#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_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_n_overlapping_mutations	i_COSMIC_overlapping_mutation_descriptions	i_COSMIC_overlapping_primary_sites	i_ChromChange	i_Chromosome_hg18	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_End_position_hg18	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_HGNC_Accession Numbers	i_HGNC_CCDS IDs	i_HGNC_Chromosome	i_HGNC_Date Modified	i_HGNC_Date Name Changed	i_HGNC_Date Symbol Changed	i_HGNC_Ensembl Gene ID	i_HGNC_Ensembl ID(supplied by Ensembl)	i_HGNC_Enzyme IDs	i_HGNC_Gene family description	i_HGNC_HGNC ID	i_HGNC_Locus Group	i_HGNC_Locus Type	i_HGNC_Name Synonyms	i_HGNC_OMIM ID(supplied by NCBI)	i_HGNC_Previous Names	i_HGNC_Previous Symbols	i_HGNC_Primary IDs	i_HGNC_Pubmed IDs	i_HGNC_Record Type	i_HGNC_RefSeq(supplied by NCBI)	i_HGNC_Secondary IDs	i_HGNC_Status	i_HGNC_Synonyms	i_HGNC_UCSC ID(supplied by UCSC)	i_HGNC_UniProt ID(supplied by UniProt)	i_HGNC_VEGA IDs	i_HGVS_coding_DNA_change	i_HGVS_genomic_change	i_HGVS_protein_change	i_ORegAnno_bin	i_Start_position_hg18	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_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
CREM	1390	broad.mit.edu	37	10	35485021	35485021	+	Intron	SNP	C	C	T	rs370167560		TCGA-AA-3679-01A-02W-0900-09	TCGA-AA-3679-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AA-3679-01A-02W-0900-09	TCGA-AA-3679-10A-01W-0900-09	g.chr10:35485021C>T	ENST00000395895.2	+	8	907				CREM_ENST00000468236.1_Missense_Mutation_p.L11F|CREM_ENST00000474931.1_Missense_Mutation_p.L11F|CREM_ENST00000460270.1_Intron|CREM_ENST00000463314.1_Intron|CREM_ENST00000488741.1_5'UTR|CREM_ENST00000490511.1_Missense_Mutation_p.L11F|CREM_ENST00000374728.3_Intron|CREM_ENST00000348787.2_Intron|CREM_ENST00000361599.4_Intron|CREM_ENST00000333809.8_Intron|CREM_ENST00000488328.1_Intron|CREM_ENST00000479070.1_Intron|CREM_ENST00000395887.3_Intron|CREM_ENST00000337656.4_Intron|CREM_ENST00000374721.3_Intron|CREM_ENST00000474362.1_Intron|CREM_ENST00000345491.3_Intron|CREM_ENST00000344351.5_5'UTR|CREM_ENST00000356917.5_Intron|CREM_ENST00000463960.1_Intron|CREM_ENST00000487763.1_Intron|CREM_ENST00000484283.1_Intron|CREM_ENST00000473940.1_Intron|CREM_ENST00000342105.3_Intron|CREM_ENST00000429130.3_Intron|CREM_ENST00000439705.1_Intron|CREM_ENST00000374734.3_Intron|CREM_ENST00000354759.3_Intron			Q03060	CREM_HUMAN	cAMP responsive element modulator						cell differentiation (GO:0030154)|glycosphingolipid metabolic process (GO:0006687)|multicellular organismal development (GO:0007275)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|rhythmic process (GO:0048511)|signal transduction (GO:0007165)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	cAMP response element binding protein binding (GO:0008140)|DNA binding (GO:0003677)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.L11F(1)		NS(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(7)|prostate(1)	14						GTCTGGCCAGCTTAGTGGTAA	0.458											OREG0020123	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.L11F												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C31T	10						.	C	,,,,,PHE/LEU,,,PHE/LEU,,,,,,,,,,,	1,4405	2.1+/-5.4	0,1,2202	140.0	117.0	125.0		,,,,,31,,,31,,,,,,,,,,,	0.8	0.0	10		125	3,8597	3.0+/-9.4	0,3,4297	no	intron,intron,intron,intron,intron,missense,utr-5,utr-5,missense,utr-5,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron	CREM	NM_181571.1,NM_182717.1,NM_182718.1,NM_182719.1,NM_182720.1,NM_182721.1,NM_182722.1,NM_182723.1,NM_182724.1,NM_182725.1,NM_182769.1,NM_182770.1,NM_182771.1,NM_182772.1,NM_182850.1,NM_182853.1,NM_183011.1,NM_183012.1,NM_183013.1,NM_183060.1	,,,,,22,,,22,,,,,,,,,,,	0,4,6499	TT,TC,CC		0.0349,0.0227,0.0308	,,,,,,,,,,,,,,,,,,,	,,,,,11/113,,,11/114,,,,,,,,,,,	35485021	4,13002	2203	4300	6503	35525027	SO:0001627	intron_variant	1390	exon1				CCDS7180.1, CCDS7181.1, CCDS7182.1, CCDS7183.1, CCDS7184.1, CCDS7185.1, CCDS7186.1, CCDS7187.1, CCDS7188.1, CCDS31181.1, CCDS53519.1, CCDS53520.1, CCDS53517.1, CCDS53518.1, CCDS53521.1, CCDS58074.1, CCDS58075.1, CCDS58076.1	10p12.1-p11.1	2013-01-10			ENSG00000095794	ENSG00000095794		"""basic leucine zipper proteins"""	2352	protein-coding gene	gene with protein product		123812				1461747, 7916662	Standard	NM_182717		Approved	hCREM-2	uc001iyb.3	Q03060	OTTHUMG00000017953	ENST00000395895.2:c.746-5358C>T	10.37:g.35485021C>T		855	35525027	NM_182721	A8K014|A8K3J7|A8K6A1|A8MPQ2|B4DXC1|C9J785|C9JZ10|E9PAR4|E9PHM1|O75519|Q14501|Q14503|Q14504|Q14505|Q14506|Q15731|Q16114|Q16116|Q5T9H7|Q5W1A6|Q5W1A7|Q5W1A8|Q5W1A9|Q5W1B0|Q5W1B2|Q7Z2Q6|Q8IVD4|Q96AG7|Q9NZ98|Q9NZ99|Q9NZB9	Missense_Mutation	SNP	ENST00000395895.2	37		.	.	.	.	.	.	.	.	.	.	C	9.301	1.053018	0.19907	2.27E-4	3.49E-4	ENSG00000095794	ENST00000474931;ENST00000468236;ENST00000490511	T;T;T	0.33216	1.43;1.5;1.42	2.87	0.793	0.18632	.	.	.	.	.	T	0.16685	0.0401	N	0.22421	0.69	0.18873	N	0.999988	B;B	0.25850	0.136;0.0	B;B	0.25140	0.058;0.001	T	0.23404	-1.0189	9	0.38643	T	0.18	.	2.522	0.04682	0.0:0.4173:0.2906:0.2921	.	11;11	A8K014;E9PAR4	.;.	F	11	ENSP00000417562:L11F;ENSP00000419810:L11F;ENSP00000417327:L11F	ENSP00000419810:L11F	L	+	1	0	CREM	35525027	0.001000	0.12720	0.000000	0.03702	0.010000	0.07245	-0.105000	0.10907	0.132000	0.18615	0.655000	0.94253	CTT		0.458	CREM-203	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_001881	
LRRC18	474354	broad.mit.edu	37	10	50121549	50121549	+	Missense_Mutation	SNP	G	G	A	rs201494402	byFrequency	TCGA-AA-3679-01A-02W-0900-09	TCGA-AA-3679-10A-01W-0900-09	G	G	G	A	G	A	Unknown	Valid	Germline	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AA-3679-01A-02W-0900-09	TCGA-AA-3679-10A-01W-0900-09	g.chr10:50121549G>A	ENST00000374160.3	-	1	728	c.652C>T	c.(652-654)Cgg>Tgg	p.R218W	WDFY4_ENST00000325239.5_Intron|RP11-523O18.7_ENST00000430438.1_RNA|LRRC18_ENST00000298124.3_Missense_Mutation_p.R218W|WDFY4_ENST00000413659.2_Intron	NM_001006939.3	NP_001006940.3	Q8N456	LRC18_HUMAN	leucine rich repeat containing 18	218						cytoplasm (GO:0005737)				NS(1)|endometrium(3)|kidney(1)|large_intestine(3)|lung(5)|ovary(2)|pancreas(1)|prostate(1)|skin(1)	18						AGGTTGTCCCGGGCGTTTTGG	0.498													G|||	2	0.000399361	0.0008	0.0	5008	,	,		19872	0.0		0.001	False		,,,				2504	0.0				p.R218W												.	.	0			c.C652T	10						.						167.0	171.0	170.0					10																	50121549		2203	4300	6503	49791555	SO:0001583	missense	474354	exon1			AY358137	CCDS31197.1	10q11.23	2011-02-10			ENSG00000165383	ENSG00000165383			23199	protein-coding gene	gene with protein product							Standard	NM_001006939		Approved	UNQ933, MGC34773, UNQ9338, VKGE9338	uc001jhd.3	Q8N456	OTTHUMG00000018182	ENST00000374160.3:c.652C>T	10.37:g.50121549G>A	ENSP00000363275:p.Arg218Trp		49791555	NM_001006939	Q6UY02	Missense_Mutation	SNP	ENST00000374160.3	37	CCDS31197.1	.	.	.	.	.	.	.	.	.	.	G	14.23	2.471973	0.43942	.	.	ENSG00000165383	ENST00000374160;ENST00000298124	T;T	0.60040	0.41;0.22	5.87	4.94	0.65067	.	0.105223	0.64402	D	0.000008	T	0.65668	0.2713	M	0.73962	2.25	0.43787	D	0.996326	D	0.71674	0.998	P	0.50791	0.65	T	0.68519	-0.5387	9	.	.	.	.	13.0508	0.58954	0.0:0.0:0.5423:0.4577	.	218	Q8N456	LRC18_HUMAN	W	218	ENSP00000363275:R218W;ENSP00000298124:R218W	.	R	-	1	2	LRRC18	49791555	0.854000	0.29725	0.288000	0.24862	0.271000	0.26615	1.917000	0.39996	1.426000	0.47256	0.655000	0.94253	CGG		0.498	LRRC18-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047964.1	NM_001006939	
ATM	472	broad.mit.edu	37	11	108121687	108121687	+	Missense_Mutation	SNP	C	C	G			TCGA-AA-3679-01A-02W-0900-09	TCGA-AA-3679-10A-01W-0900-09	C	C	C	G	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AA-3679-01A-02W-0900-09	TCGA-AA-3679-10A-01W-0900-09	g.chr11:108121687C>G	ENST00000452508.2	+	11	1684	c.1495C>G	c.(1495-1497)Caa>Gaa	p.Q499E	ATM_ENST00000278616.4_Missense_Mutation_p.Q499E			Q13315	ATM_HUMAN	ATM serine/threonine kinase	499					brain development (GO:0007420)|cell cycle arrest (GO:0007050)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to gamma radiation (GO:0071480)|DNA damage induced protein phosphorylation (GO:0006975)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|heart development (GO:0007507)|histone mRNA catabolic process (GO:0071044)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|lipoprotein catabolic process (GO:0042159)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of B cell proliferation (GO:0030889)|neuron apoptotic process (GO:0051402)|oocyte development (GO:0048599)|peptidyl-serine phosphorylation (GO:0018105)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|positive regulation of apoptotic process (GO:0043065)|positive regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043517)|positive regulation of neuron apoptotic process (GO:0043525)|pre-B cell allelic exclusion (GO:0002331)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|reciprocal meiotic recombination (GO:0007131)|replicative senescence (GO:0090399)|response to hypoxia (GO:0001666)|response to ionizing radiation (GO:0010212)|signal transduction (GO:0007165)|signal transduction involved in mitotic G2 DNA damage checkpoint (GO:0072434)|somitogenesis (GO:0001756)|telomere maintenance (GO:0000723)	cytoplasmic vesicle (GO:0031410)|nucleoplasm (GO:0005654)|spindle (GO:0005819)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA-dependent protein kinase activity (GO:0004677)|histone serine kinase activity (GO:0035174)|protein complex binding (GO:0032403)|protein dimerization activity (GO:0046983)|protein N-terminus binding (GO:0047485)|protein serine/threonine kinase activity (GO:0004674)	p.Q499E(1)		NS(4)|breast(23)|central_nervous_system(11)|endometrium(10)|haematopoietic_and_lymphoid_tissue(227)|kidney(19)|large_intestine(53)|liver(5)|lung(62)|ovary(6)|pancreas(4)|prostate(13)|skin(4)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(3)	448		all_cancers(61;9.64e-12)|all_epithelial(67;9.97e-08)|Melanoma(852;2.55e-06)|Acute lymphoblastic leukemia(157;3.95e-05)|all_hematologic(158;0.00014)|Breast(348;0.0258)|all_neural(303;0.072)		Epithelial(105;9.05e-06)|BRCA - Breast invasive adenocarcinoma(274;1.06e-05)|all cancers(92;0.000208)|Colorectal(284;0.116)|OV - Ovarian serous cystadenocarcinoma(223;0.147)	Caffeine(DB00201)	AAGTTCTGAGCAAATACAAGC	0.373			"""D, Mis, N, F, S"""		T-PLL	"""leukemia, lymphoma, medulloblastoma, glioma"""		Genes defective in diseases associated with sensitivity to DNA damaging agents	Ataxia Telangiectasia	TSP Lung(14;0.12)																											p.Q499E		yes	Rec	yes	Ataxia-telangiectasia	11	11q22.3	472	ataxia telangiectasia mutated		"""L, O"""	.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1495G	11						.						126.0	137.0	133.0					11																	108121687		2201	4298	6499	107626897	SO:0001583	missense	472	exon10	Familial Cancer Database	AT, Louis-Bar syndrome	AB209133	CCDS31669.1	11q22-q23	2014-09-17	2014-06-17		ENSG00000149311	ENSG00000149311			795	protein-coding gene	gene with protein product	"""TEL1, telomere maintenance 1, homolog (S. cerevisiae)"""	607585	"""ataxia telangiectasia mutated (includes complementation groups A, C and D)"", ""ataxia telangiectasia mutated"""	ATA, ATDC, ATC, ATD			Standard	XM_005271561		Approved	TEL1, TELO1	uc001pkb.1	Q13315	OTTHUMG00000166480	ENST00000452508.2:c.1495C>G	11.37:g.108121687C>G	ENSP00000388058:p.Gln499Glu		107626897	NM_000051	B2RNX5|O15429|Q12758|Q16551|Q93007|Q9NP02|Q9UCX7	Missense_Mutation	SNP	ENST00000452508.2	37	CCDS31669.1	.	.	.	.	.	.	.	.	.	.	C	16.99	3.274490	0.59649	.	.	ENSG00000149311	ENST00000527805;ENST00000278616;ENST00000452508	T;T;T	0.57595	0.39;0.39;0.39	6.04	5.08	0.68730	Armadillo-type fold (1);	0.115400	0.64402	D	0.000012	T	0.51702	0.1690	M	0.64997	1.995	0.41178	D	0.98621	B	0.12630	0.006	B	0.09377	0.004	T	0.46938	-0.9155	10	0.36615	T	0.2	.	16.8276	0.85935	0.0:0.8717:0.1283:0.0	.	499	Q13315	ATM_HUMAN	E	499	ENSP00000435747:Q499E;ENSP00000278616:Q499E;ENSP00000388058:Q499E	ENSP00000278616:Q499E	Q	+	1	0	ATM	107626897	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	5.617000	0.67716	2.873000	0.98535	0.561000	0.74099	CAA		0.373	ATM-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389938.1	NM_000051	
MRGPRX1	259249	broad.mit.edu	37	11	18955490	18955490	+	Missense_Mutation	SNP	C	C	T	rs531949208		TCGA-AA-3679-01A-02W-0900-09	TCGA-AA-3679-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AA-3679-01A-02W-0900-09	TCGA-AA-3679-10A-01W-0900-09	g.chr11:18955490C>T	ENST00000302797.3	-	1	1066	c.842G>A	c.(841-843)cGt>cAt	p.R281H	MRGPRX1_ENST00000526914.1_5'Flank|RP11-583F24.8_ENST00000528646.1_RNA	NM_147199.3	NP_671732.3	Q96LB2	MRGX1_HUMAN	MAS-related GPR, member X1	281					acute-phase response (GO:0006953)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)	p.R281H(1)		central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(8)|lung(12)|pancreas(2)|prostate(3)|skin(2)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	36						CCTATTTTGACGCTGCCTAAA	0.502													C|||	1	0.000199681	0.0	0.0	5008	,	,		26193	0.001		0.0	False		,,,				2504	0.0				p.R281H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G842A	11						.						70.0	69.0	69.0					11																	18955490		2194	4284	6478	18912066	SO:0001583	missense	259249	exon1				CCDS7846.1	11p15.1	2013-10-10			ENSG00000170255	ENSG00000170255		"""GPCR / Class A : Orphans"""	17962	protein-coding gene	gene with protein product		607227				11551509	Standard	NM_147199		Approved	MRGX1	uc001mpg.3	Q96LB2	OTTHUMG00000162655	ENST00000302797.3:c.842G>A	11.37:g.18955490C>T	ENSP00000305766:p.Arg281His		18912066	NM_147199	Q4V9L2|Q8TDD8|Q8TDD9	Missense_Mutation	SNP	ENST00000302797.3	37	CCDS7846.1	.	.	.	.	.	.	.	.	.	.	.	8.754	0.921979	0.17982	.	.	ENSG00000170255	ENST00000302797	T	0.39592	1.07	2.12	-1.07	0.09968	.	0.934257	0.08943	N	0.871317	T	0.40015	0.1100	M	0.80183	2.485	0.09310	N	1	B	0.16166	0.016	B	0.13407	0.009	T	0.37641	-0.9697	10	0.30078	T	0.28	.	5.0283	0.14396	0.0:0.4237:0.0:0.5763	.	281	Q96LB2	MRGX1_HUMAN	H	281	ENSP00000305766:R281H	ENSP00000305766:R281H	R	-	2	0	MRGPRX1	18912066	0.000000	0.05858	0.000000	0.03702	0.046000	0.14306	-0.934000	0.03955	-0.294000	0.08973	0.313000	0.20887	CGT		0.502	MRGPRX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369913.1	NM_147199	
OR4D9	390199	broad.mit.edu	37	11	59282405	59282405	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3679-01A-02W-0900-09	TCGA-AA-3679-10A-01W-0900-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AA-3679-01A-02W-0900-09	TCGA-AA-3679-10A-01W-0900-09	g.chr11:59282405C>A	ENST00000329328.3	+	1	20	c.20C>A	c.(19-21)aCc>aAc	p.T7N		NM_001004711.1	NP_001004711.1	Q8NGE8	OR4D9_HUMAN	olfactory receptor, family 4, subfamily D, member 9	7						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.T7N(1)		endometrium(1)|kidney(2)|large_intestine(3)|lung(14)|prostate(5)|upper_aerodigestive_tract(1)	26						AGAAATTACACCAGAGTGAAA	0.368																																					p.T7N												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C20A	11						.						94.0	92.0	93.0					11																	59282405		2201	4294	6495	59038981	SO:0001583	missense	390199	exon1			AB065861	CCDS31564.1	11q12.1	2012-08-09	2003-12-15		ENSG00000172742	ENSG00000172742		"""GPCR / Class A : Olfactory receptors"""	15178	protein-coding gene	gene with protein product			"""olfactory receptor, family 4, subfamily D, member 9 pseudogene"""				Standard	NM_001004711		Approved		uc010rkv.2	Q8NGE8	OTTHUMG00000167343	ENST00000329328.3:c.20C>A	11.37:g.59282405C>A	ENSP00000328563:p.Thr7Asn		59038981	NM_001004711	Q6IFF3	Missense_Mutation	SNP	ENST00000329328.3	37	CCDS31564.1	.	.	.	.	.	.	.	.	.	.	C	7.512	0.654918	0.14580	.	.	ENSG00000172742	ENST00000329328	T	0.04758	3.56	3.76	2.81	0.32909	.	0.199866	0.24449	U	0.038438	T	0.12092	0.0294	M	0.76170	2.325	0.09310	N	1	D	0.54397	0.966	P	0.56343	0.796	T	0.10847	-1.0612	10	0.22706	T	0.39	.	7.5371	0.27717	0.0:0.7868:0.0:0.2132	.	7	Q8NGE8	OR4D9_HUMAN	N	7	ENSP00000328563:T7N	ENSP00000328563:T7N	T	+	2	0	OR4D9	59038981	0.002000	0.14202	0.002000	0.10522	0.134000	0.20937	1.097000	0.30988	0.633000	0.30452	0.591000	0.81541	ACC		0.368	OR4D9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394237.1	NM_001004711	
STIP1	10963	broad.mit.edu	37	11	63970997	63970997	+	Nonsense_Mutation	SNP	C	C	T			TCGA-AA-3679-01A-02W-0900-09	TCGA-AA-3679-10A-01W-0900-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3679-01A-02W-0900-09	TCGA-AA-3679-10A-01W-0900-09	g.chr11:63970997C>T	ENST00000305218.4	+	13	1609	c.1462C>T	c.(1462-1464)Cga>Tga	p.R488*	STIP1_ENST00000538945.1_Nonsense_Mutation_p.R464*|STIP1_ENST00000358794.5_Nonsense_Mutation_p.R535*	NM_006819.2	NP_006810.1	P31948	STIP1_HUMAN	stress-induced phosphoprotein 1	488					response to stress (GO:0006950)	Golgi apparatus (GO:0005794)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)	p.R488*(2)		endometrium(4)|large_intestine(3)|liver(1)|lung(15)|ovary(2)|prostate(1)|skin(1)	27						TGTGAAGCGACGAGCCATGGC	0.602																																					p.R488X												.	.	2	Substitution - Nonsense(2)	large_intestine(2)	c.C1462T	11						.						51.0	39.0	43.0					11																	63970997		2201	4297	6498	63727573	SO:0001587	stop_gained	10963	exon13			BC039299	CCDS8058.1, CCDS60827.1, CCDS60828.1	11q13	2014-01-13	2014-01-13		ENSG00000168439	ENSG00000168439		"""Tetratricopeptide (TTC) repeat domain containing"""	11387	protein-coding gene	gene with protein product	"""Hsp70/Hsp90-organizing protein"""	605063	"""stress-induced-phosphoprotein 1"""			1569099	Standard	NM_006819		Approved	HOP, STI1	uc001nyk.1	P31948	OTTHUMG00000167789	ENST00000305218.4:c.1462C>T	11.37:g.63970997C>T	ENSP00000305958:p.Arg488*		63727573	NM_006819	B4DM70|F5H0T1|G3XAD8|Q3ZCU9|Q5TZU9	Nonsense_Mutation	SNP	ENST00000305218.4	37	CCDS8058.1	.	.	.	.	.	.	.	.	.	.	C	21.4	4.138224	0.77775	.	.	ENSG00000168439	ENST00000358794;ENST00000305218;ENST00000538945;ENST00000540887	.	.	.	5.21	3.23	0.37069	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-20.129	12.2256	0.54457	0.4461:0.5539:0.0:0.0	.	.	.	.	X	535;488;464;87	.	ENSP00000305958:R488X	R	+	1	2	STIP1	63727573	0.950000	0.32346	0.827000	0.32855	0.953000	0.61014	2.045000	0.41250	0.637000	0.30526	0.561000	0.74099	CGA		0.602	STIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396289.2	NM_006819	
SYTL2	54843	broad.mit.edu	37	11	85445217	85445217	+	Silent	SNP	A	A	T			TCGA-AA-3679-01A-02W-0900-09	TCGA-AA-3679-10A-01W-0900-09	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3679-01A-02W-0900-09	TCGA-AA-3679-10A-01W-0900-09	g.chr11:85445217A>T	ENST00000528231.1	-	6	1429	c.1152T>A	c.(1150-1152)tcT>tcA	p.S384S	SYTL2_ENST00000524452.1_Silent_p.S384S|SYTL2_ENST00000527523.1_Silent_p.S336S|SYTL2_ENST00000316356.4_Silent_p.S385S|SYTL2_ENST00000389960.4_Silent_p.S384S	NM_001162951.1|NM_001162953.1	NP_001156423.1|NP_001156425.1	Q9HCH5	SYTL2_HUMAN	synaptotagmin-like 2	384					exocytosis (GO:0006887)|intracellular protein transport (GO:0006886)|negative regulation of phosphatase activity (GO:0010923)|positive regulation of mucus secretion (GO:0070257)|vesicle docking involved in exocytosis (GO:0006904)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|exocytic vesicle (GO:0070382)|extrinsic component of plasma membrane (GO:0019897)|Golgi apparatus (GO:0005794)|melanosome (GO:0042470)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	neurexin family protein binding (GO:0042043)|phosphatase binding (GO:0019902)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|phosphatidylserine binding (GO:0001786)	p.S385S(1)		breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(10)|lung(22)|ovary(2)|prostate(4)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	52		Acute lymphoblastic leukemia(157;4.19e-06)|all_hematologic(158;0.0033)		KIRC - Kidney renal clear cell carcinoma(183;0.202)|Kidney(183;0.237)		TTCTGTATTGAGAAGGCTTAG	0.393																																					p.S384S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.T1152A	11						.						148.0	142.0	144.0					11																	85445217		2203	4299	6502	85122865	SO:0001819	synonymous_variant	54843	exon7			AJ303364	CCDS31649.1, CCDS31652.1, CCDS41698.1, CCDS53687.1, CCDS53688.1, CCDS53689.1	11q14.1	2014-06-13			ENSG00000137501	ENSG00000137501			15585	protein-coding gene	gene with protein product	"""chromosome 11 synaptotagmin"", ""breast cancer-associated antigen SGA-72M"", ""protein phosphatase 1, regulatory subunit 151"""	612880				10997877	Standard	XM_005274057		Approved	FLJ20163, FLJ21219, KIAA1597, exophilin-4, CHR11SYT, SLP2, SGA72M, MGC102768, PPP1R151	uc001pbb.3	Q9HCH5	OTTHUMG00000166977	ENST00000528231.1:c.1152T>A	11.37:g.85445217A>T			85122865	NM_032943	B3KRS3|B4DJT5|B4DKW3|B4DQ26|B7SA85|B7ZLX6|B7ZLX7|Q2YDA7|Q6TV07|Q6ZN59|Q6ZVC5|Q8ND34|Q96BJ2|Q9H768|Q9NXM1	Silent	SNP	ENST00000528231.1	37	CCDS53688.1																																																																																				0.393	SYTL2-007	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000392192.1	NM_206927	
AMOTL1	154810	broad.mit.edu	37	11	94592772	94592772	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3679-01A-02W-0900-09	TCGA-AA-3679-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AA-3679-01A-02W-0900-09	TCGA-AA-3679-10A-01W-0900-09	g.chr11:94592772G>A	ENST00000433060.2	+	9	2168	c.2027G>A	c.(2026-2028)cGg>cAg	p.R676Q	AMOTL1_ENST00000317829.8_Missense_Mutation_p.R626Q|AMOTL1_ENST00000317837.9_Intron	NM_130847.2	NP_570899.1	Q8IY63	AMOL1_HUMAN	angiomotin like 1	676					establishment of cell polarity involved in ameboidal cell migration (GO:0003365)|hippo signaling (GO:0035329)|positive regulation of blood vessel endothelial cell migration (GO:0043536)|Wnt signaling pathway (GO:0016055)	apical plasma membrane (GO:0016324)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|lamellipodium (GO:0030027)|tight junction (GO:0005923)	identical protein binding (GO:0042802)	p.R677Q(2)		autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(14)|lung(8)|ovary(1)|pancreas(1)|prostate(1)|urinary_tract(2)	36		Acute lymphoblastic leukemia(157;2.38e-05)|all_hematologic(158;0.00824)				AAGGAGGAGCGGATCCTGGCC	0.562																																					p.R676Q												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G2027A	11						.						45.0	49.0	48.0					11																	94592772		2201	4298	6499	94232420	SO:0001583	missense	154810	exon9			AF453742	CCDS44712.1, CCDS73368.1	11q21	2008-07-18				ENSG00000166025			17811	protein-coding gene	gene with protein product	"""junction-enriched and associated protein"""	614657				11733531	Standard	XM_005273798		Approved	JEAP	uc001pfb.3	Q8IY63		ENST00000433060.2:c.2027G>A	11.37:g.94592772G>A	ENSP00000387739:p.Arg676Gln		94232420	NM_130847	Q63HK7|Q8NDN0|Q8TEN8|Q8WXD1|Q96CM5	Missense_Mutation	SNP	ENST00000433060.2	37	CCDS44712.1	.	.	.	.	.	.	.	.	.	.	G	22.7	4.326103	0.81580	.	.	ENSG00000166025	ENST00000317829;ENST00000433060	T;T	0.19532	2.15;2.14	6.08	6.08	0.98989	Angiomotin, C-terminal (1);	0.113923	0.42821	D	0.000645	T	0.24392	0.0591	L	0.43152	1.355	0.80722	D	1	P;P	0.44734	0.842;0.659	P;B	0.46049	0.502;0.319	T	0.01033	-1.1474	10	0.15952	T	0.53	-39.5486	16.0688	0.80909	0.0:0.1332:0.8668:0.0	.	626;676	Q8IY63-2;Q8IY63	.;AMOL1_HUMAN	Q	626;676	ENSP00000320968:R626Q;ENSP00000387739:R676Q	ENSP00000320968:R626Q	R	+	2	0	AMOTL1	94232420	1.000000	0.71417	1.000000	0.80357	0.947000	0.59692	6.414000	0.73318	2.894000	0.99253	0.655000	0.94253	CGG		0.562	AMOTL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396474.3	NM_130847	
ZC3H12C	85463	broad.mit.edu	37	11	110007605	110007605	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3679-01A-02W-0900-09	TCGA-AA-3679-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AA-3679-01A-02W-0900-09	TCGA-AA-3679-10A-01W-0900-09	g.chr11:110007605C>T	ENST00000278590.3	+	2	290	c.239C>T	c.(238-240)gCg>gTg	p.A80V	ZC3H12C_ENST00000453089.2_Missense_Mutation_p.A49V|ZC3H12C_ENST00000528673.1_Missense_Mutation_p.A81V	NM_033390.1	NP_203748.1	Q9C0D7	ZC12C_HUMAN	zinc finger CCCH-type containing 12C	80							endonuclease activity (GO:0004519)|metal ion binding (GO:0046872)	p.A80V(1)		endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(11)|lung(16)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	37		all_cancers(61;3.24e-13)|all_epithelial(67;1.27e-07)|Melanoma(852;1.46e-05)|all_hematologic(158;3.66e-05)|Acute lymphoblastic leukemia(157;3.95e-05)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)|Breast(348;0.0544)		Epithelial(105;1.72e-06)|BRCA - Breast invasive adenocarcinoma(274;1.17e-05)|all cancers(92;9e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.0279)		GAAAAAGAGGCGTCTGAAGAG	0.448																																					p.A80V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C239T	11						.						61.0	58.0	59.0					11																	110007605		1946	4152	6098	109512815	SO:0001583	missense	85463	exon2				CCDS44727.1	11q22.3	2012-07-05			ENSG00000149289	ENSG00000149289		"""Zinc fingers, CCCH-type domain containing"""	29362	protein-coding gene	gene with protein product	"""MCP induced protein 3"""	615001				11214970, 18178554	Standard	NM_033390		Approved	KIAA1726, MCPIP3	uc009yxw.3	Q9C0D7	OTTHUMG00000166572	ENST00000278590.3:c.239C>T	11.37:g.110007605C>T	ENSP00000278590:p.Ala80Val		109512815	NM_033390	B4DI65|B4DR47	Missense_Mutation	SNP	ENST00000278590.3	37	CCDS44727.1	.	.	.	.	.	.	.	.	.	.	t	8.666	0.901758	0.17760	.	.	ENSG00000149289	ENST00000278590;ENST00000528673;ENST00000453089	T;T;T	0.30981	1.51;1.51;1.51	5.62	5.62	0.85841	.	.	.	.	.	T	0.07234	0.0183	N	0.00289	-1.7	0.09310	N	0.999998	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.31530	-0.9940	9	0.11182	T	0.66	-1.0609	6.3914	0.21589	0.0:0.2884:0.0:0.7116	.	81;80;80	B4DR47;B4DI65;Q9C0D7	.;.;ZC12C_HUMAN	V	80;81;49	ENSP00000278590:A80V;ENSP00000431821:A81V;ENSP00000413094:A49V	ENSP00000278590:A80V	A	+	2	0	ZC3H12C	109512815	0.021000	0.18746	1.000000	0.80357	0.098000	0.18820	0.260000	0.18424	0.966000	0.38159	-0.269000	0.10298	GCG		0.448	ZC3H12C-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000390491.1	NM_033390	
