;9.45e-06)|all cancers(17;2.05e-05)|Lung(101;0.103)|LUSC - Lung squamous cell carcinoma(112;0.154)			GAAAGGCCCACGAAGCTGGAG	0.408																																					p.V288L		.											.	COX18	90	0			c.G862T						.						98.0	97.0	97.0					4																	73923971		2203	4300	6503	SO:0001583	missense	285521	exon6			GGCCCACGAAGCT	AY957564	CCDS3554.1, CCDS75139.1	4q13.3	2013-06-12	2013-06-12		ENSG00000163626	ENSG00000163626		"""Mitochondrial respiratory chain complex assembly factors"""	26801	protein-coding gene	gene with protein product		610428	"""COX18 cytochrome c oxidase assembly homolog (S. cerevisiae)"", ""cytochrome c oxidase assembly homolog 18 (yeast)"""			16212937, 16911509	Standard	XM_005265679		Approved	FLJ38991	uc003hgm.1	Q8N8Q8	OTTHUMG00000129917	ENST00000295890.4:c.862G>T	4.37:g.73923971C>A	ENSP00000295890:p.Val288Leu	123.0	1.0		129.0	36.0	NM_173827	Q2PB66|Q2PB67|Q2PB68|Q49B97|Q6IPP9	Missense_Mutation	SNP	ENST00000295890.4	37	CCDS3554.1	.	.	.	.	.	.	.	.	.	.	C	7.047	0.563613	0.13498	.	.	ENSG00000163626	ENST00000295890;ENST00000507544	.	.	.	5.36	1.42	0.22433	.	0.461691	0.26951	N	0.021671	T	0.12390	0.0301	N	0.03967	-0.31	0.26176	N	0.979794	B;B	0.02656	0.0;0.0	B;B	0.11329	0.006;0.001	T	0.09378	-1.0677	9	0.34782	T	0.22	-15.0659	1.6981	0.02866	0.1421:0.1699:0.1316:0.5565	.	289;288	B7ZL88;Q8N8Q8	.;COX18_HUMAN	L	288;289	.	ENSP00000295890:V288L	V	-	1	0	COX18	74142835	1.000000	0.71417	1.000000	0.80357	0.621000	0.37620	0.783000	0.26802	0.868000	0.35678	-0.247000	0.11927	GTG	C|0.999;T|0.001		0.408	COX18-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000252169.2	NM_173827	
CRY1	1407	broad.mit.edu;bcgsc.ca	37	12	107486610	107486610	+	Missense_Mutation	SNP	A	A	G			TCGA-FV-A3R3-01A-11D-A22F-10	TCGA-FV-A3R3-10A-01D-A22F-10	A	A	.	.	.	.	.	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c285c2fa-24b4-47a1-874d-86e74b002b05	64edddfd-f366-4d51-a8b4-a357b2c68e6c	g.chr12:107486610A>G	ENST00000008527.5	-	1	997	c.130T>C	c.(130-132)Tcc>Ccc	p.S44P	RP11-797M17.1_ENST00000547679.1_RNA|CRY1_ENST00000550633.1_5'UTR	NM_004075.4	NP_004066.1	Q16526	CRY1_HUMAN	cryptochrome circadian clock 1	44	Photolyase/cryptochrome alpha/beta.				blue light signaling pathway (GO:0009785)|circadian regulation of gene expression (GO:0032922)|DNA damage induced protein phosphorylation (GO:0006975)|DNA repair (GO:0006281)|entrainment of circadian clock by photoperiod (GO:0043153)|gluconeogenesis (GO:0006094)|glucose homeostasis (GO:0042593)|lipid storage (GO:0019915)|negative regulation of circadian rhythm (GO:0042754)|negative regulation of G-protein coupled receptor protein signaling pathway (GO:0045744)|negative regulation of glucocorticoid receptor signaling pathway (GO:2000323)|negative regulation of glucocorticoid secretion (GO:2000850)|negative regulation of protein ubiquitination (GO:0031397)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|protein-chromophore linkage (GO:0018298)|regulation of circadian rhythm (GO:0042752)|regulation of DNA damage checkpoint (GO:2000001)|response to glucagon (GO:0033762)|response to insulin (GO:0032868)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)	blue light photoreceptor activity (GO:0009882)|core promoter binding (GO:0001047)|DNA binding (GO:0003677)|DNA photolyase activity (GO:0003913)|double-stranded DNA binding (GO:0003690)|nuclear hormone receptor binding (GO:0035257)|nucleotide binding (GO:0000166)|phosphatase binding (GO:0019902)|transcription factor binding transcription factor activity (GO:0000989)|ubiquitin binding (GO:0043130)			NS(2)|breast(2)|central_nervous_system(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(11)|ovary(3)|skin(1)	29						ACATTGGAGGAGCCGGCGAAC	0.577											OREG0022082	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.S44P		.											.	CRY1	93	0			c.T130C						.						34.0	31.0	32.0					12																	107486610		2201	4300	6501	SO:0001583	missense	1407	exon1			TGGAGGAGCCGGC	BC030519	CCDS9112.1	12q23-q24.1	2014-01-17	2014-01-17		ENSG00000008405	ENSG00000008405			2384	protein-coding gene	gene with protein product		601933	"""cryptochrome 1 (photolyase-like)"""	PHLL1		8921389	Standard	NM_004075		Approved		uc001tmi.4	Q16526	OTTHUMG00000170005	ENST00000008527.5:c.130T>C	12.37:g.107486610A>G	ENSP00000008527:p.Ser44Pro	82.0	0.0	1405	75.0	6.0	NM_004075		Missense_Mutation	SNP	ENST00000008527.5	37	CCDS9112.1	.	.	.	.	.	.	.	.	.	.	A	16.12	3.033234	0.54896	.	.	ENSG00000008405	ENST00000008527	.	.	.	5.71	5.71	0.89125	Rossmann-like alpha/beta/alpha sandwich fold (1);DNA photolyase, N-terminal (2);	0.000000	0.85682	D	0.000000	T	0.57431	0.2053	L	0.45744	1.44	0.80722	D	1	B	0.14438	0.01	B	0.21151	0.033	T	0.52660	-0.8546	9	0.33940	T	0.23	-12.4453	15.6457	0.77049	1.0:0.0:0.0:0.0	.	44	Q16526	CRY1_HUMAN	P	44	.	ENSP00000008527:S44P	S	-	1	0	CRY1	106010740	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	4.724000	0.61972	2.174000	0.68829	0.459000	0.35465	TCC	.		0.577	CRY1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406827.1	NM_004075	
DAZAP1	26528	broad.mit.edu;mdanderson.org	37	19	1434862	1434862	+	Missense_Mutation	SNP	G	G	A			TCGA-FV-A3R3-01A-11D-A22F-10	TCGA-FV-A3R3-10A-01D-A22F-10	G	G	.	.	.	.	.	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c285c2fa-24b4-47a1-874d-86e74b002b05	64edddfd-f366-4d51-a8b4-a357b2c68e6c	g.chr19:1434862G>A	ENST00000233078.4	+	12	1336	c.1175G>A	c.(1174-1176)gGa>gAa	p.G392E	DAZAP1_ENST00000336761.6_3'UTR	NM_018959.2	NP_061832.2	Q96EP5	DAZP1_HUMAN	DAZ associated protein 1	392					cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|maternal placenta development (GO:0001893)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|RNA stem-loop binding (GO:0035613)			breast(2)|endometrium(2)|large_intestine(1)|lung(3)|upper_aerodigestive_tract(1)	9		Acute lymphoblastic leukemia(61;3.02e-13)|all_hematologic(61;4.32e-09)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		AGCGGCTTTGGACGAGGGCAG	0.697																																					p.G392E		.											.	DAZAP1	153	0			c.G1175A						.						12.0	15.0	14.0					19																	1434862		2192	4279	6471	SO:0001583	missense	26528	exon12			GCTTTGGACGAGG		CCDS12065.1, CCDS12066.1	19p13.3	2013-07-16			ENSG00000071626	ENSG00000071626		"""RNA binding motif (RRM) containing"""	2683	protein-coding gene	gene with protein product	"""deleted in azoospermia associated protein 1"""	607430				10857750, 23658607	Standard	XM_005259530		Approved	MGC19907	uc002lsn.3	Q96EP5		ENST00000233078.4:c.1175G>A	19.37:g.1434862G>A	ENSP00000233078:p.Gly392Glu	23.0	0.0		24.0	10.0	NM_018959	Q96MJ3|Q9NRR9	Missense_Mutation	SNP	ENST00000233078.4	37	CCDS12065.1	.	.	.	.	.	.	.	.	.	.	G	22.0	4.233204	0.79688	.	.	ENSG00000071626	ENST00000233078	T	0.37584	1.19	5.26	5.26	0.73747	.	0.000000	0.85682	D	0.000000	T	0.48466	0.1501	N	0.24115	0.695	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.998;0.998;0.999	T	0.53606	-0.8415	10	0.87932	D	0	.	17.8389	0.88709	0.0:0.0:1.0:0.0	.	459;392;158	Q5IRN4;Q96EP5;B3KS63	.;DAZP1_HUMAN;.	E	392	ENSP00000233078:G392E	ENSP00000233078:G392E	G	+	2	0	DAZAP1	1385862	1.000000	0.71417	0.998000	0.56505	0.968000	0.65278	9.407000	0.97325	2.454000	0.82982	0.561000	0.74099	GGA	.		0.697	DAZAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449522.3	NM_170711	
DENND4A	10260	broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	15	65962395	65962395	+	Missense_Mutation	SNP	T	T	A			TCGA-FV-A3R3-01A-11D-A22F-10	TCGA-FV-A3R3-10A-01D-A22F-10	T	T	.	.	.	.	.	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c285c2fa-24b4-47a1-874d-86e74b002b05	64edddfd-f366-4d51-a8b4-a357b2c68e6c	g.chr15:65962395T>A	ENST00000431932.2	-	25	4672	c.4464A>T	c.(4462-4464)ttA>ttT	p.L1488F	DENND4A_ENST00000443035.3_Missense_Mutation_p.L1531F	NM_005848.3	NP_005839.3	Q7Z401	MYCPP_HUMAN	DENN/MADD domain containing 4A	1488					positive regulation of Rab GTPase activity (GO:0032851)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|Rab guanyl-nucleotide exchange factor activity (GO:0017112)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(17)|lung(11)|ovary(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	51						TCAGAAAGGGTAAGAAGATAT	0.363																																					p.L1531F		.											.	DENND4A	229	0			c.A4593T						.						66.0	65.0	65.0					15																	65962395		1842	4098	5940	SO:0001583	missense	10260	exon26			AAAGGGTAAGAAG	AF534403	CCDS45285.1, CCDS53949.1	15q22.31	2012-10-03	2006-01-27	2006-01-27				"""DENN/MADD domain containing"""	24321	protein-coding gene	gene with protein product		600382	"""c-myc promoter binding protein"""	MYCPBP		8056341, 12906859	Standard	NM_005848		Approved	IRLB	uc002api.3	Q7Z401		ENST00000431932.2:c.4464A>T	15.37:g.65962395T>A	ENSP00000396830:p.Leu1488Phe	103.0	1.0		89.0	9.0	NM_001144823	E7EPL3|Q14655|Q86T77|Q8IVX2|Q8NB93	Missense_Mutation	SNP	ENST00000431932.2	37	CCDS45285.1	.	.	.	.	.	.	.	.	.	.	T	19.72	3.879443	0.72294	.	.	ENSG00000174485	ENST00000443035;ENST00000431932	T;T	0.10005	2.98;2.92	5.94	-3.01	0.05463	.	0.065034	0.64402	D	0.000006	T	0.25531	0.0621	M	0.74647	2.275	0.58432	D	0.999997	D;D	0.89917	1.0;0.999	D;D	0.85130	0.996;0.997	T	0.01553	-1.1326	10	0.72032	D	0.01	.	9.5506	0.39308	0.1121:0.6924:0.0:0.1955	.	1531;1488	E7EPL3;Q7Z401	.;MYCPP_HUMAN	F	1531;1488	ENSP00000391167:L1531F;ENSP00000396830:L1488F	ENSP00000396830:L1488F	L	-	3	2	DENND4A	63749449	1.000000	0.71417	0.971000	0.41717	0.812000	0.45895	1.136000	0.31467	-0.506000	0.06558	-0.248000	0.11899	TTA	.		0.363	DENND4A-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419611.1	NM_005848	
DHX35	60625	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca;mdanderson.org	37	20	37621023	37621023	+	Silent	SNP	C	C	T	rs549854740		TCGA-FV-A3R3-01A-11D-A22F-10	TCGA-FV-A3R3-10A-01D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c285c2fa-24b4-47a1-874d-86e74b002b05	64edddfd-f366-4d51-a8b4-a357b2c68e6c	g.chr20:37621023C>T	ENST00000252011.3	+	7	570	c.537C>T	c.(535-537)caC>caT	p.H179H	DHX35_ENST00000373323.4_Silent_p.H148H|DHX35_ENST00000373325.2_Silent_p.H179H	NM_021931.3	NP_068750.2	Q9H5Z1	DHX35_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 35	179	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				mRNA splicing, via spliceosome (GO:0000398)	catalytic step 2 spliceosome (GO:0071013)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|nucleic acid binding (GO:0003676)			breast(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(6)|lung(13)|ovary(1)|skin(2)|stomach(1)|urinary_tract(2)	40		Myeloproliferative disorder(115;0.00878)				ATGAAGCCCACGAGAGGACCT	0.413													C|||	1	0.000199681	0.0	0.0	5008	,	,		19396	0.0		0.0	False		,,,				2504	0.001				p.H179H		.											.	DHX35	226	0			c.C537T						.						223.0	199.0	207.0					20																	37621023		2203	4300	6503	SO:0001819	synonymous_variant	60625	exon7			AGCCCACGAGAGG	AK026412	CCDS13310.1, CCDS54463.1	20q11.22-q12	2003-06-13	2003-06-13	2003-06-13	ENSG00000101452	ENSG00000101452		"""DEAH-boxes"""	15861	protein-coding gene	gene with protein product			"""DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 35"""	C20orf15, DDX35			Standard	NM_001190809		Approved	FLJ22759, KAIA0875	uc002xjh.3	Q9H5Z1	OTTHUMG00000032463	ENST00000252011.3:c.537C>T	20.37:g.37621023C>T		138.0	0.0		130.0	11.0	NM_021931	A2RTX3|B4E0J0|F5GXM6|Q5THR0|Q9H4H7|Q9H6T6	Silent	SNP	ENST00000252011.3	37	CCDS13310.1																																																																																			.		0.413	DHX35-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079212.2	NM_021931	
DHX37	57647	broad.mit.edu;ucsc.edu;bcgsc.ca	37	12	125455935	125455935	+	Silent	SNP	C	C	G			TCGA-FV-A3R3-01A-11D-A22F-10	TCGA-FV-A3R3-10A-01D-A22F-10	C	C	.	.	.	.	.	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c285c2fa-24b4-47a1-874d-86e74b002b05	64edddfd-f366-4d51-a8b4-a357b2c68e6c	g.chr12:125455935C>G	ENST00000308736.2	-	8	1202	c.1104G>C	c.(1102-1104)gtG>gtC	p.V368V	DHX37_ENST00000544745.1_Silent_p.V155V	NM_032656.3	NP_116045.2	Q8IY37	DHX37_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 37	368	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.						ATP binding (GO:0005524)|helicase activity (GO:0004386)|nucleic acid binding (GO:0003676)			breast(5)|cervix(1)|endometrium(9)|kidney(5)|large_intestine(11)|liver(1)|lung(27)|ovary(1)|prostate(2)|skin(3)	65	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;8.05e-05)|Epithelial(86;0.000486)|all cancers(50;0.00653)		CGATGATCACCACCTTGTACC	0.647																																					p.V368V		.											.	DHX37	227	0			c.G1104C						.						71.0	50.0	57.0					12																	125455935		2203	4300	6503	SO:0001819	synonymous_variant	57647	exon8			GATCACCACCTTG	AB040950	CCDS9261.1	12q24.31	2004-03-25	2003-06-13	2003-06-20		ENSG00000150990		"""DEAH-boxes"""	17210	protein-coding gene	gene with protein product			"""DEAD/DEAH box helicase DDX37"""	DDX37		10819331	Standard	NM_032656		Approved	KIAA1517, MGC4322, MGC2695	uc001ugy.3	Q8IY37		ENST00000308736.2:c.1104G>C	12.37:g.125455935C>G		45.0	0.0		34.0	5.0	NM_032656	Q9BUI7|Q9P211	Silent	SNP	ENST00000308736.2	37	CCDS9261.1																																																																																			.		0.647	DHX37-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_032656	
DIDO1	11083	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	20	61511712	61511712	+	Missense_Mutation	SNP	C	C	T			TCGA-FV-A3R3-01A-11D-A22F-10	TCGA-FV-A3R3-10A-01D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c285c2fa-24b4-47a1-874d-86e74b002b05	64edddfd-f366-4d51-a8b4-a357b2c68e6c	g.chr20:61511712C>T	ENST00000266070.4	-	16	5921	c.5596G>A	c.(5596-5598)Gcc>Acc	p.A1866T	DIDO1_ENST00000395343.1_Missense_Mutation_p.A1866T	NM_033081.2	NP_149072.2	Q9BTC0	DIDO1_HUMAN	death inducer-obliterator 1	1866	Pro-rich.				apoptotic signaling pathway (GO:0097190)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			NS(6)|breast(5)|central_nervous_system(1)|cervix(3)|endometrium(6)|kidney(1)|large_intestine(17)|lung(39)|ovary(8)|prostate(3)|skin(7)|stomach(2)|upper_aerodigestive_tract(1)	99	Breast(26;5.68e-08)					TGGGCGGGGGCGCCCGTCACC	0.612																																					p.A1866T	Melanoma(25;381 482 3385 5362 7955 17159 17174 40604 47095)	.											.	DIDO1	96	0			c.G5596A						.						43.0	47.0	46.0					20																	61511712		2202	4295	6497	SO:0001583	missense	11083	exon16			CGGGGGCGCCCGT	AB002331	CCDS13508.2, CCDS13509.1, CCDS33506.1	20q13.33	2013-01-28	2005-11-11	2005-11-11	ENSG00000101191	ENSG00000101191		"""Zinc fingers, PHD-type"""	2680	protein-coding gene	gene with protein product		604140	"""chromosome 20 open reading frame 158"", ""death associated transcription factor 1"""	C20orf158, DATF1		10393935	Standard	NM_033081		Approved	DIO1, dJ885L7.8, FLJ11265, KIAA0333, DIO-1, BYE1	uc002ydr.2	Q9BTC0	OTTHUMG00000032945	ENST00000266070.4:c.5596G>A	20.37:g.61511712C>T	ENSP00000266070:p.Ala1866Thr	50.0	0.0		53.0	9.0	NM_001193369	A8MY65|B9EH82|E1P5I1|O15043|Q3ZTL7|Q3ZTL8|Q4VXS1|Q4VXS2|Q4VXV8|Q4VXV9|Q96D72|Q9BQW0|Q9BW03|Q9H4G6|Q9H4G7|Q9NTU8|Q9NUM8|Q9UFB6	Missense_Mutation	SNP	ENST00000266070.4	37	CCDS33506.1	.	.	.	.	.	.	.	.	.	.	C	3.128	-0.179083	0.06380	.	.	ENSG00000101191	ENST00000266070;ENST00000395343	T;T	0.08282	3.11;3.11	4.97	-1.09	0.09904	.	0.536184	0.15455	N	0.261401	T	0.06325	0.0163	N	0.22421	0.69	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.28073	-1.0055	10	0.45353	T	0.12	-1.363	13.92	0.63926	0.0:0.5771:0.3057:0.1173	.	1866	Q9BTC0	DIDO1_HUMAN	T	1866	ENSP00000266070:A1866T;ENSP00000378752:A1866T	ENSP00000266070:A1866T	A	-	1	0	DIDO1	60982157	0.085000	0.21516	0.000000	0.03702	0.006000	0.05464	0.270000	0.18607	-0.453000	0.07076	-1.332000	0.01269	GCC	.		0.612	DIDO1-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000080091.2	NM_080796	
DTHD1	401124	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	4	36296584	36296584	+	Silent	SNP	C	C	T			TCGA-FV-A3R3-01A-11D-A22F-10	TCGA-FV-A3R3-10A-01D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c285c2fa-24b4-47a1-874d-86e74b002b05	64edddfd-f366-4d51-a8b4-a357b2c68e6c	g.chr4:36296584C>T	ENST00000456874.2	+	4	1249	c.1191C>T	c.(1189-1191)aaC>aaT	p.N397N	DTHD1_ENST00000357504.3_Silent_p.N232N|DTHD1_ENST00000507598.1_Silent_p.N437N	NM_001170700.2	NP_001164171.1	Q6ZMT9	DTHD1_HUMAN	death domain containing 1	397					signal transduction (GO:0007165)					breast(2)|central_nervous_system(1)|endometrium(2)|kidney(2)|stomach(1)	8						TTGATAAAAACAACCTTGGTT	0.373																																					p.N397N		.											.	DTHD1	46	0			c.C1191T						.						180.0	151.0	160.0					4																	36296584		692	1591	2283	SO:0001819	synonymous_variant	401124	exon4			TAAAAACAACCTT	AK094684	CCDS54754.1	4p14	2009-10-02			ENSG00000197057	ENSG00000197057			37261	protein-coding gene	gene with protein product							Standard	NM_001170700		Approved	FLJ16686	uc021xne.2	Q6ZMT9	OTTHUMG00000160371	ENST00000456874.2:c.1191C>T	4.37:g.36296584C>T		223.0	0.0		152.0	39.0	NM_001170700	B2RXK4|B4E2N7	Silent	SNP	ENST00000456874.2	37	CCDS54754.1																																																																																			.		0.373	DTHD1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001136536	
ELOVL3	83401	broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	10	103988605	103988605	+	Missense_Mutation	SNP	C	C	T	rs150611171	byFrequency	TCGA-FV-A3R3-01A-11D-A22F-10	TCGA-FV-A3R3-10A-01D-A22F-10	C	C	.	.	.	.	.	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c285c2fa-24b4-47a1-874d-86e74b002b05	64edddfd-f366-4d51-a8b4-a357b2c68e6c	g.chr10:103988605C>T	ENST00000370005.3	+	4	630	c.409C>T	c.(409-411)Cgt>Tgt	p.R137C		NM_152310.1	NP_689523.1	Q9HB03	ELOV3_HUMAN	ELOVL fatty acid elongase 3	137					cellular lipid metabolic process (GO:0044255)|fatty acid elongation, monounsaturated fatty acid (GO:0034625)|fatty acid elongation, polyunsaturated fatty acid (GO:0034626)|fatty acid elongation, saturated fatty acid (GO:0019367)|long-chain fatty-acyl-CoA biosynthetic process (GO:0035338)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)|very long-chain fatty acid biosynthetic process (GO:0042761)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	transferase activity (GO:0016740)			breast(2)|lung(10)|ovary(2)|prostate(1)|skin(1)	16		Colorectal(252;0.207)		Epithelial(162;4.47e-08)|all cancers(201;7.96e-07)		CATCATCCTGCGTAAGCGGCC	0.537													C|||	3	0.000599042	0.0	0.0	5008	,	,		20538	0.0		0.003	False		,,,				2504	0.0				p.R137C		.											.	ELOVL3	92	0			c.C409T						.	C	CYS/ARG	2,4404	4.2+/-10.8	0,2,2201	133.0	125.0	128.0		409	2.3	0.8	10	dbSNP_134	128	5,8595	4.3+/-15.6	0,5,4295	yes	missense	ELOVL3	NM_152310.1	180	0,7,6496	TT,TC,CC		0.0581,0.0454,0.0538	probably-damaging	137/271	103988605	7,12999	2203	4300	6503	SO:0001583	missense	83401	exon4			ATCCTGCGTAAGC	AF292387	CCDS7531.1	10q24	2011-05-25	2011-05-25		ENSG00000119915	ENSG00000119915			18047	protein-coding gene	gene with protein product		611815	"""elongation of very long chain fatty acids (FEN1/Elo2, SUR4/Elo3, yeast)-like 3"""				Standard	NM_152310		Approved	CIG-30	uc001kut.3	Q9HB03	OTTHUMG00000018951	ENST00000370005.3:c.409C>T	10.37:g.103988605C>T	ENSP00000359022:p.Arg137Cys	115.0	1.0		98.0	16.0	NM_152310	Q5VZL3|Q8N180	Missense_Mutation	SNP	ENST00000370005.3	37	CCDS7531.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	C	19.34	3.808858	0.70797	4.54E-4	5.81E-4	ENSG00000119915	ENST00000370005	T	0.28255	1.62	5.24	2.29	0.28610	.	0.000000	0.64402	D	0.000015	T	0.61476	0.2350	H	0.94698	3.57	0.53005	D	0.999964	D	0.89917	1.0	D	0.97110	1.0	T	0.63265	-0.6676	10	0.87932	D	0	-23.3653	8.2173	0.31519	0.2777:0.6475:0.0:0.0748	.	137	Q9HB03	ELOV3_HUMAN	C	137	ENSP00000359022:R137C	ENSP00000359022:R137C	R	+	1	0	ELOVL3	103978595	0.982000	0.34865	0.807000	0.32361	0.998000	0.95712	0.635000	0.24629	0.180000	0.19960	0.561000	0.74099	CGT	C|0.999;T|0.001		0.537	ELOVL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050030.1	NM_152310	
