#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
ZFP91	80829	broad.mit.edu	37	11	58384886	58384886	+	Missense_Mutation	SNP	G	G	C			TCGA-AA-3860-01A-02W-0900-09	TCGA-AA-3860-10A-01W-0902-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3860-01A-02W-0900-09	TCGA-AA-3860-10A-01W-0902-09	g.chr11:58384886G>C	ENST00000316059.6	+	11	1591	c.1420G>C	c.(1420-1422)Gat>Cat	p.D474H	ZFP91-CNTF_ENST00000389919.4_Missense_Mutation_p.D474H	NM_001197051.1|NM_053023.4	NP_001183980.1|NP_444251.1	Q96JP5	ZFP91_HUMAN	ZFP91 zinc finger protein	474					activation of NF-kappaB-inducing kinase activity (GO:0007250)|protein K63-linked ubiquitination (GO:0070534)	nucleus (GO:0005634)	ligase activity (GO:0016874)|metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)|ubiquitin-protein transferase activity (GO:0004842)	p.D474H(2)		cervix(1)|endometrium(4)|kidney(4)|large_intestine(4)|lung(10)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	26		Breast(21;0.00725)|all_epithelial(135;0.0101)|all_lung(304;0.24)				CACCAGCACAGATATCTTGGG	0.557																																					p.D474H												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G1420C	11						.						61.0	56.0	57.0					11																	58384886		2201	4295	6496	58141462	SO:0001583	missense	80829	exon11			AB056107	CCDS31553.1	11q12	2012-11-27	2012-11-27		ENSG00000186660	ENSG00000186660		"""Zinc fingers, C2H2-type"""	14983	protein-coding gene	gene with protein product			"""zinc finger protein homologous to Zfp91 in mouse"", ""zinc finger protein 91 homolog (mouse)"""			12738986, 20682767	Standard	NM_053023		Approved	PZF, ZNF757	uc001nmx.4	Q96JP5	OTTHUMG00000137391	ENST00000316059.6:c.1420G>C	11.37:g.58384886G>C	ENSP00000339030:p.Asp474His		58141462	NM_053023	A6NHC4|A8MSG7|Q86V47|Q96JP4|Q96QA3	Missense_Mutation	SNP	ENST00000316059.6	37	CCDS31553.1	.	.	.	.	.	.	.	.	.	.	G	19.39	3.819138	0.71028	.	.	ENSG00000186660	ENST00000316059;ENST00000389918	T	0.11930	2.73	6.16	6.16	0.99307	.	0.384489	0.26324	N	0.025022	T	0.28067	0.0692	L	0.27053	0.805	0.47994	D	0.999561	D;D	0.71674	0.998;0.996	D;D	0.74674	0.984;0.965	T	0.00523	-1.1690	10	0.56958	D	0.05	-18.5381	19.6313	0.95704	0.0:0.0:1.0:0.0	.	474;474	Q96JP5-2;Q96JP5	.;ZFP91_HUMAN	H	474	ENSP00000339030:D474H	ENSP00000374569:D474H	D	+	1	0	ZFP91	58141462	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.597000	0.74118	2.937000	0.99478	0.650000	0.86243	GAT		0.557	ZFP91-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268674.1	NM_053023	
ESRRA	2101	broad.mit.edu	37	11	64082666	64082666	+	Silent	SNP	A	A	G			TCGA-AA-3860-01A-02W-0900-09	TCGA-AA-3860-10A-01W-0902-09	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3860-01A-02W-0900-09	TCGA-AA-3860-10A-01W-0902-09	g.chr11:64082666A>G	ENST00000405666.1	+	6	1170	c.936A>G	c.(934-936)ctA>ctG	p.L312L	PRDX5_ENST00000265462.4_5'Flank|PRDX5_ENST00000352435.4_5'Flank|ESRRA_ENST00000406310.1_Silent_p.L311L|PRDX5_ENST00000347941.4_5'Flank|ESRRA_ENST00000000442.6_Silent_p.L312L	NM_001282450.1	NP_001269379.1	P11474	ERR1_HUMAN	estrogen-related receptor alpha	312	Ligand binding domain.				cartilage development (GO:0051216)|gene expression (GO:0010467)|intracellular receptor signaling pathway (GO:0030522)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of cell proliferation (GO:0042127)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|regulation of transcription, DNA-templated (GO:0006355)|transcription initiation from RNA polymerase II promoter (GO:0006367)	intercellular bridge (GO:0045171)|microtubule cytoskeleton (GO:0015630)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|protein domain specific binding (GO:0019904)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding (GO:0043565)|steroid binding (GO:0005496)|steroid hormone receptor activity (GO:0003707)|zinc ion binding (GO:0008270)	p.L312L(1)		endometrium(1)|kidney(1)|large_intestine(4)|lung(8)	14						TGCTGCAACTAGTGCGGCGGC	0.632																																					p.L312L												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.A936G	11						.						22.0	26.0	24.0					11																	64082666		1970	4152	6122	63839242	SO:0001819	synonymous_variant	2101	exon6			X51416, L38487	CCDS41667.1, CCDS60830.1	11q12	2013-01-16			ENSG00000173153	ENSG00000173153		"""Nuclear hormone receptors"""	3471	protein-coding gene	gene with protein product		601998		ESRL1		3267207	Standard	NM_004451		Approved	ERR1, ERRalpha, NR3B1, ERRa	uc001nzq.1	P11474	OTTHUMG00000150641	ENST00000405666.1:c.936A>G	11.37:g.64082666A>G			63839242	NM_004451	Q14514	Silent	SNP	ENST00000405666.1	37	CCDS41667.1	.	.	.	.	.	.	.	.	.	.	A	4.821	0.152670	0.09185	.	.	ENSG00000173153	ENST00000545035	.	.	.	4.14	-1.69	0.08186	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	7.7674	0.28988	0.1792:0.5573:0.2635:0.0	.	.	.	.	W	93	.	.	X	+	2	0	ESRRA	63839242	1.000000	0.71417	0.987000	0.45799	0.861000	0.49209	1.544000	0.36158	-0.417000	0.07461	-0.381000	0.06696	TAG		0.632	ESRRA-003	KNOWN	alternative_5_UTR|NAGNAG_splice_site|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000319304.1	NM_004451	
ATM	472	broad.mit.edu	37	11	108173724	108173724	+	Nonsense_Mutation	SNP	G	G	T			TCGA-AA-3860-01A-02W-0900-09	TCGA-AA-3860-10A-01W-0902-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AA-3860-01A-02W-0900-09	TCGA-AA-3860-10A-01W-0902-09	g.chr11:108173724G>T	ENST00000452508.2	+	37	5653	c.5464G>T	c.(5464-5466)Gaa>Taa	p.E1822*	ATM_ENST00000278616.4_Nonsense_Mutation_p.E1822*			Q13315	ATM_HUMAN	ATM serine/threonine kinase	1822					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.E1822*(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)	CACAAAATGTGAAATTCTTCA	0.333			"""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.E1822X		yes	Rec	yes	Ataxia-telangiectasia	11	11q22.3	472	ataxia telangiectasia mutated		"""L, O"""	.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.G5464T	11						.						117.0	121.0	119.0					11																	108173724		2201	4298	6499	107678934	SO:0001587	stop_gained	472	exon36	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.5464G>T	11.37:g.108173724G>T	ENSP00000388058:p.Glu1822*		107678934	NM_000051	B2RNX5|O15429|Q12758|Q16551|Q93007|Q9NP02|Q9UCX7	Nonsense_Mutation	SNP	ENST00000452508.2	37	CCDS31669.1	.	.	.	.	.	.	.	.	.	.	G	48	14.292628	0.99788	.	.	ENSG00000149311	ENST00000278616;ENST00000452508	.	.	.	5.27	5.27	0.74061	.	0.133684	0.64402	D	0.000002	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.41790	T	0.15	.	19.2496	0.93919	0.0:0.0:1.0:0.0	.	.	.	.	X	1822	.	ENSP00000278616:E1822X	E	+	1	0	ATM	107678934	1.000000	0.71417	1.000000	0.80357	0.973000	0.67179	6.177000	0.71961	2.602000	0.87976	0.650000	0.86243	GAA		0.333	ATM-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389938.1	NM_000051	
NELL2	4753	broad.mit.edu	37	12	45170849	45170849	+	Silent	SNP	A	A	G			TCGA-AA-3860-01A-02W-0900-09	TCGA-AA-3860-10A-01W-0902-09	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3860-01A-02W-0900-09	TCGA-AA-3860-10A-01W-0902-09	g.chr12:45170849A>G	ENST00000429094.2	-	7	1242	c.738T>C	c.(736-738)gaT>gaC	p.D246D	NELL2_ENST00000547172.1_5'Flank|NELL2_ENST00000437801.2_Silent_p.D296D|NELL2_ENST00000452445.2_Silent_p.D246D|NELL2_ENST00000549027.1_Silent_p.D245D|NELL2_ENST00000333837.4_Silent_p.D269D|NELL2_ENST00000551601.1_Silent_p.D245D|NELL2_ENST00000395487.2_Silent_p.D245D	NM_001145108.1	NP_001138580.1	Q99435	NELL2_HUMAN	NEL-like 2 (chicken)	246						extracellular region (GO:0005576)	calcium ion binding (GO:0005509)	p.D296D(1)|p.D246D(1)		NS(1)|breast(3)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(16)|lung(30)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	65	Lung SC(27;0.192)	Lung NSC(34;0.144)		GBM - Glioblastoma multiforme(48;0.092)		TGGCTAAAATATCCTGTAGCT	0.373																																					p.D246D												.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.T738C	12						.						158.0	149.0	152.0					12																	45170849		2203	4300	6503	43457116	SO:0001819	synonymous_variant	4753	exon7			D83018	CCDS8746.1, CCDS44863.1, CCDS44864.1, CCDS53781.1	12q12	2012-01-30	2001-11-28		ENSG00000184613	ENSG00000184613			7751	protein-coding gene	gene with protein product		602320	"""nel (chicken)-like 2"""			19249368	Standard	NM_006159		Approved	NRP2	uc010skz.1	Q99435	OTTHUMG00000169464	ENST00000429094.2:c.738T>C	12.37:g.45170849A>G			43457116	NM_001145108	B7Z2U7|B7Z5Q4|B7Z9J5|B7Z9U3|Q96JS2	Silent	SNP	ENST00000429094.2	37	CCDS8746.1																																																																																				0.373	NELL2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404180.1	NM_006159	
WDR66	144406	broad.mit.edu	37	12	122359575	122359575	+	Missense_Mutation	SNP	T	T	A			TCGA-AA-3860-01A-02W-0900-09	TCGA-AA-3860-10A-01W-0902-09	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3860-01A-02W-0900-09	TCGA-AA-3860-10A-01W-0902-09	g.chr12:122359575T>A	ENST00000288912.4	+	2	1218	c.364T>A	c.(364-366)Tca>Aca	p.S122T	WDR66_ENST00000397454.2_Missense_Mutation_p.S122T	NM_144668.5	NP_653269.3	Q8TBY9	WDR66_HUMAN	WD repeat domain 66	122							calcium ion binding (GO:0005509)	p.S122T(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(11)|liver(2)|lung(13)|ovary(2)|prostate(2)|skin(2)|soft_tissue(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	43	all_neural(191;0.0496)|Medulloblastoma(191;0.0922)			OV - Ovarian serous cystadenocarcinoma(86;0.000155)|Epithelial(86;0.000634)|BRCA - Breast invasive adenocarcinoma(302;0.248)		GTCAATCACATCAGGAATTTT	0.408																																					p.S122T	Esophageal Squamous(85;849 1794 49757 52143)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T364A	12						.						108.0	101.0	103.0					12																	122359575		1919	4146	6065	120843958	SO:0001583	missense	144406	exon2			AL833930	CCDS41853.1, CCDS53840.1	12q24.31	2014-07-31			ENSG00000158023	ENSG00000158023		"""WD repeat domain containing"""	28506	protein-coding gene	gene with protein product						17967944	Standard	NM_001178003		Approved	MGC33630, CaM-IP4	uc009zxk.3	Q8TBY9	OTTHUMG00000168948	ENST00000288912.4:c.364T>A	12.37:g.122359575T>A	ENSP00000288912:p.Ser122Thr		120843958	NM_001178003	C9J1W2|Q8IYA3|Q8N898|Q8NDE7	Missense_Mutation	SNP	ENST00000288912.4	37	CCDS41853.1	.	.	.	.	.	.	.	.	.	.	T	7.179	0.589198	0.13812	.	.	ENSG00000158023	ENST00000288912;ENST00000397454	T;T	0.06449	3.3;3.32	2.06	0.849	0.18972	.	.	.	.	.	T	0.03053	0.0090	N	0.24115	0.695	0.09310	N	1	P	0.37466	0.596	B	0.24006	0.05	T	0.44711	-0.9310	9	0.28530	T	0.3	.	4.969	0.14105	0.0:0.0:0.3184:0.6816	.	122	Q8TBY9	WDR66_HUMAN	T	122	ENSP00000288912:S122T;ENSP00000380595:S122T	ENSP00000288912:S122T	S	+	1	0	WDR66	120843958	0.000000	0.05858	0.001000	0.08648	0.001000	0.01503	0.039000	0.13884	0.240000	0.21263	-0.644000	0.03951	TCA		0.408	WDR66-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401700.1	NM_144668	
IFT88	8100	broad.mit.edu	37	13	21172813	21172813	+	Missense_Mutation	SNP	G	G	C			TCGA-AA-3860-01A-02W-0900-09	TCGA-AA-3860-10A-01W-0902-09	G	G	G	C	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AA-3860-01A-02W-0900-09	TCGA-AA-3860-10A-01W-0902-09	g.chr13:21172813G>C	ENST00000319980.6	+	12	972	c.645G>C	c.(643-645)caG>caC	p.Q215H	IFT88_ENST00000382778.4_Missense_Mutation_p.Q215H|IFT88_ENST00000351808.5_Missense_Mutation_p.Q206H|IFT88_ENST00000537103.1_Missense_Mutation_p.Q187H	NM_175605.3	NP_783195.2	Q13099	IFT88_HUMAN	intraflagellar transport 88	215					anterior/posterior pattern specification (GO:0009952)|cardiac muscle cell differentiation (GO:0055007)|cardiac septum morphogenesis (GO:0060411)|cilium morphogenesis (GO:0060271)|cochlea development (GO:0090102)|cytoplasmic microtubule organization (GO:0031122)|determination of left/right symmetry (GO:0007368)|embryonic digit morphogenesis (GO:0042733)|epidermal stem cell homeostasis (GO:0036334)|epidermis development (GO:0008544)|epithelial cell morphogenesis (GO:0003382)|eye development (GO:0001654)|forebrain morphogenesis (GO:0048853)|heart formation (GO:0060914)|inner ear receptor stereocilium organization (GO:0060122)|kidney development (GO:0001822)|liver development (GO:0001889)|lung vasculature development (GO:0060426)|negative regulation of epithelial cell proliferation (GO:0050680)|Notch signaling pathway (GO:0007219)|palate development (GO:0060021)|pancreas development (GO:0031016)|positive regulation of insulin-like growth factor receptor signaling pathway (GO:0043568)|protein localization (GO:0008104)|regulation of autophagic vacuole assembly (GO:2000785)|regulation of cilium assembly (GO:1902017)|regulation of fat cell differentiation (GO:0045598)|regulation of odontogenesis of dentin-containing tooth (GO:0042487)|regulation of protein processing (GO:0070613)|regulation of smoothened signaling pathway (GO:0008589)|response to fluid shear stress (GO:0034405)|smoothened signaling pathway (GO:0007224)|sperm axoneme assembly (GO:0007288)|spermatid nucleus elongation (GO:0007290)|spinal cord dorsal/ventral patterning (GO:0021513)|telencephalon development (GO:0021537)	acrosomal membrane (GO:0002080)|apical part of cell (GO:0045177)|axonemal basal plate (GO:0097541)|centriole (GO:0005814)|ciliary basal body (GO:0036064)|ciliary base (GO:0097546)|ciliary tip (GO:0097542)|cilium (GO:0005929)|intraciliary transport particle B (GO:0030992)|kinocilium (GO:0060091)|motile cilium (GO:0031514)|motile primary cilium (GO:0031512)|photoreceptor connecting cilium (GO:0032391)		p.Q215H(1)		breast(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(13)|ovary(1)|prostate(2)|skin(2)|urinary_tract(1)	27		all_cancers(29;5.79e-25)|all_epithelial(30;2.57e-20)|all_lung(29;3.13e-16)|Lung SC(185;0.0262)|Ovarian(182;0.0825)|Hepatocellular(188;0.244)		all cancers(112;0.000667)|Epithelial(112;0.00119)|OV - Ovarian serous cystadenocarcinoma(117;0.0141)|Lung(94;0.0183)|LUSC - Lung squamous cell carcinoma(192;0.0528)		TGGCCAGTCAGTATTCAGTTA	0.323																																					p.Q215H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G645C	13						.						125.0	125.0	125.0					13																	21172813		2202	4294	6496	20070813	SO:0001583	missense	8100	exon12			AK058172	CCDS31944.1, CCDS31945.1	13q12.1	2014-07-03	2014-07-03	2005-11-02	ENSG00000032742	ENSG00000032742		"""Intraflagellar transport homologs"", ""Tetratricopeptide (TTC) repeat domain containing"""	20606	protein-coding gene	gene with protein product	"""polaris homolog"""	600595	"""tetratricopeptide repeat domain 10"", ""intraflagellar transport 88 homolog (Chlamydomonas)"""	TTC10		7633404	Standard	XM_005266546		Approved	hTg737, Tg737, D13S1056E, MGC26259	uc001uni.3	Q13099	OTTHUMG00000016517	ENST00000319980.6:c.645G>C	13.37:g.21172813G>C	ENSP00000323580:p.Gln215His		20070813	NM_175605	A2A491|B4DUS2|Q5SZJ6|Q8N719	Missense_Mutation	SNP	ENST00000319980.6	37	CCDS31944.1	.	.	.	.	.	.	.	.	.	.	G	17.08	3.298428	0.60195	.	.	ENSG00000032742	ENST00000382778;ENST00000389374;ENST00000351808;ENST00000319980;ENST00000537103	T;T;T;T	0.76186	-0.97;-1.0;0.64;0.64	4.99	1.16	0.20824	Tetratricopeptide-like helical (1);Tetratricopeptide repeat-containing (1);	0.000000	0.85682	D	0.000000	D	0.84696	0.5529	M	0.86651	2.83	0.80722	D	1	D;D	0.67145	0.996;0.996	D;D	0.75484	0.947;0.986	T	0.82295	-0.0528	10	0.66056	D	0.02	-9.823	8.3139	0.32088	0.4003:0.0:0.5997:0.0	.	187;215	F5H6C2;Q13099	.;IFT88_HUMAN	H	215;112;206;215;187	ENSP00000372228:Q215H;ENSP00000261632:Q206H;ENSP00000323580:Q215H;ENSP00000437719:Q187H	ENSP00000323580:Q215H	Q	+	3	2	IFT88	20070813	0.549000	0.26481	0.997000	0.53966	0.985000	0.73830	-0.249000	0.08842	-0.103000	0.12175	0.591000	0.81541	CAG		0.323	IFT88-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000044075.3	NM_006531	
