#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_Mutation_Status	i_ORegAnno_bin	i_Sequence_Source	i_Sequencer	i_Sequencing_Phase	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
ABCC2	1244	broad.mit.edu	37	10	101590551	101590551	+	Silent	SNP	C	C	T	rs148081784		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr10:101590551C>T	ENST00000370449.4	+	21	2939	c.2826C>T	c.(2824-2826)gaC>gaT	p.D942D		NM_000392.3	NP_000383	Q92887	MRP2_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 2	942					cellular chloride ion homeostasis (GO:0030644)|drug transmembrane transport (GO:0006855)|prostaglandin transport (GO:0015732)|response to arsenic-containing substance (GO:0046685)|response to estrogen (GO:0043627)|response to heat (GO:0009408)|response to methotrexate (GO:0031427)|response to oxidative stress (GO:0006979)|thyroid hormone transport (GO:0070327)|transmembrane transport (GO:0055085)|transport (GO:0006810)	apical plasma membrane (GO:0016324)|cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|intercellular canaliculus (GO:0046581)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|organic anion transmembrane transporter activity (GO:0008514)	p.D942D(1)		NS(1)|breast(5)|endometrium(9)|kidney(2)|large_intestine(20)|liver(1)|lung(20)|ovary(2)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	67		Colorectal(252;0.234)		Epithelial(162;2.77e-10)|all cancers(201;2.47e-08)	Adenosine triphosphate(DB00171)|Aminohippurate(DB00345)|Arsenic trioxide(DB01169)|Atorvastatin(DB01076)|Canagliflozin(DB08907)|Carbamazepine(DB00564)|Carboplatin(DB00958)|Cisplatin(DB00515)|Clotrimazole(DB00257)|Conjugated Estrogens(DB00286)|Cyclosporine(DB00091)|Daunorubicin(DB00694)|Dexamethasone(DB01234)|Docetaxel(DB01248)|Doxorubicin(DB00997)|Eprosartan(DB00876)|Ethinyl Estradiol(DB00977)|Etoposide(DB00773)|Ezetimibe(DB00973)|Furosemide(DB00695)|Fusidic Acid(DB02703)|Gadoxetate(DB08884)|Glutathione(DB00143)|Glyburide(DB01016)|Indinavir(DB00224)|Indomethacin(DB00328)|Irinotecan(DB00762)|Ivermectin(DB00602)|Lamivudine(DB00709)|Leucovorin(DB00650)|Levetiracetam(DB01202)|Lomefloxacin(DB00978)|Lovastatin(DB00227)|Methotrexate(DB00563)|Mycophenolate mofetil(DB00688)|Nifedipine(DB01115)|Norgestimate(DB00957)|Ofloxacin(DB01165)|Olmesartan(DB00275)|Oxaliplatin(DB00526)|Paclitaxel(DB01229)|Phenobarbital(DB01174)|Phenytoin(DB00252)|Pitavastatin(DB08860)|Pranlukast(DB01411)|Pravastatin(DB00175)|Probenecid(DB01032)|Quinidine(DB00908)|Reserpine(DB00206)|Rifampicin(DB01045)|Ritonavir(DB00503)|Saquinavir(DB01232)|Simvastatin(DB00641)|Sorafenib(DB00398)|Sparfloxacin(DB01208)|Spironolactone(DB00421)|Sulfasalazine(DB00795)|Sulfinpyrazone(DB01138)|Sunitinib(DB01268)|Tamoxifen(DB00675)|Telmisartan(DB00966)|Tenofovir(DB00300)|Tetrahydrofolic acid(DB00116)|Ursodeoxycholic acid(DB01586)|Vasopressin(DB00067)|Verapamil(DB00661)|Vinblastine(DB00570)|Vincristine(DB00541)	TGAAGGAAGACGAAGAACTAG	0.423													C|||	1	0.000199681	0.0	0.0	5008	,	,		20413	0.001		0.0	False		,,,				2504	0.0				p.D942D												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C2826T	10						.						90.0	88.0	89.0					10																	101590551		2203	4300	6503	101580541	SO:0001819	synonymous_variant	1244	exon21			U63970	CCDS7484.1	10q24	2012-03-14			ENSG00000023839	ENSG00000023839		"""ATP binding cassette transporters / subfamily C"""	53	protein-coding gene	gene with protein product		601107	"""canalicular multispecific organic anion transporter 1"""	CMOAT		8797578, 9284939	Standard	XM_006717630		Approved	DJS, MRP2, cMRP	uc001kqf.2	Q92887	OTTHUMG00000018895	ENST00000370449.4:c.2826C>T	10.37:g.101590551C>T		Somatic		Capture	Illumina HiSeq	Phase_I	101580541	NM_000392	B2RMT8|Q14022|Q5T2B1|Q92500|Q92798|Q99663|Q9UMS2	Silent	SNP	ENST00000370449.4	37	CCDS7484.1																																																																																				0.423	ABCC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049825.1	NM_000392	
PKD2L1	9033	broad.mit.edu	37	10	102054399	102054399	+	Missense_Mutation	SNP	G	G	A	rs556892956	byFrequency	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr10:102054399G>A	ENST00000318222.3	-	9	1934	c.1552C>T	c.(1552-1554)Cgg>Tgg	p.R518W	PKD2L1_ENST00000353274.3_Missense_Mutation_p.R518W|PKD2L1_ENST00000338519.3_Missense_Mutation_p.R443W	NM_001253837.1|NM_016112.2	NP_001240766.1|NP_057196.2	Q9P0L9	PK2L1_HUMAN	polycystic kidney disease 2-like 1	518					cation transport (GO:0006812)|cellular response to acidic pH (GO:0071468)|detection of chemical stimulus involved in sensory perception of sour taste (GO:0001581)|detection of mechanical stimulus (GO:0050982)|potassium ion transmembrane transport (GO:0071805)|protein homotrimerization (GO:0070207)|sensory perception of sour taste (GO:0050915)|smoothened signaling pathway (GO:0007224)|sodium ion transmembrane transport (GO:0035725)	calcium channel complex (GO:0034704)|cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nonmotile primary cilium (GO:0031513)|plasma membrane (GO:0005886)	alpha-actinin binding (GO:0051393)|calcium activated cation channel activity (GO:0005227)|calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-activated potassium channel activity (GO:0015269)|cation channel activity (GO:0005261)|cytoskeletal protein binding (GO:0008092)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|sodium channel activity (GO:0005272)|sour taste receptor activity (GO:0033040)	p.R518W(1)		NS(2)|breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|lung(12)|ovary(4)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)	43		Colorectal(252;0.117)		Epithelial(162;6.15e-10)|all cancers(201;5.14e-08)		AGGATTATCCGGAACTGAGTG	0.517													G|||	2	0.000399361	0.0	0.0	5008	,	,		19527	0.0		0.0	False		,,,				2504	0.002				p.R518W												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1552T	10						.						156.0	150.0	152.0					10																	102054399		2203	4300	6503	102044389	SO:0001583	missense	9033	exon9			AF094827	CCDS7492.1	10q24.31	2011-12-16			ENSG00000107593	ENSG00000107593		"""Voltage-gated ion channels / Transient receptor potential cation channels"""	9011	protein-coding gene	gene with protein product	"""transient receptor potential cation channel, subfamily P, member 3"""	604532		PKD2L, PKDL		9878261, 9748274	Standard	NM_016112		Approved	PCL, TRPP3	uc001kqx.1	Q9P0L9	OTTHUMG00000018910	ENST00000318222.3:c.1552C>T	10.37:g.102054399G>A	ENSP00000325296:p.Arg518Trp	Somatic		Capture	Illumina HiSeq	Phase_I	102044389	NM_016112	O75972|Q5W039|Q9UP35|Q9UPA2	Missense_Mutation	SNP	ENST00000318222.3	37	CCDS7492.1	.	.	.	.	.	.	.	.	.	.	G	23.0	4.366259	0.82463	.	.	ENSG00000107593	ENST00000338519;ENST00000353274;ENST00000318222;ENST00000339977	D;D;D	0.97505	-4.41;-4.41;-4.41	5.81	4.88	0.63580	Polycystin cation channel, PKD1/PKD2 (1);	0.107879	0.64402	D	0.000006	D	0.98429	0.9477	M	0.86028	2.79	0.52501	D	0.999958	D;D	0.89917	1.0;1.0	D;D	0.91635	0.998;0.999	D	0.98982	1.0805	10	0.56958	D	0.05	-15.142	15.1087	0.72338	0.0:0.0:0.8575:0.1425	.	471;518	Q1L4F0;Q9P0L9	.;PK2L1_HUMAN	W	443;518;518;516	ENSP00000345068:R443W;ENSP00000266049:R518W;ENSP00000325296:R518W	ENSP00000325296:R518W	R	-	1	2	PKD2L1	102044389	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	1.747000	0.38298	1.401000	0.46761	0.561000	0.74099	CGG		0.517	PKD2L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049863.2	NM_016112	
DPCD	25911	broad.mit.edu	37	10	103368671	103368671	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr10:103368671G>A	ENST00000370151.4	+	5	533	c.484G>A	c.(484-486)Gcc>Acc	p.A162T	DPCD_ENST00000370147.1_3'UTR|FBXW4_ENST00000470093.1_5'Flank	NM_015448.1	NP_056263.1	Q9BVM2	DPCD_HUMAN	deleted in primary ciliary dyskinesia homolog (mouse)	162					determination of left/right symmetry (GO:0007368)|epithelial cilium movement (GO:0003351)|lateral ventricle development (GO:0021670)|left/right pattern formation (GO:0060972)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)|third ventricle development (GO:0021678)	nucleus (GO:0005634)		p.A162T(1)		endometrium(1)|large_intestine(1)|lung(2)|skin(1)	5						CTTTGCCCACGCCAACTGCAC	0.527																																					p.A162T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G484A	10						.						193.0	174.0	180.0					10																	103368671		2203	4300	6503	103358661	SO:0001583	missense	25911	exon5				CCDS7514.1	10q24.32	2012-05-03			ENSG00000166171	ENSG00000166171			24542	protein-coding gene	gene with protein product						14630615	Standard	NM_015448		Approved	DKFZP566F084, RP11-529I10.4	uc001ktn.3	Q9BVM2	OTTHUMG00000018934	ENST00000370151.4:c.484G>A	10.37:g.103368671G>A	ENSP00000359170:p.Ala162Thr	Somatic		Capture	Illumina HiSeq	Phase_I	103358661	NM_015448	A8K289|Q6QNL3|Q8N5R1|Q9UFY6	Missense_Mutation	SNP	ENST00000370151.4	37	CCDS7514.1	.	.	.	.	.	.	.	.	.	.	G	17.68	3.449443	0.63178	.	.	ENSG00000166171	ENST00000370151	T	0.32023	1.47	5.93	5.03	0.67393	.	0.053378	0.85682	D	0.000000	T	0.30479	0.0766	M	0.64404	1.975	0.80722	D	1	P	0.50066	0.931	B	0.39119	0.291	T	0.11641	-1.0579	10	0.41790	T	0.15	-0.6565	12.9988	0.58664	0.1335:0.0:0.8665:0.0	.	162	Q9BVM2	DPCD_HUMAN	T	162	ENSP00000359170:A162T	ENSP00000359170:A162T	A	+	1	0	DPCD	103358661	1.000000	0.71417	1.000000	0.80357	0.863000	0.49368	5.216000	0.65246	1.526000	0.49068	0.561000	0.74099	GCC		0.527	DPCD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049958.2		
FGF8	2253	broad.mit.edu	37	10	103534501	103534501	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr10:103534501C>T	ENST00000344255.3	-	4	291	c.292G>A	c.(292-294)Ggc>Agc	p.G98S	FGF8_ENST00000346714.3_Missense_Mutation_p.G69S|FGF8_ENST00000347978.2_Missense_Mutation_p.G80S|FGF8_ENST00000320185.2_Missense_Mutation_p.G109S|FGF8_ENST00000485728.1_5'UTR			P55075	FGF8_HUMAN	fibroblast growth factor 8 (androgen-induced)	98					anatomical structure morphogenesis (GO:0009653)|aorta morphogenesis (GO:0035909)|apoptotic process (GO:0006915)|blood vessel remodeling (GO:0001974)|BMP signaling pathway (GO:0030509)|bone development (GO:0060348)|branching involved in salivary gland morphogenesis (GO:0060445)|branching involved in ureteric bud morphogenesis (GO:0001658)|canonical Wnt signaling pathway (GO:0060070)|cell migration involved in mesendoderm migration (GO:0090134)|cell proliferation in forebrain (GO:0021846)|corticotropin hormone secreting cell differentiation (GO:0060128)|dopaminergic neuron differentiation (GO:0071542)|dorsal/ventral axon guidance (GO:0033563)|embryonic hindlimb morphogenesis (GO:0035116)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial to mesenchymal transition involved in endocardial cushion formation (GO:0003198)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|forebrain dorsal/ventral pattern formation (GO:0021798)|forebrain morphogenesis (GO:0048853)|forebrain neuron development (GO:0021884)|gastrulation (GO:0007369)|gonad development (GO:0008406)|heart looping (GO:0001947)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|lung morphogenesis (GO:0060425)|male genitalia development (GO:0030539)|MAPK cascade (GO:0000165)|mesodermal cell migration (GO:0008078)|mesonephros development (GO:0001823)|metanephros development (GO:0001656)|midbrain-hindbrain boundary development (GO:0030917)|motor neuron axon guidance (GO:0008045)|negative regulation of cardiac muscle tissue development (GO:0055026)|negative regulation of neuron apoptotic process (GO:0043524)|neural plate morphogenesis (GO:0001839)|neuroepithelial cell differentiation (GO:0060563)|neurotrophin TRK receptor signaling pathway (GO:0048011)|odontogenesis (GO:0042476)|organ induction (GO:0001759)|otic vesicle formation (GO:0030916)|outflow tract septum morphogenesis (GO:0003148)|pallium development (GO:0021543)|patterning of blood vessels (GO:0001569)|pharyngeal system development (GO:0060037)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell division (GO:0051781)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of mitosis (GO:0045840)|positive regulation of organ growth (GO:0046622)|regulation of odontogenesis of dentin-containing tooth (GO:0042487)|response to drug (GO:0042493)|response to organic cyclic compound (GO:0014070)|response to oxidative stress (GO:0006979)|signal transduction involved in regulation of gene expression (GO:0023019)|subpallium development (GO:0021544)|thyroid gland development (GO:0030878)|thyroid-stimulating hormone-secreting cell differentiation (GO:0060129)	external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|extracellular space (GO:0005615)	chemoattractant activity (GO:0042056)|growth factor activity (GO:0008083)|type 1 fibroblast growth factor receptor binding (GO:0005105)|type 2 fibroblast growth factor receptor binding (GO:0005111)	p.G109S(1)		endometrium(1)|large_intestine(1)|lung(1)|urinary_tract(2)	5		Colorectal(252;0.122)		Epithelial(162;3.94e-09)|all cancers(201;2.13e-07)		AAGGGGTCGCCGTCCTCTGCC	0.677																																					p.G69S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G205A	10						.						72.0	61.0	65.0					10																	103534501		2203	4300	6503	103524491	SO:0001583	missense	2253	exon3			D38752	CCDS7515.1, CCDS7516.1, CCDS7517.1, CCDS7518.1, CCDS73185.1	10q25-q26	2014-01-30			ENSG00000107831	ENSG00000107831		"""Endogenous ligands"""	3686	protein-coding gene	gene with protein product		600483				8595889	Standard	NM_033164		Approved	AIGF	uc001ktq.2	P55075	OTTHUMG00000018940	ENST00000344255.3:c.292G>A	10.37:g.103534501C>T	ENSP00000340039:p.Gly98Ser	Somatic		Capture	Illumina HiSeq	Phase_I	103524491	NM_033165	A1A514|Q14915|Q15766	Missense_Mutation	SNP	ENST00000344255.3	37	CCDS7517.1	.	.	.	.	.	.	.	.	.	.	C	24.2	4.508945	0.85282	.	.	ENSG00000107831	ENST00000344255;ENST00000320185;ENST00000346714;ENST00000347978	T;T;T;T	0.80653	-1.4;-1.4;-1.4;-1.4	4.52	4.52	0.55395	.	0.000000	0.85682	U	0.000000	D	0.88614	0.6484	M	0.75085	2.285	0.80722	D	1	B;B;P;D	0.67145	0.305;0.296;0.67;0.996	B;B;B;D	0.64410	0.065;0.058;0.127;0.925	D	0.90098	0.4182	10	0.66056	D	0.02	-14.1677	17.494	0.87712	0.0:1.0:0.0:0.0	.	69;80;109;98	P55075-2;P55075-3;P55075-4;P55075	.;.;.;FGF8_HUMAN	S	98;109;69;80	ENSP00000340039:G98S;ENSP00000321797:G109S;ENSP00000344306:G69S;ENSP00000321945:G80S	ENSP00000321797:G109S	G	-	1	0	FGF8	103524491	1.000000	0.71417	1.000000	0.80357	0.953000	0.61014	7.203000	0.77864	2.371000	0.80710	0.486000	0.48141	GGC		0.677	FGF8-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000049999.1	NM_006119, NM_033165	
PPRC1	23082	broad.mit.edu	37	10	103907146	103907146	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr10:103907146G>A	ENST00000278070.2	+	9	4436	c.4397G>A	c.(4396-4398)cGa>cAa	p.R1466Q	PPRC1_ENST00000413464.2_Intron|PPRC1_ENST00000370012.1_Missense_Mutation_p.R433Q|PPRC1_ENST00000489648.1_Intron	NM_015062.3	NP_055877.3	Q5VV67	PPRC1_HUMAN	peroxisome proliferator-activated receptor gamma, coactivator-related 1	1466	Arg-rich.|Ser-rich.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)	p.R1466Q(1)		central_nervous_system(1)|cervix(1)|endometrium(9)|kidney(5)|large_intestine(10)|lung(19)|ovary(1)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	56		Colorectal(252;0.122)		Epithelial(162;4.97e-08)|all cancers(201;8.99e-07)		AAGAGGTGGCGAAGGTGAGCT	0.517																																					p.R1466Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G4397A	10						.						74.0	64.0	67.0					10																	103907146		2203	4300	6503	103897136	SO:0001583	missense	23082	exon9			AF325193	CCDS7529.1, CCDS73186.1	10q24.32	2013-02-12	2006-10-17		ENSG00000148840	ENSG00000148840		"""RNA binding motif (RRM) containing"""	30025	protein-coding gene	gene with protein product			"""peroxisome proliferative activated receptor, gamma, coactivator-related 1"""			9628581, 11340167	Standard	XM_005269656		Approved	PRC, KIAA0595, MGC74642	uc001kum.3	Q5VV67	OTTHUMG00000018948	ENST00000278070.2:c.4397G>A	10.37:g.103907146G>A	ENSP00000278070:p.Arg1466Gln	Somatic		Capture	Illumina HiSeq	Phase_I	103897136	NM_015062	Q5VV66|Q6P3U5|Q6P3W1|Q76N31|Q9BUJ3|Q9BZE5|Q9Y4E0	Missense_Mutation	SNP	ENST00000278070.2	37	CCDS7529.1	.	.	.	.	.	.	.	.	.	.	G	22.5	4.299802	0.81136	.	.	ENSG00000148840	ENST00000278070;ENST00000370012	T;T	0.46063	0.88;0.88	5.76	5.76	0.90799	.	0.612146	0.15811	N	0.243450	T	0.55146	0.1902	N	0.24115	0.695	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.83275	0.996;0.989	T	0.56974	-0.7890	10	0.59425	D	0.04	.	19.972	0.97287	0.0:0.0:1.0:0.0	.	1346;1466	Q5VV67-2;Q5VV67	.;PPRC1_HUMAN	Q	1466;433	ENSP00000278070:R1466Q;ENSP00000359029:R433Q	ENSP00000278070:R1466Q	R	+	2	0	PPRC1	103897136	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	6.433000	0.73404	2.724000	0.93272	0.462000	0.41574	CGA		0.517	PPRC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050021.1	NM_015062	
NOLC1	9221	broad.mit.edu	37	10	103920362	103920362	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr10:103920362C>T	ENST00000605788.1	+	10	1488	c.1253C>T	c.(1252-1254)aCg>aTg	p.T418M	NOLC1_ENST00000405356.1_Missense_Mutation_p.T428M|NOLC1_ENST00000488254.2_Missense_Mutation_p.T419M|NOLC1_ENST00000603742.1_Missense_Mutation_p.T137M	NM_001284389.1|NM_004741.3	NP_001271318.1|NP_004732.2	Q14978	NOLC1_HUMAN	nucleolar and coiled-body phosphoprotein 1	418	11 X 12 AA approximate repeats of an acidic serine cluster.				cell cycle (GO:0007049)|mitotic nuclear division (GO:0007067)|nucleolus organization (GO:0007000)|rRNA processing (GO:0006364)	Cajal body (GO:0015030)|cytoplasm (GO:0005737)|nucleolus (GO:0005730)	ATP binding (GO:0005524)|GTP binding (GO:0005525)|poly(A) RNA binding (GO:0044822)	p.T418M(2)		breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(12)|ovary(1)|upper_aerodigestive_tract(1)	31		Colorectal(252;0.122)		Epithelial(162;5.19e-08)|all cancers(201;9.43e-07)		AAGCTTCTGACGAGAAAGGCT	0.562																																					p.T418M												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.C1253T	10						.						58.0	54.0	55.0					10																	103920362		2203	4300	6503	103910352	SO:0001583	missense	9221	exon10			Z34289	CCDS7530.1, CCDS65925.1, CCDS65926.1	10q24.32	2008-08-01			ENSG00000166197	ENSG00000166197			15608	protein-coding gene	gene with protein product		602394				7657714, 10567578	Standard	XM_005270273		Approved	P130, KIAA0035, NOPP140, NOPP130	uc001kuo.2	Q14978	OTTHUMG00000018944	ENST00000605788.1:c.1253C>T	10.37:g.103920362C>T	ENSP00000474710:p.Thr418Met	Somatic		Capture	Illumina HiSeq	Phase_I	103910352	NM_004741	Q15030|Q5VV70|Q9BUV3	Missense_Mutation	SNP	ENST00000605788.1	37	CCDS7530.1	.	.	.	.	.	.	.	.	.	.	C	1.559	-0.537277	0.04082	.	.	ENSG00000166197	ENST00000405356;ENST00000370007	T	0.33216	1.42	5.67	0.57	0.17347	.	0.634938	0.15624	N	0.252749	T	0.25680	0.0625	L	0.54323	1.7	0.09310	N	1	B;B;B	0.22080	0.064;0.064;0.038	B;B;B	0.15870	0.014;0.014;0.006	T	0.17961	-1.0352	10	0.51188	T	0.08	-0.2215	7.7611	0.28953	0.0:0.6168:0.1142:0.269	.	419;428;418	Q14978-3;Q14978-2;Q14978	.;.;NOLC1_HUMAN	M	428;418	ENSP00000385410:T428M	ENSP00000359024:T418M	T	+	2	0	NOLC1	103910352	0.000000	0.05858	0.004000	0.12327	0.000000	0.00434	-0.039000	0.12124	-0.143000	0.11334	-1.756000	0.00673	ACG		0.562	NOLC1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000050012.2	NM_004741	
GBF1	8729	broad.mit.edu	37	10	104139294	104139294	+	Silent	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr10:104139294C>T	ENST00000369983.3	+	35	4919	c.4659C>T	c.(4657-4659)tgC>tgT	p.C1553C		NM_001199378.1|NM_001199379.1|NM_004193.2	NP_001186307.1|NP_001186308.1|NP_004184.1	Q92538	GBF1_HUMAN	golgi brefeldin A resistant guanine nucleotide exchange factor 1	1553					COPI coating of Golgi vesicle (GO:0048205)|membrane organization (GO:0061024)|positive regulation of GTPase activity (GO:0043547)|post-Golgi vesicle-mediated transport (GO:0006892)|regulation of ARF protein signal transduction (GO:0032012)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)|vesicle-mediated transport (GO:0016192)|viral process (GO:0016032)	cis-Golgi network (GO:0005801)|endoplasmic reticulum lumen (GO:0005788)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|Golgi stack (GO:0005795)|membrane (GO:0016020)|mitochondrion (GO:0005739)|peroxisome (GO:0005777)|trans-Golgi network (GO:0005802)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)	p.C1553C(1)		NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(14)|kidney(8)|large_intestine(15)|lung(19)|ovary(1)|pancreas(1)|prostate(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	71		Colorectal(252;0.0236)		Epithelial(162;5.16e-08)|all cancers(201;1.19e-06)		CCTGCCTGTGCTGCGATGCCC	0.562																																					p.C1550C												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C4650T	10						.						117.0	113.0	114.0					10																	104139294		2203	4300	6503	104129284	SO:0001819	synonymous_variant	8729	exon35			D87435	CCDS7533.1	10q24	2010-02-12	2010-02-12		ENSG00000107862	ENSG00000107862			4181	protein-coding gene	gene with protein product		603698	"""golgi-specific brefeldin A resistance factor 1"""			9828135	Standard	NM_004193		Approved	KIAA0248, ARF1GEF	uc001kux.2	Q92538	OTTHUMG00000018955	ENST00000369983.3:c.4659C>T	10.37:g.104139294C>T		Somatic		Capture	Illumina HiSeq	Phase_I	104129284	NM_001199378	Q5VXX3|Q96CK6|Q96HZ3|Q9H473	Silent	SNP	ENST00000369983.3	37	CCDS7533.1																																																																																				0.562	GBF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050051.1		
CUEDC2	79004	broad.mit.edu	37	10	104183292	104183292	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr10:104183292A>G	ENST00000369937.4	-	9	900	c.755T>C	c.(754-756)gTa>gCa	p.V252A	CUEDC2_ENST00000465409.1_5'UTR|PSD_ENST00000492902.2_5'Flank	NM_024040.2	NP_076945.2	Q9H467	CUED2_HUMAN	CUE domain containing 2	252						cytoplasm (GO:0005737)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)		p.V252A(1)		autonomic_ganglia(1)|endometrium(3)|kidney(1)|large_intestine(1)|stomach(1)|upper_aerodigestive_tract(1)	8		Colorectal(252;0.122)		Epithelial(162;9.17e-09)|all cancers(201;2.16e-07)|BRCA - Breast invasive adenocarcinoma(275;0.215)		GGTGCTCACTACCTGGTTGTC	0.572											OREG0020479	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.V252A												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T755C	10						.						146.0	156.0	153.0					10																	104183292		2082	4211	6293	104173282	SO:0001583	missense	79004	exon9			BC000262	CCDS41566.1	10q24.32	2008-10-23	2004-03-04	2004-03-05	ENSG00000107874	ENSG00000107874			28352	protein-coding gene	gene with protein product		614142	"""chromosome 10 open reading frame 66"""	C10orf66		12477932	Standard	NM_024040		Approved	MGC2491	uc001kvn.2	Q9H467	OTTHUMG00000018958	ENST00000369937.4:c.755T>C	10.37:g.104183292A>G	ENSP00000358953:p.Val252Ala	Somatic	1379	Capture	Illumina HiSeq	Phase_I	104173282	NM_024040	D3DR88|Q9BWG8	Missense_Mutation	SNP	ENST00000369937.4	37	CCDS41566.1	.	.	.	.	.	.	.	.	.	.	A	18.49	3.636359	0.67130	.	.	ENSG00000107874	ENST00000369937	D	0.91180	-2.8	4.98	4.98	0.66077	.	0.259259	0.37906	N	0.001884	D	0.87509	0.6195	L	0.55481	1.735	0.52501	D	0.999957	P	0.48694	0.914	B	0.38842	0.283	D	0.89071	0.3469	10	0.87932	D	0	-0.2736	13.8601	0.63554	1.0:0.0:0.0:0.0	.	252	Q9H467	CUED2_HUMAN	A	252	ENSP00000358953:V252A	ENSP00000358953:V252A	V	-	2	0	CUEDC2	104173282	1.000000	0.71417	0.980000	0.43619	0.816000	0.46133	8.714000	0.91412	1.886000	0.54624	0.459000	0.35465	GTA		0.572	CUEDC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050060.1	NM_024040	
TMEM180	79847	broad.mit.edu	37	10	104230800	104230800	+	Silent	SNP	C	C	A	rs34328514		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr10:104230800C>A	ENST00000238936.4	+	5	867	c.630C>A	c.(628-630)gcC>gcA	p.A210A	TMEM180_ENST00000369931.3_Intron|TMEM180_ENST00000366277.2_Intron	NM_024789.3	NP_079065.2	Q14CX5	TM180_HUMAN	transmembrane protein 180	210						integral component of membrane (GO:0016021)		p.A210A(1)		breast(3)|endometrium(2)|large_intestine(3)|lung(1)|ovary(3)|skin(1)	13		Colorectal(252;0.122)		Epithelial(162;3.93e-09)|all cancers(201;1.02e-07)|BRCA - Breast invasive adenocarcinoma(275;0.215)		TTCTGGGGGCCACACAGCTGC	0.622																																					p.A210A												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C630A	10						.						58.0	70.0	66.0					10																	104230800		2203	4300	6503	104220790	SO:0001819	synonymous_variant	79847	exon5			AK026182	CCDS7535.1	10q24.32	2011-02-09	2006-10-12	2006-10-12	ENSG00000138111	ENSG00000138111			26196	protein-coding gene	gene with protein product				C10orf77		12477932	Standard	XM_006717971		Approved	FLJ22529, bA18I14.8	uc001kvt.3	Q14CX5	OTTHUMG00000018961	ENST00000238936.4:c.630C>A	10.37:g.104230800C>A		Somatic		Capture	Illumina HiSeq	Phase_I	104220790	NM_024789	Q6NWM8|Q6NWM9|Q6PEZ7|Q9H679	Silent	SNP	ENST00000238936.4	37	CCDS7535.1																																																																																				0.622	TMEM180-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050075.2	NM_024789	
WBP1L	54838	broad.mit.edu	37	10	104572927	104572927	+	Missense_Mutation	SNP	C	C	T	rs201482384		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr10:104572927C>T	ENST00000369889.4	+	4	1010	c.868C>T	c.(868-870)Cgg>Tgg	p.R290W	WBP1L_ENST00000448841.1_Missense_Mutation_p.R311W	NM_017787.4	NP_060257.4	Q9NX94	WBP1L_HUMAN	WW domain binding protein 1-like	290						integral component of membrane (GO:0016021)		p.R290W(1)									CTGCCATGTGCGGCCCCCTGG	0.637													c|||	1	0.000199681	0.0	0.0	5008	,	,		15869	0.0		0.001	False		,,,				2504	0.0				p.R290W												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C868T	10						.						58.0	65.0	63.0					10																	104572927		2203	4300	6503	104562917	SO:0001583	missense	54838	exon4			AK056285	CCDS7540.1, CCDS44473.1	10q24.33	2012-05-02	2012-05-02	2012-05-02	ENSG00000166272	ENSG00000166272			23510	protein-coding gene	gene with protein product	"""outcome predictor in acute leukemia 1"""	611129	"""chromosome 10 open reading frame 26"""	C10orf26			Standard	NM_017787		Approved	FLJ20154, OPAL1	uc001kwf.4	Q9NX94	OTTHUMG00000018968	ENST00000369889.4:c.868C>T	10.37:g.104572927C>T	ENSP00000358905:p.Arg290Trp	Somatic		Capture	Illumina HiSeq	Phase_I	104562917	NM_017787	B3KPF4|B7Z6S7|D3DR90|Q1EG70|Q2HIY7|Q5F2G6	Missense_Mutation	SNP	ENST00000369889.4	37	CCDS7540.1	.	.	.	.	.	.	.	.	.	.	c	14.53	2.561526	0.45590	.	.	ENSG00000166272	ENST00000448841;ENST00000369889	T;T	0.43688	0.94;1.01	5.93	3.89	0.44902	.	0.418166	0.28527	N	0.015032	T	0.38665	0.1049	L	0.47716	1.5	0.51233	D	0.999917	B;B	0.27192	0.171;0.04	B;B	0.19666	0.026;0.007	T	0.41963	-0.9479	10	0.87932	D	0	-16.8895	16.6667	0.85254	0.2476:0.7524:0.0:0.0	.	311;290	Q9NX94-2;Q9NX94	.;OPA1L_HUMAN	W	311;290	ENSP00000414721:R311W;ENSP00000358905:R290W	ENSP00000358905:R290W	R	+	1	2	C10orf26	104562917	1.000000	0.71417	0.991000	0.47740	0.972000	0.66771	2.761000	0.47589	1.499000	0.48617	0.556000	0.70494	CGG		0.637	WBP1L-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000050100.1	NM_017787	
ADRA2A	150	broad.mit.edu	37	10	112838875	112838875	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr10:112838875C>T	ENST00000280155.2	+	1	2086	c.1121C>T	c.(1120-1122)gCg>gTg	p.A374V		NM_000681.3	NP_000672.3	P08913	ADA2A_HUMAN	adrenoceptor alpha 2A	359					actin cytoskeleton organization (GO:0030036)|activation of MAPK activity by adrenergic receptor signaling pathway (GO:0071883)|activation of protein kinase activity (GO:0032147)|activation of protein kinase B activity (GO:0032148)|acute inflammatory response (GO:0002526)|adenylate cyclase-inhibiting adrenergic receptor signaling pathway (GO:0071881)|blood coagulation (GO:0007596)|cellular component movement (GO:0006928)|cellular response to hormone stimulus (GO:0032870)|DNA replication (GO:0006260)|energy reserve metabolic process (GO:0006112)|epidermal growth factor-activated receptor transactivation by G-protein coupled receptor signaling pathway (GO:0035625)|fear response (GO:0042596)|female pregnancy (GO:0007565)|G-protein coupled receptor signaling pathway (GO:0007186)|glucose homeostasis (GO:0042593)|intestinal absorption (GO:0050892)|negative regulation of adenylate cyclase activity (GO:0007194)|negative regulation of adrenergic receptor signaling pathway (GO:0071878)|negative regulation of calcium ion transmembrane transporter activity (GO:1901020)|negative regulation of calcium ion transport (GO:0051926)|negative regulation of calcium ion-dependent exocytosis (GO:0045955)|negative regulation of cAMP biosynthetic process (GO:0030818)|negative regulation of epinephrine secretion (GO:0032811)|negative regulation of insulin secretion (GO:0046676)|negative regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0061179)|negative regulation of lipid catabolic process (GO:0050995)|negative regulation of norepinephrine secretion (GO:0010700)|negative regulation of uterine smooth muscle contraction (GO:0070473)|phospholipase C-activating adrenergic receptor signaling pathway (GO:0071882)|platelet activation (GO:0030168)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cytokine production (GO:0001819)|positive regulation of epidermal growth factor-activated receptor activity (GO:0045741)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of membrane protein ectodomain proteolysis (GO:0051044)|positive regulation of potassium ion transport (GO:0043268)|positive regulation of vasodilation (GO:0045909)|positive regulation of wound healing (GO:0090303)|Ras protein signal transduction (GO:0007265)|regulation of insulin secretion (GO:0050796)|regulation of vasoconstriction (GO:0019229)|Rho protein signal transduction (GO:0007266)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|thermoception (GO:0050955)	basolateral plasma membrane (GO:0016323)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|synapse (GO:0045202)	alpha-1B adrenergic receptor binding (GO:0031692)|alpha-2C adrenergic receptor binding (GO:0031696)|alpha2-adrenergic receptor activity (GO:0004938)|epinephrine binding (GO:0051379)|heterotrimeric G-protein binding (GO:0032795)|norepinephrine binding (GO:0051380)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)|thioesterase binding (GO:0031996)	p.A359V(1)		breast(1)|cervix(3)|endometrium(6)|large_intestine(3)|lung(5)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	21		Breast(234;0.0735)|Lung NSC(174;0.238)		Epithelial(162;0.000316)|all cancers(201;0.00501)|BRCA - Breast invasive adenocarcinoma(275;0.118)	Amitriptyline(DB00321)|Amoxapine(DB00543)|Amphetamine(DB00182)|Apomorphine(DB00714)|Apraclonidine(DB00964)|Aripiprazole(DB01238)|Asenapine(DB06216)|Benzphetamine(DB00865)|Bethanidine(DB00217)|Brimonidine(DB00484)|Bromocriptine(DB01200)|Cabergoline(DB00248)|Carvedilol(DB01136)|Chlorpromazine(DB00477)|Clonidine(DB00575)|Clozapine(DB00363)|Desipramine(DB01151)|Dexmedetomidine(DB00633)|Dihydroergotamine(DB00320)|Dipivefrin(DB00449)|Doxepin(DB01142)|Dronedarone(DB04855)|Droxidopa(DB06262)|Ephedra(DB01363)|Epinastine(DB00751)|Epinephrine(DB00668)|Ergoloid mesylate(DB01049)|Ergotamine(DB00696)|Fenoldopam(DB00800)|Flupirtine(DB06623)|Guanabenz(DB00629)|Guanfacine(DB01018)|Lisuride(DB00589)|Lofexidine(DB04948)|Loxapine(DB00408)|Lurasidone(DB08815)|Maprotiline(DB00934)|Mephentermine(DB01365)|Methamphetamine(DB01577)|Methotrimeprazine(DB01403)|Methyldopa(DB00968)|Mianserin(DB06148)|Mirtazapine(DB00370)|Naphazoline(DB06711)|Nefazodone(DB01149)|Norepinephrine(DB00368)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Oxymetazoline(DB00935)|Paliperidone(DB01267)|Pergolide(DB01186)|Phenoxybenzamine(DB00925)|Phentolamine(DB00692)|Phenylpropanolamine(DB00397)|Pramipexole(DB00413)|Prazosin(DB00457)|Propericiazine(DB01608)|Pseudoephedrine(DB00852)|Quetiapine(DB01224)|Risperidone(DB00734)|Ropinirole(DB00268)|Tizanidine(DB00697)|Tolazoline(DB00797)|Trazodone(DB00656)|Trimipramine(DB00726)|Xylometazoline(DB06694)|Yohimbine(DB01392)|Ziprasidone(DB00246)	GCTGCCAAGGCGTCGCGCTGG	0.736																																					p.A374V	Esophageal Squamous(173;605 2658 7278 49362)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1121T	10						.						48.0	42.0	44.0					10																	112838875		2202	4298	6500	112828865	SO:0001583	missense	150	exon1			AF284095	CCDS7569.2	10q25.2	2012-08-08	2012-05-09		ENSG00000150594	ENSG00000150594		"""GPCR / Class A : Adrenoceptors : alpha"""	281	protein-coding gene	gene with protein product	"""alpha-2AAR subtype C10"", "" alpha-2A-adrenergic receptor"""	104210	"""adrenergic, alpha-2A-, receptor"""	ADRA2, ADRA2R			Standard	NM_000681		Approved	ADRAR	uc001kzo.3	P08913	OTTHUMG00000019050	ENST00000280155.2:c.1121C>T	10.37:g.112838875C>T	ENSP00000280155:p.Ala374Val	Somatic		Capture	Illumina HiSeq	Phase_I	112828865	NM_000681	B0LPF6|Q2I8G2|Q2XN99|Q86TH8|Q9BZK1	Missense_Mutation	SNP	ENST00000280155.2	37	CCDS7569.2	.	.	.	.	.	.	.	.	.	.	C	4.231	0.041702	0.08196	.	.	ENSG00000150594	ENST00000280155	T	0.35973	1.28	3.53	3.53	0.40419	GPCR, rhodopsin-like superfamily (1);	1.025860	0.07845	U	0.963731	T	0.20088	0.0483	N	0.13352	0.335	0.39986	D	0.974983	P	0.36874	0.572	B	0.35859	0.212	T	0.09185	-1.0686	10	0.13108	T	0.6	.	6.8806	0.24170	0.0:0.6991:0.1967:0.1041	.	359	P08913	ADA2A_HUMAN	V	374	ENSP00000280155:A374V	ENSP00000280155:A374V	A	+	2	0	ADRA2A	112828865	0.229000	0.23729	0.998000	0.56505	0.121000	0.20230	0.565000	0.23578	1.932000	0.55993	0.462000	0.41574	GCG		0.736	ADRA2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050372.2	NM_000681	
PLEKHS1	79949	broad.mit.edu	37	10	115540378	115540378	+	Silent	SNP	C	C	T	rs201435892	byFrequency	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr10:115540378C>T	ENST00000354462.3	+	6	593	c.435C>T	c.(433-435)atC>atT	p.I145I	PLEKHS1_ENST00000369312.4_Silent_p.I313I|PLEKHS1_ENST00000369309.1_Silent_p.I229I|PLEKHS1_ENST00000361048.1_3'UTR			Q5SXH7	PKHS1_HUMAN	pleckstrin homology domain containing, family S member 1	409								p.I313I(1)									AGCTTACCATCGGCAGGATCC	0.408													C|||	2	0.000399361	0.0015	0.0	5008	,	,		21554	0.0		0.0	False		,,,				2504	0.0				p.I313I												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C939T	10						.	C	,,	2,4404	4.2+/-10.8	0,2,2201	113.0	107.0	109.0		939,939,	-4.9	0.2	10		109	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous,utr-3	C10orf81	NM_001193434.1,NM_001193435.1,NM_024889.4	,,	0,2,6501	TT,TC,CC		0.0,0.0454,0.0154	,,	313/367,313/367,	115540378	2,13004	2203	4300	6503	115530368	SO:0001819	synonymous_variant	79949	exon11			AK027190	CCDS7583.1, CCDS53580.1, CCDS53581.1	10q26.11	2013-01-11	2012-05-31	2012-05-31	ENSG00000148735	ENSG00000148735		"""Pleckstrin homology (PH) domain containing"""	26285	protein-coding gene	gene with protein product			"""chromosome 10 open reading frame 81"""	C10orf81		12477932	Standard	NM_024889		Approved	FLJ23537, bA211N11.2	uc001lat.2	Q5SXH7	OTTHUMG00000019074	ENST00000354462.3:c.435C>T	10.37:g.115540378C>T		Somatic		Capture	Illumina HiSeq	Phase_I	115530368	NM_001193435	A8KA02|B3KX00|B6EDE1|Q5SXH8|Q5SXI0|Q6ZQR5|Q8NE42|Q9H5D9	Silent	SNP	ENST00000354462.3	37																																																																																					0.408	PLEKHS1-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000050431.2	NM_024889	
NHLRC2	374354	broad.mit.edu	37	10	115618353	115618353	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr10:115618353T>C	ENST00000369301.3	+	2	457	c.245T>C	c.(244-246)gTc>gCc	p.V82A		NM_198514.3	NP_940916.2	Q8NBF2	NHLC2_HUMAN	NHL repeat containing 2	82	Thioredoxin. {ECO:0000255|PROSITE- ProRule:PRU00691}.							p.V82A(1)		breast(1)|endometrium(2)|kidney(4)|large_intestine(3)|lung(3)|ovary(1)|upper_aerodigestive_tract(1)	15				Epithelial(162;0.017)|all cancers(201;0.0187)		AAAATAGTCGTCCTTGATTTC	0.343																																					p.V82A												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T245C	10						.						175.0	163.0	167.0					10																	115618353		2203	4300	6503	115608343	SO:0001583	missense	374354	exon2			AK090631	CCDS7585.1	10q26.11	2006-03-31			ENSG00000196865	ENSG00000196865			24731	protein-coding gene	gene with protein product						12477932	Standard	NM_198514		Approved	FLJ25621, FLJ20147, FLJ33312, MGC45492, DKFZp779F115	uc001lax.2	Q8NBF2	OTTHUMG00000019078	ENST00000369301.3:c.245T>C	10.37:g.115618353T>C	ENSP00000358307:p.Val82Ala	Somatic		Capture	Illumina HiSeq	Phase_I	115608343	NM_198514	Q8N1H1|Q8N5A6	Missense_Mutation	SNP	ENST00000369301.3	37	CCDS7585.1	.	.	.	.	.	.	.	.	.	.	T	19.99	3.928218	0.73327	.	.	ENSG00000196865	ENST00000369301	T	0.79033	-1.23	5.67	5.67	0.87782	Thioredoxin-like fold (3);	0.564177	0.18894	N	0.128233	T	0.80701	0.4673	M	0.84846	2.72	0.28423	N	0.917623	P	0.36683	0.565	B	0.36378	0.223	T	0.79042	-0.1965	10	0.56958	D	0.05	-0.9474	14.4916	0.67654	0.0:0.0:0.0:1.0	.	82	Q8NBF2	NHLC2_HUMAN	A	82	ENSP00000358307:V82A	ENSP00000358307:V82A	V	+	2	0	NHLRC2	115608343	1.000000	0.71417	0.371000	0.25978	0.811000	0.45836	7.579000	0.82511	2.148000	0.66965	0.482000	0.46254	GTC		0.343	NHLRC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050446.1	NM_198514	
TDRD1	56165	broad.mit.edu	37	10	115986880	115986880	+	Missense_Mutation	SNP	A	A	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr10:115986880A>T	ENST00000251864.2	+	23	3378	c.3225A>T	c.(3223-3225)ttA>ttT	p.L1075F	TDRD1_ENST00000369280.1_Intron|TDRD1_ENST00000369282.1_Intron|TDRD1_ENST00000422662.1_Intron|TDRD1_ENST00000369281.2_Missense_Mutation_p.L961F	NM_198795.1	NP_942090.1	Q9BXT4	TDRD1_HUMAN	tudor domain containing 1	1075					DNA methylation involved in gamete generation (GO:0043046)|gene silencing by RNA (GO:0031047)|germ cell development (GO:0007281)|meiotic nuclear division (GO:0007126)|multicellular organismal development (GO:0007275)|piRNA metabolic process (GO:0034587)|spermatogenesis (GO:0007283)	chromatoid body (GO:0033391)|cytoplasm (GO:0005737)|P granule (GO:0043186)|pi-body (GO:0071546)	metal ion binding (GO:0046872)	p.L1075F(1)		breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|lung(15)|ovary(1)|prostate(2)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(5)	48		Colorectal(252;0.172)|Breast(234;0.188)		Epithelial(162;0.0343)|all cancers(201;0.0754)		TAATGCTATTAAAAAATTTCA	0.299																																					p.L1075F												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A3225T	10						.						31.0	32.0	32.0					10																	115986880		2203	4299	6502	115976870	SO:0001583	missense	56165	exon23			AF285606	CCDS7588.1	10q26.11	2013-01-23			ENSG00000095627	ENSG00000095627		"""Tudor domain containing"""	11712	protein-coding gene	gene with protein product	"""cancer/testis antigen 41.1"""	605796				11279525	Standard	NM_198795		Approved	CT41.1	uc001lbg.1	Q9BXT4	OTTHUMG00000019083	ENST00000251864.2:c.3225A>T	10.37:g.115986880A>T	ENSP00000251864:p.Leu1075Phe	Somatic		Capture	Illumina HiSeq	Phase_I	115976870	NM_198795	A6NEN3|A6NMN2|B3KVI4|B4E2L5|D3DRC2|Q4G0Y8|Q6P518|Q9H7B3	Missense_Mutation	SNP	ENST00000251864.2	37	CCDS7588.1	.	.	.	.	.	.	.	.	.	.	A	6.440	0.449240	0.12223	.	.	ENSG00000095627	ENST00000251864;ENST00000369281	T;T	0.23754	2.78;1.89	5.91	-2.82	0.05787	.	0.000000	0.48767	D	0.000161	T	0.21307	0.0513	M	0.66939	2.045	0.54753	D	0.999988	B;B;B;B	0.22003	0.017;0.041;0.028;0.063	B;B;B;B	0.27887	0.017;0.017;0.039;0.084	T	0.15292	-1.0442	10	0.15952	T	0.53	-13.0321	8.4037	0.32601	0.3306:0.0:0.5417:0.1277	.	1075;961;1075;961	Q9BXT4;B7WPM2;Q9BXT4-3;Q9BXT4-2	TDRD1_HUMAN;.;.;.	F	1075;961	ENSP00000251864:L1075F;ENSP00000358287:L961F	ENSP00000251864:L1075F	L	+	3	2	TDRD1	115976870	0.057000	0.20700	0.095000	0.20976	0.211000	0.24417	-0.476000	0.06591	-0.778000	0.04566	-0.309000	0.09137	TTA		0.299	TDRD1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding			
VWA2	340706	broad.mit.edu	37	10	116045771	116045771	+	Silent	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr10:116045771C>T	ENST00000392982.3	+	11	1321	c.1071C>T	c.(1069-1071)gaC>gaT	p.D357D	VWA2_ENST00000603594.1_Silent_p.D357D			Q5GFL6	VWA2_HUMAN	von Willebrand factor A domain containing 2	357	VWFA 2. {ECO:0000255|PROSITE- ProRule:PRU00219}.				calcium-independent cell-matrix adhesion (GO:0007161)|protein homooligomerization (GO:0051260)|regulation of insulin receptor signaling pathway (GO:0046626)	basement membrane (GO:0005604)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	identical protein binding (GO:0042802)	p.D357D(1)		central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(7)|lung(6)|ovary(2)|prostate(1)|skin(1)|stomach(1)	26				Epithelial(162;0.036)|all cancers(201;0.0793)		CCACTCTGGACGGCTTCCTGC	0.647																																					p.D357D												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1071T	10						.						71.0	73.0	73.0					10																	116045771		2203	4300	6503	116035761	SO:0001819	synonymous_variant	340706	exon11			AK127756	CCDS7589.1, CCDS7589.2	10q25.3	2009-11-06			ENSG00000165816	ENSG00000165816			24709	protein-coding gene	gene with protein product						15580307, 14506275	Standard	NM_001272046		Approved	FLJ45857, FLJ16213, CCSP-2, AMACO, NET42	uc001lbl.2	Q5GFL6	OTTHUMG00000019082	ENST00000392982.3:c.1071C>T	10.37:g.116045771C>T		Somatic		Capture	Illumina HiSeq	Phase_I	116035761	NM_198496	A1A5D4|B5MDJ8|Q6ZS39|Q6ZWJ7|Q708C5|Q70UZ8	Silent	SNP	ENST00000392982.3	37																																																																																					0.647	VWA2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000050456.3	NM_198496	
HSPA12A	259217	broad.mit.edu	37	10	118434719	118434719	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr10:118434719G>A	ENST00000369209.3	-	12	1705	c.1601C>T	c.(1600-1602)cCg>cTg	p.P534L	RP11-498B4.5_ENST00000433600.1_RNA	NM_025015.2	NP_079291.2	O43301	HS12A_HUMAN	heat shock 70kDa protein 12A	534						extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)	p.P1155L(1)		breast(2)|endometrium(2)|kidney(1)|large_intestine(5)|lung(15)|ovary(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	32				all cancers(201;0.0158)		GTAGGTGAGCGGCGACCGGCG	0.662																																					p.P534L												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1601T	10						.						36.0	41.0	39.0					10																	118434719		2080	4188	6268	118424709	SO:0001583	missense	259217	exon12			AB007877	CCDS41569.1	10q25.3	2011-09-02	2002-08-29		ENSG00000165868	ENSG00000165868		"""Heat shock proteins / HSP70"""	19022	protein-coding gene	gene with protein product		610701	"""heat shock 70kD protein 12A"""			12552099	Standard	NM_025015		Approved	FLJ13874, KIAA0417	uc001lct.3	O43301	OTTHUMG00000019107	ENST00000369209.3:c.1601C>T	10.37:g.118434719G>A	ENSP00000358211:p.Pro534Leu	Somatic		Capture	Illumina HiSeq	Phase_I	118424709	NM_025015		Missense_Mutation	SNP	ENST00000369209.3	37	CCDS41569.1	.	.	.	.	.	.	.	.	.	.	G	21.6	4.174430	0.78452	.	.	ENSG00000165868	ENST00000369209	T	0.45668	0.89	5.84	5.84	0.93424	.	0.000000	0.85682	D	0.000000	T	0.57242	0.2040	M	0.71581	2.175	0.80722	D	1	D	0.56968	0.978	P	0.51582	0.674	T	0.56817	-0.7916	10	0.48119	T	0.1	.	20.1379	0.98040	0.0:0.0:1.0:0.0	.	534	O43301	HS12A_HUMAN	L	534	ENSP00000358211:P534L	ENSP00000358211:P534L	P	-	2	0	HSPA12A	118424709	1.000000	0.71417	0.985000	0.45067	0.638000	0.38207	9.476000	0.97823	2.779000	0.95612	0.655000	0.94253	CCG		0.662	HSPA12A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050530.1	NM_025015	
HSPA12A	259217	broad.mit.edu	37	10	118441315	118441315	+	Silent	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr10:118441315G>A	ENST00000369209.3	-	8	1013	c.909C>T	c.(907-909)tcC>tcT	p.S303S		NM_025015.2	NP_079291.2	O43301	HS12A_HUMAN	heat shock 70kDa protein 12A	303						extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)	p.S924S(2)		breast(2)|endometrium(2)|kidney(1)|large_intestine(5)|lung(15)|ovary(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	32				all cancers(201;0.0158)		CCTCCAGCTCGGACCAGATTT	0.478											OREG0020558	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.S303S												.	.	2	Substitution - coding silent(2)	large_intestine(1)|prostate(1)	c.C909T	10						.						98.0	97.0	97.0					10																	118441315		1944	4146	6090	118431305	SO:0001819	synonymous_variant	259217	exon8			AB007877	CCDS41569.1	10q25.3	2011-09-02	2002-08-29		ENSG00000165868	ENSG00000165868		"""Heat shock proteins / HSP70"""	19022	protein-coding gene	gene with protein product		610701	"""heat shock 70kD protein 12A"""			12552099	Standard	NM_025015		Approved	FLJ13874, KIAA0417	uc001lct.3	O43301	OTTHUMG00000019107	ENST00000369209.3:c.909C>T	10.37:g.118441315G>A		Somatic	1488	Capture	Illumina HiSeq	Phase_I	118431305	NM_025015		Silent	SNP	ENST00000369209.3	37	CCDS41569.1																																																																																				0.478	HSPA12A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050530.1	NM_025015	
KCNK18	338567	broad.mit.edu	37	10	118969176	118969176	+	Missense_Mutation	SNP	G	G	A	rs139101102		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr10:118969176G>A	ENST00000334549.1	+	3	521	c.521G>A	c.(520-522)cGc>cAc	p.R174H		NM_181840.1	NP_862823.1	Q7Z418	KCNKI_HUMAN	potassium channel, subfamily K, member 18	174					cellular response to pH (GO:0071467)|potassium ion export (GO:0071435)|potassium ion transport (GO:0006813)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium-activated potassium channel activity (GO:0015269)|outward rectifier potassium channel activity (GO:0015271)|potassium channel activity (GO:0005267)	p.R174H(2)		breast(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(7)|lung(24)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	41		Colorectal(252;0.19)		all cancers(201;0.0211)		TTCTTTACCCGCCCCCTCCTC	0.507																																					p.R174H												.	.	2	Substitution - Missense(2)	large_intestine(1)|kidney(1)	c.G521A	10						.	G	HIS/ARG	0,4406		0,0,2203	85.0	89.0	88.0		521	-3.3	0.0	10	dbSNP_134	88	1,8599	1.2+/-3.3	0,1,4299	no	missense	KCNK18	NM_181840.1	29	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	benign	174/385	118969176	1,13005	2203	4300	6503	118959166	SO:0001583	missense	338567	exon3			AB087138	CCDS7598.1	10q26.11	2012-03-07			ENSG00000186795	ENSG00000186795		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels, Two-P"""	19439	protein-coding gene	gene with protein product	"""TWIK related spinal cord K+ channel"""	613655				16382106	Standard	NM_181840		Approved	K2p18.1, TRESK-2, TRESK2, TRESK, TRIK	uc010qsr.2	Q7Z418	OTTHUMG00000019120	ENST00000334549.1:c.521G>A	10.37:g.118969176G>A	ENSP00000334650:p.Arg174His	Somatic		Capture	Illumina HiSeq	Phase_I	118959166	NM_181840	Q5SQQ8	Missense_Mutation	SNP	ENST00000334549.1	37	CCDS7598.1	.	.	.	.	.	.	.	.	.	.	G	9.837	1.189940	0.21954	0.0	1.16E-4	ENSG00000186795	ENST00000334549	T	0.26223	1.75	4.41	-3.26	0.05064	.	1.118960	0.06526	N	0.740624	T	0.08935	0.0221	N	0.03608	-0.345	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.22941	-1.0202	10	0.40728	T	0.16	.	1.0346	0.01545	0.2564:0.3024:0.2513:0.1898	.	174	Q7Z418	KCNKI_HUMAN	H	174	ENSP00000334650:R174H	ENSP00000334650:R174H	R	+	2	0	KCNK18	118959166	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.919000	0.04017	-0.759000	0.04684	-0.345000	0.07892	CGC		0.507	KCNK18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050562.2	NM_181840	
INPP5F	22876	broad.mit.edu	37	10	121569645	121569645	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr10:121569645G>A	ENST00000361976.2	+	14	1769	c.1603G>A	c.(1603-1605)Gca>Aca	p.A535T		NM_014937.3	NP_055752.1	Q01968	OCRL_HUMAN	inositol polyphosphate-5-phosphatase F	0	5-phosphatase.				cilium assembly (GO:0042384)|in utero embryonic development (GO:0001701)|inositol phosphate metabolic process (GO:0043647)|lipid metabolic process (GO:0006629)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phospholipid metabolic process (GO:0006644)|positive regulation of Rac GTPase activity (GO:0032855)|regulation of Rac GTPase activity (GO:0032314)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|small molecule metabolic process (GO:0044281)	clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|early endosome (GO:0005769)|extracellular vesicular exosome (GO:0070062)|Golgi stack (GO:0005795)|Golgi-associated vesicle (GO:0005798)|nucleus (GO:0005634)|photoreceptor outer segment (GO:0001750)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)	inositol phosphate phosphatase activity (GO:0052745)|phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity (GO:0004439)|Rac GTPase activator activity (GO:0030675)|Rac GTPase binding (GO:0048365)	p.A535T(1)		breast(1)|cervix(1)|endometrium(7)|kidney(4)|large_intestine(9)|lung(5)|ovary(5)|pancreas(1)|prostate(1)|skin(1)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	42		Lung NSC(174;0.109)|all_lung(145;0.142)		all cancers(201;0.00205)|BRCA - Breast invasive adenocarcinoma(275;0.158)		AAGGAAGTTAGCAGGAGTTAT	0.378																																					p.A535T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1603A	10						.						151.0	131.0	138.0					10																	121569645		2203	4300	6503	121559635	SO:0001583	missense	22876	exon14			AB023183	CCDS7616.1, CCDS58098.1	10q26.13	2009-02-03			ENSG00000198825	ENSG00000198825			17054	protein-coding gene	gene with protein product		609389				10231032, 11274189	Standard	NM_014937		Approved	SAC2, KIAA0966, hSac2	uc001leo.3	Q9Y2H2	OTTHUMG00000019158	ENST00000361976.2:c.1603G>A	10.37:g.121569645G>A	ENSP00000354519:p.Ala535Thr	Somatic		Capture	Illumina HiSeq	Phase_I	121559635	NM_014937	A6NKI1|A8KAP2|B7ZLX2|O60800|Q15684|Q15774|Q4VY09|Q4VY10|Q5JQF1|Q5JQF2|Q9UJG5|Q9UMA5	Missense_Mutation	SNP	ENST00000361976.2	37	CCDS7616.1	.	.	.	.	.	.	.	.	.	.	G	16.35	3.099020	0.56183	.	.	ENSG00000198825	ENST00000361976	T	0.26067	1.76	5.04	5.04	0.67666	.	0.114843	0.64402	D	0.000014	T	0.16938	0.0407	N	0.25485	0.75	0.80722	D	1	B	0.30824	0.296	B	0.23419	0.046	T	0.04481	-1.0948	10	0.06365	T	0.9	-16.1523	18.4265	0.90611	0.0:0.0:1.0:0.0	.	535	Q9Y2H2	SAC2_HUMAN	T	535	ENSP00000354519:A535T	ENSP00000354519:A535T	A	+	1	0	INPP5F	121559635	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.665000	0.98609	2.356000	0.79943	0.561000	0.74099	GCA		0.378	INPP5F-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050679.1	NM_014937	
DMBT1	1755	broad.mit.edu	37	10	124361388	124361388	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	G	G	G	Unknown	Wildtype	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr10:124361388G>A	ENST00000338354.3	+	29	3525	c.3419G>A	c.(3418-3420)cGa>cAa	p.R1140Q	DMBT1_ENST00000330163.4_Missense_Mutation_p.R641Q|DMBT1_ENST00000368955.3_Missense_Mutation_p.R1130Q|DMBT1_ENST00000359586.6_Intron|DMBT1_ENST00000344338.3_Missense_Mutation_p.R1130Q|DMBT1_ENST00000368909.3_Missense_Mutation_p.R1140Q|DMBT1_ENST00000368956.2_Missense_Mutation_p.R641Q			Q9UGM3	DMBT1_HUMAN	deleted in malignant brain tumors 1	1140	SRCR 9. {ECO:0000255|PROSITE- ProRule:PRU00196}.				defense response to virus (GO:0051607)|epithelial cell differentiation (GO:0030855)|induction of bacterial agglutination (GO:0043152)|innate immune response (GO:0045087)|inner cell mass cell proliferation (GO:0001833)|pattern recognition receptor signaling pathway (GO:0002221)|positive regulation of epithelial cell differentiation (GO:0030858)|protein transport (GO:0015031)|receptor-mediated endocytosis (GO:0006898)|viral process (GO:0016032)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|phagocytic vesicle membrane (GO:0030670)|proteinaceous extracellular matrix (GO:0005578)|zymogen granule membrane (GO:0042589)	calcium-dependent protein binding (GO:0048306)|scavenger receptor activity (GO:0005044)|signaling pattern recognition receptor activity (GO:0008329)|zymogen binding (GO:0035375)			breast(2)|central_nervous_system(7)|cervix(3)|endometrium(8)|kidney(1)|large_intestine(1)|lung(46)|prostate(1)|urinary_tract(3)	72		all_neural(114;0.0765)|Lung NSC(174;0.132)|all_lung(145;0.163)|Breast(234;0.238)				GTCCTATACCGAGGCTCCTGG	0.587																																					p.R1140Q	Ovarian(182;93 2026 18125 22222 38972)											.	.	0			c.G3419A	10						.						1.0	1.0	1.0					10																	124361388		102	402	504	124351378	SO:0001583	missense	1755	exon29				CCDS44490.1, CCDS44491.1, CCDS44492.1	10q25.3-q26.1	2008-08-01			ENSG00000187908	ENSG00000187908			2926	protein-coding gene	gene with protein product		601969				9288095, 17548659	Standard	NM_004406		Approved	GP340, muclin	uc001lgk.1	Q9UGM3	OTTHUMG00000019185	ENST00000338354.3:c.3419G>A	10.37:g.124361388G>A	ENSP00000342210:p.Arg1140Gln	None		Capture	Illumina HiSeq	Phase_I	124351378	NM_007329	A6NDG4|A6NDJ5|A8E4R5|B1ARE7|B1ARE8|B1ARE9|B1ARF0|B7Z8Y2|F8WEF7|Q59EX0|Q5JR26|Q6MZN4|Q96DU4|Q9UGM2|Q9UJ57|Q9UKJ4|Q9Y211|Q9Y4V9	Missense_Mutation	SNP	ENST00000338354.3	37		.	.	.	.	.	.	.	.	.	.	G	0	-2.775747	0.00080	.	.	ENSG00000187908	ENST00000338354;ENST00000368915;ENST00000341278;ENST00000368953;ENST00000339871;ENST00000368942;ENST00000327438;ENST00000344338;ENST00000339712;ENST00000330163;ENST00000368909;ENST00000368955;ENST00000368956	T;T;T;T;T;T	0.27890	1.64;1.64;1.64;1.64;1.64;1.64	3.2	-0.614	0.11590	Speract/scavenger receptor (3);Speract/scavenger receptor-related (2);	0.801389	0.10272	N	0.694661	T	0.09291	0.0229	N	0.03881	-0.34	0.09310	N	1	B;B;B;B	0.28760	0.0;0.221;0.0;0.0	B;B;B;B	0.24701	0.0;0.055;0.0;0.0	T	0.30621	-0.9972	10	0.02654	T	1	.	5.0727	0.14615	0.4332:0.0:0.4218:0.1449	.	1140;641;1130;1140	Q9UGM3-6;Q9UGM3-2;Q9UGM3-3;Q9UGM3	.;.;.;DMBT1_HUMAN	Q	1140;1140;1140;1140;1140;1140;641;1130;641;641;1140;1130;641	ENSP00000342210:R1140Q;ENSP00000343175:R1130Q;ENSP00000327747:R641Q;ENSP00000357905:R1140Q;ENSP00000357951:R1130Q;ENSP00000357952:R641Q	ENSP00000331522:R641Q	R	+	2	0	DMBT1	124351378	0.000000	0.05858	0.000000	0.03702	0.017000	0.09413	-3.368000	0.00495	-0.056000	0.13221	-0.938000	0.02693	CGA		0.587	DMBT1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000050792.2	NM_004406	
ADAM12	8038	broad.mit.edu	37	10	127789788	127789788	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr10:127789788C>T	ENST00000368679.4	-	9	1082	c.773G>A	c.(772-774)cGg>cAg	p.R258Q	ADAM12_ENST00000368676.4_Missense_Mutation_p.R258Q	NM_003474.4	NP_003465.3	O43184	ADA12_HUMAN	ADAM metallopeptidase domain 12	258	Peptidase M12B. {ECO:0000255|PROSITE- ProRule:PRU00276}.				cell adhesion (GO:0007155)|epidermal growth factor receptor signaling pathway (GO:0007173)|myoblast fusion (GO:0007520)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|SH3 domain binding (GO:0017124)|zinc ion binding (GO:0008270)	p.R258Q(2)		biliary_tract(1)|breast(7)|central_nervous_system(4)|endometrium(5)|kidney(3)|large_intestine(11)|liver(1)|lung(24)|ovary(2)|prostate(1)|skin(4)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	69		all_epithelial(44;7.06e-05)|all_lung(145;0.00563)|Lung NSC(174;0.00834)|Colorectal(57;0.102)|all_neural(114;0.107)|Breast(234;0.22)		COAD - Colon adenocarcinoma(40;0.141)|Colorectal(40;0.216)		CAACACGATCCGAATGTTCAG	0.438																																					p.R258Q												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G773A	10						.						112.0	91.0	98.0					10																	127789788		2203	4300	6503	127779778	SO:0001583	missense	8038	exon9			AF023476	CCDS7653.1, CCDS7654.1	10q26	2008-07-29	2008-07-29		ENSG00000148848	ENSG00000148848		"""ADAM metallopeptidase domain containing"""	190	protein-coding gene	gene with protein product	"""meltrin alpha"""	602714	"""a disintegrin and metalloproteinase domain 12 (meltrin alpha)"""			9417060, 18342566	Standard	NM_003474		Approved	MCMPMltna, MLTN	uc001ljk.2	O43184	OTTHUMG00000019243	ENST00000368679.4:c.773G>A	10.37:g.127789788C>T	ENSP00000357668:p.Arg258Gln	Somatic		Capture	Illumina HiSeq	Phase_I	127779778	NM_021641	O60470|Q5JRP0|Q5JRP1|Q6P9E3|Q6UWB0	Missense_Mutation	SNP	ENST00000368679.4	37	CCDS7653.1	.	.	.	.	.	.	.	.	.	.	C	32	5.149924	0.94645	.	.	ENSG00000148848	ENST00000368679;ENST00000368676;ENST00000448723	D;D;T	0.87029	-2.2;-2.2;-0.06	5.32	5.32	0.75619	Metallopeptidase, catalytic domain (1);Peptidase M12B, ADAM/reprolysin (2);	0.000000	0.64402	D	0.000001	D	0.93426	0.7903	M	0.78456	2.415	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.97110	0.999;0.998;0.999;0.999;1.0	D	0.91995	0.5606	10	0.36615	T	0.2	.	19.1925	0.93672	0.0:1.0:0.0:0.0	.	255;255;258;255;258	A8K6G4;O43184-3;O43184-2;O43184-4;O43184	.;.;.;.;ADA12_HUMAN	Q	258;258;255	ENSP00000357668:R258Q;ENSP00000357665:R258Q;ENSP00000391268:R255Q	ENSP00000357665:R258Q	R	-	2	0	ADAM12	127779778	1.000000	0.71417	0.702000	0.30337	0.939000	0.58152	5.912000	0.69948	2.767000	0.95098	0.655000	0.94253	CGG		0.438	ADAM12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050961.1		
PTPRE	5791	broad.mit.edu	37	10	129869112	129869112	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr10:129869112C>T	ENST00000254667.3	+	15	1613	c.1334C>T	c.(1333-1335)aCg>aTg	p.T445M	PTPRE_ENST00000419012.2_Missense_Mutation_p.T445M|PTPRE_ENST00000306042.5_Missense_Mutation_p.T387M	NM_006504.4	NP_006495.1	P23469	PTPRE_HUMAN	protein tyrosine phosphatase, receptor type, E	445	Tyrosine-protein phosphatase 2. {ECO:0000255|PROSITE-ProRule:PRU00160}.				negative regulation of insulin receptor signaling pathway (GO:0046627)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|regulation of mast cell activation (GO:0033003)|transmembrane receptor protein tyrosine phosphatase signaling pathway (GO:0007185)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)	p.T387M(1)|p.T445M(1)		endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(5)|lung(4)|ovary(1)|prostate(2)|skin(2)|stomach(1)|urinary_tract(1)	22		all_epithelial(44;1.66e-05)|all_lung(145;0.00456)|Lung NSC(174;0.0066)|all_neural(114;0.0936)|Colorectal(57;0.141)|Breast(234;0.166)|Melanoma(40;0.203)			Alendronate(DB00630)	AACATGAGGACGGGCAACTTG	0.542																																					p.T387M	Colon(52;977 1184 20575 41685)											.	.	2	Substitution - Missense(2)	large_intestine(2)	c.C1160T	10						.						84.0	76.0	79.0					10																	129869112		2203	4300	6503	129759102	SO:0001583	missense	5791	exon12			AF406557	CCDS7657.1, CCDS7658.1	10q26	2011-06-09			ENSG00000132334	ENSG00000132334		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"""	9669	protein-coding gene	gene with protein product		600926				8595895	Standard	NM_130435		Approved	PTPE	uc001lkb.3	P23469	OTTHUMG00000019254	ENST00000254667.3:c.1334C>T	10.37:g.129869112C>T	ENSP00000254667:p.Thr445Met	Somatic		Capture	Illumina HiSeq	Phase_I	129759102	NM_130435	Q13345|Q5VWH3|Q5VWH4|Q96KQ6	Missense_Mutation	SNP	ENST00000254667.3	37	CCDS7657.1	.	.	.	.	.	.	.	.	.	.	C	19.15	3.771908	0.69992	.	.	ENSG00000132334	ENST00000254667;ENST00000439034;ENST00000419012;ENST00000306042	T;T;T	0.11930	2.73;2.73;2.73	4.51	4.51	0.55191	Protein-tyrosine phosphatase, receptor/non-receptor type (2);	0.061183	0.64402	D	0.000005	T	0.37237	0.0996	M	0.67517	2.055	0.80722	D	1	D;P;P;P	0.89917	1.0;0.845;0.904;0.845	D;B;B;B	0.87578	0.998;0.085;0.127;0.085	T	0.23655	-1.0182	10	0.87932	D	0	.	17.4459	0.87577	0.0:1.0:0.0:0.0	.	423;445;387;445	F5H0X4;Q5VWH4;P23469-2;P23469	.;.;.;PTPRE_HUMAN	M	445;423;445;387	ENSP00000254667:T445M;ENSP00000402337:T445M;ENSP00000303350:T387M	ENSP00000254667:T445M	T	+	2	0	PTPRE	129759102	1.000000	0.71417	0.968000	0.41197	0.980000	0.70556	7.596000	0.82721	2.337000	0.79520	0.650000	0.86243	ACG		0.542	PTPRE-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050990.1		
TCERG1L	256536	broad.mit.edu	37	10	132902562	132902562	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr10:132902562C>T	ENST00000368642.4	-	10	1536	c.1451G>A	c.(1450-1452)cGc>cAc	p.R484H		NM_174937.3	NP_777597.2	Q5VWI1	TCRGL_HUMAN	transcription elongation regulator 1-like	484	FF 1.							p.R443H(1)		cervix(1)|endometrium(2)|kidney(1)|large_intestine(10)|lung(13)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	31		all_cancers(35;1.22e-10)|all_epithelial(44;2.65e-09)|Lung NSC(174;0.00188)|all_lung(145;0.00307)|Melanoma(40;0.0179)|all_neural(114;0.0424)|Breast(234;0.0743)|Colorectal(57;0.09)		all cancers(32;0.000899)|OV - Ovarian serous cystadenocarcinoma(35;0.0021)|Epithelial(32;0.00276)		CAGGAGATAGCGTGGGTCAAA	0.443																																					p.R484H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1451A	10						.						64.0	50.0	55.0					10																	132902562		2139	4088	6227	132792552	SO:0001583	missense	256536	exon10			AK096269	CCDS7662.2	10q26.3	2006-04-12			ENSG00000176769	ENSG00000176769			23533	protein-coding gene	gene with protein product							Standard	NM_174937		Approved	FLJ38950	uc001lkp.3	Q5VWI1	OTTHUMG00000019276	ENST00000368642.4:c.1451G>A	10.37:g.132902562C>T	ENSP00000357631:p.Arg484His	Somatic		Capture	Illumina HiSeq	Phase_I	132792552	NM_174937	Q5VWI2|Q86XM8	Missense_Mutation	SNP	ENST00000368642.4	37	CCDS7662.2	.	.	.	.	.	.	.	.	.	.	C	22.0	4.230349	0.79688	.	.	ENSG00000176769	ENST00000368642	T	0.57595	0.39	3.53	3.53	0.40419	FF domain (4);	0.000000	0.64402	D	0.000005	T	0.78886	0.4354	H	0.94183	3.505	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.85634	0.1272	10	0.87932	D	0	-6.8488	14.1723	0.65517	0.0:1.0:0.0:0.0	.	484	Q5VWI1	TCRGL_HUMAN	H	484	ENSP00000357631:R484H	ENSP00000357631:R484H	R	-	2	0	TCERG1L	132792552	1.000000	0.71417	0.993000	0.49108	0.990000	0.78478	6.000000	0.70678	1.953000	0.56701	0.491000	0.48974	CGC		0.443	TCERG1L-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091619.2	NM_174937	
TCERG1L	256536	broad.mit.edu	37	10	132944882	132944882	+	Missense_Mutation	SNP	T	T	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr10:132944882T>A	ENST00000368642.4	-	7	1161	c.1076A>T	c.(1075-1077)aAc>aTc	p.N359I		NM_174937.3	NP_777597.2	Q5VWI1	TCRGL_HUMAN	transcription elongation regulator 1-like	359	WW 2. {ECO:0000255|PROSITE- ProRule:PRU00224}.							p.N318I(1)		cervix(1)|endometrium(2)|kidney(1)|large_intestine(10)|lung(13)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	31		all_cancers(35;1.22e-10)|all_epithelial(44;2.65e-09)|Lung NSC(174;0.00188)|all_lung(145;0.00307)|Melanoma(40;0.0179)|all_neural(114;0.0424)|Breast(234;0.0743)|Colorectal(57;0.09)		all cancers(32;0.000899)|OV - Ovarian serous cystadenocarcinoma(35;0.0021)|Epithelial(32;0.00276)		CATCGTTGGGTTGAAGAAGAA	0.532																																					p.N359I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A1076T	10						.						138.0	123.0	128.0					10																	132944882		2203	4300	6503	132834872	SO:0001583	missense	256536	exon7			AK096269	CCDS7662.2	10q26.3	2006-04-12			ENSG00000176769	ENSG00000176769			23533	protein-coding gene	gene with protein product							Standard	NM_174937		Approved	FLJ38950	uc001lkp.3	Q5VWI1	OTTHUMG00000019276	ENST00000368642.4:c.1076A>T	10.37:g.132944882T>A	ENSP00000357631:p.Asn359Ile	Somatic		Capture	Illumina HiSeq	Phase_I	132834872	NM_174937	Q5VWI2|Q86XM8	Missense_Mutation	SNP	ENST00000368642.4	37	CCDS7662.2	.	.	.	.	.	.	.	.	.	.	T	24.8	4.572425	0.86542	.	.	ENSG00000176769	ENST00000368642	T	0.58940	0.3	4.83	4.83	0.62350	WW/Rsp5/WWP (4);	0.000000	0.64402	D	0.000009	T	0.72382	0.3453	M	0.64170	1.965	0.80722	D	1	D	0.89917	1.0	D	0.75484	0.986	T	0.75915	-0.3149	10	0.87932	D	0	-11.8799	13.8814	0.63684	0.0:0.0:0.0:1.0	.	359	Q5VWI1	TCRGL_HUMAN	I	359	ENSP00000357631:N359I	ENSP00000357631:N359I	N	-	2	0	TCERG1L	132834872	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	7.444000	0.80532	1.934000	0.56057	0.377000	0.23210	AAC		0.532	TCERG1L-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091619.2	NM_174937	
JAKMIP3	282973	broad.mit.edu	37	10	133961495	133961495	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr10:133961495G>A	ENST00000298622.4	+	13	1927	c.1789G>A	c.(1789-1791)Gag>Aag	p.E597K	JAKMIP3_ENST00000477275.1_3'UTR	NM_001105521.2	NP_001098991.1	Q5VZ66	JKIP3_HUMAN	Janus kinase and microtubule interacting protein 3	597						Golgi apparatus (GO:0005794)		p.E597K(1)		breast(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(7)|lung(10)|ovary(2)|prostate(1)|upper_aerodigestive_tract(2)	31		all_cancers(35;5.63e-09)|all_epithelial(44;9.25e-07)|Lung NSC(174;0.0108)|all_lung(145;0.0173)|Colorectal(31;0.0721)|all_neural(114;0.0726)|Breast(234;0.0949)|Glioma(114;0.172)|Melanoma(40;0.175)		OV - Ovarian serous cystadenocarcinoma(35;0.000104)|Epithelial(32;0.000142)|all cancers(32;0.000185)|BRCA - Breast invasive adenocarcinoma(275;0.224)		GCTCAGACACGAGGTGCAGGA	0.552																																					p.E597K												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1789A	10						.						122.0	97.0	106.0					10																	133961495		2201	4295	6496	133811485	SO:0001583	missense	282973	exon13			AL832756	CCDS44494.1	10q26.3	2009-04-23	2009-04-23	2008-01-28	ENSG00000188385	ENSG00000188385			23523	protein-coding gene	gene with protein product	"""neuroendocrine long coiled-coil 2"""	611198	"""chromosome 10 open reading frame 39"", ""chromosome 10 open reading frame 14"""	C10orf39, C10orf14		15277531, 17572408	Standard	NM_001105521		Approved	FLJ37857, NECC2, KIAA4091, bA140A10.5	uc001lkx.4	Q5VZ66	OTTHUMG00000150167	ENST00000298622.4:c.1789G>A	10.37:g.133961495G>A	ENSP00000298622:p.Glu597Lys	Somatic		Capture	Illumina HiSeq	Phase_I	133811485	NM_001105521	A6PW00|Q69YM6|Q6ZT29	Missense_Mutation	SNP	ENST00000298622.4	37	CCDS44494.1	.	.	.	.	.	.	.	.	.	.	G	19.21	3.784286	0.70222	.	.	ENSG00000188385	ENST00000298622	T	0.30448	1.53	4.39	4.39	0.52855	.	.	.	.	.	T	0.43964	0.1271	L	0.56199	1.76	0.43719	D	0.996199	D;P	0.65815	0.995;0.898	P;B	0.53954	0.738;0.284	T	0.46162	-0.9211	9	0.56958	D	0.05	.	16.9566	0.86261	0.0:0.0:1.0:0.0	.	34;597	Q5VZ66-2;Q5VZ66	.;JKIP3_HUMAN	K	597	ENSP00000298622:E597K	ENSP00000298622:E597K	E	+	1	0	JAKMIP3	133811485	1.000000	0.71417	0.932000	0.37286	0.074000	0.17049	8.894000	0.92506	1.999000	0.58509	0.556000	0.70494	GAG		0.552	JAKMIP3-001	KNOWN	NMD_exception|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051049.3	NM_194303	
KNDC1	85442	broad.mit.edu	37	10	135032422	135032422	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr10:135032422A>G	ENST00000304613.3	+	27	4786	c.4765A>G	c.(4765-4767)Agc>Ggc	p.S1589G	KNDC1_ENST00000368572.2_Missense_Mutation_p.S1591G			Q76NI1	VKIND_HUMAN	kinase non-catalytic C-lobe domain (KIND) containing 1	1589	Ras-GEF. {ECO:0000255|PROSITE- ProRule:PRU00168}.				cerebellar granule cell differentiation (GO:0021707)|positive regulation of protein phosphorylation (GO:0001934)|regulation of dendrite morphogenesis (GO:0048814)|small GTPase mediated signal transduction (GO:0007264)	dendrite (GO:0030425)|guanyl-nucleotide exchange factor complex (GO:0032045)|neuronal cell body (GO:0043025)	protein serine/threonine kinase activity (GO:0004674)|Ras guanyl-nucleotide exchange factor activity (GO:0005088)	p.S1589G(1)		NS(4)|breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(27)|ovary(1)|prostate(5)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	60		all_cancers(35;4.16e-10)|all_epithelial(44;2.07e-08)|Lung NSC(174;0.000845)|all_lung(145;0.00145)|all_neural(114;0.0299)|Melanoma(40;0.123)|Colorectal(31;0.173)|Glioma(114;0.203)		OV - Ovarian serous cystadenocarcinoma(35;8.77e-06)|Epithelial(32;1.13e-05)|all cancers(32;1.51e-05)		GCAGATCCTGAGCGGGCTGGA	0.597																																					p.S1589G												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A4765G	10						.						77.0	90.0	86.0					10																	135032422		2203	4300	6503	134882412	SO:0001583	missense	85442	exon27			AK074179	CCDS7674.1	10q26.3	2004-09-14	2004-04-07		ENSG00000171798	ENSG00000171798			29374	protein-coding gene	gene with protein product			"""RasGEF domain family, member 2"""	RASGEF2, C10orf23		11214970	Standard	NM_152643		Approved	KIAA1768, bB439H18.3, FLJ25027	uc001llz.1	Q76NI1	OTTHUMG00000019303	ENST00000304613.3:c.4765A>G	10.37:g.135032422A>G	ENSP00000304437:p.Ser1589Gly	Somatic		Capture	Illumina HiSeq	Phase_I	134882412	NM_152643	B0QZC5|Q5T233|Q6ZNH8|Q8TEE5|Q96LV7|Q9C095	Missense_Mutation	SNP	ENST00000304613.3	37	CCDS7674.1	.	.	.	.	.	.	.	.	.	.	A	2.530	-0.308633	0.05458	.	.	ENSG00000171798	ENST00000304613;ENST00000368572	T;T	0.36340	1.26;1.26	4.12	2.11	0.27256	Guanine-nucleotide dissociation stimulator CDC25 (3);Ras guanine nucleotide exchange factor, domain (1);	0.466103	0.23424	N	0.048323	T	0.11324	0.0276	N	0.02539	-0.55	0.25380	N	0.98862	B	0.06786	0.001	B	0.08055	0.003	T	0.35919	-0.9769	10	0.02654	T	1	-16.5307	8.1761	0.31283	0.2088:0.0:0.7912:0.0	.	1589	Q76NI1	VKIND_HUMAN	G	1589;1591	ENSP00000304437:S1589G;ENSP00000357561:S1591G	ENSP00000304437:S1589G	S	+	1	0	KNDC1	134882412	1.000000	0.71417	0.947000	0.38551	0.972000	0.66771	1.870000	0.39529	0.308000	0.22923	-0.337000	0.08149	AGC		0.597	KNDC1-006	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000277044.3	NM_152643	
TUBGCP2	10844	broad.mit.edu	37	10	135106712	135106712	+	Silent	SNP	G	G	A	rs150131271	byFrequency	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr10:135106712G>A	ENST00000252936.3	-	6	894	c.855C>T	c.(853-855)taC>taT	p.Y285Y	TUBGCP2_ENST00000543663.1_Silent_p.Y313Y|RP11-122K13.12_ENST00000424450.1_RNA|TUBGCP2_ENST00000368563.2_Silent_p.Y285Y|TUBGCP2_ENST00000368562.1_5'Flank|TUBGCP2_ENST00000417178.2_Silent_p.Y155Y			Q9BSJ2	GCP2_HUMAN	tubulin, gamma complex associated protein 2	285					G2/M transition of mitotic cell cycle (GO:0000086)|microtubule nucleation (GO:0007020)|mitotic cell cycle (GO:0000278)|protein complex assembly (GO:0006461)	centrosome (GO:0005813)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|membrane (GO:0016020)|microtubule organizing center (GO:0005815)|spindle pole (GO:0000922)		p.Y285Y(1)		breast(2)|cervix(1)|endometrium(1)|kidney(3)|large_intestine(6)|lung(16)|ovary(2)|prostate(3)|upper_aerodigestive_tract(1)	35		all_cancers(35;1.14e-09)|all_epithelial(44;5.79e-08)|Lung NSC(174;0.00263)|all_lung(145;0.0039)|all_neural(114;0.0299)|Melanoma(40;0.123)|Colorectal(31;0.172)|Glioma(114;0.203)		OV - Ovarian serous cystadenocarcinoma(35;8.87e-06)|all cancers(32;8.98e-06)|Epithelial(32;1.15e-05)		TCACCTGCCCGTACTCGAAGG	0.562													G|||	4	0.000798722	0.003	0.0	5008	,	,		19955	0.0		0.0	False		,,,				2504	0.0				p.Y285Y												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C855T	10						.	G		15,4391	21.2+/-45.6	0,15,2188	63.0	60.0	61.0		855	-2.4	0.9	10	dbSNP_134	61	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	TUBGCP2	NM_006659.2		0,17,6486	AA,AG,GG		0.0233,0.3404,0.1307		285/903	135106712	17,12989	2203	4300	6503	134956702	SO:0001819	synonymous_variant	10844	exon7			AF042379	CCDS7676.1, CCDS58104.1, CCDS58105.1	10q26.3	2008-07-28			ENSG00000130640	ENSG00000130640			18599	protein-coding gene	gene with protein product						9566967	Standard	NM_001256617		Approved	GCP2, Spc97p, SPBC97	uc010qvc.2	Q9BSJ2	OTTHUMG00000019319	ENST00000252936.3:c.855C>T	10.37:g.135106712G>A		Somatic		Capture	Illumina HiSeq	Phase_I	134956702	NM_006659	B4DM18|B7ZKL8|F5H4E0|F5H4L0|O43632|Q5VWX7	Silent	SNP	ENST00000252936.3	37	CCDS7676.1																																																																																				0.562	TUBGCP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051148.1		
AKR1E2	83592	broad.mit.edu	37	10	4877927	4877927	+	Nonsense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr10:4877927C>T	ENST00000298375.7	+	4	456	c.385C>T	c.(385-387)Cga>Tga	p.R129*	AKR1E2_ENST00000532248.1_Nonsense_Mutation_p.R129*|AKR1E2_ENST00000334019.4_Nonsense_Mutation_p.R129*|AKR1E2_ENST00000525281.1_3'UTR|AKR1E2_ENST00000345253.5_Nonsense_Mutation_p.R129*	NM_001040177.2	NP_001035267.1	Q96JD6	AKCL2_HUMAN	aldo-keto reductase family 1, member E2	129						cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	1,5-anhydro-D-fructose reductase activity (GO:0050571)	p.R129*(1)		NS(1)|endometrium(2)|kidney(2)|large_intestine(1)|lung(9)	15						CTCACATCCTCGAGTGCAGGA	0.527																																					p.R129X	NSCLC(43;343 1097 20371 28813 45509)											.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.C385T	10						.						117.0	89.0	99.0					10																	4877927		2203	4300	6503	4867927	SO:0001587	stop_gained	83592	exon4			AB040820	CCDS31134.1, CCDS59210.1, CCDS59209.1	10p15.2	2009-09-09	2009-09-09	2009-09-09	ENSG00000165568	ENSG00000165568		"""Aldo-keto reductases"""	23437	protein-coding gene	gene with protein product			"""aldo-keto reductase family 1, member C-like 2"""	AKRDC1, AKR1CL2			Standard	NM_001271021		Approved	MGC10612	uc001ihi.4	Q96JD6	OTTHUMG00000017577	ENST00000298375.7:c.385C>T	10.37:g.4877927C>T	ENSP00000298375:p.Arg129*	Somatic		Capture	Illumina HiSeq	Phase_I	4867927	NM_001040177	Q86Z16|Q86Z17|Q86Z18|Q9BU71	Nonsense_Mutation	SNP	ENST00000298375.7	37	CCDS31134.1	.	.	.	.	.	.	.	.	.	.	c	17.48	3.399049	0.62177	.	.	ENSG00000165568	ENST00000462718;ENST00000533295;ENST00000298375;ENST00000532248;ENST00000334019;ENST00000345253	.	.	.	4.12	2.29	0.28610	.	0.054940	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.46703	T	0.11	.	6.141	0.20259	0.1016:0.1905:0.708:0.0	.	.	.	.	X	25;133;129;129;129;129	.	ENSP00000298375:R129X	R	+	1	2	AKR1E2	4867927	1.000000	0.71417	0.093000	0.20910	0.011000	0.07611	3.968000	0.56809	0.705000	0.31890	-0.949000	0.02662	CGA		0.527	AKR1E2-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046520.4	NM_031436	
AKR1C4	1109	broad.mit.edu	37	10	5255064	5255064	+	Missense_Mutation	SNP	G	G	A	rs147757734	byFrequency	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr10:5255064G>A	ENST00000380448.1	+	9	1041	c.788G>A	c.(787-789)cGt>cAt	p.R263H	AKR1C4_ENST00000263126.1_Missense_Mutation_p.R263H			P17516	AK1C4_HUMAN	aldo-keto reductase family 1, member C4	263					androgen metabolic process (GO:0008209)|bile acid and bile salt transport (GO:0015721)|bile acid biosynthetic process (GO:0006699)|bile acid metabolic process (GO:0008206)|cellular response to jasmonic acid stimulus (GO:0071395)|daunorubicin metabolic process (GO:0044597)|doxorubicin metabolic process (GO:0044598)|phototransduction, visible light (GO:0007603)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	aldo-keto reductase (NADP) activity (GO:0004033)|androsterone dehydrogenase activity (GO:0047023)|bile acid transmembrane transporter activity (GO:0015125)|chlordecone reductase activity (GO:0047743)|electron carrier activity (GO:0009055)|oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor (GO:0016655)|retinal dehydrogenase activity (GO:0001758)	p.R263H(1)		NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(4)|ovary(1)|skin(2)|stomach(2)|urinary_tract(1)	18						CAGCTGCAGCGTGGGGTTGTG	0.557													G|||	2	0.000399361	0.0015	0.0	5008	,	,		19765	0.0		0.0	False		,,,				2504	0.0				p.R263H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G788A	10						.	G	HIS/ARG	5,4401	9.9+/-24.2	0,5,2198	101.0	86.0	91.0		788	3.3	1.0	10	dbSNP_134	91	0,8596		0,0,4298	no	missense	AKR1C4	NM_001818.3	29	0,5,6496	AA,AG,GG		0.0,0.1135,0.0385	probably-damaging	263/324	5255064	5,12997	2203	4298	6501	5245064	SO:0001583	missense	1109	exon7			M33375	CCDS7064.1	10p15.1	2012-12-04	2012-12-04		ENSG00000198610	ENSG00000198610	1.1.1.225	"""Aldo-keto reductases"""	387	protein-coding gene	gene with protein product	"""chlordecone reductase; 3-alpha hydroxysteroid dehydrogenase, type I; dihydrodiol dehydrogenase 4"""	600451	"""aldo-keto reductase family 1, member C4 (chlordecone reductase; 3-alpha hydroxysteroid dehydrogenase, type I; dihydrodiol dehydrogenase 4)"""	CHDR		7789999	Standard	NM_001818		Approved	DD4, HAKRA, C11, 3-alpha-HSD, CDR, MGC22581	uc001ihw.2	P17516	OTTHUMG00000017591	ENST00000380448.1:c.788G>A	10.37:g.5255064G>A	ENSP00000369814:p.Arg263His	Somatic		Capture	Illumina HiSeq	Phase_I	5245064	NM_001818	Q5T6A3|Q8WW84|Q9NS54	Missense_Mutation	SNP	ENST00000380448.1	37	CCDS7064.1	.	.	.	.	.	.	.	.	.	.	G	20.8	4.044578	0.75732	0.001135	0.0	ENSG00000198610	ENST00000380448;ENST00000263126	T;T	0.51817	0.69;0.69	3.3	3.3	0.37823	NADP-dependent oxidoreductase domain (3);	0.000000	0.64402	D	0.000017	T	0.63177	0.2489	M	0.64630	1.985	0.47009	D	0.999281	D	0.89917	1.0	D	0.77557	0.99	T	0.67055	-0.5767	10	0.87932	D	0	.	12.0585	0.53548	0.0:0.0:1.0:0.0	.	263	P17516	AK1C4_HUMAN	H	263	ENSP00000369814:R263H;ENSP00000263126:R263H	ENSP00000263126:R263H	R	+	2	0	AKR1C4	5245064	1.000000	0.71417	0.984000	0.44739	0.969000	0.65631	5.669000	0.68081	1.362000	0.46000	0.313000	0.20887	CGT		0.557	AKR1C4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046543.2	NM_001818	
FBXO18	84893	broad.mit.edu	37	10	5957384	5957384	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr10:5957384C>T	ENST00000362091.4	+	9	1530	c.1415C>T	c.(1414-1416)aCg>aTg	p.T472M	FBXO18_ENST00000397269.3_5'UTR|FBXO18_ENST00000379999.5_Missense_Mutation_p.T523M	NM_001258453.1|NM_178150.2	NP_001245382.1|NP_835363.1	Q8NFZ0	FBX18_HUMAN	F-box protein, helicase, 18	472					DNA catabolic process, endonucleolytic (GO:0000737)|positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage (GO:1902231)|positive regulation of protein phosphorylation (GO:0001934)|response to intra-S DNA damage checkpoint signaling (GO:0072429)	nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|DNA binding (GO:0003677)	p.T523M(1)		NS(2)|breast(2)|kidney(2)|large_intestine(16)|lung(9)|ovary(2)|prostate(3)|skin(3)|stomach(1)	40						AAGACCTCAACGCTGGTCAAG	0.562																																					p.T523M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1568T	10						.						88.0	65.0	73.0					10																	5957384		2203	4300	6503	5997390	SO:0001583	missense	84893	exon10			AK095343	CCDS7072.1, CCDS7073.1, CCDS73064.1	10p15.1	2004-08-24	2004-06-15		ENSG00000134452	ENSG00000134452		"""F-boxes /  ""other"""""	13620	protein-coding gene	gene with protein product		607222	"""F-box only protein 18"""			10531037, 11956208	Standard	NM_032807		Approved	FBH1, FLJ14590, Fbx18	uc001iit.4	Q8NFZ0	OTTHUMG00000017609	ENST00000362091.4:c.1415C>T	10.37:g.5957384C>T	ENSP00000355415:p.Thr472Met	Somatic		Capture	Illumina HiSeq	Phase_I	5997390	NM_032807	Q5JVB0|Q5JVB1|Q7Z4Q6|Q7Z4R0|Q8N1P5|Q8N586|Q96E82|Q96K67|Q96SW7|Q9UFB2	Missense_Mutation	SNP	ENST00000362091.4	37	CCDS7072.1	.	.	.	.	.	.	.	.	.	.	C	24.6	4.545478	0.86022	.	.	ENSG00000134452	ENST00000362091;ENST00000544954;ENST00000379999;ENST00000379994	D;D;D	0.84944	-1.92;-1.92;-1.92	5.26	5.26	0.73747	.	0.000000	0.85682	D	0.000000	D	0.93318	0.7870	M	0.84948	2.725	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.999;1.0;0.999	D	0.94054	0.7320	10	0.87932	D	0	-23.1186	18.8264	0.92121	0.0:1.0:0.0:0.0	.	523;472;398	Q8NFZ0-2;Q8NFZ0;Q2TAK1	.;FBX18_HUMAN;.	M	472;209;523;209	ENSP00000355415:T472M;ENSP00000369335:T523M;ENSP00000369330:T209M	ENSP00000355415:T472M	T	+	2	0	FBXO18	5997390	1.000000	0.71417	0.925000	0.36789	0.978000	0.69477	6.741000	0.74837	2.625000	0.88918	0.555000	0.69702	ACG		0.562	FBXO18-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046596.1	NM_032807	
RBM17	84991	broad.mit.edu	37	10	6154291	6154291	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr10:6154291G>A	ENST00000446108.1	+	8	1467	c.823G>A	c.(823-825)Ggc>Agc	p.G275S	RBM17_ENST00000379888.4_Missense_Mutation_p.G275S	NM_001145547.1	NP_001139019.1	Q96I25	SPF45_HUMAN	RNA binding motif protein 17	275	G-patch. {ECO:0000255|PROSITE- ProRule:PRU00092}.				alternative mRNA splicing, via spliceosome (GO:0000380)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)	nucleotide binding (GO:0000166)|RNA binding (GO:0003723)	p.G275S(1)		NS(1)|breast(3)|cervix(1)|endometrium(1)|kidney(4)|large_intestine(2)|lung(4)|prostate(1)|urinary_tract(2)	19						CAAGCGTGGCGGCAAGATCAT	0.602																																					p.G275S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G823A	10						.						52.0	43.0	46.0					10																	6154291		2203	4300	6503	6194297	SO:0001583	missense	84991	exon8			AF083384	CCDS7077.1	10p15.1	2013-01-28			ENSG00000134453	ENSG00000134453		"""RNA binding motif (RRM) containing"", ""G patch domain containing"""	16944	protein-coding gene	gene with protein product	"""splicing factor 45kDa"""	606935				9731529	Standard	NM_032905		Approved	SPF45, MGC14439	uc001ijb.3	Q96I25	OTTHUMG00000017618	ENST00000446108.1:c.823G>A	10.37:g.6154291G>A	ENSP00000388638:p.Gly275Ser	Somatic		Capture	Illumina HiSeq	Phase_I	6194297	NM_032905	Q96GY6	Missense_Mutation	SNP	ENST00000446108.1	37	CCDS7077.1	.	.	.	.	.	.	.	.	.	.	G	36	5.652757	0.96724	.	.	ENSG00000134453	ENST00000372795;ENST00000379888;ENST00000437845;ENST00000446108	T;T	0.58210	0.35;0.35	5.58	5.58	0.84498	D111/G-patch (3);	0.000000	0.85682	D	0.000000	T	0.81536	0.4843	M	0.94142	3.5	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.86432	0.1761	10	0.87932	D	0	-14.8451	19.5496	0.95312	0.0:0.0:1.0:0.0	.	275	Q96I25	SPF45_HUMAN	S	243;275;243;275	ENSP00000369218:G275S;ENSP00000388638:G275S	ENSP00000361881:G243S	G	+	1	0	RBM17	6194297	1.000000	0.71417	0.996000	0.52242	0.933000	0.57130	9.546000	0.98097	2.623000	0.88846	0.462000	0.41574	GGC		0.602	RBM17-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046635.1	NM_032905	
SFMBT2	57713	broad.mit.edu	37	10	7269822	7269822	+	Nonsense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr10:7269822G>A	ENST00000361972.4	-	10	1288	c.1198C>T	c.(1198-1200)Cga>Tga	p.R400*	SFMBT2_ENST00000397167.1_Nonsense_Mutation_p.R400*	NM_001018039.1	NP_001018049.1	Q5VUG0	SMBT2_HUMAN	Scm-like with four mbt domains 2	400					negative regulation of gene expression (GO:0010629)|regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	histone binding (GO:0042393)	p.R400*(1)		NS(2)|breast(3)|central_nervous_system(4)|endometrium(7)|kidney(2)|large_intestine(26)|lung(34)|ovary(5)|pancreas(2)|skin(9)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	99						CTTACATTTCGGAAGCAGAAG	0.423																																					p.R400X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.C1198T	10						.						55.0	61.0	59.0					10																	7269822		2203	4300	6503	7309828	SO:0001587	stop_gained	57713	exon10			AB046837	CCDS31138.1	10p15.1	2013-01-10	2003-11-14		ENSG00000198879	ENSG00000198879		"""Sterile alpha motif (SAM) domain containing"""	20256	protein-coding gene	gene with protein product		615392	"""Scm-related gene containing four mbt domains 2"""			10997877	Standard	NM_001029880		Approved	KIAA1617	uc009xio.2	Q5VUG0	OTTHUMG00000017630	ENST00000361972.4:c.1198C>T	10.37:g.7269822G>A	ENSP00000355109:p.Arg400*	Somatic		Capture	Illumina HiSeq	Phase_I	7309828	NM_001029880	A7MD09|Q9HCF5	Nonsense_Mutation	SNP	ENST00000361972.4	37	CCDS31138.1	.	.	.	.	.	.	.	.	.	.	G	34	5.340159	0.95783	.	.	ENSG00000198879	ENST00000361972;ENST00000397167	.	.	.	5.21	-0.233	0.13078	.	0.145674	0.64402	D	0.000009	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.17832	T	0.49	.	14.1572	0.65424	0.0:0.0:0.5051:0.4949	.	.	.	.	X	400	.	ENSP00000355109:R400X	R	-	1	2	SFMBT2	7309828	1.000000	0.71417	0.992000	0.48379	0.511000	0.34104	1.086000	0.30853	-0.210000	0.10140	-1.518000	0.00936	CGA		0.423	SFMBT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046673.1	NM_001029880	
SFMBT2	57713	broad.mit.edu	37	10	7409783	7409783	+	Silent	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr10:7409783C>T	ENST00000361972.4	-	4	354	c.264G>A	c.(262-264)ccG>ccA	p.P88P	SFMBT2_ENST00000397160.3_Silent_p.P88P|SFMBT2_ENST00000379713.3_Silent_p.P88P|SFMBT2_ENST00000379711.2_Silent_p.P88P|SFMBT2_ENST00000397167.1_Silent_p.P88P	NM_001018039.1	NP_001018049.1	Q5VUG0	SMBT2_HUMAN	Scm-like with four mbt domains 2	88					negative regulation of gene expression (GO:0010629)|regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	histone binding (GO:0042393)	p.P88P(3)		NS(2)|breast(3)|central_nervous_system(4)|endometrium(7)|kidney(2)|large_intestine(26)|lung(34)|ovary(5)|pancreas(2)|skin(9)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	99						AGTACGTGTCCGGGTTGTTCT	0.517																																					p.P88P												.	.	3	Substitution - coding silent(3)	large_intestine(2)|lung(1)	c.G264A	10						.						82.0	80.0	80.0					10																	7409783		2203	4300	6503	7449789	SO:0001819	synonymous_variant	57713	exon4			AB046837	CCDS31138.1	10p15.1	2013-01-10	2003-11-14		ENSG00000198879	ENSG00000198879		"""Sterile alpha motif (SAM) domain containing"""	20256	protein-coding gene	gene with protein product		615392	"""Scm-related gene containing four mbt domains 2"""			10997877	Standard	NM_001029880		Approved	KIAA1617	uc009xio.2	Q5VUG0	OTTHUMG00000017630	ENST00000361972.4:c.264G>A	10.37:g.7409783C>T		Somatic		Capture	Illumina HiSeq	Phase_I	7449789	NM_001029880	A7MD09|Q9HCF5	Silent	SNP	ENST00000361972.4	37	CCDS31138.1																																																																																				0.517	SFMBT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046673.1	NM_001029880	
ITIH2	3698	broad.mit.edu	37	10	7765503	7765503	+	Silent	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr10:7765503C>T	ENST00000358415.4	+	9	1123	c.957C>T	c.(955-957)ggC>ggT	p.G319G	ITIH2_ENST00000379587.4_Silent_p.G308G	NM_002216.2	NP_002207.2	P19823	ITIH2_HUMAN	inter-alpha-trypsin inhibitor heavy chain 2	319	VWFA. {ECO:0000255|PROSITE- ProRule:PRU00219}.				hyaluronan metabolic process (GO:0030212)|negative regulation of endopeptidase activity (GO:0010951)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	endopeptidase inhibitor activity (GO:0004866)|serine-type endopeptidase inhibitor activity (GO:0004867)	p.G319G(1)		NS(2)|breast(1)|endometrium(8)|kidney(1)|large_intestine(17)|lung(25)|ovary(1)|pancreas(1)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	64						ATGTGAGTGGCTCCATGTGGG	0.428																																					p.G319G												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C957T	10						.						126.0	108.0	114.0					10																	7765503		2203	4300	6503	7805509	SO:0001819	synonymous_variant	3698	exon9			X07173	CCDS31141.1	10p14	2011-10-26	2011-10-26		ENSG00000151655	ENSG00000151655			6167	protein-coding gene	gene with protein product		146640	"""inter-alpha (globulin) inhibitor, H2 polypeptide"""			1385302, 10100603	Standard	NM_002216		Approved	H2P	uc001ijs.3	P19823	OTTHUMG00000017633	ENST00000358415.4:c.957C>T	10.37:g.7765503C>T		Somatic		Capture	Illumina HiSeq	Phase_I	7805509	NM_002216	Q14659|Q15484|Q5T986	Silent	SNP	ENST00000358415.4	37	CCDS31141.1																																																																																				0.428	ITIH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046678.2	NM_002216	
CUBN	8029	broad.mit.edu	37	10	16989308	16989308	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr10:16989308G>T	ENST00000377833.4	-	36	5333	c.5268C>A	c.(5266-5268)gaC>gaA	p.D1756E		NM_001081.3	NP_001072.2	O60494	CUBN_HUMAN	cubilin (intrinsic factor-cobalamin receptor)	1756	CUB 12. {ECO:0000255|PROSITE- ProRule:PRU00059}.				cholesterol metabolic process (GO:0008203)|cobalamin metabolic process (GO:0009235)|cobalamin transport (GO:0015889)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|receptor-mediated endocytosis (GO:0006898)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|tissue homeostasis (GO:0001894)|vitamin D metabolic process (GO:0042359)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|coated pit (GO:0005905)|cytosol (GO:0005829)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|extrinsic component of external side of plasma membrane (GO:0031232)|Golgi apparatus (GO:0005794)|lysosomal lumen (GO:0043202)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|cobalamin binding (GO:0031419)|protein homodimerization activity (GO:0042803)|receptor activity (GO:0004872)|transporter activity (GO:0005215)	p.D1756E(1)		breast(8)|central_nervous_system(4)|cervix(1)|endometrium(18)|haematopoietic_and_lymphoid_tissue(3)|kidney(12)|large_intestine(42)|liver(1)|lung(107)|ovary(9)|pancreas(2)|prostate(3)|skin(9)|stomach(3)|upper_aerodigestive_tract(11)|urinary_tract(8)	241					Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)	GGGGATAAATGTCTGGGTAGC	0.443																																					p.D1756E												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C5268A	10						.						88.0	77.0	81.0					10																	16989308		2203	4300	6503	17029314	SO:0001583	missense	8029	exon36			AF034611	CCDS7113.1	10p12	2014-09-17			ENSG00000107611	ENSG00000107611			2548	protein-coding gene	gene with protein product		602997		MGA1		9572993, 9478979	Standard	NM_001081		Approved	IFCR, gp280	uc001ioo.3	O60494	OTTHUMG00000017741	ENST00000377833.4:c.5268C>A	10.37:g.16989308G>T	ENSP00000367064:p.Asp1756Glu	Somatic		Capture	Illumina HiSeq	Phase_I	17029314	NM_001081	B0YIZ4|Q5VTA6|Q96RU9	Missense_Mutation	SNP	ENST00000377833.4	37	CCDS7113.1	.	.	.	.	.	.	.	.	.	.	G	0.021	-1.422308	0.01126	.	.	ENSG00000107611	ENST00000377833	T	0.28666	1.6	5.46	-9.61	0.00550	CUB (5);	1.170240	0.06399	N	0.718458	T	0.09423	0.0232	N	0.12637	0.245	0.80722	D	1	B	0.06786	0.001	B	0.12156	0.007	T	0.39542	-0.9609	10	0.06236	T	0.91	.	1.762	0.02994	0.1449:0.2944:0.25:0.3107	.	1756	O60494	CUBN_HUMAN	E	1756	ENSP00000367064:D1756E	ENSP00000367064:D1756E	D	-	3	2	CUBN	17029314	0.000000	0.05858	0.002000	0.10522	0.213000	0.24496	-1.180000	0.03088	-1.142000	0.02869	-1.045000	0.02358	GAC		0.443	CUBN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047009.1	NM_001081	
SKIDA1	387640	broad.mit.edu	37	10	21804079	21804079	+	Silent	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr10:21804079G>A	ENST00000449193.2	-	4	4925	c.2673C>T	c.(2671-2673)ggC>ggT	p.G891G	SKIDA1_ENST00000444772.3_Silent_p.G812G	NM_207371.3	NP_997254.3	Q1XH10	SKDA1_HUMAN	SKI/DACH domain containing 1	810						nucleus (GO:0005634)		p.G891G(2)									TTGCAGAACCGCCCAGCTGCC	0.413																																					p.G891G												.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.C2673T	10						.						44.0	41.0	42.0					10																	21804079		1830	4090	5920	21844085	SO:0001819	synonymous_variant	387640	exon4			AK131456	CCDS44363.1	10p12.31	2012-06-13	2012-06-13	2012-06-13	ENSG00000180592	ENSG00000180592			32697	protein-coding gene	gene with protein product			"""chromosome 10 open reading frame 140"""	C10orf140			Standard	NM_207371		Approved	FLJ45187	uc021pnx.1	Q1XH10	OTTHUMG00000017797	ENST00000449193.2:c.2673C>T	10.37:g.21804079G>A		Somatic		Capture	Illumina HiSeq	Phase_I	21844085	NM_207371	B1ANA5|Q6ZMX4|Q8N3C3	Silent	SNP	ENST00000449193.2	37	CCDS44363.1																																																																																				0.413	SKIDA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286950.2	NM_207371	
GPR158	57512	broad.mit.edu	37	10	25887777	25887777	+	Nonsense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr10:25887777G>A	ENST00000376351.3	+	11	3581	c.3222G>A	c.(3220-3222)tgG>tgA	p.W1074*	GPR158_ENST00000490549.1_3'UTR	NM_020752.2	NP_065803.2	Q5T848	GP158_HUMAN	G protein-coupled receptor 158	1074					protein localization to plasma membrane (GO:0072659)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)	p.W1074*(1)		breast(5)|cervix(1)|endometrium(9)|kidney(10)|large_intestine(20)|lung(56)|ovary(4)|pancreas(1)|prostate(3)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	119						TATGCCTTTGGGAGAGCCAAG	0.478																																					p.W1074X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.G3222A	10						.						97.0	99.0	99.0					10																	25887777		2203	4300	6503	25927783	SO:0001587	stop_gained	57512	exon11			AB032962	CCDS31166.1	10p12.31	2012-08-21			ENSG00000151025	ENSG00000151025		"""GPCR / Class C : Orphans"""	23689	protein-coding gene	gene with protein product		614573					Standard	NM_020752		Approved	KIAA1136	uc001isj.3	Q5T848	OTTHUMG00000017832	ENST00000376351.3:c.3222G>A	10.37:g.25887777G>A	ENSP00000365529:p.Trp1074*	Somatic		Capture	Illumina HiSeq	Phase_I	25927783	NM_020752	Q6QR81|Q9ULT3	Nonsense_Mutation	SNP	ENST00000376351.3	37	CCDS31166.1	.	.	.	.	.	.	.	.	.	.	G	40	8.254357	0.98727	.	.	ENSG00000151025	ENST00000376351	.	.	.	5.37	5.37	0.77165	.	0.142764	0.49916	D	0.000129	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.09338	T	0.73	.	19.1266	0.93388	0.0:0.0:1.0:0.0	.	.	.	.	X	1074	.	ENSP00000365529:W1074X	W	+	3	0	GPR158	25927783	1.000000	0.71417	0.988000	0.46212	0.017000	0.09413	7.365000	0.79537	2.493000	0.84123	0.655000	0.94253	TGG		0.478	GPR158-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047248.2	XM_166110	
ARMC4	55130	broad.mit.edu	37	10	28196631	28196631	+	Silent	SNP	G	G	A	rs535250584		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr10:28196631G>A	ENST00000305242.5	-	17	2663	c.2571C>T	c.(2569-2571)agC>agT	p.S857S	ARMC4_ENST00000545014.1_Silent_p.S382S|ARMC4_ENST00000537576.1_Silent_p.S549S	NM_018076.2	NP_060546.2	Q5T2S8	ARMC4_HUMAN	armadillo repeat containing 4	857					cell projection organization (GO:0030030)|cilium movement (GO:0003341)|left/right axis specification (GO:0070986)|outer dynein arm assembly (GO:0036158)|ventricular system development (GO:0021591)	axoneme (GO:0005930)|ciliary base (GO:0097546)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)		p.S857S(1)		NS(2)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(7)|kidney(6)|large_intestine(17)|liver(1)|lung(17)|ovary(5)|prostate(3)|skin(8)|stomach(2)|urinary_tract(3)	75						CCCATGCTGCGCTGGCCTTCA	0.443													G|||	1	0.000199681	0.0	0.0	5008	,	,		17525	0.0		0.0	False		,,,				2504	0.001				p.S857S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C2571T	10						.						115.0	101.0	106.0					10																	28196631		2203	4300	6503	28236637	SO:0001819	synonymous_variant	55130	exon17			AL136859	CCDS7157.1	10p12.1-p11.23	2014-02-03			ENSG00000169126	ENSG00000169126		"""Armadillo repeat containing"""	25583	protein-coding gene	gene with protein product		615408				11230166	Standard	XM_005252485		Approved	FLJ10817, FLJ10376, DKFZP434P1735, CILD23	uc001itz.3	Q5T2S8	OTTHUMG00000017867	ENST00000305242.5:c.2571C>T	10.37:g.28196631G>A		Somatic		Capture	Illumina HiSeq	Phase_I	28236637	NM_018076	A8K906|B7Z7I1|Q9H0C0	Silent	SNP	ENST00000305242.5	37	CCDS7157.1																																																																																				0.443	ARMC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047339.1	NM_018076	
ZEB1	6935	broad.mit.edu	37	10	31810806	31810806	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr10:31810806C>T	ENST00000320985.10	+	7	2653	c.2543C>T	c.(2542-2544)aCg>aTg	p.T848M	ZEB1_ENST00000559858.1_3'UTR|ZEB1_ENST00000560721.2_Missense_Mutation_p.T828M|ZEB1_ENST00000446923.2_Missense_Mutation_p.T832M|ZEB1_ENST00000542815.3_Missense_Mutation_p.T781M|ZEB1_ENST00000361642.5_Missense_Mutation_p.T849M			P37275	ZEB1_HUMAN	zinc finger E-box binding homeobox 1	848					cartilage development (GO:0051216)|cell proliferation (GO:0008283)|cellular response to amino acid stimulus (GO:0071230)|cellular response to transforming growth factor beta stimulus (GO:0071560)|cochlea morphogenesis (GO:0090103)|embryonic camera-type eye morphogenesis (GO:0048596)|embryonic skeletal system morphogenesis (GO:0048704)|forebrain development (GO:0030900)|immune response (GO:0006955)|negative regulation of cell proliferation (GO:0008285)|negative regulation of epithelial cell differentiation (GO:0030857)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|pattern specification process (GO:0007389)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of mesenchymal cell proliferation (GO:0010464)|regulation of smooth muscle cell differentiation (GO:0051150)|regulation of T cell differentiation in thymus (GO:0033081)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transforming growth factor beta receptor signaling pathway (GO:0017015)|response to activity (GO:0014823)|response to nutrient levels (GO:0031667)|semicircular canal morphogenesis (GO:0048752)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|E-box binding (GO:0070888)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)	p.T848M(1)		NS(2)|breast(4)|central_nervous_system(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(14)|lung(38)|ovary(3)|skin(6)|upper_aerodigestive_tract(4)	77		Prostate(175;0.0156)				TACTCAACTACGGTCAGCCCT	0.478																																					p.T828M	Ovarian(40;423 959 14296 36701 49589)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C2483T	10						.						90.0	87.0	88.0					10																	31810806		2203	4300	6503	31850812	SO:0001583	missense	6935	exon6			AK091478	CCDS7169.1, CCDS44370.1, CCDS53505.1, CCDS53506.1, CCDS53507.1	10p11.22	2014-02-14	2007-02-15	2007-02-15	ENSG00000148516	ENSG00000148516		"""Zinc fingers, C2H2-type"", ""Homeoboxes / ZF class"""	11642	protein-coding gene	gene with protein product		189909	"""transcription factor 8 (represses interleukin 2 expression)"", ""posterior polymorphous corneal dystrophy 3"""	TCF8, PPCD3		1427828, 1840704, 15384081, 16252232	Standard	NM_001128128		Approved	BZP, ZEB, AREB6, NIL-2-A, Zfhep, Zfhx1a, FECD6	uc001ivu.4	P37275	OTTHUMG00000017907	ENST00000320985.10:c.2543C>T	10.37:g.31810806C>T	ENSP00000319248:p.Thr848Met	Somatic		Capture	Illumina HiSeq	Phase_I	31850812	NM_001174093	B4DJV0|B4DUW9|E9PCM7|F5H4I8|Q12924|Q13800|Q2KJ05|Q5T968|Q5VZ84|Q8NB68	Missense_Mutation	SNP	ENST00000320985.10	37	CCDS7169.1	.	.	.	.	.	.	.	.	.	.	C	16.64	3.178609	0.57692	.	.	ENSG00000148516	ENST00000542879;ENST00000537225;ENST00000361642;ENST00000546250;ENST00000542815;ENST00000320985;ENST00000437844;ENST00000543514;ENST00000446923	T;T;T;T;T	0.13420	2.89;2.59;2.65;2.59;2.63	5.68	5.68	0.88126	.	0.101398	0.43416	D	0.000570	T	0.30070	0.0753	L	0.40543	1.245	0.58432	D	0.999999	D;D;D;D;D;D;D;D	0.76494	0.999;0.999;0.999;0.999;0.999;0.999;0.999;0.999	D;P;P;P;P;P;P;P	0.64321	0.924;0.819;0.828;0.828;0.664;0.88;0.828;0.828	T	0.00300	-1.1835	10	0.59425	D	0.04	-9.6086	20.1615	0.98135	0.0:1.0:0.0:0.0	.	781;848;832;848;848;828;849;848	F5H4I8;F5H1R1;E9PCM7;B2RBI8;A0JLS9;Q5VZ84;Q2KJ05;P37275	.;.;.;.;.;.;.;ZEB1_HUMAN	M	630;848;849;843;781;848;828;739;832	ENSP00000444282:T630M;ENSP00000354487:T849M;ENSP00000444891:T781M;ENSP00000319248:T848M;ENSP00000391612:T832M	ENSP00000319248:T848M	T	+	2	0	ZEB1	31850812	0.999000	0.42202	0.082000	0.20525	0.715000	0.41141	5.677000	0.68142	2.835000	0.97688	0.650000	0.86243	ACG		0.478	ZEB1-018	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000419083.2	NM_030751	
ARHGAP12	94134	broad.mit.edu	37	10	32197261	32197261	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr10:32197261G>A	ENST00000344936.2	-	3	757	c.523C>T	c.(523-525)Cgc>Tgc	p.R175C	ARHGAP12_ENST00000375245.4_Missense_Mutation_p.R175C|ARHGAP12_ENST00000375250.5_Missense_Mutation_p.R175C|ARHGAP12_ENST00000396144.4_Missense_Mutation_p.R175C|ARHGAP12_ENST00000311380.4_Missense_Mutation_p.R175C	NM_001270697.1|NM_018287.6	NP_001257626.1|NP_060757.4	Q8IWW6	RHG12_HUMAN	Rho GTPase activating protein 12	175					morphogenesis of an epithelial sheet (GO:0002011)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	GTPase activator activity (GO:0005096)	p.R175C(1)		NS(1)|breast(3)|endometrium(2)|kidney(1)|large_intestine(11)|lung(10)|skin(1)|urinary_tract(2)	31		Prostate(175;0.0199)				CCAAATGAGCGTGTCCTATTC	0.453																																					p.R175C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C523T	10						.						123.0	117.0	119.0					10																	32197261		2203	4300	6503	32237267	SO:0001583	missense	94134	exon3			AY033594	CCDS7170.1, CCDS59214.1, CCDS59215.1, CCDS59216.1, CCDS73082.1	10p11.22	2013-01-10			ENSG00000165322	ENSG00000165322		"""Rho GTPase activating proteins"", ""Pleckstrin homology (PH) domain containing"""	16348	protein-coding gene	gene with protein product		610577				11854031	Standard	NM_001270695		Approved	FLJ20737, FLJ10971, FLJ21785	uc001ivz.2	Q8IWW6	OTTHUMG00000017911	ENST00000344936.2:c.523C>T	10.37:g.32197261G>A	ENSP00000345808:p.Arg175Cys	Somatic		Capture	Illumina HiSeq	Phase_I	32237267	NM_018287	B1ANY0|B1ANY1|B1ANY2|Q504X1|Q86UB3|Q8IWW7|Q8N3L1|Q9NT76	Missense_Mutation	SNP	ENST00000344936.2	37	CCDS7170.1	.	.	.	.	.	.	.	.	.	.	G	16.19	3.052340	0.55218	.	.	ENSG00000165322	ENST00000311380;ENST00000375250;ENST00000344936;ENST00000396144;ENST00000375245	T;T;T;T;T	0.08458	3.14;3.09;3.16;3.16;3.14	5.84	5.84	0.93424	.	0.463806	0.25411	N	0.030870	T	0.06050	0.0157	N	0.08118	0	0.22354	N	0.999175	P;P;D;P;P;D	0.55385	0.9;0.951;0.971;0.951;0.951;0.971	B;B;P;B;B;P	0.46758	0.296;0.326;0.526;0.326;0.326;0.526	T	0.31475	-0.9942	10	0.62326	D	0.03	.	8.0319	0.30470	0.0794:0.0:0.7505:0.1701	.	175;175;175;175;175;175	Q1RLN5;B3KR88;Q8IWW6-2;Q504X1;Q8IWW6;Q8IWW6-3	.;.;.;.;RHG12_HUMAN;.	C	175	ENSP00000310984:R175C;ENSP00000364399:R175C;ENSP00000345808:R175C;ENSP00000379448:R175C;ENSP00000364394:R175C	ENSP00000310984:R175C	R	-	1	0	ARHGAP12	32237267	0.008000	0.16893	0.997000	0.53966	0.997000	0.91878	0.924000	0.28777	2.765000	0.95021	0.655000	0.94253	CGC		0.453	ARHGAP12-009	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000047465.1		
PARD3	56288	broad.mit.edu	37	10	34630665	34630665	+	Silent	SNP	A	A	G			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr10:34630665A>G	ENST00000374789.3	-	16	2632	c.2307T>C	c.(2305-2307)ctT>ctC	p.L769L	PARD3_ENST00000350537.4_Silent_p.L753L|PARD3_ENST00000374776.1_Silent_p.L753L|PARD3_ENST00000544292.1_Silent_p.L483L|PARD3_ENST00000346874.4_Silent_p.L769L|PARD3_ENST00000374773.1_Silent_p.L766L|PARD3_ENST00000374794.3_Silent_p.L709L|PARD3_ENST00000545693.1_Silent_p.L753L|PARD3_ENST00000374788.3_Silent_p.L766L|PARD3_ENST00000545260.1_Silent_p.L709L|PARD3_ENST00000340077.5_Silent_p.L766L|PARD3_ENST00000374790.3_Silent_p.L709L	NM_019619.3	NP_062565.2	Q8TEW0	PARD3_HUMAN	par-3 family cell polarity regulator	769	Interacts with PRKCI and PRKCZ. {ECO:0000250}.				apical constriction (GO:0003383)|asymmetric cell division (GO:0008356)|axonogenesis (GO:0007409)|cell cycle (GO:0007049)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|centrosome localization (GO:0051642)|establishment of epithelial cell polarity (GO:0090162)|establishment or maintenance of cell polarity (GO:0007163)|microtubule cytoskeleton organization (GO:0000226)|myelination in peripheral nervous system (GO:0022011)|negative regulation of peptidyl-threonine phosphorylation (GO:0010801)|positive regulation of myelination (GO:0031643)|protein complex assembly (GO:0006461)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|protein targeting to membrane (GO:0006612)|regulation of actin filament-based process (GO:0032970)|regulation of cellular localization (GO:0060341)|tight junction assembly (GO:0070830)|transforming growth factor beta receptor signaling pathway (GO:0007179)|wound healing, spreading of cells (GO:0044319)	apical part of cell (GO:0045177)|axonal growth cone (GO:0044295)|cell cortex (GO:0005938)|cell junction (GO:0030054)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|cytosol (GO:0005829)|internode region of axon (GO:0033269)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|spindle (GO:0005819)|tight junction (GO:0005923)	phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|phosphatidylinositol-3-phosphate binding (GO:0032266)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)	p.L769L(1)		NS(2)|breast(4)|central_nervous_system(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(11)|lung(21)|ovary(2)|pancreas(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)	63		Breast(68;0.0707)				GATGTGGAGGAAGCACTGGCA	0.488																																					p.L769L												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.T2307C	10						.						186.0	169.0	175.0					10																	34630665		2203	4300	6503	34670671	SO:0001819	synonymous_variant	56288	exon16			AF252293	CCDS7178.1, CCDS53509.1, CCDS53510.1, CCDS53511.1, CCDS53512.1, CCDS53513.1, CCDS53514.1, CCDS53515.1, CCDS53516.1	10p11.22	2014-06-13	2013-08-28		ENSG00000148498	ENSG00000148498			16051	protein-coding gene	gene with protein product	"""atypical PKC isotype-specific interacting protein"", ""par-3 family cell polarity regulator alpha"", ""protein phosphatase 1, regulatory subunit 118"""	606745	"""par-3 (partitioning defective 3, C.elegans) homolog"", ""par-3 partitioning defective 3 homolog (C. elegans)"""			10934474	Standard	NM_001184790		Approved	PAR3, PARD3A, Bazooka, Baz, ASIP, PPP1R118	uc010qej.2	Q8TEW0	OTTHUMG00000017948	ENST00000374789.3:c.2307T>C	10.37:g.34630665A>G		Somatic		Capture	Illumina HiSeq	Phase_I	34670671	NM_001184787	F5H5T0|Q5T2U1|Q5VUA2|Q5VUA3|Q5VWV0|Q5VWV1|Q5VWV3|Q5VWV4|Q5VWV5|Q6IQ47|Q8TCZ9|Q8TEW1|Q8TEW2|Q8TEW3|Q96K28|Q96RM6|Q96RM7|Q9BY57|Q9BY58|Q9HC48|Q9NWL4|Q9NYE6	Silent	SNP	ENST00000374789.3	37	CCDS7178.1																																																																																				0.488	PARD3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047527.1	NM_019619	
ZNF33B	7582	broad.mit.edu	37	10	43089361	43089361	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr10:43089361C>T	ENST00000359467.3	-	5	1151	c.1037G>A	c.(1036-1038)cGa>cAa	p.R346Q	ZNF33B_ENST00000486187.1_RNA	NM_006955.1	NP_008886.1	Q06732	ZN33B_HUMAN	zinc finger protein 33B	346					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.R346Q(1)		breast(1)|endometrium(4)|kidney(1)|large_intestine(6)|lung(15)|skin(1)|stomach(1)	29						CCTCTGATGTCGAGTGAGATG	0.408																																					p.R346Q	Melanoma(137;1247 1767 16772 25727 43810)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1037A	10						.						123.0	120.0	121.0					10																	43089361		2203	4300	6503	42409367	SO:0001583	missense	7582	exon5			X68688, AJ491697	CCDS7198.1	10q11.2	2013-01-08	2005-03-18		ENSG00000196693	ENSG00000196693		"""Zinc fingers, C2H2-type"", ""-"""	13097	protein-coding gene	gene with protein product		194522	"""zinc finger protein 33b (KOX 31)"", ""zinc finger protein 11B"""	ZNF11B		2014798	Standard	NM_006955		Approved	KOX31, KOX2	uc001jaf.1	Q06732	OTTHUMG00000018014	ENST00000359467.3:c.1037G>A	10.37:g.43089361C>T	ENSP00000352444:p.Arg346Gln	Somatic		Capture	Illumina HiSeq	Phase_I	42409367	NM_006955	Q06731|Q32MA2|Q86XY8|Q8NDW3	Missense_Mutation	SNP	ENST00000359467.3	37	CCDS7198.1	.	.	.	.	.	.	.	.	.	.	C	0.449	-0.894608	0.02491	.	.	ENSG00000196693	ENST00000359467;ENST00000395836	T	0.26223	1.75	2.28	2.28	0.28536	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.389636	0.15539	N	0.257080	T	0.33000	0.0848	L	0.42529	1.33	0.09310	N	1	D	0.76494	0.999	P	0.61940	0.896	T	0.12218	-1.0556	10	0.11794	T	0.64	.	10.7292	0.46087	0.0:1.0:0.0:0.0	.	346	Q06732	ZN33B_HUMAN	Q	346;312	ENSP00000352444:R346Q	ENSP00000352444:R346Q	R	-	2	0	ZNF33B	42409367	0.000000	0.05858	0.989000	0.46669	0.760000	0.43138	-2.814000	0.00753	1.619000	0.50296	0.416000	0.27883	CGA		0.408	ZNF33B-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_006955	
BMS1	9790	broad.mit.edu	37	10	43288513	43288513	+	Missense_Mutation	SNP	C	C	T	rs142567948		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr10:43288513C>T	ENST00000374518.5	+	8	1073	c.1010C>T	c.(1009-1011)gCg>gTg	p.A337V		NM_014753.3	NP_055568.3	Q14692	BMS1_HUMAN	BMS1 ribosome biogenesis factor	337					ribosome assembly (GO:0042255)	nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)	p.A337V(1)		NS(1)|breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|lung(23)|ovary(2)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	62						CTGGTTTATGCGCCTCTTTCT	0.498																																					p.A337V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1010T	10						.						134.0	127.0	129.0					10																	43288513		2203	4300	6503	42608519	SO:0001583	missense	9790	exon8			BC043345	CCDS7199.1	10q11.21	2013-05-01	2013-05-01	2007-03-20	ENSG00000165733	ENSG00000165733			23505	protein-coding gene	gene with protein product		611448	"""BMS1-like, ribosome assembly protein (yeast)"", ""BMS1 homolog, ribosome assembly protein (yeast)"""	BMS1L		11779832	Standard	NM_014753		Approved	KIAA0187	uc001jaj.3	Q14692	OTTHUMG00000018020	ENST00000374518.5:c.1010C>T	10.37:g.43288513C>T	ENSP00000363642:p.Ala337Val	Somatic		Capture	Illumina HiSeq	Phase_I	42608519	NM_014753	Q5QPT5|Q86XJ9	Missense_Mutation	SNP	ENST00000374518.5	37	CCDS7199.1	.	.	.	.	.	.	.	.	.	.	c	18.65	3.670495	0.67814	.	.	ENSG00000165733	ENST00000374518	T	0.37752	1.18	5.51	4.61	0.57282	.	0.047747	0.85682	N	0.000000	T	0.40791	0.1131	M	0.75884	2.315	0.58432	D	0.99999	B	0.26935	0.164	B	0.19946	0.027	T	0.41698	-0.9494	10	0.87932	D	0	.	14.7723	0.69688	0.0:0.93:0.0:0.07	.	337	Q14692	BMS1_HUMAN	V	337	ENSP00000363642:A337V	ENSP00000363642:A337V	A	+	2	0	BMS1	42608519	1.000000	0.71417	0.986000	0.45419	0.897000	0.52465	5.620000	0.67736	1.364000	0.46038	-0.271000	0.10264	GCG		0.498	BMS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047690.2	NM_014753	
C10orf25	220979	broad.mit.edu	37	10	45496203	45496203	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr10:45496203G>T	ENST00000298298.1	-	1	133	c.105C>A	c.(103-105)agC>agA	p.S35R	CEP164P1_ENST00000456938.2_RNA|ZNF22_ENST00000298299.3_5'UTR	NM_001039380.2	NP_001034469.2	Q5T742	CJ025_HUMAN	chromosome 10 open reading frame 25	35						extracellular region (GO:0005576)		p.S35R(1)		endometrium(1)|kidney(1)|large_intestine(1)|lung(2)|stomach(1)	6						GGCGGTTACAGCTCTTGAGGT	0.522																																					p.S35R												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C105A	10						.						37.0	39.0	38.0					10																	45496203		2203	4300	6503	44816209	SO:0001583	missense	220979	exon1			AK055129	CCDS31187.1	10q11.21	2003-11-21			ENSG00000165511	ENSG00000165511			23509	protein-coding gene	gene with protein product							Standard	NM_001039380		Approved	FLJ30567	uc001jbv.2	Q5T742	OTTHUMG00000018066	ENST00000298298.1:c.105C>A	10.37:g.45496203G>T	ENSP00000298298:p.Ser35Arg	Somatic		Capture	Illumina HiSeq	Phase_I	44816209	NM_001039380	A1L424|Q96NM5	Missense_Mutation	SNP	ENST00000298298.1	37	CCDS31187.1	.	.	.	.	.	.	.	.	.	.	G	6.742	0.505661	0.12822	.	.	ENSG00000165511	ENST00000298298	T	0.37752	1.18	2.78	0.824	0.18818	.	.	.	.	.	T	0.15089	0.0364	N	0.08118	0	0.20489	N	0.999898	B	0.34161	0.439	B	0.27380	0.079	T	0.15178	-1.0446	9	0.87932	D	0	.	3.8866	0.09100	0.1478:0.253:0.5992:0.0	.	35	Q5T742	CJ025_HUMAN	R	35	ENSP00000298298:S35R	ENSP00000298298:S35R	S	-	3	2	C10orf25	44816209	0.007000	0.16637	0.000000	0.03702	0.011000	0.07611	0.560000	0.23500	0.217000	0.20800	0.563000	0.77884	AGC		0.522	C10orf25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047763.1	NM_145022	
FAM21A	387680	broad.mit.edu	37	10	47941986	47941986	+	Frame_Shift_Del	DEL	A	A	-			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	A	A	A	-	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr10:47941986delA	ENST00000358474.5	+	24	2449	c.2449delA	c.(2449-2451)aaafs	p.K818fs		NM_018232.1	NP_060702.1	Q5SNT6	FA21B_HUMAN		818					retrograde transport, endosome to Golgi (GO:0042147)	early endosome (GO:0005769)|membrane (GO:0016020)|WASH complex (GO:0071203)		p.D819fs*55(1)		endometrium(1)|kidney(1)|large_intestine(2)|lung(3)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	10						GAGAGTAGTGAAAAAAGACCA	0.323																																					p.K817fs												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.2449delA	10						.						10.0	12.0	11.0					10																	47941986		335	1676	2011	47461992	SO:0001589	frameshift_variant	55747	exon24																														ENST00000358474.5:c.2449delA	10.37:g.47941986delA	ENSP00000351259:p.Lys818fs	Somatic		Capture	Illumina HiSeq	Phase_I	47461992	NM_018232		Frame_Shift_Del	DEL	ENST00000358474.5	37	CCDS44379.1																																																																																				0.323	FAM21B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047871.2		
VSTM4	196740	broad.mit.edu	37	10	50285340	50285340	+	Silent	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr10:50285340G>A	ENST00000332853.4	-	4	581	c.558C>T	c.(556-558)tgC>tgT	p.C186C		NM_001031746.3	NP_001026916.2	Q8IW00	VSTM4_HUMAN	V-set and transmembrane domain containing 4	186						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.C186C(1)		breast(1)|endometrium(3)|kidney(1)|large_intestine(9)|liver(1)|lung(14)|skin(2)	31						GGATCCCCACGCAGCACACGA	0.517																																					p.C186C												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C558T	10						.						127.0	100.0	109.0					10																	50285340		2203	4300	6503	49955346	SO:0001819	synonymous_variant	196740	exon4			BC041414	CCDS7228.1, CCDS31198.1	10q11.23	2013-01-11	2011-07-01	2011-07-01	ENSG00000165633	ENSG00000165633		"""Immunoglobulin superfamily / V-set domain containing"""	26470	protein-coding gene	gene with protein product			"""chromosome 10 open reading frame 72"""	C10orf72			Standard	XR_246075		Approved	FLJ31737	uc001jhf.2	Q8IW00	OTTHUMG00000018184	ENST00000332853.4:c.558C>T	10.37:g.50285340G>A		Somatic		Capture	Illumina HiSeq	Phase_I	49955346	NM_001031746	B4DNI6|Q96MX7	Silent	SNP	ENST00000332853.4	37	CCDS31198.1																																																																																				0.517	VSTM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047966.2	NM_144984	
NCOA4	8031	broad.mit.edu	37	10	51579211	51579211	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr10:51579211C>T	ENST00000443446.1	+	2	299	c.70C>T	c.(70-72)Cgg>Tgg	p.R24W	NCOA4_ENST00000430396.2_Intron|NCOA4_ENST00000438493.1_Missense_Mutation_p.R40W|NCOA4_ENST00000374087.4_Missense_Mutation_p.R24W|NCOA4_ENST00000414907.2_Intron|NCOA4_ENST00000498586.1_Intron|NCOA4_ENST00000452682.1_Missense_Mutation_p.R40W|NCOA4_ENST00000344348.6_Missense_Mutation_p.R24W|NCOA4_ENST00000374082.1_Missense_Mutation_p.R24W	NM_001145262.1	NP_001138734.1	Q13772	NCOA4_HUMAN	nuclear receptor coactivator 4	24					androgen receptor signaling pathway (GO:0030521)|male gonad development (GO:0008584)|positive regulation of transcription, DNA-templated (GO:0045893)|response to hormone (GO:0009725)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	androgen receptor binding (GO:0050681)|transcription coactivator activity (GO:0003713)	p.R40W(1)|p.R24W(1)		NS(1)|central_nervous_system(1)|kidney(1)|large_intestine(1)|skin(1)	5						TAGTGATGCACGGAGGGACTT	0.448			T	RET	papillary thyroid																																p.R40W			Dom	yes		10	10q11.2	8031	nuclear receptor coactivator 4 - PTC3 (ELE1)		E	.	.	2	Substitution - Missense(2)	large_intestine(2)	c.C118T	10						.						115.0	113.0	114.0					10																	51579211		2203	4300	6503	51249217	SO:0001583	missense	8031	exon3			L49399	CCDS73092.1, CCDS73093.1, CCDS73094.1	10q11.2	2014-04-10			ENSG00000138293	ENSG00000266412			7671	protein-coding gene	gene with protein product	"""RET-activating gene ELE1"""	601984				8290261, 8643607, 24695223	Standard	NM_001145260		Approved	ARA70, RFG, ELE1, PTC3, DKFZp762E1112	uc009xon.3	Q13772	OTTHUMG00000188314	ENST00000443446.1:c.70C>T	10.37:g.51579211C>T	ENSP00000390713:p.Arg24Trp	Somatic		Capture	Illumina HiSeq	Phase_I	51249217	NM_001145261	A8K8W5|B4E260|E9PAV7|J3KQN8|Q14239	Missense_Mutation	SNP	ENST00000443446.1	37	CCDS7237.1	.	.	.	.	.	.	.	.	.	.	C	14.98	2.697722	0.48307	.	.	ENSG00000138293	ENST00000438493;ENST00000452682;ENST00000374087;ENST00000330923;ENST00000344348;ENST00000374082;ENST00000443446	T;T;T;T;T;T	0.22134	2.27;2.26;2.28;2.28;1.97;2.28	5.79	4.82	0.62117	.	0.068828	0.56097	D	0.000028	T	0.32436	0.0829	L	0.29908	0.895	0.80722	D	1	B;B;D	0.89917	0.039;0.071;1.0	B;B;D	0.65573	0.007;0.005;0.936	T	0.07616	-1.0763	10	0.87932	D	0	-18.9685	13.3197	0.60426	0.5399:0.4601:0.0:0.0	.	40;40;24	B4E260;E9PAV7;Q13772	.;.;NCOA4_HUMAN	W	40;40;24;24;24;24;24	ENSP00000405146:R40W;ENSP00000395465:R40W;ENSP00000363200:R24W;ENSP00000344552:R24W;ENSP00000363195:R24W;ENSP00000390713:R24W	ENSP00000332421:R24W	R	+	1	2	NCOA4	51249217	0.584000	0.26766	1.000000	0.80357	0.999000	0.98932	1.383000	0.34385	1.234000	0.43709	0.655000	0.94253	CGG		0.448	NCOA4-204	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048052.1	NM_005437	
FAM13C	220965	broad.mit.edu	37	10	61028434	61028434	+	Missense_Mutation	SNP	C	C	T	rs200555371		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr10:61028434C>T	ENST00000373868.2	-	8	908	c.821G>A	c.(820-822)cGc>cAc	p.R274H	FAM13C_ENST00000435852.2_Missense_Mutation_p.R274H|FAM13C_ENST00000277705.6_Missense_Mutation_p.R295H|FAM13C_ENST00000442566.3_Missense_Mutation_p.R295H|FAM13C_ENST00000419214.2_Missense_Mutation_p.R274H|FAM13C_ENST00000373867.3_Missense_Mutation_p.R191H|FAM13C_ENST00000468840.2_Missense_Mutation_p.R191H|FAM13C_ENST00000422313.2_Missense_Mutation_p.R274H	NM_198215.3	NP_937858.2	Q8NE31	FA13C_HUMAN	family with sequence similarity 13, member C	274								p.R274H(1)		NS(1)|breast(2)|endometrium(3)|kidney(2)|large_intestine(8)|lung(19)|ovary(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	45						ACAGCTGCAGCGTGAAGAACT	0.473													C|||	1	0.000199681	0.0	0.0	5008	,	,		18046	0.0		0.001	False		,,,				2504	0.0				p.R191H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G572A	10						.						50.0	48.0	49.0					10																	61028434		2203	4300	6503	60698440	SO:0001583	missense	220965	exon9			U79304	CCDS31207.1, CCDS44406.1, CCDS7255.1, CCDS53538.1	10q21	2009-09-15	2009-01-20	2009-01-20	ENSG00000148541	ENSG00000148541			19371	protein-coding gene	gene with protein product			"""family with sequence similarity 13, member C1"""	FAM13C1			Standard	NM_001001971		Approved		uc001jkn.3	Q8NE31	OTTHUMG00000018277	ENST00000373868.2:c.821G>A	10.37:g.61028434C>T	ENSP00000362975:p.Arg274His	Somatic		Capture	Illumina HiSeq	Phase_I	60698440	NM_001143773	B7ZB77|Q5T631|Q6P2M3|Q99787	Missense_Mutation	SNP	ENST00000373868.2	37	CCDS7255.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	C	11.78	1.741125	0.30865	.	.	ENSG00000148541	ENST00000373867;ENST00000373868;ENST00000442566;ENST00000277705;ENST00000419214;ENST00000468840;ENST00000435852;ENST00000422313;ENST00000468696	T;T;T;T;T;T;T;T;T	0.76968	-1.06;-1.06;-1.06;-1.06;0.86;-1.06;-1.06;-1.06;-1.06	5.32	5.32	0.75619	.	0.000000	0.64402	D	0.000001	D	0.88051	0.6333	M	0.70275	2.135	0.41939	D	0.990608	D;D;D;D;D	0.89917	1.0;0.997;0.998;1.0;1.0	D;P;P;D;D	0.91635	0.999;0.733;0.907;0.987;0.999	D	0.87987	0.2747	10	0.59425	D	0.04	-17.0059	19.8842	0.96908	0.0:1.0:0.0:0.0	.	274;191;274;274;274	B7Z2K3;B7ZB77;Q8NE31-2;Q8NE31-3;Q8NE31	.;.;.;.;FA13C_HUMAN	H	191;274;295;295;274;191;274;274;52	ENSP00000362974:R191H;ENSP00000362975:R274H;ENSP00000395661:R295H;ENSP00000277705:R295H;ENSP00000391993:R274H;ENSP00000423896:R191H;ENSP00000392302:R274H;ENSP00000400241:R274H;ENSP00000445068:R52H	ENSP00000277705:R295H	R	-	2	0	FAM13C	60698440	0.935000	0.31712	0.972000	0.41901	0.239000	0.25481	2.777000	0.47717	2.876000	0.98609	0.650000	0.86243	CGC		0.473	FAM13C-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048162.2		
CCDC6	8030	broad.mit.edu	37	10	61566688	61566688	+	Silent	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr10:61566688G>A	ENST00000263102.6	-	6	1227	c.996C>T	c.(994-996)gaC>gaT	p.D332D		NM_005436.4	NP_005427.2	Q16204	CCDC6_HUMAN	coiled-coil domain containing 6	332						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	structural constituent of cytoskeleton (GO:0005200)	p.D332D(1)	CCDC6/RET(4)	breast(3)|central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(6)|ovary(3)|stomach(1)	18				Kidney(211;0.0597)		ACCTTTCGTCGTCCATTTCTA	0.453			T	RET	NSCLC																																p.D332D			Dom	yes		10	10q21	8030	coiled-coil domain containing 6		E	.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C996T	10						.						101.0	92.0	95.0					10																	61566688		2203	4300	6503	61236694	SO:0001819	synonymous_variant	8030	exon6			S72869	CCDS7257.1	10q21.2	2006-11-09	2004-01-20		ENSG00000108091	ENSG00000108091			18782	protein-coding gene	gene with protein product	"""DNA segment, single copy, probe pH4 (transforming sequence, thyroid-1"""	601985	"""DNA segment on chromosome 10 (unique) 170"""	TST1, D10S170		8058316, 6745938	Standard	NM_005436		Approved	PTC, TPC, H4	uc001jks.4	Q16204	OTTHUMG00000018284	ENST00000263102.6:c.996C>T	10.37:g.61566688G>A		Somatic		Capture	Illumina HiSeq	Phase_I	61236694	NM_005436	Q15250|Q6GSG7	Silent	SNP	ENST00000263102.6	37	CCDS7257.1																																																																																				0.453	CCDC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048176.2	NM_005436	
ANK3	288	broad.mit.edu	37	10	61829890	61829890	+	Silent	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr10:61829890C>T	ENST00000280772.2	-	37	10940	c.10749G>A	c.(10747-10749)acG>acA	p.T3583T	ANK3_ENST00000373827.2_Intron|ANK3_ENST00000503366.1_Intron|ANK3_ENST00000355288.2_Intron	NM_020987.3	NP_066267.2	Q12955	ANK3_HUMAN	ankyrin 3, node of Ranvier (ankyrin G)	3583					axon guidance (GO:0007411)|axonogenesis (GO:0007409)|cytoskeletal anchoring at plasma membrane (GO:0007016)|establishment of protein localization (GO:0045184)|Golgi to plasma membrane protein transport (GO:0043001)|maintenance of protein location in plasma membrane (GO:0072660)|membrane assembly (GO:0071709)|mitotic cytokinesis (GO:0000281)|neuromuscular junction development (GO:0007528)|neuronal action potential (GO:0019228)|plasma membrane organization (GO:0007009)|positive regulation of cell communication by electrical coupling (GO:0010650)|positive regulation of gene expression (GO:0010628)|positive regulation of homotypic cell-cell adhesion (GO:0034112)|positive regulation of membrane depolarization during cardiac muscle cell action potential (GO:1900827)|positive regulation of membrane potential (GO:0045838)|positive regulation of protein targeting to membrane (GO:0090314)|positive regulation of sodium ion transmembrane transporter activity (GO:2000651)|positive regulation of sodium ion transport (GO:0010765)|protein localization to plasma membrane (GO:0072659)|protein targeting to plasma membrane (GO:0072661)|regulation of potassium ion transport (GO:0043266)|signal transduction (GO:0007165)	axon initial segment (GO:0043194)|basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|costamere (GO:0043034)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|intercalated disc (GO:0014704)|lateral plasma membrane (GO:0016328)|lysosome (GO:0005764)|neuromuscular junction (GO:0031594)|node of Ranvier (GO:0033268)|paranode region of axon (GO:0033270)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|sarcolemma (GO:0042383)|sarcoplasmic reticulum (GO:0016529)|spectrin-associated cytoskeleton (GO:0014731)|T-tubule (GO:0030315)|Z disc (GO:0030018)	cadherin binding (GO:0045296)|cytoskeletal protein binding (GO:0008092)|ion channel binding (GO:0044325)|protein binding, bridging (GO:0030674)|spectrin binding (GO:0030507)|structural constituent of cytoskeleton (GO:0005200)	p.T3583T(1)		NS(4)|breast(7)|central_nervous_system(5)|endometrium(19)|haematopoietic_and_lymphoid_tissue(5)|kidney(14)|large_intestine(30)|liver(2)|lung(59)|ovary(8)|pancreas(2)|prostate(5)|skin(26)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(7)	196						TTCTGGCTGGCGTTGTATCAG	0.483																																					p.T3583T												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G10749A	10						.						138.0	128.0	131.0					10																	61829890		2203	4300	6503	61499896	SO:0001819	synonymous_variant	288	exon37			U13616	CCDS7258.1, CCDS7259.1, CCDS55711.1, CCDS55712.1	10q21	2013-01-10			ENSG00000151150	ENSG00000151150		"""Ankyrin repeat domain containing"""	494	protein-coding gene	gene with protein product	"""ankyrin-3, node of Ranvier"", ""ankyrin-G"""	600465				7665168	Standard	NM_020987		Approved		uc001jky.3	Q12955	OTTHUMG00000018288	ENST00000280772.2:c.10749G>A	10.37:g.61829890C>T		Somatic		Capture	Illumina HiSeq	Phase_I	61499896	NM_020987	B1AQT2|B4DIL1|E9PE32|Q13484|Q5CZH9|Q5VXD5|Q7Z3G4|Q9H0P5	Silent	SNP	ENST00000280772.2	37	CCDS7258.1																																																																																				0.483	ANK3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048201.4	NM_020987	
ANK3	288	broad.mit.edu	37	10	61842392	61842392	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr10:61842392G>T	ENST00000280772.2	-	34	4495	c.4304C>A	c.(4303-4305)aCt>aAt	p.T1435N	Y_RNA_ENST00000365320.1_RNA|ANK3_ENST00000373827.2_Missense_Mutation_p.T1429N|ANK3_ENST00000503366.1_Missense_Mutation_p.T1436N|ANK3_ENST00000355288.2_Missense_Mutation_p.T569N	NM_020987.3	NP_066267.2	Q12955	ANK3_HUMAN	ankyrin 3, node of Ranvier (ankyrin G)	1435					axon guidance (GO:0007411)|axonogenesis (GO:0007409)|cytoskeletal anchoring at plasma membrane (GO:0007016)|establishment of protein localization (GO:0045184)|Golgi to plasma membrane protein transport (GO:0043001)|maintenance of protein location in plasma membrane (GO:0072660)|membrane assembly (GO:0071709)|mitotic cytokinesis (GO:0000281)|neuromuscular junction development (GO:0007528)|neuronal action potential (GO:0019228)|plasma membrane organization (GO:0007009)|positive regulation of cell communication by electrical coupling (GO:0010650)|positive regulation of gene expression (GO:0010628)|positive regulation of homotypic cell-cell adhesion (GO:0034112)|positive regulation of membrane depolarization during cardiac muscle cell action potential (GO:1900827)|positive regulation of membrane potential (GO:0045838)|positive regulation of protein targeting to membrane (GO:0090314)|positive regulation of sodium ion transmembrane transporter activity (GO:2000651)|positive regulation of sodium ion transport (GO:0010765)|protein localization to plasma membrane (GO:0072659)|protein targeting to plasma membrane (GO:0072661)|regulation of potassium ion transport (GO:0043266)|signal transduction (GO:0007165)	axon initial segment (GO:0043194)|basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|costamere (GO:0043034)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|intercalated disc (GO:0014704)|lateral plasma membrane (GO:0016328)|lysosome (GO:0005764)|neuromuscular junction (GO:0031594)|node of Ranvier (GO:0033268)|paranode region of axon (GO:0033270)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|sarcolemma (GO:0042383)|sarcoplasmic reticulum (GO:0016529)|spectrin-associated cytoskeleton (GO:0014731)|T-tubule (GO:0030315)|Z disc (GO:0030018)	cadherin binding (GO:0045296)|cytoskeletal protein binding (GO:0008092)|ion channel binding (GO:0044325)|protein binding, bridging (GO:0030674)|spectrin binding (GO:0030507)|structural constituent of cytoskeleton (GO:0005200)	p.T569N(1)|p.T1435N(1)		NS(4)|breast(7)|central_nervous_system(5)|endometrium(19)|haematopoietic_and_lymphoid_tissue(5)|kidney(14)|large_intestine(30)|liver(2)|lung(59)|ovary(8)|pancreas(2)|prostate(5)|skin(26)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(7)	196						TGCTGGCAGAGTGATATTTAA	0.418																																					p.T1435N												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.C4304A	10						.						184.0	179.0	181.0					10																	61842392		2203	4300	6503	61512398	SO:0001583	missense	288	exon34			U13616	CCDS7258.1, CCDS7259.1, CCDS55711.1, CCDS55712.1	10q21	2013-01-10			ENSG00000151150	ENSG00000151150		"""Ankyrin repeat domain containing"""	494	protein-coding gene	gene with protein product	"""ankyrin-3, node of Ranvier"", ""ankyrin-G"""	600465				7665168	Standard	NM_020987		Approved		uc001jky.3	Q12955	OTTHUMG00000018288	ENST00000280772.2:c.4304C>A	10.37:g.61842392G>T	ENSP00000280772:p.Thr1435Asn	Somatic		Capture	Illumina HiSeq	Phase_I	61512398	NM_020987	B1AQT2|B4DIL1|E9PE32|Q13484|Q5CZH9|Q5VXD5|Q7Z3G4|Q9H0P5	Missense_Mutation	SNP	ENST00000280772.2	37	CCDS7258.1	.	.	.	.	.	.	.	.	.	.	G	25.3	4.621003	0.87460	.	.	ENSG00000151150	ENST00000280772;ENST00000373827;ENST00000373820;ENST00000355288;ENST00000423532;ENST00000503366;ENST00000395299;ENST00000373817;ENST00000395293;ENST00000395304	T;T;T;T;T	0.78595	1.69;1.69;-1.19;1.69;1.69	5.89	5.89	0.94794	.	0.341281	0.21064	N	0.080766	D	0.89522	0.6739	M	0.81942	2.565	0.80722	D	1	D;D;D;D;D;D	0.89917	0.967;1.0;0.998;0.999;0.995;0.981	P;D;D;D;D;D	0.83275	0.852;0.996;0.973;0.994;0.948;0.966	D	0.89683	0.3892	10	0.87932	D	0	.	20.2527	0.98410	0.0:0.0:1.0:0.0	.	1436;569;1429;1435;670;569	E9PE32;A8KA62;Q5CZH9;Q12955;F5GXK0;B1AQT2	.;.;.;ANK3_HUMAN;.;.	N	1435;1429;18;569;569;1436;1415;670;1070;1070	ENSP00000280772:T1435N;ENSP00000362933:T1429N;ENSP00000362926:T18N;ENSP00000347436:T569N;ENSP00000425236:T1436N	ENSP00000280772:T1435N	T	-	2	0	ANK3	61512398	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.869000	0.99810	2.788000	0.95919	0.557000	0.71058	ACT		0.418	ANK3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048201.4	NM_020987	
ANK3	288	broad.mit.edu	37	10	61959898	61959898	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr10:61959898C>A	ENST00000280772.2	-	13	1671	c.1480G>T	c.(1480-1482)Gct>Tct	p.A494S	ANK3_ENST00000373827.2_Missense_Mutation_p.A488S|ANK3_ENST00000503366.1_Missense_Mutation_p.A477S	NM_020987.3	NP_066267.2	Q12955	ANK3_HUMAN	ankyrin 3, node of Ranvier (ankyrin G)	494					axon guidance (GO:0007411)|axonogenesis (GO:0007409)|cytoskeletal anchoring at plasma membrane (GO:0007016)|establishment of protein localization (GO:0045184)|Golgi to plasma membrane protein transport (GO:0043001)|maintenance of protein location in plasma membrane (GO:0072660)|membrane assembly (GO:0071709)|mitotic cytokinesis (GO:0000281)|neuromuscular junction development (GO:0007528)|neuronal action potential (GO:0019228)|plasma membrane organization (GO:0007009)|positive regulation of cell communication by electrical coupling (GO:0010650)|positive regulation of gene expression (GO:0010628)|positive regulation of homotypic cell-cell adhesion (GO:0034112)|positive regulation of membrane depolarization during cardiac muscle cell action potential (GO:1900827)|positive regulation of membrane potential (GO:0045838)|positive regulation of protein targeting to membrane (GO:0090314)|positive regulation of sodium ion transmembrane transporter activity (GO:2000651)|positive regulation of sodium ion transport (GO:0010765)|protein localization to plasma membrane (GO:0072659)|protein targeting to plasma membrane (GO:0072661)|regulation of potassium ion transport (GO:0043266)|signal transduction (GO:0007165)	axon initial segment (GO:0043194)|basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|costamere (GO:0043034)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|intercalated disc (GO:0014704)|lateral plasma membrane (GO:0016328)|lysosome (GO:0005764)|neuromuscular junction (GO:0031594)|node of Ranvier (GO:0033268)|paranode region of axon (GO:0033270)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|sarcolemma (GO:0042383)|sarcoplasmic reticulum (GO:0016529)|spectrin-associated cytoskeleton (GO:0014731)|T-tubule (GO:0030315)|Z disc (GO:0030018)	cadherin binding (GO:0045296)|cytoskeletal protein binding (GO:0008092)|ion channel binding (GO:0044325)|protein binding, bridging (GO:0030674)|spectrin binding (GO:0030507)|structural constituent of cytoskeleton (GO:0005200)	p.A494S(1)		NS(4)|breast(7)|central_nervous_system(5)|endometrium(19)|haematopoietic_and_lymphoid_tissue(5)|kidney(14)|large_intestine(30)|liver(2)|lung(59)|ovary(8)|pancreas(2)|prostate(5)|skin(26)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(7)	196						TTAGCTTTAGCTTCTACCTGA	0.433																																					p.A494S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1480T	10						.						92.0	82.0	86.0					10																	61959898		2203	4300	6503	61629904	SO:0001583	missense	288	exon13			U13616	CCDS7258.1, CCDS7259.1, CCDS55711.1, CCDS55712.1	10q21	2013-01-10			ENSG00000151150	ENSG00000151150		"""Ankyrin repeat domain containing"""	494	protein-coding gene	gene with protein product	"""ankyrin-3, node of Ranvier"", ""ankyrin-G"""	600465				7665168	Standard	NM_020987		Approved		uc001jky.3	Q12955	OTTHUMG00000018288	ENST00000280772.2:c.1480G>T	10.37:g.61959898C>A	ENSP00000280772:p.Ala494Ser	Somatic		Capture	Illumina HiSeq	Phase_I	61629904	NM_020987	B1AQT2|B4DIL1|E9PE32|Q13484|Q5CZH9|Q5VXD5|Q7Z3G4|Q9H0P5	Missense_Mutation	SNP	ENST00000280772.2	37	CCDS7258.1	.	.	.	.	.	.	.	.	.	.	C	24.4	4.525534	0.85600	.	.	ENSG00000151150	ENST00000280772;ENST00000373827;ENST00000503366;ENST00000395299;ENST00000395293;ENST00000395304;ENST00000536348	T;T;T	0.65549	-0.16;-0.16;-0.16	5.81	5.81	0.92471	Ankyrin repeat-containing domain (4);	0.000000	0.39985	N	0.001209	T	0.69806	0.3152	L	0.45137	1.4	0.80722	D	1	B;P;B;B;P	0.39862	0.103;0.692;0.363;0.045;0.505	B;P;B;B;B	0.50378	0.235;0.639;0.445;0.173;0.331	T	0.70396	-0.4883	10	0.87932	D	0	.	20.1454	0.98074	0.0:1.0:0.0:0.0	.	477;155;38;488;494	E9PE32;E7EMJ1;Q59G01;Q5CZH9;Q12955	.;.;.;.;ANK3_HUMAN	S	494;488;477;456;155;155;38	ENSP00000280772:A494S;ENSP00000362933:A488S;ENSP00000425236:A477S	ENSP00000280772:A494S	A	-	1	0	ANK3	61629904	1.000000	0.71417	1.000000	0.80357	0.925000	0.55904	3.900000	0.56295	2.749000	0.94314	0.650000	0.86243	GCT		0.433	ANK3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048201.4	NM_020987	
RHOBTB1	9886	broad.mit.edu	37	10	62671289	62671289	+	Silent	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr10:62671289G>A	ENST00000337910.5	-	3	349	c.12C>T	c.(10-12)gaC>gaT	p.D4D	RNU2-72P_ENST00000411175.1_RNA|RHOBTB1_ENST00000357917.4_Silent_p.D4D	NM_001242359.1|NM_014836.4	NP_001229288.1|NP_055651.1	O94844	RHBT1_HUMAN	Rho-related BTB domain containing 1	4	Rho-like.				regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|plasma membrane (GO:0005886)	GTP binding (GO:0005525)	p.D4D(1)		endometrium(4)|large_intestine(6)|lung(11)|ovary(1)|upper_aerodigestive_tract(1)	23	Prostate(12;0.0112)					CGTAGTCCATGTCAGCGTCCA	0.493																																					p.D4D												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C12T	10						.						213.0	207.0	209.0					10																	62671289		2203	4300	6503	62341295	SO:0001819	synonymous_variant	9886	exon3			AB018283	CCDS7261.1	10q22.1	2013-01-08			ENSG00000072422	ENSG00000072422		"""BTB/POZ domain containing"""	18738	protein-coding gene	gene with protein product		607351				11222756	Standard	NM_014836		Approved	KIAA0740	uc001jlh.3	O94844	OTTHUMG00000018292	ENST00000337910.5:c.12C>T	10.37:g.62671289G>A		Somatic		Capture	Illumina HiSeq	Phase_I	62341295	NM_014836		Silent	SNP	ENST00000337910.5	37	CCDS7261.1																																																																																				0.493	RHOBTB1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048220.1		
CDH23	64072	broad.mit.edu	37	10	73455225	73455225	+	Silent	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr10:73455225C>T	ENST00000224721.6	+	21	2360	c.2355C>T	c.(2353-2355)gaC>gaT	p.D785D	CDH23_ENST00000299366.7_Silent_p.D825D	NM_022124.5	NP_071407.4	Q9H251	CAD23_HUMAN	cadherin-related 23	780	Cadherin 8. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium ion transport (GO:0006816)|calcium-dependent cell-cell adhesion (GO:0016339)|cytosolic calcium ion homeostasis (GO:0051480)|equilibrioception (GO:0050957)|homophilic cell adhesion (GO:0007156)|photoreceptor cell maintenance (GO:0045494)|response to stimulus (GO:0050896)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|stereocilium (GO:0032420)	calcium ion binding (GO:0005509)	p.D785D(1)		NS(1)|breast(2)|central_nervous_system(6)|endometrium(15)|haematopoietic_and_lymphoid_tissue(5)|kidney(7)|large_intestine(27)|lung(49)|ovary(3)|pancreas(1)|prostate(7)|stomach(7)|upper_aerodigestive_tract(3)	133						CGTGGAAGGACGCACCCTACT	0.592																																					p.D780D												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C2340T	10						.						116.0	126.0	123.0					10																	73455225		2111	4228	6339	73125231	SO:0001819	synonymous_variant	64072	exon21			AY010111	CCDS53540.1, CCDS73146.1	10q22.1	2014-08-08	2010-01-25		ENSG00000107736	ENSG00000107736		"""Cadherins / Cadherin-related"""	13733	protein-coding gene	gene with protein product	"""cadherin-related family member 23"""	605516	"""cadherin related 23"", ""cadherin-like 23"""	DFNB12, USH1D		11090341	Standard	NM_022124		Approved	CDHR23	uc001jrx.4	Q9H251	OTTHUMG00000019347	ENST00000224721.6:c.2355C>T	10.37:g.73455225C>T		Somatic		Capture	Illumina HiSeq	Phase_I	73125231	NM_022124	C4IXS9|F6U049|Q5QGS1|Q5QGS2|Q5QGS5|Q5QGS6|Q5XKN2|Q6UWW1|Q96JL3|Q9H4K9	Silent	SNP	ENST00000224721.6	37																																																																																					0.592	CDH23-001	PUTATIVE	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000051227.4	NM_052836	
CDH23	64072	broad.mit.edu	37	10	73553361	73553361	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr10:73553361A>G	ENST00000224721.6	+	47	6696	c.6691A>G	c.(6691-6693)Aac>Gac	p.N2231D	CDH23_ENST00000398788.3_5'Flank	NM_022124.5	NP_071407.4	Q9H251	CAD23_HUMAN	cadherin-related 23	2226	Cadherin 21. {ECO:0000255|PROSITE- ProRule:PRU00043}.			EFLNPIQTVSVLESAEPGTVIANITAIDHDLNPKLEYHIVG IVAKDDTDRLVPNQEDAFAVNIN -> ASWEGQSHVTQAYE EAVGPPQPQVPDSTGDRHPLWGLGGFGQEHPWEGQILGGSS QAEPGLVWS (in Ref. 8; BAB61902). {ECO:0000305}.	calcium ion transport (GO:0006816)|calcium-dependent cell-cell adhesion (GO:0016339)|cytosolic calcium ion homeostasis (GO:0051480)|equilibrioception (GO:0050957)|homophilic cell adhesion (GO:0007156)|photoreceptor cell maintenance (GO:0045494)|response to stimulus (GO:0050896)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|stereocilium (GO:0032420)	calcium ion binding (GO:0005509)	p.N2231D(1)		NS(1)|breast(2)|central_nervous_system(6)|endometrium(15)|haematopoietic_and_lymphoid_tissue(5)|kidney(7)|large_intestine(27)|lung(49)|ovary(3)|pancreas(1)|prostate(7)|stomach(7)|upper_aerodigestive_tract(3)	133						CCTGGTGCCCAACCAGGAGGA	0.582																																					p.N2226D												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A6676G	10						.						49.0	54.0	52.0					10																	73553361		2097	4218	6315	73223367	SO:0001583	missense	64072	exon46			AY010111	CCDS53540.1, CCDS73146.1	10q22.1	2014-08-08	2010-01-25		ENSG00000107736	ENSG00000107736		"""Cadherins / Cadherin-related"""	13733	protein-coding gene	gene with protein product	"""cadherin-related family member 23"""	605516	"""cadherin related 23"", ""cadherin-like 23"""	DFNB12, USH1D		11090341	Standard	NM_022124		Approved	CDHR23	uc001jrx.4	Q9H251	OTTHUMG00000019347	ENST00000224721.6:c.6691A>G	10.37:g.73553361A>G	ENSP00000224721:p.Asn2231Asp	Somatic		Capture	Illumina HiSeq	Phase_I	73223367	NM_022124	C4IXS9|F6U049|Q5QGS1|Q5QGS2|Q5QGS5|Q5QGS6|Q5XKN2|Q6UWW1|Q96JL3|Q9H4K9	Missense_Mutation	SNP	ENST00000224721.6	37		.	.	.	.	.	.	.	.	.	.	G	0.828	-0.746168	0.03065	.	.	ENSG00000107736	ENST00000398860;ENST00000398855;ENST00000224721	.	.	.	4.76	0.681	0.17986	Cadherin (4);Cadherin-like (1);	0.211987	0.39210	N	0.001427	T	0.34658	0.0905	N	0.19112	0.55	0.58432	D	0.999999	B	0.02656	0.0	B	0.04013	0.001	T	0.11842	-1.0571	9	0.09843	T	0.71	.	10.089	0.42436	0.4229:0.0:0.5771:0.0	.	2226	Q9H251	CAD23_HUMAN	D	2231;2226;2229	.	ENSP00000224721:N2231D	N	+	1	0	CDH23	73223367	0.792000	0.28813	0.624000	0.29186	0.442000	0.32017	1.147000	0.31602	-0.047000	0.13423	-1.702000	0.00720	AAC		0.582	CDH23-001	PUTATIVE	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000051227.4	NM_052836	
CDH23	64072	broad.mit.edu	37	10	73567274	73567274	+	Splice_Site	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr10:73567274C>T	ENST00000224721.6	+	58	8330	c.8325C>T	c.(8323-8325)gcC>gcT	p.A2775A	CDH23_ENST00000398788.3_Splice_Site_p.A530A|CDH23_ENST00000475158.1_3'UTR	NM_022124.5	NP_071407.4	Q9H251	CAD23_HUMAN	cadherin-related 23	2770	Cadherin 26. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium ion transport (GO:0006816)|calcium-dependent cell-cell adhesion (GO:0016339)|cytosolic calcium ion homeostasis (GO:0051480)|equilibrioception (GO:0050957)|homophilic cell adhesion (GO:0007156)|photoreceptor cell maintenance (GO:0045494)|response to stimulus (GO:0050896)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|stereocilium (GO:0032420)	calcium ion binding (GO:0005509)	p.A2775A(1)		NS(1)|breast(2)|central_nervous_system(6)|endometrium(15)|haematopoietic_and_lymphoid_tissue(5)|kidney(7)|large_intestine(27)|lung(49)|ovary(3)|pancreas(1)|prostate(7)|stomach(7)|upper_aerodigestive_tract(3)	133						CACCCTCAGCCGGCAACGAAG	0.607																																					p.A530A												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1590T	10						.						34.0	40.0	38.0					10																	73567274		2081	4204	6285	73237280	SO:0001630	splice_region_variant	64072	exon12			AY010111	CCDS53540.1, CCDS73146.1	10q22.1	2014-08-08	2010-01-25		ENSG00000107736	ENSG00000107736		"""Cadherins / Cadherin-related"""	13733	protein-coding gene	gene with protein product	"""cadherin-related family member 23"""	605516	"""cadherin related 23"", ""cadherin-like 23"""	DFNB12, USH1D		11090341	Standard	NM_022124		Approved	CDHR23	uc001jrx.4	Q9H251	OTTHUMG00000019347	ENST00000224721.6:c.8324-1C>T	10.37:g.73567274C>T		Somatic		Capture	Illumina HiSeq	Phase_I	73237280	NM_001171933	C4IXS9|F6U049|Q5QGS1|Q5QGS2|Q5QGS5|Q5QGS6|Q5XKN2|Q6UWW1|Q96JL3|Q9H4K9	Silent	SNP	ENST00000224721.6	37																																																																																					0.607	CDH23-001	PUTATIVE	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000051227.4	NM_052836	Silent
PPP3CB	5532	broad.mit.edu	37	10	75198057	75198057	+	Silent	SNP	A	A	G			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr10:75198057A>G	ENST00000360663.5	-	14	1629	c.1518T>C	c.(1516-1518)tcT>tcC	p.S506S	PPP3CB_ENST00000544628.1_Silent_p.S134S|PPP3CB_ENST00000394829.2_Silent_p.S507S|PPP3CB_ENST00000394828.2_Silent_p.S497S			P16298	PP2BB_HUMAN	protein phosphatase 3, catalytic subunit, beta isozyme	506					axon extension (GO:0048675)|calcium ion-dependent exocytosis (GO:0017156)|cellular response to drug (GO:0035690)|dephosphorylation (GO:0016311)|Fc-epsilon receptor signaling pathway (GO:0038095)|heart development (GO:0007507)|innate immune response (GO:0045087)|learning (GO:0007612)|locomotion involved in locomotory behavior (GO:0031987)|memory (GO:0007613)|negative regulation of T cell mediated cytotoxicity (GO:0001915)|positive regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0035774)|positive regulation of transcription, DNA-templated (GO:0045893)|protein dephosphorylation (GO:0006470)|protein phosphorylation (GO:0006468)|regulation of insulin secretion (GO:0050796)|regulation of synaptic plasticity (GO:0048167)|response to cytokine (GO:0034097)|signal transduction (GO:0007165)|social behavior (GO:0035176)|T cell activation (GO:0042110)|T cell differentiation (GO:0030217)|T cell homeostasis (GO:0043029)|T cell proliferation (GO:0042098)	calcineurin complex (GO:0005955)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|calmodulin-dependent protein phosphatase activity (GO:0033192)|drug binding (GO:0008144)|enzyme binding (GO:0019899)|protein dimerization activity (GO:0046983)|protein phosphatase 2B binding (GO:0030346)|protein serine/threonine phosphatase activity (GO:0004722)	p.S506S(1)|p.S178S(1)		breast(1)|endometrium(3)|kidney(2)|large_intestine(7)|lung(7)|skin(1)|urinary_tract(1)	22	Prostate(51;0.0119)					CGGTGTTCAGAGAATTGAAAC	0.512																																					p.S507S												.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.T1521C	10						.						175.0	147.0	157.0					10																	75198057		2203	4300	6503	74868063	SO:0001819	synonymous_variant	5532	exon14			M29551	CCDS7328.1, CCDS44436.1, CCDS44437.1	10q22.2	2010-03-17	2010-03-05		ENSG00000107758	ENSG00000107758	3.1.3.16	"""Serine/threonine phosphatases / Protein phosphatase, catalytic subunits"""	9315	protein-coding gene	gene with protein product	"""calcineurin A beta"", ""protein phosphatase 2B, catalytic subunit, beta isoform"""	114106	"""protein phosphatase 3 (formerly 2B), catalytic subunit, beta isoform (calcineurin A beta)"", ""protein phosphatase 3 (formerly 2B), catalytic subunit, beta isoform"""	CALNB		1659808, 2558868	Standard	XM_005269944		Approved	CALNA2, CNA2, PP2Bbeta	uc001juf.3	P16298	OTTHUMG00000018472	ENST00000360663.5:c.1518T>C	10.37:g.75198057A>G		Somatic		Capture	Illumina HiSeq	Phase_I	74868063	NM_001142353	P16299|Q5F2F9|Q8N1F0|Q8N3W4	Silent	SNP	ENST00000360663.5	37	CCDS7328.1																																																																																				0.512	PPP3CB-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000048669.1	NM_021132	
SYNPO2L	79933	broad.mit.edu	37	10	75406859	75406859	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr10:75406859G>A	ENST00000394810.2	-	4	2700	c.2551C>T	c.(2551-2553)Cgg>Tgg	p.R851W	SYNPO2L_ENST00000372873.4_Missense_Mutation_p.R627W	NM_001114133.1	NP_001107605.1	Q9H987	SYP2L_HUMAN	synaptopodin 2-like	851	Pro-rich.					cytoskeleton (GO:0005856)|nucleus (GO:0005634)|Z disc (GO:0030018)		p.R627W(2)|p.R851W(1)		breast(2)|endometrium(3)|kidney(3)|large_intestine(5)|lung(6)|ovary(1)|prostate(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	26	Prostate(51;0.0112)					GGCTGATGCCGCATAAAATCT	0.577																																					p.R627W												.	.	3	Substitution - Missense(3)	kidney(2)|large_intestine(1)	c.C1879T	10						.						59.0	70.0	66.0					10																	75406859		2201	4296	6497	75076865	SO:0001583	missense	79933	exon2			AK022983	CCDS7331.1, CCDS44438.1	10q22.3	2007-12-19			ENSG00000166317	ENSG00000166317			23532	protein-coding gene	gene with protein product							Standard	XM_005270158		Approved	FLJ12921	uc001jut.4	Q9H987	OTTHUMG00000018471	ENST00000394810.2:c.2551C>T	10.37:g.75406859G>A	ENSP00000378289:p.Arg851Trp	Somatic		Capture	Illumina HiSeq	Phase_I	75076865	NM_024875	A5PKV9|Q68A20	Missense_Mutation	SNP	ENST00000394810.2	37	CCDS44438.1	.	.	.	.	.	.	.	.	.	.	G	16.62	3.172756	0.57584	.	.	ENSG00000166317	ENST00000372873;ENST00000394810	T;T	0.27720	1.65;1.98	5.08	3.02	0.34903	.	0.122449	0.53938	D	0.000053	T	0.49966	0.1588	L	0.59436	1.845	0.36226	D	0.852342	D;D	0.89917	1.0;1.0	D;D	0.72625	0.952;0.978	T	0.64210	-0.6461	10	0.72032	D	0.01	-15.751	14.6607	0.68868	0.0:0.0:0.653:0.347	.	851;627	Q9H987;Q9H987-2	SYP2L_HUMAN;.	W	627;851	ENSP00000361964:R627W;ENSP00000378289:R851W	ENSP00000361964:R627W	R	-	1	2	SYNPO2L	75076865	1.000000	0.71417	1.000000	0.80357	0.964000	0.63967	1.600000	0.36762	1.302000	0.44855	0.561000	0.74099	CGG		0.577	SYNPO2L-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316562.2	NM_024875	
KAT6B	23522	broad.mit.edu	37	10	76789769	76789769	+	Silent	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr10:76789769C>T	ENST00000287239.4	+	18	5676	c.5187C>T	c.(5185-5187)agC>agT	p.S1729S	KAT6B_ENST00000372725.1_Silent_p.S1437S|KAT6B_ENST00000372711.1_Silent_p.S1546S|KAT6B_ENST00000372714.1_Silent_p.S1437S|KAT6B_ENST00000372724.1_Silent_p.S1437S	NM_001256468.1|NM_012330.3	NP_001243397.1|NP_036462.2	Q8WYB5	KAT6B_HUMAN	K(lysine) acetyltransferase 6B	1729	Interaction with RUNX1 and RUNX2.|Ser-rich.				chromatin organization (GO:0006325)|histone acetylation (GO:0016573)|histone H3 acetylation (GO:0043966)|negative regulation of transcription, DNA-templated (GO:0045892)|nucleosome assembly (GO:0006334)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	MOZ/MORF histone acetyltransferase complex (GO:0070776)|nucleoplasm (GO:0005654)|nucleosome (GO:0000786)|nucleus (GO:0005634)	acetyltransferase activity (GO:0016407)|DNA binding (GO:0003677)|histone acetyltransferase activity (GO:0004402)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)	p.S1729S(1)									CCAACATCAGCGGGAGCTGCA	0.587																																					p.S1729S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C5187T	10						.						42.0	38.0	39.0					10																	76789769		2203	4300	6503	76459775	SO:0001819	synonymous_variant	23522	exon18			AF113514	CCDS7345.1, CCDS58084.1, CCDS58085.1	10q22.2	2013-01-28	2011-07-21	2011-07-21	ENSG00000156650	ENSG00000156650		"""Chromatin-modifying enzymes / K-acetyltransferases"", ""Zinc fingers, C2HC-type containing"", ""Zinc fingers, PHD-type"""	17582	protein-coding gene	gene with protein product	"""MOZ-related factor"""	605880	"""MYST histone acetyltransferase (monocytic leukemia) 4"""	MYST4		9205841, 10497217	Standard	NM_012330		Approved	querkopf, qkf, Morf, MOZ2, ZC2HC6B	uc001jwn.2	Q8WYB5	OTTHUMG00000018509	ENST00000287239.4:c.5187C>T	10.37:g.76789769C>T		Somatic		Capture	Illumina HiSeq	Phase_I	76459775	NM_012330	O15087|Q86Y05|Q8WU81|Q9UKW2|Q9UKW3|Q9UKX0	Silent	SNP	ENST00000287239.4	37	CCDS7345.1																																																																																				0.587	KAT6B-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048771.1	NM_012330	
KCNMA1	3778	broad.mit.edu	37	10	78651307	78651307	+	Silent	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr10:78651307G>A	ENST00000286628.8	-	26	3317	c.3318C>T	c.(3316-3318)ctC>ctT	p.L1106L	KCNMA1_ENST00000404857.1_Silent_p.L1089L|RP11-443A13.5_ENST00000458661.2_RNA|RP11-443A13.5_ENST00000609102.1_RNA|RP11-443A13.5_ENST00000595702.1_RNA|KCNMA1_ENST00000354353.5_Silent_p.L1109L|KCNMA1_ENST00000372440.1_Silent_p.L1048L|RP11-443A13.5_ENST00000429850.2_RNA|KCNMA1_ENST00000372443.1_Silent_p.L1075L|KCNMA1_ENST00000406533.3_Silent_p.L1110L|KCNMA1_ENST00000286627.5_Silent_p.L1048L|KCNMA1_ENST00000404771.3_Silent_p.L1106L	NM_001161352.1	NP_001154824.1	Q12791	KCMA1_HUMAN	potassium large conductance calcium-activated channel, subfamily M, alpha member 1	1106					blood coagulation (GO:0007596)|cellular potassium ion homeostasis (GO:0030007)|micturition (GO:0060073)|negative regulation of cell volume (GO:0045794)|positive regulation of apoptotic process (GO:0043065)|potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|regulation of membrane potential (GO:0042391)|response to calcium ion (GO:0051592)|response to carbon monoxide (GO:0034465)|response to hypoxia (GO:0001666)|response to osmotic stress (GO:0006970)|smooth muscle contraction involved in micturition (GO:0060083)|synaptic transmission (GO:0007268)	apical plasma membrane (GO:0016324)|caveola (GO:0005901)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	actin binding (GO:0003779)|calcium-activated potassium channel activity (GO:0015269)|large conductance calcium-activated potassium channel activity (GO:0060072)|metal ion binding (GO:0046872)|voltage-gated potassium channel activity (GO:0005249)	p.L1048L(1)		breast(1)|cervix(2)|endometrium(6)|kidney(3)|large_intestine(17)|lung(23)|ovary(2)|pancreas(2)|prostate(4)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	68	all_cancers(46;0.203)|all_epithelial(25;0.00604)|Prostate(51;0.0198)		OV - Ovarian serous cystadenocarcinoma(4;0.0586)|Epithelial(14;0.081)|all cancers(16;0.183)		Bendroflumethiazide(DB00436)|Chlorzoxazone(DB00356)|Cromoglicic acid(DB01003)|Diazoxide(DB01119)|Halothane(DB01159)|Hydrochlorothiazide(DB00999)|Hydroflumethiazide(DB00774)|Miconazole(DB01110)|Procaine(DB00721)	ATGGCCCATCGAGCAGAGCTA	0.572																																					p.L1089L												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C3267T	10						.						41.0	38.0	39.0					10																	78651307		2203	4300	6503	78321313	SO:0001819	synonymous_variant	3778	exon26			U11717	CCDS7352.1, CCDS60569.1, CCDS60571.1, CCDS60572.1, CCDS73156.1	10q22	2012-07-05			ENSG00000156113	ENSG00000156113		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels, calcium-activated"""	6284	protein-coding gene	gene with protein product	"""BK channel alpha subunit"""	600150		SLO		7987297, 16382103	Standard	NM_002247		Approved	KCa1.1, mSLO1	uc001jxn.3	Q12791	OTTHUMG00000018543	ENST00000286628.8:c.3318C>T	10.37:g.78651307G>A		Somatic		Capture	Illumina HiSeq	Phase_I	78321313	NM_001161353	F8WA96|Q12886|Q12917|Q12921|Q12960|Q13150|Q5JQ23|Q5SQR9|Q96LG8|Q9UBB0|Q9UCX0|Q9UQK6	Silent	SNP	ENST00000286628.8	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	0.266|0.266	-0.996030|-0.996030	0.02145|0.02145	.|.	.|.	ENSG00000156113|ENSG00000156113	ENST00000372421;ENST00000434208|ENST00000372403	.|.	.|.	.|.	5.49|5.49	-0.927|-0.927	0.10451|0.10451	.|.	.|.	.|.	.|.	.|.	.|T	.|0.48589	.|0.1508	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	.|T	.|0.35375	.|-0.9791	.|4	.|.	.|.	.|.	-8.3042|-8.3042	4.7027|4.7027	0.12835|0.12835	0.4135:0.3364:0.1831:0.0669|0.4135:0.3364:0.1831:0.0669	.|.	.|.	.|.	.|.	X|L	1037;756|999	.|.	.|.	R|S	-|-	1|2	2|0	KCNMA1|KCNMA1	78321313|78321313	0.998000|0.998000	0.40836|0.40836	0.994000|0.994000	0.49952|0.49952	0.034000|0.034000	0.12701|0.12701	0.479000|0.479000	0.22228|0.22228	-0.067000|-0.067000	0.12976|0.12976	-1.442000|-1.442000	0.01069|0.01069	CGA|TCG		0.572	KCNMA1-009	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000048885.3	NM_002247	
FAM213A	84293	broad.mit.edu	37	10	82180343	82180343	+	Silent	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr10:82180343G>A	ENST00000372181.1	+	1	590	c.120G>A	c.(118-120)aaG>aaA	p.K40K	FAM213A_ENST00000372187.5_Silent_p.K40K|FAM213A_ENST00000372185.1_Silent_p.K29K|FAM213A_ENST00000372188.1_Silent_p.K40K	NM_001243778.1|NM_001243782.1	NP_001230707.1|NP_001230711.1	Q9BRX8	F213A_HUMAN	family with sequence similarity 213, member A	40	Thioredoxin fold. {ECO:0000250}.				oxidation-reduction process (GO:0055114)|regulation of osteoclast differentiation (GO:0045670)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	antioxidant activity (GO:0016209)	p.K40K(1)									TTCTGTCCAAGCCCCAGAAAG	0.547																																					p.K40K												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G120A	10						.						71.0	70.0	71.0					10																	82180343		2203	4300	6503	82170323	SO:0001819	synonymous_variant	84293	exon2			AF086462	CCDS7368.1, CCDS58089.1	10q23.1	2011-12-08	2011-12-08	2011-12-08	ENSG00000122378	ENSG00000122378			28651	protein-coding gene	gene with protein product	"""peroxiredoxin-like 2 activated in M-CSF stimulated monocytes"""		"""chromosome 10 open reading frame 58"""	C10orf58		11483580, 19951071	Standard	NM_032333		Approved	MGC4248, PAMM	uc001kce.4	Q9BRX8	OTTHUMG00000018614	ENST00000372181.1:c.120G>A	10.37:g.82180343G>A		Somatic		Capture	Illumina HiSeq	Phase_I	82170323	NM_032333	B2RD81|Q6UW08|Q8N2K3|Q8NBK9|Q96JR0	Silent	SNP	ENST00000372181.1	37	CCDS7368.1																																																																																				0.547	FAM213A-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049077.2		
CDHR1	92211	broad.mit.edu	37	10	85962823	85962823	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr10:85962823G>T	ENST00000372117.3	+	8	830	c.727G>T	c.(727-729)Gcc>Tcc	p.A243S	CDHR1_ENST00000332904.3_Missense_Mutation_p.A243S|CDHR1_ENST00000440770.2_Missense_Mutation_p.A2S	NM_033100.2	NP_149091.1	Q96JP9	CDHR1_HUMAN	cadherin-related family member 1	243	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.		A -> V (in dbSNP:rs7086200).		cellular process (GO:0009987)|homophilic cell adhesion (GO:0007156)|photoreceptor cell maintenance (GO:0045494)	integral component of plasma membrane (GO:0005887)|photoreceptor outer segment membrane (GO:0042622)	calcium ion binding (GO:0005509)	p.A243S(1)		breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(6)|liver(1)|lung(21)|ovary(1)|prostate(1)|skin(1)	36						TCAGGACATGGCCCCTGTCTT	0.597																																					p.A243S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G727T	10						.						257.0	186.0	210.0					10																	85962823		2203	4300	6503	85952803	SO:0001583	missense	92211	exon8			AB053448	CCDS7372.1, CCDS53548.1	10q23.1	2014-01-28	2010-01-25	2010-01-25	ENSG00000148600	ENSG00000148600		"""Cadherins / Cadherin-related"""	14550	protein-coding gene	gene with protein product		609502	"""protocadherin 21"""	PCDH21		11597768	Standard	NM_001171971		Approved	KIAA1775, CORD15, RP65	uc001kcv.3	Q96JP9	OTTHUMG00000018634	ENST00000372117.3:c.727G>T	10.37:g.85962823G>T	ENSP00000361189:p.Ala243Ser	Somatic		Capture	Illumina HiSeq	Phase_I	85952803	NM_001171971	Q69YZ8|Q8IXY5	Missense_Mutation	SNP	ENST00000372117.3	37	CCDS7372.1	.	.	.	.	.	.	.	.	.	.	G	5.015	0.188381	0.09547	.	.	ENSG00000148600	ENST00000332904;ENST00000372117;ENST00000440770	T;T;T	0.41758	4.06;4.06;0.99	5.06	-0.568	0.11760	Cadherin (4);Cadherin-like (1);	0.403964	0.29355	N	0.012395	T	0.32315	0.0825	N	0.25144	0.715	0.09310	N	1	B;B;B	0.24483	0.104;0.01;0.031	B;B;B	0.23574	0.024;0.047;0.021	T	0.21008	-1.0258	10	0.44086	T	0.13	-22.3849	21.4097	0.99953	0.0:0.7839:0.2161:0.0	.	2;243;243	E7EN47;Q96JP9-2;Q96JP9	.;.;CDHR1_HUMAN	S	243;243;2	ENSP00000331063:A243S;ENSP00000361189:A243S;ENSP00000415980:A2S	ENSP00000331063:A243S	A	+	1	0	CDHR1	85952803	0.293000	0.24371	0.001000	0.08648	0.458000	0.32498	2.276000	0.43408	-0.243000	0.09653	-0.181000	0.13052	GCC		0.597	CDHR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049111.1	NM_033100	
GRID1	2894	broad.mit.edu	37	10	87407088	87407088	+	Silent	SNP	A	A	G			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr10:87407088A>G	ENST00000327946.7	-	13	2149	c.2064T>C	c.(2062-2064)taT>taC	p.Y688Y	RP11-93H12.4_ENST00000474115.2_RNA|GRID1_ENST00000536331.1_Silent_p.Y259Y|RN7SKP238_ENST00000516483.1_RNA	NM_017551.2	NP_060021.1	Q9ULK0	GRID1_HUMAN	glutamate receptor, ionotropic, delta 1	688					ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|social behavior (GO:0035176)|synaptic transmission, glutamatergic (GO:0035249)	cell junction (GO:0030054)|dendrite (GO:0030425)|extracellular vesicular exosome (GO:0070062)|ionotropic glutamate receptor complex (GO:0008328)|postsynaptic membrane (GO:0045211)	extracellular-glutamate-gated ion channel activity (GO:0005234)|ionotropic glutamate receptor activity (GO:0004970)	p.Y688Y(1)		NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(24)|lung(46)|ovary(5)|prostate(4)|skin(5)|stomach(4)|upper_aerodigestive_tract(5)	106						GGAAGTACTCATATACAGCAG	0.542										Multiple Myeloma(13;0.14)																											p.Y688Y												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.T2064C	10						.						277.0	258.0	264.0					10																	87407088		2203	4300	6503	87397068	SO:0001819	synonymous_variant	2894	exon13			AB033046	CCDS31236.1	10q22	2012-08-29			ENSG00000182771	ENSG00000182771		"""Ligand-gated ion channels / Glutamate receptors, ionotropic"", ""Glutamate receptors"""	4575	protein-coding gene	gene with protein product		610659					Standard	NM_017551		Approved	GluD1, KIAA1220	uc001kdl.1	Q9ULK0	OTTHUMG00000018650	ENST00000327946.7:c.2064T>C	10.37:g.87407088A>G		Somatic		Capture	Illumina HiSeq	Phase_I	87397068	NM_017551	B3KXD5|B7Z7L0|Q8IXT3	Silent	SNP	ENST00000327946.7	37	CCDS31236.1																																																																																				0.542	GRID1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049148.3	XM_043613	
LIPN	643418	broad.mit.edu	37	10	90534233	90534233	+	Nonsense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr10:90534233C>T	ENST00000404459.1	+	7	823	c.823C>T	c.(823-825)Cga>Tga	p.R275*		NM_001102469.1	NP_001095939.1	Q5VXI9	LIPN_HUMAN	lipase, family member N	275					lipid catabolic process (GO:0016042)	extracellular region (GO:0005576)	hydrolase activity, acting on ester bonds (GO:0016788)	p.R275*(1)		endometrium(1)|kidney(1)|large_intestine(5)|lung(1)|skin(1)	9		Colorectal(252;0.0161)		Colorectal(12;4.83e-05)|COAD - Colon adenocarcinoma(12;6.5e-05)		CCTTTAGAGTCGAATGGATGT	0.368																																					p.R275X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.C823T	10						.						113.0	107.0	109.0					10																	90534233		1849	4090	5939	90524213	SO:0001587	stop_gained	643418	exon7				CCDS44456.1	10q23.31	2013-09-20	2007-02-27	2007-02-27	ENSG00000204020	ENSG00000204020			23452	protein-coding gene	gene with protein product		613924	"""lipase-like, ab-hydrolase domain containing 4"""	LIPL4			Standard	NM_001102469		Approved	bA186O14.3	uc010qmw.2	Q5VXI9	OTTHUMG00000018694	ENST00000404459.1:c.823C>T	10.37:g.90534233C>T	ENSP00000383923:p.Arg275*	Somatic		Capture	Illumina HiSeq	Phase_I	90524213	NM_001102469	A7KIH9	Nonsense_Mutation	SNP	ENST00000404459.1	37	CCDS44456.1	.	.	.	.	.	.	.	.	.	.	C	35	5.527738	0.96446	.	.	ENSG00000204020	ENST00000404459	.	.	.	5.17	5.17	0.71159	.	0.000000	0.45606	D	0.000357	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-5.8453	15.6938	0.77477	0.0:1.0:0.0:0.0	.	.	.	.	X	275	.	ENSP00000383923:R275X	R	+	1	2	LIPN	90524213	1.000000	0.71417	1.000000	0.80357	0.971000	0.66376	3.343000	0.52167	2.695000	0.91970	0.561000	0.74099	CGA		0.368	LIPN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049254.2	XM_926751	
LIPN	643418	broad.mit.edu	37	10	90537809	90537809	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr10:90537809C>T	ENST00000404459.1	+	9	1007	c.1007C>T	c.(1006-1008)aCt>aTt	p.T336I		NM_001102469.1	NP_001095939.1	Q5VXI9	LIPN_HUMAN	lipase, family member N	336					lipid catabolic process (GO:0016042)	extracellular region (GO:0005576)	hydrolase activity, acting on ester bonds (GO:0016788)	p.T336I(1)		endometrium(1)|kidney(1)|large_intestine(5)|lung(1)|skin(1)	9		Colorectal(252;0.0161)		Colorectal(12;4.83e-05)|COAD - Colon adenocarcinoma(12;6.5e-05)		AAAGTGCCTACTGCTATTTGG	0.473																																					p.T336I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1007T	10						.						150.0	140.0	143.0					10																	90537809		1993	4154	6147	90527789	SO:0001583	missense	643418	exon9				CCDS44456.1	10q23.31	2013-09-20	2007-02-27	2007-02-27	ENSG00000204020	ENSG00000204020			23452	protein-coding gene	gene with protein product		613924	"""lipase-like, ab-hydrolase domain containing 4"""	LIPL4			Standard	NM_001102469		Approved	bA186O14.3	uc010qmw.2	Q5VXI9	OTTHUMG00000018694	ENST00000404459.1:c.1007C>T	10.37:g.90537809C>T	ENSP00000383923:p.Thr336Ile	Somatic		Capture	Illumina HiSeq	Phase_I	90527789	NM_001102469	A7KIH9	Missense_Mutation	SNP	ENST00000404459.1	37	CCDS44456.1	.	.	.	.	.	.	.	.	.	.	C	20.8	4.047746	0.75846	.	.	ENSG00000204020	ENST00000404459	T	0.71103	-0.54	5.2	5.2	0.72013	Alpha/beta hydrolase fold-1 (1);	0.092327	0.47852	D	0.000212	T	0.71508	0.3348	L	0.31526	0.94	0.41580	D	0.988736	P	0.49447	0.924	P	0.60415	0.874	T	0.62704	-0.6798	10	0.06625	T	0.88	-27.5884	18.0184	0.89248	0.0:1.0:0.0:0.0	.	336	Q5VXI9	LIPN_HUMAN	I	336	ENSP00000383923:T336I	ENSP00000383923:T336I	T	+	2	0	LIPN	90527789	0.999000	0.42202	1.000000	0.80357	0.998000	0.95712	2.090000	0.41682	2.867000	0.98391	0.637000	0.83480	ACT		0.473	LIPN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049254.2	XM_926751	
HECTD2	143279	broad.mit.edu	37	10	93252213	93252213	+	Silent	SNP	A	A	G			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr10:93252213A>G	ENST00000298068.5	+	13	1498	c.1404A>G	c.(1402-1404)ctA>ctG	p.L468L	HECTD2_ENST00000371667.1_Silent_p.L118L|HECTD2_ENST00000536715.1_Silent_p.L57L|HECTD2_ENST00000446394.1_Silent_p.L472L	NM_182765.3	NP_877497	Q5U5R9	HECD2_HUMAN	HECT domain containing E3 ubiquitin protein ligase 2	468	HECT. {ECO:0000255|PROSITE- ProRule:PRU00104}.				protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)	p.L468L(1)		breast(2)|endometrium(2)|kidney(4)|large_intestine(10)|lung(7)|skin(1)|urinary_tract(1)	27						TCCTTCTTCTAATTCGCCAAA	0.338																																					p.L468L	NSCLC(12;376 469 1699 39910 41417)											.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.A1404G	10						.						108.0	107.0	107.0					10																	93252213		2203	4299	6502	93242193	SO:0001819	synonymous_variant	143279	exon13			AK094625	CCDS7414.1, CCDS7415.1, CCDS60591.1	10q23.32	2013-09-20	2012-02-23		ENSG00000165338	ENSG00000165338			26736	protein-coding gene	gene with protein product			"""HECT domain containing 2"""			8619474, 9110174	Standard	NM_001284274		Approved	FLJ37306	uc001khl.2	Q5U5R9	OTTHUMG00000018742	ENST00000298068.5:c.1404A>G	10.37:g.93252213A>G		Somatic		Capture	Illumina HiSeq	Phase_I	93242193	NM_182765	Q5VZ97|Q5VZ98|Q5VZ99|Q8N1X7|Q8TCP5	Silent	SNP	ENST00000298068.5	37	CCDS7414.1																																																																																				0.338	HECTD2-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098620.1		
SORBS1	10580	broad.mit.edu	37	10	97192278	97192278	+	Silent	SNP	C	C	T	rs148085304	byFrequency	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr10:97192278C>T	ENST00000361941.3	-	4	254	c.228G>A	c.(226-228)tcG>tcA	p.S76S	SORBS1_ENST00000474353.2_5'UTR|SORBS1_ENST00000371241.1_Silent_p.S44S|SORBS1_ENST00000371239.1_Silent_p.S44S|SORBS1_ENST00000354106.3_Silent_p.S76S|SORBS1_ENST00000353505.5_Silent_p.S76S|SORBS1_ENST00000371249.2_Silent_p.S44S|SORBS1_ENST00000371245.3_Silent_p.S76S|SORBS1_ENST00000371247.2_Silent_p.S76S|SORBS1_ENST00000607232.1_Silent_p.S44S|SORBS1_ENST00000371246.2_Silent_p.S76S|SORBS1_ENST00000277982.5_Silent_p.S76S|SORBS1_ENST00000371227.4_Silent_p.S76S|SORBS1_ENST00000393949.1_Silent_p.S76S|SORBS1_ENST00000347291.4_Silent_p.S76S|SORBS1_ENST00000306402.6_Silent_p.S76S	NM_001034954.1	NP_001030126			sorbin and SH3 domain containing 1									p.S76S(2)		NS(1)|breast(3)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(7)|lung(19)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	42		Colorectal(252;0.0429)		Epithelial(162;1.7e-06)|all cancers(201;6.52e-05)		TGTAGGAAGACGAGGCCCGGA	0.527													C|||	3	0.000599042	0.0023	0.0	5008	,	,		17990	0.0		0.0	False		,,,				2504	0.0				p.S44S												.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.G132A	10						.	C	,,,,,,	5,4401	9.9+/-24.2	0,5,2198	98.0	101.0	100.0		228,228,228,132,132,132,228	-11.5	0.2	10	dbSNP_134	100	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	SORBS1	NM_001034954.1,NM_001034955.1,NM_001034956.1,NM_001034957.1,NM_006434.2,NM_015385.2,NM_024991.1	,,,,,,	0,5,6498	TT,TC,CC		0.0,0.1135,0.0384	,,,,,,	76/1293,76/1152,76/906,44/741,44/685,44/817,76/782	97192278	5,13001	2203	4300	6503	97182268	SO:0001819	synonymous_variant	10580	exon3			AF136381	CCDS7442.1, CCDS31252.1, CCDS31253.1, CCDS31254.1, CCDS31255.1, CCDS31256.1, CCDS73169.1	10q23.33	2011-07-25	2002-05-08		ENSG00000095637	ENSG00000095637			14565	protein-coding gene	gene with protein product	"""c-Cbl-associated protein"""	605264	"""SH3-domain protein 5 (ponsin)"""	SH3D5		10085297, 11001060	Standard	XM_005269405		Approved	FLJ12406, CAP, sh3p12, ponsin, KIAA1296	uc001kkp.3	Q9BX66	OTTHUMG00000018812	ENST00000361941.3:c.228G>A	10.37:g.97192278C>T		Somatic		Capture	Illumina HiSeq	Phase_I	97182268	NM_001034957		Silent	SNP	ENST00000361941.3	37	CCDS31255.1																																																																																				0.527	SORBS1-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000049517.1		
ALDH18A1	5832	broad.mit.edu	37	10	97366614	97366614	+	Nonsense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr10:97366614G>A	ENST00000371224.2	-	18	2430	c.2293C>T	c.(2293-2295)Cga>Tga	p.R765*	ALDH18A1_ENST00000371221.3_Nonsense_Mutation_p.R763*	NM_002860.3	NP_002851.2	P54886	P5CS_HUMAN	aldehyde dehydrogenase 18 family, member A1	765	Gamma-glutamyl phosphate reductase.				cellular amino acid biosynthetic process (GO:0008652)|cellular nitrogen compound metabolic process (GO:0034641)|citrulline biosynthetic process (GO:0019240)|glutamate metabolic process (GO:0006536)|L-proline biosynthetic process (GO:0055129)|ornithine biosynthetic process (GO:0006592)|proline biosynthetic process (GO:0006561)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|glutamate 5-kinase activity (GO:0004349)|glutamate-5-semialdehyde dehydrogenase activity (GO:0004350)|poly(A) RNA binding (GO:0044822)	p.R765*(1)		central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(7)|lung(9)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	28		Colorectal(252;0.0402)		Epithelial(162;9.1e-07)|all cancers(201;2.55e-05)		TCCTTCCCTCGCAGCAGCCAC	0.478																																					p.R763X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.C2287T	10						.						159.0	160.0	160.0					10																	97366614		2203	4300	6503	97356604	SO:0001587	stop_gained	5832	exon18			X94453	CCDS7443.1, CCDS31257.1	10q24.3-q24.6	2004-08-12	2004-08-12	2004-08-12	ENSG00000059573	ENSG00000059573		"""Aldehyde dehydrogenases"""	9722	protein-coding gene	gene with protein product		138250	"""pyrroline-5-carboxylate synthetase (glutamate gamma-semialdehyde synthetase)"""	GSAS, PYCS		8921385	Standard	XM_006717933		Approved	P5CS	uc001kkz.3	P54886	OTTHUMG00000018815	ENST00000371224.2:c.2293C>T	10.37:g.97366614G>A	ENSP00000360268:p.Arg765*	Somatic		Capture	Illumina HiSeq	Phase_I	97356604	NM_001017423	B2R5Q4|B7Z350|B7Z5X8|B7ZLP1|D3DR44|O95952|Q3KQU2|Q5T566|Q5T567|Q9UM72	Nonsense_Mutation	SNP	ENST00000371224.2	37	CCDS7443.1	.	.	.	.	.	.	.	.	.	.	G	38	7.038565	0.98021	.	.	ENSG00000059573	ENST00000371224;ENST00000371221	.	.	.	5.28	4.28	0.50868	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-6.1078	11.9245	0.52812	0.0:0.0:0.7484:0.2516	.	.	.	.	X	765;763	.	ENSP00000360265:R763X	R	-	1	2	ALDH18A1	97356604	1.000000	0.71417	0.998000	0.56505	0.988000	0.76386	3.040000	0.49799	2.479000	0.83701	0.561000	0.74099	CGA		0.478	ALDH18A1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000049552.1	NM_002860	
SLIT1	6585	broad.mit.edu	37	10	98823276	98823276	+	Silent	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr10:98823276C>T	ENST00000266058.4	-	8	974	c.729G>A	c.(727-729)tcG>tcA	p.S243S	SLIT1_ENST00000371070.4_Silent_p.S243S|ARHGAP19-SLIT1_ENST00000453547.2_3'UTR|SLIT1_ENST00000371041.3_Silent_p.S243S	NM_003061.2	NP_003052.2	O75093	SLIT1_HUMAN	slit homolog 1 (Drosophila)	243	LRRCT 1.				axon extension involved in axon guidance (GO:0048846)|axon guidance (GO:0007411)|dorsal/ventral axon guidance (GO:0033563)|establishment of nucleus localization (GO:0040023)|forebrain morphogenesis (GO:0048853)|motor neuron axon guidance (GO:0008045)|negative chemotaxis (GO:0050919)|negative regulation of axon extension involved in axon guidance (GO:0048843)|negative regulation of synapse assembly (GO:0051964)|retinal ganglion cell axon guidance (GO:0031290)|spinal cord development (GO:0021510)|tangential migration from the subventricular zone to the olfactory bulb (GO:0022028)	extracellular space (GO:0005615)	calcium ion binding (GO:0005509)|Roundabout binding (GO:0048495)	p.S243S(1)		breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(16)|lung(37)|ovary(5)|prostate(4)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	78		Colorectal(252;0.162)		Epithelial(162;2.02e-08)|all cancers(201;1.5e-06)		TGGCTGGGCCCGAGCACTGGG	0.657																																					p.S243S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G729A	10						.						23.0	25.0	24.0					10																	98823276		2203	4299	6502	98813266	SO:0001819	synonymous_variant	6585	exon8			AB011537	CCDS7453.1	10q23.3-q24	2008-08-01	2001-11-28		ENSG00000187122	ENSG00000187122			11085	protein-coding gene	gene with protein product		603742	"""slit (Drosophila) homolog 1"""	SLIL1		9693030, 9813312	Standard	NM_003061		Approved	slit1, MEGF4, Slit-1, SLIT3	uc001kmw.2	O75093	OTTHUMG00000018843	ENST00000266058.4:c.729G>A	10.37:g.98823276C>T		Somatic		Capture	Illumina HiSeq	Phase_I	98813266	NM_003061	Q5T0V1|Q8WWZ2|Q9UIL7	Silent	SNP	ENST00000266058.4	37	CCDS7453.1																																																																																				0.657	SLIT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049636.1	NM_003061	
ZDHHC16	84287	broad.mit.edu	37	10	99216547	99216547	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr10:99216547C>T	ENST00000370854.3	+	11	1222	c.1033C>T	c.(1033-1035)Cgg>Tgg	p.R345W	ZDHHC16_ENST00000353979.3_Missense_Mutation_p.R306W|ZDHHC16_ENST00000352634.4_Missense_Mutation_p.R329W|ZDHHC16_ENST00000370846.4_Missense_Mutation_p.R275W|ZDHHC16_ENST00000393760.1_Missense_Mutation_p.R345W|ZDHHC16_ENST00000495735.1_3'UTR|ZDHHC16_ENST00000345745.5_Missense_Mutation_p.R264W|ZDHHC16_ENST00000370842.2_Missense_Mutation_p.R329W	NM_032327.2	NP_115703.2	Q969W1	ZDH16_HUMAN	zinc finger, DHHC-type containing 16	345					apoptotic process (GO:0006915)|protein palmitoylation (GO:0018345)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	palmitoyltransferase activity (GO:0016409)|protein-cysteine S-palmitoyltransferase activity (GO:0019706)|zinc ion binding (GO:0008270)	p.R345W(1)		kidney(4)|large_intestine(3)|lung(3)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	14		Colorectal(252;0.0846)		Epithelial(162;5.81e-10)|all cancers(201;4.19e-08)		CTGGCTTACTCGGGTGCTCTT	0.498																																					p.R329W												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C985T	10						.						88.0	74.0	79.0					10																	99216547		2203	4300	6503	99206537	SO:0001583	missense	84287	exon10			AF258563	CCDS7460.1, CCDS7461.1, CCDS7462.1, CCDS7463.1, CCDS73176.1	10q24.1	2008-05-02			ENSG00000171307	ENSG00000171307		"""Zinc fingers, DHHC-type"""	20714	protein-coding gene	gene with protein product						12021275	Standard	NM_198043		Approved	APH2	uc001knk.3	Q969W1	OTTHUMG00000018847	ENST00000370854.3:c.1033C>T	10.37:g.99216547C>T	ENSP00000359891:p.Arg345Trp	Somatic		Capture	Illumina HiSeq	Phase_I	99206537	NM_198043	D3DR52|D3DR53|D3DR54|Q5JTG7|Q5JTH0|Q8N4Z6|Q8WY84|Q9BSV3	Missense_Mutation	SNP	ENST00000370854.3	37	CCDS7460.1	.	.	.	.	.	.	.	.	.	.	C	15.74	2.921792	0.52653	.	.	ENSG00000171307	ENST00000370854;ENST00000393760;ENST00000370846;ENST00000352634;ENST00000353979;ENST00000370842;ENST00000345745	T;T;T;T;T;T	0.72835	0.62;0.62;-0.69;0.29;0.29;-0.1	5.93	5.93	0.95920	.	0.000000	0.85682	D	0.000000	T	0.75664	0.3880	L	0.28400	0.85	0.80722	D	1	B;B;D;B;B;B;B;B	0.89917	0.122;0.027;1.0;0.016;0.116;0.06;0.055;0.059	B;B;D;B;B;B;B;B	0.74674	0.048;0.006;0.984;0.003;0.052;0.022;0.022;0.016	T	0.74813	-0.3537	10	0.44086	T	0.13	-1.3641	14.7468	0.69494	0.1447:0.8553:0.0:0.0	.	327;280;275;286;306;264;329;345	B4DNL2;E9PCL9;B1AMU0;B1AMU1;Q969W1-3;Q969W1-4;Q969W1-2;Q969W1	.;.;.;.;.;.;.;ZDH16_HUMAN	W	345;345;275;329;306;329;264	ENSP00000359891:R345W;ENSP00000377357:R345W;ENSP00000359883:R275W;ENSP00000345383:R329W;ENSP00000359879:R329W;ENSP00000304487:R264W	ENSP00000304487:R264W	R	+	1	2	ZDHHC16	99206537	0.997000	0.39634	1.000000	0.80357	0.925000	0.55904	3.616000	0.54174	2.810000	0.96702	0.655000	0.94253	CGG		0.498	ZDHHC16-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000049658.2	NM_032327	
AVPI1	60370	broad.mit.edu	37	10	99439502	99439502	+	Missense_Mutation	SNP	C	C	T	rs554930916		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr10:99439502C>T	ENST00000370626.3	-	2	728	c.161G>A	c.(160-162)cGg>cAg	p.R54Q		NM_021732.2	NP_068378.2	Q5T686	AVPI1_HUMAN	arginine vasopressin-induced 1	54					activation of MAPK activity (GO:0000187)|cell cycle (GO:0007049)			p.R54Q(1)		breast(1)|endometrium(1)|large_intestine(2)|skin(1)	5		Colorectal(252;0.162)		Epithelial(162;8.37e-11)|all cancers(201;7.94e-09)		GATCTGTGCCCGTTCCTCGGC	0.662													C|||	1	0.000199681	0.0008	0.0	5008	,	,		17905	0.0		0.0	False		,,,				2504	0.0				p.R54Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G161A	10						.						45.0	33.0	37.0					10																	99439502		2203	4300	6503	99429492	SO:0001583	missense	60370	exon2			AF131791	CCDS7470.1	10q24.2	2004-04-05			ENSG00000119986	ENSG00000119986			30898	protein-coding gene	gene with protein product						8619474, 9110174	Standard	NM_021732		Approved	VIP32, PP5395, VIT32	uc001koi.2	Q5T686	OTTHUMG00000018864	ENST00000370626.3:c.161G>A	10.37:g.99439502C>T	ENSP00000359660:p.Arg54Gln	Somatic		Capture	Illumina HiSeq	Phase_I	99429492	NM_021732	Q53G32|Q9H2R9|Q9HBN9	Missense_Mutation	SNP	ENST00000370626.3	37	CCDS7470.1	.	.	.	.	.	.	.	.	.	.	C	21.1	4.092418	0.76756	.	.	ENSG00000119986	ENST00000370626	T	0.60171	0.21	5.09	5.09	0.68999	.	.	.	.	.	T	0.71443	0.3340	L	0.61218	1.895	0.46260	D	0.998952	D	0.76494	0.999	P	0.61477	0.889	T	0.73161	-0.4070	9	0.56958	D	0.05	0.0	17.4239	0.87521	0.0:1.0:0.0:0.0	.	54	Q5T686	AVPI1_HUMAN	Q	54	ENSP00000359660:R54Q	ENSP00000359660:R54Q	R	-	2	0	AVPI1	99429492	0.998000	0.40836	0.635000	0.29338	0.990000	0.78478	5.507000	0.66999	2.637000	0.89404	0.561000	0.74099	CGG		0.662	AVPI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049736.1	NM_021732	
PRAP1	118471	broad.mit.edu	37	10	135165619	135165619	+	Silent	SNP	T	T	C			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr10:135165619T>C	ENST00000433452.2	+	4	509	c.237T>C	c.(235-237)ggT>ggC	p.G79G	ZNF511_ENST00000368554.4_Silent_p.G238G|RP11-122K13.7_ENST00000452591.1_RNA|PRAP1_ENST00000458230.1_Splice_Site|PRAP1_ENST00000423766.1_Silent_p.G80G|PRAP1_ENST00000463201.1_Splice_Site			Q96NZ9	PRAP1_HUMAN	proline-rich acidic protein 1	79						extracellular region (GO:0005576)		p.G79G(1)		large_intestine(1)|lung(2)	3		all_cancers(35;7.01e-07)|all_epithelial(44;1.45e-05)|Lung NSC(174;0.027)|all_lung(145;0.0384)|all_neural(114;0.0726)|Glioma(114;0.172)|Melanoma(40;0.175)		all cancers(32;7.08e-06)|OV - Ovarian serous cystadenocarcinoma(35;7.88e-06)|Epithelial(32;9.48e-06)		AGCCACGAGGTCAGGGCAGGG	0.627																																					p.G79G												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.T237C	10						.						68.0	69.0	69.0					10																	135165619		2203	4300	6503	135015609	SO:0001819	synonymous_variant	118471	exon4			AF421885	CCDS7679.1	10q26.3	2012-10-01			ENSG00000165828	ENSG00000165828			23304	protein-coding gene	gene with protein product		609776				14583459, 20674898	Standard	NM_001145201		Approved	UPA		Q96NZ9	OTTHUMG00000019312	ENST00000433452.2:c.237T>C	10.37:g.135165619T>C		Somatic		Capture	Illumina HiSeq	Phase_I	135015609	NM_145202	B7ZL57|B7ZL58|E9KL31|Q5VWY4|Q7Z4X5|Q8IWR3|Q8NCS2	Splice_Site	SNP	ENST00000433452.2	37	CCDS7679.1	.	.	.	.	.	.	.	.	.	.	t	6.779	0.512682	0.12944	.	.	ENSG00000165828	ENST00000458230;ENST00000415747	.	.	.	3.15	2.0	0.26442	.	.	.	.	.	.	.	.	.	.	.	0.09310	N	0.999997	.	.	.	.	.	.	.	.	.	.	.	.	.	.	5.2175	0.15350	0.0:0.1357:0.0:0.8643	.	.	.	.	.	-1	.	.	.	+	.	.	PRAP1	135015609	0.057000	0.20700	0.006000	0.13384	0.011000	0.07611	1.396000	0.34531	0.590000	0.29694	0.529000	0.55759	.		0.627	PRAP1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000051132.1	NM_145202	
TRPC6	7225	broad.mit.edu	37	11	101375176	101375176	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr11:101375176C>T	ENST00000344327.3	-	2	948	c.524G>A	c.(523-525)cGg>cAg	p.R175Q	TRPC6_ENST00000526713.1_5'Flank|TRPC6_ENST00000360497.4_Missense_Mutation_p.R175Q|TRPC6_ENST00000532133.1_Missense_Mutation_p.R175Q|TRPC6_ENST00000348423.4_Missense_Mutation_p.R175Q	NM_004621.5	NP_004612.2	Q9Y210	TRPC6_HUMAN	transient receptor potential cation channel, subfamily C, member 6	175					aging (GO:0007568)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|calcium ion transmembrane transport (GO:0070588)|cation transport (GO:0006812)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to hypoxia (GO:0071456)|ion transmembrane transport (GO:0034220)|platelet activation (GO:0030168)|positive regulation of calcium ion transport (GO:0051928)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of ion transmembrane transporter activity (GO:0032414)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|slit diaphragm (GO:0036057)	inositol 1,4,5 trisphosphate binding (GO:0070679)|store-operated calcium channel activity (GO:0015279)	p.R175Q(1)		autonomic_ganglia(1)|breast(3)|central_nervous_system(2)|endometrium(3)|kidney(3)|large_intestine(14)|lung(17)|ovary(2)|pancreas(1)|prostate(1)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	55		Acute lymphoblastic leukemia(157;0.000918)|all_hematologic(158;0.0162)		BRCA - Breast invasive adenocarcinoma(274;0.0442)		TTCCACAATCCGAACATAACC	0.443																																					p.R175Q	Colon(166;1315 1927 11094 12848 34731)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G524A	11						.						76.0	74.0	75.0					11																	101375176		2203	4299	6502	100880386	SO:0001583	missense	7225	exon2			AJ006276	CCDS8311.1	11q22.1	2014-02-04				ENSG00000137672		"""Voltage-gated ion channels / Transient receptor potential cation channels"""	12338	protein-coding gene	gene with protein product		603652	"""focal segmental glomerulosclerosis 2"""	FSGS2		9925922, 16382100, 15879175	Standard	NM_004621		Approved	TRP6	uc001pgk.4	Q9Y210		ENST00000344327.3:c.524G>A	11.37:g.101375176C>T	ENSP00000340913:p.Arg175Gln	Somatic		Capture	Illumina HiSeq	Phase_I	100880386	NM_004621	Q52M59|Q9HCW3|Q9NQA8|Q9NQA9	Missense_Mutation	SNP	ENST00000344327.3	37	CCDS8311.1	.	.	.	.	.	.	.	.	.	.	C	32	5.137646	0.94517	.	.	ENSG00000137672	ENST00000344327;ENST00000532133;ENST00000348423;ENST00000360497	T;T;T;T	0.64260	-0.09;-0.09;-0.09;-0.09	5.84	5.84	0.93424	Ankyrin repeat-containing domain (3);	0.000000	0.85682	D	0.000000	T	0.70561	0.3238	N	0.20986	0.625	0.80722	D	1	D;D;D	0.89917	1.0;0.999;1.0	D;D;D	0.91635	0.999;0.997;0.999	T	0.71784	-0.4488	10	0.52906	T	0.07	-15.2306	20.1438	0.98071	0.0:1.0:0.0:0.0	.	175;175;175	Q9Y210-3;Q9Y210-2;Q9Y210	.;.;TRPC6_HUMAN	Q	175	ENSP00000340913:R175Q;ENSP00000435574:R175Q;ENSP00000343672:R175Q;ENSP00000353687:R175Q	ENSP00000340913:R175Q	R	-	2	0	TRPC6	100880386	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	7.818000	0.86416	2.768000	0.95171	0.650000	0.86243	CGG		0.443	TRPC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394770.1	NM_004621	
DYNC2H1	79659	broad.mit.edu	37	11	102985923	102985923	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr11:102985923G>A	ENST00000375735.2	+	4	664	c.520G>A	c.(520-522)Gat>Aat	p.D174N	DYNC2H1_ENST00000398093.3_Missense_Mutation_p.D174N|DYNC2H1_ENST00000334267.7_Missense_Mutation_p.D174N	NM_001080463.1|NM_001377.2	NP_001073932.1|NP_001368.2	Q8NCM8	DYHC2_HUMAN	dynein, cytoplasmic 2, heavy chain 1	174	Stem. {ECO:0000250}.			D -> G (in Ref. 1; BAE17138). {ECO:0000305}.	antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|asymmetric protein localization (GO:0008105)|cilium assembly (GO:0042384)|determination of left/right symmetry (GO:0007368)|dorsal/ventral pattern formation (GO:0009953)|embryonic limb morphogenesis (GO:0030326)|forebrain development (GO:0030900)|Golgi organization (GO:0007030)|intraciliary retrograde transport (GO:0035721)|positive regulation of smoothened signaling pathway (GO:0045880)|protein processing (GO:0016485)|spinal cord motor neuron differentiation (GO:0021522)	apical part of cell (GO:0045177)|axoneme (GO:0005930)|cytosol (GO:0005829)|dynein complex (GO:0030286)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|motile primary cilium (GO:0031512)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|motor activity (GO:0003774)	p.D174N(1)		NS(1)|endometrium(4)|kidney(5)|large_intestine(9)|lung(9)|ovary(1)|prostate(2)|upper_aerodigestive_tract(2)	33		Acute lymphoblastic leukemia(157;0.000966)|all_hematologic(158;0.00348)		BRCA - Breast invasive adenocarcinoma(274;0.000177)|Epithelial(105;0.0785)		TACACCAAGCGATGAGTTCCA	0.323																																					p.D174N												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G520A	11						.						62.0	52.0	55.0					11																	102985923		1812	4070	5882	102491133	SO:0001583	missense	79659	exon4			AB082528	CCDS44717.1, CCDS53701.1	11q21-q22.1	2011-06-02	2005-11-24	2005-11-24	ENSG00000187240	ENSG00000187240		"""Cytoplasmic dyneins"""	2962	protein-coding gene	gene with protein product		603297	"""dynein, cytoplasmic, heavy polypeptide 2"""	DNCH2		9763680, 9373155	Standard	NM_001080463		Approved	hdhc11, DHC2, DHC1b, DYH1B	uc001phn.1	Q8NCM8	OTTHUMG00000165941	ENST00000375735.2:c.520G>A	11.37:g.102985923G>A	ENSP00000364887:p.Asp174Asn	Somatic		Capture	Illumina HiSeq	Phase_I	102491133	NM_001377	O00432|Q16693|Q3C1U8|Q4AC93|Q6ZMX7|Q6ZUM6|Q7Z363|Q8N977|Q92815|Q9HAE4	Missense_Mutation	SNP	ENST00000375735.2	37	CCDS53701.1	.	.	.	.	.	.	.	.	.	.	G	23.4	4.410138	0.83340	.	.	ENSG00000187240	ENST00000375735;ENST00000334267;ENST00000398093	T;T;T	0.59638	1.18;0.25;1.18	5.28	5.28	0.74379	.	0.279169	0.27478	U	0.019197	T	0.78666	0.4319	M	0.81497	2.545	0.58432	D	0.999999	D;D;D	0.89917	1.0;0.991;0.997	D;P;P	0.87578	0.998;0.754;0.842	T	0.81653	-0.0835	10	0.87932	D	0	.	18.9329	0.92574	0.0:0.0:1.0:0.0	.	174;174;174	Q8NCM8-3;Q8NCM8;Q8NCM8-2	.;DYHC2_HUMAN;.	N	174	ENSP00000364887:D174N;ENSP00000334021:D174N;ENSP00000381167:D174N	ENSP00000334021:D174N	D	+	1	0	DYNC2H1	102491133	1.000000	0.71417	1.000000	0.80357	0.623000	0.37688	8.909000	0.92647	2.465000	0.83290	0.655000	0.94253	GAT		0.323	DYNC2H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387196.1	XM_370652	
DYNC2H1	79659	broad.mit.edu	37	11	103070177	103070177	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr11:103070177T>C	ENST00000375735.2	+	49	8204	c.8060T>C	c.(8059-8061)cTg>cCg	p.L2687P	DYNC2H1_ENST00000398093.3_Missense_Mutation_p.L2687P|DYNC2H1_ENST00000334267.7_Intron	NM_001080463.1|NM_001377.2	NP_001073932.1|NP_001368.2	Q8NCM8	DYHC2_HUMAN	dynein, cytoplasmic 2, heavy chain 1	2687	AAA 4. {ECO:0000250}.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|asymmetric protein localization (GO:0008105)|cilium assembly (GO:0042384)|determination of left/right symmetry (GO:0007368)|dorsal/ventral pattern formation (GO:0009953)|embryonic limb morphogenesis (GO:0030326)|forebrain development (GO:0030900)|Golgi organization (GO:0007030)|intraciliary retrograde transport (GO:0035721)|positive regulation of smoothened signaling pathway (GO:0045880)|protein processing (GO:0016485)|spinal cord motor neuron differentiation (GO:0021522)	apical part of cell (GO:0045177)|axoneme (GO:0005930)|cytosol (GO:0005829)|dynein complex (GO:0030286)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|motile primary cilium (GO:0031512)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|motor activity (GO:0003774)	p.L120P(1)		NS(1)|endometrium(4)|kidney(5)|large_intestine(9)|lung(9)|ovary(1)|prostate(2)|upper_aerodigestive_tract(2)	33		Acute lymphoblastic leukemia(157;0.000966)|all_hematologic(158;0.00348)		BRCA - Breast invasive adenocarcinoma(274;0.000177)|Epithelial(105;0.0785)		GGATATGAACTGAAGCAGTTC	0.403																																					p.L2687P												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T8060C	11						.						87.0	78.0	80.0					11																	103070177		1871	4117	5988	102575387	SO:0001583	missense	79659	exon49			AB082528	CCDS44717.1, CCDS53701.1	11q21-q22.1	2011-06-02	2005-11-24	2005-11-24	ENSG00000187240	ENSG00000187240		"""Cytoplasmic dyneins"""	2962	protein-coding gene	gene with protein product		603297	"""dynein, cytoplasmic, heavy polypeptide 2"""	DNCH2		9763680, 9373155	Standard	NM_001080463		Approved	hdhc11, DHC2, DHC1b, DYH1B	uc001phn.1	Q8NCM8	OTTHUMG00000165941	ENST00000375735.2:c.8060T>C	11.37:g.103070177T>C	ENSP00000364887:p.Leu2687Pro	Somatic		Capture	Illumina HiSeq	Phase_I	102575387	NM_001377	O00432|Q16693|Q3C1U8|Q4AC93|Q6ZMX7|Q6ZUM6|Q7Z363|Q8N977|Q92815|Q9HAE4	Missense_Mutation	SNP	ENST00000375735.2	37	CCDS53701.1	.	.	.	.	.	.	.	.	.	.	T	13.38	2.221420	0.39300	.	.	ENSG00000187240	ENST00000375735;ENST00000398093	T;T	0.49139	0.79;0.79	6.17	4.85	0.62838	Dynein heavy chain, P-loop containing D4 domain (1);	0.119241	0.35124	N	0.003433	T	0.46151	0.1378	M	0.76433	2.335	0.80722	D	1	B;B	0.13594	0.008;0.007	B;B	0.14578	0.011;0.007	T	0.34378	-0.9831	10	0.23891	T	0.37	.	10.2715	0.43485	0.0:0.0973:0.0:0.9027	.	2687;2687	Q8NCM8;Q8NCM8-2	DYHC2_HUMAN;.	P	2687	ENSP00000364887:L2687P;ENSP00000381167:L2687P	ENSP00000364887:L2687P	L	+	2	0	DYNC2H1	102575387	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.076000	0.64413	0.948000	0.37687	0.533000	0.62120	CTG		0.403	DYNC2H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387196.1	XM_370652	
DDI1	414301	broad.mit.edu	37	11	103908374	103908374	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr11:103908374G>A	ENST00000302259.3	+	1	1067	c.824G>A	c.(823-825)cGa>cAa	p.R275Q	PDGFD_ENST00000393158.2_Intron|PDGFD_ENST00000302251.5_Intron	NM_001001711.2	NP_001001711.1	Q8WTU0	DDI1_HUMAN	DNA-damage inducible 1 homolog 1 (S. cerevisiae)	275							aspartic-type endopeptidase activity (GO:0004190)	p.R275Q(4)		central_nervous_system(1)|endometrium(4)|kidney(4)|large_intestine(12)|liver(2)|lung(21)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	52		Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.00648)|Melanoma(852;0.055)|all_neural(303;0.164)		BRCA - Breast invasive adenocarcinoma(274;0.00128)|Epithelial(105;0.0631)|all cancers(92;0.169)		TGTGCCGAGCGATGTAACATC	0.512																																					p.R275Q												.	.	4	Substitution - Missense(4)	large_intestine(4)	c.G824A	11						.						101.0	98.0	99.0					11																	103908374		2202	4299	6501	103413584	SO:0001583	missense	414301	exon1				CCDS31660.1	11q22.3	2010-05-04	2010-05-04			ENSG00000170967			18961	protein-coding gene	gene with protein product			"""DDI1, DNA-damage inducible 1, homolog 1 (S. cerevisiae)"""				Standard	NM_001001711		Approved	FLJ36017	uc001phr.2	Q8WTU0		ENST00000302259.3:c.824G>A	11.37:g.103908374G>A	ENSP00000302805:p.Arg275Gln	Somatic		Capture	Illumina HiSeq	Phase_I	103413584	NM_001001711	Q7Z4U6|Q8WTS3	Missense_Mutation	SNP	ENST00000302259.3	37	CCDS31660.1	.	.	.	.	.	.	.	.	.	.	G	13.06	2.123681	0.37436	.	.	ENSG00000170967	ENST00000302259	T	0.49432	0.78	5.21	0.265	0.15612	Peptidase aspartic (1);Peptidase aspartic, eukaryotic predicted (1);Peptidase aspartic, catalytic (1);	0.107337	0.64402	N	0.000009	T	0.58750	0.2144	M	0.69185	2.1	0.33245	D	0.557712	D	0.89917	1.0	D	0.66351	0.943	T	0.66027	-0.6025	10	0.54805	T	0.06	-10.5618	9.0383	0.36302	0.3767:0.0:0.6233:0.0	.	275	Q8WTU0	DDI1_HUMAN	Q	275	ENSP00000302805:R275Q	ENSP00000302805:R275Q	R	+	2	0	DDI1	103413584	1.000000	0.71417	0.006000	0.13384	0.004000	0.04260	5.863000	0.69568	-0.022000	0.13986	-1.578000	0.00866	CGA		0.512	DDI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387326.1	NM_001001711	
ATM	472	broad.mit.edu	37	11	108218036	108218036	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr11:108218036A>G	ENST00000452508.2	+	60	8804	c.8615A>G	c.(8614-8616)cAt>cGt	p.H2872R	C11orf65_ENST00000526725.1_Intron|ATM_ENST00000278616.4_Missense_Mutation_p.H2872R|C11orf65_ENST00000525729.1_Intron|ATM_ENST00000525178.1_3'UTR			Q13315	ATM_HUMAN	ATM serine/threonine kinase	2872	PI3K/PI4K. {ECO:0000255|PROSITE- ProRule:PRU00269}.		RH -> S (in T-prolymphocytic leukemia). {ECO:0000269|PubMed:9288106}.		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.H2872R(1)|p.R2871_H2872>S(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)	GGTGATAGACATGTACAGAAT	0.294			"""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.H2872R		yes	Rec	yes	Ataxia-telangiectasia	11	11q22.3	472	ataxia telangiectasia mutated		"""L, O"""	.	.	2	Substitution - Missense(1)|Complex - deletion inframe(1)	large_intestine(1)|haematopoietic_and_lymphoid_tissue(1)	c.A8615G	11						.						94.0	100.0	98.0					11																	108218036		2201	4295	6496	107723246	SO:0001583	missense	472	exon59	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.8615A>G	11.37:g.108218036A>G	ENSP00000388058:p.His2872Arg	Somatic		Capture	Illumina HiSeq	Phase_I	107723246	NM_000051	B2RNX5|O15429|Q12758|Q16551|Q93007|Q9NP02|Q9UCX7	Missense_Mutation	SNP	ENST00000452508.2	37	CCDS31669.1	.	.	.	.	.	.	.	.	.	.	A	24.5	4.540293	0.85917	.	.	ENSG00000149311	ENST00000278616;ENST00000452508	D;D	0.87650	-2.28;-2.28	5.52	5.52	0.82312	Protein kinase-like domain (1);Armadillo-type fold (1);Phosphatidylinositol 3/4-kinase, conserved site (1);Phosphatidylinositol 3-/4-kinase, catalytic (4);	0.000000	0.85682	D	0.000000	D	0.96408	0.8828	H	0.98849	4.35	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.98190	1.0462	10	0.87932	D	0	.	15.6511	0.77095	1.0:0.0:0.0:0.0	.	2872	Q13315	ATM_HUMAN	R	2872	ENSP00000278616:H2872R;ENSP00000388058:H2872R	ENSP00000278616:H2872R	H	+	2	0	ATM	107723246	1.000000	0.71417	0.999000	0.59377	0.981000	0.71138	8.850000	0.92190	2.090000	0.63153	0.454000	0.30748	CAT		0.294	ATM-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389938.1	NM_000051	
EXPH5	23086	broad.mit.edu	37	11	108382478	108382478	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr11:108382478T>C	ENST00000265843.4	-	6	3866	c.3756A>G	c.(3754-3756)atA>atG	p.I1252M	EXPH5_ENST00000525344.1_Missense_Mutation_p.I1245M|EXPH5_ENST00000524840.1_5'Flank|EXPH5_ENST00000443411.1_Missense_Mutation_p.I1064M|EXPH5_ENST00000428840.1_Missense_Mutation_p.I1176M	NM_015065.2	NP_055880	Q8NEV8	EXPH5_HUMAN	exophilin 5	1252					intracellular protein transport (GO:0006886)|keratinocyte development (GO:0003334)|multivesicular body sorting pathway (GO:0071985)|positive regulation of exocytosis (GO:0045921)|positive regulation of protein secretion (GO:0050714)	endosome (GO:0005768)	Rab GTPase binding (GO:0017137)	p.I1252M(1)		breast(3)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(13)|liver(1)|lung(34)|ovary(3)|pancreas(2)|prostate(2)|skin(11)|stomach(3)|upper_aerodigestive_tract(1)	91		all_cancers(61;3.99e-08)|Acute lymphoblastic leukemia(157;3.97e-05)|Melanoma(852;4.04e-05)|all_epithelial(67;0.000116)|all_hematologic(158;0.000315)|Breast(348;0.104)|all_neural(303;0.16)		Epithelial(105;8.1e-06)|BRCA - Breast invasive adenocarcinoma(274;1.22e-05)|all cancers(92;0.000129)|OV - Ovarian serous cystadenocarcinoma(223;0.11)|Colorectal(284;0.184)		GAGTGTAATATATTGAGACCA	0.353																																					p.I1252M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A3756G	11						.						62.0	62.0	62.0					11																	108382478		2201	4298	6499	107887688	SO:0001583	missense	23086	exon6				CCDS8341.1	11q22.3	2008-02-05			ENSG00000110723	ENSG00000110723			30578	protein-coding gene	gene with protein product	"""synaptotagmin-like homologue lacking C2 domains b"""	612878				9734811, 11773082	Standard	NM_015065		Approved	SLAC2-B	uc001pkk.3	Q8NEV8	OTTHUMG00000166536	ENST00000265843.4:c.3756A>G	11.37:g.108382478T>C	ENSP00000265843:p.Ile1252Met	Somatic		Capture	Illumina HiSeq	Phase_I	107887688	NM_015065	Q2KHM1|Q9Y4D6	Missense_Mutation	SNP	ENST00000265843.4	37	CCDS8341.1	.	.	.	.	.	.	.	.	.	.	T	13.88	2.370155	0.42003	.	.	ENSG00000110723	ENST00000265843;ENST00000428840;ENST00000443411;ENST00000525344;ENST00000526312;ENST00000533052	T;T;T;T;T;T	0.08807	3.63;3.55;3.41;3.63;3.45;3.05	5.85	-9.04	0.00734	.	0.512064	0.19508	N	0.112572	T	0.14830	0.0358	M	0.71581	2.175	0.20764	N	0.999856	D	0.76494	0.999	D	0.66351	0.943	T	0.00531	-1.1686	10	0.72032	D	0.01	-4.5686	5.6594	0.17660	0.1599:0.1432:0.5408:0.1561	.	1252	Q8NEV8	EXPH5_HUMAN	M	1252;1176;1064;1245;1176;1064	ENSP00000265843:I1252M;ENSP00000391966:I1176M;ENSP00000411390:I1064M;ENSP00000432546:I1245M;ENSP00000432683:I1176M;ENSP00000446434:I1064M	ENSP00000265843:I1252M	I	-	3	3	EXPH5	107887688	0.986000	0.35501	0.111000	0.21465	0.149000	0.21700	0.174000	0.16743	-1.179000	0.02737	-1.271000	0.01417	ATA		0.353	EXPH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390279.1	NM_015065	
C11orf87	399947	broad.mit.edu	37	11	109294853	109294853	+	Missense_Mutation	SNP	C	C	T	rs143230091		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr11:109294853C>T	ENST00000327419.6	+	2	897	c.494C>T	c.(493-495)cCg>cTg	p.P165L	RP11-708B6.2_ENST00000532929.1_RNA|RP11-708B6.2_ENST00000532992.1_RNA	NM_207645.3	NP_997528.2	Q6NUJ2	CK087_HUMAN	chromosome 11 open reading frame 87	165						integral component of membrane (GO:0016021)		p.P165L(1)		breast(2)|endometrium(1)|large_intestine(5)|lung(5)|ovary(2)|prostate(1)|urinary_tract(1)	17						TGTGCTCCTCCGCCTCCACCG	0.657																																					p.P165L												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C494T	11						.						39.0	41.0	40.0					11																	109294853		2200	4298	6498	108800063	SO:0001583	missense	399947	exon2			AB096240, BC035798	CCDS31672.1	11q22.3	2013-12-13	2013-12-13	2013-12-13	ENSG00000185742	ENSG00000185742			33788	protein-coding gene	gene with protein product	"""neuronal integral membrane protein 1"""					12477932	Standard	NM_207645		Approved	LOH11CR1A, LOC399947, NEURIM1	uc010rwb.2	Q6NUJ2		ENST00000327419.6:c.494C>T	11.37:g.109294853C>T	ENSP00000331581:p.Pro165Leu	Somatic		Capture	Illumina HiSeq	Phase_I	108800063	NM_207645	B4E169	Missense_Mutation	SNP	ENST00000327419.6	37	CCDS31672.1	.	.	.	.	.	.	.	.	.	.	C	12.13	1.845523	0.32606	.	.	ENSG00000185742	ENST00000327419	.	.	.	3.7	2.76	0.32466	.	0.224749	0.21668	U	0.070913	T	0.22244	0.0536	N	0.08118	0	0.46131	D	0.998888	P	0.34837	0.472	B	0.26202	0.067	T	0.05869	-1.0859	9	0.25106	T	0.35	-3.9511	10.4217	0.44354	0.1953:0.8047:0.0:0.0	.	165	Q6NUJ2	CK087_HUMAN	L	165	.	ENSP00000331581:P165L	P	+	2	0	C11orf87	108800063	0.063000	0.20901	1.000000	0.80357	0.988000	0.76386	0.640000	0.24705	1.101000	0.41535	0.655000	0.94253	CCG		0.657	C11orf87-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390403.1	NM_207645	