EP300	2033	broad.mit.edu;bcgsc.ca	37	22	41569690	41569690	+	Missense_Mutation	SNP	A	A	G			TCGA-FV-A3R3-01A-11D-A22F-10	TCGA-FV-A3R3-10A-01D-A22F-10	A	A	.	.	.	.	.	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c285c2fa-24b4-47a1-874d-86e74b002b05	64edddfd-f366-4d51-a8b4-a357b2c68e6c	g.chr22:41569690A>G	ENST00000263253.7	+	29	5900	c.4681A>G	c.(4681-4683)Agc>Ggc	p.S1561G	RP1-85F18.5_ENST00000420537.1_RNA|RP1-85F18.6_ENST00000415054.1_RNA	NM_001429.3	NP_001420.2	Q09472	EP300_HUMAN	E1A binding protein p300	1561	CBP/p300-type HAT. {ECO:0000255|PROSITE- ProRule:PRU01065}.				apoptotic process (GO:0006915)|cellular response to hypoxia (GO:0071456)|chromatin organization (GO:0006325)|circadian rhythm (GO:0007623)|G2/M transition of mitotic cell cycle (GO:0000086)|heart development (GO:0007507)|histone H2B acetylation (GO:0043969)|histone H4 acetylation (GO:0043967)|innate immune response (GO:0045087)|internal peptidyl-lysine acetylation (GO:0018393)|internal protein amino acid acetylation (GO:0006475)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|lung development (GO:0030324)|mitotic cell cycle (GO:0000278)|N-terminal peptidyl-lysine acetylation (GO:0018076)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nervous system development (GO:0007399)|Notch signaling pathway (GO:0007219)|organ morphogenesis (GO:0009887)|positive regulation by host of viral transcription (GO:0043923)|positive regulation of protein binding (GO:0032092)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon production (GO:0032481)|regulation of androgen receptor signaling pathway (GO:0060765)|regulation of cell cycle (GO:0051726)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|regulation of transcription, DNA-templated (GO:0006355)|regulation of tubulin deacetylation (GO:0090043)|response to estrogen (GO:0043627)|response to hypoxia (GO:0001666)|skeletal muscle tissue development (GO:0007519)|somitogenesis (GO:0001756)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	cytoplasm (GO:0005737)|histone acetyltransferase complex (GO:0000123)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	acetyltransferase activity (GO:0016407)|activating transcription factor binding (GO:0033613)|androgen receptor binding (GO:0050681)|beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|chromatin DNA binding (GO:0031490)|core promoter binding (GO:0001047)|DNA binding (GO:0003677)|histone acetyltransferase activity (GO:0004402)|lysine N-acetyltransferase activity, acting on acetyl phosphate as donor (GO:0004468)|nuclear hormone receptor binding (GO:0035257)|pre-mRNA intronic binding (GO:0097157)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|transferase activity, transferring acyl groups (GO:0016746)|zinc ion binding (GO:0008270)			NS(2)|breast(11)|central_nervous_system(7)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(31)|kidney(5)|large_intestine(31)|liver(2)|lung(33)|ovary(2)|pancreas(4)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(16)	171						CAAAAATAAGAGCAGCCTGAG	0.423			"""T,  N, F, Mis, O"""	"""MLL, RUNXBP2"""	"""colorectal, breast, pancreatic, AML, ALL, DLBCL"""				Rubinstein-Taybi syndrome																												p.S1561G		.		Rec	yes		22	22q13	2033	300 kd E1A-Binding protein gene		"""L, E"""	.	EP300	2011	0			c.A4681G						.						120.0	128.0	126.0					22																	41569690		2203	4300	6503	SO:0001583	missense	2033	exon29	Familial Cancer Database	Broad Thumb-Hallux syndrome	AATAAGAGCAGCC	U01877	CCDS14010.1	22q13.2	2011-07-01			ENSG00000100393	ENSG00000100393		"""Chromatin-modifying enzymes / K-acetyltransferases"""	3373	protein-coding gene	gene with protein product	"""histone acetyltransferase p300"""	602700				7523245	Standard	NM_001429		Approved	p300, KAT3B	uc003azl.4	Q09472	OTTHUMG00000150937	ENST00000263253.7:c.4681A>G	22.37:g.41569690A>G	ENSP00000263253:p.Ser1561Gly	170.0	0.0		121.0	6.0	NM_001429	B1AKC2	Missense_Mutation	SNP	ENST00000263253.7	37	CCDS14010.1	.	.	.	.	.	.	.	.	.	.	A	20.3	3.962913	0.74016	.	.	ENSG00000100393	ENST00000263253	D	0.93763	-3.28	5.52	5.52	0.82312	.	0.000000	0.56097	D	0.000033	D	0.93976	0.8071	N	0.26042	0.785	0.49483	D	0.999793	D	0.76494	0.999	D	0.79108	0.992	D	0.94508	0.7716	10	0.51188	T	0.08	-10.4298	15.643	0.77020	1.0:0.0:0.0:0.0	.	1561	Q09472	EP300_HUMAN	G	1561	ENSP00000263253:S1561G	ENSP00000263253:S1561G	S	+	1	0	EP300	39899636	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	7.420000	0.80191	2.094000	0.63399	0.533000	0.62120	AGC	.		0.423	EP300-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320600.1	NM_001429	
EPB41L1	2036	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	20	34761813	34761813	+	Silent	SNP	C	C	A			TCGA-FV-A3R3-01A-11D-A22F-10	TCGA-FV-A3R3-10A-01D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c285c2fa-24b4-47a1-874d-86e74b002b05	64edddfd-f366-4d51-a8b4-a357b2c68e6c	g.chr20:34761813C>A	ENST00000338074.2	+	2	275	c.114C>A	c.(112-114)ggC>ggA	p.G38G	EPB41L1_ENST00000373946.3_Intron|EPB41L1_ENST00000373941.1_Silent_p.G38G|EPB41L1_ENST00000373950.2_Intron|EPB41L1_ENST00000441639.1_Intron|EPB41L1_ENST00000202028.5_Intron	NM_001258329.1|NM_012156.2	NP_001245258.1|NP_036288.2	Q9H4G0	E41L1_HUMAN	erythrocyte membrane protein band 4.1-like 1	38					cortical actin cytoskeleton organization (GO:0030866)|synaptic transmission (GO:0007268)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extrinsic component of membrane (GO:0019898)|plasma membrane (GO:0005886)	structural molecule activity (GO:0005198)			breast(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(10)|ovary(2)|pancreas(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	37	Breast(12;0.0239)					CAGGCCACGGCCACCCAGAGG	0.662																																					p.G38G		.											.	EPB41L1	93	0			c.C114A						.						37.0	34.0	35.0					20																	34761813		2203	4300	6503	SO:0001819	synonymous_variant	2036	exon3			CCACGGCCACCCA	AB002336	CCDS13271.1, CCDS13272.1, CCDS58771.1	20q11.2-q12	2003-03-17			ENSG00000088367	ENSG00000088367			3378	protein-coding gene	gene with protein product		602879				9570967, 9828140	Standard	NM_012156		Approved	KIAA0338	uc002xfb.3	Q9H4G0	OTTHUMG00000032378	ENST00000338074.2:c.114C>A	20.37:g.34761813C>A		81.0	0.0		71.0	17.0	NM_001258329	O15046|Q4VXM6|Q4VXM7|Q4VXM8|Q4VXN4|Q6ZT61|Q8IUU7|Q96CV5|Q96L65	Silent	SNP	ENST00000338074.2	37	CCDS13271.1																																																																																			.		0.662	EPB41L1-008	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000078978.3	NM_012156	
FMN2	56776	hgsc.bcm.edu;bcgsc.ca;mdanderson.org	37	1	240371393	240371393	+	Missense_Mutation	SNP	C	C	A	rs201701711		TCGA-FV-A3R3-01A-11D-A22F-10	TCGA-FV-A3R3-10A-01D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c285c2fa-24b4-47a1-874d-86e74b002b05	64edddfd-f366-4d51-a8b4-a357b2c68e6c	g.chr1:240371393C>A	ENST00000319653.9	+	5	3511	c.3281C>A	c.(3280-3282)gCg>gAg	p.A1094E		NM_020066.4	NP_064450.3	Q9NZ56	FMN2_HUMAN	formin 2	1094	FH1.|Pro-rich.				cellular response to DNA damage stimulus (GO:0006974)|cellular response to hypoxia (GO:0071456)|establishment of meiotic spindle localization (GO:0051295)|formin-nucleated actin cable assembly (GO:0070649)|homologous chromosome movement towards spindle pole involved in homologous chromosome segregation (GO:0051758)|intracellular signal transduction (GO:0035556)|intracellular transport (GO:0046907)|multicellular organismal development (GO:0007275)|negative regulation of apoptotic process (GO:0043066)|negative regulation of protein catabolic process (GO:0042177)|oogenesis (GO:0048477)|polar body extrusion after meiotic divisions (GO:0040038)|protein transport (GO:0015031)|vesicle-mediated transport (GO:0016192)	cell cortex (GO:0005938)|cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|microvillus (GO:0005902)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)|spindle (GO:0005819)	actin binding (GO:0003779)			NS(1)|breast(7)|central_nervous_system(6)|cervix(1)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(13)|lung(87)|ovary(6)|pancreas(3)|prostate(12)|skin(7)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(2)	178	Ovarian(103;0.127)	all_cancers(173;0.013)	OV - Ovarian serous cystadenocarcinoma(106;0.0106)			CTACCCGGAGCGGGCATACCC	0.731																																					p.A1094E		.											.	FMN2	145	0			c.C3281A						.						5.0	7.0	6.0					1																	240371393		1888	3892	5780	SO:0001583	missense	56776	exon5			CCGGAGCGGGCAT	AF218942	CCDS31069.2	1q43	2008-02-05			ENSG00000155816	ENSG00000155816			14074	protein-coding gene	gene with protein product		606373				10781961	Standard	NM_020066		Approved		uc010pyd.2	Q9NZ56	OTTHUMG00000039883	ENST00000319653.9:c.3281C>A	1.37:g.240371393C>A	ENSP00000318884:p.Ala1094Glu	76.0	0.0		58.0	13.0	NM_020066	B0QZA7|B4DP05|Q59GF6|Q5VU37|Q9NZ55	Missense_Mutation	SNP	ENST00000319653.9	37	CCDS31069.2	.	.	.	.	.	.	.	.	.	.	c	7.269	0.606854	0.14002	.	.	ENSG00000155816	ENST00000319653	T	0.59083	0.29	3.16	-1.05	0.10036	Actin-binding FH2/DRF autoregulatory (1);Formin Homology 1 (2);	2.671950	0.01759	N	0.030419	T	0.42988	0.1227	L	0.33189	0.99	0.09310	N	1	B	0.06786	0.001	B	0.06405	0.002	T	0.05869	-1.0859	9	.	.	.	.	3.0177	0.06065	0.364:0.3658:0.0:0.2702	.	1094	Q9NZ56	FMN2_HUMAN	E	1094	ENSP00000318884:A1094E	.	A	+	2	0	FMN2	238438016	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.328000	0.01112	-0.352000	0.08237	-0.350000	0.07774	GCG	C|0.999;T|0.001		0.731	FMN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096217.2	XM_371352	
FPGS	2356	ucsc.edu;bcgsc.ca	37	9	130569924	130569924	+	Missense_Mutation	SNP	A	A	G			TCGA-FV-A3R3-01A-11D-A22F-10	TCGA-FV-A3R3-10A-01D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.		Illumina HiSeq	c285c2fa-24b4-47a1-874d-86e74b002b05	64edddfd-f366-4d51-a8b4-a357b2c68e6c	g.chr9:130569924A>G	ENST00000373247.2	+	8	751	c.701A>G	c.(700-702)gAt>gGt	p.D234G	FPGS_ENST00000460181.1_3'UTR|FPGS_ENST00000373225.3_Missense_Mutation_p.D184G|FPGS_ENST00000373245.1_Missense_Mutation_p.D234G|FPGS_ENST00000393706.2_Missense_Mutation_p.D208G	NM_004957.4	NP_004948.4	Q05932	FOLC_HUMAN	folylpolyglutamate synthase	234					brain development (GO:0007420)|folic acid metabolic process (GO:0046655)|liver development (GO:0001889)|nucleobase-containing compound metabolic process (GO:0006139)|one-carbon metabolic process (GO:0006730)|organ regeneration (GO:0031100)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|tetrahydrofolylpolyglutamate synthase activity (GO:0004326)			endometrium(2)|kidney(1)|lung(3)|ovary(1)	7					Methotrexate(DB00563)|Pralatrexate(DB06813)|Raltitrexed(DB00293)	CTCCTGGGGGATACGGTGGAG	0.597																																					p.D234G		.											.	FPGS	90	0			c.A701G						.						45.0	44.0	44.0					9																	130569924		2203	4300	6503	SO:0001583	missense	2356	exon8			TGGGGGATACGGT		CCDS35148.1, CCDS35149.1, CCDS75905.1	9q34.11	2013-09-19			ENSG00000136877	ENSG00000136877	6.3.2.17		3824	protein-coding gene	gene with protein product		136510					Standard	NM_004957		Approved		uc004bsg.1	Q05932	OTTHUMG00000020716	ENST00000373247.2:c.701A>G	9.37:g.130569924A>G	ENSP00000362344:p.Asp234Gly	51.0	0.0		37.0	4.0	NM_004957	B3KPW4|B7Z2Z3|F5H0K6|Q5JU19|Q5JU22|Q6P2P6	Missense_Mutation	SNP	ENST00000373247.2	37	CCDS35148.1	.	.	.	.	.	.	.	.	.	.	A	17.84	3.488509	0.64074	.	.	ENSG00000136877	ENST00000373247;ENST00000373245;ENST00000393706;ENST00000373228;ENST00000373225;ENST00000431857;ENST00000423577	T;T;T;T;T	0.35048	2.76;1.33;2.71;1.33;2.36	5.31	5.31	0.75309	Mur ligase, central (2);	0.000000	0.85682	D	0.000000	T	0.49012	0.1532	M	0.72894	2.215	0.80722	D	1	P;P	0.39576	0.679;0.679	P;P	0.47044	0.535;0.535	T	0.52328	-0.8590	10	0.59425	D	0.04	-30.3122	14.4376	0.67293	1.0:0.0:0.0:0.0	.	208;234	Q05932-4;Q05932	.;FOLC_HUMAN	G	234;234;208;234;184;184;158	ENSP00000362344:D234G;ENSP00000362342:D234G;ENSP00000377309:D208G;ENSP00000362325:D234G;ENSP00000362322:D184G	ENSP00000362322:D184G	D	+	2	0	FPGS	129609745	1.000000	0.71417	0.991000	0.47740	0.972000	0.66771	8.873000	0.92357	2.028000	0.59812	0.379000	0.24179	GAT	.		0.597	FPGS-011	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054251.1		
FSD2	123722	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	15	83451591	83451591	+	Missense_Mutation	SNP	T	T	C			TCGA-FV-A3R3-01A-11D-A22F-10	TCGA-FV-A3R3-10A-01D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c285c2fa-24b4-47a1-874d-86e74b002b05	64edddfd-f366-4d51-a8b4-a357b2c68e6c	g.chr15:83451591T>C	ENST00000334574.8	-	4	1103	c.922A>G	c.(922-924)Aca>Gca	p.T308A	FSD2_ENST00000541889.1_Missense_Mutation_p.T308A			A1L4K1	FSD2_HUMAN	fibronectin type III and SPRY domain containing 2	308										breast(2)|central_nervous_system(1)|large_intestine(5)|lung(10)	18						TCCTCTATTGTTTCCATCAGT	0.378																																					p.T308A		.											.	FSD2	90	0			c.A922G						.						305.0	288.0	293.0					15																	83451591		1894	4118	6012	SO:0001583	missense	123722	exon4			CTATTGTTTCCAT	AK122875	CCDS45332.1, CCDS61738.1	15q25.2	2013-02-11	2006-01-11	2006-01-11		ENSG00000186628		"""Fibronectin type III domain containing"""	18024	protein-coding gene	gene with protein product			"""SPRY domain containing 1"""	SPRYD1			Standard	NM_001007122		Approved	RP11-127F21	uc002bjd.2	A1L4K1		ENST00000334574.8:c.922A>G	15.37:g.83451591T>C	ENSP00000335651:p.Thr308Ala	286.0	0.0		220.0	24.0	NM_001007122	B3KVG1|B7ZM02	Missense_Mutation	SNP	ENST00000334574.8	37	CCDS45332.1	.	.	.	.	.	.	.	.	.	.	T	17.50	3.404838	0.62288	.	.	ENSG00000186628	ENST00000334574;ENST00000541889	T;T	0.63417	0.44;-0.04	6.04	3.69	0.42338	.	0.108638	0.64402	D	0.000012	T	0.58119	0.2100	M	0.66939	2.045	0.31242	N	0.695044	B;P	0.47762	0.354;0.9	B;B	0.43990	0.217;0.438	T	0.62201	-0.6904	10	0.41790	T	0.15	-13.9101	6.0078	0.19557	0.1232:0.1369:0.0:0.74	.	308;308	B7ZM02;A1L4K1	.;FSD2_HUMAN	A	308	ENSP00000335651:T308A;ENSP00000444078:T308A	ENSP00000335651:T308A	T	-	1	0	FSD2	81248645	1.000000	0.71417	0.793000	0.32043	0.950000	0.60333	2.497000	0.45354	0.497000	0.27926	0.459000	0.35465	ACA	.		0.378	FSD2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418385.1	NM_001007122	
GLI2	2736	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	2	121747077	121747077	+	Missense_Mutation	SNP	G	G	A			TCGA-FV-A3R3-01A-11D-A22F-10	TCGA-FV-A3R3-10A-01D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c285c2fa-24b4-47a1-874d-86e74b002b05	64edddfd-f366-4d51-a8b4-a357b2c68e6c	g.chr2:121747077G>A	ENST00000452319.1	+	14	3647	c.3587G>A	c.(3586-3588)gGg>gAg	p.G1196E	GLI2_ENST00000314490.11_Intron|GLI2_ENST00000361492.4_Missense_Mutation_p.G1196E					GLI family zinc finger 2											NS(1)|breast(3)|central_nervous_system(4)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(7)|lung(24)|ovary(8)|pancreas(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	64	Renal(3;0.0496)	Prostate(154;0.0623)				GCTAGCCCTGGGGGCCTGGAC	0.672																																					p.G1196E		.											.	GLI2	954	0			c.G3587A						.						13.0	17.0	15.0					2																	121747077		2182	4252	6434	SO:0001583	missense	2736	exon13			GCCCTGGGGGCCT		CCDS33283.1	2q14	2013-01-25	2009-03-05		ENSG00000074047	ENSG00000074047		"""Zinc fingers, C2H2-type"""	4318	protein-coding gene	gene with protein product	"""tax-responsive element-2 holding protein"", ""tax helper protein 1"", ""tax helper protein 2"""	165230	"""GLI-Kruppel family member GLI2"", ""glioma-associated oncogene family zinc finger 2"""			2850480, 9557682	Standard	NM_005270		Approved	THP2, HPE9, THP1	uc010flp.3	P10070	OTTHUMG00000153741	ENST00000452319.1:c.3587G>A	2.37:g.121747077G>A	ENSP00000390436:p.Gly1196Glu	63.0	0.0		78.0	19.0	NM_005270		Missense_Mutation	SNP	ENST00000452319.1	37	CCDS33283.1	.	.	.	.	.	.	.	.	.	.	G	4.102	0.016996	0.07959	.	.	ENSG00000074047	ENST00000452319;ENST00000361492	T;T	0.13196	2.61;2.61	4.72	2.81	0.32909	.	0.692268	0.14606	N	0.309348	T	0.09024	0.0223	L	0.41236	1.265	0.09310	N	1	B;P	0.36535	0.421;0.557	B;B	0.31101	0.058;0.124	T	0.22138	-1.0225	9	.	.	.	.	5.287	0.15706	0.1455:0.0:0.5539:0.3006	.	1196;851	P10070;P10070-2	GLI2_HUMAN;.	E	1196	ENSP00000390436:G1196E;ENSP00000354586:G1196E	.	G	+	2	0	GLI2	121463547	0.005000	0.15991	0.002000	0.10522	0.088000	0.18126	0.755000	0.26405	1.176000	0.42840	0.449000	0.29647	GGG	.		0.672	GLI2-009	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000332293.3	NM_005270	