CCNA1	8900	broad.mit.edu	37	13	37015258	37015258	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3860-01A-02W-0900-09	TCGA-AA-3860-10A-01W-0902-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AA-3860-01A-02W-0900-09	TCGA-AA-3860-10A-01W-0902-09	g.chr13:37015258G>A	ENST00000255465.4	+	7	1366	c.1102G>A	c.(1102-1104)Gta>Ata	p.V368I	CCNA1_ENST00000418263.1_Missense_Mutation_p.V367I|CCNA1_ENST00000449823.1_Missense_Mutation_p.V324I|CCNA1_ENST00000440264.1_Missense_Mutation_p.V324I			P78396	CCNA1_HUMAN	cyclin A1	368					G1/S transition of mitotic cell cycle (GO:0000082)|G2/M transition of mitotic cell cycle (GO:0000086)|male meiosis I (GO:0007141)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of G2/M transition of mitotic cell cycle (GO:0010389)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)|spermatogenesis (GO:0007283)	cytosol (GO:0005829)|microtubule cytoskeleton (GO:0015630)|nucleoplasm (GO:0005654)		p.V368I(1)		breast(1)|endometrium(3)|kidney(4)|large_intestine(8)|lung(10)|ovary(3)|prostate(1)|skin(2)|stomach(2)|urinary_tract(1)	35		Breast(139;0.014)|Lung SC(185;0.0548)|Prostate(109;0.174)	KIRC - Kidney renal clear cell carcinoma(5;0.119)|Kidney(79;0.169)	all cancers(112;1.91e-07)|Epithelial(112;1.22e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00623)|BRCA - Breast invasive adenocarcinoma(63;0.0119)|GBM - Glioblastoma multiforme(144;0.0242)		TGCTTAGTACGTAGCAGAGCT	0.388																																					p.V324I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G970A	13						.						137.0	115.0	123.0					13																	37015258		2203	4300	6503	35913258	SO:0001583	missense	8900	exon7			U66838	CCDS9357.1, CCDS45031.1	13q12.3-q13	2014-01-21			ENSG00000133101	ENSG00000133101			1577	protein-coding gene	gene with protein product		604036				9041194	Standard	NM_003914		Approved	CT146	uc001uvr.4	P78396	OTTHUMG00000016733	ENST00000255465.4:c.1102G>A	13.37:g.37015258G>A	ENSP00000255465:p.Val368Ile		35913258	NM_001111047	B7Z7E3|Q5T3V0|Q5U0G2|Q8IY91	Missense_Mutation	SNP	ENST00000255465.4	37	CCDS9357.1	.	.	.	.	.	.	.	.	.	.	G	11.30	1.596669	0.28445	.	.	ENSG00000133101	ENST00000440264;ENST00000449823;ENST00000418263;ENST00000255465	T;T;T;T	0.20200	2.09;2.09;2.09;2.09	5.19	5.19	0.71726	Cyclin, C-terminal (1);Cyclin-like (3);	0.202388	0.40554	N	0.001061	T	0.08846	0.0219	N	0.02169	-0.655	0.23421	N	0.997718	B;B	0.28820	0.224;0.066	B;B	0.24394	0.031;0.053	T	0.25328	-1.0135	10	0.31617	T	0.26	.	14.6497	0.68786	0.0:0.2571:0.7429:0.0	.	367;368	P78396-2;P78396	.;CCNA1_HUMAN	I	324;324;367;368	ENSP00000400666:V324I;ENSP00000409873:V324I;ENSP00000396479:V367I;ENSP00000255465:V368I	ENSP00000255465:V368I	V	+	1	0	CCNA1	35913258	0.943000	0.32029	0.954000	0.39281	0.829000	0.46940	1.091000	0.30915	2.569000	0.86673	0.563000	0.77884	GTA		0.388	CCNA1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000044514.2	NM_003914	
TEX29	121793	broad.mit.edu	37	13	111995178	111995178	+	Silent	SNP	G	G	A			TCGA-AA-3860-01A-02W-0900-09	TCGA-AA-3860-10A-01W-0902-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3860-01A-02W-0900-09	TCGA-AA-3860-10A-01W-0902-09	g.chr13:111995178G>A	ENST00000283547.1	+	5	444	c.315G>A	c.(313-315)gcG>gcA	p.A105A		NM_152324.1	NP_689537.1	Q8N6K0	TEX29_HUMAN	testis expressed 29	105						integral component of membrane (GO:0016021)		p.A105A(1)									GCGAAAAGGCGGAGTTGGCCT	0.552																																					p.A105A												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G315A	13						.						81.0	72.0	75.0					13																	111995178		2203	4300	6503	110793179	SO:0001819	synonymous_variant	121793	exon5			BC029889	CCDS9522.1	13q34	2012-03-23	2012-02-07	2012-02-07	ENSG00000153495	ENSG00000153495			20370	protein-coding gene	gene with protein product			"""chromosome 13 open reading frame 16"""	C13orf16			Standard	NM_152324		Approved	bA474D23.1, MGC35169	uc001vsa.3	Q8N6K0	OTTHUMG00000017358	ENST00000283547.1:c.315G>A	13.37:g.111995178G>A			110793179	NM_152324		Silent	SNP	ENST00000283547.1	37	CCDS9522.1																																																																																				0.552	TEX29-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045812.2	NM_152324	
ISLR2	57611	broad.mit.edu	37	15	74426699	74426700	+	Frame_Shift_Ins	INS	-	-	G			TCGA-AA-3860-01A-02W-0900-09	TCGA-AA-3860-10A-01W-0902-09	-	-					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3860-01A-02W-0900-09	TCGA-AA-3860-10A-01W-0902-09	g.chr15:74426699_74426700insG	ENST00000361742.3	+	4	2373_2374	c.1604_1605insG	c.(1603-1608)gcggggfs	p.AG535fs	ISLR2_ENST00000435464.1_Frame_Shift_Ins_p.AG535fs|ISLR2_ENST00000565540.1_Frame_Shift_Ins_p.AG535fs|ISLR2_ENST00000419208.1_Frame_Shift_Ins_p.AG535fs|ISLR2_ENST00000561975.1_Intron|ISLR2_ENST00000453268.2_Frame_Shift_Ins_p.AG535fs|ISLR2_ENST00000445793.1_Frame_Shift_Ins_p.AG535fs|ISLR2_ENST00000565159.1_Frame_Shift_Ins_p.AG535fs	NM_001130136.1|NM_020851.2	NP_001123608.1|NP_065902.1	Q6UXK2	ISLR2_HUMAN	immunoglobulin superfamily containing leucine-rich repeat 2	535					positive regulation of axon extension (GO:0045773)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.G538fs*82(1)		breast(3)|endometrium(6)|large_intestine(7)|lung(17)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	36						CTGTGTCCAGCGGGGGGCGGCG	0.748																																					p.A535fs												.	.	1	Insertion - Frameshift(1)	large_intestine(1)	c.1604_1605insG	15						.																																			72213753	SO:0001589	frameshift_variant	57611	exon4				CCDS10259.1	15q24.1	2013-01-11			ENSG00000167178	ENSG00000167178		"""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	29286	protein-coding gene	gene with protein product		614179				10819331, 12975309	Standard	NM_001130136		Approved	KIAA1465	uc010bjf.3	Q6UXK2	OTTHUMG00000137624	ENST00000361742.3:c.1610dupG	15.37:g.74426705_74426705dupG	ENSP00000355402:p.Ala535fs		72213752	NM_001130136	A8K352|Q9P263	Frame_Shift_Ins	INS	ENST00000361742.3	37	CCDS10259.1																																																																																				0.748	ISLR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269046.1	NM_020851	
SLC12A1	6557	broad.mit.edu	37	15	48536975	48536975	+	Silent	SNP	C	C	T			TCGA-AA-3860-01A-02W-0900-09	TCGA-AA-3860-10A-01W-0902-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3860-01A-02W-0900-09	TCGA-AA-3860-10A-01W-0902-09	g.chr15:48536975C>T	ENST00000558405.1	+	10	1340	c.1326C>T	c.(1324-1326)acC>acT	p.T442T	SLC12A1_ENST00000396577.3_Silent_p.T442T|SLC12A1_ENST00000380993.3_Silent_p.T442T			Q13621	S12A1_HUMAN	solute carrier family 12 (sodium/potassium/chloride transporter), member 1	442					cell death (GO:0008219)|chemical homeostasis (GO:0048878)|chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|excretion (GO:0007588)|ion transmembrane transport (GO:0034220)|ion transport (GO:0006811)|kidney development (GO:0001822)|potassium ion transport (GO:0006813)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)|transport (GO:0006810)	apical plasma membrane (GO:0016324)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	sodium:potassium:chloride symporter activity (GO:0008511)	p.T442T(1)		NS(2)|breast(3)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(14)|lung(30)|ovary(1)|prostate(2)|skin(1)	59		all_lung(180;0.00219)		all cancers(107;1.76e-09)|GBM - Glioblastoma multiforme(94;1.48e-06)	Bumetanide(DB00887)|Chlormerodrin(DB00534)|Chlorthalidone(DB00310)|Ethacrynic acid(DB00903)|Furosemide(DB00695)|Hydroflumethiazide(DB00774)|Methyclothiazide(DB00232)|Potassium Chloride(DB00761)|Quinethazone(DB01325)|Torasemide(DB00214)|Trichlormethiazide(DB01021)	GAGATGCCACCGGGAACATGA	0.468																																					p.T442T												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1326T	15						.						109.0	93.0	98.0					15																	48536975		2198	4297	6495	46324267	SO:0001819	synonymous_variant	6557	exon11				CCDS10129.2, CCDS53940.1	15q15-q21	2013-07-18	2013-07-18		ENSG00000074803	ENSG00000074803		"""Solute carriers"""	10910	protein-coding gene	gene with protein product		600839				8640224	Standard	NM_000338		Approved	NKCC2	uc010bem.3	Q13621	OTTHUMG00000131495	ENST00000558405.1:c.1326C>T	15.37:g.48536975C>T			46324267	NM_001184832	A8JYA2|E9PDW4	Silent	SNP	ENST00000558405.1	37	CCDS10129.2																																																																																				0.468	SLC12A1-006	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000417131.1		
SRCAP	10847	broad.mit.edu	37	16	30735291	30735291	+	Missense_Mutation	SNP	T	T	G			TCGA-AA-3860-01A-02W-0900-09	TCGA-AA-3860-10A-01W-0902-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AA-3860-01A-02W-0900-09	TCGA-AA-3860-10A-01W-0902-09	g.chr16:30735291T>G	ENST00000262518.4	+	25	4931	c.4546T>G	c.(4546-4548)Tct>Gct	p.S1516A	SRCAP_ENST00000395059.2_Missense_Mutation_p.S1454A|SRCAP_ENST00000344771.4_Missense_Mutation_p.S1358A	NM_006662.2	NP_006653.2	Q6ZRS2	SRCAP_HUMAN	Snf2-related CREBBP activator protein	1516	Pro-rich.				histone acetylation (GO:0016573)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|protein complex (GO:0043234)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|histone acetyltransferase activity (GO:0004402)|transcription coactivator activity (GO:0003713)	p.S1516A(1)		NS(1)|breast(3)|cervix(3)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(22)|liver(3)|lung(62)|ovary(6)|pancreas(1)|prostate(4)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(5)	136			Colorectal(24;0.198)			TCCATCCCTGTCTTCATCTCA	0.582																																					p.S1516A												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T4546G	16						.						87.0	75.0	79.0					16																	30735291		2197	4300	6497	30642792	SO:0001583	missense	10847	exon25			AB002307	CCDS10689.2	16p11.2	2009-08-06			ENSG00000080603	ENSG00000080603			16974	protein-coding gene	gene with protein product	"""Swi2/Snf2-related ATPase homolog (S. cerevisiae)"", ""domino homolog 1 (Drosophila)"""	611421				10347196, 9205841	Standard	NM_006662		Approved	KIAA0309, EAF1, SWR1, DOMO1	uc002dze.1	Q6ZRS2	OTTHUMG00000132393	ENST00000262518.4:c.4546T>G	16.37:g.30735291T>G	ENSP00000262518:p.Ser1516Ala		30642792	NM_006662	B0JZA6|O15026|Q7Z744|Q9Y5L9	Missense_Mutation	SNP	ENST00000262518.4	37	CCDS10689.2	.	.	.	.	.	.	.	.	.	.	T	10.02	1.237227	0.22711	.	.	ENSG00000080603	ENST00000262518;ENST00000395059;ENST00000344771	D;D;D	0.91011	-2.69;-2.7;-2.77	5.8	4.71	0.59529	.	0.118903	0.39083	N	0.001479	T	0.81250	0.4783	N	0.19112	0.55	0.26689	N	0.971394	B;B;B	0.11235	0.001;0.004;0.002	B;B;B	0.08055	0.002;0.003;0.001	T	0.65985	-0.6035	10	0.20046	T	0.44	-14.7981	9.7659	0.40561	0.0:0.0:0.3091:0.6909	.	1358;1454;1516	Q6ZRS2-3;Q6ZRS2-2;Q6ZRS2	.;.;SRCAP_HUMAN	A	1516;1454;1358	ENSP00000262518:S1516A;ENSP00000378499:S1454A;ENSP00000343042:S1358A	ENSP00000262518:S1516A	S	+	1	0	SRCAP	30642792	0.000000	0.05858	1.000000	0.80357	0.885000	0.51271	0.341000	0.19909	2.218000	0.71995	0.377000	0.23210	TCT		0.582	SRCAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255523.1	NM_006662	
PMFBP1	83449	broad.mit.edu	37	16	72153977	72153977	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3860-01A-02W-0900-09	TCGA-AA-3860-10A-01W-0902-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AA-3860-01A-02W-0900-09	TCGA-AA-3860-10A-01W-0902-09	g.chr16:72153977C>T	ENST00000237353.10	-	20	3041	c.2780G>A	c.(2779-2781)aGt>aAt	p.S927N	PMFBP1_ENST00000355636.6_Missense_Mutation_p.S802N|PMFBP1_ENST00000537792.1_Intron|PMFBP1_ENST00000537465.1_Missense_Mutation_p.S932N	NM_031293.2	NP_112583.2	Q8TBY8	PMFBP_HUMAN	polyamine modulated factor 1 binding protein 1	932						cytoplasm (GO:0005737)		p.S927N(1)		NS(1)|breast(3)|endometrium(1)|kidney(2)|large_intestine(7)|lung(25)|ovary(2)|skin(3)|urinary_tract(1)	45		Ovarian(137;0.179)				GACCATTACACTGTGGAGGTG	0.512																																					p.S802N												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2405A	16						.						228.0	233.0	231.0					16																	72153977		2198	4300	6498	70711478	SO:0001583	missense	83449	exon21			AF239683	CCDS32483.1	16q23.1	2008-08-04			ENSG00000118557	ENSG00000118557			17728	protein-coding gene	gene with protein product						11468771	Standard	NM_031293		Approved		uc002fcd.3	Q8TBY8	OTTHUMG00000167827	ENST00000237353.10:c.2780G>A	16.37:g.72153977C>T	ENSP00000237353:p.Ser927Asn		70711478	NM_001160213	B3KVI9|H7BY07|Q8NA09|Q9BY16|Q9H0H4	Missense_Mutation	SNP	ENST00000237353.10	37	CCDS32483.1	.	.	.	.	.	.	.	.	.	.	C	0.052	-1.247352	0.01481	.	.	ENSG00000118557	ENST00000537465;ENST00000237353;ENST00000355636	T;T;T	0.09538	2.97;2.97;3.0	4.96	2.73	0.32206	.	0.254610	0.28171	N	0.016333	T	0.01905	0.0060	N	0.00116	-2.08	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	0.44605	-0.9317	10	0.15066	T	0.55	-13.5065	8.4248	0.32723	0.0:0.2317:0.0:0.7683	.	932;927;932	Q8TBY8;Q8TBY8-2;G3V1Q7	PMFBP_HUMAN;.;.	N	932;927;802	ENSP00000443817:S932N;ENSP00000237353:S927N;ENSP00000347854:S802N	ENSP00000237353:S927N	S	-	2	0	PMFBP1	70711478	0.946000	0.32159	0.946000	0.38457	0.440000	0.31957	1.444000	0.35068	0.379000	0.24794	-0.600000	0.04104	AGT		0.512	PMFBP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000396473.2	NM_031293	
ACACA	31	broad.mit.edu	37	17	35591932	35591932	+	Silent	SNP	G	G	A	rs112050484	byFrequency	TCGA-AA-3860-01A-02W-0900-09	TCGA-AA-3860-10A-01W-0902-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3860-01A-02W-0900-09	TCGA-AA-3860-10A-01W-0902-09	g.chr17:35591932G>A	ENST00000394406.2	-	25	3283	c.3093C>T	c.(3091-3093)caC>caT	p.H1031H	ACACA_ENST00000335166.5_Silent_p.H953H|ACACA_ENST00000353139.5_Silent_p.H1068H|ACACA_ENST00000360679.3_Silent_p.H973H	NM_198836.1	NP_942133.1	Q13085	ACACA_HUMAN	acetyl-CoA carboxylase alpha	1031					acetyl-CoA metabolic process (GO:0006084)|biotin metabolic process (GO:0006768)|carnitine shuttle (GO:0006853)|cellular lipid metabolic process (GO:0044255)|energy reserve metabolic process (GO:0006112)|fatty acid biosynthetic process (GO:0006633)|lipid homeostasis (GO:0055088)|long-chain fatty-acyl-CoA biosynthetic process (GO:0035338)|malonyl-CoA biosynthetic process (GO:2001295)|multicellular organismal protein metabolic process (GO:0044268)|positive regulation of cellular metabolic process (GO:0031325)|protein homotetramerization (GO:0051289)|small molecule metabolic process (GO:0044281)|tissue homeostasis (GO:0001894)|triglyceride biosynthetic process (GO:0019432)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	acetyl-CoA carboxylase activity (GO:0003989)|ATP binding (GO:0005524)|biotin carboxylase activity (GO:0004075)|metal ion binding (GO:0046872)	p.H973H(1)|p.H1068H(1)		NS(2)|breast(5)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(24)|lung(23)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	83		Breast(25;0.00157)|Ovarian(249;0.15)			Biotin(DB00121)	TGACTTGAGCGTGAGAGAAGA	0.383																																					p.H1068H	Colon(23;82 258 739 2117 10493 24037 27661 34815 35438 36249)											.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.C3204T	17						.						219.0	178.0	192.0					17																	35591932		2203	4300	6503	32666045	SO:0001819	synonymous_variant	31	exon25			U19822	CCDS11317.1, CCDS11318.1, CCDS42302.1, CCDS42303.1	17q21	2014-05-06	2010-04-30		ENSG00000132142	ENSG00000278540	6.4.1.2		84	protein-coding gene	gene with protein product	"""acetyl-CoA carboxylase 1"""	200350	"""acetyl-Coenzyme A carboxylase alpha"""	ACAC, ACC			Standard	NM_198837		Approved	ACC1	uc002hno.3	Q13085	OTTHUMG00000188463	ENST00000394406.2:c.3093C>T	17.37:g.35591932G>A			32666045	NM_198834	B2RP68|Q6KEV6|Q6XDA8|Q7Z2G8|Q7Z561|Q7Z563|Q7Z564|Q86WB2|Q86WB3	Silent	SNP	ENST00000394406.2	37	CCDS11317.1																																																																																				0.383	ACACA-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256696.1	NM_198836	