HTR3A	3359	broad.mit.edu	37	11	113848606	113848606	+	Missense_Mutation	SNP	G	G	A	rs143359617		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr11:113848606G>A	ENST00000504030.2	+	2	626	c.181G>A	c.(181-183)Gta>Ata	p.V61I	HTR3A_ENST00000375498.2_Missense_Mutation_p.V67I|HTR3A_ENST00000506841.2_Missense_Mutation_p.V61I|HTR3A_ENST00000299961.5_Missense_Mutation_p.V46I|HTR3A_ENST00000355556.2_Missense_Mutation_p.V67I|HTR3A_ENST00000535865.1_5'UTR			P46098	5HT3A_HUMAN	5-hydroxytryptamine (serotonin) receptor 3A, ionotropic	61					cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|cellular response to growth factor stimulus (GO:0071363)|digestion (GO:0007586)|ion transmembrane transport (GO:0034220)|response to cocaine (GO:0042220)|response to ethanol (GO:0045471)|serotonin receptor signaling pathway (GO:0007210)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|transport (GO:0006810)	axon (GO:0030424)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	receptor activity (GO:0004872)|serotonin binding (GO:0051378)|serotonin receptor activity (GO:0004993)|serotonin-activated cation-selective channel activity (GO:0005232)|voltage-gated potassium channel activity (GO:0005249)	p.V61I(1)		central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(14)|prostate(1)|skin(4)|upper_aerodigestive_tract(3)	36		all_cancers(61;2.31e-17)|all_epithelial(67;2.1e-10)|all_hematologic(158;4.64e-05)|Melanoma(852;0.000312)|Acute lymphoblastic leukemia(157;0.000967)|Breast(348;0.0101)|all_neural(223;0.0281)|Prostate(24;0.0294)|Medulloblastoma(222;0.0425)		BRCA - Breast invasive adenocarcinoma(274;2.71e-06)|Epithelial(105;2.58e-05)|all cancers(92;0.000238)|OV - Ovarian serous cystadenocarcinoma(223;0.191)	Alosetron(DB00969)|Amoxapine(DB00543)|Aripiprazole(DB01238)|Chloroprocaine(DB01161)|Cisapride(DB00604)|Clozapine(DB00363)|Dolasetron(DB00757)|Ergoloid mesylate(DB01049)|Granisetron(DB00889)|Loxapine(DB00408)|Memantine(DB01043)|Methadone(DB00333)|Metoclopramide(DB01233)|Mirtazapine(DB00370)|Olanzapine(DB00334)|Ondansetron(DB00904)|Palonosetron(DB00377)|Procaine(DB00721)|Quetiapine(DB01224)|Rocuronium(DB00728)|Tapentadol(DB06204)|Trimipramine(DB00726)|Tubocurarine(DB01199)|Ziprasidone(DB00246)	GCCAACCACCGTATCCATTGA	0.582													g|||	1	0.000199681	0.0008	0.0	5008	,	,		19815	0.0		0.0	False		,,,				2504	0.0				p.V67I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G199A	11						.	A	ILE/VAL,ILE/VAL,ILE/VAL	1,4401	2.1+/-5.4	0,1,2200	135.0	102.0	113.0		199,136,199	2.6	0.0	11	dbSNP_134	113	0,8592		0,0,4296	no	missense,missense,missense	HTR3A	NM_000869.5,NM_001161772.2,NM_213621.3	29,29,29	0,1,6496	AA,AG,GG		0.0,0.0227,0.0077	probably-damaging,probably-damaging,probably-damaging	67/485,46/464,67/517	113848606	1,12993	2201	4296	6497	113353816	SO:0001583	missense	3359	exon2			D49394	CCDS8365.1, CCDS8366.1, CCDS8365.2, CCDS8366.2, CCDS53710.1	11q23.1-q23.2	2012-05-22	2012-02-03					"""5-HT (serotonin) receptors"", ""Ligand-gated ion channels / 5-HT (serotonin) receptors, ionotropic"""	5297	protein-coding gene	gene with protein product		182139	"""5-hydroxytryptamine (serotonin) receptor 3A"""	HTR3		8530095, 12867984	Standard	NM_000869		Approved	5-HT3R, 5-HT3A	uc010rxb.2	P46098		ENST00000504030.2:c.181G>A	11.37:g.113848606G>A	ENSP00000424189:p.Val61Ile	Somatic		Capture	Illumina HiSeq	Phase_I	113353816	NM_000869	B4DSY6|G5E986|O60854|Q7KZM7|Q99918|Q9BSZ9	Missense_Mutation	SNP	ENST00000504030.2	37		.	.	.	.	.	.	.	.	.	.	g	10.94	1.492271	0.26774	2.27E-4	0.0	ENSG00000166736	ENST00000504030;ENST00000355556;ENST00000375498;ENST00000506841;ENST00000299961	D;D;D;D;D	0.84873	-1.91;-1.91;-1.91;-1.91;-1.91	5.43	2.58	0.30949	.	0.202096	0.43110	N	0.000612	T	0.81884	0.4917	L	0.54908	1.71	0.80722	D	1	P;P;P	0.40834	0.593;0.489;0.73	B;B;B	0.42343	0.384;0.14;0.384	T	0.77112	-0.2708	10	0.40728	T	0.16	-13.8274	10.8722	0.46889	0.197:0.0:0.803:0.0	.	46;67;67	B4DSY6;G5E986;Q7KZM7	.;.;.	I	61;67;67;61;46	ENSP00000424189:V61I;ENSP00000347754:V67I;ENSP00000364648:V67I;ENSP00000424776:V61I;ENSP00000299961:V46I	ENSP00000299961:V46I	V	+	1	0	HTR3A	113353816	1.000000	0.71417	0.002000	0.10522	0.006000	0.05464	3.722000	0.54948	0.287000	0.22375	-0.119000	0.15052	GTA		0.582	HTR3A-001	KNOWN	upstream_ATG|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000360822.2	NM_000869	
CEP164	22897	broad.mit.edu	37	11	117265189	117265189	+	Missense_Mutation	SNP	C	C	T	rs541217768		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr11:117265189C>T	ENST00000278935.3	+	21	2887	c.2740C>T	c.(2740-2742)Cgg>Tgg	p.R914W	CEP164_ENST00000533706.1_3'UTR	NM_001271933.1|NM_014956.4	NP_001258862.1|NP_055771.4	Q9UPV0	CE164_HUMAN	centrosomal protein 164kDa	914	Glu-rich.				cilium assembly (GO:0042384)|DNA repair (GO:0006281)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)	centriole (GO:0005814)|centrosome (GO:0005813)|ciliary transition fiber (GO:0097539)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular space (GO:0005615)|nucleus (GO:0005634)		p.R914W(2)		breast(3)|central_nervous_system(1)|kidney(7)|large_intestine(12)|lung(18)|ovary(3)|prostate(3)	47	all_hematologic(175;0.0487)	Breast(348;0.00908)|Medulloblastoma(222;0.0425)|all_hematologic(192;0.196)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;4e-05)|Epithelial(105;0.0008)		TGAGGACTTGCGGCGCCGGCA	0.657																																					p.R914W												.	.	2	Substitution - Missense(2)	large_intestine(1)|prostate(1)	c.C2740T	11						.						39.0	41.0	40.0					11																	117265189		2201	4296	6497	116770399	SO:0001583	missense	22897	exon21			AB028975	CCDS31683.1	11q23.3	2014-02-20			ENSG00000110274	ENSG00000110274			29182	protein-coding gene	gene with protein product		614848				10470851, 14654843	Standard	NM_014956		Approved	KIAA1052, NPHP15	uc001prc.3	Q9UPV0	OTTHUMG00000167070	ENST00000278935.3:c.2740C>T	11.37:g.117265189C>T	ENSP00000278935:p.Arg914Trp	Somatic		Capture	Illumina HiSeq	Phase_I	116770399	NM_014956	Q6PKH9|Q7Z2X9|Q9NVS0|Q9UFJ6	Missense_Mutation	SNP	ENST00000278935.3	37	CCDS31683.1	.	.	.	.	.	.	.	.	.	.	C	10.80	1.452590	0.26074	.	.	ENSG00000110274	ENST00000278935;ENST00000529538;ENST00000375253	T	0.45276	0.9	4.55	0.0857	0.14443	.	0.333926	0.21625	N	0.071573	T	0.51500	0.1678	M	0.71581	2.175	0.20196	N	0.999921	B;D;B;B	0.89917	0.013;1.0;0.01;0.105	B;D;B;B	0.68483	0.005;0.958;0.003;0.027	T	0.42137	-0.9469	10	0.56958	D	0.05	-9.1608	1.7292	0.02928	0.2894:0.415:0.133:0.1626	.	888;688;914;917	E9PI34;Q9NTH6;Q9UPV0;Q9UPV0-2	.;.;CE164_HUMAN;.	W	914;888;795	ENSP00000278935:R914W	ENSP00000278935:R914W	R	+	1	2	CEP164	116770399	0.478000	0.25917	0.875000	0.34327	0.617000	0.37484	0.443000	0.21644	-0.185000	0.10550	-0.282000	0.10007	CGG		0.657	CEP164-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392893.1	NM_014956	
BCL9L	283149	broad.mit.edu	37	11	118773385	118773385	+	Missense_Mutation	SNP	G	G	A	rs368375563		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr11:118773385G>A	ENST00000334801.3	-	6	2031	c.1067C>T	c.(1066-1068)cCg>cTg	p.P356L	BCL9L_ENST00000526143.1_5'UTR	NM_182557.2	NP_872363.1	Q86UU0	BCL9L_HUMAN	B-cell CLL/lymphoma 9-like	356	Necessary for interaction with CTNNB1. {ECO:0000250}.|Pro-rich.				canonical Wnt signaling pathway (GO:0060070)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of cell morphogenesis (GO:0022604)|skeletal muscle cell differentiation (GO:0035914)|somatic stem cell maintenance (GO:0035019)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	beta-catenin binding (GO:0008013)|transcription coactivator activity (GO:0003713)	p.P356L(2)		NS(3)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(13)|lung(20)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|urinary_tract(2)	56	all_hematologic(175;0.0839)	Medulloblastoma(222;0.0425)|all_hematologic(192;0.103)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;7.66e-05)		GGTAGCCGTCGGGGTGTTAGG	0.706																																					p.P356L												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.C1067T	11						.	G	LEU/PRO	0,4400		0,0,2200	31.0	39.0	36.0		1067	3.8	1.0	11		36	1,8587	1.2+/-3.3	0,1,4293	no	missense	BCL9L	NM_182557.2	98	0,1,6493	AA,AG,GG		0.0116,0.0,0.0077	possibly-damaging	356/1500	118773385	1,12987	2200	4294	6494	118278595	SO:0001583	missense	283149	exon6			AB094091	CCDS8403.1	11q23.3	2012-06-06				ENSG00000186174			23688	protein-coding gene	gene with protein product		609004				12964048	Standard	NM_182557		Approved	DLNB11	uc001pug.3	Q86UU0		ENST00000334801.3:c.1067C>T	11.37:g.118773385G>A	ENSP00000335320:p.Pro356Leu	Somatic		Capture	Illumina HiSeq	Phase_I	118278595	NM_182557	A1A4C1|Q67FY1|Q6ZWJ0|Q6ZWK2	Missense_Mutation	SNP	ENST00000334801.3	37	CCDS8403.1	.	.	.	.	.	.	.	.	.	.	G	16.35	3.098305	0.56183	0.0	1.16E-4	ENSG00000186174	ENST00000334801;ENST00000526143;ENST00000392849;ENST00000431085	T	0.67171	-0.25	3.81	3.81	0.43845	.	0.000000	0.43747	D	0.000529	T	0.45696	0.1355	N	0.19112	0.55	0.51233	D	0.999917	B;B	0.31581	0.329;0.221	B;B	0.21360	0.034;0.015	T	0.48043	-0.9069	10	0.41790	T	0.15	-7.5494	9.679	0.40059	0.0974:0.0:0.9026:0.0	.	351;356	Q86UU0-2;Q86UU0	.;BCL9L_HUMAN	L	356;319;356;356	ENSP00000335320:P356L	ENSP00000335320:P356L	P	-	2	0	BCL9L	118278595	1.000000	0.71417	0.996000	0.52242	0.402000	0.30811	5.820000	0.69250	1.966000	0.57179	0.305000	0.20034	CCG		0.706	BCL9L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389653.1	NM_182557	
BCL9L	283149	broad.mit.edu	37	11	118773976	118773976	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr11:118773976C>T	ENST00000334801.3	-	4	1682	c.718G>A	c.(718-720)Gta>Ata	p.V240I	BCL9L_ENST00000526143.1_5'UTR	NM_182557.2	NP_872363.1	Q86UU0	BCL9L_HUMAN	B-cell CLL/lymphoma 9-like	240					canonical Wnt signaling pathway (GO:0060070)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of cell morphogenesis (GO:0022604)|skeletal muscle cell differentiation (GO:0035914)|somatic stem cell maintenance (GO:0035019)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	beta-catenin binding (GO:0008013)|transcription coactivator activity (GO:0003713)	p.V240I(2)		NS(3)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(13)|lung(20)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|urinary_tract(2)	56	all_hematologic(175;0.0839)	Medulloblastoma(222;0.0425)|all_hematologic(192;0.103)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;7.66e-05)		AAGACATATACGAACTGCGAG	0.697																																					p.V240I												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G718A	11						.						30.0	22.0	24.0					11																	118773976		2197	4291	6488	118279186	SO:0001583	missense	283149	exon4			AB094091	CCDS8403.1	11q23.3	2012-06-06				ENSG00000186174			23688	protein-coding gene	gene with protein product		609004				12964048	Standard	NM_182557		Approved	DLNB11	uc001pug.3	Q86UU0		ENST00000334801.3:c.718G>A	11.37:g.118773976C>T	ENSP00000335320:p.Val240Ile	Somatic		Capture	Illumina HiSeq	Phase_I	118279186	NM_182557	A1A4C1|Q67FY1|Q6ZWJ0|Q6ZWK2	Missense_Mutation	SNP	ENST00000334801.3	37	CCDS8403.1	.	.	.	.	.	.	.	.	.	.	C	16.94	3.261072	0.59431	.	.	ENSG00000186174	ENST00000334801;ENST00000526143;ENST00000392849;ENST00000431085	T	0.75589	-0.95	4.41	3.32	0.38043	.	0.000000	0.42172	D	0.000756	T	0.62392	0.2424	L	0.36672	1.1	0.48452	D	0.999652	P;P	0.44986	0.847;0.763	B;B	0.38755	0.281;0.146	T	0.65372	-0.6184	10	0.87932	D	0	-15.8928	10.4809	0.44693	0.0:0.8807:0.0:0.1193	.	235;240	Q86UU0-2;Q86UU0	.;BCL9L_HUMAN	I	240;203;240;240	ENSP00000335320:V240I	ENSP00000335320:V240I	V	-	1	0	BCL9L	118279186	1.000000	0.71417	0.994000	0.49952	0.844000	0.47949	4.333000	0.59285	0.971000	0.38288	0.555000	0.69702	GTA		0.697	BCL9L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389653.1	NM_182557	
PVRL1	5818	broad.mit.edu	37	11	119535465	119535465	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr11:119535465A>G	ENST00000264025.3	-	6	2076	c.1546T>C	c.(1546-1548)Tac>Cac	p.Y516H	PVRL1_ENST00000341398.2_Intron	NM_002855.4	NP_002846.3	Q15223	PVRL1_HUMAN	poliovirus receptor-related 1 (herpesvirus entry mediator C)	516					adherens junction organization (GO:0034332)|axon guidance (GO:0007411)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|desmosome organization (GO:0002934)|enamel mineralization (GO:0070166)|heterophilic cell-cell adhesion (GO:0007157)|homophilic cell adhesion (GO:0007156)|immune response (GO:0006955)|iron ion transport (GO:0006826)|lens morphogenesis in camera-type eye (GO:0002089)|regulation of synapse assembly (GO:0051963)|retina development in camera-type eye (GO:0060041)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|viral entry into host cell (GO:0046718)	adherens junction (GO:0005912)|axon (GO:0030424)|cell-cell adherens junction (GO:0005913)|extracellular region (GO:0005576)|growth cone membrane (GO:0032584)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|plasma membrane (GO:0005886)|synapse (GO:0045202)	carbohydrate binding (GO:0030246)|cell adhesion molecule binding (GO:0050839)|coreceptor activity (GO:0015026)|protein homodimerization activity (GO:0042803)|virion binding (GO:0046790)|virus receptor activity (GO:0001618)	p.Y516H(1)		breast(1)|endometrium(3)|kidney(2)|large_intestine(9)|liver(1)|lung(7)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	27		Breast(348;0.037)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;4.29e-05)		GGCTACACGTACCACTCCTTC	0.632																																					p.Y516H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T1546C	11						.						35.0	35.0	35.0					11																	119535465		2199	4294	6493	119040675	SO:0001583	missense	5818	exon6			X76400	CCDS8425.1, CCDS8426.1, CCDS8427.1	11q23-q24	2013-01-29	2007-06-07		ENSG00000110400	ENSG00000110400		"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	9706	protein-coding gene	gene with protein product	"""nectin"""	600644		HVEC, ED4		7721102, 9616127	Standard	NM_203285		Approved	PRR, PRR1, PVRR1, SK-12, HIgR, CLPED1, CD111, OFC7	uc001pwv.3	Q15223	OTTHUMG00000166177	ENST00000264025.3:c.1546T>C	11.37:g.119535465A>G	ENSP00000264025:p.Tyr516His	Somatic		Capture	Illumina HiSeq	Phase_I	119040675	NM_002855	O75465|Q2M3D3|Q9HBE6|Q9HBW2	Missense_Mutation	SNP	ENST00000264025.3	37	CCDS8426.1	.	.	.	.	.	.	.	.	.	.	a	21.2	4.116916	0.77323	.	.	ENSG00000110400	ENST00000264025	D	0.90504	-2.68	4.31	4.31	0.51392	.	0.000000	0.85682	D	0.000000	D	0.92156	0.7513	L	0.36672	1.1	0.80722	D	1	D	0.71674	0.998	D	0.77557	0.99	D	0.93009	0.6430	10	0.87932	D	0	.	13.3471	0.60580	1.0:0.0:0.0:0.0	.	516	Q15223	PVRL1_HUMAN	H	516	ENSP00000264025:Y516H	ENSP00000264025:Y516H	Y	-	1	0	PVRL1	119040675	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	6.917000	0.75782	1.885000	0.54596	0.392000	0.25879	TAC		0.632	PVRL1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388231.1		
GRIK4	2900	broad.mit.edu	37	11	120744870	120744870	+	Silent	SNP	C	C	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr11:120744870C>A	ENST00000527524.2	+	10	1289	c.1002C>A	c.(1000-1002)tcC>tcA	p.S334S	GRIK4_ENST00000438375.2_Silent_p.S334S|RP11-640N11.2_ENST00000505153.2_RNA	NM_001282470.1	NP_001269399.1	Q16099	GRIK4_HUMAN	glutamate receptor, ionotropic, kainate 4	334					glutamate receptor signaling pathway (GO:0007215)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|response to corticosteroid (GO:0031960)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transport (GO:0006810)	cell junction (GO:0030054)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|kainate selective glutamate receptor complex (GO:0032983)|nucleus (GO:0005634)|perikaryon (GO:0043204)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)|terminal bouton (GO:0043195)	extracellular-glutamate-gated ion channel activity (GO:0005234)|kainate selective glutamate receptor activity (GO:0015277)	p.S334S(1)		NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(20)|liver(1)|lung(29)|ovary(2)|pancreas(1)|prostate(4)|skin(2)|urinary_tract(1)	69		Breast(109;0.000868)|Medulloblastoma(222;0.0453)|all_neural(223;0.116)|all_hematologic(192;0.21)		BRCA - Breast invasive adenocarcinoma(274;1.24e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.116)		AGCCCTTGTCCTGCGGCTCGG	0.637																																					p.S334S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1002A	11						.						54.0	48.0	50.0					11																	120744870		2203	4299	6502	120250080	SO:0001819	synonymous_variant	2900	exon8			S67803	CCDS8433.1	11q23.3	2012-08-29			ENSG00000149403	ENSG00000149403		"""Ligand-gated ion channels / Glutamate receptors, ionotropic"", ""Glutamate receptors"""	4582	protein-coding gene	gene with protein product		600282		GRIK			Standard	NM_001282470		Approved	GluK4, KA1	uc009zax.1	Q16099	OTTHUMG00000048255	ENST00000527524.2:c.1002C>A	11.37:g.120744870C>A		Somatic		Capture	Illumina HiSeq	Phase_I	120250080	NM_014619	A8K9L1	Silent	SNP	ENST00000527524.2	37	CCDS8433.1																																																																																				0.637	GRIK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109760.4	NM_014619	
MUC5B	727897	broad.mit.edu	37	11	1261149	1261149	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr11:1261149C>A	ENST00000529681.1	+	28	3762	c.3704C>A	c.(3703-3705)cCc>cAc	p.P1235H	MUC5B_ENST00000447027.1_Missense_Mutation_p.P1238H|RP11-532E4.2_ENST00000532061.2_RNA	NM_002458.2	NP_002449.2	Q9HC84	MUC5B_HUMAN	mucin 5B, oligomeric mucus/gel-forming	1235	Cys-rich.				cellular protein metabolic process (GO:0044267)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to glucocorticoid stimulus (GO:0071385)|cellular response to retinoic acid (GO:0071300)|epithelial cell differentiation (GO:0030855)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|response to lipopolysaccharide (GO:0032496)|response to ozone (GO:0010193)|response to sulfur dioxide (GO:0010477)|response to vitamin A (GO:0033189)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)		p.P1238H(1)		cervix(2)|endometrium(36)|kidney(9)|lung(89)|urinary_tract(1)	137		all_cancers(49;6.97e-08)|all_epithelial(84;3.45e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.00141)|Lung(200;0.0853)|LUSC - Lung squamous cell carcinoma(625;0.1)		GCAAGGGTCCCCACAGCGGAG	0.662																																					p.P1235H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C3704A	11						.						28.0	29.0	28.0					11																	1261149		2020	4173	6193	1217725	SO:0001583	missense	727897	exon28			U95031, AF086604	CCDS44515.1, CCDS44515.2	11p15.5	2007-01-19	2006-03-14			ENSG00000117983		"""Mucins"""	7516	protein-coding gene	gene with protein product		600770	"""mucin 5, subtype B, tracheobronchial"""	MUC5		9804771	Standard	NM_002458		Approved	MG1	uc001lta.3	Q9HC84		ENST00000529681.1:c.3704C>A	11.37:g.1261149C>A	ENSP00000436812:p.Pro1235His	Somatic		Capture	Illumina HiSeq	Phase_I	1217725	NM_002458	O00447|O00573|O14985|O15494|O95291|O95451|Q14881|Q7M4S5|Q99552|Q9UE28	Missense_Mutation	SNP	ENST00000529681.1	37	CCDS44515.2	.	.	.	.	.	.	.	.	.	.	C	12.18	1.859397	0.32884	.	.	ENSG00000117983	ENST00000529681;ENST00000447027;ENST00000349637;ENST00000406844	T;T	0.17691	2.26;2.45	4.36	3.44	0.39384	.	.	.	.	.	T	0.42899	0.1223	M	0.84511	2.7	0.31675	N	0.64389	D;D	0.89917	1.0;1.0	D;D	0.70716	0.96;0.97	T	0.53641	-0.8410	9	0.87932	D	0	.	10.6143	0.45441	0.0:0.9012:0.0:0.0988	.	1928;1238	A7Y9J9;E9PBJ0	.;.	H	1235;1238;1236;1305	ENSP00000436812:P1235H;ENSP00000415793:P1238H	ENSP00000343037:P1236H	P	+	2	0	MUC5B	1217725	0.045000	0.20229	0.347000	0.25668	0.011000	0.07611	2.780000	0.47742	1.991000	0.58162	0.442000	0.29010	CCC		0.662	MUC5B-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000390041.2	XM_001126093	
SORL1	6653	broad.mit.edu	37	11	121478873	121478873	+	Missense_Mutation	SNP	A	A	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr11:121478873A>T	ENST00000260197.7	+	38	5356	c.5227A>T	c.(5227-5229)Ata>Tta	p.I1743L	SORL1_ENST00000532694.1_Missense_Mutation_p.I589L|SORL1_ENST00000534286.1_Missense_Mutation_p.I653L|SORL1_ENST00000525532.1_Missense_Mutation_p.I687L|SORL1_ENST00000527934.1_Missense_Mutation_p.I358L	NM_003105.5	NP_003096	Q92673	SORL_HUMAN	sortilin-related receptor, L(DLR class) A repeats containing	1743	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell death (GO:0008219)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|cholesterol metabolic process (GO:0008203)|lipid transport (GO:0006869)|negative regulation of aspartic-type endopeptidase activity involved in amyloid precursor protein catabolic process (GO:1902960)|negative regulation of beta-amyloid formation (GO:1902430)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of metalloendopeptidase activity involved in amyloid precursor protein catabolic process (GO:1902963)|negative regulation of neurofibrillary tangle assembly (GO:1902997)|negative regulation of neurogenesis (GO:0050768)|negative regulation of neuron death (GO:1901215)|negative regulation of protein binding (GO:0032091)|negative regulation of protein oligomerization (GO:0032460)|negative regulation of tau-protein kinase activity (GO:1902948)|positive regulation of choline O-acetyltransferase activity (GO:1902771)|positive regulation of early endosome to recycling endosome transport (GO:1902955)|positive regulation of endocytic recycling (GO:2001137)|positive regulation of ER to Golgi vesicle-mediated transport (GO:1902953)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of protein exit from endoplasmic reticulum (GO:0070863)|positive regulation of protein localization to early endosome (GO:1902966)|post-Golgi vesicle-mediated transport (GO:0006892)|protein maturation (GO:0051604)|protein retention in Golgi apparatus (GO:0045053)|protein targeting (GO:0006605)|protein targeting to Golgi (GO:0000042)|protein targeting to lysosome (GO:0006622)|receptor-mediated endocytosis (GO:0006898)|regulation of smooth muscle cell migration (GO:0014910)|signal transduction (GO:0007165)	early endosome (GO:0005769)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|Golgi cisterna (GO:0031985)|integral component of plasma membrane (GO:0005887)|low-density lipoprotein particle (GO:0034362)|membrane (GO:0016020)|multivesicular body (GO:0005771)|neuronal cell body (GO:0043025)|nuclear envelope lumen (GO:0005641)|recycling endosome (GO:0055037)|trans-Golgi network (GO:0005802)	ADP-ribosylation factor binding (GO:0030306)|beta-amyloid binding (GO:0001540)|low-density lipoprotein particle binding (GO:0030169)|transmembrane signaling receptor activity (GO:0004888)	p.I1743L(1)		NS(1)|breast(5)|central_nervous_system(1)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(14)|liver(2)|lung(34)|ovary(5)|pancreas(1)|skin(12)|stomach(2)|upper_aerodigestive_tract(2)	91		Breast(109;0.00119)|Medulloblastoma(222;0.0429)|all_neural(223;0.113)		BRCA - Breast invasive adenocarcinoma(274;3.34e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.108)		CATTACCACCATAAAAGGAAA	0.373																																					p.I1743L												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A5227T	11						.						86.0	82.0	84.0					11																	121478873		2202	4299	6501	120984083	SO:0001583	missense	6653	exon38			Y08110	CCDS8436.1	11q23.2-q24.4	2014-06-05	2011-01-25		ENSG00000137642	ENSG00000137642		"""Fibronectin type III domain containing"""	11185	protein-coding gene	gene with protein product	"""LDLR relative with 11 ligand-binding repeats"""	602005	"""chromosome 11 open reading frame 32"", ""sortilin-related receptor, L(DLR class) A repeats-containing"""	C11orf32		9157966, 8940146	Standard	NM_003105		Approved	gp250, LR11, LRP9, SorLA, SorLA-1	uc001pxx.3	Q92673	OTTHUMG00000166057	ENST00000260197.7:c.5227A>T	11.37:g.121478873A>T	ENSP00000260197:p.Ile1743Leu	Somatic		Capture	Illumina HiSeq	Phase_I	120984083	NM_003105	B2RNX7|Q92856	Missense_Mutation	SNP	ENST00000260197.7	37	CCDS8436.1	.	.	.	.	.	.	.	.	.	.	A	11.92	1.783352	0.31593	.	.	ENSG00000137642	ENST00000260197;ENST00000525532;ENST00000532694;ENST00000534286;ENST00000527934	T;T;T;T;T	0.50277	0.75;0.75;0.75;0.75;0.75	5.13	2.78	0.32641	Fibronectin, type III (1);Immunoglobulin-like fold (1);	0.717725	0.13224	N	0.404169	T	0.31009	0.0783	L	0.27053	0.805	0.23640	N	0.997227	B;B	0.10296	0.003;0.002	B;B	0.09377	0.001;0.004	T	0.21518	-1.0243	10	0.22706	T	0.39	.	7.3792	0.26845	0.7402:0.0:0.2598:0.0	.	358;1743	E9PKB0;Q92673	.;SORL_HUMAN	L	1743;687;589;653;358	ENSP00000260197:I1743L;ENSP00000434634:I687L;ENSP00000432131:I589L;ENSP00000436447:I653L;ENSP00000435405:I358L	ENSP00000260197:I1743L	I	+	1	0	SORL1	120984083	0.221000	0.23642	0.529000	0.27951	0.994000	0.84299	1.163000	0.31798	0.285000	0.22329	0.379000	0.24179	ATA		0.373	SORL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387626.2	NM_003105	
C11orf63	79864	broad.mit.edu	37	11	122756862	122756862	+	Missense_Mutation	SNP	A	A	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr11:122756862A>T	ENST00000531316.1	+	1	397	c.305A>T	c.(304-306)gAg>gTg	p.E102V	C11orf63_ENST00000227349.2_Missense_Mutation_p.E102V|C11orf63_ENST00000307257.6_Missense_Mutation_p.E102V			Q6NUN7	CK063_HUMAN	chromosome 11 open reading frame 63	102					axoneme assembly (GO:0035082)|brain development (GO:0007420)|cerebrospinal fluid secretion (GO:0033326)|ciliary basal body organization (GO:0032053)			p.E102V(1)		breast(1)|central_nervous_system(1)|endometrium(4)|kidney(4)|large_intestine(13)|lung(14)|ovary(3)|pancreas(1)|prostate(2)|skin(1)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(1)	47		Breast(109;0.00249)|Lung NSC(97;0.0177)|all_lung(97;0.018)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;5.34e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0311)		ATGGCTCGCGAGCAAAACCAC	0.488																																					p.E102V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A305T	11						.						90.0	92.0	91.0					11																	122756862		2202	4299	6501	122262072	SO:0001583	missense	79864	exon2			BC068507	CCDS8438.1, CCDS8439.1	11q24.1	2012-05-25			ENSG00000109944	ENSG00000109944			26288	protein-coding gene	gene with protein product						12477932	Standard	NM_024806		Approved	FLJ23554	uc001pym.4	Q6NUN7	OTTHUMG00000166027	ENST00000531316.1:c.305A>T	11.37:g.122756862A>T	ENSP00000431669:p.Glu102Val	Somatic		Capture	Illumina HiSeq	Phase_I	122262072	NM_024806	A8K6G0|Q96GB5|Q9H5D6	Missense_Mutation	SNP	ENST00000531316.1	37	CCDS8438.1	.	.	.	.	.	.	.	.	.	.	A	10.44	1.351476	0.24512	.	.	ENSG00000109944	ENST00000307257;ENST00000227349;ENST00000531316	T;T	0.46819	0.86;0.86	5.25	0.319	0.15873	.	1.384780	0.04305	N	0.347917	T	0.41949	0.1181	L	0.29908	0.895	0.09310	N	1	P;P	0.47677	0.815;0.899	B;P	0.45681	0.395;0.49	T	0.39396	-0.9616	10	0.52906	T	0.07	-0.8271	7.9226	0.29854	0.6305:0.0:0.3695:0.0	.	102;102	Q6NUN7;Q6NUN7-2	CK063_HUMAN;.	V	102	ENSP00000227349:E102V;ENSP00000431669:E102V	ENSP00000227349:E102V	E	+	2	0	C11orf63	122262072	0.000000	0.05858	0.000000	0.03702	0.011000	0.07611	-0.272000	0.08560	0.079000	0.16929	0.533000	0.62120	GAG		0.488	C11orf63-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387511.1	NM_024806	
CLMP	79827	broad.mit.edu	37	11	122944275	122944275	+	Silent	SNP	A	A	G			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr11:122944275A>G	ENST00000448775.2	-	7	1369	c.1029T>C	c.(1027-1029)tcT>tcC	p.S343S	CLMP_ENST00000530371.1_5'UTR	NM_024769.2	NP_079045.1	Q9H6B4	CLMP_HUMAN	CXADR-like membrane protein	343					digestive tract development (GO:0048565)	cell surface (GO:0009986)|cytoplasmic microtubule (GO:0005881)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|tight junction (GO:0005923)		p.S343S(1)		endometrium(3)|large_intestine(3)|lung(6)|ovary(1)|prostate(1)	14						TCTTTGGTTCAGAACCTCTCA	0.572																																					p.S343S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.T1029C	11						.						206.0	190.0	195.0					11																	122944275		2202	4299	6501	122449485	SO:0001819	synonymous_variant	79827	exon7			BC009371	CCDS8441.1	11q24	2013-01-29			ENSG00000166250	ENSG00000166250		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	24039	protein-coding gene	gene with protein product	"""adipocyte-specific adhesion molecule"", ""coxsackie- and adenovirus receptor-like membrane protein"", ""adipocyte adhesion molecule"""	611693				12851705, 14573622	Standard	NM_024769		Approved	ASAM, FLJ22415, ACAM	uc001pyt.3	Q9H6B4		ENST00000448775.2:c.1029T>C	11.37:g.122944275A>G		Somatic		Capture	Illumina HiSeq	Phase_I	122449485	NM_024769		Silent	SNP	ENST00000448775.2	37	CCDS8441.1																																																																																				0.572	CLMP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387542.1	NM_024769	
CLMP	79827	broad.mit.edu	37	11	122944456	122944456	+	Missense_Mutation	SNP	C	C	T	rs139133124		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr11:122944456C>T	ENST00000448775.2	-	7	1188	c.848G>A	c.(847-849)cGt>cAt	p.R283H	CLMP_ENST00000530371.1_5'UTR	NM_024769.2	NP_079045.1	Q9H6B4	CLMP_HUMAN	CXADR-like membrane protein	283					digestive tract development (GO:0048565)	cell surface (GO:0009986)|cytoplasmic microtubule (GO:0005881)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|tight junction (GO:0005923)		p.R283H(1)		endometrium(3)|large_intestine(3)|lung(6)|ovary(1)|prostate(1)	14						TTTCACAAGACGGGCTTTTGG	0.512																																					p.R283H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G848A	11						.	C	HIS/ARG	0,4404		0,0,2202	85.0	84.0	84.0		848	5.4	1.0	11	dbSNP_134	84	1,8597	1.2+/-3.3	0,1,4298	yes	missense	CLMP	NM_024769.2	29	0,1,6500	TT,TC,CC		0.0116,0.0,0.0077	benign	283/374	122944456	1,13001	2202	4299	6501	122449666	SO:0001583	missense	79827	exon7			BC009371	CCDS8441.1	11q24	2013-01-29			ENSG00000166250	ENSG00000166250		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	24039	protein-coding gene	gene with protein product	"""adipocyte-specific adhesion molecule"", ""coxsackie- and adenovirus receptor-like membrane protein"", ""adipocyte adhesion molecule"""	611693				12851705, 14573622	Standard	NM_024769		Approved	ASAM, FLJ22415, ACAM	uc001pyt.3	Q9H6B4		ENST00000448775.2:c.848G>A	11.37:g.122944456C>T	ENSP00000405577:p.Arg283His	Somatic		Capture	Illumina HiSeq	Phase_I	122449666	NM_024769		Missense_Mutation	SNP	ENST00000448775.2	37	CCDS8441.1	.	.	.	.	.	.	.	.	.	.	C	15.73	2.919237	0.52546	0.0	1.16E-4	ENSG00000166250	ENST00000448775	T	0.75367	-0.93	5.44	5.44	0.79542	.	0.108809	0.64402	D	0.000012	T	0.65842	0.2730	L	0.45051	1.395	0.45567	D	0.998512	B	0.26577	0.153	B	0.17433	0.018	T	0.62478	-0.6846	10	0.34782	T	0.22	.	13.5517	0.61736	0.0:0.9233:0.0:0.0767	.	283	Q9H6B4	CLMP_HUMAN	H	283	ENSP00000405577:R283H	ENSP00000405577:R283H	R	-	2	0	CLMP	122449666	0.994000	0.37717	1.000000	0.80357	0.952000	0.60782	2.944000	0.49034	2.559000	0.86315	0.655000	0.94253	CGT		0.512	CLMP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387542.1	NM_024769	
IGSF9B	22997	broad.mit.edu	37	11	133801988	133801988	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr11:133801988C>T	ENST00000321016.8	-	8	1318	c.1088G>A	c.(1087-1089)gGc>gAc	p.G363D	IGSF9B_ENST00000533871.2_Missense_Mutation_p.G363D			Q9UPX0	TUTLB_HUMAN	immunoglobulin superfamily, member 9B	363	Ig-like 4.				homophilic cell adhesion (GO:0007156)|positive regulation of inhibitory postsynaptic membrane potential (GO:0097151)	dendrite (GO:0030425)|inhibitory synapse (GO:0060077)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)		p.G363D(1)		breast(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(18)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	44	all_hematologic(175;0.127)	all_cancers(12;1.58e-21)|all_epithelial(12;5.17e-16)|all_lung(97;1.6e-05)|Lung NSC(97;3.86e-05)|Breast(109;0.000126)|Medulloblastoma(222;0.0245)|all_neural(223;0.0505)|Esophageal squamous(93;0.0559)		Epithelial(10;7.19e-10)|BRCA - Breast invasive adenocarcinoma(10;9.69e-09)|all cancers(11;1.23e-08)|OV - Ovarian serous cystadenocarcinoma(99;0.00328)|Lung(977;0.221)		CAGGGGACGGCCGTCCTTGTT	0.602																																					p.G363D												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1088A	11						.						69.0	86.0	80.0					11																	133801988		2136	4229	6365	133307198	SO:0001583	missense	22997	exon8			AK097578	CCDS61010.1	11q25	2013-02-11	2005-10-12	2005-11-20				"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	32326	protein-coding gene	gene with protein product		613773					Standard	NM_001277285		Approved	KIAA1030	uc031qfh.1	Q9UPX0		ENST00000321016.8:c.1088G>A	11.37:g.133801988C>T	ENSP00000317980:p.Gly363Asp	Somatic		Capture	Illumina HiSeq	Phase_I	133307198	NM_014987	G5EA26	Missense_Mutation	SNP	ENST00000321016.8	37		.	.	.	.	.	.	.	.	.	.	C	27.0	4.795547	0.90453	.	.	ENSG00000080854	ENST00000321016;ENST00000533871;ENST00000527648	T;T;T	0.81415	-1.49;-1.49;-1.49	4.89	4.89	0.63831	Immunoglobulin subtype (1);Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	.	.	.	.	D	0.89220	0.6653	M	0.75447	2.3	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.88177	0.2868	9	0.37606	T	0.19	.	18.2442	0.89979	0.0:1.0:0.0:0.0	.	363	Q9UPX0	TUTLB_HUMAN	D	363;205;363	ENSP00000317980:G363D;ENSP00000436552:G205D;ENSP00000436576:G363D	ENSP00000317980:G363D	G	-	2	0	IGSF9B	133307198	1.000000	0.71417	0.994000	0.49952	0.639000	0.38242	7.648000	0.83479	2.535000	0.85469	0.556000	0.70494	GGC		0.602	IGSF9B-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		XM_290502	
DEAF1	10522	broad.mit.edu	37	11	674719	674719	+	Silent	SNP	C	C	T	rs187523180	byFrequency	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr11:674719C>T	ENST00000382409.3	-	10	1804	c.1320G>A	c.(1318-1320)gcG>gcA	p.A440A	DEAF1_ENST00000525904.1_5'UTR|DEAF1_ENST00000338675.6_Silent_p.A351A|RP11-754B17.1_ENST00000527799.1_RNA	NM_021008.2	NP_066288.2	O75398	DEAF1_HUMAN	DEAF1 transcription factor	440	Interaction with LMO4. {ECO:0000250}.				anatomical structure morphogenesis (GO:0009653)|embryonic skeletal system development (GO:0048706)|germ cell development (GO:0007281)|negative regulation of transcription, DNA-templated (GO:0045892)|neural tube closure (GO:0001843)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of mammary gland epithelial cell proliferation (GO:0033599)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.A440A(2)		breast(2)|endometrium(3)|kidney(1)|large_intestine(4)|lung(11)|prostate(2)|upper_aerodigestive_tract(1)	24		all_cancers(49;1.24e-08)|all_epithelial(84;1.87e-05)|Breast(177;0.000286)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.106)|all_lung(207;0.136)		all cancers(45;1.76e-27)|Epithelial(43;8.42e-27)|OV - Ovarian serous cystadenocarcinoma(40;6.55e-21)|BRCA - Breast invasive adenocarcinoma(625;4.83e-05)|Lung(200;0.0259)|LUSC - Lung squamous cell carcinoma(625;0.075)		CATTGACCAACGCGGGAGGTG	0.572													C|||	2	0.000399361	0.0008	0.0	5008	,	,		17514	0.0		0.001	False		,,,				2504	0.0				p.A440A												.	.	2	Substitution - coding silent(2)	large_intestine(1)|endometrium(1)	c.G1320A	11						.	C		2,4404	4.2+/-10.8	0,2,2201	65.0	70.0	69.0		1320	-7.7	0.0	11		69	0,8600		0,0,4300	no	coding-synonymous	DEAF1	NM_021008.2		0,2,6501	TT,TC,CC		0.0,0.0454,0.0154		440/566	674719	2,13004	2203	4300	6503	664719	SO:0001819	synonymous_variant	10522	exon10			AF049460	CCDS31327.1	11p15.5	2013-01-10	2013-01-10		ENSG00000177030	ENSG00000177030		"""Zinc fingers, MYND-type"""	14677	protein-coding gene	gene with protein product		602635	"""deformed epidermal autoregulatory factor 1 (Drosophila)"""			9773984	Standard	XR_428838		Approved	NUDR, SPN, ZMYND5	uc001lqq.1	O75398	OTTHUMG00000165363	ENST00000382409.3:c.1320G>A	11.37:g.674719C>T		Somatic		Capture	Illumina HiSeq	Phase_I	664719	NM_021008	A8K1F8|A8K5R8|C7T5V5|O15152|O75399|O75510|O75511|O75512|O75513|Q9UET1	Silent	SNP	ENST00000382409.3	37	CCDS31327.1																																																																																				0.572	DEAF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383614.3	NM_021008	
OSBPL5	114879	broad.mit.edu	37	11	3129055	3129055	+	Missense_Mutation	SNP	G	G	A	rs372197696		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr11:3129055G>A	ENST00000263650.7	-	8	971	c.812C>T	c.(811-813)tCg>tTg	p.S271L	OSBPL5_ENST00000389989.3_Missense_Mutation_p.S203L|OSBPL5_ENST00000542243.1_Intron|OSBPL5_ENST00000525498.1_Missense_Mutation_p.S182L|OSBPL5_ENST00000348039.5_Missense_Mutation_p.S203L	NM_020896.3	NP_065947.1	Q9H0X9	OSBL5_HUMAN	oxysterol binding protein-like 5	271					cholesterol metabolic process (GO:0008203)|cholesterol transport (GO:0030301)|Golgi to plasma membrane transport (GO:0006893)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	cholesterol binding (GO:0015485)|oxysterol binding (GO:0008142)	p.S271L(1)		breast(2)|central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(7)|lung(8)|prostate(1)|upper_aerodigestive_tract(1)	25		all_epithelial(84;0.000236)|Medulloblastoma(188;0.00106)|Breast(177;0.00328)|Ovarian(85;0.00556)|all_neural(188;0.00681)		BRCA - Breast invasive adenocarcinoma(625;0.00607)|LUSC - Lung squamous cell carcinoma(625;0.207)		CCCACAGAGCGATGAGGGTGA	0.677																																					p.S203L												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C608T	11						.	G	LEU/SER,LEU/SER,LEU/SER	0,4404		0,0,2202	82.0	78.0	80.0		608,812,608	3.0	0.7	11		80	1,8595	1.2+/-3.3	0,1,4297	no	missense,missense,missense	OSBPL5	NM_001144063.1,NM_020896.3,NM_145638.2	145,145,145	0,1,6499	AA,AG,GG		0.0116,0.0,0.0077	possibly-damaging,possibly-damaging,possibly-damaging	203/812,271/880,203/812	3129055	1,12999	2202	4298	6500	3085631	SO:0001583	missense	114879	exon7			AF392453	CCDS31343.1, CCDS31344.1	11p15.4	2013-01-10			ENSG00000021762	ENSG00000021762		"""Oxysterol binding proteins"", ""Pleckstrin homology (PH) domain containing"""	16392	protein-coding gene	gene with protein product		606733					Standard	NM_145638		Approved	KIAA1534, ORP5	uc001lxk.2	Q9H0X9	OTTHUMG00000011702	ENST00000263650.7:c.812C>T	11.37:g.3129055G>A	ENSP00000263650:p.Ser271Leu	Somatic		Capture	Illumina HiSeq	Phase_I	3085631	NM_145638	A6NDP0|A6NJS8|Q54A90|Q8N596|Q9BZB0|Q9P1Z4	Missense_Mutation	SNP	ENST00000263650.7	37	CCDS31344.1	.	.	.	.	.	.	.	.	.	.	G	5.493	0.275895	0.10403	0.0	1.16E-4	ENSG00000021762	ENST00000263650;ENST00000389989;ENST00000525498;ENST00000348039	T;T;T;T	0.31769	1.48;1.48;1.48;1.48	3.9	2.99	0.34606	.	0.817525	0.10415	N	0.677449	T	0.23688	0.0573	L	0.56769	1.78	0.22317	N	0.999202	P;B;B;P	0.46656	0.789;0.066;0.023;0.882	B;B;B;B	0.32928	0.107;0.008;0.005;0.155	T	0.14254	-1.0479	10	0.38643	T	0.18	-9.2709	6.9915	0.24758	0.1054:0.3352:0.5594:0.0	.	182;232;203;271	B4DVB0;E7EP03;Q8N596;Q9H0X9	.;.;.;OSBL5_HUMAN	L	271;203;182;203	ENSP00000263650:S271L;ENSP00000374639:S203L;ENSP00000433342:S182L;ENSP00000302872:S203L	ENSP00000263650:S271L	S	-	2	0	OSBPL5	3085631	0.001000	0.12720	0.652000	0.29579	0.029000	0.11900	1.048000	0.30379	0.853000	0.35312	-0.384000	0.06662	TCG		0.677	OSBPL5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032332.2		
NUP98	4928	broad.mit.edu	37	11	3716744	3716744	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr11:3716744G>T	ENST00000324932.7	-	26	4522	c.4102C>A	c.(4102-4104)Ctc>Atc	p.L1368I	NUP98_ENST00000355260.3_Missense_Mutation_p.L1368I|NUP98_ENST00000359171.4_Missense_Mutation_p.L1368I|NUP98_ENST00000488828.1_5'UTR	NM_016320.4|NM_139132.3	NP_057404.2|NP_624358.2	P52948	NUP98_HUMAN	nucleoporin 98kDa	1385					carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|DNA replication (GO:0006260)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|nuclear pore complex assembly (GO:0051292)|nuclear pore organization (GO:0006999)|nucleocytoplasmic transport (GO:0006913)|protein import into nucleus, docking (GO:0000059)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytosol (GO:0005829)|nuclear envelope (GO:0005635)|nuclear inclusion body (GO:0042405)|nuclear membrane (GO:0031965)|nuclear periphery (GO:0034399)|nuclear pore (GO:0005643)|nuclear pore nuclear basket (GO:0044615)|nuclear pore outer ring (GO:0031080)|nucleoplasm (GO:0005654)	peptide binding (GO:0042277)|structural constituent of nuclear pore (GO:0017056)|transporter activity (GO:0005215)	p.L1368I(1)		NS(1)|autonomic_ganglia(1)|breast(8)|central_nervous_system(1)|endometrium(5)|kidney(5)|large_intestine(13)|liver(1)|lung(15)|ovary(2)|prostate(2)|skin(9)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	66		Medulloblastoma(188;0.0025)|Breast(177;0.00328)|all_neural(188;0.0227)		BRCA - Breast invasive adenocarcinoma(625;0.0403)|LUSC - Lung squamous cell carcinoma(625;0.116)|Lung(200;0.199)		TCTGCTTGGAGCTGATGCCAG	0.483			T	"""HOXA9, NSD1, WHSC1L1, DDX10, TOP1, HOXD13, PMX1, HOXA13, HOXD11, HOXA11, RAP1GDS1, HOXC11"""	AML																																p.L1368I			Dom	yes		11	11p15	4928	nucleoporin 98kDa		L	.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C4102A	11						.						161.0	159.0	159.0					11																	3716744		2201	4298	6499	3673320	SO:0001583	missense	4928	exon26			AF071076, AF231130, BC012906, BG773331	CCDS7746.1, CCDS31347.1, CCDS41605.1, CCDS41606.1	11p15	2008-02-26	2002-08-29		ENSG00000110713	ENSG00000110713			8068	protein-coding gene	gene with protein product		601021	"""nucleoporin 98kD"""			9166830	Standard	NM_139131		Approved	NUP96	uc001lyh.3	P52948	OTTHUMG00000011846	ENST00000324932.7:c.4102C>A	11.37:g.3716744G>T	ENSP00000316032:p.Leu1368Ile	Somatic		Capture	Illumina HiSeq	Phase_I	3673320	NM_139132	Q8IUT2|Q8WYB0|Q96E54|Q9H3Q4|Q9NT02|Q9UF57|Q9UHX0|Q9Y6J4|Q9Y6J5	Missense_Mutation	SNP	ENST00000324932.7	37	CCDS7746.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	15.20|15.20	2.762757|2.762757	0.49574|0.49574	.|.	.|.	ENSG00000110713|ENSG00000110713	ENST00000429801|ENST00000324932;ENST00000359171;ENST00000355260	.|.	.|.	.|.	5.05|5.05	5.05|5.05	0.67936|0.67936	.|.	.|0.115496	.|0.64402	.|D	.|0.000017	T|T	0.54255|0.54255	0.1847|0.1847	L|L	0.52364|0.52364	1.645|1.645	0.25889|0.25889	N|N	0.983492|0.983492	.|P;P;D	.|0.55800	.|0.928;0.928;0.973	.|B;P;P	.|0.53593	.|0.441;0.546;0.73	T|T	0.49504|0.49504	-0.8933|-0.8933	5|9	.|0.18276	.|T	.|0.48	-8.3318|-8.3318	17.8098|17.8098	0.88612|0.88612	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|1368;1368;1282	.|P52948-2;P52948-5;P52948-6	.|.;.;.	D|I	320|1368	.|.	.|ENSP00000316032:L1368I	A|L	-|-	2|1	0|0	NUP98|NUP98	3673320|3673320	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.708000|0.708000	0.40852|0.40852	4.520000|4.520000	0.60524|0.60524	2.515000|2.515000	0.84797|0.84797	0.558000|0.558000	0.71614|0.71614	GCT|CTC		0.483	NUP98-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032766.3	NM_016320	
OR52I2	143502	broad.mit.edu	37	11	4608339	4608339	+	Silent	SNP	G	G	T	rs145090174		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr11:4608339G>T	ENST00000312614.4	+	1	319	c.297G>T	c.(295-297)gtG>gtT	p.V99V		NM_001005170.2	NP_001005170.1	Q8NH67	O52I2_HUMAN	olfactory receptor, family 52, subfamily I, member 2	99						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.V99V(1)		endometrium(3)|kidney(1)|large_intestine(2)|lung(11)|pancreas(1)|skin(1)	19		Medulloblastoma(188;0.0075)|Breast(177;0.0461)|all_neural(188;0.0577)		Epithelial(150;8.45e-12)|BRCA - Breast invasive adenocarcinoma(625;0.0285)|LUSC - Lung squamous cell carcinoma(625;0.19)		TGGCTGCTGTGGACATTGTTA	0.483																																					p.V99V												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G297T	11						.						277.0	273.0	275.0					11																	4608339		2201	4298	6499	4564915	SO:0001819	synonymous_variant	143502	exon1			BK004264	CCDS31355.1	11p15.4	2012-08-09			ENSG00000226288	ENSG00000226288		"""GPCR / Class A : Olfactory receptors"""	15221	protein-coding gene	gene with protein product							Standard	NM_001005170		Approved		uc010qyh.2	Q8NH67	OTTHUMG00000165721	ENST00000312614.4:c.297G>T	11.37:g.4608339G>T		Somatic		Capture	Illumina HiSeq	Phase_I	4564915	NM_001005170	B2RNJ5|B9EKV8|Q6IFJ8	Silent	SNP	ENST00000312614.4	37	CCDS31355.1																																																																																				0.483	OR52I2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385946.1	NM_001005170	
OR51E2	81285	broad.mit.edu	37	11	4703571	4703571	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr11:4703571G>A	ENST00000396950.3	-	2	610	c.371C>T	c.(370-372)gCc>gTc	p.A124V		NM_030774.3	NP_110401.1	Q9H255	O51E2_HUMAN	olfactory receptor, family 51, subfamily E, member 2	124					cellular response to fatty acid (GO:0071398)|detection of chemical stimulus involved in sensory perception of smell (GO:0050911)|positive regulation of blood pressure (GO:0045777)|positive regulation of renin secretion into blood stream (GO:1900135)|steroid hormone mediated signaling pathway (GO:0043401)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)|signaling receptor activity (GO:0038023)|steroid hormone receptor activity (GO:0003707)	p.A124V(1)		NS(1)|central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(12)|ovary(2)|prostate(1)|skin(3)	23		Medulloblastoma(188;0.0075)|Breast(177;0.0461)|all_neural(188;0.0577)		Epithelial(150;3e-12)|BRCA - Breast invasive adenocarcinoma(625;0.00476)|LUSC - Lung squamous cell carcinoma(625;0.2)		GTGGCAGATGGCCACATAACG	0.522																																					p.A124V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C371T	11						.						59.0	48.0	52.0					11																	4703571		2201	4298	6499	4660147	SO:0001583	missense	81285	exon2			AY033942	CCDS7751.1	11p15	2012-08-09			ENSG00000167332	ENSG00000167332		"""GPCR / Class A : Olfactory receptors"""	15195	protein-coding gene	gene with protein product		611268				11118034	Standard	NM_030774		Approved	PSGR	uc001lzk.2	Q9H255	OTTHUMG00000133362	ENST00000396950.3:c.371C>T	11.37:g.4703571G>A	ENSP00000380153:p.Ala124Val	Somatic		Capture	Illumina HiSeq	Phase_I	4660147	NM_030774	B2RA63|Q6IF94	Missense_Mutation	SNP	ENST00000396950.3	37	CCDS7751.1	.	.	.	.	.	.	.	.	.	.	G	29.8	5.036563	0.93630	.	.	ENSG00000167332	ENST00000396950	T	0.00462	7.26	5.0	5.0	0.66597	GPCR, rhodopsin-like superfamily (1);	0.000000	0.46145	D	0.000304	T	0.04048	0.0113	H	0.99464	4.58	0.54753	D	0.999985	D	0.89917	1.0	D	0.87578	0.998	T	0.02126	-1.1209	10	0.87932	D	0	.	17.0368	0.86478	0.0:0.0:1.0:0.0	.	124	Q9H255	O51E2_HUMAN	V	124	ENSP00000380153:A124V	ENSP00000380153:A124V	A	-	2	0	OR51E2	4660147	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.355000	0.97087	2.613000	0.88420	0.655000	0.94253	GCC		0.522	OR51E2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257198.1	NM_030774	
OR52R1	119695	broad.mit.edu	37	11	4824753	4824753	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr11:4824753T>C	ENST00000356069.2	-	1	857	c.858A>G	c.(856-858)atA>atG	p.I286M	MMP26_ENST00000477339.1_Intron|MMP26_ENST00000380390.1_Intron|OR52R1_ENST00000380382.1_Missense_Mutation_p.I365M	NM_001005177.3	NP_001005177.3	Q8NGF1	O52R1_HUMAN	olfactory receptor, family 52, subfamily R, member 1	286						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.I285M(1)|p.I365M(1)		breast(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(14)|prostate(1)|skin(3)	29		Medulloblastoma(188;0.0025)|Breast(177;0.0184)|all_neural(188;0.0227)		Epithelial(150;4.77e-12)|BRCA - Breast invasive adenocarcinoma(625;0.00435)|LUSC - Lung squamous cell carcinoma(625;0.19)		GCATGGGAGGTATCAGTAGAT	0.473																																					p.I286M												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.A858G	11						.						132.0	132.0	132.0					11																	4824753		2201	4298	6499	4781329	SO:0001583	missense	119695	exon1			BK004282	CCDS31360.1, CCDS31360.2	11p15.4	2012-08-09			ENSG00000176937	ENSG00000176937		"""GPCR / Class A : Olfactory receptors"""	15235	protein-coding gene	gene with protein product							Standard	NM_001005177		Approved		uc021qcs.1	Q8NGF1	OTTHUMG00000066510	ENST00000356069.2:c.858A>G	11.37:g.4824753T>C	ENSP00000348368:p.Ile286Met	Somatic		Capture	Illumina HiSeq	Phase_I	4781329	NM_001005177	Q6IFI0	Missense_Mutation	SNP	ENST00000356069.2	37	CCDS31360.2	.	.	.	.	.	.	.	.	.	.	T	3.125	-0.179763	0.06380	.	.	ENSG00000176937	ENST00000356069;ENST00000380382	T;T	0.00207	8.55;8.55	5.46	-10.9	0.00192	GPCR, rhodopsin-like superfamily (1);	0.336884	0.21172	N	0.078979	T	0.00109	0.0003	L	0.47078	1.49	0.09310	N	0.999999	B	0.16802	0.019	B	0.15052	0.012	T	0.53301	-0.8458	10	0.66056	D	0.02	.	1.7126	0.02895	0.4049:0.1719:0.2668:0.1563	.	286	Q8NGF1	O52R1_HUMAN	M	286;365	ENSP00000348368:I286M;ENSP00000369742:I365M	ENSP00000348368:I286M	I	-	3	3	OR52R1	4781329	0.000000	0.05858	0.010000	0.14722	0.363000	0.29612	-4.736000	0.00192	-3.076000	0.00252	-0.417000	0.06048	ATA		0.473	OR52R1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142183.1	NM_001005177	
OR51V1	283111	broad.mit.edu	37	11	5221093	5221093	+	Missense_Mutation	SNP	C	C	T	rs182727082		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr11:5221093C>T	ENST00000321255.1	-	1	837	c.838G>A	c.(838-840)Gtg>Atg	p.V280M		NM_001004760.2	NP_001004760.2	Q9H2C8	O51V1_HUMAN	olfactory receptor, family 51, subfamily V, member 1	280					detection of chemical stimulus involved in sensory perception of smell (GO:0050911)|sensory perception of smell (GO:0007608)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.V280M(2)		endometrium(1)|kidney(2)|large_intestine(13)|lung(19)|skin(2)|upper_aerodigestive_tract(2)	39		Medulloblastoma(188;0.00225)|Breast(177;0.0155)|all_neural(188;0.0212)		Epithelial(150;2.83e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		ACGTGGGCCACGGGGGAAAGG	0.473																																					p.V280M												.	.	2	Substitution - Missense(2)	large_intestine(1)|kidney(1)	c.G838A	11						.	C	MET/VAL	0,4402		0,0,2201	119.0	106.0	110.0		838	-10.3	0.0	11		110	1,8595	1.2+/-3.3	0,1,4297	no	missense	OR51V1	NM_001004760.2	21	0,1,6498	TT,TC,CC		0.0116,0.0,0.0077	benign	280/322	5221093	1,12997	2201	4298	6499	5177669	SO:0001583	missense	283111	exon1			BK004432	CCDS31375.1	11p15.4	2012-08-09			ENSG00000176742	ENSG00000176742		"""GPCR / Class A : Olfactory receptors"""	19597	protein-coding gene	gene with protein product				OR51A12			Standard	NM_001004760		Approved		uc010qyz.2	Q9H2C8	OTTHUMG00000066671	ENST00000321255.1:c.838G>A	11.37:g.5221093C>T	ENSP00000321729:p.Val280Met	Somatic		Capture	Illumina HiSeq	Phase_I	5177669	NM_001004760		Missense_Mutation	SNP	ENST00000321255.1	37	CCDS31375.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	C	0.367	-0.936392	0.02340	0.0	1.16E-4	ENSG00000176742	ENST00000321255	T	0.71934	-0.61	5.15	-10.3	0.00346	GPCR, rhodopsin-like superfamily (1);	1.832430	0.03207	N	0.175706	T	0.59500	0.2198	M	0.71036	2.16	0.09310	N	1	B	0.34161	0.439	B	0.29598	0.104	T	0.51585	-0.8687	10	0.48119	T	0.1	.	2.5027	0.04638	0.291:0.2728:0.3341:0.1021	.	280	Q9H2C8	O51V1_HUMAN	M	280	ENSP00000321729:V280M	ENSP00000321729:V280M	V	-	1	0	OR51V1	5177669	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-5.098000	0.00151	-5.117000	0.00021	-1.224000	0.01588	GTG		0.473	OR51V1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142965.1	NM_001004760	
OR52H1	390067	broad.mit.edu	37	11	5566132	5566132	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr11:5566132A>G	ENST00000322653.4	-	1	647	c.622T>C	c.(622-624)Ttt>Ctt	p.F208L	HBG2_ENST00000380259.2_Intron	NM_001005289.1	NP_001005289.1	Q8NGJ2	O52H1_HUMAN	olfactory receptor, family 52, subfamily H, member 1	208						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.F208L(1)		NS(1)|breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(5)|ovary(1)|prostate(1)|skin(2)	20		Medulloblastoma(188;0.0075)|all_neural(188;0.0572)|Breast(177;0.0675)		Epithelial(150;5.33e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		GGAACACAAAAGCCATACCAG	0.502																																					p.F208L												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T622C	11						.						128.0	99.0	109.0					11																	5566132		2201	4297	6498	5522708	SO:0001583	missense	390067	exon1			AB065802	CCDS31386.1	11p15.4	2012-08-09			ENSG00000181616	ENSG00000181616		"""GPCR / Class A : Olfactory receptors"""	15218	protein-coding gene	gene with protein product							Standard	NM_001005289		Approved		uc010qzh.2	Q8NGJ2	OTTHUMG00000066909	ENST00000322653.4:c.622T>C	11.37:g.5566132A>G	ENSP00000326259:p.Phe208Leu	Somatic		Capture	Illumina HiSeq	Phase_I	5522708	NM_001005289	B9EH26|Q6IF79	Missense_Mutation	SNP	ENST00000322653.4	37	CCDS31386.1	.	.	.	.	.	.	.	.	.	.	A	4.181	0.032158	0.08101	.	.	ENSG00000181616	ENST00000322653	T	0.00042	8.84	5.37	4.25	0.50352	GPCR, rhodopsin-like superfamily (1);	0.200661	0.35739	N	0.003003	T	0.00073	0.0002	N	0.04655	-0.195	0.33977	D	0.647482	B	0.31581	0.329	B	0.37304	0.246	T	0.27020	-1.0086	10	0.02654	T	1	.	7.618	0.28169	0.8496:0.0:0.1504:0.0	.	208	Q8NGJ2	O52H1_HUMAN	L	208	ENSP00000326259:F208L	ENSP00000326259:F208L	F	-	1	0	OR52H1	5522708	0.059000	0.20769	1.000000	0.80357	0.873000	0.50193	0.572000	0.23684	2.032000	0.59987	0.528000	0.53228	TTT		0.502	OR52H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143400.1	NM_001005289	
HPX	3263	broad.mit.edu	37	11	6462125	6462125	+	Silent	SNP	G	G	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr11:6462125G>T	ENST00000265983.3	-	1	169	c.69C>A	c.(67-69)gcC>gcA	p.A23A	HPX_ENST00000525057.1_Intron	NM_000613.2	NP_000604.1	P02790	HEMO_HUMAN	hemopexin	23					cellular iron ion homeostasis (GO:0006879)|heme metabolic process (GO:0042168)|heme transport (GO:0015886)|hemoglobin metabolic process (GO:0020027)|positive regulation of humoral immune response mediated by circulating immunoglobulin (GO:0002925)|positive regulation of immunoglobulin production (GO:0002639)|positive regulation of interferon-gamma-mediated signaling pathway (GO:0060335)|positive regulation of tyrosine phosphorylation of Stat1 protein (GO:0042511)|viral process (GO:0016032)	blood microparticle (GO:0072562)|endocytic vesicle lumen (GO:0071682)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	heme transporter activity (GO:0015232)|metal ion binding (GO:0046872)	p.A23A(1)		endometrium(1)|large_intestine(2)|lung(11)|prostate(1)	15		Medulloblastoma(188;0.00776)|all_neural(188;0.0652)|Breast(177;0.114)		Epithelial(150;5.46e-08)|BRCA - Breast invasive adenocarcinoma(625;0.19)		GAAGAGGGGTGGCAATGGCCA	0.572																																					p.A23A												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C69A	11						.						61.0	57.0	58.0					11																	6462125		2201	4296	6497	6418701	SO:0001819	synonymous_variant	3263	exon1			J03048	CCDS7763.1	11p15.5-p15.4	2012-10-02			ENSG00000110169	ENSG00000110169			5171	protein-coding gene	gene with protein product		142290				2989777, 2842511	Standard	NM_000613		Approved		uc001mdg.2	P02790	OTTHUMG00000133399	ENST00000265983.3:c.69C>A	11.37:g.6462125G>T		Somatic		Capture	Illumina HiSeq	Phase_I	6418701	NM_000613	B2R957	Silent	SNP	ENST00000265983.3	37	CCDS7763.1																																																																																				0.572	HPX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257256.1	NM_000613	
DNHD1	144132	broad.mit.edu	37	11	6532625	6532625	+	Missense_Mutation	SNP	G	G	A	rs148449070		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr11:6532625G>A	ENST00000527990.2	+	5	1358	c.1358G>A	c.(1357-1359)cGt>cAt	p.R453H	DNHD1_ENST00000354685.3_Missense_Mutation_p.R453H|DNHD1_ENST00000254579.6_Missense_Mutation_p.R453H			Q96M86	DNHD1_HUMAN	dynein heavy chain domain 1	453					microtubule-based movement (GO:0007018)	dynein complex (GO:0030286)|extracellular vesicular exosome (GO:0070062)	microtubule motor activity (GO:0003777)	p.R453H(2)		NS(1)|autonomic_ganglia(1)|breast(4)|endometrium(13)|kidney(6)|large_intestine(11)|lung(14)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	55		Medulloblastoma(188;0.00776)|all_neural(188;0.0652)|Breast(177;0.171)		Epithelial(150;3.93e-08)|BRCA - Breast invasive adenocarcinoma(625;0.13)		CTGCTCCATCGTTGCCTAAAC	0.547																																					p.R453H												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G1358A	11						.	G	HIS/ARG,HIS/ARG	1,4401	2.1+/-5.4	0,1,2200	140.0	134.0	136.0		1358,1358	3.1	0.1	11	dbSNP_134	136	2,8590	2.2+/-6.3	0,2,4294	yes	missense,missense	DNHD1	NM_144666.2,NM_173589.3	29,29	0,3,6494	AA,AG,GG		0.0233,0.0227,0.0231	possibly-damaging,possibly-damaging	453/4754,453/598	6532625	3,12991	2201	4296	6497	6489201	SO:0001583	missense	144132	exon7			AK128064	CCDS44532.1, CCDS7767.1	11p15.4	2011-02-10		2005-11-28	ENSG00000179532	ENSG00000179532			26532	protein-coding gene	gene with protein product			"""chromosome 11 open reading frame 47"", ""dynein heavy chain domain 1-like"", ""coiled-coil domain containing 35"""	DHCD1, C11orf47, DNHD1L, CCDC35		12975309	Standard	NM_173589		Approved	FLJ32752, FLJ46184, FLJ35709, DKFZp686J0796	uc001mdw.4	Q96M86	OTTHUMG00000133403	ENST00000527990.2:c.1358G>A	11.37:g.6532625G>A	ENSP00000436180:p.Arg453His	Somatic		Capture	Illumina HiSeq	Phase_I	6489201	NM_144666	Q2NKK8|Q6UWI9|Q8NAA2|Q8TEE6|Q9NSZ9	Missense_Mutation	SNP	ENST00000527990.2	37	CCDS44532.1	.	.	.	.	.	.	.	.	.	.	G	11.94	1.790120	0.31685	2.27E-4	2.33E-4	ENSG00000179532	ENST00000254579;ENST00000354685;ENST00000527990	T;T;T	0.27402	1.67;2.66;1.67	5.32	3.11	0.35812	.	0.831941	0.10497	N	0.667688	T	0.16685	0.0401	N	0.20986	0.625	0.09310	N	1	B;P	0.38788	0.225;0.647	B;B	0.24541	0.028;0.054	T	0.08452	-1.0721	10	0.49607	T	0.09	.	8.2706	0.31842	0.1741:0.0:0.8259:0.0	.	453;453	Q96M86;Q96M86-4	DNHD1_HUMAN;.	H	453	ENSP00000254579:R453H;ENSP00000346716:R453H;ENSP00000436180:R453H	ENSP00000254579:R453H	R	+	2	0	DNHD1	6489201	0.051000	0.20477	0.073000	0.20177	0.901000	0.52897	0.550000	0.23345	0.478000	0.27488	0.655000	0.94253	CGT		0.547	DNHD1-007	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384673.2	NM_144666	
DCHS1	8642	broad.mit.edu	37	11	6649973	6649973	+	Silent	SNP	G	G	T	rs533411916		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr11:6649973G>T	ENST00000299441.3	-	13	5661	c.5250C>A	c.(5248-5250)acC>acA	p.T1750T	RP11-732A19.6_ENST00000526633.1_RNA	NM_003737.2	NP_003728.1	Q96JQ0	PCD16_HUMAN	dachsous cadherin-related 1	1750	Cadherin 16. {ECO:0000255|PROSITE- ProRule:PRU00043}.				branching involved in ureteric bud morphogenesis (GO:0001658)|calcium-dependent cell-cell adhesion (GO:0016339)|cochlea development (GO:0090102)|digestive tract development (GO:0048565)|heart morphogenesis (GO:0003007)|heterophilic cell-cell adhesion (GO:0007157)|hippo signaling (GO:0035329)|homophilic cell adhesion (GO:0007156)|neural tube development (GO:0021915)|neurogenesis (GO:0022008)|ossification involved in bone maturation (GO:0043931)|post-anal tail morphogenesis (GO:0036342)	apical part of cell (GO:0045177)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.T1750T(1)		breast(3)|central_nervous_system(1)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(4)|kidney(4)|large_intestine(16)|liver(1)|lung(41)|ovary(4)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(6)|urinary_tract(4)	103		Medulloblastoma(188;0.00263)|all_neural(188;0.026)		Epithelial(150;6.35e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		CACTCCCAAAGGTTGGTGCAT	0.592													G|||	1	0.000199681	0.0	0.0	5008	,	,		22404	0.001		0.0	False		,,,				2504	0.0				p.T1750T												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C5250A	11						.						103.0	94.0	97.0					11																	6649973		2201	4296	6497	6606549	SO:0001819	synonymous_variant	8642	exon13			AB000895	CCDS7771.1	11p15.4	2013-10-04	2013-10-04	2004-09-03	ENSG00000166341	ENSG00000166341		"""Cadherins / Cadherin-related"""	13681	protein-coding gene	gene with protein product	"""cadherin-related family member 6"""	603057	"""protocadherin 16"", ""dachsous 1 (Drosophila)"""	CDH25, PCDH16		9199196	Standard	XM_005253207		Approved	FIB1, KIAA1773, FLJ11790, CDHR6	uc001mem.1	Q96JQ0	OTTHUMG00000133398	ENST00000299441.3:c.5250C>A	11.37:g.6649973G>T		Somatic		Capture	Illumina HiSeq	Phase_I	6606549	NM_003737	O15098	Silent	SNP	ENST00000299441.3	37	CCDS7771.1																																																																																				0.592	DCHS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257258.1	NM_003737	
ZNF214	7761	broad.mit.edu	37	11	7021577	7021577	+	Missense_Mutation	SNP	T	T	C	rs150586703		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr11:7021577T>C	ENST00000278314.4	-	3	1652	c.1337A>G	c.(1336-1338)gAc>gGc	p.D446G	ZNF214_ENST00000536068.1_Missense_Mutation_p.D446G|ZNF214_ENST00000531083.1_5'Flank	NM_013249.2	NP_037381.2	Q9UL59	ZN214_HUMAN	zinc finger protein 214	446					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)	p.D446G(1)		NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(6)|lung(10)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	29				Epithelial(150;3.87e-08)|BRCA - Breast invasive adenocarcinoma(625;0.081)		CTTTCCACAGTCATCACATTT	0.428																																					p.D446G	Ovarian(22;251 657 736 21522 46864)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A1337G	11						.	T	GLY/ASP	1,4401	2.1+/-5.4	0,1,2200	120.0	124.0	123.0		1337	1.7	0.8	11	dbSNP_134	123	0,8592		0,0,4296	no	missense	ZNF214	NM_013249.2	94	0,1,6496	CC,CT,TT		0.0,0.0227,0.0077	benign	446/607	7021577	1,12993	2201	4296	6497	6978153	SO:0001583	missense	7761	exon3			AF056617	CCDS31418.1	11p15.4	2013-01-08				ENSG00000149050		"""Zinc fingers, C2H2-type"", ""-"""	13006	protein-coding gene	gene with protein product		605015					Standard	NM_013249		Approved		uc001mfa.2	Q9UL59		ENST00000278314.4:c.1337A>G	11.37:g.7021577T>C	ENSP00000278314:p.Asp446Gly	Somatic		Capture	Illumina HiSeq	Phase_I	6978153	NM_013249	B2R8Q1	Missense_Mutation	SNP	ENST00000278314.4	37	CCDS31418.1	.	.	.	.	.	.	.	.	.	.	T	7.178	0.588997	0.13812	2.27E-4	0.0	ENSG00000149050	ENST00000278314;ENST00000536068	T;T	0.07327	3.2;3.2	4.05	1.74	0.24563	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.438854	0.19485	N	0.113125	T	0.06371	0.0164	L	0.28400	0.85	0.09310	N	1	B	0.19445	0.036	B	0.19391	0.025	T	0.30880	-0.9963	10	0.72032	D	0.01	.	6.9395	0.24484	0.0:0.2013:0.0:0.7987	.	446	Q9UL59	ZN214_HUMAN	G	446	ENSP00000278314:D446G;ENSP00000445373:D446G	ENSP00000278314:D446G	D	-	2	0	ZNF214	6978153	0.000000	0.05858	0.849000	0.33467	0.988000	0.76386	0.564000	0.23563	0.371000	0.24564	0.459000	0.35465	GAC		0.428	ZNF214-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385349.1		
NLRP14	338323	broad.mit.edu	37	11	7067910	7067910	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr11:7067910G>A	ENST00000299481.4	+	5	2316	c.1970G>A	c.(1969-1971)cGc>cAc	p.R657H		NM_176822.3	NP_789792.1	Q86W24	NAL14_HUMAN	NLR family, pyrin domain containing 14	657					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)		ATP binding (GO:0005524)	p.R657H(2)		breast(3)|large_intestine(7)|lung(1)|ovary(3)|pancreas(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	21				Epithelial(150;4.62e-08)|BRCA - Breast invasive adenocarcinoma(625;0.0871)		GATGGTGATCGCATTACTCAC	0.373																																					p.R657H												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G1970A	11						.						227.0	196.0	206.0					11																	7067910		2201	4296	6497	7024486	SO:0001583	missense	338323	exon5			BK001107	CCDS7776.1	11p15.4	2006-12-08	2006-12-08	2006-12-08		ENSG00000158077		"""Nucleotide-binding domain and leucine rich repeat containing"""	22939	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 14"""	609665	"""NACHT, leucine rich repeat and PYD containing 14"""	NALP14		12563287	Standard	NM_176822		Approved	NOD5, GC-LRR, Nalp-iota, PAN8, CLR11.2	uc001mfb.1	Q86W24		ENST00000299481.4:c.1970G>A	11.37:g.7067910G>A	ENSP00000299481:p.Arg657His	Somatic		Capture	Illumina HiSeq	Phase_I	7024486	NM_176822	Q7RTR6	Missense_Mutation	SNP	ENST00000299481.4	37	CCDS7776.1	.	.	.	.	.	.	.	.	.	.	G	7.837	0.721116	0.15372	.	.	ENSG00000158077	ENST00000299481	D	0.89343	-2.5	3.99	-7.98	0.01135	.	1.873340	0.03014	N	0.149773	T	0.74596	0.3737	N	0.14661	0.345	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.66540	-0.5898	10	0.15066	T	0.55	.	5.9816	0.19411	0.71:0.0895:0.1027:0.0978	.	657	Q86W24	NAL14_HUMAN	H	657	ENSP00000299481:R657H	ENSP00000299481:R657H	R	+	2	0	NLRP14	7024486	0.000000	0.05858	0.000000	0.03702	0.089000	0.18198	-3.243000	0.00543	-2.789000	0.00357	-0.991000	0.02546	CGC		0.373	NLRP14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384551.1	NM_176822	
TUB	7275	broad.mit.edu	37	11	8122092	8122092	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr11:8122092G>A	ENST00000299506.2	+	10	1308	c.1159G>A	c.(1159-1161)Gtg>Atg	p.V387M	TUB_ENST00000534099.1_Missense_Mutation_p.V393M|TUB_ENST00000305253.4_Missense_Mutation_p.V442M	NM_177972.2	NP_813977.1	P50607	TUB_HUMAN	tubby bipartite transcription factor	387					multicellular organismal macromolecule metabolic process (GO:0044259)|phagocytosis (GO:0006909)|phototransduction (GO:0007602)|positive regulation of phagocytosis (GO:0050766)|response to hormone (GO:0009725)|retina development in camera-type eye (GO:0060041)|sensory perception of sound (GO:0007605)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	G-protein coupled photoreceptor activity (GO:0008020)|protein complex binding (GO:0032403)	p.V442M(1)		breast(1)|cervix(1)|endometrium(9)|large_intestine(7)|lung(5)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1)	26		all_lung(207;6.91e-20)|Lung NSC(207;3.36e-17)		Epithelial(150;1.69e-62)|BRCA - Breast invasive adenocarcinoma(625;8.54e-06)|LUSC - Lung squamous cell carcinoma(625;0.000184)		GAAGATGAGCGTGATTGTCCC	0.542																																					p.V387M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1159A	11						.						164.0	135.0	145.0					11																	8122092		2201	4296	6497	8078668	SO:0001583	missense	7275	exon10			U54644	CCDS7786.1, CCDS7787.1	11p15.5	2013-08-06	2013-08-06		ENSG00000166402	ENSG00000166402			12406	protein-coding gene	gene with protein product		601197	"""tubby (mouse) homolog"", ""tubby homolog (mouse)"""			8612280	Standard	NM_003320		Approved	rd5	uc001mfy.3	P50607	OTTHUMG00000165690	ENST00000299506.2:c.1159G>A	11.37:g.8122092G>A	ENSP00000299506:p.Val387Met	Somatic		Capture	Illumina HiSeq	Phase_I	8078668	NM_177972	D3DQU4|O00293|Q6B007	Missense_Mutation	SNP	ENST00000299506.2	37	CCDS7787.1	.	.	.	.	.	.	.	.	.	.	G	28.7	4.946451	0.92593	.	.	ENSG00000166402	ENST00000534099;ENST00000305253;ENST00000299506	D;D;D	0.97161	-4.27;-4.27;-4.27	4.59	4.59	0.56863	Tubby, C-terminal (4);	0.000000	0.85682	D	0.000000	D	0.98579	0.9525	M	0.87682	2.9	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.87578	0.995;0.998;0.997	D	0.99821	1.1047	10	0.87932	D	0	-0.4314	17.7363	0.88394	0.0:0.0:1.0:0.0	.	393;387;442	E9PQR4;P50607;P50607-2	.;TUB_HUMAN;.	M	393;442;387	ENSP00000434400:V393M;ENSP00000305426:V442M;ENSP00000299506:V387M	ENSP00000299506:V387M	V	+	1	0	TUB	8078668	1.000000	0.71417	0.998000	0.56505	0.993000	0.82548	9.869000	0.99810	2.277000	0.76020	0.563000	0.77884	GTG		0.542	TUB-003	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385823.1	NM_003320	
IPO7	10527	broad.mit.edu	37	11	9431628	9431628	+	Missense_Mutation	SNP	T	T	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr11:9431628T>A	ENST00000379719.3	+	4	616	c.474T>A	c.(472-474)aaT>aaA	p.N158K		NM_006391.2	NP_006382.1	O95373	IPO7_HUMAN	importin 7	158					innate immune response (GO:0045087)|protein import into nucleus (GO:0006606)|regulation of catalytic activity (GO:0050790)|signal transduction (GO:0007165)|viral process (GO:0016032)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nuclear pore (GO:0005643)	Ran GTPase binding (GO:0008536)|small GTPase regulator activity (GO:0005083)|transporter activity (GO:0005215)	p.N158K(1)		NS(1)|breast(1)|endometrium(3)|kidney(3)|large_intestine(6)|lung(12)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29				all cancers(16;8.29e-09)|Epithelial(150;4.76e-08)|BRCA - Breast invasive adenocarcinoma(625;0.0217)		TTGTGAAAAATTATGAGTAAG	0.348																																					p.N158K												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T474A	11						.						134.0	126.0	129.0					11																	9431628		2201	4296	6497	9388204	SO:0001583	missense	10527	exon4			AF098799	CCDS31425.1	11p15.3	2010-12-02	2003-03-11	2003-03-14	ENSG00000205339	ENSG00000205339		"""Importins"""	9852	protein-coding gene	gene with protein product		605586	"""RAN binding protein 7"""	RANBP7		9214382	Standard	NM_006391		Approved	Imp7	uc001mho.3	O95373	OTTHUMG00000165753	ENST00000379719.3:c.474T>A	11.37:g.9431628T>A	ENSP00000369042:p.Asn158Lys	Somatic		Capture	Illumina HiSeq	Phase_I	9388204	NM_006391	A6NNM5|B2R786|Q1RMF7|Q9H177|Q9NTE3	Missense_Mutation	SNP	ENST00000379719.3	37	CCDS31425.1	.	.	.	.	.	.	.	.	.	.	T	10.04	1.242042	0.22796	.	.	ENSG00000205339	ENST00000379719;ENST00000527431	T;T	0.65364	-0.15;-0.15	5.74	4.61	0.57282	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.34948	0.0915	N	0.16862	0.45	0.58432	D	0.999995	B	0.16603	0.018	B	0.15484	0.013	T	0.29488	-1.0010	10	0.06236	T	0.91	.	3.3207	0.07049	0.0:0.3339:0.0:0.6661	.	158	O95373	IPO7_HUMAN	K	158;96	ENSP00000369042:N158K;ENSP00000435235:N96K	ENSP00000369042:N158K	N	+	3	2	IPO7	9388204	1.000000	0.71417	1.000000	0.80357	0.926000	0.56050	3.346000	0.52190	2.191000	0.70037	0.477000	0.44152	AAT		0.348	IPO7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386022.1	NM_006391	
PDE3B	5140	broad.mit.edu	37	11	14865557	14865557	+	Silent	SNP	T	T	C			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr11:14865557T>C	ENST00000282096.4	+	12	2858	c.2505T>C	c.(2503-2505)gcT>gcC	p.A835A	PDE3B_ENST00000455098.2_Silent_p.A784A	NM_000922.3	NP_000913.2	Q13370	PDE3B_HUMAN	phosphodiesterase 3B, cGMP-inhibited	835	Catalytic. {ECO:0000250}.				angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cAMP catabolic process (GO:0006198)|cellular response to insulin stimulus (GO:0032869)|endocrine pancreas development (GO:0031018)|glucose homeostasis (GO:0042593)|insulin receptor signaling pathway (GO:0008286)|negative regulation of angiogenesis (GO:0016525)|negative regulation of cAMP-mediated signaling (GO:0043951)|negative regulation of cell adhesion (GO:0007162)|negative regulation of cell adhesion mediated by integrin (GO:0033629)|negative regulation of lipid catabolic process (GO:0050995)|regulation of insulin secretion (GO:0050796)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|guanyl-nucleotide exchange factor complex (GO:0032045)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	3',5'-cyclic-nucleotide phosphodiesterase activity (GO:0004114)|cGMP-inhibited cyclic-nucleotide phosphodiesterase activity (GO:0004119)|metal ion binding (GO:0046872)|protein kinase B binding (GO:0043422)	p.A835A(1)		NS(1)|breast(1)|endometrium(5)|kidney(3)|large_intestine(6)|lung(15)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	39					Caffeine(DB00201)	TTCTAGTGGCTACAAATGCCC	0.383																																					p.A835A												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.T2505C	11						.						102.0	99.0	100.0					11																	14865557		2200	4294	6494	14822133	SO:0001819	synonymous_variant	5140	exon12			U38178	CCDS7817.1	11p15.2	2008-03-18			ENSG00000152270	ENSG00000152270	3.1.4.17	"""Phosphodiesterases"""	8779	protein-coding gene	gene with protein product		602047				8884271, 16395595	Standard	NM_000922		Approved	HcGIP1	uc001mln.3	Q13370	OTTHUMG00000165898	ENST00000282096.4:c.2505T>C	11.37:g.14865557T>C		Somatic		Capture	Illumina HiSeq	Phase_I	14822133	NM_000922	B7ZM37|O00639|Q14408|Q6SEI4	Silent	SNP	ENST00000282096.4	37	CCDS7817.1																																																																																				0.383	PDE3B-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000386974.1	NM_000922	
PLEKHA7	144100	broad.mit.edu	37	11	16812635	16812635	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr11:16812635C>T	ENST00000355661.3	-	20	2867	c.2857G>A	c.(2857-2859)Gtg>Atg	p.V953M	PLEKHA7_ENST00000531066.1_Missense_Mutation_p.V953M|PLEKHA7_ENST00000448080.2_Missense_Mutation_p.V954M|PLEKHA7_ENST00000532079.1_Intron|PLEKHA7_ENST00000332954.4_5'UTR			Q6IQ23	PKHA7_HUMAN	pleckstrin homology domain containing, family A member 7	953					epithelial cell-cell adhesion (GO:0090136)|zonula adherens maintenance (GO:0045218)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|zonula adherens (GO:0005915)	delta-catenin binding (GO:0070097)	p.V953M(1)		breast(1)|central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(7)|lung(13)|ovary(1)|prostate(2)|skin(7)|urinary_tract(1)	37						AGGCCCCGCACAGATGTGTGC	0.677																																					p.V953M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2857A	11						.						46.0	45.0	45.0					11																	16812635		2200	4294	6494	16769211	SO:0001583	missense	144100	exon20			BC033239	CCDS31434.1	11p15	2013-01-10			ENSG00000166689	ENSG00000166689		"""Pleckstrin homology (PH) domain containing"""	27049	protein-coding gene	gene with protein product		612686				12477932	Standard	NM_175058		Approved	DKFZp686M22243	uc001mmo.3	Q6IQ23	OTTHUMG00000165954	ENST00000355661.3:c.2857G>A	11.37:g.16812635C>T	ENSP00000347883:p.Val953Met	Somatic		Capture	Illumina HiSeq	Phase_I	16769211	NM_175058	B4DK33|B4DWC3|Q86VZ7	Missense_Mutation	SNP	ENST00000355661.3	37	CCDS31434.1	.	.	.	.	.	.	.	.	.	.	C	33	5.193649	0.94960	.	.	ENSG00000166689	ENST00000531066;ENST00000355661;ENST00000448080	T;T;T	0.21191	2.02;2.02;2.02	5.52	5.52	0.82312	.	0.000000	0.85682	D	0.000000	T	0.47911	0.1471	M	0.66939	2.045	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;0.999;1.0;1.0	D;D;D;D;D	0.97110	1.0;0.999;0.997;1.0;0.999	T	0.32455	-0.9906	10	0.51188	T	0.08	-9.5797	19.7959	0.96481	0.0:1.0:0.0:0.0	.	528;953;953;954;70	Q6IQ23-3;E9PKC0;Q6IQ23;Q6IQ23-2;Q8IUS9	.;.;PKHA7_HUMAN;.;.	M	953;953;954	ENSP00000435389:V953M;ENSP00000347883:V953M;ENSP00000416895:V954M	ENSP00000347883:V953M	V	-	1	0	PLEKHA7	16769211	1.000000	0.71417	0.969000	0.41365	0.978000	0.69477	7.442000	0.80503	2.745000	0.94114	0.561000	0.74099	GTG		0.677	PLEKHA7-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000387242.2	NM_175058	
NELL1	4745	broad.mit.edu	37	11	21392488	21392488	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr11:21392488G>A	ENST00000357134.5	+	15	1791	c.1639G>A	c.(1639-1641)Gag>Aag	p.E547K	NELL1_ENST00000532434.1_Missense_Mutation_p.E547K|NELL1_ENST00000298925.5_Missense_Mutation_p.E575K|NELL1_ENST00000529218.1_3'UTR|NELL1_ENST00000325319.5_Missense_Mutation_p.E490K	NM_006157.3|NM_201551.1	NP_006148.2|NP_963845.1	Q92832	NELL1_HUMAN	NEL-like 1 (chicken)	547	EGF-like 3. {ECO:0000255|PROSITE- ProRule:PRU00076}.				cell differentiation (GO:0030154)|negative regulation of cyclin catabolic process (GO:2000599)|negative regulation of osteoblast proliferation (GO:0033689)|nervous system development (GO:0007399)|positive regulation of bone mineralization (GO:0030501)|positive regulation of osteoblast differentiation (GO:0045669)|regulation of gene expression (GO:0010468)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|nuclear envelope (GO:0005635)|perinuclear region of cytoplasm (GO:0048471)	calcium ion binding (GO:0005509)	p.E547K(1)		NS(1)|breast(3)|endometrium(5)|kidney(3)|large_intestine(15)|lung(36)|ovary(2)|prostate(3)|skin(1)|urinary_tract(1)	70						AAGCCACTGCGAGAAAGGTAA	0.428																																					p.E547K												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1639A	11						.						91.0	86.0	88.0					11																	21392488		2203	4300	6503	21349064	SO:0001583	missense	4745	exon15			AK127805	CCDS7855.1, CCDS44555.1, CCDS73267.1, CCDS73268.1	11p15.1	2008-02-01	2001-11-28		ENSG00000165973	ENSG00000165973			7750	protein-coding gene	gene with protein product		602319	"""nel (chicken)-like 1"""			8975702	Standard	NM_006157		Approved	IDH3GL, FLJ45906	uc001mqe.3	Q92832	OTTHUMG00000166042	ENST00000357134.5:c.1639G>A	11.37:g.21392488G>A	ENSP00000349654:p.Glu547Lys	Somatic		Capture	Illumina HiSeq	Phase_I	21349064	NM_006157	B2CKC1|Q4VB90|Q4VB91|Q6NSY8|Q9Y472	Missense_Mutation	SNP	ENST00000357134.5	37	CCDS7855.1	.	.	.	.	.	.	.	.	.	.	G	31	5.066121	0.93898	.	.	ENSG00000165973	ENST00000298925;ENST00000357134;ENST00000325319;ENST00000532434	D;D;D;D	0.93307	-2.26;-2.26;-2.26;-3.2	5.59	5.59	0.84812	Epidermal growth factor-like (1);Epidermal growth factor-like, type 3 (1);	0.000000	0.85682	D	0.000000	D	0.97623	0.9221	M	0.93420	3.415	0.58432	D	0.999999	D;D;D;D	0.89917	0.999;1.0;1.0;0.999	D;D;D;D	0.87578	0.988;0.981;0.998;0.972	D	0.97649	1.0153	10	0.46703	T	0.11	-20.9059	18.3657	0.90390	0.0:0.0:1.0:0.0	.	490;575;547;547	F5H6I3;B3KXR2;Q92832-2;Q92832	.;.;.;NELL1_HUMAN	K	575;547;490;547	ENSP00000298925:E575K;ENSP00000349654:E547K;ENSP00000317837:E490K;ENSP00000437170:E547K	ENSP00000298925:E575K	E	+	1	0	NELL1	21349064	1.000000	0.71417	0.990000	0.47175	0.937000	0.57800	8.192000	0.89718	2.638000	0.89438	0.650000	0.86243	GAG		0.428	NELL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387588.1	NM_006157	
LGR4	55366	broad.mit.edu	37	11	27406981	27406981	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr11:27406981C>T	ENST00000379214.4	-	5	879	c.436G>A	c.(436-438)Gag>Aag	p.E146K	LGR4_ENST00000480977.2_Missense_Mutation_p.E98K|LGR4_ENST00000389858.4_Missense_Mutation_p.E122K	NM_018490.2	NP_060960.2	Q9BXB1	LGR4_HUMAN	leucine-rich repeat containing G protein-coupled receptor 4	146					bone mineralization (GO:0030282)|bone remodeling (GO:0046849)|canonical Wnt signaling pathway involved in metanephric kidney development (GO:0061290)|cell differentiation involved in metanephros development (GO:0072202)|epithelial cell proliferation (GO:0050673)|innate immune response (GO:0045087)|male genitalia development (GO:0030539)|metanephric glomerulus development (GO:0072224)|metanephric nephron tubule morphogenesis (GO:0072282)|negative regulation of cytokine secretion (GO:0050710)|negative regulation of toll-like receptor signaling pathway (GO:0034122)|negative regulation of transcription, DNA-templated (GO:0045892)|osteoblast differentiation (GO:0001649)|positive regulation of branching involved in ureteric bud morphogenesis (GO:0090190)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of transcription, DNA-templated (GO:0045893)|spermatogenesis (GO:0007283)	integral component of plasma membrane (GO:0005887)	G-protein coupled receptor activity (GO:0004930)|transmembrane signaling receptor activity (GO:0004888)	p.E146K(1)		NS(3)|breast(2)|endometrium(3)|kidney(2)|large_intestine(11)|lung(10)|ovary(1)	32						AAACTGTCCTCGGGGACTGAG	0.473																																					p.E146K												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G436A	11						.						89.0	78.0	82.0					11																	27406981		2202	4299	6501	27363557	SO:0001583	missense	55366	exon5			AF257182	CCDS31449.1	11p14-p13	2012-08-21	2011-01-25	2004-11-12	ENSG00000205213	ENSG00000205213		"""GPCR / Class A : Orphans"""	13299	protein-coding gene	gene with protein product		606666	"""G protein-coupled receptor 48"", ""leucine-rich repeat-containing G protein-coupled receptor 4"""	GPR48		10894923	Standard	NM_018490		Approved		uc001mrj.4	Q9BXB1	OTTHUMG00000133508	ENST00000379214.4:c.436G>A	11.37:g.27406981C>T	ENSP00000368516:p.Glu146Lys	Somatic		Capture	Illumina HiSeq	Phase_I	27363557	NM_018490	A6NCH3|G5E9B3|Q8N537|Q9NYD1	Missense_Mutation	SNP	ENST00000379214.4	37	CCDS31449.1	.	.	.	.	.	.	.	.	.	.	C	19.72	3.880666	0.72294	.	.	ENSG00000205213	ENST00000379214;ENST00000389858;ENST00000480977	T;T;T	0.57595	3.63;4.27;0.39	5.79	5.79	0.91817	.	0.171099	0.50627	D	0.000102	T	0.41213	0.1149	L	0.28694	0.88	0.46678	D	0.999151	B;B	0.24882	0.051;0.113	B;B	0.26416	0.031;0.069	T	0.21930	-1.0231	10	0.14252	T	0.57	.	15.2156	0.73264	0.0:0.9308:0.0:0.0692	.	122;146	G5E9B3;Q9BXB1	.;LGR4_HUMAN	K	146;122;98	ENSP00000368516:E146K;ENSP00000374508:E122K;ENSP00000431650:E98K	ENSP00000368516:E146K	E	-	1	0	LGR4	27363557	1.000000	0.71417	0.993000	0.49108	0.987000	0.75469	4.899000	0.63245	2.725000	0.93324	0.557000	0.71058	GAG		0.473	LGR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257467.1	NM_018490	
KCNA4	3739	broad.mit.edu	37	11	30033552	30033552	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr11:30033552C>T	ENST00000328224.6	-	2	1907	c.674G>A	c.(673-675)cGc>cAc	p.R225H	KCNA4_ENST00000526518.1_5'Flank	NM_002233.3	NP_002224.1	P22459	KCNA4_HUMAN	potassium voltage-gated channel, shaker-related subfamily, member 4	225					potassium ion transport (GO:0006813)|protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	potassium ion binding (GO:0030955)|voltage-gated potassium channel activity (GO:0005249)	p.R225H(1)		central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(17)|lung(39)|ovary(3)|pancreas(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(4)|urinary_tract(1)	78					Dalfampridine(DB06637)	AAAGCTGGGGCGGTTCCTGTC	0.468																																					p.R225H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G674A	11						.						77.0	72.0	74.0					11																	30033552		1872	4113	5985	29990128	SO:0001583	missense	3739	exon2			M55514	CCDS41629.1	11p14	2012-07-05	2002-07-10			ENSG00000182255		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	6222	protein-coding gene	gene with protein product		176266	"""potassium voltage-gated channel, shaker-related subfamily, member 4-like"""	KCNA4L		2263489, 16382104	Standard	NM_002233		Approved	Kv1.4, HK1, HPCN2	uc001msk.3	P22459		ENST00000328224.6:c.674G>A	11.37:g.30033552C>T	ENSP00000328511:p.Arg225His	Somatic		Capture	Illumina HiSeq	Phase_I	29990128	NM_002233		Missense_Mutation	SNP	ENST00000328224.6	37	CCDS41629.1	.	.	.	.	.	.	.	.	.	.	C	23.0	4.359439	0.82353	.	.	ENSG00000182255	ENST00000328224	T	0.77098	-1.07	4.94	4.94	0.65067	BTB/POZ-like (1);BTB/POZ fold (2);Potassium channel, voltage dependent, Kv, tetramerisation (1);	0.063719	0.64402	D	0.000006	D	0.91496	0.7315	H	0.94345	3.525	0.80722	D	1	D	0.89917	1.0	D	0.79108	0.992	D	0.94018	0.7290	10	0.87932	D	0	.	18.1944	0.89817	0.0:1.0:0.0:0.0	.	225	P22459	KCNA4_HUMAN	H	225	ENSP00000328511:R225H	ENSP00000328511:R225H	R	-	2	0	KCNA4	29990128	1.000000	0.71417	0.998000	0.56505	0.853000	0.48598	7.787000	0.85759	2.297000	0.77311	0.655000	0.94253	CGC		0.468	KCNA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388074.2	NM_002233	
IMMP1L	196294	broad.mit.edu	37	11	31455073	31455073	+	Missense_Mutation	SNP	A	A	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr11:31455073A>T	ENST00000278200.1	-	6	561	c.366T>A	c.(364-366)aaT>aaA	p.N122K	IMMP1L_ENST00000533642.1_Missense_Mutation_p.N13K|IMMP1L_ENST00000532287.1_Missense_Mutation_p.N122K|IMMP1L_ENST00000526776.1_Missense_Mutation_p.N50K|IMMP1L_ENST00000534812.1_Missense_Mutation_p.N13K|AC108456.1_ENST00000408411.1_RNA	NM_144981.1	NP_659418.1	Q96LU5	IMP1L_HUMAN	IMP1 inner mitochondrial membrane peptidase-like (S. cerevisiae)	122					protein processing involved in protein targeting to mitochondrion (GO:0006627)	mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	serine-type peptidase activity (GO:0008236)	p.N122K(1)		breast(1)|cervix(1)|large_intestine(1)|lung(4)	7	Lung SC(675;0.225)					AATCTGTAGAATTCTGTAGAT	0.358																																					p.N122K												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T366A	11						.						95.0	91.0	93.0					11																	31455073		2202	4299	6501	31411649	SO:0001583	missense	196294	exon6				CCDS7874.1	11p13	2014-07-30			ENSG00000148950	ENSG00000148950			26317	protein-coding gene	gene with protein product		612323					Standard	NM_144981		Approved	FLJ25059	uc001msy.1	Q96LU5	OTTHUMG00000166226	ENST00000278200.1:c.366T>A	11.37:g.31455073A>T	ENSP00000278200:p.Asn122Lys	Somatic		Capture	Illumina HiSeq	Phase_I	31411649	NM_144981	D3DQZ7|Q96SH9	Missense_Mutation	SNP	ENST00000278200.1	37	CCDS7874.1	.	.	.	.	.	.	.	.	.	.	A	17.70	3.454522	0.63290	.	.	ENSG00000148950	ENST00000532287;ENST00000526776;ENST00000534812;ENST00000278200;ENST00000533642	T;T;T;T;T	0.40476	1.03;1.03;1.03;1.03;1.03	5.87	3.53	0.40419	Peptidase S24/S26A/S26B/S26C (1);Peptidase S24/S26A/S26B/S26C, beta-ribbon domain (1);	0.000000	0.85682	D	0.000000	T	0.38480	0.1042	M	0.68593	2.085	0.80722	D	1	B	0.26512	0.151	B	0.24006	0.05	T	0.17228	-1.0376	10	0.48119	T	0.1	-22.4988	7.9244	0.29865	0.8104:0.0:0.0667:0.1228	.	122	Q96LU5	IMP1L_HUMAN	K	122;50;13;122;13	ENSP00000435576:N122K;ENSP00000434280:N50K;ENSP00000432673:N13K;ENSP00000278200:N122K;ENSP00000432471:N13K	ENSP00000278200:N122K	N	-	3	2	IMMP1L	31411649	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	1.805000	0.38883	0.459000	0.27016	0.482000	0.46254	AAT		0.358	IMMP1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388496.1	NM_144981	
CAPRIN1	4076	broad.mit.edu	37	11	34098006	34098006	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr11:34098006G>A	ENST00000341394.4	+	5	779	c.590G>A	c.(589-591)cGg>cAg	p.R197Q	CAPRIN1_ENST00000529307.1_Missense_Mutation_p.R116Q|CAPRIN1_ENST00000389645.3_Missense_Mutation_p.R197Q|CAPRIN1_ENST00000532820.1_Missense_Mutation_p.R197Q|CAPRIN1_ENST00000530820.1_Missense_Mutation_p.R197Q	NM_005898.4	NP_005889.3	Q14444	CAPR1_HUMAN	cell cycle associated protein 1	197					negative regulation of translation (GO:0017148)|positive regulation of dendrite morphogenesis (GO:0050775)|positive regulation of dendritic spine morphogenesis (GO:0061003)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoplasmic mRNA processing body (GO:0000932)|cytoplasmic stress granule (GO:0010494)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)	p.R197Q(1)		breast(2)|endometrium(2)|kidney(1)|large_intestine(6)|lung(5)|ovary(1)|prostate(1)	18		Acute lymphoblastic leukemia(5;0.00045)|all_hematologic(20;0.0016)				GACCCTGAACGGGACATGAGC	0.368																																					p.R197Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G590A	11						.						90.0	96.0	94.0					11																	34098006		2202	4298	6500	34054582	SO:0001583	missense	4076	exon5			BC001731	CCDS31453.1, CCDS31454.1	11p13	2010-08-03	2007-03-27	2007-03-27	ENSG00000135387	ENSG00000135387			6743	protein-coding gene	gene with protein product	"""cytoplasmic activation/proliferation-associated protein-1"""	601178	"""membrane component, chromosome 11, surface marker 1"", ""GPI-anchored membrane protein 1"""	M11S1, GPIAP1		7657653, 16177067, 17210633, 14764709, 15471883	Standard	NM_005898		Approved	caprin-1, RNG105	uc001mvh.1	Q14444	OTTHUMG00000166248	ENST00000341394.4:c.590G>A	11.37:g.34098006G>A	ENSP00000340329:p.Arg197Gln	Somatic		Capture	Illumina HiSeq	Phase_I	34054582	NM_203364	A6NMY7|D3DR06|Q15074|Q6IMN4|Q6IMN7|Q9BV09	Missense_Mutation	SNP	ENST00000341394.4	37	CCDS31453.1	.	.	.	.	.	.	.	.	.	.	G	21.8	4.200672	0.79015	.	.	ENSG00000135387	ENST00000341394;ENST00000389645;ENST00000532820;ENST00000530820;ENST00000529307	T;T;T;T;T	0.32023	1.47;1.47;1.47;1.47;1.47	5.66	5.66	0.87406	.	0.049281	0.85682	D	0.000000	T	0.32675	0.0837	L	0.56124	1.755	0.58432	D	0.999996	P;P	0.50272	0.933;0.922	B;B	0.38194	0.229;0.267	T	0.21552	-1.0242	10	0.59425	D	0.04	.	19.7505	0.96267	0.0:0.0:1.0:0.0	.	197;197	Q14444;Q14444-2	CAPR1_HUMAN;.	Q	197;197;197;197;116	ENSP00000340329:R197Q;ENSP00000374296:R197Q;ENSP00000434150:R197Q;ENSP00000434204:R197Q;ENSP00000431581:R116Q	ENSP00000340329:R197Q	R	+	2	0	CAPRIN1	34054582	1.000000	0.71417	1.000000	0.80357	0.912000	0.54170	7.208000	0.77907	2.671000	0.90904	0.655000	0.94253	CGG		0.368	CAPRIN1-001	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000388680.2	NM_005898	
PAMR1	25891	broad.mit.edu	37	11	35457675	35457675	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr11:35457675G>A	ENST00000378880.2	-	9	1554	c.1109C>T	c.(1108-1110)cCa>cTa	p.P370L	PAMR1_ENST00000532848.1_Missense_Mutation_p.P330L|PAMR1_ENST00000278360.3_Missense_Mutation_p.P387L|PAMR1_ENST00000378878.3_Missense_Mutation_p.P259L	NM_001001991.1	NP_001001991.1	Q6UXH9	PAMR1_HUMAN	peptidase domain containing associated with muscle regeneration 1	370						extracellular region (GO:0005576)	serine-type endopeptidase activity (GO:0004252)	p.P387L(1)		breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(8)|ovary(3)|upper_aerodigestive_tract(1)	26						CTGGTGTAATGGTGTCTCCCT	0.527																																					p.P370L												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1109T	11						.						147.0	141.0	143.0					11																	35457675		2202	4298	6500	35414251	SO:0001583	missense	25891	exon9				CCDS7898.1, CCDS31460.1, CCDS60759.1, CCDS60760.1	11p13	2009-09-30			ENSG00000149090	ENSG00000149090			24554	protein-coding gene	gene with protein product	"""regeneration-associated muscle protease"""					15111323	Standard	NM_001282675		Approved	RAMP, DKFZP586H2123	uc001mwf.3	Q6UXH9	OTTHUMG00000166328	ENST00000378880.2:c.1109C>T	11.37:g.35457675G>A	ENSP00000368158:p.Pro370Leu	Somatic		Capture	Illumina HiSeq	Phase_I	35414251	NM_001001991	A8MQ58|B7ZA73|Q5EBL7|Q5JPI4|Q6N062|Q71RE9|Q96JW2|Q9Y432	Missense_Mutation	SNP	ENST00000378880.2	37	CCDS31460.1	.	.	.	.	.	.	.	.	.	.	G	31	5.058920	0.93846	.	.	ENSG00000149090	ENST00000278360;ENST00000378880;ENST00000378878;ENST00000532848;ENST00000527605	D;D;D;D;D	0.88354	-2.22;-2.24;-2.37;-2.2;-2.22	5.43	5.43	0.79202	.	0.000000	0.85682	D	0.000000	D	0.91085	0.7194	N	0.24115	0.695	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.997;0.999	D	0.92534	0.6036	10	0.87932	D	0	.	19.2398	0.93877	0.0:0.0:1.0:0.0	.	259;370;387	A8MQ58;Q6UXH9;Q6UXH9-2	.;PAMR1_HUMAN;.	L	387;370;259;330;347	ENSP00000278360:P387L;ENSP00000368158:P370L;ENSP00000368156:P259L;ENSP00000433868:P330L;ENSP00000432591:P347L	ENSP00000278360:P387L	P	-	2	0	PAMR1	35414251	1.000000	0.71417	0.992000	0.48379	0.992000	0.81027	7.398000	0.79919	2.549000	0.85964	0.561000	0.74099	CCA		0.527	PAMR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389177.1	NM_015430	
ACCS	84680	broad.mit.edu	37	11	44105040	44105040	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr11:44105040C>A	ENST00000263776.8	+	14	1755	c.1321C>A	c.(1321-1323)Ctg>Atg	p.L441M		NM_001127219.1|NM_032592.3	NP_001120691.1|NP_115981.1	Q96QU6	1A1L1_HUMAN	1-aminocyclopropane-1-carboxylate synthase homolog (Arabidopsis)(non-functional)	441					biosynthetic process (GO:0009058)		catalytic activity (GO:0003824)|protein homodimerization activity (GO:0042803)|pyridoxal phosphate binding (GO:0030170)	p.L441M(1)		breast(4)|endometrium(3)|large_intestine(11)|lung(15)|ovary(1)|skin(1)	35						CAACAAGGTGCTGCTGTCCTT	0.572																																					p.L441M	Esophageal Squamous(158;148 1889 8077 23160 41213)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1321A	11						.						89.0	78.0	82.0					11																	44105040		2203	4300	6503	44061616	SO:0001583	missense	84680	exon14			AY026508	CCDS7907.1	11p11	2008-03-12	2008-01-28		ENSG00000110455	ENSG00000110455			23989	protein-coding gene	gene with protein product		608405				11470512	Standard	NM_032592		Approved	PHACS, ACS	uc009yks.1	Q96QU6	OTTHUMG00000166427	ENST00000263776.8:c.1321C>A	11.37:g.44105040C>A	ENSP00000263776:p.Leu441Met	Somatic		Capture	Illumina HiSeq	Phase_I	44061616	NM_032592	B4E219|Q8WUL4|Q96LX5	Missense_Mutation	SNP	ENST00000263776.8	37	CCDS7907.1	.	.	.	.	.	.	.	.	.	.	C	21.6	4.174617	0.78452	.	.	ENSG00000110455	ENST00000263776	D	0.91295	-2.82	5.91	5.91	0.95273	Aminotransferase, class I/classII (1);Pyridoxal phosphate-dependent transferase, major region, subdomain 2 (1);Pyridoxal phosphate-dependent transferase, major domain (1);	0.159978	0.42548	D	0.000681	D	0.93713	0.7991	M	0.66939	2.045	0.80722	D	1	P	0.47191	0.891	P	0.55222	0.771	D	0.92250	0.5808	10	0.39692	T	0.17	-11.735	19.8936	0.96942	0.0:1.0:0.0:0.0	.	441	Q96QU6	1A1L1_HUMAN	M	441	ENSP00000263776:L441M	ENSP00000263776:L441M	L	+	1	2	ACCS	44061616	1.000000	0.71417	1.000000	0.80357	0.937000	0.57800	3.427000	0.52785	2.793000	0.96121	0.655000	0.94253	CTG		0.572	ACCS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389721.1	NM_032592	
PRDM11	56981	broad.mit.edu	37	11	45246044	45246044	+	Missense_Mutation	SNP	A	A	C			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr11:45246044A>C	ENST00000530656.1	+	7	1121	c.1121A>C	c.(1120-1122)gAc>gCc	p.D374A	PRDM11_ENST00000528980.1_Intron|CTD-2560E9.3_ENST00000527450.1_RNA|PRDM11_ENST00000424263.2_Missense_Mutation_p.D340A|PRDM11_ENST00000263765.4_Missense_Mutation_p.D374A			Q9NQV5	PRD11_HUMAN	PR domain containing 11	374							methyltransferase activity (GO:0008168)	p.D374A(1)		endometrium(3)|kidney(3)|large_intestine(5)|lung(10)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	26						TACCAGGATGACGCCTACAGT	0.577																																					p.D374A	NSCLC(118;1511 1736 6472 36603 43224)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A1121C	11						.						116.0	121.0	119.0					11																	45246044		2203	4299	6502	45202620	SO:0001583	missense	56981	exon8			AF275818	CCDS58130.1, CCDS73277.1	11p11	2008-07-21			ENSG00000019485	ENSG00000019485			13996	protein-coding gene	gene with protein product	"""PR-domain containing protein 11"""						Standard	NM_001256695		Approved	PFM8	uc031qab.1	Q9NQV5	OTTHUMG00000166478	ENST00000530656.1:c.1121A>C	11.37:g.45246044A>C	ENSP00000435976:p.Asp374Ala	Somatic		Capture	Illumina HiSeq	Phase_I	45202620	NM_020229	Q8N9F1	Missense_Mutation	SNP	ENST00000530656.1	37		.	.	.	.	.	.	.	.	.	.	A	11.33	1.607603	0.28623	.	.	ENSG00000019485	ENST00000263765;ENST00000530656;ENST00000424263	T;T;T	0.32272	1.46;1.46;1.49	5.41	4.27	0.50696	.	0.309488	0.27478	N	0.019197	T	0.20861	0.0502	N	0.19112	0.55	0.36405	D	0.863389	P	0.38827	0.649	B	0.38428	0.273	T	0.19549	-1.0302	10	0.66056	D	0.02	-10.9833	10.084	0.42406	0.9163:0.0:0.0837:0.0	.	374	Q9NQV5	PRD11_HUMAN	A	374;374;340	ENSP00000263765:D374A;ENSP00000435976:D374A;ENSP00000394314:D340A	ENSP00000263765:D374A	D	+	2	0	PRDM11	45202620	0.994000	0.37717	0.584000	0.28653	0.198000	0.23893	3.225000	0.51246	0.900000	0.36469	0.456000	0.33151	GAC		0.577	PRDM11-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000389928.1	NM_020229	
CHST1	8534	broad.mit.edu	37	11	45671693	45671693	+	Missense_Mutation	SNP	C	C	T	rs201148963		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr11:45671693C>T	ENST00000308064.2	-	4	1451	c.781G>A	c.(781-783)Ggg>Agg	p.G261R	CHST1_ENST00000533673.1_5'Flank|RP11-495O11.1_ENST00000525563.1_RNA	NM_003654.5	NP_003645.1	O43916	CHST1_HUMAN	carbohydrate (keratan sulfate Gal-6) sulfotransferase 1	261					carbohydrate metabolic process (GO:0005975)|galactose metabolic process (GO:0006012)|glycosaminoglycan metabolic process (GO:0030203)|inflammatory response (GO:0006954)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate metabolic process (GO:0042339)|polysaccharide metabolic process (GO:0005976)|small molecule metabolic process (GO:0044281)|sulfur compound metabolic process (GO:0006790)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	keratan sulfotransferase activity (GO:0045130)|sulfotransferase activity (GO:0008146)	p.G261R(1)		breast(1)|endometrium(3)|large_intestine(10)|lung(17)|pancreas(1)|prostate(2)|skin(7)|upper_aerodigestive_tract(1)	42				GBM - Glioblastoma multiforme(35;3e-06)|BRCA - Breast invasive adenocarcinoma(625;0.0781)		GGTTTCCTCCCGGTGCCGTAC	0.662																																					p.G261R												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G781A	11						.						75.0	65.0	68.0					11																	45671693		2203	4299	6502	45628269	SO:0001583	missense	8534	exon4			U65637	CCDS7913.1	11p11.2	2010-04-29			ENSG00000175264	ENSG00000175264		"""Sulfotransferases, membrane-bound"""	1969	protein-coding gene	gene with protein product		603797				9405439, 9639683	Standard	NM_003654		Approved	C6ST, KSGal6ST	uc001mys.2	O43916		ENST00000308064.2:c.781G>A	11.37:g.45671693C>T	ENSP00000309270:p.Gly261Arg	Somatic		Capture	Illumina HiSeq	Phase_I	45628269	NM_003654	D3DQP2	Missense_Mutation	SNP	ENST00000308064.2	37	CCDS7913.1	.	.	.	.	.	.	.	.	.	.	C	23.0	4.364463	0.82463	.	.	ENSG00000175264	ENST00000308064	T	0.80994	-1.44	4.89	4.89	0.63831	Sulfotransferase domain (1);	0.000000	0.85682	D	0.000000	D	0.89192	0.6645	M	0.76838	2.35	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.87240	0.2266	10	0.23891	T	0.37	-9.914	18.0436	0.89326	0.0:1.0:0.0:0.0	.	261	O43916	CHST1_HUMAN	R	261	ENSP00000309270:G261R	ENSP00000309270:G261R	G	-	1	0	CHST1	45628269	1.000000	0.71417	0.502000	0.27614	0.960000	0.62799	6.079000	0.71291	2.252000	0.74401	0.462000	0.41574	GGG		0.662	CHST1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390127.1	NM_003654	
DGKZ	8525	broad.mit.edu	37	11	46393057	46393057	+	Silent	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr11:46393057C>T	ENST00000454345.1	+	9	1352	c.1227C>T	c.(1225-1227)tgC>tgT	p.C409C	DGKZ_ENST00000543978.1_Intron|DGKZ_ENST00000456247.2_Silent_p.C220C|DGKZ_ENST00000527911.1_Silent_p.C221C|DGKZ_ENST00000318201.8_Silent_p.C198C|DGKZ_ENST00000343674.6_Silent_p.C237C|DGKZ_ENST00000532868.2_Silent_p.C225C|DGKZ_ENST00000421244.2_Silent_p.C221C|DGKZ_ENST00000395574.3_Silent_p.C187C|DGKZ_ENST00000528615.1_5'UTR	NM_001105540.1	NP_001099010.1	Q13574	DGKZ_HUMAN	diacylglycerol kinase, zeta	409					blood coagulation (GO:0007596)|cell migration (GO:0016477)|intracellular signal transduction (GO:0035556)|lipid phosphorylation (GO:0046834)|mitotic G1 DNA damage checkpoint (GO:0031571)|negative regulation of mitotic cell cycle (GO:0045930)|negative regulation of Ras protein signal transduction (GO:0046580)|phosphorylation (GO:0016310)|platelet activation (GO:0030168)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)	cytoplasm (GO:0005737)|lamellipodium (GO:0030027)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|diacylglycerol kinase activity (GO:0004143)|enzyme inhibitor activity (GO:0004857)|lipid kinase activity (GO:0001727)|metal ion binding (GO:0046872)|NAD+ kinase activity (GO:0003951)|protein C-terminus binding (GO:0008022)	p.C237C(1)|p.C409C(1)		central_nervous_system(2)|endometrium(1)|kidney(2)|large_intestine(5)|lung(12)|pancreas(1)|prostate(1)|skin(1)	25				GBM - Glioblastoma multiforme(35;0.0259)|Lung(87;0.141)		AGGTGTCCTGCTTCATGCTGC	0.692																																					p.C221C												.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.C663T	11						.						32.0	37.0	36.0					11																	46393057		2202	4299	6501	46349633	SO:0001819	synonymous_variant	8525	exon8			U51477	CCDS7918.1, CCDS41640.1, CCDS44579.1, CCDS44580.1, CCDS55757.1, CCDS55758.1, CCDS55759.1, CCDS44579.2	11p11.2	2010-11-24	2010-11-24		ENSG00000149091	ENSG00000149091	2.7.1.107		2857	protein-coding gene	gene with protein product		601441	"""diacylglycerol kinase, zeta 104kDa"""			8626588	Standard	NM_003646		Approved	DAGK5, hDGKzeta, DGK-ZETA, DAGK6	uc001ncn.1	Q13574	OTTHUMG00000166437	ENST00000454345.1:c.1227C>T	11.37:g.46393057C>T		Somatic		Capture	Illumina HiSeq	Phase_I	46349633	NM_003646	B7Z2M9|B7Z6M3|E9PPW4|F6UCU9|G3V0F6|J3KNJ6|O00542|Q6ZVG7|Q8IVW9	Silent	SNP	ENST00000454345.1	37	CCDS41640.1																																																																																				0.692	DGKZ-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000389772.1	NM_001105540	
AMBRA1	55626	broad.mit.edu	37	11	46564499	46564499	+	Silent	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr11:46564499C>T	ENST00000458649.2	-	7	1486	c.1068G>A	c.(1066-1068)tcG>tcA	p.S356S	AMBRA1_ENST00000533727.1_Silent_p.S266S|AMBRA1_ENST00000426438.1_Silent_p.S356S|AMBRA1_ENST00000528950.1_Silent_p.S356S|AMBRA1_ENST00000298834.3_Silent_p.S356S|AMBRA1_ENST00000314845.3_Silent_p.S266S|AMBRA1_ENST00000534300.1_Silent_p.S356S			Q9C0C7	AMRA1_HUMAN	autophagy/beclin-1 regulator 1	356					autophagy (GO:0006914)|cell differentiation (GO:0030154)|negative regulation of cell proliferation (GO:0008285)|negative regulation of neuron apoptotic process (GO:0043524)|neural tube development (GO:0021915)	axoneme (GO:0005930)|cytoplasm (GO:0005737)|phagocytic vesicle (GO:0045335)		p.S356S(1)|p.S266S(1)		NS(1)|breast(3)|central_nervous_system(1)|endometrium(10)|kidney(2)|large_intestine(6)|lung(10)|ovary(2)|prostate(1)|skin(1)|urinary_tract(2)	39				GBM - Glioblastoma multiforme(35;0.0435)|Lung(87;0.182)		GCTGCGTTGACGAGGCCTGCT	0.622																																					p.S266S												.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.G798A	11						.						68.0	78.0	74.0					11																	46564499		2199	4299	6498	46521075	SO:0001819	synonymous_variant	55626	exon8			AB051523	CCDS31475.1, CCDS58132.1, CCDS73281.1	11p11.2	2013-01-09			ENSG00000110497	ENSG00000110497		"""WD repeat domain containing"", ""DDB1 and CUL4 associated factors"""	25990	protein-coding gene	gene with protein product	"""WD repeat domain 94"", ""DDB1 and CUL4 associated factor 3"""	611359				17622796, 17603510, 17589504	Standard	NM_001267782		Approved	FLJ20294, KIAA1736, WDR94, DCAF3	uc001ncv.3	Q9C0C7	OTTHUMG00000166500	ENST00000458649.2:c.1068G>A	11.37:g.46564499C>T		Somatic		Capture	Illumina HiSeq	Phase_I	46521075	NM_017749	A6XN33|D3DQP8|G3V193|Q86XD6|Q9H8Z0|Q9NXE7	Silent	SNP	ENST00000458649.2	37																																																																																					0.622	AMBRA1-005	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000390103.1	NM_017749	
PTPMT1	114971	broad.mit.edu	37	11	47593081	47593081	+	Missense_Mutation	SNP	T	T	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr11:47593081T>A	ENST00000326674.9	+	4	528	c.506T>A	c.(505-507)aTc>aAc	p.I169N	PTPMT1_ENST00000534775.1_3'UTR|PTPMT1_ENST00000426530.2_Missense_Mutation_p.H141Q|PTPMT1_ENST00000326656.8_Missense_Mutation_p.I105N|NDUFS3_ENST00000533507.1_3'UTR|PTPMT1_ENST00000527079.2_3'UTR	NM_175732.2	NP_783859.1	Q8WUK0	PTPM1_HUMAN	protein tyrosine phosphatase, mitochondrial 1	169	Tyrosine-protein phosphatase.				cardiolipin biosynthetic process (GO:0032049)|glycerophospholipid biosynthetic process (GO:0046474)|inositol phosphate dephosphorylation (GO:0046855)|phosphatidylglycerol biosynthetic process (GO:0006655)|phospholipid metabolic process (GO:0006644)|protein dephosphorylation (GO:0006470)|small molecule metabolic process (GO:0044281)	mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	phosphatidylglycerophosphatase activity (GO:0008962)|phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity (GO:0004439)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)	p.I169N(1)		breast(1)|kidney(1)|large_intestine(2)|lung(1)|skin(1)	6						CGGTCATACATCCACATCAGG	0.483																																					p.H141Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T423A	11						.						99.0	94.0	96.0					11																	47593081		1919	4136	6055	47549657	SO:0001583	missense	114971	exon2			BC014048	CCDS41643.1, CCDS44593.1	11p11.2	2011-06-09			ENSG00000110536	ENSG00000110536	3.1.3.36	"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Atypical dual specificity phosphatases"""	26965	protein-coding gene	gene with protein product		609538				12477932	Standard	NM_175732		Approved	PLIP, DUSP23, MOSP	uc001nfs.4	Q8WUK0	OTTHUMG00000166892	ENST00000326674.9:c.506T>A	11.37:g.47593081T>A	ENSP00000325958:p.Ile169Asn	Somatic		Capture	Illumina HiSeq	Phase_I	47549657	NM_001143984	E9PAT8|Q7Z557|Q96CR2|Q9BXV8	Missense_Mutation	SNP	ENST00000326674.9	37	CCDS41643.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	16.83|16.83	3.230416|3.230416	0.58777|0.58777	.|.	.|.	ENSG00000110536|ENSG00000110536	ENST00000426530|ENST00000326656;ENST00000326674	.|T;D	.|0.88431	.|1.84;-2.38	6.03|6.03	6.03|6.03	0.97812|0.97812	.|Dual specificity phosphatase, catalytic domain (1);Protein-tyrosine/Dual-specificity phosphatase (1);	.|0.079210	.|0.49916	.|U	.|0.000126	D|D	0.95560|0.95560	0.8557|0.8557	M|M	0.92122|0.92122	3.275|3.275	0.51012|0.51012	D|D	0.999901|0.999901	P|D;D	0.49090|0.89917	0.919|1.0;1.0	P|D;D	0.46275|0.85130	0.51|0.944;0.997	D|D	0.95514|0.95514	0.8588|0.8588	8|10	0.87932|0.41790	D|T	0|0.15	-11.3485|-11.3485	14.788|14.788	0.69819|0.69819	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	141|105;169	E9PAT8|Q8WUK0-2;Q8WUK0	.|.;PTPM1_HUMAN	Q|N	141|105;169	.|ENSP00000325882:I105N;ENSP00000325958:I169N	ENSP00000410272:H141Q|ENSP00000325882:I105N	H|I	+|+	3|2	2|0	PTPMT1|PTPMT1	47549657|47549657	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.866000|0.866000	0.49608|0.49608	6.723000|6.723000	0.74742|0.74742	2.308000|2.308000	0.77769|0.77769	0.533000|0.533000	0.62120|0.62120	CAT|ATC		0.483	PTPMT1-002	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391746.1	XM_374879	
TRIM51	84767	broad.mit.edu	37	11	55657418	55657418	+	Splice_Site	SNP	G	G	A	rs147783452		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr11:55657418G>A	ENST00000449290.2	+	6	854	c.762G>A	c.(760-762)agG>agA	p.R254R	TRIM51_ENST00000244891.3_Splice_Site_p.R111R	NM_032681.3	NP_116070.2	Q9BSJ1	TRI51_HUMAN	tripartite motif-containing 51	254						intracellular (GO:0005622)	zinc ion binding (GO:0008270)	p.R254R(1)|p.R95R(1)									CCCCTTGCAGGTATGAGTCTC	0.453																																					p.R254R												.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.G762A	11						.	G		1,4401		0,1,2200	61.0	54.0	56.0		762		0.0	11	dbSNP_134	56	0,8592		0,0,4296	no	coding-synonymous-near-splice	SPRYD5	NM_032681.3		0,1,6496	AA,AG,GG		0.0,0.0227,0.0077		254/453	55657418	1,12993	2201	4296	6497	55413994	SO:0001630	splice_region_variant	84767	exon6			BC005014		11p11	2013-01-09	2012-05-18	2012-05-18	ENSG00000124900	ENSG00000124900		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	19023	protein-coding gene	gene with protein product			"""SPRY domain containing 5"""	SPRYD5			Standard	NM_032681		Approved	TRIM51A	uc010rip.2	Q9BSJ1	OTTHUMG00000156437	ENST00000449290.2:c.762-1G>A	11.37:g.55657418G>A		Somatic		Capture	Illumina HiSeq	Phase_I	55413994	NM_032681	A6NMG2	Silent	SNP	ENST00000449290.2	37																																																																																					0.453	TRIM51-004	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000391522.1	NM_032681	Silent
OR8K5	219453	broad.mit.edu	37	11	55927362	55927362	+	Silent	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr11:55927362C>T	ENST00000313447.1	-	1	431	c.432G>A	c.(430-432)ctG>ctA	p.L144L		NM_001004058.2	NP_001004058.2	Q8NH50	OR8K5_HUMAN	olfactory receptor, family 8, subfamily K, member 5	144						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.L144L(1)		large_intestine(3)|lung(24)|ovary(2)|pancreas(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	34	Esophageal squamous(21;0.00693)	Lung NSC(402;0.197)|all_epithelial(135;0.236)				GAATGCCCACCAGTACATGAC	0.403																																					p.L144L												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G432A	11						.						89.0	90.0	90.0					11																	55927362		2201	4296	6497	55683938	SO:0001819	synonymous_variant	219453	exon1			BK004347	CCDS31521.1	11q11	2012-08-09			ENSG00000181752	ENSG00000181752		"""GPCR / Class A : Olfactory receptors"""	15315	protein-coding gene	gene with protein product							Standard	NM_001004058		Approved		uc010rja.2	Q8NH50	OTTHUMG00000166820	ENST00000313447.1:c.432G>A	11.37:g.55927362C>T		Somatic		Capture	Illumina HiSeq	Phase_I	55683938	NM_001004058	Q6IFB5	Silent	SNP	ENST00000313447.1	37	CCDS31521.1																																																																																				0.403	OR8K5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391543.1	NM_001004058	
OR8H1	219469	broad.mit.edu	37	11	56058495	56058495	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr11:56058495G>A	ENST00000313022.2	-	1	71	c.44C>T	c.(43-45)aCg>aTg	p.T15M		NM_001005199.1	NP_001005199.1	Q8NGG4	OR8H1_HUMAN	olfactory receptor, family 8, subfamily H, member 1	15						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.T15M(1)		NS(2)|breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(18)|ovary(1)|pancreas(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	43	Esophageal squamous(21;0.00448)					TGACAGTCCCGTAAGGATGAA	0.383																																					p.T15M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C44T	11						.						106.0	102.0	104.0					11																	56058495		2201	4296	6497	55815071	SO:0001583	missense	219469	exon1			AB065836	CCDS31526.1	11q11	2012-08-09			ENSG00000181693	ENSG00000181693		"""GPCR / Class A : Olfactory receptors"""	14824	protein-coding gene	gene with protein product							Standard	NM_001005199		Approved		uc010rje.2	Q8NGG4	OTTHUMG00000162671	ENST00000313022.2:c.44C>T	11.37:g.56058495G>A	ENSP00000323595:p.Thr15Met	Somatic		Capture	Illumina HiSeq	Phase_I	55815071	NM_001005199	B2RNI7|Q6IFC5	Missense_Mutation	SNP	ENST00000313022.2	37	CCDS31526.1	.	.	.	.	.	.	.	.	.	.	G	0.036	-1.305499	0.01353	.	.	ENSG00000181693	ENST00000313022;ENST00000395186	T	0.00421	7.46	3.77	-0.664	0.11406	.	0.935374	0.09043	N	0.856952	T	0.00144	0.0004	N	0.01431	-0.87	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.22906	-1.0203	10	0.33141	T	0.24	.	1.6337	0.02737	0.5533:0.1417:0.1679:0.137	.	15	Q8NGG4	OR8H1_HUMAN	M	15;11	ENSP00000323595:T15M	ENSP00000323595:T15M	T	-	2	0	OR8H1	55815071	0.000000	0.05858	0.018000	0.16275	0.001000	0.01503	-0.185000	0.09684	-0.168000	0.10853	-0.455000	0.05494	ACG		0.383	OR8H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370019.1	NM_001005199	
CTNND1	1500	broad.mit.edu	37	11	57561544	57561544	+	Silent	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr11:57561544C>T	ENST00000399050.4	+	4	794	c.258C>T	c.(256-258)aaC>aaT	p.N86N	CTNND1_ENST00000524630.1_Silent_p.N86N|CTNND1_ENST00000361796.4_Silent_p.N86N|CTNND1_ENST00000399039.4_Silent_p.N86N|CTNND1_ENST00000426142.2_5'UTR|CTNND1_ENST00000528232.1_5'UTR|CTNND1_ENST00000531014.1_Intron|CTNND1_ENST00000532787.1_5'UTR|CTNND1_ENST00000528621.1_Silent_p.N32N|CTNND1_ENST00000526772.1_Intron|CTNND1_ENST00000525902.1_Intron|CTNND1_ENST00000361391.6_Silent_p.N86N|CTNND1_ENST00000360682.6_Silent_p.N86N|CTNND1_ENST00000428599.2_Silent_p.N86N|CTNND1_ENST00000530094.1_5'UTR|CTNND1_ENST00000532245.1_Intron|CTNND1_ENST00000529986.1_5'UTR|CTNND1_ENST00000527467.1_Intron|CTNND1_ENST00000529919.1_Silent_p.N86N|CTNND1_ENST00000529526.1_Silent_p.N32N|CTNND1_ENST00000526357.1_Silent_p.N32N|CTNND1_ENST00000532649.1_Silent_p.N32N|CTNND1_ENST00000358694.6_Silent_p.N86N|CTNND1_ENST00000361332.4_Silent_p.N86N|CTNND1_ENST00000530748.1_Silent_p.N32N|CTNND1_ENST00000526938.1_Silent_p.N86N|CTNND1_ENST00000534579.1_Silent_p.N32N|CTNND1_ENST00000532463.1_5'UTR|CTNND1_ENST00000529873.1_Silent_p.N32N|CTNND1_ENST00000415361.2_5'UTR|CTNND1_ENST00000533667.1_Intron|CTNND1_ENST00000532844.1_Silent_p.N32N	NM_001085458.1	NP_001078927.1	O60716	CTND1_HUMAN	catenin (cadherin-associated protein), delta 1	86					adherens junction organization (GO:0034332)|brain development (GO:0007420)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|regulation of transcription, DNA-templated (GO:0006355)|single organismal cell-cell adhesion (GO:0016337)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|extracellular vesicular exosome (GO:0070062)|growth cone (GO:0030426)|lamellipodium (GO:0030027)|midbody (GO:0030496)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|synapse (GO:0045202)|zonula adherens (GO:0005915)	cadherin binding (GO:0045296)|receptor binding (GO:0005102)	p.N86N(1)		breast(5)|endometrium(8)|kidney(4)|large_intestine(7)|liver(2)|lung(16)|ovary(1)|upper_aerodigestive_tract(2)	45		all_epithelial(135;0.155)				tgaaactcaacggaccccaGG	0.433																																					p.N86N												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C258T	11						.						80.0	77.0	78.0					11																	57561544		1847	4077	5924	57318120	SO:0001819	synonymous_variant	1500	exon4			AB002382	CCDS44604.1, CCDS44605.1, CCDS44606.1, CCDS44607.1, CCDS44608.1, CCDS44609.1, CCDS53632.1, CCDS53633.1, CCDS53634.1, CCDS55763.1, CCDS55764.1, CCDS55765.1, CCDS55766.1, CCDS55767.1, CCDS73290.1	11q12.1	2013-02-14				ENSG00000198561		"""Armadillo repeat containing"""	2515	protein-coding gene	gene with protein product		601045		CTNND		8808291	Standard	NM_001085460		Approved	KIAA0384, p120, p120cas, p120ctn	uc001nmc.4	O60716		ENST00000399050.4:c.258C>T	11.37:g.57561544C>T		Somatic		Capture	Illumina HiSeq	Phase_I	57318120	NM_001331	A8K939|O15088|O60713|O60714|O60715|O60935|Q6DHZ7|Q6RBX8|Q9UP71|Q9UP72|Q9UP73	De_novo_Start_OutOfFrame	SNP	ENST00000399050.4	37	CCDS44604.1																																																																																				0.433	CTNND1-006	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000393944.1	NM_001331	
ZFP91	80829	broad.mit.edu	37	11	58377437	58377437	+	Nonsense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr11:58377437C>T	ENST00000316059.6	+	3	676	c.505C>T	c.(505-507)Cga>Tga	p.R169*	ZFP91-CNTF_ENST00000389919.4_Nonsense_Mutation_p.R169*	NM_001197051.1|NM_053023.4	NP_001183980.1|NP_444251.1	Q96JP5	ZFP91_HUMAN	ZFP91 zinc finger protein	169					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.R169*(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)				AGAGAACACCCGAAGCTCTCG	0.498																																					p.R169X												.	.	2	Substitution - Nonsense(2)	large_intestine(2)	c.C505T	11						.						126.0	111.0	116.0					11																	58377437		2201	4295	6496	58134013	SO:0001587	stop_gained	80829	exon3			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.505C>T	11.37:g.58377437C>T	ENSP00000339030:p.Arg169*	Somatic		Capture	Illumina HiSeq	Phase_I	58134013	NM_053023	A6NHC4|A8MSG7|Q86V47|Q96JP4|Q96QA3	Nonsense_Mutation	SNP	ENST00000316059.6	37	CCDS31553.1	.	.	.	.	.	.	.	.	.	.	C	39	7.558931	0.98358	.	.	ENSG00000186660	ENST00000316059;ENST00000389918	.	.	.	5.42	4.47	0.54385	.	4.629640	0.00829	N	0.001654	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-7.1857	13.0115	0.58733	0.1602:0.8398:0.0:0.0	.	.	.	.	X	169	.	ENSP00000374569:R169X	R	+	1	2	ZFP91	58134013	0.966000	0.33281	0.998000	0.56505	0.989000	0.77384	2.270000	0.43355	2.811000	0.96726	0.655000	0.94253	CGA		0.498	ZFP91-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268674.1	NM_053023	
SDHAF2	54949	broad.mit.edu	37	11	61213502	61213502	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr11:61213502C>T	ENST00000301761.2	+	4	534	c.460C>T	c.(460-462)Cgt>Tgt	p.R154C	RP11-286N22.8_ENST00000543044.1_Missense_Mutation_p.R142C|SDHAF2_ENST00000543265.1_3'UTR|SDHAF2_ENST00000542074.1_3'UTR|RN7SL23P_ENST00000484055.2_RNA|RP11-286N22.8_ENST00000544880.1_Intron|SDHAF2_ENST00000537782.1_3'UTR	NM_017841.2	NP_060311.1			succinate dehydrogenase complex assembly factor 2									p.R154C(2)		large_intestine(3)|lung(4)|ovary(2)	9						GCAGAGACTGCGTGCCCCAGA	0.473											OREG0021000	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.R154C												.	.	2	Substitution - Missense(2)	large_intestine(1)|lung(1)	c.C460T	11						.						98.0	97.0	97.0					11																	61213502		2202	4299	6501	60970078	SO:0001583	missense	54949	exon4			AK000494	CCDS8007.1	11q12.2	2014-09-17	2009-08-10	2009-08-10	ENSG00000167985	ENSG00000167985		"""Mitochondrial respiratory chain complex assembly factors"""	26034	protein-coding gene	gene with protein product		613019	"""paraganglioma or familial glomus tumors 2"", ""chromosome 11 open reading frame 79"""	PGL2, C11orf79		19628817	Standard	NM_017841		Approved	FLJ20487, SDH5	uc001nrt.3	Q9NX18	OTTHUMG00000168279	ENST00000301761.2:c.460C>T	11.37:g.61213502C>T	ENSP00000301761:p.Arg154Cys	Somatic	1052	Capture	Illumina HiSeq	Phase_I	60970078	NM_017841		Missense_Mutation	SNP	ENST00000301761.2	37	CCDS8007.1	.	.	.	.	.	.	.	.	.	.	C	17.33	3.363367	0.61513	.	.	ENSG00000167985	ENST00000301761	T	0.79247	-1.25	5.55	4.64	0.57946	.	0.106899	0.64402	D	0.000005	T	0.81964	0.4934	L	0.41356	1.27	0.80722	D	1	D	0.89917	1.0	D	0.67548	0.952	T	0.82814	-0.0271	10	0.54805	T	0.06	-9.3738	13.4434	0.61127	0.0:0.923:0.0:0.077	.	154	Q9NX18	SDHF2_HUMAN	C	154	ENSP00000301761:R154C	ENSP00000440219:R142C	R	+	1	0	SDHAF2	60970078	1.000000	0.71417	0.998000	0.56505	0.984000	0.73092	3.111000	0.50360	1.367000	0.46095	0.491000	0.48974	CGT		0.473	SDHAF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398438.1	NM_017841	
AHNAK	79026	broad.mit.edu	37	11	62289853	62289853	+	Silent	SNP	G	G	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr11:62289853G>T	ENST00000378024.4	-	5	12310	c.12036C>A	c.(12034-12036)ggC>ggA	p.G4012G	AHNAK_ENST00000257247.7_Intron|AHNAK_ENST00000530124.1_Intron	NM_001620.1	NP_001611.1	Q09666	AHNK_HUMAN	AHNAK nucleoprotein	4012					protein oligomerization (GO:0051259)|regulation of RNA splicing (GO:0043484)|regulation of voltage-gated calcium channel activity (GO:1901385)	actin cytoskeleton (GO:0015629)|cell-cell contact zone (GO:0044291)|costamere (GO:0043034)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|vesicle (GO:0031982)	poly(A) RNA binding (GO:0044822)|S100 protein binding (GO:0044548)|structural molecule activity conferring elasticity (GO:0097493)	p.G4012G(1)		NS(3)|autonomic_ganglia(1)|breast(10)|central_nervous_system(5)|endometrium(17)|haematopoietic_and_lymphoid_tissue(2)|kidney(33)|large_intestine(40)|liver(1)|lung(108)|ovary(13)|pancreas(4)|prostate(5)|skin(16)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(6)	268		Melanoma(852;0.155)				TCACCTTAGGGCCTTTCAGAT	0.478																																					p.G4012G												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C12036A	11						.						192.0	201.0	198.0					11																	62289853		2202	4299	6501	62046429	SO:0001819	synonymous_variant	79026	exon5			M80899	CCDS31584.1, CCDS44625.1	11q12-q13	2008-02-05	2007-03-30		ENSG00000124942	ENSG00000124942			347	protein-coding gene	gene with protein product	"""desmoyokin"""	103390	"""AHNAK nucleoprotein (desmoyokin)"""			7987395, 12153988	Standard	NM_024060		Approved	MGC5395	uc001ntl.3	Q09666	OTTHUMG00000167558	ENST00000378024.4:c.12036C>A	11.37:g.62289853G>T		Somatic		Capture	Illumina HiSeq	Phase_I	62046429	NM_001620	A1A586	Silent	SNP	ENST00000378024.4	37	CCDS31584.1																																																																																				0.478	AHNAK-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395572.1	NM_024060	
AHNAK	79026	broad.mit.edu	37	11	62298396	62298396	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr11:62298396C>T	ENST00000378024.4	-	5	3767	c.3493G>A	c.(3493-3495)Gaa>Aaa	p.E1165K	AHNAK_ENST00000257247.7_Intron|AHNAK_ENST00000530124.1_Intron	NM_001620.1	NP_001611.1	Q09666	AHNK_HUMAN	AHNAK nucleoprotein	1165					protein oligomerization (GO:0051259)|regulation of RNA splicing (GO:0043484)|regulation of voltage-gated calcium channel activity (GO:1901385)	actin cytoskeleton (GO:0015629)|cell-cell contact zone (GO:0044291)|costamere (GO:0043034)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|vesicle (GO:0031982)	poly(A) RNA binding (GO:0044822)|S100 protein binding (GO:0044548)|structural molecule activity conferring elasticity (GO:0097493)	p.E1165K(2)		NS(3)|autonomic_ganglia(1)|breast(10)|central_nervous_system(5)|endometrium(17)|haematopoietic_and_lymphoid_tissue(2)|kidney(33)|large_intestine(40)|liver(1)|lung(108)|ovary(13)|pancreas(4)|prostate(5)|skin(16)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(6)	268		Melanoma(852;0.155)				TCTGGGGCTTCGATGTCCACC	0.552																																					p.E1165K												.	.	2	Substitution - Missense(2)	large_intestine(1)|lung(1)	c.G3493A	11						.						159.0	156.0	157.0					11																	62298396		2202	4299	6501	62054972	SO:0001583	missense	79026	exon5			M80899	CCDS31584.1, CCDS44625.1	11q12-q13	2008-02-05	2007-03-30		ENSG00000124942	ENSG00000124942			347	protein-coding gene	gene with protein product	"""desmoyokin"""	103390	"""AHNAK nucleoprotein (desmoyokin)"""			7987395, 12153988	Standard	NM_024060		Approved	MGC5395	uc001ntl.3	Q09666	OTTHUMG00000167558	ENST00000378024.4:c.3493G>A	11.37:g.62298396C>T	ENSP00000367263:p.Glu1165Lys	Somatic		Capture	Illumina HiSeq	Phase_I	62054972	NM_001620	A1A586	Missense_Mutation	SNP	ENST00000378024.4	37	CCDS31584.1	.	.	.	.	.	.	.	.	.	.	c	1.344	-0.593314	0.03771	.	.	ENSG00000124942	ENST00000378024	T	0.00526	6.8	4.99	3.1	0.35709	.	3.241920	0.01171	N	0.006878	T	0.00524	0.0017	L	0.45137	1.4	0.09310	N	1	P	0.46512	0.879	B	0.41946	0.371	T	0.56559	-0.7959	10	0.06236	T	0.91	.	8.6286	0.33906	0.0:0.7602:0.0:0.2398	.	1165	Q09666	AHNK_HUMAN	K	1165	ENSP00000367263:E1165K	ENSP00000367263:E1165K	E	-	1	0	AHNAK	62054972	0.000000	0.05858	0.007000	0.13788	0.004000	0.04260	-0.271000	0.08572	1.124000	0.41980	0.645000	0.84053	GAA		0.552	AHNAK-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395572.1	NM_024060	
TAF6L	10629	broad.mit.edu	37	11	62545450	62545450	+	Splice_Site	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr11:62545450G>A	ENST00000294168.3	+	4	436	c.235G>A	c.(235-237)Gct>Act	p.A79T	TMEM223_ENST00000527073.1_Intron	NM_006473.3	NP_006464.1	Q9Y6J9	TAF6L_HUMAN	TAF6-like RNA polymerase II, p300/CBP-associated factor (PCAF)-associated factor, 65kDa	79					chromatin organization (GO:0006325)|chromatin remodeling (GO:0006338)|DNA-templated transcription, initiation (GO:0006352)|histone H3 acetylation (GO:0043966)|regulation of sequence-specific DNA binding transcription factor activity (GO:0051090)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	histone deacetylase complex (GO:0000118)|STAGA complex (GO:0030914)	DNA binding (GO:0003677)|transcription coactivator activity (GO:0003713)	p.A79T(2)		endometrium(2)|large_intestine(5)|lung(4)|ovary(3)|prostate(1)|skin(1)	16						TTTTCCTCAGGCTGTGTGTGG	0.592																																					p.A79T												.	.	2	Substitution - Missense(2)	ovary(1)|large_intestine(1)	c.G235A	11						.						86.0	77.0	80.0					11																	62545450		2201	4299	6500	62302026	SO:0001630	splice_region_variant	10629	exon4			BC008785	CCDS8035.1	11q12.3	2008-02-01	2002-08-29		ENSG00000162227	ENSG00000162227			17305	protein-coding gene	gene with protein product		602946	"""TAF6-like RNA polymerase II, p300/CBP-associated factor (PCAF)-associated factor, 65 kD"""			9674425	Standard	NM_006473		Approved	PAF65A	uc001nvc.3	Q9Y6J9	OTTHUMG00000167610	ENST00000294168.3:c.235-1G>A	11.37:g.62545450G>A		Somatic		Capture	Illumina HiSeq	Phase_I	62302026	NM_006473	B2RAT0|Q96HA6	Missense_Mutation	SNP	ENST00000294168.3	37	CCDS8035.1	.	.	.	.	.	.	.	.	.	.	G	15.56	2.868615	0.51588	.	.	ENSG00000162227	ENST00000294168;ENST00000529509	T;T	0.47177	0.85;0.9	5.78	5.78	0.91487	.	0.000000	0.85682	D	0.000000	T	0.33673	0.0871	N	0.16478	0.41	0.80722	D	1	B;B	0.17852	0.003;0.024	B;B	0.15052	0.005;0.012	T	0.10683	-1.0619	9	.	.	.	-0.8087	17.5103	0.87758	0.0:0.0:1.0:0.0	.	79;79	B4DVM4;Q9Y6J9	.;TAF6L_HUMAN	T	79	ENSP00000294168:A79T;ENSP00000434662:A79T	.	A	+	1	0	TAF6L	62302026	1.000000	0.71417	1.000000	0.80357	0.325000	0.28411	6.833000	0.75334	2.740000	0.93945	0.455000	0.32223	GCT		0.592	TAF6L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395352.1	NM_006473	Missense_Mutation
NXF1	10482	broad.mit.edu	37	11	62567946	62567946	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr11:62567946G>A	ENST00000532297.1	-	11	1548	c.919C>T	c.(919-921)Cgg>Tgg	p.R307W	NXF1_ENST00000531709.2_Missense_Mutation_p.R307W|NXF1_ENST00000439713.2_Missense_Mutation_p.R307W|NXF1_ENST00000531131.1_Missense_Mutation_p.R170W|NXF1_ENST00000294172.2_Missense_Mutation_p.R307W			Q9UBU9	NXF1_HUMAN	nuclear RNA export factor 1	307					gene expression (GO:0010467)|mRNA export from nucleus (GO:0006406)|poly(A)+ mRNA export from nucleus (GO:0016973)|viral process (GO:0016032)	cytosol (GO:0005829)|nuclear inclusion body (GO:0042405)|nuclear pore (GO:0005643)|nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)	mRNA binding (GO:0003729)|nucleocytoplasmic transporter activity (GO:0005487)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)	p.R307W(1)		breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(4)|kidney(2)|large_intestine(9)|lung(13)|ovary(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	39						TCCAATTCCCGCTCAGACTTC	0.552																																					p.R307W												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C919T	11						.						105.0	76.0	86.0					11																	62567946		2201	4299	6500	62324522	SO:0001583	missense	10482	exon10			AF112880	CCDS8037.1, CCDS44629.1	11q12-q13	2008-07-21			ENSG00000162231	ENSG00000162231			8071	protein-coding gene	gene with protein product	"""tip associating protein"""	602647				9175835, 9660949	Standard	NM_001081491		Approved	TAP, Mex67, DKFZp667O0311	uc001nvf.1	Q9UBU9	OTTHUMG00000167612	ENST00000532297.1:c.919C>T	11.37:g.62567946G>A	ENSP00000436679:p.Arg307Trp	Somatic		Capture	Illumina HiSeq	Phase_I	62324522	NM_006362	B4E269|Q99799|Q9UQL2	Missense_Mutation	SNP	ENST00000532297.1	37	CCDS8037.1	.	.	.	.	.	.	.	.	.	.	G	9.218	1.032545	0.19590	.	.	ENSG00000162231	ENST00000294172;ENST00000532297;ENST00000530875;ENST00000439713	T;T;T;T	0.27256	1.68;1.68;1.68;1.68	4.91	0.376	0.16193	.	0.195337	0.45126	N	0.000386	T	0.10252	0.0251	N	0.12569	0.235	0.58432	D	0.999996	B;B;B;B	0.26258	0.013;0.011;0.145;0.025	B;B;B;B	0.18263	0.007;0.005;0.021;0.004	T	0.13176	-1.0519	10	0.44086	T	0.13	-3.0064	3.0203	0.06073	0.1631:0.1254:0.5516:0.1598	.	170;350;320;307	B4E227;E9PIN3;Q59E96;Q9UBU9	.;.;.;NXF1_HUMAN	W	307;307;350;307	ENSP00000294172:R307W;ENSP00000436679:R307W;ENSP00000435742:R350W;ENSP00000408864:R307W	ENSP00000294172:R307W	R	-	1	2	NXF1	62324522	0.768000	0.28519	0.961000	0.40146	0.940000	0.58332	1.135000	0.31454	0.174000	0.19809	0.650000	0.86243	CGG		0.552	NXF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395365.2	NM_006362	
SLC22A6	9356	broad.mit.edu	37	11	62744677	62744677	+	Missense_Mutation	SNP	G	G	A	rs372804378		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr11:62744677G>A	ENST00000377871.3	-	9	1810	c.1544C>T	c.(1543-1545)aCg>aTg	p.T515M	SLC22A6_ENST00000458333.2_Missense_Mutation_p.T471M|SLC22A6_ENST00000360421.4_Missense_Mutation_p.T515M|SLC22A6_ENST00000537349.1_5'Flank|SLC22A6_ENST00000421062.2_Missense_Mutation_p.T471M	NM_004790.4|NM_153278.2	NP_004781.2|NP_695010.1	Q4U2R8	S22A6_HUMAN	solute carrier family 22 (organic anion transporter), member 6	515					alpha-ketoglutarate transport (GO:0015742)|organic anion transport (GO:0015711)|protein homooligomerization (GO:0051260)|renal tubular secretion (GO:0097254)|response to methotrexate (GO:0031427)|sodium-independent organic anion transport (GO:0043252)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|caveola (GO:0005901)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	chloride ion binding (GO:0031404)|inorganic anion exchanger activity (GO:0005452)|organic anion transmembrane transporter activity (GO:0008514)|sodium-independent organic anion transmembrane transporter activity (GO:0015347)	p.T515M(1)		breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(6)|lung(18)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	36					Acetaminophen(DB00316)|Acetazolamide(DB00819)|Acetylcysteine(DB06151)|Acetylsalicylic acid(DB00945)|Aciclovir(DB00787)|Adefovir Dipivoxil(DB00718)|Aminohippurate(DB00345)|Aminophenazone(DB01424)|Amoxicillin(DB01060)|Antipyrine(DB01435)|Aspartame(DB00168)|Benzylpenicillin(DB01053)|Bromodiphenhydramine(DB01237)|Bumetanide(DB00887)|Captopril(DB01197)|Carbenicillin(DB00578)|Carprofen(DB00821)|Caspofungin(DB00520)|Cefacetrile(DB01414)|Cefadroxil(DB01140)|Cefalotin(DB00456)|Cefamandole(DB01326)|Cefazolin(DB01327)|Cefoperazone(DB01329)|Cefotaxime(DB00493)|Cefotiam(DB00229)|Cefradine(DB01333)|Ceftazidime(DB00438)|Ceftriaxone(DB01212)|Cephalexin(DB00567)|Chloramphenicol(DB00446)|Chlorothiazide(DB00880)|Chlorpropamide(DB00672)|Cidofovir(DB00369)|Cilastatin(DB01597)|Cimetidine(DB00501)|Cinoxacin(DB00827)|Cloxacillin(DB01147)|Conjugated Estrogens(DB00286)|Cyclosporine(DB00091)|Cyclothiazide(DB00606)|Dabrafenib(DB08912)|Diclofenac(DB00586)|Didanosine(DB00900)|Diflunisal(DB00861)|Dinoprost Tromethamine(DB01160)|Dinoprostone(DB00917)|Doxycycline(DB00254)|Enalapril(DB00584)|Ethacrynic acid(DB00903)|Etodolac(DB00749)|Fluorescein(DB00693)|Flurbiprofen(DB00712)|Folic Acid(DB00158)|Foscarnet(DB00529)|Furosemide(DB00695)|Ganciclovir(DB01004)|Gentamicin(DB00798)|Glyburide(DB01016)|Hydrochlorothiazide(DB00999)|Ibuprofen(DB01050)|Indomethacin(DB00328)|Ketoprofen(DB01009)|Lamivudine(DB00709)|Levofloxacin(DB01137)|Losartan(DB00678)|Meclofenamic acid(DB00939)|Methazolamide(DB00703)|Methotrexate(DB00563)|Minocycline(DB01017)|Nafcillin(DB00607)|Nalidixic Acid(DB00779)|Naproxen(DB00788)|Nateglinide(DB00731)|Norfloxacin(DB01059)|Novobiocin(DB01051)|Ofloxacin(DB01165)|Oxytetracycline(DB00595)|Phenylbutazone(DB00812)|Piperacillin(DB00319)|Piroxicam(DB00554)|Pravastatin(DB00175)|Probenecid(DB01032)|Riboflavin(DB00140)|Salicylic acid(DB00936)|Stavudine(DB00649)|Streptomycin(DB01082)|Sulindac(DB00605)|Tenofovir(DB00300)|Tetracycline(DB00759)|Tolbutamide(DB01124)|Tolmetin(DB00500)|Trifluridine(DB00432)|Valaciclovir(DB00577)|Valproic Acid(DB00313)|Vancomycin(DB00512)|Zalcitabine(DB00943)|Zidovudine(DB00495)	GTCCTGCACCGTGTCTGGCAG	0.607																																					p.T515M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1544T	11						.	G	MET/THR,MET/THR,MET/THR,MET/THR	0,4402		0,0,2201	70.0	72.0	71.0		1544,1544,1412,1412	3.5	0.7	11		71	1,8595	1.2+/-3.3	0,1,4297	no	missense,missense,missense,missense	SLC22A6	NM_004790.4,NM_153276.2,NM_153277.2,NM_153278.2	81,81,81,81	0,1,6498	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging,probably-damaging,probably-damaging,probably-damaging	515/564,515/551,471/507,471/520	62744677	1,12997	2201	4298	6499	62501253	SO:0001583	missense	9356	exon9			AF057039	CCDS8041.1, CCDS31591.1, CCDS44631.1, CCDS44632.1	11q12.3	2013-07-15			ENSG00000197901	ENSG00000197901		"""Solute carriers"""	10970	protein-coding gene	gene with protein product		607582				9762842, 9950961	Standard	NM_004790		Approved	ROAT1, PAHT, OAT1	uc001nwk.3	Q4U2R8	OTTHUMG00000167767	ENST00000377871.3:c.1544C>T	11.37:g.62744677G>A	ENSP00000367102:p.Thr515Met	Somatic		Capture	Illumina HiSeq	Phase_I	62501253	NM_004790	A8MY93|B2D0R6|O95187|O95742|Q7LDA0|Q8N192|Q9NQA6|Q9NQC2|Q9UBG6|Q9UEQ8	Missense_Mutation	SNP	ENST00000377871.3	37	CCDS31591.1	.	.	.	.	.	.	.	.	.	.	G	16.68	3.189152	0.57909	0.0	1.16E-4	ENSG00000197901	ENST00000360421;ENST00000394651;ENST00000377871;ENST00000458333;ENST00000421062	T;T;T;T	0.70045	-0.42;-0.45;-0.33;-0.28	4.48	3.52	0.40303	.	0.053431	0.64402	D	0.000001	D	0.86406	0.5925	H	0.96833	3.89	0.41067	D	0.985424	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.85130	0.994;0.994;0.997;0.994	D	0.90132	0.4207	10	0.87932	D	0	.	12.2436	0.54558	0.0:0.1865:0.8135:0.0	.	471;471;515;515	Q4U2R8-4;Q4U2R8-3;Q4U2R8;Q4U2R8-2	.;.;S22A6_HUMAN;.	M	515;494;515;471;471	ENSP00000353597:T515M;ENSP00000367102:T515M;ENSP00000396401:T471M;ENSP00000404441:T471M	ENSP00000353597:T515M	T	-	2	0	SLC22A6	62501253	1.000000	0.71417	0.743000	0.31040	0.631000	0.37964	6.012000	0.70767	2.298000	0.77334	0.561000	0.74099	ACG		0.607	SLC22A6-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000396186.1	NM_004790	
STIP1	10963	broad.mit.edu	37	11	63970997	63970997	+	Nonsense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr11:63970997C>T	ENST00000305218.4	+	13	1609	c.1462C>T	c.(1462-1464)Cga>Tga	p.R488*	STIP1_ENST00000538945.1_Nonsense_Mutation_p.R464*|STIP1_ENST00000358794.5_Nonsense_Mutation_p.R535*	NM_006819.2	NP_006810.1	P31948	STIP1_HUMAN	stress-induced phosphoprotein 1	488					response to stress (GO:0006950)	Golgi apparatus (GO:0005794)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)	p.R488*(2)		endometrium(4)|large_intestine(3)|liver(1)|lung(15)|ovary(2)|prostate(1)|skin(1)	27						TGTGAAGCGACGAGCCATGGC	0.602																																					p.R488X												.	.	2	Substitution - Nonsense(2)	large_intestine(2)	c.C1462T	11						.						51.0	39.0	43.0					11																	63970997		2201	4297	6498	63727573	SO:0001587	stop_gained	10963	exon13			BC039299	CCDS8058.1, CCDS60827.1, CCDS60828.1	11q13	2014-01-13	2014-01-13		ENSG00000168439	ENSG00000168439		"""Tetratricopeptide (TTC) repeat domain containing"""	11387	protein-coding gene	gene with protein product	"""Hsp70/Hsp90-organizing protein"""	605063	"""stress-induced-phosphoprotein 1"""			1569099	Standard	NM_006819		Approved	HOP, STI1	uc001nyk.1	P31948	OTTHUMG00000167789	ENST00000305218.4:c.1462C>T	11.37:g.63970997C>T	ENSP00000305958:p.Arg488*	Somatic		Capture	Illumina HiSeq	Phase_I	63727573	NM_006819	B4DM70|F5H0T1|G3XAD8|Q3ZCU9|Q5TZU9	Nonsense_Mutation	SNP	ENST00000305218.4	37	CCDS8058.1	.	.	.	.	.	.	.	.	.	.	C	21.4	4.138224	0.77775	.	.	ENSG00000168439	ENST00000358794;ENST00000305218;ENST00000538945;ENST00000540887	.	.	.	5.21	3.23	0.37069	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-20.129	12.2256	0.54457	0.4461:0.5539:0.0:0.0	.	.	.	.	X	535;488;464;87	.	ENSP00000305958:R488X	R	+	1	2	STIP1	63727573	0.950000	0.32346	0.827000	0.32855	0.953000	0.61014	2.045000	0.41250	0.637000	0.30526	0.561000	0.74099	CGA		0.602	STIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396289.2	NM_006819	
ATG2A	23130	broad.mit.edu	37	11	64669629	64669629	+	Silent	SNP	C	C	T	rs369030600		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr11:64669629C>T	ENST00000377264.3	-	29	4036	c.3924G>A	c.(3922-3924)gcG>gcA	p.A1308A	ATG2A_ENST00000421419.2_Silent_p.A1310A	NM_015104.2	NP_055919.2	Q2TAZ0	ATG2A_HUMAN	autophagy related 2A	1308					autophagic vacuole assembly (GO:0000045)|cellular response to nitrogen starvation (GO:0006995)|mitochondrion degradation (GO:0000422)|nucleophagy (GO:0044804)	extrinsic component of membrane (GO:0019898)|lipid particle (GO:0005811)|pre-autophagosomal structure (GO:0000407)		p.A1308A(1)		breast(3)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(19)|ovary(3)|prostate(5)|skin(1)|stomach(1)|urinary_tract(3)	55						AGATGGGCGACGCCTGAGGGA	0.647																																					p.A1308A												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G3924A	11						.	C		3,4399	6.2+/-15.9	0,3,2198	49.0	55.0	53.0		3924	3.6	1.0	11		53	0,8594		0,0,4297	no	coding-synonymous	ATG2A	NM_015104.2		0,3,6495	TT,TC,CC		0.0,0.0682,0.0231		1308/1939	64669629	3,12993	2201	4297	6498	64426205	SO:0001819	synonymous_variant	23130	exon29				CCDS31602.1	11q13.1	2014-02-12	2012-06-06		ENSG00000110046	ENSG00000110046			29028	protein-coding gene	gene with protein product			"""ATG2 autophagy related 2 homolog A (S. cerevisiae)"""			21887408	Standard	NM_015104		Approved	KIAA0404	uc001obx.3	Q2TAZ0	OTTHUMG00000066831	ENST00000377264.3:c.3924G>A	11.37:g.64669629C>T		Somatic		Capture	Illumina HiSeq	Phase_I	64426205	NM_015104	O43154|Q14DM2|Q6ZTV2|Q7Z6K8|Q8IVY5|Q8TAI8|Q96HH7	Silent	SNP	ENST00000377264.3	37	CCDS31602.1	.	.	.	.	.	.	.	.	.	.	C	7.328	0.618416	0.14129	6.82E-4	0.0	ENSG00000110046	ENST00000418259	.	.	.	4.54	3.62	0.41486	.	.	.	.	.	T	0.62233	0.2411	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.59904	-0.7366	4	.	.	.	.	11.5807	0.50889	0.0:0.3557:0.6443:0.0	.	.	.	.	I	1112	.	.	V	-	1	0	ATG2A	64426205	1.000000	0.71417	1.000000	0.80357	0.821000	0.46438	0.412000	0.21131	1.045000	0.40225	-0.256000	0.11100	GTC		0.647	ATG2A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000143224.1	NM_015104	
ATG2A	23130	broad.mit.edu	37	11	64684470	64684470	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr11:64684470G>T	ENST00000377264.3	-	1	250	c.138C>A	c.(136-138)agC>agA	p.S46R	ATG2A_ENST00000421419.2_Missense_Mutation_p.S46R	NM_015104.2	NP_055919.2	Q2TAZ0	ATG2A_HUMAN	autophagy related 2A	46					autophagic vacuole assembly (GO:0000045)|cellular response to nitrogen starvation (GO:0006995)|mitochondrion degradation (GO:0000422)|nucleophagy (GO:0044804)	extrinsic component of membrane (GO:0019898)|lipid particle (GO:0005811)|pre-autophagosomal structure (GO:0000407)		p.S46R(1)		breast(3)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(19)|ovary(3)|prostate(5)|skin(1)|stomach(1)|urinary_tract(3)	55						GCAGGGCAACGCTGCCCTTGT	0.622																																					p.S46R												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C138A	11						.						80.0	67.0	71.0					11																	64684470		2201	4297	6498	64441046	SO:0001583	missense	23130	exon1				CCDS31602.1	11q13.1	2014-02-12	2012-06-06		ENSG00000110046	ENSG00000110046			29028	protein-coding gene	gene with protein product			"""ATG2 autophagy related 2 homolog A (S. cerevisiae)"""			21887408	Standard	NM_015104		Approved	KIAA0404	uc001obx.3	Q2TAZ0	OTTHUMG00000066831	ENST00000377264.3:c.138C>A	11.37:g.64684470G>T	ENSP00000366475:p.Ser46Arg	Somatic		Capture	Illumina HiSeq	Phase_I	64441046	NM_015104	O43154|Q14DM2|Q6ZTV2|Q7Z6K8|Q8IVY5|Q8TAI8|Q96HH7	Missense_Mutation	SNP	ENST00000377264.3	37	CCDS31602.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	16.54|16.54	3.152974|3.152974	0.57259|0.57259	.|.	.|.	ENSG00000110046|ENSG00000110046	ENST00000377262|ENST00000421419;ENST00000377264;ENST00000227459	.|D;D	.|0.82803	.|-1.65;-1.65	4.84|4.84	1.89|1.89	0.25635|0.25635	.|.	.|0.150047	.|0.56097	.|N	.|0.000023	T|T	0.73225|0.73225	0.3560|0.3560	L|L	0.45581|0.45581	1.43|1.43	0.49483|0.49483	D|D	0.999798|0.999798	.|B	.|0.16603	.|0.018	.|B	.|0.20767	.|0.031	T|T	0.63857|0.63857	-0.6542|-0.6542	6|10	0.87932|0.49607	D|T	0|0.09	.|.	4.0326|4.0326	0.09716|0.09716	0.2686:0.0:0.565:0.1664|0.2686:0.0:0.565:0.1664	.|.	.|46	.|Q2TAZ0	.|ATG2A_HUMAN	S|R	44|46	.|ENSP00000410522:S46R;ENSP00000366475:S46R	ENSP00000366473:R44S|ENSP00000227459:S46R	R|S	-|-	1|3	0|2	ATG2A|ATG2A	64441046|64441046	1.000000|1.000000	0.71417|0.71417	0.910000|0.910000	0.35882|0.35882	0.891000|0.891000	0.51852|0.51852	0.619000|0.619000	0.24388|0.24388	0.302000|0.302000	0.22762|0.22762	-0.258000|-0.258000	0.10820|0.10820	CGT|AGC		0.622	ATG2A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000143224.1	NM_015104	
NAALADL1	10004	broad.mit.edu	37	11	64824858	64824858	+	Silent	SNP	T	T	C			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr11:64824858T>C	ENST00000358658.3	-	4	615	c.588A>G	c.(586-588)gtA>gtG	p.V196V	NAALADL1_ENST00000355369.2_Silent_p.V196V|NAALADL1_ENST00000355721.3_Intron|NAALADL1_ENST00000356632.3_Silent_p.V196V|NAALADL1_ENST00000340252.4_Silent_p.V196V|NAALADL1_ENST00000339885.2_Silent_p.V196V	NM_005468.2	NP_005459.2	Q9UQQ1	NALDL_HUMAN	N-acetylated alpha-linked acidic dipeptidase-like 1	196						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	carboxypeptidase activity (GO:0004180)|dipeptidase activity (GO:0016805)|metal ion binding (GO:0046872)|metallopeptidase activity (GO:0008237)|peptidase activity (GO:0008233)	p.V196V(1)		autonomic_ganglia(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(15)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)	29						CCCCACGCCCTACACCCCCAT	0.607																																					p.V196V												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.A588G	11						.						153.0	112.0	126.0					11																	64824858		2201	4297	6498	64581434	SO:0001819	synonymous_variant	10004	exon4			AF010141	CCDS31604.1	11q12	2011-08-16			ENSG00000168060	ENSG00000168060			23536	protein-coding gene	gene with protein product	"""ileal peptidase I100"""	602640				10085079	Standard	NM_005468		Approved		uc001ocn.3	Q9UQQ1	OTTHUMG00000165595	ENST00000358658.3:c.588A>G	11.37:g.64824858T>C		Somatic		Capture	Illumina HiSeq	Phase_I	64581434	NM_005468	C9J8A1|C9J964|C9JL35|C9JSN0|O43176	Silent	SNP	ENST00000358658.3	37	CCDS31604.1																																																																																				0.607	NAALADL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385162.1	NM_005468	
DPF2	5977	broad.mit.edu	37	11	65111482	65111482	+	Silent	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr11:65111482C>T	ENST00000528416.1	+	6	712	c.579C>T	c.(577-579)gcC>gcT	p.A193A	DPF2_ENST00000532264.1_3'UTR|DPF2_ENST00000415073.2_Intron|DPF2_ENST00000252268.4_Silent_p.A193A	NM_006268.4	NP_006259.1	Q92785	REQU_HUMAN	D4, zinc and double PHD fingers family 2	193					apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|zinc ion binding (GO:0008270)	p.A193A(1)		endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(7)|lung(7)|ovary(1)|prostate(1)	23						TGGGCAGTGCCCGTAAGAAGC	0.547																																					p.A193A												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C579T	11						.						82.0	74.0	77.0					11																	65111482		2201	4297	6498	64868058	SO:0001819	synonymous_variant	5977	exon6			U94585	CCDS8100.1	11q13.1	2014-05-13	2003-10-06	2003-10-08	ENSG00000133884	ENSG00000133884		"""Zinc fingers, PHD-type"""	9964	protein-coding gene	gene with protein product		601671	"""requiem, apoptosis response zinc finger gene"""	REQ		11845289	Standard	NM_006268		Approved	ubi-d4, BAF45d	uc001odm.3	Q92785	OTTHUMG00000165985	ENST00000528416.1:c.579C>T	11.37:g.65111482C>T		Somatic		Capture	Illumina HiSeq	Phase_I	64868058	NM_006268	A8K7C9|B4DT58	Silent	SNP	ENST00000528416.1	37	CCDS8100.1																																																																																				0.547	DPF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387293.3	NM_006268	
RELA	5970	broad.mit.edu	37	11	65421972	65421972	+	Frame_Shift_Del	DEL	G	G	-			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr11:65421972delG	ENST00000406246.3	-	11	1794	c.1533delC	c.(1531-1533)cccfs	p.P511fs	RELA_ENST00000525693.1_3'UTR|RELA_ENST00000308639.9_Frame_Shift_Del_p.P508fs	NM_001243984.1|NM_001243985.1|NM_021975.3	NP_001230913.1|NP_001230914.1|NP_068810.3	Q04206	TF65_HUMAN	v-rel avian reticuloendotheliosis viral oncogene homolog A	511					acetaldehyde metabolic process (GO:0006117)|aging (GO:0007568)|cellular defense response (GO:0006968)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to interleukin-1 (GO:0071347)|cellular response to interleukin-6 (GO:0071354)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to nicotine (GO:0071316)|cellular response to peptide hormone stimulus (GO:0071375)|cellular response to tumor necrosis factor (GO:0071356)|cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|Fc-epsilon receptor signaling pathway (GO:0038095)|hair follicle development (GO:0001942)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|liver development (GO:0001889)|membrane protein intracellular domain proteolysis (GO:0031293)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of apoptotic process (GO:0043066)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of protein catabolic process (GO:0042177)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|neurotrophin TRK receptor signaling pathway (GO:0048011)|nucleotide-binding oligomerization domain containing 2 signaling pathway (GO:0070431)|organ morphogenesis (GO:0009887)|positive regulation of cell proliferation (GO:0008284)|positive regulation of chondrocyte differentiation (GO:0032332)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-12 biosynthetic process (GO:0045084)|positive regulation of miRNA metabolic process (GO:2000630)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of Schwann cell differentiation (GO:0014040)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|regulation of inflammatory response (GO:0050727)|response to amino acid (GO:0043200)|response to cAMP (GO:0051591)|response to cobalamin (GO:0033590)|response to drug (GO:0042493)|response to insulin (GO:0032868)|response to interleukin-1 (GO:0070555)|response to mechanical stimulus (GO:0009612)|response to morphine (GO:0043278)|response to muramyl dipeptide (GO:0032495)|response to organic substance (GO:0010033)|response to progesterone (GO:0032570)|response to UV-B (GO:0010224)|T cell receptor signaling pathway (GO:0050852)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	activating transcription factor binding (GO:0033613)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|identical protein binding (GO:0042802)|NF-kappaB binding (GO:0051059)|phosphate ion binding (GO:0042301)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|repressing transcription factor binding (GO:0070491)|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)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001205)|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)	p.D512fs*35(1)		central_nervous_system(1)|endometrium(1)|large_intestine(4)|lung(11)|ovary(1)|urinary_tract(1)	19						GAGCTGGGTCGGGGGGCCTCT	0.627																																					p.P511fs												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.1533delC	11						.						24.0	29.0	27.0					11																	65421972		2194	4293	6487	65178548	SO:0001589	frameshift_variant	5970	exon11			Z22951	CCDS31609.1, CCDS44651.1, CCDS73322.1	11q13	2013-07-09	2013-07-09		ENSG00000173039	ENSG00000173039			9955	protein-coding gene	gene with protein product		164014	"""nuclear factor of kappa light polypeptide gene enhancer in B-cells 3"""	NFKB3		2001591	Standard	NM_021975		Approved	p65	uc001ofg.3	Q04206	OTTHUMG00000166566	ENST00000406246.3:c.1533delC	11.37:g.65421972delG	ENSP00000384273:p.Pro511fs	Somatic		Capture	Illumina HiSeq	Phase_I	65178548	NM_021975	Q6GTV1|Q6SLK1	Frame_Shift_Del	DEL	ENST00000406246.3	37	CCDS31609.1																																																																																				0.627	RELA-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000390457.2	NM_021975	
EFEMP2	30008	broad.mit.edu	37	11	65638763	65638763	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr11:65638763A>G	ENST00000307998.6	-	4	462	c.232T>C	c.(232-234)Tac>Cac	p.Y78H	EFEMP2_ENST00000528176.1_Missense_Mutation_p.Y78H	NM_016938.4	NP_058634.4	O95967	FBLN4_HUMAN	EGF containing fibulin-like extracellular matrix protein 2	78	EGF-like 1; atypical. {ECO:0000255|PROSITE-ProRule:PRU00076}.				blood coagulation (GO:0007596)|extracellular matrix organization (GO:0030198)	basement membrane (GO:0005604)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|vesicle (GO:0031982)	calcium ion binding (GO:0005509)|extracellular matrix structural constituent (GO:0005201)|transmembrane signaling receptor activity (GO:0004888)	p.Y78H(1)		cervix(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(12)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	21				READ - Rectum adenocarcinoma(159;0.169)		AGGCACAAGTAGCCCCCGTAG	0.652																																					p.Y78H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T232C	11						.						125.0	137.0	133.0					11																	65638763		2201	4296	6497	65395339	SO:0001583	missense	30008	exon4			AF109121	CCDS8116.1	11q13	2011-06-17	2011-01-25		ENSG00000172638	ENSG00000172638		"""Fibulins"""	3219	protein-coding gene	gene with protein product	"""fibulin 4"""	604633	"""EGF-containing fibulin-like extracellular matrix protein 2"""			10601734, 10982184	Standard	NR_037718		Approved	FBLN4, UPH1	uc001ofy.4	O95967	OTTHUMG00000166664	ENST00000307998.6:c.232T>C	11.37:g.65638763A>G	ENSP00000309953:p.Tyr78His	Somatic		Capture	Illumina HiSeq	Phase_I	65395339	NM_016938	A8K7R4|B3KM31|B3KQT1|O75967	Missense_Mutation	SNP	ENST00000307998.6	37	CCDS8116.1	.	.	.	.	.	.	.	.	.	.	A	29.0	4.969378	0.92855	.	.	ENSG00000172638	ENST00000528176;ENST00000307998;ENST00000526624;ENST00000527378	D;D;D;D	0.94897	-3.55;-3.55;-3.55;-3.55	4.93	4.93	0.64822	EGF-like calcium-binding, conserved site (1);EGF-like calcium-binding (1);	0.000000	0.35772	N	0.002983	D	0.96769	0.8945	M	0.77486	2.375	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.87578	0.996;0.998	D	0.97034	0.9752	10	0.66056	D	0.02	.	12.5517	0.56229	1.0:0.0:0.0:0.0	.	78;78	E9PRU1;O95967	.;FBLN4_HUMAN	H	78	ENSP00000434151:Y78H;ENSP00000309953:Y78H;ENSP00000435419:Y78H;ENSP00000435963:Y78H	ENSP00000309953:Y78H	Y	-	1	0	EFEMP2	65395339	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.486000	0.90451	2.062000	0.61559	0.533000	0.62120	TAC		0.652	EFEMP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391047.4	NM_016938	
FIBP	9158	broad.mit.edu	37	11	65652460	65652460	+	Silent	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr11:65652460G>A	ENST00000338369.2	-	7	898	c.786C>T	c.(784-786)tgC>tgT	p.C262C	FIBP_ENST00000357519.4_Silent_p.C255C|FIBP_ENST00000426652.2_5'Flank|FIBP_ENST00000533045.1_Silent_p.C252C	NM_198897.1	NP_942600.1	O43427	FIBP_HUMAN	fibroblast growth factor (acidic) intracellular binding protein	262					fibroblast growth factor receptor signaling pathway (GO:0008543)|platelet aggregation (GO:0070527)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	fibroblast growth factor binding (GO:0017134)	p.C262C(1)		endometrium(2)|kidney(1)|large_intestine(1)|lung(4)|ovary(1)|urinary_tract(1)	10				READ - Rectum adenocarcinoma(159;0.166)		GGAGAGCAGTGCACACCAGGC	0.622											OREG0021089	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.C255C												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C765T	11						.						72.0	68.0	69.0					11																	65652460		2201	4296	6497	65409036	SO:0001819	synonymous_variant	9158	exon7			AF010187	CCDS8118.1, CCDS8119.1	11q13.1	2006-06-15			ENSG00000172500	ENSG00000172500			3705	protein-coding gene	gene with protein product		608296				9806903	Standard	NM_004214		Approved	FGFIBP	uc001ogd.3	O43427	OTTHUMG00000166846	ENST00000338369.2:c.786C>T	11.37:g.65652460G>A		Somatic	1085	Capture	Illumina HiSeq	Phase_I	65409036	NM_004214	A8K0J7|Q27Q85|Q6IBQ3|Q9HD65	Silent	SNP	ENST00000338369.2	37	CCDS8119.1																																																																																				0.622	FIBP-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000391575.2	NM_198897	
PACS1	55690	broad.mit.edu	37	11	66000459	66000459	+	Missense_Mutation	SNP	G	G	A	rs201700614		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr11:66000459G>A	ENST00000320580.4	+	15	1793	c.1760G>A	c.(1759-1761)cGg>cAg	p.R587Q	PACS1_ENST00000529757.1_Missense_Mutation_p.R123Q	NM_018026.3	NP_060496.2	Q6VY07	PACS1_HUMAN	phosphofurin acidic cluster sorting protein 1	587					protein targeting to Golgi (GO:0000042)|protein targeting to plasma membrane (GO:0072661)|regulation of defense response to virus by virus (GO:0050690)|viral process (GO:0016032)	COPI-coated vesicle (GO:0030137)|cytosol (GO:0005829)	ion channel binding (GO:0044325)	p.R587Q(1)	RBM14/PACS1(2)	breast(1)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(8)|lung(8)|ovary(6)|skin(2)|urinary_tract(1)	37						CAGGACCAGCGGAAGCCTGTG	0.627																																					p.R587Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1760A	11						.	G	GLN/ARG	0,4400		0,0,2200	165.0	148.0	154.0		1760	4.4	1.0	11		154	2,8588	2.2+/-6.3	0,2,4293	yes	missense	PACS1	NM_018026.2	43	0,2,6493	AA,AG,GG		0.0233,0.0,0.0154	possibly-damaging	587/964	66000459	2,12988	2200	4295	6495	65757035	SO:0001583	missense	55690	exon15			AB033001	CCDS8129.1	11q13.1-q13.2	2008-02-05			ENSG00000175115	ENSG00000175115			30032	protein-coding gene	gene with protein product		607492				12855553, 14608369	Standard	NM_018026		Approved	FLJ10209, KIAA1175	uc001oha.2	Q6VY07	OTTHUMG00000166889	ENST00000320580.4:c.1760G>A	11.37:g.66000459G>A	ENSP00000316454:p.Arg587Gln	Somatic		Capture	Illumina HiSeq	Phase_I	65757035	NM_018026	Q6PJY6|Q6PKB6|Q7Z590|Q7Z5W4|Q8N8K6|Q96MW0|Q9NW92|Q9ULP5	Missense_Mutation	SNP	ENST00000320580.4	37	CCDS8129.1	.	.	.	.	.	.	.	.	.	.	G	12.89	2.074742	0.36566	0.0	2.33E-4	ENSG00000175115	ENST00000320580;ENST00000529757	T;T	0.44083	0.93;0.93	4.41	4.41	0.53225	.	0.452159	0.23824	N	0.044215	T	0.22551	0.0544	L	0.37630	1.12	0.80722	D	1	P	0.42993	0.797	B	0.32533	0.147	T	0.04900	-1.0919	10	0.10377	T	0.69	-24.4764	6.5689	0.22527	0.1981:0.0:0.8018:0.0	.	587	Q6VY07	PACS1_HUMAN	Q	587;123	ENSP00000316454:R587Q;ENSP00000432858:R123Q	ENSP00000316454:R587Q	R	+	2	0	PACS1	65757035	1.000000	0.71417	1.000000	0.80357	0.962000	0.63368	5.127000	0.64727	2.308000	0.77769	0.549000	0.68633	CGG		0.627	PACS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391690.2	NM_018026	
KLC2	64837	broad.mit.edu	37	11	66030380	66030380	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr11:66030380G>A	ENST00000417856.1	+	5	868	c.625G>A	c.(625-627)Gcc>Acc	p.A209T	KLC2_ENST00000394078.1_Missense_Mutation_p.A209T|RP11-755F10.3_ENST00000533576.1_RNA|KLC2_ENST00000394067.2_Missense_Mutation_p.A209T|KLC2_ENST00000394065.2_Missense_Mutation_p.A70T|KLC2_ENST00000316924.5_Missense_Mutation_p.A209T|KLC2_ENST00000421552.1_Missense_Mutation_p.A132T|KLC2_ENST00000394066.2_Missense_Mutation_p.A132T|RP11-867G23.1_ENST00000530805.1_RNA	NM_001134775.1	NP_001128247.1	Q9H0B6	KLC2_HUMAN	kinesin light chain 2	209					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|axon cargo transport (GO:0008088)|blood coagulation (GO:0007596)|microtubule-based movement (GO:0007018)	ciliary rootlet (GO:0035253)|cytosol (GO:0005829)|kinesin complex (GO:0005871)|kinesin I complex (GO:0016938)|membrane (GO:0016020)|microtubule (GO:0005874)|neuron projection (GO:0043005)|protein complex (GO:0043234)	kinesin binding (GO:0019894)|microtubule motor activity (GO:0003777)	p.A209T(1)		breast(2)|endometrium(1)|kidney(1)|large_intestine(7)|lung(3)|prostate(5)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	24						GATCCAATACGCCTCACAGGG	0.637																																					p.A209T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G625A	11						.						99.0	89.0	92.0					11																	66030380		2200	4295	6495	65786956	SO:0001583	missense	64837	exon5			AK022449	CCDS8130.1, CCDS44653.1	11q13.1	2013-01-10			ENSG00000174996	ENSG00000174996		"""Tetratricopeptide (TTC) repeat domain containing"""	20716	protein-coding gene	gene with protein product		611729				9624122	Standard	NM_022822		Approved	FLJ12387	uc001ohb.2	Q9H0B6	OTTHUMG00000133757	ENST00000417856.1:c.625G>A	11.37:g.66030380G>A	ENSP00000399403:p.Ala209Thr	Somatic		Capture	Illumina HiSeq	Phase_I	65786956	NM_001134775	A8MXL7|B2RDY4|Q9H9C8|Q9HA20	Missense_Mutation	SNP	ENST00000417856.1	37	CCDS8130.1	.	.	.	.	.	.	.	.	.	.	G	28.8	4.952521	0.92660	.	.	ENSG00000174996	ENST00000417856;ENST00000394067;ENST00000316924;ENST00000421552;ENST00000394078;ENST00000461611;ENST00000394066;ENST00000394065	T;T;T;T;T;T;T;T	0.51071	0.72;0.72;0.72;0.72;0.72;0.72;0.72;0.72	3.86	3.86	0.44501	Tetratricopeptide-like helical (1);Rabaptin, GTPase-Rab5 binding (1);Tetratricopeptide repeat-containing (1);	0.000000	0.64402	D	0.000002	T	0.61615	0.2361	L	0.56340	1.77	0.58432	D	0.999999	D;D;D;D	0.76494	0.999;0.999;0.999;0.997	D;D;D;P	0.83275	0.981;0.996;0.994;0.846	T	0.58951	-0.7545	10	0.28530	T	0.3	-16.4592	14.7237	0.69326	0.0:0.0:1.0:0.0	.	209;70;132;209	A8MX29;A8MZ87;A8MXL7;Q9H0B6	.;.;.;KLC2_HUMAN	T	209;209;209;132;209;132;132;70	ENSP00000399403:A209T;ENSP00000377631:A209T;ENSP00000314837:A209T;ENSP00000408484:A132T;ENSP00000377641:A209T;ENSP00000434538:A132T;ENSP00000377630:A132T;ENSP00000377629:A70T	ENSP00000314837:A209T	A	+	1	0	KLC2	65786956	1.000000	0.71417	0.874000	0.34290	0.941000	0.58515	9.592000	0.98245	1.976000	0.57569	0.561000	0.74099	GCC		0.637	KLC2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258200.1	NM_022822	
KLC2	64837	broad.mit.edu	37	11	66030507	66030507	+	Splice_Site	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr11:66030507G>A	ENST00000417856.1	+	5	995	c.752G>A	c.(751-753)cGg>cAg	p.R251Q	KLC2_ENST00000394078.1_Splice_Site_p.R251Q|RP11-755F10.3_ENST00000533576.1_RNA|KLC2_ENST00000394067.2_Splice_Site_p.R251Q|KLC2_ENST00000394065.2_Splice_Site_p.R112Q|KLC2_ENST00000316924.5_Splice_Site_p.R251Q|KLC2_ENST00000421552.1_Splice_Site_p.R174Q|KLC2_ENST00000394066.2_Splice_Site_p.R174Q|RP11-867G23.1_ENST00000530805.1_RNA	NM_001134775.1	NP_001128247.1	Q9H0B6	KLC2_HUMAN	kinesin light chain 2	251					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|axon cargo transport (GO:0008088)|blood coagulation (GO:0007596)|microtubule-based movement (GO:0007018)	ciliary rootlet (GO:0035253)|cytosol (GO:0005829)|kinesin complex (GO:0005871)|kinesin I complex (GO:0016938)|membrane (GO:0016020)|microtubule (GO:0005874)|neuron projection (GO:0043005)|protein complex (GO:0043234)	kinesin binding (GO:0019894)|microtubule motor activity (GO:0003777)	p.R251Q(1)		breast(2)|endometrium(1)|kidney(1)|large_intestine(7)|lung(3)|prostate(5)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	24						CTGGTCTATCGGTGAGGACTC	0.607																																					p.R251Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G752A	11						.						53.0	44.0	47.0					11																	66030507		2200	4295	6495	65787083	SO:0001630	splice_region_variant	64837	exon5			AK022449	CCDS8130.1, CCDS44653.1	11q13.1	2013-01-10			ENSG00000174996	ENSG00000174996		"""Tetratricopeptide (TTC) repeat domain containing"""	20716	protein-coding gene	gene with protein product		611729				9624122	Standard	NM_022822		Approved	FLJ12387	uc001ohb.2	Q9H0B6	OTTHUMG00000133757	ENST00000417856.1:c.752+1G>A	11.37:g.66030507G>A		Somatic		Capture	Illumina HiSeq	Phase_I	65787083	NM_001134775	A8MXL7|B2RDY4|Q9H9C8|Q9HA20	Missense_Mutation	SNP	ENST00000417856.1	37	CCDS8130.1	.	.	.	.	.	.	.	.	.	.	G	22.6	4.317351	0.81469	.	.	ENSG00000174996	ENST00000417856;ENST00000394067;ENST00000316924;ENST00000421552;ENST00000394078;ENST00000461611;ENST00000394066;ENST00000394065	T;T;T;T;T;T;T;T	0.63580	-0.05;-0.05;-0.05;-0.05;-0.05;-0.05;-0.05;-0.05	3.86	3.86	0.44501	Tetratricopeptide-like helical (1);Tetratricopeptide repeat-containing (1);	0.263091	0.29579	N	0.011757	T	0.64832	0.2634	N	0.20328	0.56	0.58432	D	0.999999	D;D;D;D	0.76494	0.985;0.999;0.999;0.998	D;D;D;P	0.68192	0.919;0.956;0.956;0.881	T	0.68202	-0.5471	10	0.48119	T	0.1	-11.6894	14.7237	0.69326	0.0:0.0:1.0:0.0	.	251;112;174;251	A8MX29;A8MZ87;A8MXL7;Q9H0B6	.;.;.;KLC2_HUMAN	Q	251;251;251;174;251;174;174;112	ENSP00000399403:R251Q;ENSP00000377631:R251Q;ENSP00000314837:R251Q;ENSP00000408484:R174Q;ENSP00000377641:R251Q;ENSP00000434538:R174Q;ENSP00000377630:R174Q;ENSP00000377629:R112Q	ENSP00000314837:R251Q	R	+	2	0	KLC2	65787083	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	9.450000	0.97607	1.976000	0.57569	0.561000	0.74099	CGG		0.607	KLC2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258200.1	NM_022822	Missense_Mutation
RAB1B	81876	broad.mit.edu	37	11	66043617	66043617	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr11:66043617C>T	ENST00000311481.6	+	6	661	c.514C>T	c.(514-516)Cgg>Tgg	p.R172W	RP11-867G23.4_ENST00000528650.1_RNA|RP11-867G23.3_ENST00000501708.1_lincRNA|RAB1B_ENST00000527397.1_Missense_Mutation_p.R140W|CNIH2_ENST00000311445.6_5'Flank|CNIH2_ENST00000528852.1_5'Flank|RP11-867G23.4_ENST00000526951.1_RNA	NM_030981.2	NP_112243.1	Q9H0U4	RAB1B_HUMAN	RAB1B, member RAS oncogene family	172					ER to Golgi vesicle-mediated transport (GO:0006888)|positive regulation of glycoprotein metabolic process (GO:1903020)|protein transport (GO:0015031)|small GTPase mediated signal transduction (GO:0007264)|virion assembly (GO:0019068)	endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|mitochondrion (GO:0005739)	GTP binding (GO:0005525)	p.R172W(1)		large_intestine(2)|lung(1)|ovary(1)|prostate(1)	5						AATCAAAAAGCGGATGGGGCC	0.602																																					p.R172W												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C514T	11						.						33.0	34.0	33.0					11																	66043617		2200	4295	6495	65800193	SO:0001583	missense	81876	exon6			AJ245875	CCDS31613.1	11q13.1	2008-02-05			ENSG00000174903	ENSG00000174903		"""RAB, member RAS oncogene"""	18370	protein-coding gene	gene with protein product		612565				9030196	Standard	NM_030981		Approved		uc001ohf.3	Q9H0U4	OTTHUMG00000166916	ENST00000311481.6:c.514C>T	11.37:g.66043617C>T	ENSP00000310226:p.Arg172Trp	Somatic		Capture	Illumina HiSeq	Phase_I	65800193	NM_030981	A8K7S1	Missense_Mutation	SNP	ENST00000311481.6	37	CCDS31613.1	.	.	.	.	.	.	.	.	.	.	C	12.98	2.100845	0.37048	.	.	ENSG00000174903	ENST00000311481;ENST00000527397	T;T	0.80480	-1.38;-1.38	3.9	2.97	0.34412	.	0.000000	0.64402	D	0.000005	T	0.61400	0.2344	N	0.14661	0.345	0.80722	D	1	P	0.35050	0.482	B	0.22880	0.042	T	0.63251	-0.6679	10	0.87932	D	0	.	10.8403	0.46710	0.1905:0.8095:0.0:0.0	.	172	Q9H0U4	RAB1B_HUMAN	W	172;140	ENSP00000310226:R172W;ENSP00000435195:R140W	ENSP00000310226:R172W	R	+	1	2	RAB1B	65800193	1.000000	0.71417	1.000000	0.80357	0.267000	0.26476	3.031000	0.49728	0.738000	0.32606	-0.823000	0.03104	CGG		0.602	RAB1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391886.2	NM_030981	
PELI3	246330	broad.mit.edu	37	11	66238807	66238807	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr11:66238807G>A	ENST00000320740.7	+	4	479	c.319G>A	c.(319-321)Gtc>Atc	p.V107I	CTD-3074O7.5_ENST00000527092.1_RNA|CTD-3074O7.5_ENST00000602951.1_RNA|PELI3_ENST00000524466.1_Missense_Mutation_p.V107I|PELI3_ENST00000531856.1_Intron|PELI3_ENST00000349459.6_Missense_Mutation_p.V83I	NM_001243136.1|NM_145065.2	NP_001230065.1|NP_659502.2	Q8N2H9	PELI3_HUMAN	pellino E3 ubiquitin protein ligase family member 3	107					defense response to Gram-negative bacterium (GO:0050829)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of protein ubiquitination (GO:0031397)|negative regulation of Toll signaling pathway (GO:0045751)|negative regulation of tumor necrosis factor-mediated signaling pathway (GO:0010804)|negative regulation of type I interferon production (GO:0032480)|positive regulation of nucleotide-binding oligomerization domain containing 2 signaling pathway (GO:0070434)|protein K63-linked ubiquitination (GO:0070534)|regulation of nucleotide-binding oligomerization domain containing 1 signaling pathway (GO:0070428)|Toll signaling pathway (GO:0008063)	cytosol (GO:0005829)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)	p.V107I(1)		breast(1)|endometrium(2)|large_intestine(4)|lung(4)|ovary(2)|prostate(1)|skin(1)	15						GAAGCCAGACGTCATGCACCA	0.647																																					p.V107I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G319A	11						.						96.0	85.0	89.0					11																	66238807		2200	4295	6495	65995383	SO:0001583	missense	246330	exon4			AL834395	CCDS31615.1, CCDS41675.1, CCDS73328.1	11q13.2	2012-02-23	2012-02-23		ENSG00000174516	ENSG00000174516		"""Pellino homologs"""	30010	protein-coding gene	gene with protein product		609827	"""pellino homolog 3 (Drosophila)"""			12874243, 15917247	Standard	NM_145065		Approved	MGC35521	uc001oic.4	Q8N2H9	OTTHUMG00000167109	ENST00000320740.7:c.319G>A	11.37:g.66238807G>A	ENSP00000322532:p.Val107Ile	Somatic		Capture	Illumina HiSeq	Phase_I	65995383	NM_145065	Q8N3E1|Q8N9Q6|Q8TAW7|Q8TED5	Missense_Mutation	SNP	ENST00000320740.7	37	CCDS31615.1	.	.	.	.	.	.	.	.	.	.	G	17.91	3.504996	0.64410	.	.	ENSG00000174516	ENST00000349459;ENST00000320740;ENST00000524466;ENST00000527230	T;T;T;T	0.42900	0.96;0.96;0.96;0.96	5.03	4.12	0.48240	.	0.170402	0.37857	N	0.001903	T	0.29945	0.0749	N	0.19112	0.55	0.37649	D	0.922329	P;P;D	0.58970	0.757;0.918;0.984	B;B;P	0.46510	0.194;0.422;0.519	T	0.19224	-1.0312	10	0.45353	T	0.12	-23.8088	7.4904	0.27458	0.1878:0.0:0.8122:0.0	.	83;107;107	Q8N2H9-2;Q8N2H9;Q8N2H9-4	.;PELI3_HUMAN;.	I	83;107;107;107	ENSP00000309848:V83I;ENSP00000322532:V107I;ENSP00000434677:V107I;ENSP00000432449:V107I	ENSP00000322532:V107I	V	+	1	0	PELI3	65995383	0.000000	0.05858	0.845000	0.33349	0.538000	0.34931	0.712000	0.25779	1.347000	0.45714	0.655000	0.94253	GTC		0.647	PELI3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000393226.1	NM_145065	
PELI3	246330	broad.mit.edu	37	11	66241211	66241211	+	Nonsense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr11:66241211C>T	ENST00000320740.7	+	7	815	c.655C>T	c.(655-657)Cga>Tga	p.R219*	CTD-3074O7.5_ENST00000527092.1_RNA|CTD-3074O7.5_ENST00000602951.1_RNA|PELI3_ENST00000524466.1_Nonsense_Mutation_p.R219*|CTD-3074O7.5_ENST00000533502.1_RNA|PELI3_ENST00000531856.1_Intron|PELI3_ENST00000349459.6_Nonsense_Mutation_p.R195*	NM_001243136.1|NM_145065.2	NP_001230065.1|NP_659502.2	Q8N2H9	PELI3_HUMAN	pellino E3 ubiquitin protein ligase family member 3	219					defense response to Gram-negative bacterium (GO:0050829)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of protein ubiquitination (GO:0031397)|negative regulation of Toll signaling pathway (GO:0045751)|negative regulation of tumor necrosis factor-mediated signaling pathway (GO:0010804)|negative regulation of type I interferon production (GO:0032480)|positive regulation of nucleotide-binding oligomerization domain containing 2 signaling pathway (GO:0070434)|protein K63-linked ubiquitination (GO:0070534)|regulation of nucleotide-binding oligomerization domain containing 1 signaling pathway (GO:0070428)|Toll signaling pathway (GO:0008063)	cytosol (GO:0005829)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)	p.R219*(1)		breast(1)|endometrium(2)|large_intestine(4)|lung(4)|ovary(2)|prostate(1)|skin(1)	15						GTCCCAGGAGCGAGCGGCCAA	0.647																																					p.R219X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.C655T	11						.						49.0	49.0	49.0					11																	66241211		2200	4295	6495	65997787	SO:0001587	stop_gained	246330	exon7			AL834395	CCDS31615.1, CCDS41675.1, CCDS73328.1	11q13.2	2012-02-23	2012-02-23		ENSG00000174516	ENSG00000174516		"""Pellino homologs"""	30010	protein-coding gene	gene with protein product		609827	"""pellino homolog 3 (Drosophila)"""			12874243, 15917247	Standard	NM_145065		Approved	MGC35521	uc001oic.4	Q8N2H9	OTTHUMG00000167109	ENST00000320740.7:c.655C>T	11.37:g.66241211C>T	ENSP00000322532:p.Arg219*	Somatic		Capture	Illumina HiSeq	Phase_I	65997787	NM_145065	Q8N3E1|Q8N9Q6|Q8TAW7|Q8TED5	Nonsense_Mutation	SNP	ENST00000320740.7	37	CCDS31615.1	.	.	.	.	.	.	.	.	.	.	C	37	6.402336	0.97537	.	.	ENSG00000174516	ENST00000349459;ENST00000320740;ENST00000524466;ENST00000526296;ENST00000528752	.	.	.	4.98	4.98	0.66077	.	0.000000	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.34782	T	0.22	-28.4758	11.0825	0.48068	0.1847:0.8153:0.0:0.0	.	.	.	.	X	195;219;219;112;6	.	ENSP00000322532:R219X	R	+	1	2	PELI3	65997787	1.000000	0.71417	1.000000	0.80357	0.966000	0.64601	1.634000	0.37123	2.746000	0.94184	0.655000	0.94253	CGA		0.647	PELI3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000393226.1	NM_145065	
PC	5091	broad.mit.edu	37	11	66619987	66619987	+	Missense_Mutation	SNP	C	C	T	rs119103242		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr11:66619987C>T	ENST00000393958.2	-	14	1841	c.1748G>A	c.(1747-1749)cGc>cAc	p.R583H	PC_ENST00000393960.1_Missense_Mutation_p.R583H|PC_ENST00000529047.1_5'Flank|PC_ENST00000393955.2_Missense_Mutation_p.R583H|PC_ENST00000528224.1_5'Flank	NM_000920.3	NP_000911.2	P11498	PYC_HUMAN	pyruvate carboxylase	583	Carboxyltransferase.		R -> L (in PC deficiency). {ECO:0000269|PubMed:19306334}.		biotin metabolic process (GO:0006768)|carbohydrate metabolic process (GO:0005975)|gluconeogenesis (GO:0006094)|glucose metabolic process (GO:0006006)|lipid metabolic process (GO:0006629)|oxaloacetate metabolic process (GO:0006107)|pyruvate metabolic process (GO:0006090)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|biotin binding (GO:0009374)|biotin carboxylase activity (GO:0004075)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)|pyruvate carboxylase activity (GO:0004736)	p.R583H(1)		cervix(1)|endometrium(3)|kidney(3)|large_intestine(9)|lung(12)|ovary(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	32		Melanoma(852;0.0525)		Lung(977;0.153)|LUSC - Lung squamous cell carcinoma(976;0.227)	Biotin(DB00121)|Pyruvic acid(DB00119)	ATCGTGGGTGCGCACACGAGT	0.617																																					p.R583H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1748A	11						.						71.0	69.0	70.0					11																	66619987		2200	4295	6495	66376563	SO:0001583	missense	5091	exon15			U04641	CCDS8152.1	11q13.4-q13.5	2012-07-11			ENSG00000173599	ENSG00000173599	6.4.1.1		8636	protein-coding gene	gene with protein product		608786				6548474	Standard	NM_022172		Approved	PCB	uc001ojn.1	P11498	OTTHUMG00000167099	ENST00000393958.2:c.1748G>A	11.37:g.66619987C>T	ENSP00000377530:p.Arg583His	Somatic		Capture	Illumina HiSeq	Phase_I	66376563	NM_001040716	B4DN00|Q16705	Missense_Mutation	SNP	ENST00000393958.2	37	CCDS8152.1	.	.	.	.	.	.	.	.	.	.	C	21.0	4.078393	0.76528	.	.	ENSG00000173599	ENST00000393955;ENST00000393958;ENST00000393960	D;D;D	0.98381	-4.9;-4.9;-4.9	5.53	5.53	0.82687	Aldolase-type TIM barrel (1);Pyruvate carboxyltransferase (2);	0.000000	0.85682	D	0.000000	D	0.99351	0.9772	H	0.96777	3.88	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.98674	1.0689	10	0.87932	D	0	-22.5396	16.9874	0.86344	0.0:1.0:0.0:0.0	.	583	P11498	PYC_HUMAN	H	583	ENSP00000377527:R583H;ENSP00000377530:R583H;ENSP00000377532:R583H	ENSP00000377527:R583H	R	-	2	0	PC	66376563	1.000000	0.71417	0.999000	0.59377	0.082000	0.17680	7.139000	0.77314	2.605000	0.88082	0.655000	0.94253	CGC		0.617	PC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393115.1	NM_001040716	
KDM2A	22992	broad.mit.edu	37	11	67012860	67012860	+	Silent	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr11:67012860C>T	ENST00000529006.2	+	14	2210	c.1764C>T	c.(1762-1764)tgC>tgT	p.C588C	KDM2A_ENST00000526258.1_3'UTR|KDM2A_ENST00000398645.2_Silent_p.C588C|KDM2A_ENST00000308783.5_Silent_p.C46C|KDM2A_ENST00000530342.1_Silent_p.C149C	NM_012308.2	NP_036440.1	Q9Y2K7	KDM2A_HUMAN	lysine (K)-specific demethylase 2A	588					histone H3-K36 demethylation (GO:0070544)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nuclear chromatin (GO:0000790)|nucleolus (GO:0005730)|nucleus (GO:0005634)	histone demethylase activity (H3-K36 specific) (GO:0051864)|unmethylated CpG binding (GO:0045322)|zinc ion binding (GO:0008270)	p.C588C(1)		NS(1)|breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(6)|lung(15)|ovary(5)|skin(1)|urinary_tract(2)	36						GCCACTACTGCAGAGACATGA	0.547																																					p.C588C												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1764T	11						.						63.0	69.0	67.0					11																	67012860		2098	4233	6331	66769436	SO:0001819	synonymous_variant	22992	exon14			BC047486	CCDS44657.1, CCDS58148.1	11q13.1	2014-02-18	2009-04-06	2009-04-06	ENSG00000173120	ENSG00000173120		"""F-boxes / Leucine-rich repeats"", ""Chromatin-modifying enzymes / K-demethylases"""	13606	protein-coding gene	gene with protein product	"""F-box protein FBL11"", ""jumonji C domain-containing histone demethylase 1A"""	605657	"""F-box and leucine-rich repeat protein 11"""	FBXL11		10231032, 10531037	Standard	NM_012308		Approved	KIAA1004, FBL11, LILINA, DKFZP434M1735, FBL7, FLJ00115, CXXC8, JHDM1A	uc001ojw.3	Q9Y2K7	OTTHUMG00000167103	ENST00000529006.2:c.1764C>T	11.37:g.67012860C>T		Somatic		Capture	Illumina HiSeq	Phase_I	66769436	NM_012308	D4QA03|E9PIL6|I3VM55|Q49A21|Q4G0M3|Q69YY8|Q9BVH5|Q9H7H5|Q9UK66	Silent	SNP	ENST00000529006.2	37	CCDS44657.1																																																																																				0.547	KDM2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393140.2	NM_012308	
CHKA	1119	broad.mit.edu	37	11	67837693	67837693	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr11:67837693G>A	ENST00000265689.4	-	6	858	c.832C>T	c.(832-834)Ctc>Ttc	p.L278F	CHKA_ENST00000356135.5_Missense_Mutation_p.L260F	NM_001277.2	NP_001268.2	P35790	CHKA_HUMAN	choline kinase alpha	278					CDP-choline pathway (GO:0006657)|choline metabolic process (GO:0019695)|glycerophospholipid biosynthetic process (GO:0046474)|lipid metabolic process (GO:0006629)|lipid transport (GO:0006869)|phosphatidylcholine biosynthetic process (GO:0006656)|phosphatidylethanolamine biosynthetic process (GO:0006646)|phospholipid metabolic process (GO:0006644)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	ATP binding (GO:0005524)|choline binding (GO:0033265)|choline kinase activity (GO:0004103)|cholinesterase activity (GO:0004104)|drug binding (GO:0008144)|ethanolamine kinase activity (GO:0004305)|signal transducer activity (GO:0004871)	p.L278F(1)		central_nervous_system(1)|endometrium(1)|large_intestine(4)|lung(5)|ovary(1)|skin(1)	13					Choline(DB00122)	TTGTAACTGAGCAATTTGTGG	0.323																																					p.L260F												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C778T	11						.						87.0	94.0	92.0					11																	67837693		2200	4294	6494	67594269	SO:0001583	missense	1119	exon5			D10704	CCDS8178.1, CCDS8179.1	11q13.1	2008-02-05	2004-04-19	2004-04-21	ENSG00000110721	ENSG00000110721	2.7.1.32		1937	protein-coding gene	gene with protein product		118491	"""choline kinase"""	CHK		1618328, 15003397	Standard	NM_001277		Approved	CKI	uc001onj.3	P35790	OTTHUMG00000167424	ENST00000265689.4:c.832C>T	11.37:g.67837693G>A	ENSP00000265689:p.Leu278Phe	Somatic		Capture	Illumina HiSeq	Phase_I	67594269	NM_212469	Q8NE29	Missense_Mutation	SNP	ENST00000265689.4	37	CCDS8178.1	.	.	.	.	.	.	.	.	.	.	G	14.62	2.589304	0.46214	.	.	ENSG00000110721	ENST00000265689;ENST00000356135;ENST00000531341	T;T;T	0.56611	0.55;0.55;0.45	5.27	5.27	0.74061	Protein kinase-like domain (1);Choline/ethanolamine kinase (1);	0.000000	0.64402	D	0.000001	T	0.54287	0.1849	L	0.33189	0.99	0.80722	D	1	D;P	0.55385	0.971;0.872	P;P	0.55161	0.77;0.688	T	0.55685	-0.8102	10	0.54805	T	0.06	-19.383	12.2702	0.54702	0.078:0.0:0.922:0.0	.	260;278	P35790-2;P35790	.;CHKA_HUMAN	F	278;260;156	ENSP00000265689:L278F;ENSP00000348454:L260F;ENSP00000435032:L156F	ENSP00000265689:L278F	L	-	1	0	CHKA	67594269	1.000000	0.71417	0.777000	0.31699	0.884000	0.51177	3.409000	0.52657	2.451000	0.82905	0.491000	0.48974	CTC		0.323	CHKA-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000394570.1	NM_001277	
SUV420H1	51111	broad.mit.edu	37	11	67925554	67925554	+	Silent	SNP	G	G	A	rs146549090	byFrequency	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr11:67925554G>A	ENST00000304363.4	-	11	2612	c.2259C>T	c.(2257-2259)aaC>aaT	p.N753N		NM_017635.3	NP_060105	Q4FZB7	SV421_HUMAN	suppressor of variegation 4-20 homolog 1 (Drosophila)	753					histone H4-K20 trimethylation (GO:0034773)|muscle organ development (GO:0007517)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	condensed nuclear chromosome, centromeric region (GO:0000780)	histone methyltransferase activity (H4-K20 specific) (GO:0042799)|histone-lysine N-methyltransferase activity (GO:0018024)	p.N753N(2)		NS(1)|breast(3)|endometrium(4)|kidney(3)|large_intestine(9)|lung(15)|ovary(2)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	46						GATTGTTATCGTTGTCATGGT	0.363													G|||	4	0.000798722	0.0023	0.0	5008	,	,		24065	0.0		0.0	False		,,,				2504	0.001				p.N753N												.	.	2	Substitution - coding silent(2)	large_intestine(1)|endometrium(1)	c.C2259T	11						.	G		6,4394	11.4+/-27.6	0,6,2194	184.0	189.0	187.0		2259	-9.7	0.0	11	dbSNP_134	187	0,8588		0,0,4294	no	coding-synonymous	SUV420H1	NM_017635.3		0,6,6488	AA,AG,GG		0.0,0.1364,0.0462		753/886	67925554	6,12982	2200	4294	6494	67682130	SO:0001819	synonymous_variant	51111	exon11			AL512763	CCDS31623.1, CCDS44660.1	11q13.2	2011-07-01			ENSG00000110066	ENSG00000110066		"""Chromatin-modifying enzymes / K-methyltransferases"""	24283	protein-coding gene	gene with protein product		610881				10810093, 11401438	Standard	NM_016028		Approved	CGI-85, KMT5B	uc001onm.1	Q4FZB7	OTTHUMG00000150484	ENST00000304363.4:c.2259C>T	11.37:g.67925554G>A		Somatic		Capture	Illumina HiSeq	Phase_I	67682130	NM_017635	B7WNX7|Q3SX56|Q4V775|Q6P150|Q96E44|Q9BUL0|Q9H022|Q9H2K3|Q9NXV3|Q9Y393	Silent	SNP	ENST00000304363.4	37	CCDS31623.1																																																																																				0.363	SUV420H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318319.1	NM_017635	
LRP5	4041	broad.mit.edu	37	11	68201131	68201131	+	Silent	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr11:68201131C>T	ENST00000294304.7	+	18	3931	c.3825C>T	c.(3823-3825)ccC>ccT	p.P1275P		NM_002335.2	NP_002326.2	O75197	LRP5_HUMAN	low density lipoprotein receptor-related protein 5	1275	LDL-receptor class A 1. {ECO:0000255|PROSITE-ProRule:PRU00124}.				adipose tissue development (GO:0060612)|anatomical structure regression (GO:0060033)|anterior/posterior pattern specification (GO:0009952)|apoptotic process involved in patterning of blood vessels (GO:1902262)|bone marrow development (GO:0048539)|bone morphogenesis (GO:0060349)|bone remodeling (GO:0046849)|branching involved in mammary gland duct morphogenesis (GO:0060444)|canonical Wnt signaling pathway (GO:0060070)|cell migration involved in gastrulation (GO:0042074)|cell-cell signaling involved in mammary gland development (GO:0060764)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|embryonic camera-type eye morphogenesis (GO:0048596)|embryonic digit morphogenesis (GO:0042733)|embryonic limb morphogenesis (GO:0030326)|embryonic retina morphogenesis in camera-type eye (GO:0060059)|endocytosis (GO:0006897)|extracellular matrix-cell signaling (GO:0035426)|gastrulation with mouth forming second (GO:0001702)|glucose catabolic process (GO:0006007)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of protein serine/threonine kinase activity (GO:0071901)|osteoblast development (GO:0002076)|positive regulation of cell proliferation (GO:0008284)|positive regulation of fat cell differentiation (GO:0045600)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of mitosis (GO:0045840)|positive regulation of osteoblast proliferation (GO:0033690)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of apoptotic process (GO:0042981)|regulation of blood pressure (GO:0008217)|regulation of bone remodeling (GO:0046850)|regulation of canonical Wnt signaling pathway (GO:0060828)|regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0061178)|response to peptide hormone (GO:0043434)|retina morphogenesis in camera-type eye (GO:0060042)|retinal blood vessel morphogenesis (GO:0061304)|somatic stem cell maintenance (GO:0035019)|Wnt signaling pathway (GO:0016055)|Wnt signaling pathway involved in dorsal/ventral axis specification (GO:0044332)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	coreceptor activity (GO:0015026)|Wnt-activated receptor activity (GO:0042813)|Wnt-protein binding (GO:0017147)	p.P1275P(1)		autonomic_ganglia(1)|breast(3)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|lung(24)|ovary(5)|pancreas(1)|prostate(1)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	63						ACTGTATCCCCGGGGCCTGGC	0.697																																					p.P1275P												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C3825T	11						.						78.0	87.0	84.0					11																	68201131		2200	4294	6494	67957707	SO:0001819	synonymous_variant	4041	exon18			AF064548	CCDS8181.1	11q13.4	2014-01-28	2003-03-12		ENSG00000162337	ENSG00000162337		"""Low density lipoprotein receptors"""	6697	protein-coding gene	gene with protein product		603506	"""osteoporosis pseudoglioma syndrome"", ""exudative vitreoretinopathy 1"""	LRP7, OPPG, EVR1		9714764, 10049586	Standard	XM_005273994		Approved	LR3, BMND1, HBM, OPS, OPTA1, VBCH2, EVR4	uc001ont.3	O75197	OTTHUMG00000167570	ENST00000294304.7:c.3825C>T	11.37:g.68201131C>T		Somatic		Capture	Illumina HiSeq	Phase_I	67957707	NM_002335	Q96TD6|Q9UES7|Q9UP66	Silent	SNP	ENST00000294304.7	37	CCDS8181.1																																																																																				0.697	LRP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395088.1	NM_002335	
IGHMBP2	3508	broad.mit.edu	37	11	68682435	68682435	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr11:68682435C>T	ENST00000255078.3	+	6	967	c.856C>T	c.(856-858)Cgg>Tgg	p.R286W		NM_002180.2	NP_002171.2	P38935	SMBP2_HUMAN	immunoglobulin mu binding protein 2	286	Leu-rich.				ATP catabolic process (GO:0006200)|cell death (GO:0008219)|DNA duplex unwinding (GO:0032508)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|protein homooligomerization (GO:0051260)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)|translation (GO:0006412)	axon (GO:0030424)|cytoplasm (GO:0005737)|growth cone (GO:0030426)|membrane (GO:0016020)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	ATP binding (GO:0005524)|ATP-dependent 5'-3' DNA helicase activity (GO:0043141)|ATP-dependent 5'-3' RNA helicase activity (GO:0032575)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)|DNA-dependent ATPase activity (GO:0008094)|ribosome binding (GO:0043022)|RNA binding (GO:0003723)|RNA-dependent ATPase activity (GO:0008186)|single-stranded DNA binding (GO:0003697)|transcription factor binding (GO:0008134)|tRNA binding (GO:0000049)|zinc ion binding (GO:0008270)	p.R286W(2)		central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(4)|liver(1)|lung(15)|ovary(2)|prostate(2)|soft_tissue(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	36			STAD - Stomach adenocarcinoma(18;0.0208)|LUAD - Lung adenocarcinoma(13;0.0713)			GGTTTTAGCGCGGAGCGACAG	0.597																																					p.R286W												.	.	2	Substitution - Missense(2)	large_intestine(1)|prostate(1)	c.C856T	11						.						112.0	100.0	104.0					11																	68682435		2200	4294	6494	68439011	SO:0001583	missense	3508	exon6			L14754	CCDS8187.1	11q13.3	2014-09-17			ENSG00000132740	ENSG00000132740		"""Zinc fingers, AN1-type domain containing"""	5542	protein-coding gene	gene with protein product	"""cardiac transcription factor 1"", ""zinc finger, AN1-type domain 7"""	600502				8349627	Standard	NM_002180		Approved	ZFAND7, SMUBP2, CATF1, SMARD1, HCSA, HMN6	uc001ook.1	P38935	OTTHUMG00000167894	ENST00000255078.3:c.856C>T	11.37:g.68682435C>T	ENSP00000255078:p.Arg286Trp	Somatic		Capture	Illumina HiSeq	Phase_I	68439011	NM_002180	A0PJD2|Q00443|Q14177	Missense_Mutation	SNP	ENST00000255078.3	37	CCDS8187.1	.	.	.	.	.	.	.	.	.	.	C	14.20	2.464362	0.43736	.	.	ENSG00000132740	ENST00000255078	D	0.83163	-1.69	3.71	2.77	0.32553	DEAD-like helicase (1);Helicase/UvrB domain (1);ATPase, AAA+ type, core (1);	0.267991	0.38381	N	0.001711	D	0.88190	0.6370	M	0.63843	1.955	0.80722	D	1	D	0.89917	1.0	D	0.76071	0.987	D	0.88114	0.2827	10	0.72032	D	0.01	-8.166	11.4816	0.50328	0.1818:0.8182:0.0:0.0	.	286	P38935	SMBP2_HUMAN	W	286	ENSP00000255078:R286W	ENSP00000255078:R286W	R	+	1	2	IGHMBP2	68439011	0.993000	0.37304	0.010000	0.14722	0.048000	0.14542	3.372000	0.52387	0.868000	0.35678	0.555000	0.69702	CGG		0.597	IGHMBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396862.1	NM_002180	
ARAP1	116985	broad.mit.edu	37	11	72414102	72414102	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr11:72414102G>A	ENST00000393609.3	-	15	2217	c.2015C>T	c.(2014-2016)aCc>aTc	p.T672I	ARAP1_ENST00000334211.8_Missense_Mutation_p.T427I|ARAP1_ENST00000495878.1_5'Flank|ARAP1_ENST00000426523.1_Missense_Mutation_p.T427I|ARAP1-AS2_ENST00000500163.2_RNA|ARAP1_ENST00000455638.2_Missense_Mutation_p.T672I|ARAP1_ENST00000393605.3_Missense_Mutation_p.T432I|ARAP1_ENST00000429686.1_Missense_Mutation_p.T366I|ARAP1_ENST00000359373.5_Missense_Mutation_p.T672I	NM_001040118.2	NP_001035207.1	Q96P48	ARAP1_HUMAN	ArfGAP with RhoGAP domain, ankyrin repeat and PH domain 1	672					actin filament reorganization involved in cell cycle (GO:0030037)|negative regulation of stress fiber assembly (GO:0051497)|positive regulation of Cdc42 GTPase activity (GO:0043089)|positive regulation of filopodium assembly (GO:0051491)|positive regulation of receptor recycling (GO:0001921)|regulation of ARF GTPase activity (GO:0032312)|regulation of cell shape (GO:0008360)|regulation of cellular component movement (GO:0051270)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)	ARF GTPase activator activity (GO:0008060)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|Rho GTPase activator activity (GO:0005100)|zinc ion binding (GO:0008270)	p.T432I(1)		cervix(2)|endometrium(2)|large_intestine(10)|lung(8)|ovary(1)|skin(3)|urinary_tract(1)	27						CAGGTCTGTGGTGGTGACTGC	0.667																																					p.T672I	Ovarian(102;1198 1520 13195 17913 37529)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C2015T	11						.						19.0	17.0	17.0					11																	72414102		2199	4291	6490	72091750	SO:0001583	missense	116985	exon15			AF411983	CCDS8217.2, CCDS41687.1, CCDS44671.1	11q13.3	2013-01-11	2008-09-22	2008-09-22	ENSG00000186635	ENSG00000186635		"""ADP-ribosylation factor GTPase activating proteins"", ""Sterile alpha motif (SAM) domain containing"", ""Pleckstrin homology (PH) domain containing"", ""Ankyrin repeat domain containing"""	16925	protein-coding gene	gene with protein product		606646	"""centaurin, delta 2"""	CENTD2			Standard	NM_001040118		Approved		uc001osu.3	Q96P48	OTTHUMG00000157102	ENST00000393609.3:c.2015C>T	11.37:g.72414102G>A	ENSP00000377233:p.Thr672Ile	Somatic		Capture	Illumina HiSeq	Phase_I	72091750	NM_001040118	A3KLL7|B2RTS2|O94879|Q4LDD5|Q59FI7|Q6PHS3|Q8WU51|Q96HP6|Q96L71	Missense_Mutation	SNP	ENST00000393609.3	37	CCDS41687.1	.	.	.	.	.	.	.	.	.	.	G	17.92	3.507275	0.64410	.	.	ENSG00000186635	ENST00000359373;ENST00000455638;ENST00000393605;ENST00000334211;ENST00000393609;ENST00000426523;ENST00000429686;ENST00000340247	T;T;T;T;T;T;T	0.08807	3.05;3.05;3.07;3.11;3.06;3.11;3.23	5.12	5.12	0.69794	.	0.126959	0.53938	D	0.000046	T	0.23133	0.0559	L	0.50333	1.59	0.33542	D	0.59498	P;D;D;P;P	0.71674	0.885;0.998;0.994;0.885;0.93	B;D;P;P;P	0.68621	0.439;0.959;0.899;0.526;0.642	T	0.03829	-1.1000	10	0.41790	T	0.15	.	17.2966	0.87171	0.0:0.0:1.0:0.0	.	427;366;672;672;432	E7EU13;B2RTS2;Q96P48-3;Q96P48;Q96P48-1	.;.;.;ARAP1_HUMAN;.	I	672;672;432;427;672;427;366;461	ENSP00000352332:T672I;ENSP00000390461:T672I;ENSP00000377230:T432I;ENSP00000335506:T427I;ENSP00000377233:T672I;ENSP00000392264:T427I;ENSP00000403127:T366I	ENSP00000335506:T427I	T	-	2	0	ARAP1	72091750	1.000000	0.71417	1.000000	0.80357	0.789000	0.44602	4.960000	0.63673	2.643000	0.89663	0.563000	0.77884	ACC		0.667	ARAP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000347428.1	NM_001040118	
ARAP1	116985	broad.mit.edu	37	11	72421468	72421468	+	Missense_Mutation	SNP	C	C	T	rs145451210		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr11:72421468C>T	ENST00000393609.3	-	10	1580	c.1378G>A	c.(1378-1380)Gtg>Atg	p.V460M	ARAP1_ENST00000334211.8_Missense_Mutation_p.V215M|ARAP1_ENST00000426523.1_Missense_Mutation_p.V215M|ARAP1_ENST00000455638.2_Missense_Mutation_p.V460M|ARAP1_ENST00000393605.3_Missense_Mutation_p.V220M|ARAP1_ENST00000429686.1_Missense_Mutation_p.V215M|ARAP1_ENST00000359373.5_Missense_Mutation_p.V460M	NM_001040118.2	NP_001035207.1	Q96P48	ARAP1_HUMAN	ArfGAP with RhoGAP domain, ankyrin repeat and PH domain 1	460	PH 2. {ECO:0000255|PROSITE- ProRule:PRU00145}.				actin filament reorganization involved in cell cycle (GO:0030037)|negative regulation of stress fiber assembly (GO:0051497)|positive regulation of Cdc42 GTPase activity (GO:0043089)|positive regulation of filopodium assembly (GO:0051491)|positive regulation of receptor recycling (GO:0001921)|regulation of ARF GTPase activity (GO:0032312)|regulation of cell shape (GO:0008360)|regulation of cellular component movement (GO:0051270)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)	ARF GTPase activator activity (GO:0008060)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|Rho GTPase activator activity (GO:0005100)|zinc ion binding (GO:0008270)	p.V220M(1)		cervix(2)|endometrium(2)|large_intestine(10)|lung(8)|ovary(1)|skin(3)|urinary_tract(1)	27						TCCCCGACCACGGCCACGTAC	0.597																																					p.V460M	Ovarian(102;1198 1520 13195 17913 37529)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1378A	11						.	C	MET/VAL,MET/VAL,MET/VAL	2,4398	4.2+/-10.8	0,2,2198	136.0	126.0	129.0		1378,643,643	5.3	1.0	11	dbSNP_134	129	0,8586		0,0,4293	no	missense,missense,missense	ARAP1	NM_001040118.2,NM_001135190.1,NM_015242.4	21,21,21	0,2,6491	TT,TC,CC		0.0,0.0455,0.0154	probably-damaging,probably-damaging,probably-damaging	460/1451,215/1134,215/1206	72421468	2,12984	2200	4293	6493	72099116	SO:0001583	missense	116985	exon10			AF411983	CCDS8217.2, CCDS41687.1, CCDS44671.1	11q13.3	2013-01-11	2008-09-22	2008-09-22	ENSG00000186635	ENSG00000186635		"""ADP-ribosylation factor GTPase activating proteins"", ""Sterile alpha motif (SAM) domain containing"", ""Pleckstrin homology (PH) domain containing"", ""Ankyrin repeat domain containing"""	16925	protein-coding gene	gene with protein product		606646	"""centaurin, delta 2"""	CENTD2			Standard	NM_001040118		Approved		uc001osu.3	Q96P48	OTTHUMG00000157102	ENST00000393609.3:c.1378G>A	11.37:g.72421468C>T	ENSP00000377233:p.Val460Met	Somatic		Capture	Illumina HiSeq	Phase_I	72099116	NM_001040118	A3KLL7|B2RTS2|O94879|Q4LDD5|Q59FI7|Q6PHS3|Q8WU51|Q96HP6|Q96L71	Missense_Mutation	SNP	ENST00000393609.3	37	CCDS41687.1	.	.	.	.	.	.	.	.	.	.	C	25.3	4.618918	0.87460	4.55E-4	0.0	ENSG00000186635	ENST00000359373;ENST00000455638;ENST00000393605;ENST00000334211;ENST00000393609;ENST00000426523;ENST00000429686;ENST00000340247	T;T;T;T;T;T;T	0.63580	-0.05;-0.05;-0.05;-0.05;-0.05;-0.05;-0.05	5.32	5.32	0.75619	Pleckstrin homology-type (1);Pleckstrin homology domain (2);	0.077649	0.51477	D	0.000086	T	0.73791	0.3632	L	0.44542	1.39	0.36776	D	0.884063	D;D;D;D;D	0.89917	0.999;1.0;1.0;1.0;0.999	P;D;D;D;D	0.80764	0.893;0.987;0.994;0.926;0.951	T	0.79369	-0.1832	10	0.72032	D	0.01	.	17.5742	0.87943	0.0:1.0:0.0:0.0	.	215;215;460;460;220	E7EU13;B2RTS2;Q96P48-3;Q96P48;Q96P48-1	.;.;.;ARAP1_HUMAN;.	M	460;460;220;215;460;215;215;249	ENSP00000352332:V460M;ENSP00000390461:V460M;ENSP00000377230:V220M;ENSP00000335506:V215M;ENSP00000377233:V460M;ENSP00000392264:V215M;ENSP00000403127:V215M	ENSP00000335506:V215M	V	-	1	0	ARAP1	72099116	0.924000	0.31332	0.980000	0.43619	0.989000	0.77384	2.003000	0.40844	2.494000	0.84150	0.563000	0.77884	GTG		0.597	ARAP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000347428.1	NM_001040118	
ARAP1	116985	broad.mit.edu	37	11	72422184	72422184	+	Silent	SNP	G	G	A	rs548349119	byFrequency	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr11:72422184G>A	ENST00000393609.3	-	9	1297	c.1095C>T	c.(1093-1095)gaC>gaT	p.D365D	ARAP1_ENST00000334211.8_Silent_p.D120D|ARAP1_ENST00000426523.1_Silent_p.D120D|ARAP1_ENST00000455638.2_Silent_p.D365D|ARAP1_ENST00000393605.3_Silent_p.D125D|ARAP1_ENST00000429686.1_Silent_p.D120D|ARAP1_ENST00000359373.5_Silent_p.D365D	NM_001040118.2	NP_001035207.1	Q96P48	ARAP1_HUMAN	ArfGAP with RhoGAP domain, ankyrin repeat and PH domain 1	365	PH 1. {ECO:0000255|PROSITE- ProRule:PRU00145}.				actin filament reorganization involved in cell cycle (GO:0030037)|negative regulation of stress fiber assembly (GO:0051497)|positive regulation of Cdc42 GTPase activity (GO:0043089)|positive regulation of filopodium assembly (GO:0051491)|positive regulation of receptor recycling (GO:0001921)|regulation of ARF GTPase activity (GO:0032312)|regulation of cell shape (GO:0008360)|regulation of cellular component movement (GO:0051270)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)	ARF GTPase activator activity (GO:0008060)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|Rho GTPase activator activity (GO:0005100)|zinc ion binding (GO:0008270)	p.D125D(1)		cervix(2)|endometrium(2)|large_intestine(10)|lung(8)|ovary(1)|skin(3)|urinary_tract(1)	27						TAGAGTAAGCGTCCTGGGGGA	0.552													G|||	4	0.000798722	0.0	0.0	5008	,	,		19889	0.0		0.0	False		,,,				2504	0.0041				p.D365D	Ovarian(102;1198 1520 13195 17913 37529)											.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1095T	11						.						65.0	60.0	61.0					11																	72422184		2200	4293	6493	72099832	SO:0001819	synonymous_variant	116985	exon9			AF411983	CCDS8217.2, CCDS41687.1, CCDS44671.1	11q13.3	2013-01-11	2008-09-22	2008-09-22	ENSG00000186635	ENSG00000186635		"""ADP-ribosylation factor GTPase activating proteins"", ""Sterile alpha motif (SAM) domain containing"", ""Pleckstrin homology (PH) domain containing"", ""Ankyrin repeat domain containing"""	16925	protein-coding gene	gene with protein product		606646	"""centaurin, delta 2"""	CENTD2			Standard	NM_001040118		Approved		uc001osu.3	Q96P48	OTTHUMG00000157102	ENST00000393609.3:c.1095C>T	11.37:g.72422184G>A		Somatic		Capture	Illumina HiSeq	Phase_I	72099832	NM_001040118	A3KLL7|B2RTS2|O94879|Q4LDD5|Q59FI7|Q6PHS3|Q8WU51|Q96HP6|Q96L71	Silent	SNP	ENST00000393609.3	37	CCDS41687.1																																																																																				0.552	ARAP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000347428.1	NM_001040118	
ATG16L2	89849	broad.mit.edu	37	11	72539930	72539930	+	Missense_Mutation	SNP	C	C	T	rs369947367		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr11:72539930C>T	ENST00000321297.5	+	17	1811	c.1673C>T	c.(1672-1674)cCg>cTg	p.P558L	ATG16L2_ENST00000534905.1_Intron	NM_033388.1	NP_203746.1	Q8NAA4	A16L2_HUMAN	autophagy related 16-like 2 (S. cerevisiae)	558					autophagy (GO:0006914)|negative stranded viral RNA replication (GO:0039689)|protein transport (GO:0015031)	cytoplasm (GO:0005737)|nucleus (GO:0005634)		p.P558L(1)		breast(1)|cervix(1)|endometrium(2)|large_intestine(1)|lung(9)	14			BRCA - Breast invasive adenocarcinoma(5;2.73e-06)			CACTACAGCCCGGACAGAAGC	0.602																																					p.P558L												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1673T	11						.						113.0	114.0	114.0					11																	72539930		2200	4293	6493	72217578	SO:0001583	missense	89849	exon17			AK024423	CCDS31634.1	11q13.4	2014-02-12	2012-06-06		ENSG00000168010	ENSG00000168010		"""WD repeat domain containing"""	25464	protein-coding gene	gene with protein product			"""ATG16 autophagy related 16-like 2 (S. cerevisiae)"""			11214971	Standard	XM_005274378		Approved	FLJ00012, WDR80, ATG16B	uc001otd.3	Q8NAA4	OTTHUMG00000167961	ENST00000321297.5:c.1673C>T	11.37:g.72539930C>T	ENSP00000326340:p.Pro558Leu	Somatic		Capture	Illumina HiSeq	Phase_I	72217578	NM_033388	A5PL30|B2RPK5|Q658V4|Q6PID3|Q8NBG0	Missense_Mutation	SNP	ENST00000321297.5	37	CCDS31634.1	.	.	.	.	.	.	.	.	.	.	C	26.2	4.711640	0.89112	.	.	ENSG00000168010	ENST00000321297;ENST00000541367	D;D	0.84800	-1.9;-1.9	5.52	5.52	0.82312	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.061993	0.64402	N	0.000007	D	0.94138	0.8120	M	0.92833	3.35	0.80722	D	1	D	0.71674	0.998	D	0.76575	0.988	D	0.95207	0.8322	10	0.87932	D	0	.	16.9157	0.86150	0.0:1.0:0.0:0.0	.	558	Q8NAA4	A16L2_HUMAN	L	558;389	ENSP00000326340:P558L;ENSP00000437412:P389L	ENSP00000326340:P558L	P	+	2	0	ATG16L2	72217578	1.000000	0.71417	0.939000	0.37840	0.851000	0.48451	6.184000	0.72008	2.610000	0.88304	0.561000	0.74099	CCG		0.602	ATG16L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397305.1	NM_033388	
P2RY2	5029	broad.mit.edu	37	11	72945734	72945734	+	Missense_Mutation	SNP	G	G	A	rs148967472		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr11:72945734G>A	ENST00000311131.2	+	3	997	c.530G>A	c.(529-531)cGc>cAc	p.R177H	P2RY2_ENST00000393596.2_Missense_Mutation_p.R177H|P2RY2_ENST00000393597.2_Missense_Mutation_p.R177H	NM_002564.2|NM_176072.1	NP_002555|NP_788086	P41231	P2RY2_HUMAN	purinergic receptor P2Y, G-protein coupled, 2	177					cellular ion homeostasis (GO:0006873)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|positive regulation of mucus secretion (GO:0070257)|regulation of vasodilation (GO:0042312)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled purinergic nucleotide receptor activity (GO:0045028)|receptor activity (GO:0004872)	p.R177H(1)		endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(3)|lung(8)|ovary(2)|prostate(1)|skin(2)|urinary_tract(2)	25					Suramin(DB04786)	ACCAGCGCGCGCGGGGGCCGC	0.721																																					p.R177H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G530A	11						.																																			72623382	SO:0001583	missense	5029	exon3			U07225	CCDS8219.1	11q13.5-q14.1	2012-08-08				ENSG00000175591		"""Purinergic receptors"", ""GPCR / Class A : Purinergic receptors, P2Y"""	8541	protein-coding gene	gene with protein product		600041				8159738, 9286708	Standard	NM_002564		Approved	P2U	uc001otj.4	P41231		ENST00000311131.2:c.530G>A	11.37:g.72945734G>A	ENSP00000310305:p.Arg177His	Somatic		Capture	Illumina HiSeq	Phase_I	72623382	NM_176072	B2R9W3|Q96EM8	Missense_Mutation	SNP	ENST00000311131.2	37	CCDS8219.1	.	.	.	.	.	.	.	.	.	.	G	12.62	1.992699	0.35131	.	.	ENSG00000175591	ENST00000393597;ENST00000311131;ENST00000393596	T;T;T	0.27104	1.69;1.69;1.69	4.94	4.94	0.65067	GPCR, rhodopsin-like superfamily (1);	11.497700	0.00166	N	0.000000	T	0.46698	0.1406	L	0.59436	1.845	0.09310	N	1	P	0.51933	0.949	P	0.58130	0.833	T	0.21211	-1.0252	10	0.51188	T	0.08	.	9.4518	0.38731	0.1653:0.0:0.8347:0.0	.	177	P41231	P2RY2_HUMAN	H	177	ENSP00000377222:R177H;ENSP00000310305:R177H;ENSP00000377221:R177H	ENSP00000310305:R177H	R	+	2	0	P2RY2	72623382	0.008000	0.16893	0.010000	0.14722	0.119000	0.20118	0.932000	0.28884	2.452000	0.82932	0.561000	0.74099	CGC		0.721	P2RY2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397336.1	NM_176072	
RAB6A	5870	broad.mit.edu	37	11	73388998	73388998	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr11:73388998A>G	ENST00000336083.3	-	8	1027	c.572T>C	c.(571-573)aTa>aCa	p.I191T	RAB6A_ENST00000310653.6_Missense_Mutation_p.I191T|RAB6A_ENST00000541588.1_Missense_Mutation_p.I87T|RAB6A_ENST00000536566.1_Missense_Mutation_p.I158T	NM_198896.1	NP_942599.1	P20340	RAB6A_HUMAN	RAB6A, member RAS oncogene family	191					antigen processing and presentation (GO:0019882)|early endosome to Golgi transport (GO:0034498)|GTP catabolic process (GO:0006184)|minus-end-directed organelle transport along microtubule (GO:0072385)|peptidyl-cysteine methylation (GO:0018125)|protein localization to Golgi apparatus (GO:0034067)|protein targeting to Golgi (GO:0000042)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)|small GTPase mediated signal transduction (GO:0007264)	cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|trans-Golgi network (GO:0005802)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|myosin V binding (GO:0031489)|protein domain specific binding (GO:0019904)	p.I191T(1)		large_intestine(2)|lung(2)	4						TTCCAGTTTTATGTCAATCAC	0.413																																					p.I191T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T572C	11						.						100.0	96.0	97.0					11																	73388998		2200	4293	6493	73066646	SO:0001583	missense	5870	exon8			AF130986	CCDS8223.1, CCDS8224.1, CCDS58155.1, CCDS58156.1	11q13.3	2008-08-08			ENSG00000175582	ENSG00000175582		"""RAB, member RAS oncogene"""	9786	protein-coding gene	gene with protein product		179513		RAB6			Standard	NM_001243718		Approved		uc001ouf.3	P20340	OTTHUMG00000134308	ENST00000336083.3:c.572T>C	11.37:g.73388998A>G	ENSP00000336850:p.Ile191Thr	Somatic		Capture	Illumina HiSeq	Phase_I	73066646	NM_198896	A8K133|B7Z772|F5H668|Q1W5D8|Q5U0A8|Q9UBE4	Missense_Mutation	SNP	ENST00000336083.3	37	CCDS8224.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	16.64|16.64	3.180516|3.180516	0.57800|0.57800	.|.	.|.	ENSG00000175582|ENSG00000175582	ENST00000310653;ENST00000336083;ENST00000393571;ENST00000536566;ENST00000541588;ENST00000540771|ENST00000541973	T;T;T;T|.	0.68479|.	-0.13;-0.13;0.32;-0.33|.	5.69|5.69	5.69|5.69	0.88448|0.88448	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|.	0.55513|.	0.1925|.	L|L	0.32530|0.32530	0.975|0.975	0.51767|0.51767	D|D	0.999936|0.999936	P;B;B|.	0.50156|.	0.932;0.036;0.272|.	P;B;B|.	0.58520|.	0.84;0.097;0.255|.	T|.	0.52525|.	-0.8564|.	10|.	0.66056|.	D|.	0.02|.	-7.1405|-7.1405	13.6893|13.6893	0.62535|0.62535	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	87;191;191|.	Q1W5D8;P20340;P20340-2|.	.;RAB6A_HUMAN;.|.	T|Q	191;191;191;158;87;69|184	ENSP00000311449:I191T;ENSP00000336850:I191T;ENSP00000437863:I158T;ENSP00000445350:I87T|.	ENSP00000311449:I191T|.	I|X	-|-	2|1	0|0	RAB6A|RAB6A	73066646|73066646	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	7.903000|7.903000	0.87398|0.87398	2.170000|2.170000	0.68504|0.68504	0.528000|0.528000	0.53228|0.53228	ATA|TAA		0.413	RAB6A-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000259241.2		