GNAS	2778	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	20	57484420	57484420	+	Missense_Mutation	SNP	C	C	T	rs11554273		TCGA-FV-A3R3-01A-11D-A22F-10	TCGA-FV-A3R3-10A-01D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c285c2fa-24b4-47a1-874d-86e74b002b05	64edddfd-f366-4d51-a8b4-a357b2c68e6c	g.chr20:57484420C>T	ENST00000371085.3	+	8	1025	c.601C>T	c.(601-603)Cgt>Tgt	p.R201C	GNAS_ENST00000464624.2_3'UTR|GNAS_ENST00000306090.10_Missense_Mutation_p.R187C|GNAS_ENST00000371100.4_Missense_Mutation_p.R844C|GNAS_ENST00000371102.4_Missense_Mutation_p.R830C|GNAS_ENST00000354359.7_Missense_Mutation_p.R202C|GNAS_ENST00000371095.3_Missense_Mutation_p.R187C|GNAS_ENST00000313949.7_3'UTR|GNAS_ENST00000265620.7_Missense_Mutation_p.R186C|GNAS_ENST00000371075.3_3'UTR	NM_000516.4	NP_000507.1	P63092	GNAS2_HUMAN	GNAS complex locus	201			R -> C (in MAS and somatotrophinoma; dbSNP:rs11554273). {ECO:0000269|PubMed:1944469, ECO:0000269|PubMed:2549426}.|R -> G (in MAS). {ECO:0000269|PubMed:10571700}.|R -> H (in MAS, somatotrophinoma and AIMAH1). {ECO:0000269|PubMed:12727968, ECO:0000269|PubMed:1594625, ECO:0000269|PubMed:1944469, ECO:0000269|PubMed:2549426}.|R -> L (in non-MAS endocrine tumors). {ECO:0000269|PubMed:7751320}.|R -> S (in AIMAH1, pituitary tumor and polyostotic fibrous dysplasia). {ECO:0000269|PubMed:12727968, ECO:0000269|PubMed:8766942, ECO:0000269|PubMed:9267696}.		activation of adenylate cyclase activity (GO:0007190)|adenylate cyclase-activating adrenergic receptor signaling pathway (GO:0071880)|adenylate cyclase-activating dopamine receptor signaling pathway (GO:0007191)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|blood coagulation (GO:0007596)|bone development (GO:0060348)|cAMP biosynthetic process (GO:0006171)|cellular response to catecholamine stimulus (GO:0071870)|cellular response to glucagon stimulus (GO:0071377)|cellular response to prostaglandin E stimulus (GO:0071380)|cognition (GO:0050890)|developmental growth (GO:0048589)|energy reserve metabolic process (GO:0006112)|hair follicle placode formation (GO:0060789)|intracellular transport (GO:0046907)|platelet aggregation (GO:0070527)|positive regulation of cAMP biosynthetic process (GO:0030819)|positive regulation of cAMP-mediated signaling (GO:0043950)|positive regulation of Ras GTPase activity (GO:0032320)|regulation of insulin secretion (GO:0050796)|sensory perception of smell (GO:0007608)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|heterotrimeric G-protein complex (GO:0005834)|intrinsic component of membrane (GO:0031224)|membrane (GO:0016020)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)	adenylate cyclase activity (GO:0004016)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|metal ion binding (GO:0046872)|signal transducer activity (GO:0004871)	p.R201C(228)|p.R844C(9)|p.R201S(5)		adrenal_gland(12)|autonomic_ganglia(1)|biliary_tract(5)|central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(4)|kidney(7)|large_intestine(37)|liver(9)|lung(9)|ovary(16)|pancreas(56)|parathyroid(5)|pituitary(228)|prostate(2)|small_intestine(1)|stomach(1)|testis(2)|thyroid(35)|upper_aerodigestive_tract(3)|urinary_tract(1)	441	all_lung(29;0.0104)		BRCA - Breast invasive adenocarcinoma(13;2.19e-08)|Colorectal(105;0.109)			GCTTCGCTGCCGTGTCCTGAC	0.428			Mis		pituitary adenoma		"""McCune-Albright syndrome; pseudohypoparathyroidism, type IA"""			TSP Lung(22;0.16)																											p.R844C	Colon(117;935 1597 6045 8307 46442)	.		Dom	yes		20	20q13.2	2778	"""guanine nucleotide binding protein (G protein), alpha stimulating activity polypeptide 1"""	yes	E	GNAS,colon,carcinoma,0	GNAS	4767	242	Substitution - Missense(242)	pituitary(141)|pancreas(35)|large_intestine(14)|ovary(12)|thyroid(10)|adrenal_gland(7)|biliary_tract(6)|parathyroid(5)|liver(3)|kidney(3)|testis(2)|upper_aerodigestive_tract(2)|autonomic_ganglia(1)|haematopoietic_and_lymphoid_tissue(1)	c.C2530T						.						80.0	78.0	79.0					20																	57484420		2203	4300	6503	SO:0001583	missense	2778	exon8			CGCTGCCGTGTCC	M21142	CCDS13471.1, CCDS13472.1, CCDS42892.1, CCDS46622.1, CCDS46623.1, CCDS46624.1	20q13.2-q13.3	2010-03-01	2001-12-19	2001-12-20	ENSG00000087460	ENSG00000087460			4392	protein-coding gene	gene with protein product	"""secretogranin VI"""	139320	"""guanine nucleotide binding protein (G protein), alpha stimulating activity polypeptide 1"""	GNAS1			Standard	NM_000516		Approved	NESP55, NESP, GNASXL, GPSA, SCG6	uc002xzw.3	O95467	OTTHUMG00000033069	ENST00000371085.3:c.601C>T	20.37:g.57484420C>T	ENSP00000360126:p.Arg201Cys	97.0	0.0		95.0	28.0	NM_080425	A6NI00|E1P5G5|P04895|Q12927|Q14433|Q32P26|Q5JWD2|Q5JWD4|Q5JWD5|Q6NR75|Q6NXS0|Q8TBC0|Q96H70	Missense_Mutation	SNP	ENST00000371085.3	37	CCDS13472.1	.	.	.	.	.	.	.	.	.	.	C	21.9	4.215896	0.79352	.	.	ENSG00000087460	ENST00000371100;ENST00000371102;ENST00000371095;ENST00000371085;ENST00000354359;ENST00000265620;ENST00000306090	D;D;D;D;D;D;D	0.99466	-5.95;-5.95;-5.95;-5.95;-5.95;-2.99;-5.95	5.53	4.53	0.55603	G protein alpha subunit, helical insertion (2);	0.000000	0.85682	D	0.000000	D	0.99775	0.9907	H	0.99732	4.735	0.80722	D	1	D;D;D;D	0.89917	0.999;0.983;0.979;1.0	D;P;P;D	0.97110	0.939;0.845;0.643;1.0	D	0.96814	0.9599	10	0.87932	D	0	.	13.0593	0.58997	0.2437:0.7563:0.0:0.0	rs11554273	201;202;186;844	P63092;A6NI00;P63092-3;Q5JWF2	GNAS2_HUMAN;.;.;GNAS1_HUMAN	C	844;830;187;201;202;186;187	ENSP00000360141:R844C;ENSP00000360143:R830C;ENSP00000360136:R187C;ENSP00000360126:R201C;ENSP00000346328:R202C;ENSP00000265620:R186C;ENSP00000304472:R187C	ENSP00000265620:R186C	R	+	1	0	GNAS	56917815	1.000000	0.71417	0.998000	0.56505	0.941000	0.58515	4.055000	0.57441	2.596000	0.87737	0.563000	0.77884	CGT	C|1.000		0.428	GNAS-015	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000080431.2	NM_000516	
GRIA2	2891	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	4	158254023	158254023	+	Missense_Mutation	SNP	G	G	A			TCGA-FV-A3R3-01A-11D-A22F-10	TCGA-FV-A3R3-10A-01D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c285c2fa-24b4-47a1-874d-86e74b002b05	64edddfd-f366-4d51-a8b4-a357b2c68e6c	g.chr4:158254023G>A	ENST00000264426.9	+	7	1214	c.935G>A	c.(934-936)cGc>cAc	p.R312H	GRIA2_ENST00000449365.1_Missense_Mutation_p.R265H|GRIA2_ENST00000296526.7_Missense_Mutation_p.R312H|GRIA2_ENST00000393815.2_Missense_Mutation_p.R265H|GRIA2_ENST00000507898.1_Missense_Mutation_p.R265H	NM_001083619.1	NP_001077088	P42262	GRIA2_HUMAN	glutamate receptor, ionotropic, AMPA 2	312					ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|cell junction (GO:0030054)|dendrite (GO:0030425)|endocytic vesicle membrane (GO:0030666)|endoplasmic reticulum (GO:0005783)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|synaptic vesicle (GO:0008021)	alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:0004971)|extracellular-glutamate-gated ion channel activity (GO:0005234)|ionotropic glutamate receptor activity (GO:0004970)			NS(1)|breast(2)|central_nervous_system(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(16)|liver(2)|lung(32)|ovary(3)|prostate(3)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	79	all_hematologic(180;0.24)	Renal(120;0.0458)		COAD - Colon adenocarcinoma(41;0.0294)	Amobarbital(DB01351)|Aprobarbital(DB01352)|Butabarbital(DB00237)|Butalbital(DB00241)|Butethal(DB01353)|Heptabarbital(DB01354)|Hexobarbital(DB01355)|Methylphenobarbital(DB00849)|Pentobarbital(DB00312)|Phenobarbital(DB01174)|Primidone(DB00794)|Quinidine barbiturate(DB01346)|Secobarbital(DB00418)|Talbutal(DB00306)|Thiopental(DB00599)	GAAGCCTTCCGCAACCTAAGG	0.463																																					p.R312H		.											.	GRIA2	515	0			c.G935A						.						99.0	105.0	103.0					4																	158254023		2203	4300	6503	SO:0001583	missense	2891	exon7			CCTTCCGCAACCT		CCDS3797.1, CCDS43274.1, CCDS43275.1	4q32.1	2012-08-29			ENSG00000120251	ENSG00000120251		"""Ligand-gated ion channels / Glutamate receptors, ionotropic"", ""Glutamate receptors"""	4572	protein-coding gene	gene with protein product		138247		GLUR2		1311100	Standard	NM_001083619		Approved	GluA2, GLURB	uc003ipl.4	P42262	OTTHUMG00000133836	ENST00000264426.9:c.935G>A	4.37:g.158254023G>A	ENSP00000264426:p.Arg312His	121.0	0.0		118.0	15.0	NM_000826	A8MT92|I6L997|Q96FP6	Missense_Mutation	SNP	ENST00000264426.9	37	CCDS43274.1	.	.	.	.	.	.	.	.	.	.	G	21.9	4.213521	0.79352	.	.	ENSG00000120251	ENST00000507898;ENST00000393815;ENST00000296526;ENST00000264426;ENST00000449365	D;D;D;D;D	0.81499	-1.5;-1.5;-1.5;-1.5;-1.5	5.09	5.09	0.68999	Extracellular ligand-binding receptor (1);	0.000000	0.85682	D	0.000000	D	0.85771	0.5774	L	0.42245	1.32	0.80722	D	1	D;B;D	0.89917	1.0;0.04;0.999	D;B;D	0.74674	0.95;0.002;0.984	D	0.83595	0.0125	10	0.28530	T	0.3	.	18.4737	0.90783	0.0:0.0:1.0:0.0	.	312;312;265	P42262;P42262-2;A8MT92	GRIA2_HUMAN;.;.	H	265;265;312;312;265	ENSP00000426845:R265H;ENSP00000377403:R265H;ENSP00000296526:R312H;ENSP00000264426:R312H;ENSP00000389837:R265H	ENSP00000264426:R312H	R	+	2	0	GRIA2	158473473	1.000000	0.71417	0.999000	0.59377	0.995000	0.86356	9.869000	0.99810	2.341000	0.79615	0.557000	0.71058	CGC	.		0.463	GRIA2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000258367.2		
ITIH6	347365	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	X	54785172	54785172	+	Silent	SNP	G	G	A			TCGA-FV-A3R3-01A-11D-A22F-10	TCGA-FV-A3R3-10A-01D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c285c2fa-24b4-47a1-874d-86e74b002b05	64edddfd-f366-4d51-a8b4-a357b2c68e6c	g.chrX:54785172G>A	ENST00000218436.6	-	8	1364	c.1335C>T	c.(1333-1335)aaC>aaT	p.N445N		NM_198510.2	NP_940912.1	Q6UXX5	ITIH6_HUMAN	inter-alpha-trypsin inhibitor heavy chain family, member 6	445	VWFA. {ECO:0000255|PROSITE- ProRule:PRU00219}.				hyaluronan metabolic process (GO:0030212)	extracellular region (GO:0005576)	serine-type endopeptidase inhibitor activity (GO:0004867)										CTATTCCCCGGTTTTCCAGGG	0.582																																					p.N445N		.											.	.	.	0			c.C1335T						.						53.0	47.0	49.0					X																	54785172		2203	4300	6503	SO:0001819	synonymous_variant	347365	exon8			TCCCCGGTTTTCC	AY358170	CCDS14361.1	Xp11.22-p11.21	2011-10-26	2011-10-26	2011-10-26	ENSG00000102313	ENSG00000102313			28907	protein-coding gene	gene with protein product			"""inter-alpha (globulin) inhibitor H5-like"""	ITIH5L		12975309	Standard	NM_198510		Approved	UNQ6369	uc004dtj.2	Q6UXX5	OTTHUMG00000021634	ENST00000218436.6:c.1335C>T	X.37:g.54785172G>A		120.0	0.0		80.0	24.0	NM_198510	A6NN03	Silent	SNP	ENST00000218436.6	37	CCDS14361.1																																																																																			.		0.582	ITIH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056814.2	NM_198510	
KRT83	3889	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	12	52712959	52712959	+	Missense_Mutation	SNP	G	G	T			TCGA-FV-A3R3-01A-11D-A22F-10	TCGA-FV-A3R3-10A-01D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c285c2fa-24b4-47a1-874d-86e74b002b05	64edddfd-f366-4d51-a8b4-a357b2c68e6c	g.chr12:52712959G>T	ENST00000293670.3	-	2	636	c.574C>A	c.(574-576)Ctg>Atg	p.L192M		NM_002282.3	NP_002273.3	P78385	KRT83_HUMAN	keratin 83	192	Coil 1B.|Rod.				aging (GO:0007568)|epidermis development (GO:0008544)|hair cycle (GO:0042633)	extracellular space (GO:0005615)|keratin filament (GO:0045095)	structural molecule activity (GO:0005198)			NS(1)|central_nervous_system(1)|endometrium(4)|large_intestine(4)|lung(9)|prostate(1)|skin(4)|stomach(7)|upper_aerodigestive_tract(1)	32	Myeloproliferative disorder(4;0.0484)|all_hematologic(5;0.088)			BRCA - Breast invasive adenocarcinoma(357;0.189)		TAGCCCTCCAGCACCTCCTGC	0.622																																					p.L192M	GBM(41;747 834 12702 24089 39393)|Esophageal Squamous(97;805 1414 12559 28198 31861)	.											.	KRT83	91	0			c.C574A						.						138.0	147.0	144.0					12																	52712959		2203	4300	6503	SO:0001583	missense	3889	exon2			CCTCCAGCACCTC	X99141	CCDS8823.1	12q13.13	2013-06-20	2006-07-17	2006-07-17	ENSG00000170523	ENSG00000170523		"""-"", ""Intermediate filaments type II, keratins (basic)"""	6460	protein-coding gene	gene with protein product	"""hard keratin type II"""	602765	"""keratin, hair, basic, 3"""	KRTHB3		9084137, 16831889	Standard	NM_002282		Approved	Hb-3	uc001saf.2	P78385	OTTHUMG00000169632	ENST00000293670.3:c.574C>A	12.37:g.52712959G>T	ENSP00000293670:p.Leu192Met	142.0	0.0		121.0	31.0	NM_002282	A1A4S9|B2RC21|Q6NT21|Q9NSB3	Missense_Mutation	SNP	ENST00000293670.3	37	CCDS8823.1	.	.	.	.	.	.	.	.	.	.	G	15.52	2.857935	0.51376	.	.	ENSG00000170523	ENST00000293670	D	0.88431	-2.38	4.81	2.89	0.33648	Filament (1);	0.000000	0.33712	U	0.004633	D	0.88047	0.6332	L	0.58428	1.81	0.27882	N	0.939653	B	0.32324	0.364	P	0.46320	0.512	T	0.80400	-0.1398	10	0.45353	T	0.12	.	3.2963	0.06968	0.0818:0.262:0.3858:0.2704	.	192	P78385	KRT83_HUMAN	M	192	ENSP00000293670:L192M	ENSP00000293670:L192M	L	-	1	2	KRT83	50999226	0.977000	0.34250	1.000000	0.80357	0.998000	0.95712	1.893000	0.39758	0.490000	0.27771	0.563000	0.77884	CTG	.		0.622	KRT83-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405182.1	NM_002282	
LIFR	3977	hgsc.bcm.edu;broad.mit.edu;mdanderson.org	37	5	38482266	38482266	+	Nonsense_Mutation	SNP	C	C	A			TCGA-FV-A3R3-01A-11D-A22F-10	TCGA-FV-A3R3-10A-01D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c285c2fa-24b4-47a1-874d-86e74b002b05	64edddfd-f366-4d51-a8b4-a357b2c68e6c	g.chr5:38482266C>A	ENST00000263409.4	-	20	2887	c.2725G>T	c.(2725-2727)Gag>Tag	p.E909*	LIFR_ENST00000453190.2_Nonsense_Mutation_p.E909*	NM_002310.5	NP_002301.1	P42702	LIFR_HUMAN	leukemia inhibitory factor receptor alpha	909					cell surface receptor signaling pathway (GO:0007166)|ciliary neurotrophic factor-mediated signaling pathway (GO:0070120)|cytokine-mediated signaling pathway (GO:0019221)|leukemia inhibitory factor signaling pathway (GO:0048861)|oncostatin-M-mediated signaling pathway (GO:0038165)|positive regulation of cell proliferation (GO:0008284)|response to cytokine (GO:0034097)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	ciliary neurotrophic factor receptor binding (GO:0005127)|growth factor binding (GO:0019838)|leukemia inhibitory factor receptor activity (GO:0004923)			NS(2)|breast(4)|endometrium(6)|kidney(2)|large_intestine(30)|liver(2)|lung(21)|ovary(3)|skin(5)|stomach(1)|urinary_tract(2)	78	all_lung(31;0.00021)					TCCAGAACCTCAACATTATTT	0.383			T	PLAG1	salivary adenoma																																p.E909X	Melanoma(13;4 730 6426 9861 34751)	.		Dom	yes		5	5p13-p12	3977	leukemia inhibitory factor receptor		E	.	LIFR	1173	0			c.G2725T						.						61.0	63.0	62.0					5																	38482266		2203	4300	6503	SO:0001587	stop_gained	3977	exon20			GAACCTCAACATT	X61615	CCDS3927.1	5p13-p12	2013-02-11	2006-05-17		ENSG00000113594	ENSG00000113594		"""CD molecules"", ""Fibronectin type III domain containing"""	6597	protein-coding gene	gene with protein product		151443	"""leukemia inhibitory factor receptor"""			1915266	Standard	NM_001127671		Approved	CD118	uc003jli.2	P42702	OTTHUMG00000131138	ENST00000263409.4:c.2725G>T	5.37:g.38482266C>A	ENSP00000263409:p.Glu909*	90.0	0.0		86.0	14.0	NM_002310	Q6LCD9	Nonsense_Mutation	SNP	ENST00000263409.4	37	CCDS3927.1	.	.	.	.	.	.	.	.	.	.	C	40	8.492486	0.98834	.	.	ENSG00000113594	ENST00000263409;ENST00000453190	.	.	.	6.06	6.06	0.98353	.	0.466719	0.26307	N	0.025129	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.45353	T	0.12	-30.0859	20.6397	0.99537	0.0:1.0:0.0:0.0	.	.	.	.	X	909	.	ENSP00000263409:E909X	E	-	1	0	LIFR	38518023	0.999000	0.42202	0.996000	0.52242	0.979000	0.70002	5.114000	0.64648	2.880000	0.98712	0.650000	0.86243	GAG	.		0.383	LIFR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253823.1	NM_002310	
PLPPR1	54886	broad.mit.edu;bcgsc.ca	37	9	104071698	104071698	+	Silent	SNP	C	C	A	rs145402155		TCGA-FV-A3R3-01A-11D-A22F-10	TCGA-FV-A3R3-10A-01D-A22F-10	C	C	.	.	.	.	.	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c285c2fa-24b4-47a1-874d-86e74b002b05	64edddfd-f366-4d51-a8b4-a357b2c68e6c	g.chr9:104071698C>A	ENST00000374874.3	+	5	1030	c.591C>A	c.(589-591)ccC>ccA	p.P197P	LPPR1_ENST00000395056.2_Silent_p.P197P	NM_207299.1	NP_997182.1	Q8TBJ4	LPPR1_HUMAN		197					nervous system development (GO:0007399)	integral component of membrane (GO:0016021)	catalytic activity (GO:0003824)										GATCCTTTCCCTCCAAACACG	0.483																																					p.P197P		.											.	.	.	0			c.C591A						.						93.0	87.0	89.0					9																	104071698		2203	4300	6503	SO:0001819	synonymous_variant	0	exon5			CTTTCCCTCCAAA																												ENST00000374874.3:c.591C>A	9.37:g.104071698C>A		63.0	0.0		48.0	4.0	NM_207299	Q5VX23|Q9NXE2	Silent	SNP	ENST00000374874.3	37	CCDS6751.1																																																																																			C|1.000;T|0.000		0.483	LPPR1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053425.1		
MID2	11043	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;mdanderson.org	37	X	107084301	107084301	+	Nonsense_Mutation	SNP	C	C	T			TCGA-FV-A3R3-01A-11D-A22F-10	TCGA-FV-A3R3-10A-01D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c285c2fa-24b4-47a1-874d-86e74b002b05	64edddfd-f366-4d51-a8b4-a357b2c68e6c	g.chrX:107084301C>T	ENST00000262843.6	+	2	954	c.406C>T	c.(406-408)Cga>Tga	p.R136*	MID2_ENST00000443968.2_Nonsense_Mutation_p.R136*	NM_012216.3|NM_052817.2	NP_036348.2|NP_438112.2	Q9UJV3	TRIM1_HUMAN	midline 2	136					innate immune response (GO:0045087)|negative regulation of viral entry into host cell (GO:0046597)|negative regulation of viral release from host cell (GO:1902187)|negative regulation of viral transcription (GO:0032897)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|protein localization to microtubule (GO:0035372)|protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)	ligase activity (GO:0016874)|microtubule binding (GO:0008017)|phosphoprotein binding (GO:0051219)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|zinc ion binding (GO:0008270)			breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(7)|ovary(1)|prostate(2)	19						GTCTAGCGAGCGAATTGCTTG	0.562																																					p.R136X		.											.	MID2	227	0			c.C406T						.						42.0	38.0	39.0					X																	107084301		2203	4300	6503	SO:0001587	stop_gained	11043	exon2			AGCGAGCGAATTG		CCDS14532.2, CCDS14533.2	Xq22.1-q22.2	2013-02-11			ENSG00000080561	ENSG00000080561		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"", ""Fibronectin type III domain containing"""	7096	protein-coding gene	gene with protein product		300204				10400986	Standard	NM_012216		Approved	FXY2, TRIM1, RNF60	uc004enl.3	Q9UJV3	OTTHUMG00000022171	ENST00000262843.6:c.406C>T	X.37:g.107084301C>T	ENSP00000262843:p.Arg136*	90.0	0.0		75.0	12.0	NM_012216	A6NEL8|A6PVI5|Q5JYF5|Q8WWK1|Q9UJR9	Nonsense_Mutation	SNP	ENST00000262843.6	37	CCDS14532.2	.	.	.	.	.	.	.	.	.	.	C	18.02	3.530285	0.64860	.	.	ENSG00000080561	ENST00000451923;ENST00000262843;ENST00000443968	.	.	.	5.94	-0.583	0.11706	.	0.168083	0.38778	N	0.001561	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.07325	T	0.83	.	17.1355	0.86738	0.7736:0.2264:0.0:0.0	.	.	.	.	X	116;136;136	.	ENSP00000262843:R136X	R	+	1	2	MID2	106970957	0.011000	0.17503	0.748000	0.31131	0.960000	0.62799	0.541000	0.23207	-0.644000	0.05465	0.600000	0.82982	CGA	.		0.562	MID2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000057852.2	NM_012216	