WSCD2	9671	broad.mit.edu	37	12	108589650	108589650	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3679-01A-02W-0900-09	TCGA-AA-3679-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AA-3679-01A-02W-0900-09	TCGA-AA-3679-10A-01W-0900-09	g.chr12:108589650G>A	ENST00000332082.4	+	3	859	c.41G>A	c.(40-42)cGg>cAg	p.R14Q	WSCD2_ENST00000547525.1_Missense_Mutation_p.R14Q|WSCD2_ENST00000261400.3_Missense_Mutation_p.R14Q|WSCD2_ENST00000549903.1_Missense_Mutation_p.R14Q			Q2TBF2	WSCD2_HUMAN	WSC domain containing 2	14						integral component of membrane (GO:0016021)		p.R14Q(1)|p.R14L(1)		breast(4)|endometrium(3)|kidney(1)|large_intestine(16)|liver(2)|lung(23)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	57						TACTTCCGCCGGAAACCTGTG	0.592																																					p.R14Q												.	.	2	Substitution - Missense(2)	large_intestine(1)|kidney(1)	c.G41A	12						.						67.0	72.0	71.0					12																	108589650		1984	4156	6140	107113780	SO:0001583	missense	9671	exon2				CCDS41828.1	12q23.3	2008-02-05				ENSG00000075035			29117	protein-coding gene	gene with protein product							Standard	NM_014653		Approved	KIAA0789	uc001tms.3	Q2TBF2		ENST00000332082.4:c.41G>A	12.37:g.108589650G>A	ENSP00000331933:p.Arg14Gln		107113780	NM_014653	B2RN48|B4DES1|Q8IY35|Q9Y4B7	Missense_Mutation	SNP	ENST00000332082.4	37	CCDS41828.1	.	.	.	.	.	.	.	.	.	.	G	36	5.802151	0.96960	.	.	ENSG00000075035	ENST00000547525;ENST00000261400;ENST00000332082;ENST00000549903	T;T;T;T	0.40225	1.07;1.04;1.07;1.04	5.74	5.74	0.90152	.	0.000000	0.85682	D	0.000000	T	0.65491	0.2696	M	0.70275	2.135	0.58432	D	0.999999	D	0.69078	0.997	D	0.70227	0.968	T	0.67264	-0.5714	10	0.87932	D	0	-35.8954	18.8897	0.92395	0.0:0.0:1.0:0.0	.	14	Q2TBF2	WSCD2_HUMAN	Q	14	ENSP00000448047:R14Q;ENSP00000261400:R14Q;ENSP00000331933:R14Q;ENSP00000447272:R14Q	ENSP00000261400:R14Q	R	+	2	0	WSCD2	107113780	1.000000	0.71417	0.993000	0.49108	0.995000	0.86356	9.317000	0.96327	2.704000	0.92352	0.655000	0.94253	CGG		0.592	WSCD2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405554.1	NM_014653	
FBXW8	26259	broad.mit.edu	37	12	117465850	117465850	+	Missense_Mutation	SNP	G	G	A	rs368052577	byFrequency	TCGA-AA-3679-01A-02W-0900-09	TCGA-AA-3679-10A-01W-0900-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3679-01A-02W-0900-09	TCGA-AA-3679-10A-01W-0900-09	g.chr12:117465850G>A	ENST00000309909.5	+	11	1752	c.1670G>A	c.(1669-1671)cGc>cAc	p.R557H	FBXW8_ENST00000455858.2_Missense_Mutation_p.R491H			Q8N3Y1	FBXW8_HUMAN	F-box and WD repeat domain containing 8	557					cell proliferation (GO:0008283)|Golgi organization (GO:0007030)|labyrinthine layer blood vessel development (GO:0060716)|positive regulation of dendrite morphogenesis (GO:0050775)|protein ubiquitination (GO:0016567)|spongiotrophoblast layer development (GO:0060712)	Cul7-RING ubiquitin ligase complex (GO:0031467)|Golgi apparatus (GO:0005794)|perinuclear region of cytoplasm (GO:0048471)|SCF ubiquitin ligase complex (GO:0019005)		p.R557H(1)		endometrium(2)|kidney(3)|large_intestine(4)|lung(8)|ovary(2)|pancreas(1)|skin(1)|stomach(1)	22	all_neural(191;0.117)|Medulloblastoma(191;0.163)			BRCA - Breast invasive adenocarcinoma(302;0.0353)		GGGCTGATCCGCGCCTATGAG	0.622													G|||	3	0.000599042	0.0	0.0	5008	,	,		17432	0.003		0.0	False		,,,				2504	0.0				p.R557H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1670A	12						.	G	HIS/ARG,HIS/ARG	0,4406		0,0,2203	98.0	75.0	83.0		1472,1670	3.8	1.0	12		83	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	FBXW8	NM_012174.1,NM_153348.2	29,29	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	benign,benign	491/533,557/599	117465850	1,13005	2203	4300	6503	115950233	SO:0001583	missense	26259	exon11			AF176707	CCDS9182.1, CCDS44988.1	12q24.23	2013-01-09	2007-02-08	2003-06-13				"""F-boxes / WD-40 domains"", ""WD repeat domain containing"""	13597	protein-coding gene	gene with protein product		609073	"""F-box only protein 29"", ""F-box and WD-40 domain protein 8"""	FBXO29		10531035, 10531037	Standard	NM_012174		Approved	FBX29, FBW6, FBW8	uc001twg.1	Q8N3Y1	OTTHUMG00000169329	ENST00000309909.5:c.1670G>A	12.37:g.117465850G>A	ENSP00000310686:p.Arg557His		115950233	NM_153348	Q9UK95	Missense_Mutation	SNP	ENST00000309909.5	37	CCDS9182.1	.	.	.	.	.	.	.	.	.	.	G	4.609	0.113274	0.08831	0.0	1.16E-4	ENSG00000174989	ENST00000309909;ENST00000455858;ENST00000505227	T;T	0.09630	2.98;2.96	4.93	3.8	0.43715	.	0.408444	0.30528	N	0.009438	T	0.05090	0.0136	N	0.10809	0.05	0.22401	N	0.999134	B;B	0.15141	0.012;0.009	B;B	0.08055	0.003;0.002	T	0.43114	-0.9411	10	0.14656	T	0.56	-7.0038	8.3216	0.32132	0.9062:0.0:0.0938:0.0	.	557;491	Q8N3Y1;Q8N3Y1-2	FBXW8_HUMAN;.	H	557;491;491	ENSP00000310686:R557H;ENSP00000389144:R491H	ENSP00000310686:R557H	R	+	2	0	FBXW8	115950233	0.989000	0.36119	0.977000	0.42913	0.406000	0.30931	2.837000	0.48191	0.734000	0.32515	-0.469000	0.05056	CGC		0.622	FBXW8-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403561.1	NM_012174	
ARHGDIB	397	broad.mit.edu	37	12	15095632	15095632	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3679-01A-02W-0900-09	TCGA-AA-3679-10A-01W-0900-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3679-01A-02W-0900-09	TCGA-AA-3679-10A-01W-0900-09	g.chr12:15095632C>A	ENST00000228945.4	-	6	574	c.430G>T	c.(430-432)Ggc>Tgc	p.G144C	ARHGDIB_ENST00000539131.1_5'UTR|ARHGDIB_ENST00000541546.1_Missense_Mutation_p.G144C|ARHGDIB_ENST00000541644.1_Missense_Mutation_p.G144C	NM_001175.4	NP_001166.3	P52566	GDIR2_HUMAN	Rho GDP dissociation inhibitor (GDI) beta	144					actin cytoskeleton organization (GO:0030036)|cellular component movement (GO:0006928)|immune response (GO:0006955)|multicellular organismal development (GO:0007275)|negative regulation of cell adhesion (GO:0007162)|regulation of catalytic activity (GO:0050790)|regulation of small GTPase mediated signal transduction (GO:0051056)|Rho protein signal transduction (GO:0007266)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	GTPase activator activity (GO:0005096)|Rho GDP-dissociation inhibitor activity (GO:0005094)	p.G144C(1)		breast(2)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(5)|prostate(1)	15						CCATAGCTGCCAACCATAAAT	0.488																																					p.G144C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G430T	12						.						87.0	73.0	78.0					12																	15095632		2203	4300	6503	14986899	SO:0001583	missense	397	exon6			L07916	CCDS8671.1	12p12.3	2014-01-30				ENSG00000111348		"""Endogenous ligands"""	679	protein-coding gene	gene with protein product		602843		RAP1GN1, GDIA2, GDID4		8434008, 8356058	Standard	NM_001175		Approved	Ly-GDI, RhoGDI2	uc001rcq.1	P52566		ENST00000228945.4:c.430G>T	12.37:g.15095632C>A	ENSP00000228945:p.Gly144Cys		14986899	NM_001175	B5BU79	Missense_Mutation	SNP	ENST00000228945.4	37	CCDS8671.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	22.7|22.7	4.323579|4.323579	0.81580|0.81580	.|.	.|.	ENSG00000111348|ENSG00000111348	ENST00000228945;ENST00000541644;ENST00000541546;ENST00000545895|ENST00000536592	.|.	.|.	.|.	4.41|4.41	4.41|4.41	0.53225|0.53225	Immunoglobulin E-set (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	D|D	0.87370|0.87370	0.6160|0.6160	H|H	0.97077|0.97077	3.935|3.935	0.80722|0.80722	D|D	1|1	D|.	0.89917|.	1.0|.	D|.	0.97110|.	1.0|.	D|D	0.91420|0.91420	0.5158|0.5158	9|5	0.87932|.	D|.	0|.	-15.9031|-15.9031	14.9714|14.9714	0.71238|0.71238	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	144|.	P52566|.	GDIR2_HUMAN|.	C|L	144|137	.|.	ENSP00000228945:G144C|.	G|W	-|-	1|2	0|0	ARHGDIB|ARHGDIB	14986899|14986899	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.987000|0.987000	0.75469|0.75469	7.247000|7.247000	0.78257|0.78257	2.457000|2.457000	0.83068|0.83068	0.650000|0.650000	0.86243|0.86243	GGC|TGG		0.488	ARHGDIB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400871.1	NM_001175	
ANO6	196527	broad.mit.edu	37	12	45695844	45695844	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3679-01A-02W-0900-09	TCGA-AA-3679-10A-01W-0900-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3679-01A-02W-0900-09	TCGA-AA-3679-10A-01W-0900-09	g.chr12:45695844G>A	ENST00000320560.8	+	2	320	c.118G>A	c.(118-120)Gaa>Aaa	p.E40K	ANO6_ENST00000441606.2_Missense_Mutation_p.E22K|ANO6_ENST00000423947.3_Missense_Mutation_p.E61K|ANO6_ENST00000426898.2_Intron|ANO6_ENST00000435642.1_Missense_Mutation_p.E40K|ANO6_ENST00000425752.2_Missense_Mutation_p.E40K	NM_001025356.2	NP_001020527.2	Q4KMQ2	ANO6_HUMAN	anoctamin 6	40					activation of blood coagulation via clotting cascade (GO:0002543)|blood coagulation (GO:0007596)|bone mineralization involved in bone maturation (GO:0035630)|calcium activated galactosylceramide scrambling (GO:0061591)|calcium activated phosphatidylcholine scrambling (GO:0061590)|calcium activated phosphatidylserine scrambling (GO:0061589)|cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|dendritic cell chemotaxis (GO:0002407)|ion transmembrane transport (GO:0034220)|phosphatidylserine exposure on blood platelet (GO:0097045)|phospholipid scrambling (GO:0017121)|positive regulation of endothelial cell apoptotic process (GO:2000353)|regulation of anion transport (GO:0044070)|transmembrane transport (GO:0055085)	cell surface (GO:0009986)|chloride channel complex (GO:0034707)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium activated cation channel activity (GO:0005227)|intracellular calcium activated chloride channel activity (GO:0005229)|phospholipid scramblase activity (GO:0017128)|voltage-gated chloride channel activity (GO:0005247)|voltage-gated ion channel activity (GO:0005244)	p.E40K(2)		central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(8)|lung(23)|ovary(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	46						GGGATCACTGGAAAGTCAGCA	0.363																																					p.E40K												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G118A	12						.						167.0	165.0	166.0					12																	45695844		2203	4300	6503	43982111	SO:0001583	missense	196527	exon2			AL832340	CCDS31782.1, CCDS44865.1, CCDS44866.1, CCDS55819.1	12q12-q13.11	2014-09-17	2008-08-28	2008-08-28				"""Ion channels / Chloride channels : Calcium activated : Anoctamins"""	25240	protein-coding gene	gene with protein product		608663	"""transmembrane protein 16F"""	TMEM16F		15067359, 24692353	Standard	NM_001025356		Approved	DKFZp313M0720	uc010slf.2	Q4KMQ2	OTTHUMG00000169564	ENST00000320560.8:c.118G>A	12.37:g.45695844G>A	ENSP00000320087:p.Glu40Lys		43982111	NM_001025356	A6NNM6|B9EGG0|E7ENK4|E9PB30|E9PCT2|Q8N3Q2	Missense_Mutation	SNP	ENST00000320560.8	37	CCDS31782.1	.	.	.	.	.	.	.	.	.	.	G	17.73	3.460668	0.63513	.	.	ENSG00000177119	ENST00000425752;ENST00000423947;ENST00000435642;ENST00000320560;ENST00000441606	T;T;T;T;T	0.69806	-0.43;-0.3;-0.43;-0.29;-0.26	4.83	2.83	0.33086	.	0.441739	0.20542	N	0.090289	T	0.55545	0.1927	L	0.57536	1.79	0.09310	N	1	B;B;B;B	0.10296	0.0;0.003;0.0;0.002	B;B;B;B	0.12156	0.0;0.001;0.0;0.007	T	0.36138	-0.9760	10	0.20046	T	0.44	.	6.0657	0.19862	0.1027:0.1914:0.706:0.0	.	22;61;40;40	E9PB30;B9EGG0;E9PCT2;Q4KMQ2	.;.;.;ANO6_HUMAN	K	40;61;40;40;22	ENSP00000391417:E40K;ENSP00000409126:E61K;ENSP00000413840:E40K;ENSP00000320087:E40K;ENSP00000413137:E22K	ENSP00000320087:E40K	E	+	1	0	ANO6	43982111	0.308000	0.24509	0.058000	0.19502	0.942000	0.58702	1.737000	0.38197	1.347000	0.45714	0.643000	0.83706	GAA		0.363	ANO6-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000404822.1	XM_113743	
PRKAG1	5571	broad.mit.edu	37	12	49396782	49396782	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3679-01A-02W-0900-09	TCGA-AA-3679-10A-01W-0900-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3679-01A-02W-0900-09	TCGA-AA-3679-10A-01W-0900-09	g.chr12:49396782C>T	ENST00000548065.1	-	12	1352	c.896G>A	c.(895-897)cGa>cAa	p.R299Q	RP11-386G11.5_ENST00000547866.1_RNA|RP11-386G11.5_ENST00000552284.1_RNA|RP11-386G11.5_ENST00000552933.1_RNA|PRKAG1_ENST00000316299.5_Missense_Mutation_p.R308Q|RP11-386G11.5_ENST00000547395.1_RNA|PRKAG1_ENST00000547306.1_Missense_Mutation_p.R248Q|PRKAG1_ENST00000552212.1_Missense_Mutation_p.R267Q|PRKAG1_ENST00000395170.3_Missense_Mutation_p.R215Q			P54619	AAKG1_HUMAN	protein kinase, AMP-activated, gamma 1 non-catalytic subunit	299	CBS 4. {ECO:0000255|PROSITE- ProRule:PRU00703}.				cell cycle arrest (GO:0007050)|fatty acid biosynthetic process (GO:0006633)|insulin receptor signaling pathway (GO:0008286)|membrane organization (GO:0061024)|positive regulation of gene expression (GO:0010628)|positive regulation of protein kinase activity (GO:0045860)|protein heterooligomerization (GO:0051291)|protein phosphorylation (GO:0006468)|regulation of glycolytic process (GO:0006110)|signal transduction (GO:0007165)|spermatogenesis (GO:0007283)	AMP-activated protein kinase complex (GO:0031588)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)	ADP binding (GO:0043531)|AMP binding (GO:0016208)|ATP binding (GO:0005524)|cAMP-dependent protein kinase activity (GO:0004691)|cAMP-dependent protein kinase regulator activity (GO:0008603)|protein kinase activity (GO:0004672)|protein kinase binding (GO:0019901)	p.R299Q(1)		cervix(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(1)|upper_aerodigestive_tract(1)	9					Acetylsalicylic acid(DB00945)	CACTACAAGTCGGTGAACCTG	0.542																																					p.R299Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G896A	12						.						146.0	119.0	128.0					12																	49396782		2203	4300	6503	47683049	SO:0001583	missense	5571	exon12			U42412	CCDS8777.1, CCDS55824.1, CCDS55825.1	12q12-q14	1998-07-16				ENSG00000181929			9385	protein-coding gene	gene with protein product		602742				8557660, 8621499	Standard	NM_002733		Approved		uc001rsz.3	P54619	OTTHUMG00000170406	ENST00000548065.1:c.896G>A	12.37:g.49396782C>T	ENSP00000447433:p.Arg299Gln		47683049	NM_002733	B4DDT7|Q8N7V9	Missense_Mutation	SNP	ENST00000548065.1	37	CCDS8777.1	.	.	.	.	.	.	.	.	.	.	C	18.01	3.526842	0.64860	.	.	ENSG00000181929	ENST00000548362;ENST00000395170;ENST00000547306;ENST00000316299;ENST00000548065;ENST00000552212;ENST00000551770;ENST00000551696	D;D;D;D;D;D;D;D	0.94687	-3.49;-3.49;-3.49;-3.49;-3.49;-3.49;-3.49;-3.49	5.18	4.28	0.50868	Aldolase-type TIM barrel (1);Cystathionine beta-synthase, core (3);	0.056121	0.64402	D	0.000001	D	0.97620	0.9220	M	0.91920	3.255	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.98472	1.0601	10	0.87932	D	0	-4.9987	14.178	0.65555	0.151:0.849:0.0:0.0	.	308;299	Q8N7V9;P54619	.;AAKG1_HUMAN	Q	64;215;248;308;299;267;219;193	ENSP00000446987:R64Q;ENSP00000378599:R215Q;ENSP00000448873:R248Q;ENSP00000323867:R308Q;ENSP00000447433:R299Q;ENSP00000448972:R267Q;ENSP00000449121:R219Q;ENSP00000447671:R193Q	ENSP00000323867:R308Q	R	-	2	0	PRKAG1	47683049	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.574000	0.82434	1.402000	0.46780	0.655000	0.94253	CGA		0.542	PRKAG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408946.1	NM_002733	
TMEM132B	114795	broad.mit.edu	37	12	126135236	126135236	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3679-01A-02W-0900-09	TCGA-AA-3679-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AA-3679-01A-02W-0900-09	TCGA-AA-3679-10A-01W-0900-09	g.chr12:126135236C>T	ENST00000299308.3	+	7	1644	c.1636C>T	c.(1636-1638)Cgg>Tgg	p.R546W	TMEM132B_ENST00000535886.1_Missense_Mutation_p.R58W	NM_052907.2	NP_443139.2	Q14DG7	T132B_HUMAN	transmembrane protein 132B	546						integral component of membrane (GO:0016021)		p.R546W(1)		NS(1)|breast(9)|central_nervous_system(1)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(11)|liver(1)|lung(45)|ovary(5)|pancreas(1)|prostate(4)|skin(15)|upper_aerodigestive_tract(3)|urinary_tract(1)	107	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000423)|Epithelial(86;0.00394)|all cancers(50;0.0362)		CAGGCCTACCCGGGAAAGCGA	0.527																																					p.R546W												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1636T	12						.						65.0	73.0	70.0					12																	126135236		2159	4278	6437	124701189	SO:0001583	missense	114795	exon7			AB067493	CCDS41859.1, CCDS66501.1	12q24.31	2006-03-02							29397	protein-coding gene	gene with protein product						11572484	Standard	NM_001286219		Approved	KIAA1906, KIAA1786	uc001uhe.1	Q14DG7		ENST00000299308.3:c.1636C>T	12.37:g.126135236C>T	ENSP00000299308:p.Arg546Trp		124701189	NM_052907	A2RRG8|Q8NA73|Q96JN9|Q96PY1	Missense_Mutation	SNP	ENST00000299308.3	37	CCDS41859.1	.	.	.	.	.	.	.	.	.	.	C	13.12	2.142698	0.37825	.	.	ENSG00000139364	ENST00000299308;ENST00000535886	T;T	0.20881	2.04;2.04	5.15	3.29	0.37713	.	0.000000	0.56097	D	0.000031	T	0.37265	0.0997	M	0.68952	2.095	0.80722	D	1	D	0.76494	0.999	P	0.60886	0.88	T	0.06789	-1.0807	10	0.54805	T	0.06	.	9.9896	0.41863	0.2796:0.5856:0.1349:0.0	.	546	Q14DG7	T132B_HUMAN	W	546;58	ENSP00000299308:R546W;ENSP00000440436:R58W	ENSP00000299308:R546W	R	+	1	2	TMEM132B	124701189	0.981000	0.34729	0.915000	0.36163	0.026000	0.11368	1.750000	0.38329	0.524000	0.28502	-0.175000	0.13238	CGG		0.527	TMEM132B-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000400043.1	NM_052907	
LHFP	10186	broad.mit.edu	37	13	39918122	39918122	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3679-01A-02W-0900-09	TCGA-AA-3679-10A-01W-0900-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3679-01A-02W-0900-09	TCGA-AA-3679-10A-01W-0900-09	g.chr13:39918122G>A	ENST00000379589.3	-	4	1016	c.554C>T	c.(553-555)aCg>aTg	p.T185M		NM_005780.2	NP_005771.1	Q9Y693	LHFP_HUMAN	lipoma HMGIC fusion partner	185						integral component of membrane (GO:0016021)	DNA binding (GO:0003677)	p.T185M(1)	HMGA2/LHFP(2)	breast(1)|endometrium(2)|large_intestine(1)|liver(1)|lung(6)|prostate(2)	13		Lung NSC(96;3.55e-06)|Breast(139;0.00408)|Ovarian(182;0.0107)|Prostate(109;0.0118)|Lung SC(185;0.0719)|Hepatocellular(188;0.114)		OV - Ovarian serous cystadenocarcinoma(117;6.48e-46)|Epithelial(112;8.43e-42)|all cancers(112;1.42e-36)|GBM - Glioblastoma multiforme(144;0.00187)|BRCA - Breast invasive adenocarcinoma(63;0.00886)|KIRC - Kidney renal clear cell carcinoma(186;0.048)|Kidney(163;0.0601)|LUSC - Lung squamous cell carcinoma(192;0.105)		AGCCAGCCACGTGCACAGCAG	0.552			T	HMGA2	lipoma																																p.T185M			Dom	yes		13	13q12	10186	lipoma HMGIC fusion partner		M	.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C554T	13						.						99.0	83.0	88.0					13																	39918122		2203	4300	6503	38816122	SO:0001583	missense	10186	exon4			AF098807	CCDS9369.1	13q12	2008-07-18			ENSG00000183722	ENSG00000183722			6586	protein-coding gene	gene with protein product		606710				10329012	Standard	NM_005780		Approved	MGC22429	uc001uxf.3	Q9Y693	OTTHUMG00000016767	ENST00000379589.3:c.554C>T	13.37:g.39918122G>A	ENSP00000368908:p.Thr185Met		38816122	NM_005780	B2R7M2|Q53FC0|Q96SH5	Missense_Mutation	SNP	ENST00000379589.3	37	CCDS9369.1	.	.	.	.	.	.	.	.	.	.	G	24.4	4.529736	0.85706	.	.	ENSG00000183722	ENST00000379589	T	0.73258	-0.73	5.24	5.24	0.73138	.	0.081758	0.50627	D	0.000108	D	0.82609	0.5074	M	0.75447	2.3	0.50813	D	0.999891	D	0.69078	0.997	D	0.63113	0.911	T	0.83184	-0.0087	9	.	.	.	.	17.8177	0.88640	0.0:0.0:1.0:0.0	.	185	Q9Y693	LHFP_HUMAN	M	185	ENSP00000368908:T185M	.	T	-	2	0	LHFP	38816122	1.000000	0.71417	0.939000	0.37840	0.946000	0.59487	9.363000	0.97131	2.459000	0.83118	0.557000	0.71058	ACG		0.552	LHFP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044619.1	NM_005780	
PCDH9	5101	broad.mit.edu	37	13	67801597	67801597	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3679-01A-02W-0900-09	TCGA-AA-3679-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AA-3679-01A-02W-0900-09	TCGA-AA-3679-10A-01W-0900-09	g.chr13:67801597G>A	ENST00000377865.2	-	1	1110	c.976C>T	c.(976-978)Cac>Tac	p.H326Y	PCDH9_ENST00000456367.1_Missense_Mutation_p.H326Y|PCDH9_ENST00000328454.5_Missense_Mutation_p.H326Y|PCDH9_ENST00000377861.3_Missense_Mutation_p.H326Y|PCDH9_ENST00000544246.1_Missense_Mutation_p.H326Y			Q9HC56	PCDH9_HUMAN	protocadherin 9	326	Cadherin 3. {ECO:0000255|PROSITE- ProRule:PRU00043}.				forebrain development (GO:0030900)|homophilic cell adhesion (GO:0007156)	cell-cell contact zone (GO:0044291)|growth cone (GO:0030426)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.H326Y(1)		breast(2)|central_nervous_system(3)|cervix(2)|endometrium(7)|kidney(4)|large_intestine(33)|lung(30)|ovary(5)|pancreas(2)|prostate(1)|skin(4)|stomach(2)|upper_aerodigestive_tract(5)|urinary_tract(3)	103		Hepatocellular(98;0.0906)|Breast(118;0.107)		GBM - Glioblastoma multiforme(99;0.00819)		GTCACTTTGTGAATGGCTGTC	0.473																																					p.H326Y												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C976T	13						.						102.0	101.0	102.0					13																	67801597		2203	4300	6503	66699598	SO:0001583	missense	5101	exon2			AF169692	CCDS9443.1, CCDS9444.1	13q21.32	2010-02-22			ENSG00000184226	ENSG00000184226		"""Cadherins / Protocadherins : Non-clustered"""	8661	protein-coding gene	gene with protein product		603581				9787079	Standard	NM_020403		Approved		uc001vik.3	Q9HC56	OTTHUMG00000017040	ENST00000377865.2:c.976C>T	13.37:g.67801597G>A	ENSP00000367096:p.His326Tyr		66699598	NM_020403	A2A6U1|Q5VT83|Q7Z3U0|Q8N3K7	Missense_Mutation	SNP	ENST00000377865.2	37	CCDS9444.1	.	.	.	.	.	.	.	.	.	.	G	15.08	2.726589	0.48833	.	.	ENSG00000184226	ENST00000544246;ENST00000377865;ENST00000456367;ENST00000328454;ENST00000377861	T;T;T;T;T	0.24723	1.84;1.84;1.84;1.84;1.84	6.17	6.17	0.99709	Cadherin (4);Cadherin-like (1);	0.000000	0.85682	D	0.000000	T	0.29256	0.0728	N	0.01761	-0.735	0.80722	D	1	P;D;D;D	0.89917	0.942;1.0;1.0;1.0	D;D;D;D	0.97110	0.943;1.0;1.0;1.0	T	0.54768	-0.8244	10	0.45353	T	0.12	.	20.8794	0.99867	0.0:0.0:1.0:0.0	.	326;326;326;326	B7ZM79;Q5VT82;Q9HC56-2;Q9HC56	.;.;.;PCDH9_HUMAN	Y	326	ENSP00000442186:H326Y;ENSP00000367096:H326Y;ENSP00000401699:H326Y;ENSP00000332060:H326Y;ENSP00000367092:H326Y	ENSP00000332060:H326Y	H	-	1	0	PCDH9	66699598	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	8.062000	0.89475	2.941000	0.99782	0.655000	0.94253	CAC		0.473	PCDH9-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000276387.1	NM_203487	
RASA3	22821	broad.mit.edu	37	13	114793340	114793340	+	Silent	SNP	C	C	T	rs575958394		TCGA-AA-3679-01A-02W-0900-09	TCGA-AA-3679-10A-01W-0900-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3679-01A-02W-0900-09	TCGA-AA-3679-10A-01W-0900-09	g.chr13:114793340C>T	ENST00000334062.7	-	6	634	c.513G>A	c.(511-513)acG>acA	p.T171T	RASA3_ENST00000389544.4_Silent_p.T139T|RASA3_ENST00000542651.1_3'UTR	NM_007368.2	NP_031394.2	Q14644	RASA3_HUMAN	RAS p21 protein activator 3	171	C2 2. {ECO:0000255|PROSITE- ProRule:PRU00041}.				calcium ion transmembrane transport (GO:0070588)|intracellular signal transduction (GO:0035556)|negative regulation of Ras protein signal transduction (GO:0046580)|positive regulation of Ras GTPase activity (GO:0032320)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)	calcium-release channel activity (GO:0015278)|GTPase activator activity (GO:0005096)|metal ion binding (GO:0046872)|Ras GTPase activator activity (GO:0005099)	p.T171T(1)		breast(1)|central_nervous_system(2)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(8)|lung(20)|ovary(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	47	Lung NSC(43;0.00814)|all_neural(89;0.0337)|Medulloblastoma(90;0.163)|Lung SC(71;0.218)	all_cancers(25;0.016)|all_epithelial(44;0.00577)|all_lung(25;0.0173)|Lung NSC(25;0.0634)|Breast(118;0.188)	BRCA - Breast invasive adenocarcinoma(86;0.128)			GTCCTGCCAGCGTCACGGTGG	0.617													c|||	1	0.000199681	0.0008	0.0	5008	,	,		17692	0.0		0.0	False		,,,				2504	0.0				p.T171T												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G513A	13						.						142.0	110.0	121.0					13																	114793340		2203	4300	6503	113811442	SO:0001819	synonymous_variant	22821	exon6				CCDS32016.1	13q34	2013-01-10			ENSG00000185989	ENSG00000185989		"""Pleckstrin homology (PH) domain containing"""	20331	protein-coding gene	gene with protein product		605182				7637787, 9382842	Standard	NM_007368		Approved	GAP1IP4BP, GAPIII	uc001vui.3	Q14644	OTTHUMG00000017399	ENST00000334062.7:c.513G>A	13.37:g.114793340C>T			113811442	NM_007368	A6NL15|F8W6X8|Q8IUY2	Silent	SNP	ENST00000334062.7	37	CCDS32016.1																																																																																				0.617	RASA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045957.2	NM_007368	
PCNXL4	64430	broad.mit.edu	37	14	60582142	60582142	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3679-01A-02W-0900-09	TCGA-AA-3679-10A-01W-0900-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AA-3679-01A-02W-0900-09	TCGA-AA-3679-10A-01W-0900-09	g.chr14:60582142G>T	ENST00000406854.1	+	4	1874	c.1320G>T	c.(1318-1320)atG>atT	p.M440I	PCNXL4_ENST00000404681.2_Missense_Mutation_p.M440I|PCNXL4_ENST00000317623.4_Missense_Mutation_p.M206I|PCNXL4_ENST00000406949.1_Missense_Mutation_p.M206I			Q63HM2	PCX4_HUMAN	pecanex-like 4 (Drosophila)	440						integral component of membrane (GO:0016021)		p.M440I(1)|p.M206I(1)									CTAGGCTCATGAAGATTGGTA	0.338																																					p.M206I												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G618T	14						.						96.0	96.0	96.0					14																	60582142		1847	4084	5931	59651895	SO:0001583	missense	64430	exon3			AK022861		14q23.1	2012-07-18	2012-07-18	2012-07-18	ENSG00000126773	ENSG00000126773			20349	protein-coding gene	gene with protein product			"""chromosome 14 open reading frame 135"""	C14orf135			Standard	NM_022495		Approved		uc001xer.4	Q63HM2	OTTHUMG00000150361	ENST00000406854.1:c.1320G>T	14.37:g.60582142G>T	ENSP00000384801:p.Met440Ile		59651895	NM_022495	A8MXM2|Q9BQG8|Q9H9F2	Missense_Mutation	SNP	ENST00000406854.1	37		.	.	.	.	.	.	.	.	.	.	G	10.47	1.359799	0.24598	.	.	ENSG00000126773	ENST00000317623;ENST00000406854;ENST00000406949;ENST00000404681	T;T;T;T	0.21932	1.98;1.98;1.99;1.98	5.8	4.9	0.64082	.	.	.	.	.	T	0.18215	0.0437	L	0.36672	1.1	0.80722	D	1	B;B	0.09022	0.001;0.002	B;B	0.09377	0.003;0.004	T	0.03240	-1.1057	9	0.22706	T	0.39	.	15.1628	0.72798	0.0685:0.0:0.9315:0.0	.	440;206	Q63HM2;B5MC47	CN135_HUMAN;.	I	206;440;206;440	ENSP00000317396:M206I;ENSP00000384801:M440I;ENSP00000385201:M206I;ENSP00000385713:M440I	ENSP00000317396:M206I	M	+	3	0	C14orf135	59651895	1.000000	0.71417	0.933000	0.37362	0.946000	0.59487	2.358000	0.44134	1.432000	0.47375	0.455000	0.32223	ATG		0.338	PCNXL4-005	KNOWN	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000317847.1	NM_022495	