PPME1	51400	broad.mit.edu	37	11	73915489	73915489	+	Splice_Site	SNP	C	C	T	rs79972734		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr11:73915489C>T	ENST00000328257.8	+	3	610	c.287C>T	c.(286-288)aCg>aTg	p.T96M	PPME1_ENST00000398427.4_Splice_Site_p.T96M|PPME1_ENST00000542710.1_3'UTR			Q9Y570	PPME1_HUMAN	protein phosphatase methylesterase 1	96					negative regulation of catalytic activity (GO:0043086)|protein demethylation (GO:0006482)|regulation of catalytic activity (GO:0050790)		protein C-terminal methylesterase activity (GO:0051722)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|protein phosphatase inhibitor activity (GO:0004864)|protein phosphatase type 2A regulator activity (GO:0008601)	p.T96M(1)		endometrium(1)|large_intestine(2)|lung(2)	5	Breast(11;3.29e-05)					GCTGTGTTCACGGTAAGTAGG	0.418																																					p.T96M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C287T	11						.						133.0	124.0	127.0					11																	73915489		1911	4115	6026	73593137	SO:0001630	splice_region_variant	51400	exon3				CCDS44678.1, CCDS60891.1	11q13.4	2014-03-14			ENSG00000214517	ENSG00000214517	3.1.1.89		30178	protein-coding gene	gene with protein product		611117				10318862	Standard	NM_016147		Approved	PME-1	uc009yty.4	Q9Y570	OTTHUMG00000168115	ENST00000328257.8:c.288+1C>T	11.37:g.73915489C>T		Somatic		Capture	Illumina HiSeq	Phase_I	73593137	NM_016147	B3KMU6|B5MEE7|J3QT22|Q8WYG8|Q9NVT5|Q9UI18	Missense_Mutation	SNP	ENST00000328257.8	37	CCDS44678.1	.	.	.	.	.	.	.	.	.	.	C	29.0	4.970723	0.92919	.	.	ENSG00000214517	ENST00000328257;ENST00000398427;ENST00000544401	T;T;T	0.66815	-0.23;-0.23;4.95	5.93	5.93	0.95920	.	0.000000	0.85682	D	0.000000	T	0.73837	0.3638	L	0.27944	0.81	0.80722	D	1	D	0.89917	1.0	D	0.71414	0.973	T	0.75303	-0.3365	10	0.62326	D	0.03	-26.654	19.1254	0.93380	0.0:1.0:0.0:0.0	.	96	Q9Y570	PPME1_HUMAN	M	96	ENSP00000329867:T96M;ENSP00000381461:T96M;ENSP00000438632:T96M	ENSP00000329867:T96M	T	+	2	0	PPME1	73593137	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	3.989000	0.56958	2.826000	0.97356	0.655000	0.94253	ACG		0.418	PPME1-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398254.1	NM_016147	Missense_Mutation
PPME1	51400	broad.mit.edu	37	11	73957184	73957184	+	Missense_Mutation	SNP	G	G	A	rs367984063		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr11:73957184G>A	ENST00000328257.8	+	10	1221	c.898G>A	c.(898-900)Ggc>Agc	p.G300S	PPME1_ENST00000398427.4_Missense_Mutation_p.G314S|PPME1_ENST00000543525.1_Missense_Mutation_p.G113S|P4HA3_ENST00000540363.1_Intron			Q9Y570	PPME1_HUMAN	protein phosphatase methylesterase 1	300					negative regulation of catalytic activity (GO:0043086)|protein demethylation (GO:0006482)|regulation of catalytic activity (GO:0050790)		protein C-terminal methylesterase activity (GO:0051722)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|protein phosphatase inhibitor activity (GO:0004864)|protein phosphatase type 2A regulator activity (GO:0008601)	p.G300S(1)		endometrium(1)|large_intestine(2)|lung(2)	5	Breast(11;3.29e-05)					ATACTGGGACGGCTGGTTCCG	0.448																																					p.G300S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G898A	11						.	G	SER/GLY	0,3694		0,0,1847	69.0	69.0	69.0		898	5.8	1.0	11		69	1,8131		0,1,4065	no	missense	PPME1	NM_016147.1	56	0,1,5912	AA,AG,GG		0.0123,0.0,0.0085	probably-damaging	300/387	73957184	1,11825	1847	4066	5913	73634832	SO:0001583	missense	51400	exon10				CCDS44678.1, CCDS60891.1	11q13.4	2014-03-14			ENSG00000214517	ENSG00000214517	3.1.1.89		30178	protein-coding gene	gene with protein product		611117				10318862	Standard	NM_016147		Approved	PME-1	uc009yty.4	Q9Y570	OTTHUMG00000168115	ENST00000328257.8:c.898G>A	11.37:g.73957184G>A	ENSP00000329867:p.Gly300Ser	Somatic		Capture	Illumina HiSeq	Phase_I	73634832	NM_016147	B3KMU6|B5MEE7|J3QT22|Q8WYG8|Q9NVT5|Q9UI18	Missense_Mutation	SNP	ENST00000328257.8	37	CCDS44678.1	.	.	.	.	.	.	.	.	.	.	G	35	5.481350	0.96307	0.0	1.23E-4	ENSG00000214517	ENST00000328257;ENST00000398427;ENST00000543525	T;T;T	0.66815	-0.23;-0.23;-0.23	5.81	5.81	0.92471	.	0.000000	0.85682	D	0.000000	T	0.77955	0.4208	L	0.49126	1.545	0.80722	D	1	D;D	0.71674	0.997;0.998	P;D	0.67900	0.9;0.954	T	0.76305	-0.3008	10	0.46703	T	0.11	-20.1847	18.847	0.92210	0.0:0.0:1.0:0.0	.	113;300	Q9Y570-2;Q9Y570	.;PPME1_HUMAN	S	300;314;113	ENSP00000329867:G300S;ENSP00000381461:G314S;ENSP00000441498:G113S	ENSP00000329867:G300S	G	+	1	0	PPME1	73634832	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	8.714000	0.91412	2.749000	0.94314	0.460000	0.39030	GGC		0.448	PPME1-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398254.1	NM_016147	
ARRB1	408	broad.mit.edu	37	11	74985178	74985178	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr11:74985178C>T	ENST00000420843.2	-	11	951	c.854G>A	c.(853-855)cGg>cAg	p.R285Q	ARRB1_ENST00000393505.4_Missense_Mutation_p.R285Q|ARRB1_ENST00000360025.3_Missense_Mutation_p.R285Q	NM_004041.4	NP_004032.2	P49407	ARRB1_HUMAN	arrestin, beta 1	285					activation of MAPK activity (GO:0000187)|apoptotic DNA fragmentation (GO:0006309)|blood coagulation (GO:0007596)|follicle-stimulating hormone signaling pathway (GO:0042699)|G-protein coupled receptor internalization (GO:0002031)|membrane organization (GO:0061024)|negative regulation of apoptotic process (GO:0043066)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of GTPase activity (GO:0034260)|negative regulation of interleukin-6 production (GO:0032715)|negative regulation of interleukin-8 production (GO:0032717)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of protein ubiquitination (GO:0031397)|Notch signaling pathway (GO:0007219)|phototransduction (GO:0007602)|platelet activation (GO:0030168)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of GTPase activity (GO:0043547)|positive regulation of histone acetylation (GO:0035066)|positive regulation of histone H4 acetylation (GO:0090240)|positive regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0035774)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of protein binding (GO:0032092)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of receptor internalization (GO:0002092)|positive regulation of Rho protein signal transduction (GO:0035025)|positive regulation of smooth muscle cell apoptotic process (GO:0034393)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|post-Golgi vesicle-mediated transport (GO:0006892)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein transport (GO:0015031)|protein ubiquitination (GO:0016567)|stress fiber assembly (GO:0043149)|transcription from RNA polymerase II promoter (GO:0006366)	basolateral plasma membrane (GO:0016323)|chromatin (GO:0000785)|coated pit (GO:0005905)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|Golgi membrane (GO:0000139)|lysosomal membrane (GO:0005765)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)|pseudopodium (GO:0031143)	angiotensin receptor binding (GO:0031701)|cysteine-type endopeptidase inhibitor activity involved in apoptotic process (GO:0043027)|enzyme inhibitor activity (GO:0004857)|GTPase activator activity (GO:0005096)|insulin-like growth factor receptor binding (GO:0005159)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)	p.R285Q(1)|p.R285L(1)		breast(4)|large_intestine(2)|lung(4)|prostate(1)	11						GGCGAGGCCCCGCTTCTCTCG	0.592																																					p.R285Q												.	.	2	Substitution - Missense(2)	large_intestine(1)|lung(1)	c.G854A	11						.						255.0	218.0	231.0					11																	74985178		2200	4293	6493	74662826	SO:0001583	missense	408	exon11			BC003636	CCDS31640.1, CCDS44684.1	11q13	2008-12-11			ENSG00000137486	ENSG00000137486			711	protein-coding gene	gene with protein product	"""arrestin 2"""	107940		ARR1		8486659	Standard	NM_004041		Approved		uc001owe.2	P49407	OTTHUMG00000165444	ENST00000420843.2:c.854G>A	11.37:g.74985178C>T	ENSP00000409581:p.Arg285Gln	Somatic		Capture	Illumina HiSeq	Phase_I	74662826	NM_020251	B6V9G8|O75625|O75630|Q2PP20|Q9BTK8	Missense_Mutation	SNP	ENST00000420843.2	37	CCDS44684.1	.	.	.	.	.	.	.	.	.	.	C	26.2	4.714295	0.89112	.	.	ENSG00000137486	ENST00000420843;ENST00000393505;ENST00000360025	T;T;T	0.11930	2.73;2.73;2.74	4.47	4.47	0.54385	Immunoglobulin E-set (1);Arrestin, C-terminal (1);Arrestin-like, C-terminal (1);	0.086330	0.47093	D	0.000252	T	0.15912	0.0383	M	0.66506	2.035	0.50632	D	0.999881	B;P	0.37525	0.346;0.598	B;B	0.30572	0.019;0.117	T	0.04281	-1.0963	10	0.49607	T	0.09	-1.0485	14.7124	0.69244	0.0:1.0:0.0:0.0	.	285;285	P49407-2;P49407	.;ARRB1_HUMAN	Q	285	ENSP00000409581:R285Q;ENSP00000377141:R285Q;ENSP00000353124:R285Q	ENSP00000353124:R285Q	R	-	2	0	ARRB1	74662826	1.000000	0.71417	1.000000	0.80357	0.890000	0.51754	7.744000	0.85034	2.053000	0.61076	0.456000	0.33151	CGG		0.592	ARRB1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000384092.3	NM_004041	
PRKRIR	5612	broad.mit.edu	37	11	76063538	76063538	+	Missense_Mutation	SNP	C	C	T	rs371539373		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr11:76063538C>T	ENST00000260045.3	-	5	761	c.656G>A	c.(655-657)cGg>cAg	p.R219Q	PRKRIR_ENST00000531878.1_5'Flank	NM_004705.2	NP_004696.2	O43422	P52K_HUMAN	protein-kinase, interferon-inducible double stranded RNA dependent inhibitor, repressor of (P58 repressor)	219					negative regulation of cell proliferation (GO:0008285)|response to stress (GO:0006950)|signal transduction (GO:0007165)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.R219Q(1)		cervix(1)|endometrium(3)|large_intestine(4)|lung(12)|ovary(2)|pancreas(1)|prostate(1)|skin(1)	25						TGTCTCAAACCGCTTTCTCAG	0.448																																					p.R219Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G656A	11						.	C	GLN/ARG	1,4383		0,1,2191	29.0	29.0	29.0		656	3.8	1.0	11		29	0,8536		0,0,4268	no	missense	PRKRIR	NM_004705.2	43	0,1,6459	TT,TC,CC		0.0,0.0228,0.0077	benign	219/762	76063538	1,12919	2192	4268	6460	75741186	SO:0001583	missense	5612	exon5			AF007393	CCDS8243.1	11q13.5	2013-01-25			ENSG00000137492	ENSG00000137492		"""THAP (C2CH-type zinc finger) domain containing"""	9440	protein-coding gene	gene with protein product	"""THAP domain containing 12"""	607374				9447982	Standard	NM_004705		Approved	P52rIPK, DAP4, THAP12	uc001oxh.1	O43422	OTTHUMG00000165280	ENST00000260045.3:c.656G>A	11.37:g.76063538C>T	ENSP00000260045:p.Arg219Gln	Somatic		Capture	Illumina HiSeq	Phase_I	75741186	NM_004705	A8K728|Q17RY9|Q8WTW1|Q9Y3Z4	Missense_Mutation	SNP	ENST00000260045.3	37	CCDS8243.1	.	.	.	.	.	.	.	.	.	.	C	15.75	2.924235	0.52653	2.28E-4	0.0	ENSG00000137492	ENST00000529901;ENST00000260045	.	.	.	4.69	3.78	0.43462	.	0.000000	0.85682	D	0.000000	T	0.56307	0.1976	M	0.63428	1.95	0.44587	D	0.997558	B	0.28584	0.216	B	0.23150	0.044	T	0.54200	-0.8329	9	0.28530	T	0.3	.	13.2357	0.59969	0.0:0.9217:0.0:0.0783	.	219	O43422	P52K_HUMAN	Q	44;219	.	ENSP00000260045:R219Q	R	-	2	0	PRKRIR	75741186	0.995000	0.38212	1.000000	0.80357	0.965000	0.64279	3.206000	0.51098	1.145000	0.42336	0.478000	0.44815	CGG		0.448	PRKRIR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383188.1	NM_004705	
CAPN5	726	broad.mit.edu	37	11	76833670	76833670	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr11:76833670C>T	ENST00000278559.3	+	12	1841	c.1652C>T	c.(1651-1653)tCg>tTg	p.S551L	CAPN5_ENST00000531028.1_Intron|CAPN5_ENST00000529629.1_Missense_Mutation_p.S551L|CAPN5_ENST00000456580.2_Missense_Mutation_p.S591L	NM_004055.4	NP_004046.2	O15484	CAN5_HUMAN	calpain 5	551	C2.				proteolysis (GO:0006508)|signal transduction (GO:0007165)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)	calcium-dependent cysteine-type endopeptidase activity (GO:0004198)	p.S551L(1)		NS(1)|breast(2)|endometrium(2)|large_intestine(7)|lung(17)|urinary_tract(1)	30						AAAGTCCGCTCGGCTGTGCAG	0.582																																					p.S551L												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1652T	11						.						112.0	95.0	101.0					11																	76833670		2200	4292	6492	76511318	SO:0001583	missense	726	exon12				CCDS8248.1	11q14	2014-01-29				ENSG00000149260			1482	protein-coding gene	gene with protein product		602537	"""vitreoretinopathy, neovascular inflammatory"""	VRNI		9503024, 9367857, 23055945	Standard	NM_004055		Approved	nCL-3, HTRA3, ADNIV	uc001oxx.3	O15484		ENST00000278559.3:c.1652C>T	11.37:g.76833670C>T	ENSP00000278559:p.Ser551Leu	Somatic		Capture	Illumina HiSeq	Phase_I	76511318	NM_004055	O00263	Missense_Mutation	SNP	ENST00000278559.3	37	CCDS8248.1	.	.	.	.	.	.	.	.	.	.	C	31	5.087404	0.94100	.	.	ENSG00000149260	ENST00000278559;ENST00000360841;ENST00000529629;ENST00000456580	T;T;T	0.74002	-0.8;-0.8;-0.8	4.79	4.79	0.61399	C2 calcium-dependent membrane targeting (2);C2 calcium/lipid-binding domain, CaLB (1);	0.000000	0.85682	D	0.000000	D	0.88009	0.6322	M	0.86651	2.83	0.80722	D	1	D;D;D;D	0.89917	1.0;0.999;0.998;1.0	D;D;D;D	0.91635	0.999;0.979;0.934;0.999	D	0.90359	0.4372	10	0.87932	D	0	.	17.1909	0.86879	0.0:1.0:0.0:0.0	.	589;591;591;551	Q59GM2;E7EV01;Q6ZRM8;O15484	.;.;.;CAN5_HUMAN	L	551;591;551;591	ENSP00000278559:S551L;ENSP00000432332:S551L;ENSP00000409996:S591L	ENSP00000278559:S551L	S	+	2	0	CAPN5	76511318	1.000000	0.71417	0.947000	0.38551	0.990000	0.78478	7.400000	0.79949	2.358000	0.79984	0.561000	0.74099	TCG		0.582	CAPN5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382564.2	NM_004055	
THRSP	7069	broad.mit.edu	37	11	77775155	77775155	+	Silent	SNP	G	G	A	rs139035297	byFrequency	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr11:77775155G>A	ENST00000281030.2	+	1	249	c.228G>A	c.(226-228)ccG>ccA	p.P76P	NDUFC2-KCTD14_ENST00000530054.1_Intron|NDUFC2-KCTD14_ENST00000528251.1_Intron	NM_003251.3	NP_003242.1	Q92748	THRSP_HUMAN	thyroid hormone responsive	76					lipid metabolic process (GO:0006629)|regulation of lipid biosynthetic process (GO:0046890)|regulation of transcription, DNA-templated (GO:0006355)|regulation of triglyceride biosynthetic process (GO:0010866)|transcription, DNA-templated (GO:0006351)	cytosol (GO:0005829)|nucleus (GO:0005634)		p.P76P(1)		breast(2)|central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(2)	7	all_cancers(14;2.23e-19)|all_epithelial(13;7.49e-22)|Breast(9;6.38e-17)|Ovarian(111;0.152)		OV - Ovarian serous cystadenocarcinoma(8;2.15e-25)			GGCTGCTGCCGCGGGAGGAGT	0.637													G|||	36	0.0071885	0.0257	0.0029	5008	,	,		21239	0.0		0.0	False		,,,				2504	0.0				p.P76P												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G228A	11						.	G	,,,	88,4312	73.6+/-111.7	0,88,2112	66.0	70.0	69.0		,,,228	-3.3	0.2	11	dbSNP_134	69	1,8583	1.2+/-3.3	0,1,4291	no	intron,intron,intron,coding-synonymous	THRSP,NDUFC2-KCTD14	NM_001203260.1,NM_001203261.1,NM_001203262.1,NM_003251.3	,,,	0,89,6403	AA,AG,GG		0.0116,2.0,0.6855	,,,	,,,76/147	77775155	89,12895	2200	4292	6492	77452803	SO:0001819	synonymous_variant	7069	exon1			Y08409	CCDS8256.1	11q14.1	2012-06-19	2010-06-25		ENSG00000151365	ENSG00000151365			11800	protein-coding gene	gene with protein product	"""SPOT14 homolog (rat)"""	601926	"""thyroid hormone responsive SPOT14 (rat) homolog"", ""lipogenic protein 1"""	LPGP1		9003802	Standard	NM_003251		Approved	SPOT14, Lpgp, S14, THRP	uc001oyx.3	Q92748	OTTHUMG00000166632	ENST00000281030.2:c.228G>A	11.37:g.77775155G>A		Somatic		Capture	Illumina HiSeq	Phase_I	77452803	NM_003251	B2R4W7	Silent	SNP	ENST00000281030.2	37	CCDS8256.1																																																																																				0.637	THRSP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390939.1	NM_003251	
TENM4	26011	broad.mit.edu	37	11	78380594	78380594	+	Missense_Mutation	SNP	C	C	T	rs373812159		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr11:78380594C>T	ENST00000278550.7	-	32	7258	c.6796G>A	c.(6796-6798)Ggt>Agt	p.G2266S		NM_001098816.2	NP_001092286.2	Q6N022	TEN4_HUMAN	teneurin transmembrane protein 4	2266					cardiac cell fate specification (GO:0060912)|cardiac muscle cell proliferation (GO:0060038)|central nervous system myelin formation (GO:0032289)|gastrulation with mouth forming second (GO:0001702)|neuron development (GO:0048666)|positive regulation of gastrulation (GO:2000543)|positive regulation of myelination (GO:0031643)|positive regulation of oligodendrocyte differentiation (GO:0048714)|self proteolysis (GO:0097264)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|neuron projection (GO:0043005)|nucleus (GO:0005634)	protein homodimerization activity (GO:0042803)	p.G2266S(1)									AAGATATCACCGCCCCGCTGC	0.602																																					p.G2266S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G6796A	11						.	C	SER/GLY	1,4335		0,1,2167	135.0	142.0	140.0		6796	-0.1	0.0	11		140	0,8528		0,0,4264	no	missense	ODZ4	NM_001098816.2	56	0,1,6431	TT,TC,CC		0.0,0.0231,0.0078	benign	2266/2770	78380594	1,12863	2168	4264	6432	78058242	SO:0001583	missense	26011	exon32			AB037723	CCDS44688.1	11q13	2012-10-02	2012-10-02	2012-10-02		ENSG00000149256			29945	protein-coding gene	gene with protein product		610084	"""odz, odd Oz/ten-m homolog 4 (Drosophila)"""	ODZ4		12000766, 10625539	Standard	NM_001098816		Approved	KIAA1302, Ten-M4	uc001ozl.4	Q6N022		ENST00000278550.7:c.6796G>A	11.37:g.78380594C>T	ENSP00000278550:p.Gly2266Ser	Somatic		Capture	Illumina HiSeq	Phase_I	78058242	NM_001098816	A6ND26|Q7Z3C7|Q96MS6|Q9P2P4|Q9Y4S2	Missense_Mutation	SNP	ENST00000278550.7	37	CCDS44688.1	.	.	.	.	.	.	.	.	.	.	C	0.021	-1.431977	0.01108	2.31E-4	0.0	ENSG00000149256	ENST00000278550;ENST00000530738	D;T	0.89875	-2.58;0.76	5.14	-0.065	0.13770	.	0.462228	0.26293	N	0.025213	T	0.61887	0.2383	N	0.00538	-1.39	0.09310	N	1	B	0.18863	0.031	B	0.08055	0.003	T	0.58896	-0.7555	9	.	.	.	.	9.9555	0.41663	0.0:0.4666:0.0:0.5334	.	2266	Q6N022	TEN4_HUMAN	S	2266;730	ENSP00000278550:G2266S;ENSP00000431711:G730S	.	G	-	1	0	ODZ4	78058242	0.003000	0.15002	0.000000	0.03702	0.072000	0.16883	1.046000	0.30354	0.063000	0.16370	-0.136000	0.14681	GGT		0.602	TENM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391406.2		
PCF11	51585	broad.mit.edu	37	11	82874870	82874870	+	Silent	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr11:82874870G>A	ENST00000298281.4	+	3	920	c.468G>A	c.(466-468)acG>acA	p.T156T		NM_015885.3	NP_056969.2	O94913	PCF11_HUMAN	PCF11 cleavage and polyadenylation factor subunit	156					gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA cleavage (GO:0006379)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	mRNA cleavage factor complex (GO:0005849)|nucleoplasm (GO:0005654)		p.T156T(1)		cervix(1)|endometrium(3)|kidney(4)|large_intestine(1)|lung(22)|ovary(1)|urinary_tract(1)	33						ATGTGAATACGTCTAGCATCC	0.328																																					p.T156T												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G468A	11						.						33.0	32.0	32.0					11																	82874870		1852	4082	5934	82552518	SO:0001819	synonymous_variant	51585	exon3			AB020631	CCDS44689.1	11q13	2013-07-02	2013-07-02		ENSG00000165494	ENSG00000165494			30097	protein-coding gene	gene with protein product		608876	"""PCF11, cleavage and polyadenylation factor II subunit, homolog (S. cerevisiae)"", ""PCF11, cleavage and polyadenylation factor subunit, homolog (S. cerevisiae)"""			11060040	Standard	NM_015885		Approved	KIAA0824	uc001ozx.4	O94913	OTTHUMG00000167031	ENST00000298281.4:c.468G>A	11.37:g.82874870G>A		Somatic		Capture	Illumina HiSeq	Phase_I	82552518	NM_015885	A6H8W7|O43671|Q6P0X8	Silent	SNP	ENST00000298281.4	37	CCDS44689.1																																																																																				0.328	PCF11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392548.2	NM_015885	
NOX4	50507	broad.mit.edu	37	11	89106611	89106611	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr11:89106611C>T	ENST00000263317.4	-	12	1362	c.1124G>A	c.(1123-1125)gGa>gAa	p.G375E	NOX4_ENST00000534731.1_Missense_Mutation_p.G375E|NOX4_ENST00000542487.1_Missense_Mutation_p.G351E|NOX4_ENST00000535633.1_Missense_Mutation_p.G351E|NOX4_ENST00000532825.1_Missense_Mutation_p.G351E|NOX4_ENST00000527956.1_Missense_Mutation_p.G351E|NOX4_ENST00000424319.1_Missense_Mutation_p.G351E|NOX4_ENST00000413594.2_Missense_Mutation_p.G396E|NOX4_ENST00000528341.1_Missense_Mutation_p.G350E|NOX4_ENST00000525196.1_Intron|NOX4_ENST00000343727.5_Missense_Mutation_p.G351E|NOX4_ENST00000531342.1_Missense_Mutation_p.G68E|NOX4_ENST00000527626.1_Missense_Mutation_p.G209E|NOX4_ENST00000375979.3_Missense_Mutation_p.G68E			Q9NPH5	NOX4_HUMAN	NADPH oxidase 4	375	FAD-binding FR-type. {ECO:0000255|PROSITE-ProRule:PRU00716}.|Mediates interaction with TLR4.				bone resorption (GO:0045453)|cardiac muscle cell differentiation (GO:0055007)|cell aging (GO:0007569)|cell morphogenesis (GO:0000902)|cellular response to cAMP (GO:0071320)|cellular response to gamma radiation (GO:0071480)|cellular response to glucose stimulus (GO:0071333)|cellular response to transforming growth factor beta stimulus (GO:0071560)|homocysteine metabolic process (GO:0050667)|inflammatory response (GO:0006954)|negative regulation of cell proliferation (GO:0008285)|oxidation-reduction process (GO:0055114)|positive regulation of apoptotic process (GO:0043065)|positive regulation of DNA biosynthetic process (GO:2000573)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of smooth muscle cell migration (GO:0014911)|positive regulation of stress fiber assembly (GO:0051496)|reactive oxygen species metabolic process (GO:0072593)|response to hypoxia (GO:0001666)|superoxide anion generation (GO:0042554)	apical plasma membrane (GO:0016324)|endoplasmic reticulum (GO:0005783)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)|NADPH oxidase complex (GO:0043020)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	electron carrier activity (GO:0009055)|flavin adenine dinucleotide binding (GO:0050660)|heme binding (GO:0020037)|modified amino acid binding (GO:0072341)|NAD(P)H oxidase activity (GO:0016174)|nucleotide binding (GO:0000166)|oxygen sensor activity (GO:0019826)|superoxide-generating NADPH oxidase activity (GO:0016175)	p.G375E(1)		NS(2)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(8)|lung(20)|ovary(2)|prostate(3)|skin(2)	44		Acute lymphoblastic leukemia(157;2.26e-05)|all_hematologic(158;0.011)				TGTCCAGTCTCCTACTATTTT	0.279																																					p.G375E												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1124A	11						.						100.0	110.0	107.0					11																	89106611		2201	4283	6484	88746259	SO:0001583	missense	50507	exon12			AF254621	CCDS8285.1, CCDS44695.1, CCDS44696.1, CCDS73361.1, CCDS73362.1	11q14.2-q21	2008-02-05			ENSG00000086991	ENSG00000086991			7891	protein-coding gene	gene with protein product		605261					Standard	NM_001143837		Approved	KOX-1, KOX	uc001pct.3	Q9NPH5	OTTHUMG00000167298	ENST00000263317.4:c.1124G>A	11.37:g.89106611C>T	ENSP00000263317:p.Gly375Glu	Somatic		Capture	Illumina HiSeq	Phase_I	88746259	NM_016931	A8K715|B7Z520|E7EMD7|Q5K3R4|Q5K3R5|Q5K3R6|Q5K3R8|Q7Z7G3|Q86V92	Missense_Mutation	SNP	ENST00000263317.4	37	CCDS8285.1	.	.	.	.	.	.	.	.	.	.	C	16.20	3.057366	0.55325	.	.	ENSG00000086991	ENST00000424319;ENST00000535633;ENST00000343727;ENST00000534731;ENST00000263317;ENST00000532825;ENST00000527956;ENST00000542487;ENST00000527626;ENST00000528341;ENST00000413594;ENST00000531342;ENST00000375979	T;T;T;T;T;T;T;T;T;T;T;D;D	0.98012	1.82;1.82;1.82;1.82;1.82;1.82;1.82;1.82;1.82;1.82;1.82;-4.05;-4.66	5.12	5.12	0.69794	Riboflavin synthase-like beta-barrel (1);FAD-binding 8 (1);Ferredoxin reductase-type FAD-binding domain (1);	0.000000	0.85682	D	0.000000	D	0.98757	0.9582	M	0.87971	2.92	0.52501	D	0.999951	D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D;D	0.97110	1.0;0.998;0.992;0.998;1.0;0.999;1.0	D	0.99505	1.0954	9	.	.	.	-12.7557	15.4797	0.75514	0.0:1.0:0.0:0.0	.	351;209;350;68;68;375;375	E9PMY6;E9PR43;E9PPP2;Q9NPH5-3;Q9NPH5-4;Q9NPH5-6;Q9NPH5	.;.;.;.;.;.;NOX4_HUMAN	E	351;351;351;375;375;351;351;351;209;350;396;68;68	ENSP00000412446:G351E;ENSP00000440172:G351E;ENSP00000344747:G351E;ENSP00000436892:G375E;ENSP00000263317:G375E;ENSP00000434924:G351E;ENSP00000433797:G351E;ENSP00000439373:G351E;ENSP00000436093:G209E;ENSP00000436970:G350E;ENSP00000405705:G396E;ENSP00000435039:G68E;ENSP00000365146:G68E	.	G	-	2	0	NOX4	88746259	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.868000	0.63021	2.382000	0.81193	0.563000	0.77884	GGA		0.279	NOX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394054.1	NM_016931	
NOX4	50507	broad.mit.edu	37	11	89185011	89185011	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr11:89185011C>A	ENST00000263317.4	-	3	444	c.206G>T	c.(205-207)aGc>aTc	p.S69I	NOX4_ENST00000534731.1_Missense_Mutation_p.S69I|NOX4_ENST00000542487.1_Missense_Mutation_p.S45I|NOX4_ENST00000535633.1_Missense_Mutation_p.S45I|NOX4_ENST00000532825.1_Missense_Mutation_p.S45I|NOX4_ENST00000527956.1_Missense_Mutation_p.S45I|NOX4_ENST00000424319.1_Missense_Mutation_p.S45I|NOX4_ENST00000413594.2_Missense_Mutation_p.S90I|NOX4_ENST00000528341.1_Missense_Mutation_p.S44I|NOX4_ENST00000525196.1_Missense_Mutation_p.S69I|NOX4_ENST00000343727.5_Missense_Mutation_p.S45I|NOX4_ENST00000531342.1_Intron|NOX4_ENST00000527626.1_Intron|NOX4_ENST00000375979.3_Intron			Q9NPH5	NOX4_HUMAN	NADPH oxidase 4	69	Ferric oxidoreductase.				bone resorption (GO:0045453)|cardiac muscle cell differentiation (GO:0055007)|cell aging (GO:0007569)|cell morphogenesis (GO:0000902)|cellular response to cAMP (GO:0071320)|cellular response to gamma radiation (GO:0071480)|cellular response to glucose stimulus (GO:0071333)|cellular response to transforming growth factor beta stimulus (GO:0071560)|homocysteine metabolic process (GO:0050667)|inflammatory response (GO:0006954)|negative regulation of cell proliferation (GO:0008285)|oxidation-reduction process (GO:0055114)|positive regulation of apoptotic process (GO:0043065)|positive regulation of DNA biosynthetic process (GO:2000573)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of smooth muscle cell migration (GO:0014911)|positive regulation of stress fiber assembly (GO:0051496)|reactive oxygen species metabolic process (GO:0072593)|response to hypoxia (GO:0001666)|superoxide anion generation (GO:0042554)	apical plasma membrane (GO:0016324)|endoplasmic reticulum (GO:0005783)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)|NADPH oxidase complex (GO:0043020)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	electron carrier activity (GO:0009055)|flavin adenine dinucleotide binding (GO:0050660)|heme binding (GO:0020037)|modified amino acid binding (GO:0072341)|NAD(P)H oxidase activity (GO:0016174)|nucleotide binding (GO:0000166)|oxygen sensor activity (GO:0019826)|superoxide-generating NADPH oxidase activity (GO:0016175)	p.S69I(1)		NS(2)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(8)|lung(20)|ovary(2)|prostate(3)|skin(2)	44		Acute lymphoblastic leukemia(157;2.26e-05)|all_hematologic(158;0.011)				AAGGATAAGGCTGCAGTTGAG	0.428																																					p.S69I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G206T	11						.						167.0	156.0	160.0					11																	89185011		2201	4299	6500	88824659	SO:0001583	missense	50507	exon3			AF254621	CCDS8285.1, CCDS44695.1, CCDS44696.1, CCDS73361.1, CCDS73362.1	11q14.2-q21	2008-02-05			ENSG00000086991	ENSG00000086991			7891	protein-coding gene	gene with protein product		605261					Standard	NM_001143837		Approved	KOX-1, KOX	uc001pct.3	Q9NPH5	OTTHUMG00000167298	ENST00000263317.4:c.206G>T	11.37:g.89185011C>A	ENSP00000263317:p.Ser69Ile	Somatic		Capture	Illumina HiSeq	Phase_I	88824659	NM_016931	A8K715|B7Z520|E7EMD7|Q5K3R4|Q5K3R5|Q5K3R6|Q5K3R8|Q7Z7G3|Q86V92	Missense_Mutation	SNP	ENST00000263317.4	37	CCDS8285.1	.	.	.	.	.	.	.	.	.	.	C	22.5	4.299192	0.81025	.	.	ENSG00000086991	ENST00000424319;ENST00000535633;ENST00000343727;ENST00000534731;ENST00000525196;ENST00000263317;ENST00000532825;ENST00000527956;ENST00000542487;ENST00000528341;ENST00000413594	D;D;D;D;D;D;D;D;D;D;D	0.90844	-2.74;-2.74;-2.74;-2.74;-2.74;-2.74;-2.74;-2.74;-2.74;-2.74;-2.74	5.15	5.15	0.70609	Flavoprotein transmembrane component (1);	0.046947	0.85682	D	0.000000	D	0.92883	0.7736	L	0.41632	1.29	0.51482	D	0.999926	P;D;D;B;P	0.71674	0.924;0.998;0.997;0.057;0.887	P;D;D;B;P	0.81914	0.836;0.961;0.995;0.072;0.645	D	0.91974	0.5589	9	.	.	.	-17.3915	17.7521	0.88438	0.0:1.0:0.0:0.0	.	45;44;69;69;69	E9PMY6;E9PPP2;E9PI95;Q9NPH5-6;Q9NPH5	.;.;.;.;NOX4_HUMAN	I	45;45;45;69;69;69;45;45;45;44;90	ENSP00000412446:S45I;ENSP00000440172:S45I;ENSP00000344747:S45I;ENSP00000436892:S69I;ENSP00000436716:S69I;ENSP00000263317:S69I;ENSP00000434924:S45I;ENSP00000433797:S45I;ENSP00000439373:S45I;ENSP00000436970:S44I;ENSP00000405705:S90I	.	S	-	2	0	NOX4	88824659	1.000000	0.71417	1.000000	0.80357	0.904000	0.53231	6.671000	0.74472	2.550000	0.86006	0.655000	0.94253	AGC		0.428	NOX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394054.1	NM_016931	
MTNR1B	4544	broad.mit.edu	37	11	92714975	92714975	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr11:92714975G>A	ENST00000257068.2	+	2	592	c.586G>A	c.(586-588)Gcc>Acc	p.A196T		NM_005959.3	NP_005950.1	P49286	MTR1B_HUMAN	melatonin receptor 1B	196					G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|glucose homeostasis (GO:0042593)|regulation of insulin secretion (GO:0050796)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|melatonin receptor activity (GO:0008502)	p.A196T(1)		central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(4)|lung(19)|ovary(1)|prostate(2)|urinary_tract(1)	33		Acute lymphoblastic leukemia(157;2.31e-05)|all_hematologic(158;0.00824)			Agomelatine(DB06594)|Melatonin(DB01065)|Ramelteon(DB00980)	CATCCAGACCGCCAGCACCCA	0.602																																					p.A196T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G586A	11						.						67.0	64.0	65.0					11																	92714975		2201	4298	6499	92354623	SO:0001583	missense	4544	exon2			AB033598	CCDS8290.1	11q21-q22	2012-08-08			ENSG00000134640	ENSG00000134640		"""GPCR / Class A : Melatonin receptors"""	7464	protein-coding gene	gene with protein product		600804					Standard	NM_005959		Approved		uc001pdk.1	P49286	OTTHUMG00000167364	ENST00000257068.2:c.586G>A	11.37:g.92714975G>A	ENSP00000257068:p.Ala196Thr	Somatic		Capture	Illumina HiSeq	Phase_I	92354623	NM_005959		Missense_Mutation	SNP	ENST00000257068.2	37	CCDS8290.1	.	.	.	.	.	.	.	.	.	.	G	5.078	0.200078	0.09652	.	.	ENSG00000134640	ENST00000257068	T	0.37058	1.22	4.21	1.29	0.21616	GPCR, rhodopsin-like superfamily (1);	0.330529	0.31721	N	0.007170	T	0.25306	0.0615	L	0.39245	1.2	0.18873	N	0.999983	B	0.23128	0.08	B	0.27715	0.082	T	0.26155	-1.0111	10	0.13853	T	0.58	-10.209	9.0644	0.36453	0.2422:0.0:0.7578:0.0	.	196	P49286	MTR1B_HUMAN	T	196	ENSP00000257068:A196T	ENSP00000257068:A196T	A	+	1	0	MTNR1B	92354623	0.993000	0.37304	0.020000	0.16555	0.062000	0.15995	4.744000	0.62118	0.171000	0.19730	0.491000	0.48974	GCC		0.602	MTNR1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394323.1		
CNTN5	53942	broad.mit.edu	37	11	100064254	100064254	+	Silent	SNP	A	A	C			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr11:100064254A>C	ENST00000524871.1	+	15	2033	c.1743A>C	c.(1741-1743)acA>acC	p.T581T	CNTN5_ENST00000528682.1_Silent_p.T581T|CNTN5_ENST00000527185.1_Silent_p.T581T|CNTN5_ENST00000524560.1_3'UTR|CNTN5_ENST00000279463.3_Silent_p.T581T|CNTN5_ENST00000418526.2_Silent_p.T507T	NM_014361.3	NP_055176.1	O94779	CNTN5_HUMAN	contactin 5	581	Ig-like C2-type 6.				cell adhesion (GO:0007155)|sensory perception of sound (GO:0007605)	anchored component of membrane (GO:0031225)|cytoplasm (GO:0005737)|plasma membrane (GO:0005886)		p.T581T(1)		NS(2)|breast(2)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(12)|lung(38)|ovary(2)|pancreas(2)|prostate(2)|skin(7)|upper_aerodigestive_tract(2)|urinary_tract(1)	81		all_hematologic(158;1.22e-05)|Acute lymphoblastic leukemia(157;3.81e-05)|Melanoma(852;0.219)		BRCA - Breast invasive adenocarcinoma(274;0.00146)|KIRC - Kidney renal clear cell carcinoma(183;0.156)|Kidney(183;0.196)		CTAAAAGAACAGAATTGACAG	0.348																																					p.T507T												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.A1521C	11						.						60.0	56.0	57.0					11																	100064254		1843	4082	5925	99569464	SO:0001819	synonymous_variant	53942	exon14			AB013802	CCDS53696.1, CCDS53697.1, CCDS58168.1	11q22.1	2013-02-11			ENSG00000149972	ENSG00000149972		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	2175	protein-coding gene	gene with protein product		607219					Standard	NM_014361		Approved	NB-2, hNB-2	uc021qpb.1	O94779	OTTHUMG00000167579	ENST00000524871.1:c.1743A>C	11.37:g.100064254A>C		Somatic		Capture	Illumina HiSeq	Phase_I	99569464	NM_175566	A1L4P0|B7ZM07|E9PKE8|O94780|Q49AF3	Silent	SNP	ENST00000524871.1	37	CCDS53696.1																																																																																				0.348	CNTN5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395148.2	NM_014361	
ACAD8	27034	broad.mit.edu	37	11	134127059	134127059	+	Silent	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr11:134127059C>T	ENST00000281182.4	+	3	394	c.288C>T	c.(286-288)ggC>ggT	p.G96G	ACAD8_ENST00000524547.1_Intron|ACAD8_ENST00000374752.4_Intron|ACAD8_ENST00000543332.1_Intron|ACAD8_ENST00000537423.1_Silent_p.G19G	NM_014384.2	NP_055199.1	Q9UKU7	ACAD8_HUMAN	acyl-CoA dehydrogenase family, member 8	96					branched-chain amino acid catabolic process (GO:0009083)|cellular nitrogen compound metabolic process (GO:0034641)|lipid metabolic process (GO:0006629)|regulation of transcription, DNA-templated (GO:0006355)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)|valine catabolic process (GO:0006574)	mitochondrial matrix (GO:0005759)	acyl-CoA dehydrogenase activity (GO:0003995)|flavin adenine dinucleotide binding (GO:0050660)	p.G96G(1)		endometrium(4)|large_intestine(3)|lung(5)|ovary(1)|urinary_tract(1)	14	all_hematologic(175;0.127)	all_cancers(12;8e-23)|all_epithelial(12;2.59e-16)|all_lung(97;1.19e-05)|Lung NSC(97;2.76e-05)|Breast(109;0.000182)|all_neural(223;0.0189)|Medulloblastoma(222;0.0245)|Esophageal squamous(93;0.0559)		Epithelial(10;1.92e-10)|all cancers(11;2.26e-09)|BRCA - Breast invasive adenocarcinoma(10;8.73e-09)|OV - Ovarian serous cystadenocarcinoma(99;0.00154)|Lung(977;0.21)	Flavin adenine dinucleotide(DB03147)	CAGATGTGGGCGGGTCTGGGC	0.532																																					p.G96G	GBM(65;238 1125 33403 41853 48889)											.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C288T	11						.						113.0	102.0	106.0					11																	134127059		2201	4297	6498	133632269	SO:0001819	synonymous_variant	27034	exon3			AF126245	CCDS8498.1	11q25	2014-09-17	2010-04-30		ENSG00000151498	ENSG00000151498			87	protein-coding gene	gene with protein product		604773	"""acyl-Coenzyme A dehydrogenase family, member 8"""			10524212	Standard	NM_014384		Approved		uc001qhk.3	Q9UKU7	OTTHUMG00000167177	ENST00000281182.4:c.288C>T	11.37:g.134127059C>T		Somatic		Capture	Illumina HiSeq	Phase_I	133632269	NM_014384	B7Z5W4|Q6ZWP6|Q9BUS8	Silent	SNP	ENST00000281182.4	37	CCDS8498.1																																																																																				0.532	ACAD8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393607.1	NM_014384	
OLR1	4973	broad.mit.edu	37	12	10313003	10313003	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr12:10313003C>T	ENST00000309539.3	-	5	683	c.623G>A	c.(622-624)cGg>cAg	p.R208Q	OLR1_ENST00000544577.1_Intron|OLR1_ENST00000432556.2_Silent_p.S161S|OLR1_ENST00000545927.1_Intron|OLR1_ENST00000543993.1_Silent_p.S57S	NM_002543.3	NP_002534.1	P78380	OLR1_HUMAN	oxidized low density lipoprotein (lectin-like) receptor 1	208	C-type lectin. {ECO:0000255|PROSITE- ProRule:PRU00040}.				blood circulation (GO:0008015)|blood coagulation (GO:0007596)|cell death (GO:0008219)|inflammatory response (GO:0006954)|leukocyte cell-cell adhesion (GO:0007159)|leukocyte migration (GO:0050900)|lipoprotein metabolic process (GO:0042157)|proteolysis (GO:0006508)|response to hydrogen peroxide (GO:0042542)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	carbohydrate binding (GO:0030246)|low-density lipoprotein receptor activity (GO:0005041)	p.R208Q(1)		breast(1)|endometrium(1)|large_intestine(2)|lung(3)|ovary(1)|pancreas(1)|skin(1)	10						GGGGTTCCTCCGAGACAGCCC	0.493																																					p.R208Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G623A	12						.						83.0	83.0	83.0					12																	10313003		2203	4300	6503	10204270	SO:0001583	missense	4973	exon5			D89050	CCDS8618.1, CCDS53745.1, CCDS53746.1	12p13.1-p12.3	2011-08-30	2006-12-07		ENSG00000173391	ENSG00000173391		"""C-type lectin domain containing"""	8133	protein-coding gene	gene with protein product		602601	"""oxidised low density lipoprotein (lectin-like) receptor 1"""			9763655	Standard	NM_002543		Approved	LOX-1, SCARE1, CLEC8A	uc001qxo.1	P78380	OTTHUMG00000168527	ENST00000309539.3:c.623G>A	12.37:g.10313003C>T	ENSP00000309124:p.Arg208Gln	Somatic		Capture	Illumina HiSeq	Phase_I	10204270	NM_002543	A8K7V9|B4DI48|G3V1I4|Q2PP00|Q7Z484	Missense_Mutation	SNP	ENST00000309539.3	37	CCDS8618.1	.	.	.	.	.	.	.	.	.	.	C	12.01	1.810326	0.32053	.	.	ENSG00000173391	ENST00000309539;ENST00000539518;ENST00000538745;ENST00000339968	T;T;T;T	0.20069	2.1;2.1;2.1;2.1	4.82	-9.65	0.00537	C-type lectin fold (1);C-type lectin-like (1);C-type lectin (3);	2.040040	0.02207	N	0.062835	T	0.15392	0.0371	.	.	.	0.09310	N	1	D	0.58268	0.982	P	0.44518	0.452	T	0.37009	-0.9724	9	0.30078	T	0.28	.	9.5264	0.39167	0.1299:0.504:0.0:0.3661	.	208	P78380	OLR1_HUMAN	Q	208;155;104;104	ENSP00000309124:R208Q;ENSP00000442389:R155Q;ENSP00000438925:R104Q;ENSP00000340572:R104Q	ENSP00000309124:R208Q	R	-	2	0	OLR1	10204270	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-1.479000	0.02327	-1.944000	0.01038	-1.047000	0.02352	CGG		0.493	OLR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400091.1	NM_002543	
MYBPC1	4604	broad.mit.edu	37	12	102025861	102025861	+	Silent	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr12:102025861C>T	ENST00000550270.1	+	6	426	c.426C>T	c.(424-426)tgC>tgT	p.C142C	MYBPC1_ENST00000550501.1_Intron|MYBPC1_ENST00000551300.1_Silent_p.C43C|MYBPC1_ENST00000541119.1_Silent_p.C130C|MYBPC1_ENST00000549145.1_Silent_p.C155C|MYBPC1_ENST00000441232.1_Silent_p.C142C|MYBPC1_ENST00000545503.2_Silent_p.C142C|MYBPC1_ENST00000361685.2_Silent_p.C167C|MYBPC1_ENST00000360610.2_Silent_p.C142C|MYBPC1_ENST00000536007.1_Silent_p.C142C|MYBPC1_ENST00000553190.1_Silent_p.C142C|MYBPC1_ENST00000392934.3_Silent_p.C129C|MYBPC1_ENST00000452455.2_Silent_p.C142C|MYBPC1_ENST00000547509.1_Silent_p.C128C|MYBPC1_ENST00000547405.1_Silent_p.C116C|MYBPC1_ENST00000361466.2_Silent_p.C167C			Q00872	MYPC1_HUMAN	myosin binding protein C, slow type	142	Ig-like C2-type 1.				cell adhesion (GO:0007155)|muscle filament sliding (GO:0030049)	cytosol (GO:0005829)|myofibril (GO:0030016)|myosin filament (GO:0032982)	structural constituent of muscle (GO:0008307)|titin binding (GO:0031432)	p.C167C(1)		breast(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|liver(1)|lung(22)|ovary(4)|prostate(1)|skin(4)|urinary_tract(2)	57						ATTACAGATGCGAGGTCACCT	0.393																																					p.C167C												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C501T	12						.						127.0	122.0	124.0					12																	102025861		2203	4300	6503	100549992	SO:0001819	synonymous_variant	4604	exon8				CCDS9083.1, CCDS9084.1, CCDS9085.1, CCDS55877.1, CCDS58268.1, CCDS58269.1, CCDS58270.1, CCDS58271.1, CCDS58272.1, CCDS58273.1	12q23.2	2013-02-11	2001-11-28		ENSG00000196091	ENSG00000196091		"""Myosin binding proteins"", ""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	7549	protein-coding gene	gene with protein product		160794	"""myosin-binding protein C, slow-type"""			8375400, 16918501	Standard	NM_002465		Approved		uc010svs.2	Q00872	OTTHUMG00000170274	ENST00000550270.1:c.426C>T	12.37:g.102025861C>T		Somatic		Capture	Illumina HiSeq	Phase_I	100549992	NM_002465	B4DKR5|B7Z8G8|B7ZL02|B7ZL09|B7ZL10|E7ESM5|E7EWS6|G3XAE8|Q15497|Q17RR7|Q569K7|Q86T48|Q86TC8|Q8N3L2	Silent	SNP	ENST00000550270.1	37	CCDS9085.1																																																																																				0.393	MYBPC1-024	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000408806.1		
NUAK1	9891	broad.mit.edu	37	12	106480538	106480538	+	Missense_Mutation	SNP	C	C	T	rs139582229		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr12:106480538C>T	ENST00000261402.2	-	3	1866	c.487G>A	c.(487-489)Gtc>Atc	p.V163I		NM_014840.2	NP_055655.1	O60285	NUAK1_HUMAN	NUAK family, SNF1-like kinase, 1	163	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cell adhesion (GO:0007155)|cellular response to DNA damage stimulus (GO:0006974)|regulation of cell adhesion (GO:0030155)|regulation of cell proliferation (GO:0042127)|regulation of cellular senescence (GO:2000772)|regulation of myosin-light-chain-phosphatase activity (GO:0035507)	cytoplasm (GO:0005737)|microtubule cytoskeleton (GO:0015630)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|p53 binding (GO:0002039)|protein serine/threonine kinase activity (GO:0004674)	p.V163I(2)		NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(8)|lung(13)|ovary(1)|prostate(2)|skin(1)|stomach(1)|urinary_tract(1)	37						ACAGCAGAGACGATCTGCCGG	0.517																																					p.V163I												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G487A	12						.	C	ILE/VAL	0,4406		0,0,2203	107.0	87.0	94.0		487	5.0	1.0	12	dbSNP_134	94	1,8599	1.2+/-3.3	0,1,4299	no	missense	NUAK1	NM_014840.2	29	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	benign	163/662	106480538	1,13005	2203	4300	6503	105004668	SO:0001583	missense	9891	exon3			AB011109	CCDS31892.1	12q23.3	2005-08-09				ENSG00000074590			14311	protein-coding gene	gene with protein product	"""AMP-activated protein kinase family member 5"""	608130				12409306, 13679856	Standard	NM_014840		Approved	ARK5, KIAA0537, NuaK1	uc001tlj.1	O60285	OTTHUMG00000169763	ENST00000261402.2:c.487G>A	12.37:g.106480538C>T	ENSP00000261402:p.Val163Ile	Somatic		Capture	Illumina HiSeq	Phase_I	105004668	NM_014840	A7MD39|Q96KA8	Missense_Mutation	SNP	ENST00000261402.2	37	CCDS31892.1	.	.	.	.	.	.	.	.	.	.	C	15.64	2.892099	0.52014	0.0	1.16E-4	ENSG00000074590	ENST00000261402;ENST00000359413;ENST00000548902	T;T	0.24908	1.83;1.83	6.03	4.96	0.65561	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.118236	0.37219	N	0.002198	T	0.15869	0.0382	N	0.05330	-0.07	0.58432	D	0.999993	B	0.22746	0.074	B	0.27170	0.077	T	0.09596	-1.0667	10	0.27785	T	0.31	.	16.1889	0.81972	0.0:0.9267:0.0:0.0733	.	163	O60285	NUAK1_HUMAN	I	163;163;32	ENSP00000261402:V163I;ENSP00000448288:V32I	ENSP00000261402:V163I	V	-	1	0	NUAK1	105004668	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	4.652000	0.61454	2.861000	0.98227	0.655000	0.94253	GTC		0.517	NUAK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405767.2	NM_014840	
STYK1	55359	broad.mit.edu	37	12	10772921	10772921	+	Missense_Mutation	SNP	C	C	T	rs375423751		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr12:10772921C>T	ENST00000075503.3	-	11	1611	c.1091G>A	c.(1090-1092)cGc>cAc	p.R364H		NM_018423.2	NP_060893.2	Q6J9G0	STYK1_HUMAN	serine/threonine/tyrosine kinase 1	364	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)	p.R364H(1)		breast(1)|central_nervous_system(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(1)|liver(1)|lung(8)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(3)	26						CTCACGCCAGCGCCAGCAGGA	0.527										HNSCC(73;0.22)																											p.R364H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1091A	12						.	C	HIS/ARG	0,4406		0,0,2203	110.0	116.0	114.0		1091	4.4	1.0	12		114	1,8599	1.2+/-3.3	0,1,4299	no	missense	STYK1	NM_018423.2	29	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	benign	364/423	10772921	1,13005	2203	4300	6503	10664188	SO:0001583	missense	55359	exon11			AF251059	CCDS8629.1	12p13.2	2005-01-21							18889	protein-coding gene	gene with protein product		611433				12841579	Standard	NM_018423		Approved	SuRTK106, DKFZp761P1010, NOK	uc001qys.2	Q6J9G0		ENST00000075503.3:c.1091G>A	12.37:g.10772921C>T	ENSP00000075503:p.Arg364His	Somatic		Capture	Illumina HiSeq	Phase_I	10664188	NM_018423	B2R9T2|Q52LR3|Q9BXY2|Q9NSH1	Missense_Mutation	SNP	ENST00000075503.3	37	CCDS8629.1	.	.	.	.	.	.	.	.	.	.	C	9.569	1.120481	0.20877	0.0	1.16E-4	ENSG00000060140	ENST00000075503	D	0.82619	-1.63	5.28	4.39	0.52855	Serine-threonine/tyrosine-protein kinase (2);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.307323	0.27696	N	0.018238	T	0.61515	0.2353	N	0.12527	0.23	0.24829	N	0.992539	B	0.06786	0.001	B	0.09377	0.004	T	0.48636	-0.9018	10	0.02654	T	1	-3.5781	6.745	0.23456	0.1753:0.7338:0.0:0.0908	.	364	Q6J9G0	STYK1_HUMAN	H	364	ENSP00000075503:R364H	ENSP00000075503:R364H	R	-	2	0	STYK1	10664188	0.059000	0.20769	1.000000	0.80357	0.425000	0.31504	-0.721000	0.04963	1.226000	0.43582	0.563000	0.77884	CGC		0.527	STYK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399622.1	NM_018423	
CKAP4	10970	broad.mit.edu	37	12	106633423	106633423	+	Silent	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr12:106633423C>T	ENST00000378026.4	-	2	1324	c.1188G>A	c.(1186-1188)tcG>tcA	p.S396S	CKAP4_ENST00000552828.1_5'Flank	NM_006825.3	NP_006816.2	Q07065	CKAP4_HUMAN	cytoskeleton-associated protein 4	396						cytoskeleton (GO:0005856)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lipid particle (GO:0005811)|membrane (GO:0016020)|plasma membrane (GO:0005886)	poly(A) RNA binding (GO:0044822)	p.S396S(1)		NS(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(8)|pancreas(1)|urinary_tract(1)	20						CAAAGGCTTCCGAGTGTCTGA	0.637																																					p.S396S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G1188A	12						.						54.0	56.0	56.0					12																	106633423		2203	4300	6503	105157553	SO:0001819	synonymous_variant	10970	exon2			X69910	CCDS9103.1	12q23.3	2006-06-23				ENSG00000136026			16991	protein-coding gene	gene with protein product						8314870	Standard	NM_006825		Approved	P63, CLIMP-63, ERGIC-63	uc001tlk.3	Q07065		ENST00000378026.4:c.1188G>A	12.37:g.106633423C>T		Somatic		Capture	Illumina HiSeq	Phase_I	105157553	NM_006825	Q504S5|Q53ES6	Silent	SNP	ENST00000378026.4	37	CCDS9103.1																																																																																				0.637	CKAP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407196.1		
ACACB	32	broad.mit.edu	37	12	109604704	109604704	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr12:109604704G>A	ENST00000338432.7	+	3	811	c.692G>A	c.(691-693)cGg>cAg	p.R231Q	ACACB_ENST00000377854.5_Missense_Mutation_p.R231Q|ACACB_ENST00000377848.3_Missense_Mutation_p.R231Q			O00763	ACACB_HUMAN	acetyl-CoA carboxylase beta	231					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)|malonyl-CoA biosynthetic process (GO:2001295)|positive regulation of cellular metabolic process (GO:0031325)|protein homotetramerization (GO:0051289)|response to drug (GO:0042493)|response to organic cyclic compound (GO:0014070)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	acetyl-CoA carboxylase activity (GO:0003989)|ATP binding (GO:0005524)|biotin binding (GO:0009374)|biotin carboxylase activity (GO:0004075)|metal ion binding (GO:0046872)	p.R231Q(1)		NS(1)|breast(2)|endometrium(9)|kidney(5)|large_intestine(20)|lung(40)|ovary(6)|pancreas(1)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	95					Adenine(DB00173)|Biotin(DB00121)	AAGAGGGGACGGGAACACAAG	0.577																																					p.R231Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G692A	12						.						89.0	81.0	84.0					12																	109604704		2203	4300	6503	108089087	SO:0001583	missense	32	exon2			U89344	CCDS31898.1	12q24.1	2010-05-07	2010-04-30		ENSG00000076555	ENSG00000076555	6.4.1.2		85	protein-coding gene	gene with protein product	"""acetyl-CoA carboxylase 2"""	601557	"""acetyl-Coenzyme A carboxylase beta"""			8670171	Standard	NM_001093		Approved	HACC275, ACC2, ACCB	uc001toc.3	O00763	OTTHUMG00000169250	ENST00000338432.7:c.692G>A	12.37:g.109604704G>A	ENSP00000341044:p.Arg231Gln	Somatic		Capture	Illumina HiSeq	Phase_I	108089087	NM_001093	A6NK36|Q16852|Q1HEC1|Q6KE87|Q6KE89|Q6TY48	Missense_Mutation	SNP	ENST00000338432.7	37	CCDS31898.1	.	.	.	.	.	.	.	.	.	.	G	20.8	4.056916	0.76074	.	.	ENSG00000076555	ENST00000338432;ENST00000377848;ENST00000377854	T;T;T	0.18016	2.24;2.24;2.24	5.15	5.15	0.70609	PreATP-grasp-like fold (1);	0.203997	0.40469	N	0.001097	T	0.21227	0.0511	L	0.55990	1.75	0.80722	D	1	P	0.51351	0.944	B	0.41946	0.371	T	0.01972	-1.1237	10	0.38643	T	0.18	.	18.2324	0.89938	0.0:0.0:1.0:0.0	.	231	O00763	ACACB_HUMAN	Q	231	ENSP00000341044:R231Q;ENSP00000367079:R231Q;ENSP00000367085:R231Q	ENSP00000341044:R231Q	R	+	2	0	ACACB	108089087	1.000000	0.71417	0.981000	0.43875	0.983000	0.72400	6.423000	0.73361	2.383000	0.81215	0.313000	0.20887	CGG		0.577	ACACB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403077.1	NM_001093	
ACACB	32	broad.mit.edu	37	12	109692038	109692038	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr12:109692038C>A	ENST00000338432.7	+	44	6184	c.6065C>A	c.(6064-6066)cCt>cAt	p.P2022H	ACACB_ENST00000543201.1_Missense_Mutation_p.P688H|ACACB_ENST00000377854.5_Missense_Mutation_p.P1952H|ACACB_ENST00000377848.3_Missense_Mutation_p.P2022H			O00763	ACACB_HUMAN	acetyl-CoA carboxylase beta	2022	Carboxyltransferase.				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)|malonyl-CoA biosynthetic process (GO:2001295)|positive regulation of cellular metabolic process (GO:0031325)|protein homotetramerization (GO:0051289)|response to drug (GO:0042493)|response to organic cyclic compound (GO:0014070)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	acetyl-CoA carboxylase activity (GO:0003989)|ATP binding (GO:0005524)|biotin binding (GO:0009374)|biotin carboxylase activity (GO:0004075)|metal ion binding (GO:0046872)	p.P2022H(1)		NS(1)|breast(2)|endometrium(9)|kidney(5)|large_intestine(20)|lung(40)|ovary(6)|pancreas(1)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	95					Adenine(DB00173)|Biotin(DB00121)	AGCCCTGTCCCTATCATCACA	0.498																																					p.P2022H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C6065A	12						.						254.0	239.0	244.0					12																	109692038		2203	4300	6503	108176421	SO:0001583	missense	32	exon43			U89344	CCDS31898.1	12q24.1	2010-05-07	2010-04-30		ENSG00000076555	ENSG00000076555	6.4.1.2		85	protein-coding gene	gene with protein product	"""acetyl-CoA carboxylase 2"""	601557	"""acetyl-Coenzyme A carboxylase beta"""			8670171	Standard	NM_001093		Approved	HACC275, ACC2, ACCB	uc001toc.3	O00763	OTTHUMG00000169250	ENST00000338432.7:c.6065C>A	12.37:g.109692038C>A	ENSP00000341044:p.Pro2022His	Somatic		Capture	Illumina HiSeq	Phase_I	108176421	NM_001093	A6NK36|Q16852|Q1HEC1|Q6KE87|Q6KE89|Q6TY48	Missense_Mutation	SNP	ENST00000338432.7	37	CCDS31898.1	.	.	.	.	.	.	.	.	.	.	C	25.5	4.646169	0.87958	.	.	ENSG00000076555	ENST00000338432;ENST00000377848;ENST00000377854;ENST00000390027;ENST00000543201	D;D;D;D	0.98862	-5.19;-5.19;-5.19;-5.19	5.27	5.27	0.74061	Acetyl-coenzyme A carboxyltransferase, C-terminal (1);Carboxyl transferase (1);	0.000000	0.85682	D	0.000000	D	0.99441	0.9802	H	0.95402	3.665	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.98479	1.0604	10	0.87932	D	0	.	18.8734	0.92325	0.0:1.0:0.0:0.0	.	2022	O00763	ACACB_HUMAN	H	2022;2022;1952;1253;688	ENSP00000341044:P2022H;ENSP00000367079:P2022H;ENSP00000367085:P1952H;ENSP00000444075:P688H	ENSP00000341044:P2022H	P	+	2	0	ACACB	108176421	1.000000	0.71417	0.975000	0.42487	0.990000	0.78478	7.660000	0.83776	2.648000	0.89879	0.655000	0.94253	CCT		0.498	ACACB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403077.1	NM_001093	
ACACB	32	broad.mit.edu	37	12	109698294	109698294	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr12:109698294A>G	ENST00000338432.7	+	48	6625	c.6506A>G	c.(6505-6507)gAc>gGc	p.D2169G	ACACB_ENST00000543201.1_3'UTR|ACACB_ENST00000377854.5_Missense_Mutation_p.D2099G|ACACB_ENST00000377848.3_Missense_Mutation_p.D2169G			O00763	ACACB_HUMAN	acetyl-CoA carboxylase beta	2169	Carboxyltransferase.				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)|malonyl-CoA biosynthetic process (GO:2001295)|positive regulation of cellular metabolic process (GO:0031325)|protein homotetramerization (GO:0051289)|response to drug (GO:0042493)|response to organic cyclic compound (GO:0014070)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	acetyl-CoA carboxylase activity (GO:0003989)|ATP binding (GO:0005524)|biotin binding (GO:0009374)|biotin carboxylase activity (GO:0004075)|metal ion binding (GO:0046872)	p.D2169G(1)		NS(1)|breast(2)|endometrium(9)|kidney(5)|large_intestine(20)|lung(40)|ovary(6)|pancreas(1)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	95					Adenine(DB00173)|Biotin(DB00121)	GACATGTATGACCAGGTGCTG	0.557																																					p.D2169G												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A6506G	12						.						141.0	125.0	131.0					12																	109698294		2203	4300	6503	108182677	SO:0001583	missense	32	exon47			U89344	CCDS31898.1	12q24.1	2010-05-07	2010-04-30		ENSG00000076555	ENSG00000076555	6.4.1.2		85	protein-coding gene	gene with protein product	"""acetyl-CoA carboxylase 2"""	601557	"""acetyl-Coenzyme A carboxylase beta"""			8670171	Standard	NM_001093		Approved	HACC275, ACC2, ACCB	uc001toc.3	O00763	OTTHUMG00000169250	ENST00000338432.7:c.6506A>G	12.37:g.109698294A>G	ENSP00000341044:p.Asp2169Gly	Somatic		Capture	Illumina HiSeq	Phase_I	108182677	NM_001093	A6NK36|Q16852|Q1HEC1|Q6KE87|Q6KE89|Q6TY48	Missense_Mutation	SNP	ENST00000338432.7	37	CCDS31898.1	.	.	.	.	.	.	.	.	.	.	A	18.33	3.600132	0.66332	.	.	ENSG00000076555	ENST00000338432;ENST00000377848;ENST00000377854;ENST00000390027	D;D;D	0.97232	-4.3;-4.3;-4.3	5.09	5.09	0.68999	Acetyl-coenzyme A carboxyltransferase, C-terminal (1);Carboxyl transferase (1);	0.044698	0.85682	D	0.000000	D	0.97720	0.9252	M	0.62154	1.92	0.80722	D	1	P	0.52170	0.951	P	0.61874	0.895	D	0.98512	1.0619	10	0.72032	D	0.01	.	15.5851	0.76475	1.0:0.0:0.0:0.0	.	2169	O00763	ACACB_HUMAN	G	2169;2169;2099;1400	ENSP00000341044:D2169G;ENSP00000367079:D2169G;ENSP00000367085:D2099G	ENSP00000341044:D2169G	D	+	2	0	ACACB	108182677	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	9.287000	0.95975	2.234000	0.73211	0.533000	0.62120	GAC		0.557	ACACB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403077.1	NM_001093	
HVCN1	84329	broad.mit.edu	37	12	111089113	111089113	+	Silent	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr12:111089113G>A	ENST00000356742.5	-	5	1305	c.552C>T	c.(550-552)ctC>ctT	p.L184L	HVCN1_ENST00000242607.8_Silent_p.L184L|HVCN1_ENST00000548312.1_Silent_p.L184L|HVCN1_ENST00000439744.2_Silent_p.L164L			Q96D96	HVCN1_HUMAN	hydrogen voltage-gated channel 1	184					cellular response to pH (GO:0071467)|cellular response to zinc ion (GO:0071294)|multicellular organism reproduction (GO:0032504)|proton transport (GO:0015992)|response to pH (GO:0009268)|response to zinc ion (GO:0010043)|single fertilization (GO:0007338)|sperm-egg recognition (GO:0035036)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	voltage-gated cation channel activity (GO:0022843)|voltage-gated proton channel activity (GO:0030171)	p.L184L(1)		NS(1)|breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(5)|lung(6)|prostate(1)|skin(1)	19						GGACAATGTCGAGGATGAATG	0.527																																					p.L184L												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C552T	12						.						114.0	102.0	106.0					12																	111089113		2203	4300	6503	109573496	SO:0001819	synonymous_variant	84329	exon6			BC007277	CCDS31900.1, CCDS58278.1	12q24.11	2011-12-09	2006-03-24	2006-03-24	ENSG00000122986	ENSG00000122986		"""Voltage-gated ion channels / Hydrogen voltage-gated channel"""	28240	protein-coding gene	gene with protein product	"""voltage sensor domain-only protein"""	611227				20961760, 16556803, 18356202, 22020278	Standard	NM_032369		Approved	MGC15619, Hv1, VSOP	uc001trs.2	Q96D96		ENST00000356742.5:c.552C>T	12.37:g.111089113G>A		Somatic		Capture	Illumina HiSeq	Phase_I	109573496	NM_032369	A8MQ37|B4DEB3|F8WCH5|Q6UW11|Q96IS5	Silent	SNP	ENST00000356742.5	37	CCDS31900.1																																																																																				0.527	HVCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404653.1	NM_032369	
HECTD4	283450	broad.mit.edu	37	12	112610509	112610509	+	Silent	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr12:112610509C>T	ENST00000430131.2	-	66	11630	c.10485G>A	c.(10483-10485)gcG>gcA	p.A3495A	HECTD4_ENST00000550722.1_Silent_p.A3771A|HECTD4_ENST00000377560.5_Silent_p.A3745A			Q9Y4D8	HECD4_HUMAN	HECT domain containing E3 ubiquitin protein ligase 4	3495					glucose homeostasis (GO:0042593)|glucose metabolic process (GO:0006006)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)	p.A3745A(1)									CAGCAGCATCCGCGGGGTCCA	0.637																																					p.A3745A												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G11235A	12						.						68.0	79.0	75.0					12																	112610509		2157	4261	6418	111094892	SO:0001819	synonymous_variant	283450	exon66			AK091473		12q24.13	2013-07-17	2012-08-14	2012-08-14	ENSG00000173064	ENSG00000173064			26611	protein-coding gene	gene with protein product			"""chromosome 12 open reading frame 51"""	C12orf51		21270382	Standard	NM_001109662		Approved	FLJ34154, KIAA0614	uc021reb.1	Q9Y4D8	OTTHUMG00000150719	ENST00000430131.2:c.10485G>A	12.37:g.112610509C>T		Somatic		Capture	Illumina HiSeq	Phase_I	111094892	NM_001109662	L8B0P6|Q3MJD5|Q6P0A0|Q7L530|Q8NB70|Q8WU73|Q96NT9|Q9NZS4|Q9UFT6	Silent	SNP	ENST00000430131.2	37																																																																																					0.637	HECTD4-202	KNOWN	basic	protein_coding	protein_coding		NM_173813	
SDS	10993	broad.mit.edu	37	12	113835055	113835055	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr12:113835055C>T	ENST00000257549.4	-	6	690	c.568G>A	c.(568-570)Gtc>Atc	p.V190I		NM_006843.2	NP_006834.2	P20132	SDHL_HUMAN	serine dehydratase	190					gluconeogenesis (GO:0006094)|L-serine catabolic process (GO:0006565)|pyruvate biosynthetic process (GO:0042866)|response to amino acid (GO:0043200)|response to cobalamin (GO:0033590)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)	L-serine ammonia-lyase activity (GO:0003941)|L-threonine ammonia-lyase activity (GO:0004794)|protein homodimerization activity (GO:0042803)|pyridoxal phosphate binding (GO:0030170)	p.V190I(1)		large_intestine(2)|lung(6)|pancreas(1)|prostate(1)|urinary_tract(1)	11					L-Serine(DB00133)	ATGGCGATGACAGGCACGTCC	0.667																																					p.V190I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G568A	12						.						78.0	65.0	69.0					12																	113835055		2203	4300	6503	112319438	SO:0001583	missense	10993	exon6			J05037	CCDS9169.1	12q24.13	2014-06-24			ENSG00000135094	ENSG00000135094	4.3.1.17		10691	protein-coding gene	gene with protein product	"""L-serine ammonia-lyase"""	182128				2674117	Standard	NM_006843		Approved	SDH	uc001tvg.3	P20132	OTTHUMG00000169554	ENST00000257549.4:c.568G>A	12.37:g.113835055C>T	ENSP00000257549:p.Val190Ile	Somatic		Capture	Illumina HiSeq	Phase_I	112319438	NM_006843	A8K9P5	Missense_Mutation	SNP	ENST00000257549.4	37	CCDS9169.1	.	.	.	.	.	.	.	.	.	.	C	2.854	-0.237746	0.05944	.	.	ENSG00000135094	ENST00000257549;ENST00000446302	D	0.96830	-4.14	4.45	-5.02	0.02982	Pyridoxal phosphate-dependent enzyme, beta subunit (2);	0.531595	0.19907	N	0.103383	D	0.86426	0.5930	N	0.05050	-0.12	0.21802	N	0.999535	B;B	0.06786	0.0;0.001	B;B	0.12837	0.008;0.008	T	0.73132	-0.4079	10	0.05436	T	0.98	-16.2009	15.4118	0.74933	0.0:0.2008:0.0:0.7992	.	190;190	Q8WW81;P20132	.;SDHL_HUMAN	I	190	ENSP00000257549:V190I	ENSP00000257549:V190I	V	-	1	0	SDS	112319438	0.000000	0.05858	0.372000	0.25991	0.967000	0.64934	-0.737000	0.04877	-1.017000	0.03367	-0.291000	0.09656	GTC		0.667	SDS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404790.1	NM_006843	
SDSL	113675	broad.mit.edu	37	12	113865908	113865908	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr12:113865908G>A	ENST00000403593.4	+	2	383	c.121G>A	c.(121-123)Gtg>Atg	p.V41M	SDSL_ENST00000345635.4_Missense_Mutation_p.V41M			Q96GA7	SDSL_HUMAN	serine dehydratase-like	41					cellular amino acid metabolic process (GO:0006520)	extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	L-serine ammonia-lyase activity (GO:0003941)|L-threonine ammonia-lyase activity (GO:0004794)|pyridoxal phosphate binding (GO:0030170)	p.V41M(1)		endometrium(1)|kidney(1)|large_intestine(4)|lung(7)|ovary(2)	15						GTGTGAGAATGTGCAGCCCAG	0.607																																					p.V41M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G121A	12						.						53.0	47.0	49.0					12																	113865908		2203	4300	6503	112350291	SO:0001583	missense	113675	exon3			AF134473	CCDS9170.1	12q24.21	2014-06-24				ENSG00000139410			30404	protein-coding gene	gene with protein product						16580895	Standard	NM_138432		Approved	SDS-RS1, cSDH	uc001tvi.3	Q96GA7		ENST00000403593.4:c.121G>A	12.37:g.113865908G>A	ENSP00000385790:p.Val41Met	Somatic		Capture	Illumina HiSeq	Phase_I	112350291	NM_138432		Missense_Mutation	SNP	ENST00000403593.4	37	CCDS9170.1	.	.	.	.	.	.	.	.	.	.	G	9.658	1.143472	0.21205	.	.	ENSG00000139410	ENST00000403593;ENST00000345635	D;D	0.96651	-4.08;-4.08	4.42	-0.214	0.13161	Pyridoxal phosphate-dependent enzyme, beta subunit (2);	0.385336	0.26311	N	0.025101	D	0.90007	0.6880	N	0.25094	0.71	0.38441	D	0.946719	B	0.15141	0.012	B	0.15870	0.014	T	0.79485	-0.1784	10	0.25751	T	0.34	-11.6328	8.9086	0.35539	0.3582:0.0:0.6418:0.0	.	41	Q96GA7	SDSL_HUMAN	M	41	ENSP00000385790:V41M;ENSP00000341117:V41M	ENSP00000341117:V41M	V	+	1	0	SDSL	112350291	0.447000	0.25673	0.913000	0.36048	0.544000	0.35116	0.736000	0.26130	-0.084000	0.12595	-0.367000	0.07326	GTG		0.607	SDSL-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404782.1	NM_138432	
FBXO21	23014	broad.mit.edu	37	12	117615422	117615422	+	Silent	SNP	G	G	A	rs149686869		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr12:117615422G>A	ENST00000330622.5	-	4	494	c.495C>T	c.(493-495)taC>taT	p.Y165Y	FBXO21_ENST00000427718.2_Silent_p.Y165Y|FBXO21_ENST00000549689.1_5'UTR			O94952	FBX21_HUMAN	F-box protein 21	165					protein ubiquitination (GO:0016567)|ubiquitin-dependent protein catabolic process (GO:0006511)	ubiquitin ligase complex (GO:0000151)	DNA binding (GO:0003677)|ubiquitin-protein transferase activity (GO:0004842)	p.Y165Y(2)		breast(4)|endometrium(3)|kidney(2)|large_intestine(6)|lung(8)|pancreas(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	29	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)			BRCA - Breast invasive adenocarcinoma(302;0.0291)		TTTTTTTTGCGTAGTATTTCC	0.343													G|||	1	0.000199681	0.0008	0.0	5008	,	,		16566	0.0		0.0	False		,,,				2504	0.0				p.Y165Y	GBM(168;452 2038 13535 17701 43680)											.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.C495T	12						.	G	,	1,4405	2.1+/-5.4	0,1,2202	96.0	94.0	95.0		495,495	-8.0	0.1	12	dbSNP_134	95	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous	FBXO21	NM_015002.2,NM_033624.2	,	0,2,6501	AA,AG,GG		0.0116,0.0227,0.0154	,	165/622,165/629	117615422	2,13004	2203	4300	6503	116099805	SO:0001819	synonymous_variant	23014	exon4			AB020682	CCDS9184.1, CCDS44989.1	12q24.23	2004-06-15	2004-06-15					"""F-boxes /  ""other"""""	13592	protein-coding gene	gene with protein product		609095	"""F-box only protein 21"""			10048485, 10531035	Standard	NM_033624		Approved	FBX21, KIAA0875	uc001twk.3	O94952	OTTHUMG00000169495	ENST00000330622.5:c.495C>T	12.37:g.117615422G>A		Somatic		Capture	Illumina HiSeq	Phase_I	116099805	NM_015002	B3KMF0|Q5BJG0|Q9H087	Silent	SNP	ENST00000330622.5	37	CCDS9184.1	.	.	.	.	.	.	.	.	.	.	G	5.822	0.335918	0.11013	2.27E-4	1.16E-4	ENSG00000135108	ENST00000550180	.	.	.	5.71	-7.98	0.01135	.	.	.	.	.	T	0.66858	0.2832	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.71974	-0.4430	4	.	.	.	-14.7377	19.9747	0.97299	0.8889:0.0:0.1111:0.0	.	.	.	.	C	109	.	.	R	-	1	0	FBXO21	116099805	0.266000	0.24112	0.143000	0.22291	0.691000	0.40173	-0.221000	0.09202	-1.683000	0.01444	-0.768000	0.03414	CGC		0.343	FBXO21-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000404409.1	NM_033624	
KSR2	283455	broad.mit.edu	37	12	117996345	117996345	+	Silent	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr12:117996345G>A	ENST00000339824.5	-	8	2086	c.1359C>T	c.(1357-1359)gcC>gcT	p.A453A	KSR2_ENST00000302438.5_Silent_p.A150A|KSR2_ENST00000545002.1_5'UTR|KSR2_ENST00000425217.1_Silent_p.A424A			Q6VAB6	KSR2_HUMAN	kinase suppressor of ras 2	453					intracellular signal transduction (GO:0035556)	cytoplasm (GO:0005737)|membrane (GO:0016020)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)	p.A485A(1)		NS(1)|breast(3)|central_nervous_system(2)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(25)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	67	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)					GACAGGGTGGGGCTTCTTTGG	0.522																																					p.A424A												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1272T	12						.						133.0	133.0	133.0					12																	117996345		1919	4137	6056	116480728	SO:0001819	synonymous_variant	283455	exon8			AY345972	CCDS61250.1	12q24.22-q24.23	2014-08-12			ENSG00000171435	ENSG00000171435			18610	protein-coding gene	gene with protein product		610737				12471243	Standard	NM_173598		Approved	FLJ25965	uc001two.2	Q6VAB6	OTTHUMG00000169020	ENST00000339824.5:c.1359C>T	12.37:g.117996345G>A		Somatic		Capture	Illumina HiSeq	Phase_I	116480728	NM_173598	A0PJT2|Q3B828|Q8N775	Silent	SNP	ENST00000339824.5	37																																																																																					0.522	KSR2-001	KNOWN	non_canonical_conserved|not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000401987.2	NM_173598	
VSIG10	54621	broad.mit.edu	37	12	118506296	118506296	+	Missense_Mutation	SNP	G	G	A	rs368996191		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr12:118506296G>A	ENST00000359236.5	-	8	1729	c.1453C>T	c.(1453-1455)Cgt>Tgt	p.R485C		NM_019086.5	NP_061959.2	Q8N0Z9	VSI10_HUMAN	V-set and immunoglobulin domain containing 10	485	Glu-rich.					integral component of membrane (GO:0016021)		p.R485C(1)		endometrium(5)|large_intestine(3)|lung(6)|skin(1)|stomach(1)|urinary_tract(1)	17						TCTCTCTCACGTGCTCCCTCC	0.493																																					p.R485C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1453T	12						.	G	CYS/ARG	0,4208		0,0,2104	190.0	189.0	190.0		1453	-7.9	0.0	12		190	1,8441		0,1,4220	no	missense	VSIG10	NM_019086.5	180	0,1,6324	AA,AG,GG		0.0118,0.0,0.0079	possibly-damaging	485/541	118506296	1,12649	2104	4221	6325	116990679	SO:0001583	missense	54621	exon8				CCDS44992.1	12q24.23	2013-01-29			ENSG00000176834	ENSG00000176834		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	26078	protein-coding gene	gene with protein product						12477932	Standard	NM_019086		Approved		uc001tws.3	Q8N0Z9		ENST00000359236.5:c.1453C>T	12.37:g.118506296G>A	ENSP00000352172:p.Arg485Cys	Somatic		Capture	Illumina HiSeq	Phase_I	116990679	NM_019086	Q9NWQ7	Missense_Mutation	SNP	ENST00000359236.5	37	CCDS44992.1	.	.	.	.	.	.	.	.	.	.	G	7.285	0.609828	0.14066	0.0	1.18E-4	ENSG00000176834	ENST00000359236	T	0.55930	0.49	4.55	-7.93	0.01156	.	3.214530	0.00972	N	0.003240	T	0.30417	0.0764	N	0.22421	0.69	0.09310	N	1	P	0.51653	0.947	B	0.36766	0.232	T	0.50338	-0.8840	10	0.39692	T	0.17	11.0702	7.1531	0.25622	0.0:0.3671:0.4012:0.2317	.	485	Q8N0Z9	VSI10_HUMAN	C	485	ENSP00000352172:R485C	ENSP00000352172:R485C	R	-	1	0	VSIG10	116990679	0.000000	0.05858	0.000000	0.03702	0.008000	0.06430	-1.008000	0.03663	-1.819000	0.01216	-0.518000	0.04402	CGT		0.493	VSIG10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401273.2	NM_019086	
SRRM4	84530	broad.mit.edu	37	12	119563215	119563215	+	Missense_Mutation	SNP	G	G	A	rs550204730		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr12:119563215G>A	ENST00000267260.4	+	7	933	c.545G>A	c.(544-546)cGc>cAc	p.R182H	SRRM4_ENST00000537597.1_3'UTR	NM_194286.3	NP_919262.2	A7MD48	SRRM4_HUMAN	serine/arginine repetitive matrix 4	182	Ser-rich.				cell differentiation (GO:0030154)|mRNA processing (GO:0006397)|nervous system development (GO:0007399)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|regulation of RNA splicing (GO:0043484)|RNA splicing (GO:0008380)|sensory perception of sound (GO:0007605)	nucleus (GO:0005634)	mRNA binding (GO:0003729)	p.R182H(1)		breast(2)|central_nervous_system(2)|endometrium(5)|kidney(1)|large_intestine(2)|lung(8)|ovary(3)|upper_aerodigestive_tract(1)	24						AAGTCTCACCGCCACCGCCAT	0.602													G|||	1	0.000199681	0.0	0.0	5008	,	,		15184	0.0		0.0	False		,,,				2504	0.001				p.R182H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G545A	12						.						38.0	49.0	45.0					12																	119563215		2004	4161	6165	118047598	SO:0001583	missense	84530	exon7			AB058756	CCDS44994.1	12q24.23	2009-09-22	2009-09-21	2009-09-21	ENSG00000139767	ENSG00000139767			29389	protein-coding gene	gene with protein product	"""neural-specific SR-related protein of 100 kDa"""	613103	"""KIAA1853"""	KIAA1853		19737518	Standard	NM_194286		Approved	nSR100	uc001txa.2	A7MD48	OTTHUMG00000168928	ENST00000267260.4:c.545G>A	12.37:g.119563215G>A	ENSP00000267260:p.Arg182His	Somatic		Capture	Illumina HiSeq	Phase_I	118047598	NM_194286	A8K5P6|B2RZH7|Q7Z5F0|Q96JH4	Missense_Mutation	SNP	ENST00000267260.4	37	CCDS44994.1	.	.	.	.	.	.	.	.	.	.	G	18.70	3.679542	0.68042	.	.	ENSG00000139767	ENST00000267260	T	0.32515	1.45	5.66	5.66	0.87406	.	0.068529	0.64402	D	0.000014	T	0.50326	0.1609	L	0.53249	1.67	0.42620	D	0.993344	D	0.89917	1.0	D	0.85130	0.997	T	0.36578	-0.9742	10	0.36615	T	0.2	-20.2207	15.2504	0.73539	0.0:0.0:1.0:0.0	.	182	A7MD48	SRRM4_HUMAN	H	182	ENSP00000267260:R182H	ENSP00000267260:R182H	R	+	2	0	SRRM4	118047598	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	3.257000	0.51500	2.648000	0.89879	0.655000	0.94253	CGC		0.602	SRRM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401640.2	NM_194286	
BCL7A	605	broad.mit.edu	37	12	122468668	122468668	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr12:122468668C>T	ENST00000261822.4	+	2	361	c.155C>T	c.(154-156)aCg>aTg	p.T52M	BCL7A_ENST00000538010.1_Missense_Mutation_p.T52M	NM_001024808.1	NP_001019979.1	Q4VC05	BCL7A_HUMAN	B-cell CLL/lymphoma 7A	52					negative regulation of transcription, DNA-templated (GO:0045892)			p.T52M(2)		haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(8)|lung(4)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	18	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000202)|Epithelial(86;0.000386)|BRCA - Breast invasive adenocarcinoma(302;0.231)		GTCCCTGTGACGGAGCCCAAG	0.582			T	MYC	BNHL																																p.T52M	GBM(17;197 467 16477 23242 44349)		Dom	yes		12	12q24.1	605	B-cell CLL/lymphoma 7A		L	.	.	2	Substitution - Missense(2)	large_intestine(2)	c.C155T	12						.						160.0	127.0	138.0					12																	122468668		2203	4300	6503	120953051	SO:0001583	missense	605	exon2			X89984	CCDS9226.1, CCDS53841.1	12q24.1	2008-07-03			ENSG00000110987	ENSG00000110987			1004	protein-coding gene	gene with protein product		601406		BCL7		8605326, 9931421	Standard	NM_020993		Approved		uc001ubo.3	Q4VC05	OTTHUMG00000168951	ENST00000261822.4:c.155C>T	12.37:g.122468668C>T	ENSP00000261822:p.Thr52Met	Somatic		Capture	Illumina HiSeq	Phase_I	120953051	NM_020993	B4DJN6|B7ZB21|Q13843|Q14CT7	Missense_Mutation	SNP	ENST00000261822.4	37	CCDS53841.1	.	.	.	.	.	.	.	.	.	.	C	17.21	3.330386	0.60743	.	.	ENSG00000110987	ENST00000538010;ENST00000261822	T;T	0.49139	0.79;0.8	5.97	5.97	0.96955	.	0.000000	0.85682	D	0.000000	T	0.64283	0.2584	L	0.42245	1.32	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.989	T	0.63681	-0.6582	10	0.72032	D	0.01	.	19.1994	0.93704	0.0:1.0:0.0:0.0	.	52;52	Q4VC05;Q4VC05-2	BCL7A_HUMAN;.	M	52	ENSP00000445868:T52M;ENSP00000261822:T52M	ENSP00000261822:T52M	T	+	2	0	BCL7A	120953051	1.000000	0.71417	0.995000	0.50966	0.027000	0.11550	5.296000	0.65698	2.837000	0.97791	0.655000	0.94253	ACG		0.582	BCL7A-002	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000401712.1		
IL31	386653	broad.mit.edu	37	12	122658468	122658468	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr12:122658468G>A	ENST00000377035.1	-	2	114	c.88C>T	c.(88-90)Cgt>Tgt	p.R30C		NM_001014336.1	NP_001014358.1	Q6EBC2	IL31_HUMAN	interleukin 31	30					immune system process (GO:0002376)	extracellular space (GO:0005615)		p.R30C(1)		central_nervous_system(2)|kidney(1)|large_intestine(4)|lung(4)|skin(1)|upper_aerodigestive_tract(1)	13	all_neural(191;0.0837)|Medulloblastoma(191;0.163)	Lung NSC(355;6.93e-05)|Breast(359;0.0544)		OV - Ovarian serous cystadenocarcinoma(86;3.27e-29)|Epithelial(86;4.86e-27)|BRCA - Breast invasive adenocarcinoma(302;0.223)		CGTAGTAAACGGACGGGCAAC	0.517																																					p.R30C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C88T	12						.						92.0	85.0	87.0					12																	122658468		2203	4300	6503	121224421	SO:0001583	missense	386653	exon2			AY499343	CCDS31919.1	12q24.31	2011-07-21			ENSG00000204671	ENSG00000204671		"""Interleukins and interleukin receptors"""	19372	protein-coding gene	gene with protein product		609509				15184896	Standard	NM_001014336		Approved	IL-31	uc001ubv.3	Q6EBC2	OTTHUMG00000168916	ENST00000377035.1:c.88C>T	12.37:g.122658468G>A	ENSP00000366234:p.Arg30Cys	Somatic		Capture	Illumina HiSeq	Phase_I	121224421	NM_001014336	A2RUQ1	Missense_Mutation	SNP	ENST00000377035.1	37	CCDS31919.1	.	.	.	.	.	.	.	.	.	.	G	9.399	1.077536	0.20227	.	.	ENSG00000204671	ENST00000377035	.	.	.	4.23	-1.56	0.08532	.	3.599670	0.00956	N	0.003029	T	0.20618	0.0496	N	0.08118	0	0.09310	N	1	B	0.32653	0.379	B	0.30855	0.121	T	0.21552	-1.0242	9	0.54805	T	0.06	7.4766	7.4031	0.26975	0.2032:0.5254:0.2714:0.0	.	30	Q6EBC2	IL31_HUMAN	C	30	.	ENSP00000366234:R30C	R	-	1	0	IL31	121224421	0.000000	0.05858	0.000000	0.03702	0.017000	0.09413	-0.956000	0.03865	-0.433000	0.07286	0.467000	0.42956	CGT		0.517	IL31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401594.1	NM_001014336	
LRRC43	254050	broad.mit.edu	37	12	122676006	122676006	+	Silent	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr12:122676006G>A	ENST00000339777.4	+	6	1009	c.981G>A	c.(979-981)ccG>ccA	p.P327P	LRRC43_ENST00000425921.1_Silent_p.P142P	NM_152759.4	NP_689972.3	Q8N309	LRC43_HUMAN	leucine rich repeat containing 43	327								p.P142P(1)		NS(1)|endometrium(1)|large_intestine(4)|lung(10)|skin(1)|upper_aerodigestive_tract(2)	19	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000312)|Epithelial(86;0.000539)|BRCA - Breast invasive adenocarcinoma(302;0.225)		TCTTAGACCCGGAACCCAGGC	0.532											OREG0022219	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.P327P												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G981A	12						.						62.0	62.0	62.0					12																	122676006		1913	4116	6029	121241959	SO:0001819	synonymous_variant	254050	exon6			AK124107	CCDS45001.1	12q24.31	2014-09-11			ENSG00000158113	ENSG00000158113			28562	protein-coding gene	gene with protein product						12477932	Standard	NM_152759		Approved	MGC35140	uc009zxm.3	Q8N309	OTTHUMG00000168915	ENST00000339777.4:c.981G>A	12.37:g.122676006G>A		Somatic	1520	Capture	Illumina HiSeq	Phase_I	121241959	NM_001098519	Q6ZVT9	Silent	SNP	ENST00000339777.4	37	CCDS45001.1																																																																																				0.532	LRRC43-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401589.1	NM_152759	
LRP6	4040	broad.mit.edu	37	12	12302006	12302006	+	Missense_Mutation	SNP	G	G	A	rs140679529	byFrequency	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr12:12302006G>A	ENST00000261349.4	-	14	3152	c.3076C>T	c.(3076-3078)Cgc>Tgc	p.R1026C	LRP6_ENST00000543091.1_Missense_Mutation_p.R1026C	NM_002336.2	NP_002327.2	O75581	LRP6_HUMAN	low density lipoprotein receptor-related protein 6	1026	Beta-propeller 4.				anterior/posterior pattern specification (GO:0009952)|axis elongation involved in somitogenesis (GO:0090245)|bone morphogenesis (GO:0060349)|bone remodeling (GO:0046849)|branching involved in mammary gland duct morphogenesis (GO:0060444)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in cardiac neural crest cell differentiation involved in heart development (GO:0061310)|canonical Wnt signaling pathway involved in neural crest cell differentiation (GO:0044335)|canonical Wnt signaling pathway involved in positive regulation of cardiac outflow tract cell proliferation (GO:0061324)|canonical Wnt signaling pathway involved in regulation of cell proliferation (GO:0044340)|cell migration involved in gastrulation (GO:0042074)|cellular response to cholesterol (GO:0071397)|cerebellum morphogenesis (GO:0021587)|cerebral cortex cell migration (GO:0021795)|cerebral cortex development (GO:0021987)|convergent extension (GO:0060026)|dopaminergic neuron differentiation (GO:0071542)|embryonic camera-type eye morphogenesis (GO:0048596)|embryonic digit morphogenesis (GO:0042733)|embryonic forelimb morphogenesis (GO:0035115)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic limb morphogenesis (GO:0030326)|embryonic pattern specification (GO:0009880)|embryonic retina morphogenesis in camera-type eye (GO:0060059)|external genitalia morphogenesis (GO:0035261)|face morphogenesis (GO:0060325)|forebrain radial glial cell differentiation (GO:0021861)|formation of radial glial scaffolds (GO:0021943)|gastrulation with mouth forming second (GO:0001702)|heart looping (GO:0001947)|mammary placode formation (GO:0060596)|midbrain development (GO:0030901)|midbrain-hindbrain boundary development (GO:0030917)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of planar cell polarity pathway involved in cardiac muscle tissue morphogenesis (GO:2000151)|negative regulation of planar cell polarity pathway involved in cardiac right atrium morphogenesis (GO:2000162)|negative regulation of planar cell polarity pathway involved in neural tube closure (GO:2000168)|negative regulation of planar cell polarity pathway involved in outflow tract morphogenesis (GO:2000164)|negative regulation of planar cell polarity pathway involved in pericardium morphogenesis (GO:2000166)|negative regulation of planar cell polarity pathway involved in ventricular septum morphogenesis (GO:2000149)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of protein serine/threonine kinase activity (GO:0071901)|negative regulation of smooth muscle cell apoptotic process (GO:0034392)|neural crest cell differentiation (GO:0014033)|neural crest formation (GO:0014029)|neural tube closure (GO:0001843)|odontogenesis of dentin-containing tooth (GO:0042475)|palate development (GO:0060021)|pericardium morphogenesis (GO:0003344)|positive regulation of apoptotic process (GO:0043065)|positive regulation of bone resorption (GO:0045780)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of cell cycle (GO:0045787)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of ossification (GO:0045778)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of Wnt signaling pathway involved in dorsal/ventral axis specification (GO:2000055)|post-anal tail morphogenesis (GO:0036342)|primitive streak formation (GO:0090009)|receptor-mediated endocytosis of low-density lipoprotein particle involved in cholesterol transport (GO:0090118)|regulation of cell development (GO:0060284)|regulation of fat cell differentiation (GO:0045598)|regulation of ossification (GO:0030278)|response to folic acid (GO:0051593)|response to peptide hormone (GO:0043434)|single organismal cell-cell adhesion (GO:0016337)|synaptic transmission (GO:0007268)|thalamus development (GO:0021794)|toxin transport (GO:1901998)|trachea cartilage morphogenesis (GO:0060535)|Wnt signaling pathway (GO:0016055)|Wnt signaling pathway involved in dorsal/ventral axis specification (GO:0044332)|Wnt signaling pathway involved in forebrain neuroblast division (GO:0021874)|Wnt signaling pathway involved in somitogenesis (GO:0090244)	cell surface (GO:0009986)|cytoplasmic vesicle (GO:0031410)|early endosome (GO:0005769)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|synapse (GO:0045202)	apolipoprotein binding (GO:0034185)|coreceptor activity involved in Wnt signaling pathway (GO:0071936)|frizzled binding (GO:0005109)|identical protein binding (GO:0042802)|kinase inhibitor activity (GO:0019210)|low-density lipoprotein receptor activity (GO:0005041)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)|toxin transporter activity (GO:0019534)|Wnt-activated receptor activity (GO:0042813)|Wnt-protein binding (GO:0017147)	p.R1026C(1)		breast(4)|central_nervous_system(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(19)|lung(28)|ovary(3)|prostate(2)|skin(7)|upper_aerodigestive_tract(5)|urinary_tract(1)	85		Prostate(47;0.0865)				TAGATGTAGCGGCTGTAAATA	0.453													G|||	4	0.000798722	0.0008	0.0	5008	,	,		18805	0.0		0.0	False		,,,				2504	0.0031				p.R1026C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C3076T	12						.	G	CYS/ARG	0,4406	2.1+/-5.4	0,0,2203	238.0	234.0	236.0		3076	3.9	1.0	12	dbSNP_134	236	2,8598	2.2+/-6.3	0,2,4298	no	missense	LRP6	NM_002336.2	180	0,2,6501	AA,AG,GG		0.0233,0.0,0.0154	probably-damaging	1026/1614	12302006	2,13004	2203	4300	6503	12193273	SO:0001583	missense	4040	exon14			AF074264	CCDS8647.1	12p13.2	2013-05-29			ENSG00000070018	ENSG00000070018		"""Low density lipoprotein receptors"""	6698	protein-coding gene	gene with protein product		603507				9704021	Standard	NM_002336		Approved	ADCAD2	uc001rah.4	O75581	OTTHUMG00000168540	ENST00000261349.4:c.3076C>T	12.37:g.12302006G>A	ENSP00000261349:p.Arg1026Cys	Somatic		Capture	Illumina HiSeq	Phase_I	12193273	NM_002336	Q17RZ2	Missense_Mutation	SNP	ENST00000261349.4	37	CCDS8647.1	.	.	.	.	.	.	.	.	.	.	G	23.3	4.397883	0.83120	0.0	2.33E-4	ENSG00000070018	ENST00000261349;ENST00000543091	D;D	0.91792	-2.91;-2.91	5.71	3.86	0.44501	Six-bladed beta-propeller, TolB-like (1);	0.000000	0.64402	U	0.000009	D	0.94981	0.8376	M	0.73753	2.245	0.80722	D	1	B;D	0.89917	0.032;1.0	B;D	0.73708	0.005;0.981	D	0.95024	0.8163	10	0.87932	D	0	.	11.2607	0.49080	0.0667:0.0:0.8072:0.1261	.	1026;1026	F5H7J9;O75581	.;LRP6_HUMAN	C	1026	ENSP00000261349:R1026C;ENSP00000442472:R1026C	ENSP00000261349:R1026C	R	-	1	0	LRP6	12193273	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.642000	0.83385	1.405000	0.46838	0.650000	0.86243	CGC		0.453	LRP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400137.1		
VPS33A	65082	broad.mit.edu	37	12	122735536	122735536	+	Silent	SNP	G	G	A	rs370198408		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr12:122735536G>A	ENST00000267199.4	-	5	706	c.594C>T	c.(592-594)tgC>tgT	p.C198C	VPS33A_ENST00000542310.1_5'Flank|RP11-512M8.5_ENST00000535844.1_Intron	NM_022916.4	NP_075067.2	Q96AX1	VP33A_HUMAN	vacuolar protein sorting 33 homolog A (S. cerevisiae)	198					lysosome localization (GO:0032418)|melanosome localization (GO:0032400)|platelet formation (GO:0030220)|protein transport (GO:0015031)|regulation of developmental pigmentation (GO:0048070)|vesicle docking involved in exocytosis (GO:0006904)|vesicle-mediated transport (GO:0016192)	early endosome (GO:0005769)|late endosome (GO:0005770)|lysosomal membrane (GO:0005765)|perinuclear region of cytoplasm (GO:0048471)		p.C198C(2)		NS(2)|breast(1)|central_nervous_system(1)|endometrium(4)|large_intestine(4)|lung(13)|ovary(1)|skin(2)	28	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000336)|Epithelial(86;0.000606)|BRCA - Breast invasive adenocarcinoma(302;0.23)		TCACCCGAGCGCATTCTCCTT	0.557																																					p.C198C												.	.	2	Substitution - coding silent(2)	large_intestine(1)|endometrium(1)	c.C594T	12						.	G		0,4406		0,0,2203	91.0	85.0	87.0		594	-2.3	1.0	12		87	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	VPS33A	NM_022916.4		0,2,6501	AA,AG,GG		0.0233,0.0,0.0154		198/597	122735536	2,13004	2203	4300	6503	121301489	SO:0001819	synonymous_variant	65082	exon5			AK026048	CCDS9231.1	12q24.31	2008-06-23	2006-04-04		ENSG00000139719	ENSG00000139719			18179	protein-coding gene	gene with protein product		610034	"""vacuolar protein sorting 33A (yeast)"""			11250079	Standard	NM_022916		Approved		uc001ucd.3	Q96AX1	OTTHUMG00000168920	ENST00000267199.4:c.594C>T	12.37:g.122735536G>A		Somatic		Capture	Illumina HiSeq	Phase_I	121301489	NM_022916	Q547V4|Q9H5Q0	Silent	SNP	ENST00000267199.4	37	CCDS9231.1																																																																																				0.557	VPS33A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401607.2		
ABCB9	23457	broad.mit.edu	37	12	123419945	123419945	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr12:123419945C>T	ENST00000542678.1	-	10	4615	c.1777G>A	c.(1777-1779)Gcc>Acc	p.A593T	ABCB9_ENST00000442028.2_Missense_Mutation_p.A593T|ABCB9_ENST00000392439.3_Missense_Mutation_p.A593T|ABCB9_ENST00000346530.5_Missense_Mutation_p.A550T|ABCB9_ENST00000540285.1_Missense_Mutation_p.A530T|ABCB9_ENST00000344275.7_Missense_Mutation_p.A593T|ABCB9_ENST00000280560.8_Missense_Mutation_p.A593T|ABCB9_ENST00000442833.2_Missense_Mutation_p.A593T			Q9NP78	ABCB9_HUMAN	ATP-binding cassette, sub-family B (MDR/TAP), member 9	593	ABC transporter. {ECO:0000255|PROSITE- ProRule:PRU00434}.				peptide transport (GO:0015833)|protein transport (GO:0015031)|transmembrane transport (GO:0055085)	integral component of endoplasmic reticulum membrane (GO:0030176)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)	ATP binding (GO:0005524)|peptide-transporting ATPase activity (GO:0015440)|protein homodimerization activity (GO:0042803)|substrate-specific transmembrane transporter activity (GO:0022891)	p.A593T(1)		central_nervous_system(1)|endometrium(2)|large_intestine(2)|lung(9)|ovary(2)|prostate(1)|skin(1)	18	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;6.84e-05)|Epithelial(86;0.000152)|BRCA - Breast invasive adenocarcinoma(302;0.111)		ATGGAGCGGGCGAACAGCACG	0.612																																					p.A550T	Ovarian(49;786 1333 9175 38236)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1648A	12						.						81.0	66.0	71.0					12																	123419945		2203	4300	6503	121985898	SO:0001583	missense	23457	exon9			U66676	CCDS9241.1, CCDS58286.1, CCDS58287.1, CCDS58288.1	12q24	2012-03-14			ENSG00000150967	ENSG00000150967		"""ATP binding cassette transporters / subfamily B"""	50	protein-coding gene	gene with protein product		605453				8894702	Standard	NM_019625		Approved	EST122234	uc001udm.4	Q9NP78		ENST00000542678.1:c.1777G>A	12.37:g.123419945C>T	ENSP00000440288:p.Ala593Thr	Somatic		Capture	Illumina HiSeq	Phase_I	121985898	NM_019624	B4E2J0|Q5W9G7|Q769F3|Q769F4|Q96AB1|Q9P208	Missense_Mutation	SNP	ENST00000542678.1	37	CCDS9241.1	.	.	.	.	.	.	.	.	.	.	C	35	5.579076	0.96565	.	.	ENSG00000150967	ENST00000280560;ENST00000540285;ENST00000346530;ENST00000392439;ENST00000542678;ENST00000442028;ENST00000546289;ENST00000542448	D;D;D;D;D;D;D;D	0.93763	-3.28;-3.28;-3.28;-3.28;-3.28;-3.28;-3.28;-3.28	5.03	5.03	0.67393	ATPase, AAA+ type, core (1);ABC transporter-like (2);	0.000000	0.85682	D	0.000000	D	0.93314	0.7869	N	0.13140	0.3	0.80722	D	1	D;D;D;P;D	0.76494	0.999;0.999;0.999;0.831;0.995	D;D;D;B;D	0.70935	0.971;0.959;0.969;0.359;0.946	D	0.95035	0.8173	10	0.72032	D	0.01	-20.3398	18.3546	0.90353	0.0:1.0:0.0:0.0	.	530;200;312;550;593	B4E2J0;B4DFR8;B3KNJ8;Q9NP78-2;Q9NP78	.;.;.;.;ABCB9_HUMAN	T	593;530;550;593;593;593;137;219	ENSP00000280560:A593T;ENSP00000441734:A530T;ENSP00000280559:A550T;ENSP00000376234:A593T;ENSP00000440288:A593T;ENSP00000394898:A593T;ENSP00000442281:A137T;ENSP00000440244:A219T	ENSP00000280560:A593T	A	-	1	0	ABCB9	121985898	0.999000	0.42202	0.977000	0.42913	0.979000	0.70002	4.028000	0.57246	2.305000	0.77605	0.563000	0.77884	GCC		0.612	ABCB9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400956.1	NM_019624	
MPHOSPH9	10198	broad.mit.edu	37	12	123687267	123687267	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr12:123687267G>A	ENST00000606320.1	-	10	1891	c.1685C>T	c.(1684-1686)tCg>tTg	p.S562L	MPHOSPH9_ENST00000392425.3_Missense_Mutation_p.S410L|MPHOSPH9_ENST00000541076.2_Missense_Mutation_p.S532L|MPHOSPH9_ENST00000302349.5_Missense_Mutation_p.S410L			Q99550	MPP9_HUMAN	M-phase phosphoprotein 9	562						centriole (GO:0005814)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|plasma membrane (GO:0005886)		p.S410L(1)		NS(1)|breast(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(18)|prostate(2)|skin(1)	33	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000182)|Epithelial(86;0.00046)|BRCA - Breast invasive adenocarcinoma(302;0.169)		GACTGAGGCCGAAGCAACCAT	0.438																																					p.S410L												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1229T	12						.						124.0	113.0	117.0					12																	123687267		2203	4300	6503	122253220	SO:0001583	missense	10198	exon6			X98258	CCDS9243.1, CCDS9243.2	12q24	2008-03-03			ENSG00000051825	ENSG00000051825			7215	protein-coding gene	gene with protein product		605501				8885239	Standard	NM_022782		Approved	MPP9	uc001uel.3	Q99550	OTTHUMG00000168849	ENST00000606320.1:c.1685C>T	12.37:g.123687267G>A	ENSP00000475489:p.Ser562Leu	Somatic		Capture	Illumina HiSeq	Phase_I	122253220	NM_022782	A1L486|A6NEE2|B3KR87|Q9H976|U3KQ28	Missense_Mutation	SNP	ENST00000606320.1	37		.	.	.	.	.	.	.	.	.	.	G	14.86	2.661958	0.47572	.	.	ENSG00000051825	ENST00000302349;ENST00000541076	T;T	0.32515	1.45;1.47	5.37	5.37	0.77165	.	1.279530	0.05202	N	0.505217	T	0.32615	0.0835	L	0.29908	0.895	0.09310	N	1	P	0.35700	0.516	B	0.36719	0.231	T	0.46652	-0.9176	10	0.42905	T	0.14	-0.0117	17.2928	0.87162	0.0:0.0:1.0:0.0	.	410	Q99550	MPP9_HUMAN	L	410	ENSP00000303597:S410L;ENSP00000445859:S410L	ENSP00000303597:S410L	S	-	2	0	MPHOSPH9	122253220	0.110000	0.22057	0.027000	0.17364	0.873000	0.50193	2.780000	0.47742	2.516000	0.84829	0.557000	0.71058	TCG		0.438	MPHOSPH9-030	NOVEL	basic	protein_coding	protein_coding	OTTHUMT00000471390.2		
C12orf65	91574	broad.mit.edu	37	12	123738488	123738488	+	Silent	SNP	A	A	G			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr12:123738488A>G	ENST00000253233.1	+	2	911	c.267A>G	c.(265-267)tcA>tcG	p.S89S	RP11-282O18.3_ENST00000541002.3_RNA|C12orf65_ENST00000366329.2_Silent_p.S89S|C12orf65_ENST00000429587.2_Silent_p.S89S|RP11-282O18.3_ENST00000543217.2_RNA	NM_152269.4	NP_689482.1	Q9H3J6	CL065_HUMAN	chromosome 12 open reading frame 65	89	GGQ domain. {ECO:0000250}.				cell death (GO:0008219)	mitochondrion (GO:0005739)	translation release factor activity (GO:0003747)	p.S89S(1)		endometrium(1)|large_intestine(1)|lung(1)|prostate(1)	4	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000595)|Epithelial(86;0.00199)		ACATCCCCTCAGGCATCGTTG	0.552																																					p.S89S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.A267G	12						.						51.0	57.0	55.0					12																	123738488		2203	4300	6503	122304441	SO:0001819	synonymous_variant	91574	exon2			AK095982	CCDS9244.1	12q24.31	2013-01-07			ENSG00000130921	ENSG00000130921			26784	protein-coding gene	gene with protein product		613541				20598281, 22688947, 23188110	Standard	NM_152269		Approved	FLJ38663, SPG55	uc001uen.3	Q9H3J6	OTTHUMG00000168852	ENST00000253233.1:c.267A>G	12.37:g.123738488A>G		Somatic		Capture	Illumina HiSeq	Phase_I	122304441	NM_001194995	Q8WUC6	Silent	SNP	ENST00000253233.1	37	CCDS9244.1																																																																																				0.552	C12orf65-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401375.1	NM_152269	
SETD8	387893	broad.mit.edu	37	12	123875243	123875243	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr12:123875243C>T	ENST00000402868.3	+	3	625	c.199C>T	c.(199-201)Cgt>Tgt	p.R67C	SETD8_ENST00000478781.2_3'UTR|SETD8_ENST00000330479.4_Missense_Mutation_p.R67C			Q9NQR1	SETD8_HUMAN	SET domain containing (lysine methyltransferase) 8	108	Ala-rich.				histone lysine methylation (GO:0034968)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|peptidyl-lysine monomethylation (GO:0018026)|regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043516)|transcription, DNA-templated (GO:0006351)	chromosome (GO:0005694)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	histone-lysine N-methyltransferase activity (GO:0018024)|p53 binding (GO:0002039)|protein-lysine N-methyltransferase activity (GO:0016279)|transcription corepressor activity (GO:0003714)	p.R67C(1)		central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(4)|prostate(3)|urinary_tract(1)	13	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.00101)|Epithelial(86;0.00425)		CTCTGGAATGCGTTTCCCCCT	0.438																																					p.R67C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C199T	12						.						110.0	105.0	106.0					12																	123875243		2203	4300	6503	122441196	SO:0001583	missense	387893	exon3			AY102937	CCDS9247.1	12q24.31	2011-07-01			ENSG00000183955	ENSG00000183955		"""Chromatin-modifying enzymes / K-methyltransferases"""	29489	protein-coding gene	gene with protein product		607240				15933070, 12086618, 12121615	Standard	NM_020382		Approved	SET8, SET07, PR-Set7, KMT5A	uc001uew.3	Q9NQR1	OTTHUMG00000150477	ENST00000402868.3:c.199C>T	12.37:g.123875243C>T	ENSP00000384629:p.Arg67Cys	Somatic		Capture	Illumina HiSeq	Phase_I	122441196	NM_020382	A8K9D0|Q86W83|Q8TD09	Missense_Mutation	SNP	ENST00000402868.3	37	CCDS9247.1	.	.	.	.	.	.	.	.	.	.	C	16.96	3.266340	0.59540	.	.	ENSG00000183955	ENST00000402868;ENST00000330479;ENST00000437502	D;D	0.98701	-5.08;-5.08	5.03	4.11	0.48088	.	0.204737	0.44483	D	0.000444	D	0.97126	0.9061	L	0.59436	1.845	0.58432	D	0.999991	B;B	0.27450	0.179;0.116	B;B	0.19391	0.019;0.025	D	0.95627	0.8686	10	0.87932	D	0	-3.2458	14.7537	0.69546	0.0:0.8542:0.1457:0.0	.	108;67	Q9NQR1;Q9NQR1-2	SETD8_HUMAN;.	C	67;67;58	ENSP00000384629:R67C;ENSP00000332995:R67C	ENSP00000332995:R67C	R	+	1	0	SETD8	122441196	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	4.700000	0.61803	1.053000	0.40415	0.561000	0.74099	CGT		0.438	SETD8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318263.1	NM_020382	
SETD8	387893	broad.mit.edu	37	12	123889471	123889471	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr12:123889471C>T	ENST00000402868.3	+	7	1124	c.698C>T	c.(697-699)aCc>aTc	p.T233I	SETD8_ENST00000330479.4_Missense_Mutation_p.T233I			Q9NQR1	SETD8_HUMAN	SET domain containing (lysine methyltransferase) 8	274					histone lysine methylation (GO:0034968)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|peptidyl-lysine monomethylation (GO:0018026)|regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043516)|transcription, DNA-templated (GO:0006351)	chromosome (GO:0005694)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	histone-lysine N-methyltransferase activity (GO:0018024)|p53 binding (GO:0002039)|protein-lysine N-methyltransferase activity (GO:0016279)|transcription corepressor activity (GO:0003714)	p.T233I(1)		central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(4)|prostate(3)|urinary_tract(1)	13	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.00101)|Epithelial(86;0.00425)		GTGATTGCCACCAAGCAGTTC	0.547																																					p.T233I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C698T	12						.						118.0	99.0	105.0					12																	123889471		2203	4300	6503	122455424	SO:0001583	missense	387893	exon7			AY102937	CCDS9247.1	12q24.31	2011-07-01			ENSG00000183955	ENSG00000183955		"""Chromatin-modifying enzymes / K-methyltransferases"""	29489	protein-coding gene	gene with protein product		607240				15933070, 12086618, 12121615	Standard	NM_020382		Approved	SET8, SET07, PR-Set7, KMT5A	uc001uew.3	Q9NQR1	OTTHUMG00000150477	ENST00000402868.3:c.698C>T	12.37:g.123889471C>T	ENSP00000384629:p.Thr233Ile	Somatic		Capture	Illumina HiSeq	Phase_I	122455424	NM_020382	A8K9D0|Q86W83|Q8TD09	Missense_Mutation	SNP	ENST00000402868.3	37	CCDS9247.1	.	.	.	.	.	.	.	.	.	.	C	31	5.097833	0.94197	.	.	ENSG00000183955	ENST00000402868;ENST00000330479;ENST00000437502	D;D;D	0.83837	-1.77;-1.77;-1.77	5.16	5.16	0.70880	SET domain (3);	0.254525	0.44688	D	0.000437	D	0.87481	0.6188	M	0.64080	1.96	0.80722	D	1	P;P	0.41345	0.746;0.701	P;B	0.50440	0.641;0.406	D	0.88448	0.3047	10	0.72032	D	0.01	-32.9929	19.0249	0.92929	0.0:1.0:0.0:0.0	.	274;233	Q9NQR1;Q9NQR1-2	SETD8_HUMAN;.	I	233;233;224	ENSP00000384629:T233I;ENSP00000332995:T233I;ENSP00000413811:T224I	ENSP00000332995:T233I	T	+	2	0	SETD8	122455424	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	7.752000	0.85141	2.573000	0.86826	0.655000	0.94253	ACC		0.547	SETD8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318263.1	NM_020382	
DHX37	57647	broad.mit.edu	37	12	125460012	125460012	+	Silent	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr12:125460012G>A	ENST00000308736.2	-	6	1031	c.933C>T	c.(931-933)gcC>gcT	p.A311A	DHX37_ENST00000544745.1_Silent_p.A98A	NM_032656.3	NP_116045.2	Q8IY37	DHX37_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 37	311	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.						ATP binding (GO:0005524)|helicase activity (GO:0004386)|nucleic acid binding (GO:0003676)	p.A311A(1)		breast(5)|cervix(1)|endometrium(9)|kidney(5)|large_intestine(11)|liver(1)|lung(27)|ovary(1)|prostate(2)|skin(3)	65	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;8.05e-05)|Epithelial(86;0.000486)|all cancers(50;0.00653)		ACATGGCCACGGCGGCCACTC	0.642																																					p.A311A												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C933T	12						.						68.0	59.0	62.0					12																	125460012		2202	4290	6492	124025965	SO:0001819	synonymous_variant	57647	exon6			AB040950	CCDS9261.1	12q24.31	2004-03-25	2003-06-13	2003-06-20		ENSG00000150990		"""DEAH-boxes"""	17210	protein-coding gene	gene with protein product			"""DEAD/DEAH box helicase DDX37"""	DDX37		10819331	Standard	NM_032656		Approved	KIAA1517, MGC4322, MGC2695	uc001ugy.3	Q8IY37		ENST00000308736.2:c.933C>T	12.37:g.125460012G>A		Somatic		Capture	Illumina HiSeq	Phase_I	124025965	NM_032656	Q9BUI7|Q9P211	Silent	SNP	ENST00000308736.2	37	CCDS9261.1																																																																																				0.642	DHX37-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_032656	
SLC15A4	121260	broad.mit.edu	37	12	129278781	129278781	+	Missense_Mutation	SNP	C	C	T	rs372794236		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr12:129278781C>T	ENST00000266771.5	-	8	1733	c.1694G>A	c.(1693-1695)cGa>cAa	p.R565Q	SLC15A4_ENST00000544112.1_Missense_Mutation_p.R228Q|SLC15A4_ENST00000545031.1_Missense_Mutation_p.R82Q	NM_145648.3	NP_663623.1	Q8N697	S15A4_HUMAN	solute carrier family 15 (oligopeptide transporter), member 4	565					ion transport (GO:0006811)|oligopeptide transport (GO:0006857)|protein transport (GO:0015031)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)	L-histidine transmembrane transporter activity (GO:0005290)|symporter activity (GO:0015293)	p.R565Q(1)		endometrium(4)|kidney(2)|large_intestine(4)|lung(11)|skin(1)	22	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;1.69e-06)|Epithelial(86;1.17e-05)|all cancers(50;5.07e-05)		GGCTCTTGATCGCTGATGGTC	0.498																																					p.R565Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1694A	12						.						107.0	108.0	107.0					12																	129278781		2203	4300	6503	127844734	SO:0001583	missense	121260	exon8			AY038999	CCDS9264.1	12q24.32	2013-07-18	2013-07-18		ENSG00000139370	ENSG00000139370		"""Solute carriers"""	23090	protein-coding gene	gene with protein product		615806	"""solute carrier family 15, member 4"""			11741232	Standard	NM_145648		Approved	PHT1, PTR4	uc001uhu.2	Q8N697	OTTHUMG00000168415	ENST00000266771.5:c.1694G>A	12.37:g.129278781C>T	ENSP00000266771:p.Arg565Gln	Somatic		Capture	Illumina HiSeq	Phase_I	127844734	NM_145648	A6H8Y9|B3KTK1|Q71M34|Q7Z5F8|Q8TAH0	Missense_Mutation	SNP	ENST00000266771.5	37	CCDS9264.1	.	.	.	.	.	.	.	.	.	.	C	8.351	0.831010	0.16820	.	.	ENSG00000139370	ENST00000266771;ENST00000545031;ENST00000544112	T;T	0.11930	4.01;2.73	5.41	3.59	0.41128	.	2.731020	0.02317	N	0.072647	T	0.11281	0.0275	L	0.27053	0.805	0.25842	N	0.984045	B	0.26400	0.148	B	0.15484	0.013	T	0.35101	-0.9802	10	0.16896	T	0.51	.	8.9158	0.35581	0.0:0.7083:0.0:0.2917	.	565	Q8N697	S15A4_HUMAN	Q	565;82;228	ENSP00000266771:R565Q;ENSP00000439946:R228Q	ENSP00000266771:R565Q	R	-	2	0	SLC15A4	127844734	0.304000	0.24472	0.576000	0.28549	0.026000	0.11368	1.232000	0.32636	0.657000	0.30906	0.655000	0.94253	CGA		0.498	SLC15A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399663.1	NM_145648	
GPRC5A	9052	broad.mit.edu	37	12	13061271	13061271	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr12:13061271G>A	ENST00000014914.5	+	2	978	c.88G>A	c.(88-90)Gtc>Atc	p.V30I	GPRC5A_ENST00000542056.1_Intron	NM_003979.3	NP_003970.1	Q8NFJ5	RAI3_HUMAN	G protein-coupled receptor, class C, group 5, member A	30					signal transduction (GO:0007165)	cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|intracellular membrane-bounded organelle (GO:0043231)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)	p.V30I(3)		breast(2)|endometrium(3)|kidney(1)|large_intestine(4)|lung(6)|ovary(1)|upper_aerodigestive_tract(1)	18		Prostate(47;0.141)		BRCA - Breast invasive adenocarcinoma(232;0.0708)	Tretinoin(DB00755)	TTGGGGCATCGTCCTAGAAAC	0.557																																					p.V30I												.	.	3	Substitution - Missense(3)	large_intestine(2)|endometrium(1)	c.G88A	12						.						85.0	80.0	82.0					12																	13061271		2203	4300	6503	12952538	SO:0001583	missense	9052	exon2			AF095448	CCDS8657.1	12p13-p12.3	2014-01-30	2014-01-30	2005-05-03		ENSG00000013588		"""GPCR / Class C : Orphans"""	9836	protein-coding gene	gene with protein product		604138	"""retinoic acid induced 3"", ""G protein-coupled receptor, family C, group 5, member A"""	RAI3, GPCR5A		9857033	Standard	NM_003979		Approved	RAIG1	uc001rba.3	Q8NFJ5		ENST00000014914.5:c.88G>A	12.37:g.13061271G>A	ENSP00000014914:p.Val30Ile	Somatic		Capture	Illumina HiSeq	Phase_I	12952538	NM_003979	B3KV45|O95357	Missense_Mutation	SNP	ENST00000014914.5	37	CCDS8657.1	.	.	.	.	.	.	.	.	.	.	G	12.76	2.033298	0.35893	.	.	ENSG00000013588	ENST00000014914;ENST00000534831	T;T	0.25749	1.78;1.82	5.36	3.52	0.40303	.	0.254509	0.33217	N	0.005144	T	0.15003	0.0362	N	0.26042	0.785	0.36116	D	0.845142	B;B	0.34255	0.445;0.445	B;B	0.25291	0.03;0.059	T	0.16541	-1.0399	10	0.22706	T	0.39	-1.3382	12.0442	0.53471	0.1419:0.0:0.8581:0.0	.	30;30	Q8NFJ5;A8K556	RAI3_HUMAN;.	I	30	ENSP00000014914:V30I;ENSP00000441627:V30I	ENSP00000014914:V30I	V	+	1	0	GPRC5A	12952538	1.000000	0.71417	0.998000	0.56505	0.157000	0.22087	4.618000	0.61211	0.627000	0.30340	-0.258000	0.10820	GTC		0.557	GPRC5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400682.1		
TMEM132D	121256	broad.mit.edu	37	12	130185052	130185052	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr12:130185052G>A	ENST00000422113.2	-	2	597	c.271C>T	c.(271-273)Cct>Tct	p.P91S	RP11-174M13.2_ENST00000544036.1_lincRNA	NM_133448.2	NP_597705.2	Q14C87	T132D_HUMAN	transmembrane protein 132D	91					negative regulation of phosphatase activity (GO:0010923)	integral component of membrane (GO:0016021)		p.P91S(1)		NS(1)|breast(6)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(33)|liver(1)|lung(69)|ovary(10)|pancreas(2)|prostate(2)|skin(7)|upper_aerodigestive_tract(5)|urinary_tract(2)	152	all_neural(191;0.101)|Medulloblastoma(191;0.163)	all_epithelial(31;0.0934)|Breast(359;0.133)		OV - Ovarian serous cystadenocarcinoma(86;0.000288)|Epithelial(86;0.0116)|all cancers(50;0.0246)		TTGAGGACAGGCAGCCTCCTG	0.512																																					p.P91S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C271T	12						.						67.0	65.0	66.0					12																	130185052		2203	4300	6503	128751005	SO:0001583	missense	121256	exon2			AB061814	CCDS9266.1	12q24.32-q24.33	2014-06-13			ENSG00000151952	ENSG00000151952			29411	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 153"""	611257				11853319, 12966072	Standard	NM_133448		Approved	KIAA1944, MOLT, PPP1R153	uc009zyl.1	Q14C87	OTTHUMG00000168400	ENST00000422113.2:c.271C>T	12.37:g.130185052G>A	ENSP00000408581:p.Pro91Ser	Somatic		Capture	Illumina HiSeq	Phase_I	128751005	NM_133448	Q14C96|Q76M59|Q8N1W9|Q8N3Q5|Q8TF57	Missense_Mutation	SNP	ENST00000422113.2	37	CCDS9266.1	.	.	.	.	.	.	.	.	.	.	G	21.1	4.105439	0.77096	.	.	ENSG00000151952	ENST00000422113	T	0.13901	2.55	5.33	5.33	0.75918	.	0.000000	0.64402	D	0.000014	T	0.46619	0.1402	M	0.88105	2.93	0.54753	D	0.999986	D	0.89917	1.0	D	0.97110	1.0	T	0.53606	-0.8415	9	.	.	.	-31.6898	19.0288	0.92946	0.0:0.0:1.0:0.0	.	91	Q14C87	T132D_HUMAN	S	91	ENSP00000408581:P91S	.	P	-	1	0	TMEM132D	128751005	1.000000	0.71417	0.086000	0.20670	0.622000	0.37654	9.623000	0.98386	2.472000	0.83506	0.555000	0.69702	CCT		0.512	TMEM132D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399592.1	NM_133448	
STX2	2054	broad.mit.edu	37	12	131291562	131291562	+	Missense_Mutation	SNP	C	C	T	rs201987693		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr12:131291562C>T	ENST00000392373.2	-	6	522	c.428G>A	c.(427-429)cGg>cAg	p.R143Q	STX2_ENST00000261653.6_Missense_Mutation_p.R143Q	NM_194356.2	NP_919337.1	P32856	STX2_HUMAN	syntaxin 2	143					acrosome reaction (GO:0007340)|cell differentiation (GO:0030154)|ectoderm development (GO:0007398)|intracellular protein transport (GO:0006886)|organ morphogenesis (GO:0009887)|regulation of blood coagulation (GO:0030193)|regulation of gene expression (GO:0010468)|signal transduction (GO:0007165)	basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|cell-cell junction (GO:0005911)|cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|membrane raft (GO:0045121)	calcium-dependent protein binding (GO:0048306)	p.R143Q(1)		breast(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(7)|prostate(1)	16	all_neural(191;0.0982)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;2.79e-06)|all cancers(50;5.27e-05)|Epithelial(86;5.29e-05)		GCCTTTGCTCCGCTCCCGAAA	0.478																																					p.R143Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G428A	12						.						119.0	104.0	109.0					12																	131291562		2203	4300	6503	129857515	SO:0001583	missense	2054	exon6			D14582	CCDS9269.1, CCDS9270.1	12q24	2008-02-05	2006-04-25	2006-04-25	ENSG00000111450	ENSG00000111450			3403	protein-coding gene	gene with protein product		132350	"""epimorphin"""	STX2B, STX2C, STX2A, EPIM		8938452, 15943887	Standard	NM_001980		Approved	EPM	uc001uio.4	P32856	OTTHUMG00000168365	ENST00000392373.2:c.428G>A	12.37:g.131291562C>T	ENSP00000376178:p.Arg143Gln	Somatic		Capture	Illumina HiSeq	Phase_I	129857515	NM_194356	Q86VW8	Missense_Mutation	SNP	ENST00000392373.2	37	CCDS9270.1	.	.	.	.	.	.	.	.	.	.	C	18.53	3.644089	0.67244	.	.	ENSG00000111450	ENST00000261653;ENST00000392373	T;T	0.23552	1.9;1.9	4.45	3.55	0.40652	t-SNARE (1);Syntaxin, N-terminal (1);	0.056687	0.64402	D	0.000001	T	0.48429	0.1499	M	0.88640	2.97	0.58432	D	0.999991	D;D;D	0.76494	0.999;0.999;0.999	P;P;P	0.56042	0.747;0.747;0.79	T	0.57418	-0.7815	10	0.72032	D	0.01	-26.5011	11.46	0.50204	0.0:0.9117:0.0:0.0883	.	143;143;143	P32856-3;P32856-2;P32856	.;.;STX2_HUMAN	Q	143	ENSP00000261653:R143Q;ENSP00000376178:R143Q	ENSP00000261653:R143Q	R	-	2	0	STX2	129857515	1.000000	0.71417	0.910000	0.35882	0.013000	0.08279	5.265000	0.65519	0.846000	0.35142	-0.258000	0.10820	CGG		0.478	STX2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000399455.2	NM_194356	
SFSWAP	6433	broad.mit.edu	37	12	132204075	132204075	+	Silent	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr12:132204075C>T	ENST00000261674.4	+	4	738	c.597C>T	c.(595-597)gaC>gaT	p.D199D	SFSWAP_ENST00000541286.1_Silent_p.D199D	NM_004592.3	NP_004583.2	Q12872	SFSWA_HUMAN	splicing factor, suppressor of white-apricot family	199					mRNA processing (GO:0006397)|mRNA splice site selection (GO:0006376)|negative regulation of mRNA splicing, via spliceosome (GO:0048025)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	RNA binding (GO:0003723)	p.D199D(1)		endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(9)|lung(8)|ovary(1)|skin(2)	25						TCCCGTCTGACGTGGAGTTGG	0.393																																					p.D199D												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C597T	12						.						132.0	122.0	126.0					12																	132204075		2203	4300	6503	130770028	SO:0001819	synonymous_variant	6433	exon4			U08377	CCDS9273.1, CCDS58290.1	12q24.33	2014-04-14	2014-04-14	2010-09-15	ENSG00000061936	ENSG00000061936			10790	protein-coding gene	gene with protein product		601945	"""splicing factor, arginine/serine-rich 8 (suppressor-of-white-apricot, Drosophila homolog)"", ""splicing factor, arginine/serine-rich 8 (suppressor-of-white-apricot homolog, Drosophila)"", ""splicing factor, suppressor of white-apricot homolog (Drosophila)"""	SFRS8		8940107	Standard	NM_004592		Approved	SWAP	uc010tbn.2	Q12872	OTTHUMG00000168319	ENST00000261674.4:c.597C>T	12.37:g.132204075C>T		Somatic		Capture	Illumina HiSeq	Phase_I	130770028	NM_004592	B2RN45|B7ZM97|F5H6B8|Q6PJF7	De_novo_Start_OutOfFrame	SNP	ENST00000261674.4	37	CCDS9273.1																																																																																				0.393	SFSWAP-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000399276.1	NM_004592	
MMP17	4326	broad.mit.edu	37	12	132325199	132325199	+	Silent	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr12:132325199C>T	ENST00000360564.1	+	4	606	c.504C>T	c.(502-504)agC>agT	p.S168S	MMP17_ENST00000535291.1_Silent_p.S84S	NM_016155.4	NP_057239.4	Q9ULZ9	MMP17_HUMAN	matrix metallopeptidase 17 (membrane-inserted)	168					positive regulation of catalytic activity (GO:0043085)	anchored component of membrane (GO:0031225)|integral component of plasma membrane (GO:0005887)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|enzyme activator activity (GO:0008047)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)	p.S168S(1)		endometrium(1)|large_intestine(3)|lung(1)	5	all_neural(191;0.0982)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;1.82e-07)|Epithelial(86;1.51e-06)|all cancers(50;2.35e-05)	Marimastat(DB00786)	AGGTCTGGAGCGACATTGCGC	0.652																																					p.S168S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C504T	12						.						107.0	93.0	98.0					12																	132325199		2203	4300	6503	130891152	SO:0001819	synonymous_variant	4326	exon4			X89576	CCDS31927.1	12q24.3	2005-08-08	2005-08-08		ENSG00000198598	ENSG00000198598			7163	protein-coding gene	gene with protein product		602285	"""matrix metalloproteinase 17 (membrane-inserted)"""			9878265	Standard	NM_016155		Approved	MT4-MMP	uc001ujc.1	Q9ULZ9	OTTHUMG00000168050	ENST00000360564.1:c.504C>T	12.37:g.132325199C>T		Somatic		Capture	Illumina HiSeq	Phase_I	130891152	NM_016155	Q14850	Silent	SNP	ENST00000360564.1	37	CCDS31927.1																																																																																				0.652	MMP17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397757.1	NM_016155	
SLC6A13	6540	broad.mit.edu	37	12	331746	331746	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr12:331746C>A	ENST00000343164.4	-	13	1519	c.1467G>T	c.(1465-1467)tgG>tgT	p.W489C	SLC6A13_ENST00000445055.2_Missense_Mutation_p.W397C|SLC6A13_ENST00000539668.1_5'UTR	NM_016615.4	NP_057699.2	Q9NSD5	S6A13_HUMAN	solute carrier family 6 (neurotransmitter transporter), member 13	489					neurotransmitter secretion (GO:0007269)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	gamma-aminobutyric acid:sodium symporter activity (GO:0005332)|neurotransmitter:sodium symporter activity (GO:0005328)	p.W489C(1)		NS(1)|autonomic_ganglia(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(7)|lung(11)|prostate(1)|urinary_tract(1)	28	all_cancers(10;0.0416)|all_epithelial(11;0.0537)|all_lung(10;0.0989)|Lung NSC(10;0.139)|Ovarian(42;0.142)		OV - Ovarian serous cystadenocarcinoma(31;0.00153)|BRCA - Breast invasive adenocarcinoma(9;0.239)			TGATAAGAGGCCATGGCCTGT	0.483																																					p.W397C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1191T	12						.						93.0	80.0	84.0					12																	331746		2203	4300	6503	202007	SO:0001583	missense	6540	exon11			U76343	CCDS8502.1, CCDS53729.1, CCDS58198.1	12p13.33	2013-07-19	2013-07-19		ENSG00000010379	ENSG00000010379		"""Solute carriers"""	11046	protein-coding gene	gene with protein product	"""GABA transporter 2"""	615097	"""solute carrier family 6 (neurotransmitter transporter, GABA), member 13"""				Standard	NM_001243392		Approved	GAT2	uc001qic.2	Q9NSD5	OTTHUMG00000168053	ENST00000343164.4:c.1467G>T	12.37:g.331746C>A	ENSP00000339260:p.Trp489Cys	Somatic		Capture	Illumina HiSeq	Phase_I	202007	NM_001190997	B4DJL1|Q8TCC2|Q8WW56	Missense_Mutation	SNP	ENST00000343164.4	37	CCDS8502.1	.	.	.	.	.	.	.	.	.	.	C	5.669	0.308069	0.10733	.	.	ENSG00000010379	ENST00000445055;ENST00000313154;ENST00000343164	T;T	0.74526	-0.85;-0.85	5.39	4.49	0.54785	.	0.250109	0.46145	D	0.000307	T	0.64472	0.2601	L	0.35644	1.08	0.58432	D	0.999993	B;B;B	0.18968	0.013;0.032;0.032	B;B;B	0.29267	0.049;0.1;0.07	T	0.58340	-0.7653	10	0.30854	T	0.27	.	8.9941	0.36041	0.1488:0.7774:0.0:0.0737	.	397;468;489	B4DJL1;B4DJS3;Q9NSD5	.;.;S6A13_HUMAN	C	397;468;489	ENSP00000407104:W397C;ENSP00000339260:W489C	ENSP00000318097:W468C	W	-	3	0	SLC6A13	202007	0.998000	0.40836	1.000000	0.80357	0.815000	0.46073	1.014000	0.29950	1.258000	0.44101	0.561000	0.74099	TGG		0.483	SLC6A13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397801.1	NM_016615	
WNK1	65125	broad.mit.edu	37	12	968524	968524	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr12:968524G>A	ENST00000315939.6	+	6	2157	c.1514G>A	c.(1513-1515)cGt>cAt	p.R505H	WNK1_ENST00000340908.4_Missense_Mutation_p.R98H|WNK1_ENST00000537687.1_Missense_Mutation_p.R505H|WNK1_ENST00000530271.2_Missense_Mutation_p.R505H|WNK1_ENST00000540360.1_3'UTR|WNK1_ENST00000535572.1_Missense_Mutation_p.R505H	NM_018979.3	NP_061852.3	Q9H4A3	WNK1_HUMAN	WNK lysine deficient protein kinase 1	505					intracellular signal transduction (GO:0035556)|ion transport (GO:0006811)|negative regulation of pancreatic juice secretion (GO:0090188)|negative regulation of phosphatase activity (GO:0010923)|neuron development (GO:0048666)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of systemic arterial blood pressure (GO:0003084)|protein phosphorylation (GO:0006468)|regulation of cellular process (GO:0050794)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|chloride channel inhibitor activity (GO:0019869)|phosphatase binding (GO:0019902)|protein kinase inhibitor activity (GO:0004860)|protein serine/threonine kinase activity (GO:0004674)	p.R505H(1)		breast(7)|central_nervous_system(1)|endometrium(3)|kidney(6)|large_intestine(15)|lung(43)|ovary(6)|prostate(3)|skin(7)|stomach(8)|upper_aerodigestive_tract(3)|urinary_tract(2)	104	all_cancers(10;0.00611)|all_epithelial(11;0.00825)|all_lung(10;0.0331)|Ovarian(42;0.0512)|Lung NSC(10;0.0632)		Epithelial(1;1.74e-08)|all cancers(1;7.04e-08)|OV - Ovarian serous cystadenocarcinoma(31;0.000423)|BRCA - Breast invasive adenocarcinoma(9;0.0149)|Colorectal(1;0.0197)			TTATGGCTACGTATTGAAGAT	0.348																																					p.R505H	Colon(19;451 567 6672 12618 28860)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1514A	12						.						66.0	75.0	72.0					12																	968524		2202	4298	6500	838785	SO:0001583	missense	65125	exon6			AJ296290	CCDS8506.1, CCDS53731.1, CCDS73419.1	12p13.3	2014-09-17	2005-01-19	2005-01-21	ENSG00000060237	ENSG00000060237			14540	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 167"""	605232	"""protein kinase, lysine deficient 1"", ""hereditary sensory neuropathy, type II"""	PRKWNK1, HSN2			Standard	NM_001184985		Approved	HSAN2, PPP1R167	uc031qfk.1	Q9H4A3	OTTHUMG00000090321	ENST00000315939.6:c.1514G>A	12.37:g.968524G>A	ENSP00000313059:p.Arg505His	Somatic		Capture	Illumina HiSeq	Phase_I	838785	NM_001184985	A1L4B0|C5HTZ5|C5HTZ6|C5HTZ7|H6WZW3|O15052|P54963|Q4VBX9|Q6IFS5|Q86WL5|Q8N673|Q96CZ6|Q9P1S9	Missense_Mutation	SNP	ENST00000315939.6	37	CCDS8506.1	.	.	.	.	.	.	.	.	.	.	G	29.4	5.003464	0.93287	.	.	ENSG00000060237	ENST00000535572;ENST00000315939;ENST00000537687;ENST00000530271;ENST00000340908	T;T;T;T;T	0.62941	-0.01;-0.01;-0.01;-0.01;-0.01	5.7	5.7	0.88788	Serine/threonine-protein kinase OSR1/WNK, CCT domain (1);	0.000000	0.64402	D	0.000006	T	0.77274	0.4106	L	0.59436	1.845	0.48632	D	0.99968	D;D	0.89917	1.0;1.0	D;D	0.91635	0.998;0.999	T	0.73630	-0.3922	10	0.35671	T	0.21	-11.035	19.82	0.96590	0.0:0.0:1.0:0.0	.	505;505	F5GWT4;Q9H4A3	.;WNK1_HUMAN	H	505;505;505;505;98	ENSP00000441972:R505H;ENSP00000313059:R505H;ENSP00000444465:R505H;ENSP00000433548:R505H;ENSP00000341292:R98H	ENSP00000313059:R505H	R	+	2	0	WNK1	838785	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.809000	0.99208	2.660000	0.90430	0.591000	0.81541	CGT		0.348	WNK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206683.1	NM_018979	
WNK1	65125	broad.mit.edu	37	12	970362	970362	+	Nonsense_Mutation	SNP	G	G	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr12:970362G>T	ENST00000315939.6	+	7	2447	c.1804G>T	c.(1804-1806)Gga>Tga	p.G602*	WNK1_ENST00000340908.4_Nonsense_Mutation_p.G195*|WNK1_ENST00000537687.1_Nonsense_Mutation_p.G602*|WNK1_ENST00000530271.2_Nonsense_Mutation_p.G602*|WNK1_ENST00000535572.1_Nonsense_Mutation_p.G602*	NM_018979.3	NP_061852.3	Q9H4A3	WNK1_HUMAN	WNK lysine deficient protein kinase 1	602					intracellular signal transduction (GO:0035556)|ion transport (GO:0006811)|negative regulation of pancreatic juice secretion (GO:0090188)|negative regulation of phosphatase activity (GO:0010923)|neuron development (GO:0048666)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of systemic arterial blood pressure (GO:0003084)|protein phosphorylation (GO:0006468)|regulation of cellular process (GO:0050794)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|chloride channel inhibitor activity (GO:0019869)|phosphatase binding (GO:0019902)|protein kinase inhibitor activity (GO:0004860)|protein serine/threonine kinase activity (GO:0004674)	p.G602*(1)		breast(7)|central_nervous_system(1)|endometrium(3)|kidney(6)|large_intestine(15)|lung(43)|ovary(6)|prostate(3)|skin(7)|stomach(8)|upper_aerodigestive_tract(3)|urinary_tract(2)	104	all_cancers(10;0.00611)|all_epithelial(11;0.00825)|all_lung(10;0.0331)|Ovarian(42;0.0512)|Lung NSC(10;0.0632)		Epithelial(1;1.74e-08)|all cancers(1;7.04e-08)|OV - Ovarian serous cystadenocarcinoma(31;0.000423)|BRCA - Breast invasive adenocarcinoma(9;0.0149)|Colorectal(1;0.0197)			TTCCCAGACAGGAATCAAGCA	0.498																																					p.G602X	Colon(19;451 567 6672 12618 28860)											.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.G1804T	12						.						118.0	101.0	107.0					12																	970362		2203	4300	6503	840623	SO:0001587	stop_gained	65125	exon7			AJ296290	CCDS8506.1, CCDS53731.1, CCDS73419.1	12p13.3	2014-09-17	2005-01-19	2005-01-21	ENSG00000060237	ENSG00000060237			14540	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 167"""	605232	"""protein kinase, lysine deficient 1"", ""hereditary sensory neuropathy, type II"""	PRKWNK1, HSN2			Standard	NM_001184985		Approved	HSAN2, PPP1R167	uc031qfk.1	Q9H4A3	OTTHUMG00000090321	ENST00000315939.6:c.1804G>T	12.37:g.970362G>T	ENSP00000313059:p.Gly602*	Somatic		Capture	Illumina HiSeq	Phase_I	840623	NM_001184985	A1L4B0|C5HTZ5|C5HTZ6|C5HTZ7|H6WZW3|O15052|P54963|Q4VBX9|Q6IFS5|Q86WL5|Q8N673|Q96CZ6|Q9P1S9	Nonsense_Mutation	SNP	ENST00000315939.6	37	CCDS8506.1	.	.	.	.	.	.	.	.	.	.	G	44	10.540476	0.99424	.	.	ENSG00000060237	ENST00000535572;ENST00000315939;ENST00000537687;ENST00000252477;ENST00000530271;ENST00000340908	.	.	.	5.73	4.84	0.62591	.	0.000000	0.64402	D	0.000004	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.56958	D	0.05	-11.6184	12.8983	0.58111	0.075:0.0:0.925:0.0	.	.	.	.	X	602;602;602;49;602;195	.	ENSP00000252477:G49X	G	+	1	0	WNK1	840623	1.000000	0.71417	0.870000	0.34147	0.842000	0.47809	6.778000	0.75043	1.431000	0.47355	0.591000	0.81541	GGA		0.498	WNK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206683.1	NM_018979	
FBXL14	144699	broad.mit.edu	37	12	1702472	1702472	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr12:1702472C>T	ENST00000339235.3	-	1	859	c.761G>A	c.(760-762)aGc>aAc	p.S254N	FBXL14_ENST00000543278.1_5'Flank|WNT5B_ENST00000537031.1_Intron	NM_152441.2	NP_689654.1	Q8N1E6	FXL14_HUMAN	F-box and leucine-rich repeat protein 14	254					protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)	ubiquitin-protein transferase activity (GO:0004842)	p.S254N(1)		endometrium(1)|kidney(1)|large_intestine(2)|lung(2)|ovary(1)|prostate(1)	8	Ovarian(42;0.107)		OV - Ovarian serous cystadenocarcinoma(31;0.00115)			GCTGCGCAGGCTGCCCATGTG	0.637																																					p.S254N												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G761A	12						.						51.0	49.0	50.0					12																	1702472		2203	4300	6503	1572733	SO:0001583	missense	144699	exon1			BC028132	CCDS8509.1	12p13.33	2011-06-09			ENSG00000171823	ENSG00000171823		"""F-boxes / Leucine-rich repeats"""	28624	protein-coding gene	gene with protein product		609081				12477932	Standard	NM_152441		Approved	MGC40195, Fbl14	uc001qjh.3	Q8N1E6	OTTHUMG00000090369	ENST00000339235.3:c.761G>A	12.37:g.1702472C>T	ENSP00000344855:p.Ser254Asn	Somatic		Capture	Illumina HiSeq	Phase_I	1572733	NM_152441		Missense_Mutation	SNP	ENST00000339235.3	37	CCDS8509.1	.	.	.	.	.	.	.	.	.	.	C	13.18	2.160423	0.38119	.	.	ENSG00000171823	ENST00000339235	T	0.02032	4.49	4.51	4.51	0.55191	.	0.237434	0.44902	D	0.000419	T	0.02727	0.0082	N	0.25957	0.775	0.40830	D	0.983583	B	0.27910	0.193	B	0.31390	0.129	T	0.61227	-0.7105	10	0.24483	T	0.36	.	17.4034	0.87467	0.0:1.0:0.0:0.0	.	254	Q8N1E6	FXL14_HUMAN	N	254	ENSP00000344855:S254N	ENSP00000344855:S254N	S	-	2	0	FBXL14	1572733	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.861000	0.62969	2.296000	0.77279	0.650000	0.86243	AGC		0.637	FBXL14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206741.1	NM_152441	
AKAP3	10566	broad.mit.edu	37	12	4736173	4736173	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr12:4736173G>A	ENST00000545990.2	-	5	2419	c.1895C>T	c.(1894-1896)cCg>cTg	p.P632L	AKAP3_ENST00000228850.1_Missense_Mutation_p.P632L|RP11-500M8.7_ENST00000536588.1_Intron	NM_001278309.1	NP_001265238.1	O75969	AKAP3_HUMAN	A kinase (PRKA) anchor protein 3	632					acrosome reaction (GO:0007340)|cellular component movement (GO:0006928)|protein localization (GO:0008104)|single fertilization (GO:0007338)|transmembrane receptor protein serine/threonine kinase signaling pathway (GO:0007178)	acrosomal vesicle (GO:0001669)|nucleus (GO:0005634)|sperm fibrous sheath (GO:0035686)|sperm principal piece (GO:0097228)	protein kinase A binding (GO:0051018)	p.P632L(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(13)|liver(1)|lung(17)|ovary(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)	51						AGACGCCAACGGTCTTTCACA	0.532																																					p.P632L												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1895T	12						.						56.0	53.0	54.0					12																	4736173		2203	4300	6503	4606434	SO:0001583	missense	10566	exon4			U85715	CCDS8531.1	12p13.3	2009-03-12				ENSG00000111254		"""A-kinase anchor proteins"""	373	protein-coding gene	gene with protein product	"""Fibrous Sheath Protein of 95 kDa"", ""cancer/testis antigen 82"""	604689				10334916, 10319321	Standard	NM_001278309		Approved	FSP95, SOB1, AKAP110, CT82	uc001qnb.4	O75969		ENST00000545990.2:c.1895C>T	12.37:g.4736173G>A	ENSP00000440994:p.Pro632Leu	Somatic		Capture	Illumina HiSeq	Phase_I	4606434	NM_006422	O75945|Q86X01|Q9UM61	Missense_Mutation	SNP	ENST00000545990.2	37	CCDS8531.1	.	.	.	.	.	.	.	.	.	.	G	10.68	1.417959	0.25552	.	.	ENSG00000111254	ENST00000228850;ENST00000545990	T;T	0.07327	3.2;3.2	5.69	5.69	0.88448	A-kinase anchor 110kDa, C-terminal (1);	0.218239	0.32640	N	0.005832	T	0.21674	0.0522	M	0.69823	2.125	0.21020	N	0.999807	D	0.58620	0.983	P	0.52627	0.704	T	0.03175	-1.1064	10	0.87932	D	0	-8.3611	16.7184	0.85404	0.0:0.0:1.0:0.0	.	632	O75969	AKAP3_HUMAN	L	632	ENSP00000228850:P632L;ENSP00000440994:P632L	ENSP00000228850:P632L	P	-	2	0	AKAP3	4606434	0.996000	0.38824	0.864000	0.33941	0.005000	0.04900	3.159000	0.50731	2.677000	0.91161	0.655000	0.94253	CCG		0.532	AKAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398911.2	NM_006422	
CD9	928	broad.mit.edu	37	12	6346971	6346971	+	Missense_Mutation	SNP	C	C	T	rs146304211		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr12:6346971C>T	ENST00000382518.1	+	9	1100	c.664C>T	c.(664-666)Cgc>Tgc	p.R222C	CD9_ENST00000481267.1_3'UTR|CD9_ENST00000382515.2_Missense_Mutation_p.R153C|CD9_ENST00000009180.4_Missense_Mutation_p.R222C			P21926	CD9_HUMAN	CD9 molecule	222					blood coagulation (GO:0007596)|brain development (GO:0007420)|cell adhesion (GO:0007155)|cellular component movement (GO:0006928)|fusion of sperm to egg plasma membrane (GO:0007342)|multicellular organism reproduction (GO:0032504)|negative regulation of cell proliferation (GO:0008285)|oligodendrocyte development (GO:0014003)|paranodal junction assembly (GO:0030913)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|response to water deprivation (GO:0009414)|single fertilization (GO:0007338)	apical plasma membrane (GO:0016324)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|platelet alpha granule membrane (GO:0031092)|vesicle (GO:0031982)		p.R222C(1)		endometrium(2)|large_intestine(1)|lung(1)|ovary(1)|prostate(1)|skin(1)|stomach(1)	8						CTGTGCTATCCGCAGGAACCG	0.438											OREG0031245	type=REGULATORY REGION|TFbs=ESR1|Dataset=Estrogen Receptor Alpha Binding Sites|EvidenceSubtype=Chromatin immunoprecipitation with tag sequencing (ChIP-TS)																									p.R222C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C664T	12						.	C	CYS/ARG	1,4405	2.1+/-5.4	0,1,2202	136.0	114.0	121.0		664	5.3	1.0	12	dbSNP_134	121	0,8600		0,0,4300	no	missense	CD9	NM_001769.3	180	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	probably-damaging	222/229	6346971	1,13005	2203	4300	6503	6217232	SO:0001583	missense	928	exon8			M38690	CCDS8540.1	12p13	2013-02-14	2006-03-28		ENSG00000010278	ENSG00000010278		"""CD molecules"", ""Tetraspanins"""	1709	protein-coding gene	gene with protein product	"""motility related protein-1"""	143030	"""CD9 antigen (p24)"""	MIC3		6198179	Standard	NM_001769		Approved	BA2, P24, TSPAN29, MRP-1	uc001qnq.2	P21926	OTTHUMG00000044400	ENST00000382518.1:c.664C>T	12.37:g.6346971C>T	ENSP00000371958:p.Arg222Cys	Somatic	633	Capture	Illumina HiSeq	Phase_I	6217232	NM_001769	D3DUQ9|Q5J7W6|Q96ES4	Missense_Mutation	SNP	ENST00000382518.1	37	CCDS8540.1	.	.	.	.	.	.	.	.	.	.	C	20.9	4.073650	0.76415	2.27E-4	0.0	ENSG00000010278	ENST00000382518;ENST00000543424;ENST00000009180;ENST00000382515	T;T;T	0.25579	2.02;2.02;1.79	6.17	5.28	0.74379	.	0.000000	0.85682	D	0.000000	T	0.63803	0.2542	H	0.95745	3.715	0.80722	D	1	D	0.89917	1.0	D	0.79784	0.993	T	0.76610	-0.2896	10	0.87932	D	0	.	15.4089	0.74902	0.0:0.8604:0.1396:0.0	.	222	P21926	CD9_HUMAN	C	222;135;222;153	ENSP00000371958:R222C;ENSP00000009180:R222C;ENSP00000371955:R153C	ENSP00000009180:R222C	R	+	1	0	CD9	6217232	1.000000	0.71417	1.000000	0.80357	0.868000	0.49771	3.271000	0.51608	1.608000	0.50180	-0.176000	0.13171	CGC		0.438	CD9-004	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000103348.1		
C1RL	51279	broad.mit.edu	37	12	7249644	7249644	+	Silent	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr12:7249644G>A	ENST00000266542.4	-	6	899	c.807C>T	c.(805-807)ggC>ggT	p.G269G	C1RL_ENST00000545280.1_Intron|C1RL_ENST00000504702.2_Intron|C1RL_ENST00000544702.1_Missense_Mutation_p.A285V	NM_016546.2	NP_057630.2	Q9NZP8	C1RL_HUMAN	complement component 1, r subcomponent-like	269	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				complement activation, classical pathway (GO:0006958)|innate immune response (GO:0045087)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	serine-type endopeptidase activity (GO:0004252)	p.G269G(1)		breast(1)|central_nervous_system(1)|endometrium(4)|large_intestine(4)|lung(2)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	16						GCAGGGCCCCGCCCCCACGGC	0.592																																					p.G269G												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C807T	12						.						50.0	50.0	50.0					12																	7249644		2203	4300	6503	7140786	SO:0001819	synonymous_variant	51279	exon6			AF178985	CCDS8573.1, CCDS73431.1	12p13.31	2008-02-05				ENSG00000139178			21265	protein-coding gene	gene with protein product		608974				12838346	Standard	XM_005253385		Approved	C1r-LP, C1RL1	uc001qsn.3	Q9NZP8		ENST00000266542.4:c.807C>T	12.37:g.7249644G>A		Somatic		Capture	Illumina HiSeq	Phase_I	7140786	NM_016546	Q53GX9	Missense_Mutation	SNP	ENST00000266542.4	37	CCDS8573.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	11.67|11.67	1.707417|1.707417	0.30322|0.30322	.|.	.|.	ENSG00000139178|ENSG00000139178	ENST00000544702|ENST00000534950	T|.	0.34667|.	1.35|.	4.74|4.74	-2.49|-2.49	0.06403|0.06403	.|.	.|.	.|.	.|.	.|.	T|T	0.38825|0.38825	0.1055|0.1055	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	B|.	0.22983|.	0.078|.	B|.	0.23852|.	0.049|.	T|T	0.32903|0.32903	-0.9889|-0.9889	8|4	0.40728|.	T|.	0.16|.	.|.	1.2309|1.2309	0.01943|0.01943	0.426:0.1118:0.2566:0.2056|0.426:0.1118:0.2566:0.2056	.|.	285|.	F5GWF3|.	.|.	V|W	285|102	ENSP00000441885:A285V|.	ENSP00000441885:A285V|.	A|R	-|-	2|1	0|2	C1RL|C1RL	7140786|7140786	0.000000|0.000000	0.05858|0.05858	0.919000|0.919000	0.36401|0.36401	0.890000|0.890000	0.51754|0.51754	-1.960000|-1.960000	0.01517|0.01517	-0.252000|-0.252000	0.09528|0.09528	-0.362000|-0.362000	0.07510|0.07510	GCG|CGG		0.592	C1RL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398367.1	NM_016546	
CLSTN3	9746	broad.mit.edu	37	12	7295807	7295807	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr12:7295807G>A	ENST00000266546.6	+	12	2197	c.1747G>A	c.(1747-1749)Gtg>Atg	p.V583M	CLSTN3_ENST00000537408.1_Missense_Mutation_p.V595M	NM_014718.3	NP_055533.2	Q9BQT9	CSTN3_HUMAN	calsyntenin 3	583					homophilic cell adhesion (GO:0007156)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|postsynaptic membrane (GO:0045211)	calcium ion binding (GO:0005509)	p.V583M(1)		NS(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(12)|lung(7)|prostate(1)|skin(1)	33						GGGGGATGATGTGGAGACCTT	0.627																																					p.V583M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1747A	12						.						126.0	115.0	119.0					12																	7295807		2203	4300	6503	7187074	SO:0001583	missense	9746	exon12			AB018269	CCDS8575.1	12p13.31	2011-07-01			ENSG00000139182	ENSG00000139182		"""Cadherins / Cadherin-related"""	18371	protein-coding gene	gene with protein product	"""cadherin-related family member 14"""	611324				12498782	Standard	NM_014718		Approved	CSTN3, KIAA0726, CDHR14	uc001qsr.3	Q9BQT9	OTTHUMG00000168167	ENST00000266546.6:c.1747G>A	12.37:g.7295807G>A	ENSP00000266546:p.Val583Met	Somatic		Capture	Illumina HiSeq	Phase_I	7187074	NM_014718	D3DUT6|O94831|Q2T9J5|Q5UE57	Missense_Mutation	SNP	ENST00000266546.6	37	CCDS8575.1	.	.	.	.	.	.	.	.	.	.	G	21.1	4.094560	0.76870	.	.	ENSG00000139182	ENST00000266546;ENST00000537408	T;T	0.34072	1.38;1.38	5.21	4.32	0.51571	.	0.124913	0.53938	D	0.000043	T	0.44953	0.1318	L	0.43152	1.355	0.38338	D	0.943981	P;D	0.54047	0.937;0.964	P;P	0.54460	0.605;0.753	T	0.49615	-0.8921	10	0.49607	T	0.09	-22.1187	15.1461	0.72653	0.0:0.0:0.8575:0.1425	.	595;583	Q5UE57;Q9BQT9	.;CSTN3_HUMAN	M	583;595	ENSP00000266546:V583M;ENSP00000440679:V595M	ENSP00000266546:V583M	V	+	1	0	CLSTN3	7187074	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	6.919000	0.75793	1.175000	0.42826	0.462000	0.41574	GTG		0.627	CLSTN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398560.2	NM_014718	
PEX5	5830	broad.mit.edu	37	12	7351701	7351701	+	Silent	SNP	C	C	T	rs138205085		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr12:7351701C>T	ENST00000455147.2	+	7	1123	c.543C>T	c.(541-543)acC>acT	p.T181T	PEX5_ENST00000266564.3_Silent_p.T181T|PEX5_ENST00000412720.2_Silent_p.T202T|PEX5_ENST00000434354.2_Silent_p.T196T|PEX5_ENST00000420616.2_Silent_p.T181T|PEX5_ENST00000266563.5_Silent_p.T181T|PEX5_ENST00000545220.1_Intron	NM_001131026.1	NP_001124498.1	P50542	PEX5_HUMAN	peroxisomal biogenesis factor 5	181					cell development (GO:0048468)|cerebral cortex cell migration (GO:0021795)|cerebral cortex neuron differentiation (GO:0021895)|endoplasmic reticulum organization (GO:0007029)|fatty acid beta-oxidation (GO:0006635)|mitochondrial membrane organization (GO:0007006)|negative regulation of protein homotetramerization (GO:1901094)|neuromuscular process (GO:0050905)|neuron migration (GO:0001764)|positive regulation of multicellular organism growth (GO:0040018)|protein import into peroxisome matrix (GO:0016558)|protein import into peroxisome matrix, docking (GO:0016560)|protein import into peroxisome matrix, translocation (GO:0016561)|protein import into peroxisome membrane (GO:0045046)|protein targeting to peroxisome (GO:0006625)|protein tetramerization (GO:0051262)|very long-chain fatty acid metabolic process (GO:0000038)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|intracellular (GO:0005622)|membrane (GO:0016020)|mitochondrion (GO:0005739)|peroxisomal matrix (GO:0005782)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)|protein complex (GO:0043234)	enzyme binding (GO:0019899)|peroxisome matrix targeting signal-1 binding (GO:0005052)|peroxisome targeting sequence binding (GO:0000268)|protein C-terminus binding (GO:0008022)|protein N-terminus binding (GO:0047485)|small GTPase binding (GO:0031267)	p.T181T(1)		breast(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(8)|ovary(1)|prostate(1)|skin(1)	21						GAACAGCCACCGATCGCTGGT	0.537																																					p.T181T												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C543T	12						.	C	,,,,	0,4406		0,0,2203	59.0	50.0	53.0		543,588,543,543,543	2.1	0.0	12	dbSNP_134	53	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PEX5	NM_000319.4,NM_001131023.1,NM_001131024.1,NM_001131025.1,NM_001131026.1	,,,,	0,2,6501	TT,TC,CC		0.0233,0.0,0.0154	,,,,	181/632,196/655,181/603,181/640,181/640	7351701	2,13004	2203	4300	6503	7242968	SO:0001819	synonymous_variant	5830	exon6			U19721	CCDS8576.1, CCDS44822.1, CCDS44823.1, CCDS44824.1, CCDS73433.1	12p	2013-01-10	2004-03-17	2004-03-19		ENSG00000139197		"""Tetratricopeptide (TTC) repeat domain containing"""	9719	protein-coding gene	gene with protein product		600414	"""peroxisome receptor 1"""	PXR1			Standard	NM_000319		Approved	PTS1R	uc010sgc.2	P50542		ENST00000455147.2:c.543C>T	12.37:g.7351701C>T		Somatic		Capture	Illumina HiSeq	Phase_I	7242968	NM_001131024	A8K891|B4DZ45|B7ZAD5|D3DUT8|Q15115|Q15266|Q96FN7	Silent	SNP	ENST00000455147.2	37	CCDS44823.1																																																																																				0.537	PEX5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398611.1	NM_000319	
FAM90A1	55138	broad.mit.edu	37	12	8377307	8377307	+	Splice_Site	SNP	C	C	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr12:8377307C>A	ENST00000538603.1	-	4	680	c.122G>T	c.(121-123)aGg>aTg	p.R41M	FAM90A1_ENST00000307435.6_Splice_Site_p.R41M	NM_018088.3	NP_060558.3	Q86YD7	F90A1_HUMAN	family with sequence similarity 90, member A1	41							nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)	p.R41M(2)		endometrium(2)|large_intestine(4)|lung(11)|ovary(1)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	25				Kidney(36;0.0866)		TAGACTTACCCTGGGATCTTC	0.632																																					p.R41M												.	.	2	Substitution - Missense(2)	large_intestine(1)|endometrium(1)	c.G122T	12						.						5.0	7.0	6.0					12																	8377307		2070	4156	6226	8268574	SO:0001630	splice_region_variant	55138	exon4			AK001270	CCDS31738.1	12p13.31	2011-08-31		2005-11-20	ENSG00000171847	ENSG00000171847			25526	protein-coding gene	gene with protein product		613041					Standard	NM_018088		Approved	FLJ10408	uc001qui.2	Q86YD7	OTTHUMG00000168641	ENST00000538603.1:c.123+1G>T	12.37:g.8377307C>A		Somatic		Capture	Illumina HiSeq	Phase_I	8268574	NM_018088	D3DUU9|Q9NVZ6	Missense_Mutation	SNP	ENST00000538603.1	37	CCDS31738.1	.	.	.	.	.	.	.	.	.	.	.	9.797	1.179622	0.21787	.	.	ENSG00000171847	ENST00000307435;ENST00000538603	T;T	0.58506	0.33;0.33	0.706	-0.381	0.12485	.	.	.	.	.	T	0.54806	0.1881	N	0.16266	0.395	0.09310	N	1	D	0.89917	1.0	D	0.85130	0.997	T	0.46596	-0.9180	8	0.87932	D	0	-14.5683	.	.	.	.	41	Q86YD7	F90A1_HUMAN	M	41	ENSP00000307798:R41M;ENSP00000445418:R41M	ENSP00000307798:R41M	R	-	2	0	FAM90A1	8268574	0.008000	0.16893	0.033000	0.17914	0.010000	0.07245	-0.864000	0.04254	-0.555000	0.06142	-1.043000	0.02367	AGG		0.632	FAM90A1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400468.1	NM_018088	Missense_Mutation
ATF7IP	55729	broad.mit.edu	37	12	14576917	14576917	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr12:14576917G>A	ENST00000540793.1	+	1	223	c.68G>A	c.(67-69)cGt>cAt	p.R23H	ATF7IP_ENST00000536444.1_Missense_Mutation_p.R23H|ATF7IP_ENST00000543189.1_Missense_Mutation_p.R23H|ATF7IP_ENST00000261168.4_Missense_Mutation_p.R23H|ATF7IP_ENST00000541654.1_3'UTR|ATF7IP_ENST00000544627.1_Missense_Mutation_p.R31H			Q6VMQ6	MCAF1_HUMAN	activating transcription factor 7 interacting protein	23					DNA methylation (GO:0006306)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of RNA polymerase II transcriptional preinitiation complex assembly (GO:0045898)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	nucleus (GO:0005634)		p.R23H(1)		cervix(1)|endometrium(7)|kidney(5)|large_intestine(10)|liver(2)|lung(22)|ovary(1)|prostate(4)|skin(1)|urinary_tract(1)	54						GTGAGTGATCGTCAGCAACTT	0.383																																					p.R23H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G68A	12						.						85.0	75.0	78.0					12																	14576917		2203	4300	6503	14468184	SO:0001583	missense	55729	exon2			AJ242978	CCDS8663.1, CCDS66326.1, CCDS66327.1, CCDS73449.1	12p13.1	2005-11-18				ENSG00000171681			20092	protein-coding gene	gene with protein product		613644				10976766, 10777215	Standard	XM_005253424		Approved	FLJ10688, p621	uc001rbw.3	Q6VMQ6		ENST00000540793.1:c.68G>A	12.37:g.14576917G>A	ENSP00000444589:p.Arg23His	Somatic		Capture	Illumina HiSeq	Phase_I	14468184	NM_018179	F5GX74|G3V1U0|Q4G0T9|Q6P3T3|Q86XW5|Q9NVJ9|Q9NWC2|Q9Y4X8	Missense_Mutation	SNP	ENST00000540793.1	37	CCDS8663.1	.	.	.	.	.	.	.	.	.	.	G	25.4	4.631164	0.87660	.	.	ENSG00000171681	ENST00000261168;ENST00000545723;ENST00000543189;ENST00000536444;ENST00000542967;ENST00000534828;ENST00000535132;ENST00000544627;ENST00000542991;ENST00000541056;ENST00000539057;ENST00000545769;ENST00000428217;ENST00000396279;ENST00000542514;ENST00000536279;ENST00000542508;ENST00000540793	T;T;T;T;T;T	0.60548	0.2;0.48;0.22;0.18;0.65;0.2	5.53	5.53	0.82687	.	0.000000	0.64402	D	0.000013	T	0.74831	0.3768	L	0.59436	1.845	0.46061	D	0.998843	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.91635	0.999;0.999;0.997;0.997;0.999	T	0.75886	-0.3159	10	0.87932	D	0	-11.0961	19.8407	0.96681	0.0:0.0:1.0:0.0	.	31;23;23;23;23	B4E2A2;B4DRL6;G3V1U0;Q6VMQ6;Q6VMQ6-2	.;.;.;MCAF1_HUMAN;.	H	23;23;23;23;23;23;23;31;23;23;23;23;23;23;23;23;23;23	ENSP00000261168:R23H;ENSP00000443179:R23H;ENSP00000445955:R23H;ENSP00000440440:R31H;ENSP00000379575:R23H;ENSP00000444589:R23H	ENSP00000261168:R23H	R	+	2	0	ATF7IP	14468184	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	7.934000	0.87649	2.763000	0.94921	0.563000	0.77884	CGT		0.383	ATF7IP-024	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000401400.1	NM_018179	
RERGL	79785	broad.mit.edu	37	12	18237463	18237463	+	Missense_Mutation	SNP	C	C	T	rs563526809		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr12:18237463C>T	ENST00000229002.2	-	5	529	c.323G>A	c.(322-324)aGt>aAt	p.S108N	RERGL_ENST00000538724.1_Missense_Mutation_p.S107N|RERGL_ENST00000541632.1_5'UTR|RERGL_ENST00000536890.1_3'UTR	NM_024730.2	NP_079006.1	Q9H628	RERGL_HUMAN	RERG/RAS-like	108	Small GTPase-like.				GTP catabolic process (GO:0006184)|small GTPase mediated signal transduction (GO:0007264)	membrane (GO:0016020)	GTP binding (GO:0005525)	p.S108N(1)		endometrium(1)|large_intestine(5)|lung(8)|prostate(1)|skin(1)|urinary_tract(1)	17						TTTACAATGACTAGTTTGTGG	0.373													C|||	1	0.000199681	0.0	0.0014	5008	,	,		17599	0.0		0.0	False		,,,				2504	0.0				p.S108N												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G323A	12						.						136.0	137.0	136.0					12																	18237463		2203	4300	6503	18128730	SO:0001583	missense	79785	exon5			AK026308	CCDS8679.1, CCDS66332.1	12p12.3	2014-08-12			ENSG00000111404	ENSG00000111404			26213	protein-coding gene	gene with protein product						24127187	Standard	NM_001286201		Approved	FLJ22655	uc001rdq.3	Q9H628	OTTHUMG00000168820	ENST00000229002.2:c.323G>A	12.37:g.18237463C>T	ENSP00000229002:p.Ser108Asn	Somatic		Capture	Illumina HiSeq	Phase_I	18128730	NM_024730		Missense_Mutation	SNP	ENST00000229002.2	37	CCDS8679.1	.	.	.	.	.	.	.	.	.	.	C	6.855	0.527121	0.13066	.	.	ENSG00000111404	ENST00000229002;ENST00000538724	T;T	0.76060	-0.9;-0.99	4.91	3.97	0.46021	.	0.213542	0.48767	D	0.000165	T	0.60689	0.2288	N	0.26092	0.79	0.80722	D	1	B;B	0.33777	0.404;0.425	B;B	0.33690	0.168;0.131	T	0.56080	-0.8038	10	0.18710	T	0.47	.	13.7232	0.62740	0.0:0.7903:0.2097:0.0	.	107;108	F5H686;Q9H628	.;RERGL_HUMAN	N	108;107	ENSP00000229002:S108N;ENSP00000437814:S107N	ENSP00000229002:S108N	S	-	2	0	RERGL	18128730	0.998000	0.40836	0.971000	0.41717	0.585000	0.36419	3.050000	0.49877	1.249000	0.43950	0.467000	0.42956	AGT		0.373	RERGL-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000401198.1	NM_024730	
SLCO1B7	338821	broad.mit.edu	37	12	21196481	21196481	+	Missense_Mutation	SNP	G	G	A	rs374188273	byFrequency	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr12:21196481G>A	ENST00000421593.2	+	6	800	c.800G>A	c.(799-801)cGa>cAa	p.R267Q	SLCO1B7_ENST00000554957.1_Missense_Mutation_p.R314Q|LST3_ENST00000381541.3_Missense_Mutation_p.R314Q|SLCO1B3_ENST00000553473.1_Intron|LST3_ENST00000540229.1_Intron	NM_001009562.4	NP_001009562.3	G3V0H7	SO1B7_HUMAN	solute carrier organic anion transporter family, member 1B7 (non-functional)	267						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	transporter activity (GO:0005215)	p.R267Q(1)		endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(25)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	46						TTGACCAACCGAAGAAAATAT	0.303													G|||	2	0.000399361	0.0008	0.0	5008	,	,		17227	0.0		0.0	False		,,,				2504	0.001				p.R267Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G800A	12						.	G	GLN/ARG	3,4167		0,3,2082	42.0	43.0	43.0		800	-6.6	0.0	12		43	0,8474		0,0,4237	no	missense	SLCO1B7	NM_001009562.4	43	0,3,6319	AA,AG,GG		0.0,0.0719,0.0237		267/641	21196481	3,12641	2085	4237	6322	21087748	SO:0001583	missense	338821	exon6			AF401642	CCDS44843.1	12p12.3	2013-05-22			ENSG00000205754	ENSG00000205754		"""Solute carriers"""	32934	protein-coding gene	gene with protein product							Standard	NM_001009562		Approved	LST3, SLC21A21		G3V0H7	OTTHUMG00000169045	ENST00000421593.2:c.800G>A	12.37:g.21196481G>A	ENSP00000394168:p.Arg267Gln	Somatic		Capture	Illumina HiSeq	Phase_I	21087748	NM_001009562	Q71QF0	Missense_Mutation	SNP	ENST00000421593.2	37	CCDS44843.1	.	.	.	.	.	.	.	.	.	.	.	0.441	-0.898736	0.02472	7.19E-4	0.0	ENSG00000257046;ENSG00000205754;ENSG00000205754	ENST00000381541;ENST00000554957;ENST00000421593	T;T;T	0.38077	1.16;1.16;1.16	3.3	-6.6	0.01824	.	2.608050	0.00824	N	0.001600	T	0.12774	0.0310	N	0.02539	-0.55	0.09310	N	1	B;B	0.09022	0.002;0.001	B;B	0.09377	0.001;0.004	T	0.20438	-1.0275	10	0.11794	T	0.64	.	7.0347	0.24987	0.4317:0.4643:0.104:0.0	.	267;314	G3V0H7;F5H094	.;.	Q	314;314;267	ENSP00000370952:R314Q;ENSP00000452013:R314Q;ENSP00000394168:R267Q	ENSP00000370952:R314Q	R	+	2	0	SLCO1B7;RP11-545J16.1	21087748	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.113000	0.10774	-1.076000	0.03125	-1.804000	0.00617	CGA		0.303	SLCO1B7-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000402066.1	NM_001009562	
SLCO1B7	338821	broad.mit.edu	37	12	21201706	21201706	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr12:21201706A>G	ENST00000421593.2	+	8	1055	c.1055A>G	c.(1054-1056)aAa>aGa	p.K352R	SLCO1B7_ENST00000554957.1_Missense_Mutation_p.K399R|LST3_ENST00000381541.3_Missense_Mutation_p.K399R|SLCO1B3_ENST00000553473.1_Intron|LST3_ENST00000540229.1_Intron	NM_001009562.4	NP_001009562.3	G3V0H7	SO1B7_HUMAN	solute carrier organic anion transporter family, member 1B7 (non-functional)	352						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	transporter activity (GO:0005215)	p.K352R(1)		endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(25)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	46						ATCATTAAAAAATTCAAATTG	0.348																																					p.K352R												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A1055G	12						.						50.0	51.0	51.0					12																	21201706		2014	4211	6225	21092973	SO:0001583	missense	338821	exon8			AF401642	CCDS44843.1	12p12.3	2013-05-22			ENSG00000205754	ENSG00000205754		"""Solute carriers"""	32934	protein-coding gene	gene with protein product							Standard	NM_001009562		Approved	LST3, SLC21A21		G3V0H7	OTTHUMG00000169045	ENST00000421593.2:c.1055A>G	12.37:g.21201706A>G	ENSP00000394168:p.Lys352Arg	Somatic		Capture	Illumina HiSeq	Phase_I	21092973	NM_001009562	Q71QF0	Missense_Mutation	SNP	ENST00000421593.2	37	CCDS44843.1	.	.	.	.	.	.	.	.	.	.	.	12.24	1.877919	0.33162	.	.	ENSG00000257046;ENSG00000205754;ENSG00000205754	ENST00000381541;ENST00000554957;ENST00000421593	T;T;T	0.78924	1.01;1.01;-1.22	3.45	0.883	0.19177	.	0.248316	0.36778	N	0.002415	T	0.66287	0.2774	L	0.39147	1.195	0.23933	N	0.996422	P;P	0.36065	0.535;0.535	B;B	0.39971	0.315;0.315	T	0.54801	-0.8239	10	0.31617	T	0.26	.	6.0829	0.19950	0.7651:0.0:0.2349:0.0	.	352;399	G3V0H7;F5H094	.;.	R	399;399;352	ENSP00000370952:K399R;ENSP00000452013:K399R;ENSP00000394168:K352R	ENSP00000370952:K399R	K	+	2	0	SLCO1B7;RP11-545J16.1	21092973	1.000000	0.71417	0.772000	0.31596	0.627000	0.37826	0.711000	0.25764	0.059000	0.16252	0.416000	0.27883	AAA		0.348	SLCO1B7-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000402066.1	NM_001009562	
SLCO1B1	10599	broad.mit.edu	37	12	21377670	21377670	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr12:21377670C>T	ENST00000256958.2	+	14	1858	c.1762C>T	c.(1762-1764)Cca>Tca	p.P588S		NM_006446.4	NP_006437.3	Q9Y6L6	SO1B1_HUMAN	solute carrier organic anion transporter family, member 1B1	588					bile acid and bile salt transport (GO:0015721)|bile acid metabolic process (GO:0008206)|organic anion transport (GO:0015711)|small molecule metabolic process (GO:0044281)|sodium-independent organic anion transport (GO:0043252)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	sodium-independent organic anion transmembrane transporter activity (GO:0015347)	p.P588S(1)		breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(14)|lung(33)|ovary(3)|pancreas(1)|prostate(1)|skin(8)|upper_aerodigestive_tract(1)	70					Acetylcysteine(DB06151)|Aminohippurate(DB00345)|Atorvastatin(DB01076)|Axitinib(DB06626)|Benzylpenicillin(DB01053)|Bezafibrate(DB01393)|Cabazitaxel(DB06772)|Caspofungin(DB00520)|Conjugated Estrogens(DB00286)|Cyclosporine(DB00091)|Dabrafenib(DB08912)|Dextrothyroxine(DB00509)|Digoxin(DB00390)|Dinoprostone(DB00917)|Eltrombopag(DB06210)|Estradiol(DB00783)|Estrone(DB00655)|Ezetimibe(DB00973)|Fexofenadine(DB00950)|Fluvastatin(DB01095)|Gadoxetate(DB08884)|Gemfibrozil(DB01241)|Indinavir(DB00224)|Irinotecan(DB00762)|L-Carnitine(DB00583)|Levothyroxine(DB00451)|Liothyronine(DB00279)|Liotrix(DB01583)|Lovastatin(DB00227)|Methotrexate(DB00563)|Mycophenolate mofetil(DB00688)|Nelfinavir(DB00220)|Olmesartan(DB00275)|Ouabain(DB01092)|Pantoprazole(DB00213)|Pazopanib(DB06589)|Penicillamine(DB00859)|Pioglitazone(DB01132)|Pitavastatin(DB08860)|Pravastatin(DB00175)|Quinidine(DB00908)|Repaglinide(DB00912)|Rifampicin(DB01045)|Rilpivirine(DB08864)|Ritonavir(DB00503)|Rosiglitazone(DB00412)|Rosuvastatin(DB01098)|Saquinavir(DB01232)|SIMEPREVIR(DB06290)|Simvastatin(DB00641)|Sirolimus(DB00877)|Sumatriptan(DB00669)|Valsartan(DB00177)|Verapamil(DB00661)	AATTCTAGCTCCAATATATTT	0.363																																					p.P588S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1762T	12						.						145.0	139.0	141.0					12																	21377670		2203	4300	6503	21268937	SO:0001583	missense	10599	exon14				CCDS8685.1	12p12	2013-05-22	2003-11-25	2003-11-26	ENSG00000134538	ENSG00000134538		"""Solute carriers"""	10959	protein-coding gene	gene with protein product		604843	"""solute carrier family 21 (organic anion transporter), member 6"""	SLC21A6		10358072	Standard	NM_006446		Approved	OATP-C, LST-1, OATP1B1	uc001req.4	Q9Y6L6	OTTHUMG00000169047	ENST00000256958.2:c.1762C>T	12.37:g.21377670C>T	ENSP00000256958:p.Pro588Ser	Somatic		Capture	Illumina HiSeq	Phase_I	21268937	NM_006446	B2R7G2|Q29R64|Q9NQ37|Q9UBF3|Q9UH89	Missense_Mutation	SNP	ENST00000256958.2	37	CCDS8685.1	.	.	.	.	.	.	.	.	.	.	C	16.02	3.002927	0.54254	.	.	ENSG00000134538	ENST00000256958	T	0.58797	0.31	3.66	3.66	0.41972	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.000000	0.85682	D	0.000000	T	0.78811	0.4342	M	0.92649	3.33	0.47778	D	0.999511	D	0.58620	0.983	D	0.66351	0.943	D	0.84130	0.0411	10	0.87932	D	0	.	12.3674	0.55236	0.0:1.0:0.0:0.0	.	588	Q9Y6L6	SO1B1_HUMAN	S	588	ENSP00000256958:P588S	ENSP00000256958:P588S	P	+	1	0	SLCO1B1	21268937	1.000000	0.71417	1.000000	0.80357	0.587000	0.36485	5.455000	0.66658	1.866000	0.54105	0.467000	0.42956	CCA		0.363	SLCO1B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402070.1	NM_006446	
KCNJ8	3764	broad.mit.edu	37	12	21919124	21919124	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr12:21919124C>T	ENST00000240662.2	-	3	1153	c.808G>A	c.(808-810)Gtg>Atg	p.V270M	RP11-59N23.1_ENST00000542489.1_RNA	NM_004982.3	NP_004973.1	Q15842	KCNJ8_HUMAN	potassium inwardly-rectifying channel, subfamily J, member 8	270					defense response to virus (GO:0051607)|heart development (GO:0007507)|kidney development (GO:0001822)|potassium ion import (GO:0010107)|potassium ion transport (GO:0006813)|response to exogenous dsRNA (GO:0043330)|response to lipopolysaccharide (GO:0032496)|response to pH (GO:0009268)|synaptic transmission (GO:0007268)|vasodilation (GO:0042311)	ATP-sensitive potassium channel complex (GO:0008282)|mitochondrion (GO:0005739)|myofibril (GO:0030016)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|voltage-gated potassium channel complex (GO:0008076)	ATP binding (GO:0005524)|ATP-activated inward rectifier potassium channel activity (GO:0015272)|inward rectifier potassium channel activity (GO:0005242)	p.V270M(1)		cervix(1)|endometrium(1)|kidney(2)|large_intestine(6)|lung(10)|ovary(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	28					Gliquidone(DB01251)|Glisoxepide(DB01289)|Glyburide(DB01016)|Levosimendan(DB00922)|Phenformin(DB00914)|Thiamylal(DB01154)|Yohimbine(DB01392)	TTGTCAATCACGTGGCAGATG	0.478																																					p.V270M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G808A	12						.						78.0	70.0	73.0					12																	21919124		2203	4300	6503	21810391	SO:0001583	missense	3764	exon3			BC000544	CCDS8692.1	12p12.1	2011-07-05			ENSG00000121361	ENSG00000121361		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels, Inwardly rectifying"""	6269	protein-coding gene	gene with protein product		600935				8595887, 16382105	Standard	NM_004982		Approved	Kir6.1	uc001rff.4	Q15842	OTTHUMG00000169093	ENST00000240662.2:c.808G>A	12.37:g.21919124C>T	ENSP00000240662:p.Val270Met	Somatic		Capture	Illumina HiSeq	Phase_I	21810391	NM_004982	O00657	Missense_Mutation	SNP	ENST00000240662.2	37	CCDS8692.1	.	.	.	.	.	.	.	.	.	.	C	17.05	3.289288	0.59976	.	.	ENSG00000121361	ENST00000240662;ENST00000539350	D	0.94862	-3.54	5.35	5.35	0.76521	Immunoglobulin E-set (1);Potassium channel, inwardly rectifying, Kir, conserved region 2 (2);Potassium channel, inwardly rectifying, Kir, cytoplasmic (1);	0.053248	0.85682	D	0.000000	D	0.94288	0.8165	M	0.78456	2.415	0.44702	D	0.99769	D	0.59357	0.985	P	0.45071	0.468	D	0.94313	0.7547	10	0.59425	D	0.04	.	13.5333	0.61633	0.0:0.9257:0.0:0.0743	.	270	Q15842	IRK8_HUMAN	M	270	ENSP00000240662:V270M	ENSP00000240662:V270M	V	-	1	0	KCNJ8	21810391	0.079000	0.21365	0.983000	0.44433	0.959000	0.62525	0.615000	0.24329	2.782000	0.95742	0.563000	0.77884	GTG		0.478	KCNJ8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402226.1	NM_004982	
KRAS	3845	broad.mit.edu	37	12	25398281	25398281	+	Missense_Mutation	SNP	C	C	T	rs112445441		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr12:25398281C>T	ENST00000256078.4	-	2	101	c.38G>A	c.(37-39)gGc>gAc	p.G13D	KRAS_ENST00000557334.1_Missense_Mutation_p.G13D|KRAS_ENST00000311936.3_Missense_Mutation_p.G13D|KRAS_ENST00000556131.1_Missense_Mutation_p.G13D	NM_033360.2	NP_203524.1	P01116	RASK_HUMAN	Kirsten rat sarcoma viral oncogene homolog	13			G -> D (in a breast carcinoma cell line and GASC; somatic mutation). {ECO:0000269|PubMed:14534542, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:3627975}.|G -> R (in pylocytic astrocytoma; somatic mutation; increase activation of the Ras pathway). {ECO:0000269|PubMed:16247081}.		actin cytoskeleton organization (GO:0030036)|activation of MAPKK activity (GO:0000186)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cytokine-mediated signaling pathway (GO:0019221)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|GTP catabolic process (GO:0006184)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|leukocyte migration (GO:0050900)|MAPK cascade (GO:0000165)|negative regulation of cell differentiation (GO:0045596)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of nitric-oxide synthase activity (GO:0051000)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of Rac protein signal transduction (GO:0035022)|Ras protein signal transduction (GO:0007265)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of synaptic transmission, GABAergic (GO:0032228)|response to glucocorticoid (GO:0051384)|response to mineralocorticoid (GO:0051385)|small GTPase mediated signal transduction (GO:0007264)|social behavior (GO:0035176)|striated muscle cell differentiation (GO:0051146)|visual learning (GO:0008542)	focal adhesion (GO:0005925)|membrane (GO:0016020)|membrane raft (GO:0045121)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	GDP binding (GO:0019003)|GMP binding (GO:0019002)|GTP binding (GO:0005525)|protein complex binding (GO:0032403)	p.G13D(3223)|p.G13V(33)|p.G13A(28)|p.G13E(3)|p.G13I(1)|p.G13N(1)|p.G13_V14>DI(1)|p.G13R(1)	UBE2L3/KRAS(2)	NS(6)|adrenal_gland(1)|autonomic_ganglia(3)|biliary_tract(532)|bone(2)|breast(32)|central_nervous_system(14)|cervix(50)|endometrium(411)|eye(4)|gastrointestinal_tract_(site_indeterminate)(7)|genital_tract(1)|haematopoietic_and_lymphoid_tissue(385)|kidney(8)|large_intestine(15267)|liver(29)|lung(3407)|oesophagus(16)|ovary(612)|pancreas(3739)|penis(1)|peritoneum(6)|prostate(96)|salivary_gland(6)|skin(45)|small_intestine(68)|soft_tissue(88)|stomach(207)|testis(17)|thymus(5)|thyroid(159)|upper_aerodigestive_tract(68)|urinary_tract(57)	25349	all_cancers(2;1e-35)|all_epithelial(2;1.97e-38)|all_lung(3;2.1e-23)|Lung NSC(3;1.16e-22)|Acute lymphoblastic leukemia(6;0.00231)|all_hematologic(7;0.00259)|Melanoma(3;0.0301)|Colorectal(261;0.11)|Ovarian(17;0.12)		OV - Ovarian serous cystadenocarcinoma(3;1.23e-21)|Epithelial(3;1.31e-20)|all cancers(3;5.45e-18)|STAD - Stomach adenocarcinoma(2;2.68e-05)			CTTGCCTACGCCACCAGCTCC	0.338	G13D(DLD1_LARGE_INTESTINE)|G13D(DV90_LUNG)|G13D(HCT116_LARGE_INTESTINE)|G13D(HCT15_LARGE_INTESTINE)|G13D(LOVO_LARGE_INTESTINE)|G13D(MDAMB231_BREAST)|G13D(NCIH647_LUNG)|G13D(NCIH747_LARGE_INTESTINE)|G13D(NOMO1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G13D(T84_LARGE_INTESTINE)|G13D(TOLEDO_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)	119	Mis		"""pancreatic, colorectal, lung, thyroid, AML, others"""				Noonan syndrome;Cardiofaciocutaneous syndrome	TSP Lung(1;<1E-08)|Multiple Myeloma(2;<1E-6)																											p.G13D	Pancreas(8;6 143 191 305 2070 2426 4376 10944 11745 26467 38091 50869)		Dom	yes		12	12p12.1	3845	v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog		"""L, E, M, O"""	KRAS,lung,NS,Substitution - Missense,-1 	.	3291	Substitution - Missense(3290)|Complex - compound substitution(1)	large_intestine(2808)|haematopoietic_and_lymphoid_tissue(94)|lung(92)|endometrium(54)|soft_tissue(38)|ovary(38)|stomach(32)|pancreas(30)|thyroid(27)|biliary_tract(21)|prostate(20)|breast(10)|cervix(4)|gastrointestinal_tract_(site_indeterminate)(3)|upper_aerodigestive_tract(3)|urinary_tract(3)|liver(3)|salivary_gland(3)|small_intestine(3)|oesophagus(2)|skin(1)|genital_tract(1)|bone(1)	c.G38A	12						.						88.0	78.0	82.0					12																	25398281		2203	4300	6503	25289548	SO:0001583	missense	3845	exon2	Familial Cancer Database	Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome;CFC, CFCS	BC010502	CCDS8702.1, CCDS8703.1	12p12.1	2014-09-17	2013-07-08	2005-01-24	ENSG00000133703	ENSG00000133703			6407	protein-coding gene	gene with protein product		190070	"""v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog"", ""v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog"""	KRAS2			Standard	NM_004985		Approved	KRAS1	uc001rgp.1	P01116		ENST00000256078.4:c.38G>A	12.37:g.25398281C>T	ENSP00000256078:p.Gly13Asp	Somatic		Capture	Illumina HiSeq	Phase_I	25289548	NM_004985	A8K8Z5|B0LPF9|P01118|Q96D10	Missense_Mutation	SNP	ENST00000256078.4	37	CCDS8703.1	.	.	.	.	.	.	.	.	.	.	C	27.8	4.867862	0.91587	.	.	ENSG00000133703	ENST00000311936;ENST00000557334;ENST00000256078;ENST00000556131	D;T;T;T	0.82803	-1.65;-0.7;-0.7;-0.7	5.68	5.68	0.88126	Small GTP-binding protein domain (1);	0.000000	0.85682	D	0.000000	D	0.90079	0.6901	M	0.93062	3.375	0.80722	D	1	B;P	0.43314	0.215;0.803	B;P	0.46172	0.175;0.506	D	0.92106	0.5692	10	0.87932	D	0	.	18.3719	0.90409	0.0:1.0:0.0:0.0	.	13;13	P01116-2;P01116	.;RASK_HUMAN	D	13	ENSP00000308495:G13D;ENSP00000452512:G13D;ENSP00000256078:G13D;ENSP00000451856:G13D	ENSP00000256078:G13D	G	-	2	0	KRAS	25289548	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.743000	0.85020	2.668000	0.90789	0.563000	0.77884	GGC		0.338	KRAS-004	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000412232.1	NM_033360	
C12orf71	728858	broad.mit.edu	37	12	27235211	27235211	+	Missense_Mutation	SNP	C	C	T	rs201692205	byFrequency	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr12:27235211C>T	ENST00000429849.2	-	1	236	c.206G>A	c.(205-207)cGc>cAc	p.R69H		NM_001080406.1	NP_001073875.1	A8MTZ7	CL071_HUMAN	chromosome 12 open reading frame 71	69								p.R69H(1)		endometrium(2)|large_intestine(1)|lung(4)|skin(1)	8						TCTCTTCATGCGTCTCCCTAT	0.532													C|||	2	0.000399361	0.0015	0.0	5008	,	,		20034	0.0		0.0	False		,,,				2504	0.0				p.R69H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G206A	12						.	C	HIS/ARG	0,3992		0,0,1996	78.0	78.0	78.0		206	-5.4	0.0	12		78	1,8347		0,1,4173	no	missense	C12orf71	NM_001080406.1	29	0,1,6169	TT,TC,CC		0.012,0.0,0.0081	benign	69/270	27235211	1,12339	1996	4174	6170	27126478	SO:0001583	missense	728858	exon1				CCDS44851.1	12p11.23	2008-07-25			ENSG00000214700	ENSG00000214700			34452	protein-coding gene	gene with protein product							Standard	NM_001080406		Approved	LOC728858	uc001rhq.3	A8MTZ7	OTTHUMG00000169274	ENST00000429849.2:c.206G>A	12.37:g.27235211C>T	ENSP00000413728:p.Arg69His	Somatic		Capture	Illumina HiSeq	Phase_I	27126478	NM_001080406		Missense_Mutation	SNP	ENST00000429849.2	37	CCDS44851.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	C	10.45	1.353208	0.24512	0.0	1.2E-4	ENSG00000214700	ENST00000398815;ENST00000429849	T	0.43688	0.94	3.32	-5.4	0.02656	.	1.042650	0.07738	U	0.946393	T	0.15176	0.0366	N	0.08118	0	0.09310	N	1	P	0.44044	0.825	B	0.31614	0.133	T	0.22765	-1.0207	10	0.62326	D	0.03	0.118	5.7494	0.18138	0.2287:0.3349:0.4364:0.0	.	69	A8MTZ7	CL071_HUMAN	H	69	ENSP00000413728:R69H	ENSP00000381796:R69H	R	-	2	0	C12orf71	27126478	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-2.069000	0.01381	-1.115000	0.02973	-0.535000	0.04281	CGC		0.532	C12orf71-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403258.1	NM_001080406	
TMTC1	83857	broad.mit.edu	37	12	29669387	29669387	+	Frame_Shift_Del	DEL	T	T	-			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr12:29669387delT	ENST00000539277.1	-	15	2260	c.2202delA	c.(2200-2202)aaafs	p.K734fs	TMTC1_ENST00000319685.8_5'UTR|TMTC1_ENST00000551659.1_Frame_Shift_Del_p.K796fs|TMTC1_ENST00000256062.5_Frame_Shift_Del_p.K626fs|TMTC1_ENST00000552618.1_Frame_Shift_Del_p.K758fs	NM_001193451.1	NP_001180380.1	Q8IUR5	TMTC1_HUMAN	transmembrane and tetratricopeptide repeat containing 1	734						integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)		p.E627fs*5(1)		breast(1)|endometrium(4)|kidney(3)|large_intestine(17)|lung(45)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	75	Lung NSC(12;7.61e-10)|Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.032)					TTTCAGCTTCTTTTGTCTGAC	0.463																																					p.K734fs												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.2202delA	12						.						140.0	129.0	133.0					12																	29669387		2203	4300	6503	29560654	SO:0001589	frameshift_variant	83857	exon15				CCDS8718.1, CCDS53772.1	12p11.22	2014-06-09	2006-01-06			ENSG00000133687		"""Tetratricopeptide (TTC) repeat domain containing"""	24099	protein-coding gene	gene with protein product		615855				24764305	Standard	NM_001193451		Approved	ARG99, OLF, FLJ31400, FLJ41625	uc021qwi.1	Q8IUR5	OTTHUMG00000169324	ENST00000539277.1:c.2202delA	12.37:g.29669387delT	ENSP00000442046:p.Lys734fs	Somatic		Capture	Illumina HiSeq	Phase_I	29560654	NM_001193451	D0EP37|F5H8B5|Q6PIU4|Q6ZSM5|Q96N52|Q9BXM2	Frame_Shift_Del	DEL	ENST00000539277.1	37	CCDS53772.1																																																																																				0.463	TMTC1-002	PUTATIVE	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000403509.1	NM_031920	
SLC38A1	81539	broad.mit.edu	37	12	46592460	46592460	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr12:46592460C>A	ENST00000398637.5	-	14	1764	c.1070G>T	c.(1069-1071)cGg>cTg	p.R357L	SLC38A1_ENST00000549049.1_Missense_Mutation_p.R357L|SLC38A1_ENST00000439706.1_Missense_Mutation_p.R357L|SLC38A1_ENST00000549633.1_5'Flank|SLC38A1_ENST00000546893.1_Missense_Mutation_p.R357L|SLC38A1_ENST00000552197.1_Missense_Mutation_p.R357L	NM_001077484.1|NM_001278387.1|NM_001278388.1|NM_001278389.1|NM_030674.3	NP_001070952.1|NP_001265316.1|NP_001265317.1|NP_001265318.1|NP_109599.3	Q9H2H9	S38A1_HUMAN	solute carrier family 38, member 1	357					amino acid transmembrane transport (GO:0003333)|amino acid transport (GO:0006865)|ion transport (GO:0006811)|neurotransmitter uptake (GO:0001504)|neutral amino acid transport (GO:0015804)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	neutral amino acid transmembrane transporter activity (GO:0015175)|sodium:amino acid symporter activity (GO:0005283)	p.R357L(2)		NS(2)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(7)|ovary(2)|prostate(1)|skin(2)	23	Lung SC(27;0.137)|Renal(347;0.236)		all cancers(1;0.00805)|OV - Ovarian serous cystadenocarcinoma(5;0.0106)|Epithelial(2;0.0344)			GACAGCCAGCCGCACTGTCAG	0.463																																					p.R357L												.	.	2	Substitution - Missense(2)	large_intestine(1)|lung(1)	c.G1070T	12						.						94.0	95.0	94.0					12																	46592460		2005	4180	6185	44878727	SO:0001583	missense	81539	exon14			AF271070	CCDS41774.1, CCDS61106.1	12q13.11	2013-05-22				ENSG00000111371		"""Solute carriers"""	13447	protein-coding gene	gene with protein product		608490				10891391	Standard	NM_030674		Approved	ATA1, NAT2, SAT1	uc001rpc.3	Q9H2H9		ENST00000398637.5:c.1070G>T	12.37:g.46592460C>A	ENSP00000381634:p.Arg357Leu	Somatic		Capture	Illumina HiSeq	Phase_I	44878727	NM_001077484	Q8NC61|Q8NCF8|Q96JX2|Q9H2Q2	Missense_Mutation	SNP	ENST00000398637.5	37	CCDS41774.1	.	.	.	.	.	.	.	.	.	.	C	26.5	4.741125	0.89573	.	.	ENSG00000111371	ENST00000549049;ENST00000439706;ENST00000398637;ENST00000546893;ENST00000552197	T;T;T;T;T	0.02631	4.22;4.22;4.22;4.22;4.22	5.58	5.58	0.84498	.	0.000000	0.64402	D	0.000006	T	0.17789	0.0427	M	0.84156	2.68	0.58432	D	0.999999	D;P	0.63880	0.993;0.936	D;P	0.66351	0.943;0.695	T	0.00116	-1.2036	10	0.66056	D	0.02	-14.0659	19.5825	0.95473	0.0:1.0:0.0:0.0	.	357;357	F8VX04;Q9H2H9	.;S38A1_HUMAN	L	357	ENSP00000449607:R357L;ENSP00000398142:R357L;ENSP00000381634:R357L;ENSP00000447853:R357L;ENSP00000449756:R357L	ENSP00000381634:R357L	R	-	2	0	SLC38A1	44878727	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	5.785000	0.68998	2.624000	0.88883	0.655000	0.94253	CGG		0.463	SLC38A1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404218.2		
RAPGEF3	10411	broad.mit.edu	37	12	48131373	48131373	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr12:48131373G>T	ENST00000449771.2	-	28	2837	c.2749C>A	c.(2749-2751)Ctc>Atc	p.L917I	RAPGEF3_ENST00000171000.4_Missense_Mutation_p.L875I|RAPGEF3_ENST00000389212.3_Missense_Mutation_p.L917I|RAPGEF3_ENST00000548919.1_Missense_Mutation_p.L808I|RP1-197B17.3_ENST00000547799.1_lincRNA|RAPGEF3_ENST00000549151.1_Missense_Mutation_p.L875I|RAPGEF3_ENST00000405493.2_Missense_Mutation_p.L875I			O95398	RPGF3_HUMAN	Rap guanine nucleotide exchange factor (GEF) 3	917					angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cAMP-mediated signaling (GO:0019933)|cell proliferation (GO:0008283)|cellular response to cAMP (GO:0071320)|energy reserve metabolic process (GO:0006112)|establishment of endothelial barrier (GO:0061028)|platelet activation (GO:0030168)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cAMP catabolic process (GO:0030822)|positive regulation of Rap GTPase activity (GO:0032854)|positive regulation of stress fiber assembly (GO:0051496)|Rap protein signal transduction (GO:0032486)|regulation of actin cytoskeleton reorganization (GO:2000249)|regulation of insulin secretion (GO:0050796)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	cAMP-dependent protein kinase complex (GO:0005952)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|plasma membrane (GO:0005886)	cAMP binding (GO:0030552)|cAMP-dependent protein kinase regulator activity (GO:0008603)|guanyl-nucleotide exchange factor activity (GO:0005085)|Rap guanyl-nucleotide exchange factor activity (GO:0017034)	p.L875I(1)		endometrium(1)|kidney(2)|large_intestine(4)|lung(9)|pancreas(1)|prostate(1)|skin(7)	25	Lung SC(27;0.192)			GBM - Glioblastoma multiforme(48;0.0375)		TCTCGGGAGAGGCGGGAGAGT	0.642																																					p.L875I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C2623A	12						.						27.0	27.0	27.0					12																	48131373		2203	4300	6503	46417640	SO:0001583	missense	10411	exon27			AK092448	CCDS31784.1, CCDS41775.1	12q13.1	2006-04-12	2004-03-26		ENSG00000079337	ENSG00000079337			16629	protein-coding gene	gene with protein product	"""exchange protein directly activated by cAMP 1"""	606057	"""RAP guanine-nucleotide-exchange factor (GEF) 3"""			10777494, 9856955	Standard	NM_001098531		Approved	cAMP-GEFI, EPAC, bcm910	uc001rpz.4	O95398	OTTHUMG00000133667	ENST00000449771.2:c.2749C>A	12.37:g.48131373G>T	ENSP00000395708:p.Leu917Ile	Somatic		Capture	Illumina HiSeq	Phase_I	46417640	NM_001098532	A8K2G5|E7EQC8|O95634|Q8WVN0	Missense_Mutation	SNP	ENST00000449771.2	37	CCDS41775.1	.	.	.	.	.	.	.	.	.	.	G	26.1	4.703370	0.88924	.	.	ENSG00000079337	ENST00000405493;ENST00000449771;ENST00000541821;ENST00000549151;ENST00000171000;ENST00000389211;ENST00000389212;ENST00000397089;ENST00000548919	T;T;T;T;T;T	0.37058	1.22;1.22;1.22;1.22;1.22;1.22	5.19	5.19	0.71726	Guanine-nucleotide dissociation stimulator CDC25 (1);Ras guanine nucleotide exchange factor, domain (1);	0.380247	0.21994	N	0.066110	T	0.51041	0.1651	L	0.51422	1.61	0.51012	D	0.999907	D	0.76494	0.999	D	0.78314	0.991	T	0.50541	-0.8816	10	0.62326	D	0.03	.	9.7639	0.40548	0.0943:0.0:0.9057:0.0	.	917	O95398	RPGF3_HUMAN	I	875;917;564;875;875;875;917;862;808	ENSP00000384521:L875I;ENSP00000395708:L917I;ENSP00000448619:L875I;ENSP00000171000:L875I;ENSP00000373864:L917I;ENSP00000448480:L808I	ENSP00000171000:L875I	L	-	1	0	RAPGEF3	46417640	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.368000	0.79567	2.423000	0.82170	0.561000	0.74099	CTC		0.642	RAPGEF3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257848.1	NM_006105	
HDAC7	51564	broad.mit.edu	37	12	48192638	48192638	+	Missense_Mutation	SNP	C	C	T	rs371297447		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr12:48192638C>T	ENST00000427332.2	-	3	227	c.71G>A	c.(70-72)cGt>cAt	p.R24H	HDAC7_ENST00000552960.1_Missense_Mutation_p.R46H|HDAC7_ENST00000354334.3_Missense_Mutation_p.R63H|HDAC7_ENST00000380610.4_Missense_Mutation_p.R80H|HDAC7_ENST00000080059.7_Missense_Mutation_p.R63H			Q8WUI4	HDAC7_HUMAN	histone deacetylase 7	24	Interaction with MEF2C. {ECO:0000250}.|Transcription repression 1. {ECO:0000250}.				cell-cell junction assembly (GO:0007043)|negative regulation of interleukin-2 production (GO:0032703)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|Notch signaling pathway (GO:0007219)|positive regulation of cell migration involved in sprouting angiogenesis (GO:0090050)|transcription, DNA-templated (GO:0006351)|vasculogenesis (GO:0001570)	cytoplasm (GO:0005737)|histone deacetylase complex (GO:0000118)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	14-3-3 protein binding (GO:0071889)|activating transcription factor binding (GO:0033613)|chromatin binding (GO:0003682)|metal ion binding (GO:0046872)|NAD-dependent histone deacetylase activity (H3-K14 specific) (GO:0032041)|NAD-dependent histone deacetylase activity (H3-K18 specific) (GO:0097372)|NAD-dependent histone deacetylase activity (H3-K9 specific) (GO:0046969)|NAD-dependent histone deacetylase activity (H4-K16 specific) (GO:0046970)|protein kinase binding (GO:0019901)|protein kinase C binding (GO:0005080)|repressing transcription factor binding (GO:0070491)|transcription corepressor activity (GO:0003714)	p.R24H(1)		breast(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(6)|lung(11)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	25				GBM - Glioblastoma multiforme(48;0.137)		GCGCTGGGGACGCTGCAGGGC	0.697																																					p.R63H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G188A	12						.	C	HIS/ARG,HIS/ARG	2,4344		0,2,2171	16.0	17.0	16.0		188,188	1.6	1.0	12		16	0,8488		0,0,4244	no	missense,missense	HDAC7	NM_001098416.2,NM_015401.3	29,29	0,2,6415	TT,TC,CC		0.0,0.046,0.0156	benign,benign	63/955,63/992	48192638	2,12832	2173	4244	6417	46478905	SO:0001583	missense	51564	exon3			AF239243	CCDS8756.2, CCDS41776.1	12q13.1	2008-02-25	2008-02-25	2008-02-25	ENSG00000061273	ENSG00000061273			14067	protein-coding gene	gene with protein product		606542	"""histone deacetylase 7A"""	HDAC7A		10922406, 10640276	Standard	NM_015401		Approved	DKFZP586J0917	uc010slo.2	Q8WUI4	OTTHUMG00000152968	ENST00000427332.2:c.71G>A	12.37:g.48192638C>T	ENSP00000404394:p.Arg24His	Somatic		Capture	Illumina HiSeq	Phase_I	46478905	NM_001098416	B3KY08|B4DWI0|B4E0Q5|Q6P1W9|Q6W9G7|Q7Z4K2|Q7Z5I1|Q96K01|Q9BR73|Q9H7L0|Q9NW41|Q9NWA9|Q9NYK9|Q9UFU7	Missense_Mutation	SNP	ENST00000427332.2	37		.	.	.	.	.	.	.	.	.	.	C	3.710	-0.059651	0.07317	4.6E-4	0.0	ENSG00000061273	ENST00000080059;ENST00000354334;ENST00000552960;ENST00000380610;ENST00000427332;ENST00000430670;ENST00000422254;ENST00000440293;ENST00000447463;ENST00000434070;ENST00000421231;ENST00000450805;ENST00000417902;ENST00000433685;ENST00000417107;ENST00000445237	T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.20463	2.07;2.07;2.07;2.07;2.07;2.07;2.07;2.07;2.07;2.07;2.07;2.07;2.07;2.07;2.07;2.07	3.92	1.59	0.23543	.	0.422380	0.23125	N	0.051651	T	0.05090	0.0136	N	0.01874	-0.695	0.22571	N	0.998972	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.40850	-0.9541	10	0.02654	T	1	.	4.5242	0.11973	0.0:0.3348:0.0:0.6652	.	63;46;63	Q8WUI4-5;Q8WUI4-6;Q8WUI4-7	.;.;.	H	63;63;46;80;24;63;24;46;24;24;24;24;46;24;24;24	ENSP00000080059:R63H;ENSP00000351326:R63H;ENSP00000448532:R46H;ENSP00000369984:R80H;ENSP00000404394:R24H;ENSP00000396159:R63H;ENSP00000410068:R24H;ENSP00000411058:R46H;ENSP00000389501:R24H;ENSP00000388561:R24H;ENSP00000412155:R24H;ENSP00000397236:R24H;ENSP00000400811:R46H;ENSP00000403149:R24H;ENSP00000387792:R24H;ENSP00000390415:R24H	ENSP00000080059:R63H	R	-	2	0	HDAC7	46478905	0.549000	0.26481	1.000000	0.80357	0.998000	0.95712	0.020000	0.13466	0.675000	0.31264	0.561000	0.74099	CGT		0.697	HDAC7-013	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000328804.2		
WNT10B	7480	broad.mit.edu	37	12	49360145	49360145	+	Silent	SNP	G	G	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr12:49360145G>T	ENST00000301061.4	-	5	1251	c.903C>A	c.(901-903)ccC>ccA	p.P301P	WNT10B_ENST00000403957.1_3'UTR|WNT10B_ENST00000407467.1_3'UTR	NM_003394.3	NP_003385.2	O00744	WN10B_HUMAN	wingless-type MMTV integration site family, member 10B	301			P -> S (in dbSNP:rs35034312). {ECO:0000269|PubMed:16477437}.		bone trabecula formation (GO:0060346)|canonical Wnt signaling pathway (GO:0060070)|cell cycle arrest (GO:0007050)|cell fate commitment (GO:0045165)|cellular response to cAMP (GO:0071320)|cellular response to hydrostatic pressure (GO:0071464)|cellular response to parathyroid hormone stimulus (GO:0071374)|cellular response to retinoic acid (GO:0071300)|chondrocyte differentiation (GO:0002062)|fungiform papilla development (GO:0061196)|G2/M transition of mitotic cell cycle (GO:0000086)|hematopoietic stem cell proliferation (GO:0071425)|lipid metabolic process (GO:0006629)|myoblast differentiation involved in skeletal muscle regeneration (GO:0014835)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuron differentiation (GO:0030182)|positive regulation of anagen (GO:0051885)|positive regulation of apoptotic process (GO:0043065)|positive regulation of bone mineralization (GO:0030501)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of cell proliferation (GO:0008284)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of G2/M transition of mitotic cell cycle (GO:0010971)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of RNA polymerase II transcriptional preinitiation complex assembly (GO:0045899)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|protein stabilization (GO:0050821)|regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032434)|regulation of skeletal muscle tissue development (GO:0048641)|sensory perception of taste (GO:0050909)|skeletal muscle fiber development (GO:0048741)|smoothened signaling pathway (GO:0007224)|Wnt signaling pathway (GO:0016055)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	frizzled binding (GO:0005109)|receptor agonist activity (GO:0048018)	p.P301P(1)		central_nervous_system(1)|large_intestine(5)|lung(12)|prostate(1)|skin(4)	23						AGAGGCGACGGGGACGCAGAC	0.647																																					p.P301P												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C903A	12						.						51.0	61.0	57.0					12																	49360145		2203	4299	6502	47646412	SO:0001819	synonymous_variant	7480	exon5			X97057	CCDS8775.1	12q13	2009-01-02			ENSG00000169884	ENSG00000169884		"""Wingless-type MMTV integration sites"""	12775	protein-coding gene	gene with protein product		601906				9121776, 9284937, 18515319	Standard	NM_003394		Approved	WNT-12, SHFM6	uc001rss.3	O00744	OTTHUMG00000150734	ENST00000301061.4:c.903C>A	12.37:g.49360145G>T		Somatic		Capture	Illumina HiSeq	Phase_I	47646412	NM_003394	B2R7A5|O00747|Q4VAJ4|Q4VAJ5|Q8WZ97	Silent	SNP	ENST00000301061.4	37	CCDS8775.1																																																																																				0.647	WNT10B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319864.1	NM_003394	
WNT10B	7480	broad.mit.edu	37	12	49360216	49360216	+	Missense_Mutation	SNP	G	G	A	rs200116103		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr12:49360216G>A	ENST00000301061.4	-	5	1180	c.832C>T	c.(832-834)Cgg>Tgg	p.R278W	WNT10B_ENST00000403957.1_3'UTR|WNT10B_ENST00000407467.1_3'UTR	NM_003394.3	NP_003385.2	O00744	WN10B_HUMAN	wingless-type MMTV integration site family, member 10B	278					bone trabecula formation (GO:0060346)|canonical Wnt signaling pathway (GO:0060070)|cell cycle arrest (GO:0007050)|cell fate commitment (GO:0045165)|cellular response to cAMP (GO:0071320)|cellular response to hydrostatic pressure (GO:0071464)|cellular response to parathyroid hormone stimulus (GO:0071374)|cellular response to retinoic acid (GO:0071300)|chondrocyte differentiation (GO:0002062)|fungiform papilla development (GO:0061196)|G2/M transition of mitotic cell cycle (GO:0000086)|hematopoietic stem cell proliferation (GO:0071425)|lipid metabolic process (GO:0006629)|myoblast differentiation involved in skeletal muscle regeneration (GO:0014835)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuron differentiation (GO:0030182)|positive regulation of anagen (GO:0051885)|positive regulation of apoptotic process (GO:0043065)|positive regulation of bone mineralization (GO:0030501)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of cell proliferation (GO:0008284)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of G2/M transition of mitotic cell cycle (GO:0010971)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of RNA polymerase II transcriptional preinitiation complex assembly (GO:0045899)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|protein stabilization (GO:0050821)|regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032434)|regulation of skeletal muscle tissue development (GO:0048641)|sensory perception of taste (GO:0050909)|skeletal muscle fiber development (GO:0048741)|smoothened signaling pathway (GO:0007224)|Wnt signaling pathway (GO:0016055)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	frizzled binding (GO:0005109)|receptor agonist activity (GO:0048018)	p.R278W(1)		central_nervous_system(1)|large_intestine(5)|lung(12)|prostate(1)|skin(4)	23						CGGCCCAGCCGCTCCCTCAAC	0.632													G|||	1	0.000199681	0.0	0.0	5008	,	,		15789	0.001		0.0	False		,,,				2504	0.0				p.R278W												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C832T	12						.						31.0	38.0	36.0					12																	49360216		2199	4292	6491	47646483	SO:0001583	missense	7480	exon5			X97057	CCDS8775.1	12q13	2009-01-02			ENSG00000169884	ENSG00000169884		"""Wingless-type MMTV integration sites"""	12775	protein-coding gene	gene with protein product		601906				9121776, 9284937, 18515319	Standard	NM_003394		Approved	WNT-12, SHFM6	uc001rss.3	O00744	OTTHUMG00000150734	ENST00000301061.4:c.832C>T	12.37:g.49360216G>A	ENSP00000301061:p.Arg278Trp	Somatic		Capture	Illumina HiSeq	Phase_I	47646483	NM_003394	B2R7A5|O00747|Q4VAJ4|Q4VAJ5|Q8WZ97	Missense_Mutation	SNP	ENST00000301061.4	37	CCDS8775.1	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	G	22.2	4.251976	0.80135	.	.	ENSG00000169884	ENST00000301061	T	0.79033	-1.23	4.43	4.43	0.53597	.	0.076059	0.52532	D	0.000080	D	0.90947	0.7154	H	0.94620	3.56	0.80722	D	1	D	0.89917	1.0	D	0.75020	0.985	D	0.93501	0.6844	10	0.87932	D	0	.	16.3501	0.83202	0.0:0.0:1.0:0.0	.	278	O00744	WN10B_HUMAN	W	278	ENSP00000301061:R278W	ENSP00000301061:R278W	R	-	1	2	WNT10B	47646483	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	3.887000	0.56197	2.484000	0.83849	0.561000	0.74099	CGG		0.632	WNT10B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319864.1	NM_003394	
KMT2D	8085	broad.mit.edu	37	12	49427267	49427267	+	Nonsense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr12:49427267G>A	ENST00000301067.7	-	39	11220	c.11221C>T	c.(11221-11223)Caa>Taa	p.Q3741*	KMT2D_ENST00000549743.1_5'Flank	NM_003482.3	NP_003473.3	O14686	KMT2D_HUMAN	lysine (K)-specific methyltransferase 2D	3741	Gln-rich.				chromatin silencing (GO:0006342)|histone H3-K4 methylation (GO:0051568)|oocyte growth (GO:0001555)|oogenesis (GO:0048477)|positive regulation of cell proliferation (GO:0008284)|positive regulation of intracellular estrogen receptor signaling pathway (GO:0033148)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|response to estrogen (GO:0043627)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)	p.Q3471*(1)									tgctgctgttgctgctgctgc	0.577																																					p.Q3741X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.C11221T	12						.						15.0	18.0	17.0					12																	49427267		2196	4294	6490	47713534	SO:0001587	stop_gained	8085	exon39			AF010403	CCDS44873.1	12q13.12	2013-05-09	2013-05-09	2013-05-09	ENSG00000167548	ENSG00000167548		"""Chromatin-modifying enzymes / K-methyltransferases"", ""Zinc fingers, PHD-type"""	7133	protein-coding gene	gene with protein product		602113	"""trinucleotide repeat containing 21"", ""myeloid/lymphoid or mixed-lineage leukemia 2"""	TNRC21, MLL2		9247308	Standard	NM_003482		Approved	ALR, MLL4, CAGL114		O14686	OTTHUMG00000166524	ENST00000301067.7:c.11221C>T	12.37:g.49427267G>A	ENSP00000301067:p.Gln3741*	Somatic		Capture	Illumina HiSeq	Phase_I	47713534	NM_003482	O14687	Nonsense_Mutation	SNP	ENST00000301067.7	37	CCDS44873.1	.	.	.	.	.	.	.	.	.	.	G	50	17.001694	0.99877	.	.	ENSG00000167548	ENST00000301067	.	.	.	5.11	5.11	0.69529	.	0.000000	0.33180	N	0.005197	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	17.6784	0.88236	0.0:0.0:1.0:0.0	.	.	.	.	X	3741	.	ENSP00000301067:Q3741X	Q	-	1	0	MLL2	47713534	1.000000	0.71417	1.000000	0.80357	0.255000	0.26057	8.707000	0.91367	2.547000	0.85894	0.462000	0.41574	CAA		0.577	KMT2D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390183.2		
KMT2D	8085	broad.mit.edu	37	12	49447880	49447880	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr12:49447880C>T	ENST00000301067.7	-	5	553	c.554G>A	c.(553-555)cGc>cAc	p.R185H		NM_003482.3	NP_003473.3	O14686	KMT2D_HUMAN	lysine (K)-specific methyltransferase 2D	185					chromatin silencing (GO:0006342)|histone H3-K4 methylation (GO:0051568)|oocyte growth (GO:0001555)|oogenesis (GO:0048477)|positive regulation of cell proliferation (GO:0008284)|positive regulation of intracellular estrogen receptor signaling pathway (GO:0033148)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|response to estrogen (GO:0043627)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)	p.R185H(1)									TCCAGGTGAGCGGCAAGGGAT	0.592																																					p.R185H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G554A	12						.						61.0	66.0	64.0					12																	49447880		2123	4235	6358	47734147	SO:0001583	missense	8085	exon5			AF010403	CCDS44873.1	12q13.12	2013-05-09	2013-05-09	2013-05-09	ENSG00000167548	ENSG00000167548		"""Chromatin-modifying enzymes / K-methyltransferases"", ""Zinc fingers, PHD-type"""	7133	protein-coding gene	gene with protein product		602113	"""trinucleotide repeat containing 21"", ""myeloid/lymphoid or mixed-lineage leukemia 2"""	TNRC21, MLL2		9247308	Standard	NM_003482		Approved	ALR, MLL4, CAGL114		O14686	OTTHUMG00000166524	ENST00000301067.7:c.554G>A	12.37:g.49447880C>T	ENSP00000301067:p.Arg185His	Somatic		Capture	Illumina HiSeq	Phase_I	47734147	NM_003482	O14687	Missense_Mutation	SNP	ENST00000301067.7	37	CCDS44873.1	.	.	.	.	.	.	.	.	.	.	C	11.87	1.767018	0.31320	.	.	ENSG00000167548	ENST00000301067	T	0.70869	-0.52	4.92	4.92	0.64577	Zinc finger, RING-type (1);Zinc finger, PHD-type (1);	0.000000	0.32473	U	0.006054	T	0.44435	0.1293	N	0.05554	-0.025	0.29511	N	0.854215	B	0.33777	0.425	B	0.20184	0.028	T	0.51196	-0.8736	10	0.87932	D	0	.	7.6403	0.28290	0.0:0.8186:0.0:0.1814	.	185	O14686	MLL2_HUMAN	H	185	ENSP00000301067:R185H	ENSP00000301067:R185H	R	-	2	0	MLL2	47734147	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	1.822000	0.39052	2.270000	0.75569	0.462000	0.41574	CGC		0.592	KMT2D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390183.2		
BCDIN3D	144233	broad.mit.edu	37	12	50232624	50232624	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr12:50232624T>C	ENST00000333924.4	-	2	450	c.409A>G	c.(409-411)Atg>Gtg	p.M137V	BCDIN3D-AS1_ENST00000549124.1_RNA|BCDIN3D-AS1_ENST00000548872.1_RNA	NM_181708.2	NP_859059.1	Q7Z5W3	BN3D2_HUMAN	BCDIN3 domain containing	137	Bin3-type SAM. {ECO:0000255|PROSITE- ProRule:PRU00848}.				miRNA metabolic process (GO:0010586)|negative regulation of pre-miRNA processing (GO:2000632)|RNA methylation (GO:0001510)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	O-methyltransferase activity (GO:0008171)|RNA methyltransferase activity (GO:0008173)	p.M137V(1)		endometrium(1)|kidney(1)|large_intestine(3)|lung(1)|ovary(1)|skin(1)|stomach(1)	9						CTTTGATTCATGAAGTCCAGG	0.453											OREG0021805	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.M137V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A409G	12						.						88.0	89.0	89.0					12																	50232624		2203	4300	6503	48518891	SO:0001583	missense	144233	exon2				CCDS8790.1	12q13.13	2008-03-12				ENSG00000186666			27050	protein-coding gene	gene with protein product							Standard	NM_181708		Approved		uc001rvh.3	Q7Z5W3	OTTHUMG00000169807	ENST00000333924.4:c.409A>G	12.37:g.50232624T>C	ENSP00000335201:p.Met137Val	Somatic	968	Capture	Illumina HiSeq	Phase_I	48518891	NM_181708	A8K829	Missense_Mutation	SNP	ENST00000333924.4	37	CCDS8790.1	.	.	.	.	.	.	.	.	.	.	T	10.65	1.409720	0.25465	.	.	ENSG00000186666	ENST00000333924	T	0.42131	0.98	5.57	4.42	0.53409	Bin3-type S-adenosyl-L-methionine binding domain (1);	0.079880	0.85682	D	0.000000	T	0.26195	0.0639	N	0.21194	0.64	0.80722	D	1	B	0.22276	0.067	B	0.12837	0.008	T	0.05533	-1.0879	10	0.19590	T	0.45	.	9.9903	0.41868	0.0:0.0806:0.0:0.9193	.	137	Q7Z5W3	BN3D2_HUMAN	V	137	ENSP00000335201:M137V	ENSP00000335201:M137V	M	-	1	0	BCDIN3D	48518891	1.000000	0.71417	1.000000	0.80357	0.302000	0.27658	6.089000	0.71384	1.049000	0.40321	0.482000	0.46254	ATG		0.453	BCDIN3D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405982.1	NM_181708	
FAIM2	23017	broad.mit.edu	37	12	50284471	50284471	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr12:50284471C>T	ENST00000320634.3	-	7	614	c.520G>A	c.(520-522)Gtc>Atc	p.V174I	FAIM2_ENST00000550890.1_Missense_Mutation_p.V128I	NM_012306.3	NP_036438.2	Q9BWQ8	LFG2_HUMAN	Fas apoptotic inhibitory molecule 2	174					apoptotic process (GO:0006915)|cerebellar granular layer development (GO:0021681)|cerebellar Purkinje cell differentiation (GO:0021702)|cerebellar Purkinje cell layer development (GO:0021680)|cerebellum development (GO:0021549)|negative regulation of apoptotic process (GO:0043066)|negative regulation of apoptotic signaling pathway (GO:2001234)|negative regulation of neuron apoptotic process (GO:0043524)|regulation of neuron apoptotic process (GO:0043523)|response to ischemia (GO:0002931)	cell junction (GO:0030054)|integral component of membrane (GO:0016021)|membrane raft (GO:0045121)|postsynaptic membrane (GO:0045211)		p.V174I(1)		endometrium(2)|large_intestine(4)|lung(4)|ovary(2)|skin(2)	14						CTTACAAAGACGGTCAGGAGA	0.592																																					p.V174I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G520A	12						.						111.0	103.0	106.0					12																	50284471		2203	4300	6503	48570738	SO:0001583	missense	23017	exon7			AB023167	CCDS8791.1	12q13	2010-03-18				ENSG00000135472			17067	protein-coding gene	gene with protein product	"""transmembrane BAX inhibitor motif containing 2"""	604306				10231032, 10535980	Standard	NM_012306		Approved	KIAA0950, LFG, NMP35, LIFEGUARD, TMBIM2, LFG2	uc001rvj.2	Q9BWQ8	OTTHUMG00000169808	ENST00000320634.3:c.520G>A	12.37:g.50284471C>T	ENSP00000321951:p.Val174Ile	Somatic		Capture	Illumina HiSeq	Phase_I	48570738	NM_012306	A8K1W6|B3KR08|Q9UJY9|Q9Y2F7	Missense_Mutation	SNP	ENST00000320634.3	37	CCDS8791.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	2.463|2.463	-0.323591|-0.323591	0.05350|0.05350	.|.	.|.	ENSG00000135472|ENSG00000135472	ENST00000552863|ENST00000320634;ENST00000550890;ENST00000550635;ENST00000552669	.|T;T;T	.|0.80566	.|1.0;1.0;-1.39	4.8|4.8	-0.366|-0.366	0.12545|0.12545	.|.	.|0.211109	.|0.48767	.|N	.|0.000163	T|T	0.43634|0.43634	0.1256|0.1256	N|N	0.00894|0.00894	-1.105|-1.105	0.26018|0.26018	N|N	0.981904|0.981904	.|B	.|0.06786	.|0.001	.|B	.|0.04013	.|0.001	T|T	0.48736|0.48736	-0.9009|-0.9009	5|10	.|0.02654	.|T	.|1	-12.1005|-12.1005	7.6192|7.6192	0.28175|0.28175	0.0:0.3911:0.0:0.6089|0.0:0.3911:0.0:0.6089	.|.	.|174	.|Q9BWQ8	.|FAIM2_HUMAN	H|I	42|174;128;174;132	.|ENSP00000321951:V174I;ENSP00000450132:V128I;ENSP00000446771:V132I	.|ENSP00000321951:V174I	R|V	-|-	2|1	0|0	FAIM2|FAIM2	48570738|48570738	0.111000|0.111000	0.22076|0.22076	0.995000|0.995000	0.50966|0.50966	0.931000|0.931000	0.56810|0.56810	0.170000|0.170000	0.16663|0.16663	-0.325000|-0.325000	0.08577|0.08577	-0.379000|-0.379000	0.06801|0.06801	CGT|GTC		0.592	FAIM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405984.1	NM_012306	
RACGAP1	29127	broad.mit.edu	37	12	50400233	50400233	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr12:50400233G>T	ENST00000427314.2	-	5	495	c.272C>A	c.(271-273)gCt>gAt	p.A91D	RACGAP1_ENST00000434422.1_Missense_Mutation_p.A91D|RACGAP1_ENST00000551016.1_Missense_Mutation_p.A91D|RACGAP1_ENST00000454520.2_Missense_Mutation_p.A91D|RACGAP1_ENST00000312377.5_Missense_Mutation_p.A91D|RACGAP1_ENST00000547905.1_Missense_Mutation_p.A91D	NM_013277.3	NP_037409.2			Rac GTPase activating protein 1									p.A91D(1)		cervix(1)|endometrium(1)|kidney(3)|large_intestine(3)|lung(6)	14						TTCGCAGTCAGCCTCAGCTCT	0.478																																					p.A91D												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C272A	12						.						206.0	175.0	186.0					12																	50400233		2203	4300	6503	48686500	SO:0001583	missense	29127	exon5				CCDS8795.1	12q13	2004-05-17				ENSG00000161800			9804	protein-coding gene	gene with protein product		604980				9497316	Standard	NM_013277		Approved	MgcRacGAP	uc001rvs.2	Q9H0H5		ENST00000427314.2:c.272C>A	12.37:g.50400233G>T	ENSP00000404190:p.Ala91Asp	Somatic		Capture	Illumina HiSeq	Phase_I	48686500	NM_013277		Missense_Mutation	SNP	ENST00000427314.2	37	CCDS8795.1	.	.	.	.	.	.	.	.	.	.	G	15.42	2.826983	0.50739	.	.	ENSG00000161800	ENST00000427314;ENST00000312377;ENST00000434422;ENST00000454520;ENST00000551016;ENST00000547905;ENST00000552310;ENST00000546595;ENST00000551145;ENST00000548824;ENST00000548644;ENST00000546723;ENST00000552921;ENST00000552157;ENST00000546764;ENST00000551876;ENST00000549777;ENST00000550651;ENST00000552004	T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.81163	-1.46;-1.46;-1.46;-1.46;-1.46;-1.46;-1.46;-1.46;-1.46;-1.0;-1.0;-1.0;-1.0;2.24;-1.0;-1.0;-1.0;-1.0;-1.0	5.48	5.48	0.80851	.	0.206953	0.50627	D	0.000116	T	0.78483	0.4290	L	0.39633	1.23	0.43330	D	0.995365	D	0.56287	0.975	P	0.50192	0.634	T	0.79914	-0.1602	10	0.62326	D	0.03	-1.5311	10.8308	0.46659	0.1457:0.0:0.8543:0.0	.	91	Q9H0H5	RGAP1_HUMAN	D	91;91;91;91;91;91;91;33;33;91;103;91;91;33;91;91;91;91;91	ENSP00000404190:A91D;ENSP00000309871:A91D;ENSP00000413241:A91D;ENSP00000404808:A91D;ENSP00000449374:A91D;ENSP00000449370:A91D;ENSP00000448697:A91D;ENSP00000449963:A33D;ENSP00000450064:A33D;ENSP00000449170:A91D;ENSP00000449620:A103D;ENSP00000449669:A91D;ENSP00000447393:A91D;ENSP00000448968:A33D;ENSP00000447177:A91D;ENSP00000449186:A91D;ENSP00000448707:A91D;ENSP00000449959:A91D;ENSP00000448136:A91D	ENSP00000309871:A91D	A	-	2	0	RACGAP1	48686500	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	4.916000	0.63362	2.580000	0.87095	0.655000	0.94253	GCT		0.478	RACGAP1-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405997.1	NM_013277	
GALNT6	11226	broad.mit.edu	37	12	51754523	51754523	+	Silent	SNP	G	G	A	rs138065864		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr12:51754523G>A	ENST00000543196.2	-	6	1354	c.1149C>T	c.(1147-1149)aaC>aaT	p.N383N	GALNT6_ENST00000356317.3_Silent_p.N383N			Q8NCL4	GALT6_HUMAN	polypeptide N-acetylgalactosaminyltransferase 6	383	Catalytic subdomain B.				cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|protein O-linked glycosylation (GO:0006493)	Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)|polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)	p.N383N(1)		endometrium(2)|large_intestine(6)|lung(7)|ovary(3)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	27						ACATTTCCACGTTCTCCCCTC	0.542																																					p.N383N												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1149T	12						.	G		1,4405	2.1+/-5.4	0,1,2202	133.0	115.0	121.0		1149	3.7	1.0	12	dbSNP_134	121	0,8600		0,0,4300	no	coding-synonymous	GALNT6	NM_007210.3		0,1,6502	AA,AG,GG		0.0,0.0227,0.0077		383/623	51754523	1,13005	2203	4300	6503	50040790	SO:0001819	synonymous_variant	11226	exon7			Y08565	CCDS8813.1	12q13	2014-03-13	2014-03-13		ENSG00000139629	ENSG00000139629		"""Glycosyltransferase family 2 domain containing"""	4128	protein-coding gene	gene with protein product	"""polypeptide GalNAc transferase 6"""	605148	"""UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 6 (GalNAc-T6)"""			10464263	Standard	NM_007210		Approved	GalNAc-T6	uc001ryl.1	Q8NCL4		ENST00000543196.2:c.1149C>T	12.37:g.51754523G>A		Somatic		Capture	Illumina HiSeq	Phase_I	50040790	NM_007210	Q8IYH4|Q9H6G2|Q9UIV5	Silent	SNP	ENST00000543196.2	37	CCDS8813.1																																																																																				0.542	GALNT6-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000469735.1	NM_007210	
ACVR1B	91	broad.mit.edu	37	12	52377920	52377920	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr12:52377920C>T	ENST00000257963.4	+	5	1026	c.949C>T	c.(949-951)Cac>Tac	p.H317Y	ACVR1B_ENST00000563121.1_3'UTR|ACVR1B_ENST00000415850.2_Missense_Mutation_p.H317Y|ACVR1B_ENST00000542485.1_Missense_Mutation_p.H265Y|ACVR1B_ENST00000426655.2_Missense_Mutation_p.H317Y|ACVR1B_ENST00000541224.1_Missense_Mutation_p.H358Y	NM_004302.4|NM_020328.3	NP_004293.1|NP_064733.3	P36896	ACV1B_HUMAN	activin A receptor, type IB	317	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activin receptor signaling pathway (GO:0032924)|central nervous system development (GO:0007417)|development of primary female sexual characteristics (GO:0046545)|extrinsic apoptotic signaling pathway (GO:0097191)|G1/S transition of mitotic cell cycle (GO:0000082)|hair follicle development (GO:0001942)|in utero embryonic development (GO:0001701)|negative regulation of cell growth (GO:0030308)|nodal signaling pathway (GO:0038092)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of activin receptor signaling pathway (GO:0032927)|positive regulation of erythrocyte differentiation (GO:0045648)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of trophoblast cell migration (GO:1901165)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)|transmembrane receptor protein serine/threonine kinase signaling pathway (GO:0007178)	cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	activin receptor activity, type I (GO:0016361)|ATP binding (GO:0005524)|inhibin binding (GO:0034711)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|receptor signaling protein serine/threonine kinase activity (GO:0004702)|SMAD binding (GO:0046332)|transforming growth factor beta-activated receptor activity (GO:0005024)|transmembrane receptor protein serine/threonine kinase activity (GO:0004675)|ubiquitin protein ligase binding (GO:0031625)	p.H317Y(1)|p.H358Y(1)		breast(5)|endometrium(4)|kidney(5)|large_intestine(12)|lung(10)|ovary(1)|pancreas(6)|prostate(1)	44				BRCA - Breast invasive adenocarcinoma(357;0.104)	Adenosine triphosphate(DB00171)	TGGGCTGGCACACCTGCACAT	0.542																																					p.H265Y												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.C793T	12						.						97.0	76.0	83.0					12																	52377920		2203	4300	6503	50664187	SO:0001583	missense	91	exon5				CCDS8816.1, CCDS44893.1, CCDS44894.1, CCDS44893.2, CCDS44894.2	12q13	2006-11-09			ENSG00000135503	ENSG00000135503			172	protein-coding gene	gene with protein product		601300		ACVRLK4		8397373	Standard	NM_020327		Approved	ALK4, SKR2, ActRIB	uc010snn.2	P36896	OTTHUMG00000167920	ENST00000257963.4:c.949C>T	12.37:g.52377920C>T	ENSP00000257963:p.His317Tyr	Somatic		Capture	Illumina HiSeq	Phase_I	50664187	NM_020327	B7Z5L8|B7Z5W5|Q15479|Q15480|Q15481|Q15482	Missense_Mutation	SNP	ENST00000257963.4	37	CCDS8816.1	.	.	.	.	.	.	.	.	.	.	C	32	5.137954	0.94517	.	.	ENSG00000135503	ENST00000257963;ENST00000541224;ENST00000426655;ENST00000415850;ENST00000542485	T;T;T;T;T	0.55760	0.5;0.5;0.5;0.5;0.5	5.28	5.28	0.74379	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.58666	0.2138	N	0.12527	0.23	0.80722	D	1	D;D;P;P	0.89917	0.965;1.0;0.847;0.847	P;D;B;P	0.97110	0.833;1.0;0.387;0.614	T	0.67162	-0.5740	10	0.87932	D	0	.	19.2879	0.94085	0.0:1.0:0.0:0.0	.	358;317;317;317	P36896-4;P36896;P36896-2;P36896-3	.;ACV1B_HUMAN;.;.	Y	317;358;317;317;265	ENSP00000257963:H317Y;ENSP00000442656:H358Y;ENSP00000390477:H317Y;ENSP00000397550:H317Y;ENSP00000442885:H265Y	ENSP00000257963:H317Y	H	+	1	0	ACVR1B	50664187	1.000000	0.71417	0.996000	0.52242	0.970000	0.65996	7.786000	0.85741	2.644000	0.89710	0.655000	0.94253	CAC		0.542	ACVR1B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397000.1	NM_020328	