MRPS28	28957	broad.mit.edu;ucsc.edu;bcgsc.ca	37	8	80942420	80942420	+	Missense_Mutation	SNP	A	A	G			TCGA-FV-A3R3-01A-11D-A22F-10	TCGA-FV-A3R3-10A-01D-A22F-10	A	A	.	.	.	.	.	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c285c2fa-24b4-47a1-874d-86e74b002b05	64edddfd-f366-4d51-a8b4-a357b2c68e6c	g.chr8:80942420A>G	ENST00000276585.4	-	1	86	c.64T>C	c.(64-66)Ttc>Ctc	p.F22L	MRPS28_ENST00000522987.1_5'UTR|MRPS28_ENST00000521434.1_5'Flank|TPD52_ENST00000537855.1_Intron|MRPS28_ENST00000521605.1_Missense_Mutation_p.F22L|RP11-92K15.3_ENST00000607017.1_lincRNA	NM_014018.2	NP_054737.1	Q9Y2Q9	RT28_HUMAN	mitochondrial ribosomal protein S28	22						mitochondrial small ribosomal subunit (GO:0005763)|mitochondrion (GO:0005739)	poly(A) RNA binding (GO:0044822)			endometrium(1)|large_intestine(1)|lung(2)|skin(1)	5	Lung NSC(7;1.86e-06)|all_lung(9;6.91e-06)		BRCA - Breast invasive adenocarcinoma(6;0.00769)|Epithelial(68;0.0208)|all cancers(69;0.0805)			GGCCTGAAGAAGAGAAACACT	0.592																																					p.F22L		.											.	MRPS28	90	0			c.T64C						.						40.0	43.0	42.0					8																	80942420		2203	4300	6503	SO:0001583	missense	28957	exon1			TGAAGAAGAGAAA	AB061209	CCDS6226.1	8q21.1-q21.2	2012-09-13			ENSG00000147586	ENSG00000147586		"""Mitochondrial ribosomal proteins / small subunits"""	14513	protein-coding gene	gene with protein product		611990				11279123, 11042152	Standard	NM_014018		Approved	MRP-S28, HSPC007, MRPS35	uc003ybp.3	Q9Y2Q9	OTTHUMG00000164642	ENST00000276585.4:c.64T>C	8.37:g.80942420A>G	ENSP00000276585:p.Phe22Leu	43.0	0.0		36.0	4.0	NM_014018	B2RDZ7|Q96Q21	Missense_Mutation	SNP	ENST00000276585.4	37	CCDS6226.1	.	.	.	.	.	.	.	.	.	.	A	10.43	1.347444	0.24426	.	.	ENSG00000147586	ENST00000276585;ENST00000521605	T	0.40756	1.02	5.38	2.96	0.34315	.	1.125180	0.06503	N	0.736579	T	0.22589	0.0545	N	0.12746	0.255	0.09310	N	0.999991	B	0.02656	0.0	B	0.06405	0.002	T	0.27536	-1.0071	10	0.09084	T	0.74	.	5.7469	0.18124	0.5854:0.33:0.0846:0.0	.	22	Q9Y2Q9	RT28_HUMAN	L	22	ENSP00000276585:F22L	ENSP00000276585:F22L	F	-	1	0	MRPS28	81104975	0.217000	0.23597	0.036000	0.18154	0.119000	0.20118	1.308000	0.33528	0.475000	0.27415	0.533000	0.62120	TTC	.		0.592	MRPS28-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379526.1	NM_014018	
MUC16	94025	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	19	9060181	9060181	+	Missense_Mutation	SNP	T	T	G			TCGA-FV-A3R3-01A-11D-A22F-10	TCGA-FV-A3R3-10A-01D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c285c2fa-24b4-47a1-874d-86e74b002b05	64edddfd-f366-4d51-a8b4-a357b2c68e6c	g.chr19:9060181T>G	ENST00000397910.4	-	3	27468	c.27265A>C	c.(27265-27267)Aca>Cca	p.T9089P		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	9091	Ser-rich.|Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						CCCCTTGATGTAGCCCCAGGA	0.478																																					p.T9089P		.											.	MUC16	566	0			c.A27265C						.						179.0	166.0	170.0					19																	9060181		1922	4131	6053	SO:0001583	missense	94025	exon3			TTGATGTAGCCCC	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"""Mucins"""	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.27265A>C	19.37:g.9060181T>G	ENSP00000381008:p.Thr9089Pro	111.0	0.0		108.0	14.0	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	.	.	.	.	.	.	.	.	.	.	t	3.272	-0.148960	0.06585	.	.	ENSG00000181143	ENST00000397910	T	0.02579	4.24	2.5	-4.99	0.03010	.	.	.	.	.	T	0.01730	0.0055	N	0.24115	0.695	.	.	.	B	0.28713	0.22	B	0.27076	0.076	T	0.44360	-0.9333	8	0.87932	D	0	.	0.1031	0.00050	0.3214:0.2327:0.1631:0.2828	.	9089	B5ME49	.	P	9089	ENSP00000381008:T9089P	ENSP00000381008:T9089P	T	-	1	0	MUC16	8921181	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-0.710000	0.05024	-1.618000	0.01568	-0.658000	0.03865	ACA	.		0.478	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
MUC4	4585	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca;mdanderson.org	37	3	195513066	195513066	+	Silent	SNP	G	G	T			TCGA-FV-A3R3-01A-11D-A22F-10	TCGA-FV-A3R3-10A-01D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c285c2fa-24b4-47a1-874d-86e74b002b05	64edddfd-f366-4d51-a8b4-a357b2c68e6c	g.chr3:195513066G>T	ENST00000463781.3	-	2	5844	c.5385C>A	c.(5383-5385)gtC>gtA	p.V1795V	MUC4_ENST00000346145.4_Intron|MUC4_ENST00000349607.4_Intron|MUC4_ENST00000475231.1_Silent_p.V1795V	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	0					cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)			NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		AAACGTCGGTGACAGGAAGAC	0.592																																					p.V1795V		.											.	MUC4	90	0			c.C5385A						.						78.0	79.0	79.0					3																	195513066		689	1591	2280	SO:0001819	synonymous_variant	4585	exon2			GTCGGTGACAGGA	AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.5385C>A	3.37:g.195513066G>T		539.0	0.0		411.0	53.0	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Silent	SNP	ENST00000463781.3	37	CCDS54700.1																																																																																			.		0.592	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
MYH9	4627	broad.mit.edu;bcgsc.ca	37	22	36737554	36737554	+	Silent	SNP	G	G	A			TCGA-FV-A3R3-01A-11D-A22F-10	TCGA-FV-A3R3-10A-01D-A22F-10	G	G	.	.	.	.	.	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c285c2fa-24b4-47a1-874d-86e74b002b05	64edddfd-f366-4d51-a8b4-a357b2c68e6c	g.chr22:36737554G>A	ENST00000216181.5	-	3	581	c.351C>T	c.(349-351)ttC>ttT	p.F117F	MYH9_ENST00000401701.1_Silent_p.F117F	NM_002473.4	NP_002464.1	P35579	MYH9_HUMAN	myosin, heavy chain 9, non-muscle	117	Myosin motor.				actin cytoskeleton reorganization (GO:0031532)|actin filament-based movement (GO:0030048)|actomyosin structure organization (GO:0031032)|angiogenesis (GO:0001525)|ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|blood vessel endothelial cell migration (GO:0043534)|cytokinesis (GO:0000910)|establishment of meiotic spindle localization (GO:0051295)|establishment of T cell polarity (GO:0001768)|in utero embryonic development (GO:0001701)|integrin-mediated signaling pathway (GO:0007229)|leukocyte migration (GO:0050900)|meiotic spindle organization (GO:0000212)|membrane protein ectodomain proteolysis (GO:0006509)|monocyte differentiation (GO:0030224)|myoblast fusion (GO:0007520)|platelet aggregation (GO:0070527)|platelet formation (GO:0030220)|protein transport (GO:0015031)|regulation of cell shape (GO:0008360)|termination of G-protein coupled receptor signaling pathway (GO:0038032)|uropod organization (GO:0032796)	actin cytoskeleton (GO:0015629)|actomyosin (GO:0042641)|actomyosin contractile ring (GO:0005826)|cell leading edge (GO:0031252)|cell-cell adherens junction (GO:0005913)|cleavage furrow (GO:0032154)|cortical cytoskeleton (GO:0030863)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|immunological synapse (GO:0001772)|membrane (GO:0016020)|myosin II complex (GO:0016460)|myosin II filament (GO:0097513)|neuromuscular junction (GO:0031594)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|ruffle (GO:0001726)|spindle (GO:0005819)|stress fiber (GO:0001725)|uropod (GO:0001931)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|actin-dependent ATPase activity (GO:0030898)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microfilament motor activity (GO:0000146)|motor activity (GO:0003774)|poly(A) RNA binding (GO:0044822)|protein anchor (GO:0043495)|protein homodimerization activity (GO:0042803)			NS(1)|breast(8)|central_nervous_system(3)|cervix(2)|endometrium(5)|kidney(4)|large_intestine(16)|lung(29)|ovary(4)|pancreas(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(6)|urinary_tract(3)	86						TGACCACACAGAACAGGCCTG	0.448			T	ALK	ALCL		"""Deafness, autosomal dominant 17, Epstein syndrome, Fechtner syndrome, May-Hegglin anomaly, Sebastian syndrome"""		Hereditary Macrothrombocytopenia, MYH9-associated																												p.F117F		.		Dom	yes		22	22q13.1	4627	"""myosin, heavy polypeptide 9, non-muscle"""	yes	L	.	MYH9	292	0			c.C351T						.						117.0	100.0	106.0					22																	36737554		2203	4300	6503	SO:0001819	synonymous_variant	4627	exon3	Familial Cancer Database	MYHIIA syndrome, incl. Fechtner Syndrome, FTNS, and May-Hegglin Anomaly, MHA	CACACAGAACAGG		CCDS13927.1	22q13.1	2014-09-17	2006-09-29		ENSG00000100345	ENSG00000100345		"""Myosins / Myosin superfamily : Class II"""	7579	protein-coding gene	gene with protein product	"""nonmuscle myosin heavy chain II-A"""	160775	"""myosin, heavy polypeptide 9, non-muscle"""	DFNA17		1860190, 11023810	Standard	NM_002473		Approved	NMMHCA, NMHC-II-A, MHA, FTNS, EPSTS	uc003apg.3	P35579	OTTHUMG00000030429	ENST00000216181.5:c.351C>T	22.37:g.36737554G>A		77.0	0.0		73.0	4.0	NM_002473	A8K6E4|O60805|Q60FE2|Q86T83	Silent	SNP	ENST00000216181.5	37	CCDS13927.1																																																																																			.		0.448	MYH9-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000259110.3	NM_002473	
NEK2	4751	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	1	211848801	211848801	+	Missense_Mutation	SNP	G	G	T			TCGA-FV-A3R3-01A-11D-A22F-10	TCGA-FV-A3R3-10A-01D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c285c2fa-24b4-47a1-874d-86e74b002b05	64edddfd-f366-4d51-a8b4-a357b2c68e6c	g.chr1:211848801G>T	ENST00000366999.4	-	1	159	c.21C>A	c.(19-21)gaC>gaA	p.D7E	RP11-122M14.1_ENST00000415202.1_RNA|NEK2_ENST00000540251.1_Intron|NEK2_ENST00000366998.3_Missense_Mutation_p.D7E	NM_002497.3	NP_002488.1	P51955	NEK2_HUMAN	NIMA-related kinase 2	7					blastocyst development (GO:0001824)|centrosome separation (GO:0051299)|chromosome segregation (GO:0007059)|G2/M transition of mitotic cell cycle (GO:0000086)|meiotic nuclear division (GO:0007126)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic sister chromatid segregation (GO:0000070)|negative regulation of centriole-centriole cohesion (GO:1903126)|negative regulation of DNA binding (GO:0043392)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of mitosis (GO:0007088)|regulation of mitotic centrosome separation (GO:0046602)|spindle assembly (GO:0051225)|spindle assembly involved in mitosis (GO:0090307)	centrosome (GO:0005813)|condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|intercellular bridge (GO:0045171)|kinetochore (GO:0000776)|microtubule (GO:0005874)|midbody (GO:0030496)|nucleus (GO:0005634)|protein complex (GO:0043234)|spindle pole (GO:0000922)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|protein phosphatase binding (GO:0019903)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|stomach(1)	3				OV - Ovarian serous cystadenocarcinoma(81;0.00203)|all cancers(67;0.0339)|Epithelial(68;0.0546)		ACACTTCATAGTCCTCAGCCC	0.647																																					p.D7E		.											.	NEK2	765	0			c.C21A						.						62.0	62.0	62.0					1																	211848801		2203	4300	6503	SO:0001583	missense	4751	exon1			TTCATAGTCCTCA	U11050	CCDS1500.1, CCDS55682.1, CCDS73024.1	1q32.3	2014-06-12	2012-11-15		ENSG00000117650	ENSG00000117650			7745	protein-coding gene	gene with protein product	"""HsPK 21"", ""protein phosphatase 1, regulatory subunit 111"""	604043	"""NIMA (never in mitosis gene a)-related kinase 2"""			8274451, 24043777	Standard	NM_002497		Approved	NLK1, NEK2A, RP67, PPP1R111	uc001hir.2	P51955	OTTHUMG00000037121	ENST00000366999.4:c.21C>A	1.37:g.211848801G>T	ENSP00000355966:p.Asp7Glu	80.0	0.0		67.0	10.0	NM_002497	Q53FD6|Q5I1Z9|Q5VXZ1|Q6NZX8|Q7Z634|Q86XH2|Q96QN9	Missense_Mutation	SNP	ENST00000366999.4	37	CCDS1500.1	.	.	.	.	.	.	.	.	.	.	G	20.7	4.035155	0.75617	.	.	ENSG00000117650	ENST00000366999;ENST00000366998	T;T	0.25749	1.78;1.78	5.35	5.35	0.76521	Protein kinase-like domain (1);	0.000000	0.85682	D	0.000000	T	0.29652	0.0740	M	0.68317	2.08	0.80722	D	1	P;P;P	0.40083	0.525;0.578;0.702	B;B;B	0.40636	0.205;0.18;0.335	T	0.01409	-1.1362	10	0.25106	T	0.35	.	12.8788	0.58006	0.074:0.0:0.926:0.0	.	7;7;7	P51955-2;P51955;P51955-4	.;NEK2_HUMAN;.	E	7	ENSP00000355966:D7E;ENSP00000355965:D7E	ENSP00000355965:D7E	D	-	3	2	NEK2	209915424	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	2.547000	0.45786	2.941000	0.99782	0.655000	0.94253	GAC	.		0.647	NEK2-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090154.1	NM_002497	
NEU1	4758	broad.mit.edu;ucsc.edu	37	6	31829947	31829947	+	Missense_Mutation	SNP	C	C	T			TCGA-FV-A3R3-01A-11D-A22F-10	TCGA-FV-A3R3-10A-01D-A22F-10	C	C	.	.	.	.	.	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c285c2fa-24b4-47a1-874d-86e74b002b05	64edddfd-f366-4d51-a8b4-a357b2c68e6c	g.chr6:31829947C>T	ENST00000375631.4	-	2	310	c.181G>A	c.(181-183)Gag>Aag	p.E61K		NM_000434.3	NP_000425.1	Q99519	NEUR1_HUMAN	sialidase 1 (lysosomal sialidase)	61					glycosphingolipid metabolic process (GO:0006687)|lipid catabolic process (GO:0016042)|oligosaccharide catabolic process (GO:0009313)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	cell junction (GO:0030054)|cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|intracellular membrane-bounded organelle (GO:0043231)|lysosomal lumen (GO:0043202)|lysosome (GO:0005764)|plasma membrane (GO:0005886)	exo-alpha-(2->3)-sialidase activity (GO:0052794)|exo-alpha-(2->6)-sialidase activity (GO:0052795)|exo-alpha-(2->8)-sialidase activity (GO:0052796)|exo-alpha-sialidase activity (GO:0004308)			kidney(1)|large_intestine(1)|lung(6)|ovary(1)|prostate(1)	10					Oseltamivir(DB00198)	AGCAGTTGCTCCATGGTCACC	0.597																																					p.E61K		.											.	NEU1	91	0			c.G181A						.						75.0	48.0	58.0					6																	31829947		1511	2708	4219	SO:0001583	missense	4758	exon2			GTTGCTCCATGGT	AF040958	CCDS4723.1	6p21	2012-10-02			ENSG00000204386	ENSG00000204386	3.2.1.18		7758	protein-coding gene	gene with protein product		608272		NEU		9054950	Standard	NM_000434		Approved		uc003nxq.4	Q99519	OTTHUMG00000031284	ENST00000375631.4:c.181G>A	6.37:g.31829947C>T	ENSP00000364782:p.Glu61Lys	65.0	0.0		42.0	3.0	NM_000434		Missense_Mutation	SNP	ENST00000375631.4	37	CCDS4723.1	.	.	.	.	.	.	.	.	.	.	C	37	6.167549	0.97343	.	.	ENSG00000204386	ENST00000375631	D	0.90004	-2.6	5.46	5.46	0.80206	Neuraminidase (1);	0.000000	0.85682	D	0.000000	D	0.92625	0.7657	M	0.72894	2.215	0.80722	D	1	D;D	0.76494	0.999;0.999	D;P	0.64877	0.93;0.89	D	0.92658	0.6139	10	0.66056	D	0.02	-9.156	16.8609	0.86018	0.0:1.0:0.0:0.0	.	61;61	E9PIF4;Q99519	.;NEUR1_HUMAN	K	61	ENSP00000364782:E61K	ENSP00000364782:E61K	E	-	1	0	NEU1	31937926	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.927000	0.75840	2.840000	0.97914	0.655000	0.94253	GAG	.		0.597	NEU1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076616.2		
NPC1	4864	broad.mit.edu;bcgsc.ca	37	18	21140425	21140425	+	Missense_Mutation	SNP	C	C	T			TCGA-FV-A3R3-01A-11D-A22F-10	TCGA-FV-A3R3-10A-01D-A22F-10	C	C	.	.	.	.	.	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c285c2fa-24b4-47a1-874d-86e74b002b05	64edddfd-f366-4d51-a8b4-a357b2c68e6c	g.chr18:21140425C>T	ENST00000269228.5	-	6	1205	c.651G>A	c.(649-651)atG>atA	p.M217I	NPC1_ENST00000540608.1_5'UTR|NPC1_ENST00000412552.2_5'Flank	NM_000271.4	NP_000262.2	O15118	NPC1_HUMAN	Niemann-Pick disease, type C1	217					adult walking behavior (GO:0007628)|autophagy (GO:0006914)|bile acid metabolic process (GO:0008206)|cellular response to low-density lipoprotein particle stimulus (GO:0071404)|cellular response to steroid hormone stimulus (GO:0071383)|cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|cholesterol transport (GO:0030301)|endocytosis (GO:0006897)|establishment of protein localization to membrane (GO:0090150)|lysosomal transport (GO:0007041)|membrane raft organization (GO:0031579)|negative regulation of cell death (GO:0060548)|negative regulation of macroautophagy (GO:0016242)|protein glycosylation (GO:0006486)|response to cadmium ion (GO:0046686)|response to drug (GO:0042493)|signal transduction (GO:0007165)	endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|membrane (GO:0016020)|membrane raft (GO:0045121)|nuclear envelope (GO:0005635)|perinuclear region of cytoplasm (GO:0048471)	cholesterol binding (GO:0015485)|hedgehog receptor activity (GO:0008158)|receptor activity (GO:0004872)|sterol transporter activity (GO:0015248)|transmembrane signaling receptor activity (GO:0004888)			breast(1)|cervix(1)|endometrium(4)|kidney(6)|large_intestine(10)|lung(13)|ovary(2)|stomach(1)	38	all_cancers(21;0.000106)|all_epithelial(16;6.57e-07)|Lung NSC(20;0.00166)|all_lung(20;0.00536)|Colorectal(14;0.0202)|Ovarian(20;0.127)					TCATGGGCTCCATCCCATGGA	0.423																																					p.M217I		.											.	NPC1	92	0			c.G651A						.						62.0	56.0	58.0					18																	21140425		2203	4300	6503	SO:0001583	missense	4864	exon6			GGGCTCCATCCCA	AF002020	CCDS11878.1	18q11.2	2014-06-17			ENSG00000141458	ENSG00000141458			7897	protein-coding gene	gene with protein product		607623				8446622	Standard	NM_000271		Approved		uc002kum.4	O15118	OTTHUMG00000131873	ENST00000269228.5:c.651G>A	18.37:g.21140425C>T	ENSP00000269228:p.Met217Ile	83.0	0.0		83.0	5.0	NM_000271	B4DET3|Q9P130	Missense_Mutation	SNP	ENST00000269228.5	37	CCDS11878.1	.	.	.	.	.	.	.	.	.	.	C	13.54	2.268896	0.40095	.	.	ENSG00000141458	ENST00000269228;ENST00000540608	D	0.92911	-3.13	5.73	5.73	0.89815	.	0.183542	0.64402	D	0.000015	D	0.89777	0.6813	L	0.43152	1.355	0.80722	D	1	B;B	0.09022	0.002;0.001	B;B	0.10450	0.005;0.003	D	0.84349	0.0531	10	0.34782	T	0.22	-39.9729	19.8932	0.96939	0.0:1.0:0.0:0.0	.	228;217	Q59GR1;O15118	.;NPC1_HUMAN	I	217;62	ENSP00000269228:M217I	ENSP00000269228:M217I	M	-	3	0	NPC1	19394423	1.000000	0.71417	1.000000	0.80357	0.932000	0.56968	5.048000	0.64238	2.698000	0.92095	0.655000	0.94253	ATG	.		0.423	NPC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254823.2	NM_000271	
NSD1	64324	broad.mit.edu;bcgsc.ca	37	5	176675231	176675231	+	Missense_Mutation	SNP	A	A	G			TCGA-FV-A3R3-01A-11D-A22F-10	TCGA-FV-A3R3-10A-01D-A22F-10	A	A	.	.	.	.	.	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c285c2fa-24b4-47a1-874d-86e74b002b05	64edddfd-f366-4d51-a8b4-a357b2c68e6c	g.chr5:176675231A>G	ENST00000439151.2	+	11	4592	c.4547A>G	c.(4546-4548)gAg>gGg	p.E1516G	NSD1_ENST00000361032.4_Missense_Mutation_p.E1413G|NSD1_ENST00000347982.4_Missense_Mutation_p.E1247G|NSD1_ENST00000354179.4_Missense_Mutation_p.E1247G	NM_022455.4	NP_071900.2	Q96L73	NSD1_HUMAN	nuclear receptor binding SET domain protein 1	1516					gastrulation with mouth forming second (GO:0001702)|histone H3-K36 methylation (GO:0010452)|histone H4-K20 methylation (GO:0034770)|histone methylation (GO:0016571)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	chromosome (GO:0005694)|nucleus (GO:0005634)	androgen receptor binding (GO:0050681)|chromatin binding (GO:0003682)|estrogen receptor binding (GO:0030331)|histone methyltransferase activity (H3-K36 specific) (GO:0046975)|histone methyltransferase activity (H4-K20 specific) (GO:0042799)|retinoic acid receptor binding (GO:0042974)|retinoid X receptor binding (GO:0046965)|thyroid hormone receptor binding (GO:0046966)|transcription cofactor activity (GO:0003712)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(13)|large_intestine(18)|lung(24)|ovary(2)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(7)|urinary_tract(3)	96	all_cancers(89;1.57e-05)|Renal(175;0.000269)|Lung NSC(126;0.00111)|all_lung(126;0.002)	all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)|Epithelial(233;0.198)	Kidney(146;0.235)		GAGACTGTTGAGGAAGGTGTA	0.493			T	NUP98	AML		Sotos Syndrome		Weaver syndrome;Sotos syndrome;Beckwith-Wiedemann syndrome	HNSCC(47;0.14)																											p.E1516G		.		Dom	yes		5	5q35	64324	nuclear receptor binding SET domain protein 1	yes	L	.	NSD1	188	0			c.A4547G						.						73.0	74.0	74.0					5																	176675231		2203	4300	6503	SO:0001583	missense	64324	exon11	Familial Cancer Database	Weaver-Smith syndrome;Cerebral Gigantism;BWS, Exomphalos-Macroglossia-Gigantism (EMG) syndrome, Wiedemann-Beckwith syndrome, WBS	CTGTTGAGGAAGG	AK026066	CCDS4412.1, CCDS4413.1	5q35	2014-09-17	2003-03-12		ENSG00000165671	ENSG00000165671		"""Chromatin-modifying enzymes / K-methyltransferases"", ""Zinc fingers, PHD-type"""	14234	protein-coding gene	gene with protein product		606681	"""Sotos syndrome"""	STO		9628876, 11896389	Standard	NM_022455		Approved	ARA267, FLJ22263, KMT3B	uc003mfr.4	Q96L73	OTTHUMG00000130846	ENST00000439151.2:c.4547A>G	5.37:g.176675231A>G	ENSP00000395929:p.Glu1516Gly	73.0	0.0		45.0	4.0	NM_022455	Q96PD8|Q96RN7	Missense_Mutation	SNP	ENST00000439151.2	37	CCDS4412.1	.	.	.	.	.	.	.	.	.	.	A	17.54	3.414901	0.62511	.	.	ENSG00000165671	ENST00000354179;ENST00000439151;ENST00000347982;ENST00000361032	D;D;D;D	0.95272	-3.66;-3.66;-3.66;-3.66	5.22	5.22	0.72569	Zinc finger, FYVE/PHD-type (1);	0.000000	0.56097	D	0.000028	D	0.96097	0.8728	L	0.56769	1.78	0.38289	D	0.942654	D;P;P	0.69078	0.997;0.607;0.714	D;B;B	0.66351	0.943;0.202;0.16	D	0.97415	1.0005	10	0.62326	D	0.03	.	15.0985	0.72253	1.0:0.0:0.0:0.0	.	1247;1413;1516	Q96L73-2;Q96L73-3;Q96L73	.;.;NSD1_HUMAN	G	1247;1516;1247;1413	ENSP00000346111:E1247G;ENSP00000395929:E1516G;ENSP00000343209:E1247G;ENSP00000354310:E1413G	ENSP00000343209:E1247G	E	+	2	0	NSD1	176607837	1.000000	0.71417	0.928000	0.36995	0.973000	0.67179	6.725000	0.74752	1.964000	0.57103	0.533000	0.62120	GAG	.		0.493	NSD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253412.2	NM_172349	