ESR2	2100	broad.mit.edu	37	14	64727347	64727347	+	Silent	SNP	G	G	A	rs143949374		TCGA-AA-3679-01A-02W-0900-09	TCGA-AA-3679-10A-01W-0900-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3679-01A-02W-0900-09	TCGA-AA-3679-10A-01W-0900-09	g.chr14:64727347G>A	ENST00000341099.4	-	5	1189	c.772C>T	c.(772-774)Ctg>Ttg	p.L258L	ESR2_ENST00000357782.2_Silent_p.L258L|ESR2_ENST00000358599.5_Silent_p.L258L|ESR2_ENST00000553796.1_Silent_p.L258L|ESR2_ENST00000555483.1_5'UTR|ESR2_ENST00000554572.1_Silent_p.L258L|ESR2_ENST00000555278.1_Silent_p.L258L|ESR2_ENST00000542956.1_Silent_p.L258L|ESR2_ENST00000557772.1_Silent_p.L258L|ESR2_ENST00000267525.6_Silent_p.L258L|ESR2_ENST00000353772.3_Silent_p.L258L	NM_001437.2	NP_001428.1	Q92731	ESR2_HUMAN	estrogen receptor 2 (ER beta)	258	Steroid-binding.				brain development (GO:0007420)|cell-cell signaling (GO:0007267)|epithelial cell maturation involved in prostate gland development (GO:0060743)|extracellular negative regulation of signal transduction (GO:1900116)|gene expression (GO:0010467)|hormone-mediated apoptotic signaling pathway (GO:0008628)|intracellular estrogen receptor signaling pathway (GO:0030520)|negative regulation of androgen receptor signaling pathway (GO:0060766)|negative regulation of cell growth (GO:0030308)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuron migration (GO:0001764)|ovarian follicle development (GO:0001541)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|prostate gland epithelium morphogenesis (GO:0060740)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)|transcription initiation from RNA polymerase II promoter (GO:0006367)|uterus development (GO:0060065)|vagina development (GO:0060068)	extracellular region (GO:0005576)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	core promoter sequence-specific DNA binding (GO:0001046)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|estrogen receptor activity (GO:0030284)|estrogen response element binding (GO:0034056)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|receptor antagonist activity (GO:0048019)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid binding (GO:0005496)|steroid hormone receptor activity (GO:0003707)|transcription coactivator activity (GO:0003713)|zinc ion binding (GO:0008270)	p.L258L(1)		central_nervous_system(2)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(5)|ovary(1)|prostate(1)|skin(3)|stomach(1)|urinary_tract(1)	23				all cancers(60;0.00916)|OV - Ovarian serous cystadenocarcinoma(108;0.0111)|BRCA - Breast invasive adenocarcinoma(234;0.0437)	Diethylstilbestrol(DB00255)|Estradiol(DB00783)|Estramustine(DB01196)|Estriol(DB04573)|Estropipate(DB04574)|Raloxifene(DB00481)|Tamoxifen(DB00675)|Trilostane(DB01108)	TCCAGCAGCAGCTCCCGCACT	0.687																																					p.L258L												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C772T	14						.	G	,,,,	1,4397		0,1,2198	23.0	25.0	24.0		772,772,772,772,772	3.9	1.0	14	dbSNP_134	24	0,8580		0,0,4290	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	ESR2	NM_001040275.1,NM_001040276.1,NM_001214902.1,NM_001214903.1,NM_001437.2	,,,,	0,1,6488	AA,AG,GG		0.0,0.0227,0.0077	,,,,	258/496,258/496,258/482,258/473,258/531	64727347	1,12977	2199	4290	6489	63797100	SO:0001819	synonymous_variant	2100	exon5			X99101	CCDS9762.1, CCDS32096.1, CCDS55920.1, CCDS61469.1, CCDS61470.1	14q21-q22	2013-01-16			ENSG00000140009	ENSG00000140009		"""Nuclear hormone receptors"""	3468	protein-coding gene	gene with protein product		601663				8769313	Standard	NM_001214902		Approved	NR3A2, Erb	uc001xha.1	Q92731	OTTHUMG00000141306	ENST00000341099.4:c.772C>T	14.37:g.64727347G>A			63797100	NM_001437	A8K8K5|G3V5M5|O60608|O60685|O60702|O60703|O75583|O75584|Q0MWT5|Q0MWT6|Q86Z31|Q9UEV6|Q9UHD3|Q9UQK9	Silent	SNP	ENST00000341099.4	37	CCDS9762.1																																																																																				0.687	ESR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000280621.1		
GABRA5	2558	broad.mit.edu	37	15	27114437	27114437	+	Missense_Mutation	SNP	C	C	A	rs373759830		TCGA-AA-3679-01A-02W-0900-09	TCGA-AA-3679-10A-01W-0900-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AA-3679-01A-02W-0900-09	TCGA-AA-3679-10A-01W-0900-09	g.chr15:27114437C>A	ENST00000335625.5	+	3	930	c.42C>A	c.(40-42)aaC>aaA	p.N14K	GABRA5_ENST00000355395.5_Missense_Mutation_p.N14K|GABRA5_ENST00000400081.3_Missense_Mutation_p.N14K|GABRA5_ENST00000557449.1_3'UTR|GABRB3_ENST00000541819.2_Intron	NM_000810.3	NP_000801.1	P31644	GBRA5_HUMAN	gamma-aminobutyric acid (GABA) A receptor, alpha 5	14					associative learning (GO:0008306)|behavioral fear response (GO:0001662)|brain development (GO:0007420)|cochlea development (GO:0090102)|gamma-aminobutyric acid signaling pathway (GO:0007214)|inner ear receptor cell development (GO:0060119)|innervation (GO:0060384)|ion transmembrane transport (GO:0034220)|negative regulation of neuron apoptotic process (GO:0043524)|sensory perception of sound (GO:0007605)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|neuronal cell body membrane (GO:0032809)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|receptor complex (GO:0043235)	chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)|receptor activity (GO:0004872)|transporter activity (GO:0005215)	p.N14K(1)		NS(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(26)|ovary(1)|upper_aerodigestive_tract(1)	49		all_lung(180;4.59e-13)|Breast(32;0.000563)|Colorectal(260;0.227)		all cancers(64;1.45e-08)|Epithelial(43;4.96e-08)|BRCA - Breast invasive adenocarcinoma(123;0.0232)|Lung(196;0.182)	Acamprosate(DB00659)|Adinazolam(DB00546)|Alprazolam(DB00404)|Amobarbital(DB01351)|Amoxapine(DB00543)|Aprobarbital(DB01352)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Butethal(DB01353)|Chlordiazepoxide(DB00475)|Cinolazepam(DB01594)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Clotiazepam(DB01559)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Fludiazepam(DB01567)|Flumazenil(DB01205)|Flunitrazepam(DB01544)|Flurazepam(DB00690)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Heptabarbital(DB01354)|Hexobarbital(DB01355)|Isoflurane(DB00753)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methylphenobarbital(DB00849)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Secobarbital(DB00418)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Thiopental(DB00599)|Topiramate(DB00273)|Triazolam(DB00897)|Zopiclone(DB01198)	TGATCAAAAACCTCCTTCTCT	0.383																																					p.N14K												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C42A	15						.						221.0	215.0	217.0					15																	27114437		1904	4110	6014	24665530	SO:0001583	missense	2558	exon3				CCDS45194.1	15q12	2012-06-22			ENSG00000186297	ENSG00000186297		"""GABA receptors"", ""Ligand-gated ion channels / GABA(A) receptors"""	4079	protein-coding gene	gene with protein product	"""GABA(A) receptor, alpha 5"""	137142				1321750	Standard	NM_000810		Approved		uc021sgi.1	P31644	OTTHUMG00000171824	ENST00000335625.5:c.42C>A	15.37:g.27114437C>A	ENSP00000335592:p.Asn14Lys		24665530	NM_001165037	A8K338|Q14DC2|Q53XL6|Q9NYT3|Q9NYT4|Q9NYT5	Missense_Mutation	SNP	ENST00000335625.5	37	CCDS45194.1	.	.	.	.	.	.	.	.	.	.	C	8.972	0.973168	0.18736	.	.	ENSG00000186297	ENST00000335625;ENST00000355395;ENST00000557484;ENST00000400081;ENST00000554038;ENST00000554596;ENST00000555060;ENST00000554599	T;T;T;T;T;T	0.80033	-0.47;-0.47;-0.47;-1.06;-1.01;-1.33	5.82	4.91	0.64330	.	0.693252	0.14819	N	0.296562	T	0.63082	0.2481	N	0.08118	0	0.26025	N	0.981811	B	0.02656	0.0	B	0.01281	0.0	T	0.52026	-0.8630	10	0.29301	T	0.29	.	10.6825	0.45823	0.0:0.9129:0.0:0.0871	.	14	P31644	GBRA5_HUMAN	K	14	ENSP00000335592:N14K;ENSP00000347557:N14K;ENSP00000382953:N14K;ENSP00000451527:N14K;ENSP00000450806:N14K;ENSP00000450717:N14K	ENSP00000335592:N14K	N	+	3	2	GABRA5	24665530	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	1.364000	0.34171	1.461000	0.47929	0.655000	0.94253	AAC		0.383	GABRA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415234.1		
UNC13C	440279	broad.mit.edu	37	15	54307993	54307993	+	Missense_Mutation	SNP	C	C	G			TCGA-AA-3679-01A-02W-0900-09	TCGA-AA-3679-10A-01W-0900-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3679-01A-02W-0900-09	TCGA-AA-3679-10A-01W-0900-09	g.chr15:54307993C>G	ENST00000260323.11	+	1	2893	c.2893C>G	c.(2893-2895)Cca>Gca	p.P965A	UNC13C_ENST00000545554.1_Missense_Mutation_p.P965A|UNC13C_ENST00000537900.1_Missense_Mutation_p.P965A	NM_001080534.1	NP_001074003.1	Q8NB66	UN13C_HUMAN	unc-13 homolog C (C. elegans)	965					exocytosis (GO:0006887)|intracellular signal transduction (GO:0035556)|synaptic transmission (GO:0007268)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|plasma membrane (GO:0005886)|presynaptic active zone (GO:0048786)	diacylglycerol binding (GO:0019992)|metal ion binding (GO:0046872)	p.P965A(2)		breast(3)|endometrium(5)|kidney(5)|large_intestine(20)|lung(70)|ovary(6)|pancreas(2)|prostate(2)|upper_aerodigestive_tract(4)|urinary_tract(4)	121				GBM - Glioblastoma multiforme(80;0.0789)|all cancers(107;0.124)		GATCACAAAGCCAAAGAGAAT	0.408																																					p.P965A												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.C2893G	15						.						64.0	61.0	62.0					15																	54307993		1853	4093	5946	52095285	SO:0001583	missense	440279	exon1			AK091491	CCDS45264.1	15q21.3	2012-10-02			ENSG00000137766	ENSG00000137766			23149	protein-coding gene	gene with protein product		614568					Standard	NM_001080534		Approved	Munc13-3, DKFZp547H074	uc021smr.1	Q8NB66	OTTHUMG00000172542	ENST00000260323.11:c.2893C>G	15.37:g.54307993C>G	ENSP00000260323:p.Pro965Ala		52095285	NM_001080534	Q0P613|Q8ND48|Q96NP3	Missense_Mutation	SNP	ENST00000260323.11	37	CCDS45264.1	.	.	.	.	.	.	.	.	.	.	C	11.71	1.720730	0.30503	.	.	ENSG00000137766	ENST00000260323;ENST00000545554;ENST00000537900	T;T;T	0.78364	-1.16;-1.17;-1.16	5.58	4.61	0.57282	.	.	.	.	.	T	0.59662	0.2210	N	0.19112	0.55	0.31041	N	0.716344	B	0.34015	0.435	B	0.27887	0.084	T	0.57300	-0.7835	9	0.15499	T	0.54	.	11.4869	0.50358	0.3202:0.6798:0.0:0.0	.	965	Q8NB66	UN13C_HUMAN	A	965	ENSP00000260323:P965A;ENSP00000438156:P965A;ENSP00000442569:P965A	ENSP00000260323:P965A	P	+	1	0	UNC13C	52095285	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.375000	0.73137	2.635000	0.89317	0.650000	0.86243	CCA		0.408	UNC13C-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000419028.3	NM_173166	
ANKDD1A	348094	broad.mit.edu	37	15	65226390	65226390	+	Missense_Mutation	SNP	C	C	T	rs537030205	byFrequency	TCGA-AA-3679-01A-02W-0900-09	TCGA-AA-3679-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AA-3679-01A-02W-0900-09	TCGA-AA-3679-10A-01W-0900-09	g.chr15:65226390C>T	ENST00000380230.3	+	9	852	c.823C>T	c.(823-825)Cgg>Tgg	p.R275W	ANKDD1A_ENST00000395720.1_Missense_Mutation_p.R275W|ANKDD1A_ENST00000395723.1_Missense_Mutation_p.R184W|ANKDD1A_ENST00000357698.3_Missense_Mutation_p.R275W	NM_182703.3	NP_874362.3	Q495B1	AKD1A_HUMAN	ankyrin repeat and death domain containing 1A	275					signal transduction (GO:0007165)			p.R275W(1)		NS(1)|endometrium(1)|large_intestine(10)|liver(2)|lung(4)|ovary(1)|prostate(2)	21						GGATGTGTCTCGGGTCCTCAT	0.532													C|||	2	0.000399361	0.0	0.0	5008	,	,		16509	0.002		0.0	False		,,,				2504	0.0				p.R275W												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C823T	15						.						129.0	109.0	115.0					15																	65226390		2202	4299	6501	63013443	SO:0001583	missense	348094	exon9				CCDS10197.2	15q22.31	2013-01-10	2006-02-16		ENSG00000166839	ENSG00000166839		"""Ankyrin repeat domain containing"""	28002	protein-coding gene	gene with protein product						12477932	Standard	NM_182703		Approved	FLJ25870	uc002aoa.3	Q495B1	OTTHUMG00000133051	ENST00000380230.3:c.823C>T	15.37:g.65226390C>T	ENSP00000369579:p.Arg275Trp		63013443	NM_182703	Q495B2|Q495B3|Q8N7A0|Q8NBS5	Missense_Mutation	SNP	ENST00000380230.3	37	CCDS10197.2	.	.	.	.	.	.	.	.	.	.	C	2.493	-0.316992	0.05386	.	.	ENSG00000166839	ENST00000380230;ENST00000357698;ENST00000395720;ENST00000395723	T;T;T;T	0.67698	-0.28;-0.27;-0.28;-0.27	3.71	1.71	0.24356	Ankyrin repeat-containing domain (3);	0.202477	0.28964	N	0.013566	T	0.67239	0.2872	M	0.91663	3.23	0.09310	N	1	B	0.24186	0.099	B	0.19946	0.027	T	0.64571	-0.6376	10	0.87932	D	0	-7.6164	4.604	0.12368	0.4208:0.4676:0.0:0.1116	.	275	Q495B1	AKD1A_HUMAN	W	275;275;275;184	ENSP00000369579:R275W;ENSP00000350329:R275W;ENSP00000379070:R275W;ENSP00000379073:R184W	ENSP00000350329:R275W	R	+	1	2	ANKDD1A	63013443	0.930000	0.31532	0.011000	0.14972	0.045000	0.14185	0.033000	0.13754	0.315000	0.23110	-0.216000	0.12614	CGG		0.532	ANKDD1A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256705.2	NM_182703	
STX4	6810	broad.mit.edu	37	16	31050969	31050969	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3679-01A-02W-0900-09	TCGA-AA-3679-10A-01W-0900-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3679-01A-02W-0900-09	TCGA-AA-3679-10A-01W-0900-09	g.chr16:31050969G>T	ENST00000313843.3	+	9	1125	c.810G>T	c.(808-810)agG>agT	p.R270S	STX4_ENST00000493902.1_3'UTR|STX4_ENST00000394998.1_Missense_Mutation_p.R268S	NM_004604.3	NP_004595.2	Q12846	STX4_HUMAN	syntaxin 4	270	Interaction with CENPF. {ECO:0000250}.				blood coagulation (GO:0007596)|intracellular protein transport (GO:0006886)|membrane organization (GO:0061024)|neurotransmitter transport (GO:0006836)|platelet activation (GO:0030168)|post-Golgi vesicle-mediated transport (GO:0006892)|SNARE complex assembly (GO:0035493)	basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lateral loop (GO:0043219)|membrane (GO:0016020)|myelin sheath adaxonal region (GO:0035749)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|SNARE complex (GO:0031201)|specific granule (GO:0042581)|trans-Golgi network (GO:0005802)|vacuole (GO:0005773)		p.R270S(1)		NS(2)|breast(1)|large_intestine(3)|lung(3)	9						AGAAGGCGAGGAAGGTGAGCC	0.587																																					p.R270S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G810T	16						.						160.0	134.0	143.0					16																	31050969		2197	4300	6497	30958470	SO:0001583	missense	6810	exon9			AF026007	CCDS10700.1, CCDS61916.1	16p11.2	2008-02-05	2006-04-25	2006-04-25	ENSG00000103496	ENSG00000103496			11439	protein-coding gene	gene with protein product		186591	"""syntaxin 4A (placental)"""	STX4A		8206394, 16339081	Standard	NM_001272095		Approved	p35-2	uc002eak.4	Q12846	OTTHUMG00000132404	ENST00000313843.3:c.810G>T	16.37:g.31050969G>T	ENSP00000317714:p.Arg270Ser		30958470	NM_004604	A8MXY0|Q15525|Q6FHE8	Missense_Mutation	SNP	ENST00000313843.3	37	CCDS10700.1	.	.	.	.	.	.	.	.	.	.	G	23.4	4.408124	0.83340	.	.	ENSG00000103496	ENST00000394998;ENST00000313843	T;T	0.54675	0.56;0.73	6.08	1.9	0.25705	.	0.051425	0.85682	D	0.000000	T	0.63803	0.2542	M	0.82517	2.595	0.36918	D	0.891221	D;D	0.69078	0.997;0.986	P;P	0.57911	0.829;0.646	T	0.67643	-0.5618	10	0.87932	D	0	-9.4065	5.3136	0.15843	0.2816:0.2529:0.4656:0.0	.	270;268	Q12846;A8MXY0	STX4_HUMAN;.	S	268;270	ENSP00000378447:R268S;ENSP00000317714:R270S	ENSP00000317714:R270S	R	+	3	2	STX4	30958470	0.999000	0.42202	0.996000	0.52242	0.992000	0.81027	0.531000	0.23052	0.449000	0.26747	0.655000	0.94253	AGG		0.587	STX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255538.3	NM_004604	
CDH11	1009	broad.mit.edu	37	16	65005485	65005485	+	Missense_Mutation	SNP	G	G	C			TCGA-AA-3679-01A-02W-0900-09	TCGA-AA-3679-10A-01W-0900-09	G	G	G	C	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AA-3679-01A-02W-0900-09	TCGA-AA-3679-10A-01W-0900-09	g.chr16:65005485G>C	ENST00000268603.4	-	11	2254	c.1639C>G	c.(1639-1641)Cga>Gga	p.R547G	CDH11_ENST00000566827.1_Missense_Mutation_p.R421G|CDH11_ENST00000394156.3_Missense_Mutation_p.R547G	NM_001797.2	NP_001788.2	P55287	CAD11_HUMAN	cadherin 11, type 2, OB-cadherin (osteoblast)	547	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				adherens junction organization (GO:0034332)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|corticospinal tract morphogenesis (GO:0021957)|homophilic cell adhesion (GO:0007156)|ossification (GO:0001503)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.R547G(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(5)|kidney(5)|large_intestine(19)|lung(40)|ovary(3)|prostate(3)|skin(2)|urinary_tract(2)	88		Ovarian(137;0.0973)		OV - Ovarian serous cystadenocarcinoma(108;0.205)		TACAAACCTCGGTTGTCTCTG	0.398			T	USP6	aneurysmal bone cysts					TSP Lung(24;0.17)																											p.R547G			Dom	yes		16	16q22.1	1009	"""cadherin 11, type 2, OB-cadherin (osteoblast)"""		M	.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1639G	16						.						121.0	112.0	115.0					16																	65005485		2203	4300	6503	63562986	SO:0001583	missense	1009	exon11			D21255	CCDS10803.1	16q21	2010-01-26			ENSG00000140937	ENSG00000140937		"""Cadherins / Major cadherins"""	1750	protein-coding gene	gene with protein product	"""OB-Cadherin"""	600023				9615235	Standard	NM_001797		Approved	OB, CAD11	uc002eoi.3	P55287	OTTHUMG00000137494	ENST00000268603.4:c.1639C>G	16.37:g.65005485G>C	ENSP00000268603:p.Arg547Gly		63562986	NM_001797	A8K5D6|A8MZC8|B7WP28|Q15065|Q15066|Q9UQ93|Q9UQ94	Missense_Mutation	SNP	ENST00000268603.4	37	CCDS10803.1	.	.	.	.	.	.	.	.	.	.	G	13.81	2.349444	0.41599	.	.	ENSG00000140937	ENST00000268603;ENST00000394156;ENST00000538390	T;T	0.56444	0.46;0.46	5.88	3.59	0.41128	Cadherin (3);Cadherin-like (1);	0.000000	0.85682	D	0.000000	T	0.47451	0.1446	N	0.16233	0.39	0.51767	D	0.999936	D;B	0.57257	0.979;0.001	P;B	0.53861	0.736;0.003	T	0.41034	-0.9531	10	0.42905	T	0.14	.	12.3625	0.55211	0.0:0.0:0.4345:0.5655	.	547;547	P55287-2;P55287	.;CAD11_HUMAN	G	547;547;530	ENSP00000268603:R547G;ENSP00000377711:R547G	ENSP00000268603:R547G	R	-	1	2	CDH11	63562986	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	0.609000	0.24238	0.466000	0.27193	-0.262000	0.10625	CGA		0.398	CDH11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268755.1	NM_033664	
CHST4	10164	broad.mit.edu	37	16	71571584	71571584	+	Missense_Mutation	SNP	G	G	A	rs201260953		TCGA-AA-3679-01A-02W-0900-09	TCGA-AA-3679-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AA-3679-01A-02W-0900-09	TCGA-AA-3679-10A-01W-0900-09	g.chr16:71571584G>A	ENST00000338482.5	+	3	1347	c.1004G>A	c.(1003-1005)cGc>cAc	p.R335H	CHST4_ENST00000539698.3_Missense_Mutation_p.R335H|RP11-510M2.5_ENST00000568523.1_RNA|ZNF19_ENST00000568446.1_Intron|CHST4_ENST00000572450.1_Missense_Mutation_p.R335H			Q8NCG5	CHST4_HUMAN	carbohydrate (N-acetylglucosamine 6-O) sulfotransferase 4	335					carbohydrate metabolic process (GO:0005975)|cell adhesion (GO:0007155)|cell-cell signaling (GO:0007267)|cellular component movement (GO:0006928)|immune response (GO:0006955)|inflammatory response (GO:0006954)|leukocyte tethering or rolling (GO:0050901)|N-acetylglucosamine metabolic process (GO:0006044)|protein sulfation (GO:0006477)|sulfur compound metabolic process (GO:0006790)	integral component of membrane (GO:0016021)|intrinsic component of Golgi membrane (GO:0031228)|trans-Golgi network (GO:0005802)	N-acetylglucosamine 6-O-sulfotransferase activity (GO:0001517)|sulfotransferase activity (GO:0008146)	p.R335H(1)		cervix(1)|kidney(3)|large_intestine(9)|lung(6)|prostate(1)|upper_aerodigestive_tract(1)	21						CAGGCTTGGCGCTGGTCTTTG	0.537											OREG0023923	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.R335H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1004A	16						.						70.0	59.0	63.0					16																	71571584		2198	4300	6498	70129085	SO:0001583	missense	10164	exon2			AF131235	CCDS10902.1	16q22.2	2008-02-05			ENSG00000140835	ENSG00000140835		"""Sulfotransferases, membrane-bound"""	1972	protein-coding gene	gene with protein product						10330415	Standard	NM_001166395		Approved	HEC-GLCNAC-6-ST, LSST	uc002fao.3	Q8NCG5	OTTHUMG00000137592	ENST00000338482.5:c.1004G>A	16.37:g.71571584G>A	ENSP00000341206:p.Arg335His	1131	70129085	NM_001166395	Q8IV46|Q9Y5R3	Missense_Mutation	SNP	ENST00000338482.5	37	CCDS10902.1	.	.	.	.	.	.	.	.	.	.	G	34	5.324831	0.95708	.	.	ENSG00000140835	ENST00000338482;ENST00000539698	D;D	0.83673	-1.75;-1.75	6.17	6.17	0.99709	Sulfotransferase domain (1);	0.000000	0.85682	D	0.000000	D	0.93949	0.8063	H	0.94264	3.515	0.58432	D	0.999991	D	0.89917	1.0	D	0.97110	1.0	D	0.94716	0.7896	10	0.87932	D	0	-8.9676	18.3732	0.90420	0.0:0.0:1.0:0.0	.	335	Q8NCG5	CHST4_HUMAN	H	335	ENSP00000341206:R335H;ENSP00000441204:R335H	ENSP00000341206:R335H	R	+	2	0	CHST4	70129085	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	9.869000	0.99810	2.941000	0.99782	0.655000	0.94253	CGC		0.537	CHST4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268992.4	NM_005769	
JPH3	57338	broad.mit.edu	37	16	87678032	87678032	+	Missense_Mutation	SNP	C	C	T	rs569623845		TCGA-AA-3679-01A-02W-0900-09	TCGA-AA-3679-10A-01W-0900-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3679-01A-02W-0900-09	TCGA-AA-3679-10A-01W-0900-09	g.chr16:87678032C>T	ENST00000284262.2	+	2	793	c.551C>T	c.(550-552)gCg>gTg	p.A184V		NM_020655.2	NP_065706.2	Q8WXH2	JPH3_HUMAN	junctophilin 3	184					calcium ion transport into cytosol (GO:0060402)|exploration behavior (GO:0035640)|learning (GO:0007612)|locomotion (GO:0040011)|memory (GO:0007613)|neuromuscular process controlling balance (GO:0050885)|regulation of neuronal synaptic plasticity (GO:0048168)|regulation of ryanodine-sensitive calcium-release channel activity (GO:0060314)	integral component of membrane (GO:0016021)|junctional membrane complex (GO:0030314)|junctional sarcoplasmic reticulum membrane (GO:0014701)|plasma membrane (GO:0005886)	calcium-release channel activity (GO:0015278)	p.A184V(2)		breast(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(3)|lung(13)|ovary(1)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	30				BRCA - Breast invasive adenocarcinoma(80;0.0287)		GCCTCTCCGGCGGTGGCCGGC	0.697													C|||	1	0.000199681	0.0	0.0014	5008	,	,		14426	0.0		0.0	False		,,,				2504	0.0				p.A184V												.	.	2	Substitution - Missense(2)	large_intestine(1)|prostate(1)	c.C551T	16						.						33.0	38.0	36.0					16																	87678032		2190	4293	6483	86235533	SO:0001583	missense	57338	exon2			AB042636	CCDS10962.1	16q24.3	2008-02-05	2002-11-13		ENSG00000154118	ENSG00000154118			14203	protein-coding gene	gene with protein product		605268	"""trinucleotide repeat containing 22"""	TNRC22		10949023, 10891348	Standard	NM_020655		Approved	JP-3, CAGL237, HDL2, JP3	uc002fkd.4	Q8WXH2	OTTHUMG00000137656	ENST00000284262.2:c.551C>T	16.37:g.87678032C>T	ENSP00000284262:p.Ala184Val		86235533	NM_020655	D3DUN2|Q8N471|Q9HDC3|Q9HDC4	Missense_Mutation	SNP	ENST00000284262.2	37	CCDS10962.1	.	.	.	.	.	.	.	.	.	.	C	13.97	2.396065	0.42512	.	.	ENSG00000154118	ENST00000537256;ENST00000284262	T	0.46451	0.87	5.03	5.03	0.67393	.	0.337477	0.31123	N	0.008204	T	0.26955	0.0660	N	0.14661	0.345	0.47374	D	0.999407	B	0.21071	0.051	B	0.11329	0.006	T	0.08186	-1.0734	10	0.12766	T	0.61	.	17.3468	0.87311	0.0:1.0:0.0:0.0	.	184	Q8WXH2	JPH3_HUMAN	V	47;184	ENSP00000284262:A184V	ENSP00000284262:A184V	A	+	2	0	JPH3	86235533	1.000000	0.71417	0.118000	0.21660	0.561000	0.35649	4.474000	0.60203	2.334000	0.79466	0.462000	0.41574	GCG		0.697	JPH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269108.2		
KSR1	8844	broad.mit.edu	37	17	25910024	25910024	+	Silent	SNP	A	A	C			TCGA-AA-3679-01A-02W-0900-09	TCGA-AA-3679-10A-01W-0900-09	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3679-01A-02W-0900-09	TCGA-AA-3679-10A-01W-0900-09	g.chr17:25910024A>C	ENST00000319524.6	+	4	873	c.873A>C	c.(871-873)ccA>ccC	p.P291P	KSR1_ENST00000398988.3_Silent_p.P154P|KSR1_ENST00000509603.2_Silent_p.P291P|KSR1_ENST00000268763.6_Silent_p.P154P			Q8IVT5	KSR1_HUMAN	kinase suppressor of ras 1	291	Poly-Pro.				Ras protein signal transduction (GO:0007265)	endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)	p.P291P(2)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|large_intestine(5)|lung(12)|prostate(2)|urinary_tract(1)	28	Lung NSC(42;0.00836)		BRCA - Breast invasive adenocarcinoma(3;0.00122)	UCEC - Uterine corpus endometrioid carcinoma (53;0.168)		CGCCCCCCCCACCCAGCCGCA	0.672																																					p.P154P	Esophageal Squamous(88;1120 1336 6324 10502 16832)											.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.A462C	17						.																																			22934151	SO:0001819	synonymous_variant	8844	exon5			U43586	CCDS58532.1	17q11.2	2012-05-23	2005-12-14	2005-12-14	ENSG00000141068	ENSG00000141068			6465	protein-coding gene	gene with protein product		601132	"""kinase suppressor of ras"""	KSR		8521512	Standard	XM_006722151		Approved	RSU2	uc031qzj.1	Q8IVT5	OTTHUMG00000132051	ENST00000319524.6:c.873A>C	17.37:g.25910024A>C			22934151	NM_014238	F8WEA9|H7BYU0|Q13476	Silent	SNP	ENST00000319524.6	37		.	.	.	.	.	.	.	.	.	.	A	10.09	1.255340	0.22965	.	.	ENSG00000141068	ENST00000398988	.	.	.	5.7	-11.4	0.00090	.	.	.	.	.	T	0.30166	0.0756	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.39961	-0.9588	4	.	.	.	.	0.5552	0.00669	0.3762:0.2168:0.1667:0.2404	.	.	.	.	P	27	.	.	T	+	1	0	KSR1	22934151	0.000000	0.05858	0.369000	0.25952	0.902000	0.53008	-5.071000	0.00154	-1.997000	0.00969	-0.475000	0.04921	ACC		0.672	KSR1-202	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_014238	
GAS2L2	246176	broad.mit.edu	37	17	34074182	34074182	+	Missense_Mutation	SNP	C	C	T	rs201782410		TCGA-AA-3679-01A-02W-0900-09	TCGA-AA-3679-10A-01W-0900-09	C	C	T	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AA-3679-01A-02W-0900-09	TCGA-AA-3679-10A-01W-0900-09	g.chr17:34074182C>T	ENST00000254466.6	-	5	965	c.938G>A	c.(937-939)cGc>cAc	p.R313H	GAS2L2_ENST00000587565.1_Missense_Mutation_p.R297H	NM_139285.3	NP_644814.1	Q8NHY3	GA2L2_HUMAN	growth arrest-specific 2 like 2	313					cell cycle arrest (GO:0007050)|microtubule bundle formation (GO:0001578)|negative regulation of microtubule depolymerization (GO:0007026)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	actin filament binding (GO:0051015)|cytoskeletal adaptor activity (GO:0008093)|microtubule binding (GO:0008017)	p.R313H(1)		central_nervous_system(1)|endometrium(1)|large_intestine(7)|lung(14)|ovary(2)|pancreas(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	35		Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0182)		GCTCTGTGAGCGGCTGATGGT	0.622																																					p.R313H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G938A	17						.	C	HIS/ARG	3,4403	6.2+/-15.9	0,3,2200	108.0	116.0	113.0		938	5.1	1.0	17		113	9,8591	7.1+/-27.0	0,9,4291	yes	missense	GAS2L2	NM_139285.3	29	0,12,6491	TT,TC,CC		0.1047,0.0681,0.0923	probably-damaging	313/881	34074182	12,12994	2203	4300	6503	31098295	SO:0001583	missense	246176	exon5			AF508784	CCDS11298.1	17q21	2014-05-06			ENSG00000132139	ENSG00000270765			24846	protein-coding gene	gene with protein product		611398				12584248	Standard	NM_139285		Approved	GAR17	uc002hjv.2	Q8NHY3	OTTHUMG00000188386	ENST00000254466.6:c.938G>A	17.37:g.34074182C>T	ENSP00000254466:p.Arg313His		31098295	NM_139285	Q8NHY4	Missense_Mutation	SNP	ENST00000254466.6	37	CCDS11298.1	.	.	.	.	.	.	.	.	.	.	C	21.5	4.161573	0.78226	6.81E-4	0.001047	ENSG00000132139	ENST00000254466	T	0.21543	2.0	5.1	5.1	0.69264	.	0.074384	0.52532	D	0.000071	T	0.43919	0.1269	M	0.63843	1.955	0.45962	D	0.998789	D	0.89917	1.0	D	0.85130	0.997	T	0.19745	-1.0296	10	0.51188	T	0.08	-20.5619	15.3692	0.74548	0.0:1.0:0.0:0.0	.	313	Q8NHY3	GA2L2_HUMAN	H	313	ENSP00000254466:R313H	ENSP00000254466:R313H	R	-	2	0	GAS2L2	31098295	1.000000	0.71417	1.000000	0.80357	0.598000	0.36846	4.545000	0.60698	2.644000	0.89710	0.561000	0.74099	CGC		0.622	GAS2L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256497.1	NM_139285	