CACNA1G	8913	broad.mit.edu	37	17	48678117	48678117	+	Nonsense_Mutation	SNP	C	C	T			TCGA-AA-3860-01A-02W-0900-09	TCGA-AA-3860-10A-01W-0902-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AA-3860-01A-02W-0900-09	TCGA-AA-3860-10A-01W-0902-09	g.chr17:48678117C>T	ENST00000359106.5	+	18	3721	c.3721C>T	c.(3721-3723)Cga>Tga	p.R1241*	CACNA1G_ENST00000354983.4_Nonsense_Mutation_p.R1218*|CACNA1G_ENST00000507609.1_Nonsense_Mutation_p.R1241*|CACNA1G_ENST00000513689.2_Nonsense_Mutation_p.R1241*|CACNA1G_ENST00000502264.1_Nonsense_Mutation_p.R1218*|CACNA1G_ENST00000510115.1_Nonsense_Mutation_p.R1218*|CACNA1G_ENST00000416767.4_Nonsense_Mutation_p.R1241*|CACNA1G_ENST00000515411.1_Nonsense_Mutation_p.R1241*|CACNA1G_ENST00000505165.1_Nonsense_Mutation_p.R1241*|CACNA1G_ENST00000514717.1_Nonsense_Mutation_p.R1218*|CACNA1G_ENST00000442258.2_Nonsense_Mutation_p.R1218*|CACNA1G_ENST00000429973.2_Nonsense_Mutation_p.R1241*|CACNA1G_ENST00000360761.4_Nonsense_Mutation_p.R1218*|CACNA1G_ENST00000512389.1_Nonsense_Mutation_p.R1241*|CACNA1G_ENST00000513964.1_Nonsense_Mutation_p.R1241*|CACNA1G_ENST00000507896.1_Nonsense_Mutation_p.R1241*|CACNA1G_ENST00000352832.5_Nonsense_Mutation_p.R1218*|CACNA1G_ENST00000507510.2_Nonsense_Mutation_p.R1241*|CACNA1G_ENST00000515765.1_Nonsense_Mutation_p.R1241*|CACNA1G_ENST00000515165.1_Nonsense_Mutation_p.R1241*|CACNA1G_ENST00000358244.5_Nonsense_Mutation_p.R1218*|CACNA1G_ENST00000514181.1_Nonsense_Mutation_p.R1241*|CACNA1G_ENST00000507336.1_Nonsense_Mutation_p.R1241*|CACNA1G_ENST00000510366.1_Nonsense_Mutation_p.R1241*|CACNA1G_ENST00000514079.1_Nonsense_Mutation_p.R1241*|CACNA1G_ENST00000503485.1_Nonsense_Mutation_p.R1241*	NM_018896.4	NP_061496.2	O43497	CAC1G_HUMAN	calcium channel, voltage-dependent, T type, alpha 1G subunit	1241					axon guidance (GO:0007411)|calcium ion import (GO:0070509)|membrane depolarization during action potential (GO:0086010)|positive regulation of calcium ion-dependent exocytosis (GO:0045956)|regulation of atrial cardiac muscle cell membrane depolarization (GO:0060371)|regulation of heart rate (GO:0002027)|regulation of membrane potential (GO:0042391)|response to nickel cation (GO:0010045)|synaptic transmission (GO:0007268)|transport (GO:0006810)	plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	low voltage-gated calcium channel activity (GO:0008332)|scaffold protein binding (GO:0097110)	p.R1241*(2)|p.R1218*(1)		breast(5)|cervix(1)|endometrium(13)|kidney(5)|lung(23)	47	Breast(11;6.7e-17)		BRCA - Breast invasive adenocarcinoma(22;7.52e-09)		Cinnarizine(DB00568)|Ethosuximide(DB00593)|Flunarizine(DB04841)|Methsuximide(DB05246)|Spironolactone(DB00421)|Trimethadione(DB00347)|Verapamil(DB00661)|Zonisamide(DB00909)	CGCGTGGATCCGAGCCCGACT	0.632																																					p.R1218X												.	.	3	Substitution - Nonsense(3)	large_intestine(3)	c.C3652T	17						.						54.0	66.0	62.0					17																	48678117		2087	4217	6304	46033116	SO:0001587	stop_gained	8913	exon17			AC004590	CCDS45730.1, CCDS45731.1, CCDS45732.1, CCDS45733.1, CCDS45734.1, CCDS45735.1, CCDS45736.1, CCDS45737.1, CCDS54142.1, CCDS54143.1, CCDS54144.1, CCDS54145.1, CCDS54146.1, CCDS58565.1, CCDS58566.1, CCDS58567.1, CCDS58568.1, CCDS58569.1, CCDS58570.1, CCDS58571.1, CCDS58572.1, CCDS58573.1, CCDS58574.1, CCDS58575.1, CCDS58576.1	17q22	2012-03-07	2007-02-16		ENSG00000006283	ENSG00000006283		"""Calcium channel subunits"", ""Voltage-gated ion channels / Calcium channels"""	1394	protein-coding gene	gene with protein product		604065				9495342, 16382099	Standard	NM_001256334		Approved	Cav3.1, NBR13	uc002irk.2	O43497	OTTHUMG00000162180	ENST00000359106.5:c.3721C>T	17.37:g.48678117C>T	ENSP00000352011:p.Arg1241*		46033116	NM_198382	D6RA64|E7EPR0|O43498|O94770|Q19QY8|Q19QY9|Q19QZ0|Q19QZ1|Q19QZ2|Q19QZ3|Q19QZ4|Q19QZ5|Q19QZ6|Q19QZ7|Q19QZ8|Q19QZ9|Q19R00|Q19R01|Q19R02|Q19R03|Q19R04|Q19R05|Q19R06|Q19R07|Q19R08|Q19R09|Q19R10|Q19R11|Q19R12|Q19R13|Q19R15|Q19R16|Q19R17|Q19R18|Q2TAC4|Q9NYU4|Q9NYU5|Q9NYU6|Q9NYU7|Q9NYU8|Q9NYU9|Q9NYV0|Q9NYV1|Q9UHN9|Q9UHP0|Q9ULU6|Q9UNG7|Q9Y5T2|Q9Y5T3	Nonsense_Mutation	SNP	ENST00000359106.5	37	CCDS45730.1	.	.	.	.	.	.	.	.	.	.	c	43	9.945755	0.99302	.	.	ENSG00000006283	ENST00000360761;ENST00000352832;ENST00000416767;ENST00000354983;ENST00000442258;ENST00000502264;ENST00000512389;ENST00000513964;ENST00000514717;ENST00000510366;ENST00000503485;ENST00000507510;ENST00000507336;ENST00000513689;ENST00000507609;ENST00000510115;ENST00000515165;ENST00000514181;ENST00000515765;ENST00000514079;ENST00000358244;ENST00000359106;ENST00000429973;ENST00000515411;ENST00000505165;ENST00000507896;ENST00000506520	.	.	.	5.46	3.32	0.38043	.	0.476775	0.22106	N	0.064553	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.09843	T	0.71	.	9.4705	0.38839	0.2553:0.5031:0.2416:0.0	.	.	.	.	X	1218;1218;1241;1218;1218;1218;1241;1241;1218;1241;1241;1241;1241;1241;1241;1218;1241;1241;1241;1241;1218;1241;1241;1241;1241;1241;56	.	ENSP00000339302:R1218X	R	+	1	2	CACNA1G	46033116	0.137000	0.22531	0.999000	0.59377	0.880000	0.50808	0.352000	0.20113	1.283000	0.44513	0.655000	0.94253	CGA		0.632	CACNA1G-013	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000367895.1	NM_018896	
CEP95	90799	broad.mit.edu	37	17	62518977	62518977	+	Silent	SNP	C	C	T			TCGA-AA-3860-01A-02W-0900-09	TCGA-AA-3860-10A-01W-0902-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3860-01A-02W-0900-09	TCGA-AA-3860-10A-01W-0902-09	g.chr17:62518977C>T	ENST00000556440.2	+	8	1383	c.873C>T	c.(871-873)gcC>gcT	p.A291A	CEP95_ENST00000553412.1_Silent_p.A127A	NM_138363.1	NP_612372.1	Q96GE4	CEP95_HUMAN	centrosomal protein 95kDa	291						centrosome (GO:0005813)|cytoplasm (GO:0005737)|spindle pole (GO:0000922)		p.A291A(2)		endometrium(1)|kidney(3)|large_intestine(5)|lung(3)|ovary(1)	13						GCTCCCCAGCCGTAAATTCTA	0.468																																					p.A291A												.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.C873T	17						.						38.0	42.0	41.0					17																	62518977		1872	4090	5962	59949439	SO:0001819	synonymous_variant	90799	exon8			AL832822	CCDS45763.1	17q24.1	2014-02-20	2011-05-06	2011-05-06	ENSG00000258890	ENSG00000258890			25141	protein-coding gene	gene with protein product			"""coiled-coil domain containing 45"""	CCDC45		21399614	Standard	NM_138363		Approved	DKFZp667E1824	uc002jem.3	Q96GE4	OTTHUMG00000179174	ENST00000556440.2:c.873C>T	17.37:g.62518977C>T			59949439	NM_138363	B4DMD2|Q96M81	Silent	SNP	ENST00000556440.2	37	CCDS45763.1																																																																																				0.468	CEP95-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445100.2	NM_138363	
TP53	7157	broad.mit.edu	37	17	7579508	7579508	+	Frame_Shift_Del	DEL	G	G	-			TCGA-AA-3860-01A-02W-0900-09	TCGA-AA-3860-10A-01W-0902-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3860-01A-02W-0900-09	TCGA-AA-3860-10A-01W-0902-09	g.chr17:7579508delG	ENST00000269305.4	-	4	368	c.179delC	c.(178-180)ccafs	p.P60fs	TP53_ENST00000420246.2_Frame_Shift_Del_p.P60fs|TP53_ENST00000359597.4_Frame_Shift_Del_p.P60fs|TP53_ENST00000445888.2_Frame_Shift_Del_p.P60fs|TP53_ENST00000413465.2_Frame_Shift_Del_p.P60fs|TP53_ENST00000455263.2_Frame_Shift_Del_p.P60fs|TP53_ENST00000574684.1_5'Flank	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	60	Interaction with HRMT1L2.		P -> L (in sporadic cancers; somatic mutation).|P -> Q (in a sporadic cancer; somatic mutation).|P -> S (in a sporadic cancer; somatic mutation).		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.0?(8)|p.P60fs*63(3)|p.G59fs*23(3)|p.E51fs*59(1)|p.D48fs*55(1)|p.P60R(1)|p.P60Q(1)|p.P60L(1)|p.P13fs*18(1)|p.S33fs*23(1)|p.D57_A76del20(1)|p.D57fs*86(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)	AGCTTCATCTGGACCTGGGTC	0.612		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.P60fs	Pancreas(47;798 1329 9957 10801)	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"""L, E, M, O"""	TP53,central_nervous_system,brain,Substitution - Missense,0 	.	23	Deletion - Frameshift(11)|Whole gene deletion(8)|Substitution - Missense(3)|Deletion - In frame(1)	central_nervous_system(4)|bone(4)|upper_aerodigestive_tract(3)|large_intestine(3)|haematopoietic_and_lymphoid_tissue(2)|prostate(2)|stomach(1)|liver(1)|lung(1)|breast(1)|pancreas(1)	c.179delC	17						.						145.0	148.0	147.0					17																	7579508		2203	4300	6503	7520233	SO:0001589	frameshift_variant	7157	exon4	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.179delC	17.37:g.7579508delG	ENSP00000269305:p.Pro60fs		7520233	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	Frame_Shift_Del	DEL	ENST00000269305.4	37	CCDS11118.1																																																																																				0.612	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546	
FOXK2	3607	broad.mit.edu	37	17	80540647	80540647	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3860-01A-02W-0900-09	TCGA-AA-3860-10A-01W-0902-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3860-01A-02W-0900-09	TCGA-AA-3860-10A-01W-0902-09	g.chr17:80540647C>T	ENST00000335255.5	+	5	1114	c.940C>T	c.(940-942)Cgt>Tgt	p.R314C	snoU13_ENST00000459591.1_RNA	NM_004514.3	NP_004505.2	Q01167	FOXK2_HUMAN	forkhead box K2	314	DNA-binding; major groove.				positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)	intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	magnesium ion binding (GO:0000287)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.R314C(2)		NS(1)|breast(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(5)|prostate(1)|urinary_tract(1)	17	Breast(20;0.00106)|all_neural(118;0.0952)		OV - Ovarian serous cystadenocarcinoma(97;0.0371)|BRCA - Breast invasive adenocarcinoma(99;0.0415)			CTCTCTGAATCGTTATTTCAT	0.378																																					p.R314C												.	.	2	Substitution - Missense(2)	large_intestine(1)|prostate(1)	c.C940T	17						.						55.0	56.0	56.0					17																	80540647		2203	4300	6503	78133936	SO:0001583	missense	3607	exon5			U58196	CCDS11813.1	17q25	2006-12-15	2004-03-09	2004-03-10	ENSG00000141568	ENSG00000141568		"""Forkhead boxes"""	6036	protein-coding gene	gene with protein product		147685	"""interleukin enhancer binding factor 1"""	ILF, ILF1		3260003	Standard	NM_004514		Approved		uc002kfn.3	Q01167	OTTHUMG00000140374	ENST00000335255.5:c.940C>T	17.37:g.80540647C>T	ENSP00000335677:p.Arg314Cys		78133936	NM_004514	A6NEP5|Q13622|Q13623|Q13624	Missense_Mutation	SNP	ENST00000335255.5	37	CCDS11813.1	.	.	.	.	.	.	.	.	.	.	C	31	5.079503	0.94050	.	.	ENSG00000141568	ENST00000535184;ENST00000335255;ENST00000531030;ENST00000526383	D;D;D	0.95656	-3.77;-3.77;-3.77	6.07	6.07	0.98685	Winged helix-turn-helix transcription repressor DNA-binding (1);Transcription factor, fork head (4);	0.000000	0.85682	D	0.000000	D	0.97495	0.9180	M	0.74881	2.28	0.80722	D	1	P;D	0.63046	0.923;0.992	P;P	0.62740	0.754;0.906	D	0.97447	1.0025	10	0.87932	D	0	.	20.6439	0.99570	0.0:1.0:0.0:0.0	.	314;314	Q01167;Q01167-2	FOXK2_HUMAN;.	C	310;314;125;194	ENSP00000335677:R314C;ENSP00000433167:R125C;ENSP00000432663:R194C	ENSP00000335677:R314C	R	+	1	0	FOXK2	78133936	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	7.671000	0.83941	2.884000	0.98904	0.655000	0.94253	CGT		0.378	FOXK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000277099.2	NM_181430	
ENOSF1	55556	broad.mit.edu	37	18	706501	706501	+	Silent	SNP	A	A	T			TCGA-AA-3860-01A-02W-0900-09	TCGA-AA-3860-10A-01W-0902-09	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3860-01A-02W-0900-09	TCGA-AA-3860-10A-01W-0902-09	g.chr18:706501A>T	ENST00000251101.7	-	2	250	c.162T>A	c.(160-162)atT>atA	p.I54I	ENOSF1_ENST00000340116.7_Silent_p.I75I|ENOSF1_ENST00000580982.1_Silent_p.I54I|ENOSF1_ENST00000383578.3_Nonsense_Mutation_p.L11*|ENOSF1_ENST00000539164.1_Silent_p.I54I|RP11-806L2.6_ENST00000580007.1_RNA	NM_017512.5	NP_059982.2	Q7L5Y1	ENOF1_HUMAN	enolase superfamily member 1	54					cellular amino acid catabolic process (GO:0009063)|cellular carbohydrate catabolic process (GO:0044275)	mitochondrion (GO:0005739)	isomerase activity (GO:0016853)|L-fuconate dehydratase activity (GO:0050023)|magnesium ion binding (GO:0000287)	p.I54I(1)		endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(3)|ovary(1)|prostate(1)	10						GAGTGAAGGTAATTCCACACC	0.458																																					p.L11X												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.T32A	18						.						158.0	132.0	141.0					18																	706501		2203	4300	6503	696501	SO:0001819	synonymous_variant	55556	exon2			X67098	CCDS11822.1, CCDS11823.1, CCDS45821.1	18p11.32	2005-01-26			ENSG00000132199	ENSG00000132199			30365	protein-coding gene	gene with protein product		607427				14508106	Standard	NM_001126123		Approved	HSRTSBETA, rTS, TYMSAS	uc002kku.4	Q7L5Y1	OTTHUMG00000131470	ENST00000251101.7:c.162T>A	18.37:g.706501A>T			696501	NM_001126123	A6NMP3|A8K9R5|B3KSL6|B3KXE4|D3DUH0|Q15407|Q15594|Q15595|Q6ZS08|Q9HAS5|Q9HAS6	Nonsense_Mutation	SNP	ENST00000251101.7	37	CCDS11822.1	.	.	.	.	.	.	.	.	.	.	A	34	5.338230	0.95758	.	.	ENSG00000132199	ENST00000383578	.	.	.	5.56	-10.6	0.00265	.	.	.	.	.	.	.	.	.	.	.	0.54753	D	0.999989	.	.	.	.	.	.	.	.	.	.	0.23302	T	0.38	.	11.0654	0.47972	0.3007:0.0:0.5598:0.1395	.	.	.	.	X	11	.	ENSP00000373072:L11X	L	-	2	0	ENOSF1	696501	0.123000	0.22298	0.078000	0.20375	0.891000	0.51852	-0.872000	0.04219	-1.651000	0.01504	-1.215000	0.01618	TTA		0.458	ENOSF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254312.2	NM_017512	
NOL4	8715	broad.mit.edu	37	18	31709929	31709929	+	Missense_Mutation	SNP	T	T	A			TCGA-AA-3860-01A-02W-0900-09	TCGA-AA-3860-10A-01W-0902-09	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AA-3860-01A-02W-0900-09	TCGA-AA-3860-10A-01W-0902-09	g.chr18:31709929T>A	ENST00000261592.5	-	2	617	c.320A>T	c.(319-321)gAt>gTt	p.D107V	NOL4_ENST00000589544.1_Missense_Mutation_p.D107V|NOL4_ENST00000538587.1_Missense_Mutation_p.D33V|NOL4_ENST00000269185.4_5'UTR|NOL4_ENST00000535475.1_5'UTR	NM_001198546.1|NM_003787.4	NP_001185475.1|NP_003778.2	O94818	NOL4_HUMAN	nucleolar protein 4	107						nucleolus (GO:0005730)	RNA binding (GO:0003723)	p.D107V(1)		NS(1)|breast(2)|endometrium(6)|kidney(1)|large_intestine(7)|lung(20)|ovary(4)|prostate(2)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	51						GTCAAAGAAATCTTCAACCAC	0.398																																					p.D107V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A320T	18						.						119.0	105.0	110.0					18																	31709929		2203	4300	6503	29963927	SO:0001583	missense	8715	exon2			AB017800	CCDS11907.2, CCDS56058.1, CCDS56059.1, CCDS59308.1	18q12	2010-05-04			ENSG00000101746	ENSG00000101746			7870	protein-coding gene	gene with protein product	"""cancer/testis antigen 125"""	603577				9813152	Standard	NM_003787		Approved	NOLP, HRIHFB2255, CT125	uc010dmi.3	O94818	OTTHUMG00000132291	ENST00000261592.5:c.320A>T	18.37:g.31709929T>A	ENSP00000261592:p.Asp107Val		29963927	NM_001198546	B4DSQ0|B7Z3Z7|F5H1E3|Q6IBS2|Q9BWF1	Missense_Mutation	SNP	ENST00000261592.5	37	CCDS11907.2	.	.	.	.	.	.	.	.	.	.	T	25.2	4.615486	0.87359	.	.	ENSG00000101746	ENST00000261592;ENST00000538587	D	0.83992	-1.79	5.61	5.61	0.85477	.	.	.	.	.	D	0.88983	0.6586	L	0.55990	1.75	0.80722	D	1	D;D;D	0.76494	0.999;0.999;0.999	D;D;D	0.83275	0.996;0.994;0.996	D	0.90023	0.4129	9	0.87932	D	0	-9.4235	14.9717	0.71238	0.0:0.0:0.0:1.0	.	33;107;107	B4DSQ0;O94818;O94818-2	.;NOL4_HUMAN;.	V	107;33	ENSP00000261592:D107V	ENSP00000261592:D107V	D	-	2	0	NOL4	29963927	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	7.536000	0.82023	2.131000	0.65755	0.477000	0.44152	GAT		0.398	NOL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255386.1	NM_003787	