POM121C	100101267	broad.mit.edu;mdanderson.org	37	7	75045350	75045350	+	IGR	SNP	G	G	A			TCGA-FV-A3R3-01A-11D-A22F-10	TCGA-FV-A3R3-10A-01D-A22F-10	G	G	.	.	.	.	.	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c285c2fa-24b4-47a1-874d-86e74b002b05	64edddfd-f366-4d51-a8b4-a357b2c68e6c	g.chr7:75045350G>A	ENST00000257665.5	-	0	5700				NSUN5P1_ENST00000393633.2_RNA			A8CG34	P121C_HUMAN	POM121 transmembrane nucleoporin C						mRNA transport (GO:0051028)|protein transport (GO:0015031)	endoplasmic reticulum (GO:0005783)|nuclear pore (GO:0005643)				central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(6)|prostate(1)|skin(1)|urinary_tract(1)	14						AGCGAGCCCTGTGCCACGCGC	0.627																																					.		.											.	NSUN5P1	22	0			.						.						21.0	23.0	22.0					7																	75045350		2199	4295	6494	SO:0001628	intergenic_variant	155400	.			AGCCCTGTGCCAC		CCDS47617.1	7q11.23	2012-03-13	2012-03-13		ENSG00000135213	ENSG00000272391			34005	protein-coding gene	gene with protein product		615754	"""POM121 membrane glycoprotein C"""			17900573	Standard	NM_001099415		Approved		uc003udk.4	A8CG34	OTTHUMG00000156238		7.37:g.75045350G>A		96.0	0.0		69.0	25.0	.	O75115|Q9Y2N3|Q9Y4S7	RNA	SNP	ENST00000257665.5	37																																																																																				.		0.627	POM121C-003	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000343919.2	NM_001099415	
PAN2	9924	ucsc.edu;bcgsc.ca	37	12	56720646	56720646	+	Silent	SNP	T	T	C			TCGA-FV-A3R3-01A-11D-A22F-10	TCGA-FV-A3R3-10A-01D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.		Illumina HiSeq	c285c2fa-24b4-47a1-874d-86e74b002b05	64edddfd-f366-4d51-a8b4-a357b2c68e6c	g.chr12:56720646T>C	ENST00000425394.2	-	7	1393	c.1017A>G	c.(1015-1017)tcA>tcG	p.S339S	PAN2_ENST00000440411.3_Silent_p.S339S|PAN2_ENST00000548043.1_Silent_p.S339S|PAN2_ENST00000257931.5_Silent_p.S339S	NM_001127460.2	NP_001120932	Q9HBH5	RDH14_HUMAN	PAN2 poly(A) specific ribonuclease subunit	0					osteoblast differentiation (GO:0001649)	endoplasmic reticulum (GO:0005783)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	oxidoreductase activity (GO:0016491)			NS(1)|breast(2)|endometrium(2)|kidney(2)|large_intestine(6)|liver(1)|lung(18)|ovary(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	41					Vitamin A(DB00162)	GCTTGCTGGCTGACACATCAA	0.562																																					p.S339S		.											.	PAN2	702	0			c.A1017G						.						94.0	93.0	94.0					12																	56720646		2203	4300	6503	SO:0001819	synonymous_variant	9924	exon7			GCTGGCTGACACA	AB014610	CCDS8915.1, CCDS44922.1, CCDS53802.1	12q13.2	2014-03-27	2014-03-27	2008-01-08		ENSG00000135473		"""Ubiquitin-specific peptidases"""	20074	protein-coding gene	gene with protein product	"""PAN2 homolog, PABP1 dependent poly A specific ribonuclease subunit (S. cerevisiae)"""		"""ubiquitin specific protease 52"", ""ubiquitin specific peptidase 52"", ""PAN2 poly(A) specific ribonuclease subunit homolog (S. cerevisiae)"""	USP52		12838346, 14583602	Standard	NM_014871		Approved	KIAA0710, hPAN2	uc001skx.3	Q504Q3	OTTHUMG00000170412	ENST00000425394.2:c.1017A>G	12.37:g.56720646T>C		33.0	0.0		38.0	4.0	NM_014871		Silent	SNP	ENST00000425394.2	37	CCDS44922.1																																																																																			.		0.562	PAN2-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000409024.1	NM_014871	
PCDHGA4	56111	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	5	140736620	140736620	+	Missense_Mutation	SNP	C	C	T			TCGA-FV-A3R3-01A-11D-A22F-10	TCGA-FV-A3R3-10A-01D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c285c2fa-24b4-47a1-874d-86e74b002b05	64edddfd-f366-4d51-a8b4-a357b2c68e6c	g.chr5:140736620C>T	ENST00000571252.1	+	1	1853	c.1853C>T	c.(1852-1854)gCa>gTa	p.A618V	PCDHGA2_ENST00000394576.2_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGB1_ENST00000523390.1_Intron	NM_018917.2	NP_061740	Q9Y5G9	PCDG4_HUMAN	protocadherin gamma subfamily A, 4	618	Cadherin 6. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			endometrium(1)|kidney(1)|lung(3)	5			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GGACTATTTGCAGTGGGGCTG	0.622																																					p.A618V		.											.	.	.	0			c.C1853T						.						37.0	45.0	42.0					5																	140736620		2197	4297	6494	SO:0001583	missense	56111	exon1			TATTTGCAGTGGG	AF152511	CCDS58979.1, CCDS58979.2, CCDS75331.1	5q31	2010-01-26						"""Cadherins / Protocadherins : Clustered"""	8702	other	protocadherin		606291				10380929	Standard	NM_018917		Approved	PCDH-GAMMA-A4		Q9Y5G9		ENST00000571252.1:c.1853C>T	5.37:g.140736620C>T	ENSP00000458570:p.Ala618Val	177.0	0.0		143.0	15.0	NM_018917	Q9Y5D3	Missense_Mutation	SNP	ENST00000571252.1	37	CCDS58979.1																																																																																			.		0.622	PCDHGA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437959.1	NM_018917	
PCK1	5105	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	20	56139383	56139383	+	Missense_Mutation	SNP	G	G	A			TCGA-FV-A3R3-01A-11D-A22F-10	TCGA-FV-A3R3-10A-01D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c285c2fa-24b4-47a1-874d-86e74b002b05	64edddfd-f366-4d51-a8b4-a357b2c68e6c	g.chr20:56139383G>A	ENST00000319441.4	+	7	1284	c.1120G>A	c.(1120-1122)Gat>Aat	p.D374N	PCK1_ENST00000535860.1_Missense_Mutation_p.D242N|PCK1_ENST00000543666.1_Missense_Mutation_p.D57N	NM_002591.3	NP_002582.3	P35558	PCKGC_HUMAN	phosphoenolpyruvate carboxykinase 1 (soluble)	374					carbohydrate metabolic process (GO:0005975)|drug metabolic process (GO:0017144)|gluconeogenesis (GO:0006094)|glucose homeostasis (GO:0042593)|glucose metabolic process (GO:0006006)|glycerol biosynthetic process from pyruvate (GO:0046327)|internal protein amino acid acetylation (GO:0006475)|oxaloacetate metabolic process (GO:0006107)|response to activity (GO:0014823)|response to insulin (GO:0032868)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	carboxylic acid binding (GO:0031406)|GDP binding (GO:0019003)|GTP binding (GO:0005525)|magnesium ion binding (GO:0000287)|manganese ion binding (GO:0030145)|phosphoenolpyruvate carboxykinase (GTP) activity (GO:0004613)			endometrium(2)|kidney(1)|large_intestine(4)|liver(2)|lung(19)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	34	Lung NSC(12;0.000764)|all_lung(29;0.00264)|Melanoma(10;0.242)		BRCA - Breast invasive adenocarcinoma(13;9.88e-12)|Epithelial(14;3.41e-08)|all cancers(14;2.13e-07)			GGAAGGCATTGATGAGCCGCT	0.557																																					p.D374N		.											.	PCK1	227	0			c.G1120A						.						104.0	91.0	96.0					20																	56139383		2203	4300	6503	SO:0001583	missense	5105	exon7			GGCATTGATGAGC		CCDS13460.1	20q13.31	2007-11-06			ENSG00000124253	ENSG00000124253	4.1.1.32		8724	protein-coding gene	gene with protein product		614168				1492743	Standard	NM_002591		Approved	PEPCK-C	uc002xyn.4	P35558	OTTHUMG00000032825	ENST00000319441.4:c.1120G>A	20.37:g.56139383G>A	ENSP00000319814:p.Asp374Asn	131.0	0.0		94.0	16.0	NM_002591	A8K437|B4DT64|Q8TCA3|Q9UJD2	Missense_Mutation	SNP	ENST00000319441.4	37	CCDS13460.1	.	.	.	.	.	.	.	.	.	.	G	13.35	2.210471	0.39102	.	.	ENSG00000124253	ENST00000540165;ENST00000319441;ENST00000543666;ENST00000535860	T;T;T	0.09911	2.93;2.93;2.93	5.31	5.31	0.75309	.	0.086985	0.85682	D	0.000000	T	0.16128	0.0388	M	0.76574	2.34	0.80722	D	1	B;B	0.15930	0.002;0.015	B;B	0.22753	0.013;0.041	T	0.01635	-1.1307	10	0.35671	T	0.21	-44.3202	12.6654	0.56840	0.0757:0.0:0.9243:0.0	.	57;374	B4DT64;P35558	.;PCKGC_HUMAN	N	56;374;57;242	ENSP00000319814:D374N;ENSP00000445767:D57N;ENSP00000444342:D242N	ENSP00000319814:D374N	D	+	1	0	PCK1	55572789	1.000000	0.71417	0.228000	0.23943	0.120000	0.20174	7.505000	0.81655	2.636000	0.89361	0.655000	0.94253	GAT	.		0.557	PCK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079851.2		
PCK1	5105	broad.mit.edu;ucsc.edu;bcgsc.ca	37	20	56139386	56139386	+	Missense_Mutation	SNP	G	G	A			TCGA-FV-A3R3-01A-11D-A22F-10	TCGA-FV-A3R3-10A-01D-A22F-10	G	G	.	.	.	.	.	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c285c2fa-24b4-47a1-874d-86e74b002b05	64edddfd-f366-4d51-a8b4-a357b2c68e6c	g.chr20:56139386G>A	ENST00000319441.4	+	7	1287	c.1123G>A	c.(1123-1125)Gag>Aag	p.E375K	PCK1_ENST00000535860.1_Missense_Mutation_p.E243K|PCK1_ENST00000543666.1_Missense_Mutation_p.E58K	NM_002591.3	NP_002582.3	P35558	PCKGC_HUMAN	phosphoenolpyruvate carboxykinase 1 (soluble)	375					carbohydrate metabolic process (GO:0005975)|drug metabolic process (GO:0017144)|gluconeogenesis (GO:0006094)|glucose homeostasis (GO:0042593)|glucose metabolic process (GO:0006006)|glycerol biosynthetic process from pyruvate (GO:0046327)|internal protein amino acid acetylation (GO:0006475)|oxaloacetate metabolic process (GO:0006107)|response to activity (GO:0014823)|response to insulin (GO:0032868)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	carboxylic acid binding (GO:0031406)|GDP binding (GO:0019003)|GTP binding (GO:0005525)|magnesium ion binding (GO:0000287)|manganese ion binding (GO:0030145)|phosphoenolpyruvate carboxykinase (GTP) activity (GO:0004613)			endometrium(2)|kidney(1)|large_intestine(4)|liver(2)|lung(19)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	34	Lung NSC(12;0.000764)|all_lung(29;0.00264)|Melanoma(10;0.242)		BRCA - Breast invasive adenocarcinoma(13;9.88e-12)|Epithelial(14;3.41e-08)|all cancers(14;2.13e-07)			AGGCATTGATGAGCCGCTAGC	0.562																																					p.E375K		.											.	PCK1	227	0			c.G1123A						.						104.0	91.0	95.0					20																	56139386		2203	4300	6503	SO:0001583	missense	5105	exon7			ATTGATGAGCCGC		CCDS13460.1	20q13.31	2007-11-06			ENSG00000124253	ENSG00000124253	4.1.1.32		8724	protein-coding gene	gene with protein product		614168				1492743	Standard	NM_002591		Approved	PEPCK-C	uc002xyn.4	P35558	OTTHUMG00000032825	ENST00000319441.4:c.1123G>A	20.37:g.56139386G>A	ENSP00000319814:p.Glu375Lys	134.0	1.0		93.0	16.0	NM_002591	A8K437|B4DT64|Q8TCA3|Q9UJD2	Missense_Mutation	SNP	ENST00000319441.4	37	CCDS13460.1	.	.	.	.	.	.	.	.	.	.	G	1.755	-0.488313	0.04352	.	.	ENSG00000124253	ENST00000540165;ENST00000319441;ENST00000543666;ENST00000535860	T;T;T	0.04234	3.67;3.67;3.67	5.31	2.24	0.28232	.	0.146062	0.64402	D	0.000009	T	0.01870	0.0059	N	0.02315	-0.6	0.49915	D	0.999839	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.46555	-0.9183	10	0.06494	T	0.89	-27.7538	12.0691	0.53605	0.0728:0.2817:0.6455:0.0	.	58;375	B4DT64;P35558	.;PCKGC_HUMAN	K	57;375;58;243	ENSP00000319814:E375K;ENSP00000445767:E58K;ENSP00000444342:E243K	ENSP00000319814:E375K	E	+	1	0	PCK1	55572792	0.998000	0.40836	0.375000	0.26029	0.048000	0.14542	2.439000	0.44846	0.300000	0.22699	-0.165000	0.13383	GAG	.		0.562	PCK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079851.2		
PDE4D	5144	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;mdanderson.org	37	5	58511685	58511685	+	Nonsense_Mutation	SNP	C	C	A			TCGA-FV-A3R3-01A-11D-A22F-10	TCGA-FV-A3R3-10A-01D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c285c2fa-24b4-47a1-874d-86e74b002b05	64edddfd-f366-4d51-a8b4-a357b2c68e6c	g.chr5:58511685C>A	ENST00000340635.6	-	2	740	c.565G>T	c.(565-567)Gag>Tag	p.E189*	PDE4D_ENST00000502575.1_Nonsense_Mutation_p.E125*|PDE4D_ENST00000507116.1_Nonsense_Mutation_p.E125*|PDE4D_ENST00000503258.1_Nonsense_Mutation_p.E59*|PDE4D_ENST00000502484.2_Nonsense_Mutation_p.E128*|PDE4D_ENST00000503947.1_5'UTR|PDE4D_ENST00000405755.2_Nonsense_Mutation_p.E67*|PDE4D_ENST00000360047.5_Nonsense_Mutation_p.E53*|PDE4D_ENST00000546160.1_Nonsense_Mutation_p.E128*	NM_001104631.1	NP_001098101.1	Q08499	PDE4D_HUMAN	phosphodiesterase 4D, cAMP-specific	189					adrenergic receptor signaling pathway (GO:0071875)|adrenergic receptor signaling pathway involved in positive regulation of heart rate (GO:0086024)|aging (GO:0007568)|cAMP catabolic process (GO:0006198)|cAMP-mediated signaling (GO:0019933)|cellular response to cAMP (GO:0071320)|cellular response to epinephrine stimulus (GO:0071872)|cellular response to lipopolysaccharide (GO:0071222)|establishment of endothelial barrier (GO:0061028)|multicellular organism growth (GO:0035264)|negative regulation of heart contraction (GO:0045822)|negative regulation of peptidyl-serine phosphorylation (GO:0033137)|negative regulation of relaxation of cardiac muscle (GO:1901898)|neutrophil chemotaxis (GO:0030593)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interleukin-2 production (GO:0032743)|positive regulation of interleukin-5 production (GO:0032754)|regulation of cardiac muscle cell contraction (GO:0086004)|regulation of cell communication by electrical coupling involved in cardiac conduction (GO:1901844)|regulation of heart rate (GO:0002027)|regulation of receptor activity (GO:0010469)|regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0010880)|regulation of ryanodine-sensitive calcium-release channel activity (GO:0060314)|smooth muscle contraction (GO:0006939)|T cell receptor signaling pathway (GO:0050852)	calcium channel complex (GO:0034704)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|membrane (GO:0016020)|plasma membrane (GO:0005886)	3',5'-cyclic-AMP phosphodiesterase activity (GO:0004115)|3',5'-cyclic-nucleotide phosphodiesterase activity (GO:0004114)|ATPase binding (GO:0051117)|beta-2 adrenergic receptor binding (GO:0031698)|cAMP binding (GO:0030552)|drug binding (GO:0008144)|enzyme binding (GO:0019899)|ion channel binding (GO:0044325)|metal ion binding (GO:0046872)|scaffold protein binding (GO:0097110)|ubiquitin protein ligase binding (GO:0031625)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(8)|pancreas(1)	15		all_cancers(5;6.5e-58)|all_epithelial(5;1.75e-57)|all_lung(5;6.84e-18)|Lung NSC(5;1.29e-17)|Melanoma(5;0.00168)|Prostate(74;0.00234)|Colorectal(97;0.00629)|Ovarian(174;0.00832)|Breast(144;0.00996)|all_hematologic(6;0.0344)|Hepatocellular(6;0.0742)|Esophageal squamous(6;0.0954)		Epithelial(2;2.6e-55)|all cancers(2;2.66e-49)|OV - Ovarian serous cystadenocarcinoma(10;1.48e-39)|Colorectal(2;8.29e-08)|Lung(2;4.47e-07)|STAD - Stomach adenocarcinoma(2;1.11e-05)|COAD - Colon adenocarcinoma(2;0.00012)|LUSC - Lung squamous cell carcinoma(2;0.000775)|LUAD - Lung adenocarcinoma(3;0.0173)|READ - Rectum adenocarcinoma(2;0.0276)	Adenosine monophosphate(DB00131)|Caffeine(DB00201)|Dyphylline(DB00651)|Ibudilast(DB05266)|Iloprost(DB01088)|Ketotifen(DB00920)|Roflumilast(DB01656)	AGGAAGGACTCCCGTCGTTGA	0.532																																					p.E189X		.											.	PDE4D	226	0			c.G565T						.						108.0	106.0	107.0					5																	58511685		1906	4121	6027	SO:0001587	stop_gained	5144	exon2			AGGACTCCCGTCG		CCDS47213.1, CCDS54858.1, CCDS54859.1, CCDS56369.1, CCDS56370.1, CCDS56371.1, CCDS56372.1, CCDS56373.1	5q12	2010-06-24	2010-06-24				3.1.4.17	"""Phosphodiesterases"""	8783	protein-coding gene	gene with protein product	"""phosphodiesterase E3 dunce homolog (Drosophila)"""	600129	"""phosphodiesterase 4D, cAMP-specific (dunce (Drosophila)-homolog phosphodiesterase E3)"""	DPDE3			Standard	NM_006203		Approved		uc003jsa.2	Q08499		ENST00000340635.6:c.565G>T	5.37:g.58511685C>A	ENSP00000345502:p.Glu189*	97.0	0.0		76.0	25.0	NM_001104631	O43433|Q13549|Q13550|Q13551|Q7Z2L8|Q8IV84|Q8IVA9|Q8IVD2|Q8IVD3|Q96HL4|Q9HCX7	Nonsense_Mutation	SNP	ENST00000340635.6	37	CCDS47213.1	.	.	.	.	.	.	.	.	.	.	C	45	11.328100	0.99547	.	.	ENSG00000113448	ENST00000340635;ENST00000356665;ENST00000360047;ENST00000507116;ENST00000503258;ENST00000405755;ENST00000502484;ENST00000546160;ENST00000502575	.	.	.	4.66	4.66	0.58398	.	0.282883	0.32918	N	0.005489	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	17.9427	0.89030	0.0:1.0:0.0:0.0	.	.	.	.	X	189;58;53;125;59;67;128;128;125	.	ENSP00000308485:E125X	E	-	1	0	PDE4D	58547442	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.776000	0.85560	2.296000	0.77279	0.591000	0.81541	GAG	.		0.532	PDE4D-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000367940.3		