KRT38	8687	broad.mit.edu	37	17	39595461	39595461	+	Silent	SNP	G	G	A			TCGA-AA-3679-01A-02W-0900-09	TCGA-AA-3679-10A-01W-0900-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3679-01A-02W-0900-09	TCGA-AA-3679-10A-01W-0900-09	g.chr17:39595461G>A	ENST00000246646.3	-	3	725	c.726C>T	c.(724-726)caC>caT	p.H242H		NM_006771.3	NP_006762.3	O76015	KRT38_HUMAN	keratin 38	242	Coil 1B.|Rod.					extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)	structural molecule activity (GO:0005198)	p.H242H(1)		breast(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(11)|ovary(1)|pancreas(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	29		Breast(137;0.000496)				ACACCTGCTCGTGGTTGCTCT	0.667																																					p.H242H												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C726T	17						.						45.0	42.0	43.0					17																	39595461		2203	4300	6503	36848987	SO:0001819	synonymous_variant	8687	exon3			Y16794	CCDS11392.1	17q21.2	2013-06-20	2006-07-17	2006-07-17	ENSG00000171360	ENSG00000171360		"""-"", ""Intermediate filaments type I, keratins (acidic)"""	6456	protein-coding gene	gene with protein product		604542	"""keratin, hair, acidic, 8"""	KRTHA8		9756910, 16831889	Standard	NM_006771		Approved		uc002hwq.1	O76015	OTTHUMG00000133439	ENST00000246646.3:c.726C>T	17.37:g.39595461G>A			36848987	NM_006771	A2RRM5|Q6A164	Silent	SNP	ENST00000246646.3	37	CCDS11392.1																																																																																				0.667	KRT38-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257307.2	NM_006771	
TP53	7157	broad.mit.edu	37	17	7577539	7577539	+	Missense_Mutation	SNP	G	G	A	rs397516437|rs121912651		TCGA-AA-3679-01A-02W-0900-09	TCGA-AA-3679-10A-01W-0900-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3679-01A-02W-0900-09	TCGA-AA-3679-10A-01W-0900-09	g.chr17:7577539G>A	ENST00000269305.4	-	7	931	c.742C>T	c.(742-744)Cgg>Tgg	p.R248W	TP53_ENST00000420246.2_Missense_Mutation_p.R248W|TP53_ENST00000455263.2_Missense_Mutation_p.R248W|TP53_ENST00000574684.1_5'Flank|TP53_ENST00000413465.2_Missense_Mutation_p.R248W|TP53_ENST00000359597.4_Missense_Mutation_p.R248W|TP53_ENST00000445888.2_Missense_Mutation_p.R248W	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	248	Interaction with AXIN1. {ECO:0000250}.|Interaction with HIPK1. {ECO:0000250}.|Interacts with the 53BP2 SH3 domain.|Required for interaction with ZNF385A.		NR -> IP (in a sporadic cancer; somatic mutation).|NR -> KW (in sporadic cancers; somatic mutation).|R -> C (in a sporadic cancer; somatic mutation).|R -> G (in sporadic cancers; somatic mutation).|R -> L (in sporadic cancers; somatic mutation). {ECO:0000269|PubMed:1394225, ECO:0000269|PubMed:7682763}.|R -> P (in sporadic cancers; somatic mutation).|R -> Q (in LFS; germline mutation and in sporadic cancers; somatic mutation; dbSNP:rs11540652). {ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:2263646, ECO:0000269|PubMed:7682763, ECO:0000269|PubMed:7887414}.|R -> W (in LFS; germline mutation and in sporadic cancers; somatic mutation). {ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:1978757, ECO:0000269|PubMed:8829627}.		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.R248W(544)|p.R155W(28)|p.R248G(12)|p.0?(8)|p.?(5)|p.N247_R248delNR(2)|p.R248fs*16(2)|p.N247_R248>KW(2)|p.M246_P250delMNRRP(2)|p.R248fs*97(2)|p.R248R(2)|p.R248fs*>39(1)|p.R248_P250delRRP(1)|p.unknown(1)|p.N247_R249delNRR(1)|p.N247_P250delNRRP(1)|p.R248C(1)|p.G245fs*14(1)|p.N247_R248>IP(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	ATGGGCCTCCGGTTCATGCCG	0.577	R248W(786O_KIDNEY)|R248W(CAS1_CENTRAL_NERVOUS_SYSTEM)|R248W(COLO320_LARGE_INTESTINE)|R248W(COLO680N_OESOPHAGUS)|R248W(DB_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248W(GCT_SOFT_TISSUE)|R248W(HCC2157_BREAST)|R248W(JIMT1_BREAST)|R248W(KO52_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248W(LUDLU1_LUNG)|R248W(LXF289_LUNG)|R248W(MIAPACA2_PANCREAS)|R248W(RD_SOFT_TISSUE)|R248W(SW837_LARGE_INTESTINE)|R248W(VCAP_PROSTATE)	111	"""Mis, N, F"""		"""breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"""	"""breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"""		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											p.R248W	Pancreas(47;798 1329 9957 10801)	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"""L, E, M, O"""	TP53,haematopoietic_and_lymphoid_tissue,lymph_node,Substitution - Missense,+1 	.	617	Substitution - Missense(585)|Whole gene deletion(8)|Deletion - In frame(7)|Unknown(6)|Insertion - Frameshift(3)|Deletion - Frameshift(3)|Complex - compound substitution(3)|Substitution - coding silent(2)	large_intestine(156)|breast(72)|ovary(42)|endometrium(38)|oesophagus(38)|skin(37)|haematopoietic_and_lymphoid_tissue(37)|central_nervous_system(35)|stomach(27)|lung(26)|upper_aerodigestive_tract(25)|urinary_tract(19)|biliary_tract(17)|pancreas(12)|prostate(10)|soft_tissue(6)|bone(6)|thyroid(4)|liver(4)|penis(2)|peritoneum(1)|vulva(1)|kidney(1)|cervix(1)	c.C742T	17	GRCh37	CM010465|CM900211	TP53	M	rs121912651	.						151.0	112.0	125.0					17																	7577539		2203	4300	6503	7518264	SO:0001583	missense	7157	exon7	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"""Li-Fraumeni syndrome"""	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.742C>T	17.37:g.7577539G>A	ENSP00000269305:p.Arg248Trp		7518264	NM_001126114	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Missense_Mutation	SNP	ENST00000269305.4	37	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	G	18.84	3.710019	0.68730	.	.	ENSG00000141510	ENST00000413465;ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000545858;ENST00000509690;ENST00000514944	D;D;D;D;D;D;D;D	0.99869	-7.34;-7.34;-7.34;-7.34;-7.34;-7.34;-7.34;-7.34	4.62	2.56	0.30785	p53, DNA-binding domain (1);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1);	0.000000	0.85682	D	0.000000	D	0.99843	0.9928	M	0.92507	3.315	0.58432	A	0.999997	D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D	0.97110	1.0;1.0;1.0;1.0;1.0;1.0	D	0.97208	0.9869	9	0.87932	D	0	-9.5643	7.568	0.27890	0.0893:0.0:0.7471:0.1636	.	248;248;155;248;248;248	P04637-2;P04637-3;E9PFT5;P04637;Q1MSW8;E7EQX7	.;.;.;P53_HUMAN;.;.	W	248;248;248;248;248;248;237;155;116;155	ENSP00000410739:R248W;ENSP00000352610:R248W;ENSP00000269305:R248W;ENSP00000398846:R248W;ENSP00000391127:R248W;ENSP00000391478:R248W;ENSP00000425104:R116W;ENSP00000423862:R155W	ENSP00000269305:R248W	R	-	1	2	TP53	7518264	1.000000	0.71417	1.000000	0.80357	0.910000	0.53928	1.447000	0.35101	0.644000	0.30656	0.462000	0.41574	CGG		0.577	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546	
SPATA20	64847	broad.mit.edu	37	17	48626535	48626535	+	Missense_Mutation	SNP	A	A	T			TCGA-AA-3679-01A-02W-0900-09	TCGA-AA-3679-10A-01W-0900-09	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3679-01A-02W-0900-09	TCGA-AA-3679-10A-01W-0900-09	g.chr17:48626535A>T	ENST00000356488.4	+	5	683	c.600A>T	c.(598-600)agA>agT	p.R200S	SPATA20_ENST00000006658.6_Missense_Mutation_p.R216S|SPATA20_ENST00000511937.1_3'UTR|SPATA20_ENST00000393244.3_Missense_Mutation_p.R156S	NM_001258372.1	NP_001245301.1	Q8TB22	SPT20_HUMAN	spermatogenesis associated 20	200					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	extracellular region (GO:0005576)	catalytic activity (GO:0003824)	p.R216S(1)		endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(5)|lung(9)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	24	Breast(11;1.23e-18)		BRCA - Breast invasive adenocarcinoma(22;9.38e-09)			TGTTGCTGAGAATACGAGAAC	0.622																																					p.R216S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A648T	17						.						52.0	56.0	55.0					17																	48626535		2203	4300	6503	45981534	SO:0001583	missense	64847	exon6				CCDS11571.1, CCDS58563.1, CCDS58564.1	17q21.33	2011-03-17			ENSG00000006282	ENSG00000006282			26125	protein-coding gene	gene with protein product	"""hypothetical protein FLJ21347"""	613939				12477932	Standard	NM_022827		Approved	FLJ21347, SSP411, Tisp78	uc002ird.3	Q8TB22	OTTHUMG00000162162	ENST00000356488.4:c.600A>T	17.37:g.48626535A>T	ENSP00000348878:p.Arg200Ser		45981534	NM_022827	Q2TA99|Q2XUZ6|Q6P0P1|Q8WVW3|Q9H747	Missense_Mutation	SNP	ENST00000356488.4	37	CCDS58563.1	.	.	.	.	.	.	.	.	.	.	A	14.74	2.624165	0.46840	.	.	ENSG00000006282	ENST00000006658;ENST00000356488;ENST00000393244	T;T;T	0.40476	1.03;1.03;1.03	5.06	-4.66	0.03329	Thioredoxin-like fold (2);Domain of unknown function DUF255 (1);	0.000000	0.85682	D	0.000000	T	0.21631	0.0521	N	0.17723	0.515	0.38161	D	0.939033	B;B;B	0.25563	0.05;0.129;0.032	B;B;B	0.28385	0.089;0.039;0.023	T	0.13335	-1.0513	10	0.14252	T	0.57	-26.8512	12.0739	0.53632	0.1746:0.1894:0.636:0.0	.	226;200;216	B4DZC5;Q8TB22;Q8TB22-2	.;SPT20_HUMAN;.	S	216;200;156	ENSP00000006658:R216S;ENSP00000348878:R200S;ENSP00000376935:R156S	ENSP00000006658:R216S	R	+	3	2	SPATA20	45981534	0.005000	0.15991	0.972000	0.41901	0.874000	0.50279	-0.839000	0.04368	-0.533000	0.06323	0.459000	0.35465	AGA		0.622	SPATA20-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000367651.1	NM_022827	
TCEB3B	51224	broad.mit.edu	37	18	44560290	44560290	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3679-01A-02W-0900-09	TCGA-AA-3679-10A-01W-0900-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AA-3679-01A-02W-0900-09	TCGA-AA-3679-10A-01W-0900-09	g.chr18:44560290G>T	ENST00000332567.4	-	1	1698	c.1346C>A	c.(1345-1347)gCc>gAc	p.A449D	KATNAL2_ENST00000356157.7_Intron|KATNAL2_ENST00000592005.1_Intron|KATNAL2_ENST00000245121.5_Intron	NM_016427.2	NP_057511.2	Q8IYF1	ELOA2_HUMAN	transcription elongation factor B polypeptide 3B (elongin A2)	449					regulation of DNA-templated transcription, elongation (GO:0032784)|transcription from RNA polymerase II promoter (GO:0006366)	integral component of membrane (GO:0016021)|nucleus (GO:0005634)	DNA binding (GO:0003677)	p.A449D(1)		breast(1)|cervix(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(15)|lung(24)|ovary(2)|pancreas(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	58						TTTCGGCCCGGCGGAATCAGC	0.602																																					p.A449D												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1346A	18						.						44.0	52.0	49.0					18																	44560290		2203	4297	6500	42814288	SO:0001583	missense	51224	exon1			BC036022	CCDS11932.1	18q21.1	2009-08-04			ENSG00000206181	ENSG00000206181			30771	protein-coding gene	gene with protein product	"""transcription elongation factor (SIII) elongin A2"", ""elongin A2"""	609522				7660129, 8244996	Standard	NM_016427		Approved	HsT832, TCEB3L	uc002lcr.1	Q8IYF1	OTTHUMG00000132649	ENST00000332567.4:c.1346C>A	18.37:g.44560290G>T	ENSP00000331302:p.Ala449Asp		42814288	NM_016427	Q9P2V9	Missense_Mutation	SNP	ENST00000332567.4	37	CCDS11932.1	.	.	.	.	.	.	.	.	.	.	G	10.36	1.329159	0.24167	.	.	ENSG00000206181	ENST00000332567	T	0.08720	3.06	1.75	0.857	0.19025	.	0.649384	0.13313	N	0.397354	T	0.06005	0.0156	L	0.38175	1.15	0.09310	N	1	P	0.37914	0.611	B	0.35114	0.196	T	0.31971	-0.9924	10	0.54805	T	0.06	-1.0955	3.9724	0.09458	0.2229:0.0:0.7771:0.0	.	449	Q8IYF1	ELOA2_HUMAN	D	449	ENSP00000331302:A449D	ENSP00000331302:A449D	A	-	2	0	TCEB3B	42814288	0.012000	0.17670	0.000000	0.03702	0.001000	0.01503	2.721000	0.47260	0.319000	0.23209	0.514000	0.50259	GCC		0.602	TCEB3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255900.1	NM_016427	
SUGP2	10147	broad.mit.edu	37	19	19130027	19130027	+	Nonsense_Mutation	SNP	G	G	A			TCGA-AA-3679-01A-02W-0900-09	TCGA-AA-3679-10A-01W-0900-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3679-01A-02W-0900-09	TCGA-AA-3679-10A-01W-0900-09	g.chr19:19130027G>A	ENST00000601879.1	-	4	2038	c.1741C>T	c.(1741-1743)Cga>Tga	p.R581*	SUGP2_ENST00000456085.2_Nonsense_Mutation_p.R350*|SUGP2_ENST00000600377.1_Nonsense_Mutation_p.R595*|SUGP2_ENST00000337018.6_Nonsense_Mutation_p.R581*|SUGP2_ENST00000452918.2_Nonsense_Mutation_p.R581*			Q8IX01	SUGP2_HUMAN	SURP and G patch domain containing 2	581					mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)	p.R581*(1)		NS(1)|breast(1)|endometrium(8)|kidney(1)|large_intestine(9)|lung(13)|ovary(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	43						TGATCTGCTCGCTGGGGGACA	0.527																																					p.R581X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.C1741T	19						.						74.0	63.0	66.0					19																	19130027		2203	4300	6503	18991027	SO:0001587	stop_gained	10147	exon4			AB002363	CCDS12392.1	19p13	2013-01-28	2010-08-10	2010-08-10	ENSG00000064607	ENSG00000064607		"""G patch domain containing"""	18641	protein-coding gene	gene with protein product		607993	"""splicing factor, arginine/serine-rich 14"""	SFRS14		12594045	Standard	NM_014884		Approved	KIAA0365	uc002nkx.2	Q8IX01		ENST00000601879.1:c.1741C>T	19.37:g.19130027G>A	ENSP00000472286:p.Arg581*		18991027	NM_014884	C9JI71|O15071|O60369|Q5JPH7|Q8WUF7	Nonsense_Mutation	SNP	ENST00000601879.1	37	CCDS12392.1	.	.	.	.	.	.	.	.	.	.	G	41	8.936283	0.99008	.	.	ENSG00000064607	ENST00000337018;ENST00000330854;ENST00000452918;ENST00000456085	.	.	.	5.59	5.59	0.84812	.	0.242179	0.29459	N	0.012093	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-13.3224	16.3093	0.82863	0.0:0.0:1.0:0.0	.	.	.	.	X	581;581;581;350	.	ENSP00000332373:R581X	R	-	1	2	SUGP2	18991027	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	3.879000	0.56138	2.639000	0.89480	0.655000	0.94253	CGA		0.527	SUGP2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000464627.1	NM_001017392	
FBXO27	126433	broad.mit.edu	37	19	39517630	39517630	+	Silent	SNP	G	G	A			TCGA-AA-3679-01A-02W-0900-09	TCGA-AA-3679-10A-01W-0900-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3679-01A-02W-0900-09	TCGA-AA-3679-10A-01W-0900-09	g.chr19:39517630G>A	ENST00000292853.4	-	5	707	c.588C>T	c.(586-588)caC>caT	p.H196H	FBXO27_ENST00000509137.2_Silent_p.H196H|FBXO27_ENST00000600828.1_Silent_p.H195H	NM_178820.3	NP_849142.1	Q8NI29	FBX27_HUMAN	F-box protein 27	196	FBA. {ECO:0000255|PROSITE- ProRule:PRU00482}.					SCF ubiquitin ligase complex (GO:0019005)	glycoprotein binding (GO:0001948)	p.H196H(1)		cervix(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(5)|ovary(1)|urinary_tract(2)	17	all_cancers(60;3.79e-07)|all_lung(34;1.26e-07)|Lung NSC(34;1.46e-07)|all_epithelial(25;4.69e-07)|Ovarian(47;0.0454)		Lung(45;0.000419)|LUSC - Lung squamous cell carcinoma(53;0.000554)			AGCCGCTGTCGTGTCGGGCTC	0.567																																					p.H196H												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C588T	19						.						108.0	106.0	107.0					19																	39517630		2203	4300	6503	44209470	SO:0001819	synonymous_variant	126433	exon5			AF436061	CCDS12527.1	19q13.2	2008-02-05	2004-06-15			ENSG00000161243		"""F-boxes /  ""other"""""	18753	protein-coding gene	gene with protein product		609099	"""F-box only protein 27"""			126433	Standard	NM_178820		Approved	Fbg5, Fbx27	uc002okh.3	Q8NI29		ENST00000292853.4:c.588C>T	19.37:g.39517630G>A			44209470	NM_178820	Q96C87	Silent	SNP	ENST00000292853.4	37	CCDS12527.1																																																																																				0.567	FBXO27-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000463281.1		
CEACAM21	90273	broad.mit.edu	37	19	42083748	42083748	+	Silent	SNP	C	C	T	rs537389102		TCGA-AA-3679-01A-02W-0900-09	TCGA-AA-3679-10A-01W-0900-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3679-01A-02W-0900-09	TCGA-AA-3679-10A-01W-0900-09	g.chr19:42083748C>T	ENST00000401445.2	+	2	287	c.261C>T	c.(259-261)caC>caT	p.H87H	CEACAM21_ENST00000482870.2_3'UTR|CEACAM21_ENST00000407170.2_5'UTR|CEACAM21_ENST00000187608.9_Silent_p.H87H			Q3KPI0	CEA21_HUMAN	carcinoembryonic antigen-related cell adhesion molecule 21	87						integral component of membrane (GO:0016021)		p.H87H(2)		endometrium(2)|large_intestine(3)|lung(6)|ovary(1)|urinary_tract(1)	13						TAGACACTCACGTTAGGACTC	0.502													c|||	1	0.000199681	0.0	0.0	5008	,	,		21730	0.0		0.0	False		,,,				2504	0.001				p.H87H												.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.C261T	19						.						102.0	106.0	104.0					19																	42083748		2160	4284	6444	46775588	SO:0001819	synonymous_variant	90273	exon2			AK023602	CCDS46086.1, CCDS46087.1, CCDS74373.1	19q13.2	2013-01-29			ENSG00000007129	ENSG00000007129		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	28834	protein-coding gene	gene with protein product						12477932	Standard	XM_005278397		Approved	R29124_1, FLJ13540	uc002ore.4	Q3KPI0	OTTHUMG00000151062	ENST00000401445.2:c.261C>T	19.37:g.42083748C>T			46775588	NM_033543	B7WNQ6|O75296|Q6UY47|Q96ER7	De_novo_Start_OutOfFrame	SNP	ENST00000401445.2	37	CCDS46086.1																																																																																				0.502	CEACAM21-005	KNOWN	non_canonical_polymorphism|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000321140.1	NM_033543	
PSG4	5672	broad.mit.edu	37	19	43698619	43698619	+	Missense_Mutation	SNP	A	A	C			TCGA-AA-3679-01A-02W-0900-09	TCGA-AA-3679-10A-01W-0900-09	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3679-01A-02W-0900-09	TCGA-AA-3679-10A-01W-0900-09	g.chr19:43698619A>C	ENST00000405312.3	-	5	1353	c.1116T>G	c.(1114-1116)ttT>ttG	p.F372L	PSG4_ENST00000244295.9_Missense_Mutation_p.F279L|PSG4_ENST00000433626.2_Missense_Mutation_p.F279L	NM_002780.3	NP_002771.2	Q00888	PSG4_HUMAN	pregnancy specific beta-1-glycoprotein 4	372	Ig-like C2-type 3.				female pregnancy (GO:0007565)	extracellular vesicular exosome (GO:0070062)		p.F279L(1)|p.F372L(1)		central_nervous_system(1)|endometrium(2)|large_intestine(8)|lung(10)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)	24		Prostate(69;0.00682)				CTGATAGCTGAAACTTCCCAT	0.458																																					p.F372L												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.T1116G	19						.						194.0	198.0	197.0					19																	43698619		2202	4295	6497	48390459	SO:0001583	missense	5672	exon5				CCDS33039.1, CCDS46093.1, CCDS62695.1	19q13.2	2013-01-29			ENSG00000243137	ENSG00000243137		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	9521	protein-coding gene	gene with protein product	"""pregnancy-specific beta-1-glycoprotein 4"""	176393				2783133	Standard	NM_002780		Approved		uc002ovy.4	Q00888	OTTHUMG00000151544	ENST00000405312.3:c.1116T>G	19.37:g.43698619A>C	ENSP00000384770:p.Phe372Leu		48390459	NM_002780	E7EX79|Q13047|Q13048|Q15234|Q15240|Q9UQ76	Missense_Mutation	SNP	ENST00000405312.3	37	CCDS46093.1	.	.	.	.	.	.	.	.	.	.	a	1.782	-0.481768	0.04383	.	.	ENSG00000243137	ENST00000244295;ENST00000405312;ENST00000433626	T;T;T	0.11169	2.8;2.8;2.8	1.4	-1.69	0.08186	Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.10895	0.0266	N	0.25332	0.735	0.09310	N	1	B;B;D	0.55800	0.046;0.001;0.973	B;B;P	0.60012	0.214;0.015;0.867	T	0.22800	-1.0206	9	0.10111	T	0.7	.	4.1586	0.10273	0.5418:0.0:0.4582:0.0	.	279;279;372	E7EX79;Q00888-2;Q00888	.;.;PSG4_HUMAN	L	279;372;279	ENSP00000244295:F279L;ENSP00000384770:F372L;ENSP00000387864:F279L	ENSP00000244295:F279L	F	-	3	2	PSG4	48390459	0.001000	0.12720	0.001000	0.08648	0.001000	0.01503	0.359000	0.20233	-0.164000	0.10927	-0.490000	0.04691	TTT		0.458	PSG4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323073.1	NM_213633	
BAX	581	broad.mit.edu	37	19	49464114	49464114	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3679-01A-02W-0900-09	TCGA-AA-3679-10A-01W-0900-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AA-3679-01A-02W-0900-09	TCGA-AA-3679-10A-01W-0900-09	g.chr19:49464114G>T	ENST00000345358.7	+	5	469	c.417G>T	c.(415-417)tgG>tgT	p.W139C	BAX_ENST00000391871.3_3'UTR|BAX_ENST00000293288.8_Missense_Mutation_p.W139C|BAX_ENST00000539787.1_3'UTR|BAX_ENST00000354470.3_Missense_Mutation_p.W90C|BAX_ENST00000415969.2_Missense_Mutation_p.W139C	NM_138761.3|NM_138764.4	NP_620116.1|NP_620119.2	Q07812	BAX_HUMAN	BCL2-associated X protein	139					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|activation of cysteine-type endopeptidase activity involved in apoptotic process by cytochrome c (GO:0008635)|activation of cysteine-type endopeptidase activity involved in apoptotic signaling pathway (GO:0097296)|apoptotic mitochondrial changes (GO:0008637)|apoptotic process (GO:0006915)|apoptotic process involved in embryonic digit morphogenesis (GO:1902263)|apoptotic process involved in patterning of blood vessels (GO:1902262)|apoptotic signaling pathway (GO:0097190)|B cell apoptotic process (GO:0001783)|B cell homeostasis (GO:0001782)|B cell homeostatic proliferation (GO:0002358)|B cell negative selection (GO:0002352)|B cell receptor apoptotic signaling pathway (GO:1990117)|blood vessel remodeling (GO:0001974)|cellular response to organic substance (GO:0071310)|cellular response to UV (GO:0034644)|cerebral cortex development (GO:0021987)|development of secondary sexual characteristics (GO:0045136)|ectopic germ cell programmed cell death (GO:0035234)|endoplasmic reticulum calcium ion homeostasis (GO:0032469)|establishment or maintenance of transmembrane electrochemical gradient (GO:0010248)|extrinsic apoptotic signaling pathway (GO:0097191)|extrinsic apoptotic signaling pathway in absence of ligand (GO:0097192)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|fertilization (GO:0009566)|germ cell development (GO:0007281)|glycosphingolipid metabolic process (GO:0006687)|homeostasis of number of cells within a tissue (GO:0048873)|hypothalamus development (GO:0021854)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|kidney development (GO:0001822)|mitochondrial fragmentation involved in apoptotic process (GO:0043653)|mitochondrial fusion (GO:0008053)|mitochondrion morphogenesis (GO:0070584)|myeloid cell homeostasis (GO:0002262)|negative regulation of apoptotic signaling pathway (GO:2001234)|negative regulation of endoplasmic reticulum calcium ion concentration (GO:0032471)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of peptidyl-serine phosphorylation (GO:0033137)|negative regulation of protein binding (GO:0032091)|neuron apoptotic process (GO:0051402)|neuron migration (GO:0001764)|odontogenesis of dentin-containing tooth (GO:0042475)|ovarian follicle development (GO:0001541)|positive regulation of apoptotic DNA fragmentation (GO:1902512)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic process involved in mammary gland involution (GO:0060058)|positive regulation of B cell apoptotic process (GO:0002904)|positive regulation of developmental pigmentation (GO:0048087)|positive regulation of endoplasmic reticulum unfolded protein response (GO:1900103)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway (GO:1901030)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of release of sequestered calcium ion into cytosol (GO:0051281)|post-embryonic camera-type eye morphogenesis (GO:0048597)|protein homooligomerization (GO:0051260)|protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:0001844)|protein oligomerization (GO:0051259)|regulation of cell cycle (GO:0051726)|regulation of mammary gland epithelial cell proliferation (GO:0033599)|regulation of mitochondrial membrane permeability involved in programmed necrotic cell death (GO:1902445)|regulation of mitochondrial membrane potential (GO:0051881)|regulation of nitrogen utilization (GO:0006808)|regulation of protein heterodimerization activity (GO:0043497)|regulation of protein homodimerization activity (GO:0043496)|release of cytochrome c from mitochondria (GO:0001836)|release of matrix enzymes from mitochondria (GO:0032976)|response to axon injury (GO:0048678)|response to gamma radiation (GO:0010332)|response to salt stress (GO:0009651)|response to toxic substance (GO:0009636)|retina development in camera-type eye (GO:0060041)|retinal cell apoptotic process (GO:1990009)|retinal cell programmed cell death (GO:0046666)|Sertoli cell proliferation (GO:0060011)|spermatid differentiation (GO:0048515)|T cell homeostatic proliferation (GO:0001777)|thymocyte apoptotic process (GO:0070242)|transformed cell apoptotic process (GO:0006927)|vagina development (GO:0060068)|viral process (GO:0016032)	BAX complex (GO:0097144)|Bcl-2 family protein complex (GO:0097136)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrial outer membrane (GO:0005741)|mitochondrial permeability transition pore complex (GO:0005757)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|pore complex (GO:0046930)	BH3 domain binding (GO:0051434)|channel activity (GO:0015267)|identical protein binding (GO:0042802)|lipid binding (GO:0008289)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)	p.W139C(1)		central_nervous_system(1)|endometrium(2)|large_intestine(1)|lung(7)|skin(2)|urinary_tract(4)	17		all_epithelial(76;5.29e-07)|all_lung(116;1.7e-06)|Lung NSC(112;3.55e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		OV - Ovarian serous cystadenocarcinoma(262;0.000159)|all cancers(93;0.00047)|GBM - Glioblastoma multiforme(486;0.018)|Epithelial(262;0.0279)		TCATGGGCTGGACATTGGACT	0.627																																					p.W90C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G270T	19						.						109.0	93.0	99.0					19																	49464114		2203	4300	6503	54155926	SO:0001583	missense	581	exon4				CCDS12742.1, CCDS12743.1, CCDS12744.1, CCDS12745.1, CCDS12745.2	19q13.3-q13.4	2014-03-07			ENSG00000087088	ENSG00000087088			959	protein-coding gene	gene with protein product		600040				8358790	Standard	NM_138761		Approved	BCL2L4	uc002plf.1	Q07812	OTTHUMG00000160476	ENST00000345358.7:c.417G>T	19.37:g.49464114G>T	ENSP00000263262:p.Trp139Cys		54155926	NM_138763	A8K4W1|P55269|Q07814|Q07815|Q8WZ49|Q9NR76|Q9NYG7|Q9UCZ6|Q9UCZ7|Q9UQD6	Missense_Mutation	SNP	ENST00000345358.7	37	CCDS12742.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	12.24|12.24	1.877514|1.877514	0.33162|0.33162	.|.	.|.	ENSG00000087088|ENSG00000087088	ENST00000506183|ENST00000345358;ENST00000415969;ENST00000354470;ENST00000293288	.|T;T;T;T	.|0.32023	.|1.47;2.7;1.47;2.7	3.13|3.13	3.13|3.13	0.36017|0.36017	.|Apoptosis regulator, Bcl2-like (1);Apoptosis regulator, Bcl-2, BH (3);	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.49660|0.49660	0.1570|0.1570	M|M	0.73217|0.73217	2.22|2.22	0.80722|0.80722	D|D	1|1	.|D;D;D;D	.|0.89917	.|0.993;1.0;1.0;1.0	.|P;D;D;D	.|0.77557	.|0.8;0.98;0.929;0.99	T|T	0.49082|0.49082	-0.8976|-0.8976	5|10	.|0.48119	.|T	.|0.1	-6.8026|-6.8026	9.991|9.991	0.41872|0.41872	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|90;139;139;139	.|Q07812-4;Q07812;Q07812-8;Q07812-2	.|.;BAX_HUMAN;.;.	V|C	73|139;139;90;139	.|ENSP00000263262:W139C;ENSP00000389971:W139C;ENSP00000346461:W90C;ENSP00000293288:W139C	.|ENSP00000293288:W139C	G|W	+|+	2|3	0|0	BAX|BAX	54155926|54155926	1.000000|1.000000	0.71417|0.71417	0.998000|0.998000	0.56505|0.56505	0.201000|0.201000	0.24016|0.24016	6.536000|6.536000	0.73842|0.73842	2.030000|2.030000	0.59900|0.59900	0.563000|0.563000	0.77884|0.77884	GGA|TGG		0.627	BAX-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360767.1	NM_138763	