TICAM1	148022	broad.mit.edu	37	19	4816464	4816465	+	Frame_Shift_Ins	INS	-	-	G			TCGA-AA-3860-01A-02W-0900-09	TCGA-AA-3860-10A-01W-0902-09	-	-					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3860-01A-02W-0900-09	TCGA-AA-3860-10A-01W-0902-09	g.chr19:4816464_4816465insG	ENST00000248244.5	-	2	2154_2155	c.1925_1926insC	c.(1924-1926)ccafs	p.P642fs		NM_182919.3	NP_891549.1	Q8IUC6	TCAM1_HUMAN	toll-like receptor adaptor molecule 1	642	Pro-rich.|Sufficient to induce apoptosis.			Missing (in Ref. 6; AAO85488). {ECO:0000305}.	apoptotic signaling pathway (GO:0097190)|defense response to virus (GO:0051607)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|lipopolysaccharide-mediated signaling pathway (GO:0031663)|macrophage activation involved in immune response (GO:0002281)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of chemokine biosynthetic process (GO:0045080)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interferon-beta biosynthetic process (GO:0045359)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of natural killer cell activation (GO:0032816)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of protein binding (GO:0032092)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of tumor necrosis factor production (GO:0032760)|positive regulation of type I interferon production (GO:0032481)|regulation of protein homodimerization activity (GO:0043496)|response to exogenous dsRNA (GO:0043330)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytosol (GO:0005829)|endosome membrane (GO:0010008)|ripoptosome (GO:0097342)	protein kinase binding (GO:0019901)|signal transducer activity (GO:0004871)	p.P643fs*>71(1)		NS(2)|breast(2)|endometrium(2)|kidney(2)|large_intestine(4)|lung(6)|ovary(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	26				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0139)		GGGAGGGCGGTGGGGGGGTGCC	0.733																																					p.P642fs												.	.	1	Insertion - Frameshift(1)	large_intestine(1)	c.1926_1927insC	19						.																																			4767465	SO:0001589	frameshift_variant	148022	exon2			AB086380	CCDS12136.1	19p13.3	2014-09-17				ENSG00000127666			18348	protein-coding gene	gene with protein product		607601				12539043, 12471095	Standard	NM_182919		Approved	TRIF, TICAM-1, MGC35334, PRVTIRB	uc002mbi.4	Q8IUC6		ENST00000248244.5:c.1926dupC	19.37:g.4816471_4816471dupG	ENSP00000248244:p.Pro642fs		4767464	NM_182919	B3Y691|O75532|Q86XP8|Q96GA0	Frame_Shift_Ins	INS	ENST00000248244.5	37	CCDS12136.1																																																																																				0.733	TICAM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450435.1	NM_014261	
PVRL2	5819	broad.mit.edu	37	19	45381521	45381522	+	Intron	INS	-	-	G			TCGA-AA-3860-01A-02W-0900-09	TCGA-AA-3860-10A-01W-0902-09	-	-					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3860-01A-02W-0900-09	TCGA-AA-3860-10A-01W-0902-09	g.chr19:45381521_45381522insG	ENST00000252483.5	+	5	1042				PVRL2_ENST00000252485.4_Frame_Shift_Ins_p.W362fs	NM_001042724.1	NP_001036189.1	Q92692	PVRL2_HUMAN	poliovirus receptor-related 2 (herpesvirus entry mediator B)						acrosome assembly (GO:0001675)|adherens junction organization (GO:0034332)|adhesion of symbiont to host (GO:0044406)|cell junction assembly (GO:0034329)|cell part morphogenesis (GO:0032990)|cell-cell junction organization (GO:0045216)|cilium organization (GO:0044782)|coreceptor-mediated virion attachment to host cell (GO:0046814)|cytoskeleton organization (GO:0007010)|establishment of mitochondrion localization (GO:0051654)|fertilization (GO:0009566)|fusion of virus membrane with host plasma membrane (GO:0019064)|homophilic cell adhesion (GO:0007156)|positive regulation of immunoglobulin mediated immune response (GO:0002891)|positive regulation of mast cell activation (GO:0033005)|positive regulation of natural killer cell mediated cytotoxicity (GO:0045954)|positive regulation of natural killer cell mediated cytotoxicity directed against tumor cell target (GO:0002860)|regulation of immune response (GO:0050776)|signal transduction (GO:0007165)|sperm mitochondrion organization (GO:0030382)|spermatid development (GO:0007286)|spermatid nucleus differentiation (GO:0007289)|susceptibility to natural killer cell mediated cytotoxicity (GO:0042271)|susceptibility to T cell mediated cytotoxicity (GO:0060370)	cell surface (GO:0009986)|cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|zonula adherens (GO:0005915)	cell adhesion molecule binding (GO:0050839)|coreceptor activity (GO:0015026)|identical protein binding (GO:0042802)|protein homodimerization activity (GO:0042803)|virus receptor activity (GO:0001618)	p.A364fs*75(1)		breast(1)|endometrium(1)|large_intestine(6)|lung(5)	13	Lung NSC(12;0.00195)|all_lung(12;0.00522)	Ovarian(192;0.0728)|all_neural(266;0.112)		OV - Ovarian serous cystadenocarcinoma(262;0.0143)		CCCGCTGGTGTGGGGGGCCGTG	0.649																																					p.W362fs												.	.	1	Insertion - Frameshift(1)	large_intestine(1)	c.1084_1085insG	19						.																																			50073362	SO:0001627	intron_variant	5819	exon6			X80038	CCDS12645.1, CCDS42576.1	19q13.32	2013-01-29			ENSG00000130202	ENSG00000130202		"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	9707	protein-coding gene	gene with protein product		600798		HVEB		7622062, 10196354	Standard	NM_001042724		Approved	PVRR2, PRR2, CD112	uc002ozw.1	Q92692	OTTHUMG00000180839	ENST00000252483.5:c.1042+3786->G	19.37:g.45381527_45381527dupG			50073361	NM_002856	A8K5L5|O75455|Q6IBI6|Q96J29	Frame_Shift_Ins	INS	ENST00000252483.5	37	CCDS42576.1																																																																																				0.649	PVRL2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000453231.1	NM_002856	
MUC16	94025	broad.mit.edu	37	19	9017469	9017469	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3860-01A-02W-0900-09	TCGA-AA-3860-10A-01W-0902-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AA-3860-01A-02W-0900-09	TCGA-AA-3860-10A-01W-0902-09	g.chr19:9017469G>A	ENST00000397910.4	-	26	38058	c.37855C>T	c.(37855-37857)Cgt>Tgt	p.R12619C		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	12621	SEA 4. {ECO:0000255|PROSITE- ProRule:PRU00188}.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)		p.R12619C(1)		NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						GGGTCAAGACGGTGGGTGCAG	0.567																																					p.R12619C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C37855T	19						.						61.0	58.0	59.0					19																	9017469		1824	4048	5872	8878469	SO:0001583	missense	94025	exon26			AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"""Mucins"""	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.37855C>T	19.37:g.9017469G>A	ENSP00000381008:p.Arg12619Cys		8878469	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	.	.	.	.	.	.	.	.	.	.	.	5.337	0.247433	0.10130	.	.	ENSG00000181143	ENST00000397910	T	0.35421	1.31	3.35	0.379	0.16213	.	.	.	.	.	T	0.38134	0.1029	M	0.63428	1.95	.	.	.	D	0.58620	0.983	P	0.51016	0.656	T	0.45483	-0.9258	8	0.87932	D	0	.	1.9401	0.03345	0.2825:0.0:0.4336:0.2839	.	12619	B5ME49	.	C	12619	ENSP00000381008:R12619C	ENSP00000381008:R12619C	R	-	1	0	MUC16	8878469	0.000000	0.05858	0.001000	0.08648	0.001000	0.01503	0.326000	0.19646	0.332000	0.23536	0.400000	0.26472	CGT		0.567	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
NLRP13	126204	broad.mit.edu	37	19	56443520	56443520	+	Missense_Mutation	SNP	G	G	A	rs145312636		TCGA-AA-3860-01A-02W-0900-09	TCGA-AA-3860-10A-01W-0902-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AA-3860-01A-02W-0900-09	TCGA-AA-3860-10A-01W-0902-09	g.chr19:56443520G>A	ENST00000342929.3	-	1	157	c.158C>T	c.(157-159)cCg>cTg	p.P53L	NLRP13_ENST00000588751.1_Missense_Mutation_p.P53L	NM_176810.2	NP_789780.2	Q86W25	NAL13_HUMAN	NLR family, pyrin domain containing 13	53	DAPIN. {ECO:0000255|PROSITE- ProRule:PRU00061}.						ATP binding (GO:0005524)	p.P53L(1)		NS(2)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(13)|lung(58)|ovary(4)|pancreas(2)|prostate(2)|skin(13)|stomach(2)|urinary_tract(1)	109		Colorectal(82;3.48e-05)|Ovarian(87;0.0481)|Renal(1328;0.218)		GBM - Glioblastoma multiforme(193;0.0642)		GGGGATACGCGGGAAGTGCCC	0.547																																					p.P53L												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C158T	19						.	G	LEU/PRO	2,4404	4.2+/-10.8	0,2,2201	56.0	59.0	58.0		158	-3.9	0.0	19	dbSNP_134	58	0,8600		0,0,4300	no	missense	NLRP13	NM_176810.2	98	0,2,6501	AA,AG,GG		0.0,0.0454,0.0154	benign	53/1044	56443520	2,13004	2203	4300	6503	61135332	SO:0001583	missense	126204	exon1			AY154468	CCDS33119.1	19q13.43	2008-02-05	2006-12-08	2006-12-08	ENSG00000173572	ENSG00000173572		"""Nucleotide-binding domain and leucine rich repeat containing"""	22937	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 13"""	609660	"""NACHT, leucine rich repeat and PYD containing 13"""	NALP13		12563287	Standard	NM_176810		Approved	NOD14, PAN13, CLR19.7	uc010ygg.2	Q86W25	OTTHUMG00000167839	ENST00000342929.3:c.158C>T	19.37:g.56443520G>A	ENSP00000343891:p.Pro53Leu		61135332	NM_176810	Q7RTR5	Missense_Mutation	SNP	ENST00000342929.3	37	CCDS33119.1	.	.	.	.	.	.	.	.	.	.	G	1.849	-0.465433	0.04476	4.54E-4	0.0	ENSG00000173572	ENST00000342929	T	0.44881	0.91	1.97	-3.94	0.04130	Pyrin (2);DEATH-like (2);	.	.	.	.	T	0.14485	0.0350	N	0.08118	0	0.09310	N	1	B	0.12013	0.005	B	0.09377	0.004	T	0.21965	-1.0230	9	0.11794	T	0.64	.	0.8137	0.01098	0.1546:0.2419:0.1985:0.4049	.	53	Q86W25	NAL13_HUMAN	L	53	ENSP00000343891:P53L	ENSP00000343891:P53L	P	-	2	0	NLRP13	61135332	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	-2.647000	0.00860	-1.503000	0.01812	-0.229000	0.12294	CCG		0.547	NLRP13-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000396560.1	NM_176810	
CELSR2	1952	broad.mit.edu	37	1	109813857	109813857	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3860-01A-02W-0900-09	TCGA-AA-3860-10A-01W-0902-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AA-3860-01A-02W-0900-09	TCGA-AA-3860-10A-01W-0902-09	g.chr1:109813857A>G	ENST00000271332.3	+	26	7676	c.7615A>G	c.(7615-7617)Atc>Gtc	p.I2539V	CELSR2_ENST00000498157.1_3'UTR	NM_001408.2	NP_001399.1	Q9HCU4	CELR2_HUMAN	cadherin, EGF LAG seven-pass G-type receptor 2	2539					cerebrospinal fluid secretion (GO:0033326)|cilium assembly (GO:0042384)|cilium movement (GO:0003341)|dendrite morphogenesis (GO:0048813)|G-protein coupled receptor signaling pathway (GO:0007186)|homophilic cell adhesion (GO:0007156)|neural plate anterior/posterior regionalization (GO:0021999)|neuron migration (GO:0001764)|neuropeptide signaling pathway (GO:0007218)|regulation of cell-cell adhesion (GO:0022407)|regulation of protein localization (GO:0032880)|regulation of transcription, DNA-templated (GO:0006355)|ventricular system development (GO:0021591)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)	p.I2539V(1)		NS(1)|autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|cervix(3)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(14)|lung(27)|ovary(5)|prostate(1)|skin(3)|urinary_tract(2)	82		all_epithelial(167;0.000114)|all_lung(203;0.000321)|Lung NSC(277;0.000626)|Breast(1374;0.244)		Colorectal(144;0.0296)|Lung(183;0.067)|COAD - Colon adenocarcinoma(174;0.114)|Epithelial(280;0.193)|all cancers(265;0.219)		CTTCCTGTACATCCTGGCGGC	0.647																																					p.I2539V	NSCLC(158;1285 2011 34800 34852 42084)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A7615G	1						.						95.0	107.0	103.0					1																	109813857		2203	4300	6503	109615380	SO:0001583	missense	1952	exon26			D87469	CCDS796.1	1p13.3	2014-08-08	2013-02-18		ENSG00000143126	ENSG00000143126		"""Cadherins / Major cadherins"", ""-"", ""GPCR / Class B : Orphans"""	3231	protein-coding gene	gene with protein product		604265	"""cadherin, EGF LAG seven-pass G-type receptor 2, flamingo (Drosophila) homolog"""	EGFL2		9693030, 10907856	Standard	NM_001408		Approved	KIAA0279, MEGF3, Flamingo1, CDHF10	uc001dxa.4	Q9HCU4	OTTHUMG00000012003	ENST00000271332.3:c.7615A>G	1.37:g.109813857A>G	ENSP00000271332:p.Ile2539Val		109615380	NM_001408	Q5T2Y7|Q92566	Missense_Mutation	SNP	ENST00000271332.3	37	CCDS796.1	.	.	.	.	.	.	.	.	.	.	A	2.685	-0.274555	0.05679	.	.	ENSG00000143126	ENST00000271332	T	0.47869	0.83	4.69	3.54	0.40534	GPCR, family 2-like (1);	.	.	.	.	T	0.06826	0.0174	N	0.05306	-0.075	0.26129	N	0.980448	B	0.02656	0.0	B	0.10450	0.005	T	0.39603	-0.9606	9	0.06099	T	0.92	.	4.8088	0.13333	0.6604:0.2089:0.1306:0.0	.	2539	Q9HCU4	CELR2_HUMAN	V	2539	ENSP00000271332:I2539V	ENSP00000271332:I2539V	I	+	1	0	CELSR2	109615380	0.685000	0.27652	1.000000	0.80357	0.995000	0.86356	1.446000	0.35090	1.971000	0.57363	0.459000	0.35465	ATC		0.647	CELSR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033200.1	NM_001408	
KCNT2	343450	broad.mit.edu	37	1	196285078	196285078	+	Silent	SNP	G	G	A			TCGA-AA-3860-01A-02W-0900-09	TCGA-AA-3860-10A-01W-0902-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3860-01A-02W-0900-09	TCGA-AA-3860-10A-01W-0902-09	g.chr1:196285078G>A	ENST00000294725.9	-	21	3342	c.2427C>T	c.(2425-2427)gcC>gcT	p.A809A	KCNT2_ENST00000367433.5_Silent_p.A785A|KCNT2_ENST00000609185.1_Silent_p.A735A|KCNT2_ENST00000451324.2_3'UTR|KCNT2_ENST00000498426.1_5'UTR|KCNT2_ENST00000367431.4_Silent_p.A735A			Q6UVM3	KCNT2_HUMAN	potassium channel, subfamily T, member 2	809					potassium ion transmembrane transport (GO:0071805)	voltage-gated potassium channel complex (GO:0008076)	ATP binding (GO:0005524)|calcium-activated potassium channel activity (GO:0015269)|voltage-gated potassium channel activity (GO:0005249)	p.A809A(1)		NS(1)|breast(4)|endometrium(5)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(16)|lung(43)|ovary(5)|pancreas(1)|prostate(1)|skin(11)|stomach(2)|upper_aerodigestive_tract(1)	97						AGTCTTCCTCGGCACTCATGG	0.443																																					p.A809A												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C2427T	1						.						143.0	116.0	125.0					1																	196285078		2203	4300	6503	194551701	SO:0001819	synonymous_variant	343450	exon21			BX647852, AY359444, AK127807	CCDS1384.1, CCDS72994.1, CCDS72995.1	1q31.3	2012-07-05			ENSG00000162687	ENSG00000162687		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels, calcium-activated"""	18866	protein-coding gene	gene with protein product	"""sodium and chloride activated ATP sensitive potassium channel"""	610044				16382103	Standard	NM_198503		Approved	KCa4.2, SLICK, SLO2.1	uc001gtd.1	Q6UVM3	OTTHUMG00000035611	ENST00000294725.9:c.2427C>T	1.37:g.196285078G>A			194551701	NM_198503	Q3SY59|Q5VTN1|Q6ZMT3	Silent	SNP	ENST00000294725.9	37	CCDS1384.1																																																																																				0.443	KCNT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086418.2	NM_198503	
ANKEF1	63926	broad.mit.edu	37	20	10030811	10030811	+	Missense_Mutation	SNP	G	G	T	rs267606072		TCGA-AA-3860-01A-02W-0900-09	TCGA-AA-3860-10A-01W-0902-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AA-3860-01A-02W-0900-09	TCGA-AA-3860-10A-01W-0902-09	g.chr20:10030811G>T	ENST00000378380.3	+	6	1923	c.1594G>T	c.(1594-1596)Gcg>Tcg	p.A532S	SNAP25-AS1_ENST00000421143.2_RNA|ANKEF1_ENST00000378392.1_Missense_Mutation_p.A532S|SNAP25-AS1_ENST00000603542.1_RNA|ANKEF1_ENST00000488991.1_3'UTR	NM_198798.1	NP_942093.1	Q9NU02	ANKE1_HUMAN	ankyrin repeat and EF-hand domain containing 1	532							calcium ion binding (GO:0005509)	p.A532S(1)									GCTAATGACGGCGTGTGCAAG	0.438																																					p.A532S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1594T	20						.						53.0	55.0	54.0					20																	10030811		2203	4299	6502	9978811	SO:0001583	missense	63926	exon6			AK025322	CCDS13108.1	20p12.2	2013-01-11	2013-01-11	2013-01-11	ENSG00000132623	ENSG00000132623		"""EF-hand domain containing"", ""Ankyrin repeat domain containing"""	15803	protein-coding gene	gene with protein product			"""ankyrin repeat domain 5"""	ANKRD5		17142250	Standard	NM_022096		Approved	FLJ21669, dJ839B4.6	uc002wnp.3	Q9NU02	OTTHUMG00000031860	ENST00000378380.3:c.1594G>T	20.37:g.10030811G>T	ENSP00000367631:p.Ala532Ser		9978811	NM_198798	B3KUQ0|Q9H6Y9	Missense_Mutation	SNP	ENST00000378380.3	37	CCDS13108.1	.	.	.	.	.	.	.	.	.	.	G	28.8	4.955826	0.92726	.	.	ENSG00000132623	ENST00000378392;ENST00000378380	T;T	0.80824	-1.42;-1.42	5.65	5.65	0.86999	Ankyrin repeat-containing domain (4);	0.000000	0.85682	D	0.000000	D	0.89993	0.6876	M	0.75150	2.29	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.89420	0.3709	10	0.54805	T	0.06	-1.657	20.0781	0.97751	0.0:0.0:1.0:0.0	.	532	Q9NU02	ANKR5_HUMAN	S	532	ENSP00000367644:A532S;ENSP00000367631:A532S	ENSP00000367631:A532S	A	+	1	0	ANKRD5	9978811	1.000000	0.71417	0.459000	0.27081	0.961000	0.63080	8.794000	0.91867	2.817000	0.96982	0.563000	0.77884	GCG		0.438	ANKEF1-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077968.2	NM_022096	