POLR2A	5430	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	17	7400976	7400976	+	Missense_Mutation	SNP	A	A	T			TCGA-FV-A3R3-01A-11D-A22F-10	TCGA-FV-A3R3-10A-01D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c285c2fa-24b4-47a1-874d-86e74b002b05	64edddfd-f366-4d51-a8b4-a357b2c68e6c	g.chr17:7400976A>T	ENST00000322644.6	+	7	1388	c.989A>T	c.(988-990)cAg>cTg	p.Q330L	POLR2A_ENST00000572844.1_Missense_Mutation_p.Q330L	NM_000937.4	NP_000928	P24928	RPB1_HUMAN	polymerase (RNA) II (DNA directed) polypeptide A, 220kDa	330					7-methylguanosine mRNA capping (GO:0006370)|DNA repair (GO:0006281)|gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|nucleotide-excision repair (GO:0006289)|positive regulation of viral transcription (GO:0050434)|regulation of transcription, DNA-templated (GO:0006355)|RNA splicing (GO:0008380)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription-coupled nucleotide-excision repair (GO:0006283)|viral process (GO:0016032)	DNA-directed RNA polymerase II, core complex (GO:0005665)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|DNA-directed RNA polymerase activity (GO:0003899)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|RNA-directed RNA polymerase activity (GO:0003968)|ubiquitin protein ligase binding (GO:0031625)			breast(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(8)|lung(17)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)	50		Prostate(122;0.173)				CAGGCCATGCAGAAGTCTGGG	0.602																																					p.Q330L		.											.	POLR2A	91	0			c.A989T						.						48.0	49.0	49.0					17																	7400976		2203	4300	6503	SO:0001583	missense	5430	exon7			CCATGCAGAAGTC			17p13.1	2013-01-21	2002-08-29		ENSG00000181222	ENSG00000181222	2.7.7.6	"""RNA polymerase subunits"""	9187	protein-coding gene	gene with protein product	"""DNA-directed RNA polymerase II largest subunit, RNA polymerase II 220 kd subunit"", ""RNA polymerase II subunit B1"""	180660	"""polymerase (RNA) II (DNA directed) polypeptide A (220kD)"""	POLR2			Standard	NM_000937		Approved	POLRA, RPB1	uc002ghf.4	P24928	OTTHUMG00000177594	ENST00000322644.6:c.989A>T	17.37:g.7400976A>T	ENSP00000314949:p.Gln330Leu	89.0	0.0		73.0	20.0	NM_000937	A6NN93|B9EH88|Q6NX41	Missense_Mutation	SNP	ENST00000322644.6	37	CCDS32548.1	.	.	.	.	.	.	.	.	.	.	A	16.49	3.138761	0.56936	.	.	ENSG00000181222	ENST00000535204;ENST00000322644	T	0.25250	1.81	5.74	5.74	0.90152	RNA polymerase, N-terminal (1);RNA polymerase Rpb1, domain 1 (1);	0.000000	0.85682	D	0.000000	T	0.46386	0.1390	M	0.74258	2.255	0.80722	D	1	P;B	0.44195	0.828;0.249	P;B	0.53912	0.737;0.143	T	0.47032	-0.9148	10	0.87932	D	0	-10.9531	15.0177	0.71600	1.0:0.0:0.0:0.0	.	330;330	P24928;Q6NX41	RPB1_HUMAN;.	L	286;330	ENSP00000314949:Q330L	ENSP00000314949:Q330L	Q	+	2	0	SLC35G6	7341700	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.444000	0.90323	2.189000	0.69895	0.460000	0.39030	CAG	.		0.602	POLR2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437967.1	NM_000937	
PRAMEF20	645425	broad.mit.edu;bcgsc.ca;mdanderson.org	37	1	13742998	13742998	+	Missense_Mutation	SNP	C	C	T	rs577731266	byFrequency	TCGA-FV-A3R3-01A-11D-A22F-10	TCGA-FV-A3R3-10A-01D-A22F-10	C	C	.	.	.	.	.	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c285c2fa-24b4-47a1-874d-86e74b002b05	64edddfd-f366-4d51-a8b4-a357b2c68e6c	g.chr1:13742998C>T	ENST00000602960.1	+	1	191	c.187C>T	c.(187-189)Cgc>Tgc	p.R63C	PRAMEF20_ENST00000316412.5_Missense_Mutation_p.R63C			Q5VT98	PRA20_HUMAN	PRAME family member 20	63					negative regulation of apoptotic process (GO:0043066)|negative regulation of cell differentiation (GO:0045596)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of cell proliferation (GO:0008284)					endometrium(1)|kidney(1)|large_intestine(1)|ovary(1)	4	Ovarian(185;0.249)	Renal(390;0.000469)|Lung NSC(185;0.00143)|all_lung(284;0.00181)|Colorectal(325;0.00215)|Breast(348;0.00224)|Myeloproliferative disorder(586;0.0393)|Hepatocellular(190;0.0623)|Ovarian(437;0.0731)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00812)|Colorectal(212;2.5e-06)|Kidney(185;4.89e-05)|COAD - Colon adenocarcinoma(227;0.000156)|KIRC - Kidney renal clear cell carcinoma(229;0.000194)|BRCA - Breast invasive adenocarcinoma(304;0.000293)|STAD - Stomach adenocarcinoma(313;0.0072)|READ - Rectum adenocarcinoma(331;0.0649)		GCCTTTCCTCCGCCTTCCTCT	0.582													c|||	2	0.000399361	0.0	0.0029	5008	,	,		12664	0.0		0.0	False		,,,				2504	0.0				p.R63C		.											.	.	.	0			c.C187T						.						16.0	18.0	17.0					1																	13742998		2175	4234	6409	SO:0001583	missense	391001	exon1			TTCCTCCGCCTTC		CCDS41265.1	1p36.21	2014-07-15			ENSG00000204478	ENSG00000204478		"""-"""	25224	protein-coding gene	gene with protein product			"""PRAME family member 21"""	PRAMEF21			Standard	NM_001099852		Approved	OTTHUMG00000007911, OTTHUMT00000008157	uc009vnv.1	Q5VT98	OTTHUMG00000007911	ENST00000602960.1:c.187C>T	1.37:g.13742998C>T	ENSP00000473584:p.Arg63Cys	323.0	0.0		263.0	12.0	NM_001100114		Missense_Mutation	SNP	ENST00000602960.1	37	CCDS41265.1	.	.	.	.	.	.	.	.	.	.	.	4.875	0.162676	0.09287	.	.	ENSG00000204478	ENST00000316412	T	0.08720	3.06	1.51	-2.08	0.07254	.	1.379330	0.04512	N	0.383110	T	0.03263	0.0095	N	0.04768	-0.165	0.09310	N	1	.	.	.	.	.	.	T	0.37314	-0.9711	8	0.22706	T	0.39	.	1.9424	0.03349	0.2652:0.3428:0.0:0.392	.	.	.	.	C	63	ENSP00000346275:R63C	ENSP00000346275:R63C	R	+	1	0	PRAMEF20	13615585	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	-1.062000	0.03468	-0.636000	0.05524	0.306000	0.20318	CGC	.		0.582	PRAMEF20-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021782.1	NM_001099852	
PSMB5	5693	broad.mit.edu;ucsc.edu;bcgsc.ca	37	14	23502649	23502649	+	Missense_Mutation	SNP	T	T	C			TCGA-FV-A3R3-01A-11D-A22F-10	TCGA-FV-A3R3-10A-01D-A22F-10	T	T	.	.	.	.	.	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c285c2fa-24b4-47a1-874d-86e74b002b05	64edddfd-f366-4d51-a8b4-a357b2c68e6c	g.chr14:23502649T>C	ENST00000361611.6	-	2	696	c.433A>G	c.(433-435)Atg>Gtg	p.M145V	PSMB5_ENST00000425762.2_Missense_Mutation_p.M42V|PSMB5_ENST00000460922.2_Intron|PSMB5_ENST00000493471.2_Missense_Mutation_p.M145V|AL132780.1_ENST00000385031.1_RNA	NM_002797.3	NP_002788.1	P28074	PSB5_HUMAN	proteasome (prosome, macropain) subunit, beta type, 5	145					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|cellular nitrogen compound metabolic process (GO:0034641)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|response to oxidative stress (GO:0006979)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|proteasome complex (GO:0000502)|proteasome core complex (GO:0005839)	threonine-type endopeptidase activity (GO:0004298)			kidney(1)|large_intestine(2)|lung(2)|ovary(1)|prostate(1)	7	all_cancers(95;3.3e-05)			GBM - Glioblastoma multiforme(265;0.0121)	Bortezomib(DB00188)|Carfilzomib(DB08889)	TGATACACCATGTTGGCAAGC	0.522																																					p.M145V		.											.	PSMB5	91	0			c.A433G						.						144.0	125.0	132.0					14																	23502649		2203	4300	6503	SO:0001583	missense	5693	exon2			ACACCATGTTGGC	D29011	CCDS9584.1, CCDS45083.1, CCDS45084.1	14q11.2	2008-08-29			ENSG00000100804	ENSG00000100804		"""Proteasome (prosome, macropain) subunits"""	9542	protein-coding gene	gene with protein product		600306				8066462, 8811196	Standard	NM_001130725		Approved	X, MB1	uc001wii.3	P28074	OTTHUMG00000028713	ENST00000361611.6:c.433A>G	14.37:g.23502649T>C	ENSP00000355325:p.Met145Val	56.0	0.0		44.0	4.0	NM_001144932	B2R4N9|B4DUM9|D3DS43|E9PAV2|Q16242|Q6PEW2|Q7Z3B5|Q86T01|Q9TNN9	Missense_Mutation	SNP	ENST00000361611.6	37	CCDS9584.1	.	.	.	.	.	.	.	.	.	.	T	16.26	3.074492	0.55646	.	.	ENSG00000100804	ENST00000361611;ENST00000493471;ENST00000425762	T;T;T	0.21361	2.01;2.01;2.01	4.88	4.88	0.63580	.	0.000000	0.85682	D	0.000000	T	0.21718	0.0523	L	0.54965	1.715	0.58432	D	0.999995	B;B	0.33583	0.418;0.206	B;B	0.30401	0.045;0.115	T	0.03278	-1.1053	10	0.52906	T	0.07	-12.1247	13.483	0.61348	0.0:0.0:0.0:1.0	.	145;145	P28074-2;P28074	.;PSB5_HUMAN	V	145;145;42	ENSP00000355325:M145V;ENSP00000452424:M145V;ENSP00000395206:M42V	ENSP00000334973:M145V	M	-	1	0	PSMB5	22572489	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	5.652000	0.67959	1.816000	0.52996	0.459000	0.35465	ATG	.		0.522	PSMB5-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071695.4	NM_002797	
PTCHD2	57540	broad.mit.edu;bcgsc.ca	37	1	11584041	11584041	+	Missense_Mutation	SNP	G	G	C			TCGA-FV-A3R3-01A-11D-A22F-10	TCGA-FV-A3R3-10A-01D-A22F-10	G	G	.	.	.	.	.	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c285c2fa-24b4-47a1-874d-86e74b002b05	64edddfd-f366-4d51-a8b4-a357b2c68e6c	g.chr1:11584041G>C	ENST00000294484.6	+	11	2543	c.2405G>C	c.(2404-2406)cGg>cCg	p.R802P	PTCHD2_ENST00000389575.3_Missense_Mutation_p.R802P	NM_020780.1	NP_065831.1	Q9P2K9	PTHD2_HUMAN	patched domain containing 2	802					cholesterol homeostasis (GO:0042632)|regulation of lipid transport (GO:0032368)|smoothened signaling pathway (GO:0007224)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|nuclear membrane (GO:0031965)	hedgehog receptor activity (GO:0008158)	p.R1019L(1)		NS(3)|breast(2)|endometrium(9)|kidney(4)|large_intestine(5)|lung(34)|ovary(3)|pancreas(1)|prostate(6)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(3)	76	Ovarian(185;0.249)	Lung NSC(185;4.16e-05)|all_lung(284;4.76e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00913)|Ovarian(437;0.00965)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;3.13e-07)|COAD - Colon adenocarcinoma(227;4.83e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000325)|Kidney(185;0.000877)|KIRC - Kidney renal clear cell carcinoma(229;0.00273)|STAD - Stomach adenocarcinoma(313;0.00766)|READ - Rectum adenocarcinoma(331;0.0549)		AACAACATCCGGACGTCCCTG	0.667																																					p.R802P		.											.	PTCHD2	209	1	Substitution - Missense(1)	lung(1)	c.G2405C						.						41.0	48.0	46.0					1																	11584041		1921	4121	6042	SO:0001583	missense	57540	exon11			ACATCCGGACGTC	AB037758	CCDS41247.1	1p36.22	2010-02-17			ENSG00000204624	ENSG00000204624			29251	protein-coding gene	gene with protein product		611251				15738394	Standard	NM_020780		Approved	KIAA1337, DISP3	uc001ash.4	Q9P2K9	OTTHUMG00000002074	ENST00000294484.6:c.2405G>C	1.37:g.11584041G>C	ENSP00000294484:p.Arg802Pro	85.0	0.0		86.0	6.0	NM_020780	Q5VTU9|Q9UJD6	Missense_Mutation	SNP	ENST00000294484.6	37	CCDS41247.1	.	.	.	.	.	.	.	.	.	.	G	14.78	2.636720	0.47049	.	.	ENSG00000204624	ENST00000294484;ENST00000389575	D;D	0.90563	-2.69;-2.69	5.25	4.34	0.51931	.	0.296407	0.32533	N	0.005963	D	0.84656	0.5520	L	0.29908	0.895	0.45250	D	0.998253	B	0.20550	0.046	B	0.18561	0.022	T	0.80228	-0.1469	10	0.42905	T	0.14	-37.5796	12.966	0.58483	0.0778:0.0:0.9222:0.0	.	802	Q9P2K9	PTHD2_HUMAN	P	802	ENSP00000294484:R802P;ENSP00000374226:R802P	ENSP00000294484:R802P	R	+	2	0	PTCHD2	11506628	1.000000	0.71417	0.999000	0.59377	0.899000	0.52679	4.823000	0.62694	1.220000	0.43490	-0.258000	0.10820	CGG	.		0.667	PTCHD2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000005770.2	XM_052561	
PTGES	9536	broad.mit.edu;mdanderson.org	37	9	132502105	132502105	+	Missense_Mutation	SNP	A	A	T			TCGA-FV-A3R3-01A-11D-A22F-10	TCGA-FV-A3R3-10A-01D-A22F-10	A	A	.	.	.	.	.	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c285c2fa-24b4-47a1-874d-86e74b002b05	64edddfd-f366-4d51-a8b4-a357b2c68e6c	g.chr9:132502105A>T	ENST00000340607.4	-	3	278	c.244T>A	c.(244-246)Ttc>Atc	p.F82I	PTGES_ENST00000481476.1_5'UTR	NM_004878.4	NP_004869.1	O14684	PTGES_HUMAN	prostaglandin E synthase	82					acute inflammatory response (GO:0002526)|arachidonic acid metabolic process (GO:0019369)|chronic inflammatory response (GO:0002544)|cyclooxygenase pathway (GO:0019371)|negative regulation of cell proliferation (GO:0008285)|prostaglandin biosynthetic process (GO:0001516)|prostaglandin metabolic process (GO:0006693)|response to calcium ion (GO:0051592)|response to cytokine (GO:0034097)|response to lipopolysaccharide (GO:0032496)|response to organic cyclic compound (GO:0014070)|response to retinoic acid (GO:0032526)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nuclear envelope lumen (GO:0005641)|perinuclear region of cytoplasm (GO:0048471)	glutathione binding (GO:0043295)|prostaglandin-E synthase activity (GO:0050220)			lung(1)|skin(1)	2		Ovarian(14;0.00556)				AGGAAAAGGAAGGGGTAGATG	0.582																																					p.F82I		.											.	PTGES	226	0			c.T244A						.						71.0	46.0	54.0					9																	132502105		2194	4294	6488	SO:0001583	missense	9536	exon3			AAAGGAAGGGGTA	AF010316	CCDS6927.1	9q34.3	2008-07-21			ENSG00000148344	ENSG00000148344			9599	protein-coding gene	gene with protein product	"""microsomal glutathione S-transferase 1-like 1"", ""tumor protein p53 inducible protein 12"", ""p53-induced gene 12"", ""microsomal prostaglandin E synthase-1"", ""glutathione S-transferase 1-like 1"", ""MGST1-like 1"""	605172		MGST1L1		9305847, 10091672	Standard	NM_004878		Approved	MGST-IV, PIG12, MGST1-L1, TP53I12	uc004byi.3	O14684	OTTHUMG00000020791	ENST00000340607.4:c.244T>A	9.37:g.132502105A>T	ENSP00000342385:p.Phe82Ile	78.0	0.0		47.0	7.0	NM_004878	O14900|Q5SZC0	Missense_Mutation	SNP	ENST00000340607.4	37	CCDS6927.1	.	.	.	.	.	.	.	.	.	.	A	31	5.065617	0.93898	.	.	ENSG00000148344	ENST00000340607	T	0.63913	-0.07	4.6	4.6	0.57074	Membrane associated eicosanoid/glutathione metabolism-like domain (1);	0.000000	0.85682	D	0.000000	D	0.82852	0.5127	M	0.92555	3.32	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.87188	0.2232	10	0.87932	D	0	-39.1868	13.6096	0.62068	1.0:0.0:0.0:0.0	.	82	O14684	PTGES_HUMAN	I	82	ENSP00000342385:F82I	ENSP00000342385:F82I	F	-	1	0	PTGES	131541926	1.000000	0.71417	0.998000	0.56505	0.994000	0.84299	9.012000	0.93624	2.048000	0.60808	0.459000	0.35465	TTC	.		0.582	PTGES-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054599.2	NM_004878	
PTPN23	25930	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca;mdanderson.org	37	3	47452056	47452056	+	Missense_Mutation	SNP	C	C	T			TCGA-FV-A3R3-01A-11D-A22F-10	TCGA-FV-A3R3-10A-01D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c285c2fa-24b4-47a1-874d-86e74b002b05	64edddfd-f366-4d51-a8b4-a357b2c68e6c	g.chr3:47452056C>T	ENST00000265562.4	+	20	2845	c.2768C>T	c.(2767-2769)aCc>aTc	p.T923I	PTPN23_ENST00000431726.1_Missense_Mutation_p.T797I	NM_015466.2	NP_056281.1	Q9H3S7	PTN23_HUMAN	protein tyrosine phosphatase, non-receptor type 23	923	His.|Pro-rich.				cilium morphogenesis (GO:0060271)|negative regulation of epithelial cell migration (GO:0010633)|peptidyl-tyrosine dephosphorylation (GO:0035335)|positive regulation of adherens junction organization (GO:1903393)|positive regulation of early endosome to late endosome transport (GO:2000643)|positive regulation of homophilic cell adhesion (GO:1903387)|protein transport (GO:0015031)|ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway (GO:0043162)	ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|early endosome (GO:0005769)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	protein kinase binding (GO:0019901)|protein tyrosine phosphatase activity (GO:0004725)			breast(3)|central_nervous_system(1)|large_intestine(5)|lung(7)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)	23				BRCA - Breast invasive adenocarcinoma(193;0.000271)|KIRC - Kidney renal clear cell carcinoma(197;0.00558)|Kidney(197;0.00632)		ACGCCTTACACCTACCCTGCA	0.682																																					p.T923I		.											.	PTPN23	227	0			c.C2768T						.						32.0	32.0	32.0					3																	47452056		2203	4300	6503	SO:0001583	missense	25930	exon20			CTTACACCTACCC	AB025194	CCDS2754.1	3p21.3	2011-06-09			ENSG00000076201	ENSG00000076201		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"""	14406	protein-coding gene	gene with protein product		606584				11095967	Standard	NM_015466		Approved	DKFZP564F0923, KIAA1471, HD-PTP	uc003crf.1	Q9H3S7	OTTHUMG00000133520	ENST00000265562.4:c.2768C>T	3.37:g.47452056C>T	ENSP00000265562:p.Thr923Ile	135.0	0.0		62.0	18.0	NM_015466	A8K0D7|Q7KZF8|Q8N6Z5|Q9BSR5|Q9P257|Q9UG03|Q9UMZ4	Missense_Mutation	SNP	ENST00000265562.4	37	CCDS2754.1	.	.	.	.	.	.	.	.	.	.	C	4.877	0.162968	0.09287	.	.	ENSG00000076201	ENST00000265562	T	0.02552	4.25	4.88	3.99	0.46301	.	0.875688	0.09919	N	0.738743	T	0.02380	0.0073	N	0.14661	0.345	0.21355	N	0.999711	B;B	0.06786	0.001;0.001	B;B	0.04013	0.001;0.001	T	0.48007	-0.9072	10	0.21540	T	0.41	-5.1617	11.0456	0.47857	0.0:0.8117:0.1883:0.0	.	797;923	B4DST5;Q9H3S7	.;PTN23_HUMAN	I	923	ENSP00000265562:T923I	ENSP00000265562:T923I	T	+	2	0	PTPN23	47427060	0.003000	0.15002	0.086000	0.20670	0.099000	0.18886	1.465000	0.35299	1.013000	0.39391	0.557000	0.71058	ACC	.		0.682	PTPN23-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257492.2	NM_015466	
PTPRQ	374462	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	12	80862537	80862537	+	Missense_Mutation	SNP	A	A	T			TCGA-FV-A3R3-01A-11D-A22F-10	TCGA-FV-A3R3-10A-01D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c285c2fa-24b4-47a1-874d-86e74b002b05	64edddfd-f366-4d51-a8b4-a357b2c68e6c	g.chr12:80862537A>T	ENST00000266688.5	+	12	947	c.947A>T	c.(946-948)aAg>aTg	p.K316M				Q9UMZ3	PTPRQ_HUMAN	protein tyrosine phosphatase, receptor type, Q	362					regulation of fat cell differentiation (GO:0045598)	integral component of membrane (GO:0016021)	protein tyrosine phosphatase activity (GO:0004725)			breast(1)|endometrium(7)|kidney(9)|lung(2)|prostate(1)|skin(2)|stomach(2)	24						ATCACAGGAAAGTCCTTTTCA	0.338																																					p.K148M		.											.	.	.	0			c.A443T						.						158.0	137.0	143.0					12																	80862537		692	1591	2283	SO:0001583	missense	374462	exon4			CAGGAAAGTCCTT	AF169351	CCDS73501.1	12q21.31	2013-02-11	2001-12-04		ENSG00000139304	ENSG00000139304		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"", ""Fibronectin type III domain containing"""	9679	protein-coding gene	gene with protein product		603317	"""deafness, autosomal recessive 84"""	DFNB84		20346435	Standard	NM_001145026		Approved		uc001sze.2	Q9UMZ3	OTTHUMG00000170171	ENST00000266688.5:c.947A>T	12.37:g.80862537A>T	ENSP00000266688:p.Lys316Met	98.0	0.0		122.0	18.0	NM_001145026		Missense_Mutation	SNP	ENST00000266688.5	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	16.31|16.31	3.087163|3.087163	0.55968|0.55968	.|.	.|.	ENSG00000139304|ENSG00000139304	ENST00000266688|ENST00000532722	T|.	0.57752|.	0.38|.	4.0|4.0	1.61|1.61	0.23674|0.23674	Fibronectin, type III (4);Immunoglobulin-like fold (1);|.	.|.	.|.	.|.	.|.	T|T	0.46483|0.46483	0.1395|0.1395	.|.	.|.	.|.	0.33448|0.33448	D|D	0.583348|0.583348	D|.	0.57571|.	0.98|.	P|.	0.59171|.	0.853|.	T|T	0.52593|0.52593	-0.8555|-0.8555	8|4	0.72032|.	D|.	0.01|.	.|.	7.0384|7.0384	0.25006|0.25006	0.7339:0.0:0.2661:0.0|0.7339:0.0:0.2661:0.0	.|.	362|.	Q9UMZ3|.	PTPRQ_HUMAN|.	M|C	316|17	ENSP00000266688:K316M|.	ENSP00000266688:K316M|.	K|S	+|+	2|1	0|0	PTPRQ|PTPRQ	79386668|79386668	0.933000|0.933000	0.31639|0.31639	0.977000|0.977000	0.42913|0.42913	0.980000|0.980000	0.70556|0.70556	1.448000|1.448000	0.35112|0.35112	0.152000|0.152000	0.19188|0.19188	0.528000|0.528000	0.53228|0.53228	AAG|AGT	.		0.338	PTPRQ-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_001145026	