PPFIA3	8541	broad.mit.edu	37	19	49643053	49643053	+	Silent	SNP	G	G	A	rs376973066		TCGA-AA-3679-01A-02W-0900-09	TCGA-AA-3679-10A-01W-0900-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3679-01A-02W-0900-09	TCGA-AA-3679-10A-01W-0900-09	g.chr19:49643053G>A	ENST00000334186.4	+	17	2554	c.2205G>A	c.(2203-2205)gcG>gcA	p.A735A	PPFIA3_ENST00000602351.1_Silent_p.A735A	NM_003660.2	NP_003651.1	O75145	LIPA3_HUMAN	protein tyrosine phosphatase, receptor type, f polypeptide (PTPRF), interacting protein (liprin), alpha 3	735					cell-matrix adhesion (GO:0007160)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|presynaptic active zone (GO:0048786)		p.A735A(1)		NS(1)|breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(4)|liver(2)|lung(16)|pancreas(1)|prostate(1)|skin(4)|urinary_tract(1)	35		all_lung(116;3.16e-06)|Lung NSC(112;6.25e-06)|all_neural(266;0.0189)|Ovarian(192;0.0392)		all cancers(93;2.36e-05)|OV - Ovarian serous cystadenocarcinoma(262;0.000203)|GBM - Glioblastoma multiforme(486;0.00307)|Epithelial(262;0.00677)		CACTGCAGGCGGGGTCCCTGG	0.662													N|||	1	0.000199681	0.0008	0.0	5008	,	,		15431	0.0		0.0	False		,,,				2504	0.0				p.A735A												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G2205A	19						.			4,4402		0,4,2199	27.0	30.0	29.0		2205	-4.5	1.0	19		29	0,8598		0,0,4299	no	coding-synonymous	PPFIA3	NM_003660.2		0,4,6498	AA,AG,GG		0.0,0.0908,0.0308		735/1195	49643053	4,13000	2203	4299	6502	54334865	SO:0001819	synonymous_variant	8541	exon17			AF034800	CCDS12758.1	19q13.33	2013-09-23			ENSG00000177380	ENSG00000177380		"""Sterile alpha motif (SAM) domain containing"""	9247	protein-coding gene	gene with protein product	"""protein tyrosine phosphatase, receptor type, f polypeptide, alpha 3"", ""liprin-alpha 3"", ""liprin"""	603144				9624153, 9734811	Standard	NM_003660		Approved	KIAA0654, LPNA3, MGC126567, MGC126569	uc002pmr.3	O75145	OTTHUMG00000183213	ENST00000334186.4:c.2205G>A	19.37:g.49643053G>A			54334865	NM_003660	A8K142|Q3MJA0|Q9H8B5|Q9UEW4	Silent	SNP	ENST00000334186.4	37	CCDS12758.1																																																																																				0.662	PPFIA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465688.1	NM_003660	
EXOSC10	5394	broad.mit.edu	37	1	11142798	11142798	+	Silent	SNP	G	G	C			TCGA-AA-3679-01A-02W-0900-09	TCGA-AA-3679-10A-01W-0900-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3679-01A-02W-0900-09	TCGA-AA-3679-10A-01W-0900-09	g.chr1:11142798G>C	ENST00000376936.4	-	10	1276	c.1227C>G	c.(1225-1227)ctC>ctG	p.L409L	EXOSC10_ENST00000304457.7_Silent_p.L409L|EXOSC10_ENST00000544779.1_Silent_p.L409L|EXOSC10_ENST00000485606.1_5'Flank	NM_001001998.1	NP_001001998.1	Q01780	EXOSX_HUMAN	exosome component 10	409					CUT catabolic process (GO:0071034)|dosage compensation by inactivation of X chromosome (GO:0009048)|histone mRNA catabolic process (GO:0071044)|maturation of 5.8S rRNA (GO:0000460)|nuclear mRNA surveillance (GO:0071028)|nuclear polyadenylation-dependent rRNA catabolic process (GO:0071035)|nuclear retention of unspliced pre-mRNA at the site of transcription (GO:0071048)|nuclear-transcribed mRNA catabolic process (GO:0000956)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|RNA phosphodiester bond hydrolysis, exonucleolytic (GO:0090503)	cytoplasm (GO:0005737)|exosome (RNase complex) (GO:0000178)|membrane (GO:0016020)|nuclear exosome (RNase complex) (GO:0000176)|nucleolus (GO:0005730)|nucleus (GO:0005634)|transcriptionally active chromatin (GO:0035327)	3'-5' exonuclease activity (GO:0008408)|exoribonuclease activity (GO:0004532)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)	p.L409L(1)		central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(9)|prostate(1)|stomach(3)|upper_aerodigestive_tract(1)	27	Ovarian(185;0.249)	Lung NSC(185;1.74e-05)|all_lung(284;2.05e-05)|Renal(390;0.000147)|Colorectal(325;0.00205)|Breast(348;0.00262)|Hepatocellular(190;0.00913)|Ovarian(437;0.00965)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;4.18e-07)|COAD - Colon adenocarcinoma(227;8.33e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000315)|Kidney(185;0.000832)|KIRC - Kidney renal clear cell carcinoma(229;0.00269)|READ - Rectum adenocarcinoma(331;0.0526)|STAD - Stomach adenocarcinoma(313;0.202)		CGTTGCAGTAGAGTTTCAGGA	0.453																																					p.L409L	Colon(179;105 1987 14326 27364 29542)											.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1227G	1						.						208.0	185.0	193.0					1																	11142798		2203	4300	6503	11065385	SO:0001819	synonymous_variant	5394	exon10			BC073788	CCDS126.1, CCDS30584.1	1p36.22	2008-02-05	2004-06-16	2004-06-18	ENSG00000171824	ENSG00000171824			9138	protein-coding gene	gene with protein product	"""polymyositis/scleroderma autoantigen 2 (100kD)"""	605960	"""polymyositis/scleroderma autoantigen 2, 100kDa"""	PMSCL2		1383382, 1644924	Standard	NM_001001998		Approved	PM-Scl, PM/Scl-100, Rrp6p, RRP6, p2, p3, p4	uc001asa.3	Q01780	OTTHUMG00000002123	ENST00000376936.4:c.1227C>G	1.37:g.11142798G>C			11065385	NM_001001998	B1AKQ0|B1AKQ1|Q15158	Silent	SNP	ENST00000376936.4	37	CCDS30584.1																																																																																				0.453	EXOSC10-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000006078.1	NM_001001998	
EXOSC10	5394	broad.mit.edu	37	1	11147931	11147931	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3679-01A-02W-0900-09	TCGA-AA-3679-10A-01W-0900-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AA-3679-01A-02W-0900-09	TCGA-AA-3679-10A-01W-0900-09	g.chr1:11147931T>C	ENST00000376936.4	-	8	920	c.871A>G	c.(871-873)Ata>Gta	p.I291V	EXOSC10_ENST00000304457.7_Missense_Mutation_p.I291V|EXOSC10_ENST00000544779.1_Missense_Mutation_p.I291V	NM_001001998.1	NP_001001998.1	Q01780	EXOSX_HUMAN	exosome component 10	291					CUT catabolic process (GO:0071034)|dosage compensation by inactivation of X chromosome (GO:0009048)|histone mRNA catabolic process (GO:0071044)|maturation of 5.8S rRNA (GO:0000460)|nuclear mRNA surveillance (GO:0071028)|nuclear polyadenylation-dependent rRNA catabolic process (GO:0071035)|nuclear retention of unspliced pre-mRNA at the site of transcription (GO:0071048)|nuclear-transcribed mRNA catabolic process (GO:0000956)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|RNA phosphodiester bond hydrolysis, exonucleolytic (GO:0090503)	cytoplasm (GO:0005737)|exosome (RNase complex) (GO:0000178)|membrane (GO:0016020)|nuclear exosome (RNase complex) (GO:0000176)|nucleolus (GO:0005730)|nucleus (GO:0005634)|transcriptionally active chromatin (GO:0035327)	3'-5' exonuclease activity (GO:0008408)|exoribonuclease activity (GO:0004532)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)	p.I291V(1)		central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(9)|prostate(1)|stomach(3)|upper_aerodigestive_tract(1)	27	Ovarian(185;0.249)	Lung NSC(185;1.74e-05)|all_lung(284;2.05e-05)|Renal(390;0.000147)|Colorectal(325;0.00205)|Breast(348;0.00262)|Hepatocellular(190;0.00913)|Ovarian(437;0.00965)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;4.18e-07)|COAD - Colon adenocarcinoma(227;8.33e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000315)|Kidney(185;0.000832)|KIRC - Kidney renal clear cell carcinoma(229;0.00269)|READ - Rectum adenocarcinoma(331;0.0526)|STAD - Stomach adenocarcinoma(313;0.202)		AGGGAGGATATGAAATGGCAT	0.393																																					p.I291V	Colon(179;105 1987 14326 27364 29542)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A871G	1						.						106.0	103.0	104.0					1																	11147931		2203	4300	6503	11070518	SO:0001583	missense	5394	exon8			BC073788	CCDS126.1, CCDS30584.1	1p36.22	2008-02-05	2004-06-16	2004-06-18	ENSG00000171824	ENSG00000171824			9138	protein-coding gene	gene with protein product	"""polymyositis/scleroderma autoantigen 2 (100kD)"""	605960	"""polymyositis/scleroderma autoantigen 2, 100kDa"""	PMSCL2		1383382, 1644924	Standard	NM_001001998		Approved	PM-Scl, PM/Scl-100, Rrp6p, RRP6, p2, p3, p4	uc001asa.3	Q01780	OTTHUMG00000002123	ENST00000376936.4:c.871A>G	1.37:g.11147931T>C	ENSP00000366135:p.Ile291Val		11070518	NM_001001998	B1AKQ0|B1AKQ1|Q15158	Missense_Mutation	SNP	ENST00000376936.4	37	CCDS30584.1	.	.	.	.	.	.	.	.	.	.	T	0.008	-1.869477	0.00547	.	.	ENSG00000171824	ENST00000376936;ENST00000304457;ENST00000544779	T;T;T	0.60797	0.16;0.16;0.16	6.17	0.766	0.18476	-5&apos (2);Ribonuclease H-like (1); exonuclease (2);3&apos (2);	0.425883	0.28151	N	0.016416	T	0.28366	0.0701	N	0.05467	-0.045	0.25020	N	0.991341	B;B	0.06786	0.001;0.001	B;B	0.18561	0.013;0.022	T	0.28776	-1.0033	10	0.02654	T	1	-12.7379	9.3973	0.38410	0.0:0.4479:0.0:0.5521	.	291;291	Q01780-2;Q01780	.;EXOSX_HUMAN	V	291	ENSP00000366135:I291V;ENSP00000307307:I291V;ENSP00000439473:I291V	ENSP00000307307:I291V	I	-	1	0	EXOSC10	11070518	0.013000	0.17824	0.031000	0.17742	0.202000	0.24057	0.115000	0.15540	0.084000	0.17077	-0.899000	0.02877	ATA		0.393	EXOSC10-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000006078.1	NM_001001998	
RHBG	57127	broad.mit.edu	37	1	156348108	156348108	+	Silent	SNP	G	G	T	rs371780489	byFrequency	TCGA-AA-3679-01A-02W-0900-09	TCGA-AA-3679-10A-01W-0900-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3679-01A-02W-0900-09	TCGA-AA-3679-10A-01W-0900-09	g.chr1:156348108G>T	ENST00000368249.1	+	4	629	c.591G>T	c.(589-591)tcG>tcT	p.S197S	RHBG_ENST00000537040.1_Intron|RHBG_ENST00000400992.2_Silent_p.S165S|RHBG_ENST00000368246.2_Silent_p.S197S|RHBG_ENST00000255013.3_Silent_p.S128S|RHBG_ENST00000451864.2_Silent_p.S165S	NM_001256396.1|NM_020407.4	NP_001243325.1|NP_065140.3	Q9H310	RHBG_HUMAN	Rh family, B glycoprotein (gene/pseudogene)	197					ammonium transmembrane transport (GO:0072488)|ammonium transport (GO:0015696)|transepithelial ammonium transport (GO:0070634)|transmembrane transport (GO:0055085)	anchored component of plasma membrane (GO:0046658)|basolateral plasma membrane (GO:0016323)|cytoplasmic vesicle (GO:0031410)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|spectrin-associated cytoskeleton (GO:0014731)	ammonium transmembrane transporter activity (GO:0008519)|ankyrin binding (GO:0030506)	p.S197S(1)		endometrium(1)|kidney(1)|large_intestine(4)|lung(9)|ovary(3)|skin(2)|stomach(1)|urinary_tract(1)	22	Hepatocellular(266;0.158)					TCGTCCTTTCGCGGGTTCTGT	0.627																																					p.S197S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G591T	1						.						102.0	109.0	107.0					1																	156348108		2060	4225	6285	154614732	SO:0001819	synonymous_variant	57127	exon4			AF193807		1q22	2013-05-22	2009-01-22		ENSG00000132677	ENSG00000132677		"""Solute carriers"""	14572	protein-coding gene	gene with protein product		607079	"""Rhesus blood group, B glycoprotein"""			10852913	Standard	NM_020407		Approved	SLC42A2	uc010pho.3	Q9H310	OTTHUMG00000024057	ENST00000368249.1:c.591G>T	1.37:g.156348108G>T			154614732	NM_020407	A8K475|Q5SZW4|Q5SZW6|Q5SZW7|Q6P193|Q6YJI2|Q6YJI3	Silent	SNP	ENST00000368249.1	37																																																																																					0.627	RHBG-001	NOVEL	basic	protein_coding	protein_coding	OTTHUMT00000060589.2	NM_001256395	
PYHIN1	149628	broad.mit.edu	37	1	158912078	158912078	+	Silent	SNP	G	G	A			TCGA-AA-3679-01A-02W-0900-09	TCGA-AA-3679-10A-01W-0900-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3679-01A-02W-0900-09	TCGA-AA-3679-10A-01W-0900-09	g.chr1:158912078G>A	ENST00000368140.1	+	5	1136	c.891G>A	c.(889-891)acG>acA	p.T297T	PYHIN1_ENST00000392252.3_Silent_p.T288T|PYHIN1_ENST00000368138.3_Silent_p.T288T|PYHIN1_ENST00000485134.1_3'UTR|PYHIN1_ENST00000392254.2_Silent_p.T297T	NM_152501.4|NM_198928.4|NM_198929.4	NP_689714.2|NP_945146.1|NP_945147.1	Q6K0P9	IFIX_HUMAN	pyrin and HIN domain family, member 1	297	HIN-200. {ECO:0000255|PROSITE- ProRule:PRU00106}.				cell cycle (GO:0007049)	nucleus (GO:0005634)		p.T297T(1)		breast(2)|endometrium(3)|large_intestine(10)|lung(32)|ovary(3)|pancreas(1)|prostate(2)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	60	all_hematologic(112;0.0378)					CTGACCAAACGTTTGAGGTTC	0.338																																					p.T288T												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G864A	1						.						49.0	51.0	50.0					1																	158912078		2203	4300	6503	157178702	SO:0001819	synonymous_variant	149628	exon5			AY185344	CCDS1178.1, CCDS1179.1, CCDS30907.1, CCDS30908.1	1q23.1	2008-02-05			ENSG00000163564	ENSG00000163564			28894	protein-coding gene	gene with protein product		612677				15122330	Standard	NM_152501		Approved	IFIX, MGC23885	uc001ftb.3	Q6K0P9	OTTHUMG00000037109	ENST00000368140.1:c.891G>A	1.37:g.158912078G>A			157178702	NM_198930	Q5T3W6|Q6K0P6|Q6K0P7|Q6K0P8|Q8WW65	Silent	SNP	ENST00000368140.1	37	CCDS1178.1																																																																																				0.338	PYHIN1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000090110.1	NM_152501	
MAST2	23139	broad.mit.edu	37	1	46497150	46497150	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3679-01A-02W-0900-09	TCGA-AA-3679-10A-01W-0900-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3679-01A-02W-0900-09	TCGA-AA-3679-10A-01W-0900-09	g.chr1:46497150G>A	ENST00000361297.2	+	24	3363	c.3080G>A	c.(3079-3081)cGc>cAc	p.R1027H	MAST2_ENST00000372009.2_Missense_Mutation_p.R957H	NM_015112.2	NP_055927.2			microtubule associated serine/threonine kinase 2									p.R1027H(1)		breast(1)|lung(3)|ovary(5)|stomach(2)	11	Acute lymphoblastic leukemia(166;0.155)|Lung SC(450;0.184)					CGTAGGGCCCGCCACCGGCTG	0.627																																					p.R1027H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G3080A	1						.						31.0	36.0	34.0					1																	46497150		2031	4188	6219	46269737	SO:0001583	missense	23139	exon24			AB047005	CCDS41326.1	1p34.1	2008-02-05			ENSG00000086015	ENSG00000086015			19035	protein-coding gene	gene with protein product		612257					Standard	NM_015112		Approved	MAST205, KIAA0807	uc001cov.3	Q6P0Q8	OTTHUMG00000008007	ENST00000361297.2:c.3080G>A	1.37:g.46497150G>A	ENSP00000354671:p.Arg1027His		46269737	NM_015112		Missense_Mutation	SNP	ENST00000361297.2	37	CCDS41326.1	.	.	.	.	.	.	.	.	.	.	G	32	5.179688	0.94846	.	.	ENSG00000086015	ENST00000361297;ENST00000372009	T;T	0.66815	-0.23;-0.18	4.02	4.02	0.46733	.	0.103590	0.64402	D	0.000003	T	0.81969	0.4935	M	0.78637	2.42	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.996;0.999	D	0.84934	0.0861	10	0.72032	D	0.01	-18.9729	17.4778	0.87664	0.0:0.0:1.0:0.0	.	957;1027	E7ERL6;Q6P0Q8	.;MAST2_HUMAN	H	1027;957	ENSP00000354671:R1027H;ENSP00000361079:R957H	ENSP00000354671:R1027H	R	+	2	0	MAST2	46269737	1.000000	0.71417	0.999000	0.59377	0.991000	0.79684	9.524000	0.98036	2.523000	0.85059	0.655000	0.94253	CGC		0.627	MAST2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021977.1	NM_015112	
PKN2	5586	broad.mit.edu	37	1	89273248	89273248	+	Silent	SNP	C	C	T			TCGA-AA-3679-01A-02W-0900-09	TCGA-AA-3679-10A-01W-0900-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3679-01A-02W-0900-09	TCGA-AA-3679-10A-01W-0900-09	g.chr1:89273248C>T	ENST00000370521.3	+	14	2330	c.1971C>T	c.(1969-1971)ttC>ttT	p.F657F	PKN2_ENST00000544045.1_Silent_p.F331F|PKN2_ENST00000370505.3_Silent_p.F500F|PKN2_ENST00000370513.5_Silent_p.F609F	NM_006256.2	NP_006247.1	Q16513	PKN2_HUMAN	protein kinase N2	657	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				apical junction assembly (GO:0043297)|apoptotic process (GO:0006915)|cell adhesion (GO:0007155)|cell cycle (GO:0007049)|cell division (GO:0051301)|epithelial cell migration (GO:0010631)|positive regulation of cytokinesis (GO:0032467)|positive regulation of mitotic cell cycle (GO:0045931)|protein phosphorylation (GO:0006468)|regulation of cell motility (GO:2000145)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)	apical junction complex (GO:0043296)|centrosome (GO:0005813)|cleavage furrow (GO:0032154)|cytoplasm (GO:0005737)|intermediate filament cytoskeleton (GO:0045111)|lamellipodium (GO:0030027)|membrane (GO:0016020)|midbody (GO:0030496)|nucleus (GO:0005634)	ATP binding (GO:0005524)|histone deacetylase binding (GO:0042826)|poly(A) RNA binding (GO:0044822)|protein kinase activity (GO:0004672)|protein kinase C activity (GO:0004697)|protein serine/threonine kinase activity (GO:0004674)	p.F657F(1)		breast(2)|endometrium(3)|kidney(3)|large_intestine(8)|lung(15)|prostate(1)|skin(1)	33		Lung NSC(277;0.123)		all cancers(265;0.0136)|Epithelial(280;0.0301)		TACAAGATTTCAGGTGTTGTG	0.308																																					p.F657F												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1971T	1						.						156.0	150.0	151.0					1																	89273248		1802	4068	5870	89045836	SO:0001819	synonymous_variant	5586	exon14			U33052	CCDS714.1	1p22	2014-04-23	2004-07-01	2004-07-01	ENSG00000065243	ENSG00000065243			9406	protein-coding gene	gene with protein product	"""cardiolipin-activated protein kinase Pak2"""	602549	"""protein kinase C-like 2"""	PRKCL2		7988719, 7851406	Standard	NM_006256		Approved	PRK2, Pak-2, STK7	uc001dmn.3	Q16513	OTTHUMG00000010074	ENST00000370521.3:c.1971C>T	1.37:g.89273248C>T			89045836	NM_006256	B4DQ21|B4DTP5|B4DVG1|D3DT24|Q08AF4|Q9H1W4	Silent	SNP	ENST00000370521.3	37	CCDS714.1																																																																																				0.308	PKN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027828.3	NM_006256	
TPR	7175	broad.mit.edu	37	1	186296594	186296594	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3679-01A-02W-0900-09	TCGA-AA-3679-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AA-3679-01A-02W-0900-09	TCGA-AA-3679-10A-01W-0900-09	g.chr1:186296594C>T	ENST00000367478.4	-	40	6183	c.5887G>A	c.(5887-5889)Gag>Aag	p.E1963K		NM_003292.2	NP_003283.2	P12270	TPR_HUMAN	translocated promoter region, nuclear basket protein	1963				Missing (in Ref. 2; CAA47021). {ECO:0000305}.	carbohydrate metabolic process (GO:0005975)|cellular response to heat (GO:0034605)|cellular response to interferon-alpha (GO:0035457)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|MAPK import into nucleus (GO:0000189)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic nuclear envelope disassembly (GO:0007077)|mitotic spindle assembly checkpoint (GO:0007094)|mRNA export from nucleus in response to heat stress (GO:0031990)|negative regulation of RNA export from nucleus (GO:0046832)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of translational initiation (GO:0045947)|nuclear pore organization (GO:0006999)|positive regulation of heterochromatin assembly (GO:0031453)|positive regulation of intracellular protein transport (GO:0090316)|positive regulation of mitotic cell cycle spindle assembly checkpoint (GO:0090267)|positive regulation of protein export from nucleus (GO:0046827)|positive regulation of protein import into nucleus (GO:0042307)|protein import into nucleus (GO:0006606)|regulation of glucose transport (GO:0010827)|regulation of mitotic sister chromatid separation (GO:0010965)|regulation of spindle assembly involved in mitosis (GO:1901673)|response to epidermal growth factor (GO:0070849)|RNA export from nucleus (GO:0006405)|RNA import into nucleus (GO:0006404)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytoplasmic dynein complex (GO:0005868)|extrinsic component of membrane (GO:0019898)|kinetochore (GO:0000776)|mitotic spindle (GO:0072686)|nuclear envelope (GO:0005635)|nuclear inclusion body (GO:0042405)|nuclear membrane (GO:0031965)|nuclear periphery (GO:0034399)|nuclear pore (GO:0005643)|nuclear pore nuclear basket (GO:0044615)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|dynein complex binding (GO:0070840)|heat shock protein binding (GO:0031072)|mitogen-activated protein kinase binding (GO:0051019)|mRNA binding (GO:0003729)|nucleocytoplasmic transporter activity (GO:0005487)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)|tubulin binding (GO:0015631)	p.E1963Q(1)|p.E1963K(1)		autonomic_ganglia(1)|breast(5)|central_nervous_system(4)|cervix(2)|endometrium(9)|kidney(12)|large_intestine(23)|liver(1)|lung(45)|ovary(2)|pancreas(1)|prostate(6)|skin(3)|stomach(1)|urinary_tract(8)	123		Breast(1374;0.000659)|Lung SC(1967;0.0262)|Prostate(1639;0.157)		Colorectal(1306;1.12e-05)|KIRC - Kidney renal clear cell carcinoma(1967;0.00553)		AAACTTACCTCATGTTCTCca	0.378			T	NTRK1	papillary thyroid																																p.E1963K			Dom	yes		1	1q25	7175	translocated promoter region		E	.	.	2	Substitution - Missense(2)	large_intestine(1)|endometrium(1)	c.G5887A	1						.						114.0	111.0	112.0					1																	186296594		1998	4168	6166	184563217	SO:0001583	missense	7175	exon40			U69668	CCDS41446.1	1q25	2012-03-13	2012-03-13		ENSG00000047410	ENSG00000047410			12017	protein-coding gene	gene with protein product		189940	"""translocated promoter region (to activated MET oncogene)"""			1611909, 15229283	Standard	NM_003292		Approved		uc001grv.3	P12270	OTTHUMG00000035580	ENST00000367478.4:c.5887G>A	1.37:g.186296594C>T	ENSP00000356448:p.Glu1963Lys		184563217	NM_003292	Q15655|Q5SWY0|Q99968	Missense_Mutation	SNP	ENST00000367478.4	37	CCDS41446.1	.	.	.	.	.	.	.	.	.	.	C	17.26	3.344681	0.61073	.	.	ENSG00000047410	ENST00000367478	T	0.25250	1.81	5.26	5.26	0.73747	.	0.181464	0.46442	D	0.000282	T	0.47040	0.1424	M	0.63843	1.955	0.58432	D	0.999995	P	0.52842	0.956	P	0.62184	0.899	T	0.37663	-0.9696	10	0.51188	T	0.08	.	17.0596	0.86543	0.0:1.0:0.0:0.0	.	1963	P12270	TPR_HUMAN	K	1963	ENSP00000356448:E1963K	ENSP00000356448:E1963K	E	-	1	0	TPR	184563217	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	4.929000	0.63455	2.451000	0.82905	0.650000	0.86243	GAG		0.378	TPR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086353.2	NM_003292	
TTLL9	164395	broad.mit.edu	37	20	30513858	30513858	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3679-01A-02W-0900-09	TCGA-AA-3679-10A-01W-0900-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AA-3679-01A-02W-0900-09	TCGA-AA-3679-10A-01W-0900-09	g.chr20:30513858G>T	ENST00000375938.4	+	10	965	c.712G>T	c.(712-714)Gct>Tct	p.A238S	TTLL9_ENST00000375921.2_Intron|TTLL9_ENST00000375934.4_Intron|TTLL9_ENST00000535842.1_Missense_Mutation_p.A238S|TTLL9_ENST00000375922.4_Intron|TTLL9_ENST00000310998.4_Intron			Q3SXZ7	TTLL9_HUMAN	tubulin tyrosine ligase-like family, member 9	238	TTL. {ECO:0000255|PROSITE- ProRule:PRU00568}.				cellular protein modification process (GO:0006464)	cilium (GO:0005929)|cytoplasm (GO:0005737)|microtubule (GO:0005874)	ligase activity (GO:0016874)	p.A238S(1)		breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(8)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	26			Colorectal(19;0.00306)|COAD - Colon adenocarcinoma(19;0.0347)			acaggtgtttgctgaatgcct	0.577																																					p.A238S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G712T	20						.						83.0	88.0	86.0					20																	30513858		2006	4181	6187	29977519	SO:0001583	missense	164395	exon10			AL031658	CCDS42863.1	20q11	2013-02-14	2005-07-28	2005-07-28		ENSG00000131044		"""Tubulin tyrosine ligase-like family"""	16118	protein-coding gene	gene with protein product			"""chromosome 20 open reading frame 125"""	C20orf125		15890843	Standard	NM_001008409		Approved	dJ310O13.1	uc010gdx.1	Q3SXZ7		ENST00000375938.4:c.712G>T	20.37:g.30513858G>T	ENSP00000365105:p.Ala238Ser		29977519	NM_001008409	A6NH06|A6NIS5|B3KSG8|Q3SXZ8|Q5JYS3|Q5JYS4	Missense_Mutation	SNP	ENST00000375938.4	37	CCDS42863.1	.	.	.	.	.	.	.	.	.	.	G	0.369	-0.935068	0.02340	.	.	ENSG00000131044	ENST00000375938;ENST00000535842	T;T	0.05081	3.5;3.5	3.23	2.26	0.28386	.	0.842315	0.10051	N	0.722288	T	0.03651	0.0104	N	0.04880	-0.145	0.09310	N	0.999999	B	0.15141	0.012	B	0.23852	0.049	T	0.45190	-0.9278	10	0.32370	T	0.25	.	7.7344	0.28806	0.0:0.0:0.7498:0.2502	.	238	Q3SXZ7	TTLL9_HUMAN	S	238	ENSP00000365105:A238S;ENSP00000442515:A238S	ENSP00000365105:A238S	A	+	1	0	TTLL9	29977519	0.000000	0.05858	0.001000	0.08648	0.001000	0.01503	0.134000	0.15932	0.917000	0.36895	-0.188000	0.12872	GCT		0.577	TTLL9-205	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001008409	
STX16	8675	broad.mit.edu	37	20	57244348	57244348	+	Splice_Site	SNP	T	T	G			TCGA-AA-3679-01A-02W-0900-09	TCGA-AA-3679-10A-01W-0900-09	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3679-01A-02W-0900-09	TCGA-AA-3679-10A-01W-0900-09	g.chr20:57244348T>G	ENST00000371141.4	+	5	1119	c.395T>G	c.(394-396)cTc>cGc	p.L132R	STX16_ENST00000358029.4_Splice_Site_p.L128R|STX16_ENST00000359617.4_Splice_Site_p.L79R|STX16_ENST00000355957.5_Splice_Site_p.L115R|STX16_ENST00000361770.5_Splice_Site_p.L115R|STX16_ENST00000361830.3_Splice_Site_p.L132R|STX16_ENST00000496003.1_Intron|STX16-NPEPL1_ENST00000530122.1_Splice_Site_p.L132R|STX16_ENST00000371132.4_Splice_Site_p.L111R	NM_001001433.2	NP_001001433.1	O14662	STX16_HUMAN	syntaxin 16	132					intra-Golgi vesicle-mediated transport (GO:0006891)|intracellular protein transport (GO:0006886)|retrograde transport, endosome to Golgi (GO:0042147)	cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|nucleolus (GO:0005730)|SNARE complex (GO:0031201)	SNAP receptor activity (GO:0005484)	p.L111R(1)		breast(1)|cervix(1)|large_intestine(3)|lung(9)|ovary(1)|pancreas(1)|urinary_tract(1)	17	all_lung(29;0.0175)		BRCA - Breast invasive adenocarcinoma(13;3.73e-09)|Epithelial(14;8.54e-06)|all cancers(14;6.89e-05)			TTCTCTTAGCTCTTCCACAGG	0.657																																					p.L111R												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T332G	20						.						15.0	18.0	17.0					20																	57244348		2161	4256	6417	56677754	SO:0001630	splice_region_variant	8675	exon4			AF038897	CCDS13468.1, CCDS13469.1, CCDS46619.1, CCDS46620.1, CCDS56199.1	20q13.32	2008-07-02			ENSG00000124222	ENSG00000124222			11431	protein-coding gene	gene with protein product		603666				9464276, 9587053, 15800843	Standard	NM_003763		Approved	hsyn16, SYN16	uc002xzi.3	O14662	OTTHUMG00000033084	ENST00000371141.4:c.394-1T>G	20.37:g.57244348T>G			56677754	NM_003763	A6NK32|A6NN69|A8MPP0|B7ZBN1|B7ZBN2|B7ZBN3|E1P5M0|E1P607|O14661|O14663|O60517|Q5W084|Q5W086|Q5W087|Q5XKI6|Q6GMS8|Q9H0Z0|Q9H1T7|Q9H1T8|Q9UIX5	Missense_Mutation	SNP	ENST00000371141.4	37	CCDS13468.1	.	.	.	.	.	.	.	.	.	.	T	34	5.291423	0.95546	.	.	ENSG00000124222	ENST00000458280;ENST00000355957;ENST00000361770;ENST00000312283;ENST00000412911;ENST00000359617;ENST00000371141;ENST00000371138;ENST00000371132;ENST00000358029;ENST00000361830;ENST00000438253	T;T;T;T;T;T;T;T;T;T;T	0.17528	2.27;2.27;2.27;2.27;2.27;2.27;2.27;2.27;2.27;2.27;2.27	5.72	5.72	0.89469	t-SNARE (1);Syntaxin, N-terminal (1);	0.062519	0.56097	U	0.000023	T	0.42675	0.1213	M	0.82132	2.575	0.80722	D	1	P;D;P;D	0.57899	0.607;0.973;0.58;0.981	P;P;B;D	0.66979	0.507;0.73;0.381;0.948	T	0.27571	-1.0070	10	0.32370	T	0.25	.	15.171	0.72872	0.0:0.0:0.0:1.0	.	128;115;111;132	Q6GMS8;O14662-4;O14662-2;O14662	.;.;.;STX16_HUMAN	R	79;115;115;79;79;79;132;79;111;128;132;74	ENSP00000388348:L79R;ENSP00000348229:L115R;ENSP00000355408:L115R;ENSP00000312086:L79R;ENSP00000416852:L79R;ENSP00000352634:L79R;ENSP00000360183:L132R;ENSP00000360173:L111R;ENSP00000350723:L128R;ENSP00000354445:L132R;ENSP00000401801:L74R	ENSP00000360180:L79R	L	+	2	0	STX16	56677754	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.633000	0.83260	2.182000	0.69389	0.533000	0.62120	CTC		0.657	STX16-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000080517.2	NM_001001433	Missense_Mutation