RIMBP3	85376	broad.mit.edu	37	22	20457514	20457514	+	Missense_Mutation	SNP	T	T	G	rs200584390		TCGA-AA-3860-01A-02W-0900-09	TCGA-AA-3860-10A-01W-0902-09	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3860-01A-02W-0900-09	TCGA-AA-3860-10A-01W-0902-09	g.chr22:20457514T>G	ENST00000426804.1	-	1	4272	c.3788A>C	c.(3787-3789)gAa>gCa	p.E1263A	SCARNA17_ENST00000516762.1_RNA|SCARNA18_ENST00000516215.1_RNA|RN7SKP131_ENST00000363006.1_RNA	NM_015672.1	NP_056487.1	Q9UFD9	RIM3A_HUMAN	RIMS binding protein 3	1263								p.E1263A(1)		breast(2)|central_nervous_system(1)|cervix(1)|endometrium(2)|large_intestine(3)|lung(1)|prostate(1)|skin(1)|urinary_tract(1)	13	Colorectal(54;0.0993)|Melanoma(16;0.165)		LUSC - Lung squamous cell carcinoma(15;0.0405)|Lung(15;0.224)			ACATTCTCCTTCTGAGCCCAG	0.592																																					p.E1263A												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A3788C	22						.																																			18837514	SO:0001583	missense	85376	exon1			AB051453	CCDS46665.1	22q11.21	2014-05-06			ENSG00000196622	ENSG00000275793			29344	protein-coding gene	gene with protein product		612699				11258795, 17855024	Standard	NM_015672		Approved	KIAA1666, RIMBP3.1, RIMBP3A	uc002zsd.4	Q9UFD9	OTTHUMG00000188355	ENST00000426804.1:c.3788A>C	22.37:g.20457514T>G	ENSP00000391564:p.Glu1263Ala		18837514	NM_015672	Q8IYP7|Q9BY94|Q9UFQ5	Missense_Mutation	SNP	ENST00000426804.1	37	CCDS46665.1	.	.	.	.	.	.	.	.	.	.	T	14.31	2.497585	0.44455	.	.	ENSG00000196622	ENST00000355186;ENST00000426804	T	0.20069	2.1	3.38	3.38	0.38709	.	0.974387	0.08394	N	0.952473	T	0.13372	0.0324	L	0.29908	0.895	0.44221	P	0.002943000000000029	B	0.33694	0.421	B	0.25140	0.058	T	0.12477	-1.0546	9	0.18276	T	0.48	-1.0666	8.3984	0.32570	0.0:0.0:0.0:1.0	.	1169	Q9UFD9	RIM3A_HUMAN	A	1169;1263	ENSP00000391564:E1263A	ENSP00000347318:E1169A	E	-	2	0	RIMBP3	18837514	0.928000	0.31464	0.559000	0.28332	0.264000	0.26372	1.444000	0.35068	1.548000	0.49413	0.347000	0.21830	GAA		0.592	RIMBP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318945.2	NM_015672	
TANC1	85461	broad.mit.edu	37	2	160031566	160031566	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3860-01A-02W-0900-09	TCGA-AA-3860-10A-01W-0902-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AA-3860-01A-02W-0900-09	TCGA-AA-3860-10A-01W-0902-09	g.chr2:160031566G>T	ENST00000263635.6	+	12	1843	c.1606G>T	c.(1606-1608)Gcc>Tcc	p.A536S	TANC1_ENST00000454300.1_Missense_Mutation_p.A430S	NM_001145909.1|NM_033394.2	NP_001139381.1|NP_203752.2	Q9C0D5	TANC1_HUMAN	tetratricopeptide repeat, ankyrin repeat and coiled-coil containing 1	536					dendritic spine maintenance (GO:0097062)|myoblast fusion (GO:0007520)|visual learning (GO:0008542)	axon terminus (GO:0043679)|cell junction (GO:0030054)|dendrite (GO:0030425)|neuronal cell body (GO:0043025)|postsynaptic membrane (GO:0045211)		p.A536S(1)		breast(3)|central_nervous_system(4)|cervix(2)|endometrium(6)|kidney(4)|large_intestine(9)|lung(25)|ovary(7)|pancreas(1)|prostate(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(2)	77						CCATCAGCTGGCCGCCTACAG	0.592																																					p.A536S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1606T	2						.						137.0	139.0	138.0					2																	160031566		2039	4198	6237	159739812	SO:0001583	missense	85461	exon12			AB051515	CCDS42766.1	2q24.2	2013-01-11			ENSG00000115183	ENSG00000115183		"""Ankyrin repeat domain containing"", ""Tetratricopeptide (TTC) repeat domain containing"""	29364	protein-coding gene	gene with protein product	"""rolling pebbles homolog B (Drosophila)"""	611397				15673434	Standard	NM_033394		Approved	KIAA1728, ROLSB	uc002uag.3	Q9C0D5	OTTHUMG00000153945	ENST00000263635.6:c.1606G>T	2.37:g.160031566G>T	ENSP00000263635:p.Ala536Ser		159739812	NM_033394	C9JD88|Q49AI8	Missense_Mutation	SNP	ENST00000263635.6	37	CCDS42766.1	.	.	.	.	.	.	.	.	.	.	G	9.388	1.074861	0.20227	.	.	ENSG00000115183	ENST00000454300;ENST00000263635	T;T	0.68331	-0.32;-0.31	5.6	3.77	0.43336	.	0.249560	0.41823	D	0.000817	T	0.35653	0.0939	N	0.03115	-0.41	0.26242	N	0.978859	B;B;B	0.13145	0.001;0.002;0.007	B;B;B	0.12156	0.001;0.002;0.007	T	0.14392	-1.0474	10	0.14656	T	0.56	.	6.3908	0.21585	0.1504:0.0:0.6834:0.1662	.	528;430;536	B9EK39;Q9C0D5-2;Q9C0D5	.;.;TANC1_HUMAN	S	430;536	ENSP00000396339:A430S;ENSP00000263635:A536S	ENSP00000263635:A536S	A	+	1	0	TANC1	159739812	0.000000	0.05858	1.000000	0.80357	0.996000	0.88848	0.186000	0.16978	2.638000	0.89438	0.655000	0.94253	GCC		0.592	TANC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333135.1		
REG1A	5967	broad.mit.edu	37	2	79350004	79350004	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3860-01A-02W-0900-09	TCGA-AA-3860-10A-01W-0902-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AA-3860-01A-02W-0900-09	TCGA-AA-3860-10A-01W-0902-09	g.chr2:79350004C>T	ENST00000233735.1	+	5	462	c.359C>T	c.(358-360)tCc>tTc	p.S120F		NM_002909.4	NP_002900.2	P05451	REG1A_HUMAN	regenerating islet-derived 1 alpha	120	C-type lectin. {ECO:0000255|PROSITE- ProRule:PRU00040}.				positive regulation of cell proliferation (GO:0008284)	extracellular vesicular exosome (GO:0070062)	carbohydrate binding (GO:0030246)|growth factor activity (GO:0008083)	p.S120F(1)		NS(1)|breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(5)|lung(26)|prostate(1)|upper_aerodigestive_tract(1)	39						TCCCTGGTCTCCTACAAGTCC	0.567																																					p.S120F												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C359T	2						.						120.0	117.0	118.0					2																	79350004		2203	4300	6503	79203512	SO:0001583	missense	5967	exon5				CCDS1964.1	2p12	2008-09-04	2008-06-04		ENSG00000115386	ENSG00000115386			9951	protein-coding gene	gene with protein product	"""pancreatic stone protein"", ""pancreatic thread protein"""	167770	"""regenerating islet-derived 1 alpha (pancreatic stone protein, pancreatic thread protein)"""	REG		2332435, 8333731	Standard	NM_002909		Approved	PSP, PTP, PSPS, PSPS1	uc002snz.3	P05451	OTTHUMG00000130016	ENST00000233735.1:c.359C>T	2.37:g.79350004C>T	ENSP00000233735:p.Ser120Phe		79203512	NM_002909	P11379|Q4ZG28	Missense_Mutation	SNP	ENST00000233735.1	37	CCDS1964.1	.	.	.	.	.	.	.	.	.	.	c	15.97	2.988446	0.53934	.	.	ENSG00000115386	ENST00000233735	T	0.19938	2.11	2.92	-2.48	0.06423	C-type lectin fold (1);C-type lectin-like (1);C-type lectin (3);	1.395990	0.05129	N	0.492187	T	0.31670	0.0804	M	0.75150	2.29	0.09310	N	1	D	0.62365	0.991	P	0.52454	0.699	T	0.34079	-0.9843	10	0.72032	D	0.01	.	3.2857	0.06931	0.2047:0.2401:0.0:0.5552	.	120	P05451	REG1A_HUMAN	F	120	ENSP00000233735:S120F	ENSP00000233735:S120F	S	+	2	0	REG1A	79203512	0.000000	0.05858	0.002000	0.10522	0.422000	0.31414	-0.323000	0.07997	-0.439000	0.07222	0.557000	0.71058	TCC		0.567	REG1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252289.1	NM_002909	
TTN	7273	broad.mit.edu	37	2	179616503	179616503	+	Intron	SNP	G	G	A			TCGA-AA-3860-01A-02W-0900-09	TCGA-AA-3860-10A-01W-0902-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AA-3860-01A-02W-0900-09	TCGA-AA-3860-10A-01W-0902-09	g.chr2:179616503G>A	ENST00000591111.1	-	45	10585				TTN-AS1_ENST00000590773.1_RNA|TTN_ENST00000589042.1_Intron|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000359218.5_Intron|TTN_ENST00000460472.2_Intron|TTN_ENST00000360870.5_Missense_Mutation_p.R3542W|TTN_ENST00000342175.6_Intron|TTN-AS1_ENST00000578746.1_RNA|TTN_ENST00000342992.6_Intron			Q8WZ42	TITIN_HUMAN	titin						adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)	p.R3542W(1)		NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			GGGATGGGCCGATTGTTATGA	0.393																																					p.R3542W												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C10624T	2						.						80.0	81.0	81.0					2																	179616503		2203	4300	6503	179324748	SO:0001627	intron_variant	7273	exon46			X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	12403	protein-coding gene	gene with protein product		188840	"""cardiomyopathy, dilated 1G (autosomal dominant)"""	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.10360+1347C>T	2.37:g.179616503G>A			179324748	NM_133379	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37		.	.	.	.	.	.	.	.	.	.	G	13.88	2.369432	0.42003	.	.	ENSG00000155657	ENST00000360870	T	0.68181	-0.31	5.86	1.35	0.21983	.	.	.	.	.	T	0.77525	0.4143	M	0.64260	1.97	0.80722	D	1	D	0.76494	0.999	D	0.66196	0.942	T	0.78723	-0.2093	9	0.66056	D	0.02	.	16.1147	0.81301	0.0:0.0:0.3089:0.6911	.	3542	Q8WZ42-6	.	W	3542	ENSP00000354117:R3542W	ENSP00000354117:R3542W	R	-	1	2	TTN	179324748	0.998000	0.40836	0.084000	0.20598	0.588000	0.36517	2.618000	0.46393	0.006000	0.14734	-0.182000	0.12963	CGG		0.393	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
COL7A1	1294	broad.mit.edu	37	3	48623672	48623672	+	Silent	SNP	A	A	G			TCGA-AA-3860-01A-02W-0900-09	TCGA-AA-3860-10A-01W-0902-09	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3860-01A-02W-0900-09	TCGA-AA-3860-10A-01W-0902-09	g.chr3:48623672A>G	ENST00000328333.8	-	27	3665	c.3558T>C	c.(3556-3558)aaT>aaC	p.N1186N	COL7A1_ENST00000454817.1_Silent_p.N1186N	NM_000094.3	NP_000085.1	Q02388	CO7A1_HUMAN	collagen, type VII, alpha 1	1186	Nonhelical region (NC1).|VWFA 2. {ECO:0000255|PROSITE- ProRule:PRU00219}.				cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|endodermal cell differentiation (GO:0035987)|epidermis development (GO:0008544)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)	basement membrane (GO:0005604)|collagen type VII trimer (GO:0005590)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)	serine-type endopeptidase inhibitor activity (GO:0004867)	p.N1186N(1)		NS(3)|breast(8)|central_nervous_system(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(18)|lung(57)|ovary(7)|prostate(5)|skin(9)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(5)	137				BRCA - Breast invasive adenocarcinoma(193;0.000293)|KIRC - Kidney renal clear cell carcinoma(197;0.00558)|Kidney(197;0.00632)		ACATCACCACATTAAGCCCTA	0.597																																					p.N1186N												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.T3558C	3						.						115.0	129.0	124.0					3																	48623672		2202	4300	6502	48598676	SO:0001819	synonymous_variant	1294	exon27			L02870	CCDS2773.1	3p21.1	2014-09-17	2008-08-01		ENSG00000114270	ENSG00000114270		"""Collagens"", ""Fibronectin type III domain containing"""	2214	protein-coding gene	gene with protein product	"""collagen VII, alpha-1 polypeptide"", ""LC collagen"""	120120	"""epidermolysis bullosa, dystrophic, dominant and recessive"""	EBDCT, EBD1, EBR1		1871109	Standard	NM_000094		Approved		uc003ctz.2	Q02388	OTTHUMG00000133541	ENST00000328333.8:c.3558T>C	3.37:g.48623672A>G			48598676	NM_000094	Q14054|Q16507	Silent	SNP	ENST00000328333.8	37	CCDS2773.1																																																																																				0.597	COL7A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257519.1	NM_000094	
FOXP1	27086	broad.mit.edu	37	3	71015207	71015207	+	Splice_Site	SNP	C	C	A			TCGA-AA-3860-01A-02W-0900-09	TCGA-AA-3860-10A-01W-0902-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AA-3860-01A-02W-0900-09	TCGA-AA-3860-10A-01W-0902-09	g.chr3:71015207C>A	ENST00000318789.4	-	20	2248	c.1723G>T	c.(1723-1725)Gct>Tct	p.A575S	FOXP1_ENST00000493089.1_Splice_Site_p.A574S|FOXP1_ENST00000484350.1_Splice_Site_p.A499S|FOXP1_ENST00000468577.1_Splice_Site_p.A511S|FOXP1_ENST00000498215.1_Splice_Site_p.A575S|FOXP1_ENST00000491238.1_Splice_Site_p.A577S|FOXP1_ENST00000475937.1_Splice_Site_p.A575S	NM_001244810.1|NM_001244813.1|NM_032682.5	NP_001231739.1|NP_001231742.1|NP_116071.2	Q9H334	FOXP1_HUMAN	forkhead box P1	575					negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.A575S(1)		breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(7)|lung(8)|ovary(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	31		Lung NSC(201;4.62e-05)|Prostate(10;0.0181)|Hepatocellular(537;0.186)|Myeloproliferative disorder(1037;0.209)		BRCA - Breast invasive adenocarcinoma(55;1.17e-05)|Epithelial(33;1.39e-05)|LUSC - Lung squamous cell carcinoma(21;2.35e-05)|Lung(16;4.26e-05)		GCCATTGAAGCCTGTCATCAA	0.423			T	PAX5	ALL																																p.A575S			Dom	yes		3	3p14.1	27086	forkhead box P1		L	.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1723T	3						.						82.0	79.0	80.0					3																	71015207		2203	4300	6503	71097897	SO:0001630	splice_region_variant	27086	exon20			AF146696	CCDS2914.1, CCDS33785.1, CCDS58837.1, CCDS58838.1, CCDS58839.1, CCDS74963.1, CCDS74964.1	3p14.1	2008-07-18			ENSG00000114861	ENSG00000114861		"""Forkhead boxes"""	3823	protein-coding gene	gene with protein product	"""fork head-related protein like B"", ""glutamine-rich factor 1"", ""PAX5/FOXP1 fusion protein"""	605515				8265594, 11751404	Standard	NM_032682		Approved	QRF1, 12CC4, HSPC215, hFKH1B	uc003doj.3	Q9H334	OTTHUMG00000158803	ENST00000318789.4:c.1723-1G>T	3.37:g.71015207C>A			71097897	NM_032682	A3QVP8|B3KV70|G5E9V8|Q8NAN6|Q9BSG9|Q9H332|Q9H333|Q9P0R1	Missense_Mutation	SNP	ENST00000318789.4	37	CCDS2914.1	.	.	.	.	.	.	.	.	.	.	C	22.6	4.317168	0.81469	.	.	ENSG00000114861	ENST00000318789;ENST00000358280;ENST00000475937;ENST00000497355;ENST00000491238;ENST00000493089;ENST00000498215;ENST00000484350;ENST00000468577	D;D;D;D;D;D;D;D	0.95171	-2.71;-2.71;-2.82;-2.82;-2.72;-2.71;-2.71;-3.63	6.17	6.17	0.99709	.	0.000000	0.85682	D	0.000000	D	0.96500	0.8858	M	0.67397	2.05	0.80722	D	1	B;P;D	0.54964	0.376;0.752;0.969	B;P;P	0.57720	0.188;0.642;0.826	D	0.95811	0.8841	10	0.59425	D	0.04	.	20.8794	0.99867	0.0:1.0:0.0:0.0	.	574;499;575	G5E9V8;Q8NAN6;Q9H334	.;.;FOXP1_HUMAN	S	575;387;575;471;577;574;575;499;511	ENSP00000318902:A575S;ENSP00000419393:A575S;ENSP00000418225:A471S;ENSP00000420736:A577S;ENSP00000418524:A574S;ENSP00000418102:A575S;ENSP00000417857:A499S;ENSP00000418883:A511S	ENSP00000318902:A575S	A	-	1	0	FOXP1	71097897	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	5.717000	0.68446	2.941000	0.99782	0.655000	0.94253	GCT		0.423	FOXP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000352250.1	NM_032682	Missense_Mutation