RXRA	6256	broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	9	137326002	137326002	+	Missense_Mutation	SNP	A	A	G			TCGA-FV-A3R3-01A-11D-A22F-10	TCGA-FV-A3R3-10A-01D-A22F-10	A	A	.	.	.	.	.	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c285c2fa-24b4-47a1-874d-86e74b002b05	64edddfd-f366-4d51-a8b4-a357b2c68e6c	g.chr9:137326002A>G	ENST00000481739.1	+	9	1242	c.1190A>G	c.(1189-1191)tAt>tGt	p.Y397C	RXRA_ENST00000356384.4_3'UTR|RXRA_ENST00000540193.1_Missense_Mutation_p.Y300C	NM_002957.4	NP_002948.1	P19793	RXRA_HUMAN	retinoid X receptor, alpha	397	Ligand-binding.				camera-type eye development (GO:0043010)|cardiac muscle cell proliferation (GO:0060038)|cellular lipid metabolic process (GO:0044255)|cholesterol metabolic process (GO:0008203)|embryo implantation (GO:0007566)|gene expression (GO:0010467)|in utero embryonic development (GO:0001701)|maternal placenta development (GO:0001893)|modulation by virus of host morphology or physiology (GO:0019048)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|peroxisome proliferator activated receptor signaling pathway (GO:0035357)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein homotetramerization (GO:0051289)|regulation of branching involved in prostate gland morphogenesis (GO:0060687)|response to retinoic acid (GO:0032526)|retinoic acid receptor signaling pathway (GO:0048384)|secretory columnal luminar epithelial cell differentiation involved in prostate glandular acinus development (GO:0060528)|small molecule metabolic process (GO:0044281)|transcription initiation from RNA polymerase II promoter (GO:0006367)|ventricular cardiac muscle cell differentiation (GO:0055012)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)|vitamin metabolic process (GO:0006766)	nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	9-cis retinoic acid receptor activity (GO:0004886)|chromatin DNA binding (GO:0031490)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|protein heterodimerization activity (GO:0046982)|retinoic acid receptor activity (GO:0003708)|retinoic acid-responsive element binding (GO:0044323)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid hormone receptor activity (GO:0003707)|transcription coactivator activity (GO:0003713)|vitamin D receptor binding (GO:0042809)|zinc ion binding (GO:0008270)	p.Y397C(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(6)|ovary(2)|prostate(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	19				OV - Ovarian serous cystadenocarcinoma(145;4.66e-08)|Epithelial(140;6.72e-08)|all cancers(34;2.22e-07)	Acitretin(DB00459)|Adapalene(DB00210)|Alitretinoin(DB00523)|Bexarotene(DB00307)|Etodolac(DB00749)	GAGAAGGTCTATGCGTCCTTG	0.637																																					p.Y397C		.											RXRA,NS,carcinoma,0	RXRA	188	1	Substitution - Missense(1)	ovary(1)	c.A1190G						.						76.0	74.0	74.0					9																	137326002		2203	4300	6503	SO:0001583	missense	6256	exon9			AGGTCTATGCGTC	X52773	CCDS35172.1	9q34	2013-01-16			ENSG00000186350	ENSG00000186350		"""Nuclear hormone receptors"""	10477	protein-coding gene	gene with protein product	"""nuclear receptor subfamily 2 group B member 1"""	180245				2159111	Standard	XM_005263409		Approved	NR2B1	uc004cfa.1	P19793	OTTHUMG00000020887	ENST00000481739.1:c.1190A>G	9.37:g.137326002A>G	ENSP00000419692:p.Tyr397Cys	30.0	0.0		15.0	5.0	NM_002957	B3KY83|Q2NL52|Q2V504	Missense_Mutation	SNP	ENST00000481739.1	37	CCDS35172.1	.	.	.	.	.	.	.	.	.	.	A	17.34	3.365328	0.61513	.	.	ENSG00000186350	ENST00000481739;ENST00000540193	D;D	0.96619	-4.07;-4.07	4.3	4.3	0.51218	Nuclear hormone receptor, ligand-binding (2);Nuclear hormone receptor, ligand-binding, core (2);	0.067294	0.64402	D	0.000009	D	0.98251	0.9421	M	0.90019	3.08	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.99289	1.0898	10	0.87932	D	0	.	13.7357	0.62815	1.0:0.0:0.0:0.0	.	397	P19793	RXRA_HUMAN	C	397;300	ENSP00000419692:Y397C;ENSP00000442123:Y300C	ENSP00000419692:Y397C	Y	+	2	0	RXRA	136465823	1.000000	0.71417	0.200000	0.23457	0.575000	0.36095	8.878000	0.92393	1.708000	0.51301	0.402000	0.26972	TAT	.		0.637	RXRA-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054949.1	NM_002957	
SASH1	23328	broad.mit.edu;ucsc.edu;bcgsc.ca	37	6	148835544	148835544	+	Missense_Mutation	SNP	A	A	G			TCGA-FV-A3R3-01A-11D-A22F-10	TCGA-FV-A3R3-10A-01D-A22F-10	A	A	.	.	.	.	.	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c285c2fa-24b4-47a1-874d-86e74b002b05	64edddfd-f366-4d51-a8b4-a357b2c68e6c	g.chr6:148835544A>G	ENST00000367467.3	+	9	1289	c.814A>G	c.(814-816)Aga>Gga	p.R272G		NM_015278.3	NP_056093.3	O94885	SASH1_HUMAN	SAM and SH3 domain containing 1	272					positive regulation of angiogenesis (GO:0045766)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of lipopolysaccharide-mediated signaling pathway (GO:0031666)|positive regulation of NIK/NF-kappaB signaling (GO:1901224)|positive regulation of p38MAPK cascade (GO:1900745)|protein polyubiquitination (GO:0000209)|regulation of protein autoubiquitination (GO:1902498)|regulation of protein K63-linked ubiquitination (GO:1900044)	membrane (GO:0016020)|protein complex (GO:0043234)	mitogen-activated protein kinase kinase kinase binding (GO:0031435)|protein C-terminus binding (GO:0008022)|protein complex scaffold (GO:0032947)|protein kinase binding (GO:0019901)			breast(4)|central_nervous_system(1)|endometrium(9)|kidney(1)|large_intestine(11)|lung(20)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	52		Ovarian(120;0.0169)		OV - Ovarian serous cystadenocarcinoma(155;5.63e-11)|GBM - Glioblastoma multiforme(68;0.0701)		TCGCAGAGTCAGAAAGAAACT	0.378																																					p.R272G		.											.	SASH1	90	0			c.A814G						.						45.0	46.0	46.0					6																	148835544		2203	4300	6503	SO:0001583	missense	23328	exon9			AGAGTCAGAAAGA	AB018333	CCDS5212.1	6q24.3	2013-01-10			ENSG00000111961	ENSG00000111961		"""SAM and SH3 domain containing"", ""Sterile alpha motif (SAM) domain containing"""	19182	protein-coding gene	gene with protein product		607955				9872452, 12771949	Standard	NM_015278		Approved	KIAA0790, dJ323M4.1, SH3D6A	uc003qme.1	O94885	OTTHUMG00000015773	ENST00000367467.3:c.814A>G	6.37:g.148835544A>G	ENSP00000356437:p.Arg272Gly	42.0	0.0		38.0	5.0	NM_015278	Q5TGN5|Q8TAI0|Q9H7R7	Missense_Mutation	SNP	ENST00000367467.3	37	CCDS5212.1	.	.	.	.	.	.	.	.	.	.	A	18.98	3.737277	0.69304	.	.	ENSG00000111961	ENST00000367467;ENST00000535767	T	0.50548	0.74	5.96	3.49	0.39957	.	0.081589	0.85682	D	0.000000	T	0.29288	0.0729	L	0.27053	0.805	0.36996	D	0.895044	D;P	0.59767	0.986;0.799	P;B	0.49637	0.617;0.395	T	0.16070	-1.0415	10	0.72032	D	0.01	-26.1488	12.9103	0.58177	0.7436:0.2564:0.0:0.0	.	253;272	Q6P4R9;O94885	.;SASH1_HUMAN	G	272;33	ENSP00000356437:R272G	ENSP00000356437:R272G	R	+	1	2	SASH1	148877237	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	2.768000	0.47645	0.466000	0.27193	-0.323000	0.08544	AGA	.		0.378	SASH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042619.1	NM_015278	
SLC5A11	115584	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca;mdanderson.org	37	16	24902218	24902218	+	Silent	SNP	A	A	G			TCGA-FV-A3R3-01A-11D-A22F-10	TCGA-FV-A3R3-10A-01D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c285c2fa-24b4-47a1-874d-86e74b002b05	64edddfd-f366-4d51-a8b4-a357b2c68e6c	g.chr16:24902218A>G	ENST00000347898.3	+	9	1315	c.693A>G	c.(691-693)ggA>ggG	p.G231G	SLC5A11_ENST00000569071.1_Intron|SLC5A11_ENST00000545376.1_Silent_p.G161G|SLC5A11_ENST00000539472.1_Silent_p.G167G|SLC5A11_ENST00000568579.1_Silent_p.G161G|SLC5A11_ENST00000424767.2_Silent_p.G196G|SLC5A11_ENST00000567758.1_Silent_p.G196G|SLC5A11_ENST00000449109.2_Intron|SLC5A11_ENST00000565769.1_Silent_p.G167G	NM_052944.3	NP_443176.2			solute carrier family 5 (sodium/inositol cotransporter), member 11											endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(6)|lung(30)|ovary(2)|prostate(2)|urinary_tract(1)	49				GBM - Glioblastoma multiforme(48;0.0365)		GGATGGAAGGACTGAAGGAGA	0.547																																					p.G231G		.											.	SLC5A11	92	0			c.A693G						.						136.0	138.0	138.0					16																	24902218		2197	4300	6497	SO:0001819	synonymous_variant	115584	exon9			GGAAGGACTGAAG	AF292385	CCDS10625.1, CCDS58437.1, CCDS58438.1, CCDS58439.1, CCDS58440.1	16p12.1	2013-07-19	2013-07-19		ENSG00000158865	ENSG00000158865		"""Solute carriers"""	23091	protein-coding gene	gene with protein product		610238	"""solute carrier family 5 (sodium/glucose cotransporter), member 11"""			12039040, 12133831	Standard	NM_001258414		Approved	KST1, SMIT2, SGLT6	uc002dmu.4	Q8WWX8	OTTHUMG00000097003	ENST00000347898.3:c.693A>G	16.37:g.24902218A>G		84.0	0.0		61.0	12.0	NM_052944		Silent	SNP	ENST00000347898.3	37	CCDS10625.1																																																																																			.		0.547	SLC5A11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214091.3	NM_052944	
SMC4	10051	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	3	160141354	160141354	+	Missense_Mutation	SNP	T	T	G			TCGA-FV-A3R3-01A-11D-A22F-10	TCGA-FV-A3R3-10A-01D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c285c2fa-24b4-47a1-874d-86e74b002b05	64edddfd-f366-4d51-a8b4-a357b2c68e6c	g.chr3:160141354T>G	ENST00000357388.3	+	14	2612	c.2161T>G	c.(2161-2163)Ttg>Gtg	p.L721V	RP11-432B6.3_ENST00000483754.1_Intron|SMC4_ENST00000469762.1_Missense_Mutation_p.L696V|SMC4_ENST00000360111.2_Missense_Mutation_p.L721V|SMC4_ENST00000344722.5_Missense_Mutation_p.L721V|SMC4_ENST00000462787.1_Missense_Mutation_p.L721V	NM_001002800.1	NP_001002800.1	Q9NTJ3	SMC4_HUMAN	structural maintenance of chromosomes 4	721	Flexible hinge.				kinetochore organization (GO:0051383)|meiotic chromosome condensation (GO:0010032)|meiotic chromosome segregation (GO:0045132)|mitotic cell cycle (GO:0000278)|mitotic chromosome condensation (GO:0007076)|mitotic sister chromatid segregation (GO:0000070)	condensin complex (GO:0000796)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein heterodimerization activity (GO:0046982)			breast(2)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(15)|lung(20)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	48			Lung(72;0.00334)|LUSC - Lung squamous cell carcinoma(72;0.00523)			AGCTGACAACTTGGATCAAGC	0.338																																					p.L721V		.											.	SMC4	291	0			c.T2161G						.						161.0	173.0	169.0					3																	160141354		2203	4300	6503	SO:0001583	missense	10051	exon13			GACAACTTGGATC	AF092564	CCDS3189.1, CCDS75046.1	3q26.1	2006-07-06	2006-07-06	2006-07-06	ENSG00000113810	ENSG00000113810		"""Structural maintenance of chromosomes proteins"""	14013	protein-coding gene	gene with protein product		605575	"""SMC4 (structural maintenance of chromosomes 4, yeast)-like 1"", ""SMC4 structural maintenance of chromosomes 4-like 1 (yeast)"""	SMC4L1		9789013, 10319587	Standard	NM_005496		Approved	hCAP-C, CAP-C	uc003fdh.3	Q9NTJ3	OTTHUMG00000159006	ENST00000357388.3:c.2161T>G	3.37:g.160141354T>G	ENSP00000349961:p.Leu721Val	85.0	0.0		103.0	24.0	NM_005496	A6NLT9|D3DNL8|O95752|Q8NDL4|Q9UNT9	Missense_Mutation	SNP	ENST00000357388.3	37	CCDS3189.1	.	.	.	.	.	.	.	.	.	.	T	18.67	3.674261	0.67928	.	.	ENSG00000113810	ENST00000357388;ENST00000360111;ENST00000469762;ENST00000462787;ENST00000344722;ENST00000545277	D;D;D;D;D	0.88741	-2.42;-2.42;-2.42;-2.42;-2.42	5.87	4.7	0.59300	SMCs flexible hinge (3);RecF/RecN/SMC (1);	0.058771	0.64402	D	0.000001	D	0.93697	0.7986	M	0.88031	2.925	0.53005	D	0.999965	D;D;B;D	0.61697	0.978;0.964;0.005;0.99	P;D;B;D	0.64237	0.833;0.919;0.034;0.923	D	0.93114	0.6519	10	0.87932	D	0	-8.8311	7.3892	0.26901	0.0:0.1099:0.1315:0.7586	.	721;696;696;721	Q9NTJ3-2;B3KXX5;E9PD53;Q9NTJ3	.;.;.;SMC4_HUMAN	V	721;721;696;721;721;315	ENSP00000349961:L721V;ENSP00000353225:L721V;ENSP00000417964:L696V;ENSP00000420734:L721V;ENSP00000341382:L721V	ENSP00000341382:L721V	L	+	1	2	SMC4	161624048	1.000000	0.71417	0.998000	0.56505	0.988000	0.76386	2.064000	0.41432	1.024000	0.39682	0.528000	0.53228	TTG	.		0.338	SMC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352862.1		
SULT2B1	6820	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	19	49090570	49090570	+	Missense_Mutation	SNP	G	G	A	rs138292714	byFrequency	TCGA-FV-A3R3-01A-11D-A22F-10	TCGA-FV-A3R3-10A-01D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c285c2fa-24b4-47a1-874d-86e74b002b05	64edddfd-f366-4d51-a8b4-a357b2c68e6c	g.chr19:49090570G>A	ENST00000201586.2	+	3	477	c.299G>A	c.(298-300)cGg>cAg	p.R100Q	SULT2B1_ENST00000323090.4_Missense_Mutation_p.R85Q	NM_177973.1	NP_814444.1	O00204	ST2B1_HUMAN	sulfotransferase family, cytosolic, 2B, member 1	100					3'-phosphoadenosine 5'-phosphosulfate metabolic process (GO:0050427)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|sulfate assimilation (GO:0000103)|xenobiotic metabolic process (GO:0006805)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	alcohol sulfotransferase activity (GO:0004027)|steroid sulfotransferase activity (GO:0050294)			central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(2)|skin(2)|urinary_tract(1)	11		all_epithelial(76;2.38e-06)|all_lung(116;4.89e-06)|Lung NSC(112;9.34e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		OV - Ovarian serous cystadenocarcinoma(262;0.000115)|all cancers(93;0.000147)|GBM - Glioblastoma multiforme(486;0.00707)|Epithelial(262;0.0178)		ATCTGGGAGCGGGCACCCTGG	0.587																																					p.R100Q		.											.	SULT2B1	91	0			c.G299A						.	G	GLN/ARG,GLN/ARG	0,4406		0,0,2203	83.0	68.0	73.0		254,299	5.0	0.1	19	dbSNP_134	73	2,8598	2.2+/-6.3	0,2,4298	yes	missense,missense	SULT2B1	NM_004605.2,NM_177973.1	43,43	0,2,6501	AA,AG,GG		0.0233,0.0,0.0154	probably-damaging,probably-damaging	85/351,100/366	49090570	2,13004	2203	4300	6503	SO:0001583	missense	6820	exon3			GGGAGCGGGCACC	U92314	CCDS12723.1, CCDS12724.1	19q13.3	2008-02-05				ENSG00000088002		"""Sulfotransferases, cytosolic"""	11459	protein-coding gene	gene with protein product		604125				9799594	Standard	NM_177973		Approved	HSST2	uc002pjl.3	O00204		ENST00000201586.2:c.299G>A	19.37:g.49090570G>A	ENSP00000201586:p.Arg100Gln	45.0	0.0		53.0	8.0	NM_177973	O00205|O75814	Missense_Mutation	SNP	ENST00000201586.2	37	CCDS12723.1	.	.	.	.	.	.	.	.	.	.	G	16.57	3.160991	0.57368	0.0	2.33E-4	ENSG00000088002	ENST00000201586;ENST00000323090	D;D	0.83673	-1.75;-1.75	4.98	4.98	0.66077	Sulfotransferase domain (1);	0.000000	0.45126	D	0.000391	D	0.91175	0.7220	M	0.81239	2.535	0.34148	D	0.667181	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.999	D	0.94718	0.7898	10	0.87932	D	0	.	16.1004	0.81167	0.0:0.0:1.0:0.0	.	85;100	O00204-2;O00204	.;ST2B1_HUMAN	Q	100;85	ENSP00000201586:R100Q;ENSP00000312880:R85Q	ENSP00000201586:R100Q	R	+	2	0	SULT2B1	53782382	1.000000	0.71417	0.082000	0.20525	0.038000	0.13279	6.908000	0.75730	2.486000	0.83907	0.579000	0.79373	CGG	G|1.000;A|0.000		0.587	SULT2B1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000466140.1	NM_004605	
SYNE1	23345	hgsc.bcm.edu;broad.mit.edu	37	6	152644792	152644792	+	Silent	SNP	C	C	T			TCGA-FV-A3R3-01A-11D-A22F-10	TCGA-FV-A3R3-10A-01D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c285c2fa-24b4-47a1-874d-86e74b002b05	64edddfd-f366-4d51-a8b4-a357b2c68e6c	g.chr6:152644792C>T	ENST00000367255.5	-	82	16339	c.15738G>A	c.(15736-15738)gaG>gaA	p.E5246E	SYNE1_ENST00000341594.5_Silent_p.E4939E|SYNE1_ENST00000265368.4_Silent_p.E5246E|SYNE1_ENST00000423061.1_Silent_p.E5175E|SYNE1_ENST00000448038.1_Silent_p.E5175E	NM_182961.3	NP_892006.3	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	5246					cell death (GO:0008219)|cytoskeletal anchoring at nuclear membrane (GO:0090286)|establishment of nucleus localization (GO:0040023)|Golgi organization (GO:0007030)|muscle cell differentiation (GO:0042692)|nuclear matrix anchoring at nuclear membrane (GO:0090292)|nucleus organization (GO:0006997)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|postsynaptic membrane (GO:0045211)|sarcomere (GO:0030017)|SUN-KASH complex (GO:0034993)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|lamin binding (GO:0005521)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)	p.E5246D(2)		NS(3)|biliary_tract(1)|breast(17)|central_nervous_system(21)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(4)|kidney(16)|large_intestine(138)|liver(1)|lung(190)|ovary(11)|pancreas(5)|prostate(12)|skin(20)|stomach(3)|upper_aerodigestive_tract(33)|urinary_tract(19)	524		Ovarian(120;0.0955)	BRCA - Breast invasive adenocarcinoma(37;0.243)	OV - Ovarian serous cystadenocarcinoma(155;2.24e-10)		GAGTTAAGAGCTCTGCTTTCG	0.488										HNSCC(10;0.0054)																											p.E5246E		.											SYNE1_ENST00000265368,NS,carcinoma,0	SYNE1	607	2	Substitution - Missense(2)	ovary(2)	c.G15738A						.						102.0	95.0	97.0					6																	152644792		2203	4300	6503	SO:0001819	synonymous_variant	23345	exon82			TAAGAGCTCTGCT	AB018339	CCDS5235.1, CCDS5236.1, CCDS5236.2	6q24.2-q25.3	2014-09-17			ENSG00000131018	ENSG00000131018			17089	protein-coding gene	gene with protein product	"""myocyte nuclear envelope protein 1"", ""nuclear envelope spectrin repeat-1"""	608441	"""chromosome 6 open reading frame 98"""	C6orf98		9872452, 10878022	Standard	NM_182961		Approved	SYNE-1B, KIAA0796, 8B, Nesprin-1, enaptin, MYNE1, CPG2, dJ45H2.2, SCAR8, ARCA1, Nesp1	uc003qou.4	Q8NF91	OTTHUMG00000015841	ENST00000367255.5:c.15738G>A	6.37:g.152644792C>T		86.0	0.0		69.0	4.0	NM_182961	E7EQI5|O94890|Q5JV19|Q5JV22|Q8N9P7|Q8TCP1|Q8WWW6|Q8WWW7|Q8WXF6|Q96N17|Q9C0A7|Q9H525|Q9H526|Q9NS36|Q9NU50|Q9UJ06|Q9UJ07|Q9ULF8	Silent	SNP	ENST00000367255.5	37	CCDS5236.2																																																																																			.		0.488	SYNE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000334755.2	NM_182961	
TEX35	84066	broad.mit.edu;bcgsc.ca	37	1	178489858	178489858	+	Missense_Mutation	SNP	A	A	G	rs35769219	byFrequency	TCGA-FV-A3R3-01A-11D-A22F-10	TCGA-FV-A3R3-10A-01D-A22F-10	A	A	.	.	.	.	.	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c285c2fa-24b4-47a1-874d-86e74b002b05	64edddfd-f366-4d51-a8b4-a357b2c68e6c	g.chr1:178489858A>G	ENST00000319416.2	+	7	504	c.392A>G	c.(391-393)aAg>aGg	p.K131R	TEX35_ENST00000367642.3_3'UTR|TEX35_ENST00000258298.2_Missense_Mutation_p.K55R|TEX35_ENST00000367639.1_Missense_Mutation_p.K139R|TEX35_ENST00000367641.3_Missense_Mutation_p.K131R|TEX35_ENST00000367643.3_Missense_Mutation_p.K131R	NM_032126.4	NP_115502.2			testis expressed 35																		CTGATGGGAAAGACTCACAGA	0.557													A|||	10	0.00199681	0.0076	0.0	5008	,	,		18013	0.0		0.0	False		,,,				2504	0.0				p.K139R		.											.	.	.	0			c.A416G						.	A	ARG/LYS,ARG/LYS,ARG/LYS,ARG/LYS	27,4379	33.5+/-64.1	0,27,2176	61.0	61.0	61.0		416,392,392,392	2.9	0.0	1	dbSNP_126	61	0,8600		0,0,4300	yes	missense,missense,missense,missense	C1orf49	NM_001170722.1,NM_001170723.1,NM_001170724.1,NM_032126.4	26,26,26,26	0,27,6476	GG,GA,AA		0.0,0.6128,0.2076	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging	139/216,131/213,131/208,131/234	178489858	27,12979	2203	4300	6503	SO:0001583	missense	84066	exon7			TGGGAAAGACTCA	AL136694	CCDS1323.1, CCDS53433.1, CCDS53434.1	1q25.2	2014-01-28	2012-06-29	2012-06-29	ENSG00000240021	ENSG00000240021			25366	protein-coding gene	gene with protein product	"""Testis-Specific Conserved gene 24kDa"""		"""chromosome 1 open reading frame 49"""	C1orf49		11230166, 17077512	Standard	NM_032126		Approved	DKFZP564J047, TSC24	uc001glt.2	Q5T0J7	OTTHUMG00000035023	ENST00000319416.2:c.392A>G	1.37:g.178489858A>G	ENSP00000323795:p.Lys131Arg	67.0	0.0		70.0	4.0	NM_001170722		Missense_Mutation	SNP	ENST00000319416.2	37	CCDS1323.1	3	0.0013736263736263737	3	0.006097560975609756	0	0.0	0	0.0	0	0.0	A	12.08	1.831404	0.32329	0.006128	0.0	ENSG00000240021	ENST00000319416;ENST00000258298;ENST00000367643;ENST00000367641;ENST00000367639	T;T;T;T;T	0.26223	1.75;1.75;1.75;1.75;1.75	4.09	2.92	0.33932	.	0.145357	0.32258	N	0.006349	T	0.21307	0.0513	L	0.52573	1.65	0.09310	N	1	P;P;P	0.50819	0.939;0.939;0.939	P;P;P	0.49708	0.62;0.62;0.62	T	0.06770	-1.0808	10	0.87932	D	0	-16.2556	6.6853	0.23142	0.7893:0.0:0.0:0.2107	rs35769219	139;131;131	Q5T0J7-2;Q5T0J7-3;Q5T0J7	.;.;CA049_HUMAN	R	131;55;131;131;139	ENSP00000323795:K131R;ENSP00000258298:K55R;ENSP00000356615:K131R;ENSP00000356613:K131R;ENSP00000356611:K139R	ENSP00000258298:K55R	K	+	2	0	C1orf49	176756481	0.005000	0.15991	0.024000	0.17045	0.238000	0.25445	0.222000	0.17699	0.696000	0.31696	0.438000	0.28831	AAG	A|0.998;G|0.002		0.557	TEX35-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000084917.1	NM_032126	