KRT85	3891	broad.mit.edu	37	12	52758769	52758769	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr12:52758769C>A	ENST00000257901.3	-	2	681	c.606G>T	c.(604-606)gaG>gaT	p.E202D	KRT85_ENST00000544265.1_5'Flank	NM_002283.3	NP_002274.1	P78386	KRT85_HUMAN	keratin 85	202	Coil 1B.|Rod.				epidermis development (GO:0008544)	extracellular space (GO:0005615)|keratin filament (GO:0045095)	structural molecule activity (GO:0005198)	p.E202D(1)		NS(1)|breast(1)|endometrium(6)|kidney(1)|large_intestine(7)|liver(1)|lung(15)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	36	Myeloproliferative disorder(4;0.0484)|all_hematologic(5;0.088)			BRCA - Breast invasive adenocarcinoma(357;0.189)		CCTCCAGCACCTCCTGCACAT	0.622																																					p.E202D												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G606T	12						.						106.0	113.0	110.0					12																	52758769		2203	4300	6503	51045036	SO:0001583	missense	3891	exon2			X99140	CCDS8824.1, CCDS73472.1	12q13.13	2013-06-20	2006-07-17	2006-07-17	ENSG00000135443	ENSG00000135443		"""-"", ""Intermediate filaments type II, keratins (basic)"""	6462	protein-coding gene	gene with protein product	"""hard keratin type II"""	602767	"""keratin, hair, basic, 5"""	KRTHB5		9084137, 16831889	Standard	NM_002283		Approved	Hb-5	uc001sag.3	P78386	OTTHUMG00000169633	ENST00000257901.3:c.606G>T	12.37:g.52758769C>A	ENSP00000257901:p.Glu202Asp	Somatic		Capture	Illumina HiSeq	Phase_I	51045036	NM_002283	Q9NSB1	Missense_Mutation	SNP	ENST00000257901.3	37	CCDS8824.1	.	.	.	.	.	.	.	.	.	.	C	9.410	1.080165	0.20309	.	.	ENSG00000135443	ENST00000257901	T	0.75704	-0.96	4.7	1.66	0.24008	Filament (1);	0.000000	0.56097	D	0.000024	T	0.53850	0.1822	L	0.36672	1.1	0.80722	D	1	B	0.17852	0.024	B	0.29353	0.101	T	0.40664	-0.9551	10	0.02654	T	1	.	1.5707	0.02614	0.228:0.4343:0.1676:0.1701	.	202	P78386	KRT85_HUMAN	D	202	ENSP00000257901:E202D	ENSP00000257901:E202D	E	-	3	2	KRT85	51045036	0.002000	0.14202	0.995000	0.50966	0.887000	0.51463	-0.159000	0.10056	0.570000	0.29347	0.491000	0.48974	GAG		0.622	KRT85-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405184.1	NM_002283	
KRT82	3888	broad.mit.edu	37	12	52799668	52799668	+	Missense_Mutation	SNP	C	C	T	rs149651491		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr12:52799668C>T	ENST00000257974.2	-	1	471	c.394G>A	c.(394-396)Gca>Aca	p.A132T	RP11-1020M18.10_ENST00000548135.1_RNA	NM_033033.3	NP_149022.3	Q9NSB4	KRT82_HUMAN	keratin 82	132	Coil 1A.|Rod.					keratin filament (GO:0045095)	structural constituent of epidermis (GO:0030280)	p.A132T(1)		endometrium(1)|kidney(2)|large_intestine(6)|liver(2)|lung(13)|ovary(1)|skin(3)|upper_aerodigestive_tract(1)	29				BRCA - Breast invasive adenocarcinoma(357;0.193)		ATGAAAGATGCGAAACGGTTG	0.567													C|||	1	0.000199681	0.0008	0.0	5008	,	,		20645	0.0		0.0	False		,,,				2504	0.0				p.A132T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G394A	12						.						287.0	265.0	273.0					12																	52799668		2203	4300	6503	51085935	SO:0001583	missense	3888	exon1			Y19207	CCDS8826.1	12q13	2013-01-16	2006-07-17	2006-07-17		ENSG00000161850		"""-"", ""Intermediate filaments type II, keratins (basic)"""	6459	protein-coding gene	gene with protein product	"""hard keratin type II 2"""	601078	"""keratin, hair, basic, 2"""	KRTHB2		2431943, 16831889	Standard	NM_033033		Approved	Hb-2	uc001sai.1	Q9NSB4	OTTHUMG00000169636	ENST00000257974.2:c.394G>A	12.37:g.52799668C>T	ENSP00000257974:p.Ala132Thr	Somatic		Capture	Illumina HiSeq	Phase_I	51085935	NM_033033		Missense_Mutation	SNP	ENST00000257974.2	37	CCDS8826.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	C	24.8	4.567412	0.86439	.	.	ENSG00000161850	ENST00000257974	D	0.95205	-3.64	4.99	4.99	0.66335	Filament (1);	0.130764	0.34200	N	0.004179	D	0.98204	0.9406	H	0.95611	3.695	0.48696	D	0.999694	D	0.89917	1.0	D	0.91635	0.999	D	0.99501	1.0953	10	0.87932	D	0	.	18.6545	0.91445	0.0:1.0:0.0:0.0	.	132	Q9NSB4	KRT82_HUMAN	T	132	ENSP00000257974:A132T	ENSP00000257974:A132T	A	-	1	0	KRT82	51085935	1.000000	0.71417	0.990000	0.47175	0.652000	0.38707	7.590000	0.82653	2.481000	0.83766	0.655000	0.94253	GCA		0.567	KRT82-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405189.1	NM_033033	
KRT71	112802	broad.mit.edu	37	12	52941728	52941728	+	Silent	SNP	G	G	A	rs137924493	byFrequency	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr12:52941728G>A	ENST00000267119.5	-	6	1086	c.1017C>T	c.(1015-1017)gaC>gaT	p.D339D		NM_033448.2	NP_258259.1	Q3SY84	K2C71_HUMAN	keratin 71	339	Coil 2.|Rod.				hair follicle morphogenesis (GO:0031069)|intermediate filament organization (GO:0045109)	extracellular vesicular exosome (GO:0070062)|keratin filament (GO:0045095)	structural molecule activity (GO:0005198)	p.D339D(1)		breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(9)|ovary(1)|skin(1)|urinary_tract(1)	22				BRCA - Breast invasive adenocarcinoma(357;0.194)		TTTTGAGGTCGTCCCCATGCC	0.537																																					p.D339D												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1017T	12						.	G		1,4405	2.1+/-5.4	0,1,2202	126.0	112.0	117.0		1017	-8.5	0.6	12	dbSNP_134	117	1,8599	1.2+/-3.3	0,1,4299	yes	coding-synonymous	KRT71	NM_033448.2		0,2,6501	AA,AG,GG		0.0116,0.0227,0.0154		339/524	52941728	2,13004	2203	4300	6503	51227995	SO:0001819	synonymous_variant	112802	exon6			AJ308600	CCDS8831.1	12q13.13	2013-01-16			ENSG00000139648	ENSG00000139648		"""-"", ""Intermediate filaments type II, keratins (basic)"""	28927	protein-coding gene	gene with protein product		608245				11982755, 12648212, 16831889	Standard	NM_033448		Approved	KRT6IRS, KRT6IRS1, K6IRS1	uc001sao.3	Q3SY84	OTTHUMG00000167831	ENST00000267119.5:c.1017C>T	12.37:g.52941728G>A		Somatic		Capture	Illumina HiSeq	Phase_I	51227995	NM_033448	B3KVC1|Q3SY85|Q96DU2	Silent	SNP	ENST00000267119.5	37	CCDS8831.1																																																																																				0.537	KRT71-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396487.1	NM_033448	
KRT71	112802	broad.mit.edu	37	12	52946854	52946854	+	Missense_Mutation	SNP	C	C	T	rs377197035	byFrequency	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr12:52946854C>T	ENST00000267119.5	-	1	77	c.8G>A	c.(7-9)cGc>cAc	p.R3H		NM_033448.2	NP_258259.1	Q3SY84	K2C71_HUMAN	keratin 71	3	Head.				hair follicle morphogenesis (GO:0031069)|intermediate filament organization (GO:0045109)	extracellular vesicular exosome (GO:0070062)|keratin filament (GO:0045095)	structural molecule activity (GO:0005198)	p.R3H(1)		breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(9)|ovary(1)|skin(1)|urinary_tract(1)	22				BRCA - Breast invasive adenocarcinoma(357;0.194)		GGTGAATTGGCGGCTCATGTT	0.597													C|||	4	0.000798722	0.0	0.0	5008	,	,		17873	0.0		0.0	False		,,,				2504	0.0041				p.R3H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G8A	12						.	C	HIS/ARG	1,4401		0,1,2200	39.0	46.0	44.0		8	5.1	1.0	12		44	0,8596		0,0,4298	no	missense	KRT71	NM_033448.2	29	0,1,6498	TT,TC,CC		0.0,0.0227,0.0077	probably-damaging	3/524	52946854	1,12997	2201	4298	6499	51233121	SO:0001583	missense	112802	exon1			AJ308600	CCDS8831.1	12q13.13	2013-01-16			ENSG00000139648	ENSG00000139648		"""-"", ""Intermediate filaments type II, keratins (basic)"""	28927	protein-coding gene	gene with protein product		608245				11982755, 12648212, 16831889	Standard	NM_033448		Approved	KRT6IRS, KRT6IRS1, K6IRS1	uc001sao.3	Q3SY84	OTTHUMG00000167831	ENST00000267119.5:c.8G>A	12.37:g.52946854C>T	ENSP00000267119:p.Arg3His	Somatic		Capture	Illumina HiSeq	Phase_I	51233121	NM_033448	B3KVC1|Q3SY85|Q96DU2	Missense_Mutation	SNP	ENST00000267119.5	37	CCDS8831.1	.	.	.	.	.	.	.	.	.	.	C	21.5	4.165782	0.78339	2.27E-4	0.0	ENSG00000139648	ENST00000267119	D	0.83163	-1.69	5.08	5.08	0.68730	.	0.000000	0.46145	D	0.000309	D	0.91297	0.7256	M	0.86573	2.825	0.41855	D	0.990199	D	0.76494	0.999	D	0.66979	0.948	D	0.92676	0.6154	10	0.72032	D	0.01	.	14.3554	0.66733	0.0:1.0:0.0:0.0	.	3	Q3SY84	K2C71_HUMAN	H	3	ENSP00000267119:R3H	ENSP00000267119:R3H	R	-	2	0	KRT71	51233121	1.000000	0.71417	1.000000	0.80357	0.862000	0.49288	2.163000	0.42377	2.532000	0.85374	0.655000	0.94253	CGC		0.597	KRT71-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396487.1	NM_033448	
KRT79	338785	broad.mit.edu	37	12	53216903	53216903	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr12:53216903G>T	ENST00000330553.5	-	7	1298	c.1264C>A	c.(1264-1266)Ctg>Atg	p.L422M		NM_175834.2	NP_787028.1	Q5XKE5	K2C79_HUMAN	keratin 79	422	Coil 2.|Rod.					extracellular vesicular exosome (GO:0070062)|keratin filament (GO:0045095)	enzyme binding (GO:0019899)|structural molecule activity (GO:0005198)	p.L422M(1)		endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(11)|ovary(2)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	30						AGCCGTGTCAGGTCCTCCTTG	0.612																																					p.L422M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1264A	12						.						98.0	91.0	93.0					12																	53216903		2203	4300	6503	51503170	SO:0001583	missense	338785	exon7			AJ564105	CCDS8839.1	12q13.13	2014-02-12	2007-07-03		ENSG00000185640	ENSG00000185640		"""-"", ""Intermediate filaments type II, keratins (basic)"""	28930	protein-coding gene	gene with protein product	"""keratin 6-like"""	611160				11683385	Standard	NM_175834		Approved	K6L, KRT6L	uc001sbb.3	Q5XKE5	OTTHUMG00000169878	ENST00000330553.5:c.1264C>A	12.37:g.53216903G>T	ENSP00000328358:p.Leu422Met	Somatic		Capture	Illumina HiSeq	Phase_I	51503170	NM_175834	Q6P465|Q7Z793	Missense_Mutation	SNP	ENST00000330553.5	37	CCDS8839.1	.	.	.	.	.	.	.	.	.	.	G	6.071	0.381379	0.11466	.	.	ENSG00000185640	ENST00000330553;ENST00000549255	D;D	0.88201	-2.35;-2.35	3.92	0.561	0.17285	Filament (1);	0.000000	0.35124	N	0.003426	T	0.76111	0.3942	N	0.04043	-0.29	0.33536	D	0.594249	P	0.50617	0.937	P	0.55345	0.774	T	0.76386	-0.2978	10	0.02654	T	1	.	4.1865	0.10400	0.2127:0.0:0.3938:0.3935	.	422	Q5XKE5	K2C79_HUMAN	M	422;8	ENSP00000328358:L422M;ENSP00000449159:L8M	ENSP00000328358:L422M	L	-	1	2	KRT79	51503170	0.997000	0.39634	0.993000	0.49108	0.148000	0.21650	1.361000	0.34136	0.097000	0.17492	-0.234000	0.12200	CTG		0.612	KRT79-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406376.1	NM_175834	
NPFF	8620	broad.mit.edu	37	12	53898576	53898576	+	IGR	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr12:53898576G>A	ENST00000267017.3	-	0	592				TARBP2_ENST00000266987.2_Missense_Mutation_p.R197Q|TARBP2_ENST00000456234.2_Missense_Mutation_p.R176Q|TARBP2_ENST00000552857.1_Missense_Mutation_p.R106Q|TARBP2_ENST00000394357.2_Missense_Mutation_p.R176Q	NM_003717.2	NP_003708.1	O15130	NPFF_HUMAN	neuropeptide FF-amide peptide precursor						acute inflammatory response to antigenic stimulus (GO:0002438)|maternal process involved in female pregnancy (GO:0060135)|negative regulation of appetite (GO:0032099)|negative regulation of heart rate (GO:0010459)|negative regulation of insulin secretion (GO:0046676)|neuropeptide signaling pathway (GO:0007218)|positive regulation of blood pressure (GO:0045777)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of membrane depolarization (GO:0003254)|regulation of sensory perception of pain (GO:0051930)|response to drug (GO:0042493)|response to morphine (GO:0043278)|somatostatin secretion (GO:0070253)|spinal cord development (GO:0021510)|synaptic transmission (GO:0007268)|vasopressin secretion (GO:0030103)	axon terminus (GO:0043679)|dendrite (GO:0030425)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|perikaryon (GO:0043204)|vesicle (GO:0031982)	receptor binding (GO:0005102)	p.R197Q(1)		haematopoietic_and_lymphoid_tissue(1)|prostate(1)|urinary_tract(1)	3						ATGACCTGTCGAGTGGAGCGT	0.587																																					p.R176Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G527A	12						.						80.0	81.0	81.0					12																	53898576		2203	4300	6503	52184843	SO:0001628	intergenic_variant	6895	exon6			AF005271	CCDS8862.1	12q13.13	2013-02-26			ENSG00000139574	ENSG00000139574		"""Endogenous ligands"""	7901	protein-coding gene	gene with protein product		604643				9224703	Standard	NM_003717		Approved	FMRFAL	uc001sdw.1	O15130	OTTHUMG00000169856		12.37:g.53898576G>A		Somatic		Capture	Illumina HiSeq	Phase_I	52184843	NM_004178	Q3SXL4	Missense_Mutation	SNP	ENST00000267017.3	37	CCDS8862.1	.	.	.	.	.	.	.	.	.	.	G	34	5.328169	0.95733	.	.	ENSG00000139546	ENST00000266987;ENST00000456234;ENST00000552857;ENST00000394357;ENST00000550407	T;T;T;T	0.77358	-1.09;-1.09;-1.09;-1.09	4.9	4.0	0.46444	Double-stranded RNA-binding (3);Double-stranded RNA-binding-like (1);	0.056895	0.64402	N	0.000002	T	0.64692	0.2621	L	0.31157	0.91	0.58432	D	0.999996	P;B	0.40731	0.728;0.202	B;B	0.35073	0.195;0.027	T	0.67971	-0.5532	10	0.52906	T	0.07	-19.8437	12.2912	0.54819	0.0841:0.0:0.9159:0.0	.	197;197	A8K3X2;Q15633	.;TRBP2_HUMAN	Q	197;176;106;176;98	ENSP00000266987:R197Q;ENSP00000416077:R176Q;ENSP00000449537:R106Q;ENSP00000377885:R176Q	ENSP00000266987:R197Q	R	+	2	0	TARBP2	52184843	1.000000	0.71417	0.998000	0.56505	0.993000	0.82548	7.392000	0.79840	1.426000	0.47256	0.491000	0.48974	CGA		0.587	NPFF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406301.1	NM_003717	
HOXC4	3221	broad.mit.edu	37	12	54447940	54447940	+	Silent	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr12:54447940G>A	ENST00000430889.2	+	1	280	c.234G>A	c.(232-234)tcG>tcA	p.S78S	HOXC4_ENST00000303406.4_Silent_p.S78S|HOXC4_ENST00000609810.1_Silent_p.S78S	NM_153633.2	NP_705897.1	P09017	HXC4_HUMAN	homeobox C4	78					multicellular organismal development (GO:0007275)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.S78S(1)		cervix(1)|kidney(2)|large_intestine(4)|lung(3)|ovary(1)|prostate(1)|urinary_tract(1)	13						CCGGCAATTCGCGAGGCCACG	0.706																																					p.S78S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G234A	12						.						33.0	41.0	38.0					12																	54447940		2203	4300	6503	52734207	SO:0001819	synonymous_variant	3221	exon3				CCDS8873.1	12q13.13	2011-06-20	2005-12-22		ENSG00000198353	ENSG00000198353		"""Homeoboxes / ANTP class : HOXL subclass"""	5126	protein-coding gene	gene with protein product		142974	"""homeo box C4"""	HOX3, HOX3E		1973146, 1358459	Standard	NM_014620		Approved		uc001sex.3	P09017	OTTHUMG00000160036	ENST00000430889.2:c.234G>A	12.37:g.54447940G>A		Somatic		Capture	Illumina HiSeq	Phase_I	52734207	NM_014620		Silent	SNP	ENST00000430889.2	37	CCDS8873.1																																																																																				0.706	HOXC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358963.1		
NFE2	4778	broad.mit.edu	37	12	54686486	54686486	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr12:54686486G>A	ENST00000540264.2	-	2	1303	c.794C>T	c.(793-795)gCg>gTg	p.A265V	RP11-968A15.8_ENST00000553061.1_RNA|NFE2_ENST00000553070.1_Missense_Mutation_p.A265V|NFE2_ENST00000312156.4_Missense_Mutation_p.A265V|NFE2_ENST00000435572.2_Missense_Mutation_p.A265V			Q16621	NFE2_HUMAN	nuclear factor, erythroid 2	265					blood circulation (GO:0008015)|blood coagulation (GO:0007596)|cell-cell signaling (GO:0007267)|hemostasis (GO:0007599)|labyrinthine layer blood vessel development (GO:0060716)|multicellular organismal development (GO:0007275)|negative regulation of bone mineralization (GO:0030502)|negative regulation of syncytium formation by plasma membrane fusion (GO:0034242)|nucleosome disassembly (GO:0006337)|positive regulation of peptidyl-lysine acetylation (GO:2000758)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	protein N-terminus binding (GO:0047485)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|WW domain binding (GO:0050699)	p.A265V(1)		breast(1)|central_nervous_system(1)|large_intestine(5)|lung(7)|upper_aerodigestive_tract(2)	16						CCGGACTAGCGCTAGCTGGCT	0.547																																					p.A265V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C794T	12						.						46.0	44.0	45.0					12																	54686486		2203	4300	6503	52972753	SO:0001583	missense	4778	exon3			BC005044	CCDS8876.1	12q13	2013-08-23	2013-08-23			ENSG00000123405		"""basic leucine zipper proteins"""	7780	protein-coding gene	gene with protein product		601490	"""nuclear factor (erythroid-derived 2), 45kD"", ""nuclear factor (erythroid-derived 2), 45kDa"""			8355703	Standard	NM_001136023		Approved	NF-E2	uc001sfr.5	Q16621		ENST00000540264.2:c.794C>T	12.37:g.54686486G>A	ENSP00000439120:p.Ala265Val	Somatic		Capture	Illumina HiSeq	Phase_I	52972753	NM_001136023	Q07720|Q6ICV9	Missense_Mutation	SNP	ENST00000540264.2	37	CCDS8876.1	.	.	.	.	.	.	.	.	.	.	G	35	5.445070	0.96187	.	.	ENSG00000123405	ENST00000312156;ENST00000435572;ENST00000540264;ENST00000553070;ENST00000553198	D;D;D;D;D	0.91295	-2.82;-2.82;-2.82;-2.82;-2.82	5.42	5.42	0.78866	Basic-leucine zipper (bZIP) transcription factor (1);Eukaryotic transcription factor, Skn-1-like, DNA-binding (2);	0.058142	0.64402	D	0.000002	D	0.95589	0.8566	M	0.84219	2.685	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.95861	0.8883	10	0.87932	D	0	-13.0461	17.0946	0.86631	0.0:0.0:1.0:0.0	.	265	Q16621	NFE2_HUMAN	V	265	ENSP00000312436:A265V;ENSP00000397185:A265V;ENSP00000439120:A265V;ENSP00000447558:A265V;ENSP00000446929:A265V	ENSP00000312436:A265V	A	-	2	0	NFE2	52972753	1.000000	0.71417	0.973000	0.42090	0.991000	0.79684	4.775000	0.62346	2.711000	0.92665	0.655000	0.94253	GCG		0.547	NFE2-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405747.1	NM_006163	
MMP19	4327	broad.mit.edu	37	12	56233331	56233331	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr12:56233331G>A	ENST00000322569.4	-	5	806	c.715C>T	c.(715-717)Ccc>Tcc	p.P239S	MMP19_ENST00000547487.1_5'Flank|MMP19_ENST00000548629.1_Missense_Mutation_p.P216S|MMP19_ENST00000394182.1_5'Flank|MMP19_ENST00000409200.3_Intron	NM_002429.4	NP_002420.1	Q99542	MMP19_HUMAN	matrix metallopeptidase 19	239					angiogenesis (GO:0001525)|cell differentiation (GO:0030154)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|luteolysis (GO:0001554)|ovarian follicle development (GO:0001541)|ovulation from ovarian follicle (GO:0001542)|proteolysis (GO:0006508)|response to cAMP (GO:0051591)|response to hormone (GO:0009725)	extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)	p.P239S(1)		endometrium(1)|kidney(2)|large_intestine(7)|lung(12)|ovary(2)|skin(2)	26					Marimastat(DB00786)	TTAAAGTGGGGCCGGTAGCCC	0.622																																					p.P239S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C715T	12						.						56.0	50.0	52.0					12																	56233331		2203	4300	6503	54519598	SO:0001583	missense	4327	exon5			X92521	CCDS8895.1, CCDS61146.1	12q14	2005-08-08	2005-08-08			ENSG00000123342			7165	protein-coding gene	gene with protein product		601807	"""matrix metalloproteinase 19"""	MMP18		9232430	Standard	NM_002429		Approved	RASI-1	uc001sib.4	Q99542	OTTHUMG00000170216	ENST00000322569.4:c.715C>T	12.37:g.56233331G>A	ENSP00000313437:p.Pro239Ser	Somatic		Capture	Illumina HiSeq	Phase_I	54519598	NM_002429	B4E030|O15278|O95606|Q99580	Missense_Mutation	SNP	ENST00000322569.4	37	CCDS8895.1	.	.	.	.	.	.	.	.	.	.	G	13.00	2.105439	0.37145	.	.	ENSG00000123342	ENST00000322569;ENST00000548629	T;T	0.16324	2.65;2.35	5.75	5.75	0.90469	Peptidase M10, metallopeptidase (1);Peptidase, metallopeptidase (1);Metallopeptidase, catalytic domain (1);	0.222920	0.46758	D	0.000272	T	0.14399	0.0348	L	0.27975	0.815	0.80722	D	1	P	0.36354	0.549	B	0.34824	0.19	T	0.04930	-1.0917	10	0.33141	T	0.24	.	17.4302	0.87537	0.0:0.0:1.0:0.0	.	239	Q99542	MMP19_HUMAN	S	239;216	ENSP00000313437:P239S;ENSP00000446979:P216S	ENSP00000313437:P239S	P	-	1	0	MMP19	54519598	0.999000	0.42202	0.992000	0.48379	0.043000	0.13939	3.119000	0.50422	2.721000	0.93114	0.511000	0.50034	CCC		0.622	MMP19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408023.1	NM_002429	
BAZ2A	11176	broad.mit.edu	37	12	56999644	56999644	+	Silent	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr12:56999644C>T	ENST00000551812.1	-	13	2662	c.2469G>A	c.(2467-2469)ccG>ccA	p.P823P	BAZ2A_ENST00000179765.5_Silent_p.P791P|BAZ2A_ENST00000549884.1_Silent_p.P821P|BAZ2A_ENST00000379441.3_Silent_p.P793P	NM_013449.3	NP_038477.2	Q9UIF9	BAZ2A_HUMAN	bromodomain adjacent to zinc finger domain, 2A	823					chromatin remodeling (GO:0006338)|chromatin silencing at rDNA (GO:0000183)|DNA methylation (GO:0006306)|heterochromatin assembly involved in chromatin silencing (GO:0070869)|histone deacetylation (GO:0016575)|histone H3-K9 methylation (GO:0051567)|histone H4 deacetylation (GO:0070933)|histone H4-K20 methylation (GO:0034770)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	chromatin silencing complex (GO:0005677)|nucleolus (GO:0005730)|rDNA heterochromatin (GO:0033553)	DNA binding (GO:0003677)|ligand-dependent nuclear receptor binding (GO:0016922)|lysine-acetylated histone binding (GO:0070577)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)	p.P823P(1)		breast(1)|cervix(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(15)|urinary_tract(1)	31						TATCCTCTGTCGGCTTCTTCA	0.493																																					p.P823P												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G2469A	12						.						46.0	45.0	46.0					12																	56999644		1929	4135	6064	55285911	SO:0001819	synonymous_variant	11176	exon13			AB032254	CCDS44924.1, CCDS73483.1	12q13.3	2013-01-28				ENSG00000076108		"""Zinc fingers, PHD-type"""	962	protein-coding gene	gene with protein product	"""TTF-I interacting peptide 5"""	605682				10662543, 11532953	Standard	XM_005268596		Approved	KIAA0314, TIP5, WALp3	uc001slq.1	Q9UIF9	OTTHUMG00000170332	ENST00000551812.1:c.2469G>A	12.37:g.56999644C>T		Somatic		Capture	Illumina HiSeq	Phase_I	55285911	NM_013449	B3KN66|O00536|O15030|Q68DI8|Q96H26	Silent	SNP	ENST00000551812.1	37	CCDS44924.1																																																																																				0.493	BAZ2A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000408561.1	NM_013449	
NAB2	4665	broad.mit.edu	37	12	57486732	57486732	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr12:57486732T>C	ENST00000300131.3	+	4	1502	c.1124T>C	c.(1123-1125)cTg>cCg	p.L375P	NAB2_ENST00000357680.4_3'UTR|NAB2_ENST00000342556.6_Missense_Mutation_p.L375P	NM_005967.3	NP_005958.1	Q15742	NAB2_HUMAN	NGFI-A binding protein 2 (EGR1 binding protein 2)	375	Necessary for nuclear localization. {ECO:0000250}.				cell proliferation (GO:0008283)|endochondral ossification (GO:0001958)|myelination (GO:0042552)|negative regulation of transcription from RNA polymerase III promoter (GO:0016480)|nervous system development (GO:0007399)|regulation of epidermis development (GO:0045682)|Schwann cell differentiation (GO:0014037)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	transcription corepressor activity (GO:0003714)	p.L375P(1)		breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(5)|ovary(1)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)	20						GGCCCTCCACTGAAGAAGCTG	0.542																																					p.L375P												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T1124C	12						.						102.0	110.0	107.0					12																	57486732		2203	4300	6503	55772999	SO:0001583	missense	4665	exon4			BC065931	CCDS8930.1	12q13.3	2008-05-14				ENSG00000166886			7627	protein-coding gene	gene with protein product		602381				8668170, 8649813	Standard	XM_005268894		Approved	MADER	uc001smz.3	Q15742		ENST00000300131.3:c.1124T>C	12.37:g.57486732T>C	ENSP00000300131:p.Leu375Pro	Somatic		Capture	Illumina HiSeq	Phase_I	55772999	NM_005967	B2RAK3|O76006|Q14797	Missense_Mutation	SNP	ENST00000300131.3	37	CCDS8930.1	.	.	.	.	.	.	.	.	.	.	T	13.70	2.315740	0.40996	.	.	ENSG00000166886	ENST00000300131;ENST00000342556	.	.	.	5.01	5.01	0.66863	.	0.217502	0.30302	N	0.009922	T	0.25717	0.0626	N	0.03608	-0.345	0.80722	D	1	B	0.06786	0.001	B	0.04013	0.001	T	0.11767	-1.0574	9	0.25751	T	0.34	-8.6337	7.3426	0.26646	0.0:0.0952:0.0:0.9048	.	375	Q15742	NAB2_HUMAN	P	375	.	ENSP00000300131:L375P	L	+	2	0	NAB2	55772999	0.993000	0.37304	1.000000	0.80357	0.994000	0.84299	2.627000	0.46469	2.107000	0.64212	0.533000	0.62120	CTG		0.542	NAB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412222.1	NM_005967	
GLI1	2735	broad.mit.edu	37	12	57861208	57861208	+	Silent	SNP	C	C	T	rs141854128		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr12:57861208C>T	ENST00000228682.2	+	9	1096	c.1005C>T	c.(1003-1005)caC>caT	p.H335H	GLI1_ENST00000546141.1_Silent_p.H294H|GLI1_ENST00000543426.1_Silent_p.H207H	NM_005269.2	NP_005260.1	P08151	GLI1_HUMAN	GLI family zinc finger 1	335					cerebellar cortex morphogenesis (GO:0021696)|digestive tract morphogenesis (GO:0048546)|dorsal/ventral pattern formation (GO:0009953)|epidermal cell differentiation (GO:0009913)|lung development (GO:0030324)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|notochord regression (GO:0060032)|osteoblast differentiation (GO:0001649)|pituitary gland development (GO:0021983)|positive regulation of cell proliferation (GO:0008284)|positive regulation of DNA replication (GO:0045740)|positive regulation of smoothened signaling pathway (GO:0045880)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|proximal/distal pattern formation (GO:0009954)|regulation of smoothened signaling pathway (GO:0008589)|smoothened signaling pathway (GO:0007224)|smoothened signaling pathway involved in regulation of cerebellar granule cell precursor cell proliferation (GO:0021938)|spermatogenesis (GO:0007283)|ventral midline development (GO:0007418)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)|primary cilium (GO:0072372)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|transcription regulatory region DNA binding (GO:0044212)	p.H335H(1)		NS(1)|breast(7)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(4)|kidney(2)|large_intestine(8)|lung(22)|ovary(6)|pancreas(2)|prostate(2)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	69			GBM - Glioblastoma multiforme(3;3.99e-32)			TGTGTGAGCACGAGGGCTGCA	0.562																																					p.H207H	Pancreas(157;841 1936 10503 41495 50368)											.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C621T	12						.	C	,,	0,4406		0,0,2203	128.0	91.0	104.0		621,882,1005	-6.3	0.8	12	dbSNP_134	104	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous,coding-synonymous	GLI1	NM_001160045.1,NM_001167609.1,NM_005269.2	,,	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	,,	207/979,294/1066,335/1107	57861208	1,13005	2203	4300	6503	56147475	SO:0001819	synonymous_variant	2735	exon7				CCDS8940.1, CCDS53806.1, CCDS53807.1	12q13.2-q13.3	2013-01-25	2009-03-05	2005-01-14		ENSG00000111087		"""Zinc fingers, C2H2-type"""	4317	protein-coding gene	gene with protein product		165220	"""glioma-associated oncogene homolog 1 (zinc finger protein)"", ""glioma-associated oncogene family zinc finger 1"""	GLI		2850480	Standard	NM_005269		Approved		uc001snx.3	P08151		ENST00000228682.2:c.1005C>T	12.37:g.57861208C>T		Somatic		Capture	Illumina HiSeq	Phase_I	56147475	NM_001160045	D0EUY3|E9PQQ9|F5H6H8|Q8TDN9	Silent	SNP	ENST00000228682.2	37	CCDS8940.1																																																																																				0.562	GLI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394197.1	NM_005269	
MBD6	114785	broad.mit.edu	37	12	57919851	57919851	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr12:57919851G>A	ENST00000355673.3	+	6	1456	c.1100G>A	c.(1099-1101)cGc>cAc	p.R367H	MBD6_ENST00000431731.2_Missense_Mutation_p.R367H	NM_052897.3	NP_443129.3	Q96DN6	MBD6_HUMAN	methyl-CpG binding domain protein 6	367	Pro-rich.					chromocenter (GO:0010369)|nucleus (GO:0005634)	chromatin binding (GO:0003682)	p.R367H(1)		breast(1)|central_nervous_system(3)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(8)|lung(8)|ovary(1)|urinary_tract(1)	31						CGTCGTCCCCGCAGACCCCCT	0.632																																					p.R367H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1100A	12						.						54.0	57.0	56.0					12																	57919851		2203	4300	6503	56206118	SO:0001583	missense	114785	exon6			AB067474	CCDS8944.1	12q13.2	2008-02-05				ENSG00000166987			20445	protein-coding gene	gene with protein product						12529184	Standard	NM_052897		Approved	KIAA1887	uc001soj.1	Q96DN6		ENST00000355673.3:c.1100G>A	12.37:g.57919851G>A	ENSP00000347896:p.Arg367His	Somatic		Capture	Illumina HiSeq	Phase_I	56206118	NM_052897	Q8N3M0|Q8NA81|Q96Q00	Missense_Mutation	SNP	ENST00000355673.3	37	CCDS8944.1	.	.	.	.	.	.	.	.	.	.	g	14.50	2.555404	0.45487	.	.	ENSG00000166987	ENST00000355673;ENST00000431731	.	.	.	3.97	3.97	0.46021	.	0.407499	0.19144	N	0.121632	T	0.50343	0.1610	N	0.08118	0	0.39480	D	0.967865	D;D	0.76494	0.999;0.999	D;D	0.78314	0.991;0.967	T	0.51748	-0.8666	8	.	.	.	-4.3366	13.4322	0.61062	0.0:0.0:1.0:0.0	.	367;367	Q6P0P0;Q96DN6	.;MBD6_HUMAN	H	367	.	.	R	+	2	0	MBD6	56206118	0.997000	0.39634	0.981000	0.43875	0.910000	0.53928	2.254000	0.43214	2.203000	0.70933	0.556000	0.70494	CGC		0.632	MBD6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407250.1		
KIF5A	3798	broad.mit.edu	37	12	57966449	57966449	+	Silent	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr12:57966449C>T	ENST00000455537.2	+	15	1930	c.1656C>T	c.(1654-1656)aaC>aaT	p.N552N	KIF5A_ENST00000286452.5_Silent_p.N463N	NM_004984.2	NP_004975.2	Q12840	KIF5A_HUMAN	kinesin family member 5A	552					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell death (GO:0008219)|cytoskeleton-dependent intracellular transport (GO:0030705)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|protein localization (GO:0008104)|synaptic transmission (GO:0007268)	cytosol (GO:0005829)|kinesin complex (GO:0005871)|membrane (GO:0016020)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|motor activity (GO:0003774)|plus-end-directed microtubule motor activity (GO:0008574)	p.N552N(1)		breast(2)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(11)|liver(1)|lung(32)|ovary(2)|prostate(2)|skin(2)	62						AGGTGCTGAACGGGCTGATGA	0.582																																					p.N552N												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1656T	12						.						201.0	165.0	177.0					12																	57966449		2203	4300	6503	56252716	SO:0001819	synonymous_variant	3798	exon15			U06698	CCDS8945.1	12q13.13	2011-07-15	2004-02-13			ENSG00000155980		"""Kinesins"""	6323	protein-coding gene	gene with protein product		602821	"""spastic paraplegia 10 (autosomal dominant)"""	SPG10		9858832, 10441583, 16489470	Standard	NM_004984		Approved	D12S1889, NKHC, MY050	uc001sor.1	Q12840	OTTHUMG00000170143	ENST00000455537.2:c.1656C>T	12.37:g.57966449C>T		Somatic		Capture	Illumina HiSeq	Phase_I	56252716	NM_004984	A6H8M5|Q4LE26	Silent	SNP	ENST00000455537.2	37	CCDS8945.1																																																																																				0.582	KIF5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407634.1	NM_004984	
OS9	10956	broad.mit.edu	37	12	58114605	58114605	+	Silent	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr12:58114605G>A	ENST00000315970.7	+	15	1958	c.1917G>A	c.(1915-1917)cgG>cgA	p.R639R	OS9_ENST00000551035.1_Silent_p.R552R|RP11-571M6.7_ENST00000549477.1_RNA|OS9_ENST00000435406.2_Silent_p.R532R|OS9_ENST00000257966.8_Silent_p.R585R|OS9_ENST00000439210.2_Silent_p.R510R|OS9_ENST00000389142.5_Silent_p.R569R|OS9_ENST00000552285.1_Silent_p.R584R|RP11-571M6.8_ENST00000548410.2_RNA|OS9_ENST00000413095.2_Silent_p.R378R|OS9_ENST00000389146.6_Silent_p.R624R	NM_001017958.2|NM_006812.3	NP_001017958.1|NP_006803.1	Q13438	OS9_HUMAN	osteosarcoma amplified 9, endoplasmic reticulum lectin	639					ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|protein retention in ER lumen (GO:0006621)|protein targeting (GO:0006605)|protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|response to endoplasmic reticulum stress (GO:0034976)	endoplasmic reticulum lumen (GO:0005788)|Hrd1p ubiquitin ligase complex (GO:0000836)	carbohydrate binding (GO:0030246)|glycoprotein binding (GO:0001948)	p.R639R(1)		autonomic_ganglia(1)|breast(1)|cervix(1)|endometrium(2)|large_intestine(4)|lung(8)|ovary(2)|prostate(1)|urinary_tract(1)	21	all_neural(12;0.00548)|Glioma(12;0.0126)|Melanoma(17;0.122)		BRCA - Breast invasive adenocarcinoma(9;0.109)			AACGCCAGCGGCAGAAAGAGC	0.627																																					p.R624R												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G1872A	12						.						59.0	60.0	60.0					12																	58114605		2203	4300	6503	56400872	SO:0001819	synonymous_variant	10956	exon15			AB002806	CCDS31843.1, CCDS31844.1, CCDS31845.1, CCDS31846.1, CCDS58246.1, CCDS58247.1, CCDS58248.1, CCDS58249.1	12q13	2009-08-26	2009-08-26						16994	protein-coding gene	gene with protein product	"""endoplasmic reticulum lectin 2"", ""erlectin 2"""	609677				8634085, 9498564, 19346256, 18264092	Standard	NM_006812		Approved	OS-9, ERLEC2	uc001spj.3	Q13438	OTTHUMG00000170284	ENST00000315970.7:c.1917G>A	12.37:g.58114605G>A		Somatic		Capture	Illumina HiSeq	Phase_I	56400872	NM_001017958	A6NDD1|A6NFR7|A6NLB2|A8K5Q9|B4DE28|B4DPX1|B4E1I6|E7ENT8|E7EW91|F8VUH2|G3XA88|O00579|Q6IBL2|Q8IZ58|Q9BW99	Silent	SNP	ENST00000315970.7	37	CCDS31843.1																																																																																				0.627	OS9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408344.1	NM_006812	
METTL21B	25895	broad.mit.edu	37	12	58174255	58174255	+	Silent	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr12:58174255G>A	ENST00000300209.8	+	3	632	c.507G>A	c.(505-507)ctG>ctA	p.L169L	METTL21B_ENST00000333012.5_3'UTR|TSFM_ENST00000540550.1_5'Flank|RP11-571M6.15_ENST00000553083.1_Intron|TSFM_ENST00000350762.5_5'Flank|TSFM_ENST00000323833.8_5'Flank|METTL21B_ENST00000551420.1_5'UTR|TSFM_ENST00000548851.1_5'Flank|TSFM_ENST00000543727.1_5'Flank|TSFM_ENST00000454289.3_5'Flank|TSFM_ENST00000550559.1_5'Flank|RP11-571M6.15_ENST00000471530.1_Intron	NM_015433.2	NP_056248.2	Q96AZ1	MT21B_HUMAN	methyltransferase like 21B	169						cytoplasm (GO:0005737)|intracellular (GO:0005622)	methyltransferase activity (GO:0008168)	p.L169L(1)		endometrium(1)|lung(1)	2						TCCAACACCTGTGCAGGCCCC	0.567																																					p.L169L												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G507A	12						.						94.0	73.0	80.0					12																	58174255		2203	4300	6503	56460522	SO:0001819	synonymous_variant	25895	exon3			AL050100, AF455816	CCDS8957.1, CCDS31848.1	12q14.1	2011-03-03	2011-03-03	2011-03-03	ENSG00000123427	ENSG00000123427			24936	protein-coding gene	gene with protein product		615258	"""family with sequence similarity 119, member B"""	FAM119B		12477932	Standard	NM_015433		Approved	DKFZP586D0919	uc001sqg.3	Q96AZ1	OTTHUMG00000170459	ENST00000300209.8:c.507G>A	12.37:g.58174255G>A		Somatic		Capture	Illumina HiSeq	Phase_I	56460522	NM_015433	Q9H749|Q9Y3W2	Silent	SNP	ENST00000300209.8	37	CCDS8957.1																																																																																				0.567	METTL21B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409268.1	NM_015433	
PPM1H	57460	broad.mit.edu	37	12	63042384	63042384	+	Missense_Mutation	SNP	C	C	T	rs540042623		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr12:63042384C>T	ENST00000228705.6	-	10	1730	c.1430G>A	c.(1429-1431)cGt>cAt	p.R477H	PPM1H_ENST00000551214.1_5'UTR|snoU13_ENST00000459527.1_RNA	NM_020700.1	NP_065751.1	Q9ULR3	PPM1H_HUMAN	protein phosphatase, Mg2+/Mn2+ dependent, 1H	477	PP2C-like.						phosphoprotein phosphatase activity (GO:0004721)	p.R477H(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(9)|ovary(1)	18			GBM - Glioblastoma multiforme(1;0.000443)|BRCA - Breast invasive adenocarcinoma(9;0.209)	GBM - Glioblastoma multiforme(28;0.0126)		ACCCCGGGCACGCATCACCAG	0.522													C|||	1	0.000199681	0.0	0.0	5008	,	,		19179	0.0		0.001	False		,,,				2504	0.0				p.R477H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1430A	12						.						57.0	60.0	59.0					12																	63042384		2095	4238	6333	61328651	SO:0001583	missense	57460	exon10			AB032983	CCDS44934.1	12q14.1	2012-04-17	2010-03-05	2004-03-26	ENSG00000111110	ENSG00000111110	3.1.3.16	"""Serine/threonine phosphatases / Protein phosphatases, Mg2+/Mn2+ dependent"""	18583	protein-coding gene	gene with protein product	"""neurite extension-related protein phosphatase related to PP2C"""		"""ras homolog gene family, member C like 1"", ""protein phosphatase 1H (PP2C domain containing)"""	ARHCL1			Standard	NM_020700		Approved	KIAA1157, FLJ13253, NERPP-2C	uc001srk.3	Q9ULR3	OTTHUMG00000169990	ENST00000228705.6:c.1430G>A	12.37:g.63042384C>T	ENSP00000228705:p.Arg477His	Somatic		Capture	Illumina HiSeq	Phase_I	61328651	NM_020700	B1Q2A9|B2RXG4|Q6PI86	Missense_Mutation	SNP	ENST00000228705.6	37	CCDS44934.1	.	.	.	.	.	.	.	.	.	.	C	33	5.268390	0.95429	.	.	ENSG00000111110	ENST00000228705	T	0.09630	2.96	5.93	5.93	0.95920	Protein phosphatase 2C-like (4);	0.122569	0.56097	D	0.000035	T	0.09512	0.0234	N	0.20304	0.555	0.80722	D	1	P	0.36048	0.534	B	0.34652	0.187	T	0.33574	-0.9863	9	.	.	.	3.064	20.3507	0.98813	0.0:1.0:0.0:0.0	.	477	Q9ULR3	PPM1H_HUMAN	H	477	ENSP00000228705:R477H	.	R	-	2	0	PPM1H	61328651	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.207000	0.77899	2.808000	0.96608	0.655000	0.94253	CGT		0.522	PPM1H-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406760.2	NM_020700	
SRGAP1	57522	broad.mit.edu	37	12	64521457	64521457	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr12:64521457G>T	ENST00000355086.3	+	20	3017	c.2493G>T	c.(2491-2493)aaG>aaT	p.K831N	SRGAP1_ENST00000543397.1_Missense_Mutation_p.K768N|SRGAP1_ENST00000357825.3_Missense_Mutation_p.K808N	NM_020762.2	NP_065813.1	Q7Z6B7	SRGP1_HUMAN	SLIT-ROBO Rho GTPase activating protein 1	831					axon guidance (GO:0007411)|cell migration (GO:0016477)|regulation of small GTPase mediated signal transduction (GO:0051056)|Rho protein signal transduction (GO:0007266)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	Rho GTPase activator activity (GO:0005100)	p.K831N(1)		breast(4)|central_nervous_system(3)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(26)|ovary(2)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	65			GBM - Glioblastoma multiforme(3;0.000139)|BRCA - Breast invasive adenocarcinoma(9;0.225)	GBM - Glioblastoma multiforme(28;0.0608)		CCTCATCCAAGGACATGAACT	0.557																																					p.K831N												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2493T	12						.						84.0	69.0	74.0					12																	64521457		2203	4300	6503	62807724	SO:0001583	missense	57522	exon20			AB037725	CCDS8967.1	12q13.13	2011-07-04			ENSG00000196935	ENSG00000196935		"""Rho GTPase activating proteins"""	17382	protein-coding gene	gene with protein product		606523				11672528	Standard	NM_020762		Approved	KIAA1304, ARHGAP13	uc010ssp.1	Q7Z6B7	OTTHUMG00000168750	ENST00000355086.3:c.2493G>T	12.37:g.64521457G>T	ENSP00000347198:p.Lys831Asn	Somatic		Capture	Illumina HiSeq	Phase_I	62807724	NM_020762	Q9H8A3|Q9P2P2	Missense_Mutation	SNP	ENST00000355086.3	37	CCDS8967.1	.	.	.	.	.	.	.	.	.	.	G	15.24	2.774823	0.49786	.	.	ENSG00000196935	ENST00000355086;ENST00000357825;ENST00000543397	T;T;T	0.19532	3.15;2.72;2.14	5.46	5.46	0.80206	Src homology-3 domain (1);	0.000000	0.36591	U	0.002508	T	0.15782	0.0380	L	0.27053	0.805	0.50313	D	0.999863	B;B	0.20887	0.049;0.001	B;B	0.25759	0.063;0.002	T	0.08659	-1.0711	9	.	.	.	.	12.949	0.58389	0.0742:0.0:0.9258:0.0	.	831;768	Q7Z6B7;G5EA48	SRGP1_HUMAN;.	N	831;808;768	ENSP00000347198:K831N;ENSP00000350480:K808N;ENSP00000437948:K768N	.	K	+	3	2	SRGAP1	62807724	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	2.393000	0.44442	2.722000	0.93159	0.650000	0.86243	AAG		0.557	SRGAP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000400896.1		
TBK1	29110	broad.mit.edu	37	12	64873877	64873877	+	Missense_Mutation	SNP	A	A	G	rs373705051		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr12:64873877A>G	ENST00000331710.5	+	7	1126	c.787A>G	c.(787-789)Atg>Gtg	p.M263V		NM_013254.3	NP_037386.1	Q9UHD2	TBK1_HUMAN	TANK-binding kinase 1	263	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				defense response to Gram-positive bacterium (GO:0050830)|defense response to virus (GO:0051607)|dendritic cell proliferation (GO:0044565)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of gene expression (GO:0010629)|negative regulation of type I interferon production (GO:0032480)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interferon-alpha production (GO:0032727)|positive regulation of interferon-beta biosynthetic process (GO:0045359)|positive regulation of interferon-beta production (GO:0032728)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon production (GO:0032481)|response to virus (GO:0009615)|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)|type I interferon production (GO:0032606)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endosome membrane (GO:0010008)	ATP binding (GO:0005524)|nucleic acid binding (GO:0003676)|phosphoprotein binding (GO:0051219)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)	p.M263V(2)		breast(2)|central_nervous_system(2)|large_intestine(7)|lung(7)|ovary(1)|pancreas(1)	20				GBM - Glioblastoma multiforme(28;0.0386)		GAGTGGAGACATGCCTGTTTC	0.403																																					p.M263V												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.A787G	12						.	A	VAL/MET	0,4406		0,0,2203	208.0	197.0	201.0		787	4.7	1.0	12		201	1,8599	1.2+/-3.3	0,1,4299	no	missense	TBK1	NM_013254.3	21	0,1,6502	GG,GA,AA		0.0116,0.0,0.0077	benign	263/730	64873877	1,13005	2203	4300	6503	63160144	SO:0001583	missense	29110	exon7			AF191838	CCDS8968.1	12q14.2	2006-06-10			ENSG00000183735	ENSG00000183735			11584	protein-coding gene	gene with protein product		604834				10581243, 10783893	Standard	NM_013254		Approved	NAK	uc001ssc.2	Q9UHD2	OTTHUMG00000168796	ENST00000331710.5:c.787A>G	12.37:g.64873877A>G	ENSP00000329967:p.Met263Val	Somatic		Capture	Illumina HiSeq	Phase_I	63160144	NM_013254	A8K4S4|Q8IYV3|Q9NUJ5	Missense_Mutation	SNP	ENST00000331710.5	37	CCDS8968.1	.	.	.	.	.	.	.	.	.	.	A	14.64	2.596526	0.46318	0.0	1.16E-4	ENSG00000183735	ENST00000331710	T	0.64803	-0.12	4.71	4.71	0.59529	Protein kinase, catalytic domain (1);	0.041694	0.85682	D	0.000000	T	0.39200	0.1069	N	0.05554	-0.025	0.48135	D	0.99959	B	0.25351	0.124	B	0.28385	0.089	T	0.26710	-1.0095	9	.	.	.	-10.1188	9.84	0.40993	0.847:0.0:0.0:0.153	.	263	Q9UHD2	TBK1_HUMAN	V	263	ENSP00000329967:M263V	.	M	+	1	0	TBK1	63160144	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	4.278000	0.58946	1.906000	0.55180	0.477000	0.44152	ATG		0.403	TBK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401130.1	NM_013254	
DYRK2	8445	broad.mit.edu	37	12	68051740	68051740	+	Silent	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr12:68051740C>T	ENST00000344096.3	+	3	1466	c.1053C>T	c.(1051-1053)ccC>ccT	p.P351P	DYRK2_ENST00000393555.3_Silent_p.P278P|RP11-335O4.3_ENST00000425371.2_RNA	NM_006482.2	NP_006473.2	Q92630	DYRK2_HUMAN	dual-specificity tyrosine-(Y)-phosphorylation regulated kinase 2	351	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cellular response to DNA damage stimulus (GO:0006974)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|negative regulation of NFAT protein import into nucleus (GO:0051534)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of glycogen biosynthetic process (GO:0045725)|protein phosphorylation (GO:0006468)|smoothened signaling pathway (GO:0007224)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)|ubiquitin ligase complex (GO:0000151)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|manganese ion binding (GO:0030145)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|protein tyrosine kinase activity (GO:0004713)|ubiquitin binding (GO:0043130)	p.P351P(1)		breast(2)|central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(7)|lung(6)|ovary(2)|prostate(2)|skin(1)|urinary_tract(1)	30			Lung(24;6.81e-05)|LUAD - Lung adenocarcinoma(15;0.00107)|LUSC - Lung squamous cell carcinoma(43;0.196)	GBM - Glioblastoma multiforme(7;0.000573)		ACCTTAAGCCCGAGAACATTT	0.448																																					p.P278P												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C834T	12						.						114.0	112.0	113.0					12																	68051740		2203	4300	6503	66338007	SO:0001819	synonymous_variant	8445	exon2			Y09216	CCDS8978.1, CCDS8979.1	12q15	2008-07-03				ENSG00000127334			3093	protein-coding gene	gene with protein product		603496				9748265	Standard	NM_003583		Approved		uc001str.4	Q92630		ENST00000344096.3:c.1053C>T	12.37:g.68051740C>T		Somatic		Capture	Illumina HiSeq	Phase_I	66338007	NM_003583	B2R9V9|Q9BRB5	Silent	SNP	ENST00000344096.3	37	CCDS8978.1																																																																																				0.448	DYRK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000402218.1		
KCNMB4	27345	broad.mit.edu	37	12	70794041	70794041	+	Missense_Mutation	SNP	T	T	G			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr12:70794041T>G	ENST00000258111.4	+	2	848	c.389T>G	c.(388-390)gTc>gGc	p.V130G		NM_014505.5	NP_055320.4	Q86W47	KCMB4_HUMAN	potassium large conductance calcium-activated channel, subfamily M, beta member 4	130					action potential (GO:0001508)|blood coagulation (GO:0007596)|detection of calcium ion (GO:0005513)|neuronal action potential (GO:0019228)|potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|regulation of neurotransmitter secretion (GO:0046928)|regulation of vasoconstriction (GO:0019229)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	calcium-activated potassium channel activity (GO:0015269)	p.V130G(1)		kidney(1)|large_intestine(4)|lung(5)	10	Renal(347;0.236)		Lung(24;0.000636)|OV - Ovarian serous cystadenocarcinoma(12;0.00243)|STAD - Stomach adenocarcinoma(21;0.0118)		Miconazole(DB01110)|Procaine(DB00721)	TTGGAAAGTGTCATGAATTGG	0.348																																					p.V130G												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T389G	12						.						171.0	165.0	167.0					12																	70794041		2203	4300	6503	69080308	SO:0001583	missense	27345	exon2			AF207992	CCDS8997.1	12q15	2006-06-10			ENSG00000135643	ENSG00000135643		"""Potassium channels"""	6289	protein-coding gene	gene with protein product		605223				10692449, 10828459	Standard	NM_014505		Approved		uc001svx.3	Q86W47	OTTHUMG00000167586	ENST00000258111.4:c.389T>G	12.37:g.70794041T>G	ENSP00000258111:p.Val130Gly	Somatic		Capture	Illumina HiSeq	Phase_I	69080308	NM_014505	Q8IVR3|Q9NPA4|Q9P0G5	Missense_Mutation	SNP	ENST00000258111.4	37	CCDS8997.1	.	.	.	.	.	.	.	.	.	.	T	16.62	3.174156	0.57692	.	.	ENSG00000135643	ENST00000258111	T	0.14893	2.47	5.83	5.83	0.93111	.	0.000000	0.64402	D	0.000001	T	0.40522	0.1120	M	0.63843	1.955	0.80722	D	1	D	0.76494	0.999	D	0.85130	0.997	T	0.19811	-1.0294	10	0.87932	D	0	-11.7075	15.1835	0.72978	0.0:0.0:0.0:1.0	.	130	Q86W47	KCMB4_HUMAN	G	130	ENSP00000258111:V130G	ENSP00000258111:V130G	V	+	2	0	KCNMB4	69080308	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.999000	0.70665	2.235000	0.73313	0.533000	0.62120	GTC		0.348	KCNMB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395208.1	NM_014505	
KCNC2	3747	broad.mit.edu	37	12	75601404	75601404	+	Silent	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr12:75601404G>A	ENST00000549446.1	-	2	1040	c.360C>T	c.(358-360)acC>acT	p.T120T	KCNC2_ENST00000298972.1_Silent_p.T120T|KCNC2_ENST00000341669.3_Silent_p.T120T|KCNC2_ENST00000393288.2_Silent_p.T120T|KCNC2_ENST00000550433.1_Silent_p.T120T|KCNC2_ENST00000350228.2_Silent_p.T120T|KCNC2_ENST00000548513.1_Silent_p.T120T|KCNC2_ENST00000540018.1_Silent_p.T120T	NM_001260497.1|NM_139137.3	NP_001247426.1|NP_631875.1	Q96PR1	KCNC2_HUMAN	potassium voltage-gated channel, Shaw-related subfamily, member 2	120					action potential (GO:0001508)|energy reserve metabolic process (GO:0006112)|protein homooligomerization (GO:0051260)|regulation of insulin secretion (GO:0050796)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)	p.T120T(2)		breast(3)|endometrium(4)|kidney(1)|large_intestine(9)|liver(1)|lung(28)|ovary(1)|pancreas(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	54					Dalfampridine(DB06637)	GCAGCTTGCCGGTGCGGTAGT	0.692																																					p.T120T												.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.C360T	12						.						28.0	32.0	31.0					12																	75601404		2203	4298	6501	73887671	SO:0001819	synonymous_variant	3747	exon2			AF268896	CCDS9005.1, CCDS9006.1, CCDS9007.1, CCDS58255.1, CCDS58256.1, CCDS58257.1	12q14.1	2012-07-05						"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	6234	protein-coding gene	gene with protein product		176256				8111118, 16382104	Standard	NM_139136		Approved	Kv3.2	uc001sxg.2	Q96PR1	OTTHUMG00000169717	ENST00000549446.1:c.360C>T	12.37:g.75601404G>A		Somatic		Capture	Illumina HiSeq	Phase_I	73887671	NM_139137	B7Z231|F5H030|J3KPP5|Q4LE77|Q86W09|Q8N1V9|Q96PR0	Silent	SNP	ENST00000549446.1	37	CCDS9007.1																																																																																				0.692	KCNC2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000405581.2	NM_153748	
OSBPL8	114882	broad.mit.edu	37	12	76786437	76786437	+	Missense_Mutation	SNP	C	C	T	rs200132037		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr12:76786437C>T	ENST00000261183.3	-	10	1332	c.853G>A	c.(853-855)Gtt>Att	p.V285I	OSBPL8_ENST00000393250.4_Missense_Mutation_p.V243I|OSBPL8_ENST00000393249.2_Missense_Mutation_p.V243I	NM_020841.4	NP_065892.1	Q9BZF1	OSBL8_HUMAN	oxysterol binding protein-like 8	285					fat cell differentiation (GO:0045444)|lipid transport (GO:0006869)|negative regulation of cell migration (GO:0030336)|negative regulation of sequestering of triglyceride (GO:0010891)|positive regulation of insulin receptor signaling pathway (GO:0046628)|positive regulation of protein kinase B signaling (GO:0051897)|protein localization to nuclear pore (GO:0090204)	membrane (GO:0016020)|nuclear membrane (GO:0031965)	cholesterol binding (GO:0015485)	p.V285I(1)		breast(1)|endometrium(3)|kidney(2)|large_intestine(6)|lung(14)|ovary(2)	28						TCTGATGAAACGCTCAGGTCA	0.423																																					p.V285I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G853A	12						.	C	ILE/VAL,ILE/VAL	0,4406		0,0,2203	270.0	207.0	228.0		727,853	1.4	1.0	12		228	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	OSBPL8	NM_001003712.1,NM_020841.4	29,29	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	benign,benign	243/848,285/890	76786437	1,13005	2203	4300	6503	75310568	SO:0001583	missense	114882	exon10			AF392452	CCDS31862.1, CCDS41814.1	12q14	2013-01-10				ENSG00000091039		"""Oxysterol binding proteins"", ""Pleckstrin homology (PH) domain containing"""	16396	protein-coding gene	gene with protein product		606736				1735225, 17991739	Standard	NM_020841		Approved	OSBP10, ORP8, MST120, MSTP120	uc001sye.1	Q9BZF1		ENST00000261183.3:c.853G>A	12.37:g.76786437C>T	ENSP00000261183:p.Val285Ile	Somatic		Capture	Illumina HiSeq	Phase_I	75310568	NM_020841	A8K1T2|E9PE66|E9PE68|Q52LQ3|Q68D75|Q8WXP8|Q9P277	Missense_Mutation	SNP	ENST00000261183.3	37	CCDS31862.1	.	.	.	.	.	.	.	.	.	.	C	8.325	0.825116	0.16678	0.0	1.16E-4	ENSG00000091039	ENST00000393249;ENST00000261183;ENST00000446075;ENST00000393250;ENST00000438913;ENST00000547540;ENST00000546946	T;T;T;T;T	0.43688	1.53;1.52;1.53;0.94;0.96	5.47	1.36	0.22044	.	0.440671	0.26684	N	0.023021	T	0.17323	0.0416	N	0.08118	0	0.22531	N	0.999013	B;B	0.09022	0.002;0.0	B;B	0.08055	0.003;0.001	T	0.11397	-1.0589	10	0.25751	T	0.34	-6.3363	3.9825	0.09501	0.2907:0.1755:0.0:0.5338	.	260;285	F8VUA7;Q9BZF1	.;OSBL8_HUMAN	I	243;285;270;243;285;285;260	ENSP00000376939:V243I;ENSP00000261183:V285I;ENSP00000376940:V243I;ENSP00000450238:V285I;ENSP00000447893:V260I	ENSP00000261183:V285I	V	-	1	0	OSBPL8	75310568	0.995000	0.38212	1.000000	0.80357	0.874000	0.50279	0.896000	0.28377	0.454000	0.26884	-0.290000	0.09829	GTT		0.423	OSBPL8-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000406357.1	NM_020841	
E2F7	144455	broad.mit.edu	37	12	77423674	77423674	+	Silent	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr12:77423674C>T	ENST00000322886.7	-	10	2056	c.1821G>A	c.(1819-1821)gaG>gaA	p.E607E	E2F7_ENST00000416496.2_Silent_p.E607E	NM_203394.2	NP_976328.2	Q96AV8	E2F7_HUMAN	E2F transcription factor 7	607					chorionic trophoblast cell differentiation (GO:0060718)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|hepatocyte differentiation (GO:0070365)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cytokinesis (GO:0032466)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0071930)|placenta development (GO:0001890)|positive regulation of DNA endoreduplication (GO:0032877)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|sprouting angiogenesis (GO:0002040)|trophoblast giant cell differentiation (GO:0060707)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	core promoter binding (GO:0001047)|identical protein binding (GO:0042802)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001227)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)	p.E607E(2)		central_nervous_system(1)|endometrium(3)|kidney(4)|large_intestine(15)|lung(14)|ovary(3)|upper_aerodigestive_tract(2)	42						TAGTGGCTGGCTCATCCTCCT	0.552																																					p.E607E												.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.G1821A	12						.						97.0	88.0	91.0					12																	77423674		2203	4300	6503	75947805	SO:0001819	synonymous_variant	144455	exon10			BC016658	CCDS9016.1	12q21.1	2008-02-05				ENSG00000165891			23820	protein-coding gene	gene with protein product		612046				12893818	Standard	NM_203394		Approved		uc001sym.4	Q96AV8	OTTHUMG00000169969	ENST00000322886.7:c.1821G>A	12.37:g.77423674C>T		Somatic		Capture	Illumina HiSeq	Phase_I	75947805	NM_203394	A6NC74|B2RMR7|B3KTZ5|B3KUP8|B5MED9	Silent	SNP	ENST00000322886.7	37	CCDS9016.1																																																																																				0.552	E2F7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406716.1	XM_084871	
NAV3	89795	broad.mit.edu	37	12	78444658	78444658	+	Silent	SNP	G	G	A	rs367740483		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr12:78444658G>A	ENST00000397909.2	+	11	2420	c.2247G>A	c.(2245-2247)ccG>ccA	p.P749P	NAV3_ENST00000266692.7_Silent_p.P749P|RP11-136F16.1_ENST00000549103.1_RNA|NAV3_ENST00000536525.2_Silent_p.P749P|NAV3_ENST00000228327.6_Silent_p.P749P			Q8IVL0	NAV3_HUMAN	neuron navigator 3	749						membrane (GO:0016020)|nuclear envelope (GO:0005635)		p.P749P(1)		NS(2)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(13)|kidney(16)|large_intestine(39)|liver(2)|lung(126)|ovary(5)|pancreas(3)|prostate(6)|skin(5)|stomach(2)|upper_aerodigestive_tract(8)|urinary_tract(1)	236						AGGCATGTCCGCGACTTCAGG	0.557										HNSCC(70;0.22)																											p.P749P												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G2247A	12						.	G		0,4004		0,0,2002	80.0	79.0	79.0		2247	-11.6	0.0	12		79	1,8345		0,1,4172	no	coding-synonymous	NAV3	NM_014903.4		0,1,6174	AA,AG,GG		0.012,0.0,0.0081		749/2364	78444658	1,12349	2002	4173	6175	76968789	SO:0001819	synonymous_variant	89795	exon11			AB023155	CCDS41815.1, CCDS66432.1	12q14.3	2008-08-05				ENSG00000067798			15998	protein-coding gene	gene with protein product	"""pore membrane and/or filament interacting like protein 1"", ""steerin 3"""	611629				12079279, 12062803	Standard	XM_005269215		Approved	KIAA0938, POMFIL1	uc001syo.3	Q8IVL0	OTTHUMG00000170001	ENST00000397909.2:c.2247G>A	12.37:g.78444658G>A		Somatic		Capture	Illumina HiSeq	Phase_I	76968789	NM_014903	Q8NFW7|Q9Y2E7	Silent	SNP	ENST00000397909.2	37																																																																																					0.557	NAV3-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000406812.1	NM_001024383	
NAV3	89795	broad.mit.edu	37	12	78515850	78515850	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr12:78515850G>A	ENST00000397909.2	+	16	4053	c.3880G>A	c.(3880-3882)Ggt>Agt	p.G1294S	NAV3_ENST00000266692.7_Intron|NAV3_ENST00000536525.2_Missense_Mutation_p.G1294S|NAV3_ENST00000228327.6_Missense_Mutation_p.G1294S			Q8IVL0	NAV3_HUMAN	neuron navigator 3	1294	Ser-rich.					membrane (GO:0016020)|nuclear envelope (GO:0005635)		p.G1294S(1)		NS(2)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(13)|kidney(16)|large_intestine(39)|liver(2)|lung(126)|ovary(5)|pancreas(3)|prostate(6)|skin(5)|stomach(2)|upper_aerodigestive_tract(8)|urinary_tract(1)	236						ACCGTCGTCCGGTACGGGCAG	0.532										HNSCC(70;0.22)																											p.G1294S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G3880A	12						.						50.0	51.0	51.0					12																	78515850		2111	4224	6335	77039981	SO:0001583	missense	89795	exon16			AB023155	CCDS41815.1, CCDS66432.1	12q14.3	2008-08-05				ENSG00000067798			15998	protein-coding gene	gene with protein product	"""pore membrane and/or filament interacting like protein 1"", ""steerin 3"""	611629				12079279, 12062803	Standard	XM_005269215		Approved	KIAA0938, POMFIL1	uc001syo.3	Q8IVL0	OTTHUMG00000170001	ENST00000397909.2:c.3880G>A	12.37:g.78515850G>A	ENSP00000381007:p.Gly1294Ser	Somatic		Capture	Illumina HiSeq	Phase_I	77039981	NM_014903	Q8NFW7|Q9Y2E7	Missense_Mutation	SNP	ENST00000397909.2	37		.	.	.	.	.	.	.	.	.	.	G	17.21	3.331546	0.60853	.	.	ENSG00000067798	ENST00000536525;ENST00000397909;ENST00000228327	T;T;T	0.27557	1.66;1.66;1.67	5.96	5.96	0.96718	.	0.000000	0.41001	U	0.000977	T	0.50514	0.1620	L	0.55481	1.735	0.80722	D	1	D;D;D	0.89917	0.998;1.0;1.0	P;D;D	0.91635	0.877;0.999;0.983	T	0.22977	-1.0201	10	0.09338	T	0.73	-18.7029	20.4082	0.99013	0.0:0.0:1.0:0.0	.	1294;1294;1294	E7EUC6;Q8IVL0;Q8IVL0-2	.;NAV3_HUMAN;.	S	1294	ENSP00000446132:G1294S;ENSP00000381007:G1294S;ENSP00000228327:G1294S	ENSP00000228327:G1294S	G	+	1	0	NAV3	77039981	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.577000	0.98196	2.814000	0.96858	0.655000	0.94253	GGT		0.532	NAV3-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000406812.1	NM_001024383	
ATP2B1	490	broad.mit.edu	37	12	90013984	90013984	+	Missense_Mutation	SNP	C	C	T	rs368317255		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr12:90013984C>T	ENST00000428670.3	-	11	2077	c.1621G>A	c.(1621-1623)Gtt>Att	p.V541I	ATP2B1_ENST00000393164.2_Missense_Mutation_p.V284I|ATP2B1_ENST00000348959.3_Missense_Mutation_p.V541I|ATP2B1_ENST00000359142.3_Missense_Mutation_p.V541I|ATP2B1_ENST00000261173.2_Missense_Mutation_p.V541I			P20020	AT2B1_HUMAN	ATPase, Ca++ transporting, plasma membrane 1	541					blood coagulation (GO:0007596)|ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)|transport (GO:0006810)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium-transporting ATPase activity (GO:0005388)|metal ion binding (GO:0046872)	p.V541I(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(13)|lung(15)|ovary(2)|prostate(2)|skin(3)|urinary_tract(1)	45						TTATTACCAACGTGACGAGGT	0.353																																					p.V541I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1621A	12						.	C	ILE/VAL,ILE/VAL	2,4404	4.2+/-10.8	0,2,2201	83.0	81.0	82.0		1621,1621	5.6	1.0	12		82	0,8600		0,0,4300	no	missense,missense	ATP2B1	NM_001001323.1,NM_001682.2	29,29	0,2,6501	TT,TC,CC		0.0,0.0454,0.0154	benign,benign	541/1177,541/1221	90013984	2,13004	2203	4300	6503	88538115	SO:0001583	missense	490	exon10			J04027	CCDS9035.1, CCDS41817.1	12q21.33	2010-04-20			ENSG00000070961	ENSG00000070961	3.6.3.8	"""ATPases / P-type"""	814	protein-coding gene	gene with protein product	"""plasma membrane calcium-transporting ATPase 1"""	108731				1674727	Standard	NM_001682		Approved	PMCA1	uc001tbh.3	P20020		ENST00000428670.3:c.1621G>A	12.37:g.90013984C>T	ENSP00000392043:p.Val541Ile	Somatic		Capture	Illumina HiSeq	Phase_I	88538115	NM_001001323	Q12992|Q12993|Q13819|Q13820|Q13821|Q16504|Q93082	Missense_Mutation	SNP	ENST00000428670.3	37	CCDS9035.1	.	.	.	.	.	.	.	.	.	.	C	28.4	4.913433	0.92178	4.54E-4	0.0	ENSG00000070961	ENST00000261173;ENST00000348959;ENST00000359142;ENST00000428670;ENST00000393164	T;T;T;T;T	0.70516	-0.49;-0.49;-0.49;-0.49;-0.49	5.58	5.58	0.84498	.	0.118619	0.56097	D	0.000024	T	0.70962	0.3284	N	0.05383	-0.06	0.80722	D	1	D;P;P	0.76494	0.999;0.752;0.856	D;B;B	0.76071	0.987;0.147;0.102	T	0.71751	-0.4498	9	.	.	.	-15.0486	19.5617	0.95375	0.0:1.0:0.0:0.0	.	541;541;541	P20020-3;P20020-2;P20020-6	.;.;.	I	541;541;541;541;284	ENSP00000261173:V541I;ENSP00000343599:V541I;ENSP00000352054:V541I;ENSP00000392043:V541I;ENSP00000376869:V284I	.	V	-	1	0	ATP2B1	88538115	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	7.818000	0.86416	2.616000	0.88540	0.467000	0.42956	GTT		0.353	ATP2B1-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406653.1	NM_001682	
LUM	4060	broad.mit.edu	37	12	91497970	91497970	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr12:91497970C>T	ENST00000266718.4	-	3	1443	c.989G>A	c.(988-990)cGt>cAt	p.R330H	LUM_ENST00000548071.1_5'UTR	NM_002345.3	NP_002336.1	P51884	LUM_HUMAN	lumican	330					carbohydrate metabolic process (GO:0005975)|cartilage development (GO:0051216)|collagen fibril organization (GO:0030199)|extracellular matrix organization (GO:0030198)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate catabolic process (GO:0042340)|keratan sulfate metabolic process (GO:0042339)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|response to growth factor (GO:0070848)|response to organic cyclic compound (GO:0014070)|small molecule metabolic process (GO:0044281)|visual perception (GO:0007601)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|fibrillar collagen trimer (GO:0005583)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)|proteinaceous extracellular matrix (GO:0005578)	collagen binding (GO:0005518)|extracellular matrix structural constituent (GO:0005201)	p.R330H(1)		central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(7)|lung(9)|skin(1)|upper_aerodigestive_tract(1)	24						GTTAGCAACACGTAGACATTC	0.378																																					p.R330H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G989A	12						.						112.0	107.0	109.0					12																	91497970		2203	4300	6503	90022101	SO:0001583	missense	4060	exon3			BT006707	CCDS9038.1	12q21.33	2014-06-13			ENSG00000139329			"""Proteoglycans / Extracellular Matrix : Small leucine-rich repeats"""	6724	protein-coding gene	gene with protein product	"""lumican proteoglycan"""	600616		LDC		7558030	Standard	NM_002345		Approved	SLRR2D	uc001tbm.3	P51884	OTTHUMG00000170074	ENST00000266718.4:c.989G>A	12.37:g.91497970C>T	ENSP00000266718:p.Arg330His	Somatic		Capture	Illumina HiSeq	Phase_I	90022101	NM_002345	B2R6R5|Q96QM7	Missense_Mutation	SNP	ENST00000266718.4	37	CCDS9038.1	.	.	.	.	.	.	.	.	.	.	C	24.7	4.564082	0.86335	.	.	ENSG00000139329	ENST00000266718	T	0.19806	2.12	5.18	5.18	0.71444	.	0.000000	0.85682	D	0.000000	T	0.49762	0.1576	M	0.78456	2.415	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.51172	-0.8739	10	0.51188	T	0.08	-17.5142	18.291	0.90130	0.0:1.0:0.0:0.0	.	330	P51884	LUM_HUMAN	H	330	ENSP00000266718:R330H	ENSP00000266718:R330H	R	-	2	0	LUM	90022101	1.000000	0.71417	0.943000	0.38184	0.610000	0.37248	6.875000	0.75551	2.394000	0.81467	0.585000	0.79938	CGT		0.378	LUM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407150.2	NM_002345	
C12orf74	338809	broad.mit.edu	37	12	93100581	93100581	+	Silent	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr12:93100581C>T	ENST00000397833.3	+	2	625	c.174C>T	c.(172-174)ggC>ggT	p.G58G	C12orf74_ENST00000544406.2_Silent_p.G58G	NM_001037671.3|NM_001178097.2	NP_001032760.1|NP_001171568.1	Q32Q52	CL074_HUMAN	chromosome 12 open reading frame 74	58								p.G58G(1)		kidney(1)|large_intestine(2)|lung(4)|prostate(1)|urinary_tract(2)	10						GGACCCGTGGCTGTGGGACAA	0.622																																					p.G58G												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C174T	12						.						46.0	49.0	48.0					12																	93100581		1890	4111	6001	91624712	SO:0001819	synonymous_variant	338809	exon2			BC043363	CCDS41819.1, CCDS53818.1	12q22	2012-08-16			ENSG00000214215	ENSG00000214215			27887	protein-coding gene	gene with protein product						12477932	Standard	NM_001037671		Approved		uc001tch.2	Q32Q52	OTTHUMG00000170105	ENST00000397833.3:c.174C>T	12.37:g.93100581C>T		Somatic		Capture	Illumina HiSeq	Phase_I	91624712	NM_001037671	F5H4P0	Silent	SNP	ENST00000397833.3	37	CCDS41819.1																																																																																				0.622	C12orf74-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000407285.1	NM_001037671	
NTN4	59277	broad.mit.edu	37	12	96077487	96077487	+	Splice_Site	SNP	G	G	A	rs371661550		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr12:96077487G>A	ENST00000343702.4	-	6	1629	c.1181C>T	c.(1180-1182)cCg>cTg	p.P394L	NTN4_ENST00000553059.1_Splice_Site_p.P394L|NTN4_ENST00000344911.4_Splice_Site_p.P357L|NTN4_ENST00000538383.1_Splice_Site_p.P357L	NM_021229.3	NP_067052.2	Q9HB63	NET4_HUMAN	netrin 4	394	Laminin EGF-like 2. {ECO:0000255|PROSITE- ProRule:PRU00460}.				axon guidance (GO:0007411)|extracellular matrix organization (GO:0030198)|neuron remodeling (GO:0016322)|regulation of branching involved in salivary gland morphogenesis by extracellular matrix-epithelial cell signaling (GO:0060668)	basement membrane (GO:0005604)|plasma membrane (GO:0005886)		p.P394L(2)		NS(2)|breast(1)|kidney(1)|large_intestine(7)|lung(8)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	25						GCAGGAACACGCTACAACAGA	0.552																																					p.P394L												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.C1181T	12						.						64.0	46.0	52.0					12																	96077487		2201	4299	6500	94601618	SO:0001630	splice_region_variant	59277	exon6			AF119916	CCDS9054.1	12q22	2013-03-01			ENSG00000074527	ENSG00000074527		"""Netrins"""	13658	protein-coding gene	gene with protein product	"""beta-netrin"", ""Netrin-4"""	610401				11038171	Standard	NM_021229		Approved		uc001tei.3	Q9HB63	OTTHUMG00000170290	ENST00000343702.4:c.1181-1C>T	12.37:g.96077487G>A		Somatic		Capture	Illumina HiSeq	Phase_I	94601618	NM_021229	B2RNC2|Q658K9|Q7L3F1|Q7L9D6|Q7Z5B6|Q9BZP1|Q9NT44|Q9P133	Missense_Mutation	SNP	ENST00000343702.4	37	CCDS9054.1	.	.	.	.	.	.	.	.	.	.	G	1.024	-0.684067	0.03353	.	.	ENSG00000074527	ENST00000343702;ENST00000344911;ENST00000538383;ENST00000553059	T;T;T;T	0.65916	-0.18;-0.18;-0.18;-0.18	5.74	-1.59	0.08453	EGF-like, laminin (2);	3.392480	0.01001	N	0.003665	T	0.63920	0.2552	M	0.67953	2.075	0.42704	D	0.993627	B;B	0.12013	0.005;0.001	B;B	0.06405	0.002;0.001	T	0.49978	-0.8881	10	0.52906	T	0.07	.	13.2731	0.60172	0.4763:0.0:0.5237:0.0	.	394;394	Q9HB63-2;Q9HB63	.;NET4_HUMAN	L	394;357;357;394	ENSP00000340998:P394L;ENSP00000339436:P357L;ENSP00000444432:P357L;ENSP00000447292:P394L	ENSP00000340998:P394L	P	-	2	0	NTN4	94601618	0.000000	0.05858	0.162000	0.22713	0.016000	0.09150	-0.242000	0.08928	-0.535000	0.06307	-0.918000	0.02743	CCG		0.552	NTN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408372.1	NM_021229	Missense_Mutation
ELK3	2004	broad.mit.edu	37	12	96617349	96617349	+	Missense_Mutation	SNP	A	A	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr12:96617349A>T	ENST00000228741.3	+	2	331	c.5A>T	c.(4-6)gAg>gTg	p.E2V	RP11-394J1.2_ENST00000551844.1_RNA|ELK3_ENST00000552142.1_Missense_Mutation_p.E2V	NM_005230.2	NP_005221.2	P41970	ELK3_HUMAN	ELK3, ETS-domain protein (SRF accessory protein 2)	2					angiogenesis (GO:0001525)|cell differentiation (GO:0030154)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|signal transduction (GO:0007165)|transcription from RNA polymerase II promoter (GO:0006366)|wound healing (GO:0042060)	intracellular membrane-bounded organelle (GO:0043231)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	purine-rich negative regulatory element binding (GO:0032422)|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 RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)	p.E2V(1)		breast(2)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(4)|liver(1)|lung(5)|ovary(2)|prostate(1)|stomach(2)	20	all_cancers(2;0.00173)					GCAGGTATGGAGAGTGCAATC	0.552																																					p.E2V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A5T	12						.						112.0	90.0	97.0					12																	96617349		2203	4300	6503	95141480	SO:0001583	missense	2004	exon2			BC017371	CCDS9060.1	12q23	2006-12-30				ENSG00000111145			3325	protein-coding gene	gene with protein product		600247				7851904	Standard	NM_005230		Approved	ERP, NET, SAP2	uc001teo.1	P41970		ENST00000228741.3:c.5A>T	12.37:g.96617349A>T	ENSP00000228741:p.Glu2Val	Somatic		Capture	Illumina HiSeq	Phase_I	95141480	NM_005230	B2R6S6|Q6FG57|Q6GU29|Q9UD17	Missense_Mutation	SNP	ENST00000228741.3	37	CCDS9060.1	.	.	.	.	.	.	.	.	.	.	a	26.7	4.766314	0.90020	.	.	ENSG00000111145	ENST00000228741;ENST00000547249;ENST00000552142;ENST00000547860	T;T;T;T	0.52057	1.36;0.68;1.81;1.1	5.48	5.48	0.80851	.	0.044561	0.85682	D	0.000000	T	0.57286	0.2043	L	0.48642	1.525	0.80722	D	1	D	0.64830	0.994	P	0.56343	0.796	T	0.61217	-0.7107	10	0.87932	D	0	.	15.5812	0.76445	1.0:0.0:0.0:0.0	.	2	P41970	ELK3_HUMAN	V	2	ENSP00000228741:E2V;ENSP00000446806:E2V;ENSP00000449430:E2V;ENSP00000447857:E2V	ENSP00000228741:E2V	E	+	2	0	ELK3	95141480	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	9.280000	0.95786	2.094000	0.63399	0.459000	0.35465	GAG		0.552	ELK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408694.1	NM_005230	
GAS2L3	283431	broad.mit.edu	37	12	101005838	101005838	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr12:101005838C>T	ENST00000539410.1	+	5	750	c.364C>T	c.(364-366)Cgg>Tgg	p.R122W	GAS2L3_ENST00000266754.5_Missense_Mutation_p.R122W|GAS2L3_ENST00000537247.1_Missense_Mutation_p.R18W|GAS2L3_ENST00000547754.1_Missense_Mutation_p.R122W			Q86XJ1	GA2L3_HUMAN	growth arrest-specific 2 like 3	122	CH. {ECO:0000255|PROSITE- ProRule:PRU00044}.				actin cytoskeleton organization (GO:0030036)|cell cycle arrest (GO:0007050)|microtubule cytoskeleton organization (GO:0000226)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)	actin binding (GO:0003779)|microtubule binding (GO:0008017)	p.R122W(1)		endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(15)|pancreas(1)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	35						ATTCTTTGCTCGGGACAATAC	0.388																																					p.R122W												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C364T	12						.						185.0	176.0	179.0					12																	101005838		2203	4300	6503	99529969	SO:0001583	missense	283431	exon6			AK095594	CCDS9079.1	12q23.1	2014-09-11			ENSG00000139354	ENSG00000139354			27475	protein-coding gene	gene with protein product							Standard	NM_174942		Approved		uc001thu.3	Q86XJ1	OTTHUMG00000170439	ENST00000539410.1:c.364C>T	12.37:g.101005838C>T	ENSP00000439672:p.Arg122Trp	Somatic		Capture	Illumina HiSeq	Phase_I	99529969	NM_174942	B2RCN2	Missense_Mutation	SNP	ENST00000539410.1	37	CCDS9079.1	.	.	.	.	.	.	.	.	.	.	C	21.8	4.205197	0.79127	.	.	ENSG00000139354	ENST00000266754;ENST00000547754;ENST00000537247;ENST00000539410	D;D;T;D	0.95103	-3.61;-3.61;0.81;-3.61	5.81	4.69	0.59074	Calponin homology domain (5);	0.102123	0.64402	D	0.000002	D	0.97898	0.9309	H	0.95114	3.625	0.45867	D	0.998725	D	0.89917	1.0	D	0.87578	0.998	D	0.98121	1.0425	10	0.87932	D	0	-18.6681	12.012	0.53293	0.6588:0.3412:0.0:0.0	.	122	Q86XJ1	GA2L3_HUMAN	W	122;122;18;122	ENSP00000266754:R122W;ENSP00000448955:R122W;ENSP00000442406:R18W;ENSP00000439672:R122W	ENSP00000266754:R122W	R	+	1	2	GAS2L3	99529969	1.000000	0.71417	1.000000	0.80357	0.960000	0.62799	4.188000	0.58351	1.069000	0.40788	0.558000	0.71614	CGG		0.388	GAS2L3-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409143.1	NM_174942	
EP400	57634	broad.mit.edu	37	12	132445192	132445192	+	Missense_Mutation	SNP	G	G	A	rs566501800		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr12:132445192G>A	ENST00000333577.4	+	2	137	c.28G>A	c.(28-30)Gtc>Atc	p.V10I	EP400_ENST00000332482.4_Missense_Mutation_p.V10I|EP400_ENST00000389562.2_Missense_Mutation_p.V10I|EP400_ENST00000389561.2_Missense_Mutation_p.V10I|EP400_ENST00000330386.6_Missense_Mutation_p.V10I			Q96L91	EP400_HUMAN	E1A binding protein p400	10					chromatin organization (GO:0006325)|histone H2A acetylation (GO:0043968)|histone H4 acetylation (GO:0043967)	NuA4 histone acetyltransferase complex (GO:0035267)|nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|Swr1 complex (GO:0000812)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|helicase activity (GO:0004386)	p.V10I(1)		NS(1)|breast(6)|central_nervous_system(10)|cervix(1)|endometrium(21)|kidney(13)|large_intestine(25)|lung(56)|ovary(5)|prostate(8)|skin(6)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(3)	161	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.198)		OV - Ovarian serous cystadenocarcinoma(86;3.01e-08)|Epithelial(86;3.43e-07)|all cancers(50;2.01e-06)		CCCCCAGAACGTCCAGCATCA	0.587													G|||	1	0.000199681	0.0008	0.0	5008	,	,		10064	0.0		0.0	False		,,,				2504	0.0				p.V10I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G28A	12						.						13.0	12.0	12.0					12																	132445192		2193	4288	6481	131011145	SO:0001583	missense	57634	exon2			U80743	CCDS31929.1, CCDS31929.2	12q24.33	2008-02-01	2002-02-05	2002-02-08		ENSG00000183495			11958	protein-coding gene	gene with protein product		606265	"""trinucleotide repeat containing 12"""	TNRC12		9225980, 11509179	Standard	NM_015409		Approved	CAGH32, KIAA1498, P400, KIAA1818, DKFZP434I225	uc001ujn.3	Q96L91		ENST00000333577.4:c.28G>A	12.37:g.132445192G>A	ENSP00000333602:p.Val10Ile	Somatic		Capture	Illumina HiSeq	Phase_I	131011145	NM_015409	O15411|Q6P2F5|Q8N8Q7|Q8NE05|Q96JK7|Q9P230	Missense_Mutation	SNP	ENST00000333577.4	37		.	.	.	.	.	.	.	.	.	.	G	9.307	1.054594	0.19907	.	.	ENSG00000183495	ENST00000537902;ENST00000333577;ENST00000389561;ENST00000389562;ENST00000332482;ENST00000330386;ENST00000423130;ENST00000541296;ENST00000542457	D;D;D;D;D	0.90197	-2.62;-2.62;-2.62;-2.63;-2.62	5.79	4.9	0.64082	.	0.357872	0.31051	N	0.008341	D	0.85375	0.5682	L	0.54323	1.7	0.22601	N	0.998948	B;B;B;P;B	0.49253	0.017;0.017;0.017;0.921;0.007	B;B;B;B;B	0.34138	0.003;0.003;0.003;0.176;0.005	T	0.80101	-0.1523	10	0.59425	D	0.04	.	11.1716	0.48575	0.1403:0.0:0.8597:0.0	.	10;10;10;10;10	Q96L91-2;Q96L91-4;Q96L91-5;F8WCN8;Q96L91-3	.;.;.;.;.	I	10	ENSP00000333602:V10I;ENSP00000374212:V10I;ENSP00000374213:V10I;ENSP00000331737:V10I;ENSP00000330620:V10I	ENSP00000330620:V10I	V	+	1	0	EP400	131011145	1.000000	0.71417	0.856000	0.33681	0.712000	0.41017	4.382000	0.59594	1.471000	0.48121	-0.214000	0.12660	GTC		0.587	EP400-203	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_015409	
NALCN	259232	broad.mit.edu	37	13	101735217	101735217	+	Silent	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr13:101735217C>T	ENST00000251127.6	-	33	3789	c.3708G>A	c.(3706-3708)ccG>ccA	p.P1236P		NM_052867.2	NP_443099.1	Q8IZF0	NALCN_HUMAN	sodium leak channel, non-selective	1236					calcium ion import (GO:0070509)|calcium ion transmembrane transport (GO:0070588)|cell death (GO:0008219)|ion transmembrane transport (GO:0034220)|membrane depolarization during action potential (GO:0086010)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	sodium channel activity (GO:0005272)|voltage-gated calcium channel activity (GO:0005245)	p.P1236P(1)		NS(1)|autonomic_ganglia(2)|breast(6)|central_nervous_system(2)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(3)|kidney(10)|large_intestine(33)|liver(2)|lung(81)|ovary(8)|pancreas(3)|prostate(5)|skin(6)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	177	all_neural(89;0.0438)|Medulloblastoma(90;0.163)|Lung SC(71;0.184)					GTACGGTCACCGGGTCCTCGA	0.527																																					p.P1236P												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G3708A	13						.						121.0	108.0	113.0					13																	101735217		2203	4300	6503	100533218	SO:0001819	synonymous_variant	259232	exon33			AY141972	CCDS9498.1	13q32.3	2012-02-21	2007-04-26	2007-04-26	ENSG00000102452	ENSG00000102452		"""Ion channels / Sodium leak channels, non-selective"""	19082	protein-coding gene	gene with protein product		611549	"""voltage gated channel like 1"""	VGCNL1		17448995	Standard	XM_006719943		Approved	bA430M15.1, CanIon	uc001vox.1	Q8IZF0	OTTHUMG00000017295	ENST00000251127.6:c.3708G>A	13.37:g.101735217C>T		Somatic		Capture	Illumina HiSeq	Phase_I	100533218	NM_052867	Q6P2S6|Q6ZMI7|Q8IZZ1|Q8TAH1	Silent	SNP	ENST00000251127.6	37	CCDS9498.1																																																																																				0.527	NALCN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045663.2	NM_052867	
BIVM	54841	broad.mit.edu	37	13	103459804	103459804	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr13:103459804C>T	ENST00000257336.1	+	3	866	c.187C>T	c.(187-189)Cgg>Tgg	p.R63W	BIVM-ERCC5_ENST00000602836.1_Missense_Mutation_p.T34M|BIVM_ENST00000419638.1_Missense_Mutation_p.R63W|BIVM_ENST00000448849.2_Intron	NM_017693.3	NP_060163.2	Q86UB2	BIVM_HUMAN	basic, immunoglobulin-like variable motif containing	63						cytoplasm (GO:0005737)|extracellular space (GO:0005615)|nucleus (GO:0005634)		p.R63W(1)		endometrium(3)|kidney(2)|large_intestine(7)|lung(10)|skin(2)|urinary_tract(1)	25	all_neural(89;0.0438)|Medulloblastoma(90;0.163)|Lung SC(71;0.211)					GACTCATACACGGGAAAAAAT	0.478																																					p.R63W												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C187T	13						.						133.0	126.0	128.0					13																	103459804		2203	4300	6503	102257805	SO:0001583	missense	2073	exon3			AF411385	CCDS9505.1, CCDS53879.1	13q33.1	2008-05-14			ENSG00000134897	ENSG00000134897			16034	protein-coding gene	gene with protein product						12036287	Standard	NM_017693		Approved	FLJ20159		Q86UB2	OTTHUMG00000017309	ENST00000257336.1:c.187C>T	13.37:g.103459804C>T	ENSP00000257336:p.Arg63Trp	Somatic		Capture	Illumina HiSeq	Phase_I	102257805	NM_017693	Q2M1J2|Q9NXM4	Missense_Mutation	SNP	ENST00000257336.1	37	CCDS9505.1	.	.	.	.	.	.	.	.	.	.	C	19.59	3.856142	0.71834	.	.	ENSG00000134897;ENSG00000134897;ENSG00000134899	ENST00000257336;ENST00000419638;ENST00000418659	.	.	.	5.97	3.12	0.35913	.	0.000000	0.85682	D	0.000000	T	0.66366	0.2782	L	0.32530	0.975	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.85130	0.997;0.973	T	0.70447	-0.4869	9	0.87932	D	0	.	15.7104	0.77623	0.5843:0.4157:0.0:0.0	.	34;63	Q59FZ7;Q86UB2	.;BIVM_HUMAN	W	63;63;34	.	ENSP00000257336:R63W	R	+	1	2	ERCC5;BIVM	102257805	0.930000	0.31532	0.995000	0.50966	0.996000	0.88848	1.126000	0.31344	0.797000	0.33971	0.655000	0.94253	CGG		0.478	BIVM-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045704.2		
DAOA	267012	broad.mit.edu	37	13	106124954	106124954	+	Silent	SNP	C	C	T	rs201139062		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr13:106124954C>T	ENST00000375936.3	+	3	247	c.201C>T	c.(199-201)gaC>gaT	p.D67D	DAOA-AS1_ENST00000448407.1_RNA|DAOA_ENST00000329625.5_5'UTR	NM_001161812.1|NM_172370.3	NP_001155284.1|NP_758958.3	P59103	DAOA_HUMAN	D-amino acid oxidase activator	67					negative regulation of D-amino-acid oxidase activity (GO:1900758)|positive regulation of catalytic activity (GO:0043085)	Golgi apparatus (GO:0005794)|mitochondrion (GO:0005739)|perinuclear region of cytoplasm (GO:0048471)	enzyme activator activity (GO:0008047)|enzyme binding (GO:0019899)	p.D67D(1)		endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(5)|skin(1)	13	Lung NSC(43;0.01)|all_neural(89;0.0741)|Lung SC(71;0.14)|Medulloblastoma(90;0.169)					GGCATGAGGACGGCTATTTGG	0.413													C|||	1	0.000199681	0.0008	0.0	5008	,	,		18053	0.0		0.0	False		,,,				2504	0.0				p.T3M												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C8T	13						.						176.0	176.0	176.0					13																	106124954		1937	4123	6060	104922955	SO:0001819	synonymous_variant	267012	exon3			AY138547	CCDS41905.1, CCDS53880.1, CCDS59242.1	13q33.2	2011-08-01			ENSG00000182346	ENSG00000182346			21191	protein-coding gene	gene with protein product	"""G72 transcript"""	607408				12364586, 15057823	Standard	NM_001161814		Approved	G72	uc010tjg.2	P59103	OTTHUMG00000041333	ENST00000375936.3:c.201C>T	13.37:g.106124954C>T		Somatic		Capture	Illumina HiSeq	Phase_I	104922955	NM_001161812	A6NKG7|Q0VAE6|Q5VX59|Q86Y17|Q8IWM4	Silent	SNP	ENST00000375936.3	37	CCDS41905.1																																																																																				0.413	DAOA-005	KNOWN	NMD_exception|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000099040.2	NM_172370	
COL4A1	1282	broad.mit.edu	37	13	110818589	110818589	+	Silent	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr13:110818589C>T	ENST00000375820.4	-	45	4132	c.4011G>A	c.(4009-4011)ccG>ccA	p.P1337P	COL4A1_ENST00000467182.1_5'Flank	NM_001845.4	NP_001836.2	P02462	CO4A1_HUMAN	collagen, type IV, alpha 1	1337	Triple-helical region.				axon guidance (GO:0007411)|basement membrane organization (GO:0071711)|blood vessel morphogenesis (GO:0048514)|brain development (GO:0007420)|cellular response to amino acid stimulus (GO:0071230)|collagen catabolic process (GO:0030574)|epithelial cell differentiation (GO:0030855)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|neuromuscular junction development (GO:0007528)|patterning of blood vessels (GO:0001569)|renal tubule morphogenesis (GO:0061333)|retinal blood vessel morphogenesis (GO:0061304)	basement membrane (GO:0005604)|collagen type IV trimer (GO:0005587)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)	extracellular matrix constituent conferring elasticity (GO:0030023)|extracellular matrix structural constituent (GO:0005201)|platelet-derived growth factor binding (GO:0048407)	p.P980P(1)|p.P1337P(1)		breast(2)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(16)|lung(57)|ovary(4)|pancreas(1)|prostate(4)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	105	all_cancers(4;9.8e-13)|all_epithelial(4;9.66e-08)|all_lung(23;3.75e-06)|Lung NSC(43;0.000274)|Colorectal(4;0.00178)|all_neural(89;0.00459)|Medulloblastoma(90;0.00596)|Lung SC(71;0.0604)	Breast(118;0.2)	BRCA - Breast invasive adenocarcinoma(86;0.11)|all cancers(43;0.145)			CTTTAGCTCCCGGGACGCCTT	0.473																																					p.P1337P												.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.G4011A	13						.						182.0	167.0	172.0					13																	110818589		2203	4300	6503	109616590	SO:0001819	synonymous_variant	1282	exon45			J04217	CCDS9511.1	13q34	2013-09-05			ENSG00000187498	ENSG00000187498		"""Collagens"""	2202	protein-coding gene	gene with protein product		120130				3691802	Standard	NM_001845		Approved		uc001vqw.4	P02462	OTTHUMG00000017342	ENST00000375820.4:c.4011G>A	13.37:g.110818589C>T		Somatic		Capture	Illumina HiSeq	Phase_I	109616590	NM_001845	A7E2W4|B1AM70|Q1P9S9|Q5VWF6|Q86X41|Q8NF88|Q9NYC5	Silent	SNP	ENST00000375820.4	37	CCDS9511.1																																																																																				0.473	COL4A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045759.3		
ATP11A	23250	broad.mit.edu	37	13	113439518	113439518	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr13:113439518G>A	ENST00000487903.1	+	2	197	c.109G>A	c.(109-111)Gca>Aca	p.A37T	ATP11A_ENST00000375645.3_Missense_Mutation_p.A37T|ATP11A_ENST00000283558.8_Missense_Mutation_p.A37T|ATP11A_ENST00000375630.2_Missense_Mutation_p.A37T			P98196	AT11A_HUMAN	ATPase, class VI, type 11A	37					phospholipid translocation (GO:0045332)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|plasma membrane (GO:0005886)|recycling endosome (GO:0055037)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)	p.A37T(1)		NS(1)|central_nervous_system(3)|cervix(1)|endometrium(6)|kidney(4)|large_intestine(12)|lung(17)|ovary(4)|skin(1)|stomach(1)|urinary_tract(1)	51	all_lung(23;0.000374)|Lung NSC(43;0.0107)|Lung SC(71;0.0753)|all_neural(89;0.0804)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)	all_lung(25;0.134)|all_epithelial(44;0.141)				ACCTCCGGGCGCAGAGGCCTA	0.557											OREG0003855	type=REGULATORY REGION|Gene=ATP11A|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay																									p.A37T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G109A	13						.						150.0	141.0	144.0					13																	113439518		2203	4300	6503	112487519	SO:0001583	missense	23250	exon2			AB028944	CCDS32011.1	13q34	2010-04-20	2007-09-19		ENSG00000068650	ENSG00000068650	3.6.3.1	"""ATPases / P-type"""	13552	protein-coding gene	gene with protein product	"""potential phospholipid-transporting ATPase IH"", ""phospholipid-translocating ATPase"""	605868	"""ATPase, Class VI, type 11A"""			11015572	Standard	NM_032189		Approved	ATPIH, ATPIS, KIAA1021	uc001vsj.4	P98196	OTTHUMG00000017371	ENST00000487903.1:c.109G>A	13.37:g.113439518G>A	ENSP00000420387:p.Ala37Thr	Somatic	1450	Capture	Illumina HiSeq	Phase_I	112487519	NM_015205	Q5VXT2	Missense_Mutation	SNP	ENST00000487903.1	37	CCDS32011.1	.	.	.	.	.	.	.	.	.	.	G	1.094	-0.663038	0.03428	.	.	ENSG00000068650	ENST00000487903;ENST00000375630;ENST00000375645;ENST00000283558	T;T;T;T	0.42131	0.98;0.98;0.98;0.98	4.83	1.93	0.25924	.	0.236952	0.43919	N	0.000512	T	0.14013	0.0339	N	0.02120	-0.675	0.23138	N	0.998232	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.27905	-1.0060	10	0.12766	T	0.61	.	7.5767	0.27939	0.377:0.0:0.623:0.0	.	37;37	E9PEJ6;P98196	.;AT11A_HUMAN	T	37	ENSP00000420387:A37T;ENSP00000364781:A37T;ENSP00000364796:A37T;ENSP00000283558:A37T	ENSP00000283558:A37T	A	+	1	0	ATP11A	112487519	0.074000	0.21230	0.022000	0.16811	0.684000	0.39900	0.399000	0.20916	0.491000	0.27793	-0.366000	0.07423	GCA		0.557	ATP11A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000045834.3	NM_015205	
MCF2L	23263	broad.mit.edu	37	13	113735527	113735527	+	Splice_Site	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr13:113735527G>A	ENST00000375608.3	+	17	1957	c.1899G>A	c.(1897-1899)agG>agA	p.R633R	MCF2L_ENST00000434480.2_Splice_Site_p.R609R|MCF2L_ENST00000375604.2_Splice_Site_p.R660R|MCF2L_ENST00000442652.2_Splice_Site_p.R633R|MCF2L_ENST00000423482.2_Splice_Site_p.R601R|MCF2L_ENST00000421756.1_Splice_Site_p.R607R|MCF2L_ENST00000375601.3_Splice_Site_p.R607R|MCF2L_ENST00000375597.4_Splice_Site_p.R601R|MCF2L_ENST00000397030.1_Splice_Site_p.R636R|MCF2L_ENST00000535094.2_Splice_Site_p.R603R			O15068	MCF2L_HUMAN	MCF.2 cell line derived transforming sequence-like	633	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.				apoptotic signaling pathway (GO:0097190)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of small GTPase mediated signal transduction (GO:0051056)|Rho protein signal transduction (GO:0007266)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|extracellular space (GO:0005615)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)	1-phosphatidylinositol binding (GO:0005545)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)	p.R601R(1)|p.R607R(1)		kidney(1)|large_intestine(5)|ovary(1)|stomach(1)	8	all_lung(23;0.000374)|Lung NSC(43;0.0107)|Lung SC(71;0.0753)|all_neural(89;0.0804)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)	all_cancers(25;0.118)|all_lung(25;0.0368)|all_epithelial(44;0.0396)|Lung NSC(25;0.129)|Breast(118;0.188)				CTGCCACCAGGCACGTGATGA	0.612																																					p.R607R												.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.G1821A	13						.						61.0	44.0	49.0					13																	113735527		2197	4295	6492	112783528	SO:0001630	splice_region_variant	23263	exon16			AB002360	CCDS9527.2, CCDS45070.1, CCDS9527.3, CCDS45070.2	13q34	2013-01-10			ENSG00000126217	ENSG00000126217		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	14576	protein-coding gene	gene with protein product		609499				9205841	Standard	NM_001112732		Approved	KIAA0362, DBS, OST, ARHGEF14	uc010tjr.2	O15068	OTTHUMG00000017377	ENST00000375608.3:c.1899-1G>A	13.37:g.113735527G>A		Somatic		Capture	Illumina HiSeq	Phase_I	112783528	NM_024979	A2A2X1|A2A2X2|A2A3G6|A2A3G8|B4DHD6|B4DIL6|E9PDN8|Q5JU56|Q5VXT1|Q6ZWD4|Q765G8|Q765G9|Q8N679	Silent	SNP	ENST00000375608.3	37		.	.	.	.	.	.	.	.	.	.	G	11.34	1.609300	0.28623	.	.	ENSG00000126217	ENST00000397017	.	.	.	4.45	3.29	0.37713	.	.	.	.	.	T	0.58163	0.2103	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.52335	-0.8589	4	.	.	.	.	8.5172	0.33253	0.1523:0.0:0.8477:0.0	.	.	.	.	T	264	.	.	A	+	1	0	MCF2L	112783528	0.984000	0.35163	0.998000	0.56505	0.723000	0.41478	0.043000	0.13971	0.657000	0.30906	0.655000	0.94253	GCA		0.612	MCF2L-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000045849.4		Silent
Unknown	0	broad.mit.edu	37	Unknown	0	0	+	IGR	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Invalid:failed_liftOver	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chrUnknown:0G>A								None (None upstream) : None (None downstream)																								0.0																																					p.G182G												.	.	0			c.C546T	13						.																																			113609281	SO:0001628	intergenic_variant	348013	exon7																															Unknown.37:g.0G>A		Somatic		Capture	Illumina HiSeq	Phase_I	113609281	NM_182614		Silent	SNP		37																																																																																				0	0								
PSPC1	55269	broad.mit.edu	37	13	20279843	20279843	+	Missense_Mutation	SNP	C	C	T	rs555623518	byFrequency	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr13:20279843C>T	ENST00000338910.4	-	8	1504	c.1345G>A	c.(1345-1347)Gca>Aca	p.A449T		NM_001042414.2	NP_001035879.1	Q8WXF1	PSPC1_HUMAN	paraspeckle component 1	449	Gly-rich.				negative regulation of transcription, DNA-templated (GO:0045892)|regulation of circadian rhythm (GO:0042752)|rhythmic process (GO:0048511)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)|paraspeckles (GO:0042382)	core promoter binding (GO:0001047)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)	p.A449T(1)		breast(1)|endometrium(1)|large_intestine(4)|lung(10)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	23		all_cancers(29;1.25e-22)|all_lung(29;1.97e-20)|all_epithelial(30;2.29e-20)|Lung NSC(5;3.36e-17)|Lung SC(185;0.0262)|Ovarian(182;0.162)		all cancers(112;4.63e-06)|Epithelial(112;2.29e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00256)|Lung(94;0.00975)|LUSC - Lung squamous cell carcinoma(192;0.0483)		CCCATATTTGCGGCTCCTTCT	0.443													C|||	6	0.00119808	0.0	0.0	5008	,	,		22587	0.006		0.0	False		,,,				2504	0.0				p.A449T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1345A	13						.						16.0	18.0	17.0					13																	20279843		1760	3983	5743	19177843	SO:0001583	missense	55269	exon8			AK001817	CCDS41870.1	13q11	2013-02-12			ENSG00000121390	ENSG00000121390		"""RNA binding motif (RRM) containing"""	20320	protein-coding gene	gene with protein product		612408				11790299	Standard	NM_001042414		Approved	PSP1, FLJ10955	uc021rgx.1	Q8WXF1	OTTHUMG00000016502	ENST00000338910.4:c.1345G>A	13.37:g.20279843C>T	ENSP00000343966:p.Ala449Thr	Somatic		Capture	Illumina HiSeq	Phase_I	19177843	NM_001042414	Q5JTQ3|Q8NCZ9|Q8WXE8|Q9NV36	Missense_Mutation	SNP	ENST00000338910.4	37	CCDS41870.1	.	.	.	.	.	.	.	.	.	.	C	13.81	2.347859	0.41599	.	.	ENSG00000121390	ENST00000338910;ENST00000422828	T	0.15487	2.42	5.17	4.33	0.51752	.	0.289012	0.38326	N	0.001737	T	0.12347	0.0300	L	0.36672	1.1	0.36368	D	0.86112	B	0.24533	0.105	B	0.11329	0.006	T	0.16276	-1.0408	10	0.19147	T	0.46	-8.1961	10.1828	0.42980	0.0:0.8463:0.0:0.1537	.	449	Q8WXF1	PSPC1_HUMAN	T	449;389	ENSP00000343966:A449T	ENSP00000343966:A449T	A	-	1	0	PSPC1	19177843	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	1.409000	0.34680	1.308000	0.44962	0.491000	0.48974	GCA		0.443	PSPC1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044037.2		
TNFRSF19	55504	broad.mit.edu	37	13	24242862	24242862	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr13:24242862A>G	ENST00000382258.4	+	9	1075	c.871A>G	c.(871-873)Act>Gct	p.T291A	TNFRSF19_ENST00000403372.2_Missense_Mutation_p.T159A|TNFRSF19_ENST00000382263.3_Missense_Mutation_p.T291A|TNFRSF19_ENST00000248484.4_Missense_Mutation_p.T291A	NM_018647.3	NP_061117.2	Q9NS68	TNR19_HUMAN	tumor necrosis factor receptor superfamily, member 19	291					apoptotic process (GO:0006915)|hair follicle development (GO:0001942)|JNK cascade (GO:0007254)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|tumor necrosis factor-mediated signaling pathway (GO:0033209)	integral component of membrane (GO:0016021)	tumor necrosis factor-activated receptor activity (GO:0005031)	p.T291A(1)		breast(1)|endometrium(4)|kidney(1)|large_intestine(4)|liver(2)|lung(5)|prostate(1)|skin(2)|stomach(1)|urinary_tract(1)	22		all_cancers(29;3.4e-22)|all_epithelial(30;8.75e-19)|all_lung(29;5.09e-18)|Lung SC(185;0.0225)|Breast(139;0.128)		all cancers(112;0.00193)|Epithelial(112;0.0137)|OV - Ovarian serous cystadenocarcinoma(117;0.0465)|GBM - Glioblastoma multiforme(144;0.184)|Lung(94;0.19)		GATGGTGCCGACTTTCTTCGG	0.493																																					p.T291A												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A871G	13						.						101.0	100.0	100.0					13																	24242862		2203	4300	6503	23140862	SO:0001583	missense	55504	exon9			AB040434	CCDS9301.1, CCDS9302.1, CCDS55893.1	13q12.11-q12.3	2008-07-18			ENSG00000127863	ENSG00000127863		"""Tumor necrosis factor receptor superfamily"""	11915	protein-coding gene	gene with protein product	"""toxicity and JNK inducer"""	606122				10764796, 10809768	Standard	NM_018647		Approved	TAJ-alpha, TROY, TAJ, TRADE	uc001uov.2	Q9NS68	OTTHUMG00000016568	ENST00000382258.4:c.871A>G	13.37:g.24242862A>G	ENSP00000371693:p.Thr291Ala	Somatic		Capture	Illumina HiSeq	Phase_I	23140862	NM_148957	A8KA09|A8KA26|B1AM40|B1AM41|B4E2I6|Q9BXZ9|Q9BY00|Q9NZV2	Missense_Mutation	SNP	ENST00000382258.4	37	CCDS9302.1	.	.	.	.	.	.	.	.	.	.	A	8.884	0.952386	0.18431	.	.	ENSG00000127863	ENST00000248484;ENST00000403372;ENST00000382258;ENST00000382263	T;T;T;T	0.75821	-0.97;1.61;-0.97;-0.97	6.07	-8.19	0.01049	.	1.069600	0.07116	N	0.843146	T	0.51210	0.1661	N	0.17082	0.46	0.09310	N	1	B;B;B	0.06786	0.001;0.0;0.0	B;B;B	0.09377	0.004;0.001;0.001	T	0.55159	-0.8184	10	0.05436	T	0.98	1.2761	15.0403	0.71785	0.2297:0.0:0.6842:0.0861	.	159;291;291	B4E2I6;Q9NS68;Q9NS68-2	.;TNR19_HUMAN;.	A	291;159;291;291	ENSP00000248484:T291A;ENSP00000385408:T159A;ENSP00000371693:T291A;ENSP00000371698:T291A	ENSP00000248484:T291A	T	+	1	0	TNFRSF19	23140862	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.333000	0.02667	-1.694000	0.01425	-0.290000	0.09829	ACT		0.493	TNFRSF19-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000044156.2	NM_018647	
RASL11A	387496	broad.mit.edu	37	13	27847385	27847385	+	Silent	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr13:27847385C>T	ENST00000241463.4	+	4	1101	c.483C>T	c.(481-483)gaC>gaT	p.D161D	RASL11A_ENST00000480803.1_3'UTR	NM_206827.1	NP_996563.1			RAS-like, family 11, member A									p.D161D(1)		breast(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(3)|prostate(1)	10		Lung SC(185;0.0161)	Colorectal(13;0.00042)|READ - Rectum adenocarcinoma(15;0.105)	all cancers(112;0.0173)|GBM - Glioblastoma multiforme(144;0.0557)|OV - Ovarian serous cystadenocarcinoma(117;0.152)|Epithelial(112;0.164)		AGACACAGGACGGTATTCAGC	0.522																																					p.D161D												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C483T	13						.						55.0	50.0	52.0					13																	27847385		2203	4300	6503	26745385	SO:0001819	synonymous_variant	387496	exon4			AY439004	CCDS9321.1	13q12.2	2014-05-09			ENSG00000122035	ENSG00000122035			23802	protein-coding gene	gene with protein product		612403				15033445	Standard	NM_206827		Approved		uc001urd.1	Q6T310	OTTHUMG00000016627	ENST00000241463.4:c.483C>T	13.37:g.27847385C>T		Somatic		Capture	Illumina HiSeq	Phase_I	26745385	NM_206827		Silent	SNP	ENST00000241463.4	37	CCDS9321.1																																																																																				0.522	RASL11A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044265.2	NM_206827	
LNX2	222484	broad.mit.edu	37	13	28127556	28127556	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr13:28127556T>C	ENST00000316334.3	-	8	1696	c.1567A>G	c.(1567-1569)Aac>Gac	p.N523D		NM_153371.3	NP_699202.1	Q8N448	LNX2_HUMAN	ligand of numb-protein X 2	523	PDZ 3. {ECO:0000255|PROSITE- ProRule:PRU00143}.				protein homooligomerization (GO:0051260)		zinc ion binding (GO:0008270)	p.N523D(1)		breast(1)|central_nervous_system(2)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(8)|lung(7)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)	31		Lung SC(185;0.0156)	Colorectal(13;0.000157)|READ - Rectum adenocarcinoma(15;0.105)	OV - Ovarian serous cystadenocarcinoma(117;0.113)|all cancers(112;0.127)|Epithelial(112;0.248)		TCAATGCCGTTGATATTTAGC	0.433																																					p.N523D												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A1567G	13						.						75.0	71.0	73.0					13																	28127556		2203	4300	6503	27025556	SO:0001583	missense	222484	exon8			AL138699	CCDS9323.1	13q12.2	2013-01-09	2004-01-22	2004-01-23	ENSG00000139517	ENSG00000139517		"""RING-type (C3HC4) zinc fingers"""	20421	protein-coding gene	gene with protein product		609733	"""PDZ domain containing ring finger 1"""	PDZRN1			Standard	NM_153371		Approved	MGC46315	uc001url.4	Q8N448	OTTHUMG00000016634	ENST00000316334.3:c.1567A>G	13.37:g.28127556T>C	ENSP00000325929:p.Asn523Asp	Somatic		Capture	Illumina HiSeq	Phase_I	27025556	NM_153371	Q5W0P0|Q6ZMH2|Q96SH4	Missense_Mutation	SNP	ENST00000316334.3	37	CCDS9323.1	.	.	.	.	.	.	.	.	.	.	T	27.5	4.836515	0.91117	.	.	ENSG00000139517	ENST00000316334	T	0.56776	0.44	5.96	5.96	0.96718	PDZ/DHR/GLGF (4);	0.000000	0.85682	D	0.000000	T	0.68063	0.2960	M	0.65320	2	0.80722	D	1	P	0.50156	0.932	P	0.59948	0.866	T	0.68678	-0.5345	10	0.52906	T	0.07	.	16.4293	0.83835	0.0:0.0:0.0:1.0	.	523	Q8N448	LNX2_HUMAN	D	523	ENSP00000325929:N523D	ENSP00000325929:N523D	N	-	1	0	LNX2	27025556	1.000000	0.71417	0.999000	0.59377	0.929000	0.56500	7.698000	0.84413	2.271000	0.75665	0.528000	0.53228	AAC		0.433	LNX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044302.2		
FRY	10129	broad.mit.edu	37	13	32747532	32747532	+	Missense_Mutation	SNP	T	T	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr13:32747532T>A	ENST00000380250.3	+	19	2676	c.2180T>A	c.(2179-2181)aTt>aAt	p.I727N		NM_023037.2	NP_075463.2	Q5TBA9	FRY_HUMAN	furry homolog (Drosophila)	727						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)		p.I727N(1)		NS(3)|breast(4)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(31)|lung(50)|ovary(5)|pancreas(1)|prostate(6)|skin(9)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	132		Lung SC(185;0.0271)		all cancers(112;4.81e-05)|Epithelial(112;0.000656)|OV - Ovarian serous cystadenocarcinoma(117;0.0123)|BRCA - Breast invasive adenocarcinoma(63;0.0295)|GBM - Glioblastoma multiforme(144;0.104)		AGTCACAGAATTCAGTCGGAA	0.453																																					p.I727N												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T2180A	13						.						135.0	136.0	136.0					13																	32747532		1979	4165	6144	31645532	SO:0001583	missense	10129	exon19			AL049784	CCDS41875.1	13q13.1	2008-02-05	2005-11-24	2005-11-24	ENSG00000073910	ENSG00000073910			20367	protein-coding gene	gene with protein product		614818	"""chromosome 13 open reading frame 14"""	C13orf14		14702039, 8812419	Standard	NM_023037		Approved	bA37E23.1, 13CDNA73, CG003	uc001utx.3	Q5TBA9	OTTHUMG00000016696	ENST00000380250.3:c.2180T>A	13.37:g.32747532T>A	ENSP00000369600:p.Ile727Asn	Somatic		Capture	Illumina HiSeq	Phase_I	31645532	NM_023037	Q9Y3N6	Missense_Mutation	SNP	ENST00000380250.3	37	CCDS41875.1	.	.	.	.	.	.	.	.	.	.	T	10.79	1.451020	0.26074	.	.	ENSG00000073910	ENST00000380250	T	0.24350	1.86	5.75	-6.35	0.01975	.	1.329840	0.04789	N	0.431283	T	0.15262	0.0368	L	0.29908	0.895	0.09310	N	1	B	0.19583	0.037	B	0.17098	0.017	T	0.28396	-1.0045	10	0.18276	T	0.48	.	8.0603	0.30629	0.0:0.3748:0.1958:0.4295	.	727	Q5TBA9	FRY_HUMAN	N	727	ENSP00000369600:I727N	ENSP00000369600:I727N	I	+	2	0	FRY	31645532	0.175000	0.23083	0.000000	0.03702	0.990000	0.78478	0.683000	0.25349	-0.838000	0.04218	0.528000	0.53228	ATT		0.453	FRY-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044405.1	NM_023037	
STARD13	90627	broad.mit.edu	37	13	33704196	33704196	+	Silent	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr13:33704196G>A	ENST00000336934.5	-	5	734	c.618C>T	c.(616-618)agC>agT	p.S206S	STARD13_ENST00000255486.4_Silent_p.S198S|STARD13_ENST00000399365.3_Silent_p.S88S	NM_001243476.1|NM_178006.3	NP_001230405.1|NP_821074.1	Q9Y3M8	STA13_HUMAN	StAR-related lipid transfer (START) domain containing 13	206					regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|lipid particle (GO:0005811)|membrane (GO:0016020)|mitochondrion (GO:0005739)	GTPase activator activity (GO:0005096)|lipid binding (GO:0008289)	p.S206S(1)		breast(2)|endometrium(2)|kidney(3)|large_intestine(6)|lung(18)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|soft_tissue(1)|upper_aerodigestive_tract(1)	40	all_epithelial(80;0.155)	Lung SC(185;0.0367)		all cancers(112;1.31e-05)|Epithelial(112;0.000142)|BRCA - Breast invasive adenocarcinoma(63;0.00936)|OV - Ovarian serous cystadenocarcinoma(117;0.0533)|Lung(94;0.143)|GBM - Glioblastoma multiforme(144;0.143)		TGCGACTGTCGCTGCCTCCAC	0.637																																					p.S206S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C618T	13						.						35.0	35.0	35.0					13																	33704196		2203	4300	6503	32602196	SO:0001819	synonymous_variant	90627	exon5			AL049801	CCDS9348.1, CCDS9349.1, CCDS9350.1	13q13.1	2013-08-13	2007-08-16		ENSG00000133121	ENSG00000133121		"""Rho GTPase activating proteins"", ""StAR-related lipid transfer (START) domain containing"""	19164	protein-coding gene	gene with protein product		609866	"""START domain containing 13"", ""long intergenic non-protein coding RNA 464"""	LINC00464		8812419	Standard	NM_178006		Approved	GT650, DLC2, ARHGAP37	uc001uuw.3	Q9Y3M8	OTTHUMG00000016708	ENST00000336934.5:c.618C>T	13.37:g.33704196G>A		Somatic		Capture	Illumina HiSeq	Phase_I	32602196	NM_178006	A2A309|A2A310|Q5HYH1|Q5TAE3|Q6UN61|Q86TP6|Q86WQ3|Q86XT1	Silent	SNP	ENST00000336934.5	37	CCDS9348.1																																																																																				0.637	STARD13-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276118.2	NM_001243466	
SOHLH2	54937	broad.mit.edu	37	13	36776096	36776096	+	Silent	SNP	A	A	G			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr13:36776096A>G	ENST00000379881.3	-	2	271	c.183T>C	c.(181-183)gaT>gaC	p.D61D	SOHLH2_ENST00000554962.1_Silent_p.D138D|SOHLH2_ENST00000317764.6_Silent_p.D61D|CCDC169-SOHLH2_ENST00000511166.1_Silent_p.D138D	NM_017826.2	NP_060296.2	Q9NX45	SOLH2_HUMAN	spermatogenesis and oogenesis specific basic helix-loop-helix 2	61					multicellular organismal development (GO:0007275)|oogenesis (GO:0048477)|regulation of transcription, DNA-templated (GO:0006355)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)	p.D61D(1)		autonomic_ganglia(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(13)|lung(5)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	26		Breast(139;0.0615)|Lung SC(185;0.0743)|Prostate(109;0.184)	KIRC - Kidney renal clear cell carcinoma(5;0.119)|Kidney(79;0.169)	all cancers(112;4.63e-08)|Epithelial(112;2.67e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.00272)|BRCA - Breast invasive adenocarcinoma(63;0.00685)|GBM - Glioblastoma multiforme(144;0.0273)		ATATGCAATCATCCAAAAGCG	0.453																																					p.D61D												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.T183C	13						.						149.0	119.0	129.0					13																	36776096		2203	4300	6503	35674096	SO:0001819	synonymous_variant	54937	exon2			AK000456	CCDS9355.1, CCDS61309.1	13q13.3	2013-05-21			ENSG00000120669	ENSG00000120669		"""Basic helix-loop-helix proteins"""	26026	protein-coding gene	gene with protein product	"""spermatogenesis associated 28"""					12477932	Standard	NM_017826		Approved	FLJ20449, TEB1, bHLHe81, SPATA28		Q9NX45	OTTHUMG00000016728	ENST00000379881.3:c.183T>C	13.37:g.36776096A>G		Somatic		Capture	Illumina HiSeq	Phase_I	35674096	NM_017826	B4DX90|Q5EGC3|Q8TC74|Q96QX4	Silent	SNP	ENST00000379881.3	37	CCDS9355.1																																																																																				0.453	SOHLH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044477.2	NM_017826	
SMAD9	4093	broad.mit.edu	37	13	37427645	37427645	+	Missense_Mutation	SNP	C	C	T	rs148698551		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr13:37427645C>T	ENST00000399275.2	-	5	1310	c.1171G>A	c.(1171-1173)Gct>Act	p.A391T	SMAD9_ENST00000379826.4_Missense_Mutation_p.A391T|SMAD9_ENST00000350148.5_Missense_Mutation_p.A354T			O15198	SMAD9_HUMAN	SMAD family member 9	391	MH2. {ECO:0000255|PROSITE- ProRule:PRU00439}.				BMP signaling pathway (GO:0030509)|bone development (GO:0060348)|cartilage development (GO:0051216)|cellular response to organic cyclic compound (GO:0071407)|hindbrain development (GO:0030902)|intracellular signal transduction (GO:0035556)|midbrain development (GO:0030901)|Mullerian duct regression (GO:0001880)|positive regulation of cell differentiation (GO:0045597)|positive regulation of transcription, DNA-templated (GO:0045893)|protein phosphorylation (GO:0006468)|response to hypoxia (GO:0001666)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|ureteric bud development (GO:0001657)	cytosol (GO:0005829)|intracellular (GO:0005622)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transforming growth factor beta receptor, pathway-specific cytoplasmic mediator activity (GO:0030618)	p.A354T(1)		NS(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(8)	18		Breast(139;0.0615)|Lung SC(185;0.0743)|Prostate(109;0.184)		all cancers(112;3.38e-07)|Epithelial(112;1.93e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00804)|BRCA - Breast invasive adenocarcinoma(63;0.0129)|GBM - Glioblastoma multiforme(144;0.026)		AGGAGCTGAGCGAAGAGCTGG	0.537																																					p.A354T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1060A	13						.	C	THR/ALA,THR/ALA	0,4406		0,0,2203	120.0	86.0	97.0		1171,1060	5.4	1.0	13	dbSNP_134	97	2,8598	2.2+/-6.3	0,2,4298	no	missense,missense	SMAD9	NM_001127217.2,NM_005905.5	58,58	0,2,6501	TT,TC,CC		0.0233,0.0,0.0154	probably-damaging,probably-damaging	391/468,354/431	37427645	2,13004	2203	4300	6503	36325645	SO:0001583	missense	4093	exon5				CCDS9360.1, CCDS45032.1	13q12-q14	2014-09-17	2006-11-06	2004-05-26	ENSG00000120693	ENSG00000120693		"""SMADs"""	6774	protein-coding gene	gene with protein product		603295	"""MAD, mothers against decapentaplegic homolog 9 (Drosophila)"", ""SMAD, mothers against DPP homolog 9 (Drosophila)"""	MADH6, MADH9		9205116	Standard	NM_001127217		Approved		uc001uvw.3	O15198	OTTHUMG00000016740	ENST00000399275.2:c.1171G>A	13.37:g.37427645C>T	ENSP00000382216:p.Ala391Thr	Somatic		Capture	Illumina HiSeq	Phase_I	36325645	NM_005905	A2A2Y6|O14989|Q5TBA1	Missense_Mutation	SNP	ENST00000399275.2	37	CCDS45032.1	.	.	.	.	.	.	.	.	.	.	C	26.8	4.772697	0.90108	0.0	2.33E-4	ENSG00000120693	ENST00000399275;ENST00000350148;ENST00000379826	D;D;D	0.97404	-4.24;-4.37;-4.24	5.42	5.42	0.78866	SMAD domain-like (1);SMAD/FHA domain (1);SMAD domain, Dwarfin-type (3);	0.000000	0.85682	D	0.000000	D	0.97636	0.9225	M	0.92691	3.335	0.80722	D	1	B;B	0.29253	0.093;0.239	B;B	0.32583	0.021;0.148	D	0.97487	1.0051	10	0.62326	D	0.03	.	18.203	0.89844	0.0:1.0:0.0:0.0	.	354;391	O15198-2;O15198	.;SMAD9_HUMAN	T	391;354;391	ENSP00000382216:A391T;ENSP00000239885:A354T;ENSP00000369154:A391T	ENSP00000239885:A354T	A	-	1	0	SMAD9	36325645	1.000000	0.71417	0.995000	0.50966	0.992000	0.81027	7.585000	0.82584	2.535000	0.85469	0.655000	0.94253	GCT		0.537	SMAD9-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000044525.2	NM_005905	
POSTN	10631	broad.mit.edu	37	13	38154761	38154761	+	Missense_Mutation	SNP	C	C	T	rs117790304		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr13:38154761C>T	ENST00000379747.4	-	11	1583	c.1466G>A	c.(1465-1467)cGc>cAc	p.R489H	POSTN_ENST00000541481.1_Missense_Mutation_p.R489H|POSTN_ENST00000379749.4_Missense_Mutation_p.R489H|POSTN_ENST00000379742.4_Missense_Mutation_p.R489H|POSTN_ENST00000379743.4_Missense_Mutation_p.R489H|POSTN_ENST00000541179.1_Missense_Mutation_p.R489H	NM_006475.2	NP_006466.2	Q15063	POSTN_HUMAN	periostin, osteoblast specific factor	489	FAS1 3. {ECO:0000255|PROSITE- ProRule:PRU00082, ECO:0000305}.				cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|regulation of Notch signaling pathway (GO:0008593)|skeletal system development (GO:0001501)|tissue development (GO:0009888)	proteinaceous extracellular matrix (GO:0005578)|trans-Golgi network (GO:0005802)	heparin binding (GO:0008201)	p.R489H(1)		cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(16)|lung(22)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	59		Lung NSC(96;2.09e-05)|Prostate(109;0.0513)|Breast(139;0.0538)|Lung SC(185;0.0743)		all cancers(112;2.48e-08)|Epithelial(112;2.78e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.000853)|BRCA - Breast invasive adenocarcinoma(63;0.013)|GBM - Glioblastoma multiforme(144;0.0154)		GATGATCTCGCGGAATATGTG	0.448													C|||	1	0.000199681	0.0	0.0	5008	,	,		17359	0.001		0.0	False		,,,				2504	0.0				p.R489H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1466A	13						.	C	HIS/ARG,HIS/ARG,HIS/ARG,HIS/ARG	0,4406		0,0,2203	315.0	290.0	298.0		1466,1466,1466,1466	2.0	1.0	13	dbSNP_132	298	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense,missense,missense	POSTN	NM_001135934.1,NM_001135935.1,NM_001135936.1,NM_006475.2	29,29,29,29	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging	489/780,489/782,489/752,489/837	38154761	1,13005	2203	4300	6503	37052761	SO:0001583	missense	10631	exon11			D13665	CCDS9364.1, CCDS45034.1, CCDS53864.1, CCDS66530.1, CCDS66531.1	13q13.3	2008-02-05			ENSG00000133110	ENSG00000133110			16953	protein-coding gene	gene with protein product		608777				8363580, 12235007	Standard	NM_006475		Approved	OSF-2, PN, periostin	uc001uwo.4	Q15063	OTTHUMG00000016751	ENST00000379747.4:c.1466G>A	13.37:g.38154761C>T	ENSP00000369071:p.Arg489His	Somatic		Capture	Illumina HiSeq	Phase_I	37052761	NM_001135934	B1ALD8|C0IMJ1|C0IMJ2|C0IMJ4|D2KRH7|F5H628|Q15064|Q29XZ0|Q3KPJ5|Q5VSY5|Q8IZF9	Missense_Mutation	SNP	ENST00000379747.4	37	CCDS9364.1	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	C	18.33	3.601401	0.66445	0.0	1.16E-4	ENSG00000133110	ENST00000541179;ENST00000379749;ENST00000379747;ENST00000379743;ENST00000379742;ENST00000541481	D;D;D;D;D;D	0.90444	-2.67;-2.67;-2.67;-2.67;-2.67;-2.67	5.03	2.0	0.26442	FAS1 domain (6);	0.278041	0.39274	N	0.001410	D	0.88455	0.6441	N	0.25647	0.755	0.34201	D	0.673149	D;P;P;P;D;B;D	0.64830	0.993;0.866;0.938;0.922;0.994;0.034;0.975	P;P;P;P;P;B;P	0.56042	0.79;0.57;0.751;0.57;0.607;0.017;0.751	D	0.89990	0.4107	10	0.66056	D	0.02	-3.8679	10.4523	0.44528	0.0:0.7556:0.0:0.2444	.	489;489;489;489;489;489;489	C0IMJ4;F5H628;B1ALD8;Q15063-3;Q15063-4;Q15063-2;Q15063	.;.;.;.;.;.;POSTN_HUMAN	H	489	ENSP00000437959:R489H;ENSP00000369073:R489H;ENSP00000369071:R489H;ENSP00000369067:R489H;ENSP00000369066:R489H;ENSP00000437953:R489H	ENSP00000369066:R489H	R	-	2	0	POSTN	37052761	0.912000	0.30974	0.994000	0.49952	0.805000	0.45488	0.123000	0.15708	0.485000	0.27652	0.563000	0.77884	CGC		0.448	POSTN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000044566.2	NM_006475	
POSTN	10631	broad.mit.edu	37	13	38158993	38158993	+	Missense_Mutation	SNP	G	G	A	rs142297717	byFrequency	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr13:38158993G>A	ENST00000379747.4	-	8	1085	c.968C>T	c.(967-969)aCg>aTg	p.T323M	POSTN_ENST00000541481.1_Missense_Mutation_p.T323M|POSTN_ENST00000379749.4_Missense_Mutation_p.T323M|POSTN_ENST00000379742.4_Missense_Mutation_p.T323M|POSTN_ENST00000379743.4_Missense_Mutation_p.T323M|POSTN_ENST00000541179.1_Missense_Mutation_p.T323M	NM_006475.2	NP_006466.2	Q15063	POSTN_HUMAN	periostin, osteoblast specific factor	323	FAS1 2. {ECO:0000255|PROSITE- ProRule:PRU00082, ECO:0000305}.				cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|regulation of Notch signaling pathway (GO:0008593)|skeletal system development (GO:0001501)|tissue development (GO:0009888)	proteinaceous extracellular matrix (GO:0005578)|trans-Golgi network (GO:0005802)	heparin binding (GO:0008201)	p.T323M(1)		cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(16)|lung(22)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	59		Lung NSC(96;2.09e-05)|Prostate(109;0.0513)|Breast(139;0.0538)|Lung SC(185;0.0743)		all cancers(112;2.48e-08)|Epithelial(112;2.78e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.000853)|BRCA - Breast invasive adenocarcinoma(63;0.013)|GBM - Glioblastoma multiforme(144;0.0154)		TCCTTCCAGCGTCTCAAAGAC	0.378																																					p.T323M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C968T	13						.	G	MET/THR,MET/THR,MET/THR,MET/THR	2,4404	4.2+/-10.8	0,2,2201	182.0	162.0	168.0		968,968,968,968	5.4	1.0	13	dbSNP_134	168	3,8597	3.0+/-9.4	0,3,4297	yes	missense,missense,missense,missense	POSTN	NM_001135934.1,NM_001135935.1,NM_001135936.1,NM_006475.2	81,81,81,81	0,5,6498	AA,AG,GG		0.0349,0.0454,0.0384	probably-damaging,probably-damaging,probably-damaging,probably-damaging	323/780,323/782,323/752,323/837	38158993	5,13001	2203	4300	6503	37056993	SO:0001583	missense	10631	exon8			D13665	CCDS9364.1, CCDS45034.1, CCDS53864.1, CCDS66530.1, CCDS66531.1	13q13.3	2008-02-05			ENSG00000133110	ENSG00000133110			16953	protein-coding gene	gene with protein product		608777				8363580, 12235007	Standard	NM_006475		Approved	OSF-2, PN, periostin	uc001uwo.4	Q15063	OTTHUMG00000016751	ENST00000379747.4:c.968C>T	13.37:g.38158993G>A	ENSP00000369071:p.Thr323Met	Somatic		Capture	Illumina HiSeq	Phase_I	37056993	NM_001135934	B1ALD8|C0IMJ1|C0IMJ2|C0IMJ4|D2KRH7|F5H628|Q15064|Q29XZ0|Q3KPJ5|Q5VSY5|Q8IZF9	Missense_Mutation	SNP	ENST00000379747.4	37	CCDS9364.1	.	.	.	.	.	.	.	.	.	.	G	22.4	4.281659	0.80692	4.54E-4	3.49E-4	ENSG00000133110	ENST00000541179;ENST00000379749;ENST00000379747;ENST00000379743;ENST00000379742;ENST00000541481;ENST00000538347	D;D;D;D;D;D	0.94828	-3.53;-3.53;-3.53;-3.53;-3.53;-3.53	5.41	5.41	0.78517	FAS1 domain (5);	0.000000	0.85682	D	0.000000	D	0.97848	0.9293	M	0.90252	3.1	0.80722	D	1	D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D;D	0.97110	1.0;0.999;1.0;0.999;0.999;1.0;1.0	D	0.98505	1.0616	10	0.72032	D	0.01	.	19.2193	0.93790	0.0:0.0:1.0:0.0	.	323;323;323;323;323;323;323	C0IMJ4;F5H628;B1ALD8;Q15063-3;Q15063-4;Q15063-2;Q15063	.;.;.;.;.;.;POSTN_HUMAN	M	323;323;323;323;323;323;240	ENSP00000437959:T323M;ENSP00000369073:T323M;ENSP00000369071:T323M;ENSP00000369067:T323M;ENSP00000369066:T323M;ENSP00000437953:T323M	ENSP00000369066:T323M	T	-	2	0	POSTN	37056993	1.000000	0.71417	0.954000	0.39281	0.693000	0.40251	9.437000	0.97535	2.524000	0.85096	0.655000	0.94253	ACG		0.378	POSTN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000044566.2	NM_006475	
SLC25A15	10166	broad.mit.edu	37	13	41381542	41381542	+	Missense_Mutation	SNP	G	G	T	rs151239794		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr13:41381542G>T	ENST00000338625.4	+	5	801	c.565G>T	c.(565-567)Ggt>Tgt	p.G189C	SLC25A15_ENST00000478827.1_3'UTR	NM_014252.3	NP_055067.1	Q9Y619	ORNT1_HUMAN	solute carrier family 25 (mitochondrial carrier; ornithine transporter) member 15	189					cellular amino acid metabolic process (GO:0006520)|cellular nitrogen compound metabolic process (GO:0034641)|L-ornithine transmembrane transport (GO:1903352)|mitochondrial ornithine transport (GO:0000066)|small molecule metabolic process (GO:0044281)|urea cycle (GO:0000050)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)	L-ornithine transmembrane transporter activity (GO:0000064)	p.G189C(1)		endometrium(4)|kidney(1)|large_intestine(3)|lung(4)|stomach(1)|urinary_tract(1)	14		Lung NSC(96;3.55e-06)|Breast(139;0.00394)|Prostate(109;0.0181)|Lung SC(185;0.0262)|Hepatocellular(188;0.194)		all cancers(112;1.48e-08)|Epithelial(112;7.51e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.000191)|GBM - Glioblastoma multiforme(144;0.00231)|BRCA - Breast invasive adenocarcinoma(63;0.0704)	L-Ornithine(DB00129)	CTTCTTCTTCGGTGGCTATGA	0.438																																					p.G189C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G565T	13						.						180.0	168.0	172.0					13																	41381542		2203	4300	6503	40279542	SO:0001583	missense	10166	exon5			AF112968	CCDS9373.1	13q14	2013-05-22			ENSG00000102743	ENSG00000102743		"""Solute carriers"""	10985	protein-coding gene	gene with protein product	"""ornithine transporter 1"""	603861		ORNT1, HHH		10369256	Standard	NM_014252		Approved	ORC1, D13S327	uc001uxn.3	Q9Y619	OTTHUMG00000016776	ENST00000338625.4:c.565G>T	13.37:g.41381542G>T	ENSP00000342267:p.Gly189Cys	Somatic		Capture	Illumina HiSeq	Phase_I	40279542	NM_014252	Q5VZD8|Q9HC45	Missense_Mutation	SNP	ENST00000338625.4	37	CCDS9373.1	.	.	.	.	.	.	.	.	.	.	G	18.13	3.556402	0.65425	.	.	ENSG00000102743	ENST00000338625;ENST00000443985	T	0.80304	-1.36	5.36	4.51	0.55191	Mitochondrial carrier domain (2);	0.000000	0.85682	D	0.000000	D	0.86343	0.5910	M	0.78637	2.42	0.80722	D	1	P;B	0.46220	0.874;0.149	P;B	0.54544	0.755;0.201	D	0.85869	0.1415	10	0.38643	T	0.18	.	13.4184	0.60982	0.076:0.0:0.924:0.0	.	129;189	B4DL63;Q9Y619	.;ORNT1_HUMAN	C	189;129	ENSP00000342267:G189C	ENSP00000342267:G189C	G	+	1	0	SLC25A15	40279542	1.000000	0.71417	0.790000	0.31976	0.814000	0.46013	7.765000	0.85310	1.400000	0.46741	-0.259000	0.10710	GGT		0.438	SLC25A15-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276149.2	NM_014252	
ELF1	1997	broad.mit.edu	37	13	41507962	41507962	+	Nonsense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr13:41507962G>A	ENST00000239882.3	-	9	1773	c.1459C>T	c.(1459-1461)Cag>Tag	p.Q487*	ELF1_ENST00000442101.1_Nonsense_Mutation_p.Q463*|ELF1_ENST00000498824.1_5'UTR	NM_172373.3	NP_758961.1	P32519	ELF1_HUMAN	E74-like factor 1 (ets domain transcription factor)	487					cell differentiation (GO:0030154)|negative regulation of T cell receptor signaling pathway (GO:0050860)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cytokine production (GO:0001817)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.Q487*(1)		NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(8)|lung(12)|ovary(1)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	37		Lung NSC(96;8.3e-05)|Prostate(109;0.0233)|Breast(139;0.0296)|Lung SC(185;0.0367)		all cancers(112;1.87e-08)|Epithelial(112;8.45e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.000202)|GBM - Glioblastoma multiforme(144;0.00266)|BRCA - Breast invasive adenocarcinoma(63;0.072)		TTTTGTGACTGCAGCATGACA	0.478																																					p.Q487X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.C1459T	13						.						142.0	149.0	146.0					13																	41507962		2203	4300	6503	40405962	SO:0001587	stop_gained	1997	exon9			M82882	CCDS9374.1	13q13	2008-07-18			ENSG00000120690	ENSG00000120690			3316	protein-coding gene	gene with protein product		189973				1545787	Standard	NM_001145353		Approved		uc001uxs.3	P32519	OTTHUMG00000016783	ENST00000239882.3:c.1459C>T	13.37:g.41507962G>A	ENSP00000239882:p.Gln487*	Somatic		Capture	Illumina HiSeq	Phase_I	40405962	NM_172373	B4E2I5|E9PDQ9|Q8N6F6|Q9UDE1	Nonsense_Mutation	SNP	ENST00000239882.3	37	CCDS9374.1	.	.	.	.	.	.	.	.	.	.	G	34	5.367152	0.95900	.	.	ENSG00000120690	ENST00000442101;ENST00000379498;ENST00000239882	.	.	.	5.44	5.44	0.79542	.	0.249544	0.36034	N	0.002821	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.72032	D	0.01	.	19.2715	0.94011	0.0:0.0:1.0:0.0	.	.	.	.	X	463;229;487	.	ENSP00000239882:Q487X	Q	-	1	0	ELF1	40405962	1.000000	0.71417	0.990000	0.47175	0.240000	0.25518	5.468000	0.66743	2.539000	0.85634	0.655000	0.94253	CAG		0.478	ELF1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044654.3	NM_172373	
ZC3H13	23091	broad.mit.edu	37	13	46559530	46559530	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr13:46559530G>A	ENST00000242848.4	-	10	1970	c.1622C>T	c.(1621-1623)aCg>aTg	p.T541M	ZC3H13_ENST00000282007.3_Missense_Mutation_p.T541M			Q5T200	ZC3HD_HUMAN	zinc finger CCCH-type containing 13	541	Arg/Ser-rich.						metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)	p.T541M(1)		cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(27)|lung(25)|ovary(2)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	79		Lung NSC(96;7.26e-05)|Breast(56;0.000118)|Prostate(109;0.00217)|Hepatocellular(98;0.0207)|Lung SC(185;0.0262)	KIRC - Kidney renal clear cell carcinoma(16;0.234)	GBM - Glioblastoma multiforme(144;4.18e-05)		CCTTATTTCCGTACGAGAACT	0.463																																					p.T541M	Esophageal Squamous(187;747 2077 11056 31291 44172)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1622T	13						.						104.0	103.0	103.0					13																	46559530		2203	4300	6503	45457531	SO:0001583	missense	23091	exon10			AB020660	CCDS9400.1	13q14.11	2012-07-05	2006-05-15	2006-05-15	ENSG00000123200	ENSG00000123200		"""Zinc fingers, CCCH-type domain containing"""	20368	protein-coding gene	gene with protein product			"""KIAA0853"""	KIAA0853		10048485	Standard	XM_005266301		Approved	DKFZp434D1812	uc001vas.1	Q5T200	OTTHUMG00000016863	ENST00000242848.4:c.1622C>T	13.37:g.46559530G>A	ENSP00000242848:p.Thr541Met	Somatic		Capture	Illumina HiSeq	Phase_I	45457531	NM_015070	A2A323|O94936|Q5T1Z9|Q7Z7J3|Q8NDT6|Q9H0L6	Missense_Mutation	SNP	ENST00000242848.4	37		.	.	.	.	.	.	.	.	.	.	G	11.42	1.632447	0.29068	.	.	ENSG00000123200	ENST00000242848;ENST00000282007;ENST00000431251	T;T	0.32272	2.46;1.46	5.73	3.97	0.46021	.	0.577114	0.17126	N	0.186008	T	0.19725	0.0474	N	0.24115	0.695	0.80722	D	1	P;P	0.46706	0.814;0.883	B;B	0.38225	0.138;0.268	T	0.01805	-1.1270	10	0.48119	T	0.1	.	10.5618	0.45150	0.0696:0.0:0.7966:0.1338	.	541;541	Q5T200;Q5T200-2	ZC3HD_HUMAN;.	M	541;541;357	ENSP00000242848:T541M;ENSP00000282007:T541M	ENSP00000242848:T541M	T	-	2	0	ZC3H13	45457531	0.998000	0.40836	0.996000	0.52242	0.942000	0.58702	3.950000	0.56676	0.859000	0.35456	-0.152000	0.13540	ACG		0.463	ZC3H13-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000044789.1	NM_015070	
FAM124A	220108	broad.mit.edu	37	13	51825615	51825615	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr13:51825615G>A	ENST00000322475.8	+	3	247	c.112G>A	c.(112-114)Gtt>Att	p.V38I	FAM124A_ENST00000280057.6_Missense_Mutation_p.V74I	NM_001242312.1	NP_001229241.1	Q86V42	F124A_HUMAN	family with sequence similarity 124A	38								p.V74I(1)		breast(1)|central_nervous_system(2)|endometrium(3)|kidney(3)|large_intestine(7)|lung(6)|ovary(1)|prostate(2)|skin(1)	26		Acute lymphoblastic leukemia(7;0.000334)|Breast(56;0.00156)|Prostate(109;0.00538)|Lung NSC(96;0.0216)|Hepatocellular(98;0.152)|Glioma(44;0.236)		GBM - Glioblastoma multiforme(99;4.25e-07)		TGAGCTTTCCGTTGAAGAGGC	0.517																																					p.V74I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G220A	13						.						57.0	58.0	57.0					13																	51825615		2203	4300	6503	50723616	SO:0001583	missense	220108	exon4			AK096364	CCDS9427.1, CCDS55900.1	13q14.3	2006-08-11			ENSG00000150510	ENSG00000150510			26413	protein-coding gene	gene with protein product						12975309	Standard	NM_145019		Approved	FLJ30707	uc001vff.2	Q86V42	OTTHUMG00000016942	ENST00000322475.8:c.112G>A	13.37:g.51825615G>A	ENSP00000324625:p.Val38Ile	Somatic		Capture	Illumina HiSeq	Phase_I	50723616	NM_145019	A2A324|Q8N8P9|Q8NE66|Q96NJ9	Missense_Mutation	SNP	ENST00000322475.8	37	CCDS55900.1	.	.	.	.	.	.	.	.	.	.	G	13.57	2.276162	0.40294	.	.	ENSG00000150510	ENST00000322475;ENST00000280057	T;T	0.49720	0.77;0.77	5.79	-0.45	0.12223	.	0.565711	0.18683	N	0.134098	T	0.37865	0.1019	M	0.63843	1.955	0.22253	N	0.999257	P;P;P	0.52170	0.951;0.889;0.531	B;B;B	0.38683	0.279;0.236;0.082	T	0.32025	-0.9922	10	0.54805	T	0.06	-24.6292	8.2828	0.31910	0.0617:0.435:0.3911:0.1122	.	38;74;38	Q86V42;Q86V42-2;Q86V42-3	F124A_HUMAN;.;.	I	38;74	ENSP00000324625:V38I;ENSP00000280057:V74I	ENSP00000280057:V74I	V	+	1	0	FAM124A	50723616	0.896000	0.30565	0.004000	0.12327	0.977000	0.68977	1.436000	0.34980	-0.458000	0.07023	0.655000	0.94253	GTT		0.517	FAM124A-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045019.3	NM_145019	
UTP14C	9724	broad.mit.edu	37	13	52604737	52604737	+	Silent	SNP	T	T	G			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr13:52604737T>G	ENST00000521776.2	+	2	2530	c.1797T>G	c.(1795-1797)gcT>gcG	p.A599A		NM_021645.5	NP_067677.4	Q5TAP6	UT14C_HUMAN	UTP14, U3 small nucleolar ribonucleoprotein, homolog C (yeast)	599					cell differentiation (GO:0030154)|meiotic nuclear division (GO:0007126)|multicellular organismal development (GO:0007275)|rRNA processing (GO:0006364)|spermatogenesis (GO:0007283)	nucleus (GO:0005634)|small-subunit processome (GO:0032040)		p.A599A(1)		breast(4)|cervix(1)|endometrium(1)|large_intestine(10)|lung(10)|ovary(3)|skin(1)|stomach(1)|urinary_tract(1)	32		Breast(56;0.00173)|Lung NSC(96;0.0108)|Prostate(109;0.0412)|Hepatocellular(98;0.152)|Glioma(44;0.236)		GBM - Glioblastoma multiforme(99;2.3e-08)		AAGCTTTTGCTGGGGATGATG	0.502																																					p.A599A												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.T1797G	13						.						90.0	95.0	93.0					13																	52604737		2203	4300	6503	51502738	SO:0001819	synonymous_variant	9724	exon2			D87455	CCDS31978.1	13q12.2-q13.3	2010-11-23	2004-06-15	2004-06-16	ENSG00000253797	ENSG00000253797			20321	protein-coding gene	gene with protein product		608969	"""KIAA0266"""	KIAA0266		9039502, 16354793	Standard	NM_021645		Approved	2700066J21Rik	uc021rjw.1	Q5TAP6	OTTHUMG00000164353	ENST00000521776.2:c.1797T>G	13.37:g.52604737T>G		Somatic		Capture	Illumina HiSeq	Phase_I	51502738	NM_021645	Q5FWG3|Q92555	Silent	SNP	ENST00000521776.2	37	CCDS31978.1																																																																																				0.502	UTP14C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045049.2	NM_021645	
PCDH17	27253	broad.mit.edu	37	13	58209099	58209100	+	Missense_Mutation	DNP	AG	AG	TA			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	AG	AG					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr13:58209099_58209100AG>TA	ENST00000377918.3	+	1	2445_2446	c.2419_2420AG>TA	c.(2419-2421)AGc>TAc	p.S807Y		NM_001040429.2	NP_001035519.1	O14917	PCD17_HUMAN	protocadherin 17	807					homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.S807>?(1)		breast(2)|central_nervous_system(2)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(30)|liver(2)|lung(54)|ovary(4)|pancreas(2)|prostate(5)|skin(3)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(2)	120		Lung NSC(96;0.027)|Prostate(109;0.0453)|Breast(118;0.128)|Hepatocellular(98;0.132)		GBM - Glioblastoma multiforme(99;1.06e-05)		CCTGCCCCTCAGCTCGCCCCGG	0.639																																					.	Melanoma(72;952 1291 1619 12849 33676)											.	.	1	Complex(1)	large_intestine(1)	c.2419_2420TA	13						.																																			57107101	SO:0001583	missense	27253	exon1			AF029343	CCDS31986.1	13q21.1	2010-01-26			ENSG00000118946	ENSG00000118946		"""Cadherins / Protocadherins : Non-clustered"""	14267	protein-coding gene	gene with protein product		611760				10835267	Standard	NM_001040429		Approved	PCDH68, PCH68	uc001vhq.1	O14917	OTTHUMG00000016992	Exception_encountered	13.37:g.58209099_58209100delinsTA	ENSP00000367151:p.Ser807Tyr	Somatic		Capture	Illumina HiSeq	Phase_I	57107100	NM_001040429	A8K1R5|Q5VVW9|Q5VVX0	Missense_Mutation	DNP	ENST00000377918.3	37	CCDS31986.1																																																																																				0.639	PCDH17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045139.1	NM_001040429	
BORA	79866	broad.mit.edu	37	13	73320709	73320709	+	Silent	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr13:73320709G>A	ENST00000390667.5	+	10	1039	c.942G>A	c.(940-942)ccG>ccA	p.P314P	BORA_ENST00000377815.3_Silent_p.P244P	NM_024808.2	NP_079084.2	Q6PGQ7	BORA_HUMAN	bora, aurora kinase A activator	314					G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|regulation of mitosis (GO:0007088)|regulation of mitotic spindle organization (GO:0060236)|regulation of protein localization (GO:0032880)	cytosol (GO:0005829)	protein kinase binding (GO:0019901)	p.P314P(1)									TAACTAATCCGTGTATCAGAA	0.398																																					p.P314P												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G942A	13						.						80.0	75.0	77.0					13																	73320709		1818	4082	5900	72218710	SO:0001819	synonymous_variant	79866	exon10			BC025367	CCDS9446.1, CCDS66560.1, CCDS9446.2, CCDS73583.1	13q22.1	2013-08-13	2011-08-09	2011-08-09	ENSG00000136122	ENSG00000136122			24724	protein-coding gene	gene with protein product		610510	"""chromosome 13 open reading frame 34"""	C13orf34		16890155, 18378770, 18566290, 19487276	Standard	NM_001286746		Approved	FLJ22624	uc001viv.1	Q6PGQ7	OTTHUMG00000017068	ENST00000390667.5:c.942G>A	13.37:g.73320709G>A		Somatic		Capture	Illumina HiSeq	Phase_I	72218710	NM_024808	B4DQ30|Q5W0P3|Q5W0P4|Q86YC6|Q96IW9|Q9H640	Silent	SNP	ENST00000390667.5	37	CCDS9446.1																																																																																				0.398	BORA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045245.3	NM_024808	
LMO7	4008	broad.mit.edu	37	13	76397791	76397791	+	Missense_Mutation	SNP	G	G	A	rs370412695		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr13:76397791G>A	ENST00000321797.8	+	13	2753	c.2032G>A	c.(2032-2034)Gca>Aca	p.A678T	LMO7_ENST00000526202.1_Missense_Mutation_p.A528T|LMO7_ENST00000357063.3_Missense_Mutation_p.A963T|LMO7_ENST00000377534.3_Missense_Mutation_p.A963T|LMO7_ENST00000341547.4_Missense_Mutation_p.A629T|LMO7_ENST00000465261.2_Missense_Mutation_p.A678T			Q8WWI1	LMO7_HUMAN	LIM domain 7	963					protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|ubiquitin ligase complex (GO:0000151)	ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.A629T(1)		NS(1)|autonomic_ganglia(1)|breast(2)|endometrium(2)|kidney(2)|large_intestine(20)|lung(15)|ovary(2)|prostate(5)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	56		Breast(118;0.0992)		GBM - Glioblastoma multiforme(99;0.0109)		AAGCCCGGACGCAAGCCAACT	0.473																																					p.A678T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2032A	13						.	G	THR/ALA,THR/ALA	0,4406		0,0,2203	107.0	95.0	100.0		1885,2032	-7.6	0.0	13		100	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	LMO7	NM_005358.5,NM_015842.2	58,58	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	benign,benign	629/1350,678/1386	76397791	1,13005	2203	4300	6503	75295792	SO:0001583	missense	4008	exon12			AF092557	CCDS9454.1, CCDS53876.1	13q22.2	2008-02-05	2004-06-15		ENSG00000136153	ENSG00000136153			6646	protein-coding gene	gene with protein product	"""F-box only protein 20"""	604362	"""LIM domain only 7"""	FBXO20		9826547, 10531035	Standard	NM_005358		Approved	FBX20, KIAA0858	uc021rkq.1	Q8WWI1	OTTHUMG00000017093	ENST00000321797.8:c.2032G>A	13.37:g.76397791G>A	ENSP00000317802:p.Ala678Thr	Somatic		Capture	Illumina HiSeq	Phase_I	75295792	NM_015842	E9PLH4|O15462|O95346|Q5TBK6|Q9UKC1|Q9UQM5|Q9Y6A7	Missense_Mutation	SNP	ENST00000321797.8	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	10.42|10.42	1.345193|1.345193	0.24426|0.24426	0.0|0.0	1.16E-4|1.16E-4	ENSG00000136153|ENSG00000136153	ENST00000341547;ENST00000357063;ENST00000377534;ENST00000377499;ENST00000321797;ENST00000526202;ENST00000465261|ENST00000447038	T;T;T;T;T;T;T|.	0.39997|.	1.05;1.05;1.05;1.05;1.05;1.05;1.05|.	5.94|5.94	-7.58|-7.58	0.01313|0.01313	.|.	2.041240|.	0.01610|.	N|.	0.022491|.	T|T	0.07188|0.07188	0.0182|0.0182	N|N	0.02011|0.02011	-0.69|-0.69	0.09310|0.09310	N|N	1|1	B;B;B;B;B|.	0.09022|.	0.0;0.001;0.001;0.0;0.002|.	B;B;B;B;B|.	0.06405|.	0.0;0.001;0.0;0.0;0.002|.	T|T	0.28138|0.28138	-1.0053|-1.0053	10|5	0.22109|.	T|.	0.4|.	2.0545|2.0545	1.8151|1.8151	0.03099|0.03099	0.1323:0.2299:0.3549:0.283|0.1323:0.2299:0.3549:0.283	.|.	528;629;963;678;911|.	E9PMS6;Q8WWI1-3;Q8WWI1;E9PLH4;F8J2B5|.	.;.;LMO7_HUMAN;.;.|.	T|H	629;963;963;577;678;528;678|586	ENSP00000342112:A629T;ENSP00000349571:A963T;ENSP00000366757:A963T;ENSP00000366719:A577T;ENSP00000317802:A678T;ENSP00000431129:A528T;ENSP00000433352:A678T|.	ENSP00000317802:A678T|.	A|R	+|+	1|2	0|0	LMO7|LMO7	75295792|75295792	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.007000|0.007000	0.05969|0.05969	-0.841000|-0.841000	0.04359|0.04359	-0.792000|-0.792000	0.04480|0.04480	0.650000|0.650000	0.86243|0.86243	GCA|CGC		0.473	LMO7-005	PUTATIVE	alternative_5_UTR|not_organism_supported|basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000045301.3	NM_005358	
LMO7	4008	broad.mit.edu	37	13	76423370	76423370	+	Nonsense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr13:76423370C>T	ENST00000321797.8	+	25	4328	c.3607C>T	c.(3607-3609)Cga>Tga	p.R1203*	LMO7_ENST00000526202.1_Nonsense_Mutation_p.R1080*|LMO7_ENST00000357063.3_Nonsense_Mutation_p.R1488*|LMO7_ENST00000377534.3_Nonsense_Mutation_p.R1488*|LMO7_ENST00000341547.4_Nonsense_Mutation_p.R1154*|LMO7_ENST00000465261.2_Nonsense_Mutation_p.R1203*			Q8WWI1	LMO7_HUMAN	LIM domain 7	1488					protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|ubiquitin ligase complex (GO:0000151)	ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.R1154*(1)		NS(1)|autonomic_ganglia(1)|breast(2)|endometrium(2)|kidney(2)|large_intestine(20)|lung(15)|ovary(2)|prostate(5)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	56		Breast(118;0.0992)		GBM - Glioblastoma multiforme(99;0.0109)		CAGCTGGATCCGACAGCGCAG	0.463																																					p.R1203X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.C3607T	13						.						137.0	113.0	121.0					13																	76423370		2203	4300	6503	75321371	SO:0001587	stop_gained	4008	exon24			AF092557	CCDS9454.1, CCDS53876.1	13q22.2	2008-02-05	2004-06-15		ENSG00000136153	ENSG00000136153			6646	protein-coding gene	gene with protein product	"""F-box only protein 20"""	604362	"""LIM domain only 7"""	FBXO20		9826547, 10531035	Standard	NM_005358		Approved	FBX20, KIAA0858	uc021rkq.1	Q8WWI1	OTTHUMG00000017093	ENST00000321797.8:c.3607C>T	13.37:g.76423370C>T	ENSP00000317802:p.Arg1203*	Somatic		Capture	Illumina HiSeq	Phase_I	75321371	NM_015842	E9PLH4|O15462|O95346|Q5TBK6|Q9UKC1|Q9UQM5|Q9Y6A7	Nonsense_Mutation	SNP	ENST00000321797.8	37		.	.	.	.	.	.	.	.	.	.	C	53	20.520979	0.99931	.	.	ENSG00000136153	ENST00000341547;ENST00000357063;ENST00000377534;ENST00000321797;ENST00000526202;ENST00000465261	.	.	.	6.02	4.09	0.47781	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-12.613	12.4639	0.55747	0.5612:0.4388:0.0:0.0	.	.	.	.	X	1154;1488;1488;1203;1080;1203	.	ENSP00000317802:R1203X	R	+	1	2	LMO7	75321371	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	3.773000	0.55333	1.510000	0.48803	0.655000	0.94253	CGA		0.463	LMO7-005	PUTATIVE	alternative_5_UTR|not_organism_supported|basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000045301.3	NM_005358	
SLITRK6	84189	broad.mit.edu	37	13	86370451	86370451	+	Nonsense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr13:86370451G>A	ENST00000400286.2	-	2	791	c.193C>T	c.(193-195)Cga>Tga	p.R65*		NM_032229.2	NP_115605.2	Q9H5Y7	SLIK6_HUMAN	SLIT and NTRK-like family, member 6	65	LRRNT 1.				adult locomotory behavior (GO:0008344)|auditory behavior (GO:0031223)|auditory receptor cell morphogenesis (GO:0002093)|axonogenesis (GO:0007409)|cochlea development (GO:0090102)|innervation (GO:0060384)|lens development in camera-type eye (GO:0002088)|linear vestibuloocular reflex (GO:0060007)|multicellular organism growth (GO:0035264)|sensory perception of sound (GO:0007605)|startle response (GO:0001964)|synapse assembly (GO:0007416)|vestibulocochlear nerve development (GO:0021562)|visual perception (GO:0007601)	cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)		p.R65*(1)		breast(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(13)|lung(18)|ovary(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_neural(89;0.117)|Medulloblastoma(90;0.163)			GBM - Glioblastoma multiforme(99;0.0456)		TGGAAAGGTCGTGATGGTGGC	0.368																																					p.R65X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.C193T	13						.						163.0	154.0	157.0					13																	86370451		1921	4119	6040	85268452	SO:0001587	stop_gained	84189	exon2			AK026427	CCDS41903.1	13q31.1	2006-04-12			ENSG00000184564	ENSG00000184564			23503	protein-coding gene	gene with protein product		609681				14557068	Standard	NM_032229		Approved	FLJ22774	uc001vll.1	Q9H5Y7	OTTHUMG00000017157	ENST00000400286.2:c.193C>T	13.37:g.86370451G>A	ENSP00000383143:p.Arg65*	Somatic		Capture	Illumina HiSeq	Phase_I	85268452	NM_032229	A8K9S8|Q495Q0|Q6AW93|Q9HAA8|Q9NT60	Nonsense_Mutation	SNP	ENST00000400286.2	37	CCDS41903.1	.	.	.	.	.	.	.	.	.	.	G	40	8.102059	0.98654	.	.	ENSG00000184564	ENST00000400286	.	.	.	6.17	3.06	0.35304	.	0.145029	0.46758	D	0.000274	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-13.0934	15.4938	0.75632	0.0:0.0:0.6112:0.3888	.	.	.	.	X	65	.	ENSP00000383143:R65X	R	-	1	2	SLITRK6	85268452	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	2.239000	0.43079	0.829000	0.34733	0.655000	0.94253	CGA		0.368	SLITRK6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045404.2	NM_032229	
GPR180	160897	broad.mit.edu	37	13	95279295	95279295	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr13:95279295A>G	ENST00000376958.4	+	9	1218	c.1193A>G	c.(1192-1194)cAg>cGg	p.Q398R		NM_180989.5	NP_851320.1	Q86V85	GP180_HUMAN	G protein-coupled receptor 180	398					G-protein coupled receptor signaling pathway (GO:0007186)|response to pheromone (GO:0019236)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)		p.Q398R(1)		breast(1)|kidney(1)|large_intestine(3)|lung(4)|urinary_tract(1)	10	all_neural(89;0.0684)|Medulloblastoma(90;0.163)					ATCCTTTGCCAGTCTGTTTCC	0.338																																					p.Q398R												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A1193G	13						.						144.0	132.0	136.0					13																	95279295		2203	4300	6503	94077296	SO:0001583	missense	160897	exon9			AF339823	CCDS9472.1	13q32.1	2006-04-05			ENSG00000152749	ENSG00000152749			28899	protein-coding gene	gene with protein product	"""intimal thickness related receptor"""	607787				12538434	Standard	NM_180989		Approved	ITR	uc001vly.3	Q86V85	OTTHUMG00000017207	ENST00000376958.4:c.1193A>G	13.37:g.95279295A>G	ENSP00000366157:p.Gln398Arg	Somatic		Capture	Illumina HiSeq	Phase_I	94077296	NM_180989	A8K1D5	Missense_Mutation	SNP	ENST00000376958.4	37	CCDS9472.1	.	.	.	.	.	.	.	.	.	.	A	13.72	2.322077	0.41096	.	.	ENSG00000152749	ENST00000376958	T	0.43688	0.94	5.52	5.52	0.82312	Rhodopsin-like GPCR transmembrane domain (1);	0.129845	0.56097	D	0.000027	T	0.38480	0.1042	L	0.48362	1.52	0.51767	D	0.999938	P	0.37708	0.606	B	0.38985	0.287	T	0.13764	-1.0497	10	0.15066	T	0.55	-9.0698	15.643	0.77020	1.0:0.0:0.0:0.0	.	398	Q86V85	GP180_HUMAN	R	398	ENSP00000366157:Q398R	ENSP00000366157:Q398R	Q	+	2	0	GPR180	94077296	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.930000	0.70104	2.088000	0.63022	0.482000	0.46254	CAG		0.338	GPR180-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045465.3	NM_180989	
ABCC4	10257	broad.mit.edu	37	13	95861752	95861752	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr13:95861752T>C	ENST00000376887.4	-	6	835	c.721A>G	c.(721-723)Atg>Gtg	p.M241V	snoU13_ENST00000459449.1_RNA|ABCC4_ENST00000536256.1_Missense_Mutation_p.M166V|ABCC4_ENST00000431522.1_Missense_Mutation_p.M241V|ABCC4_ENST00000412704.1_Missense_Mutation_p.M241V|ABCC4_ENST00000538287.1_3'UTR	NM_005845.3	NP_005836.2	O15439	MRP4_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 4	241	ABC transmembrane type-1 1. {ECO:0000255|PROSITE-ProRule:PRU00441}.				blood coagulation (GO:0007596)|oxidation-reduction process (GO:0055114)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of smooth muscle cell proliferation (GO:0048661)|response to drug (GO:0042493)|response to organic cyclic compound (GO:0014070)|response to organonitrogen compound (GO:0010243)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|platelet dense granule membrane (GO:0031088)	15-hydroxyprostaglandin dehydrogenase (NAD+) activity (GO:0016404)|ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)	p.M241V(2)		breast(1)|central_nervous_system(4)|endometrium(5)|kidney(4)|large_intestine(9)|lung(13)|ovary(1)|prostate(1)|skin(4)|urinary_tract(1)	43	all_neural(89;0.0878)|Medulloblastoma(90;0.163)				Adefovir Dipivoxil(DB00718)|Alprostadil(DB00770)|Atorvastatin(DB01076)|Cefazolin(DB01327)|Celecoxib(DB00482)|Conjugated Estrogens(DB00286)|Diclofenac(DB00586)|Dinoprostone(DB00917)|Dipyridamole(DB00975)|Fluorouracil(DB00544)|Flurbiprofen(DB00712)|Folic Acid(DB00158)|Gadoxetate(DB08884)|Glutathione(DB00143)|Ibuprofen(DB01050)|Indomethacin(DB00328)|Ketoprofen(DB01009)|Lamivudine(DB00709)|Leucovorin(DB00650)|Meloxicam(DB00814)|Mercaptopurine(DB01033)|Methotrexate(DB00563)|Nateglinide(DB00731)|Oseltamivir(DB00198)|Probenecid(DB01032)|Rosuvastatin(DB01098)|Sildenafil(DB00203)|Sorafenib(DB00398)|Sulfinpyrazone(DB01138)|Sunitinib(DB01268)|Tenofovir(DB00300)|Tioguanine(DB00352)|Ursodeoxycholic acid(DB01586)|Verapamil(DB00661)|Zidovudine(DB00495)	AGAACTGCCATCCCAGCAAGG	0.473																																					p.M241V												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.A721G	13						.						117.0	97.0	104.0					13																	95861752		2203	4300	6503	94659753	SO:0001583	missense	10257	exon6			U66682	CCDS9474.1	13q31	2012-03-14			ENSG00000125257	ENSG00000125257		"""ATP binding cassette transporters / subfamily C"""	55	protein-coding gene	gene with protein product	"""canalicular multispecific organic anion transporter (ABC superfamily)"", ""bA464I2.1 (ATP-binding cassette, sub-family C (CFTR/MRP), member 4)"", ""multidrug resistance-associated protein 4"", ""multispecific organic anion transporter B"""	605250				8894702, 9661885	Standard	NM_005845		Approved	MRP4, EST170205, MOAT-B, MOATB	uc001vmd.4	O15439	OTTHUMG00000017216	ENST00000376887.4:c.721A>G	13.37:g.95861752T>C	ENSP00000366084:p.Met241Val	Somatic		Capture	Illumina HiSeq	Phase_I	94659753	NM_001105515	A9Z1Z7|Q8IVZ4|Q8IZN6|Q8NEW8|Q9Y6J2	Missense_Mutation	SNP	ENST00000376887.4	37	CCDS9474.1	.	.	.	.	.	.	.	.	.	.	T	13.54	2.267872	0.40095	.	.	ENSG00000125257	ENST00000412704;ENST00000376887;ENST00000536256;ENST00000431522	D;D;D;D	0.88664	-2.41;-2.41;-2.41;-2.41	5.71	1.82	0.25136	ABC transporter, transmembrane domain, type 1 (1);ABC transporter, integral membrane type 1 (1);ABC transporter, transmembrane domain (1);	0.036026	0.85682	D	0.000000	T	0.76033	0.3931	N	0.21142	0.635	0.52501	D	0.999954	B;B;B;B;B	0.14012	0.002;0.009;0.004;0.009;0.002	B;B;B;B;B	0.22880	0.005;0.019;0.008;0.042;0.006	T	0.62006	-0.6945	10	0.02654	T	1	.	7.873	0.29578	0.2389:0.0:0.1251:0.636	.	166;241;241;241;241	B7Z3Q7;A8K2Q2;O15439-2;Q8IVZ4;O15439	.;.;.;.;MRP4_HUMAN	V	241;241;166;241	ENSP00000388657:M241V;ENSP00000366084:M241V;ENSP00000442024:M166V;ENSP00000398562:M241V	ENSP00000366084:M241V	M	-	1	0	ABCC4	94659753	1.000000	0.71417	0.958000	0.39756	0.755000	0.42902	3.677000	0.54619	0.077000	0.16863	0.533000	0.62120	ATG		0.473	ABCC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045478.2	NM_005845	
MBNL2	10150	broad.mit.edu	37	13	97999177	97999177	+	Missense_Mutation	SNP	T	T	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr13:97999177T>A	ENST00000376673.3	+	5	1441	c.660T>A	c.(658-660)gaT>gaA	p.D220E	MBNL2_ENST00000445661.2_Intron|MBNL2_ENST00000397601.1_Missense_Mutation_p.D220E|MBNL2_ENST00000345429.6_Missense_Mutation_p.D220E|MBNL2_ENST00000343600.4_Missense_Mutation_p.D220E			Q5VZF2	MBNL2_HUMAN	muscleblind-like splicing regulator 2	220					mRNA processing (GO:0006397)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|regulation of RNA splicing (GO:0043484)|RNA splicing (GO:0008380)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)	p.D220E(1)		endometrium(4)|large_intestine(4)|lung(7)|prostate(1)|skin(1)	17	all_neural(89;0.0982)|Medulloblastoma(90;0.163)|Lung SC(71;0.184)		BRCA - Breast invasive adenocarcinoma(86;0.218)			TTTGTATGGATTACATAAAGG	0.527																																					p.D220E												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T660A	13						.						89.0	87.0	88.0					13																	97999177		2203	4300	6503	96797178	SO:0001583	missense	10150	exon5			AF061261	CCDS9483.1, CCDS9484.1	13q31.1	2013-01-18	2012-02-23		ENSG00000139793	ENSG00000139793		"""Zinc fingers, CCCH-type domain containing"""	16746	protein-coding gene	gene with protein product		607327	"""muscleblind-like 2 (Drosophila)"""			11929853	Standard	NM_207304		Approved	MBLL, MBLL39	uc001vmz.4	Q5VZF2	OTTHUMG00000017239	ENST00000376673.3:c.660T>A	13.37:g.97999177T>A	ENSP00000365861:p.Asp220Glu	Somatic		Capture	Illumina HiSeq	Phase_I	96797178	NM_207304	Q3SXY5|Q58F19|Q8NEV3|Q8TD82	Missense_Mutation	SNP	ENST00000376673.3	37		.	.	.	.	.	.	.	.	.	.	T	26.8	4.774099	0.90108	.	.	ENSG00000139793	ENST00000397601;ENST00000343600;ENST00000345429;ENST00000376673	T;T;T;T	0.43294	0.95;0.95;0.95;0.95	5.86	5.86	0.93980	Zinc finger, CCCH-type (2);	0.000000	0.85682	D	0.000000	T	0.66954	0.2842	M	0.88450	2.955	0.80722	D	1	D;P;D	0.55172	0.97;0.775;0.958	P;B;P	0.57960	0.83;0.243;0.793	T	0.74481	-0.3651	10	0.87932	D	0	.	16.2612	0.82547	0.0:0.0:0.0:1.0	.	220;220;220	Q5VZF2;A2A3S3;Q5VZF2-2	MBNL2_HUMAN;.;.	E	220	ENSP00000380726:D220E;ENSP00000344214:D220E;ENSP00000267287:D220E;ENSP00000365861:D220E	ENSP00000344214:D220E	D	+	3	2	MBNL2	96797178	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.113000	0.57851	2.244000	0.73946	0.477000	0.44152	GAT		0.527	MBNL2-202	KNOWN	basic	protein_coding	protein_coding		NM_144778	
MBNL2	10150	broad.mit.edu	37	13	98009823	98009823	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr13:98009823G>A	ENST00000376673.3	+	6	1673	c.892G>A	c.(892-894)Gtc>Atc	p.V298I	MBNL2_ENST00000445661.2_Missense_Mutation_p.V143I|MBNL2_ENST00000397601.1_Missense_Mutation_p.V298I|MBNL2_ENST00000345429.6_Missense_Mutation_p.V298I|MBNL2_ENST00000343600.4_Missense_Mutation_p.V298I			Q5VZF2	MBNL2_HUMAN	muscleblind-like splicing regulator 2	298					mRNA processing (GO:0006397)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|regulation of RNA splicing (GO:0043484)|RNA splicing (GO:0008380)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)	p.V49I(1)|p.V298I(1)		endometrium(4)|large_intestine(4)|lung(7)|prostate(1)|skin(1)	17	all_neural(89;0.0982)|Medulloblastoma(90;0.163)|Lung SC(71;0.184)		BRCA - Breast invasive adenocarcinoma(86;0.218)			TAACCCCAGCGTCTTGCACTA	0.532																																					p.V298I												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G892A	13						.						167.0	142.0	150.0					13																	98009823		2203	4300	6503	96807824	SO:0001583	missense	10150	exon6			AF061261	CCDS9483.1, CCDS9484.1	13q31.1	2013-01-18	2012-02-23		ENSG00000139793	ENSG00000139793		"""Zinc fingers, CCCH-type domain containing"""	16746	protein-coding gene	gene with protein product		607327	"""muscleblind-like 2 (Drosophila)"""			11929853	Standard	NM_207304		Approved	MBLL, MBLL39	uc001vmz.4	Q5VZF2	OTTHUMG00000017239	ENST00000376673.3:c.892G>A	13.37:g.98009823G>A	ENSP00000365861:p.Val298Ile	Somatic		Capture	Illumina HiSeq	Phase_I	96807824	NM_207304	Q3SXY5|Q58F19|Q8NEV3|Q8TD82	Missense_Mutation	SNP	ENST00000376673.3	37		.	.	.	.	.	.	.	.	.	.	G	15.72	2.916868	0.52546	.	.	ENSG00000139793	ENST00000397601;ENST00000343600;ENST00000376679;ENST00000345429;ENST00000376673;ENST00000445661;ENST00000449284	T;T;T;T;T	0.47177	0.87;0.87;0.9;1.19;0.85	5.86	5.86	0.93980	.	0.123221	0.53938	D	0.000052	T	0.38692	0.1050	L	0.44542	1.39	0.38021	D	0.934855	P;B;P;B;B	0.41929	0.765;0.011;0.583;0.448;0.383	B;B;B;B;B	0.35470	0.184;0.006;0.124;0.058;0.203	T	0.35549	-0.9784	10	0.25751	T	0.34	.	15.7547	0.78015	0.0:0.0:0.863:0.137	.	143;298;298;298;298	B4E3F7;Q5VZF2;Q5VZF2-3;A2A3S3;Q5VZF2-2	.;MBNL2_HUMAN;.;.;.	I	298;298;49;298;298;143;48	ENSP00000380726:V298I;ENSP00000344214:V298I;ENSP00000267287:V298I;ENSP00000365861:V298I;ENSP00000406842:V143I	ENSP00000344214:V298I	V	+	1	0	MBNL2	96807824	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.595000	0.67563	2.777000	0.95525	0.591000	0.81541	GTC		0.532	MBNL2-202	KNOWN	basic	protein_coding	protein_coding		NM_144778	
TM9SF2	9375	broad.mit.edu	37	13	100172322	100172322	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr13:100172322G>A	ENST00000376387.4	+	3	462	c.272G>A	c.(271-273)cGc>cAc	p.R91H	TM9SF2_ENST00000463709.1_3'UTR	NM_004800.1	NP_004791.1	Q99805	TM9S2_HUMAN	transmembrane 9 superfamily member 2	91					transport (GO:0006810)	endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)		p.R91H(2)		endometrium(3)|kidney(1)|large_intestine(5)|lung(5)|ovary(1)|prostate(2)	17	all_neural(89;0.0837)|Medulloblastoma(90;0.18)|Lung SC(71;0.218)					GAAGGAAAGCGCCCATCTGAA	0.343																																					p.R91H												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G272A	13						.						81.0	80.0	80.0					13																	100172322		2203	4300	6503	98970323	SO:0001583	missense	9375	exon3			U81006	CCDS9493.1	13q32.2	2011-03-28			ENSG00000125304	ENSG00000125304			11865	protein-coding gene	gene with protein product		604678				9729438	Standard	NM_004800		Approved	P76	uc001voj.2	Q99805	OTTHUMG00000017272	ENST00000376387.4:c.272G>A	13.37:g.100172322G>A	ENSP00000365567:p.Arg91His	Somatic		Capture	Illumina HiSeq	Phase_I	98970323	NM_004800	A8K399|Q2TAY5	Missense_Mutation	SNP	ENST00000376387.4	37	CCDS9493.1	.	.	.	.	.	.	.	.	.	.	G	15.58	2.874852	0.51695	.	.	ENSG00000125304	ENST00000376387	T	0.41400	1.0	5.75	5.75	0.90469	.	0.095027	0.64402	D	0.000001	T	0.33059	0.0850	N	0.21097	0.63	0.53005	D	0.999963	B;B	0.31655	0.223;0.334	B;B	0.29663	0.038;0.105	T	0.05435	-1.0885	10	0.29301	T	0.29	-1.8324	19.9911	0.97363	0.0:0.0:1.0:0.0	.	91;91	E9PHW5;Q99805	.;TM9S2_HUMAN	H	91	ENSP00000365567:R91H	ENSP00000365567:R91H	R	+	2	0	TM9SF2	98970323	1.000000	0.71417	1.000000	0.80357	0.966000	0.64601	8.083000	0.89515	2.734000	0.93682	0.585000	0.79938	CGC		0.343	TM9SF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045602.3		
PCDH8	5100	broad.mit.edu	37	13	53422446	53422446	+	Frame_Shift_Del	DEL	G	G	-			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	-	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr13:53422446delG	ENST00000377942.3	-	1	329	c.126delC	c.(124-126)cccfs	p.P42fs	PCDH8_ENST00000338862.4_Frame_Shift_Del_p.P42fs	NM_002590.3	NP_002581.2	O95206	PCDH8_HUMAN	protocadherin 8	42	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell-cell signaling (GO:0007267)|homophilic cell adhesion (GO:0007156)|morphogenesis of embryonic epithelium (GO:0016331)|somitogenesis (GO:0001756)|synaptic transmission (GO:0007268)	cell junction (GO:0030054)|cell projection (GO:0042995)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	calcium ion binding (GO:0005509)	p.G43fs*13(1)		breast(1)|central_nervous_system(2)|endometrium(2)|large_intestine(5)|lung(23)|ovary(1)|skin(1)|urinary_tract(1)	36		Lung NSC(96;0.0019)|Breast(56;0.00235)|Hepatocellular(98;0.065)|Prostate(109;0.0771)|all_neural(104;0.173)		GBM - Glioblastoma multiforme(99;2.19e-08)		TGACCGTGCCGGGGGCATCCT	0.597																																					p.P42fs	GBM(36;25 841 9273 49207)											.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.126delC	13						.						94.0	88.0	90.0					13																	53422446		2203	4300	6503	52320447	SO:0001589	frameshift_variant	5100	exon1			AF061573	CCDS9438.1, CCDS9439.1	13q21.1	2010-02-22			ENSG00000136099	ENSG00000136099		"""Cadherins / Protocadherins : Non-clustered"""	8660	protein-coding gene	gene with protein product		603580				9787079, 9315676	Standard	NM_002590		Approved	PAPC, ARCADLIN	uc001vhi.3	O95206	OTTHUMG00000016979	ENST00000377942.3:c.126delC	13.37:g.53422446delG	ENSP00000367177:p.Pro42fs	Somatic		Capture	Illumina HiSeq	Phase_I	52320447	NM_032949	B4DMV7|Q5TAN1|Q5TAN2|Q8IYE9|Q96SF1	Frame_Shift_Del	DEL	ENST00000377942.3	37	CCDS9438.1																																																																																				0.597	PCDH8-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000045108.2	NM_002590	
CLYBL	171425	broad.mit.edu	37	13	100518550	100518550	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr13:100518550G>A	ENST00000376360.1	+	6	718	c.691G>A	c.(691-693)Gtc>Atc	p.V231I	CLYBL_ENST00000339105.4_Missense_Mutation_p.V231I|CLYBL_ENST00000444838.2_Missense_Mutation_p.V197I|CLYBL_ENST00000376354.1_Missense_Mutation_p.V197I|CLYBL_ENST00000376355.3_Missense_Mutation_p.V197I			Q8N0X4	CLYBL_HUMAN	citrate lyase beta like	231						mitochondrion (GO:0005739)	lyase activity (GO:0016829)|metal ion binding (GO:0046872)	p.V231I(2)		NS(1)|kidney(6)|large_intestine(6)|lung(10)|skin(2)	25	all_neural(89;0.0837)|Medulloblastoma(90;0.18)|Lung SC(71;0.184)					AAAGATTGTTGTCATAGCGAA	0.458																																					p.V231I												.	.	2	Substitution - Missense(2)	large_intestine(1)|kidney(1)	c.G691A	13						.						106.0	107.0	107.0					13																	100518550		2203	4300	6503	99316551	SO:0001583	missense	171425	exon6			AF428253	CCDS32002.1	13q32.3	2011-04-08			ENSG00000125246	ENSG00000125246			18355	protein-coding gene	gene with protein product		609686					Standard	XM_005254030		Approved	CLB	uc001vok.3	Q8N0X4	OTTHUMG00000017278	ENST00000376360.1:c.691G>A	13.37:g.100518550G>A	ENSP00000365538:p.Val231Ile	Somatic		Capture	Illumina HiSeq	Phase_I	99316551	NM_206808	Q5W0F7|Q8TDH8	Missense_Mutation	SNP	ENST00000376360.1	37	CCDS32002.1	.	.	.	.	.	.	.	.	.	.	G	14.91	2.675686	0.47781	.	.	ENSG00000125246	ENST00000376355;ENST00000376360;ENST00000444838;ENST00000376354;ENST00000339105	T;T;T;T;T	0.28069	1.63;1.63;1.63;1.63;1.63	5.75	4.87	0.63330	Aldehyde-lyase domain (1);Pyruvate/Phosphoenolpyruvate kinase (2);	0.157377	0.56097	D	0.000027	T	0.26412	0.0645	L	0.39020	1.185	0.53688	D	0.999975	B;B	0.14805	0.011;0.006	B;B	0.27608	0.081;0.033	T	0.04961	-1.0915	10	0.28530	T	0.3	-4.6304	11.9914	0.53178	0.0846:0.0:0.9154:0.0	.	197;231	B4DU60;Q8N0X4	.;CLYBL_HUMAN	I	197;231;197;197;231	ENSP00000365533:V197I;ENSP00000365538:V231I;ENSP00000404768:V197I;ENSP00000365532:V197I;ENSP00000342991:V231I	ENSP00000342991:V231I	V	+	1	0	CLYBL	99316551	1.000000	0.71417	0.031000	0.17742	0.840000	0.47671	6.209000	0.72171	1.478000	0.48253	0.650000	0.86243	GTC		0.458	CLYBL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045611.1		
DYNC1H1	1778	broad.mit.edu	37	14	102463572	102463572	+	Silent	SNP	C	C	T	rs150953878		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr14:102463572C>T	ENST00000360184.4	+	16	3929	c.3765C>T	c.(3763-3765)acC>acT	p.T1255T		NM_001376.4	NP_001367.2	Q14204	DYHC1_HUMAN	dynein, cytoplasmic 1, heavy chain 1	1255	Stem. {ECO:0000250}.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cell death (GO:0008219)|cytoplasmic mRNA processing body assembly (GO:0033962)|G2/M transition of mitotic cell cycle (GO:0000086)|microtubule-based movement (GO:0007018)|mitotic cell cycle (GO:0000278)|mitotic spindle organization (GO:0007052)|stress granule assembly (GO:0034063)|transport (GO:0006810)	centrosome (GO:0005813)|cytoplasmic dynein complex (GO:0005868)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|membrane (GO:0016020)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|poly(A) RNA binding (GO:0044822)	p.T1255T(1)		NS(1)|biliary_tract(1)|breast(4)|central_nervous_system(5)|cervix(1)|endometrium(21)|haematopoietic_and_lymphoid_tissue(3)|kidney(10)|large_intestine(28)|lung(60)|ovary(9)|pancreas(1)|prostate(6)|skin(7)|stomach(3)|upper_aerodigestive_tract(4)|urinary_tract(2)	166						GCCGCACCACCGACCTGCTGA	0.582																																					p.T1255T												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C3765T	14						.	C		0,4406		0,0,2203	51.0	47.0	49.0		3765	-11.7	0.3	14	dbSNP_134	49	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	DYNC1H1	NM_001376.4		0,2,6501	TT,TC,CC		0.0233,0.0,0.0154		1255/4647	102463572	2,13004	2203	4300	6503	101533325	SO:0001819	synonymous_variant	1778	exon16			AB002323	CCDS9966.1	14q32.31	2006-12-21	2005-11-24	2005-11-24		ENSG00000197102		"""Cytoplasmic dyneins"""	2961	protein-coding gene	gene with protein product		600112	"""dynein, cytoplasmic, heavy polypeptide 1"""	DNECL, DNCL, DNCH1		16260502, 8666668	Standard	NM_001376		Approved	Dnchc1, HL-3, p22, DHC1	uc001yks.2	Q14204		ENST00000360184.4:c.3765C>T	14.37:g.102463572C>T		Somatic		Capture	Illumina HiSeq	Phase_I	101533325	NM_001376	B0I1R0|Q6DKQ7|Q8WU28|Q92814|Q9Y4G5	Silent	SNP	ENST00000360184.4	37	CCDS9966.1																																																																																				0.582	DYNC1H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414574.1	NM_001376	
DYNC1H1	1778	broad.mit.edu	37	14	102478789	102478789	+	Silent	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr14:102478789C>T	ENST00000360184.4	+	34	7160	c.6996C>T	c.(6994-6996)cgC>cgT	p.R2332R		NM_001376.4	NP_001367.2	Q14204	DYHC1_HUMAN	dynein, cytoplasmic 1, heavy chain 1	2332	AAA 2. {ECO:0000250}.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cell death (GO:0008219)|cytoplasmic mRNA processing body assembly (GO:0033962)|G2/M transition of mitotic cell cycle (GO:0000086)|microtubule-based movement (GO:0007018)|mitotic cell cycle (GO:0000278)|mitotic spindle organization (GO:0007052)|stress granule assembly (GO:0034063)|transport (GO:0006810)	centrosome (GO:0005813)|cytoplasmic dynein complex (GO:0005868)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|membrane (GO:0016020)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|poly(A) RNA binding (GO:0044822)	p.R2332R(1)		NS(1)|biliary_tract(1)|breast(4)|central_nervous_system(5)|cervix(1)|endometrium(21)|haematopoietic_and_lymphoid_tissue(3)|kidney(10)|large_intestine(28)|lung(60)|ovary(9)|pancreas(1)|prostate(6)|skin(7)|stomach(3)|upper_aerodigestive_tract(4)|urinary_tract(2)	166						ATGGAGAGCGCCTCAGTCTTC	0.473																																					p.R2332R												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C6996T	14						.						188.0	164.0	172.0					14																	102478789		2203	4300	6503	101548542	SO:0001819	synonymous_variant	1778	exon34			AB002323	CCDS9966.1	14q32.31	2006-12-21	2005-11-24	2005-11-24		ENSG00000197102		"""Cytoplasmic dyneins"""	2961	protein-coding gene	gene with protein product		600112	"""dynein, cytoplasmic, heavy polypeptide 1"""	DNECL, DNCL, DNCH1		16260502, 8666668	Standard	NM_001376		Approved	Dnchc1, HL-3, p22, DHC1	uc001yks.2	Q14204		ENST00000360184.4:c.6996C>T	14.37:g.102478789C>T		Somatic		Capture	Illumina HiSeq	Phase_I	101548542	NM_001376	B0I1R0|Q6DKQ7|Q8WU28|Q92814|Q9Y4G5	Silent	SNP	ENST00000360184.4	37	CCDS9966.1																																																																																				0.473	DYNC1H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414574.1	NM_001376	
DYNC1H1	1778	broad.mit.edu	37	14	102508438	102508438	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr14:102508438C>T	ENST00000360184.4	+	66	12355	c.12191C>T	c.(12190-12192)aCg>aTg	p.T4064M	RP11-1017G21.4_ENST00000553701.1_RNA|RP11-1017G21.4_ENST00000557242.1_RNA|RP11-1017G21.4_ENST00000557551.1_RNA	NM_001376.4	NP_001367.2	Q14204	DYHC1_HUMAN	dynein, cytoplasmic 1, heavy chain 1	4064	AAA 6. {ECO:0000250}.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cell death (GO:0008219)|cytoplasmic mRNA processing body assembly (GO:0033962)|G2/M transition of mitotic cell cycle (GO:0000086)|microtubule-based movement (GO:0007018)|mitotic cell cycle (GO:0000278)|mitotic spindle organization (GO:0007052)|stress granule assembly (GO:0034063)|transport (GO:0006810)	centrosome (GO:0005813)|cytoplasmic dynein complex (GO:0005868)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|membrane (GO:0016020)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|poly(A) RNA binding (GO:0044822)	p.T4064M(1)		NS(1)|biliary_tract(1)|breast(4)|central_nervous_system(5)|cervix(1)|endometrium(21)|haematopoietic_and_lymphoid_tissue(3)|kidney(10)|large_intestine(28)|lung(60)|ovary(9)|pancreas(1)|prostate(6)|skin(7)|stomach(3)|upper_aerodigestive_tract(4)|urinary_tract(2)	166						GAGCAGAACACGCAGATCACT	0.542																																					p.T4064M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C12191T	14						.						113.0	90.0	98.0					14																	102508438		2203	4300	6503	101578191	SO:0001583	missense	1778	exon66			AB002323	CCDS9966.1	14q32.31	2006-12-21	2005-11-24	2005-11-24		ENSG00000197102		"""Cytoplasmic dyneins"""	2961	protein-coding gene	gene with protein product		600112	"""dynein, cytoplasmic, heavy polypeptide 1"""	DNECL, DNCL, DNCH1		16260502, 8666668	Standard	NM_001376		Approved	Dnchc1, HL-3, p22, DHC1	uc001yks.2	Q14204		ENST00000360184.4:c.12191C>T	14.37:g.102508438C>T	ENSP00000348965:p.Thr4064Met	Somatic		Capture	Illumina HiSeq	Phase_I	101578191	NM_001376	B0I1R0|Q6DKQ7|Q8WU28|Q92814|Q9Y4G5	Missense_Mutation	SNP	ENST00000360184.4	37	CCDS9966.1	.	.	.	.	.	.	.	.	.	.	C	16.02	3.004545	0.54254	.	.	ENSG00000197102	ENST00000360184	T	0.08896	3.04	5.91	5.03	0.67393	Dynein heavy chain (1);	0.101958	0.64402	D	0.000003	T	0.06917	0.0176	N	0.16903	0.455	0.51482	D	0.999928	B	0.22800	0.075	B	0.21360	0.034	T	0.29274	-1.0017	10	0.41790	T	0.15	.	15.2882	0.73846	0.0:0.9328:0.0:0.0672	.	4064	Q14204	DYHC1_HUMAN	M	4064	ENSP00000348965:T4064M	ENSP00000348965:T4064M	T	+	2	0	DYNC1H1	101578191	1.000000	0.71417	0.900000	0.35374	0.940000	0.58332	4.240000	0.58701	1.512000	0.48834	0.655000	0.94253	ACG		0.542	DYNC1H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414574.1	NM_001376	
DYNC1H1	1778	broad.mit.edu	37	14	102516871	102516871	+	Missense_Mutation	SNP	C	C	T	rs200224597		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr14:102516871C>T	ENST00000360184.4	+	78	14076	c.13912C>T	c.(13912-13914)Cgg>Tgg	p.R4638W	RP11-1017G21.4_ENST00000553701.1_RNA|RP11-1017G21.4_ENST00000557242.1_RNA	NM_001376.4	NP_001367.2	Q14204	DYHC1_HUMAN	dynein, cytoplasmic 1, heavy chain 1	4638					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cell death (GO:0008219)|cytoplasmic mRNA processing body assembly (GO:0033962)|G2/M transition of mitotic cell cycle (GO:0000086)|microtubule-based movement (GO:0007018)|mitotic cell cycle (GO:0000278)|mitotic spindle organization (GO:0007052)|stress granule assembly (GO:0034063)|transport (GO:0006810)	centrosome (GO:0005813)|cytoplasmic dynein complex (GO:0005868)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|membrane (GO:0016020)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|poly(A) RNA binding (GO:0044822)	p.R4638W(2)		NS(1)|biliary_tract(1)|breast(4)|central_nervous_system(5)|cervix(1)|endometrium(21)|haematopoietic_and_lymphoid_tissue(3)|kidney(10)|large_intestine(28)|lung(60)|ovary(9)|pancreas(1)|prostate(6)|skin(7)|stomach(3)|upper_aerodigestive_tract(4)|urinary_tract(2)	166						CTTCTACGAGCGGGGTGTCGC	0.433																																					p.R4638W												.	.	2	Substitution - Missense(2)	ovary(1)|large_intestine(1)	c.C13912T	14						.						131.0	131.0	131.0					14																	102516871		2203	4300	6503	101586624	SO:0001583	missense	1778	exon78			AB002323	CCDS9966.1	14q32.31	2006-12-21	2005-11-24	2005-11-24		ENSG00000197102		"""Cytoplasmic dyneins"""	2961	protein-coding gene	gene with protein product		600112	"""dynein, cytoplasmic, heavy polypeptide 1"""	DNECL, DNCL, DNCH1		16260502, 8666668	Standard	NM_001376		Approved	Dnchc1, HL-3, p22, DHC1	uc001yks.2	Q14204		ENST00000360184.4:c.13912C>T	14.37:g.102516871C>T	ENSP00000348965:p.Arg4638Trp	Somatic		Capture	Illumina HiSeq	Phase_I	101586624	NM_001376	B0I1R0|Q6DKQ7|Q8WU28|Q92814|Q9Y4G5	Missense_Mutation	SNP	ENST00000360184.4	37	CCDS9966.1	.	.	.	.	.	.	.	.	.	.	C	33	5.248250	0.95305	.	.	ENSG00000197102	ENST00000360184	T	0.09817	2.94	5.61	5.61	0.85477	Dynein heavy chain (1);	0.000000	0.85682	D	0.000000	T	0.44074	0.1276	M	0.90198	3.095	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.52109	-0.8619	10	0.87932	D	0	.	19.652	0.95819	0.0:1.0:0.0:0.0	.	4638	Q14204	DYHC1_HUMAN	W	4638	ENSP00000348965:R4638W	ENSP00000348965:R4638W	R	+	1	2	DYNC1H1	101586624	1.000000	0.71417	0.998000	0.56505	0.749000	0.42624	7.526000	0.81920	2.656000	0.90262	0.561000	0.74099	CGG		0.433	DYNC1H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414574.1	NM_001376	
WDR20	91833	broad.mit.edu	37	14	102675299	102675299	+	Silent	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr14:102675299C>T	ENST00000342702.3	+	3	823	c.792C>T	c.(790-792)ggC>ggT	p.G264G	WDR20_ENST00000499851.2_Silent_p.G7G|WDR20_ENST00000299135.6_3'UTR|WDR20_ENST00000454394.2_Silent_p.G295G|WDR20_ENST00000556511.2_Silent_p.G203G|WDR20_ENST00000556807.1_Silent_p.G203G|WDR20_ENST00000424963.2_Silent_p.G140G|WDR20_ENST00000322340.5_Intron|WDR20_ENST00000545563.1_Silent_p.G91G|WDR20_ENST00000335263.5_Silent_p.G264G	NM_001242418.1|NM_144574.3	NP_001229347.1|NP_653175.2	Q8TBZ3	WDR20_HUMAN	WD repeat domain 20	264								p.G264G(1)		breast(1)|large_intestine(2)|lung(4)|prostate(1)	8						ACTTTGGGGGCTTGCTGTGTG	0.547																																					p.G264G												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C792T	14						.						76.0	62.0	67.0					14																	102675299		2203	4300	6503	101745052	SO:0001819	synonymous_variant	91833	exon3			BC028387	CCDS9968.1, CCDS9969.1, CCDS9970.1, CCDS55942.1, CCDS55943.1, CCDS55944.1, CCDS55945.1	14q32.31	2013-01-09				ENSG00000140153		"""WD repeat domain containing"""	19667	protein-coding gene	gene with protein product							Standard	NM_181291		Approved	DMR, MGC33177, FLJ33659	uc010txu.2	Q8TBZ3		ENST00000342702.3:c.792C>T	14.37:g.102675299C>T		Somatic		Capture	Illumina HiSeq	Phase_I	101745052	NM_181291	B4DN18|E7EUY8|F8W9S4|G3V2F8|G3V5R0|H0YJJ1|Q86TU2|Q8NCN7|Q8WXX2|Q9UF86	Silent	SNP	ENST00000342702.3	37	CCDS9969.1	.	.	.	.	.	.	.	.	.	.	C	4.986	0.183127	0.09495	.	.	ENSG00000140153	ENST00000556511	.	.	.	5.83	4.87	0.63330	.	.	.	.	.	T	0.62551	0.2437	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.58880	-0.7558	4	.	.	.	.	11.5139	0.50509	0.3869:0.6131:0.0:0.0	.	.	.	.	F	195	.	.	L	+	1	0	WDR20	101745052	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.091000	0.41691	2.769000	0.95229	0.655000	0.94253	CTT		0.547	WDR20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414963.1	NM_181291	
ZNF839	55778	broad.mit.edu	37	14	102805557	102805557	+	Missense_Mutation	SNP	G	G	A	rs373766097		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr14:102805557G>A	ENST00000558850.1	+	7	1926	c.1576G>A	c.(1576-1578)Gct>Act	p.A526T	ZNF839_ENST00000420933.2_3'UTR|AL137229.1_ENST00000577622.1_RNA|ZNF839_ENST00000262236.5_Missense_Mutation_p.A526T|ZNF839_ENST00000559185.1_Missense_Mutation_p.A526T|ZNF839_ENST00000442396.2_Missense_Mutation_p.A642T	NM_001267827.1	NP_001254756.1	A8K0R7	ZN839_HUMAN	zinc finger protein 839	526							metal ion binding (GO:0046872)	p.A642T(1)		breast(2)|central_nervous_system(1)|endometrium(5)|large_intestine(2)|lung(5)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	19						TGCTTTGGCCGCTGGTGAGGG	0.557																																					p.A642T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1924A	14						.	A	THR/ALA	0,3852		0,0,1926	52.0	54.0	53.0		1924	-1.8	0.0	14		53	1,8293		0,1,4146	no	missense	ZNF839	NM_018335.3	58	0,1,6072	AA,AG,GG		0.0121,0.0,0.0082	benign	642/928	102805557	1,12145	1926	4147	6073	101875310	SO:0001583	missense	55778	exon7			AK093342	CCDS45164.1, CCDS58336.1	14q32.32	2010-05-06	2008-06-23	2008-06-23	ENSG00000022976	ENSG00000022976			20345	protein-coding gene	gene with protein product			"""chromosome 14 open reading frame 131"""	C14orf131			Standard	NM_018335		Approved		uc010awk.2	A8K0R7		ENST00000558850.1:c.1576G>A	14.37:g.102805557G>A	ENSP00000453363:p.Ala526Thr	Somatic		Capture	Illumina HiSeq	Phase_I	101875310	NM_018335	B3KSD2|Q53FH5|Q6GPI5|Q86TU1|Q9BQ86|Q9NUU3	Missense_Mutation	SNP	ENST00000558850.1	37	CCDS58336.1	.	.	.	.	.	.	.	.	.	.	g	11.99	1.804028	0.31869	0.0	1.21E-4	ENSG00000022976	ENST00000442396;ENST00000262236;ENST00000398436;ENST00000420933	T;T	0.18174	2.31;2.23	4.55	-1.84	0.07809	.	1.669320	0.03331	N	0.193420	T	0.07503	0.0189	N	0.24115	0.695	0.09310	N	1	B;P;P;P	0.42961	0.006;0.576;0.626;0.795	B;B;B;B	0.29267	0.004;0.048;0.05;0.1	T	0.26883	-1.0090	10	0.10902	T	0.67	.	4.8913	0.13728	0.4918:0.1625:0.3456:0.0	.	642;526;405;526	A8K0R7-5;A8K0R7-2;Q9NT83;A8K0R7	.;.;.;ZN839_HUMAN	T	642;526;194;60	ENSP00000399863:A642T;ENSP00000262236:A526T	ENSP00000262236:A526T	A	+	1	0	ZNF839	101875310	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	0.020000	0.13466	-0.219000	0.10003	-0.944000	0.02675	GCT		0.557	ZNF839-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000415492.2	NM_018335	
OR4K15	81127	broad.mit.edu	37	14	20444015	20444015	+	Missense_Mutation	SNP	G	G	A	rs139377821	byFrequency	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr14:20444015G>A	ENST00000305051.5	+	1	413	c.338G>A	c.(337-339)cGc>cAc	p.R113H		NM_001005486.1	NP_001005486.1	Q8NH41	OR4KF_HUMAN	olfactory receptor, family 4, subfamily K, member 15	113						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.R113H(1)		endometrium(3)|kidney(2)|large_intestine(6)|lung(23)|ovary(1)|prostate(2)|skin(1)|stomach(1)	39	all_cancers(95;0.00108)		Epithelial(56;9.96e-07)|all cancers(55;3.58e-06)	GBM - Glioblastoma multiforme(265;0.00327)		CTGGTTGAGCGCAAGACTATT	0.453													G|||	2	0.000399361	0.0015	0.0	5008	,	,		22221	0.0		0.0	False		,,,				2504	0.0				p.R113H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G338A	14						.						127.0	132.0	130.0					14																	20444015		2203	4297	6500	19513855	SO:0001583	missense	81127	exon1				CCDS32026.1	14q11.2	2013-09-23			ENSG00000169488	ENSG00000169488		"""GPCR / Class A : Olfactory receptors"""	15353	protein-coding gene	gene with protein product							Standard	NM_001005486		Approved	OR4K15Q	uc010tkx.2	Q8NH41	OTTHUMG00000170635	ENST00000305051.5:c.338G>A	14.37:g.20444015G>A	ENSP00000304077:p.Arg113His	Somatic		Capture	Illumina HiSeq	Phase_I	19513855	NM_001005486	B9EIL3|Q6IEZ4	Missense_Mutation	SNP	ENST00000305051.5	37	CCDS32026.1	2	9.157509157509158E-4	2	0.0040650406504065045	0	0.0	0	0.0	0	0.0	.	0.001	-3.250918	0.00022	.	.	ENSG00000169488	ENST00000305051	T	0.01584	4.75	3.6	-6.57	0.01842	GPCR, rhodopsin-like superfamily (1);	1.002150	0.08047	N	0.996093	T	0.00754	0.0025	N	0.04655	-0.195	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.47302	-0.9128	10	0.02654	T	1	.	7.8035	0.29189	0.5872:0.0:0.3023:0.1105	.	113	Q8NH41	OR4KF_HUMAN	H	113	ENSP00000304077:R113H	ENSP00000304077:R113H	R	+	2	0	OR4K15	19513855	0.000000	0.05858	0.000000	0.03702	0.017000	0.09413	-3.348000	0.00503	-1.617000	0.01570	-2.550000	0.00177	CGC		0.453	OR4K15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409883.1		
SUPT16H	11198	broad.mit.edu	37	14	21830443	21830443	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr14:21830443C>T	ENST00000216297.2	-	15	2044	c.1706G>A	c.(1705-1707)cGa>cAa	p.R569Q		NM_007192.3	NP_009123.1	Q9Y5B9	SP16H_HUMAN	suppressor of Ty 16 homolog (S. cerevisiae)	569					DNA repair (GO:0006281)|DNA replication (GO:0006260)|gene expression (GO:0010467)|nucleosome disassembly (GO:0006337)|positive regulation of DNA-templated transcription, elongation (GO:0032786)|positive regulation of viral transcription (GO:0050434)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|viral process (GO:0016032)	chromosome (GO:0005694)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)	p.R569Q(1)		breast(3)|endometrium(4)|kidney(1)|large_intestine(9)|lung(6)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	27	all_cancers(95;0.00115)		Epithelial(56;1.62e-06)|all cancers(55;1.49e-05)	GBM - Glioblastoma multiforme(265;0.0159)		AAAGTTGATTCGCAAGTAAGT	0.398																																					p.R569Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1706A	14						.						67.0	62.0	64.0					14																	21830443		2203	4300	6503	20900283	SO:0001583	missense	11198	exon15			AF152961	CCDS9569.1	14q11.1	2008-08-13	2001-11-28		ENSG00000092201	ENSG00000092201			11465	protein-coding gene	gene with protein product	"""facilitates chromatin remodeling 140 kDa subunit"""	605012	"""suppressor of Ty (S.cerevisiae) 16 homolog"""			9489704, 11239457	Standard	NM_007192		Approved	FACT, FACTP140, SPT16/CDC68, FLJ14010, FLJ10857, CDC68	uc001wao.2	Q9Y5B9	OTTHUMG00000029685	ENST00000216297.2:c.1706G>A	14.37:g.21830443C>T	ENSP00000216297:p.Arg569Gln	Somatic		Capture	Illumina HiSeq	Phase_I	20900283	NM_007192	Q6GMT8|Q6P2F1|Q6PJM1|Q9NRX0	Missense_Mutation	SNP	ENST00000216297.2	37	CCDS9569.1	.	.	.	.	.	.	.	.	.	.	C	36	5.796877	0.96952	.	.	ENSG00000092201	ENST00000216297	.	.	.	5.72	5.72	0.89469	FACT complex subunit Spt16p/Cdc68p (1);	0.000000	0.85682	D	0.000000	D	0.87849	0.6281	H	0.95114	3.625	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.90939	0.4796	9	0.87932	D	0	-4.8971	18.6573	0.91459	0.0:1.0:0.0:0.0	.	569	Q9Y5B9	SP16H_HUMAN	Q	569	.	ENSP00000216297:R569Q	R	-	2	0	SUPT16H	20900283	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	6.915000	0.75770	2.694000	0.91930	0.650000	0.86243	CGA		0.398	SUPT16H-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000074025.2		
ACIN1	22985	broad.mit.edu	37	14	23530359	23530359	+	Silent	SNP	C	C	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr14:23530359C>A	ENST00000262710.1	-	18	3960	c.3633G>T	c.(3631-3633)ctG>ctT	p.L1211L	ACIN1_ENST00000605057.1_Silent_p.L1153L|ACIN1_ENST00000555053.1_Silent_p.L1198L|ACIN1_ENST00000557515.1_Silent_p.L452L|ACIN1_ENST00000397341.3_Silent_p.L453L|ACIN1_ENST00000338631.6_Silent_p.L484L|ACIN1_ENST00000457657.1_Silent_p.L1171L|ACIN1_ENST00000357481.2_Silent_p.L453L	NM_001164814.1|NM_014977.3	NP_001158286.1|NP_055792	Q9UKV3	ACINU_HUMAN	apoptotic chromatin condensation inducer 1	1211	Arg/Asp/Glu/Lys-rich.|Sufficient for interaction with RNPS1 and SAP18 and formation of th ASAP complex. {ECO:0000250}.				apoptotic chromosome condensation (GO:0030263)|apoptotic process (GO:0006915)|ATP catabolic process (GO:0006200)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|erythrocyte differentiation (GO:0030218)|mRNA processing (GO:0006397)|negative regulation of mRNA splicing, via spliceosome (GO:0048025)|positive regulation of apoptotic process (GO:0043065)|positive regulation of monocyte differentiation (GO:0045657)|RNA splicing (GO:0008380)	ASAP complex (GO:0061574)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATPase activity (GO:0016887)|enzyme binding (GO:0019899)|nucleic acid binding (GO:0003676)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)	p.L1211L(1)		breast(1)|endometrium(6)|kidney(4)|large_intestine(9)|lung(10)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	37	all_cancers(95;1.36e-05)			GBM - Glioblastoma multiforme(265;0.00816)		AAAGGTCATCCAGCAGCTTGG	0.552																																					p.L484L												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G1452T	14						.						138.0	119.0	126.0					14																	23530359		2203	4300	6503	22600199	SO:0001819	synonymous_variant	22985	exon11			AB014570	CCDS9587.1, CCDS53887.1, CCDS53888.1, CCDS53889.1, CCDS55905.1	14q11.2	2008-11-25	2004-03-31	2004-04-01	ENSG00000100813	ENSG00000100813			17066	protein-coding gene	gene with protein product	"""functional spliceosome-associated protein 152"""	604562	"""apoptotic chromatin condensation inducer in the nucleus"""	ACINUS		9734811, 10490026	Standard	NM_014977		Approved	KIAA0670, fSAP152	uc001wit.4	Q9UKV3	OTTHUMG00000028716	ENST00000262710.1:c.3633G>T	14.37:g.23530359C>A		Somatic		Capture	Illumina HiSeq	Phase_I	22600199	NM_001164816	B2RTT4|D3DS45|O75158|Q9UG91|Q9UKV1|Q9UKV2	Silent	SNP	ENST00000262710.1	37	CCDS9587.1																																																																																				0.552	ACIN1-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000071707.3	NM_014977	
MYH6	4624	broad.mit.edu	37	14	23851679	23851679	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr14:23851679C>A	ENST00000356287.3	-	37	5783	c.5754G>T	c.(5752-5754)caG>caT	p.Q1918H	MYH6_ENST00000405093.3_Missense_Mutation_p.Q1918H			P13533	MYH6_HUMAN	myosin, heavy chain 6, cardiac muscle, alpha	1918					adult heart development (GO:0007512)|ATP catabolic process (GO:0006200)|atrial cardiac muscle tissue morphogenesis (GO:0055009)|BMP signaling pathway (GO:0030509)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle fiber development (GO:0048739)|in utero embryonic development (GO:0001701)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|myofibril assembly (GO:0030239)|regulation of ATPase activity (GO:0043462)|regulation of blood pressure (GO:0008217)|regulation of heart contraction (GO:0008016)|regulation of heart growth (GO:0060420)|regulation of heart rate (GO:0002027)|regulation of the force of heart contraction (GO:0002026)|sarcomere organization (GO:0045214)|striated muscle contraction (GO:0006941)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)|visceral muscle development (GO:0007522)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|muscle myosin complex (GO:0005859)|myofibril (GO:0030016)|myosin complex (GO:0016459)|myosin filament (GO:0032982)|nucleus (GO:0005634)|sarcomere (GO:0030017)|stress fiber (GO:0001725)|Z disc (GO:0030018)	actin-dependent ATPase activity (GO:0030898)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microfilament motor activity (GO:0000146)|protein kinase binding (GO:0019901)	p.Q1918H(1)		breast(4)|cervix(2)|endometrium(8)|kidney(2)|large_intestine(16)|liver(1)|lung(60)|ovary(2)|pancreas(3)|prostate(6)|skin(6)|stomach(3)|upper_aerodigestive_tract(4)|urinary_tract(2)	119	all_cancers(95;2.54e-05)			GBM - Glioblastoma multiforme(265;0.00764)|READ - Rectum adenocarcinoma(4;0.0289)|Colorectal(4;0.0441)		GCTTGTTGACCTGGGACTCAG	0.587																																					p.Q1918H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G5754T	14						.						168.0	151.0	157.0					14																	23851679		2203	4300	6503	22921519	SO:0001583	missense	4624	exon38			D00943	CCDS9600.1	14q11.2-q13	2014-09-17	2008-08-01		ENSG00000197616	ENSG00000197616		"""Myosins / Myosin superfamily : Class II"""	7576	protein-coding gene	gene with protein product	"""cardiomyopathy, hypertrophic 1"""	160710	"""myosin, heavy polypeptide 6, cardiac muscle, alpha (cardiomyopathy, hypertrophic 1)"""			2144212	Standard	NM_002471		Approved		uc001wjv.3	P13533	OTTHUMG00000028753	ENST00000356287.3:c.5754G>T	14.37:g.23851679C>A	ENSP00000348634:p.Gln1918His	Somatic		Capture	Illumina HiSeq	Phase_I	22921519	NM_002471	A2RTX1|D9YZU2|Q13943|Q14906|Q14907	Missense_Mutation	SNP	ENST00000356287.3	37	CCDS9600.1	.	.	.	.	.	.	.	.	.	.	C	18.31	3.596216	0.66332	.	.	ENSG00000197616	ENST00000405093;ENST00000356287	T;T	0.78364	-1.17;-1.17	4.05	3.16	0.36331	Myosin tail (1);	.	.	.	.	D	0.89322	0.6682	M	0.93808	3.46	0.49687	D	0.999819	D	0.76494	0.999	D	0.91635	0.999	D	0.89619	0.3847	9	0.87932	D	0	.	9.1014	0.36671	0.0:0.8173:0.0:0.1827	.	1918	P13533	MYH6_HUMAN	H	1918	ENSP00000386041:Q1918H;ENSP00000348634:Q1918H	ENSP00000348634:Q1918H	Q	-	3	2	MYH6	22921519	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	2.107000	0.41844	1.054000	0.40438	0.561000	0.74099	CAG		0.587	MYH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071796.3		
NGDN	25983	broad.mit.edu	37	14	23945564	23945564	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr14:23945564C>T	ENST00000408901.3	+	8	689	c.661C>T	c.(661-663)Cgt>Tgt	p.R221C	NGDN_ENST00000397154.3_Missense_Mutation_p.R221C|NGDN_ENST00000556580.1_5'UTR	NM_001042635.1|NM_015514.1	NP_001036100.1|NP_056329.1	Q8NEJ9	NGDN_HUMAN	neuroguidin, EIF4E binding protein	221					regulation of translation (GO:0006417)	cell projection (GO:0042995)|chromosome, centromeric region (GO:0000775)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)	p.R221C(1)		NS(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(6)|prostate(1)	12	all_cancers(95;0.000251)			GBM - Glioblastoma multiforme(265;0.00654)		AGAGGAAATCCGTGATGCTCG	0.527																																					p.R221C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C661T	14						.						62.0	60.0	60.0					14																	23945564		2203	4300	6503	23015404	SO:0001583	missense	25983	exon8			AK022215	CCDS32051.1, CCDS41926.1	14q11.2	2014-06-13	2006-08-02	2006-08-02	ENSG00000129460	ENSG00000129460			20271	protein-coding gene	gene with protein product		610777	"""chromosome 14 open reading frame 120"""	C14orf120		16705177	Standard	NM_001042635		Approved	DKFZP564O092, LCP5, lpd-2, NGD	uc001wjy.3	Q8NEJ9	OTTHUMG00000171501	ENST00000408901.3:c.661C>T	14.37:g.23945564C>T	ENSP00000386134:p.Arg221Cys	Somatic		Capture	Illumina HiSeq	Phase_I	23015404	NM_015514	A8K760|Q9Y400	Missense_Mutation	SNP	ENST00000408901.3	37	CCDS41926.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	24.5|24.5	4.534564|4.534564	0.85812|0.85812	.|.	.|.	ENSG00000129460|ENSG00000129460	ENST00000556483|ENST00000408901;ENST00000397154	.|T;T	.|0.34472	.|1.36;1.36	5.89|5.89	5.89|5.89	0.94794|0.94794	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.54615|0.54615	0.1869|0.1869	L|L	0.43152|0.43152	1.355|1.355	0.80722|0.80722	D|D	1|1	.|D;D	.|0.89917	.|1.0;1.0	.|D;D	.|0.74674	.|0.984;0.965	T|T	0.51036|0.51036	-0.8756|-0.8756	5|10	.|0.59425	.|D	.|0.04	-0.2676|-0.2676	19.0276|19.0276	0.92939|0.92939	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|221;221	.|Q8NEJ9-2;Q8NEJ9	.|.;NGDN_HUMAN	L|C	168|221	.|ENSP00000386134:R221C;ENSP00000380340:R221C	.|ENSP00000380340:R221C	P|R	+|+	2|1	0|0	NGDN|NGDN	23015404|23015404	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.995000|0.995000	0.86356|0.86356	2.390000|2.390000	0.44416|0.44416	2.797000|2.797000	0.96272|0.96272	0.563000|0.563000	0.77884|0.77884	CCG|CGT		0.527	NGDN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000413782.3	NM_001042635	
THTPA	79178	broad.mit.edu	37	14	24026298	24026298	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr14:24026298G>A	ENST00000288014.6	+	1	1068	c.332G>A	c.(331-333)gGc>gAc	p.G111D	RP11-66N24.4_ENST00000555446.1_RNA|THTPA_ENST00000554789.1_Intron|RP11-66N24.4_ENST00000556354.1_RNA|RP11-66N24.4_ENST00000553985.1_RNA|THTPA_ENST00000404535.3_Missense_Mutation_p.G111D|THTPA_ENST00000556015.1_Intron|THTPA_ENST00000554970.1_Intron			Q9BU02	THTPA_HUMAN	thiamine triphosphatase	111	CYTH. {ECO:0000255|PROSITE- ProRule:PRU01044}.				dephosphorylation (GO:0016311)|generation of precursor metabolites and energy (GO:0006091)|small molecule metabolic process (GO:0044281)|thiamine diphosphate metabolic process (GO:0042357)|thiamine metabolic process (GO:0006772)|thiamine-containing compound metabolic process (GO:0042723)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)	hydrolase activity (GO:0016787)|magnesium ion binding (GO:0000287)|thiamin-triphosphatase activity (GO:0050333)	p.G111D(1)		large_intestine(1)|prostate(2)	3	all_cancers(95;0.000251)			GBM - Glioblastoma multiforme(265;0.00643)		GCTGTGCTGGGCCCACTGGGG	0.587																																					p.G111D												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G332A	14						.						64.0	64.0	64.0					14																	24026298		2203	4300	6503	23096138	SO:0001583	missense	79178	exon1			AF432862	CCDS32053.1, CCDS58306.1, CCDS58307.1	14q11.2	2011-04-28					3.6.1.28		18987	protein-coding gene	gene with protein product		611612				11827967	Standard	NR_046051		Approved	THTPASE	uc001wkh.5	Q9BU02		ENST00000288014.6:c.332G>A	14.37:g.24026298G>A	ENSP00000288014:p.Gly111Asp	Somatic		Capture	Illumina HiSeq	Phase_I	23096138	NM_024328	D3DS50|G3V4J3	Missense_Mutation	SNP	ENST00000288014.6	37	CCDS32053.1	.	.	.	.	.	.	.	.	.	.	G	10.60	1.396693	0.25205	.	.	ENSG00000157306	ENST00000404535;ENST00000288014;ENST00000557630	T;T;T	0.40756	1.02;1.02;1.02	5.38	5.38	0.77491	CYTH domain (2);CYTH-like domain (1);	0.552745	0.21940	N	0.066900	T	0.29223	0.0727	L	0.31420	0.93	0.80722	D	1	B	0.28998	0.23	B	0.32090	0.14	T	0.06303	-1.0834	10	0.12103	T	0.63	-5.1343	9.9432	0.41593	0.0889:0.0:0.9111:0.0	.	111	Q9BU02	THTPA_HUMAN	D	111	ENSP00000384580:G111D;ENSP00000288014:G111D;ENSP00000452281:G111D	ENSP00000288014:G111D	G	+	2	0	THTPA	23096138	0.277000	0.24220	0.330000	0.25442	0.373000	0.29922	1.429000	0.34903	2.793000	0.96121	0.655000	0.94253	GGC		0.587	THTPA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413800.2		
JPH4	84502	broad.mit.edu	37	14	24040666	24040666	+	Missense_Mutation	SNP	C	C	T	rs140989156	byFrequency	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr14:24040666C>T	ENST00000397118.3	-	6	2176	c.1274G>A	c.(1273-1275)cGc>cAc	p.R425H	JPH4_ENST00000356300.4_Missense_Mutation_p.R425H|JPH4_ENST00000544177.1_Missense_Mutation_p.R90H	NM_032452.2	NP_115828.2	Q96JJ6	JPH4_HUMAN	junctophilin 4	425					calcium ion transport into cytosol (GO:0060402)|learning (GO:0007612)|neuromuscular process controlling balance (GO:0050885)|regulation of ryanodine-sensitive calcium-release channel activity (GO:0060314)|regulation of synaptic plasticity (GO:0048167)	dendritic shaft (GO:0043198)|integral component of membrane (GO:0016021)|junctional sarcoplasmic reticulum membrane (GO:0014701)|plasma membrane (GO:0005886)|smooth endoplasmic reticulum (GO:0005790)		p.R425H(1)		endometrium(1)|large_intestine(2)|lung(13)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	22	all_cancers(95;0.000251)			GBM - Glioblastoma multiforme(265;0.00654)		CCTGGGTCTGCGGCCTGGGTA	0.602													C|||	5	0.000998403	0.0038	0.0	5008	,	,		16622	0.0		0.0	False		,,,				2504	0.0				p.R425H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1274A	14						.	C	HIS/ARG,HIS/ARG	17,4389		0,17,2186	34.0	34.0	34.0		1274,1274	3.3	1.0	14	dbSNP_134	34	0,8594		0,0,4297	yes	missense,missense	JPH4	NM_001146028.1,NM_032452.2	29,29	0,17,6483	TT,TC,CC		0.0,0.3858,0.1308	probably-damaging,probably-damaging	425/629,425/629	24040666	17,12983	2203	4297	6500	23110506	SO:0001583	missense	84502	exon6			AB058734	CCDS9603.1	14q11	2004-05-28	2004-05-28	2004-05-28	ENSG00000092051	ENSG00000092051			20156	protein-coding gene	gene with protein product			"""junctophilin like 1"""	JPHL1		11347906	Standard	NM_032452		Approved	KIAA1831	uc001wkr.2	Q96JJ6	OTTHUMG00000028769	ENST00000397118.3:c.1274G>A	14.37:g.24040666C>T	ENSP00000380307:p.Arg425His	Somatic		Capture	Illumina HiSeq	Phase_I	23110506	NM_032452	D3DS53|Q8ND44|Q96DQ0	Missense_Mutation	SNP	ENST00000397118.3	37	CCDS9603.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	C	12.67	2.008220	0.35415	0.003858	0.0	ENSG00000092051	ENST00000356300;ENST00000397118;ENST00000543864;ENST00000267407;ENST00000544177	T;T;T	0.58060	0.36;0.36;0.77	5.17	3.34	0.38264	.	0.302778	0.17964	N	0.156092	T	0.37320	0.0999	L	0.29908	0.895	0.39073	D	0.960762	B;B	0.21452	0.056;0.013	B;B	0.15052	0.012;0.002	T	0.16867	-1.0388	10	0.36615	T	0.2	.	8.4804	0.33038	0.0:0.8165:0.0:0.1835	.	90;425	F5H1L9;Q96JJ6	.;JPH4_HUMAN	H	425;425;425;426;90	ENSP00000348648:R425H;ENSP00000380307:R425H;ENSP00000439562:R90H	ENSP00000267407:R426H	R	-	2	0	JPH4	23110506	0.989000	0.36119	1.000000	0.80357	0.999000	0.98932	-0.052000	0.11865	0.686000	0.31488	0.655000	0.94253	CGC		0.602	JPH4-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413853.1	NM_032452	
LRRC16B	90668	broad.mit.edu	37	14	24523641	24523641	+	Nonsense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr14:24523641C>T	ENST00000342740.5	+	5	437	c.283C>T	c.(283-285)Cga>Tga	p.R95*	LRRC16B_ENST00000334420.7_5'UTR	NM_138360.3	NP_612369.3	Q8ND23	LR16B_HUMAN	leucine rich repeat containing 16B	95						cytoplasm (GO:0005737)		p.R95*(1)		breast(3)|central_nervous_system(2)|cervix(3)|endometrium(7)|kidney(1)|large_intestine(9)|liver(1)|lung(15)|ovary(2)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(4)	52				GBM - Glioblastoma multiforme(265;0.019)		GGTGAGCATGCGACTGCCATC	0.622																																					p.R95X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.C283T	14						.						96.0	86.0	90.0					14																	24523641		2203	4300	6503	23593481	SO:0001587	stop_gained	90668	exon5			AI017934	CCDS32054.1	14q11.2-q12	2010-09-10	2008-02-12	2008-02-12					20272	protein-coding gene	gene with protein product		614716	"""chromosome 14 open reading frame 121"""	C14orf121		19846667	Standard	NM_138360		Approved	BC008134, crml-1, CARMIL3	uc001wlj.2	Q8ND23		ENST00000342740.5:c.283C>T	14.37:g.24523641C>T	ENSP00000340467:p.Arg95*	Somatic		Capture	Illumina HiSeq	Phase_I	23593481	NM_138360	Q8TEF7|Q96HS9	Nonsense_Mutation	SNP	ENST00000342740.5	37	CCDS32054.1	.	.	.	.	.	.	.	.	.	.	C	37	6.290664	0.97444	.	.	ENSG00000186648	ENST00000342740	.	.	.	4.7	2.78	0.32641	.	0.000000	0.64402	D	0.000006	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.06494	T	0.89	-20.4365	5.1603	0.15058	0.2068:0.6862:0.0:0.107	.	.	.	.	X	95	.	ENSP00000340467:R95X	R	+	1	2	LRRC16B	23593481	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	2.010000	0.40913	1.046000	0.40249	0.462000	0.41574	CGA		0.622	LRRC16B-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416527.1	NM_138360	
TM9SF1	10548	broad.mit.edu	37	14	24658626	24658626	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr14:24658626C>T	ENST00000261789.4	-	6	2174	c.1816G>A	c.(1816-1818)Gac>Aac	p.D606N	RP11-468E2.2_ENST00000561419.1_Nonsense_Mutation_p.W142*|TM9SF1_ENST00000524835.1_Missense_Mutation_p.D519N|TM9SF1_ENST00000528669.1_Missense_Mutation_p.D589N|IPO4_ENST00000354464.6_5'Flank|TM9SF1_ENST00000530611.1_Missense_Mutation_p.D815N|TM9SF1_ENST00000556387.1_Missense_Mutation_p.D815N	NM_006405.5	NP_006396.2	O15321	TM9S1_HUMAN	transmembrane 9 superfamily member 1	606					autophagy (GO:0006914)	cytoplasmic vesicle (GO:0031410)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)		p.D606N(1)		NS(1)|breast(4)|endometrium(3)|large_intestine(11)|lung(4)|ovary(1)	24				GBM - Glioblastoma multiforme(265;0.0183)		AGAACTCAGTCCATCTTGAGG	0.433																																					p.D606N												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1816A	14						.						105.0	110.0	109.0					14																	24658626		2203	4300	6503	23728466	SO:0001583	missense	10548	exon6			U94831	CCDS9617.1, CCDS41934.1, CCDS73623.1	14q11.2	2005-10-11			ENSG00000100926	ENSG00000100926			11864	protein-coding gene	gene with protein product						9332367	Standard	NM_006405		Approved	MP70, HMP70	uc010tob.1	O15321	OTTHUMG00000029322	ENST00000261789.4:c.1816G>A	14.37:g.24658626C>T	ENSP00000261789:p.Asp606Asn	Somatic		Capture	Illumina HiSeq	Phase_I	23728466	NM_006405	D3DS65|Q86SZ6|Q96FI8	Missense_Mutation	SNP	ENST00000261789.4	37	CCDS9617.1	.	.	.	.	.	.	.	.	.	.	C	34	5.372064	0.95923	.	.	ENSG00000100926;ENSG00000100926;ENSG00000100926;ENSG00000100926;ENSG00000254692	ENST00000261789;ENST00000528669;ENST00000556387;ENST00000524835;ENST00000530611	T;T;T;T;T	0.80653	-0.67;-0.67;-1.4;-1.39;-1.4	5.65	5.65	0.86999	.	0.000000	0.85682	D	0.000000	D	0.92166	0.7516	M	0.92122	3.275	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.93260	0.6642	10	0.87932	D	0	.	17.2626	0.87075	0.0:1.0:0.0:0.0	.	606	O15321	TM9S1_HUMAN	N	606;589;815;519;815	ENSP00000261789:D606N;ENSP00000432997:D589N;ENSP00000451949:D815N;ENSP00000434387:D519N;ENSP00000433967:D815N	ENSP00000433967:D815N	D	-	1	0	TM9SF1;RP11-468E2.1	23728466	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	6.106000	0.71511	2.941000	0.99782	0.655000	0.94253	GAC		0.433	TM9SF1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000073136.2	NM_006405	
TGM1	7051	broad.mit.edu	37	14	24728975	24728975	+	Missense_Mutation	SNP	G	G	A	rs121918731	byFrequency	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr14:24728975G>A	ENST00000206765.6	-	6	1042	c.919C>T	c.(919-921)Cgg>Tgg	p.R307W	TGM1_ENST00000544573.1_Intron	NM_000359.2	NP_000350.1	P22735	TGM1_HUMAN	transglutaminase 1	307			R -> G (in ARCI1; dbSNP:rs121918731). {ECO:0000269|PubMed:19890349}.|R -> W (in ARCI1; skin phenotype consistent with lamellar ichthyosis). {ECO:0000269|PubMed:11511296}.		cell envelope organization (GO:0043163)|cellular protein modification process (GO:0006464)|keratinization (GO:0031424)|keratinocyte differentiation (GO:0030216)|organ morphogenesis (GO:0009887)|peptide cross-linking (GO:0018149)	cell-cell adherens junction (GO:0005913)|cornified envelope (GO:0001533)|extracellular vesicular exosome (GO:0070062)|intrinsic component of membrane (GO:0031224)	metal ion binding (GO:0046872)|protein-glutamine gamma-glutamyltransferase activity (GO:0003810)	p.R307W(1)		breast(1)|central_nervous_system(3)|endometrium(3)|kidney(1)|large_intestine(5)|lung(7)|ovary(2)|prostate(2)	24				GBM - Glioblastoma multiforme(265;0.0186)	L-Glutamine(DB00130)	ATCCCCCGCCGGTCCAGGATG	0.602													G|||	2	0.000399361	0.0	0.0	5008	,	,		12687	0.001		0.001	False		,,,				2504	0.0				p.R307W												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C919T	14	GRCh37	CM012196|CM065480	TGM1	M	rs121918731	.						49.0	38.0	42.0					14																	24728975		2203	4300	6503	23798815	SO:0001583	missense	7051	exon6			D90287	CCDS9622.1	14q11.2	2013-05-02	2013-05-02		ENSG00000092295	ENSG00000092295	2.3.2.13	"""Transglutaminases"""	11777	protein-coding gene	gene with protein product	"""K polypeptide epidermal type I, protein-glutamine-gamma-glutamyltransferase"""	190195	"""transglutaminase 1 (K polypeptide epidermal type I, protein-glutamine-gamma-glutamyltransferase)"""	ICR2		11390390	Standard	NM_000359		Approved	TGASE, TGK, LI, LI1	uc001wod.3	P22735	OTTHUMG00000029329	ENST00000206765.6:c.919C>T	14.37:g.24728975G>A	ENSP00000206765:p.Arg307Trp	Somatic		Capture	Illumina HiSeq	Phase_I	23798815	NM_000359	B4DWR7|Q197M4	Missense_Mutation	SNP	ENST00000206765.6	37	CCDS9622.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	G	18.27	3.587495	0.66105	.	.	ENSG00000092295	ENST00000206765	D	0.88741	-2.42	4.9	3.04	0.35103	.	0.279630	0.37761	N	0.001944	D	0.92195	0.7525	M	0.79614	2.46	0.80722	D	1	D	0.89917	1.0	D	0.64687	0.928	D	0.90706	0.4624	10	0.87932	D	0	-26.1583	6.8272	0.23891	0.0817:0.0:0.6006:0.3177	.	307	P22735	TGM1_HUMAN	W	307	ENSP00000206765:R307W	ENSP00000206765:R307W	R	-	1	2	TGM1	23798815	0.635000	0.27199	1.000000	0.80357	0.982000	0.71751	0.889000	0.28282	0.633000	0.30452	-0.314000	0.08810	CGG		0.602	TGM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073160.6	NM_000359	
KHNYN	23351	broad.mit.edu	37	14	24900095	24900095	+	Nonsense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr14:24900095G>A	ENST00000251343.5	+	2	298	c.159G>A	c.(157-159)tgG>tgA	p.W53*	CBLN3_ENST00000267406.6_5'Flank|KHNYN_ENST00000554268.1_5'Flank|KHNYN_ENST00000553935.1_Nonsense_Mutation_p.W53*|KHNYN_ENST00000556842.1_Nonsense_Mutation_p.W53*|CBLN3_ENST00000555436.1_5'UTR			O15037	KHNYN_HUMAN	KH and NYN domain containing	53							RNA binding (GO:0003723)	p.W53*(1)		kidney(1)|large_intestine(3)|liver(1)|lung(12)|ovary(3)|pancreas(1)|prostate(3)	24						CCCACATCTGGCTGCAGCTGG	0.637																																					p.W53X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.G159A	14						.						43.0	42.0	42.0					14																	24900095		2203	4300	6503	23969935	SO:0001587	stop_gained	23351	exon2			AB002321	CCDS32058.1	14q11.2	2010-11-23	2009-10-14	2009-10-14	ENSG00000100441	ENSG00000100441			20166	protein-coding gene	gene with protein product			"""KIAA0323"""	KIAA0323		17114934	Standard	NM_015299		Approved		uc001wph.4	O15037		ENST00000251343.5:c.159G>A	14.37:g.24900095G>A	ENSP00000251343:p.Trp53*	Somatic		Capture	Illumina HiSeq	Phase_I	23969935	NM_015299	Q86TZ6|Q8IUQ2|Q96BA9	Nonsense_Mutation	SNP	ENST00000251343.5	37	CCDS32058.1	.	.	.	.	.	.	.	.	.	.	G	38	7.278549	0.98182	.	.	ENSG00000100441	ENST00000251343;ENST00000556842;ENST00000553935;ENST00000556510	.	.	.	5.34	5.34	0.76211	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	16.5458	0.84445	0.0:0.0:1.0:0.0	.	.	.	.	X	53	.	ENSP00000251343:W53X	W	+	3	0	KHNYN	23969935	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	7.067000	0.76741	2.505000	0.84491	0.549000	0.68633	TGG		0.637	KHNYN-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412928.1		
KHNYN	23351	broad.mit.edu	37	14	24909458	24909458	+	3'UTR	SNP	C	C	T	rs35580864	byFrequency	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr14:24909458C>T	ENST00000251343.5	+	0	5143				SDR39U1_ENST00000553930.1_Missense_Mutation_p.R113H|SDR39U1_ENST00000555561.1_5'UTR|SDR39U1_ENST00000538105.2_Missense_Mutation_p.R156H|SDR39U1_ENST00000399395.3_Missense_Mutation_p.R238H|SDR39U1_ENST00000554698.1_Missense_Mutation_p.R130H|SDR39U1_ENST00000555365.1_Missense_Mutation_p.R71H|SDR39U1_ENST00000399390.1_Missense_Mutation_p.R143H			O15037	KHNYN_HUMAN	KH and NYN domain containing								RNA binding (GO:0003723)	p.R263H(1)		kidney(1)|large_intestine(3)|liver(1)|lung(12)|ovary(3)|pancreas(1)|prostate(3)	24						GAAGGCTCGGCGGCCCAGGGC	0.627													C|||	3	0.000599042	0.0	0.0014	5008	,	,		20788	0.0		0.0	False		,,,				2504	0.002				p.R238H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G713A	14						.	C	,HIS/ARG	1,4131		0,1,2065	41.0	49.0	47.0		,713	3.8	1.0	14	dbSNP_126	47	22,8370		0,22,4174	yes	utr-3,missense	KHNYN,SDR39U1	NM_015299.2,NM_020195.2	,29	0,23,6239	TT,TC,CC		0.2622,0.0242,0.1836	,probably-damaging	,238/294	24909458	23,12501	2066	4196	6262	23979298	SO:0001624	3_prime_UTR_variant	56948	exon6			AB002321	CCDS32058.1	14q11.2	2010-11-23	2009-10-14	2009-10-14	ENSG00000100441	ENSG00000100441			20166	protein-coding gene	gene with protein product			"""KIAA0323"""	KIAA0323		17114934	Standard	NM_015299		Approved		uc001wph.4	O15037		ENST00000251343.5:c.*2967C>T	14.37:g.24909458C>T		Somatic		Capture	Illumina HiSeq	Phase_I	23979298	NM_020195	Q86TZ6|Q8IUQ2|Q96BA9	Missense_Mutation	SNP	ENST00000251343.5	37	CCDS32058.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	12.89|12.89	2.074106|2.074106	0.36566|0.36566	2.42E-4|2.42E-4	0.002622|0.002622	ENSG00000100445|ENSG00000100445	ENST00000556249|ENST00000399395;ENST00000336353;ENST00000399390;ENST00000553930;ENST00000538105;ENST00000554698;ENST00000555365;ENST00000553343;ENST00000555225;ENST00000555355	.|T;T;T;T;T;T;T;T;T	.|0.38240	.|1.81;1.55;1.55;1.53;1.58;1.61;1.58;1.17;1.15	4.71|4.71	3.82|3.82	0.43975|0.43975	.|NAD(P)-binding domain (1);	.|0.112497	.|0.56097	.|N	.|0.000025	T|T	0.49864|0.49864	0.1582|0.1582	H|H	0.95780|0.95780	3.72|3.72	0.48632|0.48632	D|D	0.999686|0.999686	.|P;B;B;B;P	.|0.44578	.|0.495;0.306;0.049;0.094;0.838	.|B;B;B;B;B	.|0.36808	.|0.233;0.058;0.026;0.028;0.21	T|T	0.65726|0.65726	-0.6098|-0.6098	5|10	.|0.72032	.|D	.|0.01	-17.6905|-17.6905	13.7409|13.7409	0.62847|0.62847	0.0:0.915:0.0:0.085|0.0:0.915:0.0:0.085	rs35580864|rs35580864	.|113;238;264;156;130	.|G3V5T1;Q9NRG7-2;Q9NRG7;F6RWC2;Q86TZ5	.|.;.;D39U1_HUMAN;.;.	T|H	161|238;264;143;113;156;130;71;132;71;113	.|ENSP00000382327:R238H;ENSP00000382322:R143H;ENSP00000452499:R113H;ENSP00000446077:R156H;ENSP00000452438:R130H;ENSP00000451903:R71H;ENSP00000452076:R132H;ENSP00000451593:R71H;ENSP00000450946:R113H	.|ENSP00000336854:R264H	A|R	-|-	1|2	0|0	SDR39U1|SDR39U1	23979298|23979298	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.364000|0.364000	0.29643|0.29643	5.464000|5.464000	0.66719|0.66719	0.605000|0.605000	0.29947|0.29947	-1.119000|-1.119000	0.02030|0.02030	GCC|CGC		0.627	KHNYN-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412928.1		