KIT	3815	broad.mit.edu	37	4	55561886	55561886	+	Silent	SNP	C	C	T	rs373066995		TCGA-AA-3860-01A-02W-0900-09	TCGA-AA-3860-10A-01W-0902-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3860-01A-02W-0900-09	TCGA-AA-3860-10A-01W-0902-09	g.chr4:55561886C>T	ENST00000288135.5	+	2	373	c.276C>T	c.(274-276)acC>acT	p.T92T		NM_000222.2|NM_001093772.1	NP_000213.1|NP_001087241.1	P10721	KIT_HUMAN	v-kit Hardy-Zuckerman 4 feline sarcoma viral oncogene homolog	92	Ig-like C2-type 1.				actin cytoskeleton reorganization (GO:0031532)|activation of MAPK activity (GO:0000187)|cell chemotaxis (GO:0060326)|cellular response to thyroid hormone stimulus (GO:0097067)|cytokine-mediated signaling pathway (GO:0019221)|dendritic cell cytokine production (GO:0002371)|detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|digestive tract development (GO:0048565)|ectopic germ cell programmed cell death (GO:0035234)|embryonic hemopoiesis (GO:0035162)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial cell proliferation (GO:0050673)|erythrocyte differentiation (GO:0030218)|erythropoietin-mediated signaling pathway (GO:0038162)|Fc receptor signaling pathway (GO:0038093)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|germ cell migration (GO:0008354)|glycosphingolipid metabolic process (GO:0006687)|hemopoiesis (GO:0030097)|immature B cell differentiation (GO:0002327)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|Kit signaling pathway (GO:0038109)|lamellipodium assembly (GO:0030032)|lymphoid progenitor cell differentiation (GO:0002320)|male gonad development (GO:0008584)|mast cell chemotaxis (GO:0002551)|mast cell cytokine production (GO:0032762)|mast cell degranulation (GO:0043303)|mast cell differentiation (GO:0060374)|mast cell proliferation (GO:0070662)|megakaryocyte development (GO:0035855)|melanocyte adhesion (GO:0097326)|melanocyte differentiation (GO:0030318)|melanocyte migration (GO:0097324)|myeloid progenitor cell differentiation (GO:0002318)|negative regulation of programmed cell death (GO:0043069)|neurotrophin TRK receptor signaling pathway (GO:0048011)|ovarian follicle development (GO:0001541)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|pigmentation (GO:0043473)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of JAK-STAT cascade (GO:0046427)|positive regulation of long-term neuronal synaptic plasticity (GO:0048170)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of Notch signaling pathway (GO:0045747)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of phospholipase C activity (GO:0010863)|positive regulation of pseudopodium assembly (GO:0031274)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of tyrosine phosphorylation of Stat1 protein (GO:0042511)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|positive regulation of tyrosine phosphorylation of Stat5 protein (GO:0042523)|protein autophosphorylation (GO:0046777)|regulation of cell proliferation (GO:0042127)|regulation of cell shape (GO:0008360)|regulation of developmental pigmentation (GO:0048070)|signal transduction (GO:0007165)|signal transduction by phosphorylation (GO:0023014)|somatic stem cell division (GO:0048103)|somatic stem cell maintenance (GO:0035019)|spermatid development (GO:0007286)|spermatogenesis (GO:0007283)|stem cell differentiation (GO:0048863)|stem cell maintenance (GO:0019827)|T cell differentiation (GO:0030217)|visual learning (GO:0008542)	acrosomal vesicle (GO:0001669)|cell-cell junction (GO:0005911)|cytoplasmic side of plasma membrane (GO:0009898)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|mast cell granule (GO:0042629)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cytokine binding (GO:0019955)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|stem cell factor receptor activity (GO:0005020)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)	p.T92T(1)		NS(8)|autonomic_ganglia(1)|bone(21)|breast(2)|central_nervous_system(4)|endometrium(10)|eye(12)|genital_tract(18)|haematopoietic_and_lymphoid_tissue(1820)|kidney(17)|large_intestine(17)|lung(27)|ovary(23)|pancreas(4)|prostate(1)|salivary_gland(15)|skin(228)|soft_tissue(4117)|stomach(3)|testis(55)|thymus(7)|upper_aerodigestive_tract(1)	6411	all_cancers(7;0.00453)|all_lung(4;0.000565)|Lung NSC(11;0.00129)|all_epithelial(27;0.0104)|Glioma(25;0.08)|all_neural(26;0.101)		LUSC - Lung squamous cell carcinoma(32;0.000276)|Epithelial(7;0.209)	Colorectal(1;0.0276)|COAD - Colon adenocarcinoma(1;0.171)	Dasatinib(DB01254)|Imatinib(DB00619)|Nilotinib(DB04868)|Pazopanib(DB06589)|Ponatinib(DB08901)|Regorafenib(DB08896)|Sorafenib(DB00398)|Sunitinib(DB01268)	CCACCAACACCGGCAAATACA	0.438		1	"""Mis, O"""		"""GIST, AML, TGCT, mastocytosis, mucosal melanoma"""	"""GIST, epithelioma"""	Piebald trait		Piebaldism;Mast Cell disease, Familial Clustering of;Gastrointestinal Stromal Tumors, Sporadic Multiple Primary;Familial Gastrointestinal Stromal Tumors																												p.T92T		yes	Dom	yes	Familial gastrointestinal stromal tumour	4	4q12	3815	v-kit Hardy-Zuckerman 4 feline sarcoma viral oncogene homolog	yes	"""L, M, O, E"""	.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C276T	4						.	T	,	0,4406		0,0,2203	88.0	82.0	84.0		276,276	-10.4	0.0	4		84	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous	KIT	NM_000222.2,NM_001093772.1	,	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	,	92/977,92/973	55561886	1,13005	2203	4300	6503	55256643	SO:0001819	synonymous_variant	3815	exon2	Familial Cancer Database	Piebald trait;incl.: Familial Cutaneous Mastocytosis (Urticaria Pigmentosum);Sporadic Multiple GIST;Familial GIST, incl. Multiple Familial Gastrointestinal Autonomic Nerve Tumors (GANT)	S67773	CCDS3496.1, CCDS47058.1	4q12	2014-09-17			ENSG00000157404	ENSG00000157404		"""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6342	protein-coding gene	gene with protein product		164920	"""piebald trait"""	PBT		9027509	Standard	NM_001093772		Approved	CD117, SCFR, C-Kit	uc010igr.3	P10721	OTTHUMG00000128713	ENST00000288135.5:c.276C>T	4.37:g.55561886C>T			55256643	NM_000222	B5A956|D5LXN2|D5M931|F5H8F8|Q6IQ28|Q99662|Q9UM99	Silent	SNP	ENST00000288135.5	37	CCDS3496.1																																																																																				0.438	KIT-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000250618.1		
APC	324	broad.mit.edu	37	5	112128201	112128201	+	Nonsense_Mutation	SNP	T	T	A			TCGA-AA-3860-01A-02W-0900-09	TCGA-AA-3860-10A-01W-0902-09	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AA-3860-01A-02W-0900-09	TCGA-AA-3860-10A-01W-0902-09	g.chr5:112128201T>A	ENST00000457016.1	+	7	1084	c.704T>A	c.(703-705)tTa>tAa	p.L235*	APC_ENST00000508376.2_Nonsense_Mutation_p.L235*|APC_ENST00000257430.4_Nonsense_Mutation_p.L235*			P25054	APC_HUMAN	adenomatous polyposis coli	235	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.L235*(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)		CGACAGCTTTTACAGTCCCAA	0.313		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.L235X	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"""	.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.T704A	5						.						82.0	79.0	80.0					5																	112128201		2202	4300	6502	112156100	SO:0001587	stop_gained	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.704T>A	5.37:g.112128201T>A	ENSP00000413133:p.Leu235*		112156100	NM_001127510	D3DT03|Q15162|Q15163|Q93042	Nonsense_Mutation	SNP	ENST00000457016.1	37	CCDS4107.1	.	.	.	.	.	.	.	.	.	.	T	40	8.360462	0.98777	.	.	ENSG00000134982	ENST00000457016;ENST00000257430;ENST00000508376;ENST00000512211	.	.	.	5.1	5.1	0.69264	.	0.000000	0.64402	D	0.000002	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-11.2897	15.1596	0.72771	0.0:0.0:0.0:1.0	.	.	.	.	X	235	.	ENSP00000257430:L235X	L	+	2	0	APC	112156100	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.583000	0.67484	2.038000	0.60285	0.477000	0.44152	TTA		0.313	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038	
APC	324	broad.mit.edu	37	5	112175303	112175303	+	Nonsense_Mutation	SNP	C	C	T	rs121913327		TCGA-AA-3860-01A-02W-0900-09	TCGA-AA-3860-10A-01W-0902-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3860-01A-02W-0900-09	TCGA-AA-3860-10A-01W-0902-09	g.chr5:112175303C>T	ENST00000457016.1	+	16	4392	c.4012C>T	c.(4012-4014)Cag>Tag	p.Q1338*	APC_ENST00000508376.2_Nonsense_Mutation_p.Q1338*|APC_ENST00000257430.4_Nonsense_Mutation_p.Q1338*|CTC-554D6.1_ENST00000520401.1_Intron			P25054	APC_HUMAN	adenomatous polyposis coli	1338	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.Q1338*(30)|p.L1337fs*76(4)|p.?(1)|p.K1192fs*3(1)|p.V1326fs*3(1)|p.S1335fs*70(1)|p.L1337>?(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)		CAGCAGACTGCAGGGTTCTAG	0.458	Q1338*(SW480_LARGE_INTESTINE)|Q1338*(SW620_LARGE_INTESTINE)	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.Q1320X	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,0 	.	39	Substitution - Nonsense(30)|Deletion - Frameshift(7)|Unknown(1)|Complex(1)	large_intestine(34)|thyroid(1)|biliary_tract(1)|stomach(1)|soft_tissue(1)|skin(1)	c.C3958T	5	GRCh37	CM930029	APC	M	rs121913327	.						57.0	60.0	59.0					5																	112175303		2202	4300	6502	112203202	SO:0001587	stop_gained	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.4012C>T	5.37:g.112175303C>T	ENSP00000413133:p.Gln1338*		112203202	NM_001127511	D3DT03|Q15162|Q15163|Q93042	Nonsense_Mutation	SNP	ENST00000457016.1	37	CCDS4107.1	.	.	.	.	.	.	.	.	.	.	C	39	7.909540	0.98557	.	.	ENSG00000134982	ENST00000457016;ENST00000257430;ENST00000508376	.	.	.	6.03	6.03	0.97812	.	0.226724	0.46145	D	0.000316	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-2.6325	20.1672	0.98154	0.0:1.0:0.0:0.0	.	.	.	.	X	1338	.	.	Q	+	1	0	APC	112203202	1.000000	0.71417	1.000000	0.80357	0.846000	0.48090	4.607000	0.61133	2.861000	0.98227	0.655000	0.94253	CAG		0.458	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038	
PCDHB6	56130	broad.mit.edu	37	5	140530654	140530654	+	Silent	SNP	G	G	A			TCGA-AA-3860-01A-02W-0900-09	TCGA-AA-3860-10A-01W-0902-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3860-01A-02W-0900-09	TCGA-AA-3860-10A-01W-0902-09	g.chr5:140530654G>A	ENST00000231136.1	+	1	816	c.816G>A	c.(814-816)tcG>tcA	p.S272S	PCDHB6_ENST00000543635.1_Silent_p.S136S	NM_018939.2	NP_061762.1	Q9Y5E3	PCDB6_HUMAN	protocadherin beta 6	272	Cadherin 3. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)	p.S272S(2)		cervix(1)|endometrium(14)|kidney(6)|large_intestine(16)|liver(1)|lung(33)|ovary(1)|pancreas(2)|prostate(1)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	84			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			ATGCAGGATCGTTTGGGAAGG	0.493																																					p.S272S												.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.G816A	5						.						72.0	74.0	73.0					5																	140530654		2203	4300	6503	140510838	SO:0001819	synonymous_variant	56130	exon1			AF152499	CCDS4248.1	5q31	2010-01-26			ENSG00000113211	ENSG00000113211		"""Cadherins / Protocadherins : Clustered"""	8691	other	protocadherin		606332				10380929	Standard	NM_018939		Approved	PCDH-BETA6	uc003lir.3	Q9Y5E3	OTTHUMG00000129623	ENST00000231136.1:c.816G>A	5.37:g.140530654G>A			140510838	NM_018939	B2R8R9	Silent	SNP	ENST00000231136.1	37	CCDS4248.1																																																																																				0.493	PCDHB6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251818.2	NM_018939	
PCDHB13	56123	broad.mit.edu	37	5	140594855	140594855	+	Missense_Mutation	SNP	A	A	C			TCGA-AA-3860-01A-02W-0900-09	TCGA-AA-3860-10A-01W-0902-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AA-3860-01A-02W-0900-09	TCGA-AA-3860-10A-01W-0902-09	g.chr5:140594855A>C	ENST00000341948.4	+	1	1347	c.1160A>C	c.(1159-1161)cAg>cCg	p.Q387P		NM_018933.2	NP_061756.1	Q9Y5F0	PCDBD_HUMAN	protocadherin beta 13	387	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|homophilic cell adhesion (GO:0007156)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.Q387P(1)		NS(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(14)|liver(4)|lung(24)|ovary(5)|pancreas(1)|skin(4)|upper_aerodigestive_tract(1)	66			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			TGCTCCATTCAGGAGGATCTA	0.458																																					p.Q387P												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A1160C	5						.						103.0	101.0	102.0					5																	140594855		2203	4300	6503	140575039	SO:0001583	missense	56123	exon1			AF152492	CCDS4255.1	5q31	2010-01-26			ENSG00000187372	ENSG00000187372		"""Cadherins / Protocadherins : Clustered"""	8684	other	protocadherin		606339				10380929	Standard	NM_018933		Approved	PCDH-BETA13	uc003lja.1	Q9Y5F0	OTTHUMG00000129615	ENST00000341948.4:c.1160A>C	5.37:g.140594855A>C	ENSP00000345491:p.Gln387Pro		140575039	NM_018933	A8K9V6	Missense_Mutation	SNP	ENST00000341948.4	37	CCDS4255.1	.	.	.	.	.	.	.	.	.	.	N	7.731	0.699195	0.15106	.	.	ENSG00000187372	ENST00000341948;ENST00000430318;ENST00000419217	T	0.01725	4.67	3.5	0.836	0.18891	Cadherin (4);Cadherin-like (1);	.	.	.	.	T	0.01320	0.0043	N	0.25380	0.74	0.09310	N	1	B	0.06786	0.001	B	0.11329	0.006	T	0.49818	-0.8899	9	0.11182	T	0.66	.	5.078	0.14642	0.5181:0.1645:0.0:0.3174	.	387	Q9Y5F0	PCDBD_HUMAN	P	387	ENSP00000345491:Q387P	ENSP00000345491:Q387P	Q	+	2	0	PCDHB13	140575039	0.000000	0.05858	0.008000	0.14137	0.766000	0.43426	0.309000	0.19332	-0.046000	0.13446	-1.020000	0.02445	CAG		0.458	PCDHB13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251810.1	NM_018933	
FAT2	2196	broad.mit.edu	37	5	150925879	150925879	+	Missense_Mutation	SNP	G	G	C			TCGA-AA-3860-01A-02W-0900-09	TCGA-AA-3860-10A-01W-0902-09	G	G	G	C	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AA-3860-01A-02W-0900-09	TCGA-AA-3860-10A-01W-0902-09	g.chr5:150925879G>C	ENST00000261800.5	-	9	4821	c.4809C>G	c.(4807-4809)ttC>ttG	p.F1603L		NM_001447.2	NP_001438.1	Q9NYQ8	FAT2_HUMAN	FAT atypical cadherin 2	1603	Cadherin 14. {ECO:0000255|PROSITE- ProRule:PRU00043}.				epithelial cell migration (GO:0010631)|homophilic cell adhesion (GO:0007156)	cell-cell adherens junction (GO:0005913)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.F1603L(1)		NS(6)|breast(3)|central_nervous_system(3)|cervix(5)|endometrium(15)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(61)|liver(1)|lung(60)|ovary(6)|prostate(5)|skin(5)|stomach(2)|upper_aerodigestive_tract(11)|urinary_tract(1)	196		Medulloblastoma(196;0.0912)|all_hematologic(541;0.104)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			CATTGATGTTGAAGAAACCTT	0.458																																					p.F1603L												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C4809G	5						.						77.0	72.0	74.0					5																	150925879		2203	4300	6503	150906072	SO:0001583	missense	2196	exon9			AF231022	CCDS4317.1	5q33.1	2014-07-21	2013-05-31		ENSG00000086570	ENSG00000086570		"""Cadherins / Cadherin-related"""	3596	protein-coding gene	gene with protein product	"""cadherin-related family member 9"""	604269	"""FAT tumor suppressor (Drosophila) homolog 2"", ""FAT tumor suppressor homolog 2 (Drosophila)"""			9693030	Standard	NM_001447		Approved	MEGF1, CDHF8, HFAT2, CDHR9	uc003lue.4	Q9NYQ8	OTTHUMG00000130126	ENST00000261800.5:c.4809C>G	5.37:g.150925879G>C	ENSP00000261800:p.Phe1603Leu		150906072	NM_001447	O75091|Q9NSR7	Missense_Mutation	SNP	ENST00000261800.5	37	CCDS4317.1	.	.	.	.	.	.	.	.	.	.	G	14.36	2.513134	0.44660	.	.	ENSG00000086570	ENST00000261800	D	0.82526	-1.62	5.37	3.26	0.37387	Cadherin (4);Cadherin-like (1);	0.000000	0.64402	D	0.000004	D	0.90335	0.6976	M	0.87617	2.895	0.51482	D	0.999929	D	0.76494	0.999	D	0.85130	0.997	D	0.88598	0.3148	10	0.66056	D	0.02	.	7.7667	0.28984	0.4169:0.0:0.5831:0.0	.	1603	Q9NYQ8	FAT2_HUMAN	L	1603	ENSP00000261800:F1603L	ENSP00000261800:F1603L	F	-	3	2	FAT2	150906072	0.998000	0.40836	0.654000	0.29608	0.763000	0.43281	1.370000	0.34238	0.419000	0.25927	0.313000	0.20887	TTC		0.458	FAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252434.1	NM_001447	
C6orf10	10665	broad.mit.edu	37	6	32261389	32261389	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3860-01A-02W-0900-09	TCGA-AA-3860-10A-01W-0902-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AA-3860-01A-02W-0900-09	TCGA-AA-3860-10A-01W-0902-09	g.chr6:32261389G>A	ENST00000447241.2	-	23	1233	c.1061C>T	c.(1060-1062)aCg>aTg	p.T354M	C6orf10_ENST00000527965.1_Missense_Mutation_p.T338M|C6orf10_ENST00000375007.4_Missense_Mutation_p.T352M|C6orf10_ENST00000533191.1_Missense_Mutation_p.T352M|C6orf10_ENST00000375015.4_Missense_Mutation_p.T353M|C6orf10_ENST00000442822.2_Missense_Mutation_p.T345M	NM_006781.3	NP_006772.3	Q5SRN2	CF010_HUMAN	chromosome 6 open reading frame 10	354						integral component of membrane (GO:0016021)|nucleus (GO:0005634)		p.T354M(1)		cervix(1)|endometrium(2)|kidney(1)|large_intestine(7)|lung(12)|ovary(1)|skin(1)	25						CCCACTCTTCGTTACTTGGGC	0.473																																					p.T354I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1061T	6						.						198.0	192.0	194.0					6																	32261389		1511	2709	4220	32369367	SO:0001583	missense	10665	exon23			U60665	CCDS34422.1, CCDS69082.1, CCDS75430.1	6p21.32	2012-11-20			ENSG00000204296	ENSG00000204296			13922	protein-coding gene	gene with protein product	"""testis specific basic protein"""					10803852	Standard	XM_005248810		Approved	TSBP	uc021yvs.1	Q5SRN2	OTTHUMG00000031107	ENST00000447241.2:c.1061C>T	6.37:g.32261389G>A	ENSP00000415517:p.Thr354Met		32369367	NM_006781	A2BET1|A2BET2|A6NME2|B0S7R2|B0S7R3|E9PMB1|Q5SPI9|Q5SPJ0|Q5SPK9|Q5SPL0|Q5SRN3|Q5TG25|Q5TG26|Q8N4B6	Missense_Mutation	SNP	ENST00000447241.2	37	CCDS34422.1	.	.	.	.	.	.	.	.	.	.	g	11.01	1.513923	0.27123	.	.	ENSG00000204296	ENST00000442822;ENST00000447241;ENST00000375015;ENST00000533191;ENST00000527965;ENST00000375007;ENST00000375002;ENST00000305725	T;T;T;T;T;T	0.03745	3.82;3.83;3.83;3.83;3.83;3.83	2.27	-0.52	0.11935	.	.	.	.	.	T	0.02119	0.0066	L	0.36672	1.1	0.09310	N	1	D;D	0.69078	0.988;0.997	P;P	0.53401	0.556;0.725	T	0.46414	-0.9193	9	0.49607	T	0.09	-0.4936	7.489	0.27449	0.0:0.0:0.4381:0.5619	.	354;345	Q5SRN2;C9J9T8	CF010_HUMAN;.	M	345;354;353;352;338;352;351;351	ENSP00000411164:T345M;ENSP00000415517:T354M;ENSP00000364155:T353M;ENSP00000431199:T352M;ENSP00000435103:T338M;ENSP00000364146:T352M	ENSP00000303292:T351M	T	-	2	0	C6orf10	32369367	0.000000	0.05858	0.001000	0.08648	0.001000	0.01503	0.082000	0.14847	-0.104000	0.12154	-0.275000	0.10095	ACG		0.473	C6orf10-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000076178.4	NM_006781	