THSD1	55901	broad.mit.edu;bcgsc.ca	37	13	52972291	52972300	+	Frame_Shift_Del	DEL	CTGGCTCTCT	CTGGCTCTCT	-			TCGA-FV-A3R3-01A-11D-A22F-10	TCGA-FV-A3R3-10A-01D-A22F-10	CTGGCTCTCT	CTGGCTCTCT	.	.	.	.	.	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c285c2fa-24b4-47a1-874d-86e74b002b05	64edddfd-f366-4d51-a8b4-a357b2c68e6c	g.chr13:52972291_52972300delCTGGCTCTCT	ENST00000258613.4	-	3	266_275	c.88_97delAGAGAGCCAG	c.(88-99)agagagccaggcfs	p.REPG30fs	THSD1_ENST00000349258.4_Frame_Shift_Del_p.REPG30fs|RNY4P24_ENST00000362735.1_RNA|THSD1_ENST00000544466.1_Intron	NM_018676.3	NP_061146.1	Q9NS62	THSD1_HUMAN	thrombospondin, type I, domain containing 1	30					hematopoietic progenitor cell differentiation (GO:0002244)	cell periphery (GO:0071944)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)				breast(2)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(11)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	30		Breast(56;0.000207)|Lung NSC(96;0.00145)|Hepatocellular(98;0.065)|Prostate(109;0.0771)|all_neural(104;0.173)		GBM - Glioblastoma multiforme(99;2.8e-08)		GCTACATGGCCTGGCTCTCTCAAGAGAAGA	0.414																																					p.30_33del		.											.	THSD1	94	0			c.88_97del						.																																			SO:0001589	frameshift_variant	55901	exon3			CATGGCCTGGCTC	AK096289	CCDS9432.1, CCDS9433.1	13q14.13	2010-04-20	2004-03-11		ENSG00000136114	ENSG00000136114			17754	protein-coding gene	gene with protein product			"""thrombospondin, type I, domain 1"""				Standard	NM_018676		Approved	TMTSP	uc001vgo.3	Q9NS62	OTTHUMG00000016963	ENST00000258613.4:c.88_97delAGAGAGCCAG	13.37:g.52972291_52972300delCTGGCTCTCT	ENSP00000258613:p.Arg30fs	73.0	0.0		58.0	10.0	NM_018676	A2A3J3|B2RCF5|Q6P3U1|Q6UXZ2	Frame_Shift_Del	DEL	ENST00000258613.4	37	CCDS9432.1																																																																																			.		0.414	THSD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045058.3		
TM9SF2	9375	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	13	100206607	100206607	+	Missense_Mutation	SNP	A	A	G			TCGA-FV-A3R3-01A-11D-A22F-10	TCGA-FV-A3R3-10A-01D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c285c2fa-24b4-47a1-874d-86e74b002b05	64edddfd-f366-4d51-a8b4-a357b2c68e6c	g.chr13:100206607A>G	ENST00000376387.4	+	14	1728	c.1538A>G	c.(1537-1539)gAa>gGa	p.E513G		NM_004800.1	NP_004791.1	Q99805	TM9S2_HUMAN	transmembrane 9 superfamily member 2	513					transport (GO:0006810)	endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)				endometrium(3)|kidney(1)|large_intestine(5)|lung(5)|ovary(1)|prostate(2)	17	all_neural(89;0.0837)|Medulloblastoma(90;0.18)|Lung SC(71;0.218)					CAGATTCCTGAACAGTCGTTC	0.398																																					p.E513G		.											.	TM9SF2	91	0			c.A1538G						.						169.0	159.0	162.0					13																	100206607		2203	4300	6503	SO:0001583	missense	9375	exon14			TTCCTGAACAGTC	U81006	CCDS9493.1	13q32.2	2011-03-28			ENSG00000125304	ENSG00000125304			11865	protein-coding gene	gene with protein product		604678				9729438	Standard	NM_004800		Approved	P76	uc001voj.2	Q99805	OTTHUMG00000017272	ENST00000376387.4:c.1538A>G	13.37:g.100206607A>G	ENSP00000365567:p.Glu513Gly	167.0	0.0		145.0	24.0	NM_004800	A8K399|Q2TAY5	Missense_Mutation	SNP	ENST00000376387.4	37	CCDS9493.1	.	.	.	.	.	.	.	.	.	.	A	17.73	3.462123	0.63513	.	.	ENSG00000125304	ENST00000376387	T	0.48201	0.82	5.93	5.93	0.95920	.	0.046005	0.85682	D	0.000000	T	0.57858	0.2082	M	0.87900	2.915	0.80722	D	1	B;B	0.19706	0.038;0.014	B;B	0.24394	0.053;0.053	T	0.58864	-0.7561	10	0.52906	T	0.07	-16.5071	16.3943	0.83563	1.0:0.0:0.0:0.0	.	479;513	E9PHW5;Q99805	.;TM9S2_HUMAN	G	513	ENSP00000365567:E513G	ENSP00000365567:E513G	E	+	2	0	TM9SF2	99004608	1.000000	0.71417	0.931000	0.37212	0.994000	0.84299	7.076000	0.76806	2.281000	0.76405	0.533000	0.62120	GAA	.		0.398	TM9SF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045602.3		
TTLL12	23170	ucsc.edu;bcgsc.ca	37	22	43564888	43564888	+	Missense_Mutation	SNP	A	A	G			TCGA-FV-A3R3-01A-11D-A22F-10	TCGA-FV-A3R3-10A-01D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.		Illumina HiSeq	c285c2fa-24b4-47a1-874d-86e74b002b05	64edddfd-f366-4d51-a8b4-a357b2c68e6c	g.chr22:43564888A>G	ENST00000216129.6	-	13	1738	c.1675T>C	c.(1675-1677)Ttc>Ctc	p.F559L	TTLL12_ENST00000494035.1_5'UTR	NM_015140.3	NP_055955.1	Q14166	TTL12_HUMAN	tubulin tyrosine ligase-like family, member 12	559	TTL. {ECO:0000255|PROSITE- ProRule:PRU00568}.				cellular protein modification process (GO:0006464)					central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(7)|ovary(2)|prostate(1)	13		Ovarian(80;0.221)|Glioma(61;0.222)				GCCACCTGGAACAGCTCCGTG	0.647																																					p.F559L		.											.	TTLL12	90	0			c.T1675C						.						41.0	34.0	36.0					22																	43564888		2196	4298	6494	SO:0001583	missense	23170	exon13			CCTGGAACAGCTC	D63487	CCDS14047.1	22q13.31	2013-02-14	2006-02-02		ENSG00000100304	ENSG00000100304		"""Tubulin tyrosine ligase-like family"""	28974	protein-coding gene	gene with protein product						15890843	Standard	NM_015140		Approved	KIAA0153	uc003bdp.3	Q14166	OTTHUMG00000150682	ENST00000216129.6:c.1675T>C	22.37:g.43564888A>G	ENSP00000216129:p.Phe559Leu	29.0	0.0		25.0	4.0	NM_015140	Q20WK5|Q9UGU3	Missense_Mutation	SNP	ENST00000216129.6	37	CCDS14047.1	.	.	.	.	.	.	.	.	.	.	A	19.20	3.782497	0.70222	.	.	ENSG00000100304	ENST00000216129;ENST00000423379	T	0.05513	3.43	5.29	5.29	0.74685	.	0.000000	0.85682	D	0.000000	T	0.08758	0.0217	L	0.38649	1.16	0.80722	D	1	P;P	0.44659	0.84;0.84	P;P	0.46685	0.524;0.524	T	0.42816	-0.9429	10	0.14656	T	0.56	-14.1071	15.2324	0.73401	1.0:0.0:0.0:0.0	.	559;559	B1AH89;Q14166	.;TTL12_HUMAN	L	559	ENSP00000216129:F559L	ENSP00000216129:F559L	F	-	1	0	TTLL12	41894832	1.000000	0.71417	1.000000	0.80357	0.922000	0.55478	5.508000	0.67006	2.002000	0.58637	0.260000	0.18958	TTC	.		0.647	TTLL12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319611.1	NM_015140	
VPS13C	54832	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	15	62182512	62182512	+	Missense_Mutation	SNP	T	T	C			TCGA-FV-A3R3-01A-11D-A22F-10	TCGA-FV-A3R3-10A-01D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c285c2fa-24b4-47a1-874d-86e74b002b05	64edddfd-f366-4d51-a8b4-a357b2c68e6c	g.chr15:62182512T>C	ENST00000261517.5	-	67	9266	c.9193A>G	c.(9193-9195)Acc>Gcc	p.T3065A	VPS13C_ENST00000395898.3_Missense_Mutation_p.T3022A|VPS13C_ENST00000395896.4_Missense_Mutation_p.T3065A|VPS13C_ENST00000249837.3_Missense_Mutation_p.T3022A	NM_020821.2	NP_065872.1			vacuolar protein sorting 13 homolog C (S. cerevisiae)											NS(3)|breast(4)|endometrium(4)|kidney(9)|large_intestine(26)|lung(46)|ovary(5)|prostate(6)|skin(6)|stomach(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	117						ACATCATCGGTGAAAAGCAAA	0.453																																					p.T3065A		.											.	VPS13C	92	0			c.A9193G						.						89.0	78.0	82.0					15																	62182512		2203	4300	6503	SO:0001583	missense	54832	exon67			CATCGGTGAAAAG	AJ608770	CCDS10180.1, CCDS32257.1, CCDS45272.1, CCDS58367.1	15q21.3	2009-07-09	2006-04-04		ENSG00000129003	ENSG00000129003			23594	protein-coding gene	gene with protein product		608879	"""vacuolar protein sorting 13C (yeast)"""				Standard	NM_018080		Approved	FLJ20136, FLJ10381, KIAA1421	uc002agz.3	Q709C8	OTTHUMG00000132801	ENST00000261517.5:c.9193A>G	15.37:g.62182512T>C	ENSP00000261517:p.Thr3065Ala	112.0	0.0		70.0	16.0	NM_020821		Missense_Mutation	SNP	ENST00000261517.5	37	CCDS32257.1	.	.	.	.	.	.	.	.	.	.	T	26.9	4.783518	0.90282	.	.	ENSG00000129003	ENST00000249837;ENST00000261517;ENST00000395896;ENST00000395898	T;T;T	0.52295	0.67;0.67;0.67	5.5	5.5	0.81552	.	0.000000	0.85682	D	0.000000	T	0.75332	0.3835	M	0.90870	3.155	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	0.999;0.999;1.0;0.997	T	0.81906	-0.0718	10	0.87932	D	0	.	15.6116	0.76727	0.0:0.0:0.0:1.0	.	3022;3065;3022;3065	Q709C8-4;Q709C8-2;Q709C8-3;Q709C8	.;.;.;VP13C_HUMAN	A	3022;3065;3065;3065	ENSP00000249837:T3022A;ENSP00000261517:T3065A;ENSP00000379233:T3065A	ENSP00000249837:T3022A	T	-	1	0	VPS13C	59969804	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	7.503000	0.81632	2.079000	0.62486	0.533000	0.62120	ACC	.		0.453	VPS13C-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000415997.1	NM_017684	
XRCC1	7515	ucsc.edu;bcgsc.ca	37	19	44055801	44055801	+	Missense_Mutation	SNP	A	A	G			TCGA-FV-A3R3-01A-11D-A22F-10	TCGA-FV-A3R3-10A-01D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.		Illumina HiSeq	c285c2fa-24b4-47a1-874d-86e74b002b05	64edddfd-f366-4d51-a8b4-a357b2c68e6c	g.chr19:44055801A>G	ENST00000262887.5	-	10	1668	c.1121T>C	c.(1120-1122)cTa>cCa	p.L374P	XRCC1_ENST00000543982.1_Missense_Mutation_p.L343P|L34079.3_ENST00000597119.1_RNA			P18887	XRCC1_HUMAN	X-ray repair complementing defective repair in Chinese hamster cells 1	374	BRCT 1. {ECO:0000255|PROSITE- ProRule:PRU00033}.				base-excision repair (GO:0006284)|DNA repair (GO:0006281)|hippocampus development (GO:0021766)|response to drug (GO:0042493)|response to hypoxia (GO:0001666)|response to organic substance (GO:0010033)|single strand break repair (GO:0000012)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	damaged DNA binding (GO:0003684)			breast(2)|endometrium(2)|large_intestine(4)|lung(6)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	19		Prostate(69;0.0153)				TCCCAGGCCTAGGACCTGGCT	0.632								Other BER factors																													p.L374P		.											.	XRCC1	912	0			c.T1121C						.						90.0	85.0	86.0					19																	44055801		2203	4300	6503	SO:0001583	missense	7515	exon10			AGGCCTAGGACCT	M36089	CCDS12624.1	19q13.2	2014-09-17				ENSG00000073050			12828	protein-coding gene	gene with protein product		194360		RCC		2247054	Standard	NM_006297		Approved		uc002owt.2	P18887		ENST00000262887.5:c.1121T>C	19.37:g.44055801A>G	ENSP00000262887:p.Leu374Pro	38.0	0.0		32.0	4.0	NM_006297	Q6IBS4|Q9HCB1	Missense_Mutation	SNP	ENST00000262887.5	37	CCDS12624.1	.	.	.	.	.	.	.	.	.	.	A	18.10	3.547773	0.65311	.	.	ENSG00000073050	ENST00000458471;ENST00000262887;ENST00000543982	T;T	0.79940	-1.32;-1.32	4.94	4.94	0.65067	BRCT (4);	0.135871	0.46758	D	0.000276	T	0.81607	0.4858	L	0.33339	1.005	0.58432	D	0.999999	D;B	0.71674	0.998;0.101	D;B	0.72625	0.978;0.122	T	0.79490	-0.1782	10	0.33940	T	0.23	-14.409	8.6153	0.33829	0.8287:0.0:0.0:0.1713	.	343;374	F5H8D7;P18887	.;XRCC1_HUMAN	P	388;374;343	ENSP00000262887:L374P;ENSP00000443671:L343P	ENSP00000262887:L374P	L	-	2	0	XRCC1	48747641	1.000000	0.71417	0.965000	0.40720	0.996000	0.88848	5.725000	0.68507	2.147000	0.66899	0.533000	0.62120	CTA	.		0.632	XRCC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463194.1	NM_006297	
ZBTB10	65986	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	8	81412242	81412243	+	Frame_Shift_Ins	INS	-	-	A	rs199777283		TCGA-FV-A3R3-01A-11D-A22F-10	TCGA-FV-A3R3-10A-01D-A22F-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c285c2fa-24b4-47a1-874d-86e74b002b05	64edddfd-f366-4d51-a8b4-a357b2c68e6c	g.chr8:81412242_81412243insA	ENST00000430430.1	+	3	2265_2266	c.1486_1487insA	c.(1486-1488)caafs	p.Q496fs	ZBTB10_ENST00000426744.2_Frame_Shift_Ins_p.Q496fs|ZBTB10_ENST00000455036.3_Frame_Shift_Ins_p.Q496fs|ZBTB10_ENST00000379091.4_Frame_Shift_Ins_p.Q204fs	NM_001277145.1	NP_001264074.1	Q96DT7	ZBT10_HUMAN	zinc finger and BTB domain containing 10	496					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(7)|ovary(1)|upper_aerodigestive_tract(4)	20	all_cancers(3;1.68e-09)|all_epithelial(4;5.13e-11)|Lung NSC(7;1.75e-07)|all_lung(9;7.38e-07)|Breast(3;2.96e-06)		BRCA - Breast invasive adenocarcinoma(6;0.000434)|Epithelial(68;0.00486)|all cancers(69;0.0296)			ATCACGGGATCAAAAAATTGCC	0.361																																					p.Q496fs		.											.	ZBTB10	522	0			c.1486_1487insA						.																																			SO:0001589	frameshift_variant	65986	exon2			CGGGATCAAAAAA	AK022814	CCDS47880.1, CCDS64920.1	8q13-q21.1	2013-01-09			ENSG00000205189	ENSG00000205189		"""-"", ""BTB/POZ domain containing"", ""Zinc fingers, C2H2-type"""	30953	protein-coding gene	gene with protein product						12477932	Standard	NM_001105539		Approved	RINZF, FLJ12752	uc003ybx.5	Q96DT7	OTTHUMG00000155016	ENST00000430430.1:c.1492dupA	8.37:g.81412248_81412248dupA	ENSP00000387462:p.Gln496fs	72.0	0.0		90.0	25.0	NM_023929	A4FVD0|Q86W96|Q8IXI9|Q96MH9	Frame_Shift_Ins	INS	ENST00000430430.1	37	CCDS47880.1																																																																																			.		0.361	ZBTB10-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000338055.2	NM_023929	
ZNF793	390927	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	19	38028241	38028241	+	Silent	SNP	C	C	T	rs371897623		TCGA-FV-A3R3-01A-11D-A22F-10	TCGA-FV-A3R3-10A-01D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c285c2fa-24b4-47a1-874d-86e74b002b05	64edddfd-f366-4d51-a8b4-a357b2c68e6c	g.chr19:38028241C>T	ENST00000587143.1	+	6	916	c.681C>T	c.(679-681)caC>caT	p.H227H	ZNF793_ENST00000588578.1_3'UTR|ZNF793_ENST00000542455.1_Silent_p.H227H|ZNF793_ENST00000589319.1_Intron|ZNF793_ENST00000445217.1_Silent_p.H227H			Q6ZN11	ZN793_HUMAN	zinc finger protein 793	227					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			kidney(2)|lung(1)	3			COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)			AAAAACCCCACGTCTGTAGTG	0.473																																					p.H227H	Melanoma(44;400 1431 1499 19093)	.											.	ZNF793	68	0			c.C681T						.	C		1,4047		0,1,2023	31.0	33.0	32.0		681	-6.8	0.1	19		32	0,8414		0,0,4207	no	coding-synonymous	ZNF793	NM_001013659.2		0,1,6230	TT,TC,CC		0.0,0.0247,0.0080		227/407	38028241	1,12461	2024	4207	6231	SO:0001819	synonymous_variant	390927	exon8			ACCCCACGTCTGT	AK131417	CCDS46062.1	19q13.12	2013-01-08				ENSG00000188227		"""Zinc fingers, C2H2-type"", ""-"""	33115	protein-coding gene	gene with protein product							Standard	NM_001013659		Approved		uc010efm.3	Q6ZN11		ENST00000587143.1:c.681C>T	19.37:g.38028241C>T		59.0	0.0		72.0	15.0	NM_001013659	E9PGN4|Q7Z3Q9	Silent	SNP	ENST00000587143.1	37	CCDS46062.1																																																																																			.		0.473	ZNF793-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458621.1	NM_001013659	
ZNF607	84775	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	19	38189048	38189048	+	Missense_Mutation	SNP	T	T	A	rs371361210		TCGA-FV-A3R3-01A-11D-A22F-10	TCGA-FV-A3R3-10A-01D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c285c2fa-24b4-47a1-874d-86e74b002b05	64edddfd-f366-4d51-a8b4-a357b2c68e6c	g.chr19:38189048T>A	ENST00000355202.4	-	5	2579	c.1984A>T	c.(1984-1986)Ata>Tta	p.I662L	ZNF607_ENST00000395835.3_Missense_Mutation_p.I661L|CTD-2528L19.4_ENST00000586606.2_Intron	NM_032689.4	NP_116078.4	Q96SK3	ZN607_HUMAN	zinc finger protein 607	662					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			cervix(1)|endometrium(3)|kidney(3)|large_intestine(11)|lung(8)|urinary_tract(1)	27			UCEC - Uterine corpus endometrioid carcinoma (49;0.0775)			CTATGATGTATACTAAGTTCA	0.378																																					p.I662L		.											.	ZNF607	90	0			c.A1984T						.	T	LEU/ILE,LEU/ILE	0,4406		0,0,2203	110.0	108.0	109.0		1981,1984	-3.9	0.3	19		109	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	ZNF607	NM_001172677.1,NM_032689.4	5,5	0,1,6502	AA,AT,TT		0.0116,0.0,0.0077	benign,benign	661/696,662/697	38189048	1,13005	2203	4300	6503	SO:0001583	missense	84775	exon5			GATGTATACTAAG	AK127464	CCDS33006.1, CCDS54259.1	19q13.1	2013-01-08				ENSG00000198182		"""Zinc fingers, C2H2-type"", ""-"""	28192	protein-coding gene	gene with protein product						14702039	Standard	NM_032689		Approved	MGC13071, FLJ14802	uc002ohc.2	Q96SK3		ENST00000355202.4:c.1984A>T	19.37:g.38189048T>A	ENSP00000347338:p.Ile662Leu	123.0	0.0		120.0	22.0	NM_032689	F5H141|Q6ZMN2|Q6ZMN4|Q96C40	Missense_Mutation	SNP	ENST00000355202.4	37	CCDS33006.1	.	.	.	.	.	.	.	.	.	.	T	11.15	1.553069	0.27739	0.0	1.16E-4	ENSG00000198182	ENST00000355202;ENST00000395835	T;T	0.17854	2.25;2.25	1.96	-3.91	0.04168	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.10380	0.0254	L	0.31926	0.97	0.09310	N	1	B;B	0.13145	0.004;0.007	B;B	0.17433	0.001;0.018	T	0.37454	-0.9705	9	0.29301	T	0.29	.	5.837	0.18613	0.0:0.137:0.4228:0.4402	.	662;661	Q96SK3;F5H141	ZN607_HUMAN;.	L	662;661	ENSP00000347338:I662L;ENSP00000438015:I661L	ENSP00000347338:I662L	I	-	1	0	ZNF607	42880888	0.000000	0.05858	0.340000	0.25575	0.870000	0.49936	-4.480000	0.00227	-0.467000	0.06932	0.379000	0.24179	ATA	.		0.378	ZNF607-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000459502.2	NM_032689	
ZXDA	7789	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca;mdanderson.org	37	X	57936066	57936066	+	Silent	SNP	G	G	A			TCGA-FV-A3R3-01A-11D-A22F-10	TCGA-FV-A3R3-10A-01D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c285c2fa-24b4-47a1-874d-86e74b002b05	64edddfd-f366-4d51-a8b4-a357b2c68e6c	g.chrX:57936066G>A	ENST00000358697.4	-	1	1001	c.789C>T	c.(787-789)ggC>ggT	p.G263G		NM_007156.4	NP_009087.1	P98168	ZXDA_HUMAN	zinc finger, X-linked, duplicated A	263					positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	C2H2 zinc finger domain binding (GO:0070742)|metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(2)|endometrium(9)|kidney(1)|large_intestine(7)|lung(13)|ovary(2)|prostate(2)|skin(1)	37						ACAGCACCACGCCTGGACCAG	0.731																																					p.G263G		.											.	ZXDA	131	0			c.C789T						.						9.0	10.0	10.0					X																	57936066		2182	4274	6456	SO:0001819	synonymous_variant	7789	exon1			CACCACGCCTGGA	L14787	CCDS14376.1	Xp11.21	2013-01-08			ENSG00000198205	ENSG00000198205		"""Zinc fingers, C2H2-type"""	13198	protein-coding gene	gene with protein product	"""zinc finger protein 896"""	300235				8268913	Standard	NM_007156		Approved	ZNF896	uc004dve.3	P98168	OTTHUMG00000021688	ENST00000358697.4:c.789C>T	X.37:g.57936066G>A		36.0	0.0		36.0	11.0	NM_007156	Q9UJP7	Silent	SNP	ENST00000358697.4	37	CCDS14376.1																																																																																			.		0.731	ZXDA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056925.1	NM_007156	