CTSG	1511	broad.mit.edu	37	14	25043500	25043500	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr14:25043500C>T	ENST00000216336.2	-	4	581	c.545G>A	c.(544-546)cGa>cAa	p.R182Q		NM_001911.2	NP_001902.1	P08311	CATG_HUMAN	cathepsin G	182	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				angiotensin maturation (GO:0002003)|cellular protein metabolic process (GO:0044267)|defense response to fungus (GO:0050832)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|immune response (GO:0006955)|negative regulation of growth of symbiont in host (GO:0044130)|neutrophil mediated killing of gram-positive bacterium (GO:0070946)|positive regulation of immune response (GO:0050778)|proteolysis (GO:0006508)|response to lipopolysaccharide (GO:0032496)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|secretory granule (GO:0030141)	heparin binding (GO:0008201)|peptidase activity (GO:0008233)|serine-type endopeptidase activity (GO:0004252)	p.R182Q(1)		autonomic_ganglia(1)|breast(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(12)|ovary(2)|skin(1)|urinary_tract(1)	25				GBM - Glioblastoma multiforme(265;0.0269)		AATCTGCCTTCGGGGGTCGTA	0.622																																					p.R182Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G545A	14						.						73.0	63.0	66.0					14																	25043500		2203	4300	6503	24113340	SO:0001583	missense	1511	exon4			M16117	CCDS9631.1	14q12	2013-02-25			ENSG00000100448	ENSG00000100448		"""Cathepsins"", ""Endogenous ligands"""	2532	protein-coding gene	gene with protein product		116830				2569462	Standard	NM_001911		Approved	CG	uc001wpq.3	P08311	OTTHUMG00000140182	ENST00000216336.2:c.545G>A	14.37:g.25043500C>T	ENSP00000216336:p.Arg182Gln	Somatic		Capture	Illumina HiSeq	Phase_I	24113340	NM_001911	Q6IBJ6|Q9UCA5|Q9UCU6	Missense_Mutation	SNP	ENST00000216336.2	37	CCDS9631.1	.	.	.	.	.	.	.	.	.	.	C	9.567	1.119990	0.20877	.	.	ENSG00000100448	ENST00000216336	D	0.92805	-3.11	5.01	-10.0	0.00425	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	1.320510	0.05630	N	0.581627	T	0.74442	0.3717	N	0.05510	-0.035	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.65142	-0.6240	10	0.15499	T	0.54	.	1.8609	0.03188	0.2112:0.3088:0.3202:0.1597	.	182	P08311	CATG_HUMAN	Q	182	ENSP00000216336:R182Q	ENSP00000216336:R182Q	R	-	2	0	CTSG	24113340	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.698000	0.01908	-1.847000	0.01173	-1.080000	0.02220	CGA		0.622	CTSG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276536.2	NM_001911	
ARHGAP5	394	broad.mit.edu	37	14	32562545	32562545	+	Frame_Shift_Del	DEL	T	T	-			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr14:32562545delT	ENST00000345122.3	+	2	2985	c.2670delT	c.(2668-2670)gatfs	p.D890fs	ARHGAP5_ENST00000396582.2_Intron|ARHGAP5_ENST00000432921.1_Frame_Shift_Del_p.D890fs|ARHGAP5_ENST00000433497.1_Intron|ARHGAP5_ENST00000556611.1_Frame_Shift_Del_p.D890fs|ARHGAP5_ENST00000539826.2_Frame_Shift_Del_p.D890fs	NM_001030055.1	NP_001025226.1	Q13017	RHG05_HUMAN	Rho GTPase activating protein 5	890					cell adhesion (GO:0007155)|GTP catabolic process (GO:0006184)|mammary gland development (GO:0030879)|positive regulation of cell migration (GO:0030335)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of cell size (GO:0008361)|regulation of small GTPase mediated signal transduction (GO:0051056)|Rho protein signal transduction (GO:0007266)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|Rho GTPase activator activity (GO:0005100)|SH2 domain binding (GO:0042169)	p.F892fs*9(2)		NS(2)|breast(10)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(10)|lung(12)|ovary(4)|skin(1)|stomach(1)|urinary_tract(4)	55	Hepatocellular(127;0.0604)|Prostate(35;0.15)|Breast(36;0.186)		LUAD - Lung adenocarcinoma(48;0.00192)|Lung(238;0.00714)|BRCA - Breast invasive adenocarcinoma(188;0.0952)|STAD - Stomach adenocarcinoma(7;0.173)	GBM - Glioblastoma multiforme(265;0.00566)		GCCAAGCAGATTTTTTTGAAA	0.403																																					p.D890fs	NSCLC(9;77 350 3443 29227 41353)											.	.	2	Deletion - Frameshift(2)	large_intestine(2)	c.2670delT	14						.						55.0	53.0	54.0					14																	32562545		2203	4298	6501	31632296	SO:0001589	frameshift_variant	394	exon2			U17032	CCDS32062.1, CCDS45095.1	14q12	2010-02-05						"""Rho GTPase activating proteins"""	675	protein-coding gene	gene with protein product		602680	"""growth factor independent 2"""	GFI2		8537347	Standard	XM_005267635		Approved	RhoGAP5, p190-B, p190BRhoGAP	uc001wrn.3	Q13017		ENST00000345122.3:c.2670delT	14.37:g.32562545delT	ENSP00000371897:p.Asp890fs	Somatic		Capture	Illumina HiSeq	Phase_I	31632296	NM_001030055	A1L375|A1L376|A8KAA1|D3DS89|D3DS90|Q05BE8|Q05BU8|Q59ER0|Q6DHZ3	Frame_Shift_Del	DEL	ENST00000345122.3	37	CCDS32062.1																																																																																				0.403	ARHGAP5-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000409735.1	NM_001030055	
SLC25A21	89874	broad.mit.edu	37	14	37641552	37641552	+	Missense_Mutation	SNP	A	A	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr14:37641552A>T	ENST00000331299.5	-	1	519	c.4T>A	c.(4-6)Tcc>Acc	p.S2T	SLC25A21_ENST00000557611.1_5'Flank|SLC25A21_ENST00000555449.1_Missense_Mutation_p.S2T|SLC25A21-AS1_ENST00000556667.1_5'UTR	NM_030631.3	NP_085134.1	Q9BQT8	ODC_HUMAN	solute carrier family 25 (mitochondrial oxoadipate carrier), member 21	2					cellular nitrogen compound metabolic process (GO:0034641)|lysine catabolic process (GO:0006554)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)		p.S2T(1)		NS(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(2)|pancreas(1)|prostate(1)|skin(1)	9	Esophageal squamous(585;0.164)|Breast(36;0.179)|Hepatocellular(127;0.213)		Lung(8;2.16e-08)|LUAD - Lung adenocarcinoma(9;2.16e-07)|Epithelial(34;0.0112)|all cancers(34;0.0274)|LUSC - Lung squamous cell carcinoma(13;0.149)	GBM - Glioblastoma multiforme(112;0.00204)		GGCTTGGCGGACATCTTCGCC	0.657																																					p.S2T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T4A	14						.						34.0	27.0	29.0					14																	37641552		2202	4298	6500	36711303	SO:0001583	missense	89874	exon1			AJ278148	CCDS9663.1, CCDS55913.1	14q13.3	2014-01-28	2012-03-29		ENSG00000183032	ENSG00000183032		"""Solute carriers"""	14411	protein-coding gene	gene with protein product		607571	"""solute carrier family 25 (mitochondrial oxodicarboxylate carrier), member 21"""			11083877	Standard	NM_030631		Approved	ODC1, ODC	uc001wtz.2	Q9BQT8	OTTHUMG00000140250	ENST00000331299.5:c.4T>A	14.37:g.37641552A>T	ENSP00000329452:p.Ser2Thr	Somatic		Capture	Illumina HiSeq	Phase_I	36711303	NM_001171170	A8K0L0|G3V4L5|Q3MJ99	Missense_Mutation	SNP	ENST00000331299.5	37	CCDS9663.1	.	.	.	.	.	.	.	.	.	.	A	13.27	2.185975	0.38609	.	.	ENSG00000183032	ENST00000555449;ENST00000331299	T;T	0.79247	-1.25;-1.2	3.28	2.12	0.27331	.	0.889908	0.09252	U	0.827766	T	0.60444	0.2269	N	0.17082	0.46	0.20196	N	0.99993	B	0.02656	0.0	B	0.04013	0.001	T	0.48917	-0.8992	10	0.42905	T	0.14	-4.5829	5.1373	0.14941	0.8591:0.0:0.1409:0.0	.	2	Q9BQT8	ODC_HUMAN	T	2	ENSP00000451873:S2T;ENSP00000329452:S2T	ENSP00000329452:S2T	S	-	1	0	SLC25A21	36711303	1.000000	0.71417	0.941000	0.38009	0.421000	0.31385	2.230000	0.42999	0.455000	0.26910	0.455000	0.32223	TCC		0.657	SLC25A21-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000276732.2	NM_030631	
RPL10L	140801	broad.mit.edu	37	14	47120920	47120920	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr14:47120920C>T	ENST00000298283.3	-	1	108	c.20G>A	c.(19-21)cGc>cAc	p.R7H		NM_080746.2	NP_542784.1	Q96L21	RL10L_HUMAN	ribosomal protein L10-like	7					spermatogenesis (GO:0007283)|translation (GO:0006412)	cytosolic large ribosomal subunit (GO:0022625)|membrane (GO:0016020)|nucleus (GO:0005634)|polysome (GO:0005844)	structural constituent of ribosome (GO:0003735)	p.R7H(1)		endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(20)|ovary(1)	27						CCGGTAACAGCGAGCTGGACG	0.537																																					p.R7H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G20A	14						.						70.0	74.0	73.0					14																	47120920		2203	4300	6503	46190670	SO:0001583	missense	140801	exon1			AB063608	CCDS32071.1	14q21.2	2011-09-15			ENSG00000165496	ENSG00000165496		"""L ribosomal proteins"""	17976	protein-coding gene	gene with protein product						19123937	Standard	NM_080746		Approved		uc001wwg.3	Q96L21	OTTHUMG00000157869	ENST00000298283.3:c.20G>A	14.37:g.47120920C>T	ENSP00000298283:p.Arg7His	Somatic		Capture	Illumina HiSeq	Phase_I	46190670	NM_080746	Q8IUD1	Missense_Mutation	SNP	ENST00000298283.3	37	CCDS32071.1	.	.	.	.	.	.	.	.	.	.	C	11.42	1.633653	0.29068	.	.	ENSG00000165496	ENST00000298283	T	0.76578	-1.03	4.32	4.32	0.51571	Ribosomal protein L10e/L16 (2);	0.120651	0.64402	D	0.000020	D	0.84019	0.5380	H	0.96460	3.825	0.51233	D	0.999919	B	0.14805	0.011	B	0.17098	0.017	D	0.84994	0.0896	10	0.72032	D	0.01	-17.2955	12.6152	0.56573	0.0:1.0:0.0:0.0	.	7	Q96L21	RL10L_HUMAN	H	7	ENSP00000298283:R7H	ENSP00000298283:R7H	R	-	2	0	RPL10L	46190670	0.990000	0.36364	0.817000	0.32601	0.112000	0.19704	0.588000	0.23924	2.688000	0.91661	0.655000	0.94253	CGC		0.537	RPL10L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349819.1		
TMX1	81542	broad.mit.edu	37	14	51710663	51710663	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr14:51710663C>T	ENST00000457354.2	+	2	367	c.242C>T	c.(241-243)gCg>gTg	p.A81V	SNORA70_ENST00000364506.1_RNA	NM_030755.4	NP_110382.3	Q9H3N1	TMX1_HUMAN	thioredoxin-related transmembrane protein 1	81	Thioredoxin. {ECO:0000255|PROSITE- ProRule:PRU00691}.				cell redox homeostasis (GO:0045454)|protein folding (GO:0006457)|response to endoplasmic reticulum stress (GO:0034976)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|nucleolus (GO:0005730)	disulfide oxidoreductase activity (GO:0015036)|protein disulfide isomerase activity (GO:0003756)	p.A81V(1)		endometrium(2)|large_intestine(2)|urinary_tract(1)	5						GTTAATATTGCGAAAGTAGAT	0.398																																					p.A81V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C242T	14						.						137.0	132.0	134.0					14																	51710663		1879	4099	5978	50780413	SO:0001583	missense	81542	exon2			AB048246	CCDS41953.1	14q22.1	2011-10-19	2009-02-23	2009-02-23				"""Protein disulfide isomerases"""	15487	protein-coding gene	gene with protein product	"""thioredoxin-related transmembrane protein"", ""protein disulfide isomerase family A, member 11"""	610527	"""thioredoxin domain-containing"", ""thioredoxin domain containing"", ""thioredoxin domain containing 1"""	TXNDC, TXNDC1		11152479	Standard	NM_030755		Approved	TMX, PDIA11	uc001wza.4	Q9H3N1		ENST00000457354.2:c.242C>T	14.37:g.51710663C>T	ENSP00000393316:p.Ala81Val	Somatic		Capture	Illumina HiSeq	Phase_I	50780413	NM_030755	B2R7A4|Q8N487|Q8NBN5|Q9Y4T6	Missense_Mutation	SNP	ENST00000457354.2	37	CCDS41953.1	.	.	.	.	.	.	.	.	.	.	C	21.3	4.125106	0.77436	.	.	ENSG00000139921	ENST00000457354	T	0.42513	0.97	5.73	2.82	0.32997	Thioredoxin domain (1);Thioredoxin-like fold (3);	0.094194	0.64402	D	0.000001	T	0.52322	0.1727	M	0.70595	2.14	0.58432	D	0.999995	D;P	0.54397	0.966;0.94	P;P	0.49953	0.627;0.541	T	0.60105	-0.7328	10	0.72032	D	0.01	-10.2363	15.4677	0.75416	0.0:0.5777:0.4223:0.0	.	81;81	B7Z7R5;Q9H3N1	.;TMX1_HUMAN	V	81	ENSP00000393316:A81V	ENSP00000393316:A81V	A	+	2	0	TMX1	50780413	0.997000	0.39634	1.000000	0.80357	0.994000	0.84299	3.383000	0.52471	0.390000	0.25115	0.655000	0.94253	GCG		0.398	TMX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411206.1	NM_030755	
CNIH1	10175	broad.mit.edu	37	14	54898881	54898881	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr14:54898881C>T	ENST00000216416.4	-	3	311	c.208G>A	c.(208-210)Gca>Aca	p.A70T	CNIH1_ENST00000556113.1_Missense_Mutation_p.A70T|CNIH1_ENST00000395573.4_Missense_Mutation_p.A70T|CNIH1_ENST00000557690.1_Missense_Mutation_p.A86T|CNIH1_ENST00000553660.1_Missense_Mutation_p.A47T	NM_005776.2	NP_005767.1	O95406	CNIH1_HUMAN	cornichon family AMPA receptor auxiliary protein 1	70					immune response (GO:0006955)|intracellular signal transduction (GO:0035556)|signal transduction (GO:0007165)|vesicle-mediated transport (GO:0016192)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)		p.A70T(1)									AGCCACTCTGCTGCACAAAGA	0.378																																					p.A70T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G208A	14						.						49.0	43.0	45.0					14																	54898881		2201	4294	6495	53968631	SO:0001583	missense	10175	exon3			AF031379	CCDS9717.1	14q22.1	2013-08-28	2013-08-28	2013-08-28	ENSG00000100528	ENSG00000100528			19431	protein-coding gene	gene with protein product		611287	"""cornichon homolog (Drosophila)"""	CNIH		10209299	Standard	NM_005776		Approved	TGAM77, CNIL	uc001xat.1	O95406	OTTHUMG00000152335	ENST00000216416.4:c.208G>A	14.37:g.54898881C>T	ENSP00000216416:p.Ala70Thr	Somatic		Capture	Illumina HiSeq	Phase_I	53968631	NM_005776	Q3SYM7	Missense_Mutation	SNP	ENST00000216416.4	37	CCDS9717.1	.	.	.	.	.	.	.	.	.	.	C	15.10	2.734091	0.48939	.	.	ENSG00000100528	ENST00000395573;ENST00000216416;ENST00000553660;ENST00000557690;ENST00000556113	T;T;T;T;T	0.42513	0.97;0.97;0.97;0.97;0.97	6.04	6.04	0.98038	.	0.049230	0.85682	D	0.000000	T	0.41488	0.1161	L	0.29908	0.895	0.80722	D	1	P;B	0.38863	0.65;0.011	P;B	0.45913	0.497;0.023	T	0.15636	-1.0430	10	0.42905	T	0.14	-4.8778	14.7083	0.69208	0.0:0.9314:0.0:0.0686	.	70;70	A8MVW4;O95406	.;CNIH_HUMAN	T	70;70;47;86;70	ENSP00000378940:A70T;ENSP00000216416:A70T;ENSP00000452457:A47T;ENSP00000451852:A86T;ENSP00000451142:A70T	ENSP00000216416:A70T	A	-	1	0	CNIH	53968631	1.000000	0.71417	1.000000	0.80357	0.394000	0.30568	5.708000	0.68377	2.873000	0.98535	0.563000	0.77884	GCA		0.378	CNIH1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000276896.2	NM_005776	
SAMD4A	23034	broad.mit.edu	37	14	55243162	55243162	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr14:55243162A>G	ENST00000554335.1	+	11	2611	c.1948A>G	c.(1948-1950)Aat>Gat	p.N650D	SAMD4A_ENST00000357634.3_Missense_Mutation_p.N649D|SAMD4A_ENST00000392067.3_Missense_Mutation_p.N650D|SAMD4A_ENST00000251091.5_Missense_Mutation_p.N562D|SAMD4A_ENST00000555192.1_Missense_Mutation_p.N241D			Q9UPU9	SMAG1_HUMAN	sterile alpha motif domain containing 4A	650					negative regulation of translation (GO:0017148)|positive regulation of translation (GO:0045727)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|neuron projection (GO:0043005)|synapse (GO:0045202)	poly(A) RNA binding (GO:0044822)|translation repressor activity (GO:0030371)	p.N649D(1)		breast(2)|central_nervous_system(2)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(9)|lung(10)|prostate(1)|skin(1)	29						CGGGGGCAGCAATAGCATGCC	0.597																																					p.N649D												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A1945G	14						.						98.0	110.0	106.0					14																	55243162		2203	4300	6503	54312912	SO:0001583	missense	23034	exon10			AB028976	CCDS32084.1, CCDS55917.1, CCDS55918.1, CCDS32084.2, CCDS55917.2	14q22.2	2013-01-10	2006-01-27	2006-01-27	ENSG00000020577	ENSG00000020577		"""Sterile alpha motif (SAM) domain containing"""	23023	protein-coding gene	gene with protein product	"""smaug homolog (Drosophila)"""	610747	"""sterile alpha motif domain containing 4"""	SAMD4		16221671	Standard	NM_001161577		Approved	KIAA1053, DKFZP434H0350, Smaug, SMG, SMGA, hSmaug1	uc001xbb.4	Q9UPU9	OTTHUMG00000170999	ENST00000554335.1:c.1948A>G	14.37:g.55243162A>G	ENSP00000452535:p.Asn650Asp	Somatic		Capture	Illumina HiSeq	Phase_I	54312912	NM_015589	A8MPZ5|Q0VA96|Q6PEW4	Missense_Mutation	SNP	ENST00000554335.1	37	CCDS32084.2	.	.	.	.	.	.	.	.	.	.	A	28.6	4.933919	0.92458	.	.	ENSG00000020577	ENST00000554335;ENST00000392067;ENST00000305831;ENST00000251091;ENST00000357634;ENST00000555192	.	.	.	5.41	5.41	0.78517	.	0.053280	0.64402	D	0.000001	T	0.76478	0.3993	M	0.64997	1.995	0.48087	D	0.999588	D;D;D	0.64830	0.971;0.994;0.988	P;D;P	0.73380	0.784;0.98;0.829	T	0.78617	-0.2134	9	0.62326	D	0.03	-13.7177	15.4533	0.75294	1.0:0.0:0.0:0.0	.	241;562;650	G3V2R1;Q9UPU9-3;Q9UPU9	.;.;SMAG1_HUMAN	D	650;650;562;561;649;241	.	ENSP00000251091:N279D	N	+	1	0	SAMD4A	54312912	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	8.962000	0.93254	2.035000	0.60131	0.533000	0.62120	AAT		0.597	SAMD4A-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000411186.1	NM_015589	
WDHD1	11169	broad.mit.edu	37	14	55429791	55429791	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr14:55429791G>A	ENST00000360586.3	-	19	2475	c.2410C>T	c.(2410-2412)Cgg>Tgg	p.R804W	WDHD1_ENST00000420358.2_Missense_Mutation_p.R681W|WDHD1_ENST00000421192.1_Missense_Mutation_p.R681W|WDHD1_ENST00000359167.4_Missense_Mutation_p.R322W	NM_007086.3	NP_009017.1	O75717	WDHD1_HUMAN	WD repeat and HMG-box DNA binding protein 1	804					heterochromatin maintenance (GO:0070829)|regulation of chromosome organization (GO:0033044)|RNA processing (GO:0006396)	chromosome, centromeric region (GO:0000775)|cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|RNA binding (GO:0003723)	p.R804W(1)		breast(3)|endometrium(4)|kidney(3)|large_intestine(9)|lung(13)|ovary(1)|pancreas(1)|prostate(2)|skin(4)|urinary_tract(2)	42						ATTAATTTCCGAGAGCGAGAA	0.418																																					p.R804W												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C2410T	14						.						63.0	63.0	63.0					14																	55429791		2203	4300	6503	54499541	SO:0001583	missense	11169	exon19			AJ006266	CCDS9721.1, CCDS41955.1	14q22.2	2013-01-09			ENSG00000198554	ENSG00000198554		"""WD repeat domain containing"""	23170	protein-coding gene	gene with protein product	"""CTF4, chromosome transmission fidelity factor 4 homolog (S. cerevisiae)"""	608126				9175701, 20028748	Standard	NM_007086		Approved	AND-1, CTF4, CHTF4	uc001xbm.2	O75717	OTTHUMG00000140304	ENST00000360586.3:c.2410C>T	14.37:g.55429791G>A	ENSP00000353793:p.Arg804Trp	Somatic		Capture	Illumina HiSeq	Phase_I	54499541	NM_007086	C9JW18|F6W0U7	Missense_Mutation	SNP	ENST00000360586.3	37	CCDS9721.1	.	.	.	.	.	.	.	.	.	.	G	17.98	3.521049	0.64747	.	.	ENSG00000198554	ENST00000360586;ENST00000359167;ENST00000421192	T;T;T	0.65916	0.19;0.67;-0.18	5.26	4.27	0.50696	.	0.059556	0.64402	D	0.000011	T	0.78559	0.4302	M	0.77820	2.39	0.53005	D	0.999964	D;D	0.89917	1.0;1.0	D;D	0.85130	0.997;0.993	T	0.81335	-0.0979	10	0.66056	D	0.02	.	14.6931	0.69101	0.0:0.0:0.7596:0.2403	.	322;804	F8W7P7;O75717	.;WDHD1_HUMAN	W	804;322;681	ENSP00000353793:R804W;ENSP00000352085:R322W;ENSP00000391049:R681W	ENSP00000352085:R322W	R	-	1	2	WDHD1	54499541	1.000000	0.71417	1.000000	0.80357	0.904000	0.53231	2.256000	0.43231	2.466000	0.83321	0.462000	0.41574	CGG		0.418	WDHD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276897.2	NM_007086	
KTN1	3895	broad.mit.edu	37	14	56128268	56128268	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr14:56128268G>A	ENST00000395314.3	+	32	3096	c.3028G>A	c.(3028-3030)Ggt>Agt	p.G1010S	KTN1_ENST00000395311.1_Missense_Mutation_p.G987S|KTN1_ENST00000413890.2_Missense_Mutation_p.G987S|KTN1_ENST00000395308.1_Missense_Mutation_p.G987S|KTN1_ENST00000438792.2_Missense_Mutation_p.G1010S|KTN1_ENST00000416613.1_Missense_Mutation_p.G1010S|KTN1_ENST00000395309.3_Missense_Mutation_p.G1010S|KTN1_ENST00000554507.1_Missense_Mutation_p.G305S|KTN1_ENST00000555573.1_Missense_Mutation_p.G15S	NM_001079521.1	NP_001072989.1	Q86UP2	KTN1_HUMAN	kinectin 1 (kinesin receptor)	1010					microtubule-based movement (GO:0007018)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)	p.G1010S(2)		breast(4)|central_nervous_system(1)|large_intestine(8)|lung(1)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)	19						AGAAATAAGTGGTCTCTGGAA	0.328			T	RET	papillary thryoid																																p.G1010S			Dom	yes		14	14q22.1	3895	kinectin 1 (kinesin receptor)		E	.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G3028A	14						.						98.0	106.0	104.0					14																	56128268		2203	4296	6499	55198021	SO:0001583	missense	3895	exon32				CCDS41957.1, CCDS41958.1, CCDS41959.1	14q22.1	2008-05-02			ENSG00000126777	ENSG00000126777			6467	protein-coding gene	gene with protein product		600381				9605849	Standard	NM_001079521		Approved	KIAA0004, CG1	uc001xcc.3	Q86UP2	OTTHUMG00000140312	ENST00000395314.3:c.3028G>A	14.37:g.56128268G>A	ENSP00000378725:p.Gly1010Ser	Somatic		Capture	Illumina HiSeq	Phase_I	55198021	NM_004986	B4DZ88|Q13999|Q14707|Q15387|Q17RZ5|Q5GGW3|Q86W57	Missense_Mutation	SNP	ENST00000395314.3	37	CCDS41957.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	9.715|9.715	1.158046|1.158046	0.21454|0.21454	.|.	.|.	ENSG00000126777|ENSG00000126777	ENST00000413890;ENST00000395309;ENST00000438792;ENST00000395314;ENST00000395308;ENST00000395311;ENST00000416613;ENST00000554507;ENST00000555573|ENST00000554570	T;T;T;T;T;T;T;T;T|.	0.39787|.	1.71;1.7;1.66;1.7;1.71;1.71;1.7;1.06;1.1|.	5.84|5.84	2.97|2.97	0.34412|0.34412	.|.	0.537282|.	0.18323|.	N|.	0.144722|.	T|.	0.15825|.	0.0381|.	N|N	0.04508|0.04508	-0.205|-0.205	0.09310|0.09310	N|N	0.999997|0.999997	B;B;B;B;B;B|.	0.32918|.	0.004;0.004;0.031;0.39;0.002;0.004|.	B;B;B;B;B;B|.	0.35510|.	0.009;0.017;0.023;0.204;0.023;0.034|.	T|.	0.24693|.	-1.0153|.	10|.	0.13108|.	T|.	0.6|.	0.4548|0.4548	7.2024|7.2024	0.25889|0.25889	0.1189:0.0:0.619:0.2621|0.1189:0.0:0.619:0.2621	.|.	15;1010;305;1010;987;1010|.	B7Z6P3;B4DZ88;G3V4Y7;Q86UP2-2;Q17RZ5;Q86UP2|.	.;.;.;.;.;KTN1_HUMAN|.	S|X	987;1010;1010;1010;987;987;1010;305;15|56	ENSP00000394992:G987S;ENSP00000378720:G1010S;ENSP00000391964:G1010S;ENSP00000378725:G1010S;ENSP00000378719:G987S;ENSP00000378722:G987S;ENSP00000388807:G1010S;ENSP00000452073:G305S;ENSP00000451698:G15S|.	ENSP00000378719:G987S|.	G|W	+|+	1|2	0|0	KTN1|KTN1	55198021|55198021	0.251000|0.251000	0.23961|0.23961	0.920000|0.920000	0.36463|0.36463	0.967000|0.967000	0.64934|0.64934	0.552000|0.552000	0.23376|0.23376	0.767000|0.767000	0.33267|0.33267	0.484000|0.484000	0.47621|0.47621	GGT|TGG		0.328	KTN1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000276912.2		
SLC35F4	341880	broad.mit.edu	37	14	58056152	58056152	+	Silent	SNP	G	G	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr14:58056152G>T	ENST00000339762.6	-	3	476	c.477C>A	c.(475-477)tcC>tcA	p.S159S	SLC35F4_ENST00000554729.1_5'UTR|SLC35F4_ENST00000556826.1_Silent_p.S123S			A4IF30	S35F4_HUMAN	solute carrier family 35, member F4	159					transport (GO:0006810)	integral component of membrane (GO:0016021)		p.S159S(1)		breast(1)|endometrium(4)|large_intestine(3)|lung(12)|ovary(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	24						TCAGAACCATGGACGTGCAGG	0.448																																					p.S159S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C477A	14						.						63.0	66.0	65.0					14																	58056152		2019	4193	6212	57125905	SO:0001819	synonymous_variant	341880	exon3					14q22.3	2013-05-22		2003-11-28	ENSG00000151812	ENSG00000151812		"""Solute carriers"""	19845	protein-coding gene	gene with protein product			"""chromosome 14 open reading frame 36"""	C14orf36			Standard	NM_001206920		Approved	FLJ37712	uc021rtp.1	A4IF30	OTTHUMG00000171317	ENST00000339762.6:c.477C>A	14.37:g.58056152G>T		Somatic		Capture	Illumina HiSeq	Phase_I	57125905	NM_001080455	A6NDQ3	Silent	SNP	ENST00000339762.6	37																																																																																					0.448	SLC35F4-201	KNOWN	basic	protein_coding	protein_coding		XM_292260	
ARID4A	5926	broad.mit.edu	37	14	58831166	58831166	+	Missense_Mutation	SNP	G	G	A	rs148135007		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr14:58831166G>A	ENST00000355431.3	+	20	2732	c.2359G>A	c.(2359-2361)Gaa>Aaa	p.E787K	ARID4A_ENST00000395168.3_Missense_Mutation_p.E787K|ARID4A_ENST00000431317.2_Missense_Mutation_p.E787K|ARID4A_ENST00000348476.3_Missense_Mutation_p.E787K	NM_002892.3	NP_002883.3	P29374	ARI4A_HUMAN	AT rich interactive domain 4A (RBP1-like)	787					erythrocyte development (GO:0048821)|histone H3-K4 trimethylation (GO:0080182)|histone H3-K9 trimethylation (GO:0036124)|histone H4-K20 trimethylation (GO:0034773)|negative regulation of transcription, DNA-templated (GO:0045892)|regulation of gene expression by genetic imprinting (GO:0006349)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.E787K(1)		NS(1)|breast(2)|central_nervous_system(1)|cervix(4)|endometrium(8)|kidney(2)|large_intestine(14)|lung(19)|ovary(3)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	60						GAAAGAAGCCGAAAAATCTCC	0.348																																					p.E787K												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2359A	14						.	G	LYS/GLU,LYS/GLU,LYS/GLU	0,4406		0,0,2203	36.0	41.0	39.0		2359,2359,2359	5.9	1.0	14	dbSNP_134	39	1,8591		0,1,4295	no	missense,missense,missense	ARID4A	NM_002892.3,NM_023000.2,NM_023001.2	56,56,56	0,1,6498	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging,probably-damaging,probably-damaging	787/1258,787/1204,787/1189	58831166	1,12997	2203	4296	6499	57900919	SO:0001583	missense	5926	exon20			S57153	CCDS9732.1, CCDS9733.1, CCDS45114.1	14q22.3	2013-02-07	2004-01-28	2004-01-28	ENSG00000032219	ENSG00000032219		"""-"""	9885	protein-coding gene	gene with protein product		180201	"""retinoblastoma-binding protein 1"""	RBBP1		1857421, 8455946	Standard	NM_023000		Approved	RBP1, RBP-1	uc001xdp.3	P29374	OTTHUMG00000140320	ENST00000355431.3:c.2359G>A	14.37:g.58831166G>A	ENSP00000347602:p.Glu787Lys	Somatic		Capture	Illumina HiSeq	Phase_I	57900919	NM_023000	Q15991|Q15992|Q15993	Missense_Mutation	SNP	ENST00000355431.3	37	CCDS9732.1	.	.	.	.	.	.	.	.	.	.	G	24.8	4.574929	0.86542	0.0	1.16E-4	ENSG00000032219	ENST00000355431;ENST00000348476;ENST00000395168;ENST00000431317;ENST00000417477	T;T;T;T;T	0.20069	2.33;2.31;2.28;2.31;2.1	5.9	5.9	0.94986	.	0.297142	0.36200	N	0.002728	T	0.37732	0.1014	L	0.32530	0.975	0.49483	D	0.999798	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.79108	0.992;0.986;0.992	T	0.01375	-1.1371	10	0.28530	T	0.3	-26.5688	20.2787	0.98501	0.0:0.0:1.0:0.0	.	787;787;787	P29374-3;P29374;P29374-2	.;ARI4A_HUMAN;.	K	787;787;787;787;465	ENSP00000347602:E787K;ENSP00000344556:E787K;ENSP00000378597:E787K;ENSP00000397368:E787K;ENSP00000416053:E465K	ENSP00000344556:E787K	E	+	1	0	ARID4A	57900919	1.000000	0.71417	0.954000	0.39281	0.883000	0.51084	7.138000	0.77305	2.798000	0.96311	0.650000	0.86243	GAA		0.348	ARID4A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276927.2	NM_023001	
SIX4	51804	broad.mit.edu	37	14	61186499	61186499	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr14:61186499C>T	ENST00000216513.4	-	2	1587	c.1528G>A	c.(1528-1530)Gtg>Atg	p.V510M		NM_017420.4	NP_059116.3	Q9UIU6	SIX4_HUMAN	SIX homeobox 4	510					anatomical structure morphogenesis (GO:0009653)|embryonic cranial skeleton morphogenesis (GO:0048701)|generation of neurons (GO:0048699)|inner ear morphogenesis (GO:0042472)|metanephric mesenchyme development (GO:0072075)|myoblast migration (GO:0051451)|negative regulation of neuron apoptotic process (GO:0043524)|positive regulation of branching involved in ureteric bud morphogenesis (GO:0090190)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of ureteric bud formation (GO:0072107)|regulation of branch elongation involved in ureteric bud branching (GO:0072095)|regulation of protein localization (GO:0032880)|regulation of synaptic growth at neuromuscular junction (GO:0008582)|skeletal muscle tissue development (GO:0007519)|thymus development (GO:0048538)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.V510M(1)		breast(5)|endometrium(1)|large_intestine(11)|liver(1)|lung(7)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	28				OV - Ovarian serous cystadenocarcinoma(108;0.0275)		GCCACTGACACAGGGGGCAGC	0.478																																					p.V510M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1528A	14						.						73.0	74.0	74.0					14																	61186499		2203	4300	6503	60256252	SO:0001583	missense	51804	exon2			AB024687	CCDS9749.2	14q23.1	2012-10-02	2007-07-13		ENSG00000100625	ENSG00000100625		"""Homeoboxes / SINE class"""	10890	protein-coding gene	gene with protein product		606342	"""sine oculis homeobox (Drosophila) homolog 4"", ""sine oculis homeobox homolog 4 (Drosophila)"""			10512683, 10640827	Standard	NM_017420		Approved	AREC3	uc001xfc.3	Q9UIU6	OTTHUMG00000028996	ENST00000216513.4:c.1528G>A	14.37:g.61186499C>T	ENSP00000216513:p.Val510Met	Somatic		Capture	Illumina HiSeq	Phase_I	60256252	NM_017420	Q4QQH5|Q4V764	Missense_Mutation	SNP	ENST00000216513.4	37	CCDS9749.2	.	.	.	.	.	.	.	.	.	.	C	15.85	2.953800	0.53293	.	.	ENSG00000100625	ENST00000216513;ENST00000554079;ENST00000556952	D;T	0.92299	-3.01;0.5	5.63	5.63	0.86233	.	0.247748	0.28203	N	0.016202	D	0.91068	0.7189	N	0.19112	0.55	0.41431	D	0.987862	P;D	0.53885	0.892;0.963	P;P	0.52957	0.714;0.647	D	0.92346	0.5885	10	0.66056	D	0.02	.	19.6805	0.95960	0.0:1.0:0.0:0.0	.	502;510	G3V2N2;Q9UIU6	.;SIX4_HUMAN	M	510;183;502	ENSP00000216513:V510M;ENSP00000451537:V183M	ENSP00000216513:V510M	V	-	1	0	SIX4	60256252	1.000000	0.71417	1.000000	0.80357	0.334000	0.28698	6.914000	0.75764	2.670000	0.90874	0.655000	0.94253	GTG		0.478	SIX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000072397.2		
SYT16	83851	broad.mit.edu	37	14	62547885	62547885	+	Missense_Mutation	SNP	A	A	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr14:62547885A>T	ENST00000430451.2	+	4	1524	c.1327A>T	c.(1327-1329)Atg>Ttg	p.M443L	RP11-355I22.5_ENST00000553990.1_lincRNA	NM_031914.2	NP_114120.2	Q17RD7	SYT16_HUMAN	synaptotagmin XVI	443	C2 1. {ECO:0000255|PROSITE- ProRule:PRU00041}.				exocytosis (GO:0006887)			p.M423L(1)		central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(11)|lung(12)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	35				OV - Ovarian serous cystadenocarcinoma(108;0.0438)|BRCA - Breast invasive adenocarcinoma(234;0.118)		TGCCCGGAAGATGACCCGAGA	0.557																																					p.M443L												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A1327T	14						.						33.0	36.0	35.0					14																	62547885		2177	4288	6465	61617638	SO:0001583	missense	83851	exon4			BC040924	CCDS45121.1	14q23.2	2014-07-02	2005-07-15	2005-07-15	ENSG00000139973	ENSG00000139973		"""Synaptotagmins"""	23142	protein-coding gene	gene with protein product	"""synaptotagmin XIV-related"", "" chr14 synaptotagmin"""	610950	"""synaptotagmin XIV-like"""	SYT14L		11543631	Standard	NM_031914		Approved	yt14r, CHR14SYT, Strep14	uc001xfu.1	Q17RD7	OTTHUMG00000171106	ENST00000430451.2:c.1327A>T	14.37:g.62547885A>T	ENSP00000394700:p.Met443Leu	Somatic		Capture	Illumina HiSeq	Phase_I	61617638	NM_031914	B4DZH2|B7ZL60|C9J8I3|Q707N2|Q7Z441|Q8IUU0|Q9BQR8	Missense_Mutation	SNP	ENST00000430451.2	37	CCDS45121.1	.	.	.	.	.	.	.	.	.	.	A	14.63	2.592311	0.46214	.	.	ENSG00000139973	ENST00000430451	T	0.76709	-1.04	4.97	3.84	0.44239	C2 membrane targeting protein (1);C2 calcium-dependent membrane targeting (2);C2 calcium/lipid-binding domain, CaLB (1);	0.132396	0.64402	D	0.000002	T	0.64316	0.2587	N	0.20845	0.615	0.80722	D	1	B	0.32653	0.379	B	0.37091	0.241	T	0.61806	-0.6987	10	0.44086	T	0.13	-28.3543	8.5463	0.33424	0.8301:0.0:0.1699:0.0	.	443	Q17RD7	SYT16_HUMAN	L	443	ENSP00000394700:M443L	ENSP00000394700:M443L	M	+	1	0	SYT16	61617638	1.000000	0.71417	0.994000	0.49952	0.858000	0.48976	3.625000	0.54238	1.032000	0.39892	0.533000	0.62120	ATG		0.557	SYT16-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000411700.1	NM_031914	
KCNH5	27133	broad.mit.edu	37	14	63316475	63316475	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr14:63316475G>A	ENST00000322893.7	-	8	1733	c.1465C>T	c.(1465-1467)Cgg>Tgg	p.R489W	KCNH5_ENST00000420622.2_Missense_Mutation_p.R489W|KCNH5_ENST00000394968.1_Missense_Mutation_p.R431W	NM_139318.3	NP_647479.2	Q8NCM2	KCNH5_HUMAN	potassium voltage-gated channel, subfamily H (eag-related), member 5	489					potassium ion transmembrane transport (GO:0071805)|regulation of G2/M transition of mitotic cell cycle (GO:0010389)|regulation of membrane potential (GO:0042391)|synaptic transmission (GO:0007268)	cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)|plasma membrane (GO:0005886)	phosphorelay sensor kinase activity (GO:0000155)|voltage-gated potassium channel activity (GO:0005249)	p.R489W(1)		NS(1)|biliary_tract(1)|breast(3)|central_nervous_system(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(22)|lung(33)|ovary(5)|prostate(2)|skin(17)|upper_aerodigestive_tract(4)|urinary_tract(2)	99				OV - Ovarian serous cystadenocarcinoma(108;0.00958)|BRCA - Breast invasive adenocarcinoma(234;0.168)		AGGAAGTCCCGTACATTATTC	0.393																																					p.R431W												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1291T	14						.						174.0	153.0	160.0					14																	63316475		2203	4299	6502	62386228	SO:0001583	missense	27133	exon8			U69185	CCDS9756.1, CCDS45122.1	14q23.1	2012-07-05			ENSG00000140015	ENSG00000140015		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	6254	protein-coding gene	gene with protein product		605716				9738473, 16382104	Standard	NM_139318		Approved	Kv10.2, H-EAG2, eag2	uc001xfx.3	Q8NCM2	OTTHUMG00000029041	ENST00000322893.7:c.1465C>T	14.37:g.63316475G>A	ENSP00000321427:p.Arg489Trp	Somatic		Capture	Illumina HiSeq	Phase_I	62386228	NM_172376	C9JP98	Missense_Mutation	SNP	ENST00000322893.7	37	CCDS9756.1	.	.	.	.	.	.	.	.	.	.	G	20.5	4.003978	0.74932	.	.	ENSG00000140015	ENST00000322893;ENST00000420622;ENST00000394968	D;D;D	0.96745	-4.11;-4.11;-4.11	5.21	5.21	0.72293	Cyclic nucleotide-binding-like (1);	0.000000	0.85682	D	0.000000	D	0.97967	0.9331	M	0.82630	2.6	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.87578	0.998;0.998;0.998	D	0.98442	1.0587	10	0.87932	D	0	.	13.7089	0.62656	0.0:0.0:0.8359:0.1641	.	431;489;489	Q8NCM2-3;Q8NCM2-2;Q8NCM2	.;.;KCNH5_HUMAN	W	489;489;431	ENSP00000321427:R489W;ENSP00000395439:R489W;ENSP00000378419:R431W	ENSP00000321427:R489W	R	-	1	2	KCNH5	62386228	1.000000	0.71417	0.992000	0.48379	0.997000	0.91878	5.099000	0.64554	2.566000	0.86566	0.650000	0.86243	CGG		0.393	KCNH5-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411747.1	NM_139318	
MTHFD1	4522	broad.mit.edu	37	14	64908814	64908814	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr14:64908814G>A	ENST00000545908.1	+	20	2324	c.2095G>A	c.(2095-2097)Gca>Aca	p.A699T	CTD-2555O16.2_ENST00000556640.1_RNA|MTHFD1_ENST00000216605.8_Missense_Mutation_p.A643T|CTD-2555O16.4_ENST00000609125.1_RNA			P11586	C1TC_HUMAN	methylenetetrahydrofolate dehydrogenase (NADP+ dependent) 1, methenyltetrahydrofolate cyclohydrolase, formyltetrahydrofolate synthetase	643	Formyltetrahydrofolate synthetase.				folic acid metabolic process (GO:0046655)|folic acid-containing compound biosynthetic process (GO:0009396)|histidine biosynthetic process (GO:0000105)|methionine biosynthetic process (GO:0009086)|one-carbon metabolic process (GO:0006730)|purine nucleotide biosynthetic process (GO:0006164)|small molecule metabolic process (GO:0044281)|tetrahydrofolate interconversion (GO:0035999)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|formate-tetrahydrofolate ligase activity (GO:0004329)|methenyltetrahydrofolate cyclohydrolase activity (GO:0004477)|methylenetetrahydrofolate dehydrogenase (NADP+) activity (GO:0004488)|methylenetetrahydrofolate dehydrogenase [NAD(P)+] activity (GO:0004486)	p.A643T(1)		endometrium(3)|kidney(2)|large_intestine(8)|lung(10)|ovary(2)|pancreas(1)|prostate(2)|skin(2)	30				OV - Ovarian serous cystadenocarcinoma(108;8.7e-12)|all cancers(60;3.29e-11)|BRCA - Breast invasive adenocarcinoma(234;0.0488)	Tetrahydrofolic acid(DB00116)	TGCCAACATCGCACATGGCAA	0.512																																					p.A643T	Colon(18;220 581 13419 18191 31512)|GBM(126;343 1658 28700 44425 52519)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1927A	14						.						105.0	91.0	96.0					14																	64908814		2203	4300	6503	63978567	SO:0001583	missense	4522	exon20			J04031	CCDS9763.1	14q24	2004-12-13			ENSG00000100714	ENSG00000100714	1.5.1.15, 3.5.4.-		7432	protein-coding gene	gene with protein product		172460		MTHFC, MTHFD		3053686, 2786332	Standard	NM_005956		Approved		uc001xhb.3	P11586	OTTHUMG00000141309	ENST00000545908.1:c.2095G>A	14.37:g.64908814G>A	ENSP00000438588:p.Ala699Thr	Somatic		Capture	Illumina HiSeq	Phase_I	63978567	NM_005956	B2R5Y2|G3V2B8|Q86VC9|Q9BVP5	Missense_Mutation	SNP	ENST00000545908.1	37		.	.	.	.	.	.	.	.	.	.	G	35	5.575722	0.96553	.	.	ENSG00000100714	ENST00000545908;ENST00000555709;ENST00000216605	T;T;T	0.35973	1.28;1.28;1.28	5.87	5.87	0.94306	.	0.000000	0.85682	D	0.000000	T	0.77572	0.4150	H	0.98276	4.19	0.80722	D	1	D;D	0.89917	0.999;1.0	D;D	0.97110	0.969;1.0	D	0.85463	0.1168	10	0.87932	D	0	-20.8084	20.5827	0.99408	0.0:0.0:1.0:0.0	.	699;643	F5H2F4;G3V2B8	.;.	T	699;643;699	ENSP00000438588:A699T;ENSP00000450560:A643T;ENSP00000216605:A699T	ENSP00000216605:A643T	A	+	1	0	MTHFD1	63978567	1.000000	0.71417	0.971000	0.41717	0.770000	0.43624	7.954000	0.87848	2.941000	0.99782	0.655000	0.94253	GCA		0.512	MTHFD1-002	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000412167.1		
ZBTB1	22890	broad.mit.edu	37	14	64989161	64989161	+	Silent	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr14:64989161C>T	ENST00000554015.1	+	4	1370	c.939C>T	c.(937-939)agC>agT	p.S313S	RP11-973N13.4_ENST00000554918.1_RNA|ZBTB1_ENST00000394712.2_Silent_p.S313S|ZBTB1_ENST00000358738.3_Silent_p.S313S			Q9Y2K1	ZBTB1_HUMAN	zinc finger and BTB domain containing 1	313					B cell differentiation (GO:0030183)|innate immune response (GO:0045087)|mRNA transcription from RNA polymerase II promoter (GO:0042789)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of natural killer cell differentiation (GO:0032825)|positive regulation of pro-T cell differentiation (GO:2000176)|positive regulation of T cell differentiation (GO:0045582)|positive regulation of T cell mediated immunity (GO:0002711)|protein homooligomerization (GO:0051260)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)	nuclear body (GO:0016604)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)	p.S313S(1)		kidney(1)|large_intestine(3)|lung(7)|prostate(1)|skin(1)	13		all_lung(585;0.000567)|Myeloproliferative disorder(585;0.0255)|all_neural(303;0.0294)		UCEC - Uterine corpus endometrioid carcinoma (185;0.0182)|all cancers(60;3.78e-43)|OV - Ovarian serous cystadenocarcinoma(108;1.22e-20)|BRCA - Breast invasive adenocarcinoma(234;6.75e-06)|KIRC - Kidney renal clear cell carcinoma(182;0.00269)|STAD - Stomach adenocarcinoma(64;0.012)		AAATAGCAAGCGAAGAGAAAA	0.413																																					p.S313S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C939T	14						.						41.0	45.0	44.0					14																	64989161		2202	4299	6501	64058914	SO:0001819	synonymous_variant	22890	exon2			AB023214	CCDS32097.1, CCDS45126.1	14q23.3	2013-01-09			ENSG00000126804	ENSG00000126804		"""-"", ""BTB/POZ domain containing"", ""Zinc fingers, C2H2-type"""	20259	protein-coding gene	gene with protein product						10231032	Standard	NM_014950		Approved	KIAA0997, ZNF909	uc010aqg.3	Q9Y2K1		ENST00000554015.1:c.939C>T	14.37:g.64989161C>T		Somatic		Capture	Illumina HiSeq	Phase_I	64058914	NM_014950	A8K6S8|Q86SW8	Silent	SNP	ENST00000554015.1	37	CCDS45126.1																																																																																				0.413	ZBTB1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411912.1		
MAX	4149	broad.mit.edu	37	14	65543379	65543379	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr14:65543379G>A	ENST00000358664.4	-	5	428	c.298C>T	c.(298-300)Cgt>Tgt	p.R100C	MAX_ENST00000341653.2_Intron|MAX_ENST00000284165.6_3'UTR|MAX_ENST00000555932.1_Silent_p.S13S|MAX_ENST00000557277.1_Missense_Mutation_p.R37C|MAX_ENST00000555419.1_Missense_Mutation_p.R64C|MAX_ENST00000358402.4_Missense_Mutation_p.R91C	NM_002382.4	NP_002373.3	P61244	MAX_HUMAN	MYC associated factor X	100	Leucine-zipper.				cellular response to peptide hormone stimulus (GO:0071375)|cellular response to starvation (GO:0009267)|negative regulation of gene expression (GO:0010629)|neuron apoptotic process (GO:0051402)|protein complex assembly (GO:0006461)|response to axon injury (GO:0048678)|response to insulin (GO:0032868)|retina development in camera-type eye (GO:0060041)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|MLL1 complex (GO:0071339)|nucleus (GO:0005634)|PML body (GO:0016605)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription cofactor activity (GO:0003712)	p.R100C(1)		breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(1)|lung(3)|prostate(1)|skin(1)	17				all cancers(60;0.000776)|OV - Ovarian serous cystadenocarcinoma(108;0.00359)|BRCA - Breast invasive adenocarcinoma(234;0.00999)		TCCAGTGCACGGACTAAAAGG	0.562																																					p.R91C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C271T	14						.						149.0	131.0	137.0					14																	65543379		2203	4300	6503	64613132	SO:0001583	missense	4149	exon4				CCDS9770.1, CCDS9771.1, CCDS9772.1, CCDS9774.1, CCDS41965.1	14q23	2014-09-17	2005-02-08		ENSG00000125952	ENSG00000125952		"""Basic helix-loop-helix proteins"""	6913	protein-coding gene	gene with protein product		154950	"""MAX protein"""			1557420	Standard	NM_002382		Approved	bHLHd4, bHLHd5, bHLHd6, bHLHd7, bHLHd8	uc001xif.2	P61244	OTTHUMG00000142809	ENST00000358664.4:c.298C>T	14.37:g.65543379G>A	ENSP00000351490:p.Arg100Cys	Somatic		Capture	Illumina HiSeq	Phase_I	64613132	NM_145112	A6NH73|A8K265|A8K4G4|A8K824|P25912|P52163|Q14803|Q96CY8	Missense_Mutation	SNP	ENST00000358664.4	37	CCDS9771.1	.	.	.	.	.	.	.	.	.	.	G	16.60	3.169150	0.57584	.	.	ENSG00000125952	ENST00000358402;ENST00000358664;ENST00000555419;ENST00000557277;ENST00000556892	D;D;D;D;D	0.98437	-4.93;-4.93;-4.04;-2.49;-3.36	5.93	5.93	0.95920	Helix-loop-helix DNA-binding (1);	0.212377	0.51477	D	0.000094	D	0.98836	0.9607	M	0.76170	2.325	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.71870	0.975;0.943	D	0.99843	1.1063	10	0.87932	D	0	-16.2702	19.121	0.93364	0.0:0.0:1.0:0.0	.	91;100	P61244-2;P61244	.;MAX_HUMAN	C	91;100;64;37;27	ENSP00000351175:R91C;ENSP00000351490:R100C;ENSP00000452405:R64C;ENSP00000450955:R37C;ENSP00000452206:R27C	ENSP00000351175:R91C	R	-	1	0	MAX	64613132	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	9.627000	0.98412	2.814000	0.96858	0.591000	0.81541	CGT		0.562	MAX-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286386.1	NM_197957	
GPHN	10243	broad.mit.edu	37	14	67346679	67346679	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr14:67346679G>A	ENST00000315266.5	+	5	1438	c.317G>A	c.(316-318)cGg>cAg	p.R106Q	GPHN_ENST00000478722.1_Missense_Mutation_p.R106Q|GPHN_ENST00000544752.2_3'UTR|GPHN_ENST00000305960.9_Missense_Mutation_p.R75Q|GPHN_ENST00000459628.1_Missense_Mutation_p.R88Q|GPHN_ENST00000543237.1_Missense_Mutation_p.R119Q	NM_001024218.1	NP_001019389.1	Q9NQX3	GEPH_HUMAN	gephyrin	106	MPT Mo-transferase.				establishment of synaptic specificity at neuromuscular junction (GO:0007529)|glycine receptor clustering (GO:0072579)|Mo-molybdopterin cofactor biosynthetic process (GO:0006777)|molybdopterin cofactor biosynthetic process (GO:0032324)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|inhibitory synapse (GO:0060077)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|molybdopterin adenylyltransferase activity (GO:0061598)|molybdopterin molybdotransferase activity (GO:0061599)|transferase activity (GO:0016740)	p.R106Q(1)		large_intestine(8)|liver(1)|ovary(2)|stomach(1)	12		all_cancers(7;0.0476)|all_hematologic(31;0.0116)		Epithelial(1;1.73e-08)|all cancers(60;3.15e-07)|OV - Ovarian serous cystadenocarcinoma(108;0.000275)|BRCA - Breast invasive adenocarcinoma(234;0.00323)|Colorectal(3;0.0938)|KIRC - Kidney renal clear cell carcinoma(182;0.184)		GTAATAGAACGGGAAGCACCA	0.413			T	MLL	AL																																p.R106Q			Dom	yes		14	14q24	10243	gephyrin (GPH)		L	.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G317A	14						.						90.0	84.0	86.0					14																	67346679		2203	4300	6503	66416432	SO:0001583	missense	10243	exon5			AB037806	CCDS9777.1, CCDS32103.1	14q23.3	2008-04-22			ENSG00000171723	ENSG00000171723			15465	protein-coding gene	gene with protein product		603930				1319186, 10325225, 18403029	Standard	XM_005267250		Approved	KIAA1385	uc001xix.3	Q9NQX3	OTTHUMG00000029785	ENST00000315266.5:c.317G>A	14.37:g.67346679G>A	ENSP00000312771:p.Arg106Gln	Somatic		Capture	Illumina HiSeq	Phase_I	66416432	NM_001024218	Q9H4E9|Q9P2G2	Missense_Mutation	SNP	ENST00000315266.5	37	CCDS32103.1	.	.	.	.	.	.	.	.	.	.	G	36	5.932489	0.97116	.	.	ENSG00000171723	ENST00000315266;ENST00000478722;ENST00000459628;ENST00000543237;ENST00000305960;ENST00000555456	T;T;T;T;T;T	0.77620	-1.11;-1.11;-1.11;-1.11;-1.11;-1.11	4.93	4.93	0.64822	Molybdenum cofactor synthesis (1);Molybdopterin binding (4);	0.000000	0.85682	D	0.000000	D	0.88731	0.6516	M	0.81497	2.545	0.80722	D	1	D;D;D;D;D	0.89917	0.997;1.0;1.0;0.993;0.999	D;D;D;P;P	0.81914	0.964;0.995;0.99;0.523;0.851	D	0.90204	0.4259	10	0.72032	D	0.01	-4.4638	18.4954	0.90863	0.0:0.0:1.0:0.0	.	75;119;106;106;88	F8W7D6;F5H039;Q9NQX3;Q9NQX3-2;G3V582	.;.;GEPH_HUMAN;.;.	Q	106;106;88;119;75;39	ENSP00000312771:R106Q;ENSP00000417901:R106Q;ENSP00000452220:R88Q;ENSP00000438404:R119Q;ENSP00000303019:R75Q;ENSP00000450706:R39Q	ENSP00000303019:R75Q	R	+	2	0	GPHN	66416432	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.706000	0.98722	2.440000	0.82611	0.655000	0.94253	CGG		0.413	GPHN-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000074299.2	NM_020806	
ARG2	384	broad.mit.edu	37	14	68086765	68086765	+	Missense_Mutation	SNP	A	A	C			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr14:68086765A>C	ENST00000261783.3	+	1	251	c.71A>C	c.(70-72)cAc>cCc	p.H24P	Y_RNA_ENST00000364659.1_RNA|ARG2_ENST00000556491.1_3'UTR	NM_001172.3	NP_001163.1	P78540	ARGI2_HUMAN	arginase 2	24					arginine metabolic process (GO:0006525)|cellular nitrogen compound metabolic process (GO:0034641)|nitric oxide biosynthetic process (GO:0006809)|small molecule metabolic process (GO:0044281)|striated muscle contraction (GO:0006941)|urea cycle (GO:0000050)|ureteric bud development (GO:0001657)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	arginase activity (GO:0004053)|metal ion binding (GO:0046872)	p.H24P(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(5)|ovary(1)|prostate(1)	11				all cancers(60;0.000582)|OV - Ovarian serous cystadenocarcinoma(108;0.00392)|BRCA - Breast invasive adenocarcinoma(234;0.00928)	L-Arginine(DB00125)|L-Ornithine(DB00129)	AAATCCGTCCACTCCGTGGCT	0.607																																					p.H24P												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A71C	14						.						31.0	31.0	31.0					14																	68086765		2202	4300	6502	67156518	SO:0001583	missense	384	exon1			D86724	CCDS9785.1	14q24.1	2013-05-01	2013-05-01			ENSG00000081181			664	protein-coding gene	gene with protein product		107830	"""arginase, type II"""			8954792, 8898077	Standard	NM_001172		Approved		uc001xjs.3	P78540		ENST00000261783.3:c.71A>C	14.37:g.68086765A>C	ENSP00000261783:p.His24Pro	Somatic		Capture	Illumina HiSeq	Phase_I	67156518	NM_001172	B2R690|Q6FHY8	Missense_Mutation	SNP	ENST00000261783.3	37	CCDS9785.1	.	.	.	.	.	.	.	.	.	.	A	8.677	0.904106	0.17760	.	.	ENSG00000081181	ENST00000261783	D	0.85773	-2.03	4.48	2.01	0.26516	.	0.231013	0.44902	N	0.000415	T	0.80607	0.4655	L	0.56769	1.78	0.47441	D	0.99942	B	0.10296	0.003	B	0.15870	0.014	T	0.73404	-0.3993	10	0.56958	D	0.05	.	9.3788	0.38299	0.6511:0.3489:0.0:0.0	.	24	P78540	ARGI2_HUMAN	P	24	ENSP00000261783:H24P	ENSP00000261783:H24P	H	+	2	0	ARG2	67156518	1.000000	0.71417	0.972000	0.41901	0.240000	0.25518	4.760000	0.62235	0.223000	0.20920	-0.488000	0.04728	CAC		0.607	ARG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415190.2	NM_001172	
ACTN1	87	broad.mit.edu	37	14	69346681	69346681	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr14:69346681G>A	ENST00000193403.6	-	18	2661	c.2278C>T	c.(2278-2280)Cgg>Tgg	p.R760W	ACTN1_ENST00000394419.4_Missense_Mutation_p.R760W|ACTN1_ENST00000538545.2_Missense_Mutation_p.R760W|ACTN1_ENST00000438964.2_Missense_Mutation_p.R760W|ACTN1_ENST00000376839.3_Missense_Mutation_p.R695W	NM_001102.3	NP_001093.1	P12814	ACTN1_HUMAN	actinin, alpha 1	760	EF-hand 1. {ECO:0000255|PROSITE- ProRule:PRU00448}.				actin crosslink formation (GO:0051764)|actin filament bundle assembly (GO:0051017)|blood coagulation (GO:0007596)|cell junction assembly (GO:0034329)|extracellular matrix organization (GO:0030198)|focal adhesion assembly (GO:0048041)|negative regulation of cellular component movement (GO:0051271)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of apoptotic process (GO:0042981)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|platelet alpha granule lumen (GO:0031093)|pseudopodium (GO:0031143)|Z disc (GO:0030018)	calcium ion binding (GO:0005509)|double-stranded RNA binding (GO:0003725)|integrin binding (GO:0005178)|ion channel binding (GO:0044325)|vinculin binding (GO:0017166)	p.R760W(1)		breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(5)|lung(9)|prostate(2)|urinary_tract(1)	27				BRCA - Breast invasive adenocarcinoma(234;0.00605)|all cancers(60;0.00846)|OV - Ovarian serous cystadenocarcinoma(108;0.0654)		GCTCTCACCCGGTCAAAGTGG	0.612																																					p.R760W												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C2278T	14						.						76.0	71.0	73.0					14																	69346681		2203	4300	6503	68416434	SO:0001583	missense	87	exon18			M95178	CCDS9792.1, CCDS45129.1, CCDS45130.1	14q24.1	2014-08-08			ENSG00000072110	ENSG00000072110		"""EF-hand domain containing"""	163	protein-coding gene	gene with protein product		102575				2349951	Standard	NM_001102		Approved		uc001xkm.3	P12814	OTTHUMG00000171386	ENST00000193403.6:c.2278C>T	14.37:g.69346681G>A	ENSP00000193403:p.Arg760Trp	Somatic		Capture	Illumina HiSeq	Phase_I	68416434	NM_001130005	B3V8S3|B4DHH3|B7TY16|Q1HE25|Q9BTN1	Missense_Mutation	SNP	ENST00000193403.6	37	CCDS9792.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	18.96|18.96	3.733176|3.733176	0.69189|0.69189	.|.	.|.	ENSG00000072110|ENSG00000072110	ENST00000553290|ENST00000193403;ENST00000394419;ENST00000438964;ENST00000376839;ENST00000538545;ENST00000544964	.|T;T;T;T;T;T	.|0.69685	.|-0.42;3.07;-0.42;-0.42;1.89;0.44	4.65|4.65	4.65|4.65	0.58169|0.58169	.|EF-hand-like domain (1);	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.81088|0.81088	0.4750|0.4750	M|M	0.82823|0.82823	2.61|2.61	0.48135|0.48135	D|D	0.999596|0.999596	.|D;D;D;P;D	.|0.89917	.|1.0;0.986;0.994;0.916;0.988	.|D;P;P;P;D	.|0.77557	.|0.99;0.846;0.893;0.623;0.916	T|T	0.83192|0.83192	-0.0083|-0.0083	5|10	.|0.87932	.|D	.|0	.|.	11.091|11.091	0.48115|0.48115	0.0:0.0:0.6861:0.3139|0.0:0.0:0.6861:0.3139	.|.	.|391;760;760;760;407	.|B7Z2W3;P12814-2;Q1HE25;P12814;B4DFY0	.|.;.;.;ACTN1_HUMAN;.	L|W	199|760;760;760;695;760;289	.|ENSP00000193403:R760W;ENSP00000377941:R760W;ENSP00000414272:R760W;ENSP00000366035:R695W;ENSP00000439828:R760W;ENSP00000444422:R289W	.|ENSP00000193403:R760W	P|R	-|-	2|1	0|2	ACTN1|ACTN1	68416434|68416434	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.991000|0.991000	0.79684|0.79684	4.484000|4.484000	0.60271|0.60271	2.577000|2.577000	0.86979|0.86979	0.655000|0.655000	0.94253|0.94253	CCG|CGG		0.612	ACTN1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000413233.3	NM_001102	
SLC8A3	6547	broad.mit.edu	37	14	70512793	70512793	+	Silent	SNP	C	C	T	rs199883587		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr14:70512793C>T	ENST00000381269.2	-	8	3408	c.2655G>A	c.(2653-2655)ccG>ccA	p.P885P	SLC8A3_ENST00000528359.1_Silent_p.P883P|SLC8A3_ENST00000533541.1_3'UTR|SLC8A3_ENST00000357887.3_Silent_p.P883P|SLC8A3_ENST00000394330.2_Silent_p.P242P|SLC8A3_ENST00000216568.7_Silent_p.P256P|SLC8A3_ENST00000534137.1_Silent_p.P882P|SLC8A3_ENST00000356921.2_Silent_p.P879P	NM_058240.2|NM_183002.1	NP_489479.1|NP_892114.1	P57103	NAC3_HUMAN	solute carrier family 8 (sodium/calcium exchanger), member 3	885					blood coagulation (GO:0007596)|calcium ion export from cell (GO:1990034)|calcium ion import into cell (GO:1990035)|calcium ion transport into cytosol (GO:0060402)|cell communication (GO:0007154)|cellular response to cAMP (GO:0071320)|hematopoietic progenitor cell differentiation (GO:0002244)|ion transport (GO:0006811)|telencephalon development (GO:0021537)|transmembrane transport (GO:0055085)	dendritic spine (GO:0043197)|integral component of membrane (GO:0016021)|microtubule (GO:0005874)|mitochondrion (GO:0005739)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)	calcium:sodium antiporter activity (GO:0005432)	p.P885P(1)		NS(1)|breast(3)|central_nervous_system(2)|endometrium(3)|kidney(2)|large_intestine(12)|lung(18)|ovary(2)|pancreas(2)|prostate(3)|skin(6)	54				BRCA - Breast invasive adenocarcinoma(234;0.0079)|all cancers(60;0.0102)|OV - Ovarian serous cystadenocarcinoma(108;0.0555)		CTCCCAGGTGCGGCCGCCTTC	0.597											OREG0022773	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	1	0.000199681	0.0	0.0	5008	,	,		18646	0.001		0.0	False		,,,				2504	0.0				p.P883P												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G2649A	14						.						31.0	31.0	31.0					14																	70512793		2203	4300	6503	69582546	SO:0001819	synonymous_variant	6547	exon8			AJ304852	CCDS9799.1, CCDS9800.1, CCDS35498.1, CCDS41967.1, CCDS45131.1, CCDS53904.1	14q24.1	2013-05-22	2008-09-02		ENSG00000100678	ENSG00000100678		"""Solute carriers"""	11070	protein-coding gene	gene with protein product		607991				8798769	Standard	XM_005268017		Approved	NCX3	uc001xly.3	P57103	OTTHUMG00000152342	ENST00000381269.2:c.2655G>A	14.37:g.70512793C>T		Somatic	1122	Capture	Illumina HiSeq	Phase_I	69582546	NM_033262	Q5K3P6|Q5K3P7|Q8IUE9|Q8IUF0|Q8NFI7|Q96QG1|Q96QG2	Silent	SNP	ENST00000381269.2	37	CCDS35498.1																																																																																				0.597	SLC8A3-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000390736.1		
SIPA1L1	26037	broad.mit.edu	37	14	72139291	72139291	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr14:72139291C>T	ENST00000555818.1	+	9	3404	c.3056C>T	c.(3055-3057)aCg>aTg	p.T1019M	SIPA1L1_ENST00000358550.2_Missense_Mutation_p.T1019M|SIPA1L1_ENST00000537413.1_Missense_Mutation_p.T494M|SIPA1L1_ENST00000381232.3_Missense_Mutation_p.T1019M	NM_001284247.1|NM_015556.1	NP_001271176.1|NP_056371.1	O43166	SI1L1_HUMAN	signal-induced proliferation-associated 1 like 1	1019	PDZ. {ECO:0000255|PROSITE- ProRule:PRU00143}.				actin cytoskeleton reorganization (GO:0031532)|activation of Rap GTPase activity (GO:0032861)|ephrin receptor signaling pathway (GO:0048013)|regulation of axonogenesis (GO:0050770)|regulation of dendritic spine morphogenesis (GO:0061001)|regulation of Rap GTPase activity (GO:0032317)|regulation of synaptic plasticity (GO:0048167)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|dendritic spine (GO:0043197)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)	GTPase activator activity (GO:0005096)	p.T1019M(1)		NS(1)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(11)|kidney(1)|large_intestine(22)|liver(2)|lung(25)|ovary(3)|prostate(3)|skin(3)|stomach(1)	78				all cancers(60;0.00169)|BRCA - Breast invasive adenocarcinoma(234;0.00912)|OV - Ovarian serous cystadenocarcinoma(108;0.0109)		ACATCTGTCACGGTGAAGGTT	0.597																																					p.T1019M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C3056T	14						.						79.0	65.0	70.0					14																	72139291		2203	4300	6503	71209044	SO:0001583	missense	26037	exon9			AB007900	CCDS9807.1, CCDS61490.1, CCDS61491.1	14q24.1	2003-12-11				ENSG00000197555			20284	protein-coding gene	gene with protein product						9858596	Standard	XM_005267514		Approved	KIAA0440, E6TP1	uc001xmr.1	O43166		ENST00000555818.1:c.3056C>T	14.37:g.72139291C>T	ENSP00000450832:p.Thr1019Met	Somatic		Capture	Illumina HiSeq	Phase_I	71209044	NM_015556	J3KP19|O95321|Q9UDU4|Q9UNU4	Missense_Mutation	SNP	ENST00000555818.1	37	CCDS9807.1	.	.	.	.	.	.	.	.	.	.	C	21.0	4.088273	0.76756	.	.	ENSG00000197555	ENST00000381232;ENST00000555818;ENST00000358550;ENST00000537413	T;T;T;T	0.64618	-0.11;-0.11;-0.11;-0.11	5.95	5.95	0.96441	PDZ/DHR/GLGF (2);	0.000000	0.85682	D	0.000000	T	0.80686	0.4670	M	0.75447	2.3	0.80722	D	1	D;D;D;D;D	0.89917	1.0;0.999;1.0;1.0;1.0	D;P;D;D;D	0.80764	0.982;0.902;0.994;0.975;0.94	T	0.81167	-0.1056	10	0.87932	D	0	-20.2001	20.3932	0.98965	0.0:1.0:0.0:0.0	.	494;1019;494;1019;1019	F5GYF8;A6H8W6;B4DYX7;O43166-2;O43166	.;.;.;.;SI1L1_HUMAN	M	1019;1019;1019;494	ENSP00000370630:T1019M;ENSP00000450832:T1019M;ENSP00000351352:T1019M;ENSP00000440682:T494M	ENSP00000351352:T1019M	T	+	2	0	SIPA1L1	71209044	1.000000	0.71417	0.967000	0.41034	0.917000	0.54804	6.041000	0.70988	2.824000	0.97209	0.655000	0.94253	ACG		0.597	SIPA1L1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000412806.1	NM_015556	
RGS6	9628	broad.mit.edu	37	14	72961956	72961956	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr14:72961956G>T	ENST00000553530.1	+	13	1158	c.951G>T	c.(949-951)tgG>tgT	p.W317C	RGS6_ENST00000406236.4_Missense_Mutation_p.W317C|RGS6_ENST00000554782.1_Missense_Mutation_p.W178C|RGS6_ENST00000434263.2_Missense_Mutation_p.W248C|RGS6_ENST00000343854.6_Intron|RGS6_ENST00000355512.6_Missense_Mutation_p.W317C|RGS6_ENST00000404301.2_Missense_Mutation_p.W317C|RGS6_ENST00000402788.2_Missense_Mutation_p.W317C|RGS6_ENST00000553525.1_Missense_Mutation_p.W317C|RGS6_ENST00000555571.1_Missense_Mutation_p.W317C|RGS6_ENST00000407322.4_Missense_Mutation_p.W317C|RGS6_ENST00000556437.1_Missense_Mutation_p.W317C	NM_001204417.1|NM_001204418.1|NM_001204420.1|NM_001204421.1|NM_001204422.1|NM_004296.5	NP_001191346.1|NP_001191347.1|NP_001191349.1|NP_001191350.1|NP_001191351.1|NP_004287.3	P49758	RGS6_HUMAN	regulator of G-protein signaling 6	317	G protein gamma.				G-protein coupled receptor signaling pathway (GO:0007186)|intracellular signal transduction (GO:0035556)|positive regulation of GTPase activity (GO:0043547)|positive regulation of neuron differentiation (GO:0045666)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	cytoplasm (GO:0005737)|heterotrimeric G-protein complex (GO:0005834)|plasma membrane (GO:0005886)	GTPase activator activity (GO:0005096)|signal transducer activity (GO:0004871)	p.W317C(1)		endometrium(2)|kidney(3)|large_intestine(6)|lung(14)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	33				all cancers(60;0.00309)|BRCA - Breast invasive adenocarcinoma(234;0.0281)|STAD - Stomach adenocarcinoma(64;0.0302)|OV - Ovarian serous cystadenocarcinoma(108;0.0476)		TTGCTTTGTGGGACATAGAGA	0.393																																					p.W317C	Ovarian(143;1926 2468 21071 48641)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G951T	14						.						209.0	186.0	194.0					14																	72961956		2203	4300	6503	72031709	SO:0001583	missense	9628	exon13			AF073920	CCDS9808.1, CCDS55924.1, CCDS73655.1	14q24.3	2008-07-28	2007-08-14			ENSG00000182732		"""Regulators of G-protein signaling"""	10002	protein-coding gene	gene with protein product		603894	"""regulator of G-protein signalling 6"""			10083744, 14734556	Standard	NM_004296		Approved		uc010ttn.2	P49758		ENST00000553530.1:c.951G>T	14.37:g.72961956G>T	ENSP00000452331:p.Trp317Cys	Somatic		Capture	Illumina HiSeq	Phase_I	72031709	NM_004296	C9JE95|F8W7W5|O75576|O75577|Q7Z4K3|Q7Z4K4|Q7Z4K5|Q7Z4K6|Q8TE13|Q8TE14|Q8TE15|Q8TE16|Q8TE17|Q8TE18|Q8TE19|Q8TE20|Q8TE21|Q8TE22|Q9UDS8|Q9UDT0|Q9Y245|Q9Y647	Missense_Mutation	SNP	ENST00000553530.1	37	CCDS9808.1	.	.	.	.	.	.	.	.	.	.	G	21.6	4.173816	0.78452	.	.	ENSG00000182732	ENST00000553525;ENST00000555571;ENST00000553530;ENST00000556437;ENST00000355512;ENST00000404301;ENST00000406236;ENST00000407322;ENST00000402788;ENST00000453330;ENST00000434263;ENST00000554782;ENST00000535521	T;T;T;T;T;T;T;T;T;T;T	0.25414	1.8;1.8;1.8;1.8;1.8;1.8;1.8;1.8;1.8;1.8;1.8	5.81	5.81	0.92471	G-protein gamma domain (1);	0.053397	0.85682	D	0.000000	T	0.60117	0.2244	M	0.89353	3.025	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;0.999;0.999	D;D;D;D	0.78314	0.987;0.991;0.981;0.986	T	0.66304	-0.5957	10	0.87932	D	0	-4.161	18.854	0.92244	0.0:0.0:1.0:0.0	.	248;317;322;317	B7Z7N5;P49758-2;Q59FJ8;P49758	.;.;.;RGS6_HUMAN	C	317;317;317;317;317;317;317;317;317;289;248;178;178	ENSP00000451030:W317C;ENSP00000450936:W317C;ENSP00000452331:W317C;ENSP00000451855:W317C;ENSP00000347699:W317C;ENSP00000385243:W317C;ENSP00000384218:W317C;ENSP00000384612:W317C;ENSP00000383953:W317C;ENSP00000412144:W248C;ENSP00000451912:W178C	ENSP00000347699:W317C	W	+	3	0	RGS6	72031709	1.000000	0.71417	1.000000	0.80357	0.961000	0.63080	8.586000	0.90806	2.746000	0.94184	0.655000	0.94253	TGG		0.393	RGS6-003	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000413033.2		
DCAF4	26094	broad.mit.edu	37	14	73404707	73404707	+	Missense_Mutation	SNP	G	G	T	rs151012011	byFrequency	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr14:73404707G>T	ENST00000358377.2	+	2	241	c.21G>T	c.(19-21)caG>caT	p.Q7H	DCAF4_ENST00000353777.3_Missense_Mutation_p.Q7H|DCAF4_ENST00000510612.1_3'UTR|DCAF4_ENST00000553457.1_5'UTR|DCAF4_ENST00000509153.1_Missense_Mutation_p.Q7H|DCAF4_ENST00000555042.1_Missense_Mutation_p.Q7H|DCAF4_ENST00000394234.2_Intron	NM_001163509.1|NM_015604.3	NP_001156981.1|NP_056419.2	Q8WV16	DCAF4_HUMAN	DDB1 and CUL4 associated factor 4	7					protein ubiquitination (GO:0016567)	Cul4-RING E3 ubiquitin ligase complex (GO:0080008)		p.Q7H(1)		NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(6)|ovary(1)|skin(1)	22						GTCGCTGGCAGAGTAGAAGAC	0.468																																					p.Q7H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G21T	14						.						93.0	100.0	97.0					14																	73404707		2203	4300	6503	72474460	SO:0001583	missense	26094	exon2			BC018979	CCDS9809.1, CCDS9810.1, CCDS41968.1, CCDS41968.2, CCDS55926.1	14q24.3	2013-01-09	2009-07-17	2009-07-17		ENSG00000119599		"""WD repeat domain containing"", ""DDB1 and CUL4 associated factors"""	20229	protein-coding gene	gene with protein product			"""WD repeat domain 21"", ""WD repeat domain 21A"""	WDR21, WDR21A			Standard	NM_015604		Approved	DKFZp434K114	uc010ttr.2	Q8WV16		ENST00000358377.2:c.21G>T	14.37:g.73404707G>T	ENSP00000351147:p.Gln7His	Somatic		Capture	Illumina HiSeq	Phase_I	72474460	NM_181341	B4DUT6|G3V522|Q86U31|Q8IV10|Q96K22|Q9Y4P5	Missense_Mutation	SNP	ENST00000358377.2	37	CCDS9809.1	.	.	.	.	.	.	.	.	.	.	G	13.38	2.219808	0.39201	.	.	ENSG00000119599	ENST00000358377;ENST00000353777;ENST00000509153;ENST00000555042	T;T;T;T	0.68479	0.47;-0.33;0.47;0.08	4.63	1.41	0.22369	.	1.149400	0.06322	N	0.704571	T	0.54431	0.1858	L	0.36672	1.1	0.09310	N	0.999997	B;B;B;B;B	0.09022	0.0;0.002;0.002;0.002;0.001	B;B;B;B;B	0.08055	0.001;0.003;0.003;0.001;0.001	T	0.47699	-0.9097	10	0.87932	D	0	.	3.8865	0.09100	0.2832:0.2676:0.4492:0.0	.	7;7;7;7;7	B4DUT6;Q8WV16-2;G3V522;Q86SY2;Q8WV16	.;.;.;.;DCAF4_HUMAN	H	7	ENSP00000351147:Q7H;ENSP00000345176:Q7H;ENSP00000426178:Q7H;ENSP00000452131:Q7H	ENSP00000345176:Q7H	Q	+	3	2	DCAF4	72474460	0.013000	0.17824	0.014000	0.15608	0.382000	0.30200	0.243000	0.18106	0.310000	0.22990	0.313000	0.20887	CAG		0.468	DCAF4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000361058.1	NM_015604	
RBM25	58517	broad.mit.edu	37	14	73538444	73538444	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr14:73538444C>A	ENST00000261973.7	+	2	380	c.95C>A	c.(94-96)cCt>cAt	p.P32H	RBM25_ENST00000526754.1_Missense_Mutation_p.P32H|RBM25_ENST00000525321.1_Missense_Mutation_p.P32H|RBM25_ENST00000540173.1_Missense_Mutation_p.P32H|RBM25_ENST00000527432.1_Missense_Mutation_p.P32H	NM_021239.2	NP_067062.1	P49756	RBM25_HUMAN	RNA binding motif protein 25	32					mRNA processing (GO:0006397)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|regulation of apoptotic process (GO:0042981)|RNA splicing (GO:0008380)	cytoplasm (GO:0005737)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)	mRNA binding (GO:0003729)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)	p.P32H(1)		breast(2)|central_nervous_system(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(7)|lung(6)|ovary(2)|pancreas(1)	31				BRCA - Breast invasive adenocarcinoma(234;0.00362)|OV - Ovarian serous cystadenocarcinoma(108;0.0688)		TTTCCTCCACCTGTACCTCCA	0.443																																					p.P32H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C95A	14						.						92.0	90.0	90.0					14																	73538444		2203	4300	6503	72608197	SO:0001583	missense	58517	exon2			BX647116	CCDS32113.1	14q24.3	2013-02-12	2004-04-23	2004-04-29	ENSG00000119707	ENSG00000119707		"""RNA binding motif (RRM) containing"""	23244	protein-coding gene	gene with protein product	"""functional spliceosome-associated protein 94"""	612427	"""RNA-binding region (RNP1, RRM) containing 7"""	RNPC7		9847074, 7596406	Standard	NM_021239		Approved	S164, fSAP94, NET52, Snu71	uc001xno.3	P49756	OTTHUMG00000167540	ENST00000261973.7:c.95C>A	14.37:g.73538444C>A	ENSP00000261973:p.Pro32His	Somatic		Capture	Illumina HiSeq	Phase_I	72608197	NM_021239	A0PJL9|B2RNA8|B3KT03|Q2TA72|Q5XJ17|Q6P665|Q9H6A1|Q9UEQ5|Q9UIE9	De_novo_Start_OutOfFrame	SNP	ENST00000261973.7	37	CCDS32113.1	.	.	.	.	.	.	.	.	.	.	C	16.14	3.038187	0.54896	.	.	ENSG00000119707	ENST00000261973;ENST00000540173;ENST00000527432;ENST00000531500;ENST00000525321;ENST00000526754;ENST00000525161	T;T;T;T;T;T	0.36340	1.57;1.57;1.57;1.27;1.26;1.57	5.52	5.52	0.82312	.	0.095429	0.41712	D	0.000830	T	0.42698	0.1214	L	0.39898	1.24	0.46631	D	0.999131	P;D	0.54207	0.704;0.965	B;P	0.50192	0.36;0.634	T	0.34229	-0.9837	10	0.72032	D	0.01	.	17.6121	0.88056	0.0:1.0:0.0:0.0	.	32;32	P49756;P49756-2	RBM25_HUMAN;.	H	32	ENSP00000261973:P32H;ENSP00000437934:P32H;ENSP00000431150:P32H;ENSP00000434333:P32H;ENSP00000436868:P32H;ENSP00000436225:P32H	ENSP00000261973:P32H	P	+	2	0	RBM25	72608197	1.000000	0.71417	1.000000	0.80357	0.966000	0.64601	3.761000	0.55242	2.594000	0.87642	0.585000	0.79938	CCT		0.443	RBM25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394966.1	XM_027330	
HEATR4	399671	broad.mit.edu	37	14	73989219	73989219	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr14:73989219C>T	ENST00000553558.1	-	3	959	c.638G>A	c.(637-639)cGc>cAc	p.R213H	HEATR4_ENST00000560393.1_Missense_Mutation_p.R166H|RP3-414A15.11_ENST00000553394.1_RNA|HEATR4_ENST00000334988.2_Missense_Mutation_p.R213H|RP3-414A15.2_ENST00000555972.2_RNA	NM_001220484.1	NP_001207413.1	Q86WZ0	HEAT4_HUMAN	HEAT repeat containing 4	213								p.R166H(1)		breast(3)|endometrium(2)|kidney(2)|large_intestine(7)|lung(8)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	28				BRCA - Breast invasive adenocarcinoma(234;0.00386)|OV - Ovarian serous cystadenocarcinoma(108;0.0719)		TCGGGCTGTGCGCTCGTTCAG	0.592																																					p.R166H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G497A	14						.						51.0	48.0	49.0					14																	73989219		2203	4300	6503	73058972	SO:0001583	missense	399671	exon2			BC047590	CCDS9815.1, CCDS9815.2	14q24.3	2013-09-20			ENSG00000187105	ENSG00000187105			16761	protein-coding gene	gene with protein product						15489334	Standard	NM_203309		Approved	MGC48595	uc021rwf.2	Q86WZ0	OTTHUMG00000171602	ENST00000553558.1:c.638G>A	14.37:g.73989219C>T	ENSP00000450444:p.Arg213His	Somatic		Capture	Illumina HiSeq	Phase_I	73058972	NM_203309	B7Z7V9|E9KL41	Missense_Mutation	SNP	ENST00000553558.1	37	CCDS9815.2	.	.	.	.	.	.	.	.	.	.	C	16.74	3.205528	0.58234	.	.	ENSG00000187105	ENST00000553558;ENST00000334988	T	0.45276	0.9	6.07	5.18	0.71444	.	0.000000	0.64402	D	0.000004	T	0.28896	0.0717	L	0.36672	1.1	0.35388	D	0.790534	P	0.38788	0.647	B	0.26517	0.07	T	0.46721	-0.9171	10	0.59425	D	0.04	-9.178	11.525	0.50573	0.0:0.918:0.0:0.082	.	213	Q86WZ0	HEAT4_HUMAN	H	213;166	ENSP00000450444:R213H	ENSP00000335447:R166H	R	-	2	0	HEATR4	73058972	1.000000	0.71417	1.000000	0.80357	0.093000	0.18481	2.541000	0.45735	1.577000	0.49804	0.655000	0.94253	CGC		0.592	HEATR4-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414422.2	NM_203309	
PNMA1	9240	broad.mit.edu	37	14	74179998	74179998	+	Silent	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr14:74179998G>A	ENST00000316836.3	-	1	1130	c.345C>T	c.(343-345)acC>acT	p.T115T		NM_006029.4	NP_006020.4	Q8ND90	PNMA1_HUMAN	paraneoplastic Ma antigen 1	115					inflammatory response to antigenic stimulus (GO:0002437)|positive regulation of apoptotic process (GO:0043065)	cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|nucleolus (GO:0005730)		p.T115T(1)		breast(1)|endometrium(4)|kidney(1)|large_intestine(1)|lung(1)|ovary(2)|prostate(1)|urinary_tract(2)	13				BRCA - Breast invasive adenocarcinoma(234;0.00331)|KIRC - Kidney renal clear cell carcinoma(182;0.0797)		catcttgcacggtccacccct	0.493																																					p.T115T												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C345T	14						.						80.0	84.0	83.0					14																	74179998		2203	4300	6503	73249751	SO:0001819	synonymous_variant	9240	exon1			AF037364	CCDS9818.1	14q24.3	2012-02-09	2012-02-09		ENSG00000176903	ENSG00000176903		"""Paraneoplastic Ma antigens"""	9158	protein-coding gene	gene with protein product		604010	"""paraneoplastic antigen MA1"""			10050892	Standard	NM_006029		Approved	MA1	uc001xor.1	Q8ND90	OTTHUMG00000169183	ENST00000316836.3:c.345C>T	14.37:g.74179998G>A		Somatic		Capture	Illumina HiSeq	Phase_I	73249751	NM_006029	A8K4L5|O95144|Q8NG07	Silent	SNP	ENST00000316836.3	37	CCDS9818.1																																																																																				0.493	PNMA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402774.1	NM_006029	
TMEM63C	57156	broad.mit.edu	37	14	77718233	77718233	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr14:77718233G>A	ENST00000298351.4	+	22	2284	c.2140G>A	c.(2140-2142)Gac>Aac	p.D714N		NM_020431.2	NP_065164.2	Q9P1W3	CSC1_HUMAN	transmembrane protein 63C	714					cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)	integral component of membrane (GO:0016021)	calcium activated cation channel activity (GO:0005227)	p.D714N(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(11)|ovary(1)|skin(1)	23			Kidney(204;0.164)	BRCA - Breast invasive adenocarcinoma(234;0.0342)		GATGGTTGCCGACTACGAGGT	0.567																																					p.D714N												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2140A	14						.						111.0	110.0	111.0					14																	77718233		2003	4164	6167	76787986	SO:0001583	missense	57156	exon22				CCDS45141.1	14q24.3	2014-05-30	2005-07-25	2005-07-25	ENSG00000165548	ENSG00000165548			23787	protein-coding gene	gene with protein product	"""calcium permeable stress-gated cation channel 1 homolog (Arabidopsis)"""		"""chromosome 14 open reading frame 171"""	C14orf171		24503647	Standard	NM_020431		Approved	DKFZp434P0111, CSC1, hsCSC1	uc001xtf.2	Q9P1W3	OTTHUMG00000171557	ENST00000298351.4:c.2140G>A	14.37:g.77718233G>A	ENSP00000298351:p.Asp714Asn	Somatic		Capture	Illumina HiSeq	Phase_I	76787986	NM_020431	B2RN22|B3KWJ5|Q86TS3|Q86TS4|Q9NSQ4|Q9P1W1	Missense_Mutation	SNP	ENST00000298351.4	37	CCDS45141.1	.	.	.	.	.	.	.	.	.	.	G	1.927	-0.446968	0.04572	.	.	ENSG00000165548	ENST00000298351;ENST00000536110	T	0.15139	2.45	5.32	-5.33	0.02713	.	1.570440	0.03900	N	0.280107	T	0.07638	0.0192	N	0.16478	0.41	0.09310	N	1	B	0.06786	0.001	B	0.06405	0.002	T	0.28744	-1.0034	10	0.11794	T	0.64	-0.3824	2.9422	0.05834	0.3117:0.3986:0.1874:0.1022	.	714	Q9P1W3	TM63C_HUMAN	N	714;284	ENSP00000298351:D714N	ENSP00000298351:D714N	D	+	1	0	TMEM63C	76787986	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.202000	0.09451	-0.849000	0.04158	0.561000	0.74099	GAC		0.567	TMEM63C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414193.1		
GSTZ1	2954	broad.mit.edu	37	14	77791217	77791217	+	Missense_Mutation	SNP	T	T	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr14:77791217T>A	ENST00000556627.1	+	2	151	c.20T>A	c.(19-21)aTc>aAc	p.I7N	GSTZ1_ENST00000554279.1_Missense_Mutation_p.I7N|GSTZ1_ENST00000349555.3_Missense_Mutation_p.I7N|GSTZ1_ENST00000361389.4_5'UTR|GSTZ1_ENST00000553586.1_Missense_Mutation_p.I8N|GSTZ1_ENST00000557639.1_Intron|GSTZ1_ENST00000216465.5_Missense_Mutation_p.I7N|GSTZ1_ENST00000393734.1_5'UTR|GSTZ1_ENST00000557053.1_Intron			O43708	MAAI_HUMAN	glutathione S-transferase zeta 1	7	GST N-terminal.				cellular nitrogen compound metabolic process (GO:0034641)|glutathione derivative biosynthetic process (GO:1901687)|glutathione metabolic process (GO:0006749)|L-phenylalanine catabolic process (GO:0006559)|oxidation-reduction process (GO:0055114)|small molecule metabolic process (GO:0044281)|tyrosine catabolic process (GO:0006572)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)|mitochondrion (GO:0005739)	glutathione peroxidase activity (GO:0004602)|glutathione transferase activity (GO:0004364)|maleylacetoacetate isomerase activity (GO:0016034)|protein homodimerization activity (GO:0042803)	p.I7N(1)		lung(2)|prostate(1)	3			Kidney(204;0.164)	BRCA - Breast invasive adenocarcinoma(234;0.0281)	Glutathione(DB00143)	CCTCAGCCCATCCTCTATTCC	0.572																																					p.I7N												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T20A	14						.						167.0	116.0	133.0					14																	77791217		2203	4300	6503	76860970	SO:0001583	missense	2954	exon2			U86529	CCDS9858.1, CCDS9859.1, CCDS9860.1	14q24.3	2012-06-22	2012-06-22		ENSG00000100577	ENSG00000100577	5.2.1.2, 2.5.1.18	"""Glutathione S-transferases / Soluble"""	4643	protein-coding gene	gene with protein product	"""maleylacetoacetate isomerase"""	603758	"""glutathione transferase zeta 1"""			9396740, 9417084	Standard	NM_001513		Approved	GSTZ1-1, MAAI, MAI	uc001xtj.3	O43708	OTTHUMG00000171551	ENST00000556627.1:c.20T>A	14.37:g.77791217T>A	ENSP00000450487:p.Ile7Asn	Somatic		Capture	Illumina HiSeq	Phase_I	76860970	NM_145871	A6NED0|A6NNB8|A8MWD7|B2RCK3|O15308|O75430|Q6IB17|Q7Z610|Q9BV63	Missense_Mutation	SNP	ENST00000556627.1	37		.	.	.	.	.	.	.	.	.	.	T	24.8	4.570699	0.86542	.	.	ENSG00000100577	ENST00000216465;ENST00000554279;ENST00000349555;ENST00000556627;ENST00000553586	T;T;T;T;T	0.19532	2.45;2.45;2.14;2.45;2.45	5.59	5.59	0.84812	Glutathione S-transferase, N-terminal (1);Thioredoxin-like fold (2);	0.200569	0.52532	D	0.000065	T	0.35799	0.0944	M	0.62723	1.935	0.80722	D	1	P;P	0.46220	0.716;0.874	P;P	0.52454	0.474;0.699	T	0.09729	-1.0661	10	0.72032	D	0.01	-0.8267	13.2844	0.60235	0.0:0.0:0.0:1.0	.	7;7	A6NED0;O43708	.;MAAI_HUMAN	N	7;7;7;7;8	ENSP00000216465:I7N;ENSP00000452498:I7N;ENSP00000314404:I7N;ENSP00000450487:I7N;ENSP00000451976:I8N	ENSP00000216465:I7N	I	+	2	0	GSTZ1	76860970	0.860000	0.29831	0.973000	0.42090	0.960000	0.62799	6.207000	0.72159	2.126000	0.65437	0.533000	0.62120	ATC		0.572	GSTZ1-012	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000414090.1	NM_145870	
ZC3H14	79882	broad.mit.edu	37	14	89069348	89069348	+	Missense_Mutation	SNP	A	A	C			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr14:89069348A>C	ENST00000251038.5	+	12	1916	c.1691A>C	c.(1690-1692)cAg>cCg	p.Q564P	ZC3H14_ENST00000336693.4_Intron|ZC3H14_ENST00000393514.5_Missense_Mutation_p.Q539P|ZC3H14_ENST00000406216.3_Intron|ZC3H14_ENST00000318308.6_Intron|ZC3H14_ENST00000556945.1_Intron|ZC3H14_ENST00000555900.1_Missense_Mutation_p.Q266P|ZC3H14_ENST00000359301.3_Intron|ZC3H14_ENST00000555755.1_Missense_Mutation_p.Q564P|ZC3H14_ENST00000557607.1_Intron|ZC3H14_ENST00000302216.8_Intron	NM_001160103.1|NM_001160104.1|NM_024824.4	NP_001153575.1|NP_001153576.1|NP_079100.2	Q6PJT7	ZC3HE_HUMAN	zinc finger CCCH-type containing 14	564						cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)	p.Q564P(1)		cervix(2)|endometrium(3)|kidney(2)|large_intestine(3)|lung(6)|ovary(2)|prostate(1)|skin(2)	21						CTCCACCCACAGCAGTTGCAC	0.493																																					p.Q564P												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A1691C	14						.						134.0	121.0	125.0					14																	89069348		2203	4300	6503	88139101	SO:0001583	missense	79882	exon12			AF155107	CCDS32133.1, CCDS32134.1, CCDS32135.1, CCDS32136.1, CCDS55938.1	14q31.3	2014-08-12			ENSG00000100722	ENSG00000100722		"""Zinc fingers, CCCH-type domain containing"""	20509	protein-coding gene	gene with protein product		613279				10508479	Standard	NM_024824		Approved	FLJ11806, UKp68, NY-REN-37	uc001xww.3	Q6PJT7	OTTHUMG00000170803	ENST00000251038.5:c.1691A>C	14.37:g.89069348A>C	ENSP00000251038:p.Gln564Pro	Somatic		Capture	Illumina HiSeq	Phase_I	88139101	NM_001160104	A8MY46|B4DXU8|B4DZW7|B4E2H4|G3V5R4|Q6MZU4|Q6PJ32|Q6PUI6|Q6PUI8|Q86TQ5|Q86TW0|Q86TW1|Q8NCT6|Q8NCZ3|Q8TDE2|Q9HAC9|Q9Y5A0	Missense_Mutation	SNP	ENST00000251038.5	37	CCDS32133.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	20.3|20.3	3.963072|3.963072	0.74016|0.74016	.|.	.|.	ENSG00000100722|ENSG00000100722	ENST00000251038;ENST00000393530;ENST00000353091;ENST00000555755;ENST00000393514;ENST00000555900|ENST00000556000	.|.	.|.	.|.	5.7|5.7	5.7|5.7	0.88788|0.88788	.|.	0.451004|.	0.25202|.	N|.	0.032374|.	T|T	0.69940|0.69940	0.3167|0.3167	L|L	0.60455|0.60455	1.87|1.87	0.80722|0.80722	D|D	1|1	D;B;B|.	0.71674|.	0.998;0.055;0.055|.	D;B;B|.	0.78314|.	0.991;0.02;0.034|.	T|T	0.68663|0.68663	-0.5349|-0.5349	9|5	0.40728|.	T|.	0.16|.	-3.1656|-3.1656	14.5293|14.5293	0.67912|0.67912	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	564;564;564|.	G3V5R4;Q6PJT7-2;Q6PJT7|.	.;.;ZC3HE_HUMAN|.	P|R	564;539;564;564;539;266|480	.|.	ENSP00000251038:Q564P|.	Q|S	+|+	2|1	0|0	ZC3H14|ZC3H14	88139101|88139101	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.798000|0.798000	0.45092|0.45092	6.838000|6.838000	0.75359|0.75359	2.165000|2.165000	0.68154|0.68154	0.459000|0.459000	0.35465|0.35465	CAG|AGC		0.493	ZC3H14-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000410387.1	NM_024824	
CCDC88C	440193	broad.mit.edu	37	14	91766287	91766287	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr14:91766287G>A	ENST00000389857.6	-	21	3849	c.3763C>T	c.(3763-3765)Cgg>Tgg	p.R1255W		NM_001080414.3	NP_001073883.2	Q9P219	DAPLE_HUMAN	coiled-coil domain containing 88C	1255					protein destabilization (GO:0031648)|protein homooligomerization (GO:0051260)|regulation of protein phosphorylation (GO:0001932)|Wnt signaling pathway (GO:0016055)		PDZ domain binding (GO:0030165)|protein self-association (GO:0043621)	p.R1255W(3)		central_nervous_system(3)|endometrium(2)|kidney(3)|large_intestine(2)|lung(6)|ovary(6)|pancreas(1)|urinary_tract(1)	24		all_cancers(154;0.0468)				AGCTCGCCCCGCAGCCTCTGG	0.637																																					p.R1255W												.	.	3	Substitution - Missense(3)	lung(2)|large_intestine(1)	c.C3763T	14						.						14.0	17.0	16.0					14																	91766287		2045	4191	6236	90836040	SO:0001583	missense	440193	exon21				CCDS45151.1	14q32.12	2014-07-30	2007-05-31	2007-05-31		ENSG00000015133			19967	protein-coding gene	gene with protein product	"""Dvl-associating protein with a high frequency of leucine residues"", ""spinocerebellar ataxia 40"""	611204	"""KIAA1509"""	KIAA1509		17185515, 25062847	Standard	NM_001080414		Approved	DAPLE, HkRP2, SCA40	uc010aty.3	Q9P219		ENST00000389857.6:c.3763C>T	14.37:g.91766287G>A	ENSP00000374507:p.Arg1255Trp	Somatic		Capture	Illumina HiSeq	Phase_I	90836040	NM_001080414	Q69YK1|Q7L1M2|Q86SX7|Q8IYG8	Missense_Mutation	SNP	ENST00000389857.6	37	CCDS45151.1	.	.	.	.	.	.	.	.	.	.	G	18.39	3.614099	0.66672	.	.	ENSG00000015133	ENST00000389857	T	0.15834	2.39	5.24	4.29	0.51040	.	0.147892	0.29205	U	0.012834	T	0.29093	0.0723	M	0.77103	2.36	0.80722	D	1	D	0.65815	0.995	P	0.48571	0.582	T	0.09684	-1.0663	10	0.66056	D	0.02	-25.8187	12.8795	0.58010	0.0:0.0:0.713:0.2869	.	1255	Q9P219	DAPLE_HUMAN	W	1255	ENSP00000374507:R1255W	ENSP00000374507:R1255W	R	-	1	2	CCDC88C	90836040	1.000000	0.71417	0.998000	0.56505	0.691000	0.40173	4.012000	0.57131	2.596000	0.87737	0.549000	0.68633	CGG		0.637	CCDC88C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411650.1	XM_029353	
CCDC88C	440193	broad.mit.edu	37	14	91779510	91779510	+	Missense_Mutation	SNP	C	C	T	rs185802741	byFrequency	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr14:91779510C>T	ENST00000389857.6	-	15	2736	c.2650G>A	c.(2650-2652)Ggc>Agc	p.G884S		NM_001080414.3	NP_001073883.2	Q9P219	DAPLE_HUMAN	coiled-coil domain containing 88C	884					protein destabilization (GO:0031648)|protein homooligomerization (GO:0051260)|regulation of protein phosphorylation (GO:0001932)|Wnt signaling pathway (GO:0016055)		PDZ domain binding (GO:0030165)|protein self-association (GO:0043621)	p.G884S(1)		central_nervous_system(3)|endometrium(2)|kidney(3)|large_intestine(2)|lung(6)|ovary(6)|pancreas(1)|urinary_tract(1)	24		all_cancers(154;0.0468)				TTCAGCTTGCCGGCTGCGTCC	0.602													C|||	2	0.000399361	0.0	0.0014	5008	,	,		20262	0.0		0.001	False		,,,				2504	0.0				p.G884S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2650A	14						.	C	SER/GLY	1,4217		0,1,2108	115.0	116.0	116.0		2650	-2.0	1.0	14		116	2,8452		0,2,4225	yes	missense	CCDC88C	NM_001080414.3	56	0,3,6333	TT,TC,CC		0.0237,0.0237,0.0237	benign	884/2029	91779510	3,12669	2109	4227	6336	90849263	SO:0001583	missense	440193	exon15				CCDS45151.1	14q32.12	2014-07-30	2007-05-31	2007-05-31		ENSG00000015133			19967	protein-coding gene	gene with protein product	"""Dvl-associating protein with a high frequency of leucine residues"", ""spinocerebellar ataxia 40"""	611204	"""KIAA1509"""	KIAA1509		17185515, 25062847	Standard	NM_001080414		Approved	DAPLE, HkRP2, SCA40	uc010aty.3	Q9P219		ENST00000389857.6:c.2650G>A	14.37:g.91779510C>T	ENSP00000374507:p.Gly884Ser	Somatic		Capture	Illumina HiSeq	Phase_I	90849263	NM_001080414	Q69YK1|Q7L1M2|Q86SX7|Q8IYG8	Missense_Mutation	SNP	ENST00000389857.6	37	CCDS45151.1	2	9.157509157509158E-4	0	0.0	1	0.0027624309392265192	0	0.0	1	0.0013192612137203166	C	3.308	-0.141522	0.06669	2.37E-4	2.37E-4	ENSG00000015133	ENST00000389857	T	0.12039	2.72	5.06	-1.97	0.07503	.	0.330584	0.25447	N	0.030610	T	0.03053	0.0090	N	0.01209	-0.955	0.09310	N	1	B	0.09022	0.002	B	0.04013	0.001	T	0.43294	-0.9400	10	0.02654	T	1	-6.7814	10.1945	0.43045	0.0:0.384:0.0:0.616	.	884	Q9P219	DAPLE_HUMAN	S	884	ENSP00000374507:G884S	ENSP00000374507:G884S	G	-	1	0	CCDC88C	90849263	0.000000	0.05858	0.986000	0.45419	0.734000	0.41952	0.057000	0.14279	-0.296000	0.08947	0.561000	0.74099	GGC		0.602	CCDC88C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411650.1	XM_029353	
CCDC88C	440193	broad.mit.edu	37	14	91809955	91809955	+	Silent	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr14:91809955G>A	ENST00000389857.6	-	5	473	c.387C>T	c.(385-387)ggC>ggT	p.G129G		NM_001080414.3	NP_001073883.2	Q9P219	DAPLE_HUMAN	coiled-coil domain containing 88C	129					protein destabilization (GO:0031648)|protein homooligomerization (GO:0051260)|regulation of protein phosphorylation (GO:0001932)|Wnt signaling pathway (GO:0016055)		PDZ domain binding (GO:0030165)|protein self-association (GO:0043621)	p.G129G(1)		central_nervous_system(3)|endometrium(2)|kidney(3)|large_intestine(2)|lung(6)|ovary(6)|pancreas(1)|urinary_tract(1)	24		all_cancers(154;0.0468)				GGACAGCACAGCCCAGCACCA	0.527																																					p.G129G												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C387T	14						.						62.0	69.0	66.0					14																	91809955		2111	4240	6351	90879708	SO:0001819	synonymous_variant	440193	exon5				CCDS45151.1	14q32.12	2014-07-30	2007-05-31	2007-05-31		ENSG00000015133			19967	protein-coding gene	gene with protein product	"""Dvl-associating protein with a high frequency of leucine residues"", ""spinocerebellar ataxia 40"""	611204	"""KIAA1509"""	KIAA1509		17185515, 25062847	Standard	NM_001080414		Approved	DAPLE, HkRP2, SCA40	uc010aty.3	Q9P219		ENST00000389857.6:c.387C>T	14.37:g.91809955G>A		Somatic		Capture	Illumina HiSeq	Phase_I	90879708	NM_001080414	Q69YK1|Q7L1M2|Q86SX7|Q8IYG8	Silent	SNP	ENST00000389857.6	37	CCDS45151.1																																																																																				0.527	CCDC88C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411650.1	XM_029353	
TCL1B	9623	broad.mit.edu	37	14	96157199	96157199	+	Nonsense_Mutation	SNP	C	C	T	rs542592522	byFrequency	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr14:96157199C>T	ENST00000340722.7	+	2	340	c.289C>T	c.(289-291)Cga>Tga	p.R97*	RP11-1070N10.6_ENST00000461160.1_RNA	NM_004918.3	NP_004909.1	O95988	TCL1B_HUMAN	T-cell leukemia/lymphoma 1B	97								p.R97*(1)		cervix(1)|large_intestine(2)|lung(7)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	13		all_cancers(154;0.103)		COAD - Colon adenocarcinoma(157;0.205)|Epithelial(152;0.248)		GAGGAAGTACCGAGCAGCGGA	0.622													C|||	2	0.000399361	0.0015	0.0	5008	,	,		19378	0.0		0.0	False		,,,				2504	0.0				p.R97X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.C289T	14						.						64.0	67.0	66.0					14																	96157199		2203	4300	6503	95226952	SO:0001587	stop_gained	9623	exon2			AB018563	CCDS32151.1	14q32.1	2008-09-05			ENSG00000213231	ENSG00000213231			11649	protein-coding gene	gene with protein product		603769				10077617	Standard	NM_004918		Approved	TML1	uc001yez.3	O95988	OTTHUMG00000028912	ENST00000340722.7:c.289C>T	14.37:g.96157199C>T	ENSP00000343223:p.Arg97*	Somatic		Capture	Illumina HiSeq	Phase_I	95226952	NM_004918	A6NEK7|Q6IAR7|Q9UBQ4	Nonsense_Mutation	SNP	ENST00000340722.7	37	CCDS32151.1	.	.	.	.	.	.	.	.	.	.	C	13.89	2.373322	0.42105	.	.	ENSG00000213231	ENST00000340722;ENST00000538038	.	.	.	3.29	0.145	0.14829	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	0.3086	5.8388	0.18623	0.3994:0.4212:0.1794:0.0	.	.	.	.	X	97	.	ENSP00000343223:R97X	R	+	1	2	TCL1B	95226952	0.033000	0.19621	0.034000	0.17996	0.042000	0.13812	-0.089000	0.11180	0.011000	0.14865	0.462000	0.41574	CGA		0.622	TCL1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315123.2		
BDKRB2	624	broad.mit.edu	37	14	96707546	96707546	+	Missense_Mutation	SNP	C	C	T	rs201732624		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr14:96707546C>T	ENST00000306005.3	+	3	1077	c.881C>T	c.(880-882)aCg>aTg	p.T294M	BDKRB2_ENST00000539359.1_Missense_Mutation_p.T267M|RP11-404P21.8_ENST00000553811.1_Intron|BDKRB2_ENST00000554311.1_Missense_Mutation_p.T294M|BDKRB2_ENST00000542454.2_Missense_Mutation_p.T267M	NM_000623.3	NP_000614.1	P30411	BKRB2_HUMAN	bradykinin receptor B2	294					arachidonic acid secretion (GO:0050482)|blood circulation (GO:0008015)|cell surface receptor signaling pathway (GO:0007166)|G-protein coupled receptor signaling pathway (GO:0007186)|inflammatory response (GO:0006954)|metabolic process (GO:0008152)|negative regulation of intrinsic apoptotic signaling pathway in response to osmotic stress by p53 class mediator (GO:1902239)|negative regulation of peptidyl-serine phosphorylation (GO:0033137)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|regulation of vascular permeability (GO:0043114)|regulation of vasoconstriction (GO:0019229)|response to salt stress (GO:0009651)|smooth muscle contraction (GO:0006939)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|vasoconstriction (GO:0042310)|vasodilation (GO:0042311)	endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	bradykinin receptor activity (GO:0004947)|phosphatidylinositol phospholipase C activity (GO:0004435)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|type 1 angiotensin receptor binding (GO:0031702)	p.T294M(1)		breast(1)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(5)|lung(7)|ovary(3)|skin(1)	24		all_cancers(154;0.0678)|Melanoma(154;0.155)|all_epithelial(191;0.179)		COAD - Colon adenocarcinoma(157;0.226)	Icatibant(DB06196)	TTCCTGGATACGCTGCATCGC	0.577																																					p.T294M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C881T	14						.	C	MET/THR	0,4406		0,0,2203	69.0	63.0	65.0		881	4.6	1.0	14		65	1,8599	1.2+/-3.3	0,1,4299	no	missense	BDKRB2	NM_000623.3	81	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging	294/392	96707546	1,13005	2203	4300	6503	95777299	SO:0001583	missense	624	exon3			S56772	CCDS9942.1	14q32.1-q32.2	2012-08-08				ENSG00000168398		"""GPCR / Class A : Bradykinin receptors"""	1030	protein-coding gene	gene with protein product		113503				7916737	Standard	NM_000623		Approved	BK-2	uc010avm.1	P30411		ENST00000306005.3:c.881C>T	14.37:g.96707546C>T	ENSP00000307713:p.Thr294Met	Somatic		Capture	Illumina HiSeq	Phase_I	95777299	NM_000623		Missense_Mutation	SNP	ENST00000306005.3	37	CCDS9942.1	.	.	.	.	.	.	.	.	.	.	C	15.00	2.704216	0.48412	0.0	1.16E-4	ENSG00000168398	ENST00000542454;ENST00000554311;ENST00000306005;ENST00000539359	T;T;T;T	0.37915	1.17;1.17;1.17;1.17	4.62	4.62	0.57501	GPCR, rhodopsin-like superfamily (1);	0.189976	0.45606	D	0.000354	T	0.55289	0.1911	M	0.75150	2.29	0.41443	D	0.987932	D	0.56746	0.977	P	0.55713	0.782	T	0.64007	-0.6508	10	0.72032	D	0.01	-23.0559	17.4565	0.87608	0.0:1.0:0.0:0.0	.	294	P30411	BKRB2_HUMAN	M	267;294;294;267	ENSP00000439459:T267M;ENSP00000450482:T294M;ENSP00000307713:T294M;ENSP00000438376:T267M	ENSP00000307713:T294M	T	+	2	0	BDKRB2	95777299	0.999000	0.42202	1.000000	0.80357	0.718000	0.41266	3.871000	0.56077	2.114000	0.64651	0.561000	0.74099	ACG		0.577	BDKRB2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413294.1		
SETD3	84193	broad.mit.edu	37	14	99866494	99866494	+	Nonsense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr14:99866494C>T	ENST00000331768.5	-	12	1439	c.1280G>A	c.(1279-1281)tGg>tAg	p.W427*		NM_032233.2	NP_115609.2	Q86TU7	SETD3_HUMAN	SET domain containing 3	427					histone H3-K36 methylation (GO:0010452)|peptidyl-lysine dimethylation (GO:0018027)|peptidyl-lysine monomethylation (GO:0018026)|peptidyl-lysine trimethylation (GO:0018023)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	nuclear chromatin (GO:0000790)	histone methyltransferase activity (H3-K36 specific) (GO:0046975)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|transcription coactivator activity (GO:0003713)	p.W427*(1)		NS(1)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(3)|large_intestine(8)|lung(8)|ovary(1)|skin(1)	25		all_cancers(154;0.224)|all_epithelial(191;0.0644)|Melanoma(154;0.0866)				aagaaatgtccaaagtttgac	0.378																																					p.W427X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.G1280A	14						.						90.0	86.0	88.0					14																	99866494		2203	4300	6503	98936247	SO:0001587	stop_gained	84193	exon12			AK026680	CCDS9951.1, CCDS9952.1	14q32.2	2006-02-15	2006-02-15	2006-02-15	ENSG00000183576	ENSG00000183576			20493	protein-coding gene	gene with protein product		615671	"""chromosome 14 open reading frame 154"""	C14orf154			Standard	NM_032233		Approved	FLJ23027	uc001ygc.3	Q86TU7	OTTHUMG00000028970	ENST00000331768.5:c.1280G>A	14.37:g.99866494C>T	ENSP00000327436:p.Trp427*	Somatic		Capture	Illumina HiSeq	Phase_I	98936247	NM_032233	A0PJU3|A5PLP0|B4DZE8|Q0VAQ2|Q659C0|Q86TU8|Q96GY9|Q9H5U5	Nonsense_Mutation	SNP	ENST00000331768.5	37	CCDS9951.1	.	.	.	.	.	.	.	.	.	.	C	39	7.476242	0.98309	.	.	ENSG00000183576	ENST00000331768	.	.	.	5.57	5.57	0.84162	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-14.3179	19.5529	0.95328	0.0:1.0:0.0:0.0	.	.	.	.	X	427	.	ENSP00000327436:W427X	W	-	2	0	SETD3	98936247	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	7.598000	0.82745	2.621000	0.88768	0.655000	0.94253	TGG		0.378	SETD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000072339.3	NM_032233	
EML1	2009	broad.mit.edu	37	14	100363543	100363543	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr14:100363543G>A	ENST00000262233.6	+	7	878	c.739G>A	c.(739-741)Gtc>Atc	p.V247I	EML1_ENST00000327921.9_Missense_Mutation_p.V235I|EML1_ENST00000334192.4_Missense_Mutation_p.V266I	NM_004434.2	NP_004425.2	O00423	EMAL1_HUMAN	echinoderm microtubule associated protein like 1	247	Tandem atypical propeller in EMLs.				brain development (GO:0007420)|hematopoietic progenitor cell differentiation (GO:0002244)|microtubule cytoskeleton organization (GO:0000226)|mitotic spindle organization (GO:0007052)|neuroblast proliferation (GO:0007405)	cytosol (GO:0005829)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)	calcium ion binding (GO:0005509)|microtubule binding (GO:0008017)|tubulin binding (GO:0015631)	p.V266I(1)		breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(15)|lung(9)|ovary(1)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	42		Melanoma(154;0.0879)|all_epithelial(191;0.216)				GGGAGAGACCGTCTACTTCAT	0.488																																					p.V266I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G796A	14						.						146.0	123.0	131.0					14																	100363543		2203	4300	6503	99433296	SO:0001583	missense	2009	exon8			AK023861	CCDS32154.1, CCDS32155.1	14q32	2013-01-10		2002-02-15		ENSG00000066629		"""WD repeat domain containing"""	3330	protein-coding gene	gene with protein product		602033		EMAPL		9226380, 10521658	Standard	XM_005267397		Approved	EMAP, HuEMAP, ELP79	uc001ygr.3	O00423		ENST00000262233.6:c.739G>A	14.37:g.100363543G>A	ENSP00000262233:p.Val247Ile	Somatic		Capture	Illumina HiSeq	Phase_I	99433296	NM_001008707	Q86U15|Q8N536|Q8N5C4|Q8WWL6	Missense_Mutation	SNP	ENST00000262233.6	37	CCDS32155.1	.	.	.	.	.	.	.	.	.	.	G	22.6	4.305161	0.81247	.	.	ENSG00000066629	ENST00000554479;ENST00000327921;ENST00000262233;ENST00000334192;ENST00000542138;ENST00000556714	T;T;T;T;T	0.41758	1.33;0.99;0.99;0.99;1.33	5.3	4.39	0.52855	HELP (1);Quinonprotein alcohol dehydrogenase-like (1);	0.055298	0.64402	D	0.000001	T	0.52741	0.1753	L	0.49778	1.585	0.80722	D	1	D;D;D;D;D	0.69078	0.991;0.985;0.99;0.997;0.993	P;P;P;P;P	0.56088	0.555;0.604;0.694;0.686;0.791	T	0.56208	-0.8017	10	0.56958	D	0.05	-12.4467	15.905	0.79419	0.0:0.1355:0.8645:0.0	.	235;235;247;266;266	F8W717;B7Z650;O00423;O00423-3;B3KXA3	.;.;EMAL1_HUMAN;.;.	I	234;235;247;266;266;216	ENSP00000451346:V234I;ENSP00000327384:V235I;ENSP00000262233:V247I;ENSP00000334314:V266I;ENSP00000452089:V216I	ENSP00000262233:V247I	V	+	1	0	EML1	99433296	1.000000	0.71417	0.830000	0.32933	0.663000	0.39108	6.475000	0.73582	1.215000	0.43411	0.655000	0.94253	GTC		0.488	EML1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413943.1	NM_001008707	
TRAF3	7187	broad.mit.edu	37	14	103352553	103352553	+	Missense_Mutation	SNP	G	G	A	rs540563941		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr14:103352553G>A	ENST00000560371.1	+	6	815	c.598G>A	c.(598-600)Gtg>Atg	p.V200M	TRAF3_ENST00000347662.4_Missense_Mutation_p.V200M|TRAF3_ENST00000392745.2_Missense_Mutation_p.V200M|TRAF3_ENST00000351691.5_Missense_Mutation_p.V200M|TRAF3_ENST00000539721.1_Intron	NM_003300.3|NM_145725.2	NP_003291.2|NP_663777.1	Q13114	TRAF3_HUMAN	TNF receptor-associated factor 3	200					apoptotic process (GO:0006915)|innate immune response (GO:0045087)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of type I interferon production (GO:0032480)|regulation of apoptotic process (GO:0042981)|regulation of cytokine production (GO:0001817)|regulation of defense response to virus (GO:0050688)|regulation of interferon-beta production (GO:0032648)|regulation of proteolysis (GO:0030162)|signal transduction (GO:0007165)|Toll signaling pathway (GO:0008063)|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)|tumor necrosis factor-mediated signaling pathway (GO:0033209)	CD40 receptor complex (GO:0035631)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|endosome (GO:0005768)|mitochondrion (GO:0005739)	ligase activity (GO:0016874)|signal transducer activity (GO:0004871)|thioesterase binding (GO:0031996)|tumor necrosis factor receptor binding (GO:0005164)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.V200M(1)		breast(4)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(10)|liver(2)|lung(7)|ovary(1)|prostate(2)	30		all_cancers(154;7.87e-06)|all_epithelial(191;0.0024)		Epithelial(152;9.92e-24)|all cancers(159;2.23e-21)|OV - Ovarian serous cystadenocarcinoma(161;7.85e-12)|Colorectal(3;0.0971)		CTGTCCCTGCGTGGTGGTGTC	0.587													G|||	1	0.000199681	0.0	0.0	5008	,	,		17427	0.0		0.001	False		,,,				2504	0.0				p.V200M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G598A	14						.						76.0	60.0	65.0					14																	103352553		2203	4300	6503	102422306	SO:0001583	missense	7187	exon7			U21092	CCDS9975.1, CCDS9976.1, CCDS55946.1	14q32.32	2014-09-17				ENSG00000131323			12033	protein-coding gene	gene with protein product		601896				7530216, 7859281	Standard	NM_145725		Approved	CAP-1, CD40bp, CRAF1, LAP1	uc001ymd.2	Q13114		ENST00000560371.1:c.598G>A	14.37:g.103352553G>A	ENSP00000454207:p.Val200Met	Somatic		Capture	Illumina HiSeq	Phase_I	102422306	NM_145725	B7Z8C4|Q12990|Q13076|Q13947|Q6AZX1|Q9UNL1	Missense_Mutation	SNP	ENST00000560371.1	37	CCDS9975.1	.	.	.	.	.	.	.	.	.	.	G	19.51	3.840464	0.71488	.	.	ENSG00000131323	ENST00000392745;ENST00000347662;ENST00000351691	T;T;T	0.37058	1.22;1.22;1.22	5.57	5.57	0.84162	Zinc finger, TRAF-type (1);TRAF-like (1);	0.054781	0.64402	D	0.000001	T	0.35970	0.0950	L	0.48362	1.52	0.39655	D	0.970529	B;P	0.43314	0.189;0.803	B;B	0.38683	0.051;0.279	T	0.14392	-1.0474	10	0.36615	T	0.2	-36.9231	19.8968	0.96969	0.0:0.0:1.0:0.0	.	200;200	A6NHG8;Q13114	.;TRAF3_HUMAN	M	200	ENSP00000376500:V200M;ENSP00000328003:V200M;ENSP00000332468:V200M	ENSP00000328003:V200M	V	+	1	0	TRAF3	102422306	1.000000	0.71417	1.000000	0.80357	0.909000	0.53808	6.746000	0.74866	2.779000	0.95612	0.591000	0.81541	GTG		0.587	TRAF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415735.1	NM_145725	
GOLGA6L1	283767	broad.mit.edu	37	15	22743131	22743131	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr15:22743131G>A	ENST00000560659.2	+	8	1366	c.1366G>A	c.(1366-1368)Gac>Aac	p.D456N	GOLGA6L1_ENST00000316397.3_Missense_Mutation_p.D506N			Q8N7Z2	GG6L1_HUMAN	golgin A6 family-like 1	500								p.D506N(1)		NS(1)|breast(2)|endometrium(5)|large_intestine(1)|lung(1)|skin(1)	11						gaagatgcacgaccaggagga	0.552																																					p.D506N												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1516A	15						.						3.0	2.0	3.0					15																	22743131		895	1289	2184	20294495	SO:0001583	missense	283767	exon8			AK097517	CCDS73699.1	15q11.2	2012-10-05	2010-02-12		ENSG00000197414	ENSG00000277865			37444	protein-coding gene	gene with protein product			"""golgi autoantigen, golgin subfamily a, 6-like 1"""				Standard	NM_001001413		Approved		uc010tzx.1	Q8N7Z2	OTTHUMG00000171883	ENST00000560659.2:c.1366G>A	15.37:g.22743131G>A	ENSP00000452626:p.Asp456Asn	Somatic		Capture	Illumina HiSeq	Phase_I	20294495	NM_001001413		Missense_Mutation	SNP	ENST00000560659.2	37		.	.	.	.	.	.	.	.	.	.	.	1.020	-0.685048	0.03328	.	.	ENSG00000197414	ENST00000316397;ENST00000355145	T	0.09630	2.96	.	.	.	.	.	.	.	.	T	0.07638	0.0192	N	0.19112	0.55	0.09310	N	1	.	.	.	.	.	.	T	0.38178	-0.9673	5	0.48119	T	0.1	.	.	.	.	.	.	.	.	N	506	ENSP00000320207:D506N	ENSP00000320207:D506N	D	+	1	0	GOLGA6L1	20294495	0.006000	0.16342	0.263000	0.24496	0.267000	0.26476	-0.924000	0.03996	0.149000	0.19098	0.152000	0.16155	GAC		0.552	GOLGA6L1-002	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000415616.2	NM_001001413	
NPAP1	23742	broad.mit.edu	37	15	24922024	24922024	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr15:24922024C>T	ENST00000329468.2	+	1	1484	c.1010C>T	c.(1009-1011)cCg>cTg	p.P337L		NM_018958.2	NP_061831.2	Q9NZP6	NPAP1_HUMAN	nuclear pore associated protein 1	337	Pro-rich.				cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)		p.P337L(2)									TTGCTGCTGCCGCTGCCCCCT	0.582																																					p.P337L												.	.	2	Substitution - Missense(2)	large_intestine(1)|endometrium(1)	c.C1010T	15						.						54.0	51.0	52.0					15																	24922024		2203	4300	6503	22473117	SO:0001583	missense	23742	exon1			AF179681	CCDS10015.1	15q11-q13	2012-07-19	2012-06-14	2012-06-14	ENSG00000185823	ENSG00000185823			1190	protein-coding gene	gene with protein product		610922	"""chromosome 15 open reading frame 2"""	C15orf2		10783265, 22694955	Standard	NM_018958		Approved		uc001ywo.3	Q9NZP6	OTTHUMG00000129179	ENST00000329468.2:c.1010C>T	15.37:g.24922024C>T	ENSP00000333735:p.Pro337Leu	Somatic		Capture	Illumina HiSeq	Phase_I	22473117	NM_018958		Missense_Mutation	SNP	ENST00000329468.2	37	CCDS10015.1	.	.	.	.	.	.	.	.	.	.	.	17.79	3.474963	0.63737	.	.	ENSG00000185823	ENST00000329468	T	0.08984	3.03	1.93	-3.69	0.04450	.	1.125120	0.06976	N	0.818971	T	0.12390	0.0301	L	0.39898	1.24	0.09310	N	1	D	0.71674	0.998	D	0.64321	0.924	T	0.14337	-1.0476	10	0.51188	T	0.08	.	0.2042	0.00148	0.2089:0.2628:0.2072:0.3211	.	337	Q9NZP6	CO002_HUMAN	L	337	ENSP00000333735:P337L	ENSP00000333735:P337L	P	+	2	0	C15orf2	22473117	0.001000	0.12720	0.000000	0.03702	0.892000	0.51952	-0.313000	0.08103	-1.024000	0.03338	0.313000	0.20887	CCG		0.582	NPAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251253.1	NM_018958	
ATP10A	57194	broad.mit.edu	37	15	25959112	25959112	+	Nonsense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr15:25959112G>A	ENST00000356865.6	-	10	2164	c.2053C>T	c.(2053-2055)Cag>Tag	p.Q685*		NM_024490.3	NP_077816.1	O60312	AT10A_HUMAN	ATPase, class V, type 10A	685					ion transmembrane transport (GO:0034220)|phospholipid translocation (GO:0045332)|regulation of cell shape (GO:0008360)|transmembrane transport (GO:0055085)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)	p.Q685*(1)		NS(1)|breast(2)|endometrium(8)|kidney(2)|large_intestine(33)|liver(1)|lung(41)|ovary(3)|pancreas(2)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(2)	103		all_cancers(20;5.16e-25)|all_lung(180;1.51e-14)|Acute lymphoblastic leukemia(1;2.53e-05)|all_hematologic(1;0.000267)|Breast(32;0.00125)		all cancers(64;9.48e-07)|Epithelial(43;1.69e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0252)|Lung(196;0.244)		TCTGACTCCTGCTCCTGAGCA	0.672																																					p.Q685X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.C2053T	15						.						31.0	32.0	32.0					15																	25959112		2203	4299	6502	23510205	SO:0001587	stop_gained	57194	exon10			AB011138	CCDS32178.1	15q12	2010-04-20	2007-09-19		ENSG00000206190	ENSG00000206190		"""ATPases / P-type"""	13542	protein-coding gene	gene with protein product		605855	"""ATPase, Class V, type 10C"", ""ATPase, Class V, type 10A"""	ATP10C		11015572, 9628581	Standard	NM_024490		Approved	ATPVA, ATPVC, KIAA0566	uc010ayu.3	O60312		ENST00000356865.6:c.2053C>T	15.37:g.25959112G>A	ENSP00000349325:p.Gln685*	Somatic		Capture	Illumina HiSeq	Phase_I	23510205	NM_024490	Q4G0S9|Q969I4	Nonsense_Mutation	SNP	ENST00000356865.6	37	CCDS32178.1	.	.	.	.	.	.	.	.	.	.	G	22.1	4.245566	0.80024	.	.	ENSG00000206190	ENST00000356865	.	.	.	3.41	1.48	0.22813	.	2.518930	0.01057	N	0.004564	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.06494	T	0.89	-1.2728	2.1263	0.03739	0.1068:0.2908:0.3675:0.235	.	.	.	.	X	685	.	ENSP00000349325:Q685X	Q	-	1	0	ATP10A	23510205	0.000000	0.05858	0.003000	0.11579	0.103000	0.19146	-0.099000	0.11007	0.443000	0.26582	0.561000	0.74099	CAG		0.672	ATP10A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414830.1	NM_024490	
HERC2	8924	broad.mit.edu	37	15	28419659	28419659	+	Silent	SNP	G	G	A	rs117437554	byFrequency	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr15:28419659G>A	ENST00000261609.7	-	65	10047	c.9939C>T	c.(9937-9939)cgC>cgT	p.R3313R		NM_004667.5	NP_004658.3			HECT and RLD domain containing E3 ubiquitin protein ligase 2									p.R3313R(1)		NS(1)|autonomic_ganglia(1)|breast(3)|central_nervous_system(3)|cervix(3)|endometrium(20)|kidney(11)|large_intestine(33)|lung(95)|ovary(7)|prostate(8)|skin(7)|upper_aerodigestive_tract(8)|urinary_tract(4)	204		all_lung(180;1.3e-11)|Breast(32;0.000194)|Colorectal(260;0.227)		all cancers(64;3.93e-09)|Epithelial(43;9.99e-08)|BRCA - Breast invasive adenocarcinoma(123;0.0271)|GBM - Glioblastoma multiforme(186;0.0497)|Lung(196;0.199)		CACAAGCCACGCGTGTGATCT	0.607																																					p.R3313R												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C9939T	15						.	G		9,4397	12.9+/-30.5	0,9,2194	108.0	72.0	84.0		9939	-11.4	0.1	15	dbSNP_132	84	0,8600		0,0,4300	no	coding-synonymous	HERC2	NM_004667.4		0,9,6494	AA,AG,GG		0.0,0.2043,0.0692		3313/4835	28419659	9,12997	2203	4300	6503	26093254	SO:0001819	synonymous_variant	8924	exon65			AF071172	CCDS10021.1	15q13	2012-02-23	2012-02-23		ENSG00000128731	ENSG00000128731			4868	protein-coding gene	gene with protein product		605837	"""hect domain and RLD 2"""			9949213	Standard	NM_004667		Approved	jdf2, p528, D15F37S1	uc001zbj.4	O95714	OTTHUMG00000129251	ENST00000261609.7:c.9939C>T	15.37:g.28419659G>A		Somatic		Capture	Illumina HiSeq	Phase_I	26093254	NM_004667		Silent	SNP	ENST00000261609.7	37	CCDS10021.1																																																																																				0.607	HERC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251358.2	NM_004667	
APBA2	321	broad.mit.edu	37	15	29385398	29385398	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr15:29385398C>T	ENST00000558402.1	+	8	1789	c.1190C>T	c.(1189-1191)gCg>gTg	p.A397V	APBA2_ENST00000561069.1_Missense_Mutation_p.A397V|APBA2_ENST00000558259.1_Missense_Mutation_p.A397V|APBA2_ENST00000411764.1_Missense_Mutation_p.A397V|APBA2_ENST00000558330.1_Missense_Mutation_p.A397V			Q99767	APBA2_HUMAN	amyloid beta (A4) precursor protein-binding, family A, member 2	397	PID. {ECO:0000255|PROSITE- ProRule:PRU00148}.				in utero embryonic development (GO:0001701)|locomotory behavior (GO:0007626)|multicellular organism growth (GO:0035264)|nervous system development (GO:0007399)|protein transport (GO:0015031)|regulation of gene expression (GO:0010468)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)	beta-amyloid binding (GO:0001540)	p.A397V(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(7)|liver(2)|lung(33)|stomach(1)|urinary_tract(1)	59		all_lung(180;1.73e-12)|Breast(32;2.89e-05)|Colorectal(260;0.234)		all cancers(64;7.44e-11)|Epithelial(43;5.74e-10)|GBM - Glioblastoma multiforme(186;0.026)|BRCA - Breast invasive adenocarcinoma(123;0.0286)|Lung(196;0.24)		ATGATGCAAGCGCAGGAGGCC	0.592																																					p.A397V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1190T	15						.						68.0	62.0	64.0					15																	29385398		2203	4300	6503	27172690	SO:0001583	missense	321	exon6			AB014719	CCDS10022.1, CCDS45197.1	15q11-q12	2008-07-18	2008-07-18		ENSG00000034053	ENSG00000034053			579	protein-coding gene	gene with protein product		602712	"""X11-like"", ""amyloid beta (A4) precursor protein-binding, family A, member 2 (X11-like)"""	X11L, MINT2		8955346	Standard	NM_005503		Approved	D15S1518E, LIN-10, MGC:14091, HsT16821	uc001zck.3	Q99767	OTTHUMG00000129255	ENST00000558402.1:c.1190C>T	15.37:g.29385398C>T	ENSP00000453293:p.Ala397Val	Somatic		Capture	Illumina HiSeq	Phase_I	27172690	NM_005503	E9PGI4|O60571|Q5XKC0	Missense_Mutation	SNP	ENST00000558402.1	37	CCDS10022.1	.	.	.	.	.	.	.	.	.	.	C	34	5.376774	0.95945	.	.	ENSG00000034053	ENST00000411764;ENST00000219865;ENST00000382938	T	0.56275	0.47	5.01	5.01	0.66863	Phosphotyrosine interaction domain (3);Pleckstrin homology-type (1);	0.000000	0.85682	D	0.000000	T	0.69922	0.3165	L	0.58101	1.795	0.80722	D	1	D;D;D;D	0.89917	1.0;0.998;0.999;0.999	D;D;D;D	0.83275	0.996;0.919;0.953;0.986	T	0.73084	-0.4094	10	0.72032	D	0.01	.	17.3238	0.87242	0.0:1.0:0.0:0.0	.	397;101;397;397	Q5XKC0;Q6ZVB1;E9PGI4;Q99767	.;.;.;APBA2_HUMAN	V	397;397;101	ENSP00000409312:A397V	ENSP00000219865:A397V	A	+	2	0	APBA2	27172690	1.000000	0.71417	0.988000	0.46212	0.994000	0.84299	7.587000	0.82613	2.331000	0.79229	0.555000	0.69702	GCG		0.592	APBA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251362.3	NM_005503	
TJP1	7082	broad.mit.edu	37	15	29996472	29996472	+	Silent	SNP	G	G	T	rs377130760		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr15:29996472G>T	ENST00000346128.6	-	27	5580	c.5106C>A	c.(5104-5106)ccC>ccA	p.P1702P	TJP1_ENST00000545208.2_Silent_p.P1622P|TJP1_ENST00000356107.6_Silent_p.P1702P|TJP1_ENST00000400011.2_Silent_p.P1626P	NM_003257.3|NM_175610.2	NP_003248.3|NP_783297.2	Q07157	ZO1_HUMAN	tight junction protein 1	1702	ZU5. {ECO:0000255|PROSITE- ProRule:PRU00485}.				apoptotic process (GO:0006915)|blastocyst formation (GO:0001825)|cell-cell junction assembly (GO:0007043)|cell-cell signaling involved in cell-cell junction organization (GO:1901350)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to glucose stimulus (GO:0071333)|hippo signaling (GO:0035329)|membrane organization (GO:0061024)|negative regulation of vascular permeability (GO:0043116)|response to drug (GO:0042493)|response to ethanol (GO:0045471)|response to lipopolysaccharide (GO:0032496)|response to magnetism (GO:0071000)|sensory perception of sound (GO:0007605)	apical junction complex (GO:0043296)|apical part of cell (GO:0045177)|apical plasma membrane (GO:0016324)|apicolateral plasma membrane (GO:0016327)|basolateral plasma membrane (GO:0016323)|cell junction (GO:0030054)|cell-cell adherens junction (GO:0005913)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|gap junction (GO:0005921)|intercalated disc (GO:0014704)|intercellular canaliculus (GO:0046581)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|tight junction (GO:0005923)		p.P1702P(1)		breast(4)|central_nervous_system(2)|endometrium(8)|kidney(3)|large_intestine(12)|liver(1)|lung(29)|ovary(4)|pancreas(1)|prostate(3)|urinary_tract(1)	68		all_lung(180;7.48e-11)|Breast(32;0.000153)		all cancers(64;3.29e-10)|Epithelial(43;5.34e-09)|BRCA - Breast invasive adenocarcinoma(123;0.0034)|GBM - Glioblastoma multiforme(186;0.0139)|Lung(196;0.186)		TGAGGCCATGGGGACCACACA	0.512																																					p.P1622P	Melanoma(77;681 1843 6309 6570)											.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C4866A	15						.						50.0	54.0	52.0					15																	29996472		2007	4198	6205	27783764	SO:0001819	synonymous_variant	7082	exon26				CCDS42007.1, CCDS45199.1, CCDS73702.1	15q13	2012-07-12	2012-07-12		ENSG00000104067	ENSG00000104067			11827	protein-coding gene	gene with protein product	"""zona occludens 1"", ""tight junction protein ZO-1"""	601009				8825647	Standard	XM_005254616		Approved	ZO-1, MGC133289, DKFZp686M05161	uc001zcr.3	Q07157	OTTHUMG00000137397	ENST00000346128.6:c.5106C>A	15.37:g.29996472G>T		Somatic		Capture	Illumina HiSeq	Phase_I	27783764	NM_175610	B4E3K1|Q2NKP3|Q4ZGJ6	Silent	SNP	ENST00000346128.6	37	CCDS42007.1																																																																																				0.512	TJP1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000268237.3	NM_003257	
CHRFAM7A	89832	broad.mit.edu	37	15	30664537	30664537	+	Silent	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr15:30664537G>A	ENST00000299847.2	-	7	789	c.336C>T	c.(334-336)ccC>ccT	p.P112P	CHRFAM7A_ENST00000401522.3_Silent_p.P21P|CHRFAM7A_ENST00000397827.3_Silent_p.P21P|CHRFAM7A_ENST00000567722.1_5'Flank	NM_139320.1	NP_647536.1	Q494W8	CRFM7_HUMAN	CHRNA7 (cholinergic receptor, nicotinic, alpha 7, exons 5-10) and FAM7A (family with sequence similarity 7A, exons A-E) fusion	112						integral component of membrane (GO:0016021)	extracellular ligand-gated ion channel activity (GO:0005230)	p.P112P(1)		large_intestine(3)|lung(1)|skin(2)	6		all_lung(180;3.42e-11)|Breast(32;0.000153)		all cancers(64;1.9e-15)|Epithelial(43;3.59e-12)|GBM - Glioblastoma multiforme(186;9e-05)|BRCA - Breast invasive adenocarcinoma(123;0.00177)|Lung(196;0.153)		TCCTCTTGCCGGGGATTCCTC	0.488																																					p.P112P												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C336T	15						.						27.0	29.0	29.0					15																	30664537		1560	3462	5022	28451829	SO:0001819	synonymous_variant	89832	exon7			AF029838	CCDS32184.1, CCDS42008.1	15q13.2	2013-04-24	2006-02-01		ENSG00000166664	ENSG00000166664			15781	protein-coding gene	gene with protein product		609756				11829490	Standard	NM_139320		Approved	D-10, CHRNA7-DR1	uc001zdt.1	Q494W8	OTTHUMG00000175645	ENST00000299847.2:c.336C>T	15.37:g.30664537G>A		Somatic		Capture	Illumina HiSeq	Phase_I	28451829	NM_139320	A8KAB9	Silent	SNP	ENST00000299847.2	37	CCDS32184.1																																																																																				0.488	CHRFAM7A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000430700.1	NM_148911	
RYR3	6263	broad.mit.edu	37	15	34110877	34110877	+	Silent	SNP	G	G	A	rs200309704	byFrequency	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr15:34110877G>A	ENST00000389232.4	+	76	10768	c.10698G>A	c.(10696-10698)acG>acA	p.T3566T	RYR3_ENST00000415757.3_Silent_p.T3561T	NM_001036.3	NP_001027.3	Q15413	RYR3_HUMAN	ryanodine receptor 3	3566					calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|cellular response to ATP (GO:0071318)|cellular response to caffeine (GO:0071313)|cellular response to calcium ion (GO:0071277)|cellular response to magnesium ion (GO:0071286)|ion transmembrane transport (GO:0034220)|negative regulation of cytosolic calcium ion concentration (GO:0051481)|protein homotetramerization (GO:0051289)|striated muscle contraction (GO:0006941)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|junctional membrane complex (GO:0030314)|perinuclear region of cytoplasm (GO:0048471)|sarcoplasmic reticulum membrane (GO:0033017)	calcium ion binding (GO:0005509)|calcium-induced calcium release activity (GO:0048763)|calcium-release channel activity (GO:0015278)|ryanodine-sensitive calcium-release channel activity (GO:0005219)	p.T3565T(1)		NS(3)|breast(9)|central_nervous_system(8)|cervix(2)|endometrium(29)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(55)|lung(148)|ovary(7)|pancreas(1)|prostate(13)|skin(4)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(3)	311		all_lung(180;7.18e-09)		all cancers(64;8.95e-12)|GBM - Glioblastoma multiforme(186;0.00109)|BRCA - Breast invasive adenocarcinoma(123;0.0363)		ACGCTCTCACGGAGAGGAGGT	0.517													G|||	3	0.000599042	0.0023	0.0	5008	,	,		19100	0.0		0.0	False		,,,				2504	0.0				p.T3566T												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G10698A	15						.	G		11,4119		0,11,2054	82.0	87.0	86.0		10698	-10.0	0.5	15		86	0,8410		0,0,4205	no	coding-synonymous	RYR3	NM_001036.3		0,11,6259	AA,AG,GG		0.0,0.2663,0.0877		3566/4871	34110877	11,12529	2065	4205	6270	31898169	SO:0001819	synonymous_variant	6263	exon76				CCDS45210.1, CCDS58351.1	15q14-q15	2013-01-10				ENSG00000198838		"""Ion channels / Ryanodine receptors"", ""EF-hand domain containing"""	10485	protein-coding gene	gene with protein product		180903				8276408	Standard	NM_001036		Approved		uc001zhi.3	Q15413		ENST00000389232.4:c.10698G>A	15.37:g.34110877G>A		Somatic		Capture	Illumina HiSeq	Phase_I	31898169	NM_001036	O15175|Q15412	Silent	SNP	ENST00000389232.4	37	CCDS45210.1																																																																																				0.517	RYR3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000417514.1		
FAM98B	283742	broad.mit.edu	37	15	38776701	38776701	+	IGR	SNP	A	A	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr15:38776701A>T	ENST00000491535.1	+	0	3111				FAM98B_ENST00000397609.2_Silent_p.G381G	NM_001042429.1	NP_001035894.1	Q52LJ0	FA98B_HUMAN	family with sequence similarity 98, member B							cytoplasm (GO:0005737)|nucleus (GO:0005634)|tRNA-splicing ligase complex (GO:0072669)	poly(A) RNA binding (GO:0044822)	p.G381G(1)		endometrium(2)|large_intestine(3)|lung(1)|ovary(1)|skin(1)	8		all_cancers(109;3.11e-17)|all_epithelial(112;2.64e-15)|Lung NSC(122;2.11e-11)|all_lung(180;5.61e-10)|Melanoma(134;0.0574)		GBM - Glioblastoma multiforme(113;9e-08)|BRCA - Breast invasive adenocarcinoma(123;0.0209)		GAGGAGGAGGAGGTGGTAGAG	0.642																																					p.G381G												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.A1143T	15						.						20.0	18.0	18.0					15																	38776701		1353	3061	4414	36563993	SO:0001628	intergenic_variant	283742	exon8				CCDS10047.2	15q14	2006-11-29		2005-11-20	ENSG00000171262	ENSG00000171262			26773	protein-coding gene	gene with protein product						12477932	Standard	NM_173611		Approved	FLJ38426	uc001zkc.3	Q52LJ0	OTTHUMG00000129831		15.37:g.38776701A>T		Somatic		Capture	Illumina HiSeq	Phase_I	36563993	NM_173611	A8MUW5|Q8N935	Silent	SNP	ENST00000491535.1	37	CCDS42015.1																																																																																				0.642	FAM98B-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000252071.2	NM_173611	
RPAP1	26015	broad.mit.edu	37	15	41827751	41827751	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr15:41827751G>T	ENST00000304330.4	-	5	616	c.500C>A	c.(499-501)cCa>cAa	p.P167Q	RPAP1_ENST00000561603.1_Missense_Mutation_p.P167Q|RPAP1_ENST00000568413.1_5'Flank	NM_015540.2	NP_056355.2	Q9BWH6	RPAP1_HUMAN	RNA polymerase II associated protein 1	167						nucleus (GO:0005634)	DNA binding (GO:0003677)|DNA-directed RNA polymerase activity (GO:0003899)	p.P167Q(1)		NS(1)|breast(1)|cervix(2)|endometrium(4)|kidney(4)|large_intestine(6)|lung(16)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(5)	45		all_cancers(109;6.59e-20)|all_epithelial(112;7.67e-17)|Lung NSC(122;5.34e-11)|all_lung(180;4.17e-10)|Melanoma(134;0.0179)|Ovarian(310;0.143)|Colorectal(260;0.173)		OV - Ovarian serous cystadenocarcinoma(18;2.84e-17)|GBM - Glioblastoma multiforme(113;1.68e-06)|Colorectal(105;0.0163)|BRCA - Breast invasive adenocarcinoma(123;0.117)		CCCAACTGATGGGCCCTTGGC	0.527																																					p.P167Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C500A	15						.						86.0	87.0	87.0					15																	41827751		2203	4300	6503	39615043	SO:0001583	missense	26015	exon5			BC000246	CCDS10079.1	15q14	2004-03-16			ENSG00000103932	ENSG00000103932			24567	protein-coding gene	gene with protein product		611475				10718198	Standard	XM_005254297		Approved	DKFZP727M111, KIAA1403, MGC858, FLJ12732	uc001zod.3	Q9BWH6	OTTHUMG00000130342	ENST00000304330.4:c.500C>A	15.37:g.41827751G>T	ENSP00000306123:p.Pro167Gln	Somatic		Capture	Illumina HiSeq	Phase_I	39615043	NM_015540	Q9H9I2|Q9NSQ5|Q9P2E4|Q9UFS7	Missense_Mutation	SNP	ENST00000304330.4	37	CCDS10079.1	.	.	.	.	.	.	.	.	.	.	G	15.02	2.709375	0.48517	.	.	ENSG00000103932	ENST00000304330	T	0.11930	2.73	4.73	1.79	0.24919	.	0.964070	0.08562	N	0.927397	T	0.10852	0.0265	L	0.36672	1.1	0.09310	N	1	B	0.28128	0.201	B	0.26969	0.075	T	0.36529	-0.9744	10	0.87932	D	0	-21.6357	3.9097	0.09197	0.1998:0.0:0.6113:0.189	.	167	Q9BWH6	RPAP1_HUMAN	Q	167	ENSP00000306123:P167Q	ENSP00000306123:P167Q	P	-	2	0	RPAP1	39615043	0.062000	0.20869	0.000000	0.03702	0.637000	0.38172	2.415000	0.44635	0.209000	0.20645	0.313000	0.20887	CCA		0.527	RPAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252694.2	NM_015540	
MGA	23269	broad.mit.edu	37	15	41961511	41961511	+	Missense_Mutation	SNP	G	G	A	rs528733174	byFrequency	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr15:41961511G>A	ENST00000570161.1	+	1	419	c.419G>A	c.(418-420)cGt>cAt	p.R140H	MGA_ENST00000545763.1_Missense_Mutation_p.R140H|MGA_ENST00000219905.7_Missense_Mutation_p.R140H|MGA_ENST00000389936.4_Missense_Mutation_p.R140H|MGA_ENST00000568630.1_Intron|MGA_ENST00000566586.1_Missense_Mutation_p.R140H			O43451	MGA_HUMAN	MGA, MAX dimerization protein	0					carbohydrate metabolic process (GO:0005975)|polysaccharide digestion (GO:0044245)|small molecule metabolic process (GO:0044281)|starch catabolic process (GO:0005983)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	alpha-1,4-glucosidase activity (GO:0004558)|amylase activity (GO:0016160)|carbohydrate binding (GO:0030246)|catalytic activity (GO:0003824)|glucan 1,4-alpha-glucosidase activity (GO:0004339)|maltose alpha-glucosidase activity (GO:0032450)	p.R140H(1)		NS(1)|breast(4)|central_nervous_system(3)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(18)|lung(33)|ovary(8)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	95		all_cancers(109;0.00356)|all_epithelial(112;0.0413)|all_lung(180;0.18)|Ovarian(310;0.238)		OV - Ovarian serous cystadenocarcinoma(18;1.41e-18)|GBM - Glioblastoma multiforme(113;2.15e-06)|COAD - Colon adenocarcinoma(120;0.031)|Lung(196;0.0721)|BRCA - Breast invasive adenocarcinoma(123;0.0964)|Colorectal(105;0.0998)|LUSC - Lung squamous cell carcinoma(244;0.235)	Acarbose(DB00284)|Miglitol(DB00491)|Voglibose(DB04878)	TGGAATGGTCGTTGGTGGGAA	0.408													G|||	2	0.000399361	0.0008	0.0	5008	,	,		22021	0.0		0.0	False		,,,				2504	0.001				p.R140H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G419A	15						.						285.0	283.0	283.0					15																	41961511		1885	4097	5982	39748803	SO:0001583	missense	23269	exon2			AB011090	CCDS55959.1, CCDS55960.1	15q15	2012-11-15	2012-11-15		ENSG00000174197	ENSG00000174197		"""MAX dimerization proteins"", ""T-boxes"""	14010	protein-coding gene	gene with protein product			"""MAX gene associated"""				Standard	NM_001080541		Approved	KIAA0518, MAD5, MXD5, FLJ12634	uc010ucy.2	Q8IWI9		ENST00000570161.1:c.419G>A	15.37:g.41961511G>A	ENSP00000457035:p.Arg140His	Somatic		Capture	Illumina HiSeq	Phase_I	39748803	NM_001164273	Q0VAX6|Q75ME7|Q86UM5	Missense_Mutation	SNP	ENST00000570161.1	37	CCDS55959.1	.	.	.	.	.	.	.	.	.	.	G	17.50	3.405443	0.62288	.	.	ENSG00000174197	ENST00000219905;ENST00000389936;ENST00000545763	D;D;D	0.89617	-2.54;-2.54;-2.54	5.52	5.52	0.82312	.	0.331625	0.28555	N	0.014933	D	0.89090	0.6616	N	0.21282	0.65	0.36725	D	0.881382	D;D	0.89917	0.999;1.0	D;D	0.71414	0.929;0.973	D	0.90710	0.4627	10	0.87932	D	0	.	10.2891	0.43586	0.1466:0.0:0.8534:0.0	.	140;140	F5H7K2;E7ENI0	.;.	H	140	ENSP00000219905:R140H;ENSP00000374586:R140H;ENSP00000442467:R140H	ENSP00000219905:R140H	R	+	2	0	MGA	39748803	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	3.293000	0.51779	2.767000	0.95098	0.655000	0.94253	CGT		0.408	MGA-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000420229.1	NM_001164273.1	
MAP1A	4130	broad.mit.edu	37	15	43820965	43820965	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr15:43820965G>T	ENST00000300231.5	+	4	7744	c.7294G>T	c.(7294-7296)Gct>Tct	p.A2432S	MAP1A_ENST00000399453.1_Missense_Mutation_p.A2432S|MAP1A_ENST00000382031.1_Missense_Mutation_p.A2670S			P78559	MAP1A_HUMAN	microtubule-associated protein 1A	2432					microtubule cytoskeleton organization (GO:0000226)|sensory perception of sound (GO:0007605)	cytosol (GO:0005829)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)	structural molecule activity (GO:0005198)	p.A2432S(1)		breast(5)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(11)|liver(2)|lung(19)|ovary(5)|pancreas(3)|prostate(2)|skin(6)|soft_tissue(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	66		all_cancers(109;1.03e-14)|all_epithelial(112;2.23e-12)|Lung NSC(122;2.76e-08)|all_lung(180;3.1e-07)|Melanoma(134;0.0476)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;3.05e-06)	Estramustine(DB01196)	TGAGGTCGAAGCTGGGCCCCA	0.662																																					p.A2432S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G7294T	15						.						28.0	31.0	30.0					15																	43820965		1945	4123	6068	41608257	SO:0001583	missense	4130	exon4			U38292	CCDS42031.1	15q15.3	2006-06-15			ENSG00000166963	ENSG00000166963			6835	protein-coding gene	gene with protein product		600178		MAP1L		7806212, 7629894	Standard	XM_005254385		Approved		uc001zrt.3	P78559	OTTHUMG00000059756	ENST00000300231.5:c.7294G>T	15.37:g.43820965G>T	ENSP00000300231:p.Ala2432Ser	Somatic		Capture	Illumina HiSeq	Phase_I	41608257	NM_002373	O95643|Q12973|Q15882|Q9UJT4	Missense_Mutation	SNP	ENST00000300231.5	37	CCDS42031.1	.	.	.	.	.	.	.	.	.	.	G	1.055	-0.674594	0.03378	.	.	ENSG00000166963	ENST00000382031;ENST00000399453;ENST00000300231	T;T;T	0.01388	4.96;4.95;4.96	4.63	1.24	0.21308	.	.	.	.	.	T	0.01061	0.0035	N	0.24115	0.695	0.23731	N	0.996991	B	0.14012	0.009	B	0.15052	0.012	T	0.48854	-0.8998	9	0.15952	T	0.53	-1.2903	5.0558	0.14531	0.0938:0.5073:0.2519:0.147	.	2432	P78559	MAP1A_HUMAN	S	2670;2432;2432	ENSP00000371462:A2670S;ENSP00000382380:A2432S;ENSP00000300231:A2432S	ENSP00000300231:A2432S	A	+	1	0	MAP1A	41608257	0.954000	0.32549	0.998000	0.56505	0.113000	0.19764	0.882000	0.28186	0.516000	0.28340	0.462000	0.41574	GCT		0.662	MAP1A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000132894.5	NM_002373	
SPG11	80208	broad.mit.edu	37	15	44898282	44898282	+	Nonsense_Mutation	SNP	G	G	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr15:44898282G>T	ENST00000261866.7	-	20	3477	c.3461C>A	c.(3460-3462)tCa>tAa	p.S1154*	SPG11_ENST00000535302.2_Nonsense_Mutation_p.S1154*|SPG11_ENST00000427534.2_Nonsense_Mutation_p.S1154*|SPG11_ENST00000558319.1_Nonsense_Mutation_p.S1154*	NM_025137.3	NP_079413.3	Q96JI7	SPTCS_HUMAN	spastic paraplegia 11 (autosomal recessive)	1154					cell death (GO:0008219)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)		p.S1154*(1)		autonomic_ganglia(1)|breast(5)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(4)|large_intestine(16)|lung(24)|ovary(5)|prostate(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	72		all_cancers(109;1.29e-14)|all_epithelial(112;1.26e-12)|Lung NSC(122;1.34e-07)|all_lung(180;1.21e-06)|Melanoma(134;0.0122)		all cancers(107;2.93e-22)|GBM - Glioblastoma multiforme(94;1.55e-06)|COAD - Colon adenocarcinoma(120;0.0432)|Colorectal(105;0.0484)|Lung(196;0.104)|LUSC - Lung squamous cell carcinoma(244;0.214)		ATCAAAGGGTGATAATGACTG	0.368																																					p.S1154X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.C3461A	15						.						94.0	87.0	89.0					15																	44898282		2198	4298	6496	42685574	SO:0001587	stop_gained	80208	exon20				CCDS10112.1, CCDS53939.1	15q13-q15	2007-11-13			ENSG00000104133	ENSG00000104133			11226	protein-coding gene	gene with protein product	"""spatacsin"""	610844	"""KIAA1840"""	KIAA1840		10408536, 17322883	Standard	NM_001160227		Approved	FLJ21439	uc001ztx.3	Q96JI7	OTTHUMG00000131199	ENST00000261866.7:c.3461C>A	15.37:g.44898282G>T	ENSP00000261866:p.Ser1154*	Somatic		Capture	Illumina HiSeq	Phase_I	42685574	NM_025137	A8KAX9|B9EK60|F5H3N6|Q4VC11|Q58G86|Q69YG6|Q6NW01|Q8N270|Q8TBU9|Q9H734	Nonsense_Mutation	SNP	ENST00000261866.7	37	CCDS10112.1	.	.	.	.	.	.	.	.	.	.	G	41	8.573969	0.98868	.	.	ENSG00000104133	ENST00000261866;ENST00000535302;ENST00000427534	.	.	.	5.35	0.895	0.19247	.	0.972834	0.08484	N	0.939027	.	.	.	.	.	.	0.09310	N	1	.	.	.	.	.	.	.	.	.	.	0.21540	T	0.41	.	10.732	0.46102	0.3355:0.0:0.6645:0.0	.	.	.	.	X	1154	.	ENSP00000261866:S1154X	S	-	2	0	SPG11	42685574	0.015000	0.18098	0.118000	0.21660	0.994000	0.84299	0.474000	0.22148	0.108000	0.17862	0.650000	0.86243	TCA		0.368	SPG11-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000253927.1		
USP50	373509	broad.mit.edu	37	15	50831018	50831018	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr15:50831018C>T	ENST00000532404.1	-	5	864	c.691G>A	c.(691-693)Gca>Aca	p.A231T	USP50_ENST00000530218.1_5'UTR	NM_203494.4	NP_987090.2	Q70EL3	UBP50_HUMAN	ubiquitin specific peptidase 50	236	USP.				ubiquitin-dependent protein catabolic process (GO:0006511)		ubiquitinyl hydrolase activity (GO:0036459)	p.A236T(1)		breast(1)|kidney(2)|large_intestine(4)|liver(1)|lung(5)	13				all cancers(107;0.000519)|GBM - Glioblastoma multiforme(94;0.00288)		CAGGTCAGTGCGTCTTGTTGA	0.398																																					p.A231T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G691A	15						.						89.0	84.0	85.0					15																	50831018		1874	4096	5970	48618310	SO:0001583	missense	373509	exon5			AI990110	CCDS53944.1	15q21.1	2008-02-05	2005-08-08			ENSG00000170236		"""Ubiquitin-specific peptidases"""	20079	protein-coding gene	gene with protein product			"""ubiquitin specific protease 50"""			12838346	Standard	NM_203494		Approved		uc021sky.1	Q70EL3		ENST00000532404.1:c.691G>A	15.37:g.50831018C>T	ENSP00000434676:p.Ala231Thr	Somatic		Capture	Illumina HiSeq	Phase_I	48618310	NM_203494	E9PP86	Missense_Mutation	SNP	ENST00000532404.1	37	CCDS53944.1	.	.	.	.	.	.	.	.	.	.	C	4.135	0.023356	0.08006	.	.	ENSG00000170236	ENST00000532404	T	0.27720	1.65	5.41	4.27	0.50696	Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (2);	0.247279	0.38272	N	0.001741	T	0.06280	0.0162	N	0.00204	-1.855	0.21445	N	0.999687	B	0.06786	0.001	B	0.01281	0.0	T	0.34054	-0.9844	10	0.06625	T	0.88	-9.0486	8.9624	0.35856	0.0:0.086:0.0:0.914	.	236	Q70EL3	UBP50_HUMAN	T	231	ENSP00000434676:A231T	ENSP00000434014:A6T	A	-	1	0	USP50	48618310	1.000000	0.71417	1.000000	0.80357	0.751000	0.42716	3.082000	0.50128	0.911000	0.36747	-0.290000	0.09829	GCA		0.398	USP50-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395249.1		
SPPL2A	84888	broad.mit.edu	37	15	51024859	51024859	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr15:51024859T>C	ENST00000261854.5	-	9	1229	c.955A>G	c.(955-957)Atc>Gtc	p.I319V		NM_032802.3	NP_116191.2	Q8TCT8	SPP2A_HUMAN	signal peptide peptidase like 2A	319					membrane protein ectodomain proteolysis (GO:0006509)|membrane protein intracellular domain proteolysis (GO:0031293)|regulation of immune response (GO:0050776)	extracellular vesicular exosome (GO:0070062)|Golgi-associated vesicle membrane (GO:0030660)|integral component of cytoplasmic side of endoplasmic reticulum membrane (GO:0071458)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|late endosome membrane (GO:0031902)|lysosomal membrane (GO:0005765)|plasma membrane (GO:0005886)	aspartic-type endopeptidase activity (GO:0004190)|protein homodimerization activity (GO:0042803)	p.I319V(2)		endometrium(1)|kidney(1)|large_intestine(4)|lung(6)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	15				all cancers(107;0.000712)|GBM - Glioblastoma multiforme(94;0.00314)		ATCCCCAAGATATCCTGTAAA	0.308																																					p.I319V	Melanoma(50;790 1209 4069 22965 33125)											.	.	2	Substitution - Missense(2)	large_intestine(2)	c.A955G	15						.						64.0	62.0	63.0					15																	51024859		2193	4294	6487	48812151	SO:0001583	missense	84888	exon9				CCDS10138.1	15q21.2	2012-02-21			ENSG00000138600	ENSG00000138600			30227	protein-coding gene	gene with protein product	"""intramembrane protease 3"", ""presenilin-like protein 2"""	608238				12077416, 12139484	Standard	NM_032802		Approved	IMP3, PSL2	uc001zyv.3	Q8TCT8	OTTHUMG00000131647	ENST00000261854.5:c.955A>G	15.37:g.51024859T>C	ENSP00000261854:p.Ile319Val	Somatic		Capture	Illumina HiSeq	Phase_I	48812151	NM_032802	B2RDS0|Q8TAW1|Q96SZ8	Missense_Mutation	SNP	ENST00000261854.5	37	CCDS10138.1	.	.	.	.	.	.	.	.	.	.	T	7.270	0.606856	0.14002	.	.	ENSG00000138600	ENST00000261854	T	0.18657	2.2	5.81	4.65	0.58169	.	0.113691	0.64402	D	0.000008	T	0.18467	0.0443	L	0.43152	1.355	0.42855	D	0.994092	B	0.14438	0.01	B	0.13407	0.009	T	0.04621	-1.0938	10	0.21540	T	0.41	-9.1536	13.2347	0.59963	0.0:0.0:0.1321:0.8679	.	319	Q8TCT8	PSL2_HUMAN	V	319	ENSP00000261854:I319V	ENSP00000261854:I319V	I	-	1	0	AC012100.1	48812151	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	1.674000	0.37544	2.234000	0.73211	0.524000	0.50904	ATC		0.308	SPPL2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254543.3	NM_032802	
DMXL2	23312	broad.mit.edu	37	15	51747414	51747414	+	Silent	SNP	C	C	T	rs151096557		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr15:51747414C>T	ENST00000251076.5	-	39	8759	c.8472G>A	c.(8470-8472)gcG>gcA	p.A2824A	RP11-707P17.2_ENST00000559977.1_RNA|DMXL2_ENST00000449909.3_Silent_p.A2188A|RP11-707P17.2_ENST00000560727.1_RNA|RP11-707P17.1_ENST00000561007.1_RNA|RP11-707P17.2_ENST00000559173.1_RNA|DMXL2_ENST00000543779.2_Silent_p.A2825A	NM_001174116.1|NM_015263.3	NP_001167587.1|NP_056078.2	Q8TDJ6	DMXL2_HUMAN	Dmx-like 2	2824						cell junction (GO:0030054)|extracellular space (GO:0005615)|membrane (GO:0016020)|synaptic vesicle (GO:0008021)	Rab GTPase binding (GO:0017137)	p.A2824A(1)		breast(4)|central_nervous_system(1)|cervix(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(26)|liver(1)|lung(28)|ovary(7)|prostate(7)|skin(4)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	101				all cancers(107;0.00494)		CCTCTCCATCCGCAACACCAC	0.403													C|||	1	0.000199681	0.0	0.0014	5008	,	,		18944	0.0		0.0	False		,,,				2504	0.0				p.A2824A												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G8472A	15						.	C	,,	3,4389	4.2+/-10.8	0,3,2193	169.0	139.0	150.0		8475,6564,8472	-4.5	1.0	15	dbSNP_134	150	0,8586		0,0,4293	no	coding-synonymous,coding-synonymous,coding-synonymous	DMXL2	NM_001174116.1,NM_001174117.1,NM_015263.3	,,	0,3,6486	TT,TC,CC		0.0,0.0683,0.0231	,,	2825/3038,2188/2401,2824/3037	51747414	3,12975	2196	4293	6489	49534706	SO:0001819	synonymous_variant	23312	exon39			AB020663	CCDS10141.1, CCDS53945.1, CCDS53946.1	15q21.2	2013-01-10			ENSG00000104093	ENSG00000104093		"""WD repeat domain containing"""	2938	protein-coding gene	gene with protein product	"""rabconnectin 3"""	612186					Standard	NM_001174116		Approved	RC3, KIAA0856	uc010ufy.2	Q8TDJ6	OTTHUMG00000131749	ENST00000251076.5:c.8472G>A	15.37:g.51747414C>T		Somatic		Capture	Illumina HiSeq	Phase_I	49534706	NM_015263	B2RTR3|B7ZMH3|F5GWF1|O94938	Silent	SNP	ENST00000251076.5	37	CCDS10141.1																																																																																				0.403	DMXL2-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000254671.2	NM_015263	
MYO5C	55930	broad.mit.edu	37	15	52553222	52553222	+	Missense_Mutation	SNP	T	T	G			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr15:52553222T>G	ENST00000261839.7	-	10	1311	c.1150A>C	c.(1150-1152)Acg>Ccg	p.T384P	MYO5C_ENST00000541028.1_5'UTR|MYO5C_ENST00000443683.2_Missense_Mutation_p.T327P	NM_018728.3	NP_061198.2	Q9NQX4	MYO5C_HUMAN	myosin VC	384	Myosin motor.					extracellular vesicular exosome (GO:0070062)|myosin complex (GO:0016459)	ATP binding (GO:0005524)|motor activity (GO:0003774)	p.T384P(1)		breast(1)|central_nervous_system(3)|cervix(1)|endometrium(8)|kidney(7)|large_intestine(15)|lung(12)|ovary(7)|prostate(3)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	66				all cancers(107;0.0137)		TTTACCACCGTCTCAGAGCTT	0.532																																					p.T384P												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A1150C	15						.						111.0	111.0	111.0					15																	52553222		2017	4187	6204	50340514	SO:0001583	missense	55930	exon10			AF272390	CCDS42036.1	15q21	2011-09-27				ENSG00000128833		"""Myosins / Myosin superfamily : Class V"""	7604	protein-coding gene	gene with protein product	"""myosin 5C"""	610022				11870218	Standard	NM_018728		Approved	MGC74969	uc010bff.3	Q9NQX4		ENST00000261839.7:c.1150A>C	15.37:g.52553222T>G	ENSP00000261839:p.Thr384Pro	Somatic		Capture	Illumina HiSeq	Phase_I	50340514	NM_018728	Q6P1W8	Missense_Mutation	SNP	ENST00000261839.7	37	CCDS42036.1	.	.	.	.	.	.	.	.	.	.	T	16.97	3.269018	0.59540	.	.	ENSG00000128833	ENST00000261839;ENST00000443683	D;D	0.88046	-2.33;-2.33	5.51	5.51	0.81932	Myosin head, motor domain (2);	0.000000	0.85682	D	0.000000	D	0.93635	0.7967	M	0.85462	2.755	0.80722	D	1	D	0.69078	0.997	D	0.72982	0.979	D	0.93601	0.6930	10	0.42905	T	0.14	.	15.6178	0.76780	0.0:0.0:0.0:1.0	.	384	Q9NQX4	MYO5C_HUMAN	P	384;327	ENSP00000261839:T384P;ENSP00000410582:T327P	ENSP00000261839:T384P	T	-	1	0	MYO5C	50340514	1.000000	0.71417	0.989000	0.46669	0.020000	0.10135	6.294000	0.72738	2.108000	0.64289	0.533000	0.62120	ACG		0.532	MYO5C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419562.1	NM_018728	
MYO5C	55930	broad.mit.edu	37	15	52556415	52556415	+	Missense_Mutation	SNP	G	G	A	rs189317194		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr15:52556415G>A	ENST00000261839.7	-	9	1180	c.1019C>T	c.(1018-1020)gCg>gTg	p.A340V	MYO5C_ENST00000541028.1_5'UTR|MYO5C_ENST00000443683.2_Missense_Mutation_p.A283V	NM_018728.3	NP_061198.2	Q9NQX4	MYO5C_HUMAN	myosin VC	340	Myosin motor.					extracellular vesicular exosome (GO:0070062)|myosin complex (GO:0016459)	ATP binding (GO:0005524)|motor activity (GO:0003774)	p.A340V(1)		breast(1)|central_nervous_system(3)|cervix(1)|endometrium(8)|kidney(7)|large_intestine(15)|lung(12)|ovary(7)|prostate(3)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	66				all cancers(107;0.0137)		GTTGCCCACCGCGGTGATCTG	0.468													G|||	1	0.000199681	0.0008	0.0	5008	,	,		20631	0.0		0.0	False		,,,				2504	0.0				p.A340V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1019T	15						.	G	VAL/ALA	3,3909		0,3,1953	85.0	85.0	85.0		1019	4.3	0.0	15		85	0,8294		0,0,4147	no	missense	MYO5C	NM_018728.3	64	0,3,6100	AA,AG,GG		0.0,0.0767,0.0246	possibly-damaging	340/1743	52556415	3,12203	1956	4147	6103	50343707	SO:0001583	missense	55930	exon9			AF272390	CCDS42036.1	15q21	2011-09-27				ENSG00000128833		"""Myosins / Myosin superfamily : Class V"""	7604	protein-coding gene	gene with protein product	"""myosin 5C"""	610022				11870218	Standard	NM_018728		Approved	MGC74969	uc010bff.3	Q9NQX4		ENST00000261839.7:c.1019C>T	15.37:g.52556415G>A	ENSP00000261839:p.Ala340Val	Somatic		Capture	Illumina HiSeq	Phase_I	50343707	NM_018728	Q6P1W8	Missense_Mutation	SNP	ENST00000261839.7	37	CCDS42036.1	1|1	4.578754578754579E-4|4.578754578754579E-4	1|1	0.0020325203252032522|0.0020325203252032522	0|0	0.0|0.0	0|0	0.0|0.0	0|0	0.0|0.0	G|G	8.727|8.727	0.915824|0.915824	0.17907|0.17907	7.67E-4|7.67E-4	0.0|0.0	ENSG00000128833|ENSG00000128833	ENST00000261839;ENST00000443683|ENST00000541028	D;D|.	0.87029|.	-2.2;-2.2|.	5.24|5.24	4.3|4.3	0.51218|0.51218	Myosin head, motor domain (2);|.	0.346096|.	0.29280|.	N|.	0.012605|.	T|T	0.30792|0.30792	0.0776|0.0776	L|L	0.41415|0.41415	1.275|1.275	0.09310|0.09310	N|N	1|1	P|P	0.35107|0.49696	0.484|0.927	B|B	0.35278|0.39152	0.199|0.292	T|T	0.08973|0.08973	-1.0696|-1.0696	10|8	0.48119|0.51188	T|T	0.1|0.08	.|.	14.1781|14.1781	0.65557|0.65557	0.0:0.2852:0.7147:0.0|0.0:0.2852:0.7147:0.0	.|.	340|240	Q9NQX4|F5H231	MYO5C_HUMAN|.	V|W	340;283|240	ENSP00000261839:A340V;ENSP00000410582:A283V|.	ENSP00000261839:A340V|ENSP00000445574:R240W	A|R	-|-	2|1	0|2	MYO5C|MYO5C	50343707|50343707	0.907000|0.907000	0.30839|0.30839	0.005000|0.005000	0.12908|0.12908	0.024000|0.024000	0.10985|0.10985	3.920000|3.920000	0.56446|0.56446	1.168000|1.168000	0.42723|0.42723	0.655000|0.655000	0.94253|0.94253	GCG|CGG		0.468	MYO5C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419562.1	NM_018728	
TCF12	6938	broad.mit.edu	37	15	57565320	57565320	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr15:57565320G>A	ENST00000267811.5	+	18	2070	c.1766G>A	c.(1765-1767)cGc>cAc	p.R589H	TCF12_ENST00000343827.3_Missense_Mutation_p.R419H|TCF12_ENST00000537840.1_Missense_Mutation_p.R353H|TCF12_ENST00000452095.2_Missense_Mutation_p.R609H|TCF12_ENST00000543579.1_Missense_Mutation_p.R443H|TCF12_ENST00000438423.2_Missense_Mutation_p.R613H|TCF12_ENST00000557843.1_Missense_Mutation_p.R589H|TCF12_ENST00000559703.1_Missense_Mutation_p.R246H|TCF12_ENST00000559710.1_Missense_Mutation_p.R223H|TCF12_ENST00000333725.5_Missense_Mutation_p.R613H	NM_003205.3|NM_207038.1	NP_003196.1|NP_996921.1	Q99081	HTF4_HUMAN	transcription factor 12	589	bHLH. {ECO:0000255|PROSITE- ProRule:PRU00981}.				immune response (GO:0006955)|muscle organ development (GO:0007517)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	bHLH transcription factor binding (GO:0043425)|E-box binding (GO:0070888)|enhancer binding (GO:0035326)|sequence-specific DNA binding transcription factor activity (GO:0003700)|SMAD binding (GO:0046332)|transcription factor binding (GO:0008134)	p.R613H(2)|p.R609H(2)|p.R419H(1)	TCF12/NR4A3(2)	breast(2)|central_nervous_system(5)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(1)|lung(13)|ovary(2)|prostate(1)|skin(2)|urinary_tract(1)	36		Colorectal(260;0.0907)		all cancers(107;0.000313)|GBM - Glioblastoma multiforme(80;0.00878)|STAD - Stomach adenocarcinoma(283;0.239)		GAACGCTTACGCGTGCGGGAT	0.428			T	TEC	extraskeletal myxoid chondrosarcoma																																p.R613H			Dom	yes		15	15q21	6938	"""transcription factor 12 (HTF4, helix-loop-helix transcription factors 4)"""		M	.	.	5	Substitution - Missense(5)	kidney(4)|large_intestine(1)	c.G1838A	15						.						96.0	103.0	101.0					15																	57565320		2192	4292	6484	55352612	SO:0001583	missense	6938	exon19			BC050556	CCDS10159.1, CCDS10160.1, CCDS42042.1	15q21	2013-05-21	2008-07-31		ENSG00000140262	ENSG00000140262		"""Basic helix-loop-helix proteins"""	11623	protein-coding gene	gene with protein product	"""helix-loop-helix transcription factor 4"""	600480				1886779	Standard	NM_003205		Approved	HEB, HTF4, HsT17266, bHLHb20	uc002aeb.3	Q99081	OTTHUMG00000132047	ENST00000267811.5:c.1766G>A	15.37:g.57565320G>A	ENSP00000267811:p.Arg589His	Somatic		Capture	Illumina HiSeq	Phase_I	55352612	NM_207037	Q7Z3D9|Q86TC1|Q86VM2	Missense_Mutation	SNP	ENST00000267811.5	37	CCDS10159.1	.	.	.	.	.	.	.	.	.	.	G	34	5.390505	0.95988	.	.	ENSG00000140262	ENST00000543236;ENST00000267811;ENST00000438423;ENST00000452095;ENST00000333725;ENST00000543579;ENST00000537840;ENST00000343827;ENST00000543417	D;D;D;D;D;D;D	0.99722	-6.53;-6.53;-6.53;-6.53;-6.53;-6.53;-6.53	4.72	4.72	0.59763	Helix-loop-helix DNA-binding (5);	0.000000	0.85682	D	0.000000	D	0.99778	0.9908	M	0.92923	3.36	0.80722	D	1	D;D;D;D;D;D;D;D;D;D	0.89917	1.0;0.999;1.0;1.0;0.999;1.0;1.0;0.999;1.0;0.999	D;D;D;D;D;D;D;D;D;D	0.97110	1.0;0.994;0.999;1.0;0.989;0.999;0.997;0.994;0.995;0.991	D	0.96981	0.9715	10	0.87932	D	0	-14.1354	18.0262	0.89270	0.0:0.0:1.0:0.0	.	609;223;443;353;609;641;443;419;589;613	B4DGI9;B4DZP2;B4DH96;B4E1W1;E9PGY0;F5H6Z6;F5GY10;Q99081-2;Q99081;Q99081-3	.;.;.;.;.;.;.;.;HTF4_HUMAN;.	H	641;589;613;609;613;443;353;419;201	ENSP00000267811:R589H;ENSP00000388940:R613H;ENSP00000396881:R609H;ENSP00000331057:R613H;ENSP00000440017:R443H;ENSP00000444696:R353H;ENSP00000342459:R419H	ENSP00000267811:R589H	R	+	2	0	TCF12	55352612	1.000000	0.71417	0.992000	0.48379	0.951000	0.60555	9.683000	0.98657	2.329000	0.79093	0.655000	0.94253	CGC		0.428	TCF12-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000255069.3	NM_003205	
VPS13C	54832	broad.mit.edu	37	15	62211516	62211516	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr15:62211516T>C	ENST00000261517.5	-	58	7683	c.7610A>G	c.(7609-7611)aAa>aGa	p.K2537R	VPS13C_ENST00000395898.3_Missense_Mutation_p.K2494R|VPS13C_ENST00000395896.4_Missense_Mutation_p.K2537R|VPS13C_ENST00000249837.3_Missense_Mutation_p.K2494R	NM_020821.2	NP_065872.1			vacuolar protein sorting 13 homolog C (S. cerevisiae)									p.K2537R(1)		NS(3)|breast(4)|endometrium(4)|kidney(9)|large_intestine(26)|lung(46)|ovary(5)|prostate(6)|skin(6)|stomach(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	117						GGTAATTACTTTATTCCCTTC	0.408																																					p.K2494R												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A7481G	15						.						113.0	110.0	111.0					15																	62211516		2203	4300	6503	59998808	SO:0001583	missense	54832	exon56			AJ608770	CCDS10180.1, CCDS32257.1, CCDS45272.1, CCDS58367.1	15q21.3	2009-07-09	2006-04-04		ENSG00000129003	ENSG00000129003			23594	protein-coding gene	gene with protein product		608879	"""vacuolar protein sorting 13C (yeast)"""				Standard	NM_018080		Approved	FLJ20136, FLJ10381, KIAA1421	uc002agz.3	Q709C8	OTTHUMG00000132801	ENST00000261517.5:c.7610A>G	15.37:g.62211516T>C	ENSP00000261517:p.Lys2537Arg	Somatic		Capture	Illumina HiSeq	Phase_I	59998808	NM_017684		Missense_Mutation	SNP	ENST00000261517.5	37	CCDS32257.1	.	.	.	.	.	.	.	.	.	.	T	27.3	4.819514	0.90873	.	.	ENSG00000129003	ENST00000249837;ENST00000261517;ENST00000395896;ENST00000395898	T;T;T	0.58506	0.34;0.33;0.51	5.59	5.59	0.84812	.	0.128426	0.64402	D	0.000012	T	0.74642	0.3743	M	0.77313	2.365	0.80722	D	1	P;D;P;P	0.63880	0.815;0.993;0.815;0.876	P;D;P;P	0.64042	0.646;0.921;0.646;0.638	T	0.75701	-0.3226	10	0.42905	T	0.14	.	16.0584	0.80820	0.0:0.0:0.0:1.0	.	2494;2537;2494;2537	Q709C8-4;Q709C8-2;Q709C8-3;Q709C8	.;.;.;VP13C_HUMAN	R	2494;2537;2537;2537	ENSP00000249837:K2494R;ENSP00000261517:K2537R;ENSP00000379233:K2537R	ENSP00000249837:K2494R	K	-	2	0	VPS13C	59998808	1.000000	0.71417	1.000000	0.80357	0.969000	0.65631	6.999000	0.76283	2.231000	0.72958	0.533000	0.62120	AAA		0.408	VPS13C-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000415997.1	NM_017684	
VPS13C	54832	broad.mit.edu	37	15	62300933	62300933	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr15:62300933A>G	ENST00000261517.5	-	14	1112	c.1039T>C	c.(1039-1041)Tca>Cca	p.S347P	VPS13C_ENST00000395898.3_Missense_Mutation_p.S304P|VPS13C_ENST00000395896.4_Missense_Mutation_p.S347P|VPS13C_ENST00000249837.3_Missense_Mutation_p.S304P	NM_020821.2	NP_065872.1			vacuolar protein sorting 13 homolog C (S. cerevisiae)									p.S347P(1)		NS(3)|breast(4)|endometrium(4)|kidney(9)|large_intestine(26)|lung(46)|ovary(5)|prostate(6)|skin(6)|stomach(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	117						TAATCCACTGACTCCAAAAGG	0.269																																					p.S304P												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T910C	15						.						104.0	78.0	87.0					15																	62300933		2203	4300	6503	60088225	SO:0001583	missense	54832	exon12			AJ608770	CCDS10180.1, CCDS32257.1, CCDS45272.1, CCDS58367.1	15q21.3	2009-07-09	2006-04-04		ENSG00000129003	ENSG00000129003			23594	protein-coding gene	gene with protein product		608879	"""vacuolar protein sorting 13C (yeast)"""				Standard	NM_018080		Approved	FLJ20136, FLJ10381, KIAA1421	uc002agz.3	Q709C8	OTTHUMG00000132801	ENST00000261517.5:c.1039T>C	15.37:g.62300933A>G	ENSP00000261517:p.Ser347Pro	Somatic		Capture	Illumina HiSeq	Phase_I	60088225	NM_017684		Missense_Mutation	SNP	ENST00000261517.5	37	CCDS32257.1	.	.	.	.	.	.	.	.	.	.	A	24.0	4.483123	0.84747	.	.	ENSG00000129003	ENST00000249837;ENST00000261517;ENST00000395896;ENST00000395898	T;T;T	0.45668	0.89;0.89;0.89	5.09	5.09	0.68999	.	0.159238	0.42964	D	0.000637	T	0.69024	0.3065	M	0.86740	2.835	0.80722	D	1	D;D;D;D	0.89917	0.999;1.0;1.0;1.0	D;D;D;D	0.83275	0.992;0.996;0.994;0.993	T	0.75741	-0.3211	10	0.72032	D	0.01	.	15.16	0.72775	1.0:0.0:0.0:0.0	.	304;347;304;347	Q709C8-4;Q709C8-2;Q709C8-3;Q709C8	.;.;.;VP13C_HUMAN	P	304;347;347;347	ENSP00000249837:S304P;ENSP00000261517:S347P;ENSP00000379233:S347P	ENSP00000249837:S304P	S	-	1	0	VPS13C	60088225	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.912000	0.87465	2.053000	0.61076	0.533000	0.62120	TCA		0.269	VPS13C-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000415997.1	NM_017684	
IQCH	64799	broad.mit.edu	37	15	67692501	67692501	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr15:67692501G>A	ENST00000335894.4	+	14	2021	c.1955G>A	c.(1954-1956)cGt>cAt	p.R652H	IQCH_ENST00000358767.3_Missense_Mutation_p.R388H|IQCH_ENST00000360277.4_Missense_Mutation_p.R313H|IQCH_ENST00000546225.1_Missense_Mutation_p.R309H	NM_001031715.2	NP_001026885	Q86VS3	IQCH_HUMAN	IQ motif containing H	652								p.R652H(2)		NS(1)|breast(1)|cervix(1)|endometrium(2)|large_intestine(9)|lung(9)|ovary(2)|pancreas(2)|skin(5)|upper_aerodigestive_tract(1)	33				Colorectal(3;0.0856)		CAAATACAGCGTTGGCTCTTT	0.433																																					p.R652H												.	.	2	Substitution - Missense(2)	large_intestine(1)|endometrium(1)	c.G1955A	15						.						102.0	96.0	98.0					15																	67692501		2201	4299	6500	65479555	SO:0001583	missense	64799	exon14			AY014282	CCDS10223.1, CCDS32273.1, CCDS10223.2, CCDS61680.1, CCDS61681.1	15q23	2005-10-24			ENSG00000103599	ENSG00000103599			25721	protein-coding gene	gene with protein product		612523				12477932	Standard	NM_022784		Approved	FLJ12476	uc002aqo.2	Q86VS3	OTTHUMG00000133231	ENST00000335894.4:c.1955G>A	15.37:g.67692501G>A	ENSP00000336861:p.Arg652His	Somatic		Capture	Illumina HiSeq	Phase_I	65479555	NM_001031715	A8K8W3|C9JPR6|D6RJ88|Q4G0S6|Q8NEH9|Q9BWX2|Q9H9Y1|Q9UF88	Missense_Mutation	SNP	ENST00000335894.4	37	CCDS32273.1	.	.	.	.	.	.	.	.	.	.	G	23.4	4.407769	0.83340	.	.	ENSG00000103599	ENST00000358767;ENST00000546225;ENST00000335894;ENST00000360277	T;T;T;T	0.55760	0.61;0.61;0.5;0.61	5.24	5.24	0.73138	.	0.000000	0.85682	D	0.000000	T	0.75019	0.3793	M	0.80183	2.485	0.58432	D	0.999999	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.80764	0.994;0.989;0.993	T	0.78003	-0.2374	10	0.59425	D	0.04	-24.1551	18.8189	0.92088	0.0:0.0:1.0:0.0	.	309;313;652	Q86VS3-2;Q86VS3-4;Q86VS3	.;.;IQCH_HUMAN	H	388;309;652;313	ENSP00000351617:R388H;ENSP00000444118:R309H;ENSP00000336861:R652H;ENSP00000353419:R313H	ENSP00000336861:R652H	R	+	2	0	IQCH	65479555	1.000000	0.71417	1.000000	0.80357	0.394000	0.30568	8.872000	0.92352	2.436000	0.82500	0.655000	0.94253	CGT		0.433	IQCH-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256969.1	NM_022784	
CALML4	91860	broad.mit.edu	37	15	68489809	68489809	+	Silent	SNP	C	C	T	rs554953385		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr15:68489809C>T	ENST00000467889.1	-	4	646	c.462G>A	c.(460-462)acG>acA	p.T154T	CALML4_ENST00000540479.1_Silent_p.T78T|CALML4_ENST00000448060.2_Silent_p.T107T|RP11-315D16.2_ENST00000562767.1_Missense_Mutation_p.E81K|CALML4_ENST00000395465.3_Intron	NM_033429.2	NP_219501.2	Q96GE6	CALL4_HUMAN	calmodulin-like 4	154	EF-hand 3. {ECO:0000255|PROSITE- ProRule:PRU00448}.		T -> K (in dbSNP:rs2280217).				calcium ion binding (GO:0005509)	p.T154T(1)		large_intestine(2)|lung(1)|upper_aerodigestive_tract(1)	4						CCCCCAGACTCGTGAGTTTTG	0.527													C|||	1	0.000199681	0.0	0.0	5008	,	,		20113	0.0		0.0	False		,,,				2504	0.001				p.T107T												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G321A	15						.						147.0	143.0	144.0					15																	68489809		1985	4145	6130	66276863	SO:0001819	synonymous_variant	91860	exon3			AF308287	CCDS10226.2, CCDS42052.1, CCDS66808.1	15q22.31	2013-01-10			ENSG00000129007	ENSG00000129007		"""EF-hand domain containing"""	18445	protein-coding gene	gene with protein product							Standard	NM_033429		Approved	MGC4809, NY-BR-20	uc002arb.3	Q96GE6	OTTHUMG00000133287	ENST00000467889.1:c.462G>A	15.37:g.68489809C>T		Somatic		Capture	Illumina HiSeq	Phase_I	66276863	NM_001031733	B4DL15|F8W6Y4|Q6MZY3|Q6N048|Q9H286	Silent	SNP	ENST00000467889.1	37	CCDS10226.2																																																																																				0.527	CALML4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257067.3	NM_033429	
TLE3	7090	broad.mit.edu	37	15	70358541	70358541	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr15:70358541G>A	ENST00000558939.1	-	7	1766	c.389C>T	c.(388-390)gCg>gTg	p.A130V	TLE3_ENST00000557997.1_Missense_Mutation_p.A130V|TLE3_ENST00000317509.8_Missense_Mutation_p.A130V|TLE3_ENST00000451782.2_Missense_Mutation_p.A130V|TLE3_ENST00000560939.1_Missense_Mutation_p.A135V|TLE3_ENST00000559929.1_Missense_Mutation_p.A140V|TLE3_ENST00000539550.1_Missense_Mutation_p.A74V|TLE3_ENST00000557907.1_Missense_Mutation_p.A130V|TLE3_ENST00000558379.1_Missense_Mutation_p.A130V|TLE3_ENST00000559048.1_Missense_Mutation_p.A135V|TLE3_ENST00000440567.3_Missense_Mutation_p.A123V|TLE3_ENST00000442299.2_Missense_Mutation_p.A130V|TLE3_ENST00000558201.1_Missense_Mutation_p.A136V|TLE3_ENST00000559191.1_Intron|TLE3_ENST00000560589.1_Missense_Mutation_p.A74V	NM_001282979.1|NM_001282980.1|NM_001282981.1	NP_001269908.1|NP_001269909.1|NP_001269910.1	Q04726	TLE3_HUMAN	transducin-like enhancer of split 3	130	Gln-rich.				Notch signaling pathway (GO:0007219)|organ morphogenesis (GO:0009887)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)		p.A130V(1)		breast(1)|endometrium(4)|kidney(2)|large_intestine(4)|lung(16)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	31						GAGGTGCTGCGCCTGGAGCTG	0.677																																					p.A130V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C389T	15						.						13.0	19.0	17.0					15																	70358541		2185	4283	6468	68145595	SO:0001583	missense	7090	exon7			M99438	CCDS45293.1, CCDS45294.1, CCDS58375.1, CCDS61689.1, CCDS61691.1, CCDS61692.1, CCDS73747.1	15q22	2014-03-07	2014-03-07			ENSG00000140332		"""WD repeat domain containing"""	11839	protein-coding gene	gene with protein product		600190	"""transducin-like enhancer of split 3, homolog of Drosophila E(sp1)"", ""transducin-like enhancer of split 3 (E(sp1) homolog, Drosophila)"""			8365415	Standard	XM_005254623		Approved	ESG, ESG3, KIAA1547, HsT18976, GRG3	uc002asm.2	Q04726		ENST00000558939.1:c.389C>T	15.37:g.70358541G>A	ENSP00000452871:p.Ala130Val	Somatic		Capture	Illumina HiSeq	Phase_I	68145595	NM_020908	B4DPT0|E9PD64|F8W964|Q6PI57|Q8IVV6|Q8WVR2|Q9HCM5	Missense_Mutation	SNP	ENST00000558939.1	37	CCDS45293.1	.	.	.	.	.	.	.	.	.	.	G	32	5.132990	0.94517	.	.	ENSG00000140332	ENST00000442299;ENST00000451782;ENST00000317509;ENST00000440567;ENST00000539550	T;T;T;T;T	0.56941	0.78;0.83;0.87;0.85;0.43	5.56	5.56	0.83823	Groucho/TLE, N-terminal Q-rich domain (1);	0.058754	0.64402	D	0.000002	T	0.75664	0.3880	M	0.80982	2.52	0.80722	D	1	P;P;P;P;D;P;P;P	0.89917	0.689;0.6;0.934;0.947;1.0;0.525;0.526;0.934	B;P;P;P;D;B;B;P	0.91635	0.206;0.698;0.491;0.625;0.999;0.284;0.092;0.572	T	0.77289	-0.2643	10	0.56958	D	0.05	-0.4241	19.5359	0.95254	0.0:0.0:1.0:0.0	.	123;130;130;130;130;130;135;74	F8W964;E9PD64;Q04726-3;Q6PI57;Q04726-2;Q04726;Q04726-4;F5H7D6	.;.;.;.;.;TLE3_HUMAN;.;.	V	130;130;130;123;74	ENSP00000390007:A130V;ENSP00000394717:A130V;ENSP00000319233:A130V;ENSP00000415057:A123V;ENSP00000442594:A74V	ENSP00000319233:A130V	A	-	2	0	TLE3	68145595	1.000000	0.71417	0.985000	0.45067	0.990000	0.78478	9.606000	0.98325	2.609000	0.88269	0.655000	0.94253	GCG		0.677	TLE3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000416913.1	NM_005078	
LARP6	55323	broad.mit.edu	37	15	71124560	71124560	+	Missense_Mutation	SNP	C	C	T	rs372104696		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr15:71124560C>T	ENST00000299213.8	-	3	1377	c.1307G>A	c.(1306-1308)cGt>cAt	p.R436H	RP11-138H8.7_ENST00000592096.1_lincRNA	NM_018357.2	NP_060827.2	Q9BRS8	LARP6_HUMAN	La ribonucleoprotein domain family, member 6	436					regulation of translation (GO:0006417)|RNA processing (GO:0006396)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	nucleotide binding (GO:0000166)|RNA binding (GO:0003723)	p.R436H(1)		breast(1)|cervix(1)|endometrium(1)|large_intestine(5)|lung(9)|skin(1)|upper_aerodigestive_tract(1)	19						GGCTTGGCGACGCCTCCGGAC	0.617																																					p.R436H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1307A	15						.	C	HIS/ARG	0,4398		0,0,2199	64.0	65.0	65.0		1307	5.3	1.0	15		65	1,8593	1.2+/-3.3	0,1,4296	no	missense	LARP6	NM_018357.2	29	0,1,6495	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging	436/492	71124560	1,12991	2199	4297	6496	68911614	SO:0001583	missense	55323	exon3			BC009446	CCDS10236.1, CCDS32281.1	15q23	2012-11-19			ENSG00000166173	ENSG00000166173		"""La ribonucleoprotein domain containing"""	24012	protein-coding gene	gene with protein product		611300				12477932	Standard	NM_018357		Approved	acheron, FLJ11196	uc002ass.3	Q9BRS8	OTTHUMG00000172179	ENST00000299213.8:c.1307G>A	15.37:g.71124560C>T	ENSP00000299213:p.Arg436His	Somatic		Capture	Illumina HiSeq	Phase_I	68911614	NM_018357	Q5XKE4|Q8N3N2|Q9NUR0	Missense_Mutation	SNP	ENST00000299213.8	37	CCDS32281.1	.	.	.	.	.	.	.	.	.	.	C	28.1	4.888241	0.91814	0.0	1.16E-4	ENSG00000166173	ENST00000299213	T	0.69926	-0.44	5.3	5.3	0.74995	.	0.000000	0.85682	D	0.000000	T	0.80628	0.4659	M	0.65498	2.005	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	T	0.82396	-0.0478	10	0.72032	D	0.01	-21.8005	16.4568	0.84021	0.0:1.0:0.0:0.0	.	436	Q9BRS8	LARP6_HUMAN	H	436	ENSP00000299213:R436H	ENSP00000299213:R436H	R	-	2	0	LARP6	68911614	1.000000	0.71417	0.988000	0.46212	0.981000	0.71138	5.475000	0.66787	2.471000	0.83476	0.555000	0.69702	CGT		0.617	LARP6-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417197.2	NM_018357	
THSD4	79875	broad.mit.edu	37	15	72040788	72040788	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr15:72040788G>A	ENST00000355327.3	+	14	2404	c.2270G>A	c.(2269-2271)aGg>aAg	p.R757K	THSD4_ENST00000261862.6_Missense_Mutation_p.R757K|THSD4_ENST00000357769.4_Missense_Mutation_p.R397K|THSD4_ENST00000567838.1_3'UTR			Q6ZMP0	THSD4_HUMAN	thrombospondin, type I, domain containing 4	757	TSP type-1 3. {ECO:0000255|PROSITE- ProRule:PRU00210}.				elastic fiber assembly (GO:0048251)	extracellular vesicular exosome (GO:0070062)|microfibril (GO:0001527)	metalloendopeptidase activity (GO:0004222)	p.R757K(1)		breast(1)|central_nervous_system(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(20)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	42						GTGGGACAGAGGACCCGTGAT	0.557																																					p.R757K												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2270A	15						.						147.0	166.0	159.0					15																	72040788		2180	4268	6448	69827842	SO:0001583	missense	79875	exon13			AK023772	CCDS10238.2, CCDS66817.1	15q23	2009-11-09			ENSG00000187720	ENSG00000187720			25835	protein-coding gene	gene with protein product		614476				19734141	Standard	NM_001286429		Approved	FVSY9334, PRO34005, FLJ13710, ADAMTSL6	uc002atb.1	Q6ZMP0	OTTHUMG00000133389	ENST00000355327.3:c.2270G>A	15.37:g.72040788G>A	ENSP00000347484:p.Arg757Lys	Somatic		Capture	Illumina HiSeq	Phase_I	69827842	NM_024817	B2RTY3|B4DR13|Q6MZI3|Q6UXZ8|Q9H8E4	Missense_Mutation	SNP	ENST00000355327.3	37	CCDS10238.2	.	.	.	.	.	.	.	.	.	.	G	18.21	3.573004	0.65765	.	.	ENSG00000187720	ENST00000355327;ENST00000261862;ENST00000357769	T;T;T	0.55234	0.53;0.53;0.53	4.68	4.68	0.58851	.	.	.	.	.	T	0.46288	0.1385	L	0.51914	1.62	0.45718	D	0.998624	B;P	0.38148	0.058;0.62	B;B	0.40066	0.098;0.318	T	0.36114	-0.9761	9	0.28530	T	0.3	.	9.1525	0.36971	0.1015:0.0:0.8985:0.0	.	397;757	B4DR13;Q6ZMP0	.;THSD4_HUMAN	K	757;757;397	ENSP00000347484:R757K;ENSP00000261862:R757K;ENSP00000350413:R397K	ENSP00000261862:R757K	R	+	2	0	THSD4	69827842	1.000000	0.71417	1.000000	0.80357	0.644000	0.38419	5.411000	0.66386	2.313000	0.78055	0.563000	0.77884	AGG		0.557	THSD4-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257253.2	NM_024817	
NR2E3	10002	broad.mit.edu	37	15	72104776	72104776	+	RNA	SNP	G	G	A	rs530684859		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr15:72104776G>A	ENST00000398840.2	+	0	862							Q9Y5X4	NR2E3_HUMAN	nuclear receptor subfamily 2, group E, member 3						eye photoreceptor cell development (GO:0042462)|gene expression (GO:0010467)|intracellular receptor signaling pathway (GO:0030522)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|phototransduction (GO:0007602)|positive regulation of rhodopsin gene expression (GO:0045872)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|retina development in camera-type eye (GO:0060041)|signal transduction (GO:0007165)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|visual perception (GO:0007601)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|sequence-specific DNA binding (GO:0043565)|steroid hormone receptor activity (GO:0003707)|zinc ion binding (GO:0008270)	p.S224S(1)		breast(1)|endometrium(1)|lung(1)	3						ATGAGACCTCGGCTCGCCTAC	0.597																																					p.S224S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G672A	15						.						112.0	119.0	116.0					15																	72104776		2023	4174	6197	69891830			10002	exon5				CCDS73750.1, CCDS73751.1	15q23	2013-01-16			ENSG00000031544	ENSG00000278570		"""Nuclear hormone receptors"""	7974	protein-coding gene	gene with protein product		604485				10220376	Standard	NM_016346		Approved	PNR, rd7, RP37	uc002ath.1	Q9Y5X4	OTTHUMG00000172841		15.37:g.72104776G>A		Somatic		Capture	Illumina HiSeq	Phase_I	69891830	NM_014249	B6ZGU0|Q9UHM4	Silent	SNP	ENST00000398840.2	37																																																																																					0.597	NR2E3-202	KNOWN	basic	processed_transcript	processed_transcript		NM_014249	
PARP6	56965	broad.mit.edu	37	15	72549731	72549731	+	Silent	SNP	G	G	A	rs370713698		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr15:72549731G>A	ENST00000569795.1	-	13	1644	c.957C>T	c.(955-957)ggC>ggT	p.G319G	PARP6_ENST00000287196.9_Silent_p.G319G|PARP6_ENST00000413097.2_5'UTR|PARP6_ENST00000260376.7_Silent_p.G319G			Q2NL67	PARP6_HUMAN	poly (ADP-ribose) polymerase family, member 6	319							NAD+ ADP-ribosyltransferase activity (GO:0003950)	p.G319G(1)		NS(1)|breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(8)|skin(1)|urinary_tract(1)	18						CAGACATGACGCCCAGTGTGT	0.527																																					p.G319G												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C957T	15						.	G		1,4083		0,1,2041	127.0	133.0	131.0		957	-6.4	0.9	15		131	0,8398		0,0,4199	no	coding-synonymous	PARP6	NM_020214.2		0,1,6240	AA,AG,GG		0.0,0.0245,0.0080		319/631	72549731	1,12481	2042	4199	6241	70336785	SO:0001819	synonymous_variant	56965	exon12			AL390093	CCDS10241.2	15q22	2010-02-16			ENSG00000137817	ENSG00000137817		"""Poly (ADP-ribose) polymerases"""	26921	protein-coding gene	gene with protein product						15273990	Standard	XM_005254557		Approved	pART17	uc002auc.3	Q2NL67	OTTHUMG00000133443	ENST00000569795.1:c.957C>T	15.37:g.72549731G>A		Somatic		Capture	Illumina HiSeq	Phase_I	70336785	NM_020214	Q9H7C5|Q9H9X6|Q9HAF3|Q9NPS6|Q9UFG4	Silent	SNP	ENST00000569795.1	37	CCDS10241.2																																																																																				0.527	PARP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257315.2	NM_020214	
HCN4	10021	broad.mit.edu	37	15	73616168	73616168	+	Missense_Mutation	SNP	C	C	T	rs143339036	byFrequency	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr15:73616168C>T	ENST00000261917.3	-	8	3259	c.2266G>A	c.(2266-2268)Gcg>Acg	p.A756T		NM_005477.2	NP_005468.1	Q9Y3Q4	HCN4_HUMAN	hyperpolarization activated cyclic nucleotide-gated potassium channel 4	756					blood circulation (GO:0008015)|cation transport (GO:0006812)|cellular response to cAMP (GO:0071320)|cellular response to cGMP (GO:0071321)|in utero embryonic development (GO:0001701)|muscle contraction (GO:0006936)|potassium ion transmembrane transport (GO:0071805)|regulation of heart rate (GO:0002027)|regulation of membrane potential (GO:0042391)|sodium ion transmembrane transport (GO:0035725)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|intrinsic component of plasma membrane (GO:0031226)|plasma membrane (GO:0005886)|terminal bouton (GO:0043195)	cAMP binding (GO:0030552)|cation channel activity (GO:0005261)|identical protein binding (GO:0042802)|intracellular cAMP activated cation channel activity (GO:0005222)|voltage-gated potassium channel activity (GO:0005249)|voltage-gated sodium channel activity (GO:0005248)	p.A756T(1)		NS(2)|biliary_tract(1)|breast(1)|endometrium(4)|kidney(1)|large_intestine(13)|liver(1)|lung(18)|ovary(6)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	55				COAD - Colon adenocarcinoma(1;0.142)		ACGCGGTGCGCGCAGTGGGCC	0.642																																					p.A756T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2266A	15						.	C	THR/ALA	0,4396		0,0,2198	47.0	54.0	52.0		2266	3.5	0.4	15	dbSNP_134	52	4,8590	3.7+/-12.6	0,4,4293	yes	missense	HCN4	NM_005477.2	58	0,4,6491	TT,TC,CC		0.0465,0.0,0.0308	benign	756/1204	73616168	4,12986	2198	4297	6495	71403221	SO:0001583	missense	10021	exon8			AJ132429	CCDS10248.1	15q24.1	2011-07-05			ENSG00000138622	ENSG00000138622		"""Voltage-gated ion channels / Cyclic nucleotide-regulated channels"""	16882	protein-coding gene	gene with protein product		605206				10228147, 10430953, 16382102	Standard	NM_005477		Approved		uc002avp.3	Q9Y3Q4	OTTHUMG00000137563	ENST00000261917.3:c.2266G>A	15.37:g.73616168C>T	ENSP00000261917:p.Ala756Thr	Somatic		Capture	Illumina HiSeq	Phase_I	71403221	NM_005477	Q9UMQ7	Missense_Mutation	SNP	ENST00000261917.3	37	CCDS10248.1	.	.	.	.	.	.	.	.	.	.	C	9.656	1.142729	0.21205	0.0	4.65E-4	ENSG00000138622	ENST00000261917	T	0.80214	-1.35	3.45	3.45	0.39498	.	.	.	.	.	T	0.70552	0.3237	L	0.35723	1.085	0.41831	D	0.990073	B	0.21905	0.062	B	0.16722	0.016	T	0.67313	-0.5702	9	0.33940	T	0.23	.	11.2142	0.48817	0.0:0.8138:0.1862:0.0	.	756	Q9Y3Q4	HCN4_HUMAN	T	756	ENSP00000261917:A756T	ENSP00000261917:A756T	A	-	1	0	HCN4	71403221	0.991000	0.36638	0.431000	0.26735	0.242000	0.25591	2.848000	0.48278	1.756000	0.51951	0.305000	0.20034	GCG		0.642	HCN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268900.2	NM_005477	
C15orf59	388135	broad.mit.edu	37	15	74032755	74032755	+	Missense_Mutation	SNP	C	C	T	rs565532541		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr15:74032755C>T	ENST00000569673.1	-	3	1589	c.385G>A	c.(385-387)Gag>Aag	p.E129K	C15orf59_ENST00000379822.4_Missense_Mutation_p.E129K|C15orf59_ENST00000558834.1_5'UTR			Q2T9L4	CO059_HUMAN	chromosome 15 open reading frame 59	129								p.E129K(1)		breast(1)|endometrium(2)|large_intestine(2)|lung(6)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	15						CGAGTCGACTCGGGACCATCC	0.632													C|||	1	0.000199681	0.0	0.0	5008	,	,		16583	0.0		0.0	False		,,,				2504	0.001				p.E129K												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G385A	15						.						60.0	66.0	64.0					15																	74032755		2198	4294	6492	71819808	SO:0001583	missense	388135	exon2				CCDS32289.1	15q24.1	2012-09-27			ENSG00000205363	ENSG00000205363			33753	protein-coding gene	gene with protein product							Standard	XM_005254369		Approved	MGC131524, LOC388135	uc002avy.3	Q2T9L4	OTTHUMG00000172556	ENST00000569673.1:c.385G>A	15.37:g.74032755C>T	ENSP00000457205:p.Glu129Lys	Somatic		Capture	Illumina HiSeq	Phase_I	71819808	NM_001039614		Missense_Mutation	SNP	ENST00000569673.1	37	CCDS32289.1	.	.	.	.	.	.	.	.	.	.	C	18.77	3.695619	0.68386	.	.	ENSG00000205363	ENST00000379822	T	0.43294	0.95	5.15	5.15	0.70609	.	0.192700	0.44483	D	0.000452	T	0.50752	0.1634	L	0.36672	1.1	0.48762	D	0.999702	D	0.69078	0.997	P	0.58454	0.839	T	0.42632	-0.9440	10	0.33940	T	0.23	.	18.2	0.89834	0.0:1.0:0.0:0.0	.	129	Q2T9L4	CO059_HUMAN	K	129	ENSP00000369150:E129K	ENSP00000369150:E129K	E	-	1	0	C15orf59	71819808	0.999000	0.42202	0.595000	0.28798	0.657000	0.38888	4.305000	0.59110	2.388000	0.81334	0.561000	0.74099	GAG		0.632	C15orf59-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419077.2	NM_001039614	
CYP1A2	1544	broad.mit.edu	37	15	75045573	75045573	+	Silent	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr15:75045573C>T	ENST00000343932.4	+	6	1278	c.1215C>T	c.(1213-1215)tgC>tgT	p.C405C		NM_000761.3	NP_000752.2	P05177	CP1A2_HUMAN	cytochrome P450, family 1, subfamily A, polypeptide 2	405					alkaloid metabolic process (GO:0009820)|arachidonic acid metabolic process (GO:0019369)|cellular respiration (GO:0045333)|cellular response to cadmium ion (GO:0071276)|dibenzo-p-dioxin metabolic process (GO:0018894)|drug catabolic process (GO:0042737)|drug metabolic process (GO:0017144)|epoxygenase P450 pathway (GO:0019373)|exogenous drug catabolic process (GO:0042738)|heterocycle metabolic process (GO:0046483)|hydrogen peroxide biosynthetic process (GO:0050665)|lung development (GO:0030324)|methylation (GO:0032259)|monocarboxylic acid metabolic process (GO:0032787)|monoterpenoid metabolic process (GO:0016098)|omega-hydroxylase P450 pathway (GO:0097267)|oxidation-reduction process (GO:0055114)|oxidative deethylation (GO:0071615)|oxidative demethylation (GO:0070989)|porphyrin-containing compound metabolic process (GO:0006778)|post-embryonic development (GO:0009791)|regulation of gene expression (GO:0010468)|response to estradiol (GO:0032355)|response to lipopolysaccharide (GO:0032496)|small molecule metabolic process (GO:0044281)|steroid catabolic process (GO:0006706)|toxin biosynthetic process (GO:0009403)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)|intracellular membrane-bounded organelle (GO:0043231)	aromatase activity (GO:0070330)|caffeine oxidase activity (GO:0034875)|demethylase activity (GO:0032451)|electron carrier activity (GO:0009055)|enzyme binding (GO:0019899)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|monooxygenase activity (GO:0004497)|oxidoreductase activity (GO:0016491)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen (GO:0016712)	p.C405C(1)		breast(2)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(7)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	33					"""""""Insulin(DB00071)|Acenocoumarol(DB01418)|Acetaminophen(DB00316)|Agomelatine(DB06594)|Albendazole(DB00518)|Alitretinoin(DB00523)|Almotriptan(DB00918)|Alosetron(DB00969)|Aminoglutethimide(DB00357)|Aminophenazone(DB01424)|Aminophylline(DB01223)|Amiodarone(DB01118)|Amitriptyline(DB00321)|Amlodipine(DB00381)|Anagrelide(DB00261)|Anastrozole(DB01217)|Antipyrine(DB01435)|Apixaban(DB06605)|Aprepitant(DB00673)|Asenapine(DB06216)|Atropine(DB00572)|Axitinib(DB06626)|Azelastine(DB00972)|Azithromycin(DB00207)|Benzyl alcohol(DB06770)|Betaxolol(DB00195)|Bortezomib(DB00188)|Bromazepam(DB01558)|Bromocriptine(DB01200)|Bupivacaine(DB00297)|Buprenorphine(DB00921)|Bupropion(DB01156)|Caffeine(DB00201)|Carbamazepine(DB00564)|Carmustine(DB00262)|Carvedilol(DB01136)|Chlorpromazine(DB00477)|Chlorzoxazone(DB00356)|Cilostazol(DB01166)|Cimetidine(DB00501)|Cinacalcet(DB01012)|Cinnarizine(DB00568)|Ciprofloxacin(DB00537)|Cisapride(DB00604)|Citalopram(DB00215)|Clarithromycin(DB01211)|Clenbuterol(DB01407)|Clevidipine(DB04920)|Clobetasol propionate(DB01013)|Clomifene(DB00882)|Clomipramine(DB01242)|Clonidine(DB00575)|Clopidogrel(DB00758)|Clotrimazole(DB00257)|Clozapine(DB00363)|Conjugated Estrogens(DB00286)|Cyclobenzaprine(DB00924)|Dacarbazine(DB00851)|Dapagliflozin(DB06292)|Dasatinib(DB01254)|Daunorubicin(DB00694)|Delavirdine(DB00705)|Desipramine(DB01151)|Desloratadine(DB00967)|Dexfenfluramine(DB01191)|Dexmedetomidine(DB00633)|Diazepam(DB00829)|Diclofenac(DB00586)|Dinoprostone(DB00917)|Diphenhydramine(DB01075)|Domperidone(DB01184)|Dopamine(DB00988)|Doxepin(DB01142)|Duloxetine(DB00476)|Edetic Acid(DB00974)|Efavirenz(DB00625)|Eltrombopag(DB06210)|Enoxacin(DB00467)|Epinephrine(DB00668)|Ergotamine(DB00696)|Erlotinib(DB00530)|Erythromycin(DB00199)|Estradiol(DB00783)|Estrone(DB00655)|Estropipate(DB04574)|Ethanol(DB00898)|Etoposide(DB00773)|Etoricoxib(DB01628)|Flunarizine(DB04841)|Flunitrazepam(DB01544)|Fluorouracil(DB00544)|Fluoxetine(DB00472)|Fluphenazine(DB00623)|Flutamide(DB00499)|Fluvastatin(DB01095)|Fluvoxamine(DB00176)|Frovatriptan(DB00998)|Gemfibrozil(DB01241)|Griseofulvin(DB00400)|Guanabenz(DB00629)|Haloperidol(DB00502)|Hesperetin(DB01094)|Hexobarbital(DB01355)|Iloperidone(DB04946)|Imatinib(DB00619)|Imipramine(DB00458)|Imiquimod(DB00724)|inhaled insulin(DB05278)|Insulin Aspart(DB01306)|Insulin Detemir(DB01307)|Insulin Glargine(DB00047)|Insulin Glulisine(DB01309)|Insulin Lispro(DB00046)|Insulin Regular(DB00030)|Irbesartan(DB01029)|Isoniazid(DB00951)|Ketoconazole(DB01026)|Lansoprazole(DB00448)|Leflunomide(DB01097)|Levobupivacaine(DB01002)|Levofloxacin(DB01137)|Lidocaine(DB00281)|Lomefloxacin(DB00978)|Lopinavir(DB01601)|Lorcaserin(DB04871)|Losartan(DB00678)|Lumiracoxib(DB01283)|Malathion(DB00772)|Maprotiline(DB00934)|Meclizine(DB00737)|Melatonin(DB01065)|Menadione(DB00170)|Methadone(DB00333)|Methimazole(DB00763)|Methotrimeprazine(DB01403)|Methoxsalen(DB00553)|Methoxyflurane(DB01028)|Mexiletine(DB00379)|Mianserin(DB06148)|Miconazole(DB01110)|Mirtazapine(DB00370)|Moclobemide(DB01171)|Modafinil(DB00745)|Nabumetone(DB00461)|Nafcillin(DB00607)|Naproxen(DB00788)|Nelfinavir(DB00220)|Nevirapine(DB00238)|Niclosamide(DB06803)|Nicotine(DB00184)|Nifedipine(DB01115)|Nilvadipine(DB06712)|Nisoldipine(DB00401)|Nitric Oxide(DB00435)|Nitroprusside(DB00325)|Norepinephrine(DB00368)|Norfloxacin(DB01059)|Nortriptyline(DB00540)|Ofloxacin(DB01165)|Olanzapine(DB00334)|Omeprazole(DB00338)|Ondansetron(DB00904)|Oxaliplatin(DB00526)|Oxtriphylline(DB01303)|Palonosetron(DB00377)|Pantoprazole(DB00213)|Pazopanib(DB06589)|Pefloxacin(DB00487)|Pentamidine(DB00738)|Pentoxifylline(DB00806)|Perphenazine(DB00850)|Phenobarbital(DB01174)|Phentermine(DB00191)|Phenylephrine(DB00388)|Phenylpropanolamine(DB00397)|Pimozide(DB01100)|Pipotiazine(DB01621)|Pomalidomide(DB08910)|Praziquantel(DB01058)|Primaquine(DB01087)|Primidone(DB00794)|Progesterone(DB00396)|Proguanil(DB01131)|Promazine(DB00420)|Propafenone(DB01182)|Propofol(DB00818)|Propranolol(DB00571)|Pyrazinamide(DB00339)|Quinidine(DB00908)|Quinine(DB00468)|Rabeprazole(DB01129)|Ramelteon(DB00980)|Ranitidine(DB00863)|Rasagiline(DB01367)|Rifabutin(DB00615)|Rifampicin(DB01045)|Rilpivirine(DB08864)|Riluzole(DB00740)|Ritonavir(DB00503)|Rizatriptan(DB00953)|Ropinirole(DB00268)|Ropivacaine(DB00296)|Rosiglitazone(DB00412)|Rotigotine(DB05271)|Roxithromycin(DB00778)|Secobarbital(DB00418)|Selegiline(DB01037)|Sertraline(DB01104)|SIMEPREVIR(DB06290)|Sorafenib(DB00398)|Streptozocin(DB00428)|Sulindac(DB00605)|Tamoxifen(DB00675)|Telithromycin(DB00976)|Tenofovir(DB00300)|Terbinafine(DB00857)|Thalidomide(DB01041)|Theobromine(DB01412)|Theophylline(DB00277)|Thiabendazole(DB00730)|Thioridazine(DB00679)|Thiothixene(DB01623)|Ticlopidine(DB00208)|Tioconazole(DB01007)|Tizanidine(DB00697)|Tocainide(DB01056)|Toremifene(DB00539)|Tranylcypromine(DB00752)|Triamterene(DB00384)|Trifluoperazine(DB00831)|Valproic Acid(DB00313)|Vemurafenib(DB08881)|Verapamil(DB00661)|Warfarin(DB00682)|Zafirlukast(DB00549)|Zileuton(DB00744)|Ziprasidone(DB00246)|Zolmitriptan(DB00315)|Zolpidem(DB00425)"""	CCAAGAAATGCTGTGTCTTCG	0.532																																					p.C405C												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1215T	15						.						160.0	106.0	124.0					15																	75045573		2197	4296	6493	72832626	SO:0001819	synonymous_variant	1544	exon6			AF182274	CCDS32293.1	15q24.1	2013-11-11	2003-01-14		ENSG00000140505	ENSG00000140505	1.14.14.1	"""Cytochrome P450s"""	2596	protein-coding gene	gene with protein product		124060	"""cytochrome P450, subfamily I (aromatic compound-inducible), polypeptide 2"""			15128046	Standard	NM_000761		Approved	P3-450, CP12	uc002ayr.1	P05177	OTTHUMG00000172901	ENST00000343932.4:c.1215C>T	15.37:g.75045573C>T		Somatic		Capture	Illumina HiSeq	Phase_I	72832626	NM_000761	Q16754|Q6NWU5|Q9BXX7|Q9UK49	Silent	SNP	ENST00000343932.4	37	CCDS32293.1																																																																																				0.532	CYP1A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000421263.2	NM_000761	
COX5A	9377	broad.mit.edu	37	15	75221512	75221512	+	Silent	SNP	A	A	G			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr15:75221512A>G	ENST00000322347.6	-	2	315	c.162T>C	c.(160-162)gcT>gcC	p.A54A	COX5A_ENST00000567270.1_Intron|COX5A_ENST00000568783.1_Silent_p.A54A|COX5A_ENST00000568517.1_5'UTR|COX5A_ENST00000562233.1_Silent_p.A54A|COX5A_ENST00000564811.1_Silent_p.A54A	NM_004255.3	NP_004246.2	P20674	COX5A_HUMAN	cytochrome c oxidase subunit Va	54					cellular metabolic process (GO:0044237)|hydrogen ion transmembrane transport (GO:1902600)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|mitochondrial inner membrane (GO:0005743)	cytochrome-c oxidase activity (GO:0004129)|electron carrier activity (GO:0009055)|metal ion binding (GO:0046872)	p.A54A(1)		endometrium(1)|large_intestine(1)|pancreas(1)	3						TTACCCAGCGAGCATCAAACT	0.388																																					p.A54A												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.T162C	15						.						151.0	138.0	143.0					15																	75221512		2197	4295	6492	73008565	SO:0001819	synonymous_variant	9377	exon2			M22760	CCDS10273.1	15q25	2011-07-04			ENSG00000178741	ENSG00000178741	1.9.3.1	"""Mitochondrial respiratory chain complex / Complex IV"""	2267	protein-coding gene	gene with protein product		603773				10072584, 2853101	Standard	NM_004255		Approved		uc002azi.4	P20674	OTTHUMG00000142825	ENST00000322347.6:c.162T>C	15.37:g.75221512A>G		Somatic		Capture	Illumina HiSeq	Phase_I	73008565	NM_004255	P30045|Q8TB65	Silent	SNP	ENST00000322347.6	37	CCDS10273.1																																																																																				0.388	COX5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286417.1	NM_004255	
SCAMP5	192683	broad.mit.edu	37	15	75310872	75310872	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr15:75310872G>A	ENST00000361900.6	+	7	716	c.509G>A	c.(508-510)aGc>aAc	p.S170N	SCAMP5_ENST00000568081.1_Missense_Mutation_p.S103N|SCAMP5_ENST00000545456.1_Missense_Mutation_p.S99N|SCAMP5_ENST00000425597.3_Missense_Mutation_p.S170N|SCAMP5_ENST00000562212.1_Missense_Mutation_p.S178N	NM_001178111.1	NP_001171582.1	Q8TAC9	SCAM5_HUMAN	secretory carrier membrane protein 5	170					exocytosis (GO:0006887)|negative regulation of endocytosis (GO:0045806)|positive regulation of calcium ion-dependent exocytosis (GO:0045956)|positive regulation of cytokine secretion (GO:0050715)|protein transport (GO:0015031)|response to endoplasmic reticulum stress (GO:0034976)	cell junction (GO:0030054)|cytoplasmic vesicle (GO:0031410)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|recycling endosome membrane (GO:0055038)|synapse (GO:0045202)|trans-Golgi network membrane (GO:0032588)		p.S170N(1)		large_intestine(1)|lung(1)|ovary(1)|urinary_tract(2)	5						ATCGCCCTCAGCATGGTACGT	0.542																																					p.S170N												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G509A	15						.						160.0	147.0	151.0					15																	75310872		2035	4192	6227	73097925	SO:0001583	missense	192683	exon7			AL833230	CCDS45306.1	15q24.2	2014-05-20			ENSG00000198794	ENSG00000198794		"""Secretory carrier membrane proteins"""	30386	protein-coding gene	gene with protein product		613766				12477932	Standard	NM_001178111		Approved	MGC24969	uc002azk.2	Q8TAC9	OTTHUMG00000172704	ENST00000361900.6:c.509G>A	15.37:g.75310872G>A	ENSP00000355387:p.Ser170Asn	Somatic		Capture	Illumina HiSeq	Phase_I	73097925	NM_001178111	B3KPJ7|B7Z762|D3DW71|Q8N3M4	Missense_Mutation	SNP	ENST00000361900.6	37	CCDS45306.1	.	.	.	.	.	.	.	.	.	.	G	13.88	2.368601	0.42003	.	.	ENSG00000198794	ENST00000361900;ENST00000425597;ENST00000545456	T;T;T	0.17691	2.26;2.26;2.26	4.53	4.53	0.55603	.	0.192670	0.53938	D	0.000050	T	0.09423	0.0232	N	0.12182	0.205	0.41396	D	0.987649	P;B;B	0.37276	0.589;0.328;0.029	B;B;B	0.35813	0.211;0.107;0.073	T	0.28299	-1.0048	10	0.28530	T	0.3	-7.5148	11.2095	0.48790	0.0:0.3008:0.6992:0.0	.	99;178;170	Q8TAC9-3;Q8TAC9-2;Q8TAC9	.;.;SCAM5_HUMAN	N	170;170;99	ENSP00000355387:S170N;ENSP00000406547:S170N;ENSP00000439685:S99N	ENSP00000355387:S170N	S	+	2	0	SCAMP5	73097925	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.329000	0.52060	2.338000	0.79540	0.561000	0.74099	AGC		0.542	SCAMP5-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000420015.2	NM_138967	
C15orf39	56905	broad.mit.edu	37	15	75499491	75499491	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr15:75499491C>A	ENST00000360639.2	+	2	1422	c.1102C>A	c.(1102-1104)Cca>Aca	p.P368T	C15orf39_ENST00000567617.1_Missense_Mutation_p.P368T|C15orf39_ENST00000394987.4_Missense_Mutation_p.P368T			Q6ZRI6	CO039_HUMAN	chromosome 15 open reading frame 39	368						cytoplasm (GO:0005737)		p.P368T(1)		autonomic_ganglia(1)|breast(2)|endometrium(3)|large_intestine(4)|lung(4)|skin(1)|upper_aerodigestive_tract(1)	16						TCCACGGTGCCCATTGGACTT	0.627																																					p.P368T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1102A	15						.						111.0	120.0	117.0					15																	75499491		2197	4295	6492	73286544	SO:0001583	missense	56905	exon2			AK128205	CCDS10276.1	15q23	2013-03-14	2005-10-24		ENSG00000167173	ENSG00000167173			24497	protein-coding gene	gene with protein product			"""chromosome 15 open reading frame 38~Name Same As HGNC:28782"""				Standard	NM_015492		Approved	DKFZP434H132, FLJ46337	uc002azq.4	Q6ZRI6	OTTHUMG00000142820	ENST00000360639.2:c.1102C>A	15.37:g.75499491C>A	ENSP00000353854:p.Pro368Thr	Somatic		Capture	Illumina HiSeq	Phase_I	73286544	NM_015492	B3KWI3|C9J888|Q71JB1|Q7L3S0|Q8N3F2|Q96FB6|Q9NTU5	Missense_Mutation	SNP	ENST00000360639.2	37	CCDS10276.1	.	.	.	.	.	.	.	.	.	.	C	13.20	2.165633	0.38217	.	.	ENSG00000167173	ENST00000360639;ENST00000394987	T;T	0.75367	-0.93;-0.93	4.74	4.74	0.60224	.	0.278412	0.28549	N	0.014949	T	0.81235	0.4780	L	0.60455	1.87	0.41425	D	0.987825	D	0.65815	0.995	P	0.61003	0.882	D	0.83486	0.0067	10	0.72032	D	0.01	-12.2503	13.2167	0.59865	0.0:1.0:0.0:0.0	.	368	Q6ZRI6	CO039_HUMAN	T	368	ENSP00000353854:P368T;ENSP00000378438:P368T	ENSP00000353854:P368T	P	+	1	0	C15orf39	73286544	0.093000	0.21703	0.994000	0.49952	0.706000	0.40770	0.867000	0.27968	2.175000	0.68902	0.462000	0.41574	CCA		0.627	C15orf39-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286410.1	NM_015492	
NEIL1	79661	broad.mit.edu	37	15	75646104	75646104	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr15:75646104G>A	ENST00000564784.1	+	7	1372	c.743G>A	c.(742-744)aGc>aAc	p.S248N	NEIL1_ENST00000569035.1_Missense_Mutation_p.S248N|NEIL1_ENST00000355059.4_Missense_Mutation_p.S248N|MIR631_ENST00000384904.1_RNA|RP11-817O13.6_ENST00000563660.1_lincRNA			Q96FI4	NEIL1_HUMAN	nei endonuclease VIII-like 1 (E. coli)	248					base-excision repair (GO:0006284)|negative regulation of nuclease activity (GO:0032074)|nucleotide-excision repair (GO:0006289)|response to oxidative stress (GO:0006979)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	damaged DNA binding (GO:0003684)|DNA N-glycosylase activity (GO:0019104)|DNA-(apurinic or apyrimidinic site) lyase activity (GO:0003906)|hydrolase activity, acting on glycosyl bonds (GO:0016798)|protein C-terminus binding (GO:0008022)|zinc ion binding (GO:0008270)	p.S248N(1)		breast(2)|endometrium(2)|large_intestine(4)|lung(4)|ovary(1)	13						GGGTCAGAGAGCGGGGAGGAG	0.632								Base excision repair (BER), DNA glycosylases																													p.S248N												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G743A	15						.						83.0	85.0	84.0					15																	75646104		2197	4294	6491	73433157	SO:0001583	missense	79661	exon6			AK026055	CCDS10278.1	15q33.33	2008-07-18			ENSG00000140398	ENSG00000140398			18448	protein-coding gene	gene with protein product		608844				11904416	Standard	NM_024608		Approved	FLJ22402, hFPG1, NEI1, FPG1	uc002bae.4	Q96FI4	OTTHUMG00000142821	ENST00000564784.1:c.743G>A	15.37:g.75646104G>A	ENSP00000457352:p.Ser248Asn	Somatic		Capture	Illumina HiSeq	Phase_I	73433157	NM_024608	D3DW75|Q6ZRA7|Q86XW7|Q9H6C3	Missense_Mutation	SNP	ENST00000564784.1	37	CCDS10278.1	.	.	.	.	.	.	.	.	.	.	G	4.101	0.016714	0.07959	.	.	ENSG00000140398	ENST00000355059	T	0.46451	0.87	4.47	-2.88	0.05682	.	1.306670	0.04521	N	0.384634	T	0.23806	0.0576	L	0.29908	0.895	0.09310	N	1	B	0.09022	0.002	B	0.04013	0.001	T	0.13656	-1.0501	10	0.07175	T	0.84	-0.0193	3.6038	0.08035	0.3475:0.0:0.2703:0.3821	.	248	Q96FI4	NEIL1_HUMAN	N	248	ENSP00000347170:S248N	ENSP00000347170:S248N	S	+	2	0	NEIL1	73433157	0.000000	0.05858	0.005000	0.12908	0.515000	0.34225	0.121000	0.15667	-0.654000	0.05394	0.561000	0.74099	AGC		0.632	NEIL1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419885.1	NM_024608	
MAN2C1	4123	broad.mit.edu	37	15	75648350	75648350	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr15:75648350T>C	ENST00000267978.5	-	26	3066	c.3020A>G	c.(3019-3021)gAc>gGc	p.D1007G	MAN2C1_ENST00000569482.1_Missense_Mutation_p.D984G|MIR631_ENST00000384904.1_RNA|MAN2C1_ENST00000565683.1_Missense_Mutation_p.D1024G|MAN2C1_ENST00000563622.1_Missense_Mutation_p.D908G|RP11-817O13.6_ENST00000563660.1_lincRNA	NM_006715.3	NP_006706.2	Q9NTJ4	MA2C1_HUMAN	mannosidase, alpha, class 2C, member 1	1007					mannose metabolic process (GO:0006013)		alpha-mannosidase activity (GO:0004559)|carbohydrate binding (GO:0030246)|zinc ion binding (GO:0008270)	p.D1007G(1)		central_nervous_system(4)|endometrium(4)|kidney(6)|large_intestine(6)|lung(20)|prostate(1)|stomach(1)|upper_aerodigestive_tract(2)	44						GCCAGCAGGGTCTGGTCGCTC	0.632																																					p.D1007G												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A3020G	15						.						76.0	71.0	73.0					15																	75648350		2197	4294	6491	73435403	SO:0001583	missense	4123	exon26			AF044414	CCDS32298.1, CCDS58389.1, CCDS58390.1, CCDS58391.1	15q24.2	2013-09-19			ENSG00000140400	ENSG00000140400	3.2.1.24		6827	protein-coding gene	gene with protein product		154580		MANA1, MANA		1757461, 752528	Standard	NM_006715		Approved		uc002bah.4	Q9NTJ4	OTTHUMG00000172698	ENST00000267978.5:c.3020A>G	15.37:g.75648350T>C	ENSP00000267978:p.Asp1007Gly	Somatic		Capture	Illumina HiSeq	Phase_I	73435403	NM_006715	H3BMX2|H3BQY8|H3BUT6|Q13358|Q68EM8|Q9UL64	Missense_Mutation	SNP	ENST00000267978.5	37	CCDS32298.1	.	.	.	.	.	.	.	.	.	.	T	16.23	3.063453	0.55432	.	.	ENSG00000140400	ENST00000267978	T	0.18657	2.2	4.42	3.2	0.36748	Glycosyl hydrolases 38, C-terminal (1);Glycoside hydrolase-type carbohydrate-binding (1);	0.359380	0.28742	N	0.014296	T	0.28896	0.0717	M	0.69463	2.115	0.30691	N	0.751303	P;P	0.48834	0.916;0.916	P;P	0.51487	0.671;0.538	T	0.11494	-1.0585	10	0.23302	T	0.38	-21.8397	8.8921	0.35441	0.0:0.0:0.3947:0.6053	.	984;1007	Q68EM8;Q9NTJ4	.;MA2C1_HUMAN	G	1007	ENSP00000267978:D1007G	ENSP00000267978:D1007G	D	-	2	0	MAN2C1	73435403	0.899000	0.30636	0.565000	0.28409	0.085000	0.17905	1.525000	0.35953	1.633000	0.50488	0.379000	0.24179	GAC		0.632	MAN2C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419965.1		
SNX33	257364	broad.mit.edu	37	15	75942251	75942251	+	Missense_Mutation	SNP	T	T	G			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr15:75942251T>G	ENST00000308527.5	+	1	2005	c.808T>G	c.(808-810)Ttt>Gtt	p.F270V	IMP3_ENST00000314852.2_5'Flank|IMP3_ENST00000565349.1_5'Flank	NM_153271.1	NP_695003.1	Q8WV41	SNX33_HUMAN	sorting nexin 33	270	PX. {ECO:0000255|PROSITE- ProRule:PRU00147}.				cleavage furrow formation (GO:0036089)|endocytosis (GO:0006897)|endosomal transport (GO:0016197)|endosome organization (GO:0007032)|intracellular protein transport (GO:0006886)|macropinocytosis (GO:0044351)|membrane tubulation (GO:0097320)|mitotic cytokinesis (GO:0000281)|mitotic nuclear division (GO:0007067)|negative regulation of endocytosis (GO:0045806)|negative regulation of protein localization to cell surface (GO:2000009)|positive regulation of membrane protein ectodomain proteolysis (GO:0051044)|positive regulation of protein localization to cell surface (GO:2000010)|protein import (GO:0017038)	cytoplasmic membrane-bounded vesicle (GO:0016023)|cytosol (GO:0005829)|endosome (GO:0005768)|extrinsic component of membrane (GO:0019898)|membrane (GO:0016020)	identical protein binding (GO:0042802)|phosphatidylinositol binding (GO:0035091)	p.F270V(1)		breast(2)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(3)|ovary(1)|prostate(1)|soft_tissue(1)|urinary_tract(2)	19						CTACAAACACTTTGACTGGCT	0.547																																					p.F270V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T808G	15						.						150.0	140.0	143.0					15																	75942251		2197	4294	6491	73729306	SO:0001583	missense	257364	exon1			AK091291	CCDS10283.1	15q23	2008-04-18	2008-03-25	2008-03-25	ENSG00000173548	ENSG00000173548			28468	protein-coding gene	gene with protein product			"""SH3 and PX domain containing 3"""	SH3PX3		16374509, 16782399, 18353773	Standard	NM_153271		Approved	MGC32065, SH3PXD3C, SNX30	uc002bau.3	Q8WV41	OTTHUMG00000142835	ENST00000308527.5:c.808T>G	15.37:g.75942251T>G	ENSP00000311427:p.Phe270Val	Somatic		Capture	Illumina HiSeq	Phase_I	73729306	NM_153271	B1NM17	Missense_Mutation	SNP	ENST00000308527.5	37	CCDS10283.1	.	.	.	.	.	.	.	.	.	.	T	13.18	2.160404	0.38119	.	.	ENSG00000173548	ENST00000308527	T	0.69806	-0.43	5.42	5.42	0.78866	Phox homologous domain (5);	0.000000	0.85682	D	0.000000	D	0.86339	0.5909	H	0.94385	3.53	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.90098	0.4182	10	0.87932	D	0	-19.6235	14.288	0.66258	0.0:0.0:0.0:1.0	.	270	Q8WV41	SNX33_HUMAN	V	270	ENSP00000311427:F270V	ENSP00000311427:F270V	F	+	1	0	SNX33	73729306	1.000000	0.71417	0.999000	0.59377	0.990000	0.78478	8.019000	0.88732	2.056000	0.61249	0.459000	0.35465	TTT		0.547	SNX33-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286471.1	NM_153271	
CEMIP	57214	broad.mit.edu	37	15	81239401	81239401	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr15:81239401T>C	ENST00000394685.3	+	29	4372	c.3953T>C	c.(3952-3954)tTg>tCg	p.L1318S	MESDC2_ENST00000560244.1_5'Flank|RP11-351M8.2_ENST00000560873.1_RNA|KIAA1199_ENST00000356249.5_Missense_Mutation_p.L1318S|KIAA1199_ENST00000220244.3_Missense_Mutation_p.L1318S			Q8WUJ3	CEMIP_HUMAN		1318					hyaluronan catabolic process (GO:0030214)|positive regulation of cell migration (GO:0030335)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of protein kinase C activity (GO:1900020)|positive regulation of protein targeting to membrane (GO:0090314)|positive regulation of release of sequestered calcium ion into cytosol (GO:0051281)|sensory perception of sound (GO:0007605)	clathrin-coated vesicle membrane (GO:0030665)|coated pit (GO:0005905)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	clathrin heavy chain binding (GO:0032050)|ER retention sequence binding (GO:0046923)|hyaluronic acid binding (GO:0005540)|hyalurononglucosaminidase activity (GO:0004415)	p.L1318S(1)		breast(4)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(10)|lung(14)|ovary(1)|prostate(3)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	49						GGTCTCAAGTTGAAAGGTAAG	0.502																																					p.L1318S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T3953C	15						.						66.0	67.0	66.0					15																	81239401		2203	4300	6503	79026456	SO:0001583	missense	57214	exon28																														ENST00000394685.3:c.3953T>C	15.37:g.81239401T>C	ENSP00000378177:p.Leu1318Ser	Somatic		Capture	Illumina HiSeq	Phase_I	79026456	NM_018689	Q6L9J5|Q9H1K5|Q9NPN9|Q9ULM1	Missense_Mutation	SNP	ENST00000394685.3	37	CCDS10315.1	.	.	.	.	.	.	.	.	.	.	T	20.1	3.935068	0.73442	.	.	ENSG00000103888	ENST00000220244;ENST00000394685;ENST00000356249	T;T;T	0.65916	-0.18;-0.18;-0.18	5.43	5.43	0.79202	.	0.000000	0.64402	D	0.000006	T	0.78071	0.4226	M	0.71581	2.175	0.43971	D	0.996653	D	0.76494	0.999	D	0.85130	0.997	T	0.79077	-0.1951	10	0.49607	T	0.09	-23.853	15.7715	0.78173	0.0:0.0:0.0:1.0	.	1318	Q8WUJ3	K1199_HUMAN	S	1318	ENSP00000220244:L1318S;ENSP00000378177:L1318S;ENSP00000348583:L1318S	ENSP00000220244:L1318S	L	+	2	0	KIAA1199	79026456	1.000000	0.71417	0.831000	0.32960	0.674000	0.39518	6.838000	0.75359	2.186000	0.69663	0.533000	0.62120	TTG		0.502	KIAA1199-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000291389.1		
IL16	3603	broad.mit.edu	37	15	81571200	81571200	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr15:81571200T>C	ENST00000302987.4	+	6	833	c.833T>C	c.(832-834)cTa>cCa	p.L278P	IL16_ENST00000394660.2_Missense_Mutation_p.L278P			Q14005	IL16_HUMAN	interleukin 16	278	Interaction with GRIN2A.|PDZ 1. {ECO:0000255|PROSITE- ProRule:PRU00143}.				immune response (GO:0006955)|induction of positive chemotaxis (GO:0050930)|leukocyte chemotaxis (GO:0030595)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|nucleus (GO:0005634)|plasma membrane (GO:0005886)		p.L278P(1)		NS(1)|autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(5)|large_intestine(12)|lung(20)|ovary(3)|skin(3)|stomach(1)|urinary_tract(1)	57						ATGGCTGGACTAACACATCAG	0.443																																					p.L278P												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T833C	15						.						211.0	194.0	200.0					15																	81571200		1946	4146	6092	79358255	SO:0001583	missense	3603	exon7			U82972	CCDS10317.1, CCDS42069.1, CCDS53966.1	15q26.3	2011-07-14	2011-07-14		ENSG00000172349	ENSG00000172349		"""Interleukins and interleukin receptors"""	5980	protein-coding gene	gene with protein product	"""prointerleukin 16"", ""lymphocyte chemoattractant factor"""	603035	"""interleukin 16 (lymphocyte chemoattractant factor)"""			9144227	Standard	NM_004513		Approved	LCF, IL-16, prIL-16, HsT19289, FLJ42735, FLJ16806	uc021ssh.1	Q14005	OTTHUMG00000144186	ENST00000302987.4:c.833T>C	15.37:g.81571200T>C	ENSP00000302935:p.Leu278Pro	Somatic		Capture	Illumina HiSeq	Phase_I	79358255	NM_001172128	A6NM20|A8MU65|B5TY35|B9EGR6|H3BVH5|Q16435|Q6VVE6|Q6ZMQ7|Q9UP18	Missense_Mutation	SNP	ENST00000302987.4	37	CCDS42069.1	.	.	.	.	.	.	.	.	.	.	T	18.30	3.594556	0.66219	.	.	ENSG00000172349	ENST00000394655;ENST00000394660;ENST00000355368;ENST00000302987	T;T	0.31510	1.49;1.49	4.86	4.86	0.63082	PDZ/DHR/GLGF (4);	0.000000	0.34676	N	0.003761	T	0.67655	0.2916	H	0.95850	3.73	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.999	T	0.78505	-0.2178	10	0.56958	D	0.05	.	14.5975	0.68417	0.0:0.0:0.0:1.0	.	278;278	Q14005;Q14005-2	IL16_HUMAN;.	P	278;278;110;278	ENSP00000378155:L278P;ENSP00000302935:L278P	ENSP00000302935:L278P	L	+	2	0	IL16	79358255	0.975000	0.34042	0.155000	0.22561	0.898000	0.52572	6.297000	0.72757	2.027000	0.59764	0.460000	0.39030	CTA		0.443	IL16-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000303952.1	NM_172217	
EFTUD1	79631	broad.mit.edu	37	15	82512020	82512020	+	Silent	SNP	T	T	C			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr15:82512020T>C	ENST00000268206.7	-	14	1752	c.1584A>G	c.(1582-1584)aaA>aaG	p.K528K	EFTUD1_ENST00000359445.3_Silent_p.K477K	NM_024580.5	NP_078856.4	Q7Z2Z2	ETUD1_HUMAN	elongation factor Tu GTP binding domain containing 1	528					GTP catabolic process (GO:0006184)|mature ribosome assembly (GO:0042256)		GTP binding (GO:0005525)|GTPase activity (GO:0003924)|ribosome binding (GO:0043022)|translation elongation factor activity (GO:0003746)	p.K528K(1)		cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(3)|lung(14)|ovary(1)|pancreas(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	32						GAGGACTGTATTTGGGCCCCA	0.383																																					p.K477K												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.A1431G	15						.						23.0	23.0	23.0					15																	82512020		1778	4049	5827	80299075	SO:0001819	synonymous_variant	79631	exon12			AK056656	CCDS42070.1, CCDS42071.1	15q25.2	2012-07-04			ENSG00000140598	ENSG00000140598			25789	protein-coding gene	gene with protein product	"""ribosome assembly 1 homolog (yeast)"""					14702039	Standard	NM_024580		Approved	FLJ13119, FAM42A, HsT19294, RIA1	uc002bgt.1	Q7Z2Z2	OTTHUMG00000172573	ENST00000268206.7:c.1584A>G	15.37:g.82512020T>C		Somatic		Capture	Illumina HiSeq	Phase_I	80299075	NM_001040610	A6NKY5|B7Z6I0|Q9H8Z6	Silent	SNP	ENST00000268206.7	37	CCDS42071.1																																																																																				0.383	EFTUD1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419252.1	NM_024580	
C15orf40	123207	broad.mit.edu	37	15	83679095	83679095	+	Silent	SNP	T	T	C			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr15:83679095T>C	ENST00000513601.2	-	2	139	c.132A>G	c.(130-132)gaA>gaG	p.E44E	C15orf40_ENST00000451195.3_Silent_p.E44E|RP11-382A20.5_ENST00000566841.1_RNA|RP11-382A20.7_ENST00000570202.1_RNA|C15orf40_ENST00000565712.1_Intron|C15orf40_ENST00000304177.5_Silent_p.E17E|C15orf40_ENST00000538348.2_Silent_p.E44E			Q8WUR7	CO040_HUMAN	chromosome 15 open reading frame 40	44								p.E17E(1)|p.E44E(1)		large_intestine(3)|lung(2)|skin(1)	6						GTCTCTCTGGTTCCTTGCTCT	0.438																																					p.E44E												.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.A132G	15						.						198.0	180.0	186.0					15																	83679095		2203	4300	6503	81470099	SO:0001819	synonymous_variant	123207	exon2			BC019820	CCDS32312.1, CCDS32312.2, CCDS53968.1, CCDS53969.1	15q25.2	2012-05-30			ENSG00000169609	ENSG00000169609			28443	protein-coding gene	gene with protein product							Standard	NM_144597		Approved	MGC29937	uc010uoo.1	Q8WUR7	OTTHUMG00000160473	ENST00000513601.2:c.132A>G	15.37:g.83679095T>C		Somatic		Capture	Illumina HiSeq	Phase_I	81470099	NM_001160113	A6NIC9|B2R5E7|F5GX92|F8WD31|G5EA00	Silent	SNP	ENST00000513601.2	37	CCDS32312.2																																																																																				0.438	C15orf40-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000360737.2	NM_144597	
KLHL25	64410	broad.mit.edu	37	15	86312570	86312570	+	Missense_Mutation	SNP	C	C	T	rs372508532		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr15:86312570C>T	ENST00000337975.5	-	2	746	c.472G>A	c.(472-474)Gcc>Acc	p.A158T	MIR1276_ENST00000408707.1_RNA|KLHL25_ENST00000559131.1_Intron|KLHL25_ENST00000536947.1_Missense_Mutation_p.A158T	NM_022480.3	NP_071925.2	Q9H0H3	KLH25_HUMAN	kelch-like family member 25	158	BACK.				protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|regulation of translational initiation (GO:0006446)	Cul3-RING ubiquitin ligase complex (GO:0031463)|cytoplasm (GO:0005737)		p.A158T(1)		breast(1)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(7)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	25						CACTGGTGGGCGTCCGAGAGC	0.607																																					p.A158T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G472A	15						.						69.0	68.0	68.0					15																	86312570		2202	4299	6501	84113574	SO:0001583	missense	64410	exon2				CCDS10339.1	15q25.3	2013-02-22	2013-02-22		ENSG00000183655	ENSG00000183655		"""Kelch-like"", ""BTB/POZ domain containing"""	25732	protein-coding gene	gene with protein product	"""ectodermal-neural cortex 2"""		"""kelch-like 25 (Drosophila)"""				Standard	XM_006720635		Approved	FLJ12587, ENC2, ENC-2	uc002bly.3	Q9H0H3	OTTHUMG00000148672	ENST00000337975.5:c.472G>A	15.37:g.86312570C>T	ENSP00000336800:p.Ala158Thr	Somatic		Capture	Illumina HiSeq	Phase_I	84113574	NM_022480	B2RDH2|B3KRT7	Missense_Mutation	SNP	ENST00000337975.5	37	CCDS10339.1	.	.	.	.	.	.	.	.	.	.	C	17.49	3.401712	0.62288	.	.	ENSG00000183655	ENST00000337975;ENST00000538153;ENST00000536947	T;T	0.68479	-0.33;-0.33	4.85	4.85	0.62838	BTB/Kelch-associated (2);	0.000000	0.85682	D	0.000000	T	0.61048	0.2316	L	0.43646	1.37	0.58432	D	0.999999	B	0.32160	0.358	B	0.39876	0.312	T	0.56456	-0.7976	10	0.05620	T	0.96	.	16.9559	0.86259	0.0:1.0:0.0:0.0	.	158	Q9H0H3	ENC2_HUMAN	T	158;127;158	ENSP00000336800:A158T;ENSP00000444739:A158T	ENSP00000336800:A158T	A	-	1	0	KLHL25	84113574	1.000000	0.71417	0.997000	0.53966	0.973000	0.67179	7.818000	0.86416	2.247000	0.74100	0.462000	0.41574	GCC		0.607	KLHL25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000309023.1	NM_022480	