KLC4	89953	broad.mit.edu	37	6	43039340	43039340	+	Missense_Mutation	SNP	C	C	T	rs41274918	byFrequency	TCGA-AA-3860-01A-02W-0900-09	TCGA-AA-3860-10A-01W-0902-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AA-3860-01A-02W-0900-09	TCGA-AA-3860-10A-01W-0902-09	g.chr6:43039340C>T	ENST00000394056.2	+	11	1786	c.1291C>T	c.(1291-1293)Cgg>Tgg	p.R431W	KLC4_ENST00000259708.3_Missense_Mutation_p.R449W|KLC4_ENST00000394058.1_Missense_Mutation_p.R431W|KLC4_ENST00000347162.5_Missense_Mutation_p.R431W|KLC4_ENST00000453940.2_Missense_Mutation_p.R354W|KLC4_ENST00000479388.1_Missense_Mutation_p.R431W|RP11-387M24.5_ENST00000606123.1_RNA			Q9NSK0	KLC4_HUMAN	kinesin light chain 4	431						cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	microtubule motor activity (GO:0003777)	p.R431W(1)		endometrium(2)|large_intestine(7)|lung(5)|ovary(1)|pancreas(1)|skin(3)|urinary_tract(4)	23			all cancers(41;0.00169)|Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|OV - Ovarian serous cystadenocarcinoma(102;0.0376)|KIRC - Kidney renal clear cell carcinoma(2;0.0453)			TGCAGAGGAGCGGGAGGAAAT	0.587													C|||	3	0.000599042	0.0	0.0	5008	,	,		17649	0.0		0.002	False		,,,				2504	0.001				p.R431W												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1291T	6						.	C	TRP/ARG,TRP/ARG,TRP/ARG	1,4405	2.1+/-5.4	0,1,2202	59.0	61.0	60.0		1291,1291,1345	5.8	1.0	6	dbSNP_127	60	1,8599	1.2+/-3.3	0,1,4299	yes	missense,missense,missense	KLC4	NM_201521.1,NM_201522.1,NM_201523.1	101,101,101	0,2,6501	TT,TC,CC		0.0116,0.0227,0.0154	probably-damaging,probably-damaging,probably-damaging	431/620,431/620,449/638	43039340	2,13004	2203	4300	6503	43147318	SO:0001583	missense	89953	exon10			AK055293	CCDS4882.1, CCDS4883.1, CCDS47429.1, CCDS75459.1	6p21.1	2013-01-10	2005-09-13	2005-09-13	ENSG00000137171	ENSG00000137171		"""Tetratricopeptide (TTC) repeat domain containing"""	21624	protein-coding gene	gene with protein product			"""kinesin-like 8"""	KNSL8			Standard	NM_001289034		Approved	bA387M24.3	uc003otw.1	Q9NSK0	OTTHUMG00000014720	ENST00000394056.2:c.1291C>T	6.37:g.43039340C>T	ENSP00000377620:p.Arg431Trp		43147318	NM_201521	B3KNY4|B3KPI3|B3KSQ3|B4DME9|Q66K28|Q96EG6	Missense_Mutation	SNP	ENST00000394056.2	37	CCDS4883.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	C	17.58	3.423957	0.62733	2.27E-4	1.16E-4	ENSG00000137171	ENST00000347162;ENST00000453940;ENST00000259708;ENST00000479388;ENST00000394056;ENST00000394058	T;T;T;T;T;T	0.80824	-1.4;-1.38;-1.42;-1.4;-1.4;-1.4	5.83	5.83	0.93111	.	0.000000	0.56097	D	0.000022	D	0.88381	0.6421	M	0.85859	2.78	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.937;0.999;0.998	D	0.87053	0.2148	10	0.36615	T	0.2	-22.2004	14.7934	0.69860	0.1783:0.8217:0.0:0.0	rs41274918	354;449;431	B4DME9;Q9NSK0-3;Q9NSK0	.;.;KLC4_HUMAN	W	431;354;449;431;431;431	ENSP00000340221:R431W;ENSP00000395806:R354W;ENSP00000259708:R449W;ENSP00000418031:R431W;ENSP00000377620:R431W;ENSP00000377622:R431W	ENSP00000259708:R449W	R	+	1	2	KLC4	43147318	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	1.659000	0.37387	2.765000	0.95021	0.555000	0.69702	CGG		0.587	KLC4-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040579.2	NM_138343	
CD2AP	23607	broad.mit.edu	37	6	47563641	47563641	+	Missense_Mutation	SNP	C	C	G			TCGA-AA-3860-01A-02W-0900-09	TCGA-AA-3860-10A-01W-0902-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3860-01A-02W-0900-09	TCGA-AA-3860-10A-01W-0902-09	g.chr6:47563641C>G	ENST00000359314.5	+	12	1609	c.1153C>G	c.(1153-1155)Cca>Gca	p.P385A		NM_012120.2	NP_036252.1	Q9Y5K6	CD2AP_HUMAN	CD2-associated protein	385	Pro-rich.				mitotic nuclear division (GO:0007067)|negative regulation of transforming growth factor beta1 production (GO:0032911)|positive regulation of protein localization to nucleus (GO:1900182)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein complex assembly (GO:0006461)|regulation of actin cytoskeleton reorganization (GO:2000249)|regulation of receptor-mediated endocytosis (GO:0048259)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|substrate-dependent cell migration, cell extension (GO:0006930)|vesicle organization (GO:0016050)	actin cytoskeleton (GO:0015629)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|endocytic vesicle (GO:0030139)|extracellular vesicular exosome (GO:0070062)|filamentous actin (GO:0031941)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	SH3 domain binding (GO:0017124)|structural constituent of cytoskeleton (GO:0005200)	p.P385A(1)		kidney(1)|large_intestine(9)|lung(5)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	20			Lung(136;0.105)|LUSC - Lung squamous cell carcinoma(51;0.138)			ACCAGCAGCTCCACAAGTCCC	0.373																																					p.P385A												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1153G	6						.						201.0	222.0	215.0					6																	47563641		2203	4300	6503	47671600	SO:0001583	missense	23607	exon12			AF146277	CCDS34472.1	6p12	2008-02-05			ENSG00000198087	ENSG00000198087			14258	protein-coding gene	gene with protein product		604241				10339567	Standard	NM_012120		Approved	CMS	uc003oyw.3	Q9Y5K6	OTTHUMG00000014799	ENST00000359314.5:c.1153C>G	6.37:g.47563641C>G	ENSP00000352264:p.Pro385Ala		47671600	NM_012120	A6NL34|Q5VYA3|Q9UG97	Missense_Mutation	SNP	ENST00000359314.5	37	CCDS34472.1	.	.	.	.	.	.	.	.	.	.	C	23.0	4.365814	0.82463	.	.	ENSG00000198087	ENST00000359314	T	0.32272	1.46	5.57	5.57	0.84162	.	0.919913	0.09387	N	0.809087	T	0.57213	0.2038	M	0.83483	2.645	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.53704	-0.8401	10	0.56958	D	0.05	-10.4127	19.1604	0.93529	0.0:1.0:0.0:0.0	.	385	Q9Y5K6	CD2AP_HUMAN	A	385	ENSP00000352264:P385A	ENSP00000352264:P385A	P	+	1	0	CD2AP	47671600	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	5.287000	0.65645	2.633000	0.89246	0.460000	0.39030	CCA		0.373	CD2AP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040817.2		
MYCT1	80177	broad.mit.edu	37	6	153043060	153043060	+	Missense_Mutation	SNP	G	G	A	rs201917444	byFrequency	TCGA-AA-3860-01A-02W-0900-09	TCGA-AA-3860-10A-01W-0902-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3860-01A-02W-0900-09	TCGA-AA-3860-10A-01W-0902-09	g.chr6:153043060G>A	ENST00000367245.5	+	2	388	c.380G>A	c.(379-381)cGc>cAc	p.R127H	MYCT1_ENST00000529453.1_Intron	NM_025107.2	NP_079383.2	Q8N699	MYCT1_HUMAN	myc target 1	127			R -> G (in dbSNP:rs17852097). {ECO:0000269|PubMed:15489334}.			nucleus (GO:0005634)		p.R127H(2)		NS(1)|breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(7)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	20		Ovarian(120;0.0654)		OV - Ovarian serous cystadenocarcinoma(155;1.33e-10)|BRCA - Breast invasive adenocarcinoma(81;0.143)		GGATTTTACCGCCACAGTGGC	0.512													G|||	2	0.000399361	0.0008	0.0	5008	,	,		18441	0.0		0.001	False		,,,				2504	0.0				p.R127H												.	.	2	Substitution - Missense(2)	large_intestine(1)|haematopoietic_and_lymphoid_tissue(1)	c.G380A	6						.						113.0	110.0	111.0					6																	153043060		2203	4300	6503	153084753	SO:0001583	missense	80177	exon2			AF527367	CCDS5239.1	6q25.1	2008-02-05			ENSG00000120279	ENSG00000120279			23172	protein-coding gene	gene with protein product						12477932	Standard	NM_025107		Approved	MTLC, FLJ21269	uc003qpc.4	Q8N699	OTTHUMG00000015850	ENST00000367245.5:c.380G>A	6.37:g.153043060G>A	ENSP00000356214:p.Arg127His		153084753	NM_025107	Q8N396|Q8TBE8|Q9H763	Missense_Mutation	SNP	ENST00000367245.5	37	CCDS5239.1	1|1	4.578754578754579E-4|4.578754578754579E-4	0|0	0.0|0.0	0|0	0.0|0.0	0|0	0.0|0.0	1|1	0.0013192612137203166|0.0013192612137203166	G|G	34|34	5.295720|5.295720	0.95574|0.95574	.|.	.|.	ENSG00000120279|ENSG00000120279	ENST00000532295|ENST00000367245	.|T	.|0.42513	.|0.97	5.78|5.78	5.78|5.78	0.91487|0.91487	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.58047|0.58047	0.2095|0.2095	L|L	0.59436|0.59436	1.845|1.845	0.80722|0.80722	D|D	1|1	.|D	.|0.89917	.|1.0	.|D	.|0.91635	.|0.999	T|T	0.59204|0.59204	-0.7498|-0.7498	5|10	.|0.87932	.|D	.|0	-24.7228|-24.7228	20.0096|20.0096	0.97446|0.97446	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|127	.|Q8N699	.|MYCT1_HUMAN	T|H	108|127	.|ENSP00000356214:R127H	.|ENSP00000356214:R127H	A|R	+|+	1|2	0|0	MYCT1|MYCT1	153084753|153084753	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	7.895000|7.895000	0.87343|0.87343	2.727000|2.727000	0.93392|0.93392	0.579000|0.579000	0.79373|0.79373	GCC|CGC		0.512	MYCT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042750.2	NM_025107	
ZAN	7455	broad.mit.edu	37	7	100361492	100361492	+	RNA	SNP	G	G	A	rs573564140	byFrequency	TCGA-AA-3860-01A-02W-0900-09	TCGA-AA-3860-10A-01W-0902-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3860-01A-02W-0900-09	TCGA-AA-3860-10A-01W-0902-09	g.chr7:100361492G>A	ENST00000348028.3	+	0	4215				ZAN_ENST00000443370.1_RNA|ZAN_ENST00000349350.6_RNA|ZAN_ENST00000421100.1_RNA|ZAN_ENST00000542585.1_RNA|ZAN_ENST00000449052.1_RNA|ZAN_ENST00000546213.1_RNA|ZAN_ENST00000546292.1_RNA|ZAN_ENST00000538115.1_RNA|ZAN_ENST00000427578.1_RNA			Q9Y493	ZAN_HUMAN	zonadhesin (gene/pseudogene)						binding of sperm to zona pellucida (GO:0007339)|single organismal cell-cell adhesion (GO:0016337)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.S1350S(2)		NS(2)|breast(3)|central_nervous_system(3)|endometrium(21)|kidney(6)|large_intestine(18)|lung(60)|ovary(4)|pancreas(3)|prostate(5)|skin(8)|stomach(3)|upper_aerodigestive_tract(3)	139	Lung NSC(181;0.041)|all_lung(186;0.0581)		STAD - Stomach adenocarcinoma(171;0.19)			GCAGCATGTCGGGGCCAGGGT	0.577													G|||	2	0.000399361	0.0	0.0029	5008	,	,		17719	0.0		0.0	False		,,,				2504	0.0				p.S1350S												.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.G4050A	7						.						128.0	124.0	125.0					7																	100361492		2015	4177	6192	100199428			7455	exon21			U83191		7q22.1	2013-10-10	2013-10-10		ENSG00000146839	ENSG00000146839			12857	protein-coding gene	gene with protein product		602372	"""zonadhesin"""			9799793, 17033959	Standard	NM_003386		Approved		uc003uwk.3	Q9Y493	OTTHUMG00000157037		7.37:g.100361492G>A			100199428	NM_173059	A0FKC8|D6W5W4|O00218|Q96L85|Q96L86|Q96L87|Q96L88|Q96L89|Q96L90|Q9BXN9|Q9BZ83|Q9BZ84|Q9BZ85|Q9BZ86|Q9BZ87|Q9BZ88	Silent	SNP	ENST00000348028.3	37																																																																																					0.577	ZAN-006	KNOWN	basic	polymorphic_pseudogene	polymorphic_pseudogene	OTTHUMT00000347214.1	NM_003386	
ZC3HC1	51530	broad.mit.edu	37	7	129688904	129688904	+	Missense_Mutation	SNP	T	T	A			TCGA-AA-3860-01A-02W-0900-09	TCGA-AA-3860-10A-01W-0902-09	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AA-3860-01A-02W-0900-09	TCGA-AA-3860-10A-01W-0902-09	g.chr7:129688904T>A	ENST00000358303.4	-	2	311	c.227A>T	c.(226-228)gAa>gTa	p.E76V	ZC3HC1_ENST00000311873.5_Missense_Mutation_p.E55V|ZC3HC1_ENST00000481503.1_Missense_Mutation_p.E76V|ZC3HC1_ENST00000360708.5_Missense_Mutation_p.E76V	NM_016478.3	NP_057562.3	Q86WB0	NIPA_HUMAN	zinc finger, C3HC-type containing 1	76					mitotic nuclear division (GO:0007067)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|protein ubiquitination (GO:0016567)	nuclear membrane (GO:0031965)|nucleus (GO:0005634)	protein kinase binding (GO:0019901)|zinc ion binding (GO:0008270)	p.E76V(1)		endometrium(2)|kidney(6)|large_intestine(10)|lung(2)|prostate(1)|urinary_tract(1)	22	Melanoma(18;0.0435)					AAAGAAGGCTTCTTTGCTTGT	0.413																																					p.E76V	Melanoma(115;540 1606 16325 28853 48167)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A227T	7						.						195.0	179.0	184.0					7																	129688904		2203	4300	6503	129476140	SO:0001583	missense	51530	exon2			AF151050	CCDS34753.1, CCDS64767.1, CCDS75659.1	7q32.2	2013-01-17			ENSG00000091732	ENSG00000091732		"""Zinc fingers, C3HC-type"""	29913	protein-coding gene	gene with protein product	"""nuclear interaction partner of ALK"""					11042152	Standard	XM_005250403		Approved	NIPA	uc003vpi.3	Q86WB0	OTTHUMG00000157648	ENST00000358303.4:c.227A>T	7.37:g.129688904T>A	ENSP00000351052:p.Glu76Val		129476140	NM_016478	A6NH66|Q75MF3|Q75MF4|Q8N330|Q96F75|Q9HA34|Q9NVX4|Q9P0R0	Missense_Mutation	SNP	ENST00000358303.4	37	CCDS34753.1	.	.	.	.	.	.	.	.	.	.	T	26.4	4.737487	0.89482	.	.	ENSG00000091732	ENST00000358303;ENST00000360708;ENST00000311873;ENST00000481503;ENST00000480193	T;T;T;T	0.54675	1.14;0.56;1.16;0.57	5.72	5.72	0.89469	Zinc finger, C3HC-like (1);	0.053640	0.64402	D	0.000001	T	0.69351	0.3101	L	0.61218	1.895	0.54753	D	0.999989	D	0.89917	1.0	D	0.76575	0.988	T	0.70260	-0.4921	10	0.49607	T	0.09	-15.5025	14.8789	0.70516	0.0:0.0:0.0:1.0	.	76	Q86WB0	NIPA_HUMAN	V	76;76;55;76;76	ENSP00000351052:E76V;ENSP00000353933:E76V;ENSP00000309301:E55V;ENSP00000418533:E76V	ENSP00000309301:E55V	E	-	2	0	ZC3HC1	129476140	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.398000	0.73244	2.193000	0.70182	0.477000	0.44152	GAA		0.413	ZC3HC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349316.1	NM_016478	
COL14A1	7373	broad.mit.edu	37	8	121295897	121295897	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3860-01A-02W-0900-09	TCGA-AA-3860-10A-01W-0902-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3860-01A-02W-0900-09	TCGA-AA-3860-10A-01W-0902-09	g.chr8:121295897C>T	ENST00000297848.3	+	32	4117	c.3847C>T	c.(3847-3849)Ccc>Tcc	p.P1283S	COL14A1_ENST00000309791.4_Missense_Mutation_p.P1283S|COL14A1_ENST00000247781.3_Missense_Mutation_p.P1188S	NM_021110.1	NP_066933.1			collagen, type XIV, alpha 1									p.P1283S(1)		NS(1)|autonomic_ganglia(1)|breast(11)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(9)|large_intestine(31)|lung(42)|ovary(5)|pancreas(1)|prostate(1)|skin(8)|stomach(2)|upper_aerodigestive_tract(2)	119	Lung NSC(37;6.52e-07)|Ovarian(258;0.00769)|Hepatocellular(40;0.161)		OV - Ovarian serous cystadenocarcinoma(1;6.47e-38)|STAD - Stomach adenocarcinoma(47;0.00503)			AGAAGGATTGCCCTCCGACTA	0.378																																					p.P1283S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C3847T	8						.						166.0	153.0	158.0					8																	121295897		2203	4300	6503	121365078	SO:0001583	missense	7373	exon32				CCDS34938.1	8q23	2013-02-11	2008-02-04		ENSG00000187955	ENSG00000187955		"""Collagens"", ""Fibronectin type III domain containing"""	2191	protein-coding gene	gene with protein product		120324	"""undulin"""	UND		1716629, 9427527	Standard	NM_021110		Approved		uc003yox.4	Q05707	OTTHUMG00000149877	ENST00000297848.3:c.3847C>T	8.37:g.121295897C>T	ENSP00000297848:p.Pro1283Ser		121365078	NM_021110		Missense_Mutation	SNP	ENST00000297848.3	37	CCDS34938.1	.	.	.	.	.	.	.	.	.	.	C	26.0	4.694842	0.88830	.	.	ENSG00000187955	ENST00000309791;ENST00000297848;ENST00000247781	T;T;T	0.30981	1.51;1.51;1.51	5.45	5.45	0.79879	Concanavalin A-like lectin/glucanase (1);Laminin G, thrombospondin-type, N-terminal (1);	0.000000	0.85682	D	0.000000	T	0.58779	0.2146	M	0.76574	2.34	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	T	0.61038	-0.7143	10	0.62326	D	0.03	.	19.2777	0.94039	0.0:1.0:0.0:0.0	.	1283	Q05707	COEA1_HUMAN	S	1283;1283;1188	ENSP00000311809:P1283S;ENSP00000297848:P1283S;ENSP00000247781:P1188S	ENSP00000247781:P1188S	P	+	1	0	COL14A1	121365078	1.000000	0.71417	1.000000	0.80357	0.890000	0.51754	7.818000	0.86416	2.551000	0.86045	0.462000	0.41574	CCC		0.378	COL14A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313657.2	NM_021110	