GNAS	2778	broad.mit.edu	37	20	57430099	57430099	+	Missense_Mutation	SNP	G	G	C			TCGA-AA-3679-01A-02W-0900-09	TCGA-AA-3679-10A-01W-0900-09	G	G	G	C	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AA-3679-01A-02W-0900-09	TCGA-AA-3679-10A-01W-0900-09	g.chr20:57430099G>C	ENST00000371100.4	+	1	2331	c.1779G>C	c.(1777-1779)caG>caC	p.Q593H	GNAS_ENST00000371098.2_Intron|GNAS_ENST00000371102.4_Missense_Mutation_p.Q593H|GNAS_ENST00000464624.2_3'UTR|GNAS_ENST00000313949.7_Intron|GNAS_ENST00000371099.2_Missense_Mutation_p.Q593H|GNAS_ENST00000371075.3_Intron|GNAS_ENST00000306120.3_Missense_Mutation_p.S530T	NM_001077490.1|NM_080425.2	NP_001070958.1|NP_536350.2	P63092	GNAS2_HUMAN	GNAS complex locus	0					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.Q593H(1)		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)			GCTGGTTTCAGCATCGGCGAA	0.642			Mis		pituitary adenoma		"""McCune-Albright syndrome; pseudohypoparathyroidism, type IA"""			TSP Lung(22;0.16)																											p.S531T	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	.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1592C	20						.						19.0	24.0	22.0					20																	57430099		2021	4175	6196	56863494	SO:0001583	missense	2778	exon1			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	ENST00000371100.4:c.1779G>C	20.37:g.57430099G>C	ENSP00000360141:p.Gln593His		56863494	NM_001077490	A6NI00|E1P5G5|P04895|Q12927|Q14433|Q32P26|Q5JWD2|Q5JWD4|Q5JWD5|Q6NR75|Q6NXS0|Q8TBC0|Q96H70	Missense_Mutation	SNP	ENST00000371100.4	37	CCDS46622.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	8.229|8.229	0.804142|0.804142	0.16467|0.16467	.|.	.|.	ENSG00000087460|ENSG00000087460	ENST00000371099;ENST00000371100;ENST00000371102|ENST00000306120	D;D|.	0.88896|.	-2.44;-2.44|.	3.84|3.84	1.74|1.74	0.24563|0.24563	.|.	7.952310|.	0.00166|.	N|.	0.000000|.	T|T	0.37073|0.37073	0.0990|0.0990	L|L	0.40543|0.40543	1.245|1.245	0.09310|0.09310	N|N	1|1	P|.	0.46277|.	0.875|.	B|.	0.34652|.	0.187|.	T|T	0.25012|0.25012	-1.0144|-1.0144	10|6	0.66056|0.27785	D|T	0.02|0.31	.|.	9.9115|9.9115	0.41408|0.41408	0.0:0.4063:0.5937:0.0|0.0:0.4063:0.5937:0.0	.|.	593|.	Q5JWF2|.	GNAS1_HUMAN|.	H|T	593|530	ENSP00000360141:Q593H;ENSP00000360143:Q593H|.	ENSP00000360140:Q593H|ENSP00000302237:S530T	Q|S	+|+	3|2	2|0	GNAS|GNAS	56863494|56863494	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.007000|0.007000	0.05969|0.05969	0.650000|0.650000	0.24858|0.24858	0.350000|0.350000	0.24002|0.24002	-0.502000|-0.502000	0.04539|0.04539	CAG|AGC		0.642	GNAS-001	PUTATIVE	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000080417.3	NM_000516	
TRAPPC10	7109	broad.mit.edu	37	21	45479028	45479028	+	Silent	SNP	C	C	T			TCGA-AA-3679-01A-02W-0900-09	TCGA-AA-3679-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AA-3679-01A-02W-0900-09	TCGA-AA-3679-10A-01W-0900-09	g.chr21:45479028C>T	ENST00000291574.4	+	6	898	c.723C>T	c.(721-723)gaC>gaT	p.D241D	TRAPPC10_ENST00000380221.3_Silent_p.D241D	NM_003274.4	NP_003265.3	P48553	TPC10_HUMAN	trafficking protein particle complex 10	241					sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)|vesicle-mediated transport (GO:0016192)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	sodium ion transmembrane transporter activity (GO:0015081)	p.D241D(1)		NS(1)|breast(3)|central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(10)|lung(8)|ovary(1)|prostate(2)|skin(2)|urinary_tract(4)	41						AGTTCGAGGACGCCCTGGTGC	0.473																																					p.D241D												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C723T	21						.						75.0	65.0	68.0					21																	45479028		2203	4300	6503	44303456	SO:0001819	synonymous_variant	7109	exon6			U19252	CCDS13704.1	21q22.3	2008-05-07	2008-05-07	2008-05-07	ENSG00000160218	ENSG00000160218		"""Trafficking protein particle complex"""	11868	protein-coding gene	gene with protein product	"""trafficking protein particle complex subunit 130"", ""TRAPP 130 kDa subunit"""	602103	"""transmembrane protein 1"""	TMEM1		7633421	Standard	NM_003274		Approved	EHOC-1, TRS130	uc002zea.3	P48553	OTTHUMG00000086894	ENST00000291574.4:c.723C>T	21.37:g.45479028C>T			44303456	NM_003274	Q3MIR2|Q86SI7|Q9UMD4|Q9Y4L3	De_novo_Start_OutOfFrame	SNP	ENST00000291574.4	37	CCDS13704.1																																																																																				0.473	TRAPPC10-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000195737.1	NM_003274	
PI4KA	5297	broad.mit.edu	37	22	21156277	21156277	+	Missense_Mutation	SNP	T	T	C	rs200824315		TCGA-AA-3679-01A-02W-0900-09	TCGA-AA-3679-10A-01W-0900-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AA-3679-01A-02W-0900-09	TCGA-AA-3679-10A-01W-0900-09	g.chr22:21156277T>C	ENST00000572273.1	-	14	1764	c.1534A>G	c.(1534-1536)Att>Gtt	p.I512V	PI4KA_ENST00000255882.6_Missense_Mutation_p.I570V			P42356	PI4KA_HUMAN	phosphatidylinositol 4-kinase, catalytic, alpha	512					phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi-associated vesicle membrane (GO:0030660)|membrane (GO:0016020)|plasma membrane (GO:0005886)	1-phosphatidylinositol 4-kinase activity (GO:0004430)|ATP binding (GO:0005524)	p.I512V(2)		breast(3)|endometrium(8)|kidney(9)|large_intestine(19)|lung(29)|ovary(1)|pancreas(1)|prostate(3)|salivary_gland(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	79	all_cancers(11;7.59e-25)|all_epithelial(7;1.34e-22)|Melanoma(16;0.000465)|Ovarian(15;0.00167)|Colorectal(54;0.0332)|all_neural(72;0.142)	Lung SC(17;0.0262)	LUSC - Lung squamous cell carcinoma(15;0.000536)|Lung(15;0.0108)|Epithelial(17;0.196)			ATGTTGTCAATAGCGATGTCT	0.483													T|||	1	0.000199681	0.0	0.0	5008	,	,		17331	0.0		0.001	False		,,,				2504	0.0				p.I512V	GBM(136;1332 1831 3115 23601 50806)											.	.	2	Substitution - Missense(2)	large_intestine(2)	c.A1534G	22						.						124.0	98.0	107.0					22																	21156277		2203	4300	6503	19486277	SO:0001583	missense	5297	exon14			L36151	CCDS33603.1, CCDS33603.2	22q11.21	2011-05-25	2007-08-14	2007-08-02	ENSG00000241973	ENSG00000241973			8983	protein-coding gene	gene with protein product		600286		PIK4CA		7961848, 8662589	Standard	NM_002650		Approved	PI4K-ALPHA, pi4K230	uc002zsz.5	P42356	OTTHUMG00000167440	ENST00000572273.1:c.1534A>G	22.37:g.21156277T>C	ENSP00000458238:p.Ile512Val		19486277	NM_058004	Q7Z625|Q9UPG2	Missense_Mutation	SNP	ENST00000572273.1	37		1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	T	22.5	4.302384	0.81136	.	.	ENSG00000241973	ENST00000255882	.	.	.	4.68	4.68	0.58851	.	0.000000	0.85682	D	0.000000	T	0.74268	0.3694	M	0.68317	2.08	0.80722	D	1	D;D	0.63046	0.992;0.987	P;P	0.62014	0.897;0.786	T	0.76410	-0.2969	9	0.51188	T	0.08	-18.1671	14.2883	0.66260	0.0:0.0:0.0:1.0	.	570;512	D3DX33;P42356	.;PI4KA_HUMAN	V	512	.	ENSP00000255882:I512V	I	-	1	0	PI4KA	19486277	1.000000	0.71417	1.000000	0.80357	0.876000	0.50452	7.868000	0.87116	1.975000	0.57531	0.402000	0.26972	ATT		0.483	PI4KA-202	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_058004	
MALL	7851	broad.mit.edu	37	2	110845227	110845227	+	Silent	SNP	G	G	A			TCGA-AA-3679-01A-02W-0900-09	TCGA-AA-3679-10A-01W-0900-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3679-01A-02W-0900-09	TCGA-AA-3679-10A-01W-0900-09	g.chr2:110845227G>A	ENST00000272462.2	-	3	1094	c.321C>T	c.(319-321)gcC>gcT	p.A107A	MALL_ENST00000427178.1_Intron|MIR4436B1_ENST00000583272.1_RNA	NM_005434.4	NP_005425.1	Q13021	MALL_HUMAN	mal, T-cell differentiation protein-like	107	MARVEL. {ECO:0000255|PROSITE- ProRule:PRU00581}.				cholesterol homeostasis (GO:0042632)	clathrin-coated vesicle (GO:0030136)|cytoplasmic membrane-bounded vesicle (GO:0016023)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)		p.A107A(1)		kidney(1)|large_intestine(3)|lung(1)|ovary(1)|skin(1)|stomach(1)|urinary_tract(1)	9				Epithelial(1;0.0546)|STAD - Stomach adenocarcinoma(1;0.18)		CTTGTAGGACGGCAGCGCTCA	0.522																																					p.A107A												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C321T	2						.						0.0	1.0	1.0					2																	110845227		0	1	1	110202516	SO:0001819	synonymous_variant	7851	exon3			U17077	CCDS2085.1	2q13	2008-02-05			ENSG00000144063	ENSG00000144063			6818	protein-coding gene	gene with protein product		602022				9326933	Standard	NM_005434		Approved	BENE	uc002tfk.3	Q13021	OTTHUMG00000131196	ENST00000272462.2:c.321C>T	2.37:g.110845227G>A			110202516	NM_005434	B3KWR6|Q9BTU0	Silent	SNP	ENST00000272462.2	37	CCDS2085.1																																																																																				0.522	MALL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253921.1	NM_005434	
LRP1B	53353	broad.mit.edu	37	2	141643837	141643837	+	Silent	SNP	T	T	C			TCGA-AA-3679-01A-02W-0900-09	TCGA-AA-3679-10A-01W-0900-09	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3679-01A-02W-0900-09	TCGA-AA-3679-10A-01W-0900-09	g.chr2:141643837T>C	ENST00000389484.3	-	24	4805	c.3834A>G	c.(3832-3834)agA>agG	p.R1278R		NM_018557.2	NP_061027.2	Q9NZR2	LRP1B_HUMAN	low density lipoprotein receptor-related protein 1B	1278					protein transport (GO:0015031)|receptor-mediated endocytosis (GO:0006898)	integral component of membrane (GO:0016021)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)|low-density lipoprotein receptor activity (GO:0005041)	p.R1278R(1)		NS(5)|autonomic_ganglia(1)|biliary_tract(1)|breast(3)|central_nervous_system(7)|endometrium(25)|haematopoietic_and_lymphoid_tissue(10)|kidney(27)|large_intestine(98)|liver(4)|lung(337)|ovary(15)|pancreas(6)|prostate(11)|skin(30)|stomach(2)|upper_aerodigestive_tract(19)|urinary_tract(5)	606		all_cancers(3;1.1e-60)|all_epithelial(3;1.94e-59)|all_lung(3;1.09e-24)|Lung NSC(3;5.65e-24)|Esophageal squamous(3;5.41e-13)|Renal(3;0.000147)|Breast(3;0.000527)|Hepatocellular(3;0.011)|all_neural(3;0.014)|Colorectal(150;0.101)		UCEC - Uterine corpus endometrioid carcinoma (2;0.00139)|Epithelial(1;1.25e-24)|all cancers(1;8.86e-24)|OV - Ovarian serous cystadenocarcinoma(1;2.45e-12)|LUSC - Lung squamous cell carcinoma(1;2.97e-10)|Lung(1;6.05e-09)|BRCA - Breast invasive adenocarcinoma(221;0.0103)		GACTATAGTCTCTTTTGTGAA	0.313										TSP Lung(27;0.18)																											p.R1278R	Colon(99;50 2074 2507 20106)											.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.A3834G	2						.						77.0	79.0	78.0					2																	141643837		2203	4298	6501	141360307	SO:0001819	synonymous_variant	53353	exon24			AF176832	CCDS2182.1	2q21.2	2013-05-29	2010-01-26		ENSG00000168702	ENSG00000168702		"""Low density lipoprotein receptors"""	6693	protein-coding gene	gene with protein product	"""LRP-deleted in tumors"""	608766				10766186	Standard	NM_018557		Approved	LRP-DIT, LRPDIT	uc002tvj.1	Q9NZR2	OTTHUMG00000131799	ENST00000389484.3:c.3834A>G	2.37:g.141643837T>C			141360307	NM_018557	Q8WY29|Q8WY30|Q8WY31	Silent	SNP	ENST00000389484.3	37	CCDS2182.1																																																																																				0.313	LRP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254736.2	NM_018557	
KYNU	8942	broad.mit.edu	37	2	143799648	143799648	+	Silent	SNP	G	G	T			TCGA-AA-3679-01A-02W-0900-09	TCGA-AA-3679-10A-01W-0900-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3679-01A-02W-0900-09	TCGA-AA-3679-10A-01W-0900-09	g.chr2:143799648G>T	ENST00000264170.4	+	14	1563	c.1305G>T	c.(1303-1305)gtG>gtT	p.V435V	KYNU_ENST00000409512.1_Silent_p.V435V	NM_003937.2	NP_003928.1			kynureninase									p.V435V(1)		large_intestine(10)|liver(1)|lung(18)|prostate(3)|skin(4)	36				BRCA - Breast invasive adenocarcinoma(221;0.072)		GCATTCGagtggctccagttc	0.363																																					p.V435V												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G1305T	2						.						132.0	131.0	131.0					2																	143799648		2203	4299	6502	143516118	SO:0001819	synonymous_variant	8942	exon14			U57721	CCDS2183.1, CCDS33299.1	2q22.2	2010-11-23	2010-11-23		ENSG00000115919	ENSG00000115919	3.7.1.3		6469	protein-coding gene	gene with protein product	"""L-kynurenine hydrolase"""	605197	"""kynureninase (L-kynurenine hydrolase)"""			8706755, 9180257	Standard	NM_001199241		Approved		uc002tvl.3	Q16719	OTTHUMG00000131829	ENST00000264170.4:c.1305G>T	2.37:g.143799648G>T			143516118	NM_003937		Silent	SNP	ENST00000264170.4	37	CCDS2183.1																																																																																				0.363	KYNU-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254772.1	NM_001032998	
EHD3	30845	broad.mit.edu	37	2	31457609	31457609	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3679-01A-02W-0900-09	TCGA-AA-3679-10A-01W-0900-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3679-01A-02W-0900-09	TCGA-AA-3679-10A-01W-0900-09	g.chr2:31457609G>T	ENST00000322054.5	+	1	407	c.122G>T	c.(121-123)cGc>cTc	p.R41L	EHD3_ENST00000541626.1_Missense_Mutation_p.R41L	NM_014600.2	NP_055415.1	Q9NZN3	EHD3_HUMAN	EH-domain containing 3	41					blood coagulation (GO:0007596)|endocytic recycling (GO:0032456)|protein homooligomerization (GO:0051260)|protein targeting to plasma membrane (GO:0072661)|regulation of cardiac muscle cell membrane potential (GO:0086036)	cytoplasm (GO:0005737)|endocytic vesicle (GO:0030139)|endosome membrane (GO:0010008)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|recycling endosome membrane (GO:0055038)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|nucleic acid binding (GO:0003676)	p.R41L(1)		NS(1)|breast(2)|endometrium(2)|kidney(1)|large_intestine(11)|lung(12)|ovary(1)|skin(3)	33	Acute lymphoblastic leukemia(172;0.155)					GAGCATTACCGCTTCCACGAG	0.597																																					p.R41L												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G122T	2						.						108.0	102.0	104.0					2																	31457609		2203	4300	6503	31311113	SO:0001583	missense	30845	exon1			AF181264	CCDS1774.1	2p21	2013-01-10			ENSG00000013016	ENSG00000013016		"""EF-hand domain containing"""	3244	protein-coding gene	gene with protein product		605891		PAST3		10673336	Standard	NM_014600		Approved		uc002rnu.3	Q9NZN3	OTTHUMG00000099365	ENST00000322054.5:c.122G>T	2.37:g.31457609G>T	ENSP00000327116:p.Arg41Leu		31311113	NM_014600	B4DFR5|D6W574|Q8N514|Q9NZB3	Missense_Mutation	SNP	ENST00000322054.5	37	CCDS1774.1	.	.	.	.	.	.	.	.	.	.	G	16.39	3.111116	0.56398	.	.	ENSG00000013016	ENST00000541626;ENST00000322054	T;T	0.32515	1.45;2.2	5.0	5.0	0.66597	.	0.047335	0.85682	D	0.000000	T	0.23611	0.0571	L	0.46741	1.465	0.44388	D	0.997296	B;B	0.09022	0.002;0.0	B;B	0.06405	0.002;0.001	T	0.10543	-1.0625	10	0.33141	T	0.24	-24.0634	5.9496	0.19237	0.2233:0.0:0.7767:0.0	.	41;41	B4DFR5;Q9NZN3	.;EHD3_HUMAN	L	41	ENSP00000440685:R41L;ENSP00000327116:R41L	ENSP00000327116:R41L	R	+	2	0	EHD3	31311113	1.000000	0.71417	1.000000	0.80357	0.964000	0.63967	5.609000	0.67661	2.600000	0.87896	0.561000	0.74099	CGC		0.597	EHD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216810.1	NM_014600	
UGP2	7360	broad.mit.edu	37	2	64109645	64109645	+	Missense_Mutation	SNP	A	A	C			TCGA-AA-3679-01A-02W-0900-09	TCGA-AA-3679-10A-01W-0900-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AA-3679-01A-02W-0900-09	TCGA-AA-3679-10A-01W-0900-09	g.chr2:64109645A>C	ENST00000337130.5	+	4	777	c.301A>C	c.(301-303)Ata>Cta	p.I101L	UGP2_ENST00000487469.1_3'UTR|UGP2_ENST00000445915.2_Missense_Mutation_p.I110L|UGP2_ENST00000467648.2_Missense_Mutation_p.I90L|ACA59_ENST00000515966.1_RNA|UGP2_ENST00000394417.2_Missense_Mutation_p.I90L	NM_006759.3	NP_006750.3	Q16851	UGPA_HUMAN	UDP-glucose pyrophosphorylase 2	101					carbohydrate metabolic process (GO:0005975)|cellular glucuronidation (GO:0052695)|glucose 1-phosphate metabolic process (GO:0019255)|glucose metabolic process (GO:0006006)|glycogen biosynthetic process (GO:0005978)|small molecule metabolic process (GO:0044281)|UDP-glucose metabolic process (GO:0006011)|UDP-glucuronate biosynthetic process (GO:0006065)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	glucose binding (GO:0005536)|metal ion binding (GO:0046872)|pyrimidine ribonucleotide binding (GO:0032557)|UTP:glucose-1-phosphate uridylyltransferase activity (GO:0003983)	p.I101L(1)		endometrium(2)|kidney(1)|large_intestine(8)|lung(6)|prostate(1)	18						GCCTGATAATATATCTTCCGT	0.403																																					p.I90L												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A268C	2						.						103.0	110.0	108.0					2																	64109645		2203	4300	6503	63963149	SO:0001583	missense	7360	exon4				CCDS1875.1, CCDS42690.1	2p14-p13	2012-10-02			ENSG00000169764	ENSG00000169764	2.7.7.9		12527	protein-coding gene	gene with protein product		191760	"""UDP-glucose pyrophosphorylase 1"""	UGP1			Standard	NM_006759		Approved	UGPP1	uc002scm.3	Q16851	OTTHUMG00000129513	ENST00000337130.5:c.301A>C	2.37:g.64109645A>C	ENSP00000338703:p.Ile101Leu		63963149	NM_001001521	Q07131|Q0P6K2|Q86Y81|Q9BU15	Missense_Mutation	SNP	ENST00000337130.5	37	CCDS1875.1	.	.	.	.	.	.	.	.	.	.	A	15.63	2.891549	0.52014	.	.	ENSG00000169764	ENST00000394417;ENST00000482668;ENST00000467648;ENST00000337130;ENST00000488245;ENST00000497883;ENST00000445915;ENST00000475462;ENST00000491621;ENST00000472047	T;T;T;T;T;T;T;T;T;T	0.16324	2.35;2.35;2.35;2.35;2.35;2.35;2.35;2.35;2.35;2.35	5.77	0.782	0.18567	.	0.265926	0.43110	N	0.000617	T	0.15132	0.0365	L	0.60067	1.865	0.54753	D	0.999985	B;B	0.12013	0.005;0.002	B;B	0.15484	0.013;0.013	T	0.11372	-1.0590	10	0.22109	T	0.4	-25.1732	9.558	0.39351	0.7382:0.0:0.2618:0.0	.	110;101	E7EUC7;Q16851	.;UGPA_HUMAN	L	90;90;90;101;90;93;110;90;90;90	ENSP00000377939:I90L;ENSP00000419548:I90L;ENSP00000420793:I90L;ENSP00000338703:I101L;ENSP00000419442:I90L;ENSP00000420131:I93L;ENSP00000411803:I110L;ENSP00000419335:I90L;ENSP00000420342:I90L;ENSP00000419238:I90L	ENSP00000338703:I101L	I	+	1	0	UGP2	63963149	0.998000	0.40836	0.391000	0.26233	0.995000	0.86356	1.783000	0.38664	-0.085000	0.12573	0.533000	0.62120	ATA		0.403	UGP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251688.1	NM_006759	
REG3A	5068	broad.mit.edu	37	2	79385824	79385824	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3679-01A-02W-0900-09	TCGA-AA-3679-10A-01W-0900-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AA-3679-01A-02W-0900-09	TCGA-AA-3679-10A-01W-0900-09	g.chr2:79385824G>T	ENST00000409839.3	-	3	184	c.148C>A	c.(148-150)Cac>Aac	p.H50N	AC011754.1_ENST00000415201.1_RNA|REG3A_ENST00000305165.2_Missense_Mutation_p.H50N|REG3A_ENST00000393878.1_Missense_Mutation_p.H50N	NM_002580.2|NM_138937.2	NP_002571.1|NP_620354.1	Q06141	REG3A_HUMAN	regenerating islet-derived 3 alpha	50	C-type lectin. {ECO:0000255|PROSITE- ProRule:PRU00040}.				acute-phase response (GO:0006953)|cell proliferation (GO:0008283)|heterophilic cell-cell adhesion (GO:0007157)|multicellular organismal development (GO:0007275)|negative regulation of keratinocyte differentiation (GO:0045617)|positive regulation of keratinocyte proliferation (GO:0010838)|positive regulation of wound healing (GO:0090303)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)	carbohydrate binding (GO:0030246)	p.H50N(2)		breast(2)|large_intestine(4)|lung(41)|prostate(2)|skin(1)	50						GCATAGCAGTGGGAGCCATAG	0.567																																					p.H50N												.	.	2	Substitution - Missense(2)	large_intestine(1)|lung(1)	c.C148A	2						.						110.0	98.0	102.0					2																	79385824		2203	4300	6503	79239332	SO:0001583	missense	5068	exon3			S51768	CCDS1965.1	2p12	2008-02-05	2005-02-11	2005-02-11	ENSG00000172016	ENSG00000172016			8601	protein-coding gene	gene with protein product		167805	"""pancreatitis-associated protein"""	PAP		8188210	Standard	NM_002580		Approved	HIP, REG-III, REG3, PBCGF, PAP1	uc002sof.2	Q06141	OTTHUMG00000130017	ENST00000409839.3:c.148C>A	2.37:g.79385824G>T	ENSP00000386630:p.His50Asn		79239332	NM_002580		Missense_Mutation	SNP	ENST00000409839.3	37	CCDS1965.1	.	.	.	.	.	.	.	.	.	.	G	11.15	1.552625	0.27739	.	.	ENSG00000172016	ENST00000409839;ENST00000393878;ENST00000305165	T;T;T	0.14266	2.52;2.52;2.52	3.87	-3.59	0.04583	C-type lectin fold (1);C-type lectin-like (1);C-type lectin (2);	0.576639	0.15737	N	0.247095	T	0.09730	0.0239	L	0.46885	1.475	0.09310	N	1	B	0.11235	0.004	B	0.15870	0.014	T	0.19386	-1.0307	10	0.49607	T	0.09	.	5.3159	0.15854	0.6087:0.0:0.2351:0.1562	.	50	Q06141	REG3A_HUMAN	N	50	ENSP00000386630:H50N;ENSP00000377456:H50N;ENSP00000304311:H50N	ENSP00000304311:H50N	H	-	1	0	REG3A	79239332	0.707000	0.27866	0.042000	0.18584	0.027000	0.11550	-0.289000	0.08365	-0.814000	0.04352	-0.199000	0.12753	CAC		0.567	REG3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252290.2	NM_002580	
WIPF1	7456	broad.mit.edu	37	2	175440046	175440046	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3679-01A-02W-0900-09	TCGA-AA-3679-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AA-3679-01A-02W-0900-09	TCGA-AA-3679-10A-01W-0900-09	g.chr2:175440046C>T	ENST00000392547.2	-	4	343	c.244G>A	c.(244-246)Gga>Aga	p.G82R	WIPF1_ENST00000272746.5_Missense_Mutation_p.G82R|WIPF1_ENST00000409415.3_Missense_Mutation_p.G82R|AC018890.6_ENST00000442996.1_RNA|AC018890.6_ENST00000412835.1_RNA|WIPF1_ENST00000410117.1_Missense_Mutation_p.G82R|WIPF1_ENST00000359761.3_Missense_Mutation_p.G82R|WIPF1_ENST00000409891.1_Missense_Mutation_p.G82R|AC010894.5_ENST00000454203.1_RNA|WIPF1_ENST00000392546.2_Missense_Mutation_p.G82R	NM_003387.4	NP_003378.3	O43516	WIPF1_HUMAN	WAS/WASL interacting protein family, member 1	82	Gly-rich.				actin filament-based movement (GO:0030048)|actin polymerization or depolymerization (GO:0008154)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|protein complex assembly (GO:0006461)|response to other organism (GO:0051707)	actin cytoskeleton (GO:0015629)|actin filament (GO:0005884)|cell projection (GO:0042995)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)	actin binding (GO:0003779)|profilin binding (GO:0005522)	p.G82R(1)		NS(1)|breast(1)|endometrium(5)|large_intestine(7)|lung(15)|ovary(2)|skin(1)	32						ccacctcctccgccaaatccg	0.622																																					p.G82R												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G244A	2						.						67.0	75.0	72.0					2																	175440046		2203	4300	6503	175148292	SO:0001583	missense	7456	exon4			AF031588	CCDS2260.1	2q31.2	2014-09-17	2006-10-12	2006-10-12	ENSG00000115935	ENSG00000115935			12736	protein-coding gene	gene with protein product		602357	"""Wiskott-Aldrich syndrome protein interacting protein"""	WASPIP		9405671	Standard	NM_001077269		Approved	WIP	uc002uiz.3	O43516	OTTHUMG00000132334	ENST00000392547.2:c.244G>A	2.37:g.175440046C>T	ENSP00000376330:p.Gly82Arg		175148292	NM_001077269	B8ZZM1|D3DPE4|Q15220|Q53TA9|Q6MZU9|Q9BU37|Q9UNP1	Missense_Mutation	SNP	ENST00000392547.2	37	CCDS2260.1	.	.	.	.	.	.	.	.	.	.	C	17.81	3.481516	0.63849	.	.	ENSG00000115935	ENST00000392547;ENST00000392548;ENST00000272746;ENST00000359761;ENST00000392546;ENST00000409891;ENST00000409415;ENST00000455428;ENST00000410117;ENST00000436221	D;D;D;D;D;D;D;D;D	0.96587	-4.06;-4.06;-4.06;-4.06;-4.06;-4.06;-3.94;-1.5;-1.5	4.98	1.96	0.26148	.	0.286990	0.30528	N	0.009440	D	0.94453	0.8215	L	0.48642	1.525	0.35647	D	0.811454	D;D;D;P	0.57257	0.969;0.979;0.969;0.947	P;P;P;B	0.51135	0.66;0.459;0.66;0.336	D	0.92927	0.6360	10	0.59425	D	0.04	.	6.6313	0.22859	0.139:0.7042:0.0:0.1569	.	82;82;82;82	O43516-3;E9PB87;O43516-2;O43516	.;.;.;WIPF1_HUMAN	R	82;82;82;82;82;82;82;79;82;82	ENSP00000376330:G82R;ENSP00000272746:G82R;ENSP00000352802:G82R;ENSP00000376329:G82R;ENSP00000386431:G82R;ENSP00000387150:G82R;ENSP00000391785:G79R;ENSP00000386757:G82R;ENSP00000388454:G82R	ENSP00000272746:G82R	G	-	1	0	WIPF1	175148292	0.905000	0.30787	0.002000	0.10522	0.613000	0.37349	3.216000	0.51176	0.081000	0.16988	0.462000	0.41574	GGA		0.622	WIPF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255453.1	NM_003387	
NIT2	56954	broad.mit.edu	37	3	100074045	100074045	+	Missense_Mutation	SNP	G	G	A	rs373969032		TCGA-AA-3679-01A-02W-0900-09	TCGA-AA-3679-10A-01W-0900-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3679-01A-02W-0900-09	TCGA-AA-3679-10A-01W-0900-09	g.chr3:100074045G>A	ENST00000394140.4	+	10	855	c.764G>A	c.(763-765)cGc>cAc	p.R255H		NM_020202.4	NP_064587.1	Q9NQR4	NIT2_HUMAN	nitrilase family, member 2	255	CN hydrolase. {ECO:0000255|PROSITE- ProRule:PRU00054}.				asparagine metabolic process (GO:0006528)|glutamine metabolic process (GO:0006541)|oxaloacetate metabolic process (GO:0006107)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	omega-amidase activity (GO:0050152)	p.R255H(1)		breast(1)|endometrium(1)|kidney(4)|large_intestine(3)|lung(4)|ovary(1)|prostate(2)|skin(1)	17						GCTGAAATACGCCAGCAAATC	0.423																																					p.R255H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G764A	3						.	G	HIS/ARG	0,4406		0,0,2203	77.0	75.0	75.0		764	5.8	1.0	3		75	1,8599	1.2+/-3.3	0,1,4299	no	missense	NIT2	NM_020202.4	29	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging	255/277	100074045	1,13005	2203	4300	6503	101556735	SO:0001583	missense	56954	exon10			AF284574	CCDS33806.1	3q12.3	2004-07-12			ENSG00000114021	ENSG00000114021			29878	protein-coding gene	gene with protein product						10959838	Standard	NM_020202		Approved		uc003dtv.3	Q9NQR4	OTTHUMG00000159066	ENST00000394140.4:c.764G>A	3.37:g.100074045G>A	ENSP00000377696:p.Arg255His		101556735	NM_020202	B2R9A3|D3DN47|Q8WUF0	Missense_Mutation	SNP	ENST00000394140.4	37	CCDS33806.1	.	.	.	.	.	.	.	.	.	.	G	34	5.352724	0.95830	0.0	1.16E-4	ENSG00000114021	ENST00000394140	T	0.76060	-0.99	5.78	5.78	0.91487	Nitrilase/cyanide hydratase and apolipoprotein N-acyltransferase (3);	0.050778	0.85682	D	0.000000	D	0.92080	0.7490	H	0.98048	4.135	0.80722	D	1	D	0.89917	1.0	D	0.78314	0.991	D	0.94410	0.7631	10	0.87932	D	0	-4.9614	20.0118	0.97458	0.0:0.0:1.0:0.0	.	255	Q9NQR4	NIT2_HUMAN	H	255	ENSP00000377696:R255H	ENSP00000377696:R255H	R	+	2	0	NIT2	101556735	1.000000	0.71417	1.000000	0.80357	0.937000	0.57800	8.587000	0.90810	2.733000	0.93635	0.591000	0.81541	CGC		0.423	NIT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353142.2	NM_020202	