ACAN	176	broad.mit.edu	37	15	89400154	89400154	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr15:89400154G>T	ENST00000561243.1	+	11	4338	c.4338G>T	c.(4336-4338)gaG>gaT	p.E1446D	ACAN_ENST00000439576.2_Missense_Mutation_p.E1446D|ACAN_ENST00000352105.7_Missense_Mutation_p.E1446D|ACAN_ENST00000559004.1_Missense_Mutation_p.E1446D			P16112	PGCA_HUMAN	aggrecan	1449	29 X 19 AA approximate tandem repeats of E-[IVDG]-[LV]-[EV]-[GTI]-[STA]-[ATV]- [SP]-[GA]-[VIFAD]-[GEDL]-[DE]-[LVI]-[SG]- [GERK]-[LV]-P-S-G.|CS-1.				carbohydrate metabolic process (GO:0005975)|cell adhesion (GO:0007155)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate catabolic process (GO:0042340)|keratan sulfate metabolic process (GO:0042339)|proteolysis (GO:0006508)|skeletal system development (GO:0001501)|small molecule metabolic process (GO:0044281)	extracellular region (GO:0005576)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)|proteinaceous extracellular matrix (GO:0005578)	carbohydrate binding (GO:0030246)|extracellular matrix structural constituent (GO:0005201)|hyaluronic acid binding (GO:0005540)|metal ion binding (GO:0046872)	p.E1332D(1)		NS(1)|central_nervous_system(4)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(15)|liver(2)|lung(40)|ovary(2)|prostate(5)|skin(5)|stomach(8)|upper_aerodigestive_tract(1)|urinary_tract(2)	93	Lung NSC(78;0.0392)|all_lung(78;0.077)		BRCA - Breast invasive adenocarcinoma(143;0.146)			CTGGAGTAGAGGAGATCAGCG	0.507																																					p.E1446D												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G4338T	15						.						111.0	112.0	112.0					15																	89400154		1839	4094	5933	87201158	SO:0001583	missense	176	exon12			M55172	CCDS53970.1, CCDS53971.1	15q26.1	2013-05-07	2007-02-16	2007-02-16	ENSG00000157766	ENSG00000157766		"""Immunoglobulin superfamily / V-set domain containing"", ""Proteoglycans / Extracellular Matrix : Hyalectans"""	319	protein-coding gene	gene with protein product	"""aggrecan proteoglycan"""	155760	"""chondroitin sulfate proteoglycan 1"", ""aggrecan 1"""	MSK16, CSPG1, AGC1		1985970	Standard	NM_013227		Approved	CSPGCP	uc010upo.1	P16112	OTTHUMG00000171989	ENST00000561243.1:c.4338G>T	15.37:g.89400154G>T	ENSP00000453342:p.Glu1446Asp	Somatic		Capture	Illumina HiSeq	Phase_I	87201158	NM_001135	Q13650|Q9UCD3|Q9UCP4|Q9UCP5|Q9UDE0	De_novo_Start_OutOfFrame	SNP	ENST00000561243.1	37	CCDS53970.1	.	.	.	.	.	.	.	.	.	.	-	5.922	0.354162	0.11182	.	.	ENSG00000157766	ENST00000439576;ENST00000352105;ENST00000268134	D;D	0.95980	-3.87;-3.87	3.0	-2.85	0.05734	.	.	.	.	.	D	0.94013	0.8082	M	0.77820	2.39	0.09310	N	1	P;P	0.46859	0.865;0.885	P;P	0.49047	0.497;0.599	D	0.86304	0.1682	9	0.22109	T	0.4	.	3.8662	0.09018	0.4:0.0:0.3343:0.2658	.	1446;1446	E7ENV9;E7EX88	.;.	D	1446;1446;1332	ENSP00000387356:E1446D;ENSP00000341615:E1446D	ENSP00000268134:E1332D	E	+	3	2	ACAN	87201158	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-2.408000	0.01042	-0.673000	0.05259	-0.959000	0.02639	GAG		0.507	ACAN-006	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416267.2	NM_001135	
RHCG	51458	broad.mit.edu	37	15	90020784	90020784	+	Missense_Mutation	SNP	G	G	A	rs368487303		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr15:90020784G>A	ENST00000268122.4	-	7	1144	c.1076C>T	c.(1075-1077)gCg>gTg	p.A359V	RHCG_ENST00000544600.1_Missense_Mutation_p.A359V	NM_016321.1	NP_057405.1	Q9UBD6	RHCG_HUMAN	Rh family, C glycoprotein	359					amine transport (GO:0015837)|ammonium transmembrane transport (GO:0072488)|ammonium transport (GO:0015696)|cellular ion homeostasis (GO:0006873)|epithelial cell differentiation (GO:0030855)|homeostatic process (GO:0042592)|regulation of pH (GO:0006885)|transepithelial ammonium transport (GO:0070634)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ammonium transmembrane transporter activity (GO:0008519)|ankyrin binding (GO:0030506)	p.A359V(1)		breast(1)|endometrium(2)|kidney(2)|large_intestine(5)|lung(9)|upper_aerodigestive_tract(1)|urinary_tract(1)	21	Lung NSC(78;0.0237)|all_lung(78;0.0478)					GGCGGAGGCCGCTGTCACAGC	0.567																																					p.A359V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1076T	15						.	G	VAL/ALA	0,4400		0,0,2200	60.0	51.0	54.0		1076	4.7	0.0	15		54	1,8597	1.2+/-3.3	0,1,4298	no	missense	RHCG	NM_016321.1	64	0,1,6498	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging	359/480	90020784	1,12997	2200	4299	6499	87821788	SO:0001583	missense	51458	exon7			AF081497	CCDS10351.1	15q25	2013-05-22	2006-02-23		ENSG00000140519	ENSG00000140519		"""Solute carriers"""	18140	protein-coding gene	gene with protein product		605381	"""chromosome 15 open reading frame 6"", ""Rhesus blood group, C glycoprotein"""	C15orf6		10852913	Standard	NM_016321		Approved	RHGK, PDRC2, SLC42A3	uc002bnz.2	Q9UBD6	OTTHUMG00000149647	ENST00000268122.4:c.1076C>T	15.37:g.90020784G>A	ENSP00000268122:p.Ala359Val	Somatic		Capture	Illumina HiSeq	Phase_I	87821788	NM_016321	A8K4D4|Q6X3Y4	Missense_Mutation	SNP	ENST00000268122.4	37	CCDS10351.1	.	.	.	.	.	.	.	.	.	.	G	17.25	3.342503	0.61073	0.0	1.16E-4	ENSG00000140519	ENST00000544600;ENST00000268122;ENST00000536247	T;T	0.25414	1.8;1.8	5.58	4.67	0.58626	Ammonium transporter AmtB-like (3);	0.093114	0.64402	N	0.000001	T	0.31358	0.0794	M	0.79926	2.475	0.80722	D	1	P	0.40083	0.702	B	0.35312	0.2	T	0.19063	-1.0317	9	.	.	.	-21.5	14.2562	0.66053	0.0717:0.0:0.9283:0.0	.	359	Q9UBD6	RHCG_HUMAN	V	359;359;350	ENSP00000438123:A359V;ENSP00000268122:A359V	.	A	-	2	0	RHCG	87821788	1.000000	0.71417	0.045000	0.18777	0.014000	0.08584	6.665000	0.74442	1.353000	0.45828	0.561000	0.74099	GCG		0.567	RHCG-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000312855.2	NM_016321	
BLM	641	broad.mit.edu	37	15	91326121	91326121	+	Silent	SNP	A	A	G			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr15:91326121A>G	ENST00000355112.3	+	13	2743	c.2625A>G	c.(2623-2625)gcA>gcG	p.A875A	BLM_ENST00000560136.1_3'UTR|BLM_ENST00000560509.1_Silent_p.A875A	NM_000057.2	NP_000048.1	P54132	BLM_HUMAN	Bloom syndrome, RecQ helicase-like	875					alpha-beta T cell differentiation (GO:0046632)|ATP catabolic process (GO:0006200)|cellular response to camptothecin (GO:0072757)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to hydroxyurea (GO:0072711)|cellular response to ionizing radiation (GO:0071479)|DNA double-strand break processing (GO:0000729)|DNA duplex unwinding (GO:0032508)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|DNA strand renaturation (GO:0000733)|double-strand break repair via homologous recombination (GO:0000724)|mitotic G2 DNA damage checkpoint (GO:0007095)|negative regulation of cell division (GO:0051782)|negative regulation of DNA recombination (GO:0045910)|negative regulation of mitotic recombination (GO:0045950)|negative regulation of thymocyte apoptotic process (GO:0070244)|positive regulation of alpha-beta T cell proliferation (GO:0046641)|positive regulation of transcription, DNA-templated (GO:0045893)|protein oligomerization (GO:0051259)|regulation of binding (GO:0051098)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|replication fork processing (GO:0031297)|replication fork protection (GO:0048478)|response to X-ray (GO:0010165)|telomere maintenance (GO:0000723)	cytoplasm (GO:0005737)|lateral element (GO:0000800)|male germ cell nucleus (GO:0001673)|nuclear chromosome (GO:0000228)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleus (GO:0005634)|PML body (GO:0016605)|pronucleus (GO:0045120)|replication fork (GO:0005657)	annealing helicase activity (GO:0036310)|ATP binding (GO:0005524)|ATP-dependent 3'-5' DNA helicase activity (GO:0043140)|ATP-dependent DNA helicase activity (GO:0004003)|ATP-dependent helicase activity (GO:0008026)|ATPase activity (GO:0016887)|bubble DNA binding (GO:0000405)|four-way junction helicase activity (GO:0009378)|G-quadruplex DNA binding (GO:0051880)|helicase activity (GO:0004386)|p53 binding (GO:0002039)|single-stranded DNA binding (GO:0003697)	p.A875A(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(11)|liver(4)|lung(9)|ovary(6)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	Lung NSC(78;0.0875)|all_lung(78;0.109)		Lung(145;0.189)			AAAAGGTGGCATTTGATTGCC	0.348			"""Mis, N, F"""			"""leukemia, lymphoma, skin squamous cell , other cancers"""		Genes defective in diseases associated with sensitivity to DNA damaging agents	Bloom syndrome																												p.A875A		yes	Rec		Bloom Syndrome	15	15q26.1	641	Bloom Syndrome		"""L, E"""	.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.A2625G	15						.						73.0	61.0	65.0					15																	91326121		2198	4298	6496	89127125	SO:0001819	synonymous_variant	641	exon13	Familial Cancer Database		U39817	CCDS10363.1, CCDS73782.1	15q26.1	2014-09-17	2009-03-19		ENSG00000197299	ENSG00000197299			1058	protein-coding gene	gene with protein product		604610	"""Bloom syndrome"""			9388193	Standard	NM_000057		Approved	BS, RECQL3, RECQ2	uc002bpr.3	P54132	OTTHUMG00000149834	ENST00000355112.3:c.2625A>G	15.37:g.91326121A>G		Somatic		Capture	Illumina HiSeq	Phase_I	89127125	NM_000057	Q52M96	Silent	SNP	ENST00000355112.3	37	CCDS10363.1																																																																																				0.348	BLM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313495.1		
SV2B	9899	broad.mit.edu	37	15	91769649	91769649	+	Silent	SNP	T	T	C			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr15:91769649T>C	ENST00000394232.1	+	2	626	c.156T>C	c.(154-156)ggT>ggC	p.G52G	SV2B_ENST00000557291.1_Intron|SV2B_ENST00000545111.2_Intron|SV2B_ENST00000330276.4_Silent_p.G52G	NM_014848.4	NP_055663.1	Q7L1I2	SV2B_HUMAN	synaptic vesicle glycoprotein 2B	52					neurotransmitter transport (GO:0006836)	cell junction (GO:0030054)|integral component of membrane (GO:0016021)|synaptic vesicle (GO:0008021)	transmembrane transporter activity (GO:0022857)	p.G52G(1)		NS(1)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(10)|lung(17)|ovary(4)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	42	Lung NSC(78;0.0987)|all_lung(78;0.172)		BRCA - Breast invasive adenocarcinoma(143;0.0895)			AGTACCAGGGTATCCCTCACC	0.567																																					p.G52G												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.T156C	15						.						136.0	113.0	121.0					15																	91769649		2198	4298	6496	89570653	SO:0001819	synonymous_variant	9899	exon3			AB018278	CCDS10370.1, CCDS53972.1	15q26.1	2005-01-10			ENSG00000185518	ENSG00000185518			16874	protein-coding gene	gene with protein product		185861				9872452, 7681585	Standard	NM_014848		Approved	KIAA0735, HsT19680	uc002bqv.3	Q7L1I2	OTTHUMG00000149833	ENST00000394232.1:c.156T>C	15.37:g.91769649T>C		Somatic		Capture	Illumina HiSeq	Phase_I	89570653	NM_014848	B4DH30|C6G489|O94840|Q6IAR8	Silent	SNP	ENST00000394232.1	37	CCDS10370.1																																																																																				0.567	SV2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313494.3	NM_014848	
CHD2	1106	broad.mit.edu	37	15	93567632	93567632	+	Silent	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr15:93567632C>T	ENST00000394196.4	+	39	6252	c.5184C>T	c.(5182-5184)tcC>tcT	p.S1728S		NM_001271.3	NP_001262.3	O14647	CHD2_HUMAN	chromodomain helicase DNA binding protein 2	1728					cellular response to DNA damage stimulus (GO:0006974)|chromatin modification (GO:0016568)|DNA duplex unwinding (GO:0032508)|hematopoietic stem cell differentiation (GO:0060218)|muscle organ development (GO:0007517)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|core promoter sequence-specific DNA binding (GO:0001046)|DNA binding (GO:0003677)|histone binding (GO:0042393)|poly(A) RNA binding (GO:0044822)			breast(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(5)|kidney(2)|large_intestine(10)|lung(17)|ovary(1)|prostate(2)|skin(2)|stomach(1)|urinary_tract(2)	47	Lung NSC(78;0.00976)|all_lung(78;0.016)		BRCA - Breast invasive adenocarcinoma(143;0.0282)|OV - Ovarian serous cystadenocarcinoma(32;0.0814)			GGAGGAGATCCGATGAATTTA	0.507																																					p.S1728S												.	.	0			c.C5184T	15						.						63.0	63.0	63.0					15																	93567632		1914	4141	6055	91368636	SO:0001819	synonymous_variant	1106	exon39			AF006514	CCDS10374.2, CCDS45356.1	15q26	2008-07-18			ENSG00000173575	ENSG00000173575			1917	protein-coding gene	gene with protein product		602119				9326634	Standard	NM_001042572		Approved	FLJ38614, DKFZp547I1315, DKFZp781D1727, DKFZp686E01200	uc002bsp.3	O14647	OTTHUMG00000149845	ENST00000394196.4:c.5184C>T	15.37:g.93567632C>T		Somatic		Capture	Illumina HiSeq	Phase_I	91368636	NM_001271	C6G482|Q96IP5	Silent	SNP	ENST00000394196.4	37	CCDS10374.2																																																																																				0.507	CHD2-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000313528.3	NM_001271	
IGF1R	3480	broad.mit.edu	37	15	99451929	99451929	+	Silent	SNP	C	C	T	rs542546475		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr15:99451929C>T	ENST00000268035.6	+	6	1874	c.1263C>T	c.(1261-1263)taC>taT	p.Y421Y	IGF1R_ENST00000558762.1_Silent_p.Y421Y	NM_000875.3	NP_000866.1	P08069	IGF1R_HUMAN	insulin-like growth factor 1 receptor	421					axonogenesis (GO:0007409)|brain development (GO:0007420)|epidermis development (GO:0008544)|establishment of cell polarity (GO:0030010)|exocrine pancreas development (GO:0031017)|immune response (GO:0006955)|inactivation of MAPKK activity (GO:0051389)|insulin receptor signaling pathway (GO:0008286)|insulin-like growth factor receptor signaling pathway (GO:0048009)|male sex determination (GO:0030238)|mammary gland development (GO:0030879)|negative regulation of apoptotic process (GO:0043066)|negative regulation of muscle cell apoptotic process (GO:0010656)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|peptidyl-tyrosine autophosphorylation (GO:0038083)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cytokinesis (GO:0032467)|positive regulation of DNA replication (GO:0045740)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mitosis (GO:0045840)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of steroid hormone biosynthetic process (GO:0090031)|prostate gland epithelium morphogenesis (GO:0060740)|protein autophosphorylation (GO:0046777)|protein heterooligomerization (GO:0051291)|protein tetramerization (GO:0051262)|regulation of JNK cascade (GO:0046328)|response to vitamin E (GO:0033197)|signal transduction (GO:0007165)	caveola (GO:0005901)|integral component of plasma membrane (GO:0005887)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|insulin binding (GO:0043559)|insulin receptor binding (GO:0005158)|insulin receptor substrate binding (GO:0043560)|insulin-like growth factor binding (GO:0005520)|insulin-like growth factor I binding (GO:0031994)|insulin-like growth factor-activated receptor activity (GO:0005010)|phosphatidylinositol 3-kinase binding (GO:0043548)|protein tyrosine kinase activity (GO:0004713)	p.Y421Y(1)		NS(2)|breast(1)|central_nervous_system(1)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(13)|lung(20)|ovary(1)|prostate(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	63	all_cancers(4;4.17e-14)|all_epithelial(3;4.34e-15)|Lung NSC(78;0.00175)|all_lung(78;0.00351)|Melanoma(26;0.00505)|Medulloblastoma(229;0.163)		Epithelial(2;1.94e-12)|all cancers(5;6.83e-11)|BRCA - Breast invasive adenocarcinoma(2;2.88e-09)|OV - Ovarian serous cystadenocarcinoma(32;0.00261)		"""""""Insulin(DB00071)|Insulin Glargine(DB00047)|Insulin Lispro(DB00046)|Insulin Regular(DB00030)|Mecasermin(DB01277)"""	ACTCCTTCTACGTCCTCGACA	0.507													C|||	1	0.000199681	0.0	0.0014	5008	,	,		22331	0.0		0.0	False		,,,				2504	0.0				p.Y421Y												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1263T	15						.						107.0	91.0	96.0					15																	99451929		2197	4297	6494	97269452	SO:0001819	synonymous_variant	3480	exon6			M69229	CCDS10378.1, CCDS73785.1	15q26.3	2013-02-11			ENSG00000140443	ENSG00000140443		"""CD molecules"", ""Fibronectin type III domain containing"""	5465	protein-coding gene	gene with protein product		147370				1316909	Standard	XM_006720486		Approved	JTK13, CD221, IGFIR, MGC18216, IGFR	uc002bul.3	P08069	OTTHUMG00000149851	ENST00000268035.6:c.1263C>T	15.37:g.99451929C>T		Somatic		Capture	Illumina HiSeq	Phase_I	97269452	NM_000875	B1B5Y2|Q14CV2|Q9UCC0	Silent	SNP	ENST00000268035.6	37	CCDS10378.1																																																																																				0.507	IGF1R-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000313537.2	NM_000875	
MEF2A	4205	broad.mit.edu	37	15	100252748	100252748	+	Silent	SNP	G	G	A	rs541112324	byFrequency	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr15:100252748G>A	ENST00000557785.1	+	11	1615	c.1266G>A	c.(1264-1266)ccG>ccA	p.P422P	MEF2A_ENST00000354410.5_Silent_p.P424P|MEF2A_ENST00000557942.1_Silent_p.P430P|MEF2A_ENST00000453228.2_Silent_p.P422P|MEF2A_ENST00000338042.6_Silent_p.P431P|MEF2A_ENST00000558812.1_Silent_p.P362P|MEF2A_ENST00000449277.2_Silent_p.P354P	NM_001171894.1	NP_001165365.1	Q02078	MEF2A_HUMAN	myocyte enhancer factor 2A	432	Gln/Pro-rich.				apoptotic process (GO:0006915)|cardiac conduction (GO:0061337)|cellular response to calcium ion (GO:0071277)|dendrite morphogenesis (GO:0048813)|ERK5 cascade (GO:0070375)|heart development (GO:0007507)|innate immune response (GO:0045087)|MAPK cascade (GO:0000165)|mitochondrial genome maintenance (GO:0000002)|mitochondrion distribution (GO:0048311)|muscle cell differentiation (GO:0042692)|muscle organ development (GO:0007517)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|transcription from RNA polymerase II promoter (GO:0006366)|transcription, DNA-templated (GO:0006351)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)|ventricular cardiac myofibril assembly (GO:0055005)	cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	activating transcription factor binding (GO:0033613)|chromatin binding (GO:0003682)|histone acetyltransferase binding (GO:0035035)|histone deacetylase binding (GO:0042826)|protein heterodimerization activity (GO:0046982)|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)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription coactivator activity (GO:0001105)|RNA polymerase II transcription factor binding (GO:0001085)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)|SMAD binding (GO:0046332)	p.P422P(3)|p.P424P(3)|p.P432P(1)		endometrium(2)|large_intestine(2)|lung(7)|ovary(1)	12	Lung NSC(78;0.00335)|all_lung(78;0.00659)|Melanoma(26;0.00778)|Medulloblastoma(229;0.163)		OV - Ovarian serous cystadenocarcinoma(32;0.00085)			agcagcCGCCGCCACCACCGC	0.642													G|||	176	0.0351438	0.0204	0.049	5008	,	,		8872	0.0347		0.0368	False		,,,				2504	0.044				p.P424P												.	.	7	Substitution - coding silent(7)	large_intestine(4)|endometrium(3)	c.G1272A	15	GRCh37	CD068109	MEF2A	D		.																																			98070271	SO:0001819	synonymous_variant	4205	exon11				CCDS45362.1, CCDS45363.1, CCDS53978.1, CCDS58401.1	15q26	2008-02-05	2007-04-24			ENSG00000068305		"""Myocyte enhancer factors"""	6993	protein-coding gene	gene with protein product		600660				1516833	Standard	NM_005587		Approved	RSRFC4, RSRFC9	uc002bvf.3	Q02078		ENST00000557785.1:c.1266G>A	15.37:g.100252748G>A		Somatic		Capture	Illumina HiSeq	Phase_I	98070271	NM_005587	B4DFQ7|F6XG23|O43814|Q14223|Q14224|Q59GX4|Q7Z6C9|Q96D14	Silent	SNP	ENST00000557785.1	37	CCDS53978.1																																																																																				0.642	MEF2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415985.1		
GNPTG	84572	broad.mit.edu	37	16	1412882	1412882	+	Silent	SNP	C	C	T	rs375787769		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr16:1412882C>T	ENST00000204679.4	+	10	841	c.798C>T	c.(796-798)caC>caT	p.H266H	LA16c-316G12.2_ENST00000569831.1_RNA	NM_032520.4	NP_115909.1	Q9UJJ9	GNPTG_HUMAN	N-acetylglucosamine-1-phosphate transferase, gamma subunit	266					carbohydrate phosphorylation (GO:0046835)|N-glycan processing to lysosome (GO:0016256)	extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)	protein homodimerization activity (GO:0042803)	p.H266H(1)		breast(2)|central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(2)	7		Hepatocellular(780;0.0893)				TCACCCAGCACGGCATCCCCT	0.567																																					p.H266H												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C798T	16						.	C		0,4398		0,0,2199	92.0	97.0	95.0		798	-9.6	0.1	16		95	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	GNPTG	NM_032520.4		0,1,6498	TT,TC,CC		0.0116,0.0,0.0077		266/306	1412882	1,12997	2199	4300	6499	1352883	SO:0001819	synonymous_variant	84572	exon10			BC014592	CCDS10436.1	16p13.3	2009-04-17		2004-10-01	ENSG00000090581	ENSG00000090581			23026	protein-coding gene	gene with protein product	"""GlcNAc-phosphotransferase gamma-subunit"""	607838	"""N-acetylglucosamine-1-phosphotransferase, gamma subunit"", ""chromosome 16 open reading frame 27"""	GNPTAG, C16orf27		10712439	Standard	NM_032520		Approved	CAB56184, c316G12.3	uc002clm.3	Q9UJJ9	OTTHUMG00000047835	ENST00000204679.4:c.798C>T	16.37:g.1412882C>T		Somatic		Capture	Illumina HiSeq	Phase_I	1352883	NM_032520	B2R556|Q6XYD7|Q96L13	Silent	SNP	ENST00000204679.4	37	CCDS10436.1																																																																																				0.567	GNPTG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109058.2	NM_032520	
TEKT5	146279	broad.mit.edu	37	16	10729702	10729702	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr16:10729702G>A	ENST00000283025.2	-	6	1231	c.1160C>T	c.(1159-1161)cCg>cTg	p.P387L	TEKT5_ENST00000574923.1_5'UTR	NM_144674.1	NP_653275.1	Q96M29	TEKT5_HUMAN	tektin 5	387						cilium (GO:0005929)|cytoplasm (GO:0005737)|microtubule (GO:0005874)|nucleus (GO:0005634)		p.P387L(1)		breast(2)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(9)|lung(9)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(4)	34						CACCTTCAGCGGGCCCTCCTT	0.617																																					p.P387L												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1160T	16						.						127.0	128.0	128.0					16																	10729702		2197	4300	6497	10637203	SO:0001583	missense	146279	exon6				CCDS10542.1	16p13.13	2014-01-21			ENSG00000153060	ENSG00000153060			26554	protein-coding gene	gene with protein product							Standard	NM_144674		Approved	FLJ32871, CT149	uc002czz.1	Q96M29	OTTHUMG00000129750	ENST00000283025.2:c.1160C>T	16.37:g.10729702G>A	ENSP00000283025:p.Pro387Leu	Somatic		Capture	Illumina HiSeq	Phase_I	10637203	NM_144674	A1L3Z3	Missense_Mutation	SNP	ENST00000283025.2	37	CCDS10542.1	.	.	.	.	.	.	.	.	.	.	G	19.15	3.772467	0.69992	.	.	ENSG00000153060	ENST00000283025	T	0.03181	4.02	4.56	4.56	0.56223	.	0.000000	0.56097	D	0.000031	T	0.23094	0.0558	M	0.89534	3.04	0.80722	D	1	D	0.76494	0.999	D	0.73380	0.98	T	0.09143	-1.0688	10	0.66056	D	0.02	-27.937	15.9141	0.79496	0.0:0.0:1.0:0.0	.	387	Q96M29	TEKT5_HUMAN	L	387	ENSP00000283025:P387L	ENSP00000283025:P387L	P	-	2	0	TEKT5	10637203	1.000000	0.71417	0.994000	0.49952	0.363000	0.29612	7.276000	0.78559	2.090000	0.63153	0.555000	0.69702	CCG		0.617	TEKT5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251963.1	NM_144674	
MYH11	4629	broad.mit.edu	37	16	15811172	15811172	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr16:15811172G>A	ENST00000300036.5	-	38	5438	c.5329C>T	c.(5329-5331)Cgc>Tgc	p.R1777C	NDE1_ENST00000396355.1_Intron|NDE1_ENST00000342673.5_Intron|NDE1_ENST00000396354.1_Intron|MYH11_ENST00000576790.2_Missense_Mutation_p.R1777C|MYH11_ENST00000452625.2_Missense_Mutation_p.R1784C|MYH11_ENST00000396324.3_Missense_Mutation_p.R1784C	NM_002474.2	NP_002465.1	P35749	MYH11_HUMAN	myosin, heavy chain 11, smooth muscle	1777					axon guidance (GO:0007411)|cardiac muscle fiber development (GO:0048739)|elastic fiber assembly (GO:0048251)|muscle contraction (GO:0006936)|skeletal muscle myosin thick filament assembly (GO:0030241)|smooth muscle contraction (GO:0006939)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|muscle myosin complex (GO:0005859)|myosin filament (GO:0032982)|smooth muscle contractile fiber (GO:0030485)|stress fiber (GO:0001725)	ATP binding (GO:0005524)|motor activity (GO:0003774)|structural constituent of muscle (GO:0008307)	p.R1777S(1)|p.R1784S(1)|p.R1777C(1)		NS(2)|breast(7)|central_nervous_system(1)|endometrium(11)|kidney(5)|large_intestine(34)|liver(1)|lung(37)|ovary(9)|pancreas(1)|prostate(7)|skin(7)|upper_aerodigestive_tract(1)	123						GCCGTGCTGCGCTCTGTGGCC	0.647			T	CBFB	AML																																p.R1784C			Dom	yes		16	16p13.13-p13.12	4629	"""myosin, heavy polypeptide 11, smooth muscle"""		L	.	.	3	Substitution - Missense(3)	lung(2)|large_intestine(1)	c.C5350T	16						.						54.0	53.0	53.0					16																	15811172		2197	4300	6497	15718673	SO:0001583	missense	4629	exon39			X69292	CCDS10565.1, CCDS10566.1, CCDS45423.1, CCDS45424.1	16p13.11	2011-09-27	2006-09-29		ENSG00000133392	ENSG00000133392		"""Myosins / Myosin superfamily : Class II"""	7569	protein-coding gene	gene with protein product		160745	"""myosin, heavy polypeptide 11, smooth muscle"""			7684189	Standard	NM_001040113		Approved	SMMHC, SMHC	uc002ddx.3	P35749	OTTHUMG00000129935	ENST00000300036.5:c.5329C>T	16.37:g.15811172G>A	ENSP00000300036:p.Arg1777Cys	Somatic		Capture	Illumina HiSeq	Phase_I	15718673	NM_001040114	D2JYH7|O00396|O94944|P78422|Q3MIV8|Q3MNF0|Q3MNF1	Missense_Mutation	SNP	ENST00000300036.5	37	CCDS10565.1	.	.	.	.	.	.	.	.	.	.	G	23.6	4.432019	0.83776	.	.	ENSG00000133392	ENST00000300036;ENST00000338282;ENST00000396320;ENST00000396324;ENST00000452625	T;T;T;T	0.79845	-1.31;-1.31;-1.31;-1.31	4.68	4.68	0.58851	Myosin tail (1);	0.059728	0.64402	D	0.000001	D	0.90208	0.6939	M	0.89095	3.005	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.87578	0.988;0.988;0.988;0.988;0.998	D	0.91643	0.5328	10	0.87932	D	0	.	11.8024	0.52135	0.0:0.0:0.8248:0.1752	.	1784;1777;1784;1777;1784	B1PS43;P35749;Q3MNF1;Q3MIV8;Q3MNF0	.;MYH11_HUMAN;.;.;.	C	1777;1777;1784;1784;1784	ENSP00000300036:R1777C;ENSP00000345136:R1777C;ENSP00000379616:R1784C;ENSP00000407821:R1784C	ENSP00000300036:R1777C	R	-	1	0	MYH11	15718673	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	7.871000	0.87180	2.156000	0.67533	0.561000	0.74099	CGC		0.647	MYH11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252192.2	NM_001040113	
MYH11	4629	broad.mit.edu	37	16	15812270	15812270	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr16:15812270G>A	ENST00000300036.5	-	37	5306	c.5197C>T	c.(5197-5199)Cgc>Tgc	p.R1733C	NDE1_ENST00000396355.1_Intron|NDE1_ENST00000342673.5_Intron|NDE1_ENST00000396354.1_Intron|MYH11_ENST00000576790.2_Missense_Mutation_p.R1733C|MYH11_ENST00000452625.2_Missense_Mutation_p.R1740C|MYH11_ENST00000396324.3_Missense_Mutation_p.R1740C	NM_002474.2	NP_002465.1	P35749	MYH11_HUMAN	myosin, heavy chain 11, smooth muscle	1733					axon guidance (GO:0007411)|cardiac muscle fiber development (GO:0048739)|elastic fiber assembly (GO:0048251)|muscle contraction (GO:0006936)|skeletal muscle myosin thick filament assembly (GO:0030241)|smooth muscle contraction (GO:0006939)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|muscle myosin complex (GO:0005859)|myosin filament (GO:0032982)|smooth muscle contractile fiber (GO:0030485)|stress fiber (GO:0001725)	ATP binding (GO:0005524)|motor activity (GO:0003774)|structural constituent of muscle (GO:0008307)	p.R1733C(1)		NS(2)|breast(7)|central_nervous_system(1)|endometrium(11)|kidney(5)|large_intestine(34)|liver(1)|lung(37)|ovary(9)|pancreas(1)|prostate(7)|skin(7)|upper_aerodigestive_tract(1)	123						GCCTCCAGGCGGCGCTTCTCG	0.672			T	CBFB	AML																																p.R1740C			Dom	yes		16	16p13.13-p13.12	4629	"""myosin, heavy polypeptide 11, smooth muscle"""		L	.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C5218T	16						.						28.0	22.0	24.0					16																	15812270		2196	4299	6495	15719771	SO:0001583	missense	4629	exon38			X69292	CCDS10565.1, CCDS10566.1, CCDS45423.1, CCDS45424.1	16p13.11	2011-09-27	2006-09-29		ENSG00000133392	ENSG00000133392		"""Myosins / Myosin superfamily : Class II"""	7569	protein-coding gene	gene with protein product		160745	"""myosin, heavy polypeptide 11, smooth muscle"""			7684189	Standard	NM_001040113		Approved	SMMHC, SMHC	uc002ddx.3	P35749	OTTHUMG00000129935	ENST00000300036.5:c.5197C>T	16.37:g.15812270G>A	ENSP00000300036:p.Arg1733Cys	Somatic		Capture	Illumina HiSeq	Phase_I	15719771	NM_001040114	D2JYH7|O00396|O94944|P78422|Q3MIV8|Q3MNF0|Q3MNF1	Missense_Mutation	SNP	ENST00000300036.5	37	CCDS10565.1	.	.	.	.	.	.	.	.	.	.	G	16.16	3.045815	0.55110	.	.	ENSG00000133392	ENST00000300036;ENST00000338282;ENST00000396320;ENST00000396324;ENST00000452625	D;D;D;D	0.81499	-1.5;-1.5;-1.5;-1.5	4.7	3.74	0.42951	Myosin tail (1);	0.060051	0.64402	D	0.000002	D	0.88291	0.6397	M	0.78456	2.415	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.74023	0.982;0.982;0.982;0.982;0.982	D	0.88888	0.3344	10	0.87932	D	0	.	11.9203	0.52787	0.0846:0.0:0.9154:0.0	.	1740;1733;1740;1733;1740	B1PS43;P35749;Q3MNF1;Q3MIV8;Q3MNF0	.;MYH11_HUMAN;.;.;.	C	1733;1733;1740;1740;1740	ENSP00000300036:R1733C;ENSP00000345136:R1733C;ENSP00000379616:R1740C;ENSP00000407821:R1740C	ENSP00000300036:R1733C	R	-	1	0	MYH11	15719771	1.000000	0.71417	1.000000	0.80357	0.079000	0.17450	9.624000	0.98398	0.983000	0.38602	-0.258000	0.10820	CGC		0.672	MYH11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252192.2	NM_001040113	
CRAMP1L	57585	broad.mit.edu	37	16	1719106	1719106	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr16:1719106A>G	ENST00000397412.3	+	19	3538	c.3439A>G	c.(3439-3441)Acc>Gcc	p.T1147A	CRAMP1L_ENST00000436138.3_Missense_Mutation_p.T1144A|CRAMP1L_ENST00000262317.4_Missense_Mutation_p.T522A|LA16c-431H6.6_ENST00000454337.1_3'UTR|CRAMP1L_ENST00000293925.5_Missense_Mutation_p.T1147A			Q96RY5	CRML_HUMAN	Crm, cramped-like (Drosophila)	1147	Ser-rich.					nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)	p.T1147A(1)		NS(2)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(3)|lung(6)|pancreas(1)	22						CGCCTCTCCCACCCACGACCC	0.612																																					p.T1147A												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A3439G	16						.						38.0	46.0	43.0					16																	1719106		2044	4182	6226	1659107	SO:0001583	missense	57585	exon18			AB037847	CCDS10440.2	16p13.3	2008-07-30	2001-11-28		ENSG00000007545	ENSG00000007545			14122	protein-coding gene	gene with protein product			"""Crm (Cramped Drosophila)-like"""				Standard	NM_020825		Approved	KIAA1426	uc010uvh.2	Q96RY5	OTTHUMG00000074087	ENST00000397412.3:c.3439A>G	16.37:g.1719106A>G	ENSP00000380559:p.Thr1147Ala	Somatic		Capture	Illumina HiSeq	Phase_I	1659107	NM_020825	A8MZL1|B1AJY1|Q8NDN1|Q9P2C1	Missense_Mutation	SNP	ENST00000397412.3	37	CCDS10440.2	.	.	.	.	.	.	.	.	.	.	A	19.80	3.894080	0.72639	.	.	ENSG00000007545	ENST00000397412;ENST00000293925;ENST00000436138;ENST00000262317	.	.	.	5.73	4.62	0.57501	.	0.143365	0.64402	D	0.000014	T	0.36193	0.0958	L	0.27053	0.805	0.29607	N	0.847243	P	0.44578	0.838	P	0.45099	0.469	T	0.28650	-1.0037	9	0.56958	D	0.05	-29.0243	12.9427	0.58354	0.8645:0.1355:0.0:0.0	.	1147	Q96RY5	CRML_HUMAN	A	1147;1147;1144;522	.	ENSP00000262317:T522A	T	+	1	0	CRAMP1L	1659107	0.993000	0.37304	0.998000	0.56505	0.988000	0.76386	3.292000	0.51772	0.986000	0.38683	0.533000	0.62120	ACC		0.612	CRAMP1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157297.4		
MYH11	4629	broad.mit.edu	37	16	15835450	15835450	+	Missense_Mutation	SNP	C	C	T	rs146404868		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr16:15835450C>T	ENST00000300036.5	-	22	2838	c.2729G>A	c.(2728-2730)cGg>cAg	p.R910Q	MYH11_ENST00000576790.2_Missense_Mutation_p.R910Q|MYH11_ENST00000452625.2_Missense_Mutation_p.R917Q|MYH11_ENST00000396324.3_Missense_Mutation_p.R917Q|AF001548.6_ENST00000577048.1_RNA	NM_002474.2	NP_002465.1	P35749	MYH11_HUMAN	myosin, heavy chain 11, smooth muscle	910					axon guidance (GO:0007411)|cardiac muscle fiber development (GO:0048739)|elastic fiber assembly (GO:0048251)|muscle contraction (GO:0006936)|skeletal muscle myosin thick filament assembly (GO:0030241)|smooth muscle contraction (GO:0006939)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|muscle myosin complex (GO:0005859)|myosin filament (GO:0032982)|smooth muscle contractile fiber (GO:0030485)|stress fiber (GO:0001725)	ATP binding (GO:0005524)|motor activity (GO:0003774)|structural constituent of muscle (GO:0008307)	p.R910Q(1)		NS(2)|breast(7)|central_nervous_system(1)|endometrium(11)|kidney(5)|large_intestine(34)|liver(1)|lung(37)|ovary(9)|pancreas(1)|prostate(7)|skin(7)|upper_aerodigestive_tract(1)	123						CAGCCGCACCCGCATCTCCTC	0.627			T	CBFB	AML																																p.R917Q			Dom	yes		16	16p13.13-p13.12	4629	"""myosin, heavy polypeptide 11, smooth muscle"""		L	.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2750A	16						.	C	GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG	0,4394		0,0,2197	83.0	91.0	88.0		2750,2750,2729,2729	5.0	1.0	16	dbSNP_134	88	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense,missense,missense	MYH11	NM_001040113.1,NM_001040114.1,NM_002474.2,NM_022844.2	43,43,43,43	0,1,6496	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging,probably-damaging,probably-damaging,probably-damaging	917/1946,917/1980,910/1973,910/1939	15835450	1,12993	2197	4300	6497	15742951	SO:0001583	missense	4629	exon23			X69292	CCDS10565.1, CCDS10566.1, CCDS45423.1, CCDS45424.1	16p13.11	2011-09-27	2006-09-29		ENSG00000133392	ENSG00000133392		"""Myosins / Myosin superfamily : Class II"""	7569	protein-coding gene	gene with protein product		160745	"""myosin, heavy polypeptide 11, smooth muscle"""			7684189	Standard	NM_001040113		Approved	SMMHC, SMHC	uc002ddx.3	P35749	OTTHUMG00000129935	ENST00000300036.5:c.2729G>A	16.37:g.15835450C>T	ENSP00000300036:p.Arg910Gln	Somatic		Capture	Illumina HiSeq	Phase_I	15742951	NM_001040114	D2JYH7|O00396|O94944|P78422|Q3MIV8|Q3MNF0|Q3MNF1	Missense_Mutation	SNP	ENST00000300036.5	37	CCDS10565.1	.	.	.	.	.	.	.	.	.	.	C	35	5.504715	0.96371	0.0	1.16E-4	ENSG00000133392	ENST00000300036;ENST00000338282;ENST00000396320;ENST00000396324;ENST00000452625	D;D;D;D	0.96265	-3.96;-3.96;-3.96;-3.96	5.01	5.01	0.66863	.	0.000000	0.85682	D	0.000000	D	0.98438	0.9480	M	0.91663	3.23	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;0.999;0.999;1.0	D;D;D;D;D	0.91635	0.999;0.989;0.989;0.981;0.995	D	0.98794	1.0737	10	0.42905	T	0.14	.	17.3113	0.87211	0.0:1.0:0.0:0.0	.	917;910;917;910;917	B1PS43;P35749;Q3MNF1;Q3MIV8;Q3MNF0	.;MYH11_HUMAN;.;.;.	Q	910;910;917;917;917	ENSP00000300036:R910Q;ENSP00000345136:R910Q;ENSP00000379616:R917Q;ENSP00000407821:R917Q	ENSP00000300036:R910Q	R	-	2	0	MYH11	15742951	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	7.770000	0.85390	2.330000	0.79161	0.462000	0.41574	CGG		0.627	MYH11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252192.2	NM_001040113	
SMG1	23049	broad.mit.edu	37	16	18908139	18908139	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr16:18908139C>T	ENST00000446231.2	-	2	644	c.232G>A	c.(232-234)Gct>Act	p.A78T	SMG1_ENST00000389467.3_Missense_Mutation_p.A78T|SMG1_ENST00000565224.1_Missense_Mutation_p.A52T			Q96Q15	SMG1_HUMAN	SMG1 phosphatidylinositol 3-kinase-related kinase	78	Interaction with SMG8 and SMG9.				DNA repair (GO:0006281)|gene expression (GO:0010467)|mRNA export from nucleus (GO:0006406)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|peptidyl-serine phosphorylation (GO:0018105)|phosphatidylinositol phosphorylation (GO:0046854)|protein autophosphorylation (GO:0046777)|response to stress (GO:0006950)|RNA metabolic process (GO:0016070)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)	p.A74T(1)		NS(2)|breast(8)|cervix(2)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(16)|lung(37)|ovary(1)|skin(1)|stomach(4)|urinary_tract(1)	92						TGTATGTCAGCGTGGACTCTG	0.438																																					p.A78T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G232A	16						.						10.0	10.0	10.0					16																	18908139		1633	3593	5226	18815640	SO:0001583	missense	23049	exon2			AB061371	CCDS45430.1	16p12.3	2013-07-02	2013-07-02		ENSG00000157106	ENSG00000157106			30045	protein-coding gene	gene with protein product	"""phosphatidylinositol 3-kinase-related kinase"""	607032	"""smg-1 homolog, phosphatidylinositol 3-kinase-related kinase (C. elegans)"""			9455477, 11331269, 17229728	Standard	NM_015092		Approved	LIP, KIAA0421, ATX	uc002dfm.3	Q96Q15	OTTHUMG00000166900	ENST00000446231.2:c.232G>A	16.37:g.18908139C>T	ENSP00000402515:p.Ala78Thr	Somatic		Capture	Illumina HiSeq	Phase_I	18815640	NM_015092	O43305|Q13284|Q8NFX2|Q96QV0|Q96RW3	Missense_Mutation	SNP	ENST00000446231.2	37	CCDS45430.1	.	.	.	.	.	.	.	.	.	.	C	11.53	1.666938	0.29604	.	.	ENSG00000157106	ENST00000446231;ENST00000389467;ENST00000532700	T;T;T	0.10763	2.84;2.84;2.84	4.83	-0.0359	0.13891	.	0.260438	0.30118	N	0.010367	T	0.03871	0.0109	N	0.08118	0	0.29616	N	0.846568	B	0.02656	0.0	B	0.01281	0.0	T	0.44283	-0.9338	10	0.08381	T	0.77	.	7.7183	0.28717	0.0:0.4353:0.0:0.5647	.	78	Q96Q15	SMG1_HUMAN	T	78;78;52	ENSP00000402515:A78T;ENSP00000374118:A78T;ENSP00000432825:A52T	ENSP00000374118:A78T	A	-	1	0	SMG1	18815640	0.929000	0.31497	0.938000	0.37757	0.994000	0.84299	0.115000	0.15540	0.107000	0.17824	0.555000	0.69702	GCT		0.438	SMG1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000391817.1	NM_015092	
KNOP1	400506	broad.mit.edu	37	16	19721832	19721832	+	Splice_Site	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr16:19721832G>A	ENST00000219837.7	-	4	1142	c.1064C>T	c.(1063-1065)aCg>aTg	p.T355M	AC002550.5_ENST00000565916.1_RNA|KNOP1_ENST00000568230.1_Splice_Site_p.T34M	NM_001012991.2	NP_001013009.2	Q1ED39	KNOP1_HUMAN	lysine-rich nucleolar protein 1	355	Interaction with ZNF106. {ECO:0000250}.					nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)	p.T355M(1)									CAAACTTACCGTCCACTTCCT	0.577																																					p.T355M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1064T	16						.						113.0	132.0	126.0					16																	19721832		2131	4233	6364	19629333	SO:0001630	splice_region_variant	400506	exon4			BC047010	CCDS42127.1	16p12.3	2013-03-12	2013-03-12	2013-03-12	ENSG00000103550	ENSG00000103550			34404	protein-coding gene	gene with protein product	"""family with sequence similarity 191, member A"", ""testis-specific gene 118"""		"""chromosome 16 open reading frame 88"""	C16orf88			Standard	NM_001012991		Approved	101F10.1, FAM191A, TSG118	uc002dgq.3	Q1ED39		ENST00000219837.7:c.1065+1C>T	16.37:g.19721832G>A		Somatic		Capture	Illumina HiSeq	Phase_I	19629333	NM_001012991	O43328|Q5FWF3	Missense_Mutation	SNP	ENST00000219837.7	37	CCDS42127.1	.	.	.	.	.	.	.	.	.	.	G	9.009	0.982122	0.18889	.	.	ENSG00000103550	ENST00000219837	T	0.26223	1.75	4.36	-1.68	0.08212	.	.	.	.	.	T	0.12774	0.0310	L	0.28740	0.885	0.09310	N	1	B	0.18461	0.028	B	0.14023	0.01	T	0.32188	-0.9916	8	.	.	.	-5.9576	0.4677	0.00526	0.3197:0.1266:0.2954:0.2583	.	355	Q1ED39	CP088_HUMAN	M	355	ENSP00000219837:T355M	.	T	-	2	0	C16orf88	19629333	0.001000	0.12720	0.031000	0.17742	0.072000	0.16883	-0.503000	0.06383	-0.127000	0.11661	-0.670000	0.03821	ACG		0.577	KNOP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000435993.2	NM_001012991	Missense_Mutation
DNAH3	55567	broad.mit.edu	37	16	20948094	20948094	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr16:20948094C>A	ENST00000261383.3	-	60	11735	c.11736G>T	c.(11734-11736)gaG>gaT	p.E3912D	DNAH3_ENST00000415178.1_3'UTR	NM_017539.1	NP_060009.1	Q8TD57	DYH3_HUMAN	dynein, axonemal, heavy chain 3	3912					cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|microtubule motor activity (GO:0003777)	p.E3912D(2)		NS(3)|autonomic_ganglia(1)|breast(12)|central_nervous_system(3)|cervix(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(4)|kidney(10)|large_intestine(42)|liver(2)|lung(57)|ovary(14)|pancreas(1)|prostate(7)|skin(11)|stomach(5)|upper_aerodigestive_tract(7)|urinary_tract(6)	202				GBM - Glioblastoma multiforme(48;0.207)		TAAAGACTTCCTCTAGCTCCG	0.557																																					p.E3912D												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G11736T	16						.						75.0	66.0	69.0					16																	20948094		2201	4300	6501	20855595	SO:0001583	missense	55567	exon60			U83574	CCDS10594.1	16p12.2	2008-08-01	2006-09-04		ENSG00000158486	ENSG00000158486		"""Axonemal dyneins"""	2949	protein-coding gene	gene with protein product		603334	"""dynein, axonemal, heavy polypeptide 3"""			9256245, 9373155	Standard	NM_017539		Approved	Dnahc3b, DLP3, Hsadhc3, DKFZp434N074	uc010vbe.2	Q8TD57	OTTHUMG00000090677	ENST00000261383.3:c.11736G>T	16.37:g.20948094C>A	ENSP00000261383:p.Glu3912Asp	Somatic		Capture	Illumina HiSeq	Phase_I	20855595	NM_017539	O00437|O15437|O43326|Q3C0H2|Q8WUP9|Q9UEM3|Q9UEM5|Q9UG35	Missense_Mutation	SNP	ENST00000261383.3	37	CCDS10594.1	.	.	.	.	.	.	.	.	.	.	C	21.0	4.087953	0.76642	.	.	ENSG00000158486	ENST00000261383	T	0.11385	2.78	5.85	3.58	0.41010	Dynein heavy chain (1);	0.000000	0.85682	D	0.000000	T	0.24624	0.0597	M	0.63208	1.945	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.00904	-1.1520	10	0.51188	T	0.08	.	6.4983	0.22153	0.0:0.643:0.0:0.357	.	3912	Q8TD57	DYH3_HUMAN	D	3912	ENSP00000261383:E3912D	ENSP00000261383:E3912D	E	-	3	2	DNAH3	20855595	0.994000	0.37717	1.000000	0.80357	0.991000	0.79684	0.432000	0.21461	1.481000	0.48307	0.655000	0.94253	GAG		0.557	DNAH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207361.1	NM_017539	
TRAF7	84231	broad.mit.edu	37	16	2220647	2220647	+	Silent	SNP	C	C	T	rs200035101	byFrequency	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr16:2220647C>T	ENST00000326181.6	+	5	396	c.264C>T	c.(262-264)tcC>tcT	p.S88S		NM_032271.2	NP_115647.2	Q6Q0C0	TRAF7_HUMAN	TNF receptor-associated factor 7, E3 ubiquitin protein ligase	88					activation of MAPKKK activity (GO:0000185)|apoptotic process (GO:0006915)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of MAPK cascade (GO:0043410)|protein ubiquitination (GO:0016567)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasmic vesicle (GO:0031410)|ubiquitin ligase complex (GO:0000151)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.S88S(1)		breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(8)|ovary(1)|pancreas(1)|prostate(2)|skin(1)	23						GCTCCGACTCCGCCATCTCTG	0.687													C|||	5	0.000998403	0.0	0.0	5008	,	,		13766	0.004		0.001	False		,,,				2504	0.0				p.S88S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C264T	16						.	C		1,4369		0,1,2184	44.0	40.0	41.0		264	-9.6	0.0	16		41	0,8596		0,0,4298	no	coding-synonymous	TRAF7	NM_032271.2		0,1,6482	TT,TC,CC		0.0,0.0229,0.0077		88/671	2220647	1,12965	2185	4298	6483	2160648	SO:0001819	synonymous_variant	84231	exon5			AL136921	CCDS10461.1	16p13.3	2013-01-10	2012-02-23	2004-06-04	ENSG00000131653	ENSG00000131653		"""RING-type (C3HC4) zinc fingers"", ""WD repeat domain containing"""	20456	protein-coding gene	gene with protein product		606692	"""ring finger and WD repeat domain 1"", ""TNF receptor-associated factor 7"""	RFWD1		11230166, 15001576	Standard	NM_032271		Approved	RNF119, DKFZp586I021, MGC7807	uc002cow.3	Q6Q0C0	OTTHUMG00000128826	ENST00000326181.6:c.264C>T	16.37:g.2220647C>T		Somatic		Capture	Illumina HiSeq	Phase_I	2160648	NM_032271	Q9H073	Silent	SNP	ENST00000326181.6	37	CCDS10461.1																																																																																				0.687	TRAF7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250762.1	NM_032271	
DNAH3	55567	broad.mit.edu	37	16	20975196	20975196	+	Missense_Mutation	SNP	G	G	A	rs530510705		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr16:20975196G>A	ENST00000261383.3	-	53	10009	c.10010C>T	c.(10009-10011)aCg>aTg	p.T3337M	DNAH3_ENST00000415178.1_3'UTR	NM_017539.1	NP_060009.1	Q8TD57	DYH3_HUMAN	dynein, axonemal, heavy chain 3	3337					cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|microtubule motor activity (GO:0003777)	p.T3337M(2)		NS(3)|autonomic_ganglia(1)|breast(12)|central_nervous_system(3)|cervix(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(4)|kidney(10)|large_intestine(42)|liver(2)|lung(57)|ovary(14)|pancreas(1)|prostate(7)|skin(11)|stomach(5)|upper_aerodigestive_tract(7)|urinary_tract(6)	202				GBM - Glioblastoma multiforme(48;0.207)		CTCGCTCTTCGTGCTGTGGGT	0.473													G|||	1	0.000199681	0.0008	0.0	5008	,	,		24191	0.0		0.0	False		,,,				2504	0.0				p.T3337M												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.C10010T	16						.						158.0	123.0	135.0					16																	20975196		2201	4300	6501	20882697	SO:0001583	missense	55567	exon53			U83574	CCDS10594.1	16p12.2	2008-08-01	2006-09-04		ENSG00000158486	ENSG00000158486		"""Axonemal dyneins"""	2949	protein-coding gene	gene with protein product		603334	"""dynein, axonemal, heavy polypeptide 3"""			9256245, 9373155	Standard	NM_017539		Approved	Dnahc3b, DLP3, Hsadhc3, DKFZp434N074	uc010vbe.2	Q8TD57	OTTHUMG00000090677	ENST00000261383.3:c.10010C>T	16.37:g.20975196G>A	ENSP00000261383:p.Thr3337Met	Somatic		Capture	Illumina HiSeq	Phase_I	20882697	NM_017539	O00437|O15437|O43326|Q3C0H2|Q8WUP9|Q9UEM3|Q9UEM5|Q9UG35	Missense_Mutation	SNP	ENST00000261383.3	37	CCDS10594.1	.	.	.	.	.	.	.	.	.	.	G	4.510	0.094706	0.08681	.	.	ENSG00000158486	ENST00000261383	D	0.86694	-2.16	5.78	-11.6	0.00059	.	2.041410	0.01831	N	0.034701	T	0.74160	0.3680	L	0.33093	0.98	0.09310	N	1	P	0.45715	0.865	B	0.37346	0.247	T	0.73263	-0.4038	10	0.72032	D	0.01	.	5.4467	0.16539	0.1232:0.3796:0.0824:0.4148	.	3337	Q8TD57	DYH3_HUMAN	M	3337	ENSP00000261383:T3337M	ENSP00000261383:T3337M	T	-	2	0	DNAH3	20882697	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-2.467000	0.00993	-2.052000	0.00902	-1.119000	0.02030	ACG		0.473	DNAH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207361.1	NM_017539	
SCNN1B	6338	broad.mit.edu	37	16	23391835	23391835	+	Missense_Mutation	SNP	G	G	A	rs112069765		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr16:23391835G>A	ENST00000343070.2	+	13	1812	c.1636G>A	c.(1636-1638)Gac>Aac	p.D546N	SCNN1B_ENST00000307331.5_Missense_Mutation_p.D591N|SCNN1B_ENST00000568085.1_Missense_Mutation_p.D510N|SCNN1B_ENST00000568923.1_Missense_Mutation_p.D519N	NM_000336.2	NP_000327.2	P51168	SCNNB_HUMAN	sodium channel, non-voltage-gated 1, beta subunit	546					excretion (GO:0007588)|ion transmembrane transport (GO:0034220)|multicellular organismal water homeostasis (GO:0050891)|response to stimulus (GO:0050896)|sensory perception of taste (GO:0050909)|sodium ion homeostasis (GO:0055078)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|sodium channel complex (GO:0034706)	ligand-gated sodium channel activity (GO:0015280)|WW domain binding (GO:0050699)	p.D546N(1)		breast(2)|endometrium(3)|kidney(2)|large_intestine(5)|liver(2)|lung(8)|ovary(3)|pancreas(1)|prostate(3)|skin(1)|stomach(1)|urinary_tract(1)	32				GBM - Glioblastoma multiforme(48;0.0465)	Amiloride(DB00594)|Triamterene(DB00384)	GATCATCATCGACTTTGTGTG	0.617																																					p.D546N												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1636A	16						.	G	ASN/ASP	1,4393	2.1+/-5.4	0,1,2196	173.0	173.0	173.0		1636	4.8	1.0	16	dbSNP_132	173	0,8600		0,0,4300	no	missense	SCNN1B	NM_000336.2	23	0,1,6496	AA,AG,GG		0.0,0.0228,0.0077	probably-damaging	546/641	23391835	1,12993	2197	4300	6497	23299336	SO:0001583	missense	6338	exon13			X87159	CCDS10609.1	16p12.2-p12.1	2012-02-28	2012-02-28		ENSG00000168447	ENSG00000168447		"""Ion channels / Sodium channel, nonvoltage-gated"", ""Sodium channels"""	10600	protein-coding gene	gene with protein product	"""Liddle syndrome"""	600760	"""sodium channel, nonvoltage-gated 1, beta"", ""sodium channel, non-voltage-gated 1, beta"""				Standard	NM_000336		Approved	ENaCbeta	uc002dln.3	P51168	OTTHUMG00000131608	ENST00000343070.2:c.1636G>A	16.37:g.23391835G>A	ENSP00000345751:p.Asp546Asn	Somatic		Capture	Illumina HiSeq	Phase_I	23299336	NM_000336	C5HTZ2|O60891|Q96KG2|Q9UJ32|Q9UMU5	Missense_Mutation	SNP	ENST00000343070.2	37	CCDS10609.1	.	.	.	.	.	.	.	.	.	.	G	27.0	4.788612	0.90367	2.28E-4	0.0	ENSG00000168447	ENST00000343070;ENST00000307331	T;T	0.79247	-1.25;-1.25	4.85	4.85	0.62838	.	0.000000	0.64402	D	0.000001	T	0.77452	0.4132	N	0.08118	0	0.54753	D	0.999981	D	0.89917	1.0	D	0.73380	0.98	D	0.83593	0.0124	10	0.87932	D	0	-10.5837	16.981	0.86327	0.0:0.0:1.0:0.0	.	546	P51168	SCNNB_HUMAN	N	546;591	ENSP00000345751:D546N;ENSP00000302874:D591N	ENSP00000302874:D591N	D	+	1	0	SCNN1B	23299336	1.000000	0.71417	0.996000	0.52242	0.996000	0.88848	7.218000	0.77991	2.230000	0.72887	0.643000	0.83706	GAC		0.617	SCNN1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254495.2		
ERN2	10595	broad.mit.edu	37	16	23717720	23717720	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr16:23717720G>T	ENST00000457008.2	-	7	558	c.520C>A	c.(520-522)Cca>Aca	p.P174T	ERN2_ENST00000256797.4_Missense_Mutation_p.P222T					endoplasmic reticulum to nucleus signaling 2									p.P222T(1)		large_intestine(2)|lung(2)|ovary(2)	6				GBM - Glioblastoma multiforme(48;0.0156)		CGCAGGGCTGGGGCTCTTGGG	0.582																																					p.P222T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C664A	16						.						46.0	46.0	46.0					16																	23717720		2197	4295	6492	23625221	SO:0001583	missense	10595	exon7			AA527544	CCDS32407.1	16p12.2	2008-02-05	2007-08-14			ENSG00000134398			16942	protein-coding gene	gene with protein product		604034	"""ER to nucleus signalling 2"""			9755171, 11175748	Standard	NM_033266		Approved	IRE1b	uc002dma.4	Q76MJ5		ENST00000457008.2:c.520C>A	16.37:g.23717720G>T	ENSP00000413812:p.Pro174Thr	Somatic		Capture	Illumina HiSeq	Phase_I	23625221	NM_033266		Missense_Mutation	SNP	ENST00000457008.2	37		.	.	.	.	.	.	.	.	.	.	G	13.73	2.323965	0.41096	.	.	ENSG00000134398	ENST00000256797;ENST00000457008	T;T	0.56776	0.44;0.44	5.67	5.67	0.87782	Quinonprotein alcohol dehydrogenase-like (2);	0.233186	0.45867	D	0.000338	T	0.41971	0.1182	L	0.29908	0.895	0.18873	N	0.999986	B;B;B	0.32245	0.002;0.361;0.242	B;B;B	0.32864	0.011;0.154;0.073	T	0.23868	-1.0176	10	0.15066	T	0.55	.	17.2499	0.87039	0.0:0.0:1.0:0.0	.	174;174;174	Q76MJ5;E7ETG2;A5YM65	ERN2_HUMAN;.;.	T	222;174	ENSP00000256797:P222T;ENSP00000413812:P174T	ENSP00000256797:P222T	P	-	1	0	ERN2	23625221	0.997000	0.39634	0.195000	0.23364	0.964000	0.63967	5.172000	0.65003	2.677000	0.91161	0.462000	0.41574	CCA		0.582	ERN2-002	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000434886.1		
PRKCB	5579	broad.mit.edu	37	16	24202517	24202517	+	Missense_Mutation	SNP	G	G	A	rs563116744		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr16:24202517G>A	ENST00000321728.7	+	16	2004	c.1829G>A	c.(1828-1830)cGc>cAc	p.R610H	PRKCB_ENST00000303531.7_Missense_Mutation_p.R610H	NM_212535.2	NP_997700.1	P05771	KPCB_HUMAN	protein kinase C, beta	610	AGC-kinase C-terminal.				apoptotic process (GO:0006915)|B cell activation (GO:0042113)|B cell receptor signaling pathway (GO:0050853)|blood coagulation (GO:0007596)|calcium ion transport (GO:0006816)|cellular calcium ion homeostasis (GO:0006874)|cellular response to carbohydrate stimulus (GO:0071322)|histone H3-T6 phosphorylation (GO:0035408)|intracellular signal transduction (GO:0035556)|lipoprotein transport (GO:0042953)|negative regulation of glucose transport (GO:0010829)|negative regulation of insulin receptor signaling pathway (GO:0046627)|platelet activation (GO:0030168)|positive regulation of angiogenesis (GO:0045766)|positive regulation of B cell receptor signaling pathway (GO:0050861)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030949)|protein phosphorylation (GO:0006468)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	androgen receptor binding (GO:0050681)|ATP binding (GO:0005524)|calcium channel regulator activity (GO:0005246)|chromatin binding (GO:0003682)|histone binding (GO:0042393)|histone kinase activity (H3-T6 specific) (GO:0035403)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|protein kinase C activity (GO:0004697)|protein kinase C binding (GO:0005080)|protein serine/threonine kinase activity (GO:0004674)|zinc ion binding (GO:0008270)	p.R610H(2)		central_nervous_system(3)|large_intestine(1)|lung(2)|ovary(3)	9					Tamoxifen(DB00675)|Vitamin E(DB00163)	AAACTTGAACGCAAAGAGATC	0.478													G|||	1	0.000199681	0.0	0.0	5008	,	,		18802	0.0		0.0	False		,,,				2504	0.001				p.R610H												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G1829A	16						.						120.0	122.0	122.0					16																	24202517		2197	4300	6497	24110018	SO:0001583	missense	5579	exon16			M13975	CCDS10618.1, CCDS10619.1	16p12	2009-07-10	2008-08-18	2008-08-18	ENSG00000166501	ENSG00000166501	2.7.11.1		9395	protein-coding gene	gene with protein product		176970	"""protein kinase C, beta 1"""	PRKCB2, PKCB, PRKCB1		3658678	Standard	NM_002738		Approved		uc002dme.3	P05771	OTTHUMG00000131615	ENST00000321728.7:c.1829G>A	16.37:g.24202517G>A	ENSP00000318315:p.Arg610His	Somatic		Capture	Illumina HiSeq	Phase_I	24110018	NM_212535	C5IFJ8|D3DWF5|O43744|P05127|Q15138|Q93060|Q9UE49|Q9UE50|Q9UEH8|Q9UJ30|Q9UJ33	Missense_Mutation	SNP	ENST00000321728.7	37	CCDS10618.1	.	.	.	.	.	.	.	.	.	.	G	18.05	3.536078	0.64972	.	.	ENSG00000166501	ENST00000321728;ENST00000303531	T;T	0.54071	0.59;0.59	5.79	5.79	0.91817	AGC-kinase, C-terminal (2);Protein kinase-like domain (1);	0.124523	0.56097	D	0.000028	T	0.42787	0.1218	L	0.31207	0.915	0.42943	D	0.994353	B;B	0.21225	0.053;0.031	B;B	0.14578	0.011;0.005	T	0.24154	-1.0168	10	0.18710	T	0.47	.	18.5987	0.91239	0.0:0.0:1.0:0.0	.	610;610	P05771-2;P05771	.;KPCB_HUMAN	H	610	ENSP00000318315:R610H;ENSP00000305355:R610H	ENSP00000305355:R610H	R	+	2	0	PRKCB	24110018	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	2.857000	0.48349	2.744000	0.94065	0.650000	0.86243	CGC		0.478	PRKCB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254504.2	NM_212535	
RBBP6	5930	broad.mit.edu	37	16	24573231	24573231	+	Silent	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr16:24573231G>A	ENST00000319715.4	+	10	1470	c.1038G>A	c.(1036-1038)ccG>ccA	p.P346P	RBBP6_ENST00000381039.3_Silent_p.P346P|RBBP6_ENST00000348022.2_Silent_p.P346P	NM_006910.4	NP_008841.2	Q7Z6E9	RBBP6_HUMAN	retinoblastoma binding protein 6	346					embryonic organ development (GO:0048568)|in utero embryonic development (GO:0001701)|multicellular organism growth (GO:0035264)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|somite development (GO:0061053)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	ligase activity (GO:0016874)|poly(A) RNA binding (GO:0044822)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.P346P(1)		NS(1)|breast(3)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(10)|lung(17)|ovary(4)|pancreas(1)|prostate(2)|urinary_tract(1)	46				GBM - Glioblastoma multiforme(48;0.0518)		TACCACCTCCGAGACCACTGA	0.428																																					p.P346P												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G1038A	16						.						134.0	133.0	134.0					16																	24573231		2197	4300	6497	24480732	SO:0001819	synonymous_variant	5930	exon10				CCDS10621.1, CCDS10622.1, CCDS45444.1	16p12.2	2008-08-04	2001-11-28		ENSG00000122257	ENSG00000122257			9889	protein-coding gene	gene with protein product	"""proliferation potential-related protein"""	600938	"""retinoblastoma-binding protein 6"""			8595913, 16396680	Standard	NM_006910		Approved	P2P-R, PACT, SNAMA	uc002dmh.3	Q7Z6E9	OTTHUMG00000096991	ENST00000319715.4:c.1038G>A	16.37:g.24573231G>A		Somatic		Capture	Illumina HiSeq	Phase_I	24480732	NM_018703	Q147T5|Q15290|Q6DKH4|Q6P4C2|Q6YNC9|Q7Z6E8|Q8N0V2|Q96PH3|Q9H3I8|Q9H5M5|Q9NPX4	Silent	SNP	ENST00000319715.4	37	CCDS10621.1																																																																																				0.428	RBBP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214067.2	NM_006910	
TNRC6A	27327	broad.mit.edu	37	16	24802272	24802272	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr16:24802272C>T	ENST00000395799.3	+	6	2438	c.2309C>T	c.(2308-2310)aCt>aTt	p.T770I	TNRC6A_ENST00000315183.7_Missense_Mutation_p.T770I	NM_014494.2	NP_055309.2	Q8NDV7	TNR6A_HUMAN	trinucleotide repeat containing 6A	770	Interaction with argonaute family proteins.|Sufficient for interaction with AGO1 and AGO4.				cellular response to starvation (GO:0009267)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|gene expression (GO:0010467)|innate immune response (GO:0045087)|negative regulation of translation involved in gene silencing by miRNA (GO:0035278)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch signaling pathway (GO:0007219)|phosphatidylinositol-mediated signaling (GO:0048015)	cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|micro-ribonucleoprotein complex (GO:0035068)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)	p.T770I(1)		breast(1)|cervix(1)|endometrium(13)|kidney(5)|large_intestine(13)|liver(1)|lung(20)|ovary(3)|skin(2)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	64				GBM - Glioblastoma multiforme(48;0.0394)		ATAGATAAGACTAGCCCTAAT	0.517																																					p.T770I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C2309T	16						.						45.0	49.0	48.0					16																	24802272		2194	4300	6494	24709773	SO:0001583	missense	27327	exon6			U80739	CCDS10624.2	16p11.2	2009-09-22	2004-12-17	2004-12-17	ENSG00000090905	ENSG00000090905		"""Trinucleotide (CAG) repeat containing"""	11969	protein-coding gene	gene with protein product		610739	"""trinucleotide repeat containing 6"""	TNRC6		9225980	Standard	NM_014494		Approved	CAGH26, KIAA1460, GW182	uc002dmm.3	Q8NDV7	OTTHUMG00000096999	ENST00000395799.3:c.2309C>T	16.37:g.24802272C>T	ENSP00000379144:p.Thr770Ile	Somatic		Capture	Illumina HiSeq	Phase_I	24709773	NM_014494	C9JAR8|O15408|Q658L5|Q6NVB5|Q8NEZ0|Q8TBT8|Q8TCR0|Q9NV59|Q9P268	Missense_Mutation	SNP	ENST00000395799.3	37	CCDS10624.2	.	.	.	.	.	.	.	.	.	.	C	10.24	1.296577	0.23650	.	.	ENSG00000090905	ENST00000315183;ENST00000395799	T;T	0.11821	2.74;2.74	5.72	5.72	0.89469	.	0.202066	0.35615	N	0.003090	T	0.14227	0.0344	N	0.14661	0.345	0.80722	D	1	B;B;P	0.46395	0.429;0.255;0.877	P;B;B	0.45971	0.499;0.192;0.276	T	0.02909	-1.1095	10	0.52906	T	0.07	-0.5012	19.8807	0.96899	0.0:1.0:0.0:0.0	.	517;770;770	Q8NDV7-2;Q8NDV7-6;Q8NDV7	.;.;TNR6A_HUMAN	I	770	ENSP00000326900:T770I;ENSP00000379144:T770I	ENSP00000326900:T770I	T	+	2	0	TNRC6A	24709773	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	3.954000	0.56708	2.700000	0.92200	0.563000	0.77884	ACT		0.517	TNRC6A-001	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000214081.1	NM_020847	
HS3ST4	9951	broad.mit.edu	37	16	26147442	26147442	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr16:26147442G>A	ENST00000331351.5	+	2	1636	c.1244G>A	c.(1243-1245)cGg>cAg	p.R415Q	HS3ST4_ENST00000475436.1_3'UTR	NM_006040.2	NP_006031.2	Q9Y661	HS3S4_HUMAN	heparan sulfate (glucosamine) 3-O-sulfotransferase 4	415					heparan sulfate proteoglycan metabolic process (GO:0030201)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	[heparan sulfate]-glucosamine 3-sulfotransferase 1 activity (GO:0008467)	p.R415Q(1)		breast(2)|endometrium(3)|large_intestine(1)|lung(9)	15				GBM - Glioblastoma multiforme(48;0.0988)		AGCAAAGGTCGGACTCATCCT	0.458																																					p.R415Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1244A	16						.						57.0	51.0	53.0					16																	26147442		1568	3582	5150	26054943	SO:0001583	missense	9951	exon2			AF105378	CCDS53995.1	16p11.2	2008-03-12			ENSG00000182601	ENSG00000182601	2.8.2.23	"""Sulfotransferases, membrane-bound"""	5200	protein-coding gene	gene with protein product		604059				9988767	Standard	NM_006040		Approved	3OST4	uc002dof.3	Q9Y661	OTTHUMG00000059978	ENST00000331351.5:c.1244G>A	16.37:g.26147442G>A	ENSP00000330606:p.Arg415Gln	Somatic		Capture	Illumina HiSeq	Phase_I	26054943	NM_006040	Q5QI42|Q8NDC2	Missense_Mutation	SNP	ENST00000331351.5	37	CCDS53995.1	.	.	.	.	.	.	.	.	.	.	G	34	5.377931	0.95945	.	.	ENSG00000182601	ENST00000331351	T	0.57436	0.4	5.56	5.56	0.83823	Sulfotransferase domain (1);	0.000000	0.64402	U	0.000006	T	0.71829	0.3386	M	0.85859	2.78	0.80722	D	1	D	0.71674	0.998	P	0.55615	0.78	T	0.77164	-0.2688	10	0.72032	D	0.01	.	18.5023	0.90887	0.0:0.0:1.0:0.0	.	415	Q9Y661	HS3S4_HUMAN	Q	415	ENSP00000330606:R415Q	ENSP00000330606:R415Q	R	+	2	0	HS3ST4	26054943	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.823000	0.99369	2.602000	0.87976	0.655000	0.94253	CGG		0.458	HS3ST4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000133286.2	NM_006040	
ATXN2L	11273	broad.mit.edu	37	16	28847674	28847674	+	3'UTR	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr16:28847674G>A	ENST00000336783.4	+	0	3483				ATXN2L_ENST00000395547.2_Missense_Mutation_p.R1056H|ATXN2L_ENST00000564304.1_Intron|ATXN2L_ENST00000570200.1_Intron|ATXN2L_ENST00000340394.8_Intron|ATXN2L_ENST00000325215.6_Intron|ATXN2L_ENST00000382686.4_Intron|RP11-24N18.1_ENST00000563565.1_RNA	NM_007245.3	NP_009176.2	Q8WWM7	ATX2L_HUMAN	ataxin 2-like						regulation of cytoplasmic mRNA processing body assembly (GO:0010603)|stress granule assembly (GO:0034063)	cytoplasm (GO:0005737)|cytoplasmic stress granule (GO:0010494)|membrane (GO:0016020)|nuclear speck (GO:0016607)	poly(A) RNA binding (GO:0044822)	p.R1056H(1)		breast(1)|endometrium(4)|kidney(3)|large_intestine(7)|lung(14)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	36						AGCCACAGTCGCCGCCGCCAG	0.672																																					p.R1056H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G3167A	16						.						53.0	60.0	58.0					16																	28847674		2197	4300	6497	28755175	SO:0001624	3_prime_UTR_variant	11273	exon23				CCDS10639.1, CCDS10640.1, CCDS10641.1, CCDS32423.1, CCDS45451.1, CCDS58443.1	16p11	2008-02-05			ENSG00000168488	ENSG00000168488			31326	protein-coding gene	gene with protein product		607931				11784712, 14769358	Standard	NM_007245		Approved	A2lp, A2D	uc002dqy.4	Q8WWM7	OTTHUMG00000097038	ENST00000336783.4:c.*88G>A	16.37:g.28847674G>A		Somatic		Capture	Illumina HiSeq	Phase_I	28755175	NM_148414	A8K1R6|B9EGM2|E9PAR9|O95135|Q63ZY4|Q6NVJ8|Q6PJW6|Q8IU61|Q8IU95|Q8WWM3|Q8WWM4|Q8WWM5|Q8WWM6|Q99703	Missense_Mutation	SNP	ENST00000336783.4	37	CCDS10641.1	.	.	.	.	.	.	.	.	.	.	.	13.95	2.389390	0.42410	.	.	ENSG00000168488	ENST00000395547	T	0.48522	0.81	5.06	5.06	0.68205	.	0.328529	0.22217	N	0.063001	T	0.36991	0.0987	.	.	.	0.80722	D	1	P	0.52577	0.954	B	0.38378	0.272	T	0.21177	-1.0253	9	0.36615	T	0.2	-0.0488	13.8062	0.63233	0.0:0.0:1.0:0.0	.	1056	Q8WWM7-3	.	H	1056	ENSP00000378917:R1056H	ENSP00000378917:R1056H	R	+	2	0	ATXN2L	28755175	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.178000	0.58284	2.645000	0.89757	0.551000	0.68910	CGC		0.672	ATXN2L-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000214139.1	NM_007245	
SH2B1	25970	broad.mit.edu	37	16	28883862	28883862	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr16:28883862G>A	ENST00000322610.8	+	10	2172	c.1733G>A	c.(1732-1734)cGt>cAt	p.R578H	SH2B1_ENST00000538342.1_Missense_Mutation_p.R242H|SH2B1_ENST00000359285.5_Missense_Mutation_p.R578H|SH2B1_ENST00000395532.4_Missense_Mutation_p.R578H|SH2B1_ENST00000563674.1_Intron|SH2B1_ENST00000545570.1_Missense_Mutation_p.R268H|SH2B1_ENST00000337120.5_Missense_Mutation_p.R578H			Q9NRF2	SH2B1_HUMAN	SH2B adaptor protein 1	578	SH2. {ECO:0000255|PROSITE- ProRule:PRU00191}.				blood coagulation (GO:0007596)|cellular component movement (GO:0006928)|intracellular signal transduction (GO:0035556)|lamellipodium assembly (GO:0030032)|positive regulation of mitosis (GO:0045840)|regulation of DNA biosynthetic process (GO:2000278)	cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)	signal transducer activity (GO:0004871)	p.R578H(1)		endometrium(2)|kidney(1)|large_intestine(2)|lung(12)|ovary(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	25						CAGCACCTGCGTTTGTCGCTG	0.637																																					p.R578H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1733A	16						.						104.0	93.0	97.0					16																	28883862		2197	4300	6497	28791363	SO:0001583	missense	25970	exon7			AK055104	CCDS32424.1, CCDS53996.1, CCDS53997.1	16p11.2	2013-02-14						"""Pleckstrin homology (PH) domain containing"", ""SH2 domain containing"""	30417	protein-coding gene	gene with protein product	"""SH2-B homolog"""	608937				11827956, 10594240	Standard	NM_001145812		Approved	FLJ30542, SH2B	uc002drl.3	Q9NRF2		ENST00000322610.8:c.1733G>A	16.37:g.28883862G>A	ENSP00000321221:p.Arg578His	Somatic		Capture	Illumina HiSeq	Phase_I	28791363	NM_015503	A8K2R7|Q96FK3|Q96SX3|Q9NRF1|Q9NRF3|Q9P2P7|Q9Y3Y3	Missense_Mutation	SNP	ENST00000322610.8	37	CCDS53996.1	.	.	.	.	.	.	.	.	.	.	g	25.0	4.591910	0.86953	.	.	ENSG00000178188	ENST00000322610;ENST00000545570;ENST00000359285;ENST00000538342;ENST00000395532;ENST00000337120	T;T;T;T;T;T	0.56275	0.47;0.47;0.47;0.47;0.47;0.47	5.23	5.23	0.72850	SH2 motif (4);	0.064947	0.64402	D	0.000007	T	0.77731	0.4174	M	0.88979	2.995	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.87578	0.995;0.995;0.996;0.998;0.998	T	0.82579	-0.0387	10	0.87932	D	0	-32.504	17.5753	0.87946	0.0:0.0:1.0:0.0	.	242;268;578;578;578	B4DLN5;F5GXU7;Q9NRF2-2;Q9NRF2-3;Q9NRF2	.;.;.;.;SH2B1_HUMAN	H	578;268;578;242;578;578	ENSP00000321221:R578H;ENSP00000440354:R268H;ENSP00000352232:R578H;ENSP00000438784:R242H;ENSP00000378903:R578H;ENSP00000337163:R578H	ENSP00000321221:R578H	R	+	2	0	SH2B1	28791363	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.485000	0.81204	2.433000	0.82419	0.651000	0.88453	CGT		0.637	SH2B1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000432666.1	NM_015503	
DOC2A	8448	broad.mit.edu	37	16	30018552	30018552	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr16:30018552C>T	ENST00000350119.4	-	6	786	c.596G>A	c.(595-597)cGc>cAc	p.R199H	DOC2A_ENST00000564979.1_Missense_Mutation_p.R199H|DOC2A_ENST00000564944.1_Missense_Mutation_p.R199H	NM_001282062.1|NM_001282063.1|NM_001282068.1|NM_003586.2	NP_001268991.1|NP_001268992.1|NP_001268997.1|NP_003577.2	Q14183	DOC2A_HUMAN	double C2-like domains, alpha	199					nervous system development (GO:0007399)|regulation of calcium ion-dependent exocytosis (GO:0017158)|synaptic transmission (GO:0007268)|synaptic vesicle exocytosis (GO:0016079)	cell junction (GO:0030054)|lysosome (GO:0005764)|membrane (GO:0016020)|neuron projection (GO:0043005)|synaptic vesicle (GO:0008021)	calcium-dependent phospholipid binding (GO:0005544)|transporter activity (GO:0005215)	p.R199H(1)		central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(2)|ovary(2)	9						CTTGAGGCGGCGGAGGGGCAC	0.637																																					p.R199H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G596A	16						.						55.0	54.0	54.0					16																	30018552		2197	4300	6497	29926053	SO:0001583	missense	8448	exon6			D31897	CCDS10666.1	16p11.2	2014-07-02			ENSG00000149927	ENSG00000149927		"""Synaptotagmins"""	2985	protein-coding gene	gene with protein product		604567				7826360, 9736751	Standard	NM_003586		Approved		uc002dvn.3	Q14183	OTTHUMG00000132109	ENST00000350119.4:c.596G>A	16.37:g.30018552C>T	ENSP00000340017:p.Arg199His	Somatic		Capture	Illumina HiSeq	Phase_I	29926053	NM_003586	B4DEJ2|H3BNH6|Q6P4G4|Q7Z5G0|Q8IVX0	Missense_Mutation	SNP	ENST00000350119.4	37	CCDS10666.1	.	.	.	.	.	.	.	.	.	.	C	21.7	4.184957	0.78677	.	.	ENSG00000149927	ENST00000350119	T	0.40476	1.03	5.44	4.47	0.54385	C2 calcium-dependent membrane targeting (1);C2 calcium/lipid-binding domain, CaLB (1);	0.000000	0.52532	D	0.000072	T	0.56572	0.1994	L	0.59436	1.845	0.44918	D	0.997934	D	0.76494	0.999	D	0.65140	0.932	T	0.58216	-0.7675	10	0.62326	D	0.03	.	12.4597	0.55725	0.0:0.9155:0.0:0.0845	.	199	Q14183	DOC2A_HUMAN	H	199	ENSP00000340017:R199H	ENSP00000340017:R199H	R	-	2	0	DOC2A	29926053	0.993000	0.37304	1.000000	0.80357	0.919000	0.55068	1.506000	0.35747	2.552000	0.86080	0.491000	0.48974	CGC		0.637	DOC2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255148.2	NM_003586	
MAPK3	5595	broad.mit.edu	37	16	30133325	30133325	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr16:30133325G>A	ENST00000263025.4	-	2	257	c.173C>T	c.(172-174)tCg>tTg	p.S58L	MAPK3_ENST00000395202.1_Missense_Mutation_p.S58L|MAPK3_ENST00000322266.5_Missense_Mutation_p.S58L|MAPK3_ENST00000403394.1_Missense_Mutation_p.S58L|MAPK3_ENST00000395200.1_Missense_Mutation_p.S29L|MAPK3_ENST00000484663.1_5'UTR|MAPK3_ENST00000395199.3_Missense_Mutation_p.S58L	NM_002746.2	NP_002737.2	P27361	MK03_HUMAN	mitogen-activated protein kinase 3	58	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of MAPK activity (GO:0000187)|activation of MAPKK activity (GO:0000186)|apoptotic process (GO:0006915)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|BMP signaling pathway (GO:0030509)|cartilage development (GO:0051216)|caveolin-mediated endocytosis (GO:0072584)|cell cycle (GO:0007049)|cellular response to mechanical stimulus (GO:0071260)|cytokine-mediated signaling pathway (GO:0019221)|DNA damage induced protein phosphorylation (GO:0006975)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|gene expression (GO:0010467)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|interleukin-1-mediated signaling pathway (GO:0070498)|JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)|lipopolysaccharide-mediated signaling pathway (GO:0031663)|MAPK cascade (GO:0000165)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of apolipoprotein binding (GO:2000657)|neurotrophin TRK receptor signaling pathway (GO:0048011)|organ morphogenesis (GO:0009887)|peptidyl-tyrosine autophosphorylation (GO:0038083)|phosphorylation (GO:0016310)|platelet activation (GO:0030168)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of histone acetylation (GO:0035066)|positive regulation of histone phosphorylation (GO:0033129)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein phosphorylation (GO:0006468)|Ras protein signal transduction (GO:0007265)|regulation of cytoskeleton organization (GO:0051493)|regulation of early endosome to late endosome transport (GO:2000641)|regulation of Golgi inheritance (GO:0090170)|regulation of sequence-specific DNA binding transcription factor activity (GO:0051090)|regulation of stress-activated MAPK cascade (GO:0032872)|response to epidermal growth factor (GO:0070849)|response to exogenous dsRNA (GO:0043330)|sensory perception of pain (GO:0019233)|small GTPase mediated signal transduction (GO:0007264)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|transcription from RNA polymerase I promoter (GO:0006360)|transcription initiation from RNA polymerase I promoter (GO:0006361)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)|viral process (GO:0016032)	caveola (GO:0005901)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|early endosome (GO:0005769)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|late endosome (GO:0005770)|microtubule cytoskeleton (GO:0015630)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|pseudopodium (GO:0031143)	ATP binding (GO:0005524)|MAP kinase activity (GO:0004707)|phosphatase binding (GO:0019902)	p.S58L(1)								Arsenic trioxide(DB01169)|Sulindac(DB00605)	GTCATAGGCCGAGCTGAGGGG	0.647																																					p.S58L												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C173T	16						.						51.0	41.0	44.0					16																	30133325		2197	4300	6497	30040826	SO:0001583	missense	5595	exon2			M84490	CCDS10672.1, CCDS42148.1, CCDS42149.1	16p11.2	2011-06-10			ENSG00000102882	ENSG00000102882	2.7.11.1	"""Mitogen-activated protein kinase cascade / Kinases"""	6877	protein-coding gene	gene with protein product		601795		PRKM3		9628824	Standard	NM_001109891		Approved	ERK1, p44mapk, p44erk1	uc002dws.3	P27361	OTTHUMG00000132149	ENST00000263025.4:c.173C>T	16.37:g.30133325G>A	ENSP00000263025:p.Ser58Leu	Somatic		Capture	Illumina HiSeq	Phase_I	30040826	NM_001040056	A8CZ58|B0LPG3|Q8NHX1	Missense_Mutation	SNP	ENST00000263025.4	37	CCDS10672.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	34|34	5.354046|5.354046	0.95830|0.95830	.|.	.|.	ENSG00000102882|ENSG00000102882	ENST00000495629;ENST00000481230|ENST00000263025;ENST00000322266;ENST00000403394;ENST00000395200;ENST00000395202;ENST00000395199	.|T;T;T;T;T;T	.|0.64803	.|-0.12;-0.12;-0.12;-0.12;-0.12;-0.12	5.63|5.63	5.63|5.63	0.86233|0.86233	.|Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.61640|0.61640	0.2363|0.2363	N|N	0.03917|0.03917	-0.325|-0.325	0.80722|0.80722	D|D	1|1	.|P;D;D	.|0.89917	.|0.503;1.0;0.998	.|B;D;P	.|0.72982	.|0.18;0.979;0.822	T|T	0.73594|0.73594	-0.3933|-0.3933	5|10	.|0.87932	.|D	.|0	-1.3996|-1.3996	18.4484|18.4484	0.90695|0.90695	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|58;58;58	.|P27361-2;P27361-3;P27361	.|.;.;MK03_HUMAN	W|L	19;12|58;58;58;29;58;58	.|ENSP00000263025:S58L;ENSP00000327293:S58L;ENSP00000384895:S58L;ENSP00000378626:S29L;ENSP00000378628:S58L;ENSP00000378625:S58L	.|ENSP00000263025:S58L	R|S	-|-	1|2	2|0	MAPK3|MAPK3	30040826|30040826	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.857000|0.857000	0.48899|0.48899	9.807000|9.807000	0.99171|0.99171	2.655000|2.655000	0.90218|0.90218	0.462000|0.462000	0.41574|0.41574	CGG|TCG		0.647	MAPK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255196.2		
ITGAL	3683	broad.mit.edu	37	16	30518158	30518158	+	Missense_Mutation	SNP	G	G	A	rs369554955		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr16:30518158G>A	ENST00000356798.6	+	21	2669	c.2489G>A	c.(2488-2490)cGc>cAc	p.R830H	MIR4518_ENST00000580665.1_RNA|ITGAL_ENST00000358164.5_Missense_Mutation_p.R746H|ITGAL_ENST00000433423.2_Intron	NM_002209.2	NP_002200.2	P20701	ITAL_HUMAN	integrin, alpha L (antigen CD11A (p180), lymphocyte function-associated antigen 1; alpha polypeptide)	830					activated T cell proliferation (GO:0050798)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|cellular component movement (GO:0006928)|extracellular matrix organization (GO:0030198)|heterophilic cell-cell adhesion (GO:0007157)|inflammatory response (GO:0006954)|integrin-mediated signaling pathway (GO:0007229)|leukocyte cell-cell adhesion (GO:0007159)|leukocyte migration (GO:0050900)|positive regulation of calcium-mediated signaling (GO:0050850)|positive regulation of cell-cell adhesion (GO:0022409)|positive regulation of T cell proliferation (GO:0042102)|receptor clustering (GO:0043113)|regulation of immune response (GO:0050776)|signal transduction (GO:0007165)|T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell (GO:0002291)	cell surface (GO:0009986)|cell-cell junction (GO:0005911)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|immunological synapse (GO:0001772)|integrin alphaL-beta2 complex (GO:0034687)|integrin complex (GO:0008305)|membrane (GO:0016020)|plasma membrane (GO:0005886)	cell adhesion molecule binding (GO:0050839)|ICAM-3 receptor activity (GO:0030369)|metal ion binding (GO:0046872)	p.R830H(1)		breast(1)|central_nervous_system(3)|cervix(1)|endometrium(10)|kidney(4)|large_intestine(12)|lung(32)|ovary(3)|prostate(4)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	76					Antithymocyte globulin(DB00098)|Efalizumab(DB00095)|Lovastatin(DB00227)	CTCTCCTTCCGCAAGGTGGAG	0.612																																					p.R746H	NSCLC(110;1462 1641 3311 33990 49495)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2237A	16						.		HIS/ARG,HIS/ARG	0,4394		0,0,2197	105.0	103.0	104.0		2237,2489	5.2	1.0	16		104	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	ITGAL	NM_001114380.1,NM_002209.2	29,29	0,1,6496	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging,probably-damaging	746/1087,830/1171	30518158	1,12993	2197	4300	6497	30425659	SO:0001583	missense	3683	exon19				CCDS32433.1, CCDS45461.1	16p13.1-p11	2010-03-23				ENSG00000005844		"""CD molecules"", ""Integrins"""	6148	protein-coding gene	gene with protein product		153370		CD11A		3284962	Standard	NM_002209		Approved	LFA-1	uc002dyi.4	P20701		ENST00000356798.6:c.2489G>A	16.37:g.30518158G>A	ENSP00000349252:p.Arg830His	Somatic		Capture	Illumina HiSeq	Phase_I	30425659	NM_001114380	O43746|Q45H73|Q96HB1|Q9UBC8	Missense_Mutation	SNP	ENST00000356798.6	37	CCDS32433.1	.	.	.	.	.	.	.	.	.	.	g	20.2	3.951474	0.73787	0.0	1.16E-4	ENSG00000005844	ENST00000356798;ENST00000358164	T;T	0.48522	0.81;0.81	5.2	5.2	0.72013	Integrin alpha-2 (1);	0.000000	0.39341	N	0.001386	T	0.67059	0.2853	M	0.80847	2.515	0.80722	D	1	D;D	0.76494	0.999;0.998	P;P	0.61397	0.888;0.888	T	0.72337	-0.4324	10	0.87932	D	0	.	14.2982	0.66329	0.0:0.0:1.0:0.0	.	746;830	Q96HB1;P20701	.;ITAL_HUMAN	H	830;746	ENSP00000349252:R830H;ENSP00000350886:R746H	ENSP00000349252:R830H	R	+	2	0	ITGAL	30425659	1.000000	0.71417	0.997000	0.53966	0.683000	0.39861	4.994000	0.63901	2.452000	0.82932	0.437000	0.28790	CGC		0.612	ITGAL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434508.2		
SRCAP	10847	broad.mit.edu	37	16	30724941	30724941	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr16:30724941G>A	ENST00000262518.4	+	16	2787	c.2402G>A	c.(2401-2403)cGc>cAc	p.R801H	SRCAP_ENST00000395059.2_Missense_Mutation_p.R801H|SRCAP_ENST00000344771.4_Missense_Mutation_p.R801H|SNORA30_ENST00000384028.1_RNA	NM_006662.2	NP_006653.2	Q6ZRS2	SRCAP_HUMAN	Snf2-related CREBBP activator protein	801					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.R801H(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)			CAGTCTCATCGCGAGTTCAAG	0.522																																					p.R801H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2402A	16						.						190.0	167.0	175.0					16																	30724941		2197	4300	6497	30632442	SO:0001583	missense	10847	exon16			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.2402G>A	16.37:g.30724941G>A	ENSP00000262518:p.Arg801His	Somatic		Capture	Illumina HiSeq	Phase_I	30632442	NM_006662	B0JZA6|O15026|Q7Z744|Q9Y5L9	Missense_Mutation	SNP	ENST00000262518.4	37	CCDS10689.2	.	.	.	.	.	.	.	.	.	.	G	19.11	3.764112	0.69878	.	.	ENSG00000080603	ENST00000262518;ENST00000395059;ENST00000344771	D;D;D	0.93307	-3.2;-3.2;-3.2	5.54	5.54	0.83059	DEAD-like helicase (1);SNF2-related (1);	0.000000	0.56097	D	0.000025	D	0.94817	0.8326	L	0.33189	0.99	0.80722	D	1	D;D;D	0.89917	0.965;1.0;1.0	P;D;D	0.91635	0.661;0.999;0.999	D	0.95030	0.8168	10	0.66056	D	0.02	-8.1585	18.4191	0.90582	0.0:0.0:1.0:0.0	.	801;801;801	Q6ZRS2-3;Q6ZRS2-2;Q6ZRS2	.;.;SRCAP_HUMAN	H	801	ENSP00000262518:R801H;ENSP00000378499:R801H;ENSP00000343042:R801H	ENSP00000262518:R801H	R	+	2	0	SRCAP	30632442	1.000000	0.71417	0.994000	0.49952	0.987000	0.75469	3.758000	0.55220	2.884000	0.98904	0.655000	0.94253	CGC		0.522	SRCAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255523.1	NM_006662	
RNF40	9810	broad.mit.edu	37	16	30778093	30778093	+	Missense_Mutation	SNP	G	G	A	rs146102570		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr16:30778093G>A	ENST00000324685.6	+	11	1760	c.1325G>A	c.(1324-1326)cGc>cAc	p.R442H	RNF40_ENST00000357890.5_Missense_Mutation_p.R342H|RNF40_ENST00000402121.3_Missense_Mutation_p.R134H|RNF40_ENST00000563683.1_Missense_Mutation_p.R402H	NM_001207033.1|NM_014771.3	NP_001193962.1|NP_055586	O75150	BRE1B_HUMAN	ring finger protein 40, E3 ubiquitin protein ligase	442					histone H2B ubiquitination (GO:0033523)|histone monoubiquitination (GO:0010390)|ubiquitin-dependent protein catabolic process (GO:0006511)	HULC complex (GO:0033503)|membrane (GO:0016020)|neuron projection (GO:0043005)|nucleus (GO:0005634)|ubiquitin ligase complex (GO:0000151)	ligase activity (GO:0016874)|protein homodimerization activity (GO:0042803)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.R442H(1)		central_nervous_system(2)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(6)|lung(10)|prostate(2)	30			Colorectal(24;0.198)			AAGAAGCTACGCACAGAGGTC	0.577																																					p.R442H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1325A	16						.	G	HIS/ARG,HIS/ARG,HIS/ARG	0,4394		0,0,2197	68.0	48.0	55.0		1325,1025,1325	6.1	1.0	16	dbSNP_134	55	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense,missense	RNF40	NM_001207033.1,NM_001207034.1,NM_014771.3	29,29,29	0,1,6496	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging,probably-damaging,probably-damaging	442/1001,342/902,442/1002	30778093	1,12993	2197	4300	6497	30685594	SO:0001583	missense	9810	exon11			AB014561	CCDS10691.1, CCDS55994.1	16p11.2-p11.1	2012-02-23	2012-02-23		ENSG00000103549	ENSG00000103549		"""RING-type (C3HC4) zinc fingers"""	16867	protein-coding gene	gene with protein product	"""BRE1 E3 ubiquitin ligase homolog B (S. cerevisiae)"""	607700	"""ring finger protein 40"""			9734811, 10944455, 12121982	Standard	NM_014771		Approved	KIAA0661, RBP95, BRE1B, STARING	uc002dzq.3	O75150	OTTHUMG00000132394	ENST00000324685.6:c.1325G>A	16.37:g.30778093G>A	ENSP00000325677:p.Arg442His	Somatic		Capture	Illumina HiSeq	Phase_I	30685594	NM_014771	Q6AHZ6|Q6N005|Q7L3T6|Q8N615|Q96T18|Q9BSV9|Q9HC82	Missense_Mutation	SNP	ENST00000324685.6	37	CCDS10691.1	.	.	.	.	.	.	.	.	.	.	G	35	5.543763	0.96474	0.0	1.16E-4	ENSG00000103549	ENST00000324685;ENST00000357890;ENST00000402121	T;T;T	0.46819	0.94;1.14;0.86	6.07	6.07	0.98685	.	0.000000	0.85682	D	0.000000	T	0.74215	0.3687	M	0.84585	2.705	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.91635	0.999;0.999;0.999;0.999	T	0.76594	-0.2902	10	0.87932	D	0	-11.8124	19.4154	0.94694	0.0:0.0:1.0:0.0	.	134;342;442;442	F8W8Z4;O75150-4;A8K6K1;O75150	.;.;.;BRE1B_HUMAN	H	442;342;134	ENSP00000325677:R442H;ENSP00000350563:R342H;ENSP00000384942:R134H	ENSP00000325677:R442H	R	+	2	0	RNF40	30685594	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	9.164000	0.94755	2.884000	0.98904	0.655000	0.94253	CGC		0.577	RNF40-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255524.2	NM_014771	
ZNF213	7760	broad.mit.edu	37	16	3188458	3188458	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr16:3188458C>T	ENST00000396878.3	+	3	914	c.439C>T	c.(439-441)Cgg>Tgg	p.R147W	ZNF213_ENST00000416391.2_Silent_p.A13A|ZNF213_ENST00000574902.1_Missense_Mutation_p.R147W|ZNF213_ENST00000576416.1_Missense_Mutation_p.R147W	NM_001134655.1|NM_004220.2	NP_001128127.1|NP_004211.1	O14771	ZN213_HUMAN	zinc finger protein 213	147					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.R147W(1)		haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(5)|ovary(1)|prostate(4)|upper_aerodigestive_tract(1)	16						GGCTGCAGGCCGGGGATCCCA	0.677																																					p.R147W												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C439T	16						.						33.0	41.0	38.0					16																	3188458		2197	4299	6496	3128459	SO:0001583	missense	7760	exon3			AF017433	CCDS10495.1	16p13.3	2014-05-13	2007-02-20	2007-02-20	ENSG00000085644	ENSG00000085644		"""Zinc fingers, C2H2-type"", ""-"", ""-"", ""-"""	13005	protein-coding gene	gene with protein product		608387				9653642, 10023065	Standard	NM_004220		Approved	CR53, ZKSCAN21, ZSCAN53	uc010uws.2	O14771	OTTHUMG00000177519	ENST00000396878.3:c.439C>T	16.37:g.3188458C>T	ENSP00000380087:p.Arg147Trp	Somatic		Capture	Illumina HiSeq	Phase_I	3128459	NM_001134655	A8K1B9|B4DMG6|Q96IS1	Missense_Mutation	SNP	ENST00000396878.3	37	CCDS10495.1	.	.	.	.	.	.	.	.	.	.	C	18.15	3.560595	0.65538	.	.	ENSG00000085644	ENST00000396878	T	0.05580	3.42	4.91	4.91	0.64330	.	0.796770	0.10643	N	0.650809	T	0.05547	0.0146	N	0.08118	0	0.29859	N	0.827774	D	0.56968	0.978	P	0.44477	0.451	T	0.26326	-1.0106	10	0.66056	D	0.02	.	13.4563	0.61201	0.0:1.0:0.0:0.0	.	147	O14771	ZN213_HUMAN	W	147	ENSP00000380087:R147W	ENSP00000380087:R147W	R	+	1	2	ZNF213	3128459	0.263000	0.24083	0.081000	0.20488	0.034000	0.12701	2.357000	0.44125	2.532000	0.85374	0.655000	0.94253	CGG		0.677	ZNF213-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437334.1	NM_004220	
TRIM72	493829	broad.mit.edu	37	16	31234182	31234182	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr16:31234182G>A	ENST00000322122.3	+	6	1059	c.775G>A	c.(775-777)Gcc>Acc	p.A259T		NM_001008274.3	NP_001008275.2			tripartite motif containing 72, E3 ubiquitin protein ligase									p.A259T(2)		breast(1)|endometrium(2)|large_intestine(2)|lung(9)|skin(1)	15						TCCCCCACCCGCCCGTCTGGA	0.617																																					p.A259T												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G775A	16						.						54.0	55.0	55.0					16																	31234182		2197	4300	6497	31141683	SO:0001583	missense	493829	exon6			AK090695	CCDS32437.1	16p11.2	2014-02-10	2014-02-10					"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	32671	protein-coding gene	gene with protein product	"""mitsugumin 53"""	613288	"""tripartite motif-containing 72"", ""tripartite motif containing 72"""			20399744, 23354051	Standard	NM_001008274		Approved	MG53	uc002ebn.2	Q6ZMU5		ENST00000322122.3:c.775G>A	16.37:g.31234182G>A	ENSP00000312675:p.Ala259Thr	Somatic		Capture	Illumina HiSeq	Phase_I	31141683	NM_001008274		Missense_Mutation	SNP	ENST00000322122.3	37	CCDS32437.1	.	.	.	.	.	.	.	.	.	.	G	14.83	2.653900	0.47362	.	.	ENSG00000177238	ENST00000322122	T	0.62941	-0.01	5.25	5.25	0.73442	.	0.187177	0.37577	N	0.002023	T	0.51568	0.1682	L	0.53249	1.67	0.39036	D	0.960036	P	0.45078	0.85	B	0.28553	0.091	T	0.58470	-0.7631	10	0.25106	T	0.35	.	17.6162	0.88068	0.0:0.0:1.0:0.0	.	259	Q6ZMU5	TRI72_HUMAN	T	259	ENSP00000312675:A259T	ENSP00000312675:A259T	A	+	1	0	TRIM72	31141683	1.000000	0.71417	0.941000	0.38009	0.542000	0.35054	3.729000	0.54999	2.444000	0.82710	0.561000	0.74099	GCC		0.617	TRIM72-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433567.1	NM_001008274	
ITGAD	3681	broad.mit.edu	37	16	31409192	31409192	+	Missense_Mutation	SNP	G	G	A	rs148236672		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr16:31409192G>A	ENST00000389202.2	+	5	438	c.389G>A	c.(388-390)cGc>cAc	p.R130H		NM_005353.2	NP_005344.2	Q13349	ITAD_HUMAN	integrin, alpha D	130					activated T cell proliferation (GO:0050798)|extracellular matrix organization (GO:0030198)|heterotypic cell-cell adhesion (GO:0034113)|immune response (GO:0006955)|integrin-mediated signaling pathway (GO:0007229)	cell surface (GO:0009986)|integrin complex (GO:0008305)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)	p.R130H(1)		breast(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|liver(2)|lung(43)|ovary(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	71						CTGGGCTCGCGCTGGGAGATC	0.642																																					p.R130H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G389A	16						.						39.0	34.0	35.0					16																	31409192		2197	4300	6497	31316693	SO:0001583	missense	3681	exon5			U40274	CCDS32438.1	16p13.1-p11	2010-03-23				ENSG00000156886		"""CD molecules"", ""Integrins"""	6146	protein-coding gene	gene with protein product		602453				8666289, 9598326	Standard	NM_005353		Approved	CD11d, ADB2	uc002ebv.1	Q13349		ENST00000389202.2:c.389G>A	16.37:g.31409192G>A	ENSP00000373854:p.Arg130His	Somatic		Capture	Illumina HiSeq	Phase_I	31316693	NM_005353	Q15575|Q15576	Missense_Mutation	SNP	ENST00000389202.2	37	CCDS32438.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	8.478|8.478	0.859138|0.859138	0.17178|0.17178	.|.	.|.	ENSG00000156886|ENSG00000156886	ENST00000316569|ENST00000444228;ENST00000389202	.|T	.|0.58797	.|0.31	3.86|3.86	0.98|0.98	0.19750|0.19750	.|.	.|.	.|.	.|.	.|.	T|T	0.27765|0.27765	0.0683|0.0683	N|N	0.01874|0.01874	-0.695|-0.695	0.09310|0.09310	N|N	1|1	.|B;B;B	.|0.10296	.|0.003;0.003;0.001	.|B;B;B	.|0.08055	.|0.003;0.002;0.002	T|T	0.19095|0.19095	-1.0316|-1.0316	6|9	0.30854|0.49607	T|T	0.27|0.09	.|.	6.4965|6.4965	0.22146|0.22146	0.5477:0.0:0.4523:0.0|0.5477:0.0:0.4523:0.0	.|.	.|130;146;130	.|B7Z6V7;Q59H14;Q13349	.|.;.;ITAD_HUMAN	T|H	38|146;130	.|ENSP00000373854:R130H	ENSP00000323325:A38T|ENSP00000373854:R130H	A|R	+|+	1|2	0|0	ITGAD|ITGAD	31316693|31316693	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.047000|0.047000	0.14425|0.14425	0.563000|0.563000	0.23547|0.23547	0.055000|0.055000	0.16094|0.16094	-0.238000|-0.238000	0.12139|0.12139	GCT|CGC		0.642	ITGAD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432836.1	NM_005353	
ITGAD	3681	broad.mit.edu	37	16	31414843	31414843	+	Missense_Mutation	SNP	A	A	C			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr16:31414843A>C	ENST00000389202.2	+	7	630	c.581A>C	c.(580-582)aAc>aCc	p.N194T	RP11-120K18.2_ENST00000567545.1_RNA	NM_005353.2	NP_005344.2	Q13349	ITAD_HUMAN	integrin, alpha D	194	VWFA. {ECO:0000255|PROSITE- ProRule:PRU00219}.				activated T cell proliferation (GO:0050798)|extracellular matrix organization (GO:0030198)|heterotypic cell-cell adhesion (GO:0034113)|immune response (GO:0006955)|integrin-mediated signaling pathway (GO:0007229)	cell surface (GO:0009986)|integrin complex (GO:0008305)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)	p.N194T(1)		breast(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|liver(2)|lung(43)|ovary(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	71						CAGTACTCAAACCTCCTGAAG	0.517																																					p.N194T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A581C	16						.						120.0	98.0	105.0					16																	31414843		2197	4300	6497	31322344	SO:0001583	missense	3681	exon7			U40274	CCDS32438.1	16p13.1-p11	2010-03-23				ENSG00000156886		"""CD molecules"", ""Integrins"""	6146	protein-coding gene	gene with protein product		602453				8666289, 9598326	Standard	NM_005353		Approved	CD11d, ADB2	uc002ebv.1	Q13349		ENST00000389202.2:c.581A>C	16.37:g.31414843A>C	ENSP00000373854:p.Asn194Thr	Somatic		Capture	Illumina HiSeq	Phase_I	31322344	NM_005353	Q15575|Q15576	Missense_Mutation	SNP	ENST00000389202.2	37	CCDS32438.1	.	.	.	.	.	.	.	.	.	.	A	14.40	2.525436	0.44969	.	.	ENSG00000156886	ENST00000316569;ENST00000444228;ENST00000389202	T	0.21361	2.01	4.57	2.33	0.28932	von Willebrand factor, type A (3);	.	.	.	.	T	0.11879	0.0289	N	0.14661	0.345	0.09310	N	1	B;B;B	0.24651	0.108;0.087;0.049	B;B;B	0.28784	0.094;0.023;0.023	T	0.37619	-0.9698	9	0.24483	T	0.36	.	7.2954	0.26391	0.813:0.0:0.187:0.0	.	194;210;194	B7Z6V7;Q59H14;Q13349	.;.;ITAD_HUMAN	T	58;210;194	ENSP00000373854:N194T	ENSP00000323325:N58T	N	+	2	0	ITGAD	31322344	0.001000	0.12720	0.002000	0.10522	0.664000	0.39144	1.398000	0.34554	0.288000	0.22398	0.328000	0.21473	AAC		0.517	ITGAD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432836.1	NM_005353	
MEFV	4210	broad.mit.edu	37	16	3293534	3293534	+	Silent	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr16:3293534G>A	ENST00000219596.1	-	10	1992	c.1953C>T	c.(1951-1953)ggC>ggT	p.G651G	MEFV_ENST00000536379.1_Silent_p.G440G|MEFV_ENST00000541159.1_3'UTR|MEFV_ENST00000339854.4_Silent_p.G471G	NM_000243.2	NP_000234.1	O15553	MEFV_HUMAN	Mediterranean fever	651	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.				inflammatory response (GO:0006954)|innate immune response (GO:0045087)|negative regulation of inflammatory response (GO:0050728)|negative regulation of interleukin-1 beta production (GO:0032691)|negative regulation of interleukin-12 production (GO:0032695)|negative regulation of macrophage inflammatory protein 1 alpha production (GO:0071641)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|positive regulation of cysteine-type endopeptidase activity (GO:2001056)	cell projection (GO:0042995)|cytosol (GO:0005829)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|nucleus (GO:0005634)	actin binding (GO:0003779)|zinc ion binding (GO:0008270)	p.G651G(1)		NS(2)|biliary_tract(1)|breast(5)|central_nervous_system(2)|endometrium(2)|kidney(3)|large_intestine(6)|lung(19)|ovary(3)|prostate(1)|skin(6)	50						AGTAACGGCGGCCAGAGAGGA	0.537																																					p.G651G												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1953T	16						.						97.0	102.0	100.0					16																	3293534		2197	4300	6497	3233535	SO:0001819	synonymous_variant	4210	exon10			AF018080	CCDS10498.1, CCDS55981.1	16p13.3	2014-09-17			ENSG00000103313	ENSG00000103313		"""Tripartite motif containing / Tripartite motif containing"""	6998	protein-coding gene	gene with protein product	"""pyrin"""	608107		MEF		9288094	Standard	NM_000243		Approved	FMF, TRIM20	uc002cun.1	O15553	OTTHUMG00000129324	ENST00000219596.1:c.1953C>T	16.37:g.3293534G>A		Somatic		Capture	Illumina HiSeq	Phase_I	3233535	NM_000243	D3DUC0|F5H0Q3|Q3MJ84|Q96PN4|Q96PN5	Silent	SNP	ENST00000219596.1	37	CCDS10498.1																																																																																				0.537	MEFV-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251464.1	NM_000243	
ZNF75A	7627	broad.mit.edu	37	16	3367832	3367832	+	Missense_Mutation	SNP	G	G	A	rs370943522		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr16:3367832G>A	ENST00000574298.1	+	6	1327	c.854G>A	c.(853-855)cGg>cAg	p.R285Q	ZNF75A_ENST00000498240.2_3'UTR	NM_153028.2	NP_694573.1	Q96N20	ZN75A_HUMAN	zinc finger protein 75a	285					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.R285Q(1)		breast(1)|large_intestine(3)|lung(7)|prostate(1)	12						TTCAGCAGGCGGTCAAGCCTT	0.453																																					p.R285Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G854A	16						.	G	GLN/ARG	1,4393		0,1,2196	54.0	57.0	56.0		854	4.5	1.0	16		56	0,8600		0,0,4300	no	missense	ZNF75A	NM_153028.2	43	0,1,6496	AA,AG,GG		0.0,0.0228,0.0077	probably-damaging	285/297	3367832	1,12993	2197	4300	6497	3307833	SO:0001583	missense	7627	exon6			X91826	CCDS10501.1	16p13.11	2013-01-08			ENSG00000162086	ENSG00000162086		"""Zinc fingers, C2H2-type"", ""-"""	13146	protein-coding gene	gene with protein product		601473				8661144	Standard	NM_153028		Approved	FLJ31529	uc002cut.4	Q96N20	OTTHUMG00000129356	ENST00000574298.1:c.854G>A	16.37:g.3367832G>A	ENSP00000459566:p.Arg285Gln	Somatic		Capture	Illumina HiSeq	Phase_I	3307833	NM_153028	Q0VDI8|Q92669	Missense_Mutation	SNP	ENST00000574298.1	37	CCDS10501.1	.	.	.	.	.	.	.	.	.	.	G	10.63	1.403287	0.25291	2.28E-4	0.0	ENSG00000162086	ENST00000293995	.	.	.	4.46	4.46	0.54185	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.40908	D	0.000992	T	0.22975	0.0555	L	0.43554	1.36	0.09310	N	1	P	0.35077	0.483	B	0.14578	0.011	T	0.15321	-1.0441	9	0.31617	T	0.26	.	8.5503	0.33447	0.1048:0.0:0.8952:0.0	.	285	Q96N20	ZN75A_HUMAN	Q	285	.	ENSP00000293995:R285Q	R	+	2	0	ZNF75A	3307833	0.006000	0.16342	0.997000	0.53966	0.952000	0.60782	1.683000	0.37638	2.459000	0.83118	0.557000	0.71058	CGG		0.453	ZNF75A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251506.2	NM_153028	
ZNF597	146434	broad.mit.edu	37	16	3486828	3486828	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr16:3486828C>T	ENST00000301744.4	-	4	1106	c.871G>A	c.(871-873)Gta>Ata	p.V291I		NM_152457.1	NP_689670.1	Q96LX8	ZN597_HUMAN	zinc finger protein 597	291					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.V291I(1)		endometrium(1)|kidney(1)|large_intestine(3)|lung(5)|ovary(1)|skin(1)|urinary_tract(1)	13						GGGCCTGATACGAATGTTTCC	0.463																																					p.V291I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G871A	16						.						102.0	98.0	99.0					16																	3486828		2197	4300	6497	3426829	SO:0001583	missense	146434	exon4			AK057633	CCDS10505.1	16p13.3	2013-01-08			ENSG00000167981	ENSG00000167981		"""Zinc fingers, C2H2-type"", ""-"""	26573	protein-coding gene	gene with protein product		614685				12477932	Standard	NM_152457		Approved	FLJ33071	uc002cvd.3	Q96LX8	OTTHUMG00000129359	ENST00000301744.4:c.871G>A	16.37:g.3486828C>T	ENSP00000301744:p.Val291Ile	Somatic		Capture	Illumina HiSeq	Phase_I	3426829	NM_152457		Missense_Mutation	SNP	ENST00000301744.4	37	CCDS10505.1	.	.	.	.	.	.	.	.	.	.	C	9.146	1.015109	0.19355	.	.	ENSG00000167981	ENST00000301744	T	0.06849	3.25	4.76	-6.55	0.01854	.	1.230950	0.05969	N	0.641970	T	0.02380	0.0073	N	0.01874	-0.695	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.42292	-0.9460	10	0.54805	T	0.06	3.8964	0.7026	0.00910	0.3739:0.2384:0.1109:0.2769	.	291	Q96LX8	ZN597_HUMAN	I	291	ENSP00000301744:V291I	ENSP00000301744:V291I	V	-	1	0	ZNF597	3426829	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.931000	0.03967	-1.452000	0.01931	-0.247000	0.11927	GTA		0.463	ZNF597-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251511.2	NM_152457	
SLX4	84464	broad.mit.edu	37	16	3639799	3639799	+	Silent	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr16:3639799G>A	ENST00000294008.3	-	12	4480	c.3840C>T	c.(3838-3840)agC>agT	p.S1280S		NM_032444.2	NP_115820.2	Q8IY92	SLX4_HUMAN	SLX4 structure-specific endonuclease subunit	1280	Interaction with PLK1 and TERF2-TERF2IP.				DNA catabolic process, endonucleolytic (GO:0000737)|DNA double-strand break processing involved in repair via single-strand annealing (GO:0010792)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|double-strand break repair via homologous recombination (GO:0000724)|nucleotide-excision repair (GO:0006289)|positive regulation of catalytic activity (GO:0043085)|response to intra-S DNA damage checkpoint signaling (GO:0072429)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|Slx1-Slx4 complex (GO:0033557)	5'-flap endonuclease activity (GO:0017108)|enzyme activator activity (GO:0008047)	p.S1280S(1)		breast(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(18)|lung(20)|ovary(3)|pancreas(1)|prostate(7)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	76						CGGCCAGCCCGCTCCTGAGGC	0.637								Direct reversal of damage																													p.S1280S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C3840T	16						.						99.0	97.0	98.0					16																	3639799		2197	4300	6497	3579800	SO:0001819	synonymous_variant	84464	exon12			AB058687	CCDS10506.2	16p13.3	2014-09-17	2013-06-05	2010-09-13	ENSG00000188827	ENSG00000188827		"""Fanconi anemia, complementation groups"", ""BTB/POZ domain containing"""	23845	protein-coding gene	gene with protein product	"""Fanconi anemia, complementation group P"""	613278	"""BTB (POZ) domain containing 12"", ""SLX4 structure-specific endonuclease subunit homolog (S. cerevisiae)"""	BTBD12		11347906, 19595721	Standard	NM_032444		Approved	KIAA1784, KIAA1987, FANCP	uc002cvp.2	Q8IY92	OTTHUMG00000074089	ENST00000294008.3:c.3840C>T	16.37:g.3639799G>A		Somatic		Capture	Illumina HiSeq	Phase_I	3579800	NM_032444	Q69YT8|Q8TF15|Q96JP1	Silent	SNP	ENST00000294008.3	37	CCDS10506.2																																																																																				0.637	SLX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157301.3	NM_032444	
SLX4	84464	broad.mit.edu	37	16	3658481	3658481	+	Missense_Mutation	SNP	G	G	A	rs140876043		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr16:3658481G>A	ENST00000294008.3	-	2	1125	c.485C>T	c.(484-486)aCg>aTg	p.T162M		NM_032444.2	NP_115820.2	Q8IY92	SLX4_HUMAN	SLX4 structure-specific endonuclease subunit	162	Interaction with SLX4IP, ERCC4 and MSH2.				DNA catabolic process, endonucleolytic (GO:0000737)|DNA double-strand break processing involved in repair via single-strand annealing (GO:0010792)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|double-strand break repair via homologous recombination (GO:0000724)|nucleotide-excision repair (GO:0006289)|positive regulation of catalytic activity (GO:0043085)|response to intra-S DNA damage checkpoint signaling (GO:0072429)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|Slx1-Slx4 complex (GO:0033557)	5'-flap endonuclease activity (GO:0017108)|enzyme activator activity (GO:0008047)	p.T162M(1)		breast(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(18)|lung(20)|ovary(3)|pancreas(1)|prostate(7)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	76						CTGGTTACCCGTCTGGGTGTT	0.532								Direct reversal of damage																													p.T162M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C485T	16						.	G	MET/THR	0,4394		0,0,2197	112.0	114.0	114.0		485	5.5	1.0	16	dbSNP_134	114	2,8598	2.2+/-6.3	0,2,4298	yes	missense	SLX4	NM_032444.2	81	0,2,6495	AA,AG,GG		0.0233,0.0,0.0154	possibly-damaging	162/1835	3658481	2,12992	2197	4300	6497	3598482	SO:0001583	missense	84464	exon2			AB058687	CCDS10506.2	16p13.3	2014-09-17	2013-06-05	2010-09-13	ENSG00000188827	ENSG00000188827		"""Fanconi anemia, complementation groups"", ""BTB/POZ domain containing"""	23845	protein-coding gene	gene with protein product	"""Fanconi anemia, complementation group P"""	613278	"""BTB (POZ) domain containing 12"", ""SLX4 structure-specific endonuclease subunit homolog (S. cerevisiae)"""	BTBD12		11347906, 19595721	Standard	NM_032444		Approved	KIAA1784, KIAA1987, FANCP	uc002cvp.2	Q8IY92	OTTHUMG00000074089	ENST00000294008.3:c.485C>T	16.37:g.3658481G>A	ENSP00000294008:p.Thr162Met	Somatic		Capture	Illumina HiSeq	Phase_I	3598482	NM_032444	Q69YT8|Q8TF15|Q96JP1	Missense_Mutation	SNP	ENST00000294008.3	37	CCDS10506.2	.	.	.	.	.	.	.	.	.	.	G	16.93	3.259187	0.59321	0.0	2.33E-4	ENSG00000188827	ENST00000294008	T	0.01258	5.09	5.53	5.53	0.82687	.	0.310015	0.23519	N	0.047312	T	0.03608	0.0103	N	0.22421	0.69	0.26667	N	0.9718	D	0.89917	1.0	P	0.61275	0.886	T	0.40270	-0.9572	10	0.87932	D	0	.	15.3162	0.74081	0.0:0.0:1.0:0.0	.	162	Q8IY92	SLX4_HUMAN	M	162	ENSP00000294008:T162M	ENSP00000294008:T162M	T	-	2	0	SLX4	3598482	1.000000	0.71417	0.961000	0.40146	0.669000	0.39330	4.929000	0.63455	2.749000	0.94314	0.650000	0.86243	ACG		0.532	SLX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157301.3	NM_032444	
TRAP1	10131	broad.mit.edu	37	16	3713478	3713478	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr16:3713478G>A	ENST00000246957.5	-	14	1743	c.1655C>T	c.(1654-1656)aCg>aTg	p.T552M	DNASE1_ENST00000414110.2_Intron|TRAP1_ENST00000538171.1_Missense_Mutation_p.T499M|DNASE1_ENST00000575152.1_3'UTR|TRAP1_ENST00000573872.1_5'Flank|TRAP1_ENST00000575671.1_Missense_Mutation_p.T343M	NM_016292.2	NP_057376.2	Q12931	TRAP1_HUMAN	TNF receptor-associated protein 1	552					chaperone-mediated protein folding (GO:0061077)|negative regulation of cellular respiration (GO:1901856)|negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway (GO:1902176)|regulation of reactive oxygen species metabolic process (GO:2000377)|response to stress (GO:0006950)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)|mitochondrial intermembrane space (GO:0005758)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)|protein kinase binding (GO:0019901)|tumor necrosis factor receptor binding (GO:0005164)	p.T552M(1)		central_nervous_system(2)|endometrium(3)|kidney(2)|large_intestine(3)|lung(7)|skin(1)|upper_aerodigestive_tract(1)	19		Ovarian(90;0.0261)				GACTATGTCCGTCTCCACAGA	0.557																																					p.T552M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1655T	16						.						144.0	131.0	135.0					16																	3713478		2197	4300	6497	3653479	SO:0001583	missense	10131	exon14			AF154108	CCDS10508.1, CCDS61824.1	16p13.3	2011-09-02			ENSG00000126602	ENSG00000126602		"""Heat shock proteins / HSPC"""	16264	protein-coding gene	gene with protein product		606219				10652318, 7876093	Standard	NM_016292		Approved	HSP75, HSP90L	uc002cvt.4	Q12931	OTTHUMG00000129427	ENST00000246957.5:c.1655C>T	16.37:g.3713478G>A	ENSP00000246957:p.Thr552Met	Somatic		Capture	Illumina HiSeq	Phase_I	3653479	NM_016292	B4DR68|D3DUC8|F5H897|O43642|O75235|Q9UHL5	Missense_Mutation	SNP	ENST00000246957.5	37	CCDS10508.1	.	.	.	.	.	.	.	.	.	.	G	16.20	3.054865	0.55325	.	.	ENSG00000126602	ENST00000246957;ENST00000538171	T;T	0.09538	2.97;2.97	5.83	5.83	0.93111	Ribosomal protein S5 domain 2-type fold (1);	0.051349	0.85682	D	0.000000	T	0.13628	0.0330	L	0.34521	1.04	0.80722	D	1	P;P	0.35844	0.468;0.524	B;B	0.38842	0.186;0.283	T	0.01805	-1.1270	10	0.87932	D	0	-22.3614	19.112	0.93319	0.0:0.0:1.0:0.0	.	499;552	F5H897;Q12931	.;TRAP1_HUMAN	M	552;499	ENSP00000246957:T552M;ENSP00000442070:T499M	ENSP00000246957:T552M	T	-	2	0	TRAP1	3653479	1.000000	0.71417	0.828000	0.32881	0.181000	0.23173	9.394000	0.97261	2.764000	0.94973	0.557000	0.71058	ACG		0.557	TRAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251586.2	NM_016292	
ADCY9	115	broad.mit.edu	37	16	4029167	4029167	+	Missense_Mutation	SNP	C	C	T	rs144986362		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr16:4029167C>T	ENST00000294016.3	-	8	3167	c.2629G>A	c.(2629-2631)Gca>Aca	p.A877T		NM_001116.3	NP_001107.2	O60503	ADCY9_HUMAN	adenylate cyclase 9	877					activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|neurotrophin TRK receptor signaling pathway (GO:0048011)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	axon (GO:0030424)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	adenylate cyclase activity (GO:0004016)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)	p.A877T(1)		breast(4)|central_nervous_system(1)|cervix(2)|endometrium(5)|kidney(3)|large_intestine(11)|lung(9)|ovary(5)|prostate(4)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	47						ACGGCCAGTGCGGGAAGCGAC	0.582													C|||	1	0.000199681	0.0	0.0	5008	,	,		16725	0.0		0.0	False		,,,				2504	0.001				p.A877T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2629A	16						.	C	THR/ALA	2,4392	4.2+/-10.8	0,2,2195	131.0	124.0	126.0		2629	5.6	0.2	16	dbSNP_134	126	1,8599	1.2+/-3.3	0,1,4299	no	missense	ADCY9	NM_001116.3	58	0,3,6494	TT,TC,CC		0.0116,0.0455,0.0231	benign	877/1354	4029167	3,12991	2197	4300	6497	3969168	SO:0001583	missense	115	exon8			AF036927	CCDS32382.1	16p13.3	2013-02-04				ENSG00000162104	4.6.1.1	"""Adenylate cyclases"""	240	protein-coding gene	gene with protein product		603302				9628827	Standard	NM_001116		Approved	AC9	uc002cvx.3	O60503		ENST00000294016.3:c.2629G>A	16.37:g.4029167C>T	ENSP00000294016:p.Ala877Thr	Somatic		Capture	Illumina HiSeq	Phase_I	3969168	NM_001116	A7E2V5|A7E2X2|D3DUD1|O60273|Q4ZHT9|Q4ZIR5|Q9BWT4|Q9UGP2	Missense_Mutation	SNP	ENST00000294016.3	37	CCDS32382.1	.	.	.	.	.	.	.	.	.	.	C	14.81	2.647550	0.47258	4.55E-4	1.16E-4	ENSG00000162104	ENST00000294016	D	0.84223	-1.82	5.59	5.59	0.84812	.	0.053693	0.85682	D	0.000000	T	0.78591	0.4307	L	0.45581	1.43	0.54753	D	0.999983	P	0.42456	0.78	B	0.28991	0.097	T	0.77576	-0.2536	10	0.20519	T	0.43	.	19.5959	0.95538	0.0:1.0:0.0:0.0	.	877	O60503	ADCY9_HUMAN	T	877	ENSP00000294016:A877T	ENSP00000294016:A877T	A	-	1	0	ADCY9	3969168	1.000000	0.71417	0.241000	0.24154	0.007000	0.05969	4.618000	0.61211	2.617000	0.88574	0.655000	0.94253	GCA		0.582	ADCY9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438076.1		
DNAJA3	9093	broad.mit.edu	37	16	4498739	4498739	+	Silent	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr16:4498739C>T	ENST00000262375.6	+	9	1208	c.1131C>T	c.(1129-1131)ccC>ccT	p.P377P	DNAJA3_ENST00000355296.4_Silent_p.P377P|DNAJA3_ENST00000431375.2_Silent_p.P224P	NM_005147.5	NP_005138.3	Q96EY1	DNJA3_HUMAN	DnaJ (Hsp40) homolog, subfamily A, member 3	377					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|activation-induced cell death of T cells (GO:0006924)|cell aging (GO:0007569)|mitochondrial DNA replication (GO:0006264)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of interferon-gamma-mediated signaling pathway (GO:0060336)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of programmed cell death (GO:0043069)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuromuscular junction development (GO:0007528)|positive regulation of apoptotic process (GO:0043065)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of T cell proliferation (GO:0042102)|protein folding (GO:0006457)|protein stabilization (GO:0050821)|response to heat (GO:0009408)|response to interferon-gamma (GO:0034341)|skeletal muscle acetylcholine-gated channel clustering (GO:0071340)|small GTPase mediated signal transduction (GO:0007264)|T cell differentiation in thymus (GO:0033077)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extrinsic component of plasma membrane (GO:0019897)|intracellular membrane-bounded organelle (GO:0043231)|mitochondrial matrix (GO:0005759)|mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)|neuromuscular junction (GO:0031594)|nucleus (GO:0005634)|postsynaptic membrane (GO:0045211)	ATP binding (GO:0005524)|interferon-gamma receptor binding (GO:0005133)|metal ion binding (GO:0046872)|NF-kappaB binding (GO:0051059)|protein kinase binding (GO:0019901)|small GTPase regulator activity (GO:0005083)|transcription factor binding (GO:0008134)	p.P377P(1)		NS(1)|breast(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|ovary(2)|upper_aerodigestive_tract(2)	15						TATAGATCCCCCCTGGGACTC	0.463																																					p.P377P												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1131T	16						.						43.0	40.0	41.0					16																	4498739		2197	4300	6497	4438740	SO:0001819	synonymous_variant	9093	exon9			AF061749	CCDS10515.1, CCDS45400.1, CCDS66930.1	16p13.3	2011-09-02			ENSG00000103423	ENSG00000103423		"""Heat shock proteins / DNAJ (HSP40)"""	11808	protein-coding gene	gene with protein product		608382		TID1		9683573	Standard	NM_005147		Approved	hTid-1	uc002cwk.3	Q96EY1	OTTHUMG00000129470	ENST00000262375.6:c.1131C>T	16.37:g.4498739C>T		Somatic		Capture	Illumina HiSeq	Phase_I	4438740	NM_001135110	B2RAJ5|B4DI33|E7ES32|O75472|Q8WUJ6|Q8WXJ3|Q96D76|Q96IV1|Q9NYH8	Silent	SNP	ENST00000262375.6	37	CCDS10515.1																																																																																				0.463	DNAJA3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251633.1		
TGFB1I1	7041	broad.mit.edu	37	16	31484787	31484787	+	Silent	SNP	T	T	C			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr16:31484787T>C	ENST00000394863.3	+	2	169	c.39T>C	c.(37-39)acT>acC	p.T13T	TGFB1I1_ENST00000361773.3_5'UTR|TGFB1I1_ENST00000394858.2_5'UTR|TGFB1I1_ENST00000567607.1_5'UTR	NM_001042454.2	NP_001035919.1	O43294	TGFI1_HUMAN	transforming growth factor beta 1 induced transcript 1	13	Interaction with PTK2B/PYK2.|Transcription activation. {ECO:0000250}.				androgen receptor signaling pathway (GO:0030521)|cell adhesion (GO:0007155)|cell fate commitment (GO:0045165)|epithelial cell differentiation (GO:0030855)|morphogenesis of embryonic epithelium (GO:0016331)|negative regulation of cell proliferation (GO:0008285)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|response to heat (GO:0009408)|transcription from RNA polymerase II promoter (GO:0006366)|ubiquitin-dependent SMAD protein catabolic process (GO:0030579)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|focal adhesion (GO:0005925)|intracellular (GO:0005622)|nucleus (GO:0005634)	androgen receptor binding (GO:0050681)|I-SMAD binding (GO:0070411)|Roundabout binding (GO:0048495)|transcription coactivator activity (GO:0003713)|zinc ion binding (GO:0008270)			lung(8)|upper_aerodigestive_tract(1)	9						ACCTGGAGACTACCACCTCGC	0.602																																					p.T13T												.	.	0			c.T39C	16						.						51.0	55.0	53.0					16																	31484787		2197	4300	6497	31392288	SO:0001819	synonymous_variant	7041	exon2			AB007836	CCDS10713.1, CCDS42156.1	16p11	2008-02-05			ENSG00000140682	ENSG00000140682			11767	protein-coding gene	gene with protein product		602353				9422762, 10075738	Standard	NM_015927		Approved	Hic-5, TSC-5, ARA55, HIC-5	uc002ecd.2	O43294	OTTHUMG00000132467	ENST00000394863.3:c.39T>C	16.37:g.31484787T>C		Somatic		Capture	Illumina HiSeq	Phase_I	31392288	NM_001042454	B2R8D5|Q9BPW3|Q9Y2V5	Silent	SNP	ENST00000394863.3	37	CCDS42156.1																																																																																				0.602	TGFB1I1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255630.3		
NUDT16L1	84309	broad.mit.edu	37	16	4744986	4744986	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr16:4744986T>C	ENST00000304301.6	+	3	475	c.442T>C	c.(442-444)Tac>Cac	p.Y148H	NUDT16L1_ENST00000405142.1_3'UTR|NUDT16L1_ENST00000586536.1_Missense_Mutation_p.V171A|NUDT16L1_ENST00000586252.1_Intron	NM_032349.3	NP_115725.1	Q9BRJ7	SDOS_HUMAN	nudix (nucleoside diphosphate linked moiety X)-type motif 16-like 1	148	Interaction with PXN. {ECO:0000250}.					cytoplasm (GO:0005737)	hydrolase activity (GO:0016787)|poly(A) RNA binding (GO:0044822)|snoRNA binding (GO:0030515)	p.Y148H(1)		endometrium(1)|large_intestine(1)|lung(1)|skin(1)	4						GGTCCCGCTGTACACCCAGAA	0.642																																					p.Y148H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T442C	16						.						48.0	39.0	42.0					16																	4744986		2197	4300	6497	4684987	SO:0001583	missense	84309	exon3			BC006223	CCDS10519.1, CCDS59257.1	16p13.3	2008-02-05			ENSG00000168101	ENSG00000168101		"""Nudix motif containing"""	28154	protein-coding gene	gene with protein product						11805099	Standard	NM_032349		Approved	SDOS	uc002cxe.3	Q9BRJ7	OTTHUMG00000129471	ENST00000304301.6:c.442T>C	16.37:g.4744986T>C	ENSP00000306670:p.Tyr148His	Somatic		Capture	Illumina HiSeq	Phase_I	4684987	NM_032349	Q8NAI2	Missense_Mutation	SNP	ENST00000304301.6	37	CCDS10519.1	.	.	.	.	.	.	.	.	.	.	T	18.99	3.739360	0.69304	.	.	ENSG00000168101	ENST00000304301	T	0.52057	0.68	4.52	4.52	0.55395	NUDIX hydrolase domain-like (1);	5.567940	0.00616	N	0.000427	T	0.69360	0.3102	L	0.58583	1.82	0.80722	D	1	D	0.76494	0.999	D	0.75020	0.985	T	0.44787	-0.9305	10	0.52906	T	0.07	.	12.7052	0.57058	0.0:0.0:0.0:1.0	.	148	Q9BRJ7	SDOS_HUMAN	H	148	ENSP00000306670:Y148H	ENSP00000306670:Y148H	Y	+	1	0	NUDT16L1	4684987	1.000000	0.71417	0.990000	0.47175	0.992000	0.81027	5.712000	0.68407	1.676000	0.50930	0.533000	0.62120	TAC		0.642	NUDT16L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251634.1	NM_032349	
SEPT12	124404	broad.mit.edu	37	16	4828088	4828088	+	Splice_Site	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr16:4828088G>A	ENST00000268231.8	-	9	1137	c.874C>T	c.(874-876)Cgc>Tgc	p.R292C	SEPT12_ENST00000396693.5_Splice_Site_p.R246C	NM_144605.4	NP_653206.2	Q8IYM1	SEP12_HUMAN	septin 12	292	Septin-type G.				cell cycle (GO:0007049)|cell division (GO:0051301)	cleavage furrow (GO:0032154)|microtubule cytoskeleton (GO:0015630)|midbody (GO:0030496)|perinuclear region of cytoplasm (GO:0048471)|septin complex (GO:0031105)|sperm annulus (GO:0097227)|spindle (GO:0005819)|stress fiber (GO:0001725)	GDP binding (GO:0019003)|GTP binding (GO:0005525)|phosphatidylinositol binding (GO:0035091)|protein homodimerization activity (GO:0042803)	p.R292C(1)		NS(1)|cervix(1)|endometrium(3)|large_intestine(5)|lung(8)|skin(2)|stomach(3)	23						CACCCTCACCGGATAAGCAGG	0.627																																					p.R292C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C874T	16						.						59.0	55.0	57.0					16																	4828088		2197	4300	6497	4768089	SO:0001630	splice_region_variant	124404	exon9			AK058139	CCDS10522.1, CCDS53987.1	16p13.3	2013-01-21			ENSG00000140623	ENSG00000140623		"""Septins"""	26348	protein-coding gene	gene with protein product		611562				14611653, 15915442	Standard	NM_001154458		Approved	FLJ25410	uc002cxq.3	Q8IYM1	OTTHUMG00000129481	ENST00000268231.8:c.875+1C>T	16.37:g.4828088G>A		Somatic		Capture	Illumina HiSeq	Phase_I	4768089	NM_144605	Q0P6B0|Q1PBH0|Q96LL0	Missense_Mutation	SNP	ENST00000268231.8	37	CCDS10522.1	.	.	.	.	.	.	.	.	.	.	G	21.9	4.215876	0.79352	.	.	ENSG00000140623	ENST00000396693;ENST00000268231	T;T	0.54279	0.58;0.58	4.72	4.72	0.59763	.	0.000000	0.85682	D	0.000000	T	0.74612	0.3739	M	0.83384	2.64	0.58432	D	0.999999	D;D	0.89917	1.0;1.0	D;D	0.77004	0.987;0.989	T	0.78858	-0.2038	10	0.72032	D	0.01	.	16.7906	0.85589	0.0:0.0:1.0:0.0	.	246;292	Q8IYM1-2;Q8IYM1	.;SEP12_HUMAN	C	246;292	ENSP00000379922:R246C;ENSP00000268231:R292C	ENSP00000268231:R292C	R	-	1	0	SEPT12	4768089	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	4.610000	0.61155	2.607000	0.88179	0.561000	0.74099	CGC		0.627	SEPT12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251645.2	NM_144605	Missense_Mutation
PPL	5493	broad.mit.edu	37	16	4953943	4953943	+	Silent	SNP	C	C	T	rs200847749		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr16:4953943C>T	ENST00000345988.2	-	3	350	c.261G>A	c.(259-261)gcG>gcA	p.A87A	PPL_ENST00000590782.2_Silent_p.A87A	NM_002705.4	NP_002696	O60437	PEPL_HUMAN	periplakin	87					keratinization (GO:0031424)	cell junction (GO:0030054)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	structural constituent of cytoskeleton (GO:0005200)	p.A87A(1)		breast(6)|central_nervous_system(1)|endometrium(11)|kidney(5)|large_intestine(12)|lung(12)|ovary(4)|prostate(5)|skin(3)|stomach(1)|urinary_tract(2)	62						TGGCCGCATCCGCCTCTAGCA	0.622													C|||	1	0.000199681	0.0008	0.0	5008	,	,		17938	0.0		0.0	False		,,,				2504	0.0				p.A87A												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G261A	16						.						84.0	70.0	75.0					16																	4953943		2197	4300	6497	4893944	SO:0001819	synonymous_variant	5493	exon3			AF013717	CCDS10526.1	16p13.3	2008-02-05			ENSG00000118898	ENSG00000118898			9273	protein-coding gene	gene with protein product		602871				9570964, 9521878	Standard	NM_002705		Approved		uc002cyd.1	O60437	OTTHUMG00000129528	ENST00000345988.2:c.261G>A	16.37:g.4953943C>T		Somatic		Capture	Illumina HiSeq	Phase_I	4893944	NM_002705	O60314|O60454|Q14C98	Silent	SNP	ENST00000345988.2	37	CCDS10526.1																																																																																				0.622	PPL-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251715.1	NM_002705	
NETO2	81831	broad.mit.edu	37	16	47162257	47162257	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr16:47162257C>A	ENST00000562435.1	-	4	844	c.460G>T	c.(460-462)Gca>Tca	p.A154S	NETO2_ENST00000303155.5_Missense_Mutation_p.A154S	NM_018092.4	NP_060562.3	Q8NC67	NETO2_HUMAN	neuropilin (NRP) and tolloid (TLL)-like 2	154	CUB 1. {ECO:0000255|PROSITE- ProRule:PRU00059}.				regulation of kainate selective glutamate receptor activity (GO:2000312)	kainate selective glutamate receptor complex (GO:0032983)|postsynaptic density (GO:0014069)		p.A154S(1)		breast(1)|cervix(1)|endometrium(1)|large_intestine(8)|lung(11)|prostate(1)|skin(2)|upper_aerodigestive_tract(4)	29		all_cancers(37;0.00114)|all_lung(18;0.00432)|Lung NSC(13;0.0384)|Breast(268;0.174)				GAATATTTTGCTCGAAATCCC	0.358										HNSCC(25;0.065)																											p.A154S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G460T	16						.						73.0	77.0	76.0					16																	47162257		2202	4300	6502	45719758	SO:0001583	missense	81831	exon4			AK001292	CCDS10727.1, CCDS58460.1	16q11.2	2008-08-04			ENSG00000171208	ENSG00000171208			14644	protein-coding gene	gene with protein product		607974				11943477	Standard	NM_018092		Approved	FLJ10430, NEOT2	uc002eer.2	Q8NC67	OTTHUMG00000133101	ENST00000562435.1:c.460G>T	16.37:g.47162257C>A	ENSP00000455169:p.Ala154Ser	Somatic		Capture	Illumina HiSeq	Phase_I	45719758	NM_018092	J3KNF1|Q7Z381|Q8ND51|Q96SP4|Q9NVY8	Missense_Mutation	SNP	ENST00000562435.1	37	CCDS10727.1	.	.	.	.	.	.	.	.	.	.	C	18.32	3.597852	0.66332	.	.	ENSG00000171208	ENST00000303155	T	0.36157	1.27	5.71	5.71	0.89125	CUB (5);	0.158899	0.56097	D	0.000025	T	0.64405	0.2595	H	0.96333	3.805	0.54753	D	0.999988	B;P;P	0.43231	0.126;0.801;0.801	B;P;B	0.46419	0.143;0.516;0.252	T	0.76332	-0.2998	10	0.87932	D	0	.	19.8604	0.96781	0.0:1.0:0.0:0.0	.	18;154;154	B7Z4I7;Q32NC3;Q8NC67	.;.;NETO2_HUMAN	S	154	ENSP00000306726:A154S	ENSP00000306726:A154S	A	-	1	0	NETO2	45719758	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	2.983000	0.49345	2.699000	0.92147	0.650000	0.86243	GCA		0.358	NETO2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256766.2	NM_018092	
NOD2	64127	broad.mit.edu	37	16	50745017	50745017	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr16:50745017G>A	ENST00000300589.2	+	4	1300	c.1195G>A	c.(1195-1197)Gac>Aac	p.D399N	RP11-327F22.6_ENST00000602304.1_RNA	NM_022162.1	NP_071445.1	Q9HC29	NOD2_HUMAN	nucleotide-binding oligomerization domain containing 2	399	NACHT. {ECO:0000255|PROSITE- ProRule:PRU00136}.				activation of MAPK activity (GO:0000187)|activation of MAPK activity involved in innate immune response (GO:0035419)|cellular response to muramyl dipeptide (GO:0071225)|cellular response to peptidoglycan (GO:0071224)|cytokine production involved in immune response (GO:0002367)|defense response (GO:0006952)|defense response to bacterium (GO:0042742)|defense response to Gram-positive bacterium (GO:0050830)|detection of bacterium (GO:0016045)|detection of biotic stimulus (GO:0009595)|detection of muramyl dipeptide (GO:0032498)|immunoglobulin production involved in immunoglobulin mediated immune response (GO:0002381)|innate immune response (GO:0045087)|innate immune response in mucosa (GO:0002227)|intracellular signal transduction (GO:0035556)|JNK cascade (GO:0007254)|macrophage inflammatory protein-1 alpha production (GO:0071608)|maintenance of gastrointestinal epithelium (GO:0030277)|microglial cell activation involved in immune response (GO:0002282)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of growth of symbiont in host (GO:0044130)|negative regulation of inflammatory response to antigenic stimulus (GO:0002862)|negative regulation of interferon-gamma production (GO:0032689)|negative regulation of interleukin-12 production (GO:0032695)|negative regulation of interleukin-18 production (GO:0032701)|negative regulation of interleukin-2 production (GO:0032703)|negative regulation of macrophage apoptotic process (GO:2000110)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of T cell mediated immunity (GO:0002710)|negative regulation of toll-like receptor 2 signaling pathway (GO:0034136)|negative regulation of tumor necrosis factor production (GO:0032720)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing 2 signaling pathway (GO:0070431)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|pathogen-associated molecular pattern dependent induction by symbiont of host innate immune response (GO:0052033)|positive regulation of B cell activation (GO:0050871)|positive regulation of biosynthetic process of antibacterial peptides active against Gram-positive bacteria (GO:0006965)|positive regulation of dendritic cell antigen processing and presentation (GO:0002606)|positive regulation of dendritic cell cytokine production (GO:0002732)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of gamma-delta T cell activation (GO:0046645)|positive regulation of humoral immune response mediated by circulating immunoglobulin (GO:0002925)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-1 beta production (GO:0032731)|positive regulation of interleukin-1 beta secretion (GO:0050718)|positive regulation of interleukin-10 production (GO:0032733)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of interleukin-17 production (GO:0032740)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of JNK cascade (GO:0046330)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of nitric-oxide synthase biosynthetic process (GO:0051770)|positive regulation of Notch signaling pathway (GO:0045747)|positive regulation of oxidoreductase activity (GO:0051353)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phagocytosis (GO:0050766)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of prostaglandin-E synthase activity (GO:2000363)|positive regulation of prostaglandin-endoperoxide synthase activity (GO:0060585)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of stress-activated MAPK cascade (GO:0032874)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tumor necrosis factor production (GO:0032760)|positive regulation of type 2 immune response (GO:0002830)|protein oligomerization (GO:0051259)|regulation of inflammatory response (GO:0050727)|regulation of neutrophil chemotaxis (GO:0090022)|response to exogenous dsRNA (GO:0043330)|response to lipopolysaccharide (GO:0032496)|response to muramyl dipeptide (GO:0032495)|response to nutrient (GO:0007584)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|vesicle (GO:0031982)	ATP binding (GO:0005524)|CARD domain binding (GO:0050700)|enzyme binding (GO:0019899)|muramyl dipeptide binding (GO:0032500)|peptidoglycan binding (GO:0042834)|protein kinase binding (GO:0019901)	p.D399N(1)		cervix(1)|endometrium(5)|kidney(3)|large_intestine(7)|lung(30)|ovary(3)|skin(3)	52		all_cancers(37;0.0156)				CTCCCCGACCGACCCCACCTC	0.592																																					p.D399N												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1195A	16						.						62.0	65.0	64.0					16																	50745017		2198	4300	6498	49302518	SO:0001583	missense	64127	exon4			AF178930	CCDS10746.1	16q12	2014-09-17	2006-12-08	2006-12-08	ENSG00000167207	ENSG00000167207		"""Nucleotide-binding domain and leucine rich repeat containing"""	5331	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and CARD domain containing 2"", ""NOD-like receptor C2"", ""NLR family, CARD domain containing 2"""	605956	"""caspase recruitment domain family, member 15"""	IBD1, CARD15		7809109, 8587604	Standard	XM_005256084		Approved	BLAU, CD, PSORAS1, CLR16.3, NLRC2	uc002egm.1	Q9HC29	OTTHUMG00000133171	ENST00000300589.2:c.1195G>A	16.37:g.50745017G>A	ENSP00000300589:p.Asp399Asn	Somatic		Capture	Illumina HiSeq	Phase_I	49302518	NM_022162	E2JEQ6|Q96RH5|Q96RH6|Q96RH8	Missense_Mutation	SNP	ENST00000300589.2	37	CCDS10746.1	.	.	.	.	.	.	.	.	.	.	G	13.68	2.309814	0.40895	.	.	ENSG00000167207	ENST00000526417;ENST00000300589	T	0.78816	-1.21	5.59	4.64	0.57946	NACHT nucleoside triphosphatase (1);	0.388025	0.25313	N	0.031570	T	0.77538	0.4145	L	0.42245	1.32	0.30724	N	0.747918	D;P;D	0.59357	0.985;0.932;0.985	P;B;P	0.51582	0.674;0.386;0.674	T	0.78748	-0.2083	10	0.72032	D	0.01	.	12.3351	0.55062	0.082:0.0:0.918:0.0	.	183;372;399	D6CHF9;Q9HC29-2;Q9HC29	.;.;NOD2_HUMAN	N	372;399	ENSP00000300589:D399N	ENSP00000300589:D399N	D	+	1	0	NOD2	49302518	0.431000	0.25546	0.359000	0.25824	0.221000	0.24807	1.126000	0.31344	1.380000	0.46344	0.561000	0.74099	GAC		0.592	NOD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256876.2	NM_022162	
SALL1	6299	broad.mit.edu	37	16	51171334	51171334	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr16:51171334C>A	ENST00000251020.4	-	3	3697	c.3664G>T	c.(3664-3666)Gcg>Tcg	p.A1222S	SALL1_ENST00000440970.1_Missense_Mutation_p.A1125S|SALL1_ENST00000541611.1_Missense_Mutation_p.A45S|SALL1_ENST00000566102.1_3'UTR	NM_002968.2	NP_002959.2	Q9NSC2	SALL1_HUMAN	spalt-like transcription factor 1	1222					adrenal gland development (GO:0030325)|branching involved in ureteric bud morphogenesis (GO:0001658)|embryonic digestive tract development (GO:0048566)|embryonic digit morphogenesis (GO:0042733)|forelimb morphogenesis (GO:0035136)|gonad development (GO:0008406)|heart development (GO:0007507)|hindlimb morphogenesis (GO:0035137)|histone deacetylation (GO:0016575)|inductive cell-cell signaling (GO:0031129)|kidney development (GO:0001822)|kidney epithelium development (GO:0072073)|limb development (GO:0060173)|mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003337)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|neural tube closure (GO:0001843)|olfactory bulb interneuron differentiation (GO:0021889)|olfactory bulb mitral cell layer development (GO:0061034)|olfactory nerve development (GO:0021553)|outer ear morphogenesis (GO:0042473)|pituitary gland development (GO:0021983)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of Wnt signaling pathway (GO:0030177)|regulation of neural precursor cell proliferation (GO:2000177)|transcription, DNA-templated (GO:0006351)|ureteric bud development (GO:0001657)|ureteric bud invasion (GO:0072092)|ventricular septum development (GO:0003281)	chromocenter (GO:0010369)|cytoplasm (GO:0005737)|heterochromatin (GO:0000792)|nucleus (GO:0005634)|NuRD complex (GO:0016581)	beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.A1222S(1)		NS(4)|breast(2)|central_nervous_system(2)|endometrium(3)|kidney(5)|large_intestine(25)|lung(61)|ovary(3)|prostate(6)|skin(12)|upper_aerodigestive_tract(3)	126		all_cancers(37;0.0322)	COAD - Colon adenocarcinoma(2;0.24)			GATCTTGCCGCCAAATCCTTC	0.572																																					p.A1222S	GBM(103;1352 1446 1855 4775 8890)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G3664T	16						.						58.0	54.0	56.0					16																	51171334		2198	4300	6498	49728835	SO:0001583	missense	6299	exon3			X98833	CCDS10747.1, CCDS45483.1	16q12.1	2014-09-17	2013-10-17		ENSG00000103449	ENSG00000103449		"""Zinc fingers, C2H2-type"""	10524	protein-coding gene	gene with protein product		602218	"""sal (Drosophila)-like 1"", ""sal-like 1 (Drosophila)"""	TBS		9425907	Standard	NM_002968		Approved	Hsal1, ZNF794	uc021tie.1	Q9NSC2	OTTHUMG00000133176	ENST00000251020.4:c.3664G>T	16.37:g.51171334C>A	ENSP00000251020:p.Ala1222Ser	Somatic		Capture	Illumina HiSeq	Phase_I	49728835	NM_002968	Q99881|Q9NSC3|Q9P1R0	Missense_Mutation	SNP	ENST00000251020.4	37	CCDS10747.1	.	.	.	.	.	.	.	.	.	.	C	9.919	1.211594	0.22289	.	.	ENSG00000103449	ENST00000251020;ENST00000440970;ENST00000457559;ENST00000541611	T;T;T	0.51071	0.72;0.72;0.72	5.53	5.53	0.82687	.	0.109628	0.64402	D	0.000009	T	0.38401	0.1039	L	0.28458	0.855	0.43360	D	0.995439	B;B	0.27498	0.18;0.006	B;B	0.20577	0.03;0.007	T	0.11494	-1.0585	10	0.25106	T	0.35	-15.4979	19.4677	0.94950	0.0:1.0:0.0:0.0	.	1222;45	Q9NSC2;F5H733	SALL1_HUMAN;.	S	1222;1125;1186;45	ENSP00000251020:A1222S;ENSP00000407914:A1125S;ENSP00000442827:A45S	ENSP00000251020:A1222S	A	-	1	0	SALL1	49728835	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	3.833000	0.55790	2.603000	0.88011	0.643000	0.83706	GCG		0.572	SALL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256883.2	NM_002968	
CES5A	221223	broad.mit.edu	37	16	55880681	55880681	+	Splice_Site	SNP	C	C	T	rs16955812	byFrequency	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr16:55880681C>T	ENST00000290567.9	-	12	1616	c.1495G>A	c.(1495-1497)Ggg>Agg	p.G499R	CES5A_ENST00000541580.1_5'UTR|CES5A_ENST00000521992.1_Splice_Site_p.G528R|CES5A_ENST00000319165.9_Splice_Site_p.G449R|CES5A_ENST00000518005.1_Splice_Site_p.G393R|CES5A_ENST00000520435.1_Splice_Site_p.G469R	NM_001143685.1	NP_001137157.1	Q6NT32	EST5A_HUMAN	carboxylesterase 5A	499			G -> R (in dbSNP:rs16955812).			extracellular region (GO:0005576)	carboxylic ester hydrolase activity (GO:0052689)	p.G528R(1)|p.G449R(1)		breast(2)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(8)|lung(13)|ovary(4)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	39						TTTACTTACCCGGTTCGAGCA	0.522													c|||	92	0.0183706	0.0651	0.0086	5008	,	,		18080	0.0		0.0	False		,,,				2504	0.0				p.G499R												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G1495A	16						.	C	ARG/GLY,ARG/GLY,ARG/GLY	250,4146		4,242,1952	214.0	213.0	214.0		1495,1582,1345	4.5	0.9	16	dbSNP_123	214	3,8597		0,3,4297	yes	missense-near-splice,missense-near-splice,missense-near-splice	CES5A	NM_001143685.1,NM_001190158.1,NM_145024.2	125,125,125	4,245,6249	TT,TC,CC		0.0349,5.687,1.9468	probably-damaging,probably-damaging,probably-damaging	499/576,528/605,449/526	55880681	253,12743	2198	4300	6498	54438182	SO:0001630	splice_region_variant	221223	exon12			AK090997	CCDS10755.1, CCDS45490.1, CCDS54012.1	16q13	2010-10-12	2010-10-12	2010-10-12	ENSG00000159398	ENSG00000159398	3.1.1.1	"""Carboxylesterases"""	26459	protein-coding gene	gene with protein product			"""carboxylesterase 7"""	CES7		20931200	Standard	NM_145024		Approved	FLJ31547, CES4C1, CES5, CAUXIN	uc021tir.1	Q6NT32	OTTHUMG00000133236	ENST00000290567.9:c.1496+1G>A	16.37:g.55880681C>T		Somatic		Capture	Illumina HiSeq	Phase_I	54438182	NM_001143685	B7Z252|B7ZLB6|Q8NBC8|Q96DN9	Missense_Mutation	SNP	ENST00000290567.9	37	CCDS45490.1	38	0.0173992673992674	36	0.07317073170731707	2	0.0055248618784530384	0	0.0	0	0.0	.	15.12	2.737936	0.49045	0.05687	3.49E-4	ENSG00000159398	ENST00000521992;ENST00000319165;ENST00000518005;ENST00000290567;ENST00000520435;ENST00000541580	T;T;T;T;T	0.75260	-0.92;-0.92;-0.92;-0.92;-0.92	5.45	4.5	0.54988	Carboxylesterase, type B (1);	0.471386	0.17999	N	0.154980	T	0.49184	0.1542	H	0.94462	3.54	0.46542	D	0.999099	D;D	0.89917	1.0;0.999	D;D	0.97110	1.0;0.959	T	0.76913	-0.2783	10	0.66056	D	0.02	.	12.6097	0.56544	0.0:0.9188:0.0:0.0812	rs16955812;rs52827358;rs16955812	499;449	Q6NT32;Q6NT32-2	EST5A_HUMAN;.	R	528;449;393;499;469;279	ENSP00000428864:G528R;ENSP00000324271:G449R;ENSP00000428571:G393R;ENSP00000290567:G499R;ENSP00000428887:G469R	ENSP00000290567:G499R	G	-	1	0	CES5A	54438182	0.997000	0.39634	0.887000	0.34795	0.085000	0.17905	4.036000	0.57304	1.439000	0.47511	-0.126000	0.14955	GGG		0.522	CES5A-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000256975.3	NM_145024	Missense_Mutation
GPR97	222487	broad.mit.edu	37	16	57713122	57713122	+	Missense_Mutation	SNP	G	G	A	rs376154437		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr16:57713122G>A	ENST00000333493.4	+	5	687	c.526G>A	c.(526-528)Gtg>Atg	p.V176M	GPR97_ENST00000450388.3_Missense_Mutation_p.V56M|RP11-405F3.4_ENST00000563062.1_RNA|GPR97_ENST00000327655.6_5'UTR	NM_170776.4	NP_740746.4	Q86Y34	GPR97_HUMAN	G protein-coupled receptor 97	176					neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)	p.V176M(1)|p.V176L(1)		breast(1)|central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(9)|lung(7)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	30						TGGCAGCGGCGTGTTGAACAA	0.642																																					p.V176M												.	.	2	Substitution - Missense(2)	large_intestine(1)|lung(1)	c.G526A	16						.						110.0	102.0	104.0					16																	57713122		2198	4300	6498	56270623	SO:0001583	missense	222487	exon5			AY140959	CCDS10786.1	16q13	2014-08-08			ENSG00000182885	ENSG00000182885		"""-"", ""GPCR / Class B : Orphans"""	13728	protein-coding gene	gene with protein product						12435584, 222487	Standard	NM_170776		Approved	Pb99, PGR26	uc002emh.3	Q86Y34	OTTHUMG00000133458	ENST00000333493.4:c.526G>A	16.37:g.57713122G>A	ENSP00000332900:p.Val176Met	Somatic		Capture	Illumina HiSeq	Phase_I	56270623	NM_170776	Q6ZMF4|Q86SL9|Q8IZF1	Missense_Mutation	SNP	ENST00000333493.4	37	CCDS10786.1	.	.	.	.	.	.	.	.	.	.	G	14.29	2.492240	0.44352	.	.	ENSG00000182885	ENST00000333493;ENST00000450388	T;T	0.35236	1.32;1.42	4.99	4.99	0.66335	.	0.000000	0.49305	D	0.000147	T	0.61362	0.2341	M	0.78049	2.395	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.66300	-0.5958	10	0.72032	D	0.01	.	14.9828	0.71324	0.0:0.0:1.0:0.0	.	176	Q86Y34	GPR97_HUMAN	M	176;56	ENSP00000332900:V176M;ENSP00000404803:V56M	ENSP00000332900:V176M	V	+	1	0	GPR97	56270623	0.989000	0.36119	0.873000	0.34254	0.068000	0.16541	1.625000	0.37029	2.296000	0.77279	0.491000	0.48974	GTG		0.642	GPR97-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257333.2	NM_170776	
GPR97	222487	broad.mit.edu	37	16	57719693	57719693	+	Silent	SNP	G	G	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr16:57719693G>T	ENST00000333493.4	+	11	1556	c.1395G>T	c.(1393-1395)gcG>gcT	p.A465A	GPR97_ENST00000450388.3_Silent_p.A345A|RP11-405F3.4_ENST00000563062.1_RNA|GPR97_ENST00000327655.6_Silent_p.A255A	NM_170776.4	NP_740746.4	Q86Y34	GPR97_HUMAN	G protein-coupled receptor 97	465				A -> V (in Ref. 4; AAH64508). {ECO:0000305}.	neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)	p.A465A(1)		breast(1)|central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(9)|lung(7)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	30						GTGCTACAGCGGTCAAGGAGC	0.607																																					p.A465A												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G1395T	16						.						129.0	108.0	115.0					16																	57719693		2198	4300	6498	56277194	SO:0001819	synonymous_variant	222487	exon11			AY140959	CCDS10786.1	16q13	2014-08-08			ENSG00000182885	ENSG00000182885		"""-"", ""GPCR / Class B : Orphans"""	13728	protein-coding gene	gene with protein product						12435584, 222487	Standard	NM_170776		Approved	Pb99, PGR26	uc002emh.3	Q86Y34	OTTHUMG00000133458	ENST00000333493.4:c.1395G>T	16.37:g.57719693G>T		Somatic		Capture	Illumina HiSeq	Phase_I	56277194	NM_170776	Q6ZMF4|Q86SL9|Q8IZF1	Silent	SNP	ENST00000333493.4	37	CCDS10786.1																																																																																				0.607	GPR97-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257333.2	NM_170776	
GPR97	222487	broad.mit.edu	37	16	57722356	57722356	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr16:57722356T>C	ENST00000333493.4	+	12	1794	c.1633T>C	c.(1633-1635)Tcc>Ccc	p.S545P	GPR97_ENST00000450388.3_Missense_Mutation_p.S425P|RP11-405F3.4_ENST00000563062.1_RNA|GPR97_ENST00000327655.6_Intron	NM_170776.4	NP_740746.4	Q86Y34	GPR97_HUMAN	G protein-coupled receptor 97	545					neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)	p.S545P(1)		breast(1)|central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(9)|lung(7)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	30						CCAGGCCCACTCCGCATCTca	0.557																																					p.S545P												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T1633C	16						.						143.0	128.0	133.0					16																	57722356		2198	4300	6498	56279857	SO:0001583	missense	222487	exon12			AY140959	CCDS10786.1	16q13	2014-08-08			ENSG00000182885	ENSG00000182885		"""-"", ""GPCR / Class B : Orphans"""	13728	protein-coding gene	gene with protein product						12435584, 222487	Standard	NM_170776		Approved	Pb99, PGR26	uc002emh.3	Q86Y34	OTTHUMG00000133458	ENST00000333493.4:c.1633T>C	16.37:g.57722356T>C	ENSP00000332900:p.Ser545Pro	Somatic		Capture	Illumina HiSeq	Phase_I	56279857	NM_170776	Q6ZMF4|Q86SL9|Q8IZF1	Missense_Mutation	SNP	ENST00000333493.4	37	CCDS10786.1	.	.	.	.	.	.	.	.	.	.	T	16.44	3.123970	0.56613	.	.	ENSG00000182885	ENST00000333493;ENST00000450388	T;T	0.32515	1.45;1.53	5.53	0.014	0.14098	.	.	.	.	.	T	0.23886	0.0578	L	0.27053	0.805	0.09310	N	1	D	0.54397	0.966	P	0.47299	0.543	T	0.14559	-1.0468	9	0.66056	D	0.02	.	6.7486	0.23475	0.3918:0.0:0.1045:0.5037	.	545	Q86Y34	GPR97_HUMAN	P	545;425	ENSP00000332900:S545P;ENSP00000404803:S425P	ENSP00000332900:S545P	S	+	1	0	GPR97	56279857	0.000000	0.05858	0.000000	0.03702	0.137000	0.21094	-0.129000	0.10515	-0.306000	0.08818	0.459000	0.35465	TCC		0.557	GPR97-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257333.2	NM_170776	
KIFC3	3801	broad.mit.edu	37	16	57799480	57799480	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr16:57799480G>A	ENST00000379655.4	-	11	1660	c.1403C>T	c.(1402-1404)gCt>gTt	p.A468V	KIFC3_ENST00000543930.1_Missense_Mutation_p.A329V|KIFC3_ENST00000465878.2_Missense_Mutation_p.A329V|KIFC3_ENST00000540079.2_Missense_Mutation_p.A366V|KIFC3_ENST00000539578.1_Missense_Mutation_p.A410V|KIFC3_ENST00000541240.1_Missense_Mutation_p.A490V|KIFC3_ENST00000421376.2_Missense_Mutation_p.A329V|KIFC3_ENST00000562903.1_Missense_Mutation_p.A329V|KIFC3_ENST00000445690.2_Missense_Mutation_p.A468V	NM_005550.3	NP_005541.3	Q9BVG8	KIFC3_HUMAN	kinesin family member C3	468	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				ATP catabolic process (GO:0006200)|epithelial cell-cell adhesion (GO:0090136)|Golgi organization (GO:0007030)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|visual perception (GO:0007601)|zonula adherens maintenance (GO:0045218)	centrosome (GO:0005813)|cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|kinesin complex (GO:0005871)|membrane (GO:0016020)|microtubule (GO:0005874)|zonula adherens (GO:0005915)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)	p.A468V(1)		breast(2)|central_nervous_system(3)|endometrium(4)|large_intestine(3)|lung(6)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	23		all_neural(199;0.224)				GAAAGTCACAGCATTGGTGGC	0.587																																					p.A468V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1403T	16						.						169.0	105.0	127.0					16																	57799480		2197	4300	6497	56356981	SO:0001583	missense	3801	exon11			BC001211	CCDS10789.2, CCDS45493.1, CCDS45494.1	16q13-q21	2008-02-05			ENSG00000140859	ENSG00000140859		"""Kinesins"""	6326	protein-coding gene	gene with protein product		604535				9782090	Standard	NM_001130099		Approved		uc002emp.3	Q9BVG8	OTTHUMG00000133455	ENST00000379655.4:c.1403C>T	16.37:g.57799480G>A	ENSP00000368976:p.Ala468Val	Somatic		Capture	Illumina HiSeq	Phase_I	56356981	NM_001130100	A8K6S2|B7Z484|O75299|Q49A29|Q49AQ0|Q59G19|Q8IUT3|Q96HW6	Missense_Mutation	SNP	ENST00000379655.4	37	CCDS10789.2	.	.	.	.	.	.	.	.	.	.	G	0.014	-1.582182	0.00879	.	.	ENSG00000140859	ENST00000379655;ENST00000445690;ENST00000421376;ENST00000541240;ENST00000540079;ENST00000543930;ENST00000539578	T;T;T;T;T;T;T	0.73469	-0.75;-0.75;-0.75;-0.75;-0.75;-0.75;-0.75	5.4	3.46	0.39613	Kinesin, motor domain (4);	0.516885	0.22773	N	0.055813	T	0.38904	0.1058	N	0.01297	-0.9	0.09310	N	1	B;B;B;B;B;B;B	0.16396	0.003;0.017;0.005;0.002;0.001;0.009;0.004	B;B;B;B;B;B;B	0.10450	0.003;0.003;0.003;0.001;0.002;0.005;0.005	T	0.37454	-0.9705	10	0.02654	T	1	.	8.3689	0.32404	0.2365:0.0:0.7635:0.0	.	490;410;329;366;173;468;329	B7Z484;F5H4I9;B7Z896;F5H3M2;B7Z3I6;Q9BVG8;A8K6S2	.;.;.;.;.;KIFC3_HUMAN;.	V	468;468;329;490;366;329;410	ENSP00000368976:A468V;ENSP00000401696:A468V;ENSP00000396399:A329V;ENSP00000442008:A490V;ENSP00000438805:A366V;ENSP00000444012:A329V;ENSP00000444884:A410V	ENSP00000368976:A468V	A	-	2	0	KIFC3	56356981	0.220000	0.23631	0.320000	0.25306	0.001000	0.01503	2.811000	0.47986	0.677000	0.31305	-0.140000	0.14226	GCT		0.587	KIFC3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257329.2	NM_005550	
USB1	79650	broad.mit.edu	37	16	58043956	58043956	+	Missense_Mutation	SNP	G	G	A	rs199886884		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr16:58043956G>A	ENST00000563149.1	+	3	453	c.389G>A	c.(388-390)cGc>cAc	p.R130H	USB1_ENST00000561743.1_Missense_Mutation_p.R79H|USB1_ENST00000423271.3_Missense_Mutation_p.R130H|USB1_ENST00000219281.3_Missense_Mutation_p.R130H|USB1_ENST00000565662.1_3'UTR|USB1_ENST00000539737.2_Missense_Mutation_p.R130H	NM_001204911.1	NP_001191840.1			U6 snRNA biogenesis 1									p.R130H(1)									GTGGTTCTGCGCCACCACTGG	0.592													G|||	0	0.0	0.0	0.0	5008	,	,		15332	0.0		0.0	False		,,,				2504	0.0				p.R130H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G389A	16						.						170.0	128.0	142.0					16																	58043956		2198	4300	6498	56601457	SO:0001583	missense	79650	exon3			AK023216	CCDS10791.1, CCDS55997.1, CCDS55998.1	16q13	2014-09-17	2012-08-21	2012-08-21	ENSG00000103005	ENSG00000103005			25792	protein-coding gene	gene with protein product	"""HVSL motif containing 1"", ""poikiloderma with neutropenia"", ""U six biogenesis 1"", ""mutated in poikiloderma with neutropenia protein 1"""	613276	"""chromosome 16 open reading frame 57"""	C16orf57		20004881, 20503306, 22899009	Standard	NM_024598		Approved	FLJ13154, HVSL1, Mpn1	uc002emz.3	Q9BQ65	OTTHUMG00000133456	ENST00000563149.1:c.389G>A	16.37:g.58043956G>A	ENSP00000454692:p.Arg130His	Somatic		Capture	Illumina HiSeq	Phase_I	56601457	NM_024598		Missense_Mutation	SNP	ENST00000563149.1	37		1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	G	35	5.414500	0.96092	.	.	ENSG00000103005	ENST00000219281;ENST00000543731;ENST00000539737;ENST00000423271	T;T;T	0.59364	0.96;0.27;0.27	5.34	5.34	0.76211	.	0.000000	0.85682	D	0.000000	T	0.77831	0.4189	M	0.81239	2.535	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.87578	0.989;0.998;0.991	T	0.78715	-0.2096	10	0.46703	T	0.11	-22.3439	18.0258	0.89269	0.0:0.0:1.0:0.0	.	130;130;130	B4DZW5;B4DWE3;Q9BQ65	.;.;CP057_HUMAN	H	130;78;130;130	ENSP00000219281:R130H;ENSP00000446143:R130H;ENSP00000409792:R130H	ENSP00000219281:R130H	R	+	2	0	C16orf57	56601457	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.969000	0.70422	2.490000	0.84030	0.655000	0.94253	CGC		0.592	USB1-003	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000429953.1	NM_024598	
CDH11	1009	broad.mit.edu	37	16	65016004	65016004	+	Silent	SNP	G	G	A	rs180715892		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr16:65016004G>A	ENST00000268603.4	-	8	1815	c.1200C>T	c.(1198-1200)acC>acT	p.T400T	CDH11_ENST00000394156.3_Silent_p.T400T|CDH11_ENST00000566827.1_Silent_p.T274T	NM_001797.2	NP_001788.2	P55287	CAD11_HUMAN	cadherin 11, type 2, OB-cadherin (osteoblast)	400	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				adherens junction organization (GO:0034332)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|corticospinal tract morphogenesis (GO:0021957)|homophilic cell adhesion (GO:0007156)|ossification (GO:0001503)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.T400T(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(5)|kidney(5)|large_intestine(19)|lung(40)|ovary(3)|prostate(3)|skin(2)|urinary_tract(2)	88		Ovarian(137;0.0973)		OV - Ovarian serous cystadenocarcinoma(108;0.205)		TCCCAACCACGGTGCCAGCAG	0.498			T	USP6	aneurysmal bone cysts					TSP Lung(24;0.17)			G|||	1	0.000199681	0.0	0.0014	5008	,	,		17216	0.0		0.0	False		,,,				2504	0.0				p.T400T			Dom	yes		16	16q22.1	1009	"""cadherin 11, type 2, OB-cadherin (osteoblast)"""		M	.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1200T	16						.	G		1,4405	2.1+/-5.4	0,1,2202	134.0	120.0	125.0		1200	-9.2	0.5	16		125	0,8600		0,0,4300	no	coding-synonymous	CDH11	NM_001797.2		0,1,6502	AA,AG,GG		0.0,0.0227,0.0077		400/797	65016004	1,13005	2203	4300	6503	63573505	SO:0001819	synonymous_variant	1009	exon8			D21255	CCDS10803.1	16q21	2010-01-26			ENSG00000140937	ENSG00000140937		"""Cadherins / Major cadherins"""	1750	protein-coding gene	gene with protein product	"""OB-Cadherin"""	600023				9615235	Standard	NM_001797		Approved	OB, CAD11	uc002eoi.3	P55287	OTTHUMG00000137494	ENST00000268603.4:c.1200C>T	16.37:g.65016004G>A		Somatic		Capture	Illumina HiSeq	Phase_I	63573505	NM_001797	A8K5D6|A8MZC8|B7WP28|Q15065|Q15066|Q9UQ93|Q9UQ94	Silent	SNP	ENST00000268603.4	37	CCDS10803.1																																																																																				0.498	CDH11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268755.1	NM_033664	
CMTM1	113540	broad.mit.edu	37	16	66600453	66600453	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr16:66600453G>T	ENST00000457188.2	+	1	158	c.37G>T	c.(37-39)Gca>Tca	p.A13S	CMTM1_ENST00000336328.6_Missense_Mutation_p.A13S|CMTM1_ENST00000533953.1_Missense_Mutation_p.A13S|CMTM1_ENST00000379500.2_Missense_Mutation_p.A13S|CMTM1_ENST00000328020.6_Missense_Mutation_p.A13S|CMTM1_ENST00000531885.1_Missense_Mutation_p.A13S|CMTM1_ENST00000332695.7_Missense_Mutation_p.A13S|CMTM1_ENST00000528324.1_Missense_Mutation_p.A13S|CMTM1_ENST00000535705.1_Missense_Mutation_p.A13S|CMTM1_ENST00000529506.1_5'UTR|CKLF-CMTM1_ENST00000527729.1_Intron|CMTM1_ENST00000533666.1_Missense_Mutation_p.A13S	NM_181269.2	NP_851786.1	Q8IZ96	CKLF1_HUMAN	CKLF-like MARVEL transmembrane domain containing 1	13					chemotaxis (GO:0006935)	extracellular space (GO:0005615)|integral component of membrane (GO:0016021)		p.A13S(1)		breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(2)	7		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0702)|Epithelial(162;0.222)		GTCATCCGAGGCACCTTCAGG	0.622																																					p.A13S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G37T	16						.						89.0	72.0	78.0					16																	66600453		2201	4300	6501	65157954	SO:0001583	missense	113540	exon1			AF278577	CCDS10810.1, CCDS10811.1, CCDS10812.2, CCDS45503.1, CCDS45504.1, CCDS54019.1, CCDS54020.1, CCDS54021.1	16q22.1	2009-10-06	2005-11-08	2005-11-08	ENSG00000089505	ENSG00000089505			19172	protein-coding gene	gene with protein product		607884	"""chemokine-like factor super family 1"", ""chemokine-like factor superfamily 1"""	CKLFSF1		12782130	Standard	NM_181268		Approved	CKLFH1a, CKLFH	uc002epr.4	Q8IZ96	OTTHUMG00000137502	ENST00000457188.2:c.37G>T	16.37:g.66600453G>T	ENSP00000405729:p.Ala13Ser	Somatic		Capture	Illumina HiSeq	Phase_I	65157954	NM_181296	Q2PPY5|Q6PEV5|Q8IU76|Q8IU83|Q8IU86|Q8IU93|Q8IZ87|Q8IZ88|Q8IZ89|Q8IZ90|Q8IZ91|Q8IZ92|Q8IZ93|Q8IZ94|Q8IZ95|Q96JC2|Q96JC3	Missense_Mutation	SNP	ENST00000457188.2	37	CCDS45503.1	.	.	.	.	.	.	.	.	.	.	G	9.263	1.043807	0.19748	.	.	ENSG00000089505	ENST00000535705;ENST00000332695;ENST00000336328;ENST00000528324;ENST00000531885;ENST00000457188;ENST00000533666;ENST00000533953;ENST00000379500;ENST00000328020;ENST00000379490	T;T;T;T;T;T;T;T;T;T	0.69926	-0.2;0.58;0.57;1.81;0.32;1.6;-0.44;0.48;1.18;1.27	3.73	-2.16	0.07080	.	.	.	.	.	T	0.42585	0.1209	.	.	.	0.09310	N	1	B;P;P;P;P;B;P;B;P	0.41041	0.395;0.582;0.582;0.582;0.582;0.244;0.582;0.244;0.736	B;B;B;B;B;B;B;B;B	0.35655	0.112;0.207;0.207;0.207;0.207;0.038;0.207;0.063;0.207	T	0.30060	-0.9991	8	0.32370	T	0.25	4.7784	1.4481	0.02368	0.1888:0.3127:0.3388:0.1598	.	13;13;13;13;13;13;13;13;13	E9PIL3;Q6PEV5;E9PAX0;Q8IZ96-5;Q8IZ96-6;Q8IZ96-7;Q8IZ96;Q8IZ96-4;Q8IZ96-15	.;.;.;.;.;.;CKLF1_HUMAN;.;.	S	13	ENSP00000443374:A13S;ENSP00000331428:A13S;ENSP00000337119:A13S;ENSP00000432398:A13S;ENSP00000432687:A13S;ENSP00000405729:A13S;ENSP00000435020:A13S;ENSP00000435786:A13S;ENSP00000368814:A13S;ENSP00000330061:A13S	ENSP00000330061:A13S	A	+	1	0	CMTM1	65157954	0.000000	0.05858	0.000000	0.03702	0.019000	0.09904	-0.946000	0.03905	-0.340000	0.08388	0.603000	0.83216	GCA		0.622	CMTM1-015	NOVEL	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000390261.2	NM_052999	
CES3	23491	broad.mit.edu	37	16	66997155	66997155	+	Silent	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr16:66997155C>T	ENST00000303334.4	+	2	227	c.156C>T	c.(154-156)ggC>ggT	p.G52G	RP11-361L15.4_ENST00000566869.1_RNA|CES3_ENST00000394037.1_Silent_p.G52G	NM_024922.5	NP_079198.2	Q6UWW8	EST3_HUMAN	carboxylesterase 3	52						endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)	carboxylic ester hydrolase activity (GO:0052689)	p.G52G(1)		breast(1)|central_nervous_system(2)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(4)|lung(6)|ovary(3)|skin(1)	24		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0488)|Epithelial(162;0.127)		GCGTGAAGGGCACAGACCGCC	0.647																																					p.G52G												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C156T	16						.						77.0	79.0	78.0					16																	66997155		2200	4300	6500	65554656	SO:0001819	synonymous_variant	23491	exon2			AK025389	CCDS10826.1, CCDS54022.1, CCDS54023.1	16q22.1	2014-05-13	2008-07-25		ENSG00000172828	ENSG00000172828		"""Carboxylesterases"""	1865	protein-coding gene	gene with protein product	"""esterase 31"", ""brain carboxylesterase BR3"""	605279	"""carboxylesterase 3 (brain)"""			10518925, 14581373, 15100172, 20931200	Standard	NM_001185176		Approved	FLJ21736, ES31	uc002eqt.3	Q6UWW8	OTTHUMG00000137525	ENST00000303334.4:c.156C>T	16.37:g.66997155C>T		Somatic		Capture	Illumina HiSeq	Phase_I	65554656	NM_001185177	B2Z3W9|F5H242|Q7Z6J1|Q9H6X7	Silent	SNP	ENST00000303334.4	37	CCDS10826.1																																																																																				0.647	CES3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000268848.1	NM_024922	
E2F4	1874	broad.mit.edu	37	16	67226189	67226189	+	Missense_Mutation	SNP	A	A	C			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr16:67226189A>C	ENST00000379378.3	+	1	118	c.59A>C	c.(58-60)aAg>aCg	p.K20T	EXOC3L1_ENST00000562887.1_5'Flank|EXOC3L1_ENST00000314586.6_5'Flank	NM_001950.3	NP_001941.2	Q16254	E2F4_HUMAN	E2F transcription factor 4, p107/p130-binding	20					blood circulation (GO:0008015)|cell volume homeostasis (GO:0006884)|cilium assembly (GO:0042384)|epithelial cell development (GO:0002064)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|organ morphogenesis (GO:0009887)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of cell proliferation (GO:0042127)|regulation of cell size (GO:0008361)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|protein domain specific binding (GO:0019904)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)	p.K20T(1)		breast(4)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(2)	11		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.000697)|Epithelial(162;0.00303)|all cancers(182;0.0325)		CGGCACGAAAAGAGCCTGGGA	0.721																																					p.K20T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A59C	16						.						23.0	20.0	21.0					16																	67226189		2190	4294	6484	65783690	SO:0001583	missense	1874	exon1			BC021050	CCDS32464.1	16q22.1	2014-05-06			ENSG00000205250	ENSG00000205250			3118	protein-coding gene	gene with protein product		600659				7958924, 7892279	Standard	NM_001950		Approved	E2F-4	uc002erz.3	Q16254	OTTHUMG00000172975	ENST00000379378.3:c.59A>C	16.37:g.67226189A>C	ENSP00000368686:p.Lys20Thr	Somatic		Capture	Illumina HiSeq	Phase_I	65783690	NM_001950	A6NGR8|B5BU56|Q12991|Q15328	Missense_Mutation	SNP	ENST00000379378.3	37	CCDS32464.1	.	.	.	.	.	.	.	.	.	.	A	14.84	2.656011	0.47467	.	.	ENSG00000205250	ENST00000379378	T	0.11712	2.75	4.55	4.55	0.56014	Transcription factor E2F/dimerisation partner (TDP) (1);Winged helix-turn-helix transcription repressor DNA-binding (1);	0.047521	0.85682	D	0.000000	T	0.23171	0.0560	L	0.39326	1.205	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.00728	-1.1591	10	0.44086	T	0.13	-13.3585	13.1726	0.59606	1.0:0.0:0.0:0.0	.	20	Q16254	E2F4_HUMAN	T	20	ENSP00000368686:K20T	ENSP00000368686:K20T	K	+	2	0	E2F4	65783690	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	8.663000	0.91134	2.044000	0.60594	0.533000	0.62120	AAG		0.721	E2F4-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000421565.1	NM_001950	
FHOD1	29109	broad.mit.edu	37	16	67265246	67265246	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr16:67265246C>T	ENST00000258201.4	-	17	2759	c.2512G>A	c.(2512-2514)Ggc>Agc	p.G838S		NM_013241.2	NP_037373.2	Q9Y613	FHOD1_HUMAN	formin homology 2 domain containing 1	838	FH2. {ECO:0000255|PROSITE- ProRule:PRU00774}.				positive regulation of stress fiber assembly (GO:0051496)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|membrane (GO:0016020)|nucleus (GO:0005634)	identical protein binding (GO:0042802)	p.G838S(1)		breast(4)|endometrium(3)|kidney(3)|large_intestine(5)|lung(7)|ovary(3)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	34		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.000691)|Epithelial(162;0.00462)|all cancers(182;0.0434)		AGCTCAAAGCCGCTGCTCTGA	0.587																																					p.G838S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2512A	16						.						85.0	80.0	82.0					16																	67265246		2198	4300	6498	65822747	SO:0001583	missense	29109	exon17			AF113615	CCDS10834.1	16q22	2008-02-22			ENSG00000135723	ENSG00000135723			17905	protein-coding gene	gene with protein product		606881				10352228, 16112087	Standard	NM_013241		Approved	FHOS	uc002esl.3	Q9Y613	OTTHUMG00000137521	ENST00000258201.4:c.2512G>A	16.37:g.67265246C>T	ENSP00000258201:p.Gly838Ser	Somatic		Capture	Illumina HiSeq	Phase_I	65822747	NM_013241	Q59F76|Q6Y1F2|Q76MS8|Q8N521	Missense_Mutation	SNP	ENST00000258201.4	37	CCDS10834.1	.	.	.	.	.	.	.	.	.	.	C	23.5	4.422238	0.83559	.	.	ENSG00000135723	ENST00000258201	D	0.86865	-2.18	5.39	4.42	0.53409	Actin-binding FH2/DRF autoregulatory (1);Actin-binding FH2 (3);	0.000000	0.85682	D	0.000000	D	0.93478	0.7919	M	0.86268	2.805	0.80722	D	1	D	0.76494	0.999	D	0.74674	0.984	D	0.94226	0.7472	10	0.87932	D	0	.	13.9406	0.64052	0.1533:0.8467:0.0:0.0	.	838	Q9Y613	FHOD1_HUMAN	S	838	ENSP00000258201:G838S	ENSP00000258201:G838S	G	-	1	0	FHOD1	65822747	1.000000	0.71417	0.992000	0.48379	0.985000	0.73830	7.818000	0.86416	1.229000	0.43630	0.561000	0.74099	GGC		0.587	FHOD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268844.2		
FHOD1	29109	broad.mit.edu	37	16	67270509	67270509	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr16:67270509T>C	ENST00000258201.4	-	11	1517	c.1270A>G	c.(1270-1272)Atc>Gtc	p.I424V		NM_013241.2	NP_037373.2	Q9Y613	FHOD1_HUMAN	formin homology 2 domain containing 1	424	GBD/FH3. {ECO:0000255|PROSITE- ProRule:PRU00579}.				positive regulation of stress fiber assembly (GO:0051496)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|membrane (GO:0016020)|nucleus (GO:0005634)	identical protein binding (GO:0042802)	p.I424V(1)		breast(4)|endometrium(3)|kidney(3)|large_intestine(5)|lung(7)|ovary(3)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	34		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.000691)|Epithelial(162;0.00462)|all cancers(182;0.0434)		GCCACAGAGATGGTAGGAAAA	0.627																																					p.I424V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A1270G	16						.						47.0	46.0	46.0					16																	67270509		2198	4300	6498	65828010	SO:0001583	missense	29109	exon11			AF113615	CCDS10834.1	16q22	2008-02-22			ENSG00000135723	ENSG00000135723			17905	protein-coding gene	gene with protein product		606881				10352228, 16112087	Standard	NM_013241		Approved	FHOS	uc002esl.3	Q9Y613	OTTHUMG00000137521	ENST00000258201.4:c.1270A>G	16.37:g.67270509T>C	ENSP00000258201:p.Ile424Val	Somatic		Capture	Illumina HiSeq	Phase_I	65828010	NM_013241	Q59F76|Q6Y1F2|Q76MS8|Q8N521	Missense_Mutation	SNP	ENST00000258201.4	37	CCDS10834.1	.	.	.	.	.	.	.	.	.	.	T	11.30	1.597037	0.28445	.	.	ENSG00000135723	ENST00000258201	T	0.21932	1.98	5.49	-2.81	0.05805	GTPase-binding/formin homology 3 (1);	1.046230	0.07554	N	0.915959	T	0.10337	0.0253	N	0.19112	0.55	0.09310	N	0.999999	B	0.02656	0.0	B	0.01281	0.0	T	0.35822	-0.9773	10	0.27785	T	0.31	.	3.009	0.06038	0.1197:0.161:0.4604:0.2588	.	424	Q9Y613	FHOD1_HUMAN	V	424	ENSP00000258201:I424V	ENSP00000258201:I424V	I	-	1	0	FHOD1	65828010	0.259000	0.24043	0.429000	0.26710	0.914000	0.54420	0.057000	0.14279	-0.123000	0.11745	0.459000	0.35465	ATC		0.627	FHOD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268844.2		
PLEKHG4	25894	broad.mit.edu	37	16	67319312	67319312	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr16:67319312G>A	ENST00000360461.5	+	13	4850	c.2315G>A	c.(2314-2316)cGc>cAc	p.R772H	PLEKHG4_ENST00000450733.1_Missense_Mutation_p.R691H|PLEKHG4_ENST00000379344.3_Missense_Mutation_p.R772H|PLEKHG4_ENST00000427155.2_Missense_Mutation_p.R772H	NM_001129727.1|NM_015432.3	NP_001123199.1|NP_056247.1	Q58EX7	PKHG4_HUMAN	pleckstrin homology domain containing, family G (with RhoGef domain) member 4	772	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.						Rho guanyl-nucleotide exchange factor activity (GO:0005089)	p.R772H(1)		central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(14)|ovary(2)|pancreas(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	37				OV - Ovarian serous cystadenocarcinoma(108;0.00376)|Epithelial(162;0.0173)|all cancers(182;0.116)|Kidney(780;0.119)		CAGGGCCTCCGCGGTCAGCGT	0.632																																					p.R772H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2315A	16						.						95.0	102.0	100.0					16																	67319312		2198	4300	6498	65876813	SO:0001583	missense	25894	exon15			AK024475	CCDS32466.1, CCDS45512.1	16q22.1	2013-01-11						"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	24501	protein-coding gene	gene with protein product	"""puratrophin-1"""	609526	"""spinocerebellar ataxia 4"""	SCA4		16491300, 16001362	Standard	NM_015432		Approved	DKFZP434I216, ARHGEF44	uc010cef.3	Q58EX7		ENST00000360461.5:c.2315G>A	16.37:g.67319312G>A	ENSP00000353646:p.Arg772His	Somatic		Capture	Illumina HiSeq	Phase_I	65876813	NM_001129727	Q4G0J8|Q4H485|Q56A69|Q9H7K4|Q9UFW0	Missense_Mutation	SNP	ENST00000360461.5	37	CCDS32466.1	.	.	.	.	.	.	.	.	.	.	G	34	5.339348	0.95783	.	.	ENSG00000196155	ENST00000360461;ENST00000427155;ENST00000379344;ENST00000450733	T;T;T;T	0.63417	-0.04;-0.04;-0.04;-0.04	4.91	4.91	0.64330	Dbl homology (DH) domain (5);	0.000000	0.33834	N	0.004504	T	0.81828	0.4905	M	0.87456	2.885	0.58432	D	0.999995	D;D	0.89917	1.0;1.0	D;D	0.97110	0.999;1.0	D	0.84592	0.0667	10	0.52906	T	0.07	.	17.0854	0.86610	0.0:0.0:1.0:0.0	.	691;772	Q58EX7-2;Q58EX7	.;PKHG4_HUMAN	H	772;772;772;691	ENSP00000353646:R772H;ENSP00000401118:R772H;ENSP00000368649:R772H;ENSP00000398030:R691H	ENSP00000353646:R772H	R	+	2	0	PLEKHG4	65876813	1.000000	0.71417	1.000000	0.80357	0.648000	0.38561	9.809000	0.99208	2.290000	0.77057	0.561000	0.74099	CGC		0.632	PLEKHG4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000421395.2	NM_015432	
SLC12A4	6560	broad.mit.edu	37	16	67991926	67991926	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr16:67991926T>C	ENST00000316341.3	-	4	504	c.364A>G	c.(364-366)Atg>Gtg	p.M122V	SLC12A4_ENST00000576616.1_Missense_Mutation_p.M122V|SLC12A4_ENST00000572037.1_Missense_Mutation_p.M74V|SLC12A4_ENST00000338335.3_Missense_Mutation_p.M122V|SLC12A4_ENST00000537830.2_Missense_Mutation_p.M116V|SLC12A4_ENST00000422611.2_Missense_Mutation_p.M124V|SLC12A4_ENST00000572010.1_5'UTR|SLC12A4_ENST00000541864.2_Missense_Mutation_p.M91V	NM_001145961.1|NM_005072.4	NP_001139433.1|NP_005063.1	Q9UP95	S12A4_HUMAN	solute carrier family 12 (potassium/chloride transporter), member 4	122					cell volume homeostasis (GO:0006884)|chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|ion transport (GO:0006811)|potassium ion transport (GO:0006813)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|plasma membrane (GO:0005886)	potassium:chloride symporter activity (GO:0015379)|protein kinase binding (GO:0019901)	p.M122V(1)		breast(3)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(3)|lung(2)|ovary(2)|prostate(4)|skin(2)|urinary_tract(3)	29		Ovarian(137;0.192)		OV - Ovarian serous cystadenocarcinoma(108;0.0042)|Epithelial(162;0.0185)|all cancers(182;0.121)	Bumetanide(DB00887)|Potassium Chloride(DB00761)	TACACCCCCATGAGGGTGCCC	0.597																																					p.M91V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A271G	16						.						68.0	61.0	64.0					16																	67991926		2198	4300	6498	66549427	SO:0001583	missense	6560	exon4				CCDS10855.1, CCDS54030.1, CCDS54031.1, CCDS54032.1	16q22.1	2013-07-18	2013-07-18		ENSG00000124067	ENSG00000124067		"""Solute carriers"""	10913	protein-coding gene	gene with protein product		604119				8663127	Standard	NM_005072		Approved	KCC1	uc010ceu.2	Q9UP95	OTTHUMG00000137535	ENST00000316341.3:c.364A>G	16.37:g.67991926T>C	ENSP00000318557:p.Met122Val	Somatic		Capture	Illumina HiSeq	Phase_I	66549427	NM_001145964	B4DF69|B4DR04|B4DZ82|B7ZAV0|F5H066|F5H0S9|F5H3C0|O60632|O75893|Q13953|Q96LD5	Missense_Mutation	SNP	ENST00000316341.3	37	CCDS10855.1	.	.	.	.	.	.	.	.	.	.	T	22.8	4.337041	0.81801	.	.	ENSG00000124067	ENST00000422611;ENST00000541864;ENST00000537830;ENST00000338335;ENST00000316341	D;D;D;D;D	0.88509	-1.86;-1.85;-1.85;-2.39;-1.86	4.92	4.92	0.64577	.	0.000000	0.85682	D	0.000000	D	0.93255	0.7851	M	0.72118	2.19	0.80722	D	1	B;B;P;D;B;B;B	0.57571	0.02;0.017;0.946;0.98;0.007;0.007;0.007	B;B;D;D;B;B;B	0.70227	0.07;0.016;0.968;0.968;0.022;0.022;0.01	D	0.92786	0.6244	10	0.39692	T	0.17	.	14.848	0.70275	0.0:0.0:0.0:1.0	.	124;122;91;74;116;122;122	F5H3C0;B4DF30;F5H066;B4DF69;F5H0S9;Q9UP95-2;Q9UP95	.;.;.;.;.;.;S12A4_HUMAN	V	124;91;116;122;122	ENSP00000395983:M124V;ENSP00000438334:M91V;ENSP00000445962:M116V;ENSP00000343374:M122V;ENSP00000318557:M122V	ENSP00000318557:M122V	M	-	1	0	SLC12A4	66549427	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.997000	0.88414	1.974000	0.57490	0.482000	0.46254	ATG		0.597	SLC12A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268864.4	NM_005072	
CDH1	999	broad.mit.edu	37	16	68835711	68835711	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr16:68835711A>G	ENST00000261769.5	+	3	493	c.302A>G	c.(301-303)tAc>tGc	p.Y101C	CDH1_ENST00000562836.1_3'UTR|CDH1_ENST00000422392.2_Missense_Mutation_p.Y101C	NM_004360.3	NP_004351.1	P12830	CADH1_HUMAN	cadherin 1, type 1, E-cadherin (epithelial)	101					adherens junction organization (GO:0034332)|apoptotic process (GO:0006915)|calcium-dependent cell-cell adhesion (GO:0016339)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to amino acid stimulus (GO:0071230)|cellular response to indole-3-methanol (GO:0071681)|cellular response to lithium ion (GO:0071285)|cochlea development (GO:0090102)|epithelial cell morphogenesis (GO:0003382)|establishment of protein localization to plasma membrane (GO:0090002)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|homophilic cell adhesion (GO:0007156)|intestinal epithelial cell development (GO:0060576)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of epithelial cell proliferation (GO:0050680)|neuron projection development (GO:0031175)|pituitary gland development (GO:0021983)|positive regulation of transcription factor import into nucleus (GO:0042993)|positive regulation of transcription, DNA-templated (GO:0045893)|protein homooligomerization (GO:0051260)|protein localization to plasma membrane (GO:0072659)|protein metabolic process (GO:0019538)|regulation of branching involved in salivary gland morphogenesis (GO:0060693)|regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043281)|regulation of immune response (GO:0050776)|regulation of neuron migration (GO:2001222)|regulation of protein localization to cell surface (GO:2000008)|regulation of water loss via skin (GO:0033561)|response to drug (GO:0042493)|response to toxic substance (GO:0009636)|salivary gland cavitation (GO:0060662)|sensory perception of sound (GO:0007605)|single organismal cell-cell adhesion (GO:0016337)|synapse assembly (GO:0007416)|tight junction assembly (GO:0070830)|trophectodermal cell differentiation (GO:0001829)	actin cytoskeleton (GO:0015629)|aggresome (GO:0016235)|apical junction complex (GO:0043296)|apical part of cell (GO:0045177)|axon terminus (GO:0043679)|basolateral plasma membrane (GO:0016323)|catenin complex (GO:0016342)|cell junction (GO:0030054)|cell surface (GO:0009986)|cell-cell adherens junction (GO:0005913)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|endosome (GO:0005768)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|lateral loop (GO:0043219)|lateral plasma membrane (GO:0016328)|node of Ranvier (GO:0033268)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|Schmidt-Lanterman incisure (GO:0043220)|trans-Golgi network (GO:0005802)	ankyrin binding (GO:0030506)|beta-catenin binding (GO:0008013)|calcium ion binding (GO:0005509)|cell adhesion molecule binding (GO:0050839)|gamma-catenin binding (GO:0045295)|glycoprotein binding (GO:0001948)|GTPase activating protein binding (GO:0032794)	p.?(2)|p.Y101C(1)		NS(6)|biliary_tract(8)|breast(161)|central_nervous_system(4)|endometrium(9)|kidney(4)|large_intestine(13)|lung(13)|oesophagus(3)|ovary(2)|prostate(3)|soft_tissue(2)|stomach(76)|thyroid(1)|upper_aerodigestive_tract(3)|urinary_tract(3)	311		all_neural(199;0.0189)|Ovarian(137;0.0563)		Epithelial(162;8.44e-05)|all cancers(182;0.000404)|OV - Ovarian serous cystadenocarcinoma(108;0.000426)|BRCA - Breast invasive adenocarcinoma(181;0.0261)		TTCTTGGTCTACGCCTGGGAC	0.507			"""Mis, N, F, S"""		"""lobular breast, gastric"""	gastric			Hereditary Diffuse Gastric Cancer																												p.Y101C		yes	Rec	yes	Familial gastric carcinoma	16	16q22.1	999	"""cadherin 1, type 1, E-cadherin (epithelial) (ECAD)"""		E	.	.	3	Unknown(2)|Substitution - Missense(1)	breast(2)|large_intestine(1)	c.A302G	16						.						143.0	130.0	135.0					16																	68835711		2198	4300	6498	67393212	SO:0001583	missense	999	exon3	Familial Cancer Database	HDGC	L08599	CCDS10869.1	16q22.1	2014-09-17			ENSG00000039068	ENSG00000039068		"""CD molecules"", ""Cadherins / Major cadherins"""	1748	protein-coding gene	gene with protein product	"""E-Cadherin"""	192090		UVO		9925936	Standard	NM_004360		Approved	uvomorulin, CD324	uc002ewg.1	P12830	OTTHUMG00000137561	ENST00000261769.5:c.302A>G	16.37:g.68835711A>G	ENSP00000261769:p.Tyr101Cys	Somatic		Capture	Illumina HiSeq	Phase_I	67393212	NM_004360	A8K1U7|Q13799|Q14216|Q15855|Q16194|Q4PJ14|Q9UII8	Missense_Mutation	SNP	ENST00000261769.5	37	CCDS10869.1	.	.	.	.	.	.	.	.	.	.	A	2.410	-0.335564	0.05278	.	.	ENSG00000039068	ENST00000261769;ENST00000379120;ENST00000268794;ENST00000422392	T;T	0.44881	0.91;0.91	5.43	3.1	0.35709	Cadherin prodomain-like (1);Cadherin-like (1);	0.546940	0.16467	N	0.213150	T	0.44912	0.1316	L	0.38175	1.15	0.21386	N	0.999708	P;D	0.63046	0.83;0.992	P;P	0.59948	0.796;0.866	T	0.21008	-1.0258	10	0.49607	T	0.09	.	5.6052	0.17374	0.6902:0.1553:0.1545:0.0	.	101;101	Q9UII8;P12830	.;CADH1_HUMAN	C	101	ENSP00000261769:Y101C;ENSP00000414946:Y101C	ENSP00000261769:Y101C	Y	+	2	0	CDH1	67393212	0.826000	0.29277	0.027000	0.17364	0.148000	0.21650	2.791000	0.47829	0.403000	0.25479	0.459000	0.35465	TAC		0.507	CDH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268897.2	NM_004360	
CDH1	999	broad.mit.edu	37	16	68853297	68853297	+	Silent	SNP	G	G	A	rs35741240	byFrequency	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr16:68853297G>A	ENST00000261769.5	+	11	1871	c.1680G>A	c.(1678-1680)acG>acA	p.T560T	CDH1_ENST00000562836.1_3'UTR|CDH1_ENST00000422392.2_Silent_p.T499T|RP11-354M1.2_ENST00000563916.1_RNA	NM_004360.3	NP_004351.1	P12830	CADH1_HUMAN	cadherin 1, type 1, E-cadherin (epithelial)	560	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				adherens junction organization (GO:0034332)|apoptotic process (GO:0006915)|calcium-dependent cell-cell adhesion (GO:0016339)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to amino acid stimulus (GO:0071230)|cellular response to indole-3-methanol (GO:0071681)|cellular response to lithium ion (GO:0071285)|cochlea development (GO:0090102)|epithelial cell morphogenesis (GO:0003382)|establishment of protein localization to plasma membrane (GO:0090002)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|homophilic cell adhesion (GO:0007156)|intestinal epithelial cell development (GO:0060576)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of epithelial cell proliferation (GO:0050680)|neuron projection development (GO:0031175)|pituitary gland development (GO:0021983)|positive regulation of transcription factor import into nucleus (GO:0042993)|positive regulation of transcription, DNA-templated (GO:0045893)|protein homooligomerization (GO:0051260)|protein localization to plasma membrane (GO:0072659)|protein metabolic process (GO:0019538)|regulation of branching involved in salivary gland morphogenesis (GO:0060693)|regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043281)|regulation of immune response (GO:0050776)|regulation of neuron migration (GO:2001222)|regulation of protein localization to cell surface (GO:2000008)|regulation of water loss via skin (GO:0033561)|response to drug (GO:0042493)|response to toxic substance (GO:0009636)|salivary gland cavitation (GO:0060662)|sensory perception of sound (GO:0007605)|single organismal cell-cell adhesion (GO:0016337)|synapse assembly (GO:0007416)|tight junction assembly (GO:0070830)|trophectodermal cell differentiation (GO:0001829)	actin cytoskeleton (GO:0015629)|aggresome (GO:0016235)|apical junction complex (GO:0043296)|apical part of cell (GO:0045177)|axon terminus (GO:0043679)|basolateral plasma membrane (GO:0016323)|catenin complex (GO:0016342)|cell junction (GO:0030054)|cell surface (GO:0009986)|cell-cell adherens junction (GO:0005913)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|endosome (GO:0005768)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|lateral loop (GO:0043219)|lateral plasma membrane (GO:0016328)|node of Ranvier (GO:0033268)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|Schmidt-Lanterman incisure (GO:0043220)|trans-Golgi network (GO:0005802)	ankyrin binding (GO:0030506)|beta-catenin binding (GO:0008013)|calcium ion binding (GO:0005509)|cell adhesion molecule binding (GO:0050839)|gamma-catenin binding (GO:0045295)|glycoprotein binding (GO:0001948)|GTPase activating protein binding (GO:0032794)	p.T560T(1)|p.?(1)		NS(6)|biliary_tract(8)|breast(161)|central_nervous_system(4)|endometrium(9)|kidney(4)|large_intestine(13)|lung(13)|oesophagus(3)|ovary(2)|prostate(3)|soft_tissue(2)|stomach(76)|thyroid(1)|upper_aerodigestive_tract(3)|urinary_tract(3)	311		all_neural(199;0.0189)|Ovarian(137;0.0563)		Epithelial(162;8.44e-05)|all cancers(182;0.000404)|OV - Ovarian serous cystadenocarcinoma(108;0.000426)|BRCA - Breast invasive adenocarcinoma(181;0.0261)		AGAACAGCACGTACACAGCCC	0.542			"""Mis, N, F, S"""		"""lobular breast, gastric"""	gastric			Hereditary Diffuse Gastric Cancer																												p.T560T		yes	Rec	yes	Familial gastric carcinoma	16	16q22.1	999	"""cadherin 1, type 1, E-cadherin (epithelial) (ECAD)"""		E	.	.	2	Unknown(1)|Substitution - coding silent(1)	large_intestine(1)|breast(1)	c.G1680A	16						.						106.0	85.0	92.0					16																	68853297		2198	4300	6498	67410798	SO:0001819	synonymous_variant	999	exon11	Familial Cancer Database	HDGC	L08599	CCDS10869.1	16q22.1	2014-09-17			ENSG00000039068	ENSG00000039068		"""CD molecules"", ""Cadherins / Major cadherins"""	1748	protein-coding gene	gene with protein product	"""E-Cadherin"""	192090		UVO		9925936	Standard	NM_004360		Approved	uvomorulin, CD324	uc002ewg.1	P12830	OTTHUMG00000137561	ENST00000261769.5:c.1680G>A	16.37:g.68853297G>A		Somatic		Capture	Illumina HiSeq	Phase_I	67410798	NM_004360	A8K1U7|Q13799|Q14216|Q15855|Q16194|Q4PJ14|Q9UII8	Silent	SNP	ENST00000261769.5	37	CCDS10869.1																																																																																				0.542	CDH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268897.2	NM_004360	
CLEC18C	283971	broad.mit.edu	37	16	70211271	70211271	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr16:70211271C>T	ENST00000569347.2	+	3	598	c.344C>T	c.(343-345)gCg>gTg	p.A115V	CLEC18C_ENST00000314151.8_Missense_Mutation_p.A115V|CLEC18C_ENST00000541793.2_Missense_Mutation_p.A115V|CLEC18C_ENST00000561612.1_Intron|CLEC18C_ENST00000536907.2_Missense_Mutation_p.A115V	NM_173619.2	NP_775890.2	Q8NCF0	CL18C_HUMAN	C-type lectin domain family 18, member C	115	SCP.					extracellular region (GO:0005576)	carbohydrate binding (GO:0030246)	p.A115V(1)		endometrium(3)|large_intestine(6)|lung(1)	10						CTGCTGCCCGCGGGCTTGGCG	0.662																																					p.A115V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C344T	16						.						49.0	57.0	54.0					16																	70211271		2196	4299	6495	68768772	SO:0001583	missense	283971	exon3			AL833339	CCDS32473.1	16q22.1	2010-04-27	2009-03-10	2009-03-10		ENSG00000157335		"""C-type lectin domain containing"""	28538	protein-coding gene	gene with protein product						12477932	Standard	XM_005255906		Approved	MGC34761		Q8NCF0		ENST00000569347.2:c.344C>T	16.37:g.70211271C>T	ENSP00000455920:p.Ala115Val	Somatic		Capture	Illumina HiSeq	Phase_I	68768772	NM_173619	Q8IUW8	Missense_Mutation	SNP	ENST00000569347.2	37	CCDS32473.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	N|N	0.480|0.480	-0.880119|-0.880119	0.02530|0.02530	.|.	.|.	ENSG00000157335|ENSG00000157335	ENST00000541793;ENST00000314151;ENST00000433156;ENST00000536907|ENST00000539438	T;T;T|.	0.08282|.	3.11;3.11;3.11|.	4.32|4.32	-8.63|-8.63	0.00878|0.00878	CAP domain (3);|.	2.079320|.	0.01636|.	N|.	0.023788|.	T|T	0.29158|0.29158	0.0725|0.0725	L|L	0.49778|0.49778	1.585|1.585	0.09310|0.09310	N|N	1|1	B|.	0.09022|.	0.002|.	B|.	0.06405|.	0.002|.	T|T	0.14643|0.14643	-1.0465|-1.0465	10|6	0.27785|0.38643	T|T	0.31|0.18	.|.	1.3459|1.3459	0.02163|0.02163	0.354:0.1611:0.0888:0.3961|0.354:0.1611:0.0888:0.3961	.|.	115|.	Q8NCF0|.	CL18C_HUMAN|.	V|W	115|112	ENSP00000444875:A115V;ENSP00000326538:A115V;ENSP00000444726:A115V|.	ENSP00000326538:A115V|ENSP00000445424:R112W	A|R	+|+	2|1	0|2	CLEC18C|CLEC18C	68768772|68768772	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.007000|0.007000	0.05969|0.05969	-6.990000|-6.990000	0.00047|0.00047	-4.194000|-4.194000	0.00066|0.00066	-0.887000|-0.887000	0.02937|0.02937	GCG|CGG		0.662	CLEC18C-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000434588.2	NM_173619	
ZNF821	55565	broad.mit.edu	37	16	71894204	71894204	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr16:71894204C>T	ENST00000565601.1	-	7	1363	c.956G>A	c.(955-957)cGg>cAg	p.R319Q	ZNF821_ENST00000564134.1_3'UTR|ZNF821_ENST00000446827.2_Missense_Mutation_p.R277Q|ZNF821_ENST00000425432.1_Missense_Mutation_p.R319Q|ATXN1L_ENST00000569119.1_Intron|ZNF821_ENST00000313565.6_Missense_Mutation_p.R277Q	NM_001201553.1	NP_001188482.1	O75541	ZN821_HUMAN	zinc finger protein 821	319					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.R277Q(1)		endometrium(1)|kidney(1)|large_intestine(5)|lung(4)|ovary(2)	13						CCGCTGCAGCCGGCGTGCCCG	0.677																																					p.R277Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G830A	16						.						26.0	27.0	27.0					16																	71894204		2196	4299	6495	70451705	SO:0001583	missense	55565	exon6			AF070588	CCDS32481.1, CCDS56006.1, CCDS73911.1	16q22.3	2008-05-02				ENSG00000102984		"""Zinc fingers, C2H2-type"""	28043	protein-coding gene	gene with protein product						8619474, 9110174	Standard	NM_017530		Approved		uc021tlb.1	O75541		ENST00000565601.1:c.956G>A	16.37:g.71894204C>T	ENSP00000455648:p.Arg319Gln	Somatic		Capture	Illumina HiSeq	Phase_I	70451705	NM_017530	A6NK48|B4DKK4|D3DWS3	Missense_Mutation	SNP	ENST00000565601.1	37	CCDS56006.1	.	.	.	.	.	.	.	.	.	.	C	35	5.557380	0.96514	.	.	ENSG00000102984	ENST00000425432;ENST00000313565;ENST00000446827	T;T;T	0.11169	4.41;2.8;2.8	5.97	5.97	0.96955	.	0.000000	0.85682	D	0.000000	T	0.32912	0.0845	L	0.60067	1.865	0.80722	D	1	D;D;D	0.71674	0.997;0.998;0.997	D;D;D	0.72982	0.968;0.979;0.968	T	0.00377	-1.1778	10	0.87932	D	0	-12.1548	20.4214	0.99039	0.0:1.0:0.0:0.0	.	319;277;319	B4DKK4;O75541-2;O75541	.;.;ZN821_HUMAN	Q	319;277;277	ENSP00000398089:R319Q;ENSP00000313822:R277Q;ENSP00000405908:R277Q	ENSP00000313822:R277Q	R	-	2	0	ZNF821	70451705	1.000000	0.71417	0.956000	0.39512	0.994000	0.84299	7.475000	0.81041	2.820000	0.97059	0.655000	0.94253	CGG		0.677	ZNF821-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434180.1	NM_017530	
ZFHX3	463	broad.mit.edu	37	16	72984449	72984449	+	Silent	SNP	A	A	G			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr16:72984449A>G	ENST00000268489.5	-	3	3807	c.3135T>C	c.(3133-3135)tgT>tgC	p.C1045C	ZFHX3_ENST00000397992.5_Silent_p.C131C	NM_006885.3	NP_008816.3	Q15911	ZFHX3_HUMAN	zinc finger homeobox 3	1045					brain development (GO:0007420)|cell cycle arrest (GO:0007050)|muscle organ development (GO:0007517)|negative regulation of myoblast differentiation (GO:0045662)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of myoblast differentiation (GO:0045663)|regulation of neuron differentiation (GO:0045664)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	mitochondrion (GO:0005739)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	enzyme binding (GO:0019899)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)	p.C1045C(1)		NS(3)|breast(7)|cervix(2)|endometrium(18)|haematopoietic_and_lymphoid_tissue(5)|kidney(8)|large_intestine(22)|liver(1)|lung(46)|ovary(5)|pancreas(1)|prostate(15)|skin(6)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(11)	153		Ovarian(137;0.13)				TGTAGTAGTCACAGGCGTTGC	0.602																																					p.C1045C												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.T3135C	16						.						102.0	81.0	88.0					16																	72984449		2198	4300	6498	71541950	SO:0001819	synonymous_variant	463	exon3			D10250	CCDS10908.1, CCDS54035.1	16q22.3	2012-03-09	2007-08-09	2007-08-09	ENSG00000140836	ENSG00000140836		"""Zinc fingers, C2H2-type"", ""Homeoboxes / ZF class"""	777	protein-coding gene	gene with protein product		104155	"""AT-binding transcription factor 1"""	ATBF1		1719379, 7592926	Standard	NM_006885		Approved	ZNF927	uc002fck.3	Q15911	OTTHUMG00000137599	ENST00000268489.5:c.3135T>C	16.37:g.72984449A>G		Somatic		Capture	Illumina HiSeq	Phase_I	71541950	NM_006885	D3DWS8|O15101|Q13719	Silent	SNP	ENST00000268489.5	37	CCDS10908.1																																																																																				0.602	ZFHX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269008.1	NM_006885	
WDR59	79726	broad.mit.edu	37	16	74919552	74919552	+	Splice_Site	SNP	G	G	A	rs147964482		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr16:74919552G>A	ENST00000262144.6	-	25	2818	c.2688C>T	c.(2686-2688)atC>atT	p.I896I		NM_030581.3	NP_085058.3	Q6PJI9	WDR59_HUMAN	WD repeat domain 59	896								p.I896I(1)		breast(3)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(13)|ovary(1)|prostate(1)	27						CATACTCACCGATCCCTTTGT	0.448																																					p.I896I												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C2688T	16						.	G		0,4396		0,0,2198	107.0	98.0	101.0		2688	-10.7	0.6	16	dbSNP_134	101	1,8599	1.2+/-3.3	0,1,4299	yes	coding-synonymous-near-splice	WDR59	NM_030581.3		0,1,6497	AA,AG,GG		0.0116,0.0,0.0077		896/975	74919552	1,12995	2198	4300	6498	73477053	SO:0001630	splice_region_variant	79726	exon25			AB067510	CCDS32488.1	16q22.3	2013-01-09				ENSG00000103091		"""WD repeat domain containing"""	25706	protein-coding gene	gene with protein product						11572484	Standard	XM_005256146		Approved	FLJ12270	uc002fdh.1	Q6PJI9		ENST00000262144.6:c.2689+1C>T	16.37:g.74919552G>A		Somatic		Capture	Illumina HiSeq	Phase_I	73477053	NM_030581	B3KRC3|Q71RE7|Q96PW5|Q9BSW6|Q9HA43	Silent	SNP	ENST00000262144.6	37	CCDS32488.1																																																																																				0.448	WDR59-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410601.3	NM_030581	Silent
WDR59	79726	broad.mit.edu	37	16	74983682	74983682	+	Missense_Mutation	SNP	G	G	A	rs201171908		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr16:74983682G>A	ENST00000262144.6	-	5	471	c.341C>T	c.(340-342)gCg>gTg	p.A114V	WDR59_ENST00000562331.1_5'Flank	NM_030581.3	NP_085058.3	Q6PJI9	WDR59_HUMAN	WD repeat domain 59	114								p.A114V(1)		breast(3)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(13)|ovary(1)|prostate(1)	27						CTCAAACACCGCCCAGTCCAA	0.458																																					p.A114V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C341T	16						.	G	VAL/ALA	0,4396		0,0,2198	82.0	75.0	77.0		341	5.6	1.0	16		77	3,8597	3.0+/-9.4	0,3,4297	yes	missense	WDR59	NM_030581.3	64	0,3,6495	AA,AG,GG		0.0349,0.0,0.0231	benign	114/975	74983682	3,12993	2198	4300	6498	73541183	SO:0001583	missense	79726	exon5			AB067510	CCDS32488.1	16q22.3	2013-01-09				ENSG00000103091		"""WD repeat domain containing"""	25706	protein-coding gene	gene with protein product						11572484	Standard	XM_005256146		Approved	FLJ12270	uc002fdh.1	Q6PJI9		ENST00000262144.6:c.341C>T	16.37:g.74983682G>A	ENSP00000262144:p.Ala114Val	Somatic		Capture	Illumina HiSeq	Phase_I	73541183	NM_030581	B3KRC3|Q71RE7|Q96PW5|Q9BSW6|Q9HA43	Missense_Mutation	SNP	ENST00000262144.6	37	CCDS32488.1	.	.	.	.	.	.	.	.	.	.	G	22.9	4.345904	0.82022	0.0	3.49E-4	ENSG00000103091	ENST00000262144;ENST00000536050	T	0.61392	0.11	5.62	5.62	0.85841	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.059144	0.64402	D	0.000002	T	0.52500	0.1738	L	0.32530	0.975	0.51233	D	0.999919	P;P	0.52577	0.954;0.851	B;B	0.42798	0.361;0.398	T	0.56323	-0.7998	10	0.52906	T	0.07	-13.5715	19.6676	0.95898	0.0:0.0:1.0:0.0	.	114;114	Q6PJI9-2;Q6PJI9	.;WDR59_HUMAN	V	114;93	ENSP00000262144:A114V	ENSP00000262144:A114V	A	-	2	0	WDR59	73541183	1.000000	0.71417	1.000000	0.80357	0.959000	0.62525	9.197000	0.94985	2.656000	0.90262	0.563000	0.77884	GCG		0.458	WDR59-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410601.3	NM_030581	
HSD17B2	3294	broad.mit.edu	37	16	82101901	82101901	+	Missense_Mutation	SNP	G	G	A	rs373965697		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr16:82101901G>A	ENST00000199936.4	+	2	585	c.392G>A	c.(391-393)cGc>cAc	p.R131H	RP11-510J16.5_ENST00000567021.1_RNA	NM_002153.2	NP_002144.1	P37059	DHB2_HUMAN	hydroxysteroid (17-beta) dehydrogenase 2	131					in utero embryonic development (GO:0001701)|placenta development (GO:0001890)|response to retinoic acid (GO:0032526)|steroid biosynthetic process (GO:0006694)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	17-alpha,20-alpha-dihydroxypregn-4-en-3-one dehydrogenase activity (GO:0047006)|estradiol 17-beta-dehydrogenase activity (GO:0004303)|testosterone dehydrogenase (NAD+) activity (GO:0047035)	p.R131H(1)		breast(2)|central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(1)|ovary(1)|upper_aerodigestive_tract(1)	10						TGCTCTCCGCGCCTCTCGGTG	0.527																																					p.R131H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G392A	16						.	G	HIS/ARG	0,4402		0,0,2201	76.0	64.0	68.0		392	4.4	0.0	16		68	1,8599	1.2+/-3.3	0,1,4299	no	missense	HSD17B2	NM_002153.2	29	0,1,6500	AA,AG,GG		0.0116,0.0,0.0077	benign	131/388	82101901	1,13001	2201	4300	6501	80659402	SO:0001583	missense	3294	exon2				CCDS10936.1	16q24.1-q24.2	2011-09-14			ENSG00000086696	ENSG00000086696	1.1.1.62	"""Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 2"""	5211	protein-coding gene	gene with protein product	"""short chain dehydrogenase/reductase family 9C, member 2"""	109685				7759109, 19027726	Standard	NM_002153		Approved	HSD17, SDR9C2	uc002fgv.3	P37059	OTTHUMG00000137631	ENST00000199936.4:c.392G>A	16.37:g.82101901G>A	ENSP00000199936:p.Arg131His	Somatic		Capture	Illumina HiSeq	Phase_I	80659402	NM_002153	B2R7T4	Missense_Mutation	SNP	ENST00000199936.4	37	CCDS10936.1	.	.	.	.	.	.	.	.	.	.	G	10.89	1.479284	0.26511	0.0	1.16E-4	ENSG00000086696	ENST00000199936	T	0.47528	0.84	5.33	4.38	0.52667	NAD(P)-binding domain (1);	0.362193	0.29100	N	0.013150	T	0.44052	0.1275	L	0.59967	1.855	0.09310	N	1	P	0.35411	0.5	B	0.37198	0.243	T	0.39683	-0.9602	10	0.45353	T	0.12	.	9.5063	0.39048	0.1601:0.0:0.8399:0.0	.	131	P37059	DHB2_HUMAN	H	131	ENSP00000199936:R131H	ENSP00000199936:R131H	R	+	2	0	HSD17B2	80659402	0.004000	0.15560	0.012000	0.15200	0.010000	0.07245	1.466000	0.35310	1.256000	0.44068	0.650000	0.86243	CGC		0.527	HSD17B2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269057.2	NM_002153	
DNAAF1	123872	broad.mit.edu	37	16	84199465	84199465	+	Missense_Mutation	SNP	C	C	T	rs536922836		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr16:84199465C>T	ENST00000378553.5	+	7	1064	c.940C>T	c.(940-942)Cgg>Tgg	p.R314W	DNAAF1_ENST00000563818.1_3'UTR|DNAAF1_ENST00000334315.5_Missense_Mutation_p.R314W	NM_178452.4	NP_848547.4	Q8NEP3	DAAF1_HUMAN	dynein, axonemal, assembly factor 1	314					axonemal dynein complex assembly (GO:0070286)|cilium morphogenesis (GO:0060271)|cilium movement (GO:0003341)|determination of digestive tract left/right asymmetry (GO:0071907)|determination of liver left/right asymmetry (GO:0071910)|determination of pancreatic left/right asymmetry (GO:0035469)|epithelial cilium movement involved in determination of left/right asymmetry (GO:0060287)|heart looping (GO:0001947)|inner dynein arm assembly (GO:0036159)|left/right pattern formation (GO:0060972)|lung development (GO:0030324)|motile cilium assembly (GO:0044458)|outer dynein arm assembly (GO:0036158)|regulation of cilium beat frequency (GO:0003356)	axoneme (GO:0005930)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	dynein binding (GO:0045502)	p.R314W(1)		NS(1)|endometrium(7)|kidney(1)|large_intestine(6)|lung(15)|ovary(4)|pancreas(1)|prostate(1)|stomach(4)|urinary_tract(1)	41						GAGCAGGGAGCGGAAGAAGAT	0.527																																					p.R314W												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C940T	16						.						177.0	166.0	170.0					16																	84199465		2200	4300	6500	82756966	SO:0001583	missense	123872	exon7			BC024009	CCDS10943.2	16q24.1	2012-05-03	2011-06-09	2011-06-09	ENSG00000154099	ENSG00000154099			30539	protein-coding gene	gene with protein product	"""outer row dynein assembly 7 homolog (Chlamydomonas)"""	613190	"""leucine rich repeat containing 50"""	LRRC50		19944405	Standard	NM_178452		Approved	FLJ25330, ODA7, CILD13	uc002fhl.4	Q8NEP3	OTTHUMG00000128517	ENST00000378553.5:c.940C>T	16.37:g.84199465C>T	ENSP00000367815:p.Arg314Trp	Somatic		Capture	Illumina HiSeq	Phase_I	82756966	NM_178452	B4DJA3|Q69YI8|Q69YJ0|Q69YW5|Q96LP3|Q96MB6	Missense_Mutation	SNP	ENST00000378553.5	37	CCDS10943.2	.	.	.	.	.	.	.	.	.	.	C	17.13	3.309929	0.60414	.	.	ENSG00000154099	ENST00000334315;ENST00000378553	T;T	0.37915	1.17;1.59	5.66	3.52	0.40303	.	0.400743	0.25842	N	0.027960	T	0.58821	0.2149	M	0.82823	2.61	0.35554	D	0.80413	D;D	0.89917	1.0;0.998	D;P	0.65010	0.931;0.84	T	0.72054	-0.4406	10	0.87932	D	0	-2.4457	12.8511	0.57858	0.3274:0.6726:0.0:0.0	.	62;314	Q8NEP3-2;Q8NEP3	.;DAAF1_HUMAN	W	314	ENSP00000334593:R314W;ENSP00000367815:R314W	ENSP00000334593:R314W	R	+	1	2	DNAAF1	82756966	1.000000	0.71417	0.692000	0.30179	0.099000	0.18886	3.969000	0.56816	2.673000	0.90976	0.650000	0.86243	CGG		0.527	DNAAF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250328.3	NM_178452	
LMF1	64788	broad.mit.edu	37	16	904627	904627	+	Missense_Mutation	SNP	G	G	A	rs555435528		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr16:904627G>A	ENST00000262301.11	-	11	1627	c.1609C>T	c.(1609-1611)Cgg>Tgg	p.R537W	LMF1_ENST00000568897.1_Missense_Mutation_p.R320W|LMF1_ENST00000399843.2_Missense_Mutation_p.R537W|LMF1_ENST00000543238.1_Missense_Mutation_p.R300W	NM_022773.2	NP_073610.2	Q96S06	LMF1_HUMAN	lipase maturation factor 1	537					chylomicron remnant clearance (GO:0034382)|ER to Golgi vesicle-mediated transport (GO:0006888)|positive regulation of lipoprotein lipase activity (GO:0051006)|protein glycosylation in Golgi (GO:0033578)|protein maturation (GO:0051604)|protein secretion (GO:0009306)|regulation of cholesterol metabolic process (GO:0090181)|regulation of triglyceride metabolic process (GO:0090207)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)		p.R537W(1)		central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(7)|ovary(1)|prostate(1)|stomach(2)|urinary_tract(1)	18		Hepatocellular(780;0.00308)				ATCCTCTTCCGCACCCACCAC	0.667																																					p.R537W												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1609T	16						.						24.0	31.0	29.0					16																	904627		2058	4181	6239	844628	SO:0001583	missense	64788	exon11			AK022743	CCDS45373.1	16p13.3	2008-02-05	2007-11-29	2007-11-29	ENSG00000103227	ENSG00000103227			14154	protein-coding gene	gene with protein product		611761	"""chromosome 16 open reading frame 26"", ""transmembrane protein 112"""	C16orf26, TMEM112		11157797, 17994020	Standard	NM_022773		Approved	FLJ12681, JFP11, FLJ22302, TMEM112A	uc021tae.1	Q96S06	OTTHUMG00000047848	ENST00000262301.11:c.1609C>T	16.37:g.904627G>A	ENSP00000262301:p.Arg537Trp	Somatic		Capture	Illumina HiSeq	Phase_I	844628	NM_022773	Q68CJ3|Q96FJ4|Q9H6G4|Q9H9K7	Missense_Mutation	SNP	ENST00000262301.11	37	CCDS45373.1	.	.	.	.	.	.	.	.	.	.	G	17.77	3.471234	0.63625	.	.	ENSG00000103227	ENST00000262301;ENST00000399843;ENST00000540070;ENST00000543238	T;T;T	0.48201	0.82;0.82;0.82	4.4	4.4	0.53042	.	0.000000	0.64402	U	0.000001	T	0.77811	0.4186	H	0.96080	3.765	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.85554	0.1223	10	0.87932	D	0	-2.3535	14.4706	0.67514	0.0:0.0:1.0:0.0	.	537	Q96S06	LMF1_HUMAN	W	537;537;320;300	ENSP00000262301:R537W;ENSP00000382737:R537W;ENSP00000437418:R300W	ENSP00000262301:R537W	R	-	1	2	LMF1	844628	1.000000	0.71417	0.265000	0.24526	0.785000	0.44390	3.543000	0.53633	1.995000	0.58328	0.462000	0.41574	CGG		0.667	LMF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000109071.3	NM_022773	
LMF1	64788	broad.mit.edu	37	16	929712	929712	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr16:929712G>A	ENST00000262301.11	-	6	773	c.755C>T	c.(754-756)gCg>gTg	p.A252V	LMF1_ENST00000568897.1_Missense_Mutation_p.A35V|LMF1_ENST00000399843.2_Missense_Mutation_p.A252V|LMF1_ENST00000543238.1_Missense_Mutation_p.A15V|LMF1_ENST00000568268.1_5'UTR	NM_022773.2	NP_073610.2	Q96S06	LMF1_HUMAN	lipase maturation factor 1	252					chylomicron remnant clearance (GO:0034382)|ER to Golgi vesicle-mediated transport (GO:0006888)|positive regulation of lipoprotein lipase activity (GO:0051006)|protein glycosylation in Golgi (GO:0033578)|protein maturation (GO:0051604)|protein secretion (GO:0009306)|regulation of cholesterol metabolic process (GO:0090181)|regulation of triglyceride metabolic process (GO:0090207)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)		p.A252V(1)		central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(7)|ovary(1)|prostate(1)|stomach(2)|urinary_tract(1)	18		Hepatocellular(780;0.00308)				CAGGTAGTACGCCACAGGATT	0.657																																					p.A252V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C755T	16						.						56.0	67.0	63.0					16																	929712		2155	4251	6406	869713	SO:0001583	missense	64788	exon6			AK022743	CCDS45373.1	16p13.3	2008-02-05	2007-11-29	2007-11-29	ENSG00000103227	ENSG00000103227			14154	protein-coding gene	gene with protein product		611761	"""chromosome 16 open reading frame 26"", ""transmembrane protein 112"""	C16orf26, TMEM112		11157797, 17994020	Standard	NM_022773		Approved	FLJ12681, JFP11, FLJ22302, TMEM112A	uc021tae.1	Q96S06	OTTHUMG00000047848	ENST00000262301.11:c.755C>T	16.37:g.929712G>A	ENSP00000262301:p.Ala252Val	Somatic		Capture	Illumina HiSeq	Phase_I	869713	NM_022773	Q68CJ3|Q96FJ4|Q9H6G4|Q9H9K7	Missense_Mutation	SNP	ENST00000262301.11	37	CCDS45373.1	.	.	.	.	.	.	.	.	.	.	G	23.4	4.413040	0.83449	.	.	ENSG00000103227	ENST00000262301;ENST00000399843;ENST00000540070;ENST00000545827;ENST00000543238	T;T;T	0.27557	1.66;1.66;1.66	5.06	5.06	0.68205	.	0.138683	0.48767	D	0.000170	T	0.60157	0.2247	M	0.89287	3.02	0.80722	D	1	D	0.67145	0.996	P	0.61275	0.886	T	0.69654	-0.5087	10	0.72032	D	0.01	-24.079	17.3999	0.87456	0.0:0.0:1.0:0.0	.	252	Q96S06	LMF1_HUMAN	V	252;252;35;6;15	ENSP00000262301:A252V;ENSP00000382737:A252V;ENSP00000437418:A15V	ENSP00000262301:A252V	A	-	2	0	LMF1	869713	1.000000	0.71417	0.987000	0.45799	0.003000	0.03518	7.923000	0.87546	2.356000	0.79943	0.555000	0.69702	GCG		0.657	LMF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000109071.3	NM_022773	
METTL22	79091	broad.mit.edu	37	16	8738510	8738510	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr16:8738510G>T	ENST00000381920.3	+	10	1365	c.1107G>T	c.(1105-1107)aaG>aaT	p.K369N	METTL22_ENST00000561758.1_Missense_Mutation_p.K313N|METTL22_ENST00000568967.1_3'UTR	NM_024109.2	NP_077014.2	Q9BUU2	MET22_HUMAN	methyltransferase like 22	369						nucleus (GO:0005634)	methyltransferase activity (GO:0008168)	p.K369N(1)		large_intestine(5)|lung(4)	9						CAGATGGCAAGCTGCGCTTCG	0.622																																					p.K369N												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1107T	16						.						87.0	89.0	88.0					16																	8738510		2054	4195	6249	8646011	SO:0001583	missense	79091	exon10			AK022495	CCDS10533.2	16p13.2	2014-07-15	2011-03-03	2011-03-03	ENSG00000067365	ENSG00000067365			28368	protein-coding gene	gene with protein product		615261	"""chromosome 16 open reading frame 68"""	C16orf68		24140279	Standard	XM_005255570		Approved	FLJ12433,MGC2654	uc002cyz.3	Q9BUU2	OTTHUMG00000129694	ENST00000381920.3:c.1107G>T	16.37:g.8738510G>T	ENSP00000371345:p.Lys369Asn	Somatic		Capture	Illumina HiSeq	Phase_I	8646011	NM_024109	B2RD29|D3DUF2|Q6XYB4|Q9HA03	Missense_Mutation	SNP	ENST00000381920.3	37	CCDS10533.2	.	.	.	.	.	.	.	.	.	.	G	11.71	1.720786	0.30503	.	.	ENSG00000067365	ENST00000381920	T	0.20200	2.09	5.47	-0.976	0.10286	.	1.032410	0.07674	N	0.935886	T	0.16257	0.0391	L	0.42245	1.32	0.21220	N	0.999759	B;B	0.02656	0.0;0.0	B;B	0.08055	0.003;0.002	T	0.33828	-0.9853	10	0.35671	T	0.21	-26.8196	5.7859	0.18333	0.2327:0.5157:0.2515:0.0	.	144;369	Q9BUU2-3;Q9BUU2	.;MET22_HUMAN	N	369	ENSP00000371345:K369N	ENSP00000371345:K369N	K	+	3	2	METTL22	8646011	0.001000	0.12720	0.102000	0.21198	0.742000	0.42306	-0.140000	0.10342	-0.005000	0.14395	-0.458000	0.05436	AAG		0.622	METTL22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251901.1	NM_024109	
FAM92B	339145	broad.mit.edu	37	16	85143971	85143971	+	Missense_Mutation	SNP	G	G	A	rs201987292		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr16:85143971G>A	ENST00000539556.1	-	2	271	c.116C>T	c.(115-117)aCg>aTg	p.T39M		NM_198491.1	NP_940893.1	Q6ZTR7	FA92B_HUMAN	family with sequence similarity 92, member B	39								p.T39M(1)		breast(1)|central_nervous_system(1)|kidney(1)|large_intestine(5)|lung(6)|ovary(1)|prostate(1)	16						CAGCCGGGCCGTCTTGCGCGT	0.637																																					p.T39M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C116T	16						.	G	MET/THR	0,4396		0,0,2198	51.0	53.0	53.0		116	4.4	1.0	16		53	1,8599	1.2+/-3.3	0,1,4299	no	missense	FAM92B	NM_198491.1	81	0,1,6497	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging	39/305	85143971	1,12995	2198	4300	6498	83701472	SO:0001583	missense	339145	exon2				CCDS32500.1	16q24.1	2005-09-22				ENSG00000153789			24781	protein-coding gene	gene with protein product						12477932	Standard	NM_198491		Approved	FLJ44299	uc021tlz.1	Q6ZTR7		ENST00000539556.1:c.116C>T	16.37:g.85143971G>A	ENSP00000443411:p.Thr39Met	Somatic		Capture	Illumina HiSeq	Phase_I	83701472	NM_198491		Missense_Mutation	SNP	ENST00000539556.1	37	CCDS32500.1	.	.	.	.	.	.	.	.	.	.	G	21.2	4.111062	0.77210	0.0	1.16E-4	ENSG00000153789	ENST00000393246;ENST00000539556	T	0.58652	0.32	5.38	4.43	0.53597	.	0.080569	0.50627	D	0.000102	T	0.70842	0.3270	M	0.84846	2.72	0.40513	D	0.980756	D	0.60160	0.987	P	0.53593	0.73	T	0.77236	-0.2662	10	0.72032	D	0.01	-18.1994	12.1699	0.54152	0.0842:0.0:0.9158:0.0	.	39	Q6ZTR7	FA92B_HUMAN	M	39	ENSP00000443411:T39M	ENSP00000376937:T39M	T	-	2	0	FAM92B	83701472	1.000000	0.71417	0.980000	0.43619	0.688000	0.40055	4.242000	0.58714	1.272000	0.44329	0.561000	0.74099	ACG		0.637	FAM92B-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_198491	