PHYHIP	9796	broad.mit.edu	37	8	22078878	22078878	+	Silent	SNP	G	G	A			TCGA-AA-3860-01A-02W-0900-09	TCGA-AA-3860-10A-01W-0902-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3860-01A-02W-0900-09	TCGA-AA-3860-10A-01W-0902-09	g.chr8:22078878G>A	ENST00000321613.3	-	6	1437	c.981C>T	c.(979-981)agC>agT	p.S327S	PHYHIP_ENST00000454243.2_Silent_p.S327S	NM_001099335.1	NP_001092805.1	Q92561	PHYIP_HUMAN	phytanoyl-CoA 2-hydroxylase interacting protein	327								p.S327S(1)		endometrium(1)|kidney(1)|large_intestine(4)|lung(3)|upper_aerodigestive_tract(1)	10				Colorectal(74;0.0152)|COAD - Colon adenocarcinoma(73;0.0629)		AGCGGCCCACGCTGATGTTGC	0.637																																					p.S327S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C981T	8						.						37.0	41.0	40.0					8																	22078878		2061	4195	6256	22134823	SO:0001819	synonymous_variant	9796	exon5			D87463	CCDS43723.1	8p21.2	2010-02-17	2006-01-09		ENSG00000168490	ENSG00000168490			16865	protein-coding gene	gene with protein product		608511	"""phytanoyl-CoA hydroxylase interacting protein"", ""DYRK1A interacting protein 3"""	DYRK1AP3		9039502, 10686344	Standard	NM_014759		Approved	KIAA0273, PAHX-AP	uc003xbj.4	Q92561	OTTHUMG00000163776	ENST00000321613.3:c.981C>T	8.37:g.22078878G>A			22134823	NM_014759	D3DSR1|Q8N4I9	Silent	SNP	ENST00000321613.3	37	CCDS43723.1																																																																																				0.637	PHYHIP-002	PUTATIVE	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000375388.1	NM_014759	
LYN	4067	broad.mit.edu	37	8	56922602	56922602	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3860-01A-02W-0900-09	TCGA-AA-3860-10A-01W-0902-09	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3860-01A-02W-0900-09	TCGA-AA-3860-10A-01W-0902-09	g.chr8:56922602A>G	ENST00000519728.1	+	13	1768	c.1472A>G	c.(1471-1473)gAc>gGc	p.D491G	LYN_ENST00000520220.2_Missense_Mutation_p.D470G	NM_002350.3	NP_002341.1	P07948	LYN_HUMAN	LYN proto-oncogene, Src family tyrosine kinase	491	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				B cell homeostasis (GO:0001782)|B cell receptor signaling pathway (GO:0050853)|blood coagulation (GO:0007596)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to extracellular stimulus (GO:0031668)|cellular response to heat (GO:0034605)|cellular response to retinoic acid (GO:0071300)|cytokine secretion (GO:0050663)|dendritic cell differentiation (GO:0097028)|erythrocyte differentiation (GO:0030218)|Fc receptor mediated inhibitory signaling pathway (GO:0002774)|Fc receptor mediated stimulatory signaling pathway (GO:0002431)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|histamine secretion by mast cell (GO:0002553)|immune response-regulating cell surface receptor signaling pathway (GO:0002768)|innate immune response (GO:0045087)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)|leukocyte migration (GO:0050900)|lipopolysaccharide-mediated signaling pathway (GO:0031663)|negative regulation of B cell proliferation (GO:0030889)|negative regulation of cell proliferation (GO:0008285)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of immune response (GO:0050777)|negative regulation of intracellular signal transduction (GO:1902532)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of mast cell proliferation (GO:0070667)|negative regulation of myeloid leukocyte differentiation (GO:0002762)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of toll-like receptor 2 signaling pathway (GO:0034136)|negative regulation of toll-like receptor 4 signaling pathway (GO:0034144)|neuron projection development (GO:0031175)|oligodendrocyte development (GO:0014003)|peptidyl-tyrosine phosphorylation (GO:0018108)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of B cell receptor signaling pathway (GO:0050861)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cellular component movement (GO:0051272)|positive regulation of dendritic cell apoptotic process (GO:2000670)|positive regulation of Fc receptor mediated stimulatory signaling pathway (GO:0060369)|positive regulation of glial cell proliferation (GO:0060252)|positive regulation of mast cell proliferation (GO:0070668)|positive regulation of neuron projection development (GO:0010976)|positive regulation of oligodendrocyte progenitor proliferation (GO:0070447)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of stress-activated protein kinase signaling cascade (GO:0070304)|positive regulation of tyrosine phosphorylation of STAT protein (GO:0042531)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of B cell apoptotic process (GO:0002902)|regulation of B cell receptor signaling pathway (GO:0050855)|regulation of cell adhesion mediated by integrin (GO:0033628)|regulation of cytokine production (GO:0001817)|regulation of cytokine secretion (GO:0050707)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of erythrocyte differentiation (GO:0045646)|regulation of inflammatory response (GO:0050727)|regulation of mast cell activation (GO:0033003)|regulation of mast cell degranulation (GO:0043304)|regulation of monocyte chemotaxis (GO:0090025)|regulation of platelet aggregation (GO:0090330)|regulation of protein phosphorylation (GO:0001932)|regulation of release of sequestered calcium ion into cytosol (GO:0051279)|response to amino acid (GO:0043200)|response to axon injury (GO:0048678)|response to carbohydrate (GO:0009743)|response to drug (GO:0042493)|response to hormone (GO:0009725)|response to insulin (GO:0032868)|response to organic cyclic compound (GO:0014070)|response to sterol depletion (GO:0006991)|response to toxic substance (GO:0009636)|signal transduction (GO:0007165)|signal transduction by phosphorylation (GO:0023014)|T cell costimulation (GO:0031295)|tolerance induction to self antigen (GO:0002513)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integrin alpha2-beta1 complex (GO:0034666)|mast cell granule (GO:0042629)|membrane raft (GO:0045121)|mitochondrial crista (GO:0030061)|mitochondrial intermembrane space (GO:0005758)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)	ATP binding (GO:0005524)|enzyme binding (GO:0019899)|glycosphingolipid binding (GO:0043208)|ion channel binding (GO:0044325)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)	p.D491G(1)		breast(4)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(8)|ovary(1)|upper_aerodigestive_tract(1)	22		all_lung(136;0.0555)|Lung NSC(129;0.0726)|all_epithelial(80;0.0772)	Epithelial(17;0.000834)|all cancers(17;0.00598)		Bosutinib(DB06616)|Ponatinib(DB08901)	CCAACGTTTGACTACTTACAG	0.522																																					p.D491G												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A1472G	8						.						104.0	94.0	97.0					8																	56922602		2203	4300	6503	57085156	SO:0001583	missense	4067	exon13			M16038	CCDS6162.1, CCDS47859.1	8q13	2014-06-25	2014-06-25		ENSG00000254087	ENSG00000254087		"""SH2 domain containing"""	6735	protein-coding gene	gene with protein product		165120	"""v-yes-1 Yamaguchi sarcoma viral related oncogene homolog"""			3561390	Standard	NM_002350		Approved	JTK8	uc003xsk.4	P07948	OTTHUMG00000044345	ENST00000519728.1:c.1472A>G	8.37:g.56922602A>G	ENSP00000428924:p.Asp491Gly		57085156	NM_002350	A0AVQ5	Missense_Mutation	SNP	ENST00000519728.1	37	CCDS6162.1	.	.	.	.	.	.	.	.	.	.	A	24.7	4.561310	0.86335	.	.	ENSG00000254087	ENST00000519728;ENST00000520220	D;D	0.82803	-1.65;-1.65	5.95	5.95	0.96441	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.089469	0.85682	D	0.000000	D	0.82930	0.5144	N	0.12853	0.265	0.80722	D	1	P;P	0.45531	0.86;0.852	P;P	0.60345	0.873;0.854	D	0.86313	0.1687	10	0.87932	D	0	.	16.4237	0.83790	1.0:0.0:0.0:0.0	.	561;491	Q6NUK7;P07948	.;LYN_HUMAN	G	491;470	ENSP00000428924:D491G;ENSP00000428424:D470G	ENSP00000428924:D491G	D	+	2	0	LYN	57085156	1.000000	0.71417	0.514000	0.27761	0.514000	0.34195	9.339000	0.96797	2.279000	0.76181	0.533000	0.62120	GAC		0.522	LYN-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378155.1	NM_002350	
ASAP1	50807	broad.mit.edu	37	8	131073149	131073149	+	Silent	SNP	C	C	T	rs141392919		TCGA-AA-3860-01A-02W-0900-09	TCGA-AA-3860-10A-01W-0902-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3860-01A-02W-0900-09	TCGA-AA-3860-10A-01W-0902-09	g.chr8:131073149C>T	ENST00000518721.1	-	28	3095	c.2868G>A	c.(2866-2868)ccG>ccA	p.P956P	ASAP1_ENST00000357668.1_Silent_p.P956P	NM_001247996.1|NM_018482.3	NP_001234925.1|NP_060952.2	Q9ULH1	ASAP1_HUMAN	ArfGAP with SH3 domain, ankyrin repeat and PH domain 1	956	Pro-rich.				cilium morphogenesis (GO:0060271)|regulation of ARF GTPase activity (GO:0032312)	cytoplasm (GO:0005737)|membrane (GO:0016020)	ARF GTPase activator activity (GO:0008060)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|zinc ion binding (GO:0008270)	p.P956P(1)		breast(5)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(13)|lung(22)|ovary(6)|pancreas(1)|prostate(1)|skin(3)|stomach(1)	68						CTGGCTTAGGCGGCAAATCTC	0.577																																					p.P956P												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G2868A	8						.						84.0	101.0	95.0					8																	131073149		2203	4300	6503	131142331	SO:0001819	synonymous_variant	50807	exon27			AB033075	CCDS6362.1, CCDS75788.1	8q24.1-q24.2	2013-01-11	2008-09-22	2008-09-22	ENSG00000153317	ENSG00000153317		"""ADP-ribosylation factor GTPase activating proteins"", ""Pleckstrin homology (PH) domain containing"", ""Ankyrin repeat domain containing"""	2720	protein-coding gene	gene with protein product	"""centaurin, beta 4"""	605953	"""development and differentiation enhancing factor 1"""	DDEF1		9819391	Standard	NM_018482		Approved	PAP, KIAA1249, ZG14P, CENTB4	uc003yta.2	Q9ULH1	OTTHUMG00000164772	ENST00000518721.1:c.2868G>A	8.37:g.131073149C>T			131142331	NM_018482	B2RNV3	Silent	SNP	ENST00000518721.1	37	CCDS6362.1	.	.	.	.	.	.	.	.	.	.	C	7.533	0.659171	0.14645	.	.	ENSG00000153317	ENST00000524124;ENST00000519483	.	.	.	5.24	-3.99	0.04069	.	.	.	.	.	T	0.37625	0.1010	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.36768	-0.9734	4	.	.	.	.	1.2317	0.01944	0.203:0.3425:0.1786:0.2758	.	.	.	.	T	777;313	.	.	A	-	1	0	ASAP1	131142331	0.942000	0.31987	0.982000	0.44146	0.775000	0.43874	-0.042000	0.12063	-0.600000	0.05790	-0.294000	0.09567	GCC		0.577	ASAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380170.1	NM_018482	
ERCC6L	54821	broad.mit.edu	37	X	71426422	71426422	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3860-01A-02W-0900-09	TCGA-AA-3860-10A-01W-0902-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AA-3860-01A-02W-0900-09	TCGA-AA-3860-10A-01W-0902-09	g.chrX:71426422C>T	ENST00000334463.3	-	2	2330	c.2195G>A	c.(2194-2196)aGa>aAa	p.R732K	PIN4_ENST00000423432.2_Intron|ERCC6L_ENST00000373657.1_Missense_Mutation_p.R609K	NM_017669.2	NP_060139.2	Q2NKX8	ERC6L_HUMAN	excision repair cross-complementation group 6-like	732					mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)	cytosol (GO:0005829)|kinetochore (GO:0000776)|membrane (GO:0016020)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)	p.R732K(1)		breast(2)|cervix(1)|endometrium(9)|kidney(4)|large_intestine(9)|lung(9)|ovary(3)|skin(1)	38	Renal(35;0.156)					TACAGGTTCTCTTAGCCAGGC	0.408																																					p.R732K												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2195A	X						.						89.0	82.0	84.0					X																	71426422		2203	4300	6503	71343147	SO:0001583	missense	54821	exon2			AK000112	CCDS35329.1	Xq13.1	2014-03-07	2014-03-07		ENSG00000186871	ENSG00000186871			20794	protein-coding gene	gene with protein product	"""PLK1-interacting checkpoint helicase"""	300687	"""excision repair cross-complementing rodent repair deficiency, complementation group 6-like"""			17218258	Standard	NM_017669		Approved	FLJ20105, PICH, RAD26L	uc004eaq.1	Q2NKX8	OTTHUMG00000021810	ENST00000334463.3:c.2195G>A	X.37:g.71426422C>T	ENSP00000334675:p.Arg732Lys		71343147	NM_017669	Q8NCI1|Q96H93|Q9NXQ8	Missense_Mutation	SNP	ENST00000334463.3	37	CCDS35329.1	.	.	.	.	.	.	.	.	.	.	C	14.46	2.541804	0.45280	.	.	ENSG00000186871	ENST00000373657;ENST00000334463	D;D	0.90900	-2.72;-2.75	5.25	0.512	0.16994	.	.	.	.	.	T	0.77961	0.4209	N	0.15975	0.35	0.09310	N	1	B	0.15141	0.012	B	0.12156	0.007	T	0.62455	-0.6851	9	0.27785	T	0.31	-0.2731	2.8505	0.05556	0.1454:0.5114:0.1409:0.2024	.	732	Q2NKX8	ERC6L_HUMAN	K	609;732	ENSP00000362761:R609K;ENSP00000334675:R732K	ENSP00000334675:R732K	R	-	2	0	ERCC6L	71343147	0.196000	0.23350	0.007000	0.13788	0.925000	0.55904	0.518000	0.22847	0.041000	0.15688	0.594000	0.82650	AGA		0.408	ERCC6L-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057174.2	NM_017669	
ZCCHC5	203430	broad.mit.edu	37	X	77913703	77913703	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3860-01A-02W-0900-09	TCGA-AA-3860-10A-01W-0902-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AA-3860-01A-02W-0900-09	TCGA-AA-3860-10A-01W-0902-09	g.chrX:77913703G>T	ENST00000321110.1	-	2	510	c.215C>A	c.(214-216)gCa>gAa	p.A72E		NM_152694.2	NP_689907.1	Q8N8U3	ZCHC5_HUMAN	zinc finger, CCHC domain containing 5	72	Pro-rich.						nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)	p.A72E(1)		breast(3)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(6)|lung(18)|ovary(1)|prostate(1)|skin(1)	37						CTCCCAGGCTGCTGGGGGATT	0.587																																					p.A72E												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C215A	X						.						23.0	23.0	23.0					X																	77913703		2203	4300	6503	77800359	SO:0001583	missense	203430	exon2			AK096184	CCDS14440.1	Xq13.3	2008-02-05			ENSG00000179300	ENSG00000179300		"""Zinc fingers, CCHC domain containing"""	22997	protein-coding gene	gene with protein product						15716091, 16093683	Standard	NM_152694		Approved	FLJ38865, Mar3, Mart3, ZHC5	uc004edc.1	Q8N8U3	OTTHUMG00000021892	ENST00000321110.1:c.215C>A	X.37:g.77913703G>T	ENSP00000316794:p.Ala72Glu		77800359	NM_152694	B2RMZ0|Q5JQE9	Missense_Mutation	SNP	ENST00000321110.1	37	CCDS14440.1	.	.	.	.	.	.	.	.	.	.	G	0.010	-1.749477	0.00669	.	.	ENSG00000179300	ENST00000321110	T	0.22134	1.97	3.13	-1.11	0.09840	.	.	.	.	.	T	0.11324	0.0276	N	0.24115	0.695	0.09310	N	1	B	0.21452	0.056	B	0.15052	0.012	T	0.38520	-0.9657	9	0.06757	T	0.87	.	11.6496	0.51282	0.0:0.0:0.2334:0.7666	.	72	Q8N8U3	ZCHC5_HUMAN	E	72	ENSP00000316794:A72E	ENSP00000316794:A72E	A	-	2	0	ZCCHC5	77800359	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-0.091000	0.11146	-0.426000	0.07360	-0.371000	0.07208	GCA		0.587	ZCCHC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057319.1	NM_152694	
AFF2	2334	broad.mit.edu	37	X	148037375	148037375	+	Silent	SNP	C	C	A			TCGA-AA-3860-01A-02W-0900-09	TCGA-AA-3860-10A-01W-0902-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3860-01A-02W-0900-09	TCGA-AA-3860-10A-01W-0902-09	g.chrX:148037375C>A	ENST00000370460.2	+	11	2279	c.1800C>A	c.(1798-1800)ccC>ccA	p.P600P	AFF2_ENST00000342251.3_Silent_p.P567P|AFF2_ENST00000370457.5_Silent_p.P567P|AFF2_ENST00000286437.5_Silent_p.P241P	NM_001169123.1|NM_002025.3	NP_001162594.1|NP_002016.2	P51816	AFF2_HUMAN	AF4/FMR2 family, member 2	600					brain development (GO:0007420)|learning or memory (GO:0007611)|mRNA processing (GO:0006397)|regulation of RNA splicing (GO:0043484)|RNA splicing (GO:0008380)	nuclear speck (GO:0016607)	G-quadruplex RNA binding (GO:0002151)	p.P241P(1)|p.P600P(1)		breast(5)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(29)|liver(2)|lung(39)|ovary(4)|pancreas(5)|prostate(1)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	109	Acute lymphoblastic leukemia(192;6.56e-05)					GTCCACGGCCCACTCAGAAAA	0.463																																					p.P600P												.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.C1800A	X						.						87.0	92.0	90.0					X																	148037375		2203	4299	6502	147845075	SO:0001819	synonymous_variant	2334	exon11			U48436	CCDS14684.1, CCDS55521.1, CCDS76040.1	Xq28	2008-02-05	2005-06-27	2005-06-27	ENSG00000155966	ENSG00000155966			3776	protein-coding gene	gene with protein product		300806	"""fragile X mental retardation 2"""	FMR2			Standard	NM_002025		Approved	FRAXE	uc004fcp.3	P51816	OTTHUMG00000022613	ENST00000370460.2:c.1800C>A	X.37:g.148037375C>A			147845075	NM_002025	A2RTY4|B4DXD5|B7WNQ1|B7ZLD6|B7ZLD9|O43786|O60215|P78407|Q13521|Q14323|Q7Z2F7|Q7Z400|Q9UNA5	Silent	SNP	ENST00000370460.2	37	CCDS14684.1																																																																																				0.463	AFF2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058673.2	NM_002025	