CBLB	868	broad.mit.edu	37	3	105389107	105389107	+	Nonsense_Mutation	SNP	G	G	A			TCGA-AA-3679-01A-02W-0900-09	TCGA-AA-3679-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AA-3679-01A-02W-0900-09	TCGA-AA-3679-10A-01W-0900-09	g.chr3:105389107G>A	ENST00000264122.4	-	18	2980	c.2659C>T	c.(2659-2661)Cag>Tag	p.Q887*	CBLB_ENST00000394027.3_Nonsense_Mutation_p.Q865*|CBLB_ENST00000407712.1_Nonsense_Mutation_p.Q102*	NM_170662.3	NP_733762.2	Q13191	CBLB_HUMAN	Cbl proto-oncogene B, E3 ubiquitin protein ligase	887	Pro-rich.				cell surface receptor signaling pathway (GO:0007166)|immune response (GO:0006955)|intracellular signal transduction (GO:0035556)|negative regulation of alpha-beta T cell proliferation (GO:0046642)|negative regulation of T cell receptor signaling pathway (GO:0050860)|NLS-bearing protein import into nucleus (GO:0006607)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of T cell anergy (GO:0002669)|signal transduction (GO:0007165)|T cell activation (GO:0042110)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|ligase activity (GO:0016874)|signal transducer activity (GO:0004871)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.Q887*(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(8)|liver(1)|lung(20)|ovary(3)|prostate(1)|skin(3)|stomach(2)|urinary_tract(2)	49						TCATAGTCCTGTGATGTTCTG	0.378			Mis S		AML																																p.Q887X	GBM(93;588 1337 9788 29341 43499)		Rec	yes		3	3q13.11	868	Cas-Br-M (murine) ecotropic retroviral transforming sequence b		L	.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.C2659T	3						.						163.0	142.0	149.0					3																	105389107		2203	4300	6503	106871797	SO:0001587	stop_gained	868	exon18			U26710	CCDS2948.1	3q	2013-07-09	2013-07-09		ENSG00000114423	ENSG00000114423		"""RING-type (C3HC4) zinc fingers"""	1542	protein-coding gene	gene with protein product		604491	"""Cas-Br-M (murine) ectropic retroviral transforming sequence b"", ""Cas-Br-M (murine) ecotropic retroviral transforming sequence b"""			7784085	Standard	XM_005247853		Approved	RNF56, Cbl-b	uc003dwc.3	Q13191	OTTHUMG00000150654	ENST00000264122.4:c.2659C>T	3.37:g.105389107G>A	ENSP00000264122:p.Gln887*		106871797	NM_170662	A8K9S7|B7WNM4|Q13192|Q13193|Q3LIC0|Q63Z43|Q8IVC5	Nonsense_Mutation	SNP	ENST00000264122.4	37	CCDS2948.1	.	.	.	.	.	.	.	.	.	.	G	39	7.565334	0.98361	.	.	ENSG00000114423	ENST00000394030;ENST00000264122;ENST00000407712;ENST00000394027	.	.	.	5.72	5.72	0.89469	.	0.052578	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	-13.6891	18.4242	0.90604	0.0:0.0:1.0:0.0	.	.	.	.	X	226;887;102;865	.	ENSP00000264122:Q887X	Q	-	1	0	CBLB	106871797	1.000000	0.71417	0.983000	0.44433	0.978000	0.69477	6.338000	0.72963	2.865000	0.98341	0.655000	0.94253	CAG		0.378	CBLB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319417.2	NM_170662	
MB21D2	151963	broad.mit.edu	37	3	192516874	192516874	+	Silent	SNP	A	A	G			TCGA-AA-3679-01A-02W-0900-09	TCGA-AA-3679-10A-01W-0900-09	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3679-01A-02W-0900-09	TCGA-AA-3679-10A-01W-0900-09	g.chr3:192516874A>G	ENST00000392452.2	-	2	1097	c.777T>C	c.(775-777)gaT>gaC	p.D259D		NM_178496.3	NP_848591.2	Q8IYB1	M21D2_HUMAN	Mab-21 domain containing 2	259							protein complex binding (GO:0032403)	p.D257D(1)		endometrium(3)|kidney(1)|large_intestine(4)|lung(17)|ovary(3)|prostate(2)|upper_aerodigestive_tract(1)	31						TAATCTTCCCATCCCAAAAGT	0.498																																					p.D259D												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.T777C	3						.						64.0	61.0	62.0					3																	192516874		2203	4300	6503	193999568	SO:0001819	synonymous_variant	151963	exon2			AK056276	CCDS3302.2	3q28-q29	2011-02-23	2011-02-23	2011-02-23	ENSG00000180611	ENSG00000180611			30438	protein-coding gene	gene with protein product			"""chromosome 3 open reading frame 59"""	C3orf59		12477932	Standard	NM_178496		Approved		uc011bsp.2	Q8IYB1	OTTHUMG00000155768	ENST00000392452.2:c.777T>C	3.37:g.192516874A>G			193999568	NM_178496	Q86VD8	Silent	SNP	ENST00000392452.2	37	CCDS3302.2																																																																																				0.498	MB21D2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341543.1	NM_178496	
ADAMTS9	56999	broad.mit.edu	37	3	64606905	64606905	+	Nonsense_Mutation	SNP	G	G	A			TCGA-AA-3679-01A-02W-0900-09	TCGA-AA-3679-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AA-3679-01A-02W-0900-09	TCGA-AA-3679-10A-01W-0900-09	g.chr3:64606905G>A	ENST00000498707.1	-	19	3040	c.2698C>T	c.(2698-2700)Cga>Tga	p.R900*	ADAMTS9_ENST00000295903.4_Nonsense_Mutation_p.R872*	NM_182920.1	NP_891550.1	Q9P2N4	ATS9_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 9	900	TSP type-1 2. {ECO:0000255|PROSITE- ProRule:PRU00210}.				glycoprotein catabolic process (GO:0006516)|multicellular organismal development (GO:0007275)|positive regulation of melanocyte differentiation (GO:0045636)|protein transport (GO:0015031)|proteolysis (GO:0006508)|vesicle-mediated transport (GO:0016192)	endoplasmic reticulum (GO:0005783)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)	p.R900*(1)		breast(3)|central_nervous_system(4)|cervix(1)|endometrium(9)|kidney(4)|large_intestine(17)|liver(4)|lung(43)|ovary(3)|prostate(3)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	100		Lung NSC(201;0.00682)		BRCA - Breast invasive adenocarcinoma(55;0.00142)|Kidney(15;0.00202)|KIRC - Kidney renal clear cell carcinoma(15;0.00221)		ACAAGTTTTCGTTTCCGTTCC	0.423																																					p.R900X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.C2698T	3						.						57.0	57.0	57.0					3																	64606905		2203	4300	6503	64581945	SO:0001587	stop_gained	56999	exon19			AF261918	CCDS2903.1	3p14.1	2008-05-15	2005-08-19		ENSG00000163638	ENSG00000163638		"""ADAM metallopeptidases with thrombospondin type 1 motif"""	13202	protein-coding gene	gene with protein product		605421	"""a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 9"""			10936055	Standard	NM_182920		Approved	KIAA1312	uc003dmg.3	Q9P2N4	OTTHUMG00000158722	ENST00000498707.1:c.2698C>T	3.37:g.64606905G>A	ENSP00000418735:p.Arg900*		64581945	NM_182920	A1L4L0|B7ZVX9|B9ZVN0|Q9NR29	Nonsense_Mutation	SNP	ENST00000498707.1	37	CCDS2903.1	.	.	.	.	.	.	.	.	.	.	G	40	8.201228	0.98704	.	.	ENSG00000163638	ENST00000295903;ENST00000498707	.	.	.	5.96	3.96	0.45880	.	0.000000	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	13.6819	0.62491	0.0:0.0:0.5993:0.4007	.	.	.	.	X	872;900	.	ENSP00000295903:R872X	R	-	1	2	ADAMTS9	64581945	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	3.292000	0.51772	1.466000	0.48025	0.585000	0.79938	CGA		0.423	ADAMTS9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351891.1		
ARHGAP31	57514	broad.mit.edu	37	3	119134369	119134369	+	Frame_Shift_Del	DEL	G	G	-			TCGA-AA-3679-01A-02W-0900-09	TCGA-AA-3679-10A-01W-0900-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3679-01A-02W-0900-09	TCGA-AA-3679-10A-01W-0900-09	g.chr3:119134369delG	ENST00000264245.4	+	12	4125	c.3593delG	c.(3592-3594)aggfs	p.R1198fs		NM_020754.2	NP_065805.2	Q2M1Z3	RHG31_HUMAN	Rho GTPase activating protein 31	1198					regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cell junction (GO:0030054)|cytosol (GO:0005829)|lamellipodium (GO:0030027)	GTPase activator activity (GO:0005096)	p.A1199fs*106(1)		breast(5)|central_nervous_system(1)|cervix(1)|endometrium(10)|kidney(3)|large_intestine(11)|lung(29)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	67						TGCCAGGCCAGGGCGGTCCCA	0.582																																					p.R1198fs	Pancreas(7;176 297 5394 51128 51241)											.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.3593delG	3						.						53.0	58.0	56.0					3																	119134369		2031	4190	6221	120617059	SO:0001589	frameshift_variant	57514	exon12				CCDS43135.1	3q13.33	2011-06-29			ENSG00000031081	ENSG00000031081		"""Rho GTPase activating proteins"""	29216	protein-coding gene	gene with protein product		610911				9786927, 12819203, 16519628	Standard	NM_020754		Approved	CDGAP	uc003ecj.4	Q2M1Z3	OTTHUMG00000159362	ENST00000264245.4:c.3593delG	3.37:g.119134369delG	ENSP00000264245:p.Arg1198fs		120617059	NM_020754	Q9ULL6	Frame_Shift_Del	DEL	ENST00000264245.4	37	CCDS43135.1																																																																																				0.582	ARHGAP31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354942.2		
PCYT1A	5130	broad.mit.edu	37	3	195997349	195997349	+	Silent	SNP	C	C	T	rs200496999	byFrequency	TCGA-AA-3679-01A-02W-0900-09	TCGA-AA-3679-10A-01W-0900-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3679-01A-02W-0900-09	TCGA-AA-3679-10A-01W-0900-09	g.chr3:195997349C>T	ENST00000292823.2	-	3	226	c.54G>A	c.(52-54)gcG>gcA	p.A18A	PCYT1A_ENST00000491544.1_5'UTR|RP11-447L10.1_ENST00000431391.1_3'UTR|PCYT1A_ENST00000419333.1_Silent_p.A18A|PCYT1A_ENST00000431016.1_Silent_p.A18A	NM_005017.2	NP_005008.2	P49585	PCY1A_HUMAN	phosphate cytidylyltransferase 1, choline, alpha	18					CDP-choline pathway (GO:0006657)|glycerophospholipid biosynthetic process (GO:0046474)|phosphatidylcholine biosynthetic process (GO:0006656)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum membrane (GO:0005789)|glycogen granule (GO:0042587)	choline-phosphate cytidylyltransferase activity (GO:0004105)|lipid binding (GO:0008289)	p.A18A(2)		cervix(1)|endometrium(3)|large_intestine(8)|lung(5)|ovary(1)	18	all_cancers(143;1.19e-08)|Ovarian(172;0.0634)|Breast(254;0.206)		Epithelial(36;1.28e-24)|all cancers(36;1.01e-22)|OV - Ovarian serous cystadenocarcinoma(49;3.88e-19)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.00259)	Choline(DB00122)|Lamivudine(DB00709)	TGGGTCCGGGCGCCTCTTTTC	0.483													C|||	2	0.000399361	0.0	0.0014	5008	,	,		18184	0.0		0.0	False		,,,				2504	0.001				p.A18A												.	.	2	Substitution - coding silent(2)	large_intestine(1)|lung(1)	c.G54A	3						.						232.0	231.0	232.0					3																	195997349		2203	4300	6503	197481746	SO:0001819	synonymous_variant	5130	exon3			L28957	CCDS3315.1	3q29	2010-07-19	2005-09-05		ENSG00000161217	ENSG00000161217	2.7.7.15		8754	protein-coding gene	gene with protein product	"""phosphate cytidylyltransferase 1, choline, alpha isoform"""	123695	"""phosphate cytidylyltransferase 1, choline, alpha isoform"""	PCYT1		7918629	Standard	NM_005017		Approved	CT, CTPCT	uc003fwg.3	P49585	OTTHUMG00000155670	ENST00000292823.2:c.54G>A	3.37:g.195997349C>T			197481746	NM_005017	A9LYK9|D3DXB1|Q86Y88	Silent	SNP	ENST00000292823.2	37	CCDS3315.1																																																																																				0.483	PCYT1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341147.1	NM_005017	
TUBB7P	56604	broad.mit.edu	37	4	190904562	190904562	+	IGR	SNP	C	C	G	rs531850339	byFrequency	TCGA-AA-3679-01A-02W-0900-09	TCGA-AA-3679-10A-01W-0900-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3679-01A-02W-0900-09	TCGA-AA-3679-10A-01W-0900-09	g.chr4:190904562C>G								FRG1 (20203 upstream) : RNA5SP174 (31730 downstream)														p.G140R(1)									CCAGTCCCCCCACCCAGGGAG	0.562													.|||	4	0.000798722	0.0008	0.0	5008	,	,		15673	0.002		0.0	False		,,,				2504	0.001				p.W140S												.	.	1	Substitution - Missense(1)	endometrium(1)	c.G419C	4						.						7.0	10.0	9.0					4																	190904562		1902	3990	5892	191141556	SO:0001628	intergenic_variant	56604	exon4																															4.37:g.190904562C>G			191141556	NM_020040		Missense_Mutation	SNP		37																																																																																				0	0.562								
APC	324	broad.mit.edu	37	5	112128143	112128143	+	Splice_Site	SNP	C	C	T	rs62619935		TCGA-AA-3679-01A-02W-0900-09	TCGA-AA-3679-10A-01W-0900-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3679-01A-02W-0900-09	TCGA-AA-3679-10A-01W-0900-09	g.chr5:112128143C>T	ENST00000457016.1	+	7	1026	c.646C>T	c.(646-648)Cga>Tga	p.R216*	APC_ENST00000508376.2_Splice_Site_p.R216*|APC_ENST00000257430.4_Splice_Site_p.R216*			P25054	APC_HUMAN	adenomatous polyposis coli	216	Leu-rich.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.R216*(12)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		TTTATTTTAGCGAAGAATAGC	0.323		12	"""D, Mis, N, F, S"""		"""colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"""	"""colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"""			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											p.R216X	NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"""E, M, O"""	.	.	12	Substitution - Nonsense(12)	large_intestine(12)	c.C646T	5	GRCh37	CM992133	APC	M	rs62619935	.						52.0	51.0	51.0					5																	112128143		2202	4300	6502	112156042	SO:0001630	splice_region_variant	324	exon8	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"", ""Armadillo repeat containing"""	583	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 46"""	611731	"""adenomatosis polyposis coli"""			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.646-1C>T	5.37:g.112128143C>T			112156042	NM_001127510	D3DT03|Q15162|Q15163|Q93042	Nonsense_Mutation	SNP	ENST00000457016.1	37	CCDS4107.1	.	.	.	.	.	.	.	.	.	.	C	39	7.466758	0.98302	.	.	ENSG00000134982	ENST00000457016;ENST00000257430;ENST00000508376;ENST00000512211	.	.	.	5.19	2.99	0.34606	.	0.630262	0.16042	N	0.232387	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-5.2274	1.7088	0.02888	0.2899:0.3634:0.2259:0.1208	rs62619935	.	.	.	X	216	.	.	R	+	1	2	APC	112156042	1.000000	0.71417	1.000000	0.80357	0.934000	0.57294	0.662000	0.25038	1.304000	0.44892	-0.158000	0.13435	CGA		0.323	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038	Nonsense_Mutation
APC	324	broad.mit.edu	37	5	112175212	112175216	+	Frame_Shift_Del	DEL	AAAAG	AAAAG	-	rs121913224		TCGA-AA-3679-01A-02W-0900-09	TCGA-AA-3679-10A-01W-0900-09	AAAAG	AAAAG					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3679-01A-02W-0900-09	TCGA-AA-3679-10A-01W-0900-09	g.chr5:112175212_112175216delAAAAG	ENST00000457016.1	+	16	4301_4305	c.3921_3925delAAAAG	c.(3919-3927)ataaaagaafs	p.KE1308fs	APC_ENST00000508376.2_Frame_Shift_Del_p.KE1308fs|APC_ENST00000257430.4_Frame_Shift_Del_p.KE1308fs|CTC-554D6.1_ENST00000520401.1_Intron			P25054	APC_HUMAN	adenomatous polyposis coli	1308	Responsible for down-regulation through a process mediated by direct ubiquitination.|Ser-rich.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.E1309fs*6(51)|p.E1309fs*4(42)|p.E1309*(25)|p.I1307fs*6(12)|p.K1308*(6)|p.I1307fs*7(2)|p.I1311fs*4(2)|p.K1308fs*6(1)|p.I1307fs*13(1)|p.?(1)|p.E1309fs*5(1)|p.K1192fs*3(1)|p.?fs(1)|p.E1309K(1)|p.K1308E(1)|p.K1308fs*4(1)|p.I1307fs*14(1)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		TAGCAGAAATAAAAGAAAAGATTGG	0.424		12	"""D, Mis, N, F, S"""		"""colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"""	"""colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"""			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											p.1289_1291del	NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"""E, M, O"""	APC,large_intestine,colon,Substitution - Nonsense,-1 	.	150	Deletion - Frameshift(61)|Insertion - Frameshift(54)|Substitution - Nonsense(31)|Substitution - Missense(2)|Unknown(1)|Complex - frameshift(1)	large_intestine(145)|stomach(2)|upper_aerodigestive_tract(1)|soft_tissue(1)|skin(1)	c.3867_3871del	5	GRCh37	CD040160|CD084022|CD941590|CD972006|CM086765|CM920052	APC	D|M		.																																			112203115	SO:0001589	frameshift_variant	324	exon14	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"", ""Armadillo repeat containing"""	583	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 46"""	611731	"""adenomatosis polyposis coli"""			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.3921_3925delAAAAG	5.37:g.112175217_112175221delAAAAG	ENSP00000413133:p.Lys1308fs		112203111	NM_001127511	D3DT03|Q15162|Q15163|Q93042	Frame_Shift_Del	DEL	ENST00000457016.1	37	CCDS4107.1																																																																																				0.424	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038	
HIST1H2BM	8342	broad.mit.edu	37	6	27783025	27783025	+	Silent	SNP	C	C	T	rs140232303		TCGA-AA-3679-01A-02W-0900-09	TCGA-AA-3679-10A-01W-0900-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3679-01A-02W-0900-09	TCGA-AA-3679-10A-01W-0900-09	g.chr6:27783025C>T	ENST00000359465.4	+	1	204	c.204C>T	c.(202-204)aaC>aaT	p.N68N	HIST1H2AJ_ENST00000333151.3_5'Flank	NM_003521.2	NP_003512.1	Q99879	H2B1M_HUMAN	histone cluster 1, H2bm	68					chromatin organization (GO:0006325)|nucleosome assembly (GO:0006334)	extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|nucleosome (GO:0000786)|nucleus (GO:0005634)	DNA binding (GO:0003677)	p.N68N(1)		NS(1)|breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(2)	12						CCTTCGTCAACGACATCTTTG	0.562																																					p.N68N												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C204T	6						.						153.0	140.0	145.0					6																	27783025		2203	4300	6503	27891004	SO:0001819	synonymous_variant	8342	exon1			Z83738	CCDS4629.1	6p22.1	2011-01-27	2006-10-11	2003-02-28	ENSG00000196374	ENSG00000273703		"""Histones / Replication-dependent"""	4750	protein-coding gene	gene with protein product		602802	"""H2B histone family, member E"", ""histone 1, H2bm"""	H2BFE		9439656, 12408966	Standard	NM_003521		Approved	H2B/e, dJ160A22.3	uc003njo.3	Q99879	OTTHUMG00000014489	ENST00000359465.4:c.204C>T	6.37:g.27783025C>T			27891004	NM_003521	Q6NWQ3	Silent	SNP	ENST00000359465.4	37	CCDS4629.1																																																																																				0.562	HIST1H2BM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040157.1	NM_003521	
NELFE	7936	broad.mit.edu	37	6	31922416	31922417	+	Silent	DNP	GA	GA	TG			TCGA-AA-3679-01A-02W-0900-09	TCGA-AA-3679-10A-01W-0900-09	GA	GA					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3679-01A-02W-0900-09	TCGA-AA-3679-10A-01W-0900-09	g.chr6:31922416_31922417GA>TG	ENST00000375429.3	-	7	883_884	c.657_658TC>CA	c.(655-660)gaTCgg>gaCAgg	p.219_220DR>DR	NELFE_ENST00000375425.5_Silent_p.226_227DR>DR|NELFE_ENST00000444811.2_Silent_p.189_190DR>DR|MIR1236_ENST00000408340.1_RNA	NM_002904.5	NP_002895.3	P18615	NELFE_HUMAN	negative elongation factor complex member E	219	30 X 2 AA approximate tandem repeats of R-[DSNE].				gene expression (GO:0010467)|negative regulation of transcription elongation from RNA polymerase II promoter (GO:0034244)|positive regulation of viral transcription (GO:0050434)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|viral process (GO:0016032)	NELF complex (GO:0032021)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)	p.D219>?(1)									tcccgatcccgatccctgtccc	0.639																																					.												.	.	1	Complex(1)	large_intestine(1)	c.657_658CA	6						.																																			32030396	SO:0001819	synonymous_variant	7936	exon7			M33230	CCDS4730.1	6p21.3	2013-02-12	2013-01-31	2013-01-31	ENSG00000204356	ENSG00000204356		"""RNA binding motif (RRM) containing"""	13974	protein-coding gene	gene with protein product		154040	"""RD RNA-binding protein"", ""RD RNA binding protein"""	RDBP			Standard	XM_006715205		Approved	RD, D6S45, NELF-E, RDP	uc003nyk.3	P18615	OTTHUMG00000031046	ENST00000375429.3:c.657_658delinsTG	6.37:g.31922416_31922417delinsTG			32030395	NM_002904	A2BE08|B4DUN1|B4DYX9|Q5JP74|Q5JP75|Q96F56|Q9NPK2	Silent	DNP	ENST00000375429.3	37	CCDS4730.1																																																																																				0.639	NELFE-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000076047.4		
KCNK17	89822	broad.mit.edu	37	6	39272407	39272407	+	Missense_Mutation	SNP	G	G	A	rs376144090		TCGA-AA-3679-01A-02W-0900-09	TCGA-AA-3679-10A-01W-0900-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3679-01A-02W-0900-09	TCGA-AA-3679-10A-01W-0900-09	g.chr6:39272407G>A	ENST00000373231.4	-	3	609	c.377C>T	c.(376-378)aCg>aTg	p.T126M	KCNK17_ENST00000453413.2_Missense_Mutation_p.T126M	NM_031460.3	NP_113648.2	Q96T54	KCNKH_HUMAN	potassium channel, subfamily K, member 17	126					potassium ion transport (GO:0006813)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	potassium channel activity (GO:0005267)|voltage-gated ion channel activity (GO:0005244)	p.T126M(1)		endometrium(1)|kidney(1)|large_intestine(3)|lung(6)|ovary(1)|skin(2)	14						GGCAGCCATCGTGTTGGGGCT	0.617																																					p.T126M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C377T	6						.						132.0	132.0	132.0					6																	39272407		2203	4300	6503	39380385	SO:0001583	missense	89822	exon3			AF358910	CCDS4842.1, CCDS47419.1	6p21	2012-03-07			ENSG00000124780	ENSG00000124780		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels, Two-P"""	14465	protein-coding gene	gene with protein product		607370				16382106	Standard	NM_031460		Approved	K2p17.1, TALK-2, TALK2, TASK4, TASK-4	uc003ooo.3	Q96T54	OTTHUMG00000014646	ENST00000373231.4:c.377C>T	6.37:g.39272407G>A	ENSP00000362328:p.Thr126Met		39380385	NM_031460	E9PB46|Q5TCF4|Q8TAW4|Q9BXD1|Q9H592	Missense_Mutation	SNP	ENST00000373231.4	37	CCDS4842.1	.	.	.	.	.	.	.	.	.	.	G	16.49	3.138888	0.56936	.	.	ENSG00000124780	ENST00000373231;ENST00000453413	T;T	0.35236	1.32;1.32	4.87	3.99	0.46301	Ion transport 2 (1);	0.106404	0.38058	N	0.001831	T	0.60996	0.2312	H	0.96333	3.805	0.24601	N	0.993771	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	T	0.64516	-0.6389	10	0.87932	D	0	.	12.6479	0.56746	0.0:0.1662:0.8338:0.0	.	126;126	E9PB46;Q96T54	.;KCNKH_HUMAN	M	126	ENSP00000362328:T126M;ENSP00000401271:T126M	ENSP00000362328:T126M	T	-	2	0	KCNK17	39380385	1.000000	0.71417	0.010000	0.14722	0.597000	0.36814	6.211000	0.72182	1.013000	0.39391	0.561000	0.74099	ACG		0.617	KCNK17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040453.2	NM_031460	
BAI3	577	broad.mit.edu	37	6	69945014	69945014	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3679-01A-02W-0900-09	TCGA-AA-3679-10A-01W-0900-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AA-3679-01A-02W-0900-09	TCGA-AA-3679-10A-01W-0900-09	g.chr6:69945014G>T	ENST00000370598.1	+	19	3519	c.2698G>T	c.(2698-2700)Gca>Tca	p.A900S	BAI3_ENST00000238918.8_Missense_Mutation_p.A106S	NM_001704.2	NP_001695	O60242	BAI3_HUMAN	brain-specific angiogenesis inhibitor 3	900					G-protein coupled receptor signaling pathway (GO:0007186)|negative regulation of angiogenesis (GO:0016525)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)	p.A900S(1)		NS(2)|breast(4)|central_nervous_system(5)|endometrium(5)|kidney(2)|large_intestine(28)|liver(1)|lung(111)|ovary(10)|pancreas(4)|prostate(7)|skin(22)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(4)	210		all_lung(197;0.212)				AGTTGTCTATGCAGCATTATG	0.383																																					p.A900S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2698T	6						.						229.0	213.0	218.0					6																	69945014		2203	4300	6503	70001735	SO:0001583	missense	577	exon19			AB005299	CCDS4968.1	6q12	2014-08-08			ENSG00000135298	ENSG00000135298		"""-"", ""GPCR / Class B : Orphans"""	945	protein-coding gene	gene with protein product		602684				9533023	Standard	NM_001704		Approved	KIAA0550	uc003pev.4	O60242	OTTHUMG00000014982	ENST00000370598.1:c.2698G>T	6.37:g.69945014G>T	ENSP00000359630:p.Ala900Ser		70001735	NM_001704	B7Z1K0|O60297|Q2NKN6|Q5VY37|Q9BX54	Missense_Mutation	SNP	ENST00000370598.1	37	CCDS4968.1	.	.	.	.	.	.	.	.	.	.	G	15.54	2.865229	0.51482	.	.	ENSG00000135298	ENST00000370598;ENST00000238918	T;T	0.37411	1.2;1.2	5.81	5.81	0.92471	GPCR, family 2-like (1);	0.053226	0.64402	D	0.000001	T	0.28466	0.0704	L	0.35793	1.09	0.80722	D	1	B;B;P	0.50819	0.393;0.089;0.939	B;B;P	0.45753	0.253;0.187;0.492	T	0.02852	-1.1102	10	0.54805	T	0.06	.	20.0805	0.97772	0.0:0.0:1.0:0.0	.	106;900;900	B7Z356;A8K0Y1;O60242	.;.;BAI3_HUMAN	S	900;106	ENSP00000359630:A900S;ENSP00000238918:A106S	ENSP00000238918:A106S	A	+	1	0	BAI3	70001735	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	8.062000	0.89475	2.755000	0.94549	0.650000	0.86243	GCA		0.383	BAI3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041120.1		
IGF2R	3482	broad.mit.edu	37	6	160454078	160454078	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3679-01A-02W-0900-09	TCGA-AA-3679-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AA-3679-01A-02W-0900-09	TCGA-AA-3679-10A-01W-0900-09	g.chr6:160454078G>A	ENST00000356956.1	+	9	1298	c.1150G>A	c.(1150-1152)Gtg>Atg	p.V384M		NM_000876.2	NP_000867	P11717	MPRI_HUMAN	insulin-like growth factor 2 receptor	384					insulin-like growth factor receptor signaling pathway (GO:0048009)|liver development (GO:0001889)|organ regeneration (GO:0031100)|positive regulation of apoptotic process (GO:0043065)|post-embryonic development (GO:0009791)|receptor-mediated endocytosis (GO:0006898)|response to retinoic acid (GO:0032526)|signal transduction (GO:0007165)|spermatogenesis (GO:0007283)	cell surface (GO:0009986)|clathrin coat (GO:0030118)|endocytic vesicle (GO:0030139)|endosome (GO:0005768)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|late endosome (GO:0005770)|lysosome (GO:0005764)|membrane (GO:0016020)|nuclear envelope lumen (GO:0005641)|perinuclear region of cytoplasm (GO:0048471)|trans-Golgi network transport vesicle (GO:0030140)	G-protein coupled receptor activity (GO:0004930)|glycoprotein binding (GO:0001948)|identical protein binding (GO:0042802)|insulin-like growth factor-activated receptor activity (GO:0005010)|mannose binding (GO:0005537)|phosphoprotein binding (GO:0051219)|receptor activity (GO:0004872)|retinoic acid binding (GO:0001972)|transporter activity (GO:0005215)	p.V384M(1)		breast(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(27)|lung(31)|ovary(3)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	95		Breast(66;0.000777)|Ovarian(120;0.0305)		OV - Ovarian serous cystadenocarcinoma(65;2.45e-17)|BRCA - Breast invasive adenocarcinoma(81;1.09e-05)	Mecasermin(DB01277)	AGTTTGCCAAGTGAAAAAGAG	0.378																																					p.V384M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1150A	6						.						92.0	88.0	89.0					6																	160454078		2203	4300	6503	160374068	SO:0001583	missense	3482	exon9			J03528	CCDS5273.1	6q25.3	2014-09-16			ENSG00000197081	ENSG00000197081		"""CD molecules"""	5467	protein-coding gene	gene with protein product	"""cation-independent mannose-6 phosphate receptor"""	147280					Standard	NM_000876		Approved	CD222, MPRI, MPR1, CIMPR, M6P-R	uc003qta.3	P11717	OTTHUMG00000015945	ENST00000356956.1:c.1150G>A	6.37:g.160454078G>A	ENSP00000349437:p.Val384Met		160374068	NM_000876	Q7Z7G9|Q96PT5	Missense_Mutation	SNP	ENST00000356956.1	37	CCDS5273.1	.	.	.	.	.	.	.	.	.	.	G	13.80	2.346076	0.41599	.	.	ENSG00000197081	ENST00000356956	T	0.03272	3.99	4.81	3.89	0.44902	Mannose-6-phosphate receptor, binding (1);	0.401868	0.25148	N	0.032763	T	0.07999	0.0200	M	0.81614	2.55	0.36501	D	0.869014	D	0.61080	0.989	D	0.64144	0.922	T	0.10847	-1.0612	10	0.34782	T	0.22	-8.3593	10.7206	0.46038	0.0948:0.0:0.9052:0.0	.	384	P11717	MPRI_HUMAN	M	384	ENSP00000349437:V384M	ENSP00000349437:V384M	V	+	1	0	IGF2R	160374068	1.000000	0.71417	0.720000	0.30636	0.027000	0.11550	3.948000	0.56660	1.067000	0.40740	-0.345000	0.07892	GTG		0.378	IGF2R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042931.1	NM_000876	