CDK10	8558	broad.mit.edu	37	16	89757906	89757906	+	Silent	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr16:89757906G>A	ENST00000353379.7	+	4	331	c.288G>A	c.(286-288)ccG>ccA	p.P96P	CDK10_ENST00000331006.8_Silent_p.P49P|CDK10_ENST00000505473.1_Silent_p.P25P|CDK10_ENST00000514965.1_3'UTR	NM_001098533.2|NM_001160367.1|NM_052988.4	NP_001092003.2|NP_001153839.1|NP_443714.3	Q15131	CDK10_HUMAN	cyclin-dependent kinase 10	96	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.		P -> L (in dbSNP:rs55819627). {ECO:0000269|PubMed:17344846}.		negative regulation of cell proliferation (GO:0008285)|traversing start control point of mitotic cell cycle (GO:0007089)		ATP binding (GO:0005524)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)	p.P96P(1)		ovary(1)	1		Lung NSC(15;2.19e-05)|all_lung(18;3.07e-05)|all_hematologic(23;0.0256)		BRCA - Breast invasive adenocarcinoma(80;0.0276)		TGCGTCATCCGAACATCGTGG	0.642																																					p.P25P												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G75A	16						.						73.0	68.0	70.0					16																	89757906		2198	4300	6498	88285407	SO:0001819	synonymous_variant	8558	exon4			L33264	CCDS10984.2, CCDS32514.1, CCDS32514.2	16q24.3	2011-11-08	2007-11-21		ENSG00000185324	ENSG00000185324		"""Cyclin-dependent kinases"""	1770	protein-coding gene	gene with protein product		603464	"""cyclin-dependent kinase (CDC2-like) 10"""			8208557, 8084611	Standard	NM_052988		Approved	PISSLRE	uc010cio.3	Q15131	OTTHUMG00000138049	ENST00000353379.7:c.288G>A	16.37:g.89757906G>A		Somatic		Capture	Illumina HiSeq	Phase_I	88285407	NM_001098533	A8K370|A8K8I6|A8MXU6|B3KQJ3|B7Z420|D3DX82|D3DX83|Q0VGZ7|Q15130|Q6PJC0	Silent	SNP	ENST00000353379.7	37	CCDS10984.2																																																																																				0.642	CDK10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269925.2		
SLX4	84464	broad.mit.edu	37	16	3639380	3639380	+	Frame_Shift_Del	DEL	G	G	-			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	-	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr16:3639380delG	ENST00000294008.3	-	12	4899	c.4259delC	c.(4258-4260)ccafs	p.P1420fs		NM_032444.2	NP_115820.2	Q8IY92	SLX4_HUMAN	SLX4 structure-specific endonuclease subunit	1420	Interaction with MUS81.|Interaction with PLK1 and TERF2-TERF2IP.				DNA catabolic process, endonucleolytic (GO:0000737)|DNA double-strand break processing involved in repair via single-strand annealing (GO:0010792)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|double-strand break repair via homologous recombination (GO:0000724)|nucleotide-excision repair (GO:0006289)|positive regulation of catalytic activity (GO:0043085)|response to intra-S DNA damage checkpoint signaling (GO:0072429)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|Slx1-Slx4 complex (GO:0033557)	5'-flap endonuclease activity (GO:0017108)|enzyme activator activity (GO:0008047)	p.P1420fs*30(1)		breast(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(18)|lung(20)|ovary(3)|pancreas(1)|prostate(7)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	76						AATTGGAATTGGGGGGTCACT	0.627								Direct reversal of damage																													p.P1420fs												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.4259delC	16						.						63.0	70.0	68.0					16																	3639380		2137	4218	6355	3579381	SO:0001589	frameshift_variant	84464	exon12			AB058687	CCDS10506.2	16p13.3	2014-09-17	2013-06-05	2010-09-13	ENSG00000188827	ENSG00000188827		"""Fanconi anemia, complementation groups"", ""BTB/POZ domain containing"""	23845	protein-coding gene	gene with protein product	"""Fanconi anemia, complementation group P"""	613278	"""BTB (POZ) domain containing 12"", ""SLX4 structure-specific endonuclease subunit homolog (S. cerevisiae)"""	BTBD12		11347906, 19595721	Standard	NM_032444		Approved	KIAA1784, KIAA1987, FANCP	uc002cvp.2	Q8IY92	OTTHUMG00000074089	ENST00000294008.3:c.4259delC	16.37:g.3639380delG	ENSP00000294008:p.Pro1420fs	Somatic		Capture	Illumina HiSeq	Phase_I	3579381	NM_032444	Q69YT8|Q8TF15|Q96JP1	Frame_Shift_Del	DEL	ENST00000294008.3	37	CCDS10506.2																																																																																				0.627	SLX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157301.3	NM_032444	
USP7	7874	broad.mit.edu	37	16	8987895	8987895	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr16:8987895C>T	ENST00000344836.4	-	31	3467	c.3269G>A	c.(3268-3270)cGc>cAc	p.R1090H	USP7_ENST00000381886.4_Missense_Mutation_p.R1074H|USP7_ENST00000535863.1_Missense_Mutation_p.R991H	NM_003470.2	NP_003461.2	Q93009	UBP7_HUMAN	ubiquitin specific peptidase 7 (herpes virus-associated)	1090					maintenance of DNA methylation (GO:0010216)|multicellular organismal development (GO:0007275)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|protein deubiquitination (GO:0016579)|regulation of sequence-specific DNA binding transcription factor activity (GO:0051090)|transcription-coupled nucleotide-excision repair (GO:0006283)|ubiquitin-dependent protein catabolic process (GO:0006511)|viral process (GO:0016032)	cytosol (GO:0005829)|nucleus (GO:0005634)	cysteine-type endopeptidase activity (GO:0004197)|p53 binding (GO:0002039)|protein C-terminus binding (GO:0008022)|transcription factor binding (GO:0008134)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)	p.R1090H(1)		autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(13)|lung(20)|ovary(3)|skin(2)|upper_aerodigestive_tract(1)	48						GTAAGTGTAGCGACTCCTCTT	0.507																																					p.R1090H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G3269A	16						.						189.0	178.0	181.0					16																	8987895		2197	4300	6497	8895396	SO:0001583	missense	7874	exon31			Z72499	CCDS32385.1, CCDS66941.1	16p13.3	2008-04-11	2005-08-08			ENSG00000187555		"""Ubiquitin-specific peptidases"""	12630	protein-coding gene	gene with protein product		602519	"""ubiquitin specific protease 7 (herpes virus-associated)"""	HAUSP		12838346, 9925944	Standard	NM_003470		Approved		uc002czl.2	Q93009		ENST00000344836.4:c.3269G>A	16.37:g.8987895C>T	ENSP00000343535:p.Arg1090His	Somatic		Capture	Illumina HiSeq	Phase_I	8895396	NM_003470	A6NMY8|B7Z815|H0Y3G8	Missense_Mutation	SNP	ENST00000344836.4	37	CCDS32385.1	.	.	.	.	.	.	.	.	.	.	C	24.7	4.560082	0.86335	.	.	ENSG00000187555	ENST00000344836;ENST00000381886;ENST00000535863	T;T	0.08102	3.13;3.14	5.85	4.9	0.64082	.	0.000000	0.85682	D	0.000000	T	0.22820	0.0551	L	0.50333	1.59	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.76575	0.988;0.98	T	0.00638	-1.1632	10	0.39692	T	0.17	.	14.9195	0.70826	0.0:0.9316:0.0:0.0684	.	1090;1074	Q93009;B7Z815	UBP7_HUMAN;.	H	1090;1098;991	ENSP00000343535:R1090H;ENSP00000443646:R991H	ENSP00000343535:R1090H	R	-	2	0	USP7	8895396	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.363000	0.79516	1.490000	0.48466	0.650000	0.86243	CGC		0.507	USP7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434268.2		
USP7	7874	broad.mit.edu	37	16	9014216	9014216	+	Splice_Site	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr16:9014216G>A	ENST00000344836.4	-	5	809	c.611C>T	c.(610-612)gCg>gTg	p.A204V	USP7_ENST00000566224.1_5'Flank|USP7_ENST00000381886.4_Splice_Site_p.A188V|USP7_ENST00000535863.1_Splice_Site_p.A105V	NM_003470.2	NP_003461.2	Q93009	UBP7_HUMAN	ubiquitin specific peptidase 7 (herpes virus-associated)	204	Interaction with TSPYL5.|Interaction with p53/TP53, MDM2 and EBNA1.|Necessary for nuclear localization.				maintenance of DNA methylation (GO:0010216)|multicellular organismal development (GO:0007275)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|protein deubiquitination (GO:0016579)|regulation of sequence-specific DNA binding transcription factor activity (GO:0051090)|transcription-coupled nucleotide-excision repair (GO:0006283)|ubiquitin-dependent protein catabolic process (GO:0006511)|viral process (GO:0016032)	cytosol (GO:0005829)|nucleus (GO:0005634)	cysteine-type endopeptidase activity (GO:0004197)|p53 binding (GO:0002039)|protein C-terminus binding (GO:0008022)|transcription factor binding (GO:0008134)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)	p.A204V(1)		autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(13)|lung(20)|ovary(3)|skin(2)|upper_aerodigestive_tract(1)	48						AAAAACTTACGCAACTCCATG	0.378																																					p.A204V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C611T	16						.						98.0	96.0	96.0					16																	9014216		2197	4300	6497	8921717	SO:0001630	splice_region_variant	7874	exon5			Z72499	CCDS32385.1, CCDS66941.1	16p13.3	2008-04-11	2005-08-08			ENSG00000187555		"""Ubiquitin-specific peptidases"""	12630	protein-coding gene	gene with protein product		602519	"""ubiquitin specific protease 7 (herpes virus-associated)"""	HAUSP		12838346, 9925944	Standard	NM_003470		Approved		uc002czl.2	Q93009		ENST00000344836.4:c.611+1C>T	16.37:g.9014216G>A		Somatic		Capture	Illumina HiSeq	Phase_I	8921717	NM_003470	A6NMY8|B7Z815|H0Y3G8	Missense_Mutation	SNP	ENST00000344836.4	37	CCDS32385.1	.	.	.	.	.	.	.	.	.	.	G	22.6	4.307568	0.81247	.	.	ENSG00000187555	ENST00000344836;ENST00000381886;ENST00000535863;ENST00000544549;ENST00000542333	T;T;T	0.06933	3.25;3.24;3.24	5.63	5.63	0.86233	.	0.046134	0.85682	D	0.000000	T	0.07999	0.0200	L	0.33485	1.01	0.80722	D	1	B;B	0.30021	0.265;0.265	B;B	0.06405	0.002;0.002	T	0.34551	-0.9824	9	.	.	.	.	19.6876	0.95986	0.0:0.0:1.0:0.0	.	204;188	Q93009;B7Z815	UBP7_HUMAN;.	V	204;212;105;105;146	ENSP00000343535:A204V;ENSP00000443646:A105V;ENSP00000439272:A146V	.	A	-	2	0	USP7	8921717	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.751000	0.98889	2.659000	0.90383	0.655000	0.94253	GCG		0.378	USP7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434268.2		Missense_Mutation
GRIN2A	2903	broad.mit.edu	37	16	10032029	10032029	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr16:10032029G>A	ENST00000396573.2	-	4	1103	c.794C>T	c.(793-795)aCg>aTg	p.T265M	GRIN2A_ENST00000562109.1_Missense_Mutation_p.T265M|GRIN2A_ENST00000404927.2_Missense_Mutation_p.T265M|GRIN2A_ENST00000535259.1_Missense_Mutation_p.T108M|GRIN2A_ENST00000566670.1_5'UTR|GRIN2A_ENST00000330684.3_Missense_Mutation_p.T265M|GRIN2A_ENST00000396575.2_Missense_Mutation_p.T265M	NM_000833.3	NP_000824.1	Q12879	NMDE1_HUMAN	glutamate receptor, ionotropic, N-methyl D-aspartate 2A	265					directional locomotion (GO:0033058)|dopamine metabolic process (GO:0042417)|glutamate receptor signaling pathway (GO:0007215)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|learning or memory (GO:0007611)|memory (GO:0007613)|negative regulation of protein catabolic process (GO:0042177)|neurogenesis (GO:0022008)|positive regulation of apoptotic process (GO:0043065)|protein localization (GO:0008104)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of sensory perception of pain (GO:0051930)|regulation of synaptic plasticity (GO:0048167)|response to amphetamine (GO:0001975)|response to drug (GO:0042493)|response to ethanol (GO:0045471)|response to wounding (GO:0009611)|sensory perception of pain (GO:0019233)|serotonin metabolic process (GO:0042428)|sleep (GO:0030431)|startle response (GO:0001964)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transport (GO:0006810)|visual learning (GO:0008542)	cell junction (GO:0030054)|cell surface (GO:0009986)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|integral component of plasma membrane (GO:0005887)|N-methyl-D-aspartate selective glutamate receptor complex (GO:0017146)|neuronal postsynaptic density (GO:0097481)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)|synaptic vesicle (GO:0008021)	calcium channel activity (GO:0005262)|extracellular-glutamate-gated ion channel activity (GO:0005234)|N-methyl-D-aspartate selective glutamate receptor activity (GO:0004972)|zinc ion binding (GO:0008270)	p.T265M(1)		NS(7)|breast(5)|cervix(1)|endometrium(11)|kidney(6)|large_intestine(36)|lung(71)|ovary(4)|prostate(9)|skin(45)|upper_aerodigestive_tract(2)|urinary_tract(1)	198					Acamprosate(DB00659)|Acetylcysteine(DB06151)|Atomoxetine(DB00289)|Felbamate(DB00949)|Gabapentin(DB00996)|Glycine(DB00145)|Halothane(DB01159)|Ketobemidone(DB06738)|Memantine(DB01043)|Milnacipran(DB04896)|Pentobarbital(DB00312)|Pethidine(DB00454)|Phenobarbital(DB01174)|Secobarbital(DB00418)	GATGAGCTCCGTGTTCCCAGA	0.552																																					p.T265M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C794T	16						.						71.0	60.0	64.0					16																	10032029		2197	4300	6497	9939530	SO:0001583	missense	2903	exon3				CCDS10539.1, CCDS45407.1	16p13.2	2012-08-29			ENSG00000183454	ENSG00000183454		"""Ligand-gated ion channels / Glutamate receptors, ionotropic"", ""Glutamate receptors"""	4585	protein-coding gene	gene with protein product		138253		NMDAR2A		9480759	Standard	XM_005255267		Approved	GluN2A	uc002czo.4	Q12879	OTTHUMG00000129721	ENST00000396573.2:c.794C>T	16.37:g.10032029G>A	ENSP00000379818:p.Thr265Met	Somatic		Capture	Illumina HiSeq	Phase_I	9939530	NM_001134408	O00669|Q17RZ6	Missense_Mutation	SNP	ENST00000396573.2	37	CCDS10539.1	.	.	.	.	.	.	.	.	.	.	g	20.2	3.947562	0.73787	.	.	ENSG00000183454	ENST00000396573;ENST00000404927;ENST00000535259;ENST00000330684;ENST00000396575	D;D;D;D;D	0.82803	-1.65;-1.65;-1.65;-1.65;-1.65	5.2	5.2	0.72013	Extracellular ligand-binding receptor (1);	0.156108	0.56097	D	0.000024	D	0.87293	0.6141	L	0.58669	1.825	0.41827	D	0.990057	P;P;D	0.69078	0.81;0.939;0.997	B;P;P	0.56343	0.24;0.489;0.796	D	0.86740	0.1954	9	.	.	.	.	18.0961	0.89490	0.0:0.0:1.0:0.0	.	108;265;265	F5GZ52;Q17RZ6;Q12879	.;.;NMDE1_HUMAN	M	265;265;108;265;265	ENSP00000379818:T265M;ENSP00000385872:T265M;ENSP00000441572:T108M;ENSP00000332549:T265M;ENSP00000379820:T265M	.	T	-	2	0	GRIN2A	9939530	1.000000	0.71417	0.952000	0.39060	0.986000	0.74619	6.481000	0.73608	2.582000	0.87167	0.561000	0.74099	ACG		0.552	GRIN2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251930.3		
NLRC5	84166	broad.mit.edu	37	16	57113024	57113024	+	Frame_Shift_Del	DEL	C	C	-	rs186267475		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	-	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr16:57113024delC	ENST00000262510.6	+	44	5369	c.5144delC	c.(5143-5145)tccfs	p.S1715fs	NLRC5_ENST00000539144.1_Frame_Shift_Del_p.S1686fs|NLRC5_ENST00000308149.7_Frame_Shift_Del_p.S1686fs|NLRC5_ENST00000436936.1_3'UTR	NM_032206.4	NP_115582.4	Q86WI3	NLRC5_HUMAN	NLR family, CARD domain containing 5	1715				S -> F (in Ref. 7; BAB55096/BAB55098). {ECO:0000305}.	defense response to virus (GO:0051607)|innate immune response (GO:0045087)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of type I interferon production (GO:0032480)|negative regulation of type I interferon-mediated signaling pathway (GO:0060339)|positive regulation of interferon-gamma-mediated signaling pathway (GO:0060335)|positive regulation of MHC class I biosynthetic process (GO:0045345)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon-mediated signaling pathway (GO:0060340)|regulation of kinase activity (GO:0043549)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)	p.H1717fs*29(1)		NS(2)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(16)|lung(21)|ovary(8)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	75		all_neural(199;0.225)				CTGGATGGATCCCCCCATTTG	0.647																																					p.S1715fs												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.5144delC	16						.						56.0	66.0	63.0					16																	57113024		2198	4299	6497	55670525	SO:0001589	frameshift_variant	84166	exon44			AF389420	CCDS10773.1	16q13	2008-02-05			ENSG00000140853	ENSG00000140853		"""Nucleotide-binding domain and leucine rich repeat containing"""	29933	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and CARD domain containing 5"", ""NOD-like receptor C5"""	613537				12615073	Standard	NM_032206		Approved	NOD27, CLR16.1, FLJ21709	uc021tiu.1	Q86WI3	OTTHUMG00000133470	ENST00000262510.6:c.5144delC	16.37:g.57113024delC	ENSP00000262510:p.Ser1715fs	Somatic		Capture	Illumina HiSeq	Phase_I	55670525	NM_032206	B5MEF1|C9JMD8|Q6P4A6|Q86VM7|Q8NF42|Q8TEE2|Q8TEJ1|Q969L7	Frame_Shift_Del	DEL	ENST00000262510.6	37	CCDS10773.1																																																																																				0.647	NLRC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257346.1	NM_032206	
TCF25	22980	broad.mit.edu	37	16	89970553	89970553	+	Missense_Mutation	SNP	G	G	C			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	C	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr16:89970553G>C	ENST00000263346.8	+	13	1465	c.1409G>C	c.(1408-1410)aGt>aCt	p.S470T	TCF25_ENST00000263347.7_Missense_Mutation_p.S235T|RP11-566K11.7_ENST00000570217.1_RNA	NM_014972.2	NP_055787.1	Q9BQ70	TCF25_HUMAN	transcription factor 25 (basic helix-loop-helix)	470					heart development (GO:0007507)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.S470T(1)		breast(1)|endometrium(2)|large_intestine(1)|lung(8)|ovary(3)|skin(1)|urinary_tract(2)	18		all_cancers(9;4.71e-08)|Lung NSC(15;0.000192)|all_lung(18;0.000319)|all_neural(9;0.0122)|all_hematologic(23;0.027)		BRCA - Breast invasive adenocarcinoma(80;0.0288)		GAGTCTTGCAGTGTGCGGCCC	0.622																																					p.S470T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1409C	16						.						43.0	37.0	39.0					16																	89970553		2194	4298	6492	88498054	SO:0001583	missense	22980	exon13			AF322111	CCDS10987.1	16q24.3	2008-02-05			ENSG00000141002	ENSG00000141002			29181	protein-coding gene	gene with protein product		612326				12107429, 16574069	Standard	NM_014972		Approved	Nulp1, KIAA1049	uc002fpb.2	Q9BQ70	OTTHUMG00000138986	ENST00000263346.8:c.1409G>C	16.37:g.89970553G>C	ENSP00000263346:p.Ser470Thr	Somatic		Capture	Illumina HiSeq	Phase_I	88498054	NM_014972	Q2MK75|Q9UPV3	Missense_Mutation	SNP	ENST00000263346.8	37	CCDS10987.1	.	.	.	.	.	.	.	.	.	.	G	12.26	1.883671	0.33255	.	.	ENSG00000141002	ENST00000263346;ENST00000263347	.	.	.	5.09	5.09	0.68999	.	0.195805	0.53938	D	0.000045	T	0.61211	0.2329	L	0.46614	1.455	0.44055	D	0.996798	P;P	0.49635	0.515;0.926	B;P	0.49561	0.268;0.615	T	0.62001	-0.6946	9	0.46703	T	0.11	.	17.6691	0.88211	0.0:0.0:1.0:0.0	.	235;470	Q9H384;Q9BQ70	.;TCF25_HUMAN	T	470;235	.	ENSP00000263346:S470T	S	+	2	0	TCF25	88498054	1.000000	0.71417	1.000000	0.80357	0.237000	0.25408	4.723000	0.61965	2.645000	0.89757	0.462000	0.41574	AGT		0.622	TCF25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000272875.2	NM_014972	
SLC43A2	124935	broad.mit.edu	37	17	1520020	1520020	+	Silent	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr17:1520020C>T	ENST00000301335.5	-	3	292	c.204G>A	c.(202-204)ggG>ggA	p.G68G	SLC43A2_ENST00000571650.1_Silent_p.G68G|SLC43A2_ENST00000382147.4_Silent_p.G68G|snoU13_ENST00000459614.1_RNA	NM_001284498.1|NM_001284499.1	NP_001271427.1|NP_001271428.1	Q8N370	LAT4_HUMAN	solute carrier family 43 (amino acid system L transporter), member 2	68					amino acid transport (GO:0006865)|ion transport (GO:0006811)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	L-amino acid transmembrane transporter activity (GO:0015179)	p.G68G(1)		endometrium(4)|large_intestine(4)|liver(1)|lung(2)|upper_aerodigestive_tract(1)	12				UCEC - Uterine corpus endometrioid carcinoma (25;0.0883)		CCTCCTCGTGCCCCGGCTCTG	0.582																																					p.G68G												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G204A	17						.						87.0	71.0	77.0					17																	1520020		2203	4300	6503	1466770	SO:0001819	synonymous_variant	124935	exon3			BC027923	CCDS11006.1, CCDS67107.1, CCDS67108.1	17p13.3	2013-07-17	2013-07-17		ENSG00000167703	ENSG00000167703		"""Solute carriers"""	23087	protein-coding gene	gene with protein product		610791				23268354	Standard	NM_001284498		Approved	MGC34680	uc002fsv.3	Q8N370	OTTHUMG00000090345	ENST00000301335.5:c.204G>A	17.37:g.1520020C>T		Somatic		Capture	Illumina HiSeq	Phase_I	1466770	NM_152346	B7Z6X9|C9JNU8|D3DTH9|Q5CD75|Q6IPM1|Q8NBX1|Q8NC21|Q8WZ00	Silent	SNP	ENST00000301335.5	37	CCDS11006.1																																																																																				0.582	SLC43A2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000206717.4	NM_152346	
MYH13	8735	broad.mit.edu	37	17	10233778	10233778	+	Silent	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr17:10233778C>T	ENST00000418404.3	-	20	2524	c.2361G>A	c.(2359-2361)acG>acA	p.T787T	RP11-401O9.3_ENST00000577743.1_RNA|MYH13_ENST00000252172.4_Silent_p.T787T			Q9UKX3	MYH13_HUMAN	myosin, heavy chain 13, skeletal muscle	787	IQ. {ECO:0000255|PROSITE- ProRule:PRU00116}.				cellular response to starvation (GO:0009267)|metabolic process (GO:0008152)|muscle contraction (GO:0006936)	extracellular vesicular exosome (GO:0070062)|muscle myosin complex (GO:0005859)|myofibril (GO:0030016)|myosin filament (GO:0032982)	ATP binding (GO:0005524)|microfilament motor activity (GO:0000146)	p.T787T(2)		breast(3)|cervix(2)|endometrium(11)|kidney(7)|large_intestine(21)|lung(48)|ovary(7)|skin(2)|upper_aerodigestive_tract(5)|urinary_tract(2)	108						TTGTCATCAGCGTCACCAGCT	0.532																																					p.T787T												.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.G2361A	17						.						90.0	93.0	92.0					17																	10233778		2193	4300	6493	10174503	SO:0001819	synonymous_variant	8735	exon21			AF075248	CCDS45613.1	17p13	2011-09-27	2006-09-29			ENSG00000006788		"""Myosins / Myosin superfamily : Class II"""	7571	protein-coding gene	gene with protein product	"""extraocular muscle myosin heavy chain"", ""extraocular myosin heavy chain"""	603487	"""myosin, heavy polypeptide 13, skeletal muscle"""			9806854	Standard	NM_003802		Approved	MyHC-eo	uc002gmk.1	Q9UKX3		ENST00000418404.3:c.2361G>A	17.37:g.10233778C>T		Somatic		Capture	Illumina HiSeq	Phase_I	10174503	NM_003802	O95252|Q9P0U8	Silent	SNP	ENST00000418404.3	37	CCDS45613.1																																																																																				0.532	MYH13-003	KNOWN	alternative_3_UTR|alternative_5_UTR|NMD_exception|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442255.1	NM_003802	
NCOR1	9611	broad.mit.edu	37	17	15968278	15968278	+	Silent	SNP	T	T	C			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr17:15968278T>C	ENST00000268712.3	-	34	5264	c.5007A>G	c.(5005-5007)ggA>ggG	p.G1669G	NCOR1_ENST00000395851.1_Silent_p.G1685G|NCOR1_ENST00000395857.3_Silent_p.G253G	NM_006311.3	NP_006302.2	O75376	NCOR1_HUMAN	nuclear receptor corepressor 1	1669	Interaction with C1D. {ECO:0000250}.|Interaction with ETO.				CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation (GO:0002361)|cellular lipid metabolic process (GO:0044255)|cholesterol homeostasis (GO:0042632)|chromatin modification (GO:0016568)|circadian regulation of gene expression (GO:0032922)|definitive erythrocyte differentiation (GO:0060318)|gene expression (GO:0010467)|negative regulation of JNK cascade (GO:0046329)|negative regulation of phosphatidylinositol 3-kinase signaling (GO:0014067)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|Notch signaling pathway (GO:0007219)|positive regulation of histone deacetylation (GO:0031065)|regulation of fatty acid transport (GO:2000191)|regulation of glycolytic process by negative regulation of transcription from RNA polymerase II promoter (GO:0072362)|regulation of lipid transport by negative regulation of transcription from RNA polymerase II promoter (GO:0072368)|regulation of multicellular organism growth (GO:0040014)|small molecule metabolic process (GO:0044281)|spindle assembly (GO:0051225)|thalamus development (GO:0021794)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle microtubule (GO:0005876)|transcription factor complex (GO:0005667)|transcriptional repressor complex (GO:0017053)	chromatin binding (GO:0003682)|histone deacetylase binding (GO:0042826)|histone deacetylase regulator activity (GO:0035033)|nuclear hormone receptor binding (GO:0035257)|RNA polymerase II activating transcription factor binding (GO:0001102)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)|transcription regulatory region DNA binding (GO:0044212)	p.G1669G(1)		NS(2)|breast(13)|central_nervous_system(2)|cervix(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(17)|lung(26)|ovary(1)|prostate(7)|skin(2)|upper_aerodigestive_tract(6)|urinary_tract(10)	107				UCEC - Uterine corpus endometrioid carcinoma (92;0.101)		GAGTGCTTGTTCCCCCTGGAT	0.433																																					p.G1685G												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.A5055G	17						.						197.0	170.0	179.0					17																	15968278		2203	4300	6503	15909003	SO:0001819	synonymous_variant	9611	exon33			AF044209	CCDS11175.1, CCDS54094.1, CCDS54095.1	17p11.2	2014-06-12	2010-06-10		ENSG00000141027	ENSG00000141027			7672	protein-coding gene	gene with protein product	"""thyroid hormone- and retinoic acid receptor-associated corepressor 1"", ""protein phosphatase 1, regulatory subunit 109"""	600849	"""nuclear receptor co-repressor 1"""			7566114, 9724795	Standard	NM_006311		Approved	N-CoR, hCIT529I10, TRAC1, hN-CoR, KIAA1047, MGC104216, PPP1R109	uc002gpo.3	O75376	OTTHUMG00000059309	ENST00000268712.3:c.5007A>G	17.37:g.15968278T>C		Somatic		Capture	Illumina HiSeq	Phase_I	15909003	NM_001190440	B3DLF8|E9PGV6|Q86YY0|Q9UPV5|Q9UQ18	Silent	SNP	ENST00000268712.3	37	CCDS11175.1																																																																																				0.433	NCOR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131751.5	NM_006311	
ZNF287	57336	broad.mit.edu	37	17	16470734	16470734	+	Missense_Mutation	SNP	C	C	A	rs146385284	byFrequency	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr17:16470734C>A	ENST00000395824.1	-	2	929	c.312G>T	c.(310-312)gaG>gaT	p.E104D	ZNF287_ENST00000461555.1_5'Flank|ZNF287_ENST00000395825.3_Missense_Mutation_p.E104D			Q9HBT7	ZN287_HUMAN	zinc finger protein 287	97	SCAN box. {ECO:0000255|PROSITE- ProRule:PRU00187}.				positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cytokine biosynthetic process (GO:0042035)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.E97D(1)		breast(1)|endometrium(3)|kidney(2)|large_intestine(7)|lung(5)|prostate(1)|urinary_tract(1)	20				UCEC - Uterine corpus endometrioid carcinoma (92;0.083)		AAGTCCTAACCTCACCAGGCA	0.502																																					p.E104D												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G312T	17						.						85.0	86.0	85.0					17																	16470734		2203	4300	6503	16411459	SO:0001583	missense	57336	exon2			AF217227	CCDS11179.2	17p11.2	2013-01-09			ENSG00000141040	ENSG00000141040		"""Zinc fingers, C2H2-type"", ""-"", ""-"", ""-"""	13502	protein-coding gene	gene with protein product							Standard	NM_020653		Approved	ZKSCAN13, ZSCAN45	uc002gqi.2	Q9HBT7	OTTHUMG00000058993	ENST00000395824.1:c.312G>T	17.37:g.16470734C>A	ENSP00000379168:p.Glu104Asp	Somatic		Capture	Illumina HiSeq	Phase_I	16411459	NM_020653	Q6IAG1	Missense_Mutation	SNP	ENST00000395824.1	37	CCDS11179.2	.	.	.	.	.	.	.	.	.	.	C	16.25	3.069249	0.55539	.	.	ENSG00000141040	ENST00000395825;ENST00000395824	T;T	0.07567	3.18;3.18	5.06	2.04	0.26737	Retrovirus capsid, C-terminal (1);Transcription regulator SCAN (3);	0.000000	0.47852	D	0.000219	T	0.15262	0.0368	L	0.38649	1.16	0.27046	N	0.963882	D	0.69078	0.997	D	0.79108	0.992	T	0.02526	-1.1146	10	0.62326	D	0.03	.	6.9207	0.24387	0.0:0.7195:0.0:0.2805	.	97	Q9HBT7	ZN287_HUMAN	D	104	ENSP00000379169:E104D;ENSP00000379168:E104D	ENSP00000379168:E104D	E	-	3	2	ZNF287	16411459	0.963000	0.33076	1.000000	0.80357	0.994000	0.84299	0.254000	0.18314	0.422000	0.26005	-0.136000	0.14681	GAG		0.502	ZNF287-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130504.1		
MPRIP	23164	broad.mit.edu	37	17	17030083	17030083	+	Missense_Mutation	SNP	G	G	A	rs372089723		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr17:17030083G>A	ENST00000341712.4	+	4	335	c.335G>A	c.(334-336)cGc>cAc	p.R112H	MPRIP_ENST00000395811.5_Missense_Mutation_p.R112H|MPRIP_ENST00000444976.1_Missense_Mutation_p.R112H|MPRIP_ENST00000395804.3_Missense_Mutation_p.R112H			Q6WCQ1	MPRIP_HUMAN	myosin phosphatase Rho interacting protein	112	Interaction with F-actin. {ECO:0000250}.|PH 1. {ECO:0000255|PROSITE- ProRule:PRU00145}.					actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)		p.R112H(1)		biliary_tract(1)|breast(1)|endometrium(4)|kidney(2)|large_intestine(6)|lung(9)|ovary(3)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	31						GGGGAGGGCCGCACGGGCCAG	0.597																																					p.R112H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G335A	17						.						87.0	82.0	84.0					17																	17030083		2203	4300	6503	16970808	SO:0001583	missense	23164	exon4			BC014102	CCDS32578.1, CCDS42268.1	17p11.2	2013-01-10			ENSG00000133030	ENSG00000133030		"""Pleckstrin homology (PH) domain containing"""	30321	protein-coding gene	gene with protein product	"""Rho interacting protein 3"""	612935				10048485	Standard	NM_201274		Approved	RHOIP3, M-RIP, p116Rip	uc002gqy.2	Q6WCQ1	OTTHUMG00000059276	ENST00000341712.4:c.335G>A	17.37:g.17030083G>A	ENSP00000342379:p.Arg112His	Somatic		Capture	Illumina HiSeq	Phase_I	16970808	NM_015134	Q3KQZ5|Q5FB94|Q6DHW2|Q7Z5Y2|Q8N390|Q96G40	Missense_Mutation	SNP	ENST00000341712.4	37	CCDS32578.1	.	.	.	.	.	.	.	.	.	.	G	29.0	4.968482	0.92855	.	.	ENSG00000133030	ENST00000444976;ENST00000395811;ENST00000395804;ENST00000341712	D;D;D;D	0.93019	-3.15;-3.15;-3.15;-3.15	5.59	5.59	0.84812	Pleckstrin homology-type (1);Pleckstrin homology domain (3);	.	.	.	.	D	0.96140	0.8742	L	0.58101	1.795	0.54753	D	0.999985	D;D	0.89917	1.0;0.998	D;D	0.83275	0.996;0.953	D	0.96228	0.9166	9	0.72032	D	0.01	.	19.5944	0.95530	0.0:0.0:1.0:0.0	.	112;112	Q6WCQ1-2;Q6WCQ1	.;MPRIP_HUMAN	H	112	ENSP00000400189:R112H;ENSP00000379156:R112H;ENSP00000379149:R112H;ENSP00000342379:R112H	ENSP00000342379:R112H	R	+	2	0	MPRIP	16970808	1.000000	0.71417	0.995000	0.50966	0.989000	0.77384	5.313000	0.65798	2.642000	0.89623	0.561000	0.74099	CGC		0.597	MPRIP-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000131587.1	NM_015134	
MYO15A	51168	broad.mit.edu	37	17	18047264	18047264	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr17:18047264C>A	ENST00000205890.5	+	28	6465	c.6127C>A	c.(6127-6129)Ctg>Atg	p.L2043M	snoU13_ENST00000459354.1_RNA	NM_016239.3	NP_057323.3	Q9UKN7	MYO15_HUMAN	myosin XVA	2043	Tail.				inner ear morphogenesis (GO:0042472)|locomotory behavior (GO:0007626)|sensory perception of sound (GO:0007605)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|myosin complex (GO:0016459)|stereocilium (GO:0032420)	ATP binding (GO:0005524)|motor activity (GO:0003774)	p.L2043M(1)		breast(5)|central_nervous_system(2)|endometrium(17)|kidney(3)|large_intestine(16)|lung(27)|ovary(3)|pancreas(1)|prostate(6)|skin(13)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	99	all_neural(463;0.228)					CACACTGCCCCTGGACATCAA	0.597																																					p.L2043M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C6127A	17						.						45.0	47.0	46.0					17																	18047264		2071	4206	6277	17987989	SO:0001583	missense	51168	exon27			AF144094	CCDS42271.1	17p11.2	2011-09-27			ENSG00000091536	ENSG00000091536		"""Myosins / Myosin superfamily : Class XV"""	7594	protein-coding gene	gene with protein product		602666		DFNB3, MYO15		9603736	Standard	NM_016239		Approved		uc021trl.1	Q9UKN7	OTTHUMG00000059390	ENST00000205890.5:c.6127C>A	17.37:g.18047264C>A	ENSP00000205890:p.Leu2043Met	Somatic		Capture	Illumina HiSeq	Phase_I	17987989	NM_016239	B4DFC7	Missense_Mutation	SNP	ENST00000205890.5	37	CCDS42271.1	.	.	.	.	.	.	.	.	.	.	C	17.21	3.331998	0.60853	.	.	ENSG00000091536	ENST00000205890	D	0.88431	-2.38	5.28	4.3	0.51218	.	.	.	.	.	D	0.93631	0.7966	M	0.77103	2.36	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.93402	0.6761	9	0.51188	T	0.08	.	13.2882	0.60255	0.0:0.9232:0.0:0.0768	.	2043	Q9UKN7	MYO15_HUMAN	M	2043	ENSP00000205890:L2043M	ENSP00000205890:L2043M	L	+	1	2	MYO15A	17987989	1.000000	0.71417	1.000000	0.80357	0.956000	0.61745	4.528000	0.60580	2.472000	0.83506	0.462000	0.41574	CTG		0.597	MYO15A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132048.1	NM_016239	
TOP3A	7156	broad.mit.edu	37	17	18208457	18208457	+	Silent	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr17:18208457G>A	ENST00000321105.5	-	5	682	c.468C>T	c.(466-468)atC>atT	p.I156I	TOP3A_ENST00000582230.1_5'Flank|TOP3A_ENST00000542570.1_Silent_p.I61I	NM_004618.3	NP_004609.1	Q13472	TOP3A_HUMAN	topoisomerase (DNA) III alpha	156	Toprim. {ECO:0000255|PROSITE- ProRule:PRU00995}.				DNA topological change (GO:0006265)|meiotic nuclear division (GO:0007126)	chromosome (GO:0005694)|nucleus (GO:0005634)|PML body (GO:0016605)	DNA binding (GO:0003677)|DNA topoisomerase type I activity (GO:0003917)|zinc ion binding (GO:0008270)	p.I156I(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(7)|lung(15)|ovary(1)|skin(6)|stomach(2)|urinary_tract(1)	36						TCTCAAACCCGATGTTTTCGC	0.448																																					p.I156I												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C468T	17						.						134.0	132.0	133.0					17																	18208457		2203	4300	6503	18149182	SO:0001819	synonymous_variant	7156	exon5			U43431	CCDS11194.1	17p12-p11.2	2014-02-18			ENSG00000177302	ENSG00000177302			11992	protein-coding gene	gene with protein product	"""zinc finger, GRF-type containing 7"""	601243		TOP3		9450867	Standard	NM_004618		Approved	ZGRF7	uc002gsx.1	Q13472	OTTHUMG00000059391	ENST00000321105.5:c.468C>T	17.37:g.18208457G>A		Somatic		Capture	Illumina HiSeq	Phase_I	18149182	NM_004618	A8KA61|B4DK80|D3DXC7|Q13473	Silent	SNP	ENST00000321105.5	37	CCDS11194.1	.	.	.	.	.	.	.	.	.	.	G	7.074	0.568832	0.13560	.	.	ENSG00000177302	ENST00000412083	.	.	.	5.61	-11.2	0.00127	.	.	.	.	.	T	0.71039	0.3293	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.80441	-0.1381	4	.	.	.	-23.0834	21.9845	0.99964	0.3016:0.0:0.6984:0.0	.	.	.	.	W	136	.	.	R	-	1	2	TOP3A	18149182	0.002000	0.14202	0.198000	0.23420	0.670000	0.39368	-1.079000	0.03410	-2.592000	0.00456	-0.937000	0.02696	CGG		0.448	TOP3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132052.2		
DPH1	1801	broad.mit.edu	37	17	1936801	1936801	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr17:1936801C>T	ENST00000263083.6	+	2	124	c.79C>T	c.(79-81)Cgg>Tgg	p.R27W	DPH1_ENST00000570477.1_5'UTR	NM_001383.3	NP_001374.3	Q9BZG8	DPH1_HUMAN	diphthamide biosynthesis 1	27					cell proliferation (GO:0008283)|peptidyl-diphthamide biosynthetic process from peptidyl-histidine (GO:0017183)|translation (GO:0006412)	cytoplasm (GO:0005737)|nucleus (GO:0005634)		p.R27W(1)		endometrium(3)|large_intestine(2)|lung(6)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	17						CATTCTAGGTCGGGCCCCTCG	0.587																																					p.R27W												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C79T	17						.						52.0	56.0	55.0					17																	1936801		1845	4081	5926	1883551	SO:0001583	missense	1801	exon2			S81752	CCDS42228.1	17p13.3	2013-05-02	2013-05-02	2005-06-03	ENSG00000108963	ENSG00000108963			3003	protein-coding gene	gene with protein product	"""ovarian tumor suppressor candidate 1"""	603527	"""diptheria toxin resistance protein required for diphthamide biosynthesis-like 1 (S. cerevisiae)"", ""DPH-like 1 (S. cerevisiae)"", ""DPH1 homolog (S. cerevisiae)"""	DPH2L, DPH2L1		8603384, 15485916, 22869748	Standard	NM_001383		Approved	OVCA1	uc002fts.3	Q9BZG8	OTTHUMG00000177724	ENST00000263083.6:c.79C>T	17.37:g.1936801C>T	ENSP00000263083:p.Arg27Trp	Somatic		Capture	Illumina HiSeq	Phase_I	1883551	NM_001383	D3DTI3|Q16439|Q4VBA2|Q9BTW7|Q9UCY0	Missense_Mutation	SNP	ENST00000263083.6	37	CCDS42228.1	.	.	.	.	.	.	.	.	.	.	C	13.85	2.360846	0.41801	.	.	ENSG00000108963	ENST00000263083	T	0.34072	1.38	5.41	5.41	0.78517	.	0.288137	0.31246	N	0.007985	T	0.56108	0.1963	M	0.76328	2.33	0.80722	D	1	D;D;D	0.76494	0.999;0.999;0.99	D;D;P	0.64776	0.929;0.929;0.492	T	0.59043	-0.7528	10	0.62326	D	0.03	-12.5373	11.2708	0.49138	0.0:0.9155:0.0:0.0845	.	37;37;27	E7ENH3;B4DNK0;Q9BZG8	.;.;DPH1_HUMAN	W	27	ENSP00000263083:R27W	ENSP00000263083:R27W	R	+	1	2	DPH1	1883551	0.982000	0.34865	0.984000	0.44739	0.018000	0.09664	0.707000	0.25704	2.539000	0.85634	0.655000	0.94253	CGG		0.587	DPH1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000438660.1	NM_001383	
FAM83G	644815	broad.mit.edu	37	17	18874870	18874870	+	Silent	SNP	G	G	A	rs377066158		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr17:18874870G>A	ENST00000388995.6	-	6	2497	c.2274C>T	c.(2272-2274)ccC>ccT	p.P758P	SLC5A10_ENST00000417251.2_Intron|SLC5A10_ENST00000395643.2_Intron|FAM83G_ENST00000585154.2_Silent_p.P758P|SLC5A10_ENST00000395642.1_Intron|SLC5A10_ENST00000317977.6_Intron|SLC5A10_ENST00000395645.3_Intron|FAM83G_ENST00000345041.4_Silent_p.P758P|SLC5A10_ENST00000395647.2_Intron			A6ND36	FA83G_HUMAN	family with sequence similarity 83, member G	758					BMP signaling pathway (GO:0030509)	cytosol (GO:0005829)|nucleus (GO:0005634)		p.P758P(1)		central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(3)|lung(7)|ovary(2)|prostate(3)|stomach(1)	22						TTGGGCTGCCGGGATCCGGAA	0.647																																					p.P758P												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C2274T	17						.	G	,,	1,3895		0,1,1947	61.0	71.0	68.0		2274,,	-9.1	0.0	17		68	1,8275		0,1,4137	no	coding-synonymous,intron,intron	SLC5A10,FAM83G	NM_001039999.2,NM_001042450.1,NM_152351.3	,,	0,2,6084	AA,AG,GG		0.0121,0.0257,0.0164	,,	758/824,,	18874870	2,12170	1948	4138	6086	18815595	SO:0001819	synonymous_variant	644815	exon6			AK123558	CCDS42276.1	17p11.2	2014-05-01	2006-03-22		ENSG00000188522	ENSG00000188522			32554	protein-coding gene	gene with protein product	"""protein associated with SMAD1"""	615886				24554596	Standard	NM_001039999		Approved	FLJ41564, PAWS1	uc002guw.3	A6ND36	OTTHUMG00000059411	ENST00000388995.6:c.2274C>T	17.37:g.18874870G>A		Somatic		Capture	Illumina HiSeq	Phase_I	18815595	NM_001039999	Q3KQZ4|Q6ZW60	Silent	SNP	ENST00000388995.6	37	CCDS42276.1																																																																																				0.647	FAM83G-002	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253108.4		
MAPK7	5598	broad.mit.edu	37	17	19284064	19284064	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr17:19284064G>A	ENST00000308406.5	+	4	928	c.542G>A	c.(541-543)cGt>cAt	p.R181H	MAPK7_ENST00000299612.7_Missense_Mutation_p.R42H|B9D1_ENST00000575403.1_5'Flank|B9D1_ENST00000468679.3_5'Flank|MFAP4_ENST00000574313.2_5'Flank|MAPK7_ENST00000571657.1_Intron|MAPK7_ENST00000395602.4_Missense_Mutation_p.R181H|MAPK7_ENST00000395604.3_Missense_Mutation_p.R181H|B9D1_ENST00000477478.2_5'Flank	NM_139033.2	NP_620602.2	Q13164	MK07_HUMAN	mitogen-activated protein kinase 7	181	Necessary for oligomerization. {ECO:0000250}.|Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cAMP-mediated signaling (GO:0019933)|cell cycle (GO:0007049)|cell differentiation (GO:0030154)|cellular response to growth factor stimulus (GO:0071363)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to laminar fluid shear stress (GO:0071499)|cellular response to transforming growth factor beta stimulus (GO:0071560)|innate immune response (GO:0045087)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of cAMP catabolic process (GO:0030821)|negative regulation of cyclic-nucleotide phosphodiesterase activity (GO:0051344)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|negative regulation of heterotypic cell-cell adhesion (GO:0034115)|negative regulation of inflammatory response (GO:0050728)|negative regulation of NFAT protein import into nucleus (GO:0051534)|negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway (GO:1902176)|negative regulation of response to cytokine stimulus (GO:0060761)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-serine phosphorylation (GO:0018105)|positive regulation of protein metabolic process (GO:0051247)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase II promoter in response to stress (GO:0036003)|regulation of angiogenesis (GO:0045765)|signal transduction (GO:0007165)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)	ATP binding (GO:0005524)|MAP kinase activity (GO:0004707)|mitogen-activated protein kinase binding (GO:0051019)	p.R181H(1)		autonomic_ganglia(1)|central_nervous_system(4)|endometrium(5)|kidney(2)|large_intestine(4)|lung(9)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	30	all_cancers(12;2.87e-05)|all_epithelial(12;0.00114)|Hepatocellular(7;0.00345)|Breast(13;0.206)					GTCATCCACCGTGACCTGAAG	0.562																																					p.R181H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G542A	17						.						143.0	112.0	123.0					17																	19284064		2203	4300	6503	19224657	SO:0001583	missense	5598	exon4			U25278	CCDS11206.1, CCDS11207.1	17p11.2	2011-06-09			ENSG00000166484	ENSG00000166484	2.7.11.24	"""Mitogen-activated protein kinase cascade / Kinases"""	6880	protein-coding gene	gene with protein product	"""BMK1 kinase"", ""extracellular-signal-regulated kinase 5"""	602521		PRKM7		10072598, 7759517	Standard	NM_139032		Approved	BMK1, ERK5	uc002gvp.3	Q13164	OTTHUMG00000059587	ENST00000308406.5:c.542G>A	17.37:g.19284064G>A	ENSP00000311005:p.Arg181His	Somatic		Capture	Illumina HiSeq	Phase_I	19224657	NM_139033	Q16634|Q59F50|Q6QLU7|Q7L4P4|Q969G1|Q96G51	Missense_Mutation	SNP	ENST00000308406.5	37	CCDS11206.1	.	.	.	.	.	.	.	.	.	.	G	26.4	4.736000	0.89482	.	.	ENSG00000166484	ENST00000308406;ENST00000299612;ENST00000443215;ENST00000395604;ENST00000395602	T;T;T;T;T	0.65178	-0.14;-0.14;-0.14;-0.14;-0.14	4.74	4.74	0.60224	Serine/threonine-protein kinase-like domain (1);MAP kinase, conserved site (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	D	0.87462	0.6183	H	0.98833	4.345	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.92539	0.6040	10	0.87932	D	0	-11.2351	15.5975	0.76599	0.0:0.0:1.0:0.0	.	181	Q13164	MK07_HUMAN	H	181;42;181;181;181	ENSP00000311005:R181H;ENSP00000299612:R42H;ENSP00000412902:R181H;ENSP00000378968:R181H;ENSP00000378966:R181H	ENSP00000299612:R42H	R	+	2	0	MAPK7	19224657	1.000000	0.71417	0.957000	0.39632	0.995000	0.86356	9.327000	0.96396	2.335000	0.79485	0.561000	0.74099	CGT		0.562	MAPK7-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132506.1	NM_139033	
ULK2	9706	broad.mit.edu	37	17	19687020	19687020	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr17:19687020G>A	ENST00000395544.4	-	22	2949	c.2450C>T	c.(2449-2451)aCg>aTg	p.T817M	ULK2_ENST00000361658.2_Missense_Mutation_p.T817M	NM_014683.3	NP_055498.3	Q8IYT8	ULK2_HUMAN	unc-51 like autophagy activating kinase 2	817	CTD-like region.				autophagic vacuole assembly (GO:0000045)|axon extension (GO:0048675)|negative regulation of collateral sprouting (GO:0048671)|protein autophosphorylation (GO:0046777)|regulation of autophagy (GO:0010506)|response to starvation (GO:0042594)|signal transduction (GO:0007165)	ATG1/UKL1 signaling complex (GO:0034273)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|pre-autophagosomal structure membrane (GO:0034045)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)	p.T817M(1)		large_intestine(1)|skin(4)|stomach(1)	6	all_cancers(12;4.97e-05)|all_epithelial(12;0.00362)|Breast(13;0.186)					CTCCATCAGCGTCTCCTCCGG	0.473																																					p.T817M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C2450T	17						.						96.0	108.0	104.0					17																	19687020		2203	4300	6503	19627612	SO:0001583	missense	9706	exon22			AB014523	CCDS11213.1	17p11.2	2014-02-12	2013-07-02		ENSG00000083290	ENSG00000083290	2.7.11.1		13480	protein-coding gene	gene with protein product		608650	"""unc-51 (C. elegans)-like kinase 2"", ""unc-51-like kinase 2 (C. elegans)"""			10557072	Standard	NM_014683		Approved	KIAA0623, Unc51.2, ATG1B	uc002gwn.3	Q8IYT8	OTTHUMG00000059511	ENST00000395544.4:c.2450C>T	17.37:g.19687020G>A	ENSP00000378914:p.Thr817Met	Somatic		Capture	Illumina HiSeq	Phase_I	19627612	NM_001142610	A8MY69|O75119	Missense_Mutation	SNP	ENST00000395544.4	37	CCDS11213.1	.	.	.	.	.	.	.	.	.	.	G	19.55	3.848913	0.71603	.	.	ENSG00000083290	ENST00000361658;ENST00000395544	T;T	0.47177	0.85;0.85	5.58	5.58	0.84498	Serine/threonine-protein kinase, C-terminal (1);	0.049019	0.85682	D	0.000000	T	0.71290	0.3322	M	0.78049	2.395	0.50313	D	0.999864	D	0.89917	1.0	D	0.91635	0.999	T	0.74444	-0.3663	10	0.87932	D	0	-15.2126	18.5624	0.91105	0.0:0.0:1.0:0.0	.	817	Q8IYT8	ULK2_HUMAN	M	817	ENSP00000354877:T817M;ENSP00000378914:T817M	ENSP00000354877:T817M	T	-	2	0	ULK2	19627612	1.000000	0.71417	0.886000	0.34754	0.395000	0.30598	9.403000	0.97302	2.611000	0.88343	0.655000	0.94253	ACG		0.473	ULK2-001	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132375.2	NM_014683	
USP22	23326	broad.mit.edu	37	17	20931957	20931957	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr17:20931957C>T	ENST00000261497.4	-	2	405	c.202G>A	c.(202-204)Gtc>Atc	p.V68I	USP22_ENST00000455117.2_5'UTR|USP22_ENST00000537526.2_Missense_Mutation_p.V56I	NM_015276.1	NP_056091.1	Q9UPT9	UBP22_HUMAN	ubiquitin specific peptidase 22	68					cell cycle (GO:0007049)|chromatin organization (GO:0006325)|embryo development (GO:0009790)|histone deubiquitination (GO:0016578)|histone H4 acetylation (GO:0043967)|histone ubiquitination (GO:0016574)|positive regulation of mitotic cell cycle (GO:0045931)|positive regulation of transcription, DNA-templated (GO:0045893)|protein deubiquitination (GO:0016579)|transcription, DNA-templated (GO:0006351)|ubiquitin-dependent protein catabolic process (GO:0006511)	SAGA complex (GO:0000124)	enzyme binding (GO:0019899)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|transcription coactivator activity (GO:0003713)|ubiquitin-specific protease activity (GO:0004843)|zinc ion binding (GO:0008270)	p.V290I(1)		endometrium(2)|kidney(3)|large_intestine(2)|lung(6)|ovary(1)|prostate(1)	15						TTGAGGTGGACGCCACAGACA	0.517																																					p.V68I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G202A	17						.						58.0	62.0	61.0					17																	20931957		2065	4206	6271	20872549	SO:0001583	missense	23326	exon2			AB028986	CCDS42285.1	17p11.2	2006-11-24	2005-08-08		ENSG00000124422	ENSG00000124422		"""Ubiquitin-specific peptidases"""	12621	protein-coding gene	gene with protein product		612116	"""ubiquitin specific protease 22"", ""ubiquitin specific peptidase 3-like"""	USP3L		12838346	Standard	NM_015276		Approved	KIAA1063	uc002gym.4	Q9UPT9	OTTHUMG00000133621	ENST00000261497.4:c.202G>A	17.37:g.20931957C>T	ENSP00000261497:p.Val68Ile	Somatic		Capture	Illumina HiSeq	Phase_I	20872549	NM_015276	A0JNS3|Q2NLE2|Q6MZY4|Q8TBS8|Q96IW5	Missense_Mutation	SNP	ENST00000261497.4	37	CCDS42285.1	.	.	.	.	.	.	.	.	.	.	c	15.70	2.911092	0.52439	.	.	ENSG00000124422	ENST00000455117;ENST00000537526;ENST00000261497	T;T	0.42131	0.98;0.98	4.96	2.94	0.34122	Zinc finger, RING/FYVE/PHD-type (1);Zinc finger, UBP-type (2);	0.517985	0.18900	N	0.128068	T	0.23572	0.0570	N	0.14661	0.345	0.27658	N	0.947165	B;B	0.10296	0.001;0.003	B;B	0.15484	0.003;0.013	T	0.18745	-1.0327	10	0.17369	T	0.5	.	10.2541	0.43385	0.0:0.7891:0.1364:0.0744	.	56;68	Q9UPT9-2;Q9UPT9	.;UBP22_HUMAN	I	136;56;68	ENSP00000440950:V56I;ENSP00000261497:V68I	ENSP00000261497:V68I	V	-	1	0	USP22	20872549	0.984000	0.35163	0.021000	0.16686	0.966000	0.64601	2.659000	0.46741	0.485000	0.27652	0.655000	0.94253	GTC		0.517	USP22-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444169.1		
KSR1	8844	broad.mit.edu	37	17	25944415	25944415	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr17:25944415G>A	ENST00000319524.6	+	20	2654	c.2654G>A	c.(2653-2655)cGg>cAg	p.R885Q	KSR1_ENST00000582410.1_Missense_Mutation_p.R99Q|KSR1_ENST00000509603.2_Missense_Mutation_p.R863Q|KSR1_ENST00000268763.6_Missense_Mutation_p.R748Q|KSR1_ENST00000398988.3_Missense_Mutation_p.R748Q			Q8IVT5	KSR1_HUMAN	kinase suppressor of ras 1	885					Ras protein signal transduction (GO:0007265)	endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)	p.R885Q(1)|p.R863Q(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|large_intestine(5)|lung(12)|prostate(2)|urinary_tract(1)	28	Lung NSC(42;0.00836)		BRCA - Breast invasive adenocarcinoma(3;0.00122)	UCEC - Uterine corpus endometrioid carcinoma (53;0.168)		AAGCTGAACCGGCGGCTCTCC	0.607																																					p.R748Q	Esophageal Squamous(88;1120 1336 6324 10502 16832)											.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G2243A	17						.						34.0	37.0	36.0					17																	25944415		1978	4157	6135	22968542	SO:0001583	missense	8844	exon20			U43586	CCDS58532.1	17q11.2	2012-05-23	2005-12-14	2005-12-14	ENSG00000141068	ENSG00000141068			6465	protein-coding gene	gene with protein product		601132	"""kinase suppressor of ras"""	KSR		8521512	Standard	XM_006722151		Approved	RSU2	uc031qzj.1	Q8IVT5	OTTHUMG00000132051	ENST00000319524.6:c.2654G>A	17.37:g.25944415G>A	ENSP00000323178:p.Arg885Gln	Somatic		Capture	Illumina HiSeq	Phase_I	22968542	NM_014238	F8WEA9|H7BYU0|Q13476	Missense_Mutation	SNP	ENST00000319524.6	37		.	.	.	.	.	.	.	.	.	.	G	19.26	3.793582	0.70452	.	.	ENSG00000141068	ENST00000319524;ENST00000509603;ENST00000268763;ENST00000398982	T;T;T	0.81078	-1.41;-1.45;-1.39	5.56	5.56	0.83823	Protein kinase-like domain (1);	0.000000	0.85682	D	0.000000	D	0.84588	0.5505	L	0.27053	0.805	0.80722	D	1	D;D	0.89917	1.0;0.996	D;D	0.83275	0.996;0.971	D	0.85790	0.1367	10	0.56958	D	0.05	.	18.5192	0.90945	0.0:0.0:1.0:0.0	.	883;863	Q8IVT5;F5H0K8	KSR1_HUMAN;.	Q	885;863;748;748	ENSP00000323178:R885Q;ENSP00000438795:R863Q;ENSP00000268763:R748Q	ENSP00000268763:R748Q	R	+	2	0	KSR1	22968542	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.785000	0.85724	2.614000	0.88457	0.557000	0.71058	CGG		0.607	KSR1-202	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_014238	
SLC13A2	9058	broad.mit.edu	37	17	26818764	26818764	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr17:26818764G>A	ENST00000314669.5	+	6	1192	c.772G>A	c.(772-774)Ggc>Agc	p.G258S	SLC13A2_ENST00000537681.1_Missense_Mutation_p.G187S|SLC13A2_ENST00000545060.1_Missense_Mutation_p.G215S|SLC13A2_ENST00000444914.3_Missense_Mutation_p.G307S	NM_003984.3	NP_003975.1	Q13183	S13A2_HUMAN	solute carrier family 13 (sodium-dependent dicarboxylate transporter), member 2	258					dicarboxylic acid transport (GO:0006835)|transmembrane transport (GO:0055085)|transport (GO:0006810)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	low-affinity sodium:dicarboxylate symporter activity (GO:0015361)	p.G258S(1)		breast(2)|endometrium(2)|kidney(1)|large_intestine(8)|lung(10)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	26	all_lung(13;0.000871)|Lung NSC(42;0.0027)			UCEC - Uterine corpus endometrioid carcinoma (53;0.154)	Succinic acid(DB00139)	CCCCCAAAACGGCAACGTGGT	0.597																																					p.G215S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G643A	17						.						161.0	138.0	146.0					17																	26818764		2203	4300	6503	23842891	SO:0001583	missense	9058	exon5			U26209	CCDS11231.1, CCDS54098.1	17p13.2	2013-05-22			ENSG00000007216	ENSG00000007216		"""Solute carriers"""	10917	protein-coding gene	gene with protein product		604148				8967342, 10343111	Standard	NM_001145975		Approved	NaDC-1	uc010wan.2	Q13183	OTTHUMG00000132523	ENST00000314669.5:c.772G>A	17.37:g.26818764G>A	ENSP00000316202:p.Gly258Ser	Somatic		Capture	Illumina HiSeq	Phase_I	23842891	NM_001145976	B2RBI9|B4DPL1|E7ETH5|Q4VAR7	Missense_Mutation	SNP	ENST00000314669.5	37	CCDS11231.1	.	.	.	.	.	.	.	.	.	.	G	8.108	0.778259	0.16120	.	.	ENSG00000007216	ENST00000314669;ENST00000444914;ENST00000545060;ENST00000541739;ENST00000537681	T;T;T;T	0.03951	3.75;3.75;3.75;3.75	5.52	-3.14	0.05250	.	1.067880	0.07043	N	0.830449	T	0.03434	0.0099	L	0.45285	1.41	0.09310	N	1	P;B;B;P;B	0.34892	0.468;0.094;0.053;0.474;0.053	B;B;B;B;B	0.25405	0.04;0.053;0.06;0.036;0.037	T	0.46303	-0.9201	10	0.12103	T	0.63	-26.0201	6.92	0.24383	0.1311:0.4086:0.3797:0.0806	.	215;307;214;187;258	F5GWV6;E7ETH5;B4E1M6;G3V1L2;Q13183	.;.;.;.;S13A2_HUMAN	S	258;307;215;214;187	ENSP00000316202:G258S;ENSP00000392411:G307S;ENSP00000441935:G215S;ENSP00000440802:G187S	ENSP00000316202:G258S	G	+	1	0	SLC13A2	23842891	0.000000	0.05858	0.000000	0.03702	0.249000	0.25844	0.235000	0.17948	-0.293000	0.08986	0.557000	0.71058	GGC		0.597	SLC13A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255722.1	NM_003984	
KIAA0100	9703	broad.mit.edu	37	17	26946934	26946934	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr17:26946934G>A	ENST00000528896.2	-	30	5538	c.5464C>T	c.(5464-5466)Cgg>Tgg	p.R1822W	SPAG5-AS1_ENST00000424210.1_RNA|KIAA0100_ENST00000389003.3_Missense_Mutation_p.R1679W|KIAA0100_ENST00000544884.1_Missense_Mutation_p.R1679W|SPAG5-AS1_ENST00000414744.1_RNA|KIAA0100_ENST00000579924.2_5'Flank	NM_014680.3	NP_055495.2	Q14667	K0100_HUMAN	KIAA0100	1822						extracellular region (GO:0005576)		p.R1822W(1)		breast(3)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(13)|lung(23)|ovary(2)|prostate(2)|skin(6)|stomach(2)|urinary_tract(3)	68	Lung NSC(42;0.00431)					ACATGCTGCCGCACAGCCTCC	0.493																																					p.R1822W												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C5464T	17						.						99.0	91.0	94.0					17																	26946934		2203	4300	6503	23971061	SO:0001583	missense	9703	exon30			D43947	CCDS32595.1	17q11.2	2012-11-29			ENSG00000007202	ENSG00000007202			28960	protein-coding gene	gene with protein product	"""cancer/testis antigen 101"", ""breast cancer overexpressed gene 1"""	610664				16289875	Standard	NM_014680		Approved	DKFZp686M0843, MGC111488, BCOX1, CT101, BCOX	uc002hbu.3	Q14667	OTTHUMG00000166587	ENST00000528896.2:c.5464C>T	17.37:g.26946934G>A	ENSP00000436773:p.Arg1822Trp	Somatic		Capture	Illumina HiSeq	Phase_I	23971061	NM_014680	A6NCX3|Q3SYN5|Q49A07|Q5H9T4|Q6WG74|Q6ZP51|Q96HH8	Missense_Mutation	SNP	ENST00000528896.2	37	CCDS32595.1	.	.	.	.	.	.	.	.	.	.	G	17.99	3.522641	0.64747	.	.	ENSG00000007202	ENST00000005905;ENST00000389003;ENST00000528896;ENST00000544884	T;T	0.55413	0.52;0.52	5.53	3.24	0.37175	FMP27,  C-terminal (1);	0.051185	0.64402	D	0.000001	T	0.71929	0.3398	M	0.80332	2.49	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.77117	-0.2706	10	0.72032	D	0.01	.	13.3585	0.60642	0.0:0.0:0.5836:0.4164	.	1822	Q14667	K0100_HUMAN	W	1822;1792;1822;1679	ENSP00000436773:R1822W;ENSP00000446443:R1679W	ENSP00000005905:R1822W	R	-	1	2	KIAA0100	23971061	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	1.408000	0.34668	1.435000	0.47434	0.655000	0.94253	CGG		0.493	KIAA0100-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390571.3	NM_014680	
SUPT6H	6830	broad.mit.edu	37	17	27030737	27030737	+	IGR	SNP	G	G	A	rs201634767	byFrequency	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr17:27030737G>A	ENST00000314616.6	+	0	6518				PROCA1_ENST00000439862.3_Missense_Mutation_p.R286W|PROCA1_ENST00000579650.1_5'Flank|PROCA1_ENST00000301039.2_Missense_Mutation_p.R284W|PROCA1_ENST00000581289.1_3'UTR	NM_003170.3	NP_003161.2	Q7KZ85	SPT6H_HUMAN	suppressor of Ty 6 homolog (S. cerevisiae)						chromatin remodeling (GO:0006338)|mRNA processing (GO:0006397)|mRNA transport (GO:0051028)|negative regulation of histone H3-K27 methylation (GO:0061086)|positive regulation of transcription elongation from RNA polymerase II promoter (GO:0032968)|regulation of isotype switching (GO:0045191)|regulation of mRNA export from nucleus (GO:0010793)|regulation of mRNA processing (GO:0050684)|regulation of muscle cell differentiation (GO:0051147)|regulation of transcription, DNA-templated (GO:0006355)|RNA splicing (GO:0008380)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	nucleus (GO:0005634)	DNA binding (GO:0003677)|histone binding (GO:0042393)|hydrolase activity, acting on ester bonds (GO:0016788)|poly(A) RNA binding (GO:0044822)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.R284W(1)		NS(4)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(9)|kidney(2)|large_intestine(15)|lung(21)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	64	Lung NSC(42;0.00431)					CCCTGCCCCCGGCCATTGTAA	0.572													G|||	2	0.000399361	0.0015	0.0	5008	,	,		17012	0.0		0.0	False		,,,				2504	0.0				p.R284W												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C850T	17						.	G	TRP/ARG	1,4405	2.1+/-5.4	0,1,2202	101.0	99.0	100.0		850	1.4	0.0	17		100	0,8600		0,0,4300	no	missense	PROCA1	NM_152465.1	101	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	probably-damaging	284/337	27030737	1,13005	2203	4300	6503	24054864	SO:0001628	intergenic_variant	147011	exon4			U38658	CCDS32596.1	17q11.2	2013-02-14	2001-11-28			ENSG00000109111		"""SH2 domain containing"""	11470	protein-coding gene	gene with protein product		601333	"""suppressor of Ty (S.cerevisiae) 6 homolog"""			8786132	Standard	XM_005258026		Approved	KIAA0162, SPT6H	uc002hby.3	Q7KZ85			17.37:g.27030737G>A		Somatic		Capture	Illumina HiSeq	Phase_I	24054864	NM_152465	A7E2B4|Q15737|Q6GMQ4|Q7KYW9|Q7LDK4|Q8N526|Q92775|Q96AH3|Q9BTH9|Q9BTI2	Missense_Mutation	SNP	ENST00000314616.6	37	CCDS32596.1	2	9.157509157509158E-4	2	0.0040650406504065045	0	0.0	0	0.0	0	0.0	G	14.82	2.649646	0.47362	2.27E-4	0.0	ENSG00000167525	ENST00000301039;ENST00000439862;ENST00000415329	T;T	0.05025	3.51;3.51	5.1	1.4	0.22301	.	0.474042	0.19164	N	0.121110	T	0.08537	0.0212	N	0.19112	0.55	0.09310	N	1	B;D;D	0.76494	0.004;0.999;0.999	B;P;P	0.62298	0.001;0.9;0.9	T	0.16719	-1.0393	10	0.54805	T	0.06	-0.9737	5.4087	0.16336	0.0977:0.0:0.4784:0.4239	.	312;286;284	Q8NCQ7;G5E9R8;Q8NCQ7-2	PRCA1_HUMAN;.;.	W	284;286;312	ENSP00000301039:R284W;ENSP00000411400:R286W	ENSP00000301039:R284W	R	-	1	2	PROCA1	24054864	0.001000	0.12720	0.011000	0.14972	0.660000	0.38997	-0.066000	0.11598	0.627000	0.30340	-0.119000	0.15052	CGG		0.572	SUPT6H-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446422.2	NM_003170	
PHF12	57649	broad.mit.edu	37	17	27238234	27238234	+	Missense_Mutation	SNP	G	G	A	rs139914566		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr17:27238234G>A	ENST00000332830.4	-	10	2921	c.2111C>T	c.(2110-2112)aCg>aTg	p.T704M	PHF12_ENST00000577226.1_Missense_Mutation_p.T704M|PHF12_ENST00000582655.1_5'UTR	NM_001033561.1	NP_001028733.1			PHD finger protein 12									p.T704M(1)		breast(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(6)|lung(8)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	30	all_cancers(5;1.95e-14)|all_epithelial(6;5e-18)|Lung NSC(42;0.01)		Epithelial(11;1.64e-05)|all cancers(11;7.47e-05)|BRCA - Breast invasive adenocarcinoma(11;9.79e-05)			TATGGATAACGTGCCGGGGCT	0.547																																					p.T704M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C2111T	17						.	G	MET/THR	0,4406		0,0,2203	165.0	132.0	143.0		2111	5.9	1.0	17	dbSNP_134	143	1,8599	1.2+/-3.3	0,1,4299	no	missense	PHF12	NM_001033561.1	81	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	possibly-damaging	704/1005	27238234	1,13005	2203	4300	6503	24262360	SO:0001583	missense	57649	exon10			AB040956	CCDS11247.1, CCDS32598.1	17q11.2	2013-01-28			ENSG00000109118	ENSG00000109118		"""Zinc fingers, PHD-type"""	20816	protein-coding gene	gene with protein product						11390640	Standard	XM_005258015		Approved	PF1, KIAA1523	uc002hdg.1	Q96QT6	OTTHUMG00000132676	ENST00000332830.4:c.2111C>T	17.37:g.27238234G>A	ENSP00000329933:p.Thr704Met	Somatic		Capture	Illumina HiSeq	Phase_I	24262360	NM_001033561		Missense_Mutation	SNP	ENST00000332830.4	37	CCDS32598.1	.	.	.	.	.	.	.	.	.	.	G	19.54	3.846582	0.71603	0.0	1.16E-4	ENSG00000109118	ENST00000332830;ENST00000378879	D	0.94687	-3.49	5.89	5.89	0.94794	.	0.104089	0.64402	D	0.000006	D	0.96408	0.8828	L	0.50333	1.59	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;0.998;1.0	D;D;P;D	0.80764	0.994;0.994;0.747;0.994	D	0.96574	0.9425	10	0.87932	D	0	-0.7477	18.8256	0.92117	0.0:0.0:1.0:0.0	.	686;704;704;704	B4DFE2;Q2TAK2;C9J9G2;Q96QT6	.;.;.;PHF12_HUMAN	M	704	ENSP00000329933:T704M	ENSP00000329933:T704M	T	-	2	0	PHF12	24262360	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.159000	0.77483	2.793000	0.96121	0.655000	0.94253	ACG		0.547	PHF12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255941.1	NM_020889	
CLUH	23277	broad.mit.edu	37	17	2597230	2597230	+	Silent	SNP	G	G	A	rs371996237		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr17:2597230G>A	ENST00000570628.2	-	19	3183	c.3078C>T	c.(3076-3078)ctC>ctT	p.L1026L	CLUH_ENST00000435359.1_Silent_p.L1026L|CLUH_ENST00000538975.1_Silent_p.L1026L			O75153	CLU_HUMAN	clustered mitochondria (cluA/CLU1) homolog	1026					intracellular distribution of mitochondria (GO:0048312)	cytoplasm (GO:0005737)		p.L1027L(1)									GGAGGCGGGCGAGGAGGCGCA	0.632																																					p.L1026L												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C3078T	17						.	A		2,4234		0,2,2116	27.0	38.0	34.0		3078	-6.5	1.0	17		34	1,8447		0,1,4223	no	coding-synonymous	KIAA0664	NM_015229.3		0,3,6339	AA,AG,GG		0.0118,0.0472,0.0237		1026/1310	2597230	3,12681	2118	4224	6342	2543980	SO:0001819	synonymous_variant	23277	exon19			AB014564	CCDS45572.1	17p13.3	2012-12-18	2012-11-30	2012-11-30	ENSG00000132361	ENSG00000132361			29094	protein-coding gene	gene with protein product			"""KIAA0664"""	KIAA0664			Standard	XM_005256567		Approved	CLU1	uc002fuy.1	O75153	OTTHUMG00000177575	ENST00000570628.2:c.3078C>T	17.37:g.2597230G>A		Somatic		Capture	Illumina HiSeq	Phase_I	2543980	NM_015229	Q6AHY2|Q6P3X7|Q6ZUG8|Q8N4U7|Q9BTA3|Q9H979	Silent	SNP	ENST00000570628.2	37	CCDS45572.1																																																																																				0.632	CLUH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437807.2	NM_015229	
ANKRD13B	124930	broad.mit.edu	37	17	27935076	27935076	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr17:27935076G>A	ENST00000394859.3	+	3	477	c.323G>A	c.(322-324)cGg>cAg	p.R108Q	RP11-68I3.2_ENST00000581474.1_RNA	NM_152345.4	NP_689558.4	Q86YJ7	AN13B_HUMAN	ankyrin repeat domain 13B	108						endosome (GO:0005768)|plasma membrane (GO:0005886)		p.R108Q(1)		cervix(1)|large_intestine(2)|lung(9)|ovary(1)|prostate(1)|skin(2)	16						GACTACCAGCGGGTGGTGAAG	0.682																																					p.R108Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G323A	17						.						39.0	45.0	43.0					17																	27935076		2203	4300	6503	24959202	SO:0001583	missense	124930	exon3			AK092673	CCDS11251.1	17q11.2	2013-01-10			ENSG00000198720	ENSG00000198720		"""Ankyrin repeat domain containing"""	26363	protein-coding gene	gene with protein product		615124					Standard	NM_152345		Approved	FLJ25555	uc002hei.3	Q86YJ7	OTTHUMG00000132731	ENST00000394859.3:c.323G>A	17.37:g.27935076G>A	ENSP00000378328:p.Arg108Gln	Somatic		Capture	Illumina HiSeq	Phase_I	24959202	NM_152345	Q8N7S9	Missense_Mutation	SNP	ENST00000394859.3	37	CCDS11251.1	.	.	.	.	.	.	.	.	.	.	G	36	5.840711	0.97009	.	.	ENSG00000198720	ENST00000394859	T	0.57273	0.41	6.03	6.03	0.97812	.	0.097830	0.64402	D	0.000004	T	0.53802	0.1819	L	0.31294	0.92	0.80722	D	1	P	0.40000	0.698	P	0.46208	0.507	T	0.51810	-0.8658	10	0.52906	T	0.07	-32.0316	20.177	0.98182	0.0:0.0:1.0:0.0	.	108	Q86YJ7	AN13B_HUMAN	Q	108	ENSP00000378328:R108Q	ENSP00000378328:R108Q	R	+	2	0	ANKRD13B	24959202	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	9.726000	0.98782	2.854000	0.98071	0.655000	0.94253	CGG		0.682	ANKRD13B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256077.1	NM_152345	
SLC6A4	6532	broad.mit.edu	37	17	28545151	28545151	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr17:28545151G>A	ENST00000401766.2	-	4	1195	c.683C>T	c.(682-684)gCt>gTt	p.A228V	SLC6A4_ENST00000261707.3_Missense_Mutation_p.A228V			P31645	SC6A4_HUMAN	solute carrier family 6 (neurotransmitter transporter), member 4	228					brain morphogenesis (GO:0048854)|cellular response to cGMP (GO:0071321)|cellular response to retinoic acid (GO:0071300)|circadian rhythm (GO:0007623)|memory (GO:0007613)|monoamine transport (GO:0015844)|negative regulation of cerebellar granule cell precursor proliferation (GO:0021941)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of organ growth (GO:0046621)|negative regulation of synaptic transmission, dopaminergic (GO:0032227)|positive regulation of cell cycle (GO:0045787)|positive regulation of gene expression (GO:0010628)|protein homooligomerization (GO:0051260)|protein oligomerization (GO:0051259)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to hypoxia (GO:0001666)|response to nutrient (GO:0007584)|response to toxic substance (GO:0009636)|serotonin transport (GO:0006837)|serotonin uptake (GO:0051610)|social behavior (GO:0035176)|sperm ejaculation (GO:0042713)|thalamus development (GO:0021794)|vasoconstriction (GO:0042310)	cytosol (GO:0005829)|endomembrane system (GO:0012505)|endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)	actin filament binding (GO:0051015)|cocaine binding (GO:0019811)|monoamine transmembrane transporter activity (GO:0008504)|Rab GTPase binding (GO:0017137)|serotonin transmembrane transporter activity (GO:0015222)|serotonin:sodium symporter activity (GO:0005335)	p.A228V(1)		breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(8)|ovary(1)|prostate(1)|skin(4)	25					Amitriptyline(DB00321)|Amoxapine(DB00543)|Amphetamine(DB00182)|Atomoxetine(DB00289)|Chlorphenamine(DB01114)|Citalopram(DB00215)|Clomipramine(DB01242)|Cocaine(DB00907)|Desipramine(DB01151)|Desvenlafaxine(DB06700)|Dexfenfluramine(DB01191)|Dexmethylphenidate(DB06701)|Dextromethorphan(DB00514)|Dopamine(DB00988)|Doxepin(DB01142)|Duloxetine(DB00476)|Ephedra(DB01363)|Escitalopram(DB01175)|Fluoxetine(DB00472)|Fluvoxamine(DB00176)|Imipramine(DB00458)|Levomilnacipran(DB08918)|Loxapine(DB00408)|Mazindol(DB00579)|Methamphetamine(DB01577)|Methylphenidate(DB00422)|Mianserin(DB06148)|Milnacipran(DB04896)|Minaprine(DB00805)|Mirtazapine(DB00370)|Nefazodone(DB01149)|Nortriptyline(DB00540)|Paroxetine(DB00715)|Pethidine(DB00454)|Phentermine(DB00191)|Protriptyline(DB00344)|Pseudoephedrine(DB00852)|Sertraline(DB01104)|Sibutramine(DB01105)|Tapentadol(DB06204)|Tramadol(DB00193)|Trazodone(DB00656)|Trimipramine(DB00726)|Venlafaxine(DB00285)|Verapamil(DB00661)|Vilazodone(DB06684)	AAATTCTTCAGCAGGGGACGT	0.552																																					p.A228V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C683T	17						.						134.0	123.0	127.0					17																	28545151		2203	4300	6503	25569277	SO:0001583	missense	6532	exon5			L05568	CCDS11256.1	17q11.2	2014-01-30	2013-07-19		ENSG00000108576	ENSG00000108576		"""Solute carriers"""	11050	protein-coding gene	gene with protein product	"""serotonin transporter 1"""	182138	"""solute carrier family 6 (neurotransmitter transporter, serotonin), member 4"", ""5-hydroxytryptamine (serotonin) transporter"", ""obsessive-compulsive disorder 1"""	HTT, OCD1		7681602, 19806148	Standard	NM_001045		Approved	5-HTT, SERT1	uc002hey.5	P31645	OTTHUMG00000132751	ENST00000401766.2:c.683C>T	17.37:g.28545151G>A	ENSP00000385822:p.Ala228Val	Somatic		Capture	Illumina HiSeq	Phase_I	25569277	NM_001045	Q5EE02	Missense_Mutation	SNP	ENST00000401766.2	37	CCDS11256.1	.	.	.	.	.	.	.	.	.	.	G	34	5.311208	0.95655	.	.	ENSG00000108576	ENST00000394821;ENST00000401766;ENST00000261707	T;T	0.73897	-0.79;-0.79	6.17	6.17	0.99709	.	0.000000	0.85682	D	0.000000	T	0.81083	0.4749	L	0.35542	1.07	0.80722	D	1	D	0.89917	1.0	D	0.80764	0.994	T	0.77161	-0.2689	10	0.33141	T	0.24	.	19.8676	0.96824	0.0:0.0:1.0:0.0	.	228	P31645	SC6A4_HUMAN	V	270;228;228	ENSP00000385822:A228V;ENSP00000261707:A228V	ENSP00000261707:A228V	A	-	2	0	SLC6A4	25569277	1.000000	0.71417	0.577000	0.28562	0.877000	0.50540	7.904000	0.87408	2.941000	0.99782	0.655000	0.94253	GCT		0.552	SLC6A4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256115.3	NM_001045	
PSMD11	5717	broad.mit.edu	37	17	30806366	30806366	+	Missense_Mutation	SNP	G	G	A	rs201116985		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr17:30806366G>A	ENST00000261712.3	+	10	1273	c.1010G>A	c.(1009-1011)cGa>cAa	p.R337Q	PSMD11_ENST00000457654.2_Missense_Mutation_p.R337Q	NM_001270482.1|NM_002815.3	NP_001257411.1|NP_002806.2	O00231	PSD11_HUMAN	proteasome (prosome, macropain) 26S subunit, non-ATPase, 11	337	PCI.				anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|cellular nitrogen compound metabolic process (GO:0034641)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|proteasome assembly (GO:0043248)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|stem cell differentiation (GO:0048863)|ubiquitin-dependent protein catabolic process (GO:0006511)|viral process (GO:0016032)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|proteasome accessory complex (GO:0022624)|proteasome complex (GO:0000502)|proteasome regulatory particle (GO:0005838)		p.R337Q(1)		breast(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(7)|ovary(1)|skin(4)|upper_aerodigestive_tract(1)	19		Breast(31;0.159)|Ovarian(249;0.182)	BRCA - Breast invasive adenocarcinoma(9;0.109)			AATCTGATCCGAGTCATTGAG	0.517																																					p.R337Q	Ovarian(130;1038 1716 9294 11987 19279)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1010A	17						.						133.0	128.0	130.0					17																	30806366		2203	4300	6503	27830479	SO:0001583	missense	5717	exon10			AB003102	CCDS11272.1	17q12	2008-05-22			ENSG00000108671	ENSG00000108671		"""Proteasome (prosome, macropain) subunits"""	9556	protein-coding gene	gene with protein product		604449				9426256, 9119060	Standard	NM_001270482		Approved	S9, p44.5, MGC3844, Rpn6	uc010cta.2	O00231	OTTHUMG00000132811	ENST00000261712.3:c.1010G>A	17.37:g.30806366G>A	ENSP00000261712:p.Arg337Gln	Somatic		Capture	Illumina HiSeq	Phase_I	27830479	NM_002815	A8K3I7|E1P663|O00495|Q53FT5	Missense_Mutation	SNP	ENST00000261712.3	37	CCDS11272.1	.	.	.	.	.	.	.	.	.	.	G	35	5.573109	0.96553	.	.	ENSG00000108671	ENST00000261712	T	0.27557	1.66	5.41	5.41	0.78517	Winged helix-turn-helix transcription repressor DNA-binding (1);Proteasome component (PCI) domain (2);	0.000000	0.85682	D	0.000000	T	0.59729	0.2215	M	0.86268	2.805	0.80722	D	1	D	0.76494	0.999	D	0.66716	0.946	T	0.64922	-0.6293	10	0.87932	D	0	-2.6927	16.7464	0.85473	0.0:0.0:1.0:0.0	.	337	O00231	PSD11_HUMAN	Q	337	ENSP00000261712:R337Q	ENSP00000261712:R337Q	R	+	2	0	PSMD11	27830479	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	9.657000	0.98554	2.826000	0.97356	0.561000	0.74099	CGA		0.517	PSMD11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256252.2	NM_002815	
NLE1	54475	broad.mit.edu	37	17	33463189	33463189	+	Splice_Site	SNP	C	C	T	rs201219885		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr17:33463189C>T	ENST00000442241.4	-	9	1049	c.1010G>A	c.(1009-1011)cGg>cAg	p.R337Q	NLE1_ENST00000593176.1_5'Flank|NLE1_ENST00000586869.1_Splice_Site_p.R45Q|NLE1_ENST00000360831.5_Splice_Site_p.R295Q	NM_001014445.1|NM_018096.3	NP_001014445.1|NP_060566.2	Q9NVX2	NLE1_HUMAN	notchless homolog 1 (Drosophila)	337					hematopoietic stem cell homeostasis (GO:0061484)|inner cell mass cell differentiation (GO:0001826)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic signaling pathway (GO:2001268)|negative regulation of mitotic cell cycle (GO:0045930)|Notch signaling pathway (GO:0007219)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|ribosomal large subunit biogenesis (GO:0042273)	nucleolus (GO:0005730)|nucleus (GO:0005634)		p.R337Q(1)		NS(1)|breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(4)|ovary(1)|prostate(2)	22		Ovarian(249;0.17)				CACACTCACCCGCACGAGGTT	0.557																																					p.R45Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G134A	17						.						168.0	171.0	170.0					17																	33463189		2203	4300	6503	30487302	SO:0001630	splice_region_variant	54475	exon8				CCDS11291.1, CCDS45647.1	17q12	2013-01-10		2005-08-09	ENSG00000073536	ENSG00000073536		"""WD repeat domain containing"""	19889	protein-coding gene	gene with protein product	"""Notchless gene homolog, (Drosophila)"""						Standard	XM_005257989		Approved	FLJ10458	uc002hiy.1	Q9NVX2	OTTHUMG00000132928	ENST00000442241.4:c.1011+1G>A	17.37:g.33463189C>T		Somatic		Capture	Illumina HiSeq	Phase_I	30487302	NM_001014445	O60868|Q59GJ8|Q9BU54	Missense_Mutation	SNP	ENST00000442241.4	37	CCDS11291.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	10.96|10.96	1.498230|1.498230	0.26861|0.26861	.|.	.|.	ENSG00000073536|ENSG00000073536	ENST00000436188|ENST00000442241;ENST00000360831;ENST00000537697	.|T	.|0.57436	.|0.4	5.1|5.1	5.1|5.1	0.69264|0.69264	.|WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.42720|0.42720	0.1215|0.1215	N|N	0.15975|0.15975	0.35|0.35	0.58432|0.58432	D|D	0.999999|0.999999	.|B;D	.|0.57571	.|0.175;0.98	.|B;P	.|0.49637	.|0.031;0.617	T|T	0.19516|0.19516	-1.0303|-1.0303	5|10	.|0.23891	.|T	.|0.37	-33.76|-33.76	13.8693|13.8693	0.63608|0.63608	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|313;337	.|B4E074;Q9NVX2	.|.;NLE1_HUMAN	R|Q	117|337;45;313	.|ENSP00000413572:R337Q	.|ENSP00000354075:R45Q	G|R	-|-	1|2	0|0	NLE1|NLE1	30487302|30487302	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.526000|0.526000	0.34562|0.34562	5.878000|5.878000	0.69682|0.69682	2.657000|2.657000	0.90304|0.90304	0.563000|0.563000	0.77884|0.77884	GGG|CGG		0.557	NLE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256441.2	NM_018096	Missense_Mutation
TRPV1	7442	broad.mit.edu	37	17	3494310	3494310	+	Silent	SNP	C	C	T	rs200555594	byFrequency	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr17:3494310C>T	ENST00000571088.1	-	4	765	c.552G>A	c.(550-552)acG>acA	p.T184T	TRPV1_ENST00000310522.5_Silent_p.T184T|SHPK_ENST00000572705.1_Silent_p.T184T|TRPV1_ENST00000399759.3_Silent_p.T184T|TRPV1_ENST00000399756.4_Silent_p.T184T|TRPV1_ENST00000174621.6_Silent_p.T182T|TRPV1_ENST00000425167.2_Silent_p.T184T|TRPV1_ENST00000576351.1_Silent_p.T184T	NM_018727.5	NP_061197.4	Q8NER1	TRPV1_HUMAN	transient receptor potential cation channel, subfamily V, member 1	184					calcium ion transmembrane transport (GO:0070588)|cell surface receptor signaling pathway (GO:0007166)|cellular response to alkaloid (GO:0071312)|cellular response to ATP (GO:0071318)|chemosensory behavior (GO:0007635)|ion transmembrane transport (GO:0034220)|thermoception (GO:0050955)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cell junction (GO:0030054)|cell projection (GO:0042995)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|intrinsic component of plasma membrane (GO:0031226)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	ATP binding (GO:0005524)|calcium channel activity (GO:0005262)|calcium-release channel activity (GO:0015278)|excitatory extracellular ligand-gated ion channel activity (GO:0005231)|phosphoprotein binding (GO:0051219)|transmembrane signaling receptor activity (GO:0004888)	p.T184T(1)		central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(5)|ovary(1)|prostate(1)|urinary_tract(1)	17				Lung(1;0.055)|COAD - Colon adenocarcinoma(5;0.0896)|LUAD - Lung adenocarcinoma(1115;0.131)	Alpha-Linolenic Acid(DB00132)|Aspartame(DB00168)|Icosapent(DB00159)	TCAGGCTGTCCGTTTGCCGCG	0.637													C|||	20	0.00399361	0.0	0.0	5008	,	,		19704	0.0198		0.0	False		,,,				2504	0.0				p.T184T	Melanoma(38;962 1762 15789)											.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G552A	17						.	C	,,,	1,4253		0,1,2126	63.0	65.0	64.0		552,552,552,552	-10.4	0.2	17		64	1,8447		0,1,4223	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	TRPV1	NM_018727.5,NM_080704.3,NM_080705.3,NM_080706.3	,,,	0,2,6349	TT,TC,CC		0.0118,0.0235,0.0157	,,,	184/840,184/840,184/840,184/840	3494310	2,12700	2127	4224	6351	3441059	SO:0001819	synonymous_variant	7442	exon4			AJ272063	CCDS45576.1	17p13.2	2014-08-12	2002-01-29	2002-02-01	ENSG00000196689	ENSG00000262304		"""Voltage-gated ion channels / Transient receptor potential cation channels"", ""Ankyrin repeat domain containing"""	12716	protein-coding gene	gene with protein product		602076	"""vanilloid receptor subtype 1"""	VR1		9349813, 11549313, 16382100	Standard	NM_018727		Approved		uc010vrt.2	Q8NER1	OTTHUMG00000177649	ENST00000571088.1:c.552G>A	17.37:g.3494310C>T		Somatic		Capture	Illumina HiSeq	Phase_I	3441059	NM_018727	A2RUA9|Q3LU47|Q9H0G9|Q9H303|Q9H304|Q9NQ74|Q9NY22	Silent	SNP	ENST00000571088.1	37	CCDS45576.1																																																																																				0.637	TRPV1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438254.1	NM_018727	
SLFN13	146857	broad.mit.edu	37	17	33769111	33769111	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr17:33769111C>T	ENST00000285013.6	-	5	1668	c.1393G>A	c.(1393-1395)Gca>Aca	p.A465T	SLFN13_ENST00000526861.1_Missense_Mutation_p.A465T|SLFN13_ENST00000533791.1_Missense_Mutation_p.A465T|SLFN13_ENST00000542635.1_Missense_Mutation_p.A465T|SLFN13_ENST00000534689.1_Missense_Mutation_p.A147T|SLFN13_ENST00000360502.2_Missense_Mutation_p.A147T	NM_144682.5	NP_653283.3	Q68D06	SLN13_HUMAN	schlafen family member 13	465						intracellular (GO:0005622)	ATP binding (GO:0005524)	p.A465T(1)		NS(1)|breast(1)|endometrium(1)|large_intestine(10)|lung(8)|ovary(3)|pancreas(1)|prostate(5)|stomach(1)	31				UCEC - Uterine corpus endometrioid carcinoma (308;0.0185)		CTGTTCTGTGCTATCAGCAGA	0.542																																					p.A465T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1393A	17						.						103.0	90.0	95.0					17																	33769111		2203	4298	6501	30793224	SO:0001583	missense	146857	exon5			AL832726	CCDS32620.1	17q12	2006-04-05				ENSG00000154760			26481	protein-coding gene	gene with protein product		614957				9846487	Standard	NM_144682		Approved	FLJ31952	uc002hjl.2	Q68D06		ENST00000285013.6:c.1393G>A	17.37:g.33769111C>T	ENSP00000285013:p.Ala465Thr	Somatic		Capture	Illumina HiSeq	Phase_I	30793224	NM_144682	E1P645|Q658M1|Q6ZS51|Q96A81	Missense_Mutation	SNP	ENST00000285013.6	37	CCDS32620.1	.	.	.	.	.	.	.	.	.	.	c	14.38	2.516954	0.44763	.	.	ENSG00000154760	ENST00000285013;ENST00000360502;ENST00000526861;ENST00000542635;ENST00000534689	T;T;T;T;T	0.04551	4.18;3.6;4.18;4.18;3.6	3.05	-0.827	0.10802	.	0.146879	0.31519	N	0.007505	T	0.05044	0.0135	L	0.56396	1.775	0.18873	N	0.999982	B;B	0.28233	0.204;0.015	B;B	0.27887	0.084;0.008	T	0.27434	-1.0074	10	0.59425	D	0.04	.	5.3439	0.15998	0.4042:0.3979:0.1979:0.0	.	147;465	Q68D06-2;Q68D06	.;SLN13_HUMAN	T	465;147;465;465;147	ENSP00000285013:A465T;ENSP00000353692:A147T;ENSP00000434439:A465T;ENSP00000444016:A465T;ENSP00000435442:A147T	ENSP00000285013:A465T	A	-	1	0	SLFN13	30793224	0.000000	0.05858	0.260000	0.24451	0.640000	0.38277	-0.573000	0.05874	-0.215000	0.10063	0.194000	0.17425	GCA		0.542	SLFN13-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381883.1	NM_144682	
FBXL20	84961	broad.mit.edu	37	17	37420430	37420430	+	Missense_Mutation	SNP	T	T	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr17:37420430T>A	ENST00000264658.6	-	14	1461	c.1201A>T	c.(1201-1203)Agg>Tgg	p.R401W	FBXL20_ENST00000577399.1_Missense_Mutation_p.R403W|FBXL20_ENST00000583610.1_Missense_Mutation_p.R401W|FBXL20_ENST00000394294.3_Missense_Mutation_p.R369W	NM_032875.2	NP_116264.2	Q96IG2	FXL20_HUMAN	F-box and leucine-rich repeat protein 20	401					behavioral fear response (GO:0001662)	cytoplasm (GO:0005737)		p.R401W(1)		breast(2)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(8)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	22			LUAD - Lung adenocarcinoma(14;0.146)			ATTTTTACCCTGAGTCTCTTG	0.413																																					p.R401W												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A1201T	17						.						131.0	122.0	125.0					17																	37420430		2203	4300	6503	34673956	SO:0001583	missense	84961	exon14			BC007557	CCDS32640.1, CCDS54116.1	17q21.2	2011-06-09				ENSG00000108306		"""F-boxes / Leucine-rich repeats"""	24679	protein-coding gene	gene with protein product		609086				12477932	Standard	NM_032875		Approved	MGC15482, Fbl2, Fbl20	uc002hrt.3	Q96IG2		ENST00000264658.6:c.1201A>T	17.37:g.37420430T>A	ENSP00000264658:p.Arg401Trp	Somatic		Capture	Illumina HiSeq	Phase_I	34673956	NM_032875	A8K729|Q38J52	Missense_Mutation	SNP	ENST00000264658.6	37	CCDS32640.1	.	.	.	.	.	.	.	.	.	.	T	22.0	4.228120	0.79576	.	.	ENSG00000108306	ENST00000264658;ENST00000394294	T;T	0.02395	4.31;4.31	5.9	5.9	0.94986	.	0.045115	0.85682	D	0.000000	T	0.14614	0.0353	M	0.80982	2.52	0.80722	D	1	D;D	0.89917	1.0;0.999	D;D	0.71870	0.975;0.941	T	0.00094	-1.2078	10	0.62326	D	0.03	.	11.9173	0.52774	0.0:0.0:0.1452:0.8548	.	369;401	Q96IG2-2;Q96IG2	.;FXL20_HUMAN	W	401;369	ENSP00000264658:R401W;ENSP00000377832:R369W	ENSP00000264658:R401W	R	-	1	2	FBXL20	34673956	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	2.137000	0.42130	2.254000	0.74563	0.460000	0.39030	AGG		0.413	FBXL20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444315.2	NM_032875	
MED24	9862	broad.mit.edu	37	17	38176550	38176550	+	Missense_Mutation	SNP	G	G	A	rs142219986		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr17:38176550G>A	ENST00000394128.2	-	24	2761	c.2680C>T	c.(2680-2682)Cgg>Tgg	p.R894W	MED24_ENST00000394126.1_Missense_Mutation_p.R919W|MED24_ENST00000356271.3_Missense_Mutation_p.R881W|MED24_ENST00000501516.3_Missense_Mutation_p.R913W|MED24_ENST00000394127.2_Missense_Mutation_p.R881W	NM_014815.3	NP_055630.2	O75448	MED24_HUMAN	mediator complex subunit 24	894					androgen receptor signaling pathway (GO:0030521)|gene expression (GO:0010467)|intracellular steroid hormone receptor signaling pathway (GO:0030518)|positive regulation of transcription, DNA-templated (GO:0045893)|protein heterooligomerization (GO:0051291)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|stem cell maintenance (GO:0019827)|transcription initiation from RNA polymerase II promoter (GO:0006367)	mediator complex (GO:0016592)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	histone acetyltransferase activity (GO:0004402)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|receptor activity (GO:0004872)|RNA polymerase II transcription cofactor activity (GO:0001104)|thyroid hormone receptor binding (GO:0046966)|transcription cofactor activity (GO:0003712)|vitamin D receptor binding (GO:0042809)	p.R894W(1)		autonomic_ganglia(1)|breast(2)|endometrium(9)|large_intestine(10)|lung(14)|ovary(1)|prostate(2)|skin(1)|urinary_tract(1)	41	Colorectal(19;0.000442)					AGAGGGTCCCGCATGTTGACC	0.627																																					p.R881W												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C2641T	17						.	G	TRP/ARG,TRP/ARG	0,4406		0,0,2203	67.0	58.0	61.0		2641,2680	2.3	1.0	17	dbSNP_134	61	2,8596		0,2,4297	no	missense,missense	MED24	NM_001079518.1,NM_014815.3	101,101	0,2,6500	AA,AG,GG		0.0233,0.0,0.0154	probably-damaging,probably-damaging	881/977,894/990	38176550	2,13002	2203	4299	6502	35430076	SO:0001583	missense	9862	exon23			AF055995	CCDS11359.1, CCDS42315.1	17q21.2	2007-07-30	2007-07-30	2007-07-30	ENSG00000008838	ENSG00000008838			22963	protein-coding gene	gene with protein product		607000	"""thyroid hormone receptor associated protein 4"", ""cofactor required for Sp1 transcriptional activation, subunit 4, 100kDa"""	THRAP4, CRSP4			Standard	NM_001079518		Approved	TRAP100, KIAA0130, DRIP100, CRSP100	uc002htt.3	O75448	OTTHUMG00000133329	ENST00000394128.2:c.2680C>T	17.37:g.38176550G>A	ENSP00000377686:p.Arg894Trp	Somatic		Capture	Illumina HiSeq	Phase_I	35430076	NM_001079518	A8K4S5|B3KMR9|Q14143|Q9NNY5	Missense_Mutation	SNP	ENST00000394128.2	37	CCDS11359.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	13.28|13.28	2.189132|2.189132	0.38707|0.38707	0.0|0.0	2.33E-4|2.33E-4	ENSG00000008838|ENSG00000008838	ENST00000422942|ENST00000394126;ENST00000356271;ENST00000394128;ENST00000394127;ENST00000536318;ENST00000431269	.|T;T	.|0.53640	.|0.61;0.61	4.58|4.58	2.26|2.26	0.28386|0.28386	.|Mediator complex, subunit Med24, N-terminal (1);	.|0.043531	.|0.85682	.|D	.|0.000000	T|T	0.58722|0.58722	0.2142|0.2142	L|L	0.50333|0.50333	1.59|1.59	0.58432|0.58432	D|D	0.999996|0.999996	.|D;D;D;D;D	.|0.76494	.|0.999;0.999;0.999;0.999;0.999	.|D;D;D;D;D	.|0.68353	.|0.928;0.912;0.928;0.957;0.928	T|T	0.59080|0.59080	-0.7521|-0.7521	5|10	.|0.87932	.|D	.|0	-24.9096|-24.9096	11.5466|11.5466	0.50696|0.50696	0.0:0.0:0.2899:0.7101|0.0:0.0:0.2899:0.7101	.|.	.|804;804;881;894;836	.|F8W9R9;B4E1A5;O75448-2;O75448;F5H0K1	.|.;.;.;MED24_HUMAN;.	V|W	191|894;894;894;881;836;804	.|ENSP00000377686:R894W;ENSP00000377685:R881W	.|ENSP00000348610:R894W	A|R	-|-	2|1	0|2	MED24|MED24	35430076|35430076	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.991000|0.991000	0.79684|0.79684	2.205000|2.205000	0.42770|0.42770	0.338000|0.338000	0.23692|0.23692	-0.275000|-0.275000	0.10095|0.10095	GCG|CGG		0.627	MED24-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257147.2	NM_014815	
MED24	9862	broad.mit.edu	37	17	38179499	38179499	+	Missense_Mutation	SNP	G	G	A	rs145215690		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr17:38179499G>A	ENST00000394128.2	-	20	2216	c.2135C>T	c.(2134-2136)aCg>aTg	p.T712M	MED24_ENST00000394126.1_Missense_Mutation_p.T737M|MED24_ENST00000356271.3_Missense_Mutation_p.T699M|MED24_ENST00000501516.3_Missense_Mutation_p.T731M|MED24_ENST00000394127.2_Missense_Mutation_p.T699M	NM_014815.3	NP_055630.2	O75448	MED24_HUMAN	mediator complex subunit 24	712					androgen receptor signaling pathway (GO:0030521)|gene expression (GO:0010467)|intracellular steroid hormone receptor signaling pathway (GO:0030518)|positive regulation of transcription, DNA-templated (GO:0045893)|protein heterooligomerization (GO:0051291)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|stem cell maintenance (GO:0019827)|transcription initiation from RNA polymerase II promoter (GO:0006367)	mediator complex (GO:0016592)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	histone acetyltransferase activity (GO:0004402)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|receptor activity (GO:0004872)|RNA polymerase II transcription cofactor activity (GO:0001104)|thyroid hormone receptor binding (GO:0046966)|transcription cofactor activity (GO:0003712)|vitamin D receptor binding (GO:0042809)	p.T712M(1)		autonomic_ganglia(1)|breast(2)|endometrium(9)|large_intestine(10)|lung(14)|ovary(1)|prostate(2)|skin(1)|urinary_tract(1)	41	Colorectal(19;0.000442)					AAAAATGTCCGTCAGCACCTC	0.602																																					p.T699M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C2096T	17						.	G	MET/THR,MET/THR	1,4405	2.1+/-5.4	0,1,2202	65.0	60.0	62.0		2096,2135	2.5	0.9	17	dbSNP_134	62	0,8600		0,0,4300	no	missense,missense	MED24	NM_001079518.1,NM_014815.3	81,81	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	possibly-damaging,possibly-damaging	699/977,712/990	38179499	1,13005	2203	4300	6503	35433025	SO:0001583	missense	9862	exon19			AF055995	CCDS11359.1, CCDS42315.1	17q21.2	2007-07-30	2007-07-30	2007-07-30	ENSG00000008838	ENSG00000008838			22963	protein-coding gene	gene with protein product		607000	"""thyroid hormone receptor associated protein 4"", ""cofactor required for Sp1 transcriptional activation, subunit 4, 100kDa"""	THRAP4, CRSP4			Standard	NM_001079518		Approved	TRAP100, KIAA0130, DRIP100, CRSP100	uc002htt.3	O75448	OTTHUMG00000133329	ENST00000394128.2:c.2135C>T	17.37:g.38179499G>A	ENSP00000377686:p.Thr712Met	Somatic		Capture	Illumina HiSeq	Phase_I	35433025	NM_001079518	A8K4S5|B3KMR9|Q14143|Q9NNY5	Missense_Mutation	SNP	ENST00000394128.2	37	CCDS11359.1	.	.	.	.	.	.	.	.	.	.	G	10.08	1.252321	0.22880	2.27E-4	0.0	ENSG00000008838	ENST00000394126;ENST00000356271;ENST00000394128;ENST00000535071;ENST00000394127;ENST00000536318;ENST00000535508;ENST00000501516;ENST00000431269	T;T;T	0.44881	0.91;0.91;0.91	4.43	2.45	0.29901	Mediator complex, subunit Med24, N-terminal (1);	0.173450	0.49916	D	0.000123	T	0.24198	0.0586	L	0.40543	1.245	0.30146	N	0.803478	P;B;P;B;B;B	0.41624	0.757;0.109;0.676;0.132;0.16;0.221	B;B;B;B;B;B	0.30029	0.11;0.006;0.063;0.011;0.018;0.016	T	0.23013	-1.0200	10	0.51188	T	0.08	-8.8074	5.0149	0.14331	0.2512:0.1532:0.5956:0.0	.	662;622;622;699;712;654	F5H5K2;F8W9R9;B4E1A5;O75448-2;O75448;F5H0K1	.;.;.;.;MED24_HUMAN;.	M	712;712;712;662;699;654;273;183;622	ENSP00000377686:T712M;ENSP00000443344:T662M;ENSP00000377685:T699M	ENSP00000348610:T712M	T	-	2	0	MED24	35433025	0.971000	0.33674	0.904000	0.35570	0.997000	0.91878	1.967000	0.40491	0.500000	0.27991	0.561000	0.74099	ACG		0.602	MED24-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257147.2	NM_014815	
NR1D1	9572	broad.mit.edu	37	17	38252961	38252961	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr17:38252961C>T	ENST00000246672.3	-	3	1072	c.442G>A	c.(442-444)Gcc>Acc	p.A148T		NM_021724.3	NP_068370.1	P20393	NR1D1_HUMAN	nuclear receptor subfamily 1, group D, member 1	148	Crucial for activation of GJA1. {ECO:0000250}.				cell differentiation (GO:0030154)|cellular response to lipopolysaccharide (GO:0071222)|circadian regulation of gene expression (GO:0032922)|circadian temperature homeostasis (GO:0060086)|gene expression (GO:0010467)|glycogen biosynthetic process (GO:0005978)|intracellular receptor signaling pathway (GO:0030522)|negative regulation of receptor biosynthetic process (GO:0010871)|negative regulation of toll-like receptor 4 signaling pathway (GO:0034144)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of bile acid biosynthetic process (GO:0070859)|positive regulation of transcription, DNA-templated (GO:0045893)|proteasomal protein catabolic process (GO:0010498)|regulation of cholesterol homeostasis (GO:2000188)|regulation of circadian rhythm (GO:0042752)|regulation of fat cell differentiation (GO:0045598)|regulation of gluconeogenesis by regulation of transcription from RNA polymerase II promoter (GO:0035947)|regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0061178)|regulation of lipid metabolic process (GO:0019216)|regulation of type B pancreatic cell proliferation (GO:0061469)|response to leptin (GO:0044321)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|dendritic spine (GO:0043197)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	core promoter sequence-specific DNA binding (GO:0001046)|heme binding (GO:0020037)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|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)|steroid hormone receptor activity (GO:0003707)|transcription corepressor activity (GO:0003714)|transcription corepressor binding (GO:0001222)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)	p.A148T(2)		endometrium(1)|large_intestine(5)|lung(2)|skin(1)|upper_aerodigestive_tract(2)	11	Colorectal(19;0.000442)					CCCTCGCAGGCGTGCACACCG	0.637																																					p.A148T												.	.	2	Substitution - Missense(2)	large_intestine(1)|endometrium(1)	c.G442A	17						.						75.0	60.0	65.0					17																	38252961		2203	4300	6503	35506487	SO:0001583	missense	9572	exon3			X72631	CCDS11361.1	17q11.2	2013-01-16			ENSG00000126368	ENSG00000126368		"""Nuclear hormone receptors"""	7962	protein-coding gene	gene with protein product		602408		THRAL		1971514	Standard	NM_021724		Approved	ear-1, hRev, Rev-ErbAalpha, THRA1	uc002htz.3	P20393	OTTHUMG00000133327	ENST00000246672.3:c.442G>A	17.37:g.38252961C>T	ENSP00000246672:p.Ala148Thr	Somatic		Capture	Illumina HiSeq	Phase_I	35506487	NM_021724	Q0P5Z4|Q15304	Missense_Mutation	SNP	ENST00000246672.3	37	CCDS11361.1	.	.	.	.	.	.	.	.	.	.	C	21.5	4.152650	0.78001	.	.	ENSG00000126368	ENST00000246672	D	0.96802	-4.13	4.64	4.64	0.57946	Zinc finger, NHR/GATA-type (1);Zinc finger, nuclear hormone receptor-type (6);	0.000000	0.64402	D	0.000001	D	0.96482	0.8852	L	0.39326	1.205	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.94534	0.7739	10	0.14656	T	0.56	.	16.4298	0.83837	0.0:1.0:0.0:0.0	.	148	P20393	NR1D1_HUMAN	T	148	ENSP00000246672:A148T	ENSP00000246672:A148T	A	-	1	0	NR1D1	35506487	0.980000	0.34600	0.988000	0.46212	0.054000	0.15201	2.592000	0.46171	2.400000	0.81607	0.563000	0.77884	GCC		0.637	NR1D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257135.1		
RAPGEFL1	51195	broad.mit.edu	37	17	38345551	38345551	+	Silent	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr17:38345551G>A	ENST00000456989.2	+	6	631	c.585G>A	c.(583-585)acG>acA	p.T195T	RAPGEFL1_ENST00000544503.1_Silent_p.T189T|RAPGEFL1_ENST00000540388.1_3'UTR|RAPGEFL1_ENST00000436615.3_Silent_p.T140T|RAPGEFL1_ENST00000264644.6_Silent_p.T140T			Q9UHV5	RPGFL_HUMAN	Rap guanine nucleotide exchange factor (GEF)-like 1	346					G-protein coupled receptor signaling pathway (GO:0007186)|nervous system development (GO:0007399)|positive regulation of GTPase activity (GO:0043547)|small GTPase mediated signal transduction (GO:0007264)	membrane (GO:0016020)	guanyl-nucleotide exchange factor activity (GO:0005085)	p.T140T(1)		breast(1)|central_nervous_system(2)|kidney(1)|large_intestine(2)|lung(5)|ovary(1)|prostate(2)|skin(1)	15						GCTCTGTGACGGAGAAACTTC	0.557																																					p.T140T	Esophageal Squamous(28;274 750 6870 14218 42203)											.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G420A	17						.						163.0	165.0	165.0					17																	38345551		2203	4300	6503	35599077	SO:0001819	synonymous_variant	51195	exon6			AF117946	CCDS11363.1	17q21.2	2006-08-01	2004-03-26		ENSG00000108352	ENSG00000108352			17428	protein-coding gene	gene with protein product	"""Link guanine nucleotide exchange factor II"""		"""RAP guanine-nucleotide-exchange factor (GEF)-like 1"""				Standard	NM_016339		Approved	Link-GEFII	uc010cwu.1	Q9UHV5	OTTHUMG00000133325	ENST00000456989.2:c.585G>A	17.37:g.38345551G>A		Somatic		Capture	Illumina HiSeq	Phase_I	35599077	NM_016339		Silent	SNP	ENST00000456989.2	37																																																																																					0.557	RAPGEFL1-005	PUTATIVE	non_canonical_conserved|basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000397518.1	NM_016339	
ITGAE	3682	broad.mit.edu	37	17	3660366	3660366	+	Silent	SNP	C	C	T	rs148305090	byFrequency	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr17:3660366C>T	ENST00000263087.4	-	10	1181	c.1083G>A	c.(1081-1083)ccG>ccA	p.P361P		NM_002208.4	NP_002199.3	P38570	ITAE_HUMAN	integrin, alpha E (antigen CD103, human mucosal lymphocyte antigen 1; alpha polypeptide)	361	VWFA. {ECO:0000255|PROSITE- ProRule:PRU00219}.				cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|integrin-mediated signaling pathway (GO:0007229)	external side of plasma membrane (GO:0009897)|integrin complex (GO:0008305)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)	p.P361P(1)		NS(1)|breast(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(13)|lung(14)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	41				UCEC - Uterine corpus endometrioid carcinoma (3;0.0813)		GGGTCTCATCCGGGTCTGAGG	0.567													C|||	2	0.000399361	0.0008	0.0	5008	,	,		20442	0.0		0.0	False		,,,				2504	0.001				p.P361P	NSCLC(182;635 2928 8995 38788)											.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G1083A	17						.	C		3,4403	6.2+/-15.9	0,3,2200	282.0	263.0	269.0		1083	-6.2	0.0	17	dbSNP_134	269	3,8597	3.0+/-9.4	0,3,4297	no	coding-synonymous	ITGAE	NM_002208.4		0,6,6497	TT,TC,CC		0.0349,0.0681,0.0461		361/1180	3660366	6,13000	2203	4300	6503	3607115	SO:0001819	synonymous_variant	3682	exon10			L25851	CCDS32531.1	17p13	2010-03-23				ENSG00000083457		"""CD molecules"", ""Integrins"""	6147	protein-coding gene	gene with protein product		604682				8119947	Standard	NM_002208		Approved	CD103, HUMINAE	uc002fwo.4	P38570		ENST00000263087.4:c.1083G>A	17.37:g.3660366C>T		Somatic		Capture	Illumina HiSeq	Phase_I	3607115	NM_002208	Q17RS6|Q9NZU9	Silent	SNP	ENST00000263087.4	37	CCDS32531.1																																																																																				0.567	ITGAE-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438169.1	NM_002208	
SMARCE1	6605	broad.mit.edu	37	17	38793808	38793808	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr17:38793808G>A	ENST00000348513.6	-	5	953	c.173C>T	c.(172-174)aCg>aTg	p.T58M	SMARCE1_ENST00000578044.1_De_novo_Start_InFrame|SMARCE1_ENST00000544009.1_De_novo_Start_InFrame|SMARCE1_ENST00000431889.2_Missense_Mutation_p.T40M|SMARCE1_ENST00000377808.4_Missense_Mutation_p.T23M|SMARCE1_ENST00000400122.3_De_novo_Start_InFrame|KRT222_ENST00000476049.1_Intron|SMARCE1_ENST00000580419.1_Missense_Mutation_p.T23M	NM_003079.4	NP_003070.3	Q969G3	SMCE1_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily e, member 1	58	Pro-rich.				ATP-dependent chromatin remodeling (GO:0043044)|chromatin remodeling (GO:0006338)|metabolic process (GO:0008152)|negative regulation of transcription, DNA-templated (GO:0045892)|nervous system development (GO:0007399)|nucleosome disassembly (GO:0006337)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	nBAF complex (GO:0071565)|npBAF complex (GO:0071564)|nuclear chromatin (GO:0000790)|nuclear chromosome (GO:0000228)|nucleus (GO:0005634)|protein complex (GO:0043234)|SWI/SNF complex (GO:0016514)|transcriptional repressor complex (GO:0017053)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|ligand-dependent nuclear receptor binding (GO:0016922)|N-acetyltransferase activity (GO:0008080)|protein N-terminus binding (GO:0047485)|RNA binding (GO:0003723)|transcription coactivator activity (GO:0003713)	p.T58M(1)		large_intestine(1)	1		Breast(137;0.000812)				TTTTGGAATCGTGATACCAGA	0.438																																					p.T58M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C173T	17						.						108.0	97.0	101.0					17																	38793808		2203	4299	6502	36047334	SO:0001583	missense	6605	exon5			AF035262	CCDS11370.1	17q21.2	2006-09-20			ENSG00000073584	ENSG00000073584			11109	protein-coding gene	gene with protein product		603111				9435219	Standard	NM_003079		Approved	BAF57	uc002hux.2	Q969G3	OTTHUMG00000133367	ENST00000348513.6:c.173C>T	17.37:g.38793808G>A	ENSP00000323967:p.Thr58Met	Somatic		Capture	Illumina HiSeq	Phase_I	36047334	NM_003079	B3KMC1|B4DFR4|C0IMW4|C0IMW5|C0IMW7|H7C3F6|O43539	Missense_Mutation	SNP	ENST00000348513.6	37	CCDS11370.1	.	.	.	.	.	.	.	.	.	.	G	12.53	1.966447	0.34659	.	.	ENSG00000073584	ENST00000348513;ENST00000431889;ENST00000377808	D;D;T	0.93712	-3.27;-3.27;2.3	5.78	5.78	0.91487	High mobility group, superfamily (1);	0.044902	0.85682	D	0.000000	D	0.92870	0.7732	N	0.19112	0.55	0.80722	D	1	D;D;D;D	0.76494	0.999;0.999;0.989;0.989	P;P;P;P	0.56088	0.732;0.791;0.548;0.548	D	0.93500	0.6843	10	0.66056	D	0.02	.	20.3754	0.98918	0.0:0.0:1.0:0.0	.	23;40;23;58	C0IMW5;B4DGM3;C0IMW4;Q969G3	.;.;.;SMCE1_HUMAN	M	58;40;23	ENSP00000323967:T58M;ENSP00000445370:T40M;ENSP00000367039:T23M	ENSP00000323967:T58M	T	-	2	0	SMARCE1	36047334	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.334000	0.59291	2.894000	0.99253	0.591000	0.81541	ACG		0.438	SMARCE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257203.1	NM_003079	
KRT27	342574	broad.mit.edu	37	17	38935973	38935973	+	Silent	SNP	C	C	T	rs373395779		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr17:38935973C>T	ENST00000301656.3	-	4	865	c.825G>A	c.(823-825)gcG>gcA	p.A275A	KRT27_ENST00000540723.1_5'Flank	NM_181537.3	NP_853515.2			keratin 27									p.A275A(1)		NS(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(6)|ovary(1)|prostate(3)|skin(1)|stomach(1)	21		Breast(137;0.000812)				ACCAGGCCTCCGCGTCCCTGC	0.652																																					p.A275A												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G825A	17						.	C		0,4406		0,0,2203	37.0	36.0	37.0		825	-11.0	0.4	17		37	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	KRT27	NM_181537.3		0,1,6502	TT,TC,CC		0.0116,0.0,0.0077		275/460	38935973	1,13005	2203	4300	6503	36189499	SO:0001819	synonymous_variant	342574	exon4			AJ564206	CCDS11375.1	17q21.2	2013-01-16	2006-07-17	2006-07-17	ENSG00000171446	ENSG00000171446		"""-"", ""Intermediate filaments type I, keratins (acidic)"""	30841	protein-coding gene	gene with protein product			"""keratin 25C"""	KRT25C		16831889	Standard	NM_181537		Approved		uc002hvg.3	Q7Z3Y8	OTTHUMG00000133371	ENST00000301656.3:c.825G>A	17.37:g.38935973C>T		Somatic		Capture	Illumina HiSeq	Phase_I	36189499	NM_181537		Silent	SNP	ENST00000301656.3	37	CCDS11375.1																																																																																				0.652	KRT27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257216.1	NM_181537	
NT5C3B	115024	broad.mit.edu	37	17	39991473	39991473	+	Nonsense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr17:39991473G>A	ENST00000435506.2	-	3	232	c.163C>T	c.(163-165)Cga>Tga	p.R55*	KLHL10_ENST00000293303.4_5'Flank|NT5C3B_ENST00000269534.8_Nonsense_Mutation_p.R47*|NT5C3B_ENST00000521789.1_Nonsense_Mutation_p.R22*|RN7SL871P_ENST00000583512.1_RNA			Q969T7	5NT3B_HUMAN	5'-nucleotidase, cytosolic IIIB	55					nucleotide metabolic process (GO:0009117)	cytoplasm (GO:0005737)	5'-nucleotidase activity (GO:0008253)|magnesium ion binding (GO:0000287)|nucleotide binding (GO:0000166)	p.R47*(2)									GAAGGGCATCGCTTTCCATTA	0.398																																					p.R55X												.	.	2	Substitution - Nonsense(2)	large_intestine(2)	c.C163T	17						.						123.0	109.0	114.0					17																	39991473		2203	4300	6503	37244999	SO:0001587	stop_gained	115024	exon3				CCDS11410.1, CCDS11410.2	17q21.2	2013-01-31	2013-01-31	2013-01-31	ENSG00000141698	ENSG00000141698	3.1.3.5		28300	protein-coding gene	gene with protein product			"""5'-nucleotidase, cytosolic III-like"""	NT5C3L		23223233	Standard	NM_052935		Approved	MGC20781	uc021txo.1	Q969T7	OTTHUMG00000133499	ENST00000435506.2:c.163C>T	17.37:g.39991473G>A	ENSP00000389948:p.Arg55*	Somatic		Capture	Illumina HiSeq	Phase_I	37244999	NM_052935	A8MWB9|C9JKC4|Q7L3B7	Nonsense_Mutation	SNP	ENST00000435506.2	37	CCDS11410.2	.	.	.	.	.	.	.	.	.	.	G	23.8	4.459824	0.84317	.	.	ENSG00000141698	ENST00000269534;ENST00000521789;ENST00000393911;ENST00000435506;ENST00000415460	.	.	.	4.56	1.09	0.20402	.	0.062956	0.64402	D	0.000013	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	1.8599	12.7824	0.57485	0.0:0.0:0.435:0.5649	.	.	.	.	X	47;22;89;55;55	.	ENSP00000269534:R47X	R	-	1	2	NT5C3L	37244999	0.979000	0.34478	0.995000	0.50966	0.988000	0.76386	1.004000	0.29822	0.492000	0.27815	0.558000	0.71614	CGA		0.398	NT5C3B-008	NOVEL	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257430.2	NM_052935	
KAT2A	2648	broad.mit.edu	37	17	40269779	40269779	+	Missense_Mutation	SNP	G	G	A	rs377593132		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr17:40269779G>A	ENST00000225916.5	-	9	1398	c.1345C>T	c.(1345-1347)Cgt>Tgt	p.R449C		NM_021078.2	NP_066564.2	Q92830	KAT2A_HUMAN	K(lysine) acetyltransferase 2A	449					cell proliferation (GO:0008283)|chromatin organization (GO:0006325)|chromatin remodeling (GO:0006338)|histone deubiquitination (GO:0016578)|histone H3 acetylation (GO:0043966)|histone H3-K14 acetylation (GO:0044154)|in utero embryonic development (GO:0001701)|metencephalon development (GO:0022037)|midbrain development (GO:0030901)|multicellular organism growth (GO:0035264)|neural tube closure (GO:0001843)|positive regulation of gluconeogenesis (GO:0045722)|regulation of protein stability (GO:0031647)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|somitogenesis (GO:0001756)|telencephalon development (GO:0021537)|transcription from RNA polymerase II promoter (GO:0006366)|viral process (GO:0016032)	Ada2/Gcn5/Ada3 transcription activator complex (GO:0005671)|extracellular space (GO:0005615)|mitotic spindle (GO:0072686)|nucleoplasm (GO:0005654)|STAGA complex (GO:0030914)|transcription factor TFTC complex (GO:0033276)	chromatin binding (GO:0003682)|H3 histone acetyltransferase activity (GO:0010484)|histone acetyltransferase activity (GO:0004402)|histone acetyltransferase activity (H4-K12 specific) (GO:0043997)|histone deacetylase binding (GO:0042826)|transcription coactivator activity (GO:0003713)	p.R449C(1)		central_nervous_system(1)|endometrium(3)|large_intestine(1)|lung(4)|ovary(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	18						CCCATCACACGGAGCCGCTTG	0.592																																					p.R449C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1345T	17						.	G	CYS/ARG	0,4406		0,0,2203	46.0	38.0	41.0		1345	4.7	1.0	17		41	1,8599	1.2+/-3.3	0,1,4299	no	missense	KAT2A	NM_021078.2	180	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging	449/838	40269779	1,13005	2203	4300	6503	37523305	SO:0001583	missense	2648	exon9			AF029777	CCDS11417.1	17q12-q21	2011-07-01	2008-07-04	2008-07-04	ENSG00000108773	ENSG00000108773		"""Chromatin-modifying enzymes / K-acetyltransferases"""	4201	protein-coding gene	gene with protein product		602301	"""GCN5 general control of amino-acid synthesis 5-like 2 (yeast)"""	GCN5L2		8552087	Standard	NM_021078		Approved	GCN5, PCAF-b	uc002hyx.2	Q92830	OTTHUMG00000133504	ENST00000225916.5:c.1345C>T	17.37:g.40269779G>A	ENSP00000225916:p.Arg449Cys	Somatic		Capture	Illumina HiSeq	Phase_I	37523305	NM_021078	Q8N1A2|Q9UCW1	Missense_Mutation	SNP	ENST00000225916.5	37	CCDS11417.1	.	.	.	.	.	.	.	.	.	.	G	25.7	4.660217	0.88154	0.0	1.16E-4	ENSG00000108773	ENST00000225916	T	0.07021	3.23	4.7	4.7	0.59300	.	0.000000	0.85682	D	0.000000	T	0.29355	0.0731	M	0.77103	2.36	0.80722	D	1	D	0.89917	1.0	D	0.63703	0.917	T	0.09335	-1.0679	10	0.87932	D	0	-9.2086	17.6406	0.88135	0.0:0.0:1.0:0.0	.	449	Q92830	KAT2A_HUMAN	C	449	ENSP00000225916:R449C	ENSP00000225916:R449C	R	-	1	0	KAT2A	37523305	1.000000	0.71417	0.998000	0.56505	0.963000	0.63663	6.579000	0.74036	2.164000	0.68074	0.561000	0.74099	CGT		0.592	KAT2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257458.1	NM_021078	
ATP2A3	489	broad.mit.edu	37	17	3839671	3839671	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr17:3839671G>A	ENST00000352011.3	-	16	2468	c.2414C>T	c.(2413-2415)aCg>aTg	p.T805M	ATP2A3_ENST00000397043.3_Missense_Mutation_p.T805M|ATP2A3_ENST00000359983.3_Missense_Mutation_p.T805M|ATP2A3_ENST00000309890.7_Missense_Mutation_p.T805M|ATP2A3_ENST00000397039.1_De_novo_Start_InFrame|ATP2A3_ENST00000397035.3_Missense_Mutation_p.T805M|ATP2A3_ENST00000397041.3_Missense_Mutation_p.T805M			Q93084	AT2A3_HUMAN	ATPase, Ca++ transporting, ubiquitous	805					blood coagulation (GO:0007596)|calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)|transport (GO:0006810)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|platelet dense tubular network membrane (GO:0031095)|sarcoplasmic reticulum (GO:0016529)	ATP binding (GO:0005524)|calcium-transporting ATPase activity (GO:0005388)|metal ion binding (GO:0046872)	p.T805M(1)		breast(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(11)|ovary(3)|prostate(1)|skin(3)|stomach(1)|urinary_tract(1)	36				LUAD - Lung adenocarcinoma(1115;0.000692)|Lung(3;0.0766)		GCCCAGAGCCGTGGCAGGTAG	0.622																																					p.T805M	GBM(32;29 774 15719 37967)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C2414T	17						.						76.0	78.0	77.0					17																	3839671		2203	4300	6503	3786420	SO:0001583	missense	489	exon16				CCDS11041.1, CCDS11042.1, CCDS42234.1, CCDS45579.1, CCDS45580.1	17p13.3	2012-10-22			ENSG00000074370	ENSG00000074370	3.6.3.8	"""ATPases / P-type"""	813	protein-coding gene	gene with protein product	"""sarcoplasmic/endoplasmic reticulum calcium ATPase 3"", ""calcium pump 3"""	601929				8809064	Standard	NM_005173		Approved	SERCA3	uc002fwy.2	Q93084		ENST00000352011.3:c.2414C>T	17.37:g.3839671G>A	ENSP00000301387:p.Thr805Met	Somatic		Capture	Illumina HiSeq	Phase_I	3786420	NM_174955	A8MZG0|D3DTJ8|O60900|O60901|O75501|O75502|Q16115|Q6JHX1|Q8TEX5|Q8TEX6	Missense_Mutation	SNP	ENST00000352011.3	37	CCDS11041.1	.	.	.	.	.	.	.	.	.	.	G	21.3	4.131325	0.77549	.	.	ENSG00000074370	ENST00000397043;ENST00000352011;ENST00000359983;ENST00000397041;ENST00000397045;ENST00000309890;ENST00000397035	D;D;D;D;D;D	0.95821	-3.82;-3.82;-3.82;-3.82;-3.82;-3.82	4.16	4.16	0.48862	ATPase, P-type cation-transporter, C-terminal (1);ATPase, P-type,  transmembrane domain (1);	0.000000	0.85682	D	0.000000	D	0.97617	0.9219	M	0.83384	2.64	0.80722	D	1	D;D;D;D;D;D	0.89917	1.0;0.987;0.996;0.995;0.995;0.987	D;P;P;P;P;P	0.87578	0.998;0.52;0.551;0.52;0.52;0.52	D	0.97484	1.0049	10	0.49607	T	0.09	.	16.7249	0.85419	0.0:0.0:1.0:0.0	.	805;805;805;805;805;805	Q93084-4;Q93084-2;Q93084;Q93084-6;G3XAE1;Q93084-3	.;.;AT2A3_HUMAN;.;.;.	M	805	ENSP00000380236:T805M;ENSP00000301387:T805M;ENSP00000353072:T805M;ENSP00000380234:T805M;ENSP00000312577:T805M;ENSP00000380229:T805M	ENSP00000312577:T805M	T	-	2	0	ATP2A3	3786420	1.000000	0.71417	0.963000	0.40424	0.828000	0.46876	9.657000	0.98554	2.607000	0.88179	0.561000	0.74099	ACG		0.622	ATP2A3-015	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000438401.1	NM_174953	
PTRF	284119	broad.mit.edu	37	17	40557353	40557353	+	Silent	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr17:40557353C>T	ENST00000357037.5	-	2	944	c.525G>A	c.(523-525)tcG>tcA	p.S175S		NM_012232.5	NP_036364.2			polymerase I and transcript release factor									p.S175S(1)		breast(2)|central_nervous_system(1)|endometrium(1)|large_intestine(4)|lung(5)|ovary(1)|prostate(2)|urinary_tract(1)	17		all_cancers(22;0.00146)|Breast(137;0.00116)|all_epithelial(22;0.0134)		BRCA - Breast invasive adenocarcinoma(366;0.193)		GCAGCGCCTCCGACTCTTTCA	0.647																																					p.S175S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G525A	17						.						81.0	88.0	86.0					17																	40557353		2203	4300	6503	37810879	SO:0001819	synonymous_variant	284119	exon2			AF000421	CCDS11425.1	17q21.31	2011-04-20				ENSG00000177469			9688	protein-coding gene	gene with protein product		603198				9582279	Standard	NM_012232		Approved	cavin-1, CAVIN1	uc002hzo.3	Q6NZI2		ENST00000357037.5:c.525G>A	17.37:g.40557353C>T		Somatic		Capture	Illumina HiSeq	Phase_I	37810879	NM_012232		Silent	SNP	ENST00000357037.5	37	CCDS11425.1																																																																																				0.647	PTRF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449938.1	NM_012232	
MLX	6945	broad.mit.edu	37	17	40720554	40720554	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr17:40720554G>A	ENST00000246912.4	+	3	361	c.308G>A	c.(307-309)aGt>aAt	p.S103N	MLX_ENST00000435881.2_Missense_Mutation_p.S49N|MLX_ENST00000346833.4_Intron	NM_170607.2	NP_733752.1	Q9UH92	MLX_HUMAN	MLX, MAX dimerization protein	103					energy reserve metabolic process (GO:0006112)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nucleocytoplasmic transport (GO:0006913)|positive regulation of cellular metabolic process (GO:0031325)|regulation of transcription, DNA-templated (GO:0006355)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001227)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)	p.S103N(1)		kidney(3)|large_intestine(4)|lung(1)|ovary(1)|urinary_tract(1)	10		all_cancers(22;4.26e-05)|Breast(137;0.000153)|all_epithelial(22;0.00148)		BRCA - Breast invasive adenocarcinoma(366;0.129)		GGTTCCACCAGTGCCTCTTCT	0.537																																					p.S49N	GBM(121;657 1601 4665 24731 34640)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G146A	17						.						139.0	139.0	139.0					17																	40720554		2203	4300	6503	37974080	SO:0001583	missense	6945	exon3			AF213668	CCDS11430.1, CCDS42341.1, CCDS45687.1	17q21.1	2013-05-21	2012-11-15	2005-02-11		ENSG00000108788		"""MAX dimerization proteins"", ""Basic helix-loop-helix proteins"""	11645	protein-coding gene	gene with protein product		602976	"""transcription factor-like 4"", ""MAX-like protein X"""	TCFL4		8973301	Standard	NM_170607		Approved	MAD7, MXD7, bHLHd13	uc002iag.3	Q9UH92		ENST00000246912.4:c.308G>A	17.37:g.40720554G>A	ENSP00000246912:p.Ser103Asn	Somatic		Capture	Illumina HiSeq	Phase_I	37974080	NM_198204	A8K2J3|B2RAV8|B2RD73|Q53XM6|Q96FL2|Q9H2V0|Q9H2V1|Q9H2V2|Q9NXN3	Missense_Mutation	SNP	ENST00000246912.4	37	CCDS11430.1	.	.	.	.	.	.	.	.	.	.	G	32	5.115769	0.94339	.	.	ENSG00000108788	ENST00000246912;ENST00000435881	T;T	0.80824	-1.42;-1.14	5.4	5.4	0.78164	.	0.000000	0.85682	D	0.000000	T	0.76126	0.3944	L	0.47716	1.5	0.80722	D	1	B;B	0.26547	0.152;0.008	B;B	0.24974	0.057;0.007	T	0.70215	-0.4933	10	0.20046	T	0.44	-9.5411	18.9633	0.92685	0.0:0.0:1.0:0.0	.	103;49	Q9UH92;Q9UH92-3	MLX_HUMAN;.	N	103;49	ENSP00000246912:S103N;ENSP00000416627:S49N	ENSP00000246912:S103N	S	+	2	0	MLX	37974080	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	9.512000	0.98008	2.813000	0.96785	0.561000	0.74099	AGT		0.537	MLX-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000450415.1	NM_170607	
TUBG1	7283	broad.mit.edu	37	17	40765685	40765685	+	Silent	SNP	C	C	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr17:40765685C>A	ENST00000251413.3	+	7	689	c.627C>A	c.(625-627)gcC>gcA	p.A209A		NM_001070.4	NP_001061.2	P23258	TBG1_HUMAN	tubulin, gamma 1	209					cytoplasmic microtubule organization (GO:0031122)|G2/M transition of mitotic cell cycle (GO:0000086)|meiotic spindle organization (GO:0000212)|microtubule cytoskeleton organization (GO:0000226)|microtubule nucleation (GO:0007020)|mitotic cell cycle (GO:0000278)	apical part of cell (GO:0045177)|cell leading edge (GO:0031252)|centriole (GO:0005814)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|gamma-tubulin complex (GO:0000930)|nonmotile primary cilium (GO:0031513)|pericentriolar material (GO:0000242)|polar microtubule (GO:0005827)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|structural constituent of cytoskeleton (GO:0005200)	p.A209A(1)		endometrium(2)|kidney(2)|large_intestine(2)|lung(4)|ovary(1)|prostate(1)	12		Breast(137;0.00116)		BRCA - Breast invasive adenocarcinoma(366;0.129)	Vinblastine(DB00570)	ACAACACAGCCCTGAACCGGA	0.562																																					p.A209A	Colon(20;114 698 11420 22864)											.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C627A	17						.						176.0	166.0	169.0					17																	40765685		2203	4300	6503	38019211	SO:0001819	synonymous_variant	7283	exon7			BC000619	CCDS11433.1	17q21.31	2010-03-15	2000-01-20		ENSG00000131462	ENSG00000131462		"""Tubulins"""	12417	protein-coding gene	gene with protein product		191135	"""tubulin, gamma polypeptide"""	TUBG		1904010	Standard	NM_001070		Approved	TUBGCP1	uc002ian.3	P23258		ENST00000251413.3:c.627C>A	17.37:g.40765685C>A		Somatic		Capture	Illumina HiSeq	Phase_I	38019211	NM_001070	Q53X79|Q9BW59	Silent	SNP	ENST00000251413.3	37	CCDS11433.1																																																																																				0.562	TUBG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450548.1	NM_001070	
CNTD1	124817	broad.mit.edu	37	17	40957864	40957864	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr17:40957864C>T	ENST00000588408.1	+	4	818	c.542C>T	c.(541-543)aCt>aTt	p.T181I	CNTD1_ENST00000315066.5_3'UTR|CNTD1_ENST00000588527.1_Missense_Mutation_p.T98I	NM_173478.2	NP_775749.2	Q8N815	CNTD1_HUMAN	cyclin N-terminal domain containing 1	181								p.T181I(1)		central_nervous_system(2)|large_intestine(2)|lung(4)|ovary(1)|skin(1)	10		Breast(137;0.00104)		BRCA - Breast invasive adenocarcinoma(366;0.0749)		AATCTGCCCACTCCCCTGGCA	0.438																																					p.T181I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C542T	17						.						96.0	91.0	93.0					17																	40957864		2203	4300	6503	38211390	SO:0001583	missense	124817	exon4			AK097456	CCDS11440.1	17q21.31	2014-07-03	2006-03-31	2006-03-31	ENSG00000176563	ENSG00000176563			26847	protein-coding gene	gene with protein product			"""cyclin N-terminal domain containing"""	CNTD		24891606	Standard	NM_173478		Approved	FLJ40137	uc002ibm.4	Q8N815		ENST00000588408.1:c.542C>T	17.37:g.40957864C>T	ENSP00000465204:p.Thr181Ile	Somatic		Capture	Illumina HiSeq	Phase_I	38211390	NM_173478	Q658Q6|Q8NEP1	Missense_Mutation	SNP	ENST00000588408.1	37	CCDS11440.1	.	.	.	.	.	.	.	.	.	.	C	26.0	4.692597	0.88735	.	.	ENSG00000176563	ENST00000315066	.	.	.	5.78	5.78	0.91487	.	0.099069	0.64402	D	0.000001	T	0.76399	0.3982	M	0.62723	1.935	0.42978	D	0.994459	D	0.69078	0.997	P	0.60789	0.879	T	0.77968	-0.2388	9	0.87932	D	0	-16.3614	20.0085	0.97443	0.0:1.0:0.0:0.0	.	181	Q8N815	CNTD1_HUMAN	I	181	.	ENSP00000316647:T181I	T	+	2	0	CNTD1	38211390	1.000000	0.71417	0.998000	0.56505	0.995000	0.86356	4.284000	0.58983	2.723000	0.93209	0.650000	0.86243	ACT		0.438	CNTD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452398.1	NM_173478	
G6PC3	92579	broad.mit.edu	37	17	42153097	42153097	+	Missense_Mutation	SNP	G	G	A	rs140785361		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr17:42153097G>A	ENST00000269097.4	+	6	958	c.727G>A	c.(727-729)Gtg>Atg	p.V243M		NM_138387.3	NP_612396.1	Q9BUM1	G6PC3_HUMAN	glucose 6 phosphatase, catalytic, 3	243					carbohydrate metabolic process (GO:0005975)|gluconeogenesis (GO:0006094)|glucose 6-phosphate metabolic process (GO:0051156)|glucose transport (GO:0015758)|glucose-6-phosphate transport (GO:0015760)|hexose transport (GO:0008645)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	glucose-6-phosphatase activity (GO:0004346)	p.V243M(1)		endometrium(2)|large_intestine(5)|lung(1)|ovary(2)|skin(1)	11		Breast(137;0.00637)|Prostate(33;0.0313)		BRCA - Breast invasive adenocarcinoma(366;0.113)		GTGGATACACGTGGATAGCCG	0.622																																					p.V243M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G727A	17						.	A	MET/VAL	1,4405	825.9+/-416.6	0,1,2202	79.0	74.0	75.0		727	-10.8	0.0	17	dbSNP_134	75	1,8599	818.9+/-406.8	0,1,4299	yes	missense	G6PC3	NM_138387.3	21	0,2,6501	AA,AG,GG		0.0116,0.0227,0.0154	benign	243/347	42153097	2,13004	2203	4300	6503	39508623	SO:0001583	missense	92579	exon6			BC021574	CCDS11476.1	17q21.31	2014-09-17				ENSG00000141349			24861	protein-coding gene	gene with protein product		611045				12370122, 12965222	Standard	NM_138387		Approved	UGRP	uc002iex.3	Q9BUM1		ENST00000269097.4:c.727G>A	17.37:g.42153097G>A	ENSP00000269097:p.Val243Met	Somatic		Capture	Illumina HiSeq	Phase_I	39508623	NM_138387	Q8WU15	Missense_Mutation	SNP	ENST00000269097.4	37	CCDS11476.1	.	.	.	.	.	.	.	.	.	.	A	0.014	-1.576050	0.00887	2.27E-4	1.16E-4	ENSG00000141349	ENST00000269097	T	0.76186	-1.0	5.4	-10.8	0.00216	.	0.959880	0.08658	N	0.912947	T	0.41190	0.1148	N	0.04297	-0.235	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.42137	-0.9469	10	0.28530	T	0.3	-34.8653	4.3225	0.11023	0.5298:0.0647:0.1629:0.2426	.	243	Q9BUM1	G6PC3_HUMAN	M	243	ENSP00000269097:V243M	ENSP00000269097:V243M	V	+	1	0	G6PC3	39508623	0.000000	0.05858	0.000000	0.03702	0.405000	0.30901	-4.983000	0.00163	-5.197000	0.00019	-2.029000	0.00425	GTG		0.622	G6PC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457675.1	NM_138387	
HDAC5	10014	broad.mit.edu	37	17	42156199	42156199	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr17:42156199C>T	ENST00000393622.2	-	25	3458	c.3127G>A	c.(3127-3129)Gca>Aca	p.A1043T	HDAC5_ENST00000225983.6_Missense_Mutation_p.A1044T|HDAC5_ENST00000586802.1_Missense_Mutation_p.A1043T|HDAC5_ENST00000336057.5_Missense_Mutation_p.A958T	NM_001015053.1|NM_005474.4	NP_001015053.1|NP_005465.2	Q9UQL6	HDAC5_HUMAN	histone deacetylase 5	1043					B cell activation (GO:0042113)|B cell differentiation (GO:0030183)|cellular response to insulin stimulus (GO:0032869)|chromatin modification (GO:0016568)|chromatin organization (GO:0006325)|chromatin remodeling (GO:0006338)|chromatin silencing (GO:0006342)|heart development (GO:0007507)|histone deacetylation (GO:0016575)|inflammatory response (GO:0006954)|multicellular organismal response to stress (GO:0033555)|negative regulation of cell migration involved in sprouting angiogenesis (GO:0090051)|negative regulation of myotube differentiation (GO:0010832)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|Notch signaling pathway (GO:0007219)|osteoblast development (GO:0002076)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of gene expression, epigenetic (GO:0040029)|regulation of myotube differentiation (GO:0010830)|regulation of protein binding (GO:0043393)|regulation of skeletal muscle fiber development (GO:0048742)|response to cocaine (GO:0042220)|response to drug (GO:0042493)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|histone deacetylase complex (GO:0000118)|nuclear body (GO:0016604)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	core promoter binding (GO:0001047)|histone deacetylase activity (GO:0004407)|metal ion binding (GO:0046872)|NAD-dependent histone deacetylase activity (H3-K14 specific) (GO:0032041)|NAD-dependent histone deacetylase activity (H3-K18 specific) (GO:0097372)|NAD-dependent histone deacetylase activity (H3-K9 specific) (GO:0046969)|NAD-dependent histone deacetylase activity (H4-K16 specific) (GO:0046970)|protein kinase C binding (GO:0005080)|repressing transcription factor binding (GO:0070491)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)	p.A1043T(2)		central_nervous_system(1)|endometrium(5)|large_intestine(4)|lung(7)|ovary(1)|prostate(2)|skin(1)	21		Breast(137;0.00637)|Prostate(33;0.0313)		BRCA - Breast invasive adenocarcinoma(366;0.118)		GTGGCCACTGCGTTGATGTTG	0.592																																					p.A1044T												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G3130A	17						.						167.0	148.0	155.0					17																	42156199		2203	4300	6503	39511725	SO:0001583	missense	10014	exon25			AF249731	CCDS32663.1, CCDS45696.1	17q21	2008-07-18					3.5.1.98		14068	protein-coding gene	gene with protein product		605315				10220385, 9610721	Standard	XM_005256905		Approved	KIAA0600, NY-CO-9, FLJ90614	uc002iff.1	Q9UQL6		ENST00000393622.2:c.3127G>A	17.37:g.42156199C>T	ENSP00000377244:p.Ala1043Thr	Somatic		Capture	Illumina HiSeq	Phase_I	39511725	NM_001015053	C9JFV9|O60340|O60528|Q96DY4	Missense_Mutation	SNP	ENST00000393622.2	37	CCDS45696.1	.	.	.	.	.	.	.	.	.	.	C	17.81	3.480576	0.63849	.	.	ENSG00000108840	ENST00000225983;ENST00000393622;ENST00000336057	T;T;T	0.56941	0.43;0.43;0.69	4.88	3.92	0.45320	Histone deacetylase domain (1);	0.000000	0.85682	D	0.000000	T	0.71753	0.3377	M	0.81614	2.55	0.80722	D	1	D;D;D	0.89917	0.999;1.0;1.0	D;D;D	0.91635	0.927;0.999;0.997	T	0.75505	-0.3294	10	0.66056	D	0.02	-8.8397	12.1613	0.54105	0.0:0.9159:0.0:0.0841	.	958;1044;1043	Q9UQL6-2;Q9UQL6-3;Q9UQL6	.;.;HDAC5_HUMAN	T	1044;1043;958	ENSP00000225983:A1044T;ENSP00000377244:A1043T;ENSP00000337290:A958T	ENSP00000225983:A1044T	A	-	1	0	HDAC5	39511725	1.000000	0.71417	0.759000	0.31340	0.070000	0.16714	7.552000	0.82192	1.287000	0.44583	-0.136000	0.14681	GCA		0.592	HDAC5-201	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000457686.1	NM_001015053	
TMUB2	79089	broad.mit.edu	37	17	42271702	42271702	+	IGR	SNP	C	C	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr17:42271702C>A	ENST00000587989.1	+	0	1969				ATXN7L3_ENST00000593073.1_5'UTR|ATXN7L3_ENST00000389384.4_Missense_Mutation_p.G325C|ATXN7L3_ENST00000454077.2_Missense_Mutation_p.G332C			Q71RG4	TMUB2_HUMAN	transmembrane and ubiquitin-like domain containing 2							integral component of membrane (GO:0016021)		p.G325C(1)		endometrium(2)|kidney(2)|large_intestine(1)|lung(3)	8		Breast(137;0.00765)|Prostate(33;0.0181)		BRCA - Breast invasive adenocarcinoma(366;0.113)		TTGTTGGAACCTAGGCCGGAG	0.527																																					p.G332C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G994T	17						.						144.0	146.0	145.0					17																	42271702		2018	4192	6210	39627228	SO:0001628	intergenic_variant	56970	exon12				CCDS11479.1, CCDS54134.1	17q21	2006-06-27				ENSG00000168591			28459	protein-coding gene	gene with protein product						8619474, 9110174	Standard	NM_177441		Approved	MGC3123	uc002ifo.3	Q71RG4			17.37:g.42271702C>A		Somatic		Capture	Illumina HiSeq	Phase_I	39627228	NM_020218	B3KU81|Q8NDI2|Q9BPZ5|Q9HAG3	Missense_Mutation	SNP	ENST00000587989.1	37	CCDS54134.1	.	.	.	.	.	.	.	.	.	.	C	9.207	1.030045	0.19512	.	.	ENSG00000087152	ENST00000454077;ENST00000389384;ENST00000541672	.	.	.	5.29	4.26	0.50523	.	0.450348	0.22453	U	0.059879	T	0.33323	0.0859	N	0.24115	0.695	0.35688	D	0.814593	B;P	0.38617	0.221;0.64	B;B	0.40329	0.041;0.326	T	0.44892	-0.9298	9	0.87932	D	0	.	6.5058	0.22194	0.0:0.8361:0.0:0.1639	.	325;332	Q14CW9;Q14CW9-2	AT7L3_HUMAN;.	C	332;325;107	.	ENSP00000374035:G325C	G	-	1	0	ATXN7L3	39627228	0.346000	0.24844	0.988000	0.46212	0.020000	0.10135	1.279000	0.33191	2.761000	0.94854	0.655000	0.94253	GGT		0.527	TMUB2-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000457711.1	NM_177441	
CYB5D2	124936	broad.mit.edu	37	17	4053288	4053288	+	Silent	SNP	T	T	C			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr17:4053288T>C	ENST00000301391.3	+	2	854	c.354T>C	c.(352-354)aaT>aaC	p.N118N	CYB5D2_ENST00000575251.1_Silent_p.N6N|CYB5D2_ENST00000573984.1_Silent_p.N6N|CYB5D2_ENST00000575411.2_3'UTR	NM_144611.3	NP_653212.1	Q8WUJ1	NEUFC_HUMAN	cytochrome b5 domain containing 2	118	Cytochrome b5 heme-binding.				nervous system development (GO:0007399)	extracellular region (GO:0005576)	heme binding (GO:0020037)	p.N118N(1)		breast(1)|large_intestine(3)|liver(2)|ovary(1)	7						CACTTCACAATTGGCTTTCAT	0.483																																					p.N118N												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.T354C	17						.						150.0	126.0	135.0					17																	4053288		2203	4300	6503	4000037	SO:0001819	synonymous_variant	124936	exon2			AK172844	CCDS11044.1, CCDS58501.1	17p13.2	2006-03-10							28471	protein-coding gene	gene with protein product							Standard	NM_144611		Approved	MGC32124	uc002fxm.4	Q8WUJ1		ENST00000301391.3:c.354T>C	17.37:g.4053288T>C		Somatic		Capture	Illumina HiSeq	Phase_I	4000037	NM_144611	B2R7R6|D3DTJ9|I3L1K2	Silent	SNP	ENST00000301391.3	37	CCDS11044.1																																																																																				0.483	CYB5D2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438698.1	NM_144611	
UBTF	7343	broad.mit.edu	37	17	42284924	42284924	+	Silent	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr17:42284924G>A	ENST00000302904.4	-	20	2559	c.2067C>T	c.(2065-2067)gaC>gaT	p.D689D	CTB-175E5.7_ENST00000586560.1_RNA|UBTF_ENST00000526094.1_Silent_p.D652D|UBTF_ENST00000529383.1_Silent_p.D689D|UBTF_ENST00000533177.1_Silent_p.D652D|UBTF_ENST00000343638.5_Silent_p.D652D|UBTF_ENST00000393606.3_Silent_p.D652D|UBTF_ENST00000527034.1_Missense_Mutation_p.T651M|UBTF_ENST00000436088.1_Silent_p.D689D			P17480	UBF1_HUMAN	upstream binding transcription factor, RNA polymerase I	689	Asp/Glu/Ser-rich (acidic).				chromatin silencing at rDNA (GO:0000183)|gene expression (GO:0010467)|positive regulation of transcription from RNA polymerase I promoter (GO:0045943)|regulation of transcription from RNA polymerase I promoter (GO:0006356)|termination of RNA polymerase I transcription (GO:0006363)|transcription elongation from RNA polymerase I promoter (GO:0006362)|transcription from RNA polymerase I promoter (GO:0006360)|transcription initiation from RNA polymerase I promoter (GO:0006361)	nucleolus (GO:0005730)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)	p.D689D(1)|p.D689E(1)		breast(1)|central_nervous_system(2)|endometrium(1)|large_intestine(9)|lung(10)|ovary(1)|prostate(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	29		Breast(137;0.00765)|Prostate(33;0.0181)		BRCA - Breast invasive adenocarcinoma(366;0.114)		cttcatcctcgtcctcgtcat	0.567																																					p.D652D												.	.	2	Substitution - Missense(1)|Substitution - coding silent(1)	upper_aerodigestive_tract(1)|large_intestine(1)	c.C1956T	17						.						201.0	131.0	154.0					17																	42284924		2203	4300	6503	39640450	SO:0001819	synonymous_variant	7343	exon19			BC042297	CCDS11480.1, CCDS42346.1	17q21.31	2014-03-25			ENSG00000108312	ENSG00000108312			12511	protein-coding gene	gene with protein product		600673				9126496	Standard	NM_001076683		Approved	UBF, NOR-90, UBF1, UBF2	uc010czs.3	P17480	OTTHUMG00000167585	ENST00000302904.4:c.2067C>T	17.37:g.42284924G>A		Somatic		Capture	Illumina HiSeq	Phase_I	39640450	NM_001076683	A8K6R8	Silent	SNP	ENST00000302904.4	37	CCDS11480.1	.	.	.	.	.	.	.	.	.	.	g	8.332	0.826630	0.16749	.	.	ENSG00000108312	ENST00000527034	D	0.98550	-4.99	5.05	-10.1	0.00402	.	.	.	.	.	D	0.96565	0.8879	.	.	.	0.80722	D	1	.	.	.	.	.	.	D	0.90224	0.4274	6	0.46703	T	0.11	-2.0028	7.5819	0.27970	0.1935:0.3956:0.342:0.0689	.	.	.	.	M	651	ENSP00000431539:T651M	ENSP00000431539:T651M	T	-	2	0	UBTF	39640450	0.000000	0.05858	0.006000	0.13384	0.967000	0.64934	-6.026000	0.00085	-3.966000	0.00086	-0.458000	0.05436	ACG		0.567	UBTF-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395205.1	NM_014233	
EFTUD2	9343	broad.mit.edu	37	17	42929110	42929110	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr17:42929110G>A	ENST00000426333.2	-	27	3088	c.2791C>T	c.(2791-2793)Cgg>Tgg	p.R931W	EFTUD2_ENST00000592576.1_Missense_Mutation_p.R921W|EFTUD2_ENST00000402521.3_Missense_Mutation_p.R896W|EFTUD2_ENST00000591382.1_Missense_Mutation_p.R931W	NM_001142605.1|NM_001258354.1|NM_004247.3	NP_001136077.1|NP_001245283.1|NP_004238.3	Q15029	U5S1_HUMAN	elongation factor Tu GTP binding domain containing 2	931					gene expression (GO:0010467)|GTP catabolic process (GO:0006184)|mRNA processing (GO:0006397)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)	Cajal body (GO:0015030)|catalytic step 2 spliceosome (GO:0071013)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|poly(A) RNA binding (GO:0044822)	p.R931W(1)		breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(9)|ovary(1)|prostate(2)|skin(1)|urinary_tract(2)	32		Prostate(33;0.109)				ATGAATTCCCGGGCCAGGTGA	0.552																																					p.R931W	Ovarian(10;65 485 10258 29980 30707)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C2791T	17						.						34.0	28.0	30.0					17																	42929110		2203	4300	6503	40284636	SO:0001583	missense	9343	exon27			D21163	CCDS11489.1, CCDS45707.1, CCDS59295.1	17q21.31	2014-08-12			ENSG00000108883	ENSG00000108883			30858	protein-coding gene	gene with protein product	"""U5 snRNP specific protein, 116 kD"""	603892				9233818	Standard	NM_004247		Approved	U5-116KD, Snrp116, Snu114, SNRNP116	uc002ihn.2	Q15029	OTTHUMG00000179865	ENST00000426333.2:c.2791C>T	17.37:g.42929110G>A	ENSP00000392094:p.Arg931Trp	Somatic		Capture	Illumina HiSeq	Phase_I	40284636	NM_004247	B4DK30|B4DMC0|D3DX58|K7EJ81|Q9BUR0	Missense_Mutation	SNP	ENST00000426333.2	37	CCDS11489.1	.	.	.	.	.	.	.	.	.	.	G	21.9	4.212418	0.79240	.	.	ENSG00000108883	ENST00000426333;ENST00000262414;ENST00000402521	T;T	0.32272	1.46;1.46	5.15	5.15	0.70609	Translation elongation factor EFG/EF2, C-terminal (1);	0.000000	0.85682	D	0.000000	T	0.66489	0.2794	H	0.95850	3.73	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.75408	-0.3328	10	0.87932	D	0	-16.2892	11.9895	0.53168	0.0:0.0:0.7154:0.2846	.	921;931	B4DMC0;Q15029	.;U5S1_HUMAN	W	931;921;896	ENSP00000392094:R931W;ENSP00000385873:R896W	ENSP00000262414:R921W	R	-	1	2	EFTUD2	40284636	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	3.325000	0.52030	2.861000	0.98227	0.650000	0.86243	CGG		0.552	EFTUD2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448672.1	NM_004247	
NMT1	4836	broad.mit.edu	37	17	43180340	43180340	+	Nonsense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr17:43180340C>T	ENST00000592782.1	+	10	1146	c.1015C>T	c.(1015-1017)Cga>Tga	p.R339*	NMT1_ENST00000258960.2_Nonsense_Mutation_p.R339*			P30419	NMT1_HUMAN	N-myristoyltransferase 1	339					apoptotic process (GO:0006915)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|N-terminal protein myristoylation (GO:0006499)|phototransduction, visible light (GO:0007603)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|protein lipoylation (GO:0009249)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|rhodopsin mediated signaling pathway (GO:0016056)|viral process (GO:0016032)	actin cytoskeleton (GO:0015629)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|plasma membrane (GO:0005886)	catalytic activity (GO:0003824)|glycylpeptide N-tetradecanoyltransferase activity (GO:0004379)	p.R339*(1)		breast(2)|endometrium(2)|kidney(1)|large_intestine(1)|lung(1)|prostate(1)	8		Prostate(33;0.155)				AGCTGGGCTGCGACCAATGGA	0.537																																					p.R339X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.C1015T	17						.						95.0	93.0	94.0					17																	43180340		2203	4300	6503	40535866	SO:0001587	stop_gained	4836	exon9				CCDS11494.1	17q21.31	2012-10-02			ENSG00000136448	ENSG00000136448			7857	protein-coding gene	gene with protein product	"""alternative, short form NMT-S"", ""myristoyl-CoA:protein N-myristoyltransferase"", ""long form, NMT-L"""	160993				1570339	Standard	NM_021079		Approved	NMT	uc002ihz.3	P30419	OTTHUMG00000180003	ENST00000592782.1:c.1015C>T	17.37:g.43180340C>T	ENSP00000468424:p.Arg339*	Somatic		Capture	Illumina HiSeq	Phase_I	40535866	NM_021079	A8K7C1|Q9UE09	Nonsense_Mutation	SNP	ENST00000592782.1	37	CCDS11494.1	.	.	.	.	.	.	.	.	.	.	C	27.0	4.793384	0.90453	.	.	ENSG00000136448	ENST00000258960	.	.	.	5.14	3.11	0.35812	.	0.061170	0.64402	D	0.000006	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-5.0969	6.6753	0.23090	0.1424:0.7079:0.0:0.1497	.	.	.	.	X	339	.	ENSP00000258960:R339X	R	+	1	2	NMT1	40535866	1.000000	0.71417	0.942000	0.38095	0.817000	0.46193	1.742000	0.38248	1.406000	0.46857	0.650000	0.86243	CGA		0.537	NMT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449239.1	NM_021079	
MAP3K14-AS1	100133991	broad.mit.edu	37	17	43347913	43347913	+	RNA	SNP	C	C	T	rs572439695		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr17:43347913C>T	ENST00000585780.1	+	0	4950				MAP3K14-AS1_ENST00000586450.1_RNA|MAP3K14-AS1_ENST00000592422.1_RNA|MAP3K14-AS1_ENST00000588504.1_RNA|MAP3K14_ENST00000344686.2_RNA|MAP3K14-AS1_ENST00000588698.1_RNA|MAP3K14-AS1_ENST00000585351.1_RNA|MAP3K14-AS1_ENST00000590100.1_RNA					MAP3K14 antisense RNA 1									p.P613P(1)									CCCTCACAGGCGGAGGCTCGC	0.627																																					p.R613H												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G1838A	17						.						28.0	33.0	32.0					17																	43347913		1995	4177	6172	40703696			9020	exon11			AK311429, BC031942		17q21.31	2014-06-16			ENSG00000267278	ENSG00000267278		"""Long non-coding RNAs"""	44359	non-coding RNA	RNA, long non-coding							Standard	NR_024435		Approved		uc002iit.4		OTTHUMG00000180362		17.37:g.43347913C>T		Somatic		Capture	Illumina HiSeq	Phase_I	40703696	NM_003954		Silent	SNP	ENST00000585780.1	37																																																																																					0.627	MAP3K14-AS1-008	KNOWN	basic	antisense	antisense	OTTHUMT00000450941.1	NR_024434	
ARHGAP27	201176	broad.mit.edu	37	17	43472970	43472970	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr17:43472970A>G	ENST00000428638.1	-	17	2521	c.2522T>C	c.(2521-2523)aTg>aCg	p.M841T	ARHGAP27_ENST00000376922.2_Missense_Mutation_p.M500T|ARHGAP27_ENST00000455881.1_Missense_Mutation_p.M500T|ARHGAP27_ENST00000532038.1_Missense_Mutation_p.M619T|ARHGAP27_ENST00000532891.2_Missense_Mutation_p.M819T|ARHGAP27_ENST00000582826.1_5'Flank|ARHGAP27_ENST00000442348.1_Missense_Mutation_p.M814T|CTB-39G8.3_ENST00000592389.1_RNA|ARHGAP27_ENST00000528384.1_Missense_Mutation_p.M473T			Q6ZUM4	RHG27_HUMAN	Rho GTPase activating protein 27	841	Rho-GAP. {ECO:0000255|PROSITE- ProRule:PRU00172}.				positive regulation of Cdc42 GTPase activity (GO:0043089)|positive regulation of Rac GTPase activity (GO:0032855)|receptor-mediated endocytosis (GO:0006898)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|intracellular (GO:0005622)|membrane (GO:0016020)	Rac GTPase activator activity (GO:0030675)|SH3 domain binding (GO:0017124)	p.M500T(1)		endometrium(4)|large_intestine(9)|lung(3)|skin(1)	17	Renal(3;0.0405)					CTGCACCGACATGCGGTTCTG	0.667																																					p.M500T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T1499C	17						.						32.0	28.0	29.0					17																	43472970		2203	4300	6503	40828753	SO:0001583	missense	201176	exon17			AK125535	CCDS11498.1, CCDS74082.1	17q21.31	2013-01-10			ENSG00000159314	ENSG00000159314		"""Rho GTPase activating proteins"", ""Pleckstrin homology (PH) domain containing"""	31813	protein-coding gene	gene with protein product		610591	"""SH3 domain containing 20"""	SH3D20		15147912	Standard	NM_199282		Approved	CAMGAP1, FLJ43547, SH3P20	uc002iix.3	Q6ZUM4	OTTHUMG00000166982	ENST00000428638.1:c.2522T>C	17.37:g.43472970A>G	ENSP00000403323:p.Met841Thr	Somatic		Capture	Illumina HiSeq	Phase_I	40828753	NM_199282	A4FU35|A8K3N5|C9JTF3|Q494U0|Q6NWZ8|Q8WY58	Missense_Mutation	SNP	ENST00000428638.1	37		.	.	.	.	.	.	.	.	.	.	A	22.4	4.285907	0.80803	.	.	ENSG00000159314	ENST00000532038;ENST00000376922;ENST00000528384;ENST00000532891;ENST00000428638;ENST00000442348;ENST00000455881	T;T;T;T;T;T;T	0.40225	1.04;1.04;1.04;1.04;1.04;1.04;1.04	4.45	4.45	0.53987	Rho GTPase-activating protein domain (4);Rho GTPase activation protein (1);	0.000000	0.85682	D	0.000000	T	0.76335	0.3973	H	0.98646	4.29	0.80722	D	1	D;D	0.76494	0.999;0.984	D;D	0.97110	1.0;0.986	D	0.84481	0.0605	10	0.87932	D	0	.	11.7204	0.51678	1.0:0.0:0.0:0.0	.	814;841	F8WBX1;Q6ZUM4	.;RHG27_HUMAN	T	619;500;473;819;841;814;500	ENSP00000432762:M619T;ENSP00000366121:M500T;ENSP00000431591:M473T;ENSP00000433942:M819T;ENSP00000403323:M841T;ENSP00000409330:M814T;ENSP00000408235:M500T	ENSP00000366121:M500T	M	-	2	0	ARHGAP27	40828753	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	9.009000	0.93606	1.881000	0.54492	0.448000	0.29417	ATG		0.667	ARHGAP27-202	KNOWN	basic	protein_coding	protein_coding		NM_199282	
SPPL2C	162540	broad.mit.edu	37	17	43922344	43922344	+	Silent	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr17:43922344C>T	ENST00000329196.5	+	1	89	c.72C>T	c.(70-72)taC>taT	p.Y24Y	MAPT-AS1_ENST00000581125.1_RNA|MAPT-AS1_ENST00000579244.1_RNA|MAPT-AS1_ENST00000579599.1_RNA	NM_175882.2	NP_787078.2	Q8IUH8	SPP2C_HUMAN	signal peptide peptidase like 2C	24						endoplasmic reticulum membrane (GO:0005789)|integral component of cytoplasmic side of endoplasmic reticulum membrane (GO:0071458)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)	aspartic-type endopeptidase activity (GO:0004190)|protein homodimerization activity (GO:0042803)	p.Y24Y(1)									GGGGAAAGTACGGCGTGGCCC	0.622																																					p.Y24Y												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C72T	17						.						96.0	80.0	86.0					17																	43922344		2203	4300	6503	41278124	SO:0001819	synonymous_variant	162540	exon1				CCDS32673.1	17q21.31	2014-02-12			ENSG00000185294	ENSG00000185294			28902	protein-coding gene	gene with protein product	"""intramembrane protease 5"""	608284				12139484	Standard	NM_175882		Approved	IMP5	uc010wka.2	Q8IUH8		ENST00000329196.5:c.72C>T	17.37:g.43922344C>T		Somatic		Capture	Illumina HiSeq	Phase_I	41278124	NM_175882	Q8TC67|Q8WVZ6	Silent	SNP	ENST00000329196.5	37	CCDS32673.1																																																																																				0.622	SPPL2C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441156.1	NM_175882	
MAPT	4137	broad.mit.edu	37	17	44051760	44051760	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr17:44051760C>T	ENST00000571987.1	+	3	230	c.230C>T	c.(229-231)gCa>gTa	p.A77V	MAPT_ENST00000431008.3_Missense_Mutation_p.A77V|MAPT_ENST00000574436.1_Missense_Mutation_p.A77V|MAPT_ENST00000262410.5_Missense_Mutation_p.A77V|MAPT_ENST00000340799.5_Intron|MAPT_ENST00000446361.3_Intron|MAPT_ENST00000535772.1_Missense_Mutation_p.A77V|MAPT_ENST00000415613.2_Missense_Mutation_p.A77V|MAPT_ENST00000347967.5_Intron|MAPT_ENST00000576518.1_5'UTR|MAPT_ENST00000420682.2_Intron|MAPT_ENST00000334239.8_Intron|MAPT_ENST00000351559.5_Missense_Mutation_p.A77V|MAPT_ENST00000570299.1_Intron|MAPT_ENST00000344290.5_Missense_Mutation_p.A77V			P10636	TAU_HUMAN	microtubule-associated protein tau	77					adult walking behavior (GO:0007628)|apoptotic process (GO:0006915)|axon cargo transport (GO:0008088)|axon extension (GO:0048675)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|generation of neurons (GO:0048699)|microtubule cytoskeleton organization (GO:0000226)|mitochondrion transport along microtubule (GO:0047497)|negative regulation of intracellular transport (GO:0032387)|neuron migration (GO:0001764)|positive regulation of axon extension (GO:0045773)|positive regulation of microtubule polymerization (GO:0031116)|regulation of autophagy (GO:0010506)|regulation of microtubule polymerization (GO:0031113)|regulation of microtubule-based movement (GO:0060632)	axon (GO:0030424)|axoneme (GO:0005930)|cytoplasmic ribonucleoprotein granule (GO:0036464)|cytosol (GO:0005829)|growth cone (GO:0030426)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|nuclear periphery (GO:0034399)|plasma membrane (GO:0005886)|tubulin complex (GO:0045298)	apolipoprotein binding (GO:0034185)|enzyme binding (GO:0019899)|lipoprotein particle binding (GO:0071813)|microtubule binding (GO:0008017)|SH3 domain binding (GO:0017124)|structural constituent of cytoskeleton (GO:0005200)	p.A77V(1)		breast(1)|endometrium(4)|kidney(1)|large_intestine(9)|lung(14)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	38		Melanoma(429;0.216)			Docetaxel(DB01248)|Paclitaxel(DB01229)	GATGTGACAGCACCCTTAGTG	0.617																																					p.A77V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C230T	17						.						33.0	31.0	32.0					17																	44051760		2203	4300	6503	41407596	SO:0001583	missense	4137	exon4			J03778	CCDS11499.1, CCDS11500.1, CCDS11501.1, CCDS11502.1, CCDS45715.1, CCDS45716.1, CCDS56033.1	17q21	2014-09-17			ENSG00000186868	ENSG00000186868			6893	protein-coding gene	gene with protein product	"""G protein beta1/gamma2 subunit-interacting factor 1"", ""microtubule-associated protein tau, isoform 4"", ""protein phosphatase 1, regulatory subunit 103"""	157140		DDPAC, MAPTL		7936241, 3131773	Standard	NM_001123067		Approved	MTBT1, tau, PPND, FTDP-17, TAU, MSTD, MTBT2, FLJ31424, MGC138549, PPP1R103	uc010dau.3	P10636	OTTHUMG00000168833	ENST00000571987.1:c.230C>T	17.37:g.44051760C>T	ENSP00000458742:p.Ala77Val	Somatic		Capture	Illumina HiSeq	Phase_I	41407596	NM_016835	P18518|Q14799|Q15549|Q15550|Q15551|Q1RMF6|Q53YB1|Q5CZI7|Q5XWF0|Q6QT54|Q9UDJ3|Q9UMH0|Q9UQ96	Missense_Mutation	SNP	ENST00000571987.1	37	CCDS11501.1	.	.	.	.	.	.	.	.	.	.	C	27.6	4.849434	0.91277	.	.	ENSG00000186868	ENST00000344290;ENST00000262410;ENST00000351559;ENST00000535772;ENST00000415613	T;T;T;T;T	0.26373	2.12;2.12;1.74;1.98;2.12	5.94	5.94	0.96194	.	0.000000	0.44097	D	0.000498	T	0.47229	0.1434	L	0.54323	1.7	0.80722	D	1	D;D;D	0.76494	0.997;0.998;0.999	D;D;D	0.85130	0.995;0.987;0.997	T	0.22103	-1.0226	10	0.51188	T	0.08	-16.1209	15.8634	0.79043	0.0:1.0:0.0:0.0	.	77;77;77	P10636-9;P10636-8;P10636	.;.;TAU_HUMAN	V	77	ENSP00000340820:A77V;ENSP00000262410:A77V;ENSP00000303214:A77V;ENSP00000443028:A77V;ENSP00000410838:A77V	ENSP00000262410:A77V	A	+	2	0	MAPT	41407596	0.995000	0.38212	0.984000	0.44739	0.846000	0.48090	4.413000	0.59795	2.826000	0.97356	0.561000	0.74099	GCA		0.617	MAPT-008	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000440133.1	NM_016835	
KANSL1	284058	broad.mit.edu	37	17	44117146	44117146	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr17:44117146C>A	ENST00000262419.6	-	8	2595	c.2125G>T	c.(2125-2127)Gca>Tca	p.A709S	KANSL1_ENST00000572904.1_Missense_Mutation_p.A709S|KANSL1_ENST00000432791.1_Missense_Mutation_p.A709S|KANSL1_ENST00000393476.3_Missense_Mutation_p.A66S|KANSL1_ENST00000574590.1_Missense_Mutation_p.A709S|KANSL1_ENST00000575318.1_Missense_Mutation_p.A709S	NM_001193466.1	NP_001180395	Q7Z3B3	KANL1_HUMAN	KAT8 regulatory NSL complex subunit 1	709					chromatin organization (GO:0006325)|histone H4-K16 acetylation (GO:0043984)|histone H4-K5 acetylation (GO:0043981)|histone H4-K8 acetylation (GO:0043982)	histone acetyltransferase complex (GO:0000123)|MLL1 complex (GO:0071339)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)		p.A709S(1)									GGCATGGGTGCTCTGTGCTTA	0.502																																					p.A709S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2125T	17						.						133.0	124.0	127.0					17																	44117146		2203	4300	6503	41472993	SO:0001583	missense	284058	exon8			BX538006	CCDS11503.1, CCDS11503.2, CCDS74084.1	17q21.31	2012-02-20	2012-02-20	2012-02-20	ENSG00000120071	ENSG00000120071			24565	protein-coding gene	gene with protein product	"""centromere protein 36"""	612452	"""KIAA1267"""	KIAA1267		10574462	Standard	NM_015443		Approved	DKFZP727C091, MSL1v1, CENP-36, NSL1	uc002ikd.3	Q7Z3B3		ENST00000262419.6:c.2125G>T	17.37:g.44117146C>A	ENSP00000262419:p.Ala709Ser	Somatic		Capture	Illumina HiSeq	Phase_I	41472993	NM_015443	A8K5E4|Q6AW85|Q8IYH1|Q9BRH0|Q9NTE7|Q9UFT0|Q9ULF3	Missense_Mutation	SNP	ENST00000262419.6	37	CCDS11503.1	.	.	.	.	.	.	.	.	.	.	C	6.414	0.444586	0.12164	.	.	ENSG00000120071	ENST00000262419;ENST00000432791;ENST00000393476	T;T;T	0.23348	2.7;2.7;1.91	6.05	0.655	0.17839	.	0.487699	0.25114	N	0.033032	T	0.13329	0.0323	L	0.38531	1.155	0.29809	N	0.831837	B;B;B;B	0.30686	0.05;0.161;0.16;0.29	B;B;B;B	0.26094	0.033;0.033;0.059;0.066	T	0.26467	-1.0102	10	0.10111	T	0.7	-0.4189	5.3573	0.16067	0.1241:0.538:0.0:0.338	.	40;40;709;709	B3KT49;Q7Z3B3-2;C9JHY2;Q7Z3B3	.;.;.;K1267_HUMAN	S	709;709;66	ENSP00000262419:A709S;ENSP00000387393:A709S;ENSP00000377117:A66S	ENSP00000262419:A709S	A	-	1	0	KIAA1267	41472993	0.984000	0.35163	0.998000	0.56505	0.602000	0.36980	0.225000	0.17757	0.160000	0.19432	-0.158000	0.13435	GCA		0.502	KANSL1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440274.1	NM_015443	
NSF	4905	broad.mit.edu	37	17	44827147	44827147	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr17:44827147G>T	ENST00000398238.4	+	18	2024	c.1917G>T	c.(1915-1917)aaG>aaT	p.K639N	NSF_ENST00000225282.8_Missense_Mutation_p.K545N|NSF_ENST00000575068.1_Missense_Mutation_p.K634N	NM_006178.3	NP_006169.2	P46459	NSF_HUMAN	N-ethylmaleimide-sensitive factor	639				K -> M (in Ref. 4; BAF82893). {ECO:0000305}.	exocytosis (GO:0006887)|plasma membrane fusion (GO:0045026)|positive regulation of receptor recycling (GO:0001921)|potassium ion transport (GO:0006813)|protein transport (GO:0015031)|synaptic transmission (GO:0007268)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|lysosomal membrane (GO:0005765)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled (GO:0042623)|metal ion binding (GO:0046872)|PDZ domain binding (GO:0030165)|protein complex binding (GO:0032403)|protein kinase binding (GO:0019901)|syntaxin-1 binding (GO:0017075)	p.K639N(1)		kidney(2)|large_intestine(1)|liver(2)|lung(7)|ovary(1)|upper_aerodigestive_tract(1)	14		Melanoma(429;0.203)	BRCA - Breast invasive adenocarcinoma(9;0.0257)	BRCA - Breast invasive adenocarcinoma(366;0.241)		AGGGCCGCAAGCTTCTTATCA	0.418																																					p.K639N	Ovarian(25;472 742 1472 36813 50223)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1917T	17						.						94.0	90.0	91.0					17																	44827147		1937	4148	6085	42182314	SO:0001583	missense	4905	exon18				CCDS42354.1	17q21	2010-04-21			ENSG00000073969	ENSG00000073969		"""ATPases / AAA-type"""	8016	protein-coding gene	gene with protein product	"""N-ethylmaleimide-sensitive factor-like protein"""	601633				1315316, 8875895	Standard	NM_006178		Approved	SKD2	uc002iku.3	P46459	OTTHUMG00000134315	ENST00000398238.4:c.1917G>T	17.37:g.44827147G>T	ENSP00000381293:p.Lys639Asn	Somatic		Capture	Illumina HiSeq	Phase_I	42182314	NM_006178	A8K2D9|B4DFA2|Q8N6D7|Q9UKZ2	Missense_Mutation	SNP	ENST00000398238.4	37	CCDS42354.1	.	.	.	.	.	.	.	.	.	.	G	15.73	2.919848	0.52653	.	.	ENSG00000073969	ENST00000398238;ENST00000225282	D;D	0.92858	-3.12;-3.12	5.38	4.42	0.53409	ATPase, AAA-type, core (1);ATPase, AAA+ type, core (1);	0.000000	0.85682	D	0.000000	D	0.92325	0.7565	L	0.28694	0.88	0.80722	D	1	D	0.54772	0.968	D	0.68039	0.955	D	0.90794	0.4689	10	0.30078	T	0.28	-14.5017	14.0397	0.64667	0.0729:0.0:0.9271:0.0	.	639	P46459	NSF_HUMAN	N	639;545	ENSP00000381293:K639N;ENSP00000225282:K545N	ENSP00000225282:K545N	K	+	3	2	NSF	42182314	1.000000	0.71417	1.000000	0.80357	0.110000	0.19582	5.412000	0.66392	1.278000	0.44430	-0.251000	0.11542	AAG		0.418	NSF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259348.2	NM_006178	
NFE2L1	4779	broad.mit.edu	37	17	46135912	46135912	+	Missense_Mutation	SNP	T	T	G			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr17:46135912T>G	ENST00000362042.3	+	6	1844	c.1228T>G	c.(1228-1230)Tcc>Gcc	p.S410A	NFE2L1_ENST00000582155.1_Missense_Mutation_p.S222A|NFE2L1_ENST00000536222.1_Missense_Mutation_p.S254A|NFE2L1_ENST00000583378.1_Missense_Mutation_p.S211A|NFE2L1_ENST00000357480.5_Missense_Mutation_p.S380A|NFE2L1_ENST00000361665.3_Missense_Mutation_p.S399A|NFE2L1_ENST00000585291.1_Missense_Mutation_p.S380A|RP5-890E16.4_ENST00000583349.1_RNA	NM_003204.2	NP_003195.1	Q14494	NF2L1_HUMAN	nuclear factor, erythroid 2-like 1	410					anatomical structure morphogenesis (GO:0009653)|erythrocyte differentiation (GO:0030218)|heme biosynthetic process (GO:0006783)|inflammatory response (GO:0006954)|transcription from RNA polymerase II promoter (GO:0006366)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	RNA polymerase II transcription factor binding transcription factor activity involved in positive regulation of transcription (GO:0001190)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription cofactor activity (GO:0003712)	p.S410A(1)		cervix(1)|endometrium(3)|kidney(9)|large_intestine(7)|lung(7)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	32						CACCTTCGGCTCCACCAACCT	0.607																																					p.S410A												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T1228G	17						.						80.0	81.0	81.0					17																	46135912		2203	4300	6503	43490911	SO:0001583	missense	4779	exon6			AK090459	CCDS11524.1	17q21.3	2013-08-23	2013-08-23			ENSG00000082641		"""basic leucine zipper proteins"""	7781	protein-coding gene	gene with protein product		163260	"""nuclear factor (erythroid-derived 2)-like 1"""	TCF11		8248256, 9501099	Standard	NM_003204		Approved	NRF1, LCR-F1, FLJ00380	uc002imz.4	Q14494		ENST00000362042.3:c.1228T>G	17.37:g.46135912T>G	ENSP00000354855:p.Ser410Ala	Somatic		Capture	Illumina HiSeq	Phase_I	43490911	NM_003204	D3DTU3|D3DTU5|Q12877|Q96FN6	Missense_Mutation	SNP	ENST00000362042.3	37	CCDS11524.1	.	.	.	.	.	.	.	.	.	.	T	1.185	-0.637121	0.03557	.	.	ENSG00000082641	ENST00000362042;ENST00000361665;ENST00000357480;ENST00000536222	T;T	0.08546	3.08;3.08	5.62	3.3	0.37823	.	0.296211	0.38111	N	0.001812	T	0.03871	0.0109	N	0.12569	0.235	0.30108	N	0.806861	B;B;B;B	0.06786	0.0;0.0;0.0;0.001	B;B;B;B	0.06405	0.002;0.001;0.001;0.001	T	0.37009	-0.9724	10	0.10111	T	0.7	-23.6367	7.2447	0.26115	0.0:0.0774:0.1462:0.7764	.	254;222;380;410	F5H1B7;B4DYE1;Q14494-2;Q14494	.;.;.;NF2L1_HUMAN	A	429;410;380;254	ENSP00000350072:S380A;ENSP00000445811:S254A	ENSP00000350072:S380A	S	+	1	0	NFE2L1	43490911	1.000000	0.71417	1.000000	0.80357	0.614000	0.37383	2.202000	0.42743	0.977000	0.38444	0.454000	0.30748	TCC		0.607	NFE2L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443019.1	NM_003204	
IGF2BP1	10642	broad.mit.edu	37	17	47123644	47123644	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr17:47123644C>T	ENST00000290341.3	+	14	1884	c.1550C>T	c.(1549-1551)aCg>aTg	p.T517M	IGF2BP1_ENST00000431824.2_Missense_Mutation_p.T378M	NM_006546.3	NP_006537.3	Q9NZI8	IF2B1_HUMAN	insulin-like growth factor 2 mRNA binding protein 1	517	KH 4. {ECO:0000255|PROSITE- ProRule:PRU00117}.|Necessary for interaction with ELAVL4 and binding to TAU mRNA. {ECO:0000250}.				CRD-mediated mRNA stabilization (GO:0070934)|gene expression (GO:0010467)|mRNA transport (GO:0051028)|negative regulation of translation (GO:0017148)|regulation of cytokine biosynthetic process (GO:0042035)|regulation of mRNA stability involved in response to stress (GO:0010610)	CRD-mediated mRNA stability complex (GO:0070937)|cytoplasm (GO:0005737)|cytoplasmic stress granule (GO:0010494)|cytosol (GO:0005829)|dendrite (GO:0030425)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	mRNA 3'-UTR binding (GO:0003730)|mRNA 5'-UTR binding (GO:0048027)|mRNA binding (GO:0003729)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|translation regulator activity (GO:0045182)	p.T517M(1)		breast(1)|endometrium(3)|kidney(2)|large_intestine(8)|lung(12)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	31						CAGAATTTGACGGCAGCTGAG	0.542																																					p.T378M	Esophageal Squamous(198;1041 2123 8248 37119 38268)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1133T	17						.						93.0	83.0	87.0					17																	47123644		2203	4300	6503	44478643	SO:0001583	missense	10642	exon12			AF198254	CCDS11543.1, CCDS54138.1	17q21.32	2013-02-12			ENSG00000159217	ENSG00000159217		"""RNA binding motif (RRM) containing"""	28866	protein-coding gene	gene with protein product	"""IGF II mRNA binding protein 1"""	608288				9891060, 11992722	Standard	NM_001160423		Approved	IMP-1	uc002iom.3	Q9NZI8	OTTHUMG00000161173	ENST00000290341.3:c.1550C>T	17.37:g.47123644C>T	ENSP00000290341:p.Thr517Met	Somatic		Capture	Illumina HiSeq	Phase_I	44478643	NM_001160423	C9JT33	Missense_Mutation	SNP	ENST00000290341.3	37	CCDS11543.1	.	.	.	.	.	.	.	.	.	.	C	35	5.501371	0.96371	.	.	ENSG00000159217	ENST00000290341;ENST00000431824	T;T	0.45668	0.89;0.89	5.65	5.65	0.86999	K Homology (1);K Homology, type 1, subgroup (1);K Homology, type 1 (1);	0.049761	0.85682	D	0.000000	T	0.68659	0.3025	M	0.81239	2.535	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.78314	0.991;0.986	T	0.70817	-0.4769	10	0.87932	D	0	-10.5378	19.5069	0.95121	0.0:1.0:0.0:0.0	.	378;517	C9JT33;Q9NZI8	.;IF2B1_HUMAN	M	517;378	ENSP00000290341:T517M;ENSP00000389135:T378M	ENSP00000290341:T517M	T	+	2	0	IGF2BP1	44478643	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	7.618000	0.83043	2.941000	0.99782	0.655000	0.94253	ACG		0.542	IGF2BP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364046.1	NM_006546	
NGFR	4804	broad.mit.edu	37	17	47590210	47590210	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr17:47590210T>C	ENST00000172229.3	+	6	1248	c.1123T>C	c.(1123-1125)Tcc>Ccc	p.S375P	RP5-1029K10.2_ENST00000514506.1_RNA|NGFR_ENST00000504201.1_Missense_Mutation_p.S281P	NM_002507.3	NP_002498.1	P08138	TNR16_HUMAN	nerve growth factor receptor	375	Death. {ECO:0000255|PROSITE- ProRule:PRU00064}.				apoptotic signaling pathway (GO:0097190)|axon guidance (GO:0007411)|central nervous system development (GO:0007417)|circadian regulation of gene expression (GO:0032922)|detection of temperature stimulus (GO:0016048)|glucose homeostasis (GO:0042593)|hair follicle morphogenesis (GO:0031069)|intracellular protein transport (GO:0006886)|membrane protein intracellular domain proteolysis (GO:0031293)|negative regulation of apoptotic process (GO:0043066)|negative regulation of axonogenesis (GO:0050771)|negative regulation of cell cycle (GO:0045786)|negative regulation of fibroblast growth factor receptor signaling pathway (GO:0040037)|negative regulation of hair follicle development (GO:0051799)|nerve development (GO:0021675)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of axonogenesis (GO:0050772)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of odontogenesis of dentin-containing tooth (GO:0042488)|regulation of axonogenesis (GO:0050770)|regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043281)|regulation of glucose import in response to insulin stimulus (GO:2001273)	cell surface (GO:0009986)|cytosol (GO:0005829)|endosome (GO:0005768)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|neuronal postsynaptic density (GO:0097481)|nucleoplasm (GO:0005654)|plasma membrane (GO:0005886)	death receptor activity (GO:0005035)|Rab GTPase binding (GO:0017137)|receptor activity (GO:0004872)|signal transducer activity (GO:0004871)|transmembrane signaling receptor activity (GO:0004888)|ubiquitin protein ligase binding (GO:0031625)	p.S375P(1)		central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(4)|liver(1)|lung(7)|ovary(1)	17	all_cancers(4;1.45e-13)|Breast(4;6.34e-28)|all_epithelial(4;4.95e-17)					GCACATAGACTCCTTTACCCA	0.692																																					p.S375P												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T1123C	17						.						40.0	45.0	43.0					17																	47590210		2203	4299	6502	44945209	SO:0001583	missense	4804	exon6			M14764	CCDS11549.1	17q21-q22	2013-05-22	2010-04-28		ENSG00000064300	ENSG00000064300		"""Tumor necrosis factor receptor superfamily"", ""CD molecules"""	7809	protein-coding gene	gene with protein product	"""low affinity nerve growth factor receptor"", ""TNFR superfamily, member 16"""	162010	"""nerve growth factor receptor (TNFR superfamily, member 16)"""			3022937, 3006050	Standard	NM_002507		Approved	TNFRSF16, CD271, p75NTR	uc002ioz.4	P08138	OTTHUMG00000161495	ENST00000172229.3:c.1123T>C	17.37:g.47590210T>C	ENSP00000172229:p.Ser375Pro	Somatic		Capture	Illumina HiSeq	Phase_I	44945209	NM_002507	B2R961|B4E096	Missense_Mutation	SNP	ENST00000172229.3	37	CCDS11549.1	.	.	.	.	.	.	.	.	.	.	T	18.45	3.625610	0.66901	.	.	ENSG00000064300	ENST00000172229;ENST00000504201	D;D	0.85773	-2.03;-2.03	4.85	4.85	0.62838	Death (3);DEATH-like (2);	0.518968	0.18685	N	0.134040	T	0.80144	0.4569	N	0.21448	0.665	0.32473	N	0.542543	P	0.50369	0.934	P	0.50708	0.648	T	0.80668	-0.1280	10	0.30854	T	0.27	-31.3336	8.9476	0.35769	0.1659:0.0:0.0:0.8341	.	375	P08138	TNR16_HUMAN	P	375;281	ENSP00000172229:S375P;ENSP00000421731:S281P	ENSP00000172229:S375P	S	+	1	0	NGFR	44945209	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	1.529000	0.35996	1.812000	0.52913	0.459000	0.35465	TCC		0.692	NGFR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365150.1		
CHAD	1101	broad.mit.edu	37	17	48545768	48545768	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr17:48545768G>A	ENST00000508540.1	-	1	559	c.407C>T	c.(406-408)aCt>aTt	p.T136I	ACSF2_ENST00000541920.1_Intron|ACSF2_ENST00000427954.2_Intron|ACSF2_ENST00000502667.1_Intron|ACSF2_ENST00000506085.1_3'UTR|ACSF2_ENST00000504392.1_Intron|ACSF2_ENST00000300441.4_Intron|CHAD_ENST00000258969.4_Missense_Mutation_p.T136I	NM_001267.2	NP_001258.2	O15335	CHAD_HUMAN	chondroadherin	136					bone development (GO:0060348)|cartilage condensation (GO:0001502)|negative regulation of bone trabecula formation (GO:1900155)	proteinaceous extracellular matrix (GO:0005578)		p.T136I(1)		central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(7)|lung(2)|ovary(2)	15	Breast(11;1.93e-18)		BRCA - Breast invasive adenocarcinoma(22;1.55e-09)			GGGCAGCTCAGTGACCTTGTT	0.602																																					p.T136I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C407T	17						.						56.0	49.0	51.0					17																	48545768		2203	4300	6503	45900767	SO:0001583	missense	1101	exon1			U96767	CCDS11568.1	17q21.33	2008-02-05			ENSG00000136457	ENSG00000136457		"""Proteoglycans / Extracellular Matrix : Small leucine-rich repeats"""	1909	protein-coding gene	gene with protein product	"""chondroadherin proteoglycan"""	602178				9344663	Standard	NM_001267		Approved	SLRR4A	uc010dbr.3	O15335	OTTHUMG00000162129	ENST00000508540.1:c.407C>T	17.37:g.48545768G>A	ENSP00000423812:p.Thr136Ile	Somatic		Capture	Illumina HiSeq	Phase_I	45900767	NM_001267	A8K812|Q6GTU0|Q96RJ5	Missense_Mutation	SNP	ENST00000508540.1	37	CCDS11568.1	.	.	.	.	.	.	.	.	.	.	G	11.49	1.653461	0.29425	.	.	ENSG00000136457	ENST00000508540;ENST00000258969	T;T	0.58797	0.31;0.31	4.77	3.76	0.43208	.	0.354385	0.29752	N	0.011297	T	0.53578	0.1805	M	0.74258	2.255	0.31088	N	0.711141	B	0.09022	0.002	B	0.10450	0.005	T	0.53143	-0.8480	10	0.25751	T	0.34	.	9.9493	0.41630	0.0819:0.1528:0.7653:0.0	.	136	O15335	CHAD_HUMAN	I	136	ENSP00000423812:T136I;ENSP00000258969:T136I	ENSP00000258969:T136I	T	-	2	0	CHAD	45900767	0.999000	0.42202	0.962000	0.40283	0.990000	0.78478	2.880000	0.48530	2.478000	0.83669	0.563000	0.77884	ACT		0.602	CHAD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367447.3	NM_001267	
RSAD1	55316	broad.mit.edu	37	17	48560712	48560712	+	Nonsense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr17:48560712C>T	ENST00000258955.2	+	6	1001	c.916C>T	c.(916-918)Cga>Tga	p.R306*		NM_018346.1	NP_060816.1	Q9HA92	RSAD1_HUMAN	radical S-adenosyl methionine domain containing 1	306					porphyrin-containing compound biosynthetic process (GO:0006779)	mitochondrion (GO:0005739)	4 iron, 4 sulfur cluster binding (GO:0051539)|coproporphyrinogen oxidase activity (GO:0004109)|metal ion binding (GO:0046872)	p.R306*(1)		breast(1)|endometrium(4)|large_intestine(3)|lung(5)|ovary(1)|prostate(1)|skin(1)	16	Breast(11;1.93e-18)		BRCA - Breast invasive adenocarcinoma(22;1.55e-09)			GGCCCATGGACGATTTATGCC	0.532																																					p.R306X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.C916T	17						.						37.0	39.0	38.0					17																	48560712		2203	4300	6503	45915711	SO:0001587	stop_gained	55316	exon6			AK002026	CCDS11569.1	17q21.33	2004-11-08			ENSG00000136444	ENSG00000136444			25634	protein-coding gene	gene with protein product						12477932	Standard	NM_018346		Approved	FLJ11164	uc002iqw.1	Q9HA92	OTTHUMG00000162126	ENST00000258955.2:c.916C>T	17.37:g.48560712C>T	ENSP00000258955:p.Arg306*	Somatic		Capture	Illumina HiSeq	Phase_I	45915711	NM_018346	B4DMW0|Q53HV8|Q86VC4|Q9BRY7|Q9NUS7	Nonsense_Mutation	SNP	ENST00000258955.2	37	CCDS11569.1	.	.	.	.	.	.	.	.	.	.	C	13.63	2.294188	0.40594	.	.	ENSG00000136444	ENST00000258955	.	.	.	5.28	4.28	0.50868	.	0.229060	0.36200	N	0.002733	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-1.9491	13.4545	0.61191	0.2844:0.7155:0.0:0.0	.	.	.	.	X	306	.	ENSP00000258955:R306X	R	+	1	2	RSAD1	45915711	0.983000	0.35010	0.958000	0.39756	0.087000	0.18053	1.299000	0.33424	1.309000	0.44985	0.655000	0.94253	CGA		0.532	RSAD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367413.1	NM_018346	
EPN3	55040	broad.mit.edu	37	17	48614046	48614046	+	Silent	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr17:48614046C>T	ENST00000268933.3	+	2	708	c.129C>T	c.(127-129)atC>atT	p.I43I	EPN3_ENST00000541226.1_Intron|RP11-94C24.8_ENST00000513017.1_RNA|EPN3_ENST00000537145.1_Intron	NM_017957.2	NP_060427.2	Q9H201	EPN3_HUMAN	epsin 3	43	ENTH. {ECO:0000255|PROSITE- ProRule:PRU00243}.					clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|extracellular vesicular exosome (GO:0070062)|extrinsic component of plasma membrane (GO:0019897)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	lipid binding (GO:0008289)	p.I43I(1)		breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(3)|lung(1)|ovary(1)|prostate(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	14	Breast(11;1.23e-18)		BRCA - Breast invasive adenocarcinoma(22;2.88e-09)			TGTCCGAGATCGCTGACCTGA	0.592																																					p.I43I												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C129T	17						.						84.0	78.0	80.0					17																	48614046		2203	4300	6503	45969045	SO:0001819	synonymous_variant	55040	exon2			AF324241	CCDS11570.1	17q21.33	2008-07-18				ENSG00000049283			18235	protein-coding gene	gene with protein product		607264				10951261, 11359770	Standard	NM_017957		Approved	FLJ20778, MGC129899	uc002ira.4	Q9H201		ENST00000268933.3:c.129C>T	17.37:g.48614046C>T		Somatic		Capture	Illumina HiSeq	Phase_I	45969045	NM_017957	A8K6J3|A8KAB2|Q9BVN6|Q9NWK2	Silent	SNP	ENST00000268933.3	37	CCDS11570.1																																																																																				0.592	EPN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367573.1	NM_017957	
CACNA1G	8913	broad.mit.edu	37	17	48650000	48650000	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr17:48650000G>A	ENST00000359106.5	+	6	832	c.832G>A	c.(832-834)Ggc>Agc	p.G278S	CACNA1G_ENST00000507609.1_Missense_Mutation_p.G278S|CACNA1G_ENST00000513689.2_Missense_Mutation_p.G278S|CACNA1G_ENST00000507510.2_Missense_Mutation_p.G278S|CACNA1G_ENST00000507336.1_Missense_Mutation_p.G278S|CACNA1G_ENST00000502264.1_Missense_Mutation_p.G278S|CACNA1G_ENST00000442258.2_Missense_Mutation_p.G278S|CACNA1G_ENST00000514717.1_Missense_Mutation_p.G278S|CACNA1G_ENST00000507896.1_Missense_Mutation_p.G278S|CACNA1G_ENST00000503485.1_Missense_Mutation_p.G278S|CACNA1G_ENST00000515411.1_Missense_Mutation_p.G278S|CACNA1G_ENST00000510115.1_Missense_Mutation_p.G278S|CACNA1G_ENST00000515765.1_Missense_Mutation_p.G278S|CACNA1G_ENST00000429973.2_Missense_Mutation_p.G278S|CACNA1G_ENST00000360761.4_Missense_Mutation_p.G278S|CACNA1G_ENST00000358244.5_Missense_Mutation_p.G278S|CACNA1G_ENST00000505165.1_Missense_Mutation_p.G278S|CACNA1G_ENST00000513964.1_Missense_Mutation_p.G278S|CACNA1G_ENST00000416767.4_Missense_Mutation_p.G278S|CACNA1G_ENST00000515165.1_Missense_Mutation_p.G278S|CACNA1G_ENST00000514079.1_Missense_Mutation_p.G278S|CACNA1G_ENST00000354983.4_Missense_Mutation_p.G278S|CACNA1G_ENST00000512389.1_Missense_Mutation_p.G278S|CACNA1G_ENST00000352832.5_Missense_Mutation_p.G278S|CACNA1G_ENST00000510366.1_Missense_Mutation_p.G278S|CACNA1G_ENST00000514181.1_Missense_Mutation_p.G278S	NM_018896.4	NP_061496.2	O43497	CAC1G_HUMAN	calcium channel, voltage-dependent, T type, alpha 1G subunit	278					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.G278S(3)		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)	ACGCGAGAACGGCATGCGGTC	0.647																																					p.G278S												.	.	3	Substitution - Missense(3)	large_intestine(3)	c.G832A	17						.						20.0	23.0	22.0					17																	48650000		2080	4205	6285	46004999	SO:0001583	missense	8913	exon6			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.832G>A	17.37:g.48650000G>A	ENSP00000352011:p.Gly278Ser	Somatic		Capture	Illumina HiSeq	Phase_I	46004999	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	Missense_Mutation	SNP	ENST00000359106.5	37	CCDS45730.1	.	.	.	.	.	.	.	.	.	.	g	35	5.527848	0.96446	.	.	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	D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D	0.97665	-4.29;-4.29;-4.48;-4.23;-4.28;-4.27;-4.31;-4.38;-4.35;-4.36;-4.37;-4.24;-4.26;-4.32;-4.27;-4.22;-4.31;-4.26;-4.24;-4.31;-4.29;-4.26;-4.3;-4.24;-4.31;-4.31	5.36	5.36	0.76844	Ion transport (1);	0.000000	0.43110	D	0.000603	D	0.98454	0.9485	M	0.81341	2.54	0.80722	D	1	D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;0.999;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;0.999	D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D	0.97110	0.999;1.0;1.0;0.999;1.0;1.0;0.999;1.0;0.999;1.0;1.0;0.967;1.0;1.0;0.999;1.0;0.971;0.993;1.0;1.0;0.999;1.0;0.999;0.999;0.999;0.951	D	0.98974	1.0802	10	0.54805	T	0.06	.	19.1515	0.93491	0.0:0.0:1.0:0.0	.	278;278;278;278;278;278;278;278;278;278;278;278;278;278;278;278;278;278;278;278;278;278;278;278;278;278	Q19QZ5;Q19QZ1;Q19QZ4;Q19R07;Q19QY8;Q19R10;Q19QZ6;Q19QZ3;Q19R06;Q19R00;Q19R04;O43497-10;Q19QZ9;Q19QZ7;Q19R08;Q19QZ8;Q19R03;O43497-4;Q19R02;Q19R12;Q19R17;Q19R11;Q2TAC4;O43497;Q19R13;O43497-11	.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;CAC1G_HUMAN;.;.	S	278	ENSP00000353990:G278S;ENSP00000339302:G278S;ENSP00000392390:G278S;ENSP00000347078:G278S;ENSP00000409759:G278S;ENSP00000425522:G278S;ENSP00000426261:G278S;ENSP00000425451:G278S;ENSP00000422407:G278S;ENSP00000426814:G278S;ENSP00000427238:G278S;ENSP00000423112:G278S;ENSP00000420918:G278S;ENSP00000426172:G278S;ENSP00000423045:G278S;ENSP00000427173:G278S;ENSP00000426098:G278S;ENSP00000425698:G278S;ENSP00000426232:G278S;ENSP00000423317:G278S;ENSP00000350979:G278S;ENSP00000352011:G278S;ENSP00000414388:G278S;ENSP00000423155:G278S;ENSP00000422268:G278S;ENSP00000421518:G278S	ENSP00000339302:G278S	G	+	1	0	CACNA1G	46004999	1.000000	0.71417	0.997000	0.53966	0.979000	0.70002	9.293000	0.96082	2.541000	0.85698	0.505000	0.49811	GGC		0.647	CACNA1G-013	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000367895.1	NM_018896	
KIF1C	10749	broad.mit.edu	37	17	4927270	4927270	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr17:4927270G>A	ENST00000320785.5	+	23	3493	c.3136G>A	c.(3136-3138)Gca>Aca	p.A1046T		NM_006612.5	NP_006603.2	O43896	KIF1C_HUMAN	kinesin family member 1C	1046	Pro-rich.				ATP catabolic process (GO:0006200)|cell death (GO:0008219)|cytoskeleton-dependent intracellular transport (GO:0030705)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)|vesicle-mediated transport (GO:0016192)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|motor activity (GO:0003774)|plus-end-directed microtubule motor activity (GO:0008574)|poly(A) RNA binding (GO:0044822)	p.A1046T(1)		NS(2)|breast(4)|endometrium(4)|kidney(2)|large_intestine(8)|lung(6)|skin(1)|urinary_tract(3)	30						AGCGGGTTCTGCACAGCCTGA	0.697																																					p.A1046T	Melanoma(96;1023 1447 10250 19259 33730)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G3136A	17						.						41.0	48.0	46.0					17																	4927270		2203	4300	6503	4867994	SO:0001583	missense	10749	exon23			U91329	CCDS11065.1	17p13.2	2014-03-03			ENSG00000129250	ENSG00000129250		"""Kinesins"""	6317	protein-coding gene	gene with protein product		603060	"""spastic ataxia 2 (autosomal recessive)"""	SAX2		9685376, 24319291, 24482476	Standard	NM_006612		Approved	SPAX2, SPG58	uc002gan.2	O43896	OTTHUMG00000099451	ENST00000320785.5:c.3136G>A	17.37:g.4927270G>A	ENSP00000320821:p.Ala1046Thr	Somatic		Capture	Illumina HiSeq	Phase_I	4867994	NM_006612	D3DTL6|O75186|Q5U618	Missense_Mutation	SNP	ENST00000320785.5	37	CCDS11065.1	.	.	.	.	.	.	.	.	.	.	G	0.013	-1.636572	0.00806	.	.	ENSG00000129250	ENST00000320785	T	0.74737	-0.87	4.79	-1.45	0.08828	.	.	.	.	.	T	0.47728	0.1461	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.32134	-0.9918	9	0.08599	T	0.76	.	9.3857	0.38340	0.6794:0.0:0.3206:0.0	.	1046	O43896	KIF1C_HUMAN	T	1046	ENSP00000320821:A1046T	ENSP00000320821:A1046T	A	+	1	0	KIF1C	4867994	0.000000	0.05858	0.000000	0.03702	0.203000	0.24098	-1.084000	0.03393	-0.105000	0.12132	0.561000	0.74099	GCA		0.697	KIF1C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216916.1		
SLC52A1	55065	broad.mit.edu	37	17	4936850	4936850	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr17:4936850C>T	ENST00000424747.1	-	3	1646	c.934G>A	c.(934-936)Gcc>Acc	p.A312T	SLC52A1_ENST00000512825.2_Missense_Mutation_p.A312T|SLC52A1_ENST00000254853.5_Missense_Mutation_p.A312T	NM_001104577.1	NP_001098047.1	Q9NWF4	S52A1_HUMAN	solute carrier family 52 (riboflavin transporter), member 1	312					riboflavin transport (GO:0032218)	integral component of plasma membrane (GO:0005887)	riboflavin transporter activity (GO:0032217)|virus receptor activity (GO:0001618)	p.A312T(1)									AGGTGGTAGGCCAGGCGCCCA	0.642																																					p.A312T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G934A	17						.						72.0	62.0	65.0					17																	4936850		2203	4300	6503	4877574	SO:0001583	missense	55065	exon3			AY070775	CCDS11066.1	17p13.3	2013-07-17	2013-07-17	2012-02-29	ENSG00000132517	ENSG00000132517		"""Solute carriers"""	30225	protein-coding gene	gene with protein product	"""riboflavin transporter 1"""	607883	"""G protein-coupled receptor 172B"""	GPR172B		12740431, 18632736	Standard	NM_001104577		Approved	FLJ10060, GPCR42, PAR2, hRFT1, RFVT1	uc002gao.4	Q9NWF4	OTTHUMG00000099448	ENST00000424747.1:c.934G>A	17.37:g.4936850C>T	ENSP00000399979:p.Ala312Thr	Somatic		Capture	Illumina HiSeq	Phase_I	4877574	NM_017986	B5MEV1|B5MEV2|Q6P9E0|Q86UT0	Missense_Mutation	SNP	ENST00000424747.1	37	CCDS11066.1	.	.	.	.	.	.	.	.	.	.	C	16.63	3.175673	0.57692	.	.	ENSG00000132517	ENST00000254853;ENST00000512825;ENST00000424747	T;T;T	0.74209	-0.82;-0.82;-0.82	0.784	0.784	0.18578	.	0.121080	0.56097	N	0.000028	T	0.60547	0.2277	L	0.41710	1.295	0.40470	D	0.98033	B;B	0.19073	0.033;0.008	B;B	0.24269	0.052;0.028	T	0.52215	-0.8605	10	0.30854	T	0.27	.	7.3913	0.26911	0.0:1.0:0.0:0.0	.	312;312	F5H5Y1;Q9NWF4	.;RFT_HUMAN	T	312	ENSP00000254853:A312T;ENSP00000443026:A312T;ENSP00000399979:A312T	ENSP00000254853:A312T	A	-	1	0	GPR172B	4877574	1.000000	0.71417	0.998000	0.56505	0.994000	0.84299	0.794000	0.26958	0.699000	0.31761	0.563000	0.77884	GCC		0.642	SLC52A1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216913.1	NM_017986	
ABCC3	8714	broad.mit.edu	37	17	48741100	48741100	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr17:48741100G>A	ENST00000285238.8	+	9	1137	c.1057G>A	c.(1057-1059)Gct>Act	p.A353T	ABCC3_ENST00000427699.1_Missense_Mutation_p.A353T	NM_003786.3	NP_003777.2	O15438	MRP3_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 3	353	ABC transmembrane type-1 1. {ECO:0000255|PROSITE-ProRule:PRU00441}.				bile acid and bile salt transport (GO:0015721)|bile acid metabolic process (GO:0008206)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|organic anion transmembrane transporter activity (GO:0008514)	p.A353T(1)		breast(1)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(6)|liver(1)|lung(11)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	33			BRCA - Breast invasive adenocarcinoma(22;3.05e-09)		Cisplatin(DB00515)|Clotrimazole(DB00257)|Conjugated Estrogens(DB00286)|Cyclosporine(DB00091)|Doxorubicin(DB00997)|Etoposide(DB00773)|Ezetimibe(DB00973)|Fluorouracil(DB00544)|Folic Acid(DB00158)|Gadoxetate(DB08884)|Glutathione(DB00143)|Glyburide(DB01016)|Indomethacin(DB00328)|Lamivudine(DB00709)|Leucovorin(DB00650)|Methotrexate(DB00563)|Metyrapone(DB01011)|Nifedipine(DB01115)|Omeprazole(DB00338)|Phenobarbital(DB01174)|Probenecid(DB01032)|Rifampicin(DB01045)|Sulfinpyrazone(DB01138)|Verapamil(DB00661)|Vincristine(DB00541)	CTTCCTGGTGGCTGGGCTGAT	0.557																																					p.A353T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1057A	17						.						131.0	122.0	125.0					17																	48741100		2203	4300	6503	46096099	SO:0001583	missense	8714	exon9			Y17151	CCDS32681.1, CCDS45739.1	17q21	2012-03-14			ENSG00000108846	ENSG00000108846		"""ATP binding cassette transporters / subfamily C"""	54	protein-coding gene	gene with protein product	"""canalicular multispecific organic anion transporter 2"""	604323				8894702, 9827529	Standard	NM_003786		Approved	MRP3, cMOAT2, EST90757, MLP2, MOAT-D	uc002isl.3	O15438	OTTHUMG00000162245	ENST00000285238.8:c.1057G>A	17.37:g.48741100G>A	ENSP00000285238:p.Ala353Thr	Somatic		Capture	Illumina HiSeq	Phase_I	46096099	NM_001144070	B2RPA9|D3DTX9|O60265|O60922|O75621|O95078|O95289|O95290|Q86X85|Q9UN52	Missense_Mutation	SNP	ENST00000285238.8	37	CCDS32681.1	.	.	.	.	.	.	.	.	.	.	G	17.31	3.357180	0.61293	.	.	ENSG00000108846	ENST00000427699;ENST00000285238	D;D	0.90324	-2.65;-2.65	4.54	3.55	0.40652	ABC transporter, transmembrane domain, type 1 (1);ABC transporter, integral membrane type 1 (1);ABC transporter, transmembrane domain (1);	0.000000	0.85682	D	0.000000	D	0.93956	0.8065	M	0.77406	2.37	0.80722	D	1	P;D;P	0.67145	0.946;0.996;0.743	P;D;B	0.67382	0.732;0.951;0.386	D	0.92337	0.5878	10	0.23891	T	0.37	-19.9491	13.9121	0.63873	0.0:0.0:0.8464:0.1536	.	128;353;353	D3DTY0;O15438;O15438-5	.;MRP3_HUMAN;.	T	353	ENSP00000395160:A353T;ENSP00000285238:A353T	ENSP00000285238:A353T	A	+	1	0	ABCC3	46096099	1.000000	0.71417	1.000000	0.80357	0.847000	0.48162	9.396000	0.97270	1.074000	0.40909	-0.282000	0.10007	GCT		0.557	ABCC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368083.2	NM_020038	
KIF2B	84643	broad.mit.edu	37	17	51901020	51901020	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr17:51901020C>T	ENST00000268919.4	+	1	782	c.626C>T	c.(625-627)cCg>cTg	p.P209L		NM_032559.4	NP_115948.4	Q8N4N8	KIF2B_HUMAN	kinesin family member 2B	209					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|ATP catabolic process (GO:0006200)|blood coagulation (GO:0007596)|metabolic process (GO:0008152)|microtubule depolymerization (GO:0007019)|microtubule-based movement (GO:0007018)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|regulation of chromosome segregation (GO:0051983)	cytosol (GO:0005829)|kinesin complex (GO:0005871)|kinetochore (GO:0000776)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)	p.P209L(1)		NS(1)|breast(2)|endometrium(7)|kidney(2)|large_intestine(15)|lung(58)|ovary(5)|prostate(4)|skin(7)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	104						CTGGAGCCCCCGCAAGAACAT	0.537																																					p.P209L												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C626T	17						.						73.0	62.0	66.0					17																	51901020		2203	4300	6503	49256019	SO:0001583	missense	84643	exon1			AF333335	CCDS32685.1	17q22	2014-08-12			ENSG00000141200	ENSG00000141200		"""Kinesins"""	29443	protein-coding gene	gene with protein product		615142				11416179	Standard	NM_032559		Approved		uc002iua.2	Q8N4N8	OTTHUMG00000177756	ENST00000268919.4:c.626C>T	17.37:g.51901020C>T	ENSP00000268919:p.Pro209Leu	Somatic		Capture	Illumina HiSeq	Phase_I	49256019	NM_032559	Q96MA2|Q9BXG6	Missense_Mutation	SNP	ENST00000268919.4	37	CCDS32685.1	.	.	.	.	.	.	.	.	.	.	C	1.139	-0.650158	0.03506	.	.	ENSG00000141200	ENST00000268919;ENST00000416491	T	0.15952	2.38	5.37	-4.73	0.03259	.	0.827724	0.10270	N	0.694831	T	0.08358	0.0208	N	0.16790	0.44	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.34229	-0.9837	10	0.31617	T	0.26	.	7.8622	0.29516	0.0:0.3321:0.337:0.3309	.	209	Q8N4N8	KIF2B_HUMAN	L	209;132	ENSP00000268919:P209L	ENSP00000268919:P209L	P	+	2	0	KIF2B	49256019	0.000000	0.05858	0.003000	0.11579	0.002000	0.02628	-2.144000	0.01296	-0.843000	0.04189	-1.749000	0.00680	CCG		0.537	KIF2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438854.1	NM_032559	
BZRAP1	9256	broad.mit.edu	37	17	56403666	56403666	+	Silent	SNP	C	C	T	rs369879329		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr17:56403666C>T	ENST00000343736.4	-	3	721	c.558G>A	c.(556-558)acG>acA	p.T186T	BZRAP1-AS1_ENST00000578334.1_RNA|BZRAP1-AS1_ENST00000579527.1_RNA|BZRAP1_ENST00000355701.3_Silent_p.T186T|BZRAP1_ENST00000268893.6_Silent_p.T186T|BZRAP1-AS1_ENST00000580515.1_RNA			O95153	RIMB1_HUMAN	benzodiazepine receptor (peripheral) associated protein 1	186						cytoplasm (GO:0005737)|mitochondrion (GO:0005739)	benzodiazepine receptor binding (GO:0030156)	p.T186T(2)		cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(11)|liver(2)|lung(16)|ovary(1)|prostate(1)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	54	Medulloblastoma(34;0.127)|all_neural(34;0.237)					CCCTCAGGTTCGTTTCCTGCA	0.632																																					p.T186T												.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.G558A	17						.						90.0	89.0	89.0					17																	56403666		2203	4300	6503	53758665	SO:0001819	synonymous_variant	9256	exon3			AB014512	CCDS11605.1, CCDS45742.1	17q22-q23	2014-01-09	2014-01-09						16831	protein-coding gene	gene with protein product		610764				9734811, 9915832	Standard	NM_004758		Approved	PRAX-1, KIAA0612, RIM-BP1, RIMBP1	uc002ivx.5	O95153		ENST00000343736.4:c.558G>A	17.37:g.56403666C>T		Somatic		Capture	Illumina HiSeq	Phase_I	53758665	NM_004758	O75111|Q8N5W3	Silent	SNP	ENST00000343736.4	37	CCDS11605.1																																																																																				0.632	BZRAP1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000443980.1	NM_004758	
TEX14	56155	broad.mit.edu	37	17	56679902	56679902	+	Silent	SNP	T	T	C			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr17:56679902T>C	ENST00000240361.8	-	12	1489	c.1404A>G	c.(1402-1404)gtA>gtG	p.V468V	TEX14_ENST00000349033.5_Silent_p.V462V|TEX14_ENST00000389934.3_Silent_p.V462V			Q8IWB6	TEX14_HUMAN	testis expressed 14	468	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				attachment of spindle microtubules to kinetochore (GO:0008608)|intercellular bridge organization (GO:0043063)|male meiosis (GO:0007140)|mitotic sister chromatid separation (GO:0051306)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of cytokinesis (GO:0032466)|negative regulation of protein binding (GO:0032091)	cell (GO:0005623)|cytoplasm (GO:0005737)|intercellular bridge (GO:0045171)|kinetochore (GO:0000776)|midbody (GO:0030496)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein kinase binding (GO:0019901)	p.V462V(1)|p.V468V(1)		breast(6)|endometrium(5)|kidney(3)|large_intestine(22)|liver(1)|lung(24)|ovary(4)|pancreas(1)|prostate(1)|skin(5)|stomach(5)|upper_aerodigestive_tract(1)|urinary_tract(3)	81	Medulloblastoma(34;0.127)|all_neural(34;0.237)					TCCCCGAGACTACGGCTTTTT	0.408																																					p.V462V												.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.A1386G	17						.						80.0	76.0	77.0					17																	56679902		2203	4300	6503	54034901	SO:0001819	synonymous_variant	56155	exon12			AF285601	CCDS32692.1, CCDS32693.1, CCDS56042.1	17q22	2013-09-20	2007-03-13		ENSG00000121101	ENSG00000121101			11737	protein-coding gene	gene with protein product	"""cancer/testis antigen 113"""	605792	"""testis expressed sequence 14"""			11279525, 12711554	Standard	NM_031272		Approved	CT113	uc010dcz.2	Q8IWB6	OTTHUMG00000179245	ENST00000240361.8:c.1404A>G	17.37:g.56679902T>C		Somatic		Capture	Illumina HiSeq	Phase_I	54034901	NM_198393	A6NH19|Q7RTP3|Q8ND97|Q9BXT9	Silent	SNP	ENST00000240361.8	37	CCDS56042.1																																																																																				0.408	TEX14-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000445446.1		
CLTC	1213	broad.mit.edu	37	17	57754436	57754436	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr17:57754436C>T	ENST00000269122.3	+	17	2957	c.2683C>T	c.(2683-2685)Cgt>Tgt	p.R895C	CLTC_ENST00000393043.1_Missense_Mutation_p.R895C|CLTC_ENST00000579815.1_3'UTR|CLTC_ENST00000579456.1_Intron	NM_004859.3	NP_004850.1	Q00610	CLH1_HUMAN	clathrin, heavy chain (Hc)	895	Heavy chain arm.|Proximal segment.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|intracellular protein transport (GO:0006886)|membrane organization (GO:0061024)|mitotic nuclear division (GO:0007067)|negative regulation of hyaluronan biosynthetic process (GO:1900126)|negative regulation of protein localization to plasma membrane (GO:1903077)|osteoblast differentiation (GO:0001649)|post-Golgi vesicle-mediated transport (GO:0006892)|receptor internalization (GO:0031623)|receptor-mediated endocytosis (GO:0006898)|transferrin transport (GO:0033572)	clathrin coat (GO:0030118)|clathrin coat of coated pit (GO:0030132)|clathrin coat of trans-Golgi network vesicle (GO:0030130)|clathrin complex (GO:0071439)|clathrin-coated endocytic vesicle membrane (GO:0030669)|clathrin-coated vesicle (GO:0030136)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|spindle (GO:0005819)|trans-Golgi network membrane (GO:0032588)|vesicle (GO:0031982)	clathrin light chain binding (GO:0032051)|double-stranded RNA binding (GO:0003725)|poly(A) RNA binding (GO:0044822)|protein kinase binding (GO:0019901)|structural molecule activity (GO:0005198)	p.R895C(1)	CLTC/ALK(44)|CLTC/TFE3(2)	breast(2)|large_intestine(6)|ovary(1)	9	all_neural(34;0.0878)|Medulloblastoma(34;0.0922)					GAGATTTCTTCGTGAAAATCC	0.458			T	"""ALK, TFE3"""	"""ALCL, renal """																																p.R895C			Dom	yes		17	17q11-qter	1213	"""clathrin, heavy polypeptide (Hc)"""		L	.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C2683T	17						.						97.0	100.0	99.0					17																	57754436		2203	4300	6503	55109218	SO:0001583	missense	1213	exon17			X55878	CCDS32696.1, CCDS74115.1	17q23.1	2013-09-19	2006-09-29		ENSG00000141367	ENSG00000141367			2092	protein-coding gene	gene with protein product		118955	"""clathrin, heavy polypeptide (Hc)"", ""clathrin, heavy chain"", ""clathrin, heavy polypeptide-like 2"""	CLTCL2		1765375, 7584026	Standard	NM_004859		Approved	Hc	uc002ixq.1	Q00610	OTTHUMG00000134279	ENST00000269122.3:c.2683C>T	17.37:g.57754436C>T	ENSP00000269122:p.Arg895Cys	Somatic		Capture	Illumina HiSeq	Phase_I	55109218	NM_004859	D3DU00|Q6N0A0|Q86TF2	Missense_Mutation	SNP	ENST00000269122.3	37	CCDS32696.1	.	.	.	.	.	.	.	.	.	.	C	22.6	4.307221	0.81247	.	.	ENSG00000141367	ENST00000269122;ENST00000393043	T;T	0.21191	2.02;2.02	5.45	5.45	0.79879	Tetratricopeptide-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.48572	0.1507	M	0.82323	2.585	0.80722	D	1	D;P	0.65815	0.995;0.772	P;P	0.59171	0.853;0.719	T	0.54153	-0.8336	10	0.72032	D	0.01	.	19.2912	0.94100	0.0:1.0:0.0:0.0	.	895;895	Q00610;Q00610-2	CLH1_HUMAN;.	C	895	ENSP00000269122:R895C;ENSP00000376763:R895C	ENSP00000269122:R895C	R	+	1	0	CLTC	55109218	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.647000	0.61418	2.569000	0.86673	0.557000	0.71058	CGT		0.458	CLTC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258859.1	NM_004859	
USP32	84669	broad.mit.edu	37	17	58286133	58286133	+	Silent	SNP	C	C	G			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	G	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr17:58286133C>G	ENST00000300896.4	-	23	2849	c.2655G>C	c.(2653-2655)ggG>ggC	p.G885G	USP32_ENST00000592339.1_Silent_p.G555G	NM_032582.3	NP_115971.2	Q8NFA0	UBP32_HUMAN	ubiquitin specific peptidase 32	885	USP.				protein deubiquitination (GO:0016579)|ubiquitin-dependent protein catabolic process (GO:0006511)	Golgi apparatus (GO:0005794)|membrane (GO:0016020)	calcium ion binding (GO:0005509)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)	p.G885G(1)		NS(3)|breast(5)|endometrium(5)|kidney(4)|large_intestine(12)|liver(1)|lung(24)|pancreas(1)|prostate(3)|skin(3)|urinary_tract(1)	62	all_neural(34;0.0878)|Medulloblastoma(34;0.0922)		Epithelial(12;2.02e-11)|all cancers(12;5.23e-10)|Colorectal(3;0.198)			ATCTTAGCTGCCCATGGAACA	0.368																																					p.G885G												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G2655C	17						.						38.0	42.0	41.0					17																	58286133		2187	4286	6473	55640915	SO:0001819	synonymous_variant	84669	exon23			AF533230	CCDS32697.1	17q23.3	2013-01-10	2005-08-08		ENSG00000170832	ENSG00000170832		"""Ubiquitin-specific peptidases"", ""EF-hand domain containing"""	19143	protein-coding gene	gene with protein product		607740	"""ubiquitin specific protease 32"""			12838346	Standard	NM_032582		Approved	NY-REN-60, USP10	uc002iyo.1	Q8NFA0		ENST00000300896.4:c.2655G>C	17.37:g.58286133C>G		Somatic		Capture	Illumina HiSeq	Phase_I	55640915	NM_032582	Q7Z5T3|Q9BX85|Q9Y591	Silent	SNP	ENST00000300896.4	37	CCDS32697.1																																																																																				0.368	USP32-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449235.2	NM_032582	
PPM1D	8493	broad.mit.edu	37	17	58740537	58740537	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr17:58740537C>T	ENST00000305921.3	+	6	1674	c.1442C>T	c.(1441-1443)gCc>gTc	p.A481V	RNU6-623P_ENST00000363143.1_RNA	NM_003620.3	NP_003611.1	O15297	PPM1D_HUMAN	protein phosphatase, Mg2+/Mn2+ dependent, 1D	481					G2/M transition of mitotic cell cycle (GO:0000086)|negative regulation of cell proliferation (GO:0008285)|peptidyl-threonine dephosphorylation (GO:0035970)|protein dephosphorylation (GO:0006470)|response to bacterium (GO:0009617)|response to radiation (GO:0009314)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|protein serine/threonine phosphatase activity (GO:0004722)	p.A481V(1)		haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(5)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	15	all_neural(34;0.0878)|Medulloblastoma(34;0.0922)		Epithelial(12;6.75e-12)|all cancers(12;1.96e-10)			TGCGCTAAAGCCCTGACTTTA	0.383											OREG0031485	type=REGULATORY REGION|TFbs=ESR1|Dataset=Estrogen Receptor Alpha Binding Sites|EvidenceSubtype=Chromatin immunoprecipitation with tag sequencing (ChIP-TS)																									p.A481V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1442T	17						.						103.0	96.0	98.0					17																	58740537		2203	4300	6503	56095319	SO:0001583	missense	8493	exon6			U78305	CCDS11625.1	17q23.3	2014-09-17	2010-03-05		ENSG00000170836	ENSG00000170836		"""Serine/threonine phosphatases / Protein phosphatases, Mg2+/Mn2+ dependent"""	9277	protein-coding gene	gene with protein product	"""wild-type p53-induced phosphatase 1"", ""protein phosphatase 2C, delta isoform"""	605100	"""protein phosphatase 1D magnesium-dependent, delta isoform"""			9177166	Standard	NM_003620		Approved	Wip1, PP2C-DELTA	uc002iyt.2	O15297		ENST00000305921.3:c.1442C>T	17.37:g.58740537C>T	ENSP00000306682:p.Ala481Val	Somatic	1033	Capture	Illumina HiSeq	Phase_I	56095319	NM_003620	Q53XP4|Q6P991|Q8IVR6	Missense_Mutation	SNP	ENST00000305921.3	37	CCDS11625.1	.	.	.	.	.	.	.	.	.	.	C	15.58	2.874726	0.51695	.	.	ENSG00000170836	ENST00000305921	T	0.55413	0.52	6.08	3.93	0.45458	.	0.609539	0.18362	N	0.143526	T	0.41949	0.1181	N	0.24115	0.695	0.36056	D	0.841101	B	0.27853	0.191	B	0.23275	0.045	T	0.52411	-0.8579	10	0.56958	D	0.05	-0.8166	18.294	0.90139	0.0:0.7445:0.2555:0.0	.	481	O15297	PPM1D_HUMAN	V	481	ENSP00000306682:A481V	ENSP00000306682:A481V	A	+	2	0	PPM1D	56095319	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	2.854000	0.48325	1.553000	0.49476	0.591000	0.81541	GCC		0.383	PPM1D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449474.1	NM_003620	
INTS2	57508	broad.mit.edu	37	17	59971158	59971158	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr17:59971158G>A	ENST00000444766.3	-	13	1765	c.1690C>T	c.(1690-1692)Cgt>Tgt	p.R564C	INTS2_ENST00000251334.6_Missense_Mutation_p.R556C	NM_020748.2	NP_065799	Q9H0H0	INT2_HUMAN	integrator complex subunit 2	564					snRNA processing (GO:0016180)	integral component of membrane (GO:0016021)|integrator complex (GO:0032039)|intracellular (GO:0005622)|membrane (GO:0016020)		p.R564C(1)		NS(1)|breast(2)|cervix(2)|endometrium(3)|kidney(2)|large_intestine(6)|lung(15)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	38						GTAAAGGAACGGCTCCTGAGA	0.383																																					p.R564C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1690T	17						.						58.0	55.0	56.0					17																	59971158		1856	4099	5955	57325940	SO:0001583	missense	57508	exon13			AB033113	CCDS45750.1	17q23.2	2006-04-26	2006-03-15	2006-03-15		ENSG00000108506			29241	protein-coding gene	gene with protein product		611346	"""KIAA1287"""	KIAA1287		16239144	Standard	NR_026641		Approved	INT2	uc002izn.3	Q9H0H0		ENST00000444766.3:c.1690C>T	17.37:g.59971158G>A	ENSP00000414237:p.Arg564Cys	Somatic		Capture	Illumina HiSeq	Phase_I	57325940	NM_020748	Q9ULD3	Missense_Mutation	SNP	ENST00000444766.3	37	CCDS45750.1	.	.	.	.	.	.	.	.	.	.	G	21.9	4.217238	0.79352	.	.	ENSG00000108506	ENST00000444766;ENST00000251334	T	0.56776	0.44	5.74	4.69	0.59074	.	0.000000	0.85682	D	0.000000	T	0.72145	0.3424	M	0.74647	2.275	0.80722	D	1	D	0.89917	1.0	D	0.79108	0.992	T	0.72821	-0.4177	9	.	.	.	-14.0847	17.4726	0.87650	0.0:0.0:0.8674:0.1326	.	564	Q9H0H0	INT2_HUMAN	C	564;563	ENSP00000414237:R564C	.	R	-	1	0	INTS2	57325940	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	4.989000	0.63870	2.723000	0.93209	0.655000	0.94253	CGT		0.383	INTS2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000445368.1	NM_020748	
MRC2	9902	broad.mit.edu	37	17	60743591	60743591	+	Silent	SNP	C	C	T	rs564657391		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr17:60743591C>T	ENST00000303375.5	+	3	1059	c.657C>T	c.(655-657)taC>taT	p.Y219Y		NM_006039.4	NP_006030.2	Q9UBG0	MRC2_HUMAN	mannose receptor, C type 2	219	Fibronectin type-II. {ECO:0000255|PROSITE-ProRule:PRU00479}.				collagen catabolic process (GO:0030574)|endocytosis (GO:0006897)|osteoblast differentiation (GO:0001649)	focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	carbohydrate binding (GO:0030246)|collagen binding (GO:0005518)	p.Y219Y(1)		NS(1)|breast(1)|central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(11)|lung(28)|ovary(2)|prostate(1)|skin(3)	53						CCCAGGACTACGGCAAAGACG	0.642																																					p.Y219Y												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C657T	17						.						40.0	32.0	35.0					17																	60743591		2202	4298	6500	58097323	SO:0001819	synonymous_variant	9902	exon3			AB014609	CCDS11634.1	17q23	2011-08-30				ENSG00000011028		"""CD molecules"", ""C-type lectin domain containing"""	16875	protein-coding gene	gene with protein product		612264				9734811, 8702911	Standard	NM_006039		Approved	KIAA0709, ENDO180, CLEC13E, CD280	uc002jad.4	Q9UBG0		ENST00000303375.5:c.657C>T	17.37:g.60743591C>T		Somatic		Capture	Illumina HiSeq	Phase_I	58097323	NM_006039	A6H8K4|D3DU08|Q7LGE7|Q9Y5P9	Silent	SNP	ENST00000303375.5	37	CCDS11634.1																																																																																				0.642	MRC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445152.1		
SCN4A	6329	broad.mit.edu	37	17	62026823	62026823	+	Silent	SNP	G	G	A	rs73992419	byFrequency	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr17:62026823G>A	ENST00000435607.1	-	15	2995	c.2919C>T	c.(2917-2919)ccC>ccT	p.P973P	SCN4A_ENST00000578147.1_Silent_p.P973P	NM_000334.4	NP_000325.4	P35499	SCN4A_HUMAN	sodium channel, voltage-gated, type IV, alpha subunit	973					membrane depolarization during action potential (GO:0086010)|muscle contraction (GO:0006936)|neuronal action potential (GO:0019228)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|voltage-gated sodium channel complex (GO:0001518)	voltage-gated sodium channel activity (GO:0005248)	p.P973P(1)		breast(4)|central_nervous_system(3)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(23)|lung(40)|ovary(3)|pancreas(1)|prostate(6)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	101					Diclofenac(DB00586)|Flecainide(DB01195)|Propofol(DB00818)|Valproic Acid(DB00313)|Zonisamide(DB00909)	GGTCCTCCTCGGGGGGCTTGT	0.637													G|||	201	0.0401358	0.1483	0.0058	5008	,	,		17985	0.001		0.0	False		,,,				2504	0.0				p.P973P												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C2919T	17						.	G		372,3532		17,338,1597	32.0	38.0	36.0		2919	-8.4	0.2	17	dbSNP_130	36	4,8306		0,4,4151	no	coding-synonymous	SCN4A	NM_000334.4		17,342,5748	AA,AG,GG		0.0481,9.5287,3.0784		973/1837	62026823	376,11838	1952	4155	6107	59380555	SO:0001819	synonymous_variant	6329	exon15			U24693		17q23.3	2012-02-26	2007-01-23					"""Sodium channels"", ""Voltage-gated ion channels / Sodium channels"""	10591	protein-coding gene	gene with protein product		603967		HYKPP		1654742, 1659948, 16382098	Standard	XM_005257566		Approved	Nav1.4, HYPP, SkM1	uc002jds.1	P35499		ENST00000435607.1:c.2919C>T	17.37:g.62026823G>A		Somatic		Capture	Illumina HiSeq	Phase_I	59380555	NM_000334	Q15478|Q16447|Q7Z6B1	Silent	SNP	ENST00000435607.1	37	CCDS45761.1																																																																																				0.637	SCN4A-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_000334	
SCN4A	6329	broad.mit.edu	37	17	62038709	62038709	+	Silent	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr17:62038709C>T	ENST00000435607.1	-	11	1765	c.1689G>A	c.(1687-1689)ccG>ccA	p.P563P	SCN4A_ENST00000578147.1_Silent_p.P563P	NM_000334.4	NP_000325.4	P35499	SCN4A_HUMAN	sodium channel, voltage-gated, type IV, alpha subunit	563					membrane depolarization during action potential (GO:0086010)|muscle contraction (GO:0006936)|neuronal action potential (GO:0019228)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|voltage-gated sodium channel complex (GO:0001518)	voltage-gated sodium channel activity (GO:0005248)	p.P563P(1)		breast(4)|central_nervous_system(3)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(23)|lung(40)|ovary(3)|pancreas(1)|prostate(6)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	101					Diclofenac(DB00586)|Flecainide(DB01195)|Propofol(DB00818)|Valproic Acid(DB00313)|Zonisamide(DB00909)	ACTTCAGCCACGGGGCGCAGC	0.567																																					p.P563P												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G1689A	17						.						199.0	208.0	205.0					17																	62038709		2096	4210	6306	59392441	SO:0001819	synonymous_variant	6329	exon11			U24693		17q23.3	2012-02-26	2007-01-23					"""Sodium channels"", ""Voltage-gated ion channels / Sodium channels"""	10591	protein-coding gene	gene with protein product		603967		HYKPP		1654742, 1659948, 16382098	Standard	XM_005257566		Approved	Nav1.4, HYPP, SkM1	uc002jds.1	P35499		ENST00000435607.1:c.1689G>A	17.37:g.62038709C>T		Somatic		Capture	Illumina HiSeq	Phase_I	59392441	NM_000334	Q15478|Q16447|Q7Z6B1	Silent	SNP	ENST00000435607.1	37	CCDS45761.1																																																																																				0.567	SCN4A-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_000334	
APOH	350	broad.mit.edu	37	17	64219836	64219836	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr17:64219836G>A	ENST00000205948.6	-	4	432	c.395C>T	c.(394-396)cCg>cTg	p.P132L		NM_000042.2	NP_000033.2	P02749	APOH_HUMAN	apolipoprotein H (beta-2-glycoprotein I)	132	Sushi 2. {ECO:0000255|PROSITE- ProRule:PRU00302}.				blood coagulation, intrinsic pathway (GO:0007597)|negative regulation of angiogenesis (GO:0016525)|negative regulation of blood coagulation (GO:0030195)|negative regulation of endothelial cell migration (GO:0010596)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of fibrinolysis (GO:0051918)|negative regulation of myeloid cell apoptotic process (GO:0033033)|negative regulation of smooth muscle cell apoptotic process (GO:0034392)|plasminogen activation (GO:0031639)|positive regulation of blood coagulation (GO:0030194)|positive regulation of lipoprotein lipase activity (GO:0051006)|regulation of fibrinolysis (GO:0051917)|triglyceride metabolic process (GO:0006641)|triglyceride transport (GO:0034197)	cell surface (GO:0009986)|chylomicron (GO:0042627)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|high-density lipoprotein particle (GO:0034364)|very-low-density lipoprotein particle (GO:0034361)	glycoprotein binding (GO:0001948)|heparin binding (GO:0008201)|identical protein binding (GO:0042802)|lipid binding (GO:0008289)|lipoprotein lipase activator activity (GO:0060230)|phospholipid binding (GO:0005543)	p.P132L(1)		central_nervous_system(1)|kidney(3)|large_intestine(5)|lung(6)|skin(1)|upper_aerodigestive_tract(1)	17			BRCA - Breast invasive adenocarcinoma(6;9.74e-08)			AGGAAGCTCCGGGCTCCATTT	0.453																																					p.P132L	Melanoma(155;624 1882 16869 48804 51309)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C395T	17						.						108.0	106.0	107.0					17																	64219836		2203	4300	6503	61650298	SO:0001583	missense	350	exon4				CCDS11663.1	17q24.2	2013-01-24				ENSG00000091583		"""Apolipoproteins"""	616	protein-coding gene	gene with protein product	"""beta-2-glycoprotein I"""	138700		B2G1		1582254	Standard	NM_000042		Approved	BG	uc002jfn.4	P02749		ENST00000205948.6:c.395C>T	17.37:g.64219836G>A	ENSP00000205948:p.Pro132Leu	Somatic		Capture	Illumina HiSeq	Phase_I	61650298	NM_000042	B2R9M3|Q9UCN7	Missense_Mutation	SNP	ENST00000205948.6	37	CCDS11663.1	.	.	.	.	.	.	.	.	.	.	g	3.277	-0.147836	0.06627	.	.	ENSG00000091583	ENST00000205948	T	0.25579	1.79	5.59	-2.55	0.06288	Complement control module (2);Sushi/SCR/CCP (3);	1.007670	0.07948	N	0.980419	T	0.26593	0.0650	M	0.86740	2.835	0.09310	N	1	D	0.52996	0.957	B	0.33042	0.157	T	0.46091	-0.9216	10	0.45353	T	0.12	.	9.4954	0.38984	0.0749:0.0:0.2944:0.6307	.	132	P02749	APOH_HUMAN	L	132	ENSP00000205948:P132L	ENSP00000205948:P132L	P	-	2	0	APOH	61650298	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-0.552000	0.06020	-0.020000	0.14032	-0.397000	0.06425	CCG		0.453	APOH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446926.1	NM_000042	