DDC	1644	broad.mit.edu	37	7	50607722	50607722	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3679-01A-02W-0900-09	TCGA-AA-3679-10A-01W-0900-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3679-01A-02W-0900-09	TCGA-AA-3679-10A-01W-0900-09	g.chr7:50607722G>A	ENST00000444124.2	-	3	406	c.206C>T	c.(205-207)aCg>aTg	p.T69M	DDC_ENST00000426377.1_Intron|DDC_ENST00000431062.1_Missense_Mutation_p.T69M|DDC_ENST00000380984.4_Missense_Mutation_p.T69M|DDC_ENST00000357936.5_Missense_Mutation_p.T69M|AC018705.5_ENST00000454521.1_RNA|DDC_ENST00000489162.1_5'UTR	NM_001082971.1	NP_001076440	P20711	DDC_HUMAN	dopa decarboxylase (aromatic L-amino acid decarboxylase)	69	2 X approximate tandem repeats.				catecholamine biosynthetic process (GO:0042423)|cellular amino acid metabolic process (GO:0006520)|cellular nitrogen compound metabolic process (GO:0034641)|cellular response to alkaloid (GO:0071312)|cellular response to drug (GO:0035690)|cellular response to growth factor stimulus (GO:0071363)|circadian rhythm (GO:0007623)|dopamine biosynthetic process (GO:0042416)|indolalkylamine biosynthetic process (GO:0046219)|isoquinoline alkaloid metabolic process (GO:0033076)|multicellular organismal aging (GO:0010259)|phytoalexin metabolic process (GO:0052314)|response to pyrethroid (GO:0046684)|serotonin biosynthetic process (GO:0042427)|small molecule metabolic process (GO:0044281)|synaptic vesicle amine transport (GO:0015842)	axon (GO:0030424)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|neuronal cell body (GO:0043025)|synaptic vesicle (GO:0008021)	amino acid binding (GO:0016597)|aromatic-L-amino-acid decarboxylase activity (GO:0004058)|enzyme binding (GO:0019899)|L-dopa decarboxylase activity (GO:0036468)|pyridoxal phosphate binding (GO:0030170)	p.T69M(1)		breast(1)|endometrium(4)|kidney(3)|large_intestine(2)|lung(23)|ovary(4)|skin(2)|stomach(1)	40	Glioma(55;0.08)|all_neural(89;0.245)				Amantadine(DB00915)|Carbidopa(DB00190)|Cycloserine(DB00260)|Droxidopa(DB06262)|Flupentixol(DB00875)|L-DOPA(DB01235)|L-Tryptophan(DB00150)|Methyldopa(DB00968)	GTGCCAGTGCGTCACCTGCAT	0.647																																					p.T69M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C206T	7						.						93.0	75.0	81.0					7																	50607722		2202	4300	6502	50575216	SO:0001583	missense	1644	exon3				CCDS5511.1, CCDS56485.1, CCDS56486.1, CCDS56487.1, CCDS75598.1, CCDS75599.1	7p12.1	2012-08-30			ENSG00000132437	ENSG00000132437	4.1.1.28		2719	protein-coding gene	gene with protein product		107930				1612608	Standard	NM_001082971		Approved	AADC	uc003tpf.4	P20711	OTTHUMG00000023353	ENST00000444124.2:c.206C>T	7.37:g.50607722G>A	ENSP00000403644:p.Thr69Met		50575216	NM_000790	C9IYA0|E7ER62|E7EU95|Q16723|Q5W5T9|Q75MJ6	Missense_Mutation	SNP	ENST00000444124.2	37	CCDS5511.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	23.9|23.9	4.476472|4.476472	0.84640|0.84640	.|.	.|.	ENSG00000132437|ENSG00000132437	ENST00000430300|ENST00000357936;ENST00000431062;ENST00000444124;ENST00000380984	.|T;T;T;T	.|0.39787	.|1.06;1.06;1.06;1.06	5.5|5.5	5.5|5.5	0.81552|0.81552	.|Pyridoxal phosphate-dependent transferase, major domain (1);	.|0.045704	.|0.85682	.|D	.|0.000000	T|T	0.76579|0.76579	0.4007|0.4007	H|H	0.95816|0.95816	3.725|3.725	0.58432|0.58432	D|D	0.999999|0.999999	.|D;D	.|0.89917	.|1.0;1.0	.|D;D	.|0.91635	.|0.999;0.999	D|D	0.83972|0.83972	0.0327|0.0327	5|10	.|0.87932	.|D	.|0	-10.3752|-10.3752	19.4023|19.4023	0.94635|0.94635	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|69;69	.|Q53Y41;P20711	.|.;DDC_HUMAN	C|M	35|69	.|ENSP00000350616:T69M;ENSP00000399184:T69M;ENSP00000403644:T69M;ENSP00000370371:T69M	.|ENSP00000350616:T69M	R|T	-|-	1|2	0|0	DDC|DDC	50575216|50575216	1.000000|1.000000	0.71417|0.71417	0.999000|0.999000	0.59377|0.59377	0.920000|0.920000	0.55202|0.55202	6.744000|6.744000	0.74854|0.74854	2.573000|2.573000	0.86826|0.86826	0.655000|0.655000	0.94253|0.94253	CGC|ACG		0.647	DDC-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342593.1		
SEMA3D	223117	broad.mit.edu	37	7	84697536	84697536	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3679-01A-02W-0900-09	TCGA-AA-3679-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AA-3679-01A-02W-0900-09	TCGA-AA-3679-10A-01W-0900-09	g.chr7:84697536G>A	ENST00000284136.6	-	5	603	c.560C>T	c.(559-561)cCt>cTt	p.P187L	SEMA3D_ENST00000444867.1_Missense_Mutation_p.P187L	NM_152754.2	NP_689967.2	O95025	SEM3D_HUMAN	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3D	187	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				cell differentiation (GO:0030154)|nervous system development (GO:0007399)	extracellular region (GO:0005576)|membrane (GO:0016020)	receptor activity (GO:0004872)	p.P187L(1)		NS(1)|breast(2)|cervix(1)|endometrium(9)|kidney(2)|large_intestine(19)|lung(29)|ovary(3)|pancreas(1)|prostate(4)|skin(2)	73						AGGCTGCTGAGGATCGAAAGG	0.348																																					p.P187L	Ovarian(63;442 1191 17318 29975 31528)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C560T	7						.						102.0	100.0	101.0					7																	84697536		2203	4300	6503	84535472	SO:0001583	missense	223117	exon5			BC029590	CCDS34676.1	7q21.11	2013-01-11			ENSG00000153993	ENSG00000153993		"""Semaphorins"", ""Immunoglobulin superfamily / V-set domain containing"""	10726	protein-coding gene	gene with protein product		609907					Standard	NM_152754		Approved	coll-2, Sema-Z2	uc003uic.3	O95025	OTTHUMG00000154569	ENST00000284136.6:c.560C>T	7.37:g.84697536G>A	ENSP00000284136:p.Pro187Leu		84535472	NM_152754	A6NK46|Q6UW77|Q8NCQ1	Missense_Mutation	SNP	ENST00000284136.6	37	CCDS34676.1	.	.	.	.	.	.	.	.	.	.	G	32	5.134607	0.94517	.	.	ENSG00000153993	ENST00000284136;ENST00000444867	T;T	0.36157	1.27;1.27	5.49	5.49	0.81192	WD40/YVTN repeat-like-containing domain (1);Semaphorin/CD100 antigen (4);	0.045565	0.85682	D	0.000000	T	0.72614	0.3482	H	0.94847	3.59	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.80578	-0.1320	10	0.87932	D	0	.	19.7306	0.96180	0.0:0.0:1.0:0.0	.	187;187	C9JYT6;O95025	.;SEM3D_HUMAN	L	187	ENSP00000284136:P187L;ENSP00000401366:P187L	ENSP00000284136:P187L	P	-	2	0	SEMA3D	84535472	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	9.407000	0.97325	2.707000	0.92482	0.655000	0.94253	CCT		0.348	SEMA3D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336084.2	NM_152754	
MFHAS1	9258	broad.mit.edu	37	8	8747813	8747813	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3679-01A-02W-0900-09	TCGA-AA-3679-10A-01W-0900-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AA-3679-01A-02W-0900-09	TCGA-AA-3679-10A-01W-0900-09	g.chr8:8747813T>C	ENST00000276282.6	-	1	3342	c.2756A>G	c.(2755-2757)tAt>tGt	p.Y919C		NM_004225.2	NP_004216.2	Q9Y4C4	MFHA1_HUMAN	malignant fibrous histiocytoma amplified sequence 1	919								p.Y919C(1)		endometrium(1)|kidney(3)|large_intestine(7)|lung(6)|ovary(1)|prostate(2)|stomach(1)	21		Hepatocellular(245;0.217)		COAD - Colon adenocarcinoma(149;0.124)		TTTCCCTCTATAGGCAAAGAT	0.473																																					p.Y919C	Melanoma(103;1201 2045 17515 28966)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A2756G	8						.						80.0	83.0	82.0					8																	8747813		2203	4300	6503	8785223	SO:0001583	missense	9258	exon1			AB016816	CCDS34844.1	8p23.1	2014-03-07			ENSG00000147324	ENSG00000147324			16982	protein-coding gene	gene with protein product	"""leucine rich repeat containing 65"", ""malignant fibrous histiocytoma-amplified sequences with leucine-rich tandem repeats 1"""	605352				9973190	Standard	NM_004225		Approved	MASL1, LRRC65	uc003wsj.1	Q9Y4C4	OTTHUMG00000163676	ENST00000276282.6:c.2756A>G	8.37:g.8747813T>C	ENSP00000276282:p.Tyr919Cys		8785223	NM_004225	Q96CI0	Missense_Mutation	SNP	ENST00000276282.6	37	CCDS34844.1	.	.	.	.	.	.	.	.	.	.	T	15.89	2.967418	0.53507	.	.	ENSG00000147324	ENST00000276282	T	0.37584	1.19	4.98	3.83	0.44106	.	0.076976	0.53938	D	0.000048	T	0.35098	0.0920	M	0.66939	2.045	0.53688	D	0.999972	B	0.14805	0.011	B	0.15052	0.012	T	0.14090	-1.0485	10	0.39692	T	0.17	.	9.782	0.40653	0.0:0.0805:0.0:0.9195	.	919	Q9Y4C4	MFHA1_HUMAN	C	919	ENSP00000276282:Y919C	ENSP00000276282:Y919C	Y	-	2	0	MFHAS1	8785223	1.000000	0.71417	0.014000	0.15608	0.934000	0.57294	7.448000	0.80631	0.948000	0.37687	0.533000	0.62120	TAT		0.473	MFHAS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374724.2	NM_004225	
PRKDC	5591	broad.mit.edu	37	8	48706925	48706925	+	Silent	SNP	G	G	C			TCGA-AA-3679-01A-02W-0900-09	TCGA-AA-3679-10A-01W-0900-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3679-01A-02W-0900-09	TCGA-AA-3679-10A-01W-0900-09	g.chr8:48706925G>C	ENST00000314191.2	-	75	10649	c.10593C>G	c.(10591-10593)ccC>ccG	p.P3531P	PRKDC_ENST00000338368.3_Silent_p.P3531P|PRKDC_ENST00000523565.1_5'UTR	NM_006904.6	NP_008835.5	P78527	PRKDC_HUMAN	protein kinase, DNA-activated, catalytic polypeptide	3532	FAT. {ECO:0000255|PROSITE- ProRule:PRU00534}.				B cell lineage commitment (GO:0002326)|brain development (GO:0007420)|cellular protein modification process (GO:0006464)|cellular response to insulin stimulus (GO:0032869)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via nonhomologous end joining (GO:0006303)|ectopic germ cell programmed cell death (GO:0035234)|heart development (GO:0007507)|immunoglobulin V(D)J recombination (GO:0033152)|innate immune response (GO:0045087)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|negative regulation of protein phosphorylation (GO:0001933)|peptidyl-serine phosphorylation (GO:0018105)|positive regulation of apoptotic process (GO:0043065)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon production (GO:0032481)|pro-B cell differentiation (GO:0002328)|protein destabilization (GO:0031648)|regulation of circadian rhythm (GO:0042752)|response to gamma radiation (GO:0010332)|rhythmic process (GO:0048511)|signal transduction involved in mitotic G1 DNA damage checkpoint (GO:0072431)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell receptor V(D)J recombination (GO:0033153)|telomere maintenance (GO:0000723)	cytosol (GO:0005829)|DNA-dependent protein kinase-DNA ligase 4 complex (GO:0005958)|membrane (GO:0016020)|nonhomologous end joining complex (GO:0070419)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA-dependent protein kinase activity (GO:0004677)|poly(A) RNA binding (GO:0044822)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|transcription factor binding (GO:0008134)	p.P3531P(1)|p.P3532P(1)		NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(9)|cervix(3)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(30)|lung(56)|ovary(6)|pancreas(1)|prostate(8)|skin(7)	147		all_cancers(86;0.0336)|all_epithelial(80;0.00111)|Lung NSC(129;0.00363)|all_lung(136;0.00391)			Caffeine(DB00201)	TTATGATGAAGGGATAAACAA	0.438								Non-homologous end-joining																													p.P3532R	Esophageal Squamous(79;1091 1253 12329 31680 40677)											.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.C10595G	8						.						98.0	90.0	92.0					8																	48706925		1881	4114	5995	48869478	SO:0001819	synonymous_variant	5591	exon74				CCDS75734.1, CCDS75735.1	8q11	2014-09-17				ENSG00000253729	2.7.11.1		9413	protein-coding gene	gene with protein product		600899		HYRC, HYRC1		7638222	Standard	NM_001081640		Approved	DNPK1, p350, DNAPK, XRCC7, DNA-PKcs	uc003xqi.3	P78527		ENST00000314191.2:c.10593C>G	8.37:g.48706925G>C			48869478	NM_001081640	P78528|Q13327|Q13337|Q14175|Q59H99|Q7Z611|Q96SE6|Q9UME3	Silent	SNP	ENST00000314191.2	37																																																																																					0.438	PRKDC-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_001081640	
MTSS1	9788	broad.mit.edu	37	8	125565357	125565357	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3679-01A-02W-0900-09	TCGA-AA-3679-10A-01W-0900-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3679-01A-02W-0900-09	TCGA-AA-3679-10A-01W-0900-09	g.chr8:125565357C>T	ENST00000518547.1	-	14	2617	c.2144G>A	c.(2143-2145)aGt>aAt	p.S715N	NDUFB9_ENST00000522532.1_Intron|MTSS1_ENST00000378017.3_Missense_Mutation_p.S690N|MTSS1_ENST00000431961.2_Missense_Mutation_p.S433N|MTSS1_ENST00000523587.1_5'UTR|MTSS1_ENST00000354184.4_Missense_Mutation_p.S433N|MTSS1_ENST00000395508.2_Missense_Mutation_p.S489N|MTSS1_ENST00000524090.1_Missense_Mutation_p.S605N|MTSS1_ENST00000325064.5_Missense_Mutation_p.S719N	NM_001282971.1|NM_014751.4	NP_001269900.1|NP_055566.3	O43312	MTSS1_HUMAN	metastasis suppressor 1	715	Pro-rich.				actin cytoskeleton organization (GO:0030036)|actin filament polymerization (GO:0030041)|adherens junction maintenance (GO:0034334)|bone mineralization (GO:0030282)|cell adhesion (GO:0007155)|cellular component movement (GO:0006928)|cellular response to fluid shear stress (GO:0071498)|epithelial cell proliferation involved in renal tubule morphogenesis (GO:2001013)|filopodium assembly (GO:0046847)|glomerulus morphogenesis (GO:0072102)|in utero embryonic development (GO:0001701)|magnesium ion homeostasis (GO:0010960)|microspike assembly (GO:0030035)|negative regulation of epithelial cell proliferation (GO:0050680)|nephron tubule epithelial cell differentiation (GO:0072160)|positive regulation of actin filament bundle assembly (GO:0032233)|renal tubule morphogenesis (GO:0061333)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	actin cytoskeleton (GO:0015629)|adherens junction (GO:0005912)|cytoplasm (GO:0005737)|endocytic vesicle (GO:0030139)|ruffle (GO:0001726)	actin monomer binding (GO:0003785)|identical protein binding (GO:0042802)|receptor binding (GO:0005102)	p.S715N(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(5)|lung(14)|ovary(1)|prostate(2)|skin(1)|stomach(1)|urinary_tract(1)	37	Ovarian(258;0.00438)|all_neural(195;0.00459)|Hepatocellular(40;0.108)		STAD - Stomach adenocarcinoma(47;0.00288)			TGCAGGGTCACTCTCTGGAAT	0.552																																					p.S715N	Esophageal Squamous(160;622 1893 3862 8546 12509)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2144A	8						.						242.0	238.0	240.0					8																	125565357		2203	4300	6503	125634538	SO:0001583	missense	9788	exon14			AF086645	CCDS6353.1, CCDS64968.1, CCDS64969.1	8p22	2008-02-05			ENSG00000170873	ENSG00000170873			20443	protein-coding gene	gene with protein product		608486				12482861, 12082544	Standard	XM_005251111		Approved	KIAA0429, MIMA, MIMB, MIM	uc003yrk.2	O43312	OTTHUMG00000048189	ENST00000518547.1:c.2144G>A	8.37:g.125565357C>T	ENSP00000429064:p.Ser715Asn		125634538	NM_014751	J3KNK6|Q8TCA2|Q96RX2	Missense_Mutation	SNP	ENST00000518547.1	37	CCDS6353.1	.	.	.	.	.	.	.	.	.	.	C	4.698	0.129779	0.08981	.	.	ENSG00000170873	ENST00000378017;ENST00000518547;ENST00000354184;ENST00000395508;ENST00000325064;ENST00000431961;ENST00000524090	T;T;T;T;T;T;T	0.30981	1.52;1.52;1.52;1.52;1.52;1.52;1.51	6.17	5.3	0.74995	.	0.487974	0.20506	N	0.090997	T	0.15392	0.0371	N	0.14661	0.345	0.09310	N	1	B;B;B;B;B;P;B	0.45827	0.0;0.001;0.121;0.001;0.192;0.867;0.001	B;B;B;B;B;B;B	0.39617	0.0;0.001;0.035;0.001;0.07;0.305;0.002	T	0.07635	-1.0762	10	0.25106	T	0.35	-0.7461	5.8121	0.18471	0.1316:0.5835:0.2147:0.0703	.	605;489;690;715;690;433;364	E7EWW5;B7Z3B6;A5YM41;O43312;O43312-4;O43312-2;Q6ZTG0	.;.;.;MTSS1_HUMAN;.;.;.	N	690;715;433;489;719;433;605	ENSP00000367256:S690N;ENSP00000429064:S715N;ENSP00000346119:S433N;ENSP00000378884:S489N;ENSP00000322804:S719N;ENSP00000393606:S433N;ENSP00000428319:S605N	ENSP00000322804:S719N	S	-	2	0	MTSS1	125634538	0.000000	0.05858	0.808000	0.32385	0.064000	0.16182	0.427000	0.21379	1.627000	0.50400	0.655000	0.94253	AGT		0.552	MTSS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109625.3	NM_014751	
DOCK8	81704	broad.mit.edu	37	9	420430	420430	+	Silent	SNP	G	G	A			TCGA-AA-3679-01A-02W-0900-09	TCGA-AA-3679-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AA-3679-01A-02W-0900-09	TCGA-AA-3679-10A-01W-0900-09	g.chr9:420430G>A	ENST00000453981.1	+	31	3982	c.3870G>A	c.(3868-3870)gcG>gcA	p.A1290A	DOCK8_ENST00000432829.2_Silent_p.A1222A|DOCK8_ENST00000469391.1_Silent_p.A1190A|DOCK8_ENST00000493666.2_3'UTR|DOCK8_ENST00000382329.1_Silent_p.A757A			Q8NF50	DOCK8_HUMAN	dedicator of cytokinesis 8	1290					blood coagulation (GO:0007596)|dendritic cell migration (GO:0036336)|immunological synapse formation (GO:0001771)|memory T cell proliferation (GO:0061485)|negative regulation of T cell apoptotic process (GO:0070233)|small GTPase mediated signal transduction (GO:0007264)	cell leading edge (GO:0031252)|cytosol (GO:0005829)|membrane (GO:0016020)	guanyl-nucleotide exchange factor activity (GO:0005085)	p.A1222A(1)|p.A1290A(1)		breast(1)|central_nervous_system(5)|endometrium(2)|kidney(6)|large_intestine(13)|lung(22)|ovary(3)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(6)	65		all_cancers(5;2.13e-17)|all_epithelial(5;2.15e-12)|all_lung(10;6.69e-11)|Lung NSC(10;1.08e-10)|Acute lymphoblastic leukemia(5;0.000242)|all_hematologic(5;0.00317)|Breast(48;0.0151)|Prostate(43;0.128)		all cancers(5;9.3e-07)|GBM - Glioblastoma multiforme(5;2.41e-06)|Epithelial(6;0.00557)|Lung(218;0.00942)		TGCTGAACGCGGACACTACTC	0.493																																					p.A1190A												.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.G3570A	9						.						122.0	103.0	109.0					9																	420430		2203	4300	6503	410430	SO:0001819	synonymous_variant	81704	exon29			AK090429	CCDS6440.1, CCDS6440.2, CCDS55283.1, CCDS55284.1	9p24.3	2014-09-17			ENSG00000107099	ENSG00000107099			19191	protein-coding gene	gene with protein product		611432				11214971	Standard	NM_203447		Approved	FLJ00026, FLJ00152, ZIR8, FLJ00346	uc003zgf.2	Q8NF50	OTTHUMG00000078789	ENST00000453981.1:c.3870G>A	9.37:g.420430G>A			410430	NM_001190458	A2A350|A2BDF2|A4FU78|B7ZLP0|E9PH09|Q3MV16|Q5JPJ1|Q8TEP1|Q8WUY2|Q9BYJ5|Q9H1Q2|Q9H1Q3|Q9H308|Q9H7P2	Silent	SNP	ENST00000453981.1	37	CCDS6440.2																																																																																				0.493	DOCK8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000171792.5	XM_036307	
KIAA1045	23349	broad.mit.edu	37	9	34976636	34976636	+	Missense_Mutation	SNP	C	C	T	rs557271865		TCGA-AA-3679-01A-02W-0900-09	TCGA-AA-3679-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AA-3679-01A-02W-0900-09	TCGA-AA-3679-10A-01W-0900-09	g.chr9:34976636C>T	ENST00000242315.3	+	5	830	c.748C>T	c.(748-750)Cgc>Tgc	p.R250C	KIAA1045_ENST00000544237.1_Missense_Mutation_p.R250C|KIAA1045_ENST00000476115.2_3'UTR	NM_015297.1	NP_056112.1	Q9UPV7	K1045_HUMAN	KIAA1045	250							metal ion binding (GO:0046872)	p.R250C(1)		breast(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(4)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	19			LUSC - Lung squamous cell carcinoma(32;0.00575)			GCAGGCGGCCCGCCAGTTTGC	0.622													C|||	1	0.000199681	0.0	0.0	5008	,	,		20025	0.0		0.001	False		,,,				2504	0.0				p.R250C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C748T	9						.						52.0	59.0	57.0					9																	34976636		2015	4154	6169	34966636	SO:0001583	missense	23349	exon5			AB028968	CCDS43796.1	9p13.2	2008-02-05			ENSG00000122733	ENSG00000122733			29180	protein-coding gene	gene with protein product						10470851	Standard	NM_015297		Approved		uc003zvr.3	Q9UPV7	OTTHUMG00000019844	ENST00000242315.3:c.748C>T	9.37:g.34976636C>T	ENSP00000242315:p.Arg250Cys		34966636	NM_015297	B7Z253|Q58FE9|Q5T662	Missense_Mutation	SNP	ENST00000242315.3	37	CCDS43796.1	.	.	.	.	.	.	.	.	.	.	C	21.9	4.211992	0.79240	.	.	ENSG00000122733	ENST00000544237;ENST00000242315	T;T	0.24723	1.84;1.84	4.92	4.92	0.64577	EF-hand-like domain (1);	0.514426	0.20658	N	0.088064	T	0.20536	0.0494	N	0.19112	0.55	0.41134	D	0.985908	P	0.52577	0.954	B	0.43123	0.409	T	0.04065	-1.0980	10	0.56958	D	0.05	-5.5969	15.2674	0.73672	0.0:1.0:0.0:0.0	.	250	Q9UPV7	K1045_HUMAN	C	250	ENSP00000444138:R250C;ENSP00000242315:R250C	ENSP00000242315:R250C	R	+	1	0	KIAA1045	34966636	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	3.712000	0.54875	2.282000	0.76494	0.561000	0.74099	CGC		0.622	KIAA1045-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052256.2	XM_048592	
IARS	3376	broad.mit.edu	37	9	95027380	95027380	+	Missense_Mutation	SNP	G	G	A	rs371250371		TCGA-AA-3679-01A-02W-0900-09	TCGA-AA-3679-10A-01W-0900-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3679-01A-02W-0900-09	TCGA-AA-3679-10A-01W-0900-09	g.chr9:95027380G>A	ENST00000375643.3	-	16	1797	c.1531C>T	c.(1531-1533)Cgc>Tgc	p.R511C	IARS_ENST00000443024.2_Missense_Mutation_p.R511C|IARS_ENST00000375629.3_De_novo_Start_OutOfFrame|IARS_ENST00000447699.2_Missense_Mutation_p.R401C	NM_013417.2	NP_038203.2	P41252	SYIC_HUMAN	isoleucyl-tRNA synthetase	511					gene expression (GO:0010467)|isoleucyl-tRNA aminoacylation (GO:0006428)|osteoblast differentiation (GO:0001649)|tRNA aminoacylation for protein translation (GO:0006418)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	aminoacyl-tRNA editing activity (GO:0002161)|ATP binding (GO:0005524)|isoleucine-tRNA ligase activity (GO:0004822)	p.R511C(1)		breast(3)|endometrium(2)|kidney(4)|large_intestine(7)|lung(14)|ovary(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	35					L-Isoleucine(DB00167)	TTCCCACAGCGTGAAGGAATG	0.423																																					p.R511C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1531T	9						.	G	CYS/ARG,CYS/ARG	0,4406		0,0,2203	67.0	58.0	61.0		1531,1531	5.4	1.0	9		61	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	IARS	NM_013417.2,NM_002161.4	180,180	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	benign,benign	511/1263,511/1263	95027380	1,13005	2203	4300	6503	94067201	SO:0001583	missense	3376	exon16			AB209234	CCDS6694.1	9q21	2011-07-01	2007-02-26		ENSG00000196305	ENSG00000196305	6.1.1.5	"""Aminoacyl tRNA synthetases / Class I"""	5330	protein-coding gene	gene with protein product	"""isoleucine tRNA ligase 1, cytoplasmic"""	600709				8812440	Standard	NM_002161		Approved	ILRS, IARS1	uc004aru.4	P41252	OTTHUMG00000020219	ENST00000375643.3:c.1531C>T	9.37:g.95027380G>A	ENSP00000364794:p.Arg511Cys		94067201	NM_013417	A8KAE9|Q5TCD0|Q7Z3T4|Q9H588	Missense_Mutation	SNP	ENST00000375643.3	37	CCDS6694.1	.	.	.	.	.	.	.	.	.	.	G	16.74	3.208001	0.58343	0.0	1.16E-4	ENSG00000196305	ENST00000375643;ENST00000443024;ENST00000447699;ENST00000375660	T;T;T	0.37411	1.2;1.2;1.2	5.4	5.4	0.78164	Rossmann-like alpha/beta/alpha sandwich fold (1);Aminoacyl-tRNA synthetase, class Ia (1);	0.107205	0.64402	D	0.000004	T	0.40862	0.1134	L	0.58669	1.825	0.80722	D	1	B;B	0.17268	0.01;0.021	B;B	0.20955	0.032;0.013	T	0.28235	-1.0050	10	0.62326	D	0.03	-4.1376	18.7647	0.91868	0.0:0.0:1.0:0.0	.	511;356	P41252;Q6P0M4	SYIC_HUMAN;.	C	511;511;401;511	ENSP00000364794:R511C;ENSP00000406448:R511C;ENSP00000415020:R401C	ENSP00000364794:R511C	R	-	1	0	IARS	94067201	1.000000	0.71417	0.983000	0.44433	0.943000	0.58893	5.473000	0.66774	2.539000	0.85634	0.491000	0.48974	CGC		0.423	IARS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053059.2	NM_002161	
EXOSC2	23404	broad.mit.edu	37	9	133570879	133570879	+	Splice_Site	SNP	G	G	T			TCGA-AA-3679-01A-02W-0900-09	TCGA-AA-3679-10A-01W-0900-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3679-01A-02W-0900-09	TCGA-AA-3679-10A-01W-0900-09	g.chr9:133570879G>T	ENST00000372358.5	+	2	194	c.123G>T	c.(121-123)cgG>cgT	p.R41R	EXOSC2_ENST00000546165.1_Splice_Site_p.R41R|EXOSC2_ENST00000372351.3_Splice_Site_p.R41R|EXOSC2_ENST00000372352.3_Splice_Site_p.R41R			Q13868	EXOS2_HUMAN	exosome component 2	41					exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay (GO:0043928)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|positive regulation of cell growth (GO:0030307)|RNA metabolic process (GO:0016070)|RNA phosphodiester bond hydrolysis, exonucleolytic (GO:0090503)|rRNA processing (GO:0006364)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|exosome (RNase complex) (GO:0000178)|nucleus (GO:0005634)	3'-5'-exoribonuclease activity (GO:0000175)|7S RNA binding (GO:0008312)	p.R41R(1)		breast(1)|endometrium(1)|large_intestine(3)|ovary(1)	6		Acute lymphoblastic leukemia(5;0.0508)|all_hematologic(13;0.0588)		OV - Ovarian serous cystadenocarcinoma(145;0.000324)		CTTGCATCAGGGGCCATGGAA	0.463																																					p.R41R	Pancreas(134;1683 1824 10118 27928 31640)											.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G123T	9						.						203.0	197.0	200.0					9																	133570879		2203	4300	6503	132560700	SO:0001630	splice_region_variant	23404	exon2			AK001916	CCDS6935.1, CCDS65160.1, CCDS65161.1	9q34	2008-02-05			ENSG00000130713	ENSG00000130713			17097	protein-coding gene	gene with protein product	"""homolog of yeast RRP4 (ribosomal RNA processing 4), 3' 5' exoribonuclease (RRP4)"""	602238				8600032, 1538749	Standard	XM_005272176		Approved	hRrp4p, Rrp4p, RRP4, p7	uc004bzu.2	Q13868	OTTHUMG00000020811	ENST00000372358.5:c.123-1G>T	9.37:g.133570879G>T			132560700	NM_014285	A3KFL3|B4DKK6|Q9NUY4	Silent	SNP	ENST00000372358.5	37	CCDS6935.1																																																																																				0.463	EXOSC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054673.1	NM_014285	Silent
POU3F4	5456	broad.mit.edu	37	X	82763392	82763392	+	Silent	SNP	G	G	A			TCGA-AA-3679-01A-02W-0900-09	TCGA-AA-3679-10A-01W-0900-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3679-01A-02W-0900-09	TCGA-AA-3679-10A-01W-0900-09	g.chrX:82763392G>A	ENST00000373200.2	+	1	124	c.60G>A	c.(58-60)gcG>gcA	p.A20A	RP3-326L13.3_ENST00000607789.1_lincRNA|RP3-326L13.2_ENST00000607095.1_RNA	NM_000307.3	NP_000298	P49335	PO3F4_HUMAN	POU class 3 homeobox 4	20					cochlea morphogenesis (GO:0090103)|forebrain neuron differentiation (GO:0021879)|negative regulation of mesenchymal cell apoptotic process (GO:2001054)|sensory perception of sound (GO:0007605)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	AT DNA binding (GO:0003680)|double-stranded DNA binding (GO:0003690)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.A20A(1)		breast(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(10)|lung(14)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)	37						TAGTCCATGCGGACTCTGCGG	0.557																																					p.A20A												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G60A	X						.						62.0	45.0	51.0					X																	82763392		2203	4300	6503	82650048	SO:0001819	synonymous_variant	5456	exon1			X82324	CCDS14450.1	Xq21.1	2011-06-20	2007-07-13		ENSG00000196767	ENSG00000196767		"""Homeoboxes / POU class"""	9217	protein-coding gene	gene with protein product	"""brain-4"""	300039	"""POU domain class 3, transcription factor 4"""	DFN3		7911044, 7581392	Standard	NM_000307		Approved	BRN4, OTF9, DFNX2	uc004eeg.2	P49335	OTTHUMG00000021919	ENST00000373200.2:c.60G>A	X.37:g.82763392G>A			82650048	NM_000307	B2RC71|Q5H9G9|Q99410	Silent	SNP	ENST00000373200.2	37	CCDS14450.1																																																																																				0.557	POU3F4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057368.2	NM_000307	