HELZ	9931	broad.mit.edu	37	17	65134178	65134178	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr17:65134178G>A	ENST00000358691.5	-	22	2988	c.2822C>T	c.(2821-2823)gCg>gTg	p.A941V	HELZ_ENST00000580168.1_Missense_Mutation_p.A942V	NM_014877.3	NP_055692	P42694	HELZ_HUMAN	helicase with zinc finger	941						membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)	p.A941V(1)		NS(1)|breast(5)|endometrium(9)|kidney(3)|large_intestine(11)|liver(1)|lung(24)|ovary(1)|pancreas(1)|prostate(1)|skin(8)|upper_aerodigestive_tract(2)|urinary_tract(2)	69	all_cancers(12;1.24e-11)|Breast(2;1.05e-17)|all_epithelial(3;3.87e-13)					CTTCCCCCACGCTACTGGCCA	0.388																																					p.A941V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C2822T	17						.						147.0	150.0	149.0					17																	65134178		2144	4238	6382	62564640	SO:0001583	missense	9931	exon22			D29677	CCDS42374.1	17q24.2	2013-01-18			ENSG00000198265	ENSG00000198265		"""Zinc fingers, CCCH-type domain containing"""	16878	protein-coding gene	gene with protein product	"""down-regulated in human cancers"""	606699				10471385, 12691822	Standard	NM_014877		Approved	KIAA0054, HUMORF5, DHRC	uc002jfx.4	P42694	OTTHUMG00000179555	ENST00000358691.5:c.2822C>T	17.37:g.65134178G>A	ENSP00000351524:p.Ala941Val	Somatic		Capture	Illumina HiSeq	Phase_I	62564640	NM_014877	I6L9H4	Missense_Mutation	SNP	ENST00000358691.5	37	CCDS42374.1	.	.	.	.	.	.	.	.	.	.	G	17.34	3.364768	0.61513	.	.	ENSG00000198265	ENST00000358691	D	0.82526	-1.62	5.24	5.24	0.73138	.	0.102559	0.64402	D	0.000003	D	0.87928	0.6301	L	0.48935	1.535	0.80722	D	1	D;P	0.76494	0.999;0.944	D;P	0.63033	0.91;0.487	D	0.88575	0.3132	10	0.59425	D	0.04	-10.9121	18.8583	0.92262	0.0:0.0:1.0:0.0	.	942;941	B7ZLW2;P42694	.;HELZ_HUMAN	V	941	ENSP00000351524:A941V	ENSP00000351524:A941V	A	-	2	0	HELZ	62564640	1.000000	0.71417	0.992000	0.48379	0.996000	0.88848	9.476000	0.97823	2.437000	0.82529	0.655000	0.94253	GCG		0.388	HELZ-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000447068.1	NM_014877	
SLC16A6	9120	broad.mit.edu	37	17	66267318	66267318	+	Missense_Mutation	SNP	C	C	T	rs138575233	byFrequency	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr17:66267318C>T	ENST00000327268.4	-	6	1147	c.983G>A	c.(982-984)cGc>cAc	p.R328H	ARSG_ENST00000448504.2_Intron|SLC16A6_ENST00000580666.1_Missense_Mutation_p.R328H	NM_001174166.1	NP_001167637.1	O15403	MOT7_HUMAN	solute carrier family 16, member 6	328					monocarboxylic acid transport (GO:0015718)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	monocarboxylic acid transmembrane transporter activity (GO:0008028)|symporter activity (GO:0015293)	p.R328H(1)		large_intestine(3)|lung(8)|prostate(1)|skin(1)|urinary_tract(2)	15	all_cancers(12;1.24e-09)		BRCA - Breast invasive adenocarcinoma(8;3.17e-08)|LUSC - Lung squamous cell carcinoma(166;0.24)		Pyruvic acid(DB00119)	AAAAGCAGCGCGGTCCTGGTC	0.443													C|||	5	0.000998403	0.003	0.0014	5008	,	,		19704	0.0		0.0	False		,,,				2504	0.0				p.R328H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G983A	17						.	C	HIS/ARG,HIS/ARG,	35,4371	40.8+/-73.8	0,35,2168	67.0	66.0	66.0		983,983,	3.6	0.0	17	dbSNP_134	66	0,8600		0,0,4300	yes	missense,missense,intron	SLC16A6,ARSG	NM_001174166.1,NM_004694.4,NM_014960.3	29,29,	0,35,6468	TT,TC,CC		0.0,0.7944,0.2691	benign,benign,	328/524,328/524,	66267318	35,12971	2203	4300	6503	63778913	SO:0001583	missense	9120	exon5			U79745	CCDS11675.1	17q24.2	2013-07-18	2013-07-18		ENSG00000108932	ENSG00000108932		"""Solute carriers"""	10927	protein-coding gene	gene with protein product		603880	"""solute carrier family 16 (monocarboxylic acid transporters), member 6"", ""solute carrier family 16, member 6 (monocarboxylic acid transporter 7)"""			9425115	Standard	NM_004694		Approved	MCT6, MCT7	uc002jgz.2	O15403	OTTHUMG00000179812	ENST00000327268.4:c.983G>A	17.37:g.66267318C>T	ENSP00000319991:p.Arg328His	Somatic		Capture	Illumina HiSeq	Phase_I	63778913	NM_004694	Q6P1X3	Missense_Mutation	SNP	ENST00000327268.4	37	CCDS11675.1	2	9.157509157509158E-4	1	0.0020325203252032522	1	0.0027624309392265192	0	0.0	0	0.0	C	9.840	1.190762	0.21954	0.007944	0.0	ENSG00000108932	ENST00000327268	T	0.58652	0.32	4.59	3.62	0.41486	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.809119	0.11608	N	0.547048	T	0.33904	0.0879	L	0.34521	1.04	0.09310	N	1	B	0.13145	0.007	B	0.14023	0.01	T	0.23297	-1.0192	10	0.40728	T	0.16	.	3.7925	0.08726	0.1932:0.6028:0.0:0.204	.	328	O15403	MOT7_HUMAN	H	328	ENSP00000319991:R328H	ENSP00000319991:R328H	R	-	2	0	SLC16A6	63778913	0.000000	0.05858	0.008000	0.14137	0.881000	0.50899	-0.033000	0.12246	1.143000	0.42306	0.484000	0.47621	CGC		0.443	SLC16A6-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448323.1	NM_004694	
ABCA5	23461	broad.mit.edu	37	17	67304435	67304435	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr17:67304435C>T	ENST00000392676.3	-	5	608	c.544G>A	c.(544-546)Gct>Act	p.A182T	ABCA5_ENST00000588877.1_Missense_Mutation_p.A182T|ABCA5_ENST00000392677.2_Missense_Mutation_p.A182T			Q8WWZ7	ABCA5_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 5	182					cholesterol efflux (GO:0033344)|high-density lipoprotein particle remodeling (GO:0034375)|negative regulation of macrophage derived foam cell differentiation (GO:0010745)|reverse cholesterol transport (GO:0043691)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|late endosome (GO:0005770)|lysosome (GO:0005764)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)	p.A182T(1)		breast(2)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(18)|lung(19)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|urinary_tract(1)	54	Breast(10;3.72e-11)				Tacrolimus(DB00864)	ATAATGGCAGCATCTATGGAT	0.348																																					p.A182T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G544A	17						.						85.0	91.0	89.0					17																	67304435		2203	4300	6503	64816030	SO:0001583	missense	23461	exon5			U66672	CCDS11685.1	17q24.3	2012-03-14			ENSG00000154265	ENSG00000154265		"""ATP binding cassette transporters / subfamily A"""	35	protein-coding gene	gene with protein product		612503				8894702	Standard	NM_172232		Approved	EST90625	uc002jig.2	Q8WWZ7		ENST00000392676.3:c.544G>A	17.37:g.67304435C>T	ENSP00000376443:p.Ala182Thr	Somatic		Capture	Illumina HiSeq	Phase_I	64816030	NM_172232	Q8IVJ2|Q96LJ1|Q96MS4|Q96PZ9|Q9NY14	Missense_Mutation	SNP	ENST00000392676.3	37	CCDS11685.1	.	.	.	.	.	.	.	.	.	.	C	18.24	3.580213	0.65992	.	.	ENSG00000154265	ENST00000392677;ENST00000392676	D;D	0.87334	-2.24;-2.24	4.65	2.65	0.31530	.	0.109580	0.40222	N	0.001142	D	0.87188	0.6115	L	0.59967	1.855	0.37866	D	0.929879	B;P	0.48230	0.204;0.907	B;P	0.54460	0.283;0.753	D	0.84433	0.0578	9	.	.	.	.	5.8449	0.18661	0.1523:0.6831:0.0:0.1646	.	182;182	Q8WWZ7-2;Q8WWZ7	.;ABCA5_HUMAN	T	182	ENSP00000376444:A182T;ENSP00000376443:A182T	.	A	-	1	0	ABCA5	64816030	1.000000	0.71417	0.999000	0.59377	0.986000	0.74619	2.774000	0.47694	0.396000	0.25283	-0.384000	0.06662	GCT		0.348	ABCA5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000450654.1	NM_018672	
NXN	64359	broad.mit.edu	37	17	722782	722782	+	Silent	SNP	C	C	T	rs532150840	byFrequency	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr17:722782C>T	ENST00000336868.3	-	5	808	c.717G>A	c.(715-717)tcG>tcA	p.S239S	NXN_ENST00000575801.1_Silent_p.S131S|NXN_ENST00000537628.2_5'UTR|NXN_ENST00000538650.1_5'UTR	NM_022463.4	NP_071908.2	Q6DKJ4	NXN_HUMAN	nucleoredoxin	239	Thioredoxin. {ECO:0000255|PROSITE- ProRule:PRU00691}.				cardiovascular system development (GO:0072358)|cell differentiation (GO:0030154)|negative regulation of protein ubiquitination (GO:0031397)|negative regulation of Wnt signaling pathway (GO:0030178)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	protein-disulfide reductase activity (GO:0047134)|thioredoxin-disulfide reductase activity (GO:0004791)	p.S239S(1)		breast(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(2)|ovary(2)|pancreas(1)|prostate(1)	13				UCEC - Uterine corpus endometrioid carcinoma (25;0.0237)		AGGACTCCTCCGACCTACAGA	0.617													C|||	2	0.000399361	0.0	0.0	5008	,	,		16790	0.0		0.0	False		,,,				2504	0.002				p.S239S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G717A	17						.						71.0	66.0	68.0					17																	722782		2203	4300	6503	669532	SO:0001819	synonymous_variant	64359	exon5				CCDS10998.1, CCDS56013.1	17p13	2007-08-10			ENSG00000167693	ENSG00000167693			18008	protein-coding gene	gene with protein product		612895					Standard	NM_022463		Approved	FLJ12614, NRX	uc002fsa.3	Q6DKJ4	OTTHUMG00000090307	ENST00000336868.3:c.717G>A	17.37:g.722782C>T		Somatic		Capture	Illumina HiSeq	Phase_I	669532	NM_022463	B4DXQ0|D3DTH2|Q3SWW6|Q6P3U6|Q7L4C6|Q9H9Q1	Silent	SNP	ENST00000336868.3	37	CCDS10998.1																																																																																				0.617	NXN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206669.1		
FBXO39	162517	broad.mit.edu	37	17	6690670	6690670	+	Nonsense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr17:6690670C>T	ENST00000321535.4	+	4	1382	c.1252C>T	c.(1252-1254)Cag>Tag	p.Q418*		NM_153230.2	NP_694962.1	Q8N4B4	FBX39_HUMAN	F-box protein 39	418								p.Q418*(1)		NS(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(7)|lung(5)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	26						CAAGACCCTGCAGGAAATTTA	0.413																																					p.Q418X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.C1252T	17						.						135.0	128.0	130.0					17																	6690670		2203	4300	6503	6631394	SO:0001587	stop_gained	162517	exon4			BC034782	CCDS11082.1	17p13.2	2014-01-21			ENSG00000177294	ENSG00000177294		"""F-boxes /  ""other"""""	28565	protein-coding gene	gene with protein product		609106				12477932	Standard	NM_153230		Approved	MGC35179, Fbx39, CT144	uc010vtg.2	Q8N4B4	OTTHUMG00000102062	ENST00000321535.4:c.1252C>T	17.37:g.6690670C>T	ENSP00000321386:p.Gln418*	Somatic		Capture	Illumina HiSeq	Phase_I	6631394	NM_153230		Nonsense_Mutation	SNP	ENST00000321535.4	37	CCDS11082.1	.	.	.	.	.	.	.	.	.	.	C	37	6.342788	0.97489	.	.	ENSG00000177294	ENST00000321535	.	.	.	5.23	4.25	0.50352	.	0.232714	0.30575	N	0.009323	.	.	.	.	.	.	0.58432	D	0.999998	.	.	.	.	.	.	.	.	.	.	0.05833	T	0.94	-23.8429	11.5397	0.50659	0.179:0.821:0.0:0.0	.	.	.	.	X	418	.	ENSP00000321386:Q418X	Q	+	1	0	FBXO39	6631394	0.973000	0.33851	1.000000	0.80357	0.896000	0.52359	0.945000	0.29056	1.327000	0.45338	0.555000	0.69702	CAG		0.413	FBXO39-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219866.2	NM_153230	
KCNJ2	3759	broad.mit.edu	37	17	68171231	68171231	+	Silent	SNP	C	C	T	rs141965142		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr17:68171231C>T	ENST00000243457.3	+	2	434	c.51C>T	c.(49-51)gaC>gaT	p.D17D	KCNJ2_ENST00000535240.1_Silent_p.D17D	NM_000891.2	NP_000882.1	P63252	KCNJ2_HUMAN	potassium inwardly-rectifying channel, subfamily J, member 2	17					cardiac muscle cell action potential involved in contraction (GO:0086002)|cellular potassium ion homeostasis (GO:0030007)|cellular response to mechanical stimulus (GO:0071260)|magnesium ion transport (GO:0015693)|membrane depolarization during cardiac muscle cell action potential (GO:0086012)|membrane repolarization during action potential (GO:0086011)|membrane repolarization during cardiac muscle cell action potential (GO:0086013)|positive regulation of potassium ion transmembrane transport (GO:1901381)|potassium ion import (GO:0010107)|potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|protein homotetramerization (GO:0051289)|regulation of heart rate by cardiac conduction (GO:0086091)|regulation of membrane repolarization (GO:0060306)|regulation of resting membrane potential (GO:0060075)|regulation of skeletal muscle contraction via regulation of action potential (GO:0014861)|relaxation of cardiac muscle (GO:0055119)|relaxation of skeletal muscle (GO:0090076)|synaptic transmission (GO:0007268)	dendritic spine (GO:0043197)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|intercalated disc (GO:0014704)|intrinsic component of membrane (GO:0031224)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|rough endoplasmic reticulum (GO:0005791)|smooth endoplasmic reticulum (GO:0005790)|T-tubule (GO:0030315)|voltage-gated potassium channel complex (GO:0008076)	inward rectifier potassium channel activity (GO:0005242)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|voltage-gated potassium channel activity involved in cardiac muscle cell action potential repolarization (GO:0086008)	p.D17D(1)		breast(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(3)|lung(13)|skin(1)|urinary_tract(1)	25	Breast(10;1.64e-08)					CAGAAGAAGACGGTATGAAGT	0.522													C|||	1	0.000199681	0.0008	0.0	5008	,	,		20539	0.0		0.0	False		,,,				2504	0.0				p.D17D												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C51T	17						.						74.0	70.0	71.0					17																	68171231		2203	4300	6503	65682826	SO:0001819	synonymous_variant	3759	exon2			AF011904	CCDS11688.1	17q24.3	2014-09-17				ENSG00000123700		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels, Inwardly rectifying"""	6263	protein-coding gene	gene with protein product		600681				7696590, 11240146, 16382105	Standard	NM_000891		Approved	Kir2.1, IRK1, LQT7	uc002jir.3	P63252		ENST00000243457.3:c.51C>T	17.37:g.68171231C>T		Somatic		Capture	Illumina HiSeq	Phase_I	65682826	NM_000891	O15110|P48049	Silent	SNP	ENST00000243457.3	37	CCDS11688.1																																																																																				0.522	KCNJ2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450889.1	NM_000891	
OTOP2	92736	broad.mit.edu	37	17	72920984	72920984	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr17:72920984G>A	ENST00000580223.1	+	1	287	c.257G>A	c.(256-258)cGc>cAc	p.R86H	USH1G_ENST00000319642.1_5'Flank|OTOP2_ENST00000331427.4_Missense_Mutation_p.R86H			Q7RTS6	OTOP2_HUMAN	otopetrin 2	86						integral component of membrane (GO:0016021)		p.R86H(1)		breast(4)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(13)|ovary(3)|prostate(4)|skin(1)|urinary_tract(2)	39	all_lung(278;0.172)|Lung NSC(278;0.207)					CGAACCGTGCGCTGCCCCTGC	0.667																																					p.R86H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G257A	17						.						42.0	25.0	31.0					17																	72920984		2200	4294	6494	70432579	SO:0001583	missense	92736	exon2			BK000567	CCDS11708.1	17q25.3	2006-09-20				ENSG00000183034			19657	protein-coding gene	gene with protein product		607827				12651873	Standard	NM_178160		Approved		uc010wrp.2	Q7RTS6		ENST00000580223.1:c.257G>A	17.37:g.72920984G>A	ENSP00000463837:p.Arg86His	Somatic		Capture	Illumina HiSeq	Phase_I	70432579	NM_178160		Missense_Mutation	SNP	ENST00000580223.1	37	CCDS11708.1	.	.	.	.	.	.	.	.	.	.	G	16.64	3.179779	0.57800	.	.	ENSG00000183034	ENST00000331427	T	0.12569	2.67	4.12	4.12	0.48240	.	0.061097	0.64402	D	0.000007	T	0.30355	0.0762	M	0.68317	2.08	0.40991	D	0.984859	D	0.89917	1.0	D	0.63957	0.92	T	0.03287	-1.1052	10	0.52906	T	0.07	-7.6456	11.2125	0.48806	0.0898:0.0:0.9102:0.0	.	86	Q7RTS6	OTOP2_HUMAN	H	86	ENSP00000332528:R86H	ENSP00000332528:R86H	R	+	2	0	OTOP2	70432579	0.476000	0.25901	0.631000	0.29282	0.055000	0.15305	3.704000	0.54815	2.122000	0.65172	0.555000	0.69702	CGC		0.667	OTOP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445306.1	NM_178160	
RECQL5	9400	broad.mit.edu	37	17	73623540	73623540	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr17:73623540C>T	ENST00000317905.5	-	20	3097	c.2938G>A	c.(2938-2940)Gaa>Aaa	p.E980K	RECQL5_ENST00000443199.2_5'UTR|RECQL5_ENST00000423245.2_Missense_Mutation_p.E953K	NM_004259.6	NP_004250.4	O94762	RECQ5_HUMAN	RecQ protein-like 5	980					chromosome separation (GO:0051304)|DNA duplex unwinding (GO:0032508)|DNA metabolic process (GO:0006259)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|mitotic nuclear division (GO:0007067)|negative regulation of transcription elongation from RNA polymerase II promoter (GO:0034244)	cytoplasm (GO:0005737)|DNA-directed RNA polymerase II, holoenzyme (GO:0016591)|nuclear membrane (GO:0031965)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|DNA helicase activity (GO:0003678)|nucleic acid binding (GO:0003676)|RNA polymerase II core binding (GO:0000993)	p.E953K(1)		breast(1)|cervix(3)|endometrium(3)|kidney(7)|large_intestine(7)|lung(8)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(5)	36	all_cancers(13;2.73e-08)|Breast(9;6.04e-09)|all_epithelial(9;6.79e-09)		all cancers(21;1.15e-06)|Epithelial(20;2.19e-06)|Lung(188;0.101)|LUSC - Lung squamous cell carcinoma(166;0.112)			CAGTCAGCTTCGCTCTCGCAC	0.627								Other identified genes with known or suspected DNA repair function																													p.E980K												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2938A	17						.						69.0	79.0	75.0					17																	73623540		2035	4180	6215	71135135	SO:0001583	missense	9400	exon20			AB006533	CCDS32735.1, CCDS42380.1, CCDS45777.1	17q25	2014-03-07	2014-03-07	2014-03-07	ENSG00000108469	ENSG00000108469			9950	protein-coding gene	gene with protein product	"""RecQ protein 5"""	603781				9878247	Standard	NM_004259		Approved	RecQ5, FLJ90603	uc010dgl.3	O94762		ENST00000317905.5:c.2938G>A	17.37:g.73623540C>T	ENSP00000317636:p.Glu980Lys	Somatic		Capture	Illumina HiSeq	Phase_I	71135135	NM_004259	Q9H0B1|Q9P1W7|Q9UNC8	Missense_Mutation	SNP	ENST00000317905.5	37	CCDS42380.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	15.53|15.53	2.861009|2.861009	0.51482|0.51482	.|.	.|.	ENSG00000108469|ENSG00000108469	ENST00000423245|ENST00000443199;ENST00000317905	.|T	.|0.70045	.|-0.45	5.23|5.23	3.24|3.24	0.37175|0.37175	.|.	.|0.266722	.|0.36002	.|N	.|0.002854	.|T	.|0.75561	.|0.3866	M|M	0.69823|0.69823	2.125|2.125	0.80722|0.80722	D|D	1|1	.|D;D;D	.|0.76494	.|0.998;0.998;0.999	.|P;P;P	.|0.60117	.|0.869;0.869;0.823	.|T	.|0.77335	.|-0.2626	.|10	.|0.59425	.|D	.|0.04	.|-6.3524	10.8742|10.8742	0.46902|0.46902	0.0:0.8485:0.0:0.1515|0.0:0.8485:0.0:0.1515	.|.	.|980;953;176	.|O94762;Q6P4G0;Q6FIC9	.|RECQ5_HUMAN;.;.	.|K	-1|575;980	.|ENSP00000317636:E980K	.|ENSP00000317636:E980K	.|E	-|-	.|1	.|0	RECQL5|RECQL5	71135135|71135135	0.998000|0.998000	0.40836|0.40836	0.933000|0.933000	0.37362|0.37362	0.817000|0.817000	0.46193|0.46193	2.918000|2.918000	0.48829|0.48829	1.213000|1.213000	0.43380|0.43380	0.563000|0.563000	0.77884|0.77884	.|GAA		0.627	RECQL5-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448207.1	NM_004259	
QRICH2	84074	broad.mit.edu	37	17	74287751	74287751	+	Silent	SNP	G	G	A	rs147682958		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr17:74287751G>A	ENST00000262765.5	-	4	2738	c.2559C>T	c.(2557-2559)taC>taT	p.Y853Y		NM_032134.1	NP_115510.1	Q9H0J4	QRIC2_HUMAN	glutamine rich 2	853								p.Y853Y(1)		breast(3)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(6)|lung(17)|ovary(4)|pancreas(2)|prostate(3)|skin(2)|stomach(4)	62						ACACCTGGCCGTATTGTTCTC	0.468																																					p.Y853Y												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C2559T	17						.	A		0,4406		0,0,2203	124.0	116.0	119.0		2559	-4.0	0.0	17	dbSNP_134	119	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	QRICH2	NM_032134.1		0,1,6502	AA,AG,GG		0.0116,0.0,0.0077		853/1664	74287751	1,13005	2203	4300	6503	71799346	SO:0001819	synonymous_variant	84074	exon4			AK058102	CCDS32741.1	17q25.1	2009-03-19			ENSG00000129646	ENSG00000129646			25326	protein-coding gene	gene with protein product							Standard	NM_032134		Approved	DKFZP434P0316	uc002jrd.1	Q9H0J4	OTTHUMG00000167578	ENST00000262765.5:c.2559C>T	17.37:g.74287751G>A		Somatic		Capture	Illumina HiSeq	Phase_I	71799346	NM_032134	A2RRE1|Q96LM3	Silent	SNP	ENST00000262765.5	37	CCDS32741.1																																																																																				0.468	QRICH2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395140.1	NM_032134	
QRICH2	84074	broad.mit.edu	37	17	74288292	74288292	+	Missense_Mutation	SNP	C	C	T	rs556024715		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr17:74288292C>T	ENST00000262765.5	-	4	2197	c.2018G>A	c.(2017-2019)cGt>cAt	p.R673H		NM_032134.1	NP_115510.1	Q9H0J4	QRIC2_HUMAN	glutamine rich 2	673	Gln-rich.							p.R673H(1)		breast(3)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(6)|lung(17)|ovary(4)|pancreas(2)|prostate(3)|skin(2)|stomach(4)	62						gaccaaaccacgctgaactgc	0.557													C|||	1	0.000199681	0.0	0.0	5008	,	,		27828	0.001		0.0	False		,,,				2504	0.0				p.R673H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2018A	17						.						100.0	94.0	96.0					17																	74288292		2203	4300	6503	71799887	SO:0001583	missense	84074	exon4			AK058102	CCDS32741.1	17q25.1	2009-03-19			ENSG00000129646	ENSG00000129646			25326	protein-coding gene	gene with protein product							Standard	NM_032134		Approved	DKFZP434P0316	uc002jrd.1	Q9H0J4	OTTHUMG00000167578	ENST00000262765.5:c.2018G>A	17.37:g.74288292C>T	ENSP00000262765:p.Arg673His	Somatic		Capture	Illumina HiSeq	Phase_I	71799887	NM_032134	A2RRE1|Q96LM3	Missense_Mutation	SNP	ENST00000262765.5	37	CCDS32741.1	.	.	.	.	.	.	.	.	.	.	T	5.498	0.276884	0.10403	.	.	ENSG00000129646	ENST00000262765;ENST00000301613	T	0.22336	1.96	4.48	-8.97	0.00758	.	.	.	.	.	T	0.08223	0.0205	N	0.14661	0.345	0.09310	N	1	B;B	0.19073	0.033;0.001	B;B	0.11329	0.006;0.0	T	0.27706	-1.0066	9	0.24483	T	0.36	7.6465	5.3595	0.16079	0.0636:0.2872:0.181:0.4681	.	673;673	B5MD94;Q9H0J4	.;QRIC2_HUMAN	H	673	ENSP00000262765:R673H	ENSP00000262765:R673H	R	-	2	0	QRICH2	71799887	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-5.731000	0.00102	-2.153000	0.00793	-3.310000	0.00045	CGT		0.557	QRICH2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395140.1	NM_032134	
PRPSAP1	5635	broad.mit.edu	37	17	74340789	74340789	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr17:74340789G>A	ENST00000446526.3	-	3	698	c.253C>T	c.(253-255)Cgt>Tgt	p.R85C	PRPSAP1_ENST00000324684.4_5'UTR	NM_002766.2	NP_002757.2	Q14558	KPRA_HUMAN	phosphoribosyl pyrophosphate synthetase-associated protein 1	56					negative regulation of kinase activity (GO:0033673)|nucleobase-containing compound metabolic process (GO:0006139)|nucleotide biosynthetic process (GO:0009165)	ribose phosphate diphosphokinase complex (GO:0002189)	enzyme inhibitor activity (GO:0004857)|magnesium ion binding (GO:0000287)|ribose phosphate diphosphokinase activity (GO:0004749)	p.R56C(1)		cervix(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(3)|ovary(1)|skin(1)|urinary_tract(1)	17						TCTTGGCCACGAACAGATTCT	0.279																																					p.R85C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C253T	17						.						95.0	105.0	102.0					17																	74340789		2203	4300	6503	71852384	SO:0001583	missense	5635	exon3			D61391	CCDS11743.2	17q24-q25	2008-07-18			ENSG00000161542	ENSG00000161542			9466	protein-coding gene	gene with protein product		601249				8660991	Standard	NM_002766		Approved	PAP39	uc010wta.1	Q14558	OTTHUMG00000155969	ENST00000446526.3:c.253C>T	17.37:g.74340789G>A	ENSP00000414624:p.Arg85Cys	Somatic		Capture	Illumina HiSeq	Phase_I	71852384	NM_002766	B2R6M4|Q96H06	Missense_Mutation	SNP	ENST00000446526.3	37	CCDS11743.2	.	.	.	.	.	.	.	.	.	.	g	20.9	4.073517	0.76415	.	.	ENSG00000161542	ENST00000446526;ENST00000442767	D;D	0.93604	-3.25;-3.25	4.8	4.8	0.61643	.	0.000000	0.85682	D	0.000000	D	0.97711	0.9249	H	0.95917	3.74	0.80722	D	1	D	0.89917	1.0	D	0.72982	0.979	D	0.98810	1.0743	10	0.87932	D	0	.	15.8622	0.79035	0.0:0.0:1.0:0.0	.	85	Q14558-2	.	C	85;43	ENSP00000414624:R85C;ENSP00000402126:R43C	ENSP00000402126:R43C	R	-	1	0	PRPSAP1	71852384	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.457000	0.66672	2.525000	0.85131	0.539000	0.68188	CGT		0.279	PRPSAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342480.2	NM_002766	
JMJD6	23210	broad.mit.edu	37	17	74714887	74714887	+	Missense_Mutation	SNP	G	G	A	rs377582812		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr17:74714887G>A	ENST00000397625.4	-	6	1250	c.1136C>T	c.(1135-1137)aCg>aTg	p.T379M	JMJD6_ENST00000585429.1_Missense_Mutation_p.R333C|JMJD6_ENST00000445478.2_Missense_Mutation_p.T379M	NM_015167.2	NP_055982.2	Q6NYC1	JMJD6_HUMAN	jumonji domain containing 6	379					cell surface receptor signaling pathway (GO:0007166)|erythrocyte development (GO:0048821)|heart development (GO:0007507)|histone H3-R2 demethylation (GO:0070078)|histone H4-R3 demethylation (GO:0070079)|kidney development (GO:0001822)|lung development (GO:0030324)|macrophage activation (GO:0042116)|mRNA processing (GO:0006397)|peptidyl-lysine hydroxylation to 5-hydroxy-L-lysine (GO:0018395)|recognition of apoptotic cell (GO:0043654)|regulation of mRNA splicing, via spliceosome (GO:0048024)|regulation of transcription, DNA-templated (GO:0006355)|retina development in camera-type eye (GO:0060041)|RNA splicing (GO:0008380)|sprouting angiogenesis (GO:0002040)|T cell differentiation in thymus (GO:0033077)|transcription, DNA-templated (GO:0006351)	nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	histone demethylase activity (H3-R2 specific) (GO:0033746)|histone demethylase activity (H4-R3 specific) (GO:0033749)|identical protein binding (GO:0042802)|iron ion binding (GO:0005506)|peptidyl-lysine 5-dioxygenase activity (GO:0070815)|receptor activity (GO:0004872)|RNA binding (GO:0003723)|single-stranded RNA binding (GO:0003727)	p.T379M(1)		endometrium(2)|kidney(5)|large_intestine(2)|lung(3)|ovary(2)|skin(2)	16						CATGCTGCACGTCCTCCTCTT	0.587													G|||	1	0.000199681	0.0008	0.0	5008	,	,		19238	0.0		0.0	False		,,,				2504	0.0				p.T379M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1136T	17						.	G	MET/THR,MET/THR	1,4281		0,1,2140	103.0	109.0	107.0		1136,1136	6.2	1.0	17		107	1,8477		0,1,4238	no	missense,missense	JMJD6	NM_001081461.1,NM_015167.2	81,81	0,2,6378	AA,AG,GG		0.0118,0.0234,0.0157	possibly-damaging,possibly-damaging	379/415,379/404	74714887	2,12758	2141	4239	6380	72226482	SO:0001583	missense	23210	exon6			AB011157	CCDS42383.1, CCDS42384.1	17q25	2007-11-20	2007-02-16	2007-02-16	ENSG00000070495	ENSG00000070495			19355	protein-coding gene	gene with protein product		604914	"""phosphatidylserine receptor"""	PTDSR		11877474	Standard	NM_015167		Approved	PTDSR1, KIAA0585	uc002jsn.1	Q6NYC1	OTTHUMG00000169267	ENST00000397625.4:c.1136C>T	17.37:g.74714887G>A	ENSP00000380750:p.Thr379Met	Somatic		Capture	Illumina HiSeq	Phase_I	72226482	NM_015167	B3KMN8|B4DGX1|Q86VY0|Q8IUM5|Q9Y4E2	Missense_Mutation	SNP	ENST00000397625.4	37	CCDS42384.1	.	.	.	.	.	.	.	.	.	.	G	19.82	3.897658	0.72639	2.34E-4	1.18E-4	ENSG00000070495	ENST00000445478;ENST00000397625	.	.	.	6.17	6.17	0.99709	.	0.147725	0.64402	D	0.000011	T	0.53110	0.1776	L	0.44542	1.39	0.39769	D	0.972137	P;D	0.54397	0.902;0.966	B;P	0.48815	0.387;0.591	T	0.53690	-0.8403	9	0.46703	T	0.11	-21.1336	13.9957	0.64397	0.0685:0.0:0.9315:0.0	.	379;379	Q6NYC1;Q6NYC1-3	JMJD6_HUMAN;.	M	379	.	ENSP00000380750:T379M	T	-	2	0	JMJD6	72226482	1.000000	0.71417	0.989000	0.46669	0.990000	0.78478	5.269000	0.65542	2.941000	0.99782	0.655000	0.94253	ACG		0.587	JMJD6-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403211.1	NM_015167	
SEC14L1	6397	broad.mit.edu	37	17	75202891	75202891	+	Silent	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr17:75202891C>T	ENST00000413679.2	+	13	1726	c.1423C>T	c.(1423-1425)Ctg>Ttg	p.L475L	SEC14L1_ENST00000443798.4_Silent_p.L475L|SEC14L1_ENST00000436233.4_Silent_p.L475L|SEC14L1_ENST00000591437.1_Silent_p.L441L|SEC14L1_ENST00000431431.2_Silent_p.L441L|SEC14L1_ENST00000430767.4_Silent_p.L475L|SEC14L1_ENST00000585618.1_Silent_p.L475L|SEC14L1_ENST00000392476.2_Silent_p.L475L	NM_001143998.1|NM_001143999.1|NM_003003.3	NP_001137470|NP_001137471|NP_002994	Q92503	S14L1_HUMAN	SEC14-like 1 (S. cerevisiae)	475	CRAL-TRIO. {ECO:0000255|PROSITE- ProRule:PRU00056}.				transport (GO:0006810)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)		p.L475L(1)		NS(1)|endometrium(4)|kidney(3)|large_intestine(4)|lung(12)|ovary(3)|prostate(2)|skin(2)	31						TGGAGGCCTGCTGGATTACAT	0.498																																					p.L475L												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1423T	17						.						135.0	123.0	127.0					17																	75202891		2203	4300	6503	72714486	SO:0001819	synonymous_variant	6397	exon13			D67029	CCDS11752.1, CCDS42385.1, CCDS45789.1	17q25.2	2008-02-01	2001-11-28			ENSG00000129657			10698	protein-coding gene	gene with protein product		601504	"""SEC14 (S. cerevisiae)-like 1"""	SEC14L		8697811	Standard	NM_001143998		Approved	PRELID4A	uc002jto.3	Q92503		ENST00000413679.2:c.1423C>T	17.37:g.75202891C>T		Somatic		Capture	Illumina HiSeq	Phase_I	72714486	NM_001039573	A8K4E8|B4DDI5|D5G3K1|Q99780	Silent	SNP	ENST00000413679.2	37	CCDS11752.1																																																																																				0.498	SEC14L1-201	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000436240.1	NM_003003	
SENP3	26168	broad.mit.edu	37	17	7468154	7468154	+	Nonsense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr17:7468154C>T	ENST00000429205.2	+	3	977	c.928C>T	c.(928-930)Cga>Tga	p.R310*	SENP3-EIF4A1_ENST00000579777.1_RNA|SENP3_ENST00000578868.1_3'UTR|SENP3_ENST00000321337.7_Nonsense_Mutation_p.R310*			Q9H4L4	SENP3_HUMAN	SUMO1/sentrin/SMT3 specific peptidase 3	310						cytoplasm (GO:0005737)|MLL1 complex (GO:0071339)|nucleolus (GO:0005730)	cysteine-type peptidase activity (GO:0008234)	p.R310*(1)		central_nervous_system(1)|ovary(1)	2		Prostate(122;0.157)				CAGCCCCCTGCGAGAGGAGCA	0.612																																					p.R310X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.C928T	17						.						37.0	44.0	42.0					17																	7468154		1999	4169	6168	7408878	SO:0001587	stop_gained	26168	exon3			AK000923	CCDS73958.1	17p13	2012-05-02	2005-08-17			ENSG00000161956			17862	protein-coding gene	gene with protein product		612844	"""SUMO1/sentrin/SMT3 specific protease 3"""			10806345, 11230166	Standard	NM_015670		Approved	DKFZP586K0919, SSP3, DKFZp762A152, SMT3IP1, Ulp1	uc002ghm.3	Q9H4L4		ENST00000429205.2:c.928C>T	17.37:g.7468154C>T	ENSP00000403712:p.Arg310*	Somatic		Capture	Illumina HiSeq	Phase_I	7408878	NM_015670	Q66K15|Q86VS7|Q96PS4|Q9Y3W9	Nonsense_Mutation	SNP	ENST00000429205.2	37		.	.	.	.	.	.	.	.	.	.	C	40	8.365470	0.98779	.	.	ENSG00000161956	ENST00000321337;ENST00000429205	.	.	.	5.98	4.99	0.66335	.	0.234093	0.32671	N	0.005787	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-8.2587	11.9485	0.52942	0.3159:0.6841:0.0:0.0	.	.	.	.	X	310	.	ENSP00000314029:R310X	R	+	1	2	SENP3	7408878	0.982000	0.34865	0.954000	0.39281	0.994000	0.84299	1.263000	0.33004	1.493000	0.48517	0.591000	0.81541	CGA		0.612	SENP3-202	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_015670	
TMC6	11322	broad.mit.edu	37	17	76115097	76115097	+	Silent	SNP	G	G	A	rs150820026	byFrequency	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr17:76115097G>A	ENST00000590602.1	-	15	2001	c.1842C>T	c.(1840-1842)ccC>ccT	p.P614P	TMC6_ENST00000306591.7_Intron|TMC6_ENST00000322933.4_Silent_p.P193P|TMC6_ENST00000592076.1_Intron|TMC6_ENST00000322914.3_Silent_p.P614P|TMC6_ENST00000591436.1_Silent_p.P193P|TMC6_ENST00000392467.3_Silent_p.P614P			Q7Z403	TMC6_HUMAN	transmembrane channel-like 6	614					ion transport (GO:0006811)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nuclear membrane (GO:0031965)		p.P614P(1)		NS(1)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(5)|upper_aerodigestive_tract(1)	14			BRCA - Breast invasive adenocarcinoma(99;0.00269)|Lung(188;0.0973)			TCTGCACGGCGGGGAGGAGGG	0.677													G|||	6	0.00119808	0.0045	0.0	5008	,	,		16344	0.0		0.0	False		,,,				2504	0.0				p.P614P												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1842T	17						.	G	,	2,4394		0,2,2196	19.0	17.0	18.0		1842,1842	-9.2	0.5	17	dbSNP_134	18	0,8594		0,0,4297	yes	coding-synonymous,coding-synonymous	TMC6	NM_001127198.1,NM_007267.6	,	0,2,6493	AA,AG,GG		0.0,0.0455,0.0154	,	614/806,614/806	76115097	2,12988	2198	4297	6495	73626692	SO:0001819	synonymous_variant	11322	exon15			AY057379	CCDS32748.1	17q25.3	2014-09-17	2005-11-10	2005-11-10	ENSG00000141524	ENSG00000141524			18021	protein-coding gene	gene with protein product		605828	"""epidermodysplasia verruciformis 1"""	EVER1		12426567	Standard	NM_007267		Approved	LAK-4P, EVIN1	uc002juk.2	Q7Z403	OTTHUMG00000177466	ENST00000590602.1:c.1842C>T	17.37:g.76115097G>A		Somatic		Capture	Illumina HiSeq	Phase_I	73626692	NM_007267	O43284|Q45VJ2|Q8IU98|Q8IUI7|Q8IWU8|Q8TEQ7|Q9HAG5	Silent	SNP	ENST00000590602.1	37	CCDS32748.1																																																																																				0.677	TMC6-007	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437146.1		
TIMP2	7077	broad.mit.edu	37	17	76851793	76851793	+	Missense_Mutation	SNP	C	C	T	rs201845164	byFrequency	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr17:76851793C>T	ENST00000262768.7	-	5	917	c.619G>A	c.(619-621)Gcg>Acg	p.A207T	TIMP2_ENST00000585421.1_Missense_Mutation_p.A130T|TIMP2_ENST00000536189.2_Missense_Mutation_p.A130T|RP11-323N12.5_ENST00000587434.1_RNA|TIMP2_ENST00000586057.1_Missense_Mutation_p.A130T	NM_003255.4	NP_003246.1	P16035	TIMP2_HUMAN	TIMP metallopeptidase inhibitor 2	207					aging (GO:0007568)|cellular response to organic substance (GO:0071310)|central nervous system development (GO:0007417)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|negative regulation of cell proliferation (GO:0008285)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of mitotic cell cycle (GO:0045930)|negative regulation of proteolysis (GO:0045861)|negative regulation of Ras protein signal transduction (GO:0046580)|positive regulation of adenylate cyclase activity (GO:0045762)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of neuron differentiation (GO:0045666)|regulation of Rap protein signal transduction (GO:0032487)|response to cytokine (GO:0034097)|response to drug (GO:0042493)	basement membrane (GO:0005604)|cell surface (GO:0009986)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|growth cone (GO:0030426)|neuronal cell body (GO:0043025)	enzyme activator activity (GO:0008047)|metal ion binding (GO:0046872)|metalloendopeptidase inhibitor activity (GO:0008191)	p.A207T(1)		central_nervous_system(2)	2			BRCA - Breast invasive adenocarcinoma(99;0.0101)|OV - Ovarian serous cystadenocarcinoma(97;0.194)			GGGGGCGCCGCGCCGCGGTAC	0.597													C|||	2	0.000399361	0.0	0.0	5008	,	,		16656	0.002		0.0	False		,,,				2504	0.0				p.A207T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G619A	17						.						61.0	52.0	55.0					17																	76851793		2203	4300	6503	74363388	SO:0001583	missense	7077	exon5				CCDS11758.1	17q25	2008-07-18	2005-08-08		ENSG00000035862	ENSG00000035862			11821	protein-coding gene	gene with protein product		188825	"""tissue inhibitor of metalloproteinase 2"""			1427908	Standard	NM_003255		Approved	CSC-21K	uc002jwf.3	P16035	OTTHUMG00000154517	ENST00000262768.7:c.619G>A	17.37:g.76851793C>T	ENSP00000262768:p.Ala207Thr	Somatic		Capture	Illumina HiSeq	Phase_I	74363388	NM_003255	Q16121|Q93006|Q9UDF7	Missense_Mutation	SNP	ENST00000262768.7	37	CCDS11758.1	2	9.157509157509158E-4	0	0.0	0	0.0	2	0.0034965034965034965	0	0.0	c	11.58	1.682471	0.29872	.	.	ENSG00000035862	ENST00000262768;ENST00000536189	D;D	0.94862	-3.54;-3.37	5.72	3.74	0.42951	Tissue inhibitor of metalloproteinases-like, OB-fold (1);	0.468894	0.21672	N	0.070856	D	0.88303	0.6400	N	0.19112	0.55	0.09310	N	1	B	0.06786	0.001	B	0.01281	0.0	T	0.74365	-0.3689	10	0.21540	T	0.41	.	13.083	0.59123	0.0:0.8985:0.0:0.1015	.	207	P16035	TIMP2_HUMAN	T	207;130	ENSP00000262768:A207T;ENSP00000441724:A130T	ENSP00000262768:A207T	A	-	1	0	TIMP2	74363388	0.000000	0.05858	0.223000	0.23860	0.968000	0.65278	0.616000	0.24344	0.885000	0.36088	0.651000	0.88453	GCG		0.597	TIMP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335662.1	NM_003255	
CBX2	84733	broad.mit.edu	37	17	77755566	77755566	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr17:77755566C>T	ENST00000310942.4	+	4	358	c.254C>T	c.(253-255)gCc>gTc	p.A85V	CBX2_ENST00000269399.5_Missense_Mutation_p.A85V	NM_005189.2	NP_005180.1	Q14781	CBX2_HUMAN	chromobox homolog 2	85					cell differentiation (GO:0030154)|chromatin modification (GO:0016568)|development of primary sexual characteristics (GO:0045137)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	euchromatin (GO:0000791)|heterochromatin (GO:0000792)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PcG protein complex (GO:0031519)|PRC1 complex (GO:0035102)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)	p.A85V(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(8)|upper_aerodigestive_tract(1)	16			OV - Ovarian serous cystadenocarcinoma(97;0.0102)|BRCA - Breast invasive adenocarcinoma(99;0.0224)			AAGCTCACTGCCATGTCCTCC	0.637																																					p.A85V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C254T	17						.						52.0	63.0	59.0					17																	77755566		2203	4300	6503	75370161	SO:0001583	missense	84733	exon4			BC004252, BG354579	CCDS11764.1, CCDS32757.1	17q25.3	2010-07-06	2010-06-24		ENSG00000173894	ENSG00000173894			1552	protein-coding gene	gene with protein product	"""Pc class homolog (Drosophila)"""	602770	"""chromobox homolog 2 (Drosophila Pc class)"", ""cell division cycle associated 6"""	CDCA6		7782071, 2477932	Standard	NM_005189		Approved	MGC10561	uc002jxc.3	Q14781		ENST00000310942.4:c.254C>T	17.37:g.77755566C>T	ENSP00000308750:p.Ala85Val	Somatic		Capture	Illumina HiSeq	Phase_I	75370161	NM_032647	Q0VDA5|Q9BTB1	Missense_Mutation	SNP	ENST00000310942.4	37	CCDS32757.1	.	.	.	.	.	.	.	.	.	.	C	10.45	1.354476	0.24512	.	.	ENSG00000173894	ENST00000310942;ENST00000269399	.	.	.	5.25	1.67	0.24075	AT hook, DNA-binding motif (1);	0.639543	0.14902	N	0.291730	T	0.21509	0.0518	N	0.08118	0	0.19575	N	0.999965	B;B	0.16396	0.0;0.017	B;B	0.12837	0.0;0.008	T	0.17289	-1.0374	9	0.38643	T	0.18	.	8.6138	0.33820	0.0:0.1499:0.0:0.8501	.	85;85	Q14781;Q14781-2	CBX2_HUMAN;.	V	85	.	ENSP00000269399:A85V	A	+	2	0	CBX2	75370161	0.939000	0.31865	0.001000	0.08648	0.188000	0.23474	1.993000	0.40747	-0.006000	0.14370	0.655000	0.94253	GCC		0.637	CBX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437040.1	NM_032647	
TBC1D16	125058	broad.mit.edu	37	17	77987304	77987304	+	Missense_Mutation	SNP	A	A	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr17:77987304A>T	ENST00000310924.2	-	2	158	c.43T>A	c.(43-45)Tcg>Acg	p.S15T		NM_001271844.1|NM_001271845.1|NM_019020.2	NP_001258773.1|NP_001258774.1|NP_061893.2	Q8TBP0	TBC16_HUMAN	TBC1 domain family, member 16	15							Rab GTPase activator activity (GO:0005097)	p.S15T(1)		NS(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(13)|ovary(1)|prostate(3)	28	all_neural(118;0.167)		OV - Ovarian serous cystadenocarcinoma(97;0.00739)|BRCA - Breast invasive adenocarcinoma(99;0.0819)			AGGAGGTCCGAGGCTTTGGAG	0.652																																					p.S15T	Ovarian(14;397 562 4850 31922 49378)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T43A	17						.						19.0	20.0	19.0					17																	77987304		2198	4297	6495	75601899	SO:0001583	missense	125058	exon2			AL157485	CCDS11766.1, CCDS62351.1, CCDS62352.1, CCDS62353.1	17q25.3	2013-07-10				ENSG00000167291			28356	protein-coding gene	gene with protein product						23019362	Standard	NM_019020		Approved	MGC25062, FLJ20748	uc002jxj.4	Q8TBP0		ENST00000310924.2:c.43T>A	17.37:g.77987304A>T	ENSP00000309794:p.Ser15Thr	Somatic		Capture	Illumina HiSeq	Phase_I	75601899	NM_019020	B9A6L7|I3L1E0|I3L4U2|Q8N3Z4|Q96DH7	Missense_Mutation	SNP	ENST00000310924.2	37	CCDS11766.1	.	.	.	.	.	.	.	.	.	.	A	25.1	4.601451	0.87055	.	.	ENSG00000167291	ENST00000310924	T	0.09723	2.95	4.99	4.99	0.66335	.	2.085870	0.02428	N	0.083281	T	0.37293	0.0998	M	0.61703	1.905	0.80722	D	1	D	0.69078	0.997	D	0.73380	0.98	T	0.00014	-1.2408	10	0.66056	D	0.02	-16.2208	14.6705	0.68939	1.0:0.0:0.0:0.0	.	15	Q8TBP0	TBC16_HUMAN	T	15	ENSP00000309794:S15T	ENSP00000309794:S15T	S	-	1	0	TBC1D16	75601899	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	8.899000	0.92544	1.857000	0.53885	0.477000	0.44152	TCG		0.652	TBC1D16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437145.1	NM_019020	
CARD14	79092	broad.mit.edu	37	17	78178056	78178056	+	Missense_Mutation	SNP	C	C	T	rs577478029		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr17:78178056C>T	ENST00000573882.1	+	19	2850	c.2314C>T	c.(2314-2316)Cgc>Tgc	p.R772C	RP11-334C17.5_ENST00000572730.1_RNA|RP11-334C17.5_ENST00000573346.1_RNA|RP11-334C17.5_ENST00000573935.1_RNA|CARD14_ENST00000344227.2_Missense_Mutation_p.R772C|RP11-334C17.5_ENST00000570309.1_RNA|RP11-334C17.5_ENST00000576824.1_RNA			Q9BXL6	CAR14_HUMAN	caspase recruitment domain family, member 14	772					activation of NF-kappaB-inducing kinase activity (GO:0007250)|apoptotic process (GO:0006915)|negative regulation of apoptotic process (GO:0043066)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of protein phosphorylation (GO:0001934)|tumor necrosis factor-mediated signaling pathway (GO:0033209)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	CARD domain binding (GO:0050700)	p.R772C(1)		NS(1)|cervix(1)|endometrium(1)|large_intestine(2)|lung(11)|ovary(5)|prostate(1)|skin(1)	23	all_neural(118;0.0952)		OV - Ovarian serous cystadenocarcinoma(97;0.017)|BRCA - Breast invasive adenocarcinoma(99;0.0908)			GAAGCTGGTCCGCATCGTCAG	0.572													C|||	1	0.000199681	0.0008	0.0	5008	,	,		19688	0.0		0.0	False		,,,				2504	0.0				p.R772C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C2314T	17						.						53.0	45.0	47.0					17																	78178056		2202	4299	6501	75792651	SO:0001583	missense	79092	exon17			AF322642	CCDS11768.1, CCDS58605.1	17q25.3	2014-09-04			ENSG00000141527	ENSG00000141527			16446	protein-coding gene	gene with protein product		607211	"""psoriasis susceptibility 2"""	PSORS2		11278692, 11356195, 22521418	Standard	NM_052819		Approved	CARMA2, BIMP2	uc031res.1	Q9BXL6	OTTHUMG00000177549	ENST00000573882.1:c.2314C>T	17.37:g.78178056C>T	ENSP00000458715:p.Arg772Cys	Somatic		Capture	Illumina HiSeq	Phase_I	75792651	NM_024110	B8QQJ3|Q9BVB5	Missense_Mutation	SNP	ENST00000573882.1	37	CCDS11768.1	.	.	.	.	.	.	.	.	.	.	C	21.5	4.164137	0.78339	.	.	ENSG00000141527	ENST00000344227	T	0.05925	3.37	4.08	4.08	0.47627	.	0.414174	0.25073	N	0.033360	T	0.22399	0.0540	M	0.69823	2.125	0.80722	D	1	D	0.89917	1.0	D	0.65987	0.94	T	0.01657	-1.1302	10	0.87932	D	0	-22.9344	15.054	0.71897	0.0:1.0:0.0:0.0	.	772	Q9BXL6	CAR14_HUMAN	C	772	ENSP00000344549:R772C	ENSP00000344549:R772C	R	+	1	0	CARD14	75792651	0.972000	0.33761	1.000000	0.80357	0.980000	0.70556	2.084000	0.41625	1.826000	0.53198	0.467000	0.42956	CGC		0.572	CARD14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437507.1		
RPTOR	57521	broad.mit.edu	37	17	78857651	78857651	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr17:78857651G>A	ENST00000306801.3	+	16	2083	c.1721G>A	c.(1720-1722)cGc>cAc	p.R574H	RPTOR_ENST00000544334.2_Intron|RPTOR_ENST00000575542.1_3'UTR	NM_020761.2	NP_065812.1	Q8N122	RPTOR_HUMAN	regulatory associated protein of MTOR, complex 1	574					cell cycle arrest (GO:0007050)|cell growth (GO:0016049)|cellular response to amino acid stimulus (GO:0071230)|cellular response to nutrient levels (GO:0031669)|insulin receptor signaling pathway (GO:0008286)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|positive regulation of TOR signaling (GO:0032008)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|regulation of cell size (GO:0008361)|TOR signaling (GO:0031929)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|TORC1 complex (GO:0031931)	14-3-3 protein binding (GO:0071889)|protein complex binding (GO:0032403)|protein kinase binding (GO:0019901)|RNA polymerase III type 1 promoter DNA binding (GO:0001030)|RNA polymerase III type 2 promoter DNA binding (GO:0001031)|RNA polymerase III type 3 promoter DNA binding (GO:0001032)|TFIIIC-class transcription factor binding (GO:0001156)	p.R574H(1)		breast(1)|endometrium(4)|kidney(1)|large_intestine(12)|lung(17)|ovary(3)|prostate(1)|skin(1)|stomach(1)|urinary_tract(3)	44						CCCTTGCTGCGCCAGTGGGTG	0.637																																					p.R574H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1721A	17						.						73.0	68.0	70.0					17																	78857651		2203	4300	6503	76472246	SO:0001583	missense	57521	exon16				CCDS11773.1, CCDS54175.1	17q25.3	2013-01-10				ENSG00000141564		"""WD repeat domain containing"""	30287	protein-coding gene	gene with protein product	"""regulatory associated protein of mTOR"""	607130				10718198, 12150926	Standard	NM_001163034		Approved	KOG1, Mip1, KIAA1303, raptor	uc002jyt.1	Q8N122		ENST00000306801.3:c.1721G>A	17.37:g.78857651G>A	ENSP00000307272:p.Arg574His	Somatic		Capture	Illumina HiSeq	Phase_I	76472246	NM_020761	B2RN36|C6KEF2|F5H7J5|Q8N4V9|Q8TB32|Q9P2P3	Missense_Mutation	SNP	ENST00000306801.3	37	CCDS11773.1	.	.	.	.	.	.	.	.	.	.	G	32	5.124193	0.94429	.	.	ENSG00000141564	ENST00000306801	T	0.49432	0.78	4.68	4.68	0.58851	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.75693	0.3884	M	0.92923	3.36	0.80722	D	1	D	0.89917	1.0	D	0.69479	0.964	T	0.83204	-0.0077	10	0.72032	D	0.01	.	18.0063	0.89210	0.0:0.0:1.0:0.0	.	574	Q8N122	RPTOR_HUMAN	H	574	ENSP00000307272:R574H	ENSP00000307272:R574H	R	+	2	0	RPTOR	76472246	1.000000	0.71417	1.000000	0.80357	0.913000	0.54294	9.159000	0.94728	2.322000	0.78497	0.558000	0.71614	CGC		0.637	RPTOR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438125.1	NM_020761	
BAIAP2	10458	broad.mit.edu	37	17	79060365	79060365	+	Silent	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr17:79060365G>A	ENST00000321300.6	+	6	567	c.474G>A	c.(472-474)tcG>tcA	p.S158S	BAIAP2_ENST00000321280.7_Silent_p.S158S|BAIAP2_ENST00000573894.1_3'UTR|BAIAP2_ENST00000575712.1_Silent_p.S158S|BAIAP2_ENST00000428708.2_Silent_p.S158S|BAIAP2_ENST00000575245.1_Silent_p.S191S|BAIAP2_ENST00000435091.3_Silent_p.S158S|BAIAP2_ENST00000392411.3_Silent_p.S80S	NM_001144888.1|NM_017451.2	NP_001138360.1|NP_059345.1	Q9UQB8	BAIP2_HUMAN	BAI1-associated protein 2	158	IMD. {ECO:0000255|PROSITE- ProRule:PRU00668}.				actin crosslink formation (GO:0051764)|actin filament bundle assembly (GO:0051017)|axonogenesis (GO:0007409)|dendrite development (GO:0016358)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|filopodium assembly (GO:0046847)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of cell shape (GO:0008360)|regulation of synaptic plasticity (GO:0048167)|response to bacterium (GO:0009617)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)	cytoskeletal adaptor activity (GO:0008093)|identical protein binding (GO:0042802)|proline-rich region binding (GO:0070064)|protein C-terminus binding (GO:0008022)	p.S158S(1)		breast(1)|central_nervous_system(2)|endometrium(3)|kidney(2)|large_intestine(3)|lung(6)|skin(1)	18	all_neural(118;0.101)		BRCA - Breast invasive adenocarcinoma(99;0.0228)|OV - Ovarian serous cystadenocarcinoma(97;0.0524)			AGAAGTACTCGGACAAGGAGC	0.627																																					p.S158S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G474A	17						.						76.0	80.0	78.0					17																	79060365		2203	4300	6503	76674960	SO:0001819	synonymous_variant	10458	exon6			AB015019	CCDS11775.1, CCDS11776.1, CCDS11777.1, CCDS45806.1	17q25.3	2014-09-11			ENSG00000175866				947	protein-coding gene	gene with protein product		605475				10343108	Standard	NM_017451		Approved	BAP2	uc002jzg.2	Q9UQB8	OTTHUMG00000177698	ENST00000321300.6:c.474G>A	17.37:g.79060365G>A		Somatic		Capture	Illumina HiSeq	Phase_I	76674960	NM_006340	O43858|Q53HB1|Q86WC1|Q8N5C0|Q96CR7|Q9UBR3|Q9UQ43	Silent	SNP	ENST00000321300.6	37	CCDS11775.1																																																																																				0.627	BAIAP2-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000438553.1		
TMEM105	284186	broad.mit.edu	37	17	79288240	79288240	+	Missense_Mutation	SNP	G	G	A	rs576997633	byFrequency	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr17:79288240G>A	ENST00000332900.1	-	2	572	c.23C>T	c.(22-24)gCg>gTg	p.A8V		NM_178520.3	NP_848615.1	Q8N8V8	TM105_HUMAN	transmembrane protein 105	8						integral component of membrane (GO:0016021)		p.A8V(1)		NS(1)|large_intestine(3)|lung(1)|ovary(2)	7	all_neural(118;0.0804)|Melanoma(429;0.242)		BRCA - Breast invasive adenocarcinoma(99;0.0272)|OV - Ovarian serous cystadenocarcinoma(97;0.0892)			CTTCAAGGACGCCCTCCTCAC	0.647													G|||	6	0.00119808	0.0	0.0	5008	,	,		13667	0.0		0.0	False		,,,				2504	0.0061				p.A8V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C23T	17						.						52.0	41.0	45.0					17																	79288240		2200	4298	6498	76902835	SO:0001583	missense	284186	exon2			AK096111	CCDS11781.1	17q25.3	2008-04-21	2008-04-21	2008-04-21		ENSG00000185332			26794	protein-coding gene	gene with protein product							Standard	NM_178520		Approved	FLJ38792	uc002kad.2	Q8N8V8		ENST00000332900.1:c.23C>T	17.37:g.79288240G>A	ENSP00000329795:p.Ala8Val	Somatic		Capture	Illumina HiSeq	Phase_I	76902835	NM_178520		Missense_Mutation	SNP	ENST00000332900.1	37	CCDS11781.1	.	.	.	.	.	.	.	.	.	.	G	8.688	0.906731	0.17833	.	.	ENSG00000185332	ENST00000332900	T	0.54479	0.57	4.22	-2.05	0.07321	.	.	.	.	.	T	0.26085	0.0636	N	0.08118	0	0.09310	N	1	B	0.24132	0.098	B	0.15484	0.013	T	0.16958	-1.0385	9	0.87932	D	0	.	4.1465	0.10219	0.4578:0.1795:0.3628:0.0	.	8	Q8N8V8	TM105_HUMAN	V	8	ENSP00000329795:A8V	ENSP00000329795:A8V	A	-	2	0	TMEM105	76902835	0.000000	0.05858	0.001000	0.08648	0.179000	0.23085	-2.483000	0.00980	-0.181000	0.10619	-0.254000	0.11334	GCG		0.647	TMEM105-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439607.1	NM_178520	
TRPV1	7442	broad.mit.edu	37	17	3491525	3491527	+	In_Frame_Del	DEL	TTC	TTC	-			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	TTC	TTC					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr17:3491525_3491527delTTC	ENST00000571088.1	-	7	1392_1394	c.1179_1181delGAA	c.(1177-1182)aagaac>aac	p.K393del	TRPV1_ENST00000310522.5_Intron|SHPK_ENST00000572705.1_In_Frame_Del_p.K393del|TRPV1_ENST00000399759.3_In_Frame_Del_p.K393del|TRPV1_ENST00000399756.4_In_Frame_Del_p.K393del|TRPV1_ENST00000174621.6_In_Frame_Del_p.K391del|TRPV1_ENST00000425167.2_In_Frame_Del_p.K404del|TRPV1_ENST00000576351.1_In_Frame_Del_p.K393del	NM_018727.5	NP_061197.4	Q8NER1	TRPV1_HUMAN	transient receptor potential cation channel, subfamily V, member 1	393					calcium ion transmembrane transport (GO:0070588)|cell surface receptor signaling pathway (GO:0007166)|cellular response to alkaloid (GO:0071312)|cellular response to ATP (GO:0071318)|chemosensory behavior (GO:0007635)|ion transmembrane transport (GO:0034220)|thermoception (GO:0050955)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cell junction (GO:0030054)|cell projection (GO:0042995)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|intrinsic component of plasma membrane (GO:0031226)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	ATP binding (GO:0005524)|calcium channel activity (GO:0005262)|calcium-release channel activity (GO:0015278)|excitatory extracellular ligand-gated ion channel activity (GO:0005231)|phosphoprotein binding (GO:0051219)|transmembrane signaling receptor activity (GO:0004888)	p.K393delK(1)|p.K404delK(1)		central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(5)|ovary(1)|prostate(1)|urinary_tract(1)	17				Lung(1;0.055)|COAD - Colon adenocarcinoma(5;0.0896)|LUAD - Lung adenocarcinoma(1115;0.131)	Alpha-Linolenic Acid(DB00132)|Aspartame(DB00168)|Icosapent(DB00159)	CAGCACCGAGTTCTTCTCGCAGG	0.655																																					p.393_394del	Melanoma(38;962 1762 15789)											.	.	2	Deletion - In frame(2)	large_intestine(2)	c.1179_1181del	17						.																																			3438276	SO:0001651	inframe_deletion	7442	exon7			AJ272063	CCDS45576.1	17p13.2	2014-08-12	2002-01-29	2002-02-01	ENSG00000196689	ENSG00000262304		"""Voltage-gated ion channels / Transient receptor potential cation channels"", ""Ankyrin repeat domain containing"""	12716	protein-coding gene	gene with protein product		602076	"""vanilloid receptor subtype 1"""	VR1		9349813, 11549313, 16382100	Standard	NM_018727		Approved		uc010vrt.2	Q8NER1	OTTHUMG00000177649	ENST00000571088.1:c.1179_1181delGAA	17.37:g.3491528_3491530delTTC	ENSP00000461007:p.Lys393del	Somatic		Capture	Illumina HiSeq	Phase_I	3438274	NM_018727	A2RUA9|Q3LU47|Q9H0G9|Q9H303|Q9H304|Q9NQ74|Q9NY22	In_Frame_Del	DEL	ENST00000571088.1	37	CCDS45576.1																																																																																				0.655	TRPV1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438254.1	NM_018727	
ALOX15B	247	broad.mit.edu	37	17	7942706	7942706	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr17:7942706G>T	ENST00000380183.4	+	2	289	c.150G>T	c.(148-150)gaG>gaT	p.E50D	ALOX15B_ENST00000572022.1_Missense_Mutation_p.E50D|ALOX15B_ENST00000380173.2_Missense_Mutation_p.E50D|ALOX15B_ENST00000573359.1_Missense_Mutation_p.E50D	NM_001141.2	NP_001132.2	O15296	LX15B_HUMAN	arachidonate 15-lipoxygenase, type B	50	PLAT. {ECO:0000255|PROSITE- ProRule:PRU00152}.				apoptotic process (GO:0006915)|arachidonic acid metabolic process (GO:0019369)|hepoxilin biosynthetic process (GO:0051122)|linoleic acid metabolic process (GO:0043651)|lipid metabolic process (GO:0006629)|lipoxygenase pathway (GO:0019372)|negative regulation of cell cycle (GO:0045786)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of growth (GO:0045926)|positive regulation of chemokine secretion (GO:0090197)|positive regulation of keratinocyte differentiation (GO:0045618)|positive regulation of macrophage derived foam cell differentiation (GO:0010744)|positive regulation of peroxisome proliferator activated receptor signaling pathway (GO:0035360)|prostate gland development (GO:0030850)|regulation of epithelial cell differentiation (GO:0030856)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|intracellular (GO:0005622)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	arachidonate 15-lipoxygenase activity (GO:0050473)|arachidonate 8(S)-lipoxygenase activity (GO:0036403)|calcium ion binding (GO:0005509)|iron ion binding (GO:0005506)|linoleate 13S-lipoxygenase activity (GO:0016165)|lipid binding (GO:0008289)	p.E50D(1)		NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(5)|lung(3)|ovary(1)|prostate(2)|skin(2)|stomach(4)|upper_aerodigestive_tract(1)	24						CCCCTCAGGAGGAGGACTTCC	0.692																																					p.E50D												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G150T	17						.						27.0	27.0	27.0					17																	7942706		2203	4300	6503	7883431	SO:0001583	missense	247	exon2			U78294	CCDS11128.1, CCDS32558.1, CCDS32559.1	17p13.1	2013-03-20	2006-01-16		ENSG00000179593	ENSG00000179593	1.13.11.33	"""Arachidonate lipoxygenases"""	434	protein-coding gene	gene with protein product		603697	"""arachidonate 15-lipoxygenase, second type"""			9177185	Standard	NM_001039130		Approved	15-LOX-2	uc002gju.3	O15296	OTTHUMG00000108181	ENST00000380183.4:c.150G>T	17.37:g.7942706G>T	ENSP00000369530:p.Glu50Asp	Somatic		Capture	Illumina HiSeq	Phase_I	7883431	NM_001039130	D3DTR2|Q8IYQ2|Q8TEV3|Q8TEV4|Q8TEV5|Q8TEV6|Q9UKM4	Missense_Mutation	SNP	ENST00000380183.4	37	CCDS11128.1	.	.	.	.	.	.	.	.	.	.	G	11.71	1.718496	0.30503	.	.	ENSG00000179593	ENST00000380173;ENST00000339694;ENST00000380183	T;T	0.66099	-0.19;-0.19	3.58	2.58	0.30949	Lipoxygenase, LH2 (4);Lipase/lipooxygenase, PLAT/LH2 (1);	0.670290	0.14327	N	0.326635	T	0.56441	0.1985	L	0.57536	1.79	0.29922	N	0.822638	B;B;B;B	0.20550	0.012;0.01;0.037;0.046	B;B;B;B	0.19148	0.014;0.008;0.014;0.024	T	0.57670	-0.7771	10	0.62326	D	0.03	-18.9338	9.6718	0.40017	0.1137:0.0:0.8862:0.0	.	50;50;50;50	B4DNW8;O15296-2;O15296-4;O15296	.;.;.;LX15B_HUMAN	D	50	ENSP00000369520:E50D;ENSP00000369530:E50D	ENSP00000344337:E50D	E	+	3	2	ALOX15B	7883431	0.571000	0.26659	1.000000	0.80357	0.886000	0.51366	1.373000	0.34272	0.755000	0.32990	0.591000	0.81541	GAG		0.692	ALOX15B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226985.2		
ALOX12B	242	broad.mit.edu	37	17	7976993	7976993	+	Silent	SNP	A	A	G			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr17:7976993A>G	ENST00000319144.4	-	13	1997	c.1737T>C	c.(1735-1737)gcT>gcC	p.A579A	ALOX12B_ENST00000577351.1_Intron	NM_001139.2	NP_001130.1	O75342	LX12B_HUMAN	arachidonate 12-lipoxygenase, 12R type	579	Lipoxygenase. {ECO:0000255|PROSITE- ProRule:PRU00726}.				arachidonic acid metabolic process (GO:0019369)|ceramide biosynthetic process (GO:0046513)|establishment of skin barrier (GO:0061436)|hepoxilin biosynthetic process (GO:0051122)|linoleic acid metabolic process (GO:0043651)|lipoxygenase pathway (GO:0019372)|oxidation-reduction process (GO:0055114)|positive regulation of gene expression (GO:0010628)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mucus secretion (GO:0070257)|protein lipidation (GO:0006497)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	cytosol (GO:0005829)	arachidonate 12-lipoxygenase activity (GO:0004052)|iron ion binding (GO:0005506)|linoleate 9S-lipoxygenase activity (GO:1990136)|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen (GO:0016702)	p.A579A(1)		endometrium(5)|kidney(1)|large_intestine(3)|lung(5)|prostate(1)|stomach(1)	16						TGTTGACAGCAGCGTGCTTGG	0.582										Multiple Myeloma(8;0.094)	OREG0024152	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.A579A												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.T1737C	17						.						90.0	74.0	79.0					17																	7976993		2203	4300	6503	7917718	SO:0001819	synonymous_variant	242	exon13			AF038461	CCDS11129.1	17p13.1	2008-03-18			ENSG00000179477	ENSG00000179477	1.13.11.-	"""Arachidonate lipoxygenases"""	430	protein-coding gene	gene with protein product		603741				9618483	Standard	NM_001139		Approved	12R-LOX	uc002gjy.1	O75342	OTTHUMG00000108180	ENST00000319144.4:c.1737T>C	17.37:g.7976993A>G		Somatic	645	Capture	Illumina HiSeq	Phase_I	7917718	NM_001139		Silent	SNP	ENST00000319144.4	37	CCDS11129.1																																																																																				0.582	ALOX12B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226984.3		
PER1	5187	broad.mit.edu	37	17	8050604	8050604	+	Silent	SNP	G	G	A	rs146375404	byFrequency	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr17:8050604G>A	ENST00000317276.4	-	13	1830	c.1593C>T	c.(1591-1593)aaC>aaT	p.N531N	PER1_ENST00000354903.5_Silent_p.N515N|PER1_ENST00000581082.1_Silent_p.N511N|PER1_ENST00000578089.1_5'Flank	NM_002616.2	NP_002607.2	O15534	PER1_HUMAN	period circadian clock 1	531					circadian regulation of gene expression (GO:0032922)|circadian regulation of translation (GO:0097167)|circadian rhythm (GO:0007623)|entrainment of circadian clock (GO:0009649)|entrainment of circadian clock by photoperiod (GO:0043153)|histone H3 acetylation (GO:0043966)|histone H3 deacetylation (GO:0070932)|histone H4 acetylation (GO:0043967)|negative regulation of glucocorticoid receptor signaling pathway (GO:2000323)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of JNK cascade (GO:0046329)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|posttranscriptional regulation of gene expression (GO:0010608)|regulation of circadian rhythm (GO:0042752)|regulation of cytokine production involved in inflammatory response (GO:1900015)|regulation of hair cycle (GO:0042634)|regulation of p38MAPK cascade (GO:1900744)|regulation of sodium ion transport (GO:0002028)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin DNA binding (GO:0031490)|E-box binding (GO:0070888)|kinase binding (GO:0019900)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|signal transducer activity (GO:0004871)|transcription factor binding transcription factor activity (GO:0000989)|ubiquitin protein ligase binding (GO:0031625)	p.N531N(1)		breast(4)|central_nervous_system(1)|endometrium(2)|kidney(7)|large_intestine(3)|lung(15)|ovary(4)|pancreas(1)|prostate(5)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	47						CATCACCCCCGTTGCTATCAC	0.657			T	ETV6	"""AML, CMML"""			Other conserved DNA damage response genes					G|||	8	0.00159744	0.0053	0.0	5008	,	,		16393	0.0		0.001	False		,,,				2504	0.0				p.N531N			Dom	yes		17	17p13.1-17p12	5187	period homolog 1 (Drosophila)		L	.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1593T	17						.	G		8,4396		0,8,2194	26.0	21.0	23.0		1593	-4.8	1.0	17	dbSNP_134	23	0,8592		0,0,4296	no	coding-synonymous	PER1	NM_002616.2		0,8,6490	AA,AG,GG		0.0,0.1817,0.0616		531/1291	8050604	8,12988	2202	4296	6498	7991329	SO:0001819	synonymous_variant	5187	exon13			AB002107	CCDS11131.1	17p13.1	2012-12-13	2012-12-13			ENSG00000179094			8845	protein-coding gene	gene with protein product		602260	"""period (Drosophila) homolog 1"", ""period homolog 1 (Drosophila)"""	PER		9323128	Standard	NM_002616		Approved	RIGUI	uc002gkd.3	O15534		ENST00000317276.4:c.1593C>T	17.37:g.8050604G>A		Somatic		Capture	Illumina HiSeq	Phase_I	7991329	NM_002616	B2RPA8|B4DI49|D3DTR3	Silent	SNP	ENST00000317276.4	37	CCDS11131.1																																																																																				0.657	PER1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441481.2		
C17orf59	54785	broad.mit.edu	37	17	8092521	8092521	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr17:8092521A>G	ENST00000389017.4	-	1	1043	c.938T>C	c.(937-939)aTg>aCg	p.M313T	MIR3676_ENST00000579470.1_RNA	NM_017622.2	NP_060092.2	Q96GS4	CQ059_HUMAN	chromosome 17 open reading frame 59	313								p.M179T(1)		large_intestine(2)|lung(3)|urinary_tract(1)	6						CTTGATGCTCATGTCCACGGC	0.667																																					p.M313T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T938C	17						.						77.0	69.0	72.0					17																	8092521		2203	4300	6503	8033246	SO:0001583	missense	54785	exon1			BC018880	CCDS11133.2	17p13.1	2005-12-16			ENSG00000196544	ENSG00000196544			25939	protein-coding gene	gene with protein product						12477932	Standard	NM_017622		Approved	FLJ20014	uc010vut.2	Q96GS4	OTTHUMG00000153930	ENST00000389017.4:c.938T>C	17.37:g.8092521A>G	ENSP00000373669:p.Met313Thr	Somatic		Capture	Illumina HiSeq	Phase_I	8033246	NM_017622	Q53HS4|Q9NXW8	Missense_Mutation	SNP	ENST00000389017.4	37	CCDS11133.2	.	.	.	.	.	.	.	.	.	.	A	18.68	3.676223	0.67928	.	.	ENSG00000196544	ENST00000389017	.	.	.	5.49	5.49	0.81192	.	0.045949	0.85682	D	0.000000	T	0.63153	0.2487	L	0.36672	1.1	0.52501	D	0.999956	D	0.69078	0.997	D	0.67725	0.953	T	0.59380	-0.7465	9	0.25106	T	0.35	-18.2423	11.972	0.53069	1.0:0.0:0.0:0.0	.	313	Q96GS4	CQ059_HUMAN	T	313	.	ENSP00000373669:M313T	M	-	2	0	C17orf59	8033246	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	8.435000	0.90297	2.086000	0.62901	0.459000	0.35465	ATG		0.667	C17orf59-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333072.1	NM_017622	
RCVRN	5957	broad.mit.edu	37	17	9808215	9808215	+	Missense_Mutation	SNP	C	C	T	rs117017774	byFrequency	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr17:9808215C>T	ENST00000226193.5	-	1	723	c.283G>A	c.(283-285)Gcg>Acg	p.A95T		NM_002903.2	NP_002894.1	P35243	RECO_HUMAN	recoverin	95	EF-hand 2. {ECO:0000255|PROSITE- ProRule:PRU00448}.				phototransduction, visible light (GO:0007603)|positive regulation of guanylate cyclase activity (GO:0031284)|regulation of calcium ion transport (GO:0051924)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|rhodopsin mediated signaling pathway (GO:0016056)|signal transduction (GO:0007165)|visual perception (GO:0007601)	dendrite (GO:0030425)	calcium ion binding (GO:0005509)|calcium sensitive guanylate cyclase activator activity (GO:0008048)	p.A95T(1)		endometrium(1)|kidney(1)|large_intestine(6)|lung(3)|upper_aerodigestive_tract(1)	12						GTCTTGCCCGCGGTGGTCATG	0.592													C|||	6	0.00119808	0.0	0.0	5008	,	,		20133	0.006		0.0	False		,,,				2504	0.0				p.A95T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G283A	17						.						179.0	133.0	149.0					17																	9808215		2203	4300	6503	9748940	SO:0001583	missense	5957	exon1			BC001720	CCDS11151.1	17p13.1	2013-01-10		2006-09-26	ENSG00000109047	ENSG00000109047		"""EF-hand domain containing"""	9937	protein-coding gene	gene with protein product		179618		RCV1		1387789, 12507501, 1467959, 12789533	Standard	NM_002903		Approved		uc002gme.1	P35243	OTTHUMG00000130268	ENST00000226193.5:c.283G>A	17.37:g.9808215C>T	ENSP00000226193:p.Ala95Thr	Somatic		Capture	Illumina HiSeq	Phase_I	9748940	NM_002903	Q53XL0	Missense_Mutation	SNP	ENST00000226193.5	37	CCDS11151.1	5	0.0022893772893772895	0	0.0	0	0.0	5	0.008741258741258742	0	0.0	C	13.55	2.270705	0.40194	.	.	ENSG00000109047	ENST00000226193	T	0.42131	0.98	4.98	1.55	0.23275	EF-hand-like domain (1);	0.332646	0.31922	N	0.006843	T	0.09598	0.0236	N	0.01109	-1.01	0.09310	N	0.999997	B	0.02656	0.0	B	0.01281	0.0	T	0.20240	-1.0281	10	0.62326	D	0.03	.	6.2287	0.20722	0.4382:0.4729:0.0:0.0889	.	95	P35243	RECO_HUMAN	T	95	ENSP00000226193:A95T	ENSP00000226193:A95T	A	-	1	0	RCVRN	9748940	0.000000	0.05858	0.006000	0.13384	0.989000	0.77384	-0.011000	0.12721	0.593000	0.29745	0.655000	0.94253	GCG		0.592	RCVRN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252600.2	NM_002903	
SIRT7	51547	broad.mit.edu	37	17	79870453	79870453	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr17:79870453G>A	ENST00000328666.6	-	10	1104	c.1042C>T	c.(1042-1044)Cgt>Tgt	p.R348C	PCYT2_ENST00000331285.3_5'Flank|PCYT2_ENST00000538936.2_5'Flank|PCYT2_ENST00000571105.1_5'Flank|PCYT2_ENST00000570391.1_5'Flank|PCYT2_ENST00000538721.2_5'Flank|PCYT2_ENST00000570388.1_5'Flank	NM_016538.2	NP_057622.1	Q9NRC8	SIR7_HUMAN	sirtuin 7	348					histone H3 deacetylation (GO:0070932)|histone H4 deacetylation (GO:0070933)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription on exit from mitosis (GO:0007072)|rRNA transcription (GO:0009303)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleolus organizer region (GO:0005731)	chromatin binding (GO:0003682)|metal ion binding (GO:0046872)|NAD+ binding (GO:0070403)|NAD-dependent histone deacetylase activity (H3-K18 specific) (GO:0097372)	p.R348C(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(6)|prostate(1)|upper_aerodigestive_tract(1)	13	all_neural(118;0.0878)|Ovarian(332;0.12)		BRCA - Breast invasive adenocarcinoma(99;0.0165)|OV - Ovarian serous cystadenocarcinoma(97;0.0382)			TCACCAGCACGCAGGGGAGTC	0.652																																					p.R348C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1042T	17						.						32.0	38.0	36.0					17																	79870453		2202	4300	6502	77463745	SO:0001583	missense	51547	exon10			AF233395	CCDS11792.1	17q25.3	2010-06-25	2010-06-25			ENSG00000187531			14935	protein-coding gene	gene with protein product		606212	"""sirtuin (silent mating type information regulation 2, S.cerevisiae, homolog) 7"", ""sirtuin (silent mating type information regulation 2 homolog) 7 (S. cerevisiae)"""			10873683, 16618798	Standard	NM_016538		Approved		uc002kcj.2	Q9NRC8		ENST00000328666.6:c.1042C>T	17.37:g.79870453G>A	ENSP00000329466:p.Arg348Cys	Somatic		Capture	Illumina HiSeq	Phase_I	77463745	NM_016538	A8K2K0|B3KSU8|Q3MIK4|Q9NSZ6|Q9NUS6	Missense_Mutation	SNP	ENST00000328666.6	37	CCDS11792.1	.	.	.	.	.	.	.	.	.	.	G	14.83	2.653013	0.47362	.	.	ENSG00000187531	ENST00000328666	T	0.18338	2.22	4.74	4.74	0.60224	.	0.211286	0.37761	N	0.001942	T	0.15003	0.0362	L	0.32530	0.975	0.50632	D	0.999885	B;B	0.25719	0.132;0.132	B;B	0.12156	0.007;0.007	T	0.03662	-1.1015	10	0.45353	T	0.12	-10.5962	16.6571	0.85231	0.0:0.0:1.0:0.0	.	348;348	A8K2K0;Q9NRC8	.;SIRT7_HUMAN	C	348	ENSP00000329466:R348C	ENSP00000329466:R348C	R	-	1	0	SIRT7	77463745	0.845000	0.29573	0.951000	0.38953	0.935000	0.57460	2.590000	0.46154	2.466000	0.83321	0.491000	0.48974	CGT		0.652	SIRT7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439961.1	NM_016538	
APCDD1	147495	broad.mit.edu	37	18	10468502	10468502	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr18:10468502G>T	ENST00000355285.5	+	2	449	c.95G>T	c.(94-96)aGc>aTc	p.S32I	APCDD1_ENST00000578882.1_Missense_Mutation_p.S32I	NM_153000.4	NP_694545.1			adenomatosis polyposis coli down-regulated 1									p.S32I(1)		NS(1)|breast(1)|endometrium(3)|large_intestine(5)|lung(7)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	22				READ - Rectum adenocarcinoma(15;0.08)		CATCCAGACAGCAGGTCTCAT	0.483																																					p.S32I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G95T	18						.						140.0	143.0	142.0					18																	10468502		2203	4300	6503	10458502	SO:0001583	missense	147495	exon2			AB056722	CCDS11849.1	18p11.21	2006-07-07			ENSG00000154856	ENSG00000154856			15718	protein-coding gene	gene with protein product		607479				12384519	Standard	NM_153000		Approved	B7323	uc002kom.4	Q8J025	OTTHUMG00000131635	ENST00000355285.5:c.95G>T	18.37:g.10468502G>T	ENSP00000347433:p.Ser32Ile	Somatic		Capture	Illumina HiSeq	Phase_I	10458502	NM_153000		Missense_Mutation	SNP	ENST00000355285.5	37	CCDS11849.1	.	.	.	.	.	.	.	.	.	.	G	11.30	1.598672	0.28445	.	.	ENSG00000154856	ENST00000355285;ENST00000423585	T	0.39229	1.09	5.29	5.29	0.74685	.	0.128466	0.64402	D	0.000001	T	0.43787	0.1263	L	0.54323	1.7	0.44539	D	0.997491	P	0.49090	0.919	P	0.45506	0.483	T	0.45071	-0.9286	10	0.72032	D	0.01	-51.9768	12.6248	0.56623	0.0763:0.0:0.9237:0.0	.	32	Q8J025	APCD1_HUMAN	I	32;83	ENSP00000347433:S32I	ENSP00000347433:S32I	S	+	2	0	APCDD1	10458502	1.000000	0.71417	1.000000	0.80357	0.831000	0.47069	5.819000	0.69243	2.637000	0.89404	0.655000	0.94253	AGC		0.483	APCDD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254529.2	NM_153000	
NAPG	8774	broad.mit.edu	37	18	10532792	10532792	+	Splice_Site	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr18:10532792C>T	ENST00000322897.6	+	3	278	c.209C>T	c.(208-210)gCt>gTt	p.A70V	NAPG_ENST00000542979.1_5'UTR	NM_003826.2	NP_003817.1	Q99747	SNAG_HUMAN	N-ethylmaleimide-sensitive factor attachment protein, gamma	70					intra-Golgi vesicle-mediated transport (GO:0006891)|intracellular protein transport (GO:0006886)|membrane fusion (GO:0061025)|protein complex assembly (GO:0006461)|protein stabilization (GO:0050821)	extracellular vesicular exosome (GO:0070062)|lysosomal membrane (GO:0005765)|mitochondrion (GO:0005739)		p.A70V(1)		large_intestine(2)|lung(2)	4						AATAATAGGGCGTATCTTTTT	0.323																																					p.A70V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C209T	18						.						27.0	28.0	28.0					18																	10532792		1801	4066	5867	10522792	SO:0001630	splice_region_variant	8774	exon3			U78107	CCDS45827.1	18p11.21	2013-02-28			ENSG00000134265	ENSG00000134265			7642	protein-coding gene	gene with protein product	"""gamma SNAP"""	603216				9269766	Standard	NM_003826		Approved		uc002kon.3	Q99747	OTTHUMG00000179119	ENST00000322897.6:c.209+1C>T	18.37:g.10532792C>T		Somatic		Capture	Illumina HiSeq	Phase_I	10522792	NM_003826	B4DFC9|Q9BUV1	Missense_Mutation	SNP	ENST00000322897.6	37	CCDS45827.1	.	.	.	.	.	.	.	.	.	.	C	17.88	3.497125	0.64186	.	.	ENSG00000134265	ENST00000322897	T	0.76060	-0.99	5.92	5.92	0.95590	Tetratricopeptide-like helical (1);	0.092733	0.85682	D	0.000000	T	0.66346	0.2780	L	0.27053	0.805	0.80722	D	1	B	0.22909	0.077	B	0.16722	0.016	T	0.59461	-0.7450	10	0.39692	T	0.17	0.7413	20.3214	0.98679	0.0:1.0:0.0:0.0	.	70	Q99747	SNAG_HUMAN	V	70	ENSP00000324628:A70V	ENSP00000324628:A70V	A	+	2	0	NAPG	10522792	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.326000	0.79133	2.804000	0.96469	0.655000	0.94253	GCT		0.323	NAPG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444873.1	NM_003826	Missense_Mutation
CEP192	55125	broad.mit.edu	37	18	13055897	13055897	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr18:13055897C>T	ENST00000325971.8	+	17	3113	c.1520C>T	c.(1519-1521)aCa>aTa	p.T507I	CEP192_ENST00000430049.2_Missense_Mutation_p.T628I|CEP192_ENST00000506447.1_Missense_Mutation_p.T1103I			Q8TEP8	CE192_HUMAN	centrosomal protein 192kDa	507					centrosome duplication (GO:0051298)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|negative regulation of phosphatase activity (GO:0010923)|spindle assembly (GO:0051225)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)	phosphatase binding (GO:0019902)	p.T1103I(1)|p.T507I(1)		NS(1)|breast(4)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(12)|lung(36)|ovary(4)|pancreas(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	71						GGAAAAGGAACATTATCATCT	0.378																																					p.T1103I												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.C3308T	18						.						59.0	58.0	59.0					18																	13055897		2203	4300	6503	13045897	SO:0001583	missense	55125	exon19			AK074074	CCDS32792.1, CCDS32792.2	18p11.21	2014-02-20				ENSG00000101639		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	25515	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 62"""					11230166, 14654843	Standard	NM_032142		Approved	KIAA1569, FLJ10352, PPP1R62	uc010xac.2	Q8TEP8		ENST00000325971.8:c.1520C>T	18.37:g.13055897C>T	ENSP00000317156:p.Thr507Ile	Somatic		Capture	Illumina HiSeq	Phase_I	13045897	NM_032142	A0A060A9S4|E9PF99|Q8WYT8|Q9H0F4|Q9NW27	Missense_Mutation	SNP	ENST00000325971.8	37		.	.	.	.	.	.	.	.	.	.	C	7.891	0.732390	0.15507	.	.	ENSG00000101639	ENST00000506447;ENST00000325971;ENST00000399863;ENST00000430049	T;T;T	0.24723	1.84;1.84;1.84	3.7	2.78	0.32641	.	0.813289	0.10500	N	0.667417	T	0.16599	0.0399	L	0.29908	0.895	0.09310	N	1	B;B;B	0.24368	0.021;0.021;0.102	B;B;B	0.19391	0.01;0.016;0.025	T	0.23619	-1.0183	10	0.42905	T	0.14	-0.003	3.8616	0.08998	0.1662:0.5754:0.162:0.0965	.	628;1103;507	C9JT09;E9PF99;Q8TEP8	.;.;CE192_HUMAN	I	1103;507;507;628	ENSP00000427550:T1103I;ENSP00000317156:T507I;ENSP00000389190:T628I	ENSP00000317156:T507I	T	+	2	0	CEP192	13045897	0.000000	0.05858	0.001000	0.08648	0.195000	0.23768	0.435000	0.21510	0.798000	0.33994	0.514000	0.50259	ACA		0.378	CEP192-201	KNOWN	basic	protein_coding	protein_coding		NM_032142	
USP14	9097	broad.mit.edu	37	18	202914	202914	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr18:202914C>T	ENST00000261601.7	+	11	1002	c.911C>T	c.(910-912)aCg>aTg	p.T304M	USP14_ENST00000400266.3_Missense_Mutation_p.T293M|USP14_ENST00000582707.1_Missense_Mutation_p.T269M|USP14_ENST00000383589.2_Missense_Mutation_p.T258M	NM_005151.3	NP_005142.1	P54578	UBP14_HUMAN	ubiquitin specific peptidase 14 (tRNA-guanine transglycosylase)	304	USP.				negative regulation of endopeptidase activity (GO:0010951)|protein deubiquitination (GO:0016579)|regulation of chemotaxis (GO:0050920)|regulation of proteasomal protein catabolic process (GO:0061136)|synaptic transmission (GO:0007268)|ubiquitin-dependent protein catabolic process (GO:0006511)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)|proteasome complex (GO:0000502)|synapse (GO:0045202)	cysteine-type endopeptidase activity (GO:0004197)|endopeptidase inhibitor activity (GO:0004866)|proteasome binding (GO:0070628)|tRNA guanylyltransferase activity (GO:0008193)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)	p.T304M(1)		endometrium(1)|large_intestine(1)|lung(5)|ovary(2)|skin(2)	11		all_cancers(4;0.0896)|Myeloproliferative disorder(11;0.0412)				CAGTCTCCAACGTTGCAAAGA	0.323																																					p.T304M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C911T	18						.						78.0	78.0	78.0					18																	202914		2203	4300	6503	192914	SO:0001583	missense	9097	exon11			U30888	CCDS32780.1, CCDS32781.1	18p11.32	2006-10-06	2005-08-08			ENSG00000101557		"""Ubiquitin-specific peptidases"""	12612	protein-coding gene	gene with protein product		607274	"""ubiquitin specific protease 14 (tRNA-guanine transglycosylase)"""			12838346	Standard	NM_001037334		Approved	TGT	uc002kkf.1	P54578		ENST00000261601.7:c.911C>T	18.37:g.202914C>T	ENSP00000261601:p.Thr304Met	Somatic		Capture	Illumina HiSeq	Phase_I	192914	NM_005151	J3QRZ5|Q53XY5	Missense_Mutation	SNP	ENST00000261601.7	37	CCDS32780.1	.	.	.	.	.	.	.	.	.	.	c	33	5.239135	0.95240	.	.	ENSG00000101557	ENST00000261601;ENST00000383589;ENST00000400266	T;T	0.32988	1.43;1.44	5.79	5.79	0.91817	Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (2);	0.144405	0.64402	D	0.000006	T	0.59702	0.2213	M	0.84219	2.685	0.80722	D	1	D;D;D	0.63880	0.993;0.977;0.987	P;P;P	0.62491	0.903;0.867;0.896	T	0.63743	-0.6568	10	0.87932	D	0	-17.9951	20.0361	0.97558	0.0:1.0:0.0:0.0	.	293;269;304	B7Z4N8;A6NJA2;P54578	.;.;UBP14_HUMAN	M	304;269;293	ENSP00000261601:T304M;ENSP00000383125:T293M	ENSP00000261601:T304M	T	+	2	0	USP14	192914	1.000000	0.71417	1.000000	0.80357	0.965000	0.64279	7.295000	0.78780	2.740000	0.93945	0.563000	0.77884	ACG		0.323	USP14-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440305.3	NM_005151	
CEP192	55125	broad.mit.edu	37	18	13069738	13069738	+	Splice_Site	SNP	T	T	C			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr18:13069738T>C	ENST00000325971.8	+	25	4862	c.3269T>C	c.(3268-3270)gTc>gCc	p.V1090A	CEP192_ENST00000430049.2_Splice_Site_p.V1211A|CEP192_ENST00000506447.1_Splice_Site_p.V1686A			Q8TEP8	CE192_HUMAN	centrosomal protein 192kDa	1090					centrosome duplication (GO:0051298)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|negative regulation of phosphatase activity (GO:0010923)|spindle assembly (GO:0051225)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)	phosphatase binding (GO:0019902)	p.V1686A(1)|p.V1090A(1)		NS(1)|breast(4)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(12)|lung(36)|ovary(4)|pancreas(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	71						TATATTTAGGTCCCAGAACAA	0.403																																					p.V1686A												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.T5057C	18						.						106.0	107.0	106.0					18																	13069738		2203	4300	6503	13059738	SO:0001630	splice_region_variant	55125	exon27			AK074074	CCDS32792.1, CCDS32792.2	18p11.21	2014-02-20				ENSG00000101639		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	25515	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 62"""					11230166, 14654843	Standard	NM_032142		Approved	KIAA1569, FLJ10352, PPP1R62	uc010xac.2	Q8TEP8		ENST00000325971.8:c.3268-1T>C	18.37:g.13069738T>C		Somatic		Capture	Illumina HiSeq	Phase_I	13059738	NM_032142	A0A060A9S4|E9PF99|Q8WYT8|Q9H0F4|Q9NW27	Missense_Mutation	SNP	ENST00000325971.8	37		.	.	.	.	.	.	.	.	.	.	T	15.29	2.788985	0.49997	.	.	ENSG00000101639	ENST00000506447;ENST00000325971;ENST00000399863;ENST00000430049	T;T;T	0.40756	1.02;1.02;1.02	5.47	5.47	0.80525	.	0.615222	0.16629	N	0.206147	T	0.33498	0.0865	L	0.39898	1.24	0.80722	D	1	B;B;B	0.32467	0.372;0.247;0.25	B;B;B	0.33392	0.163;0.078;0.075	T	0.10200	-1.0640	10	0.25751	T	0.34	-6.0845	9.6858	0.40098	0.0:0.0821:0.0:0.9179	.	1211;1686;288	C9JT09;E9PF99;Q9HCK3	.;.;.	A	1686;1090;1090;1211	ENSP00000427550:V1686A;ENSP00000317156:V1090A;ENSP00000389190:V1211A	ENSP00000317156:V1090A	V	+	2	0	CEP192	13059738	1.000000	0.71417	0.997000	0.53966	0.949000	0.60115	2.014000	0.40951	2.091000	0.63221	0.459000	0.35465	GTC		0.403	CEP192-201	KNOWN	basic	protein_coding	protein_coding		NM_032142	Missense_Mutation
NPC1	4864	broad.mit.edu	37	18	21136549	21136549	+	Silent	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr18:21136549G>A	ENST00000269228.5	-	8	1538	c.984C>T	c.(982-984)agC>agT	p.S328S	NPC1_ENST00000540608.1_5'UTR|NPC1_ENST00000412552.2_Silent_p.S78S	NM_000271.4	NP_000262.2	O15118	NPC1_HUMAN	Niemann-Pick disease, type C1	328					adult walking behavior (GO:0007628)|autophagy (GO:0006914)|bile acid metabolic process (GO:0008206)|cellular response to low-density lipoprotein particle stimulus (GO:0071404)|cellular response to steroid hormone stimulus (GO:0071383)|cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|cholesterol transport (GO:0030301)|endocytosis (GO:0006897)|establishment of protein localization to membrane (GO:0090150)|lysosomal transport (GO:0007041)|membrane raft organization (GO:0031579)|negative regulation of cell death (GO:0060548)|negative regulation of macroautophagy (GO:0016242)|protein glycosylation (GO:0006486)|response to cadmium ion (GO:0046686)|response to drug (GO:0042493)|signal transduction (GO:0007165)	endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|membrane (GO:0016020)|membrane raft (GO:0045121)|nuclear envelope (GO:0005635)|perinuclear region of cytoplasm (GO:0048471)	cholesterol binding (GO:0015485)|hedgehog receptor activity (GO:0008158)|receptor activity (GO:0004872)|sterol transporter activity (GO:0015248)|transmembrane signaling receptor activity (GO:0004888)	p.S328S(1)		breast(1)|cervix(1)|endometrium(4)|kidney(6)|large_intestine(10)|lung(13)|ovary(2)|stomach(1)	38	all_cancers(21;0.000106)|all_epithelial(16;6.57e-07)|Lung NSC(20;0.00166)|all_lung(20;0.00536)|Colorectal(14;0.0202)|Ovarian(20;0.127)					CAAATGCTGCGCTGACAGGGT	0.562																																					p.S328S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C984T	18						.						33.0	33.0	33.0					18																	21136549		2203	4300	6503	19390547	SO:0001819	synonymous_variant	4864	exon8			AF002020	CCDS11878.1	18q11.2	2014-06-17			ENSG00000141458	ENSG00000141458			7897	protein-coding gene	gene with protein product		607623				8446622	Standard	NM_000271		Approved		uc002kum.4	O15118	OTTHUMG00000131873	ENST00000269228.5:c.984C>T	18.37:g.21136549G>A		Somatic		Capture	Illumina HiSeq	Phase_I	19390547	NM_000271	B4DET3|Q9P130	Silent	SNP	ENST00000269228.5	37	CCDS11878.1																																																																																				0.562	NPC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254823.2	NM_000271	
ZNF521	25925	broad.mit.edu	37	18	22804373	22804373	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr18:22804373C>T	ENST00000361524.3	-	4	3657	c.3509G>A	c.(3508-3510)aGc>aAc	p.S1170N	ZNF521_ENST00000584787.1_Missense_Mutation_p.S950N|ZNF521_ENST00000538137.2_Missense_Mutation_p.S1170N	NM_015461.2	NP_056276.1	Q96K83	ZN521_HUMAN	zinc finger protein 521	1170					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|protein domain specific binding (GO:0019904)	p.S1170N(1)		NS(1)|breast(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(21)|lung(97)|ovary(5)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	149	all_cancers(21;0.0025)|all_epithelial(16;3.62e-05)|Ovarian(20;0.0991)					CAACTGTGTGCTGTTGCTGTC	0.483			T	PAX5	ALL																																p.S1170N			Dom	yes		18	18q11.2	25925	zinc finger protein 521		L	.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G3509A	18						.						162.0	150.0	154.0					18																	22804373		2203	4300	6503	21058371	SO:0001583	missense	25925	exon4			AK027354	CCDS32806.1	18q11.2	2013-01-08				ENSG00000198795		"""Zinc fingers, C2H2-type"""	24605	protein-coding gene	gene with protein product	"""early hematopoietic zinc finger"""	610974				11984006, 14630787	Standard	NM_015461		Approved	EHZF, Evi3	uc002kvk.2	Q96K83		ENST00000361524.3:c.3509G>A	18.37:g.22804373C>T	ENSP00000354794:p.Ser1170Asn	Somatic		Capture	Illumina HiSeq	Phase_I	21058371	NM_015461	A3QVP7|B0YJB7|Q8IXI0|Q8TES6|Q9C065|Q9HAL5|Q9UFK4	Missense_Mutation	SNP	ENST00000361524.3	37	CCDS32806.1	.	.	.	.	.	.	.	.	.	.	C	11.87	1.766270	0.31228	.	.	ENSG00000198795	ENST00000361524;ENST00000538137;ENST00000399425	T;T	0.09911	2.94;2.93	5.98	5.1	0.69264	.	0.190754	0.53938	D	0.000043	T	0.07143	0.0181	N	0.14661	0.345	0.34447	D	0.700231	B	0.06786	0.001	B	0.08055	0.003	T	0.24368	-1.0162	10	0.15066	T	0.55	-18.7303	15.6243	0.76840	0.0:0.9334:0.0:0.0666	.	1170	Q96K83	ZN521_HUMAN	N	1170;1204;1170	ENSP00000354794:S1170N;ENSP00000382352:S1170N	ENSP00000354794:S1170N	S	-	2	0	ZNF521	21058371	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	2.307000	0.43682	2.835000	0.97688	0.650000	0.86243	AGC		0.483	ZNF521-001	KNOWN	overlapping_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446781.2	NM_015461	
ZNF521	25925	broad.mit.edu	37	18	22804685	22804685	+	Missense_Mutation	SNP	T	T	G			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr18:22804685T>G	ENST00000361524.3	-	4	3345	c.3197A>C	c.(3196-3198)aAg>aCg	p.K1066T	ZNF521_ENST00000584787.1_Missense_Mutation_p.K846T|ZNF521_ENST00000538137.2_Missense_Mutation_p.K1066T|ZNF521_ENST00000579111.1_5'Flank	NM_015461.2	NP_056276.1	Q96K83	ZN521_HUMAN	zinc finger protein 521	1066					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|protein domain specific binding (GO:0019904)	p.K1066T(1)		NS(1)|breast(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(21)|lung(97)|ovary(5)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	149	all_cancers(21;0.0025)|all_epithelial(16;3.62e-05)|Ovarian(20;0.0991)					AGATGCGCACTTATACAGTTT	0.502			T	PAX5	ALL																																p.K1066T			Dom	yes		18	18q11.2	25925	zinc finger protein 521		L	.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A3197C	18						.						73.0	62.0	66.0					18																	22804685		2203	4300	6503	21058683	SO:0001583	missense	25925	exon4			AK027354	CCDS32806.1	18q11.2	2013-01-08				ENSG00000198795		"""Zinc fingers, C2H2-type"""	24605	protein-coding gene	gene with protein product	"""early hematopoietic zinc finger"""	610974				11984006, 14630787	Standard	NM_015461		Approved	EHZF, Evi3	uc002kvk.2	Q96K83		ENST00000361524.3:c.3197A>C	18.37:g.22804685T>G	ENSP00000354794:p.Lys1066Thr	Somatic		Capture	Illumina HiSeq	Phase_I	21058683	NM_015461	A3QVP7|B0YJB7|Q8IXI0|Q8TES6|Q9C065|Q9HAL5|Q9UFK4	Missense_Mutation	SNP	ENST00000361524.3	37	CCDS32806.1	.	.	.	.	.	.	.	.	.	.	T	11.84	1.759253	0.31137	.	.	ENSG00000198795	ENST00000361524;ENST00000538137;ENST00000399425	T;T	0.10288	2.92;2.89	5.86	5.86	0.93980	.	0.000000	0.85682	D	0.000000	T	0.21881	0.0527	L	0.27053	0.805	0.47407	D	0.999414	D	0.89917	1.0	D	0.80764	0.994	T	0.01786	-1.1274	10	0.41790	T	0.15	-33.6182	16.2652	0.82574	0.0:0.0:0.0:1.0	.	1066	Q96K83	ZN521_HUMAN	T	1066;1100;1066	ENSP00000354794:K1066T;ENSP00000382352:K1066T	ENSP00000354794:K1066T	K	-	2	0	ZNF521	21058683	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.698000	0.84413	2.241000	0.73720	0.528000	0.53228	AAG		0.502	ZNF521-001	KNOWN	overlapping_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446781.2	NM_015461	
TAF4B	6875	broad.mit.edu	37	18	23854787	23854787	+	Splice_Site	SNP	C	C	T	rs202073070		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr18:23854787C>T	ENST00000269142.5	+	4	1756	c.758C>T	c.(757-759)cCg>cTg	p.P253L	TAF4B_ENST00000578121.1_Splice_Site_p.P253L|TAF4B_ENST00000400466.2_Splice_Site_p.P253L	NM_005640.1	NP_005631.1	Q92750	TAF4B_HUMAN	TAF4b RNA polymerase II, TATA box binding protein (TBP)-associated factor, 105kDa	253					gene expression (GO:0010467)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor TFIID complex (GO:0005669)	DNA binding (GO:0003677)|NF-kappaB binding (GO:0051059)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.P253L(1)		breast(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(13)|prostate(1)|skin(1)	29	all_cancers(21;0.00151)|Lung NSC(5;0.000401)|all_lung(6;0.00115)|Ovarian(20;0.124)		Epithelial(2;9.57e-07)|all cancers(3;5.15e-06)|OV - Ovarian serous cystadenocarcinoma(3;1.96e-05)|LUSC - Lung squamous cell carcinoma(2;0.00594)|Lung(2;0.0267)			AATCTTTCTCCGGTAAGCTCT	0.388													C|||	1	0.000199681	0.0008	0.0	5008	,	,		18088	0.0		0.0	False		,,,				2504	0.0				p.P253L												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C758T	18						.						163.0	151.0	155.0					18																	23854787		1868	4105	5973	22108785	SO:0001630	splice_region_variant	6875	exon4			Y09321	CCDS42421.1	18q11.1	2008-08-01	2002-08-29	2001-12-07		ENSG00000141384			11538	protein-coding gene	gene with protein product	"""TATA box binding protein (TBP)-associated factor 4B"""	601689	"""TATA box binding protein (TBP)-associated factor, RNA polymerase II, C2, 105kD"""	TAF2C2		8858156, 10849440	Standard	XM_005258339		Approved	TAFII105	uc002kvu.4	Q92750		ENST00000269142.5:c.759+1C>T	18.37:g.23854787C>T		Somatic		Capture	Illumina HiSeq	Phase_I	22108785	NM_005640	Q29YA4|Q29YA5	Missense_Mutation	SNP	ENST00000269142.5	37	CCDS42421.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	C	9.870	1.198661	0.22121	.	.	ENSG00000141384	ENST00000418698;ENST00000269142;ENST00000400466	T;T;T	0.40225	1.04;1.04;1.04	5.66	4.6	0.57074	.	0.541958	0.20720	N	0.086926	T	0.30947	0.0781	L	0.36672	1.1	0.43390	D	0.995506	B;B	0.30709	0.023;0.291	B;B	0.18871	0.008;0.023	T	0.07673	-1.0760	10	0.32370	T	0.25	-10.3177	13.7632	0.62979	0.0:0.9162:0.0:0.0838	.	253;253	Q92750;A4PBF7	TAF4B_HUMAN;.	L	253	ENSP00000389365:P253L;ENSP00000269142:P253L;ENSP00000383314:P253L	ENSP00000269142:P253L	P	+	2	0	TAF4B	22108785	1.000000	0.71417	0.999000	0.59377	0.338000	0.28826	2.976000	0.49289	2.680000	0.91292	0.655000	0.94253	CCG		0.388	TAF4B-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000446260.3	NM_005640	Missense_Mutation
TAF4B	6875	broad.mit.edu	37	18	23901113	23901113	+	Silent	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr18:23901113C>T	ENST00000269142.5	+	11	3080	c.2082C>T	c.(2080-2082)ggC>ggT	p.G694G	TAF4B_ENST00000578121.1_Silent_p.G699G	NM_005640.1	NP_005631.1	Q92750	TAF4B_HUMAN	TAF4b RNA polymerase II, TATA box binding protein (TBP)-associated factor, 105kDa	694	Histone-fold.				gene expression (GO:0010467)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor TFIID complex (GO:0005669)	DNA binding (GO:0003677)|NF-kappaB binding (GO:0051059)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.G694G(1)		breast(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(13)|prostate(1)|skin(1)	29	all_cancers(21;0.00151)|Lung NSC(5;0.000401)|all_lung(6;0.00115)|Ovarian(20;0.124)		Epithelial(2;9.57e-07)|all cancers(3;5.15e-06)|OV - Ovarian serous cystadenocarcinoma(3;1.96e-05)|LUSC - Lung squamous cell carcinoma(2;0.00594)|Lung(2;0.0267)			GACTACGAGGCCTTCTAGAAA	0.398																																					p.G694G												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C2082T	18						.						87.0	79.0	81.0					18																	23901113		1886	4116	6002	22155111	SO:0001819	synonymous_variant	6875	exon11			Y09321	CCDS42421.1	18q11.1	2008-08-01	2002-08-29	2001-12-07		ENSG00000141384			11538	protein-coding gene	gene with protein product	"""TATA box binding protein (TBP)-associated factor 4B"""	601689	"""TATA box binding protein (TBP)-associated factor, RNA polymerase II, C2, 105kD"""	TAF2C2		8858156, 10849440	Standard	XM_005258339		Approved	TAFII105	uc002kvu.4	Q92750		ENST00000269142.5:c.2082C>T	18.37:g.23901113C>T		Somatic		Capture	Illumina HiSeq	Phase_I	22155111	NM_005640	Q29YA4|Q29YA5	Silent	SNP	ENST00000269142.5	37	CCDS42421.1																																																																																				0.398	TAF4B-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000446260.3	NM_005640	
DSG1	1828	broad.mit.edu	37	18	28908192	28908192	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr18:28908192G>A	ENST00000257192.4	+	4	469	c.257G>A	c.(256-258)cGc>cAc	p.R86H		NM_001942.2	NP_001933.2	Q02413	DSG1_HUMAN	desmoglein 1	86	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				apoptotic process (GO:0006915)|calcium-dependent cell-cell adhesion (GO:0016339)|cell-cell junction assembly (GO:0007043)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|homophilic cell adhesion (GO:0007156)|maternal process involved in female pregnancy (GO:0060135)|protein stabilization (GO:0050821)|response to progesterone (GO:0032570)|single organismal cell-cell adhesion (GO:0016337)	apical plasma membrane (GO:0016324)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lateral plasma membrane (GO:0016328)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|gamma-catenin binding (GO:0045295)|toxic substance binding (GO:0015643)	p.R86H(1)		NS(2)|central_nervous_system(2)|endometrium(5)|kidney(7)|large_intestine(11)|lung(36)|ovary(3)|prostate(1)|skin(7)|stomach(1)|upper_aerodigestive_tract(1)	76			OV - Ovarian serous cystadenocarcinoma(10;0.00559)			GTTACATACCGCATCTCTGGA	0.373																																					p.R86H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G257A	18						.						96.0	93.0	94.0					18																	28908192		2203	4299	6502	27162190	SO:0001583	missense	1828	exon4			X56654	CCDS11896.1	18q12.1	2014-05-13			ENSG00000134760	ENSG00000134760		"""Cadherins / Major cadherins"""	3048	protein-coding gene	gene with protein product		125670		DSG		1889810	Standard	NM_001942		Approved	CDHF4	uc002kwp.3	Q02413	OTTHUMG00000131983	ENST00000257192.4:c.257G>A	18.37:g.28908192G>A	ENSP00000257192:p.Arg86His	Somatic		Capture	Illumina HiSeq	Phase_I	27162190	NM_001942	B7Z845	Missense_Mutation	SNP	ENST00000257192.4	37	CCDS11896.1	.	.	.	.	.	.	.	.	.	.	G	21.4	4.138491	0.77775	.	.	ENSG00000134760	ENST00000257192	T	0.53640	0.61	5.59	4.72	0.59763	Cadherin (4);Cadherin-like (1);	0.309404	0.28595	N	0.014796	T	0.43590	0.1254	L	0.43152	1.355	0.80722	D	1	P	0.47910	0.902	P	0.45406	0.479	T	0.39187	-0.9626	10	0.54805	T	0.06	.	9.8534	0.41070	0.0732:0.1397:0.7871:0.0	.	86	Q02413	DSG1_HUMAN	H	86	ENSP00000257192:R86H	ENSP00000257192:R86H	R	+	2	0	DSG1	27162190	0.998000	0.40836	1.000000	0.80357	0.991000	0.79684	2.536000	0.45693	1.357000	0.45904	0.563000	0.77884	CGC		0.373	DSG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254947.1	NM_001942	
B4GALT6	9331	broad.mit.edu	37	18	29211052	29211052	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr18:29211052T>C	ENST00000306851.5	-	6	942	c.646A>G	c.(646-648)Atg>Gtg	p.M216V	B4GALT6_ENST00000383131.3_Missense_Mutation_p.M177V|B4GALT6_ENST00000237019.7_Missense_Mutation_p.M177V	NM_004775.3	NP_004766.2	Q9UBX8	B4GT6_HUMAN	UDP-Gal:betaGlcNAc beta 1,4- galactosyltransferase, polypeptide 6	216					carbohydrate metabolic process (GO:0005975)|cellular protein metabolic process (GO:0044267)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate metabolic process (GO:0042339)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|small molecule metabolic process (GO:0044281)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	galactosyltransferase activity (GO:0008378)|metal ion binding (GO:0046872)	p.M216V(1)		breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(6)|lung(6)|pancreas(1)	20			OV - Ovarian serous cystadenocarcinoma(10;0.00791)			CTGTCTTTCATGGCCTCTTTG	0.443																																					p.M216V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A646G	18						.						99.0	91.0	94.0					18																	29211052		2203	4300	6503	27465050	SO:0001583	missense	9331	exon6			AF038664	CCDS11900.1	18q11	2013-02-19			ENSG00000118276	ENSG00000118276		"""Beta 4-glycosyltransferases"""	929	protein-coding gene	gene with protein product	"""UDP-Gal:glucosylceramide beta-1,4-galactosyltransferase"""	604017				9597550, 12180132	Standard	NM_004775		Approved	beta4GalT-VI	uc002kwz.4	Q9UBX8	OTTHUMG00000131980	ENST00000306851.5:c.646A>G	18.37:g.29211052T>C	ENSP00000306459:p.Met216Val	Somatic		Capture	Illumina HiSeq	Phase_I	27465050	NM_004775	O60514|Q6NT09	Missense_Mutation	SNP	ENST00000306851.5	37	CCDS11900.1	.	.	.	.	.	.	.	.	.	.	T	16.24	3.066594	0.55539	.	.	ENSG00000118276	ENST00000306851;ENST00000237019;ENST00000383131	T;T;T	0.33654	1.4;1.4;1.4	5.5	5.5	0.81552	.	0.051146	0.85682	D	0.000000	T	0.43211	0.1237	M	0.75777	2.31	0.46336	D	0.998997	B;B;B	0.28026	0.198;0.081;0.099	B;B;B	0.28465	0.085;0.09;0.085	T	0.44952	-0.9294	10	0.87932	D	0	0.1657	15.8986	0.79356	0.0:0.0:0.0:1.0	.	177;177;216	Q6NT09;G3XA83;Q9UBX8	.;.;B4GT6_HUMAN	V	216;177;177	ENSP00000306459:M216V;ENSP00000237019:M177V;ENSP00000372613:M177V	ENSP00000237019:M177V	M	-	1	0	B4GALT6	27465050	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	6.119000	0.71590	2.223000	0.72356	0.477000	0.44152	ATG		0.443	B4GALT6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254942.2	NM_004775	
MEP1B	4225	broad.mit.edu	37	18	29790608	29790608	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr18:29790608T>C	ENST00000269202.6	+	10	1111	c.1064T>C	c.(1063-1065)cTg>cCg	p.L355P	MEP1B_ENST00000581447.1_Missense_Mutation_p.L355P	NM_005925.2	NP_005916.2	Q16820	MEP1B_HUMAN	meprin A, beta	355	MAM. {ECO:0000255|PROSITE- ProRule:PRU00128}.				digestion (GO:0007586)|inflammatory response (GO:0006954)	extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)	p.L355P(1)		cervix(1)|endometrium(1)|kidney(2)|large_intestine(6)|lung(9)|ovary(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	23						AGTGATCAACTGAACATCTAT	0.413																																					p.L355P												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T1064C	18						.						110.0	107.0	108.0					18																	29790608		1895	4113	6008	28044606	SO:0001583	missense	4225	exon10			X81333	CCDS45846.1	18q12.2-q12.3	2003-12-17				ENSG00000141434	3.4.24.18		7020	protein-coding gene	gene with protein product		600389				7774936	Standard	NM_005925		Approved		uc002kxj.4	Q16820		ENST00000269202.6:c.1064T>C	18.37:g.29790608T>C	ENSP00000269202:p.Leu355Pro	Somatic		Capture	Illumina HiSeq	Phase_I	28044606	NM_005925	B7ZM35|B9EGL6|Q670J1	Missense_Mutation	SNP	ENST00000269202.6	37	CCDS45846.1	.	.	.	.	.	.	.	.	.	.	T	22.2	4.251515	0.80135	.	.	ENSG00000141434	ENST00000269202	T	0.08370	3.1	5.33	5.33	0.75918	Concanavalin A-like lectin/glucanase (1);MAM domain (3);	0.000000	0.85682	D	0.000000	T	0.40595	0.1123	H	0.94964	3.605	0.80722	D	1	D	0.89917	1.0	D	0.79784	0.993	T	0.56986	-0.7888	10	0.87932	D	0	-10.7061	15.2911	0.73868	0.0:0.0:0.0:1.0	.	355	Q16820	MEP1B_HUMAN	P	355	ENSP00000269202:L355P	ENSP00000269202:L355P	L	+	2	0	MEP1B	28044606	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.648000	0.83479	2.027000	0.59764	0.477000	0.44152	CTG		0.413	MEP1B-001	KNOWN	NAGNAG_splice_site|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447755.1	NM_005925	
MYOM1	8736	broad.mit.edu	37	18	3067309	3067309	+	Missense_Mutation	SNP	G	G	A	rs560579909	byFrequency	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr18:3067309G>A	ENST00000356443.4	-	38	5342	c.5009C>T	c.(5008-5010)gCg>gTg	p.A1670V	MYOM1_ENST00000400569.3_Missense_Mutation_p.A1670V|MYOM1_ENST00000261606.7_Missense_Mutation_p.A1574V	NM_003803.3|NM_019856.1	NP_003794.3|NP_062830.1	P52179	MYOM1_HUMAN	myomesin 1	1670					muscle contraction (GO:0006936)	M band (GO:0031430)|striated muscle myosin thick filament (GO:0005863)	identical protein binding (GO:0042802)|protein homodimerization activity (GO:0042803)|structural constituent of muscle (GO:0008307)	p.A1670V(1)		NS(2)|autonomic_ganglia(1)|central_nervous_system(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|lung(20)|ovary(4)|pancreas(1)|prostate(4)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	77						GGCCATCCTCGCCTCCTCCTC	0.602																																					p.A1574V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C4721T	18						.						30.0	36.0	34.0					18																	3067309		2199	4299	6498	3057309	SO:0001583	missense	8736	exon37			AF185573	CCDS45823.1, CCDS45824.1	18p11.31	2014-09-17	2012-10-17		ENSG00000101605	ENSG00000101605		"""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	7613	protein-coding gene	gene with protein product	"""skelemin"""	603508	"""myomesin 1 (skelemin) (185kD)"", ""myomesin 1 (skelemin) 185kDa"", ""myomesin 1, 185kDa"""			9806852	Standard	NM_019856		Approved		uc002klp.3	P52179	OTTHUMG00000178209	ENST00000356443.4:c.5009C>T	18.37:g.3067309G>A	ENSP00000348821:p.Ala1670Val	Somatic		Capture	Illumina HiSeq	Phase_I	3057309	NM_019856	Q14BD6|Q6H969|Q6ZUU0	Missense_Mutation	SNP	ENST00000356443.4	37	CCDS45824.1	.	.	.	.	.	.	.	.	.	.	G	8.529	0.870666	0.17322	.	.	ENSG00000101605	ENST00000356443;ENST00000400569;ENST00000261606	T;T;T	0.48201	0.95;0.95;0.82	5.23	3.33	0.38152	.	0.322732	0.30752	N	0.008946	T	0.27384	0.0672	L	0.29908	0.895	0.19575	N	0.999964	B;B	0.28378	0.209;0.136	B;B	0.17433	0.018;0.009	T	0.08310	-1.0728	10	0.21540	T	0.41	.	4.9273	0.13900	0.1628:0.0:0.5494:0.2878	.	1574;1670	P52179-2;P52179	.;MYOM1_HUMAN	V	1670;1670;1574	ENSP00000348821:A1670V;ENSP00000383413:A1670V;ENSP00000261606:A1574V	ENSP00000261606:A1574V	A	-	2	0	MYOM1	3057309	0.995000	0.38212	0.797000	0.32132	0.603000	0.37013	1.966000	0.40481	1.166000	0.42689	0.655000	0.94253	GCG		0.602	MYOM1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000441037.2	NM_003803	
ASXL3	80816	broad.mit.edu	37	18	31325872	31325872	+	Silent	SNP	A	A	G	rs369151165		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr18:31325872A>G	ENST00000269197.5	+	12	6060	c.6060A>G	c.(6058-6060)ccA>ccG	p.P2020P		NM_030632.1	NP_085135.1	Q9C0F0	ASXL3_HUMAN	additional sex combs like transcriptional regulator 3	2020	Pro-rich.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.P2020P(1)		breast(3)|endometrium(3)|kidney(3)|large_intestine(6)|lung(22)|ovary(2)|pancreas(1)|skin(2)|urinary_tract(1)	43						cgccgccgccaccgcctcccc	0.602																																					p.P2020P												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.A6060G	18						.	A		0,3808		0,0,1904	19.0	24.0	22.0		6060	-7.4	0.0	18		22	1,8217		0,1,4108	no	coding-synonymous	ASXL3	NM_030632.1		0,1,6012	GG,GA,AA		0.0122,0.0,0.0083		2020/2249	31325872	1,12025	1904	4109	6013	29579870	SO:0001819	synonymous_variant	80816	exon12			AB051500	CCDS45847.1	18q11	2014-06-17	2014-06-17	2007-02-01		ENSG00000141431			29357	protein-coding gene	gene with protein product		615115	"""KIAA1713"", ""additional sex combs like 3 (Drosophila)"""	KIAA1713		11214970	Standard	NM_030632		Approved		uc010dmg.1	Q9C0F0		ENST00000269197.5:c.6060A>G	18.37:g.31325872A>G		Somatic		Capture	Illumina HiSeq	Phase_I	29579870	NM_030632	Q6ZMX6|Q96MU3|Q9UFC5	Silent	SNP	ENST00000269197.5	37	CCDS45847.1																																																																																				0.602	ASXL3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441865.2		
PIK3C3	5289	broad.mit.edu	37	18	39637995	39637995	+	Silent	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr18:39637995G>A	ENST00000262039.4	+	22	2498	c.2412G>A	c.(2410-2412)acG>acA	p.T804T	PIK3C3_ENST00000398870.3_Silent_p.T741T|PIK3C3_ENST00000593098.1_Silent_p.T289T|PIK3C3_ENST00000588156.1_Silent_p.T28T	NM_002647.2	NP_002638.2	Q8NEB9	PK3C3_HUMAN	phosphatidylinositol 3-kinase, catalytic subunit type 3	804	PI3K/PI4K. {ECO:0000255|PROSITE- ProRule:PRU00269}.				autophagic vacuole assembly (GO:0000045)|cytokinesis (GO:0000910)|early endosome to late endosome transport (GO:0045022)|endosome organization (GO:0007032)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|protein processing (GO:0016485)|regulation of protein secretion (GO:0050708)|response to leucine (GO:0043201)|small molecule metabolic process (GO:0044281)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)	axoneme (GO:0005930)|cytosol (GO:0005829)|late endosome (GO:0005770)|membrane (GO:0016020)|midbody (GO:0030496)|phagocytic vesicle (GO:0045335)|phosphatidylinositol 3-kinase complex (GO:0005942)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|ATP binding (GO:0005524)|protein kinase activity (GO:0004672)	p.T804T(1)		breast(2)|cervix(2)|endometrium(3)|kidney(2)|large_intestine(10)|liver(1)|lung(25)|ovary(1)|skin(2)|urinary_tract(1)	49						AGTGTTACACGGCTTTCCTCC	0.403										TSP Lung(28;0.18)																											p.T804T	NSCLC(37;552 1060 2683 16430 37914)											.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G2412A	18						.						74.0	72.0	73.0					18																	39637995		2203	4300	6503	37891993	SO:0001819	synonymous_variant	5289	exon22			Z46973	CCDS11920.1	18q12.3	2012-07-13	2012-07-13		ENSG00000078142	ENSG00000078142	2.7.1.137		8974	protein-coding gene	gene with protein product		602609	"""phosphoinositide-3-kinase, class 3"""			7628435	Standard	NM_002647		Approved	Vps34	uc002lap.3	Q8NEB9	OTTHUMG00000132593	ENST00000262039.4:c.2412G>A	18.37:g.39637995G>A		Somatic		Capture	Illumina HiSeq	Phase_I	37891993	NM_002647	Q15134	Silent	SNP	ENST00000262039.4	37	CCDS11920.1																																																																																				0.403	PIK3C3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255804.1	NM_002647	
SLC14A2	8170	broad.mit.edu	37	18	43205654	43205654	+	Missense_Mutation	SNP	C	C	T	rs200534486		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr18:43205654C>T	ENST00000255226.6	+	3	973	c.157C>T	c.(157-159)Cgg>Tgg	p.R53W	SLC14A2_ENST00000586448.1_Missense_Mutation_p.R53W	NM_007163.3	NP_009094.3	Q15849	UT2_HUMAN	solute carrier family 14 (urea transporter), member 2	53					transmembrane transport (GO:0055085)|urea transport (GO:0015840)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	cell adhesion molecule binding (GO:0050839)|urea transmembrane transporter activity (GO:0015204)	p.R53W(1)		NS(1)|central_nervous_system(1)|endometrium(5)|kidney(4)|large_intestine(8)|lung(35)|ovary(1)|prostate(1)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	63						AAAGGATCTCCGGTCTTCCAA	0.468													C|||	1	0.000199681	0.0	0.0	5008	,	,		20474	0.0		0.0	False		,,,				2504	0.001				p.R53W												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C157T	18						.						47.0	45.0	45.0					18																	43205654		2203	4300	6503	41459652	SO:0001583	missense	8170	exon3			X96969	CCDS11924.1	18q12.1-q21.1	2013-05-22			ENSG00000132874	ENSG00000132874		"""Solute carriers"""	10919	protein-coding gene	gene with protein product		601611				8647271	Standard	NM_007163		Approved	HUT2, UT2	uc010dnj.3	Q15849	OTTHUMG00000132616	ENST00000255226.6:c.157C>T	18.37:g.43205654C>T	ENSP00000255226:p.Arg53Trp	Somatic		Capture	Illumina HiSeq	Phase_I	41459652	NM_007163	A8K8Q7|Q2TBD6|Q96PH5	Missense_Mutation	SNP	ENST00000255226.6	37	CCDS11924.1	.	.	.	.	.	.	.	.	.	.	C	23.3	4.402210	0.83230	.	.	ENSG00000132874	ENST00000255226;ENST00000323329	T;T	0.57907	0.98;0.37	5.79	5.79	0.91817	.	0.246322	0.34750	N	0.003720	T	0.71829	0.3386	M	0.70595	2.14	0.42164	D	0.991614	D;D	0.89917	1.0;1.0	D;D	0.87578	0.993;0.998	T	0.74365	-0.3689	10	0.87932	D	0	-18.7503	15.5155	0.75822	0.0:1.0:0.0:0.0	.	53;53	Q15849;E7EPU1	UT2_HUMAN;.	W	53	ENSP00000255226:R53W;ENSP00000320689:R53W	ENSP00000255226:R53W	R	+	1	2	SLC14A2	41459652	0.771000	0.28555	0.974000	0.42286	0.915000	0.54546	1.183000	0.32041	2.737000	0.93849	0.650000	0.86243	CGG		0.468	SLC14A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255858.1		
EPG5	57724	broad.mit.edu	37	18	43484051	43484051	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr18:43484051C>T	ENST00000282041.5	-	25	4395	c.4361G>A	c.(4360-4362)cGc>cAc	p.R1454H	EPG5_ENST00000585906.1_5'UTR	NM_020964.2	NP_066015.2	Q9HCE0	EPG5_HUMAN	ectopic P-granules autophagy protein 5 homolog (C. elegans)	1454					autophagic vacuole maturation (GO:0097352)|autophagy (GO:0006914)|endocytic recycling (GO:0032456)			p.R1454H(1)		NS(1)|breast(9)|central_nervous_system(3)|cervix(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(22)|lung(35)|ovary(2)|pancreas(1)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	95						ATGATAGATGCGCTCCATGTT	0.443																																					p.R1454H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G4361A	18						.						146.0	140.0	142.0					18																	43484051		1982	4168	6150	41738049	SO:0001583	missense	57724	exon25			AK023817	CCDS11926.2	18q12.3	2011-03-02	2011-03-02	2011-03-02	ENSG00000152223	ENSG00000152223			29331	protein-coding gene	gene with protein product		615068	"""KIAA1632"""	KIAA1632		10997877, 20550938	Standard	XM_005258323		Approved	hEPG5	uc002lbm.3	Q9HCE0	OTTHUMG00000132626	ENST00000282041.5:c.4361G>A	18.37:g.43484051C>T	ENSP00000282041:p.Arg1454His	Somatic		Capture	Illumina HiSeq	Phase_I	41738049	NM_020964	A2BDF3|Q9H8C8	Missense_Mutation	SNP	ENST00000282041.5	37	CCDS11926.2	.	.	.	.	.	.	.	.	.	.	C	25.8	4.673560	0.88445	.	.	ENSG00000152223	ENST00000282041;ENST00000308403	T	0.11063	2.81	6.04	6.04	0.98038	.	.	.	.	.	T	0.29976	0.0750	L	0.59436	1.845	0.80722	D	1	D	0.89917	1.0	D	0.69824	0.966	T	0.00074	-1.2124	9	0.62326	D	0.03	-10.9235	16.2018	0.82087	0.1408:0.8592:0.0:0.0	.	1454	Q9HCE0	EPG5_HUMAN	H	1454;329	ENSP00000282041:R1454H	ENSP00000282041:R1454H	R	-	2	0	EPG5	41738049	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	5.041000	0.64196	2.873000	0.98535	0.563000	0.77884	CGC		0.443	EPG5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445081.1	NM_020964	
EPG5	57724	broad.mit.edu	37	18	43495562	43495562	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr18:43495562G>A	ENST00000282041.5	-	20	3641	c.3607C>T	c.(3607-3609)Cgg>Tgg	p.R1203W	EPG5_ENST00000585906.1_5'UTR	NM_020964.2	NP_066015.2	Q9HCE0	EPG5_HUMAN	ectopic P-granules autophagy protein 5 homolog (C. elegans)	1203					autophagic vacuole maturation (GO:0097352)|autophagy (GO:0006914)|endocytic recycling (GO:0032456)			p.R1203W(1)		NS(1)|breast(9)|central_nervous_system(3)|cervix(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(22)|lung(35)|ovary(2)|pancreas(1)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	95						AGCAGACTCCGGTCACAGTGG	0.498																																					p.R1203W												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C3607T	18						.						88.0	91.0	90.0					18																	43495562		2179	4272	6451	41749560	SO:0001583	missense	57724	exon20			AK023817	CCDS11926.2	18q12.3	2011-03-02	2011-03-02	2011-03-02	ENSG00000152223	ENSG00000152223			29331	protein-coding gene	gene with protein product		615068	"""KIAA1632"""	KIAA1632		10997877, 20550938	Standard	XM_005258323		Approved	hEPG5	uc002lbm.3	Q9HCE0	OTTHUMG00000132626	ENST00000282041.5:c.3607C>T	18.37:g.43495562G>A	ENSP00000282041:p.Arg1203Trp	Somatic		Capture	Illumina HiSeq	Phase_I	41749560	NM_020964	A2BDF3|Q9H8C8	Missense_Mutation	SNP	ENST00000282041.5	37	CCDS11926.2	.	.	.	.	.	.	.	.	.	.	G	15.22	2.770346	0.49680	.	.	ENSG00000152223	ENST00000282041;ENST00000308403	T	0.10860	2.83	5.51	4.63	0.57726	.	0.113146	0.35870	N	0.002924	T	0.26702	0.0653	L	0.53249	1.67	0.46823	D	0.999212	D;D	0.89917	1.0;1.0	D;D	0.67231	0.95;0.95	T	0.01036	-1.1473	10	0.72032	D	0.01	-15.6179	13.6988	0.62595	0.0:0.0:0.6626:0.3374	.	1203;1203	Q9HCE0-2;Q9HCE0	.;EPG5_HUMAN	W	1203;78	ENSP00000282041:R1203W	ENSP00000282041:R1203W	R	-	1	2	EPG5	41749560	1.000000	0.71417	1.000000	0.80357	0.288000	0.27193	4.605000	0.61119	1.315000	0.45114	-0.188000	0.12872	CGG		0.498	EPG5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445081.1	NM_020964	
TCEB3B	51224	broad.mit.edu	37	18	44560277	44560277	+	Silent	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr18:44560277C>T	ENST00000332567.4	-	1	1711	c.1359G>A	c.(1357-1359)acG>acA	p.T453T	KATNAL2_ENST00000592005.1_Intron|KATNAL2_ENST00000356157.7_Intron|KATNAL2_ENST00000245121.5_Intron	NM_016427.2	NP_057511.2	Q8IYF1	ELOA2_HUMAN	transcription elongation factor B polypeptide 3B (elongin A2)	453					regulation of DNA-templated transcription, elongation (GO:0032784)|transcription from RNA polymerase II promoter (GO:0006366)	integral component of membrane (GO:0016021)|nucleus (GO:0005634)	DNA binding (GO:0003677)	p.T453T(1)		breast(1)|cervix(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(15)|lung(24)|ovary(2)|pancreas(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	58						GGCTGGGCACCGTTTTCGGCC	0.607																																					p.T453T												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G1359A	18						.						49.0	58.0	55.0					18																	44560277		2203	4300	6503	42814275	SO:0001819	synonymous_variant	51224	exon1			BC036022	CCDS11932.1	18q21.1	2009-08-04			ENSG00000206181	ENSG00000206181			30771	protein-coding gene	gene with protein product	"""transcription elongation factor (SIII) elongin A2"", ""elongin A2"""	609522				7660129, 8244996	Standard	NM_016427		Approved	HsT832, TCEB3L	uc002lcr.1	Q8IYF1	OTTHUMG00000132649	ENST00000332567.4:c.1359G>A	18.37:g.44560277C>T		Somatic		Capture	Illumina HiSeq	Phase_I	42814275	NM_016427	Q9P2V9	Silent	SNP	ENST00000332567.4	37	CCDS11932.1																																																																																				0.607	TCEB3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255900.1	NM_016427	
ZBTB7C	201501	broad.mit.edu	37	18	45566339	45566339	+	Silent	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr18:45566339C>T	ENST00000588982.1	-	3	1641	c.1140G>A	c.(1138-1140)ccG>ccA	p.P380P	ZBTB7C_ENST00000586438.1_Silent_p.P380P|ZBTB7C_ENST00000332053.2_Silent_p.P380P|ZBTB7C_ENST00000535628.2_Silent_p.P380P|ZBTB7C_ENST00000590800.1_Silent_p.P380P			A1YPR0	ZBT7C_HUMAN	zinc finger and BTB domain containing 7C	380							metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)	p.P380P(1)		endometrium(8)|kidney(1)|large_intestine(7)|lung(3)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	23						TCATGTGCCGCGGCAGCTTCC	0.647																																					p.P380P												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G1140A	18						.						67.0	71.0	70.0					18																	45566339		2203	4300	6503	43820337	SO:0001819	synonymous_variant	201501	exon2			Y14591	CCDS32830.1	18q21.1	2013-01-08		2005-04-07	ENSG00000184828	ENSG00000184828		"""-"", ""Zinc fingers, C2H2-type"", ""BTB/POZ domain containing"""	31700	protein-coding gene	gene with protein product			"""zinc finger and BTB domain containing 36"""	ZBTB36			Standard	NM_001039360		Approved	ZNF857C	uc002ldb.3	A1YPR0		ENST00000588982.1:c.1140G>A	18.37:g.45566339C>T		Somatic		Capture	Illumina HiSeq	Phase_I	43820337	NM_001039360	O73453	Silent	SNP	ENST00000588982.1	37	CCDS32830.1																																																																																				0.647	ZBTB7C-025	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450731.1	NM_001039360	
ACAA2	10449	broad.mit.edu	37	18	47329180	47329180	+	Silent	SNP	G	G	A	rs151022375	byFrequency	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr18:47329180G>A	ENST00000285093.10	-	2	535	c.60C>T	c.(58-60)taC>taT	p.Y20Y	RP11-886H22.1_ENST00000590532.2_3'UTR|ACAA2_ENST00000587994.1_Silent_p.Y17Y|ACAA2_ENST00000589432.1_De_novo_Start_OutOfFrame	NM_006111.2	NP_006102.2	P42765	THIM_HUMAN	acetyl-CoA acyltransferase 2	20					cellular response to hypoxia (GO:0071456)|cholesterol biosynthetic process (GO:0006695)|fatty acid metabolic process (GO:0006631)|negative regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902109)|negative regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway (GO:1901029)	extracellular vesicular exosome (GO:0070062)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	acetyl-CoA C-acyltransferase activity (GO:0003988)|poly(A) RNA binding (GO:0044822)	p.Y20Y(1)		large_intestine(2)|lung(7)|ovary(1)	10						GAAGGCCTCCGTAAGCTCCAA	0.458																																					p.Y20Y												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C60T	18						.						114.0	104.0	107.0					18																	47329180		2203	4300	6503	45583178	SO:0001819	synonymous_variant	10449	exon2			D16294	CCDS11939.1	18q21	2010-04-30	2010-04-30		ENSG00000167315	ENSG00000167315	2.3.1.16		83	protein-coding gene	gene with protein product	"""mitochondrial 3-oxoacyl-Coenzyme A thiolase"""	604770	"""acetyl-Coenzyme A acyltransferase 2"""			8241273	Standard	NM_006111		Approved	DSAEC	uc002ldw.4	P42765	OTTHUMG00000132667	ENST00000285093.10:c.60C>T	18.37:g.47329180G>A		Somatic		Capture	Illumina HiSeq	Phase_I	45583178	NM_006111	Q9BUT6	Silent	SNP	ENST00000285093.10	37	CCDS11939.1																																																																																				0.458	ACAA2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255921.2	NM_006111	
ME2	4200	broad.mit.edu	37	18	48458652	48458652	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr18:48458652A>G	ENST00000321341.5	+	13	1611	c.1339A>G	c.(1339-1341)Agt>Ggt	p.S447G	ME2_ENST00000585680.1_3'UTR|ME2_ENST00000382927.3_Missense_Mutation_p.S447G	NM_002396.4	NP_002387.1	P23368	MAOM_HUMAN	malic enzyme 2, NAD(+)-dependent, mitochondrial	447					malate metabolic process (GO:0006108)	intracellular membrane-bounded organelle (GO:0043231)|mitochondrion (GO:0005739)	electron carrier activity (GO:0009055)|malate dehydrogenase (decarboxylating) (NAD+) activity (GO:0004471)|metal ion binding (GO:0046872)|NAD binding (GO:0051287)|oxaloacetate decarboxylase activity (GO:0008948)	p.S447G(1)		breast(2)|endometrium(1)|kidney(2)|large_intestine(4)|lung(11)|upper_aerodigestive_tract(3)	23		Colorectal(6;0.0273)|all_epithelial(6;0.118)		Colorectal(21;0.0313)|READ - Rectum adenocarcinoma(32;0.105)|STAD - Stomach adenocarcinoma(97;0.184)		TGCCAGTGGCAGTCCATTTGG	0.363																																					p.S447G												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A1339G	18						.						124.0	121.0	122.0					18																	48458652		2203	4300	6503	46712650	SO:0001583	missense	4200	exon13			M55905	CCDS11948.1, CCDS54187.1	18q21	2012-10-02			ENSG00000082212	ENSG00000082212	1.1.1.40		6984	protein-coding gene	gene with protein product		154270				1993674	Standard	NM_002396		Approved		uc002ley.3	P23368	OTTHUMG00000132694	ENST00000321341.5:c.1339A>G	18.37:g.48458652A>G	ENSP00000321070:p.Ser447Gly	Somatic		Capture	Illumina HiSeq	Phase_I	46712650	NM_001168335	B2R8J2|Q9BWL6|Q9BYG1|Q9H4B2	Missense_Mutation	SNP	ENST00000321341.5	37	CCDS11948.1	.	.	.	.	.	.	.	.	.	.	A	24.8	4.575954	0.86645	.	.	ENSG00000082212	ENST00000321341;ENST00000382927	T;T	0.48201	0.82;0.82	5.18	5.18	0.71444	Malic enzyme, NAD-binding (2);NAD(P)-binding domain (1);	0.000000	0.85682	D	0.000000	T	0.75287	0.3829	M	0.92833	3.35	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.997;0.998	T	0.82141	-0.0604	10	0.87932	D	0	-22.8849	14.3033	0.66368	1.0:0.0:0.0:0.0	.	447;447	Q9BWL6;P23368	.;MAOM_HUMAN	G	447	ENSP00000321070:S447G;ENSP00000372384:S447G	ENSP00000321070:S447G	S	+	1	0	ME2	46712650	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	8.526000	0.90588	2.089000	0.63090	0.459000	0.35465	AGT		0.363	ME2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255991.1	NM_002396	
C18orf54	162681	broad.mit.edu	37	18	51888161	51888161	+	Silent	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr18:51888161G>A	ENST00000300091.5	+	3	764	c.432G>A	c.(430-432)ccG>ccA	p.P144P	C18orf54_ENST00000382911.4_Silent_p.P144P|C18orf54_ENST00000578138.1_Intron	NM_173529.4	NP_775800.3	Q8IYD9	LAS2_HUMAN	chromosome 18 open reading frame 54	144						extracellular region (GO:0005576)		p.P144P(1)		breast(1)|central_nervous_system(1)|endometrium(3)|large_intestine(3)|lung(5)|ovary(1)|skin(1)	15				Colorectal(16;0.0206)|READ - Rectum adenocarcinoma(59;0.186)		ATGTTGGACCGAGTCACCGAA	0.428																																					p.P144P												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G432A	18						.						92.0	78.0	82.0					18																	51888161		2203	4300	6503	50142159	SO:0001819	synonymous_variant	162681	exon3			AK126503	CCDS11956.1, CCDS74223.1	18q21	2012-10-24			ENSG00000166845	ENSG00000166845			13796	protein-coding gene	gene with protein product	"""lung adenoma susceptibility protein 2"""	613258					Standard	XM_005258201		Approved	MGC33382, LAS2	uc031rij.1	Q8IYD9	OTTHUMG00000132703	ENST00000300091.5:c.432G>A	18.37:g.51888161G>A		Somatic		Capture	Illumina HiSeq	Phase_I	50142159	NM_173529	I7HFJ6|Q6MZU3|Q6ZTL6	Silent	SNP	ENST00000300091.5	37	CCDS11956.1																																																																																				0.428	C18orf54-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256001.1	NM_173529	
FECH	2235	broad.mit.edu	37	18	55222145	55222145	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr18:55222145C>T	ENST00000262093.5	-	8	995	c.844G>A	c.(844-846)Gcc>Acc	p.A282T	FECH_ENST00000382873.3_Missense_Mutation_p.A288T	NM_000140.3|NM_001012515.2	NP_000131.2|NP_001012533.1	P22830	HEMH_HUMAN	ferrochelatase	282					cellular response to dexamethasone stimulus (GO:0071549)|cholesterol metabolic process (GO:0008203)|detection of UV (GO:0009589)|erythrocyte differentiation (GO:0030218)|generation of precursor metabolites and energy (GO:0006091)|heme biosynthetic process (GO:0006783)|iron ion homeostasis (GO:0055072)|porphyrin-containing compound metabolic process (GO:0006778)|protoporphyrinogen IX metabolic process (GO:0046501)|regulation of eIF2 alpha phosphorylation by heme (GO:0010999)|regulation of gene expression (GO:0010468)|regulation of hemoglobin biosynthetic process (GO:0046984)|response to arsenic-containing substance (GO:0046685)|response to drug (GO:0042493)|response to ethanol (GO:0045471)|response to insecticide (GO:0017085)|response to lead ion (GO:0010288)|response to light stimulus (GO:0009416)|response to methylmercury (GO:0051597)|response to platinum ion (GO:0070541)|small molecule metabolic process (GO:0044281)|very-low-density lipoprotein particle assembly (GO:0034379)	mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)	2 iron, 2 sulfur cluster binding (GO:0051537)|ferrochelatase activity (GO:0004325)|ferrous iron binding (GO:0008198)|heme binding (GO:0020037)|iron-responsive element binding (GO:0030350)	p.A288T(1)		central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(5)|prostate(1)|upper_aerodigestive_tract(1)	15		Colorectal(73;0.227)				TGGACAGTGGCGCTTACCTCC	0.577																																					p.A288T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G862A	18						.						101.0	93.0	95.0					18																	55222145		2203	4300	6503	53373143	SO:0001583	missense	2235	exon8			D00726	CCDS11964.1, CCDS32836.1	18q21.2-q21.3	2010-05-11	2010-05-11		ENSG00000066926	ENSG00000066926	4.99.1.1		3647	protein-coding gene	gene with protein product	"""protoporphyria"""	612386	"""ferrochelatase (protoporphyria)"""			1838349	Standard	NM_001012515		Approved		uc002lgp.4	P22830	OTTHUMG00000132740	ENST00000262093.5:c.844G>A	18.37:g.55222145C>T	ENSP00000262093:p.Ala282Thr	Somatic		Capture	Illumina HiSeq	Phase_I	53373143	NM_001012515	A8KA72|Q8IXN1|Q8NAN0	Missense_Mutation	SNP	ENST00000262093.5	37	CCDS11964.1	.	.	.	.	.	.	.	.	.	.	C	31	5.077259	0.94000	.	.	ENSG00000066926	ENST00000262093;ENST00000382873	D;D	0.97279	-4.32;-4.32	5.77	5.77	0.91146	.	0.000000	0.85682	D	0.000000	D	0.98131	0.9383	M	0.79011	2.435	0.80722	D	1	D;D	0.76494	0.999;0.999	P;P	0.60415	0.874;0.801	D	0.98145	1.0438	10	0.51188	T	0.08	-26.0171	19.5894	0.95501	0.0:1.0:0.0:0.0	.	282;288	P22830;P22830-2	HEMH_HUMAN;.	T	282;288	ENSP00000262093:A282T;ENSP00000372326:A288T	ENSP00000262093:A282T	A	-	1	0	FECH	53373143	1.000000	0.71417	0.980000	0.43619	0.403000	0.30841	7.248000	0.78268	2.720000	0.93068	0.557000	0.71058	GCC		0.577	FECH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256098.1		
FECH	2235	broad.mit.edu	37	18	55230168	55230168	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr18:55230168G>A	ENST00000262093.5	-	6	794	c.643C>T	c.(643-645)Cgg>Tgg	p.R215W	FECH_ENST00000382873.3_Missense_Mutation_p.R221W	NM_000140.3|NM_001012515.2	NP_000131.2|NP_001012533.1	P22830	HEMH_HUMAN	ferrochelatase	215					cellular response to dexamethasone stimulus (GO:0071549)|cholesterol metabolic process (GO:0008203)|detection of UV (GO:0009589)|erythrocyte differentiation (GO:0030218)|generation of precursor metabolites and energy (GO:0006091)|heme biosynthetic process (GO:0006783)|iron ion homeostasis (GO:0055072)|porphyrin-containing compound metabolic process (GO:0006778)|protoporphyrinogen IX metabolic process (GO:0046501)|regulation of eIF2 alpha phosphorylation by heme (GO:0010999)|regulation of gene expression (GO:0010468)|regulation of hemoglobin biosynthetic process (GO:0046984)|response to arsenic-containing substance (GO:0046685)|response to drug (GO:0042493)|response to ethanol (GO:0045471)|response to insecticide (GO:0017085)|response to lead ion (GO:0010288)|response to light stimulus (GO:0009416)|response to methylmercury (GO:0051597)|response to platinum ion (GO:0070541)|small molecule metabolic process (GO:0044281)|very-low-density lipoprotein particle assembly (GO:0034379)	mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)	2 iron, 2 sulfur cluster binding (GO:0051537)|ferrochelatase activity (GO:0004325)|ferrous iron binding (GO:0008198)|heme binding (GO:0020037)|iron-responsive element binding (GO:0030350)	p.R221W(1)		central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(5)|prostate(1)|upper_aerodigestive_tract(1)	15		Colorectal(73;0.227)				GTGGGCTTCCGTCCCACTTGA	0.458																																					p.R221W												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C661T	18						.						177.0	127.0	144.0					18																	55230168		2203	4300	6503	53381166	SO:0001583	missense	2235	exon6			D00726	CCDS11964.1, CCDS32836.1	18q21.2-q21.3	2010-05-11	2010-05-11		ENSG00000066926	ENSG00000066926	4.99.1.1		3647	protein-coding gene	gene with protein product	"""protoporphyria"""	612386	"""ferrochelatase (protoporphyria)"""			1838349	Standard	NM_001012515		Approved		uc002lgp.4	P22830	OTTHUMG00000132740	ENST00000262093.5:c.643C>T	18.37:g.55230168G>A	ENSP00000262093:p.Arg215Trp	Somatic		Capture	Illumina HiSeq	Phase_I	53381166	NM_001012515	A8KA72|Q8IXN1|Q8NAN0	Missense_Mutation	SNP	ENST00000262093.5	37	CCDS11964.1	.	.	.	.	.	.	.	.	.	.	G	12.30	1.896325	0.33442	.	.	ENSG00000066926	ENST00000262093;ENST00000382873	D;D	0.97352	-4.35;-4.35	5.88	2.19	0.27852	.	0.863268	0.10675	N	0.647056	D	0.93262	0.7853	N	0.25647	0.755	0.09310	N	1	D;D	0.62365	0.985;0.991	B;P	0.45099	0.408;0.469	D	0.86089	0.1549	10	0.37606	T	0.19	-6.7949	7.1416	0.25558	0.0:0.1406:0.4598:0.3997	.	215;221	P22830;P22830-2	HEMH_HUMAN;.	W	215;221	ENSP00000262093:R215W;ENSP00000372326:R221W	ENSP00000262093:R215W	R	-	1	2	FECH	53381166	0.157000	0.22836	0.001000	0.08648	0.178000	0.23041	1.555000	0.36277	0.135000	0.18707	0.655000	0.94253	CGG		0.458	FECH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256098.1		
EPB41L3	23136	broad.mit.edu	37	18	5397204	5397204	+	Silent	SNP	C	C	T	rs79015463	byFrequency	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr18:5397204C>T	ENST00000341928.2	-	18	3034	c.2694G>A	c.(2692-2694)acG>acA	p.T898T	EPB41L3_ENST00000400111.3_Silent_p.T676T|EPB41L3_ENST00000544123.1_Silent_p.T729T|EPB41L3_ENST00000540638.2_Silent_p.T676T|EPB41L3_ENST00000342933.3_Silent_p.T898T|EPB41L3_ENST00000427684.2_Silent_p.T195T|EPB41L3_ENST00000542652.2_5'UTR|EPB41L3_ENST00000542146.1_Silent_p.T203T	NM_012307.2	NP_036439.2	Q9Y2J2	E41L3_HUMAN	erythrocyte membrane protein band 4.1-like 3	898	C-terminal (CTD).				apoptotic process (GO:0006915)|cortical actin cytoskeleton organization (GO:0030866)|cortical cytoskeleton organization (GO:0030865)|cytoskeletal anchoring at plasma membrane (GO:0007016)|myelin maintenance (GO:0043217)|neuron projection morphogenesis (GO:0048812)|paranodal junction assembly (GO:0030913)|protein localization to juxtaparanode region of axon (GO:0071205)|protein localization to paranode region of axon (GO:0002175)|protein localization to plasma membrane (GO:0072659)|regulation of cell shape (GO:0008360)	axolemma (GO:0030673)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extrinsic component of membrane (GO:0019898)|juxtaparanode region of axon (GO:0044224)|paranode region of axon (GO:0033270)|plasma membrane (GO:0005886)	structural constituent of cytoskeleton (GO:0005200)	p.T898T(1)		breast(1)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(24)|lung(52)|ovary(5)|prostate(4)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	105						TAGCCCCCTCCGTCAAGGCAG	0.602													C|||	4	0.000798722	0.0	0.0	5008	,	,		18401	0.001		0.0	False		,,,				2504	0.0031				p.T898T												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G2694A	18						.						116.0	97.0	104.0					18																	5397204		2203	4300	6503	5387204	SO:0001819	synonymous_variant	23136	exon18			AB023204	CCDS11838.1, CCDS62381.1, CCDS62382.1	18p11.32	2006-06-28			ENSG00000082397	ENSG00000082397			3380	protein-coding gene	gene with protein product		605331				9828140, 9892180	Standard	NM_012307		Approved	DAL1, KIAA0987, 4.1B	uc002kmt.1	Q9Y2J2	OTTHUMG00000131562	ENST00000341928.2:c.2694G>A	18.37:g.5397204C>T		Somatic		Capture	Illumina HiSeq	Phase_I	5387204	NM_012307	B7Z4I5|F5GX05|O95713|Q9BRP5	Silent	SNP	ENST00000341928.2	37	CCDS11838.1																																																																																				0.602	EPB41L3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254424.1	NM_012307	
NARS	4677	broad.mit.edu	37	18	55270050	55270050	+	Silent	SNP	A	A	C			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr18:55270050A>C	ENST00000256854.5	-	12	1832	c.1377T>G	c.(1375-1377)acT>acG	p.T459T	NARS_ENST00000423481.2_Silent_p.T210T	NM_004539.3	NP_004530.1	O43776	SYNC_HUMAN	asparaginyl-tRNA synthetase	459					asparaginyl-tRNA aminoacylation (GO:0006421)|gene expression (GO:0010467)|tRNA aminoacylation for protein translation (GO:0006418)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	asparagine-tRNA ligase activity (GO:0004816)|ATP binding (GO:0005524)|nucleic acid binding (GO:0003676)	p.T459T(1)		breast(1)|endometrium(5)|large_intestine(5)|lung(8)|skin(1)	20		Colorectal(73;0.227)			L-Asparagine(DB00174)	TGACAGATTCAGTAAGACGGG	0.418																																					p.T459T												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.T1377G	18						.						79.0	70.0	73.0					18																	55270050		2203	4300	6503	53421048	SO:0001819	synonymous_variant	4677	exon12			D84273	CCDS32837.1	18q21.31	2014-05-06			ENSG00000134440	ENSG00000134440	6.1.1.22	"""Aminoacyl tRNA synthetases / Class II"""	7643	protein-coding gene	gene with protein product	"""asparagine tRNA ligase 1, cytoplasmic"""	108410				6836455, 9421509	Standard	NM_004539		Approved	NARS1	uc002lgs.2	O43776	OTTHUMG00000180125	ENST00000256854.5:c.1377T>G	18.37:g.55270050A>C		Somatic		Capture	Illumina HiSeq	Phase_I	53421048	NM_004539	B4DG16|Q53GU6	Silent	SNP	ENST00000256854.5	37	CCDS32837.1																																																																																				0.418	NARS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449872.2	NM_004539	
KIAA1468	57614	broad.mit.edu	37	18	59894589	59894589	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr18:59894589G>A	ENST00000398130.2	+	6	1158	c.926G>A	c.(925-927)cGg>cAg	p.R309Q	KIAA1468_ENST00000256858.6_Missense_Mutation_p.R309Q	NM_020854.3	NP_065905.2	Q9P260	K1468_HUMAN	KIAA1468	309								p.R309Q(1)|p.R309L(1)		autonomic_ganglia(1)|breast(4)|endometrium(4)|kidney(4)|large_intestine(7)|lung(20)|ovary(2)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	47		Colorectal(73;0.186)				CAACTCTACCGGGATTTTGGA	0.343																																					p.R309Q												.	.	2	Substitution - Missense(2)	large_intestine(1)|kidney(1)	c.G926A	18						.						87.0	85.0	85.0					18																	59894589		1844	4083	5927	58045569	SO:0001583	missense	57614	exon6			BC011992	CCDS11979.2	18q21.33	2005-11-03			ENSG00000134444	ENSG00000134444			29289	protein-coding gene	gene with protein product						11973628	Standard	NM_020854		Approved	HsT885, HsT3308, FLJ33841	uc002lil.3	Q9P260	OTTHUMG00000132780	ENST00000398130.2:c.926G>A	18.37:g.59894589G>A	ENSP00000381198:p.Arg309Gln	Somatic		Capture	Illumina HiSeq	Phase_I	58045569	NM_020854		Missense_Mutation	SNP	ENST00000398130.2	37	CCDS11979.2	.	.	.	.	.	.	.	.	.	.	G	36	5.616885	0.96649	.	.	ENSG00000134444	ENST00000398130;ENST00000256858	T;T	0.48522	0.81;0.81	5.75	5.75	0.90469	.	0.055575	0.64402	D	0.000001	T	0.72358	0.3450	M	0.79693	2.465	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.999	T	0.72243	-0.4350	9	.	.	.	-7.8131	19.9576	0.97228	0.0:0.0:1.0:0.0	.	309;309	Q9P260-2;Q9P260	.;K1468_HUMAN	Q	309	ENSP00000381198:R309Q;ENSP00000256858:R309Q	.	R	+	2	0	KIAA1468	58045569	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	9.578000	0.98200	2.720000	0.93068	0.557000	0.71058	CGG		0.343	KIAA1468-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256187.1	NM_020854	
CDH19	28513	broad.mit.edu	37	18	64172238	64172238	+	Silent	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr18:64172238C>T	ENST00000262150.2	-	12	2422	c.2130G>A	c.(2128-2130)ccG>ccA	p.P710P		NM_021153.3	NP_066976.1	Q96JQ0	PCD16_HUMAN	cadherin 19, type 2	0	Cadherin 7. {ECO:0000255|PROSITE- ProRule:PRU00043}.				branching involved in ureteric bud morphogenesis (GO:0001658)|calcium-dependent cell-cell adhesion (GO:0016339)|cochlea development (GO:0090102)|digestive tract development (GO:0048565)|heart morphogenesis (GO:0003007)|heterophilic cell-cell adhesion (GO:0007157)|hippo signaling (GO:0035329)|homophilic cell adhesion (GO:0007156)|neural tube development (GO:0021915)|neurogenesis (GO:0022008)|ossification involved in bone maturation (GO:0043931)|post-anal tail morphogenesis (GO:0036342)	apical part of cell (GO:0045177)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.P710P(1)		NS(1)|breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(13)|lung(22)|ovary(1)|prostate(3)|skin(7)	61		Esophageal squamous(42;0.0132)				GAGGGGCACACGGATCAGTAT	0.493																																					p.P710P												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G2130A	18						.						132.0	126.0	128.0					18																	64172238		2203	4300	6503	62323218	SO:0001819	synonymous_variant	28513	exon12			AJ007607	CCDS11994.1, CCDS59325.1	18q22.1	2010-01-26			ENSG00000071991	ENSG00000071991		"""Cadherins / Major cadherins"""	1758	protein-coding gene	gene with protein product		603016				10995570	Standard	NM_021153		Approved	CDH7	uc002lkc.2	Q9H159	OTTHUMG00000132802	ENST00000262150.2:c.2130G>A	18.37:g.64172238C>T		Somatic		Capture	Illumina HiSeq	Phase_I	62323218	NM_021153	O15098	Silent	SNP	ENST00000262150.2	37	CCDS11994.1																																																																																				0.493	CDH19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256219.1	NM_021153	
LAMA1	284217	broad.mit.edu	37	18	6966164	6966164	+	Silent	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr18:6966164G>A	ENST00000389658.3	-	49	7125	c.7032C>T	c.(7030-7032)taC>taT	p.Y2344Y		NM_005559.3	NP_005550.2	P25391	LAMA1_HUMAN	laminin, alpha 1	2344	Laminin G-like 2. {ECO:0000255|PROSITE- ProRule:PRU00122}.				axon guidance (GO:0007411)|branching involved in salivary gland morphogenesis (GO:0060445)|cell adhesion (GO:0007155)|cell surface receptor signaling pathway (GO:0007166)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|establishment of epithelial cell apical/basal polarity (GO:0045198)|extracellular matrix organization (GO:0030198)|morphogenesis of an epithelial sheet (GO:0002011)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of embryonic development (GO:0045995)|retinal blood vessel morphogenesis (GO:0061304)	basement membrane (GO:0005604)|cell-cell junction (GO:0005911)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|laminin-1 complex (GO:0005606)|laminin-3 complex (GO:0005608)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)|glycosphingolipid binding (GO:0043208)	p.Y2344Y(1)		NS(4)|breast(7)|central_nervous_system(3)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(49)|liver(1)|lung(71)|ovary(9)|pancreas(3)|prostate(5)|skin(11)|stomach(7)|upper_aerodigestive_tract(8)|urinary_tract(3)	205		Colorectal(10;0.172)				ATGAACCCAGGTAGAGAAGAA	0.448																																					p.Y2344Y												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C7032T	18						.						74.0	61.0	65.0					18																	6966164		2203	4300	6503	6956164	SO:0001819	synonymous_variant	284217	exon49			X58531	CCDS32787.1	18p11.3	2013-03-01			ENSG00000101680	ENSG00000101680		"""Laminins"""	6481	protein-coding gene	gene with protein product		150320		LAMA		2591971	Standard	NM_005559		Approved		uc002knm.3	P25391	OTTHUMG00000133478	ENST00000389658.3:c.7032C>T	18.37:g.6966164G>A		Somatic		Capture	Illumina HiSeq	Phase_I	6956164	NM_005559		Silent	SNP	ENST00000389658.3	37	CCDS32787.1																																																																																				0.448	LAMA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257369.1	NM_005559	
LAMA1	284217	broad.mit.edu	37	18	6974995	6974995	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr18:6974995G>A	ENST00000389658.3	-	46	6623	c.6530C>T	c.(6529-6531)gCc>gTc	p.A2177V	RN7SL537P_ENST00000584392.1_RNA	NM_005559.3	NP_005550.2	P25391	LAMA1_HUMAN	laminin, alpha 1	2177	Laminin G-like 1. {ECO:0000255|PROSITE- ProRule:PRU00122}.				axon guidance (GO:0007411)|branching involved in salivary gland morphogenesis (GO:0060445)|cell adhesion (GO:0007155)|cell surface receptor signaling pathway (GO:0007166)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|establishment of epithelial cell apical/basal polarity (GO:0045198)|extracellular matrix organization (GO:0030198)|morphogenesis of an epithelial sheet (GO:0002011)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of embryonic development (GO:0045995)|retinal blood vessel morphogenesis (GO:0061304)	basement membrane (GO:0005604)|cell-cell junction (GO:0005911)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|laminin-1 complex (GO:0005606)|laminin-3 complex (GO:0005608)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)|glycosphingolipid binding (GO:0043208)	p.A2177V(1)		NS(4)|breast(7)|central_nervous_system(3)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(49)|liver(1)|lung(71)|ovary(9)|pancreas(3)|prostate(5)|skin(11)|stomach(7)|upper_aerodigestive_tract(8)|urinary_tract(3)	205		Colorectal(10;0.172)				CCACAGGAAGGCCACTCTCCC	0.557																																					p.A2177V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C6530T	18						.						63.0	56.0	58.0					18																	6974995		2203	4300	6503	6964995	SO:0001583	missense	284217	exon46			X58531	CCDS32787.1	18p11.3	2013-03-01			ENSG00000101680	ENSG00000101680		"""Laminins"""	6481	protein-coding gene	gene with protein product		150320		LAMA		2591971	Standard	NM_005559		Approved		uc002knm.3	P25391	OTTHUMG00000133478	ENST00000389658.3:c.6530C>T	18.37:g.6974995G>A	ENSP00000374309:p.Ala2177Val	Somatic		Capture	Illumina HiSeq	Phase_I	6964995	NM_005559		Missense_Mutation	SNP	ENST00000389658.3	37	CCDS32787.1	.	.	.	.	.	.	.	.	.	.	G	24.9	4.579123	0.86645	.	.	ENSG00000101680	ENST00000389658	T	0.75821	-0.97	5.38	4.5	0.54988	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Laminin G domain (2);Laminin G, subdomain 1 (1);	0.245531	0.32987	N	0.005415	T	0.67306	0.2879	N	0.17248	0.465	0.36854	D	0.888068	P	0.40970	0.734	P	0.49301	0.606	T	0.67325	-0.5699	10	0.16896	T	0.51	.	14.4821	0.67590	0.0715:0.0:0.9285:0.0	.	2177	P25391	LAMA1_HUMAN	V	2177	ENSP00000374309:A2177V	ENSP00000374309:A2177V	A	-	2	0	LAMA1	6964995	1.000000	0.71417	1.000000	0.80357	0.843000	0.47879	4.273000	0.58914	1.398000	0.46701	0.643000	0.83706	GCC		0.557	LAMA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257369.1	NM_005559	
DOK6	220164	broad.mit.edu	37	18	67068504	67068504	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr18:67068504A>G	ENST00000382713.5	+	1	214	c.24A>G	c.(22-24)atA>atG	p.I8M		NM_152721.5	NP_689934.2	Q6PKX4	DOK6_HUMAN	docking protein 6	8	PH.							p.I8M(1)		central_nervous_system(1)|cervix(1)|endometrium(1)|large_intestine(6)|lung(6)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	20		Colorectal(73;0.083)|Esophageal squamous(42;0.131)				TTAACGACATAGTCAAGCAGG	0.687																																					p.I8M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A24G	18						.						45.0	38.0	41.0					18																	67068504		2201	4300	6501	65219484	SO:0001583	missense	220164	exon1			AK057795	CCDS32841.1	18q22.2	2013-01-10	2005-01-18	2005-01-18		ENSG00000206052		"""Pleckstrin homology (PH) domain containing"""	28301	protein-coding gene	gene with protein product		611402	"""docking protein 5-like"""	DOK5L		15286081	Standard	NM_152721		Approved	MGC20785, HsT3226	uc002lkl.3	Q6PKX4		ENST00000382713.5:c.24A>G	18.37:g.67068504A>G	ENSP00000372160:p.Ile8Met	Somatic		Capture	Illumina HiSeq	Phase_I	65219484	NM_152721	A6NNG3|Q4V9S3|Q8WUZ8|Q96HI2|Q96LU2	Missense_Mutation	SNP	ENST00000382713.5	37	CCDS32841.1	.	.	.	.	.	.	.	.	.	.	A	19.44	3.828765	0.71258	.	.	ENSG00000206052	ENST00000382713	T	0.76578	-1.03	4.08	-1.67	0.08238	Pleckstrin homology-type (1);Pleckstrin homology domain (2);	0.062472	0.64402	D	0.000006	T	0.78972	0.4368	L	0.54323	1.7	0.39237	D	0.963783	D	0.89917	1.0	D	0.80764	0.994	T	0.75393	-0.3333	10	0.72032	D	0.01	.	2.965	0.05905	0.3544:0.4185:0.0904:0.1367	.	8	Q6PKX4	DOK6_HUMAN	M	8	ENSP00000372160:I8M	ENSP00000372160:I8M	I	+	3	3	DOK6	65219484	0.996000	0.38824	1.000000	0.80357	0.999000	0.98932	0.349000	0.20055	0.068000	0.16574	0.533000	0.62120	ATA		0.687	DOK6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442969.1	NM_152721	
LAMA1	284217	broad.mit.edu	37	18	7080337	7080337	+	Missense_Mutation	SNP	C	C	T	rs147676957		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr18:7080337C>T	ENST00000389658.3	-	2	274	c.181G>A	c.(181-183)Gtc>Atc	p.V61I	RP11-76K13.3_ENST00000581502.1_RNA	NM_005559.3	NP_005550.2	P25391	LAMA1_HUMAN	laminin, alpha 1	61	Laminin N-terminal. {ECO:0000255|PROSITE- ProRule:PRU00466}.				axon guidance (GO:0007411)|branching involved in salivary gland morphogenesis (GO:0060445)|cell adhesion (GO:0007155)|cell surface receptor signaling pathway (GO:0007166)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|establishment of epithelial cell apical/basal polarity (GO:0045198)|extracellular matrix organization (GO:0030198)|morphogenesis of an epithelial sheet (GO:0002011)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of embryonic development (GO:0045995)|retinal blood vessel morphogenesis (GO:0061304)	basement membrane (GO:0005604)|cell-cell junction (GO:0005911)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|laminin-1 complex (GO:0005606)|laminin-3 complex (GO:0005608)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)|glycosphingolipid binding (GO:0043208)	p.V61I(1)		NS(4)|breast(7)|central_nervous_system(3)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(49)|liver(1)|lung(71)|ovary(9)|pancreas(3)|prostate(5)|skin(11)|stomach(7)|upper_aerodigestive_tract(8)|urinary_tract(3)	205		Colorectal(10;0.172)				GGGTTTCGGACGGGCCGACCT	0.547													C|||	1	0.000199681	0.0	0.0014	5008	,	,		17068	0.0		0.0	False		,,,				2504	0.0				p.V61I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G181A	18						.	C	ILE/VAL	2,4404	4.2+/-10.8	0,2,2201	84.0	84.0	84.0		181	-1.9	0.0	18	dbSNP_134	84	15,8585	10.5+/-38.8	0,15,4285	yes	missense	LAMA1	NM_005559.3	29	0,17,6486	TT,TC,CC		0.1744,0.0454,0.1307	benign	61/3076	7080337	17,12989	2203	4300	6503	7070337	SO:0001583	missense	284217	exon2			X58531	CCDS32787.1	18p11.3	2013-03-01			ENSG00000101680	ENSG00000101680		"""Laminins"""	6481	protein-coding gene	gene with protein product		150320		LAMA		2591971	Standard	NM_005559		Approved		uc002knm.3	P25391	OTTHUMG00000133478	ENST00000389658.3:c.181G>A	18.37:g.7080337C>T	ENSP00000374309:p.Val61Ile	Somatic		Capture	Illumina HiSeq	Phase_I	7070337	NM_005559		Missense_Mutation	SNP	ENST00000389658.3	37	CCDS32787.1	1	4.578754578754579E-4	0	0.0	1	0.0027624309392265192	0	0.0	0	0.0	C	6.934	0.542140	0.13250	4.54E-4	0.001744	ENSG00000101680	ENST00000389658	T	0.17854	2.25	5.68	-1.86	0.07760	Laminin, N-terminal (3);	0.529728	0.17841	N	0.160205	T	0.07863	0.0197	L	0.27053	0.805	0.09310	N	1	B	0.20261	0.043	B	0.24974	0.057	T	0.38178	-0.9673	10	0.09843	T	0.71	.	3.1497	0.06484	0.0912:0.3068:0.3406:0.2614	.	61	P25391	LAMA1_HUMAN	I	61	ENSP00000374309:V61I	ENSP00000374309:V61I	V	-	1	0	LAMA1	7070337	0.008000	0.16893	0.000000	0.03702	0.095000	0.18619	0.129000	0.15830	-0.421000	0.07416	0.650000	0.86243	GTC		0.547	LAMA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257369.1	NM_005559	
CNDP2	55748	broad.mit.edu	37	18	72173141	72173141	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr18:72173141G>A	ENST00000324262.4	+	4	578	c.262G>A	c.(262-264)Gac>Aac	p.D88N	CNDP2_ENST00000579847.1_Missense_Mutation_p.D88N|CNDP2_ENST00000324301.8_Intron	NM_018235.2	NP_060705.2	Q96KP4	CNDP2_HUMAN	CNDP dipeptidase 2 (metallopeptidase M20 family)	88					cellular nitrogen compound metabolic process (GO:0034641)|glutathione biosynthetic process (GO:0006750)|glutathione derivative biosynthetic process (GO:1901687)|small molecule metabolic process (GO:0044281)|sulfur amino acid metabolic process (GO:0000096)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	carboxypeptidase activity (GO:0004180)|dipeptidase activity (GO:0016805)|metal ion binding (GO:0046872)|metallopeptidase activity (GO:0008237)|tripeptidase activity (GO:0034701)	p.D88N(1)		breast(1)|cervix(1)|endometrium(3)|large_intestine(7)|lung(5)|ovary(2)|skin(2)|stomach(3)	24		Esophageal squamous(42;0.131)|Prostate(75;0.173)		BRCA - Breast invasive adenocarcinoma(31;0.22)		GCTGGGCTCCGACCCACAGAA	0.612																																					p.D88N												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G262A	18						.						53.0	51.0	52.0					18																	72173141		2203	4300	6503	70324121	SO:0001583	missense	55748	exon4			AK001692	CCDS12006.1, CCDS54190.1	18q22.3	2014-07-14	2004-07-12		ENSG00000133313	ENSG00000133313	3.4.13.18		24437	protein-coding gene	gene with protein product	"""cytosolic nonspecific dipeptidase"""	169800	"""peptidase A"""	PEPA		12473676	Standard	NM_018235		Approved	FLJ10830, CN2, HsT2298, CPGL	uc002llm.2	Q96KP4	OTTHUMG00000132853	ENST00000324262.4:c.262G>A	18.37:g.72173141G>A	ENSP00000325548:p.Asp88Asn	Somatic		Capture	Illumina HiSeq	Phase_I	70324121	NM_018235	B3KUG4|Q8WY59|Q9BQ94|Q9NVB4	Missense_Mutation	SNP	ENST00000324262.4	37	CCDS12006.1	.	.	.	.	.	.	.	.	.	.	G	10.95	1.496041	0.26774	.	.	ENSG00000133313	ENST00000324262	T	0.08193	3.12	5.39	4.52	0.55395	.	0.146293	0.64402	N	0.000011	T	0.12603	0.0306	M	0.72894	2.215	0.80722	D	1	B;B	0.26318	0.146;0.146	B;B	0.19946	0.027;0.017	T	0.01839	-1.1263	10	0.56958	D	0.05	-0.0173	13.7793	0.63073	0.0744:0.0:0.9256:0.0	.	88;88	B4DV28;Q96KP4	.;CNDP2_HUMAN	N	88	ENSP00000325548:D88N	ENSP00000325548:D88N	D	+	1	0	CNDP2	70324121	1.000000	0.71417	0.011000	0.14972	0.014000	0.08584	6.515000	0.73751	1.281000	0.44480	0.557000	0.71058	GAC		0.612	CNDP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256327.1	NM_018235	
ZNF407	55628	broad.mit.edu	37	18	72775188	72775188	+	Silent	SNP	G	G	A	rs199635552		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr18:72775188G>A	ENST00000299687.5	+	8	5511	c.5511G>A	c.(5509-5511)gcG>gcA	p.A1837A		NM_017757.2	NP_060227.2	Q9C0G0	ZN407_HUMAN	zinc finger protein 407	1837					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)	p.A1837A(1)		central_nervous_system(1)|endometrium(6)|kidney(7)|large_intestine(21)|lung(23)|ovary(4)|prostate(3)|upper_aerodigestive_tract(2)	67		Esophageal squamous(42;0.131)|Prostate(75;0.173)		BRCA - Breast invasive adenocarcinoma(31;0.184)		TCACCGCGGCGGCCTTGGCAG	0.622													G|||	1	0.000199681	0.0	0.0	5008	,	,		15697	0.001		0.0	False		,,,				2504	0.0				p.A1837A												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G5511A	18						.						87.0	101.0	96.0					18																	72775188		2063	4201	6264	70904176	SO:0001819	synonymous_variant	55628	exon8			AB051490	CCDS45885.1, CCDS54191.1, CCDS58634.1	18q23	2013-01-08			ENSG00000215421	ENSG00000215421		"""Zinc fingers, C2H2-type"""	19904	protein-coding gene	gene with protein product		615894				11214970	Standard	NM_017757		Approved	FLJ20307, FLJ13839, KIAA1703	uc002llw.2	Q9C0G0		ENST00000299687.5:c.5511G>A	18.37:g.72775188G>A		Somatic		Capture	Illumina HiSeq	Phase_I	70904176	NM_017757	B5MD54|Q96MY0|Q9H8A1|Q9NXD4|Q9NXD7	Silent	SNP	ENST00000299687.5	37	CCDS45885.1																																																																																				0.622	ZNF407-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444903.1	NM_017757	
ZNF236	7776	broad.mit.edu	37	18	74592156	74592156	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr18:74592156G>A	ENST00000253159.8	+	8	1264	c.1066G>A	c.(1066-1068)Gac>Aac	p.D356N	ZNF236_ENST00000320610.9_Missense_Mutation_p.D358N	NM_007345.3	NP_031371.3	Q9UL36	ZN236_HUMAN	zinc finger protein 236	356					cellular response to glucose stimulus (GO:0071333)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.D356N(2)		NS(1)|breast(2)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(14)|lung(43)|ovary(7)|pancreas(1)|prostate(6)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	94		Prostate(75;0.0405)|Esophageal squamous(42;0.129)|Melanoma(33;0.132)		OV - Ovarian serous cystadenocarcinoma(15;4.36e-06)|BRCA - Breast invasive adenocarcinoma(31;0.0686)		GGCGGTGAGCGACGTCATCCA	0.627																																					p.D356N												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G1066A	18						.						43.0	48.0	46.0					18																	74592156		2011	4160	6171	72721144	SO:0001583	missense	7776	exon8			AF085243	CCDS42447.1	18q22-q23	2013-01-08				ENSG00000130856		"""Zinc fingers, C2H2-type"""	13028	protein-coding gene	gene with protein product		604760				10458916	Standard	NM_007345		Approved		uc002lmi.3	Q9UL36		ENST00000253159.8:c.1066G>A	18.37:g.74592156G>A	ENSP00000253159:p.Asp356Asn	Somatic		Capture	Illumina HiSeq	Phase_I	72721144	NM_007345	B2RTX9|Q9UL37	Missense_Mutation	SNP	ENST00000253159.8	37	CCDS42447.1	.	.	.	.	.	.	.	.	.	.	g	18.11	3.550209	0.65311	.	.	ENSG00000130856	ENST00000253159;ENST00000543926;ENST00000320610	T;T	0.11063	2.81;2.97	5.27	4.4	0.53042	.	0.057281	0.64402	N	0.000003	T	0.30603	0.0770	M	0.69823	2.125	0.42380	D	0.992481	D;D	0.89917	1.0;1.0	D;D	0.83275	0.974;0.996	T	0.03184	-1.1063	10	0.32370	T	0.25	.	14.1434	0.65334	0.0726:0.0:0.9274:0.0	.	356;356	Q9NWI2;Q9UL36	.;ZN236_HUMAN	N	356	ENSP00000253159:D356N;ENSP00000444524:D356N	ENSP00000253159:D356N	D	+	1	0	ZNF236	72721144	1.000000	0.71417	0.057000	0.19452	0.279000	0.26890	7.378000	0.79679	1.232000	0.43678	-0.224000	0.12420	GAC		0.627	ZNF236-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000445776.1		
ATP9B	374868	broad.mit.edu	37	18	76856576	76856576	+	Nonsense_Mutation	SNP	C	C	T	rs376702405		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr18:76856576C>T	ENST00000426216.2	+	2	237	c.220C>T	c.(220-222)Cga>Tga	p.R74*	ATP9B_ENST00000307671.7_Nonsense_Mutation_p.R74*|ATP9B_ENST00000591464.1_3'UTR|ATP9B_ENST00000458297.2_Nonsense_Mutation_p.R22*|ATP9B_ENST00000586722.1_Nonsense_Mutation_p.R74*	NM_198531.3	NP_940933.3	O43861	ATP9B_HUMAN	ATPase, class II, type 9B	74					establishment of protein localization to Golgi (GO:0072600)|phospholipid translocation (GO:0045332)	integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)|trans-Golgi network (GO:0005802)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)	p.R74*(1)		NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(15)|ovary(3)|prostate(1)|skin(2)|stomach(1)	38		Esophageal squamous(42;0.018)|Melanoma(33;0.0964)|Prostate(75;0.171)		OV - Ovarian serous cystadenocarcinoma(15;1.44e-07)|BRCA - Breast invasive adenocarcinoma(31;0.0405)		CACCTTACCACGAGCCAGGAT	0.453																																					p.R74X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.C220T	18						.	C	stop/ARG	0,4406		0,0,2203	208.0	172.0	184.0		220	4.0	0.0	18		184	1,8599	1.2+/-3.3	0,1,4299	no	stop-gained	ATP9B	NM_198531.3		0,1,6502	TT,TC,CC		0.0116,0.0,0.0077		74/1148	76856576	1,13005	2203	4300	6503	74957564	SO:0001587	stop_gained	374868	exon2			R51412	CCDS12014.1	18q23	2010-04-20	2007-09-19		ENSG00000166377	ENSG00000166377		"""ATPases / P-type"""	13541	protein-coding gene	gene with protein product		614446	"""ATPase, Class II, type 9B"""			9548971, 11015572	Standard	NM_198531		Approved	ATPIIB	uc002lmx.3	O43861	OTTHUMG00000132898	ENST00000426216.2:c.220C>T	18.37:g.76856576C>T	ENSP00000398076:p.Arg74*	Somatic		Capture	Illumina HiSeq	Phase_I	74957564	NM_198531	O60872|Q08AD8|Q08AD9	Nonsense_Mutation	SNP	ENST00000426216.2	37	CCDS12014.1	.	.	.	.	.	.	.	.	.	.	C	18.86	3.713615	0.68730	0.0	1.16E-4	ENSG00000166377	ENST00000426216;ENST00000307671;ENST00000458297	.	.	.	5.03	4.02	0.46733	.	0.074441	0.50627	D	0.000109	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.07813	T	0.8	.	10.6409	0.45592	0.422:0.578:0.0:0.0	.	.	.	.	X	74;74;22	.	ENSP00000304500:R74X	R	+	1	2	ATP9B	74957564	0.995000	0.38212	0.041000	0.18516	0.016000	0.09150	2.248000	0.43160	2.511000	0.84671	0.563000	0.77884	CGA		0.453	ATP9B-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256402.3	NM_198531	
ATP9B	374868	broad.mit.edu	37	18	77037137	77037137	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr18:77037137G>A	ENST00000426216.2	+	13	1369	c.1352G>A	c.(1351-1353)cGg>cAg	p.R451Q	ATP9B_ENST00000307671.7_Missense_Mutation_p.R451Q	NM_198531.3	NP_940933.3	O43861	ATP9B_HUMAN	ATPase, class II, type 9B	451					establishment of protein localization to Golgi (GO:0072600)|phospholipid translocation (GO:0045332)	integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)|trans-Golgi network (GO:0005802)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)	p.R451Q(1)		NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(15)|ovary(3)|prostate(1)|skin(2)|stomach(1)	38		Esophageal squamous(42;0.018)|Melanoma(33;0.0964)|Prostate(75;0.171)		OV - Ovarian serous cystadenocarcinoma(15;1.44e-07)|BRCA - Breast invasive adenocarcinoma(31;0.0405)		ACGGTCGTTCGGACCAGCACT	0.473																																					p.R451Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1352A	18						.						177.0	158.0	164.0					18																	77037137		2203	4300	6503	75138125	SO:0001583	missense	374868	exon13			R51412	CCDS12014.1	18q23	2010-04-20	2007-09-19		ENSG00000166377	ENSG00000166377		"""ATPases / P-type"""	13541	protein-coding gene	gene with protein product		614446	"""ATPase, Class II, type 9B"""			9548971, 11015572	Standard	NM_198531		Approved	ATPIIB	uc002lmx.3	O43861	OTTHUMG00000132898	ENST00000426216.2:c.1352G>A	18.37:g.77037137G>A	ENSP00000398076:p.Arg451Gln	Somatic		Capture	Illumina HiSeq	Phase_I	75138125	NM_198531	O60872|Q08AD8|Q08AD9	Missense_Mutation	SNP	ENST00000426216.2	37	CCDS12014.1	.	.	.	.	.	.	.	.	.	.	G	34	5.410787	0.96072	.	.	ENSG00000166377	ENST00000426216;ENST00000307671	D;D	0.91011	-2.77;-2.77	5.4	5.4	0.78164	.	0.000000	0.85682	D	0.000000	D	0.95436	0.8518	M	0.82323	2.585	0.80722	D	1	D;D	0.76494	0.999;0.999	P;D	0.64237	0.84;0.923	D	0.95672	0.8724	10	0.87932	D	0	.	19.5384	0.95264	0.0:0.0:1.0:0.0	.	451;451	O43861;O43861-2	ATP9B_HUMAN;.	Q	451	ENSP00000398076:R451Q;ENSP00000304500:R451Q	ENSP00000304500:R451Q	R	+	2	0	ATP9B	75138125	1.000000	0.71417	0.994000	0.49952	0.897000	0.52465	9.053000	0.93860	2.687000	0.91594	0.655000	0.94253	CGG		0.473	ATP9B-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256402.3	NM_198531	
DSG3	1830	broad.mit.edu	37	18	29044177	29044177	+	Frame_Shift_Del	DEL	C	C	-			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	-	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr18:29044177delC	ENST00000257189.4	+	9	1186	c.1103delC	c.(1102-1104)accfs	p.T368fs		NM_001944.2	NP_001935.2	P32926	DSG3_HUMAN	desmoglein 3	368	Cadherin 3. {ECO:0000255|PROSITE- ProRule:PRU00043}.				apoptotic process (GO:0006915)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|homophilic cell adhesion (GO:0007156)	cell junction (GO:0030054)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.P369fs*6(1)		breast(1)|central_nervous_system(2)|cervix(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(28)|ovary(4)|prostate(1)|skin(8)|upper_aerodigestive_tract(1)	62			OV - Ovarian serous cystadenocarcinoma(10;0.00504)			GTTCAGTCAACCCCAGTCACA	0.373																																					p.T368fs												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.1103delC	18						.						94.0	89.0	90.0					18																	29044177		2203	4300	6503	27298175	SO:0001589	frameshift_variant	1830	exon9			M76482	CCDS11898.1	18q12.1	2010-06-24	2010-06-24		ENSG00000134757	ENSG00000134757		"""Cadherins / Major cadherins"""	3050	protein-coding gene	gene with protein product	"""pemphigus vulgaris antigen"""	169615	"""desmoglein 3 (pemphigus vulgaris antigen)"""			1601426	Standard	NM_001944		Approved	CDHF6	uc002kws.3	P32926	OTTHUMG00000131985	ENST00000257189.4:c.1103delC	18.37:g.29044177delC	ENSP00000257189:p.Thr368fs	Somatic		Capture	Illumina HiSeq	Phase_I	27298175	NM_001944	A8K2V2	Frame_Shift_Del	DEL	ENST00000257189.4	37	CCDS11898.1																																																																																				0.373	DSG3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254949.1	NM_001944	
CTDP1	9150	broad.mit.edu	37	18	77477579	77477579	+	Missense_Mutation	SNP	G	G	A	rs372703325		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr18:77477579G>A	ENST00000299543.7	+	9	2260	c.2113G>A	c.(2113-2115)Gtg>Atg	p.V705M	CTDP1_ENST00000075430.7_Missense_Mutation_p.V705M	NM_001202504.1|NM_004715.4	NP_001189433.1|NP_004706.3	Q9Y5B0	CTDP1_HUMAN	CTD (carboxy-terminal domain, RNA polymerase II, polypeptide A) phosphatase, subunit 1	705	BRCT. {ECO:0000255|PROSITE- ProRule:PRU00033}.				exit from mitosis (GO:0010458)|gene expression (GO:0010467)|positive regulation of viral transcription (GO:0050434)|protein dephosphorylation (GO:0006470)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|viral process (GO:0016032)	actin cytoskeleton (GO:0015629)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|midbody (GO:0030496)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle (GO:0005819)|spindle midzone (GO:0051233)|spindle pole (GO:0000922)	CTD phosphatase activity (GO:0008420)|DNA-directed RNA polymerase activity (GO:0003899)	p.V705M(1)		autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(14)|ovary(2)|prostate(2)|urinary_tract(1)	35		Esophageal squamous(42;0.0157)|Melanoma(33;0.144)		OV - Ovarian serous cystadenocarcinoma(15;5.2e-06)|BRCA - Breast invasive adenocarcinoma(31;0.0277)		ACACCTGCACGTGGTCAACCC	0.657																																					p.V705M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2113A	18						.	G	MET/VAL,MET/VAL,MET/VAL	0,4406		0,0,2203	84.0	83.0	83.0		1756,2113,2113	5.1	1.0	18		83	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense,missense	CTDP1	NM_001202504.1,NM_004715.4,NM_048368.3	21,21,21	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging,probably-damaging,probably-damaging	586/843,705/962,705/868	77477579	1,13005	2203	4300	6503	75578567	SO:0001583	missense	9150	exon9			AF081287	CCDS12017.1, CCDS12018.1, CCDS74239.1	18q23	2014-09-17			ENSG00000060069	ENSG00000060069		"""Serine/threonine phosphatases / CTD aspartate-based phosphatases"""	2498	protein-coding gene	gene with protein product		604927				9405607, 9765293	Standard	NM_004715		Approved	FCP1	uc002lnh.2	Q9Y5B0	OTTHUMG00000132920	ENST00000299543.7:c.2113G>A	18.37:g.77477579G>A	ENSP00000299543:p.Val705Met	Somatic		Capture	Illumina HiSeq	Phase_I	75578567	NM_048368	A8MY97|Q7Z644|Q96BZ1|Q9Y6F5	Missense_Mutation	SNP	ENST00000299543.7	37	CCDS12017.1	.	.	.	.	.	.	.	.	.	.	G	19.12	3.765549	0.69878	0.0	1.16E-4	ENSG00000060069	ENST00000299543;ENST00000075430	D;D	0.86297	-2.1;-2.1	5.09	5.09	0.68999	BRCT (3);	0.058193	0.64402	D	0.000002	D	0.92071	0.7487	M	0.77406	2.37	0.54753	D	0.999983	D;D;D	0.89917	0.999;1.0;1.0	D;D;D	0.76071	0.961;0.983;0.987	D	0.91982	0.5595	10	0.56958	D	0.05	-46.7263	9.3073	0.37883	0.1598:0.0:0.8402:0.0	.	586;705;705	Q9Y5B0-3;Q9Y5B0-4;Q9Y5B0	.;.;CTDP1_HUMAN	M	705	ENSP00000299543:V705M;ENSP00000075430:V705M	ENSP00000075430:V705M	V	+	1	0	CTDP1	75578567	1.000000	0.71417	0.981000	0.43875	0.793000	0.44817	3.842000	0.55858	2.355000	0.79922	0.563000	0.77884	GTG		0.657	CTDP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256432.1	NM_004715	
ANGPTL6	83854	broad.mit.edu	37	19	10204056	10204056	+	Silent	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr19:10204056G>A	ENST00000253109.4	-	5	1429	c.1191C>T	c.(1189-1191)agC>agT	p.S397S	ANGPTL6_ENST00000589181.1_Silent_p.S357S|ANGPTL6_ENST00000592641.1_Silent_p.S397S	NM_031917.2	NP_114123.2	Q8NI99	ANGL6_HUMAN	angiopoietin-like 6	397	Fibrinogen C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00739}.				angiogenesis (GO:0001525)|cell differentiation (GO:0030154)	extracellular vesicular exosome (GO:0070062)|secretory granule (GO:0030141)		p.S397S(1)		endometrium(1)|kidney(1)|large_intestine(2)|lung(6)|ovary(1)|pancreas(1)	12			OV - Ovarian serous cystadenocarcinoma(20;3.58e-08)|Epithelial(33;2.5e-05)|all cancers(31;5.96e-05)			TATCCACGGTGCTGAAGGGCT	0.562											OREG0006893	type=TRANSCRIPTION FACTOR BINDING SITE|Gene=FLJ11286|TFbs=REST|Dataset=NRSF/REST ChIPSeq sites|EvidenceSubtype=Chromatin immunoprecipitation with tag sequencing (ChIP-TS)																									p.S397S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1191T	19						.						119.0	106.0	110.0					19																	10204056		2203	4300	6503	10065056	SO:0001819	synonymous_variant	83854	exon5			AB054064	CCDS12224.1	19p13.2	2013-02-06				ENSG00000130812		"""Fibrinogen C domain containing"""	23140	protein-coding gene	gene with protein product	"""angiopoietin-related protein 5"""	609336				12871997	Standard	NM_031917		Approved	ARP5, AGF	uc002mmy.1	Q8NI99		ENST00000253109.4:c.1191C>T	19.37:g.10204056G>A		Somatic	662	Capture	Illumina HiSeq	Phase_I	10065056	NM_031917	A5PKV7|Q9BZZ0	Silent	SNP	ENST00000253109.4	37	CCDS12224.1																																																																																				0.562	ANGPTL6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451142.1	NM_031917	
DOCK6	57572	broad.mit.edu	37	19	11347514	11347514	+	Silent	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr19:11347514G>A	ENST00000294618.7	-	19	2126	c.2115C>T	c.(2113-2115)ggC>ggT	p.G705G	RN7SL298P_ENST00000581369.1_RNA|C19orf80_ENST00000252453.8_5'Flank|C19orf80_ENST00000591200.1_5'Flank|DOCK6_ENST00000319867.7_Silent_p.G9G	NM_020812.3	NP_065863.2	Q96HP0	DOCK6_HUMAN	dedicator of cytokinesis 6	705	DHR-1.				blood coagulation (GO:0007596)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	guanyl-nucleotide exchange factor activity (GO:0005085)	p.G705G(1)		breast(1)|central_nervous_system(1)|endometrium(11)|large_intestine(8)|liver(2)|lung(9)|ovary(4)|prostate(1)|skin(1)|urinary_tract(1)	39						CACTGAACACGCCCTTGTGAC	0.677																																					p.G705G												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C2115T	19						.						25.0	32.0	30.0					19																	11347514		2030	4043	6073	11208514	SO:0001819	synonymous_variant	57572	exon19				CCDS45975.1	19p13.2	2011-08-04			ENSG00000130158	ENSG00000130158			19189	protein-coding gene	gene with protein product		614194				12432077	Standard	NM_020812		Approved	KIAA1395, ZIR1	uc002mqs.5	Q96HP0		ENST00000294618.7:c.2115C>T	19.37:g.11347514G>A		Somatic		Capture	Illumina HiSeq	Phase_I	11208514	NM_020812	A6H8X5|Q7Z7P4|Q9P2F2	Silent	SNP	ENST00000294618.7	37	CCDS45975.1																																																																																				0.677	DOCK6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453155.1	NM_020812	
RAB3D	9545	broad.mit.edu	37	19	11446143	11446143	+	Missense_Mutation	SNP	C	C	T	rs145958698	byFrequency	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr19:11446143C>T	ENST00000222120.3	-	4	712	c.452G>A	c.(451-453)cGg>cAg	p.R151Q	RAB3D_ENST00000589655.1_Missense_Mutation_p.R151Q	NM_004283.3	NP_004274.1	O95716	RAB3D_HUMAN	RAB3D, member RAS oncogene family	151					exocytosis (GO:0006887)|GTP catabolic process (GO:0006184)|peptidyl-cysteine methylation (GO:0018125)|protein transport (GO:0015031)|regulation of exocytosis (GO:0017157)|small GTPase mediated signal transduction (GO:0007264)	extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)|transport vesicle (GO:0030133)|zymogen granule (GO:0042588)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|myosin V binding (GO:0031489)	p.R151Q(1)		cervix(1)|endometrium(3)|kidney(1)|large_intestine(3)|liver(1)|lung(3)|ovary(2)	14						GGCGAGCCTCCGGCCATCCTC	0.607													C|||	3	0.000599042	0.0008	0.0	5008	,	,		20260	0.001		0.0	False		,,,				2504	0.001				p.R151Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G452A	19						.	C	GLN/ARG	3,4403	6.2+/-15.9	0,3,2200	73.0	60.0	64.0		452	-4.9	0.9	19	dbSNP_134	64	0,8600		0,0,4300	yes	missense	RAB3D	NM_004283.3	43	0,3,6500	TT,TC,CC		0.0,0.0681,0.0231	benign	151/220	11446143	3,13003	2203	4300	6503	11307143	SO:0001583	missense	9545	exon4			AF081353	CCDS12257.1	19p13.2	2012-10-02			ENSG00000105514	ENSG00000105514		"""RAB, member RAS oncogene"""	9779	protein-coding gene	gene with protein product	"""Rab3D upregulated with myeloid differentiation"", ""glioblastoma overexpressed"""	604350		GOV		10023084, 10072586	Standard	NM_004283		Approved	RAB16, D2-2, RAD3D	uc002mqx.3	O95716	OTTHUMG00000180835	ENST00000222120.3:c.452G>A	19.37:g.11446143C>T	ENSP00000222120:p.Arg151Gln	Somatic		Capture	Illumina HiSeq	Phase_I	11307143	NM_004283		Missense_Mutation	SNP	ENST00000222120.3	37	CCDS12257.1	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	C	3.925	-0.017258	0.07681	6.81E-4	0.0	ENSG00000105514	ENST00000222120	T	0.76186	-1.0	4.62	-4.93	0.03066	Small GTP-binding protein domain (1);	0.591766	0.17639	N	0.167102	T	0.38558	0.1045	N	0.01134	-0.995	0.36253	D	0.854043	B	0.06786	0.001	B	0.06405	0.002	T	0.12734	-1.0536	10	0.22706	T	0.39	.	12.5284	0.56100	0.0:0.3557:0.0:0.6443	.	151	O95716	RAB3D_HUMAN	Q	151	ENSP00000222120:R151Q	ENSP00000222120:R151Q	R	-	2	0	RAB3D	11307143	0.000000	0.05858	0.884000	0.34674	0.732000	0.41865	-1.327000	0.02682	-0.651000	0.05415	0.448000	0.29417	CGG		0.607	RAB3D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453211.1	NM_004283	
PRKCSH	5589	broad.mit.edu	37	19	11559765	11559765	+	Silent	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr19:11559765G>A	ENST00000589838.1	+	14	1302	c.1302G>A	c.(1300-1302)tcG>tcA	p.S434S	PRKCSH_ENST00000591462.1_Silent_p.S431S|PRKCSH_ENST00000412601.1_Silent_p.S431S|PRKCSH_ENST00000252455.2_Silent_p.S434S|PRKCSH_ENST00000587327.1_Silent_p.S431S|PRKCSH_ENST00000592741.1_Silent_p.S441S			P14314	GLU2B_HUMAN	protein kinase C substrate 80K-H	434	PRKCSH.				cellular protein metabolic process (GO:0044267)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|liver development (GO:0001889)|N-glycan processing (GO:0006491)|negative regulation of neuron projection development (GO:0010977)|nitrogen compound metabolic process (GO:0006807)|post-translational protein modification (GO:0043687)|protein folding (GO:0006457)|protein heterooligomerization (GO:0051291)|protein N-linked glycosylation via asparagine (GO:0018279)|renal system development (GO:0072001)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|intracellular (GO:0005622)	calcium ion binding (GO:0005509)|ion channel binding (GO:0044325)|phosphoprotein binding (GO:0051219)|protein kinase C binding (GO:0005080)|RNA binding (GO:0003723)	p.S434S(1)		breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(7)|ovary(2)|pancreas(1)|prostate(3)	19						AGCTTGTCTCGCAGAAACCCA	0.652																																					p.S434S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G1302A	19						.						104.0	111.0	109.0					19																	11559765		2203	4300	6503	11420765	SO:0001819	synonymous_variant	5589	exon15				CCDS32911.1, CCDS45977.1, CCDS74286.1	19p13.2	2014-01-30			ENSG00000130175	ENSG00000130175	2.7.11.1	"""EF-hand domain containing"""	9411	protein-coding gene	gene with protein product		177060	"""polycystic liver disease"""	G19P1, PCLD, PLD1		12529853	Standard	NM_002743		Approved		uc002mrt.3	P14314	OTTHUMG00000182029	ENST00000589838.1:c.1302G>A	19.37:g.11559765G>A		Somatic		Capture	Illumina HiSeq	Phase_I	11420765	NM_002743	A8K318|Q96BU9|Q96D06|Q9P0W9	Silent	SNP	ENST00000589838.1	37	CCDS32911.1																																																																																				0.652	PRKCSH-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000458817.1		
ECSIT	51295	broad.mit.edu	37	19	11624044	11624044	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr19:11624044G>A	ENST00000270517.7	-	4	700	c.565C>T	c.(565-567)Cgc>Tgc	p.R189C	ECSIT_ENST00000591352.1_Intron|ECSIT_ENST00000417981.2_Intron|ECSIT_ENST00000592312.1_Missense_Mutation_p.R73C|ECSIT_ENST00000588998.1_Intron|ECSIT_ENST00000252440.7_Missense_Mutation_p.R189C|ECSIT_ENST00000591104.1_Missense_Mutation_p.R189C|RN7SL833P_ENST00000498758.2_RNA	NM_016581.4	NP_057665.2	Q9BQ95	ECSIT_HUMAN	ECSIT signalling integrator	189					BMP signaling pathway (GO:0030509)|innate immune response (GO:0045087)|mesoderm formation (GO:0001707)|oxidation-reduction process (GO:0055114)|regulation of oxidoreductase activity (GO:0051341)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	oxidoreductase activity, acting on NAD(P)H (GO:0016651)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)	p.R189C(1)		kidney(2)|large_intestine(3)|lung(1)|ovary(1)|prostate(2)|skin(1)|urinary_tract(1)	11						TAGCTTTTGCGTCCAAAGATC	0.587																																					p.R189C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C565T	19						.						129.0	91.0	104.0					19																	11624044		2203	4300	6503	11485044	SO:0001583	missense	51295	exon4			BC005119	CCDS12262.1, CCDS45979.1, CCDS45980.1, CCDS59353.1	19p13.2	2013-05-24	2013-05-24			ENSG00000130159		"""Mitochondrial respiratory chain complex assembly factors"""	29548	protein-coding gene	gene with protein product	"""signaling intermediate in Toll pathway evolutionarily conserved ortholog (mouse)"""	608388	"""ECSIT homolog (Drosophila)"""			10465784, 22982022	Standard	NM_001142464		Approved	SITPEC	uc002msb.3	Q9BQ95		ENST00000270517.7:c.565C>T	19.37:g.11624044G>A	ENSP00000270517:p.Arg189Cys	Somatic		Capture	Illumina HiSeq	Phase_I	11485044	NM_001142464	E9PAN9|K7EMM0|Q96HQ7|Q9NYI1	Missense_Mutation	SNP	ENST00000270517.7	37	CCDS12262.1	.	.	.	.	.	.	.	.	.	.	g	16.75	3.208564	0.58343	.	.	ENSG00000130159	ENST00000270517;ENST00000252440	T;T	0.78364	-1.17;-1.17	4.81	3.69	0.42338	.	0.476980	0.22850	N	0.054872	D	0.82834	0.5123	M	0.77103	2.36	0.43564	D	0.995885	D;D	0.76494	0.998;0.999	P;P	0.57679	0.804;0.825	D	0.83825	0.0249	10	0.72032	D	0.01	-17.5163	7.552	0.27802	0.0:0.1512:0.5836:0.2652	.	189;189	Q9BQ95-2;Q9BQ95	.;ECSIT_HUMAN	C	189	ENSP00000270517:R189C;ENSP00000252440:R189C	ENSP00000252440:R189C	R	-	1	0	ECSIT	11485044	0.316000	0.24580	0.198000	0.23420	0.936000	0.57629	3.159000	0.50731	2.384000	0.81235	0.546000	0.68486	CGC		0.587	ECSIT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442603.2	NM_016581	
ZNF823	55552	broad.mit.edu	37	19	11833064	11833064	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr19:11833064C>T	ENST00000341191.6	-	4	1438	c.1285G>A	c.(1285-1287)Ggt>Agt	p.G429S	ZNF823_ENST00000545749.1_Missense_Mutation_p.G247S	NM_001080493.2	NP_001073962.1	P16415	ZN823_HUMAN	zinc finger protein 823	429					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.G429S(1)		breast(1)|endometrium(4)|kidney(1)|large_intestine(3)|lung(10)|ovary(2)|prostate(1)|upper_aerodigestive_tract(4)	26						CGAAGGGAACCGGCAAGACTG	0.423										HNSCC(68;0.2)																											p.G429S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1285A	19						.						63.0	70.0	68.0					19																	11833064		2201	4300	6501	11694064	SO:0001583	missense	55552	exon4			X51760	CCDS45981.1	19p13.2	2013-01-08			ENSG00000197933	ENSG00000197933		"""Zinc fingers, C2H2-type"", ""-"""	30936	protein-coding gene	gene with protein product	"""ZFP 36 for a zinc finger protein"""						Standard	XM_006722789		Approved	HSZFP36	uc002msm.2	P16415	OTTHUMG00000156528	ENST00000341191.6:c.1285G>A	19.37:g.11833064C>T	ENSP00000340683:p.Gly429Ser	Somatic		Capture	Illumina HiSeq	Phase_I	11694064	NM_001080493	A0PJL4|B7Z8D4|Q6P4A9	Missense_Mutation	SNP	ENST00000341191.6	37	CCDS45981.1	.	.	.	.	.	.	.	.	.	.	N	0.006	-2.093744	0.00364	.	.	ENSG00000197933	ENST00000545749;ENST00000341191;ENST00000431998	T;T;T	0.35236	1.32;2.91;1.32	0.566	-1.13	0.09775	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.08403	0.0209	N	0.01631	-0.79	0.09310	N	1	B	0.15473	0.013	B	0.08055	0.003	T	0.19451	-1.0305	9	0.02654	T	1	.	0.1512	0.00093	0.2508:0.2557:0.2505:0.243	.	429	P16415	ZN823_HUMAN	S	247;429;385	ENSP00000440162:G247S;ENSP00000340683:G429S;ENSP00000410654:G385S	ENSP00000340683:G429S	G	-	1	0	ZNF823	11694064	0.000000	0.05858	0.000000	0.03702	0.289000	0.27227	-2.075000	0.01374	-1.203000	0.02652	0.184000	0.17185	GGT		0.423	ZNF823-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344516.2	NM_001080493	
GCDH	2639	broad.mit.edu	37	19	13008224	13008224	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr19:13008224G>A	ENST00000222214.5	+	10	1275	c.1064G>A	c.(1063-1065)cGc>cAc	p.R355H	GCDH_ENST00000457854.1_Missense_Mutation_p.R355H|GCDH_ENST00000422947.2_Missense_Mutation_p.R311H|GCDH_ENST00000591470.1_Missense_Mutation_p.R355H			Q92947	GCDH_HUMAN	glutaryl-CoA dehydrogenase	355			R -> C (in GA1).|R -> H (in GA1).		cellular nitrogen compound metabolic process (GO:0034641)|fatty acid oxidation (GO:0019395)|fatty-acyl-CoA biosynthetic process (GO:0046949)|lysine catabolic process (GO:0006554)|small molecule metabolic process (GO:0044281)|tryptophan metabolic process (GO:0006568)	mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	fatty-acyl-CoA binding (GO:0000062)|flavin adenine dinucleotide binding (GO:0050660)|glutaryl-CoA dehydrogenase activity (GO:0004361)	p.R355H(1)		autonomic_ganglia(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(8)	19					Flavin adenine dinucleotide(DB03147)	CAGCTCGGCCGCTTGAAGGAC	0.612																																					p.R355H	GBM(123;875 1636 7726 16444 26754)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1064A	19	GRCh37	CM980875	GCDH	M		.						38.0	39.0	39.0					19																	13008224		2203	4300	6503	12869224	SO:0001583	missense	2639	exon10			AF012342	CCDS12286.1	19p13.2	2010-04-30	2010-04-30			ENSG00000105607	1.3.99.7		4189	protein-coding gene	gene with protein product		608801	"""glutaryl-Coenzyme A dehydrogenase"""			1438360, 8088809	Standard	NM_000159		Approved	ACAD5	uc002mvq.4	Q92947		ENST00000222214.5:c.1064G>A	19.37:g.13008224G>A	ENSP00000222214:p.Arg355His	Somatic		Capture	Illumina HiSeq	Phase_I	12869224	NM_013976	A8K2Z2|O14719	Missense_Mutation	SNP	ENST00000222214.5	37	CCDS12286.1	.	.	.	.	.	.	.	.	.	.	G	32	5.151112	0.94645	.	.	ENSG00000105607	ENST00000457854;ENST00000222214;ENST00000421816;ENST00000422947	D;D;D	0.96168	-3.93;-3.93;-3.93	5.17	5.17	0.71159	Acyl-CoA dehydrogenase/oxidase C-terminal (2);Acyl-CoA oxidase/dehydrogenase, type 1 (1);	0.000000	0.85682	D	0.000000	D	0.97914	0.9314	M	0.93150	3.385	0.80722	D	1	D;D;D;D;D	0.65815	0.993;0.974;0.995;0.993;0.963	P;P;P;P;P	0.58577	0.763;0.634;0.841;0.781;0.576	D	0.98720	1.0708	10	0.66056	D	0.02	.	16.5109	0.84284	0.0:0.0:1.0:0.0	.	311;191;322;355;355	B4DK85;B4DUY0;B4DQF2;Q92947;Q92947-2	.;.;.;GCDH_HUMAN;.	H	355;355;322;311	ENSP00000394872:R355H;ENSP00000222214:R355H;ENSP00000394821:R311H	ENSP00000222214:R355H	R	+	2	0	GCDH	12869224	1.000000	0.71417	0.999000	0.59377	0.944000	0.59088	7.618000	0.83043	2.575000	0.86900	0.563000	0.77884	CGC		0.612	GCDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451897.1		
FARSA	2193	broad.mit.edu	37	19	13041434	13041434	+	Missense_Mutation	SNP	C	C	T	rs368745199		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr19:13041434C>T	ENST00000314606.4	-	2	295	c.277G>A	c.(277-279)Gag>Aag	p.E93K	FARSA_ENST00000423140.2_Missense_Mutation_p.E93K|FARSA_ENST00000588025.1_Missense_Mutation_p.E133K|CTC-425F1.2_ENST00000592636.1_RNA	NM_004461.2	NP_004452.1	Q9Y285	SYFA_HUMAN	phenylalanyl-tRNA synthetase, alpha subunit	93					gene expression (GO:0010467)|phenylalanyl-tRNA aminoacylation (GO:0006432)|tRNA aminoacylation for protein translation (GO:0006418)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)	ATP binding (GO:0005524)|phenylalanine-tRNA ligase activity (GO:0004826)|poly(A) RNA binding (GO:0044822)|tRNA binding (GO:0000049)	p.E93K(1)		NS(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(9)|ovary(3)|upper_aerodigestive_tract(1)	20					L-Phenylalanine(DB00120)	ACCATAAGCTCGCTCTGGGCC	0.637																																					p.E93K												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G277A	19						.	C	LYS/GLU	0,4406		0,0,2203	61.0	50.0	53.0		277	4.3	1.0	19		53	1,8599	1.2+/-3.3	0,1,4299	no	missense	FARSA	NM_004461.2	56	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	benign	93/509	13041434	1,13005	2203	4300	6503	12902434	SO:0001583	missense	2193	exon2			U07424	CCDS12287.1	19p13.2	2014-05-06	2007-02-23	2007-02-23	ENSG00000179115	ENSG00000179115	6.1.1.20	"""Aminoacyl tRNA synthetases / Class II"""	3592	protein-coding gene	gene with protein product	"""phenylalanine tRNA ligase 1, alpha, cytoplasmic"""	602918	"""phenylalanine-tRNA synthetase-like"", ""phenylalanyl-tRNA synthetase-like, alpha subunit"""	FARSL, FARSLA		9177188	Standard	NM_004461		Approved	CML33	uc002mvs.2	Q9Y285	OTTHUMG00000180569	ENST00000314606.4:c.277G>A	19.37:g.13041434C>T	ENSP00000320309:p.Glu93Lys	Somatic		Capture	Illumina HiSeq	Phase_I	12902434	NM_004461	B4E363|Q9NSD8|Q9Y4W8	Missense_Mutation	SNP	ENST00000314606.4	37	CCDS12287.1	.	.	.	.	.	.	.	.	.	.	C	15.93	2.979152	0.53827	0.0	1.16E-4	ENSG00000179115	ENST00000314606;ENST00000423140	T;T	0.65916	-0.18;0.43	5.41	4.34	0.51931	.	0.265245	0.42294	D	0.000721	T	0.58807	0.2148	L	0.59967	1.855	0.48185	D	0.999609	B;B	0.18310	0.027;0.004	B;B	0.11329	0.006;0.002	T	0.56432	-0.7980	10	0.39692	T	0.17	-9.457	14.8958	0.70644	0.0:0.8553:0.1447:0.0	.	93;93	B4E363;Q9Y285	.;SYFA_HUMAN	K	93	ENSP00000320309:E93K;ENSP00000396548:E93K	ENSP00000320309:E93K	E	-	1	0	FARSA	12902434	0.989000	0.36119	1.000000	0.80357	0.896000	0.52359	2.738000	0.47401	1.236000	0.43740	0.561000	0.74099	GAG		0.637	FARSA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451935.1	NM_004461	
RAD23A	5886	broad.mit.edu	37	19	13058787	13058787	+	Silent	SNP	C	C	T	rs555882027		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr19:13058787C>T	ENST00000586534.1	+	2	259	c.198C>T	c.(196-198)atC>atT	p.I66I	RAD23A_ENST00000541222.1_5'UTR|RAD23A_ENST00000316856.3_Silent_p.I66I|RAD23A_ENST00000588826.2_3'UTR|RAD23A_ENST00000592268.1_Silent_p.I66I			P54725	RD23A_HUMAN	RAD23 homolog A (S. cerevisiae)	66	Ubiquitin-like. {ECO:0000255|PROSITE- ProRule:PRU00214}.				nucleotide-excision repair (GO:0006289)|positive regulation of viral genome replication (GO:0045070)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032434)|viral process (GO:0016032)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|proteasome complex (GO:0000502)	damaged DNA binding (GO:0003684)|polyubiquitin binding (GO:0031593)|single-stranded DNA binding (GO:0003697)|ubiquitin-specific protease binding (GO:1990381)	p.I66I(1)		central_nervous_system(1)|endometrium(2)|large_intestine(3)|lung(2)|ovary(2)|prostate(1)|skin(1)	12						ACTATCGCATCGATGAGAAGA	0.567								Nucleotide excision repair (NER)																													p.I66I												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C198T	19						.						176.0	155.0	162.0					19																	13058787		2203	4300	6503	12919787	SO:0001819	synonymous_variant	5886	exon2				CCDS12289.1, CCDS59357.1, CCDS59358.1	19p13.2	2008-07-17	2001-11-28			ENSG00000179262			9812	protein-coding gene	gene with protein product	"""RAD23, yeast homolog, A"""	600061	"""RAD23 (S. cerevisiae) homolog A"""			7851894	Standard	NM_005053		Approved	HHR23A, MGC111083	uc002mvw.2	P54725		ENST00000586534.1:c.198C>T	19.37:g.13058787C>T		Somatic		Capture	Illumina HiSeq	Phase_I	12919787	NM_005053	K7ESE3|Q59EU8|Q5M7Z1	Silent	SNP	ENST00000586534.1	37	CCDS12289.1																																																																																				0.567	RAD23A-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000452752.1	NM_005053	
RAD23A	5886	broad.mit.edu	37	19	13059152	13059152	+	Silent	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr19:13059152G>A	ENST00000586534.1	+	3	457	c.396G>A	c.(394-396)acG>acA	p.T132T	RAD23A_ENST00000541222.1_5'UTR|RAD23A_ENST00000316856.3_Silent_p.T132T|RAD23A_ENST00000588826.2_3'UTR|RAD23A_ENST00000592268.1_Silent_p.T132T			P54725	RD23A_HUMAN	RAD23 homolog A (S. cerevisiae)	132					nucleotide-excision repair (GO:0006289)|positive regulation of viral genome replication (GO:0045070)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032434)|viral process (GO:0016032)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|proteasome complex (GO:0000502)	damaged DNA binding (GO:0003684)|polyubiquitin binding (GO:0031593)|single-stranded DNA binding (GO:0003697)|ubiquitin-specific protease binding (GO:1990381)	p.T132T(1)		central_nervous_system(1)|endometrium(2)|large_intestine(3)|lung(2)|ovary(2)|prostate(1)|skin(1)	12						CCCCCACGACGTCCCCAGAGT	0.642								Nucleotide excision repair (NER)																													p.T132T												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G396A	19						.						38.0	44.0	42.0					19																	13059152		2203	4300	6503	12920152	SO:0001819	synonymous_variant	5886	exon3				CCDS12289.1, CCDS59357.1, CCDS59358.1	19p13.2	2008-07-17	2001-11-28			ENSG00000179262			9812	protein-coding gene	gene with protein product	"""RAD23, yeast homolog, A"""	600061	"""RAD23 (S. cerevisiae) homolog A"""			7851894	Standard	NM_005053		Approved	HHR23A, MGC111083	uc002mvw.2	P54725		ENST00000586534.1:c.396G>A	19.37:g.13059152G>A		Somatic		Capture	Illumina HiSeq	Phase_I	12920152	NM_005053	K7ESE3|Q59EU8|Q5M7Z1	Silent	SNP	ENST00000586534.1	37	CCDS12289.1																																																																																				0.642	RAD23A-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000452752.1	NM_005053	
TRMT1	55621	broad.mit.edu	37	19	13216195	13216195	+	Silent	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr19:13216195G>A	ENST00000592062.1	-	17	2289	c.1719C>T	c.(1717-1719)gaC>gaT	p.D573D	TRMT1_ENST00000357720.4_Silent_p.D573D|LYL1_ENST00000264824.4_5'Flank|TRMT1_ENST00000221504.8_Silent_p.D544D|TRMT1_ENST00000437766.1_Silent_p.D573D			Q9NXH9	TRM1_HUMAN	tRNA methyltransferase 1 homolog (S. cerevisiae)	573							metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|tRNA (guanine-N2-)-methyltransferase activity (GO:0004809)|tRNA binding (GO:0000049)	p.D573D(1)		endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(5)|ovary(1)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(1)	14			OV - Ovarian serous cystadenocarcinoma(19;6.08e-22)	GBM - Glioblastoma multiforme(1328;0.0356)		CCATAGCTTCGTCGGCCGCCT	0.637																																					p.D573D												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1719T	19						.						63.0	68.0	66.0					19																	13216195		2203	4300	6503	13077195	SO:0001819	synonymous_variant	55621	exon15			AF196479	CCDS12293.1, CCDS45997.1	19p13.13	2012-06-12	2012-06-12						25980	protein-coding gene	gene with protein product		611669				10982862	Standard	NM_001142554		Approved	FLJ20244, TRM1	uc002mwl.3	Q9NXH9		ENST00000592062.1:c.1719C>T	19.37:g.13216195G>A		Somatic		Capture	Illumina HiSeq	Phase_I	13077195	NM_017722	O76103|Q548Y5|Q8WVA6	Silent	SNP	ENST00000592062.1	37	CCDS12293.1																																																																																				0.637	TRMT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452780.2	NM_017722	
CCDC130	81576	broad.mit.edu	37	19	13869999	13869999	+	Silent	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr19:13869999G>A	ENST00000586600.1	+	9	989	c.486G>A	c.(484-486)gcG>gcA	p.A162A	CCDC130_ENST00000587019.1_3'UTR|CCDC130_ENST00000221554.8_Silent_p.A162A			P13994	CC130_HUMAN	coiled-coil domain containing 130	162					response to virus (GO:0009615)			p.A162A(1)		endometrium(2)|kidney(1)|large_intestine(3)|ovary(1)|skin(2)|urinary_tract(1)	10			OV - Ovarian serous cystadenocarcinoma(19;6.02e-23)|Epithelial(5;2.58e-18)			TCAAGAAGGCGCTGCCCACAC	0.632																																					p.A162A												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G486A	19						.						32.0	32.0	32.0					19																	13869999		2201	4299	6500	13730999	SO:0001819	synonymous_variant	81576	exon8			AF250306	CCDS12296.1	19p13.13	2008-02-05				ENSG00000104957			28118	protein-coding gene	gene with protein product						3203696	Standard	NM_030818		Approved	MGC10471	uc002mxc.1	P13994		ENST00000586600.1:c.486G>A	19.37:g.13869999G>A		Somatic		Capture	Illumina HiSeq	Phase_I	13730999	NM_030818	Q9BQ72	Silent	SNP	ENST00000586600.1	37	CCDS12296.1																																																																																				0.632	CCDC130-001	KNOWN	alternative_5_UTR|upstream_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453216.2	NM_030818	
RFX1	5989	broad.mit.edu	37	19	14076457	14076457	+	Silent	SNP	G	G	A	rs139336544		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr19:14076457G>A	ENST00000254325.4	-	15	2328	c.2094C>T	c.(2092-2094)gaC>gaT	p.D698D		NM_002918.4	NP_002909.4	P22670	RFX1_HUMAN	regulatory factor X, 1 (influences HLA class II expression)	698					immune response (GO:0006955)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)	p.D698D(1)		NS(1)|breast(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(8)|ovary(2)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)	21			OV - Ovarian serous cystadenocarcinoma(19;6.67e-23)			GCCGCAGCACGTCGGGAATGA	0.657																																					p.D698D												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C2094T	19						.						87.0	68.0	74.0					19																	14076457		2201	4300	6501	13937457	SO:0001819	synonymous_variant	5989	exon15				CCDS12301.1	19p13.1	2008-07-17				ENSG00000132005			9982	protein-coding gene	gene with protein product	"""trans-acting regulatory factor 1"", ""enhancer factor C"", ""MHC class II regulatory factor RFX"""	600006				1505960, 8289803	Standard	NM_002918		Approved	EF-C	uc002mxv.3	P22670		ENST00000254325.4:c.2094C>T	19.37:g.14076457G>A		Somatic		Capture	Illumina HiSeq	Phase_I	13937457	NM_002918		Silent	SNP	ENST00000254325.4	37	CCDS12301.1																																																																																				0.657	RFX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458510.1	NM_002918	
PRKACA	5566	broad.mit.edu	37	19	14208433	14208433	+	Silent	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr19:14208433G>A	ENST00000308677.4	-	7	796	c.600C>T	c.(598-600)tgC>tgT	p.C200C	PRKACA_ENST00000350356.3_5'UTR|PRKACA_ENST00000589994.1_Silent_p.C192C|PRKACA_ENST00000590853.1_Intron	NM_002730.3	NP_002721.1	P17612	KAPCA_HUMAN	protein kinase, cAMP-dependent, catalytic, alpha	200	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|blood coagulation (GO:0007596)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|carbohydrate metabolic process (GO:0005975)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cellular response to epinephrine stimulus (GO:0071872)|cellular response to glucagon stimulus (GO:0071377)|cellular response to glucose stimulus (GO:0071333)|cellular response to parathyroid hormone stimulus (GO:0071374)|cytosolic calcium ion homeostasis (GO:0051480)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|G2/M transition of mitotic cell cycle (GO:0000086)|gluconeogenesis (GO:0006094)|glucose metabolic process (GO:0006006)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|mesoderm formation (GO:0001707)|mitotic cell cycle (GO:0000278)|negative regulation of smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:1901621)|neural tube closure (GO:0001843)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of protein export from nucleus (GO:0046827)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of cardiac muscle contraction (GO:0055117)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of heart rate (GO:0002027)|regulation of insulin secretion (GO:0050796)|regulation of osteoblast differentiation (GO:0045667)|regulation of proteasomal protein catabolic process (GO:0061136)|regulation of protein binding (GO:0043393)|regulation of protein processing (GO:0070613)|regulation of ryanodine-sensitive calcium-release channel activity (GO:0060314)|regulation of synaptic transmission (GO:0050804)|regulation of tight junction assembly (GO:2000810)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|sperm capacitation (GO:0048240)|transmembrane transport (GO:0055085)|triglyceride catabolic process (GO:0019433)|water transport (GO:0006833)	AMP-activated protein kinase complex (GO:0031588)|calcium channel complex (GO:0034704)|cAMP-dependent protein kinase complex (GO:0005952)|centrosome (GO:0005813)|ciliary base (GO:0097546)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|motile cilium (GO:0031514)|neuromuscular junction (GO:0031594)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sperm midpiece (GO:0097225)	ATP binding (GO:0005524)|cAMP-dependent protein kinase activity (GO:0004691)|protein kinase A regulatory subunit binding (GO:0034237)|protein kinase binding (GO:0019901)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|ubiquitin protein ligase binding (GO:0031625)	p.C200C(1)		central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(3)|lung(5)|ovary(1)|prostate(1)	16						CAGGGGTGCCGCACAAGGTCC	0.637																																					p.C200C												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C600T	19						.						46.0	49.0	48.0					19																	14208433		2203	4300	6503	14069433	SO:0001819	synonymous_variant	5566	exon7				CCDS12304.1, CCDS12305.1	19p13.1	2012-10-02				ENSG00000072062	2.7.11.1		9380	protein-coding gene	gene with protein product		601639				8884279	Standard	NM_002730		Approved	PKACa	uc002myc.3	P17612		ENST00000308677.4:c.600C>T	19.37:g.14208433G>A		Somatic		Capture	Illumina HiSeq	Phase_I	14069433	NM_002730	Q32P54|Q9H2Y0|Q9NRB4|Q9NRH9	Silent	SNP	ENST00000308677.4	37	CCDS12304.1																																																																																				0.637	PRKACA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459004.1	NM_002730	
SLC1A6	6511	broad.mit.edu	37	19	15065029	15065029	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr19:15065029C>T	ENST00000221742.3	-	7	1289	c.1282G>A	c.(1282-1284)Gcc>Acc	p.A428T	SLC1A6_ENST00000430939.2_Missense_Mutation_p.A364T|SLC1A6_ENST00000600144.1_Missense_Mutation_p.A350T	NM_005071.1	NP_005062.1	P48664	EAA4_HUMAN	solute carrier family 1 (high affinity aspartate/glutamate transporter), member 6	428					aspartate transport (GO:0015810)|ion transport (GO:0006811)|L-glutamate transport (GO:0015813)|regulation of membrane potential (GO:0042391)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	L-aspartate transmembrane transporter activity (GO:0015183)|L-glutamate transmembrane transporter activity (GO:0005313)|sodium:dicarboxylate symporter activity (GO:0017153)	p.A428T(1)		breast(1)|central_nervous_system(2)|endometrium(6)|large_intestine(8)|liver(1)|lung(12)|ovary(3)|pancreas(3)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	42						TCGTAGAGGGCAGTGCCATCC	0.617																																					p.A428T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1282A	19						.						90.0	80.0	83.0					19																	15065029		2203	4300	6503	14926029	SO:0001583	missense	6511	exon7				CCDS12321.1, CCDS62578.1	19p13.12	2013-07-15			ENSG00000105143	ENSG00000105143		"""Solute carriers"""	10944	protein-coding gene	gene with protein product		600637				7791878	Standard	NM_005071		Approved	EAAT4	uc002naa.2	P48664	OTTHUMG00000183351	ENST00000221742.3:c.1282G>A	19.37:g.15065029C>T	ENSP00000221742:p.Ala428Thr	Somatic		Capture	Illumina HiSeq	Phase_I	14926029	NM_005071	Q8N753	Missense_Mutation	SNP	ENST00000221742.3	37	CCDS12321.1	.	.	.	.	.	.	.	.	.	.	c	33	5.203134	0.95033	.	.	ENSG00000105143	ENST00000430939;ENST00000221742	T;T	0.75938	-0.98;0.0	4.52	4.52	0.55395	Sodium:dicarboxylate symporter, conserved site (1);	0.054945	0.64402	D	0.000001	D	0.85725	0.5763	M	0.78285	2.405	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.999	D	0.87584	0.2486	10	0.87932	D	0	-29.334	15.1319	0.72530	0.0:1.0:0.0:0.0	.	364;428	E7EV13;P48664	.;EAA4_HUMAN	T	364;428	ENSP00000409386:A364T;ENSP00000221742:A428T	ENSP00000221742:A428T	A	-	1	0	SLC1A6	14926029	1.000000	0.71417	0.993000	0.49108	0.992000	0.81027	7.472000	0.80996	2.518000	0.84900	0.546000	0.68486	GCC		0.617	SLC1A6-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466283.1	NM_005071	
SYDE1	85360	broad.mit.edu	37	19	15221487	15221487	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr19:15221487G>A	ENST00000342784.2	+	4	1262	c.1231G>A	c.(1231-1233)Ggc>Agc	p.G411S	SYDE1_ENST00000600440.1_Missense_Mutation_p.G344S|SYDE1_ENST00000600252.1_Missense_Mutation_p.G68S	NM_033025.4	NP_149014.3	Q6ZW31	SYDE1_HUMAN	synapse defective 1, Rho GTPase, homolog 1 (C. elegans)	411	Rho-GAP. {ECO:0000255|PROSITE- ProRule:PRU00172}.				activation of Rho GTPase activity (GO:0032862)|positive regulation of synaptic transmission (GO:0050806)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|synaptic vesicle docking involved in exocytosis (GO:0016081)|synaptonemal complex assembly (GO:0007130)	cerebellar mossy fiber (GO:0044300)|cytosol (GO:0005829)|synaptic membrane (GO:0097060)	Rho GTPase activator activity (GO:0005100)	p.G411S(1)		endometrium(4)|kidney(1)|large_intestine(7)|lung(2)|ovary(1)|pancreas(1)|skin(1)	17						GCGGCCCCCCGGCCAGGTGCC	0.706																																					p.G411S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1231A	19						.						10.0	13.0	12.0					19																	15221487		2189	4273	6462	15082487	SO:0001583	missense	85360	exon4			BC029926	CCDS12324.1, CCDS74299.1	19p13.12	2008-02-05				ENSG00000105137			25824	protein-coding gene	gene with protein product						12477932	Standard	XM_005260126		Approved	7h3, FLJ13511	uc002nah.1	Q6ZW31		ENST00000342784.2:c.1231G>A	19.37:g.15221487G>A	ENSP00000341489:p.Gly411Ser	Somatic		Capture	Illumina HiSeq	Phase_I	15082487	NM_033025	Q7L2I8|Q8N6J2|Q9H8K4	Missense_Mutation	SNP	ENST00000342784.2	37	CCDS12324.1	.	.	.	.	.	.	.	.	.	.	G	9.943	1.218057	0.22373	.	.	ENSG00000105137	ENST00000342784	T	0.41758	0.99	4.97	4.97	0.65823	Rho GTPase-activating protein domain (3);Rho GTPase activation protein (1);	0.376195	0.24260	N	0.040085	T	0.21022	0.0506	N	0.19112	0.55	0.33051	D	0.532682	B;P;B	0.43314	0.274;0.803;0.274	B;B;B	0.25884	0.053;0.064;0.053	T	0.25676	-1.0125	10	0.09843	T	0.71	.	15.7126	0.77644	0.0:0.0:1.0:0.0	.	344;344;411	B2RD93;Q6ZW31-2;Q6ZW31	.;.;SYDE1_HUMAN	S	411	ENSP00000341489:G411S	ENSP00000341489:G411S	G	+	1	0	SYDE1	15082487	0.001000	0.12720	0.945000	0.38365	0.602000	0.36980	0.537000	0.23144	2.324000	0.78689	0.491000	0.48974	GGC		0.706	SYDE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465666.1	NM_033025	
NOTCH3	4854	broad.mit.edu	37	19	15281154	15281154	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr19:15281154G>A	ENST00000263388.2	-	27	5177	c.5102C>T	c.(5101-5103)gCg>gTg	p.A1701V		NM_000435.2	NP_000426.2	Q9UM47	NOTC3_HUMAN	notch 3	1701					forebrain development (GO:0030900)|gene expression (GO:0010467)|glomerular capillary formation (GO:0072104)|negative regulation of neuron differentiation (GO:0045665)|neuron fate commitment (GO:0048663)|Notch receptor processing (GO:0007220)|Notch signaling pathway (GO:0007219)|positive regulation of smooth muscle cell proliferation (GO:0048661)|regulation of transcription, DNA-templated (GO:0006355)|transcription initiation from RNA polymerase II promoter (GO:0006367)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)	p.A1701V(2)		breast(4)|central_nervous_system(3)|endometrium(10)|kidney(3)|large_intestine(16)|liver(1)|lung(31)|ovary(8)|prostate(3)|skin(7)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(1)	93			OV - Ovarian serous cystadenocarcinoma(3;2.6e-20)|Epithelial(3;1.34e-16)|all cancers(3;5.13e-15)			CATGCCCAGCGCGTCCTGGCC	0.652																																					p.A1701V												.	.	2	Substitution - Missense(2)	large_intestine(1)|central_nervous_system(1)	c.C5102T	19						.						37.0	39.0	38.0					19																	15281154		2203	4300	6503	15142154	SO:0001583	missense	4854	exon27			U97669	CCDS12326.1	19p13.2-p13.1	2013-01-10	2010-06-24			ENSG00000074181		"""Ankyrin repeat domain containing"""	7883	protein-coding gene	gene with protein product		600276	"""Notch (Drosophila) homolog 3"", ""Notch homolog 3 (Drosophila)"""	CADASIL		7835890	Standard	NM_000435		Approved	CASIL	uc002nan.3	Q9UM47		ENST00000263388.2:c.5102C>T	19.37:g.15281154G>A	ENSP00000263388:p.Ala1701Val	Somatic		Capture	Illumina HiSeq	Phase_I	15142154	NM_000435	Q9UEB3|Q9UPL3|Q9Y6L8	Missense_Mutation	SNP	ENST00000263388.2	37	CCDS12326.1	.	.	.	.	.	.	.	.	.	.	G	23.7	4.445904	0.84101	.	.	ENSG00000074181	ENST00000263388	D	0.82081	-1.57	3.97	3.97	0.46021	.	.	.	.	.	D	0.88081	0.6341	M	0.64404	1.975	0.46078	D	0.998855	D	0.76494	0.999	P	0.62740	0.906	D	0.88353	0.2982	9	0.46703	T	0.11	.	14.9888	0.71371	0.0:0.0:1.0:0.0	.	1701	Q9UM47	NOTC3_HUMAN	V	1701	ENSP00000263388:A1701V	ENSP00000263388:A1701V	A	-	2	0	NOTCH3	15142154	1.000000	0.71417	0.434000	0.26772	0.938000	0.57974	7.650000	0.83521	2.056000	0.61249	0.591000	0.81541	GCG		0.652	NOTCH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465714.1	NM_000435	
NOTCH3	4854	broad.mit.edu	37	19	15296398	15296398	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr19:15296398G>T	ENST00000263388.2	-	13	2119	c.2044C>A	c.(2044-2046)Ctc>Atc	p.L682I		NM_000435.2	NP_000426.2	Q9UM47	NOTC3_HUMAN	notch 3	682	EGF-like 17; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				forebrain development (GO:0030900)|gene expression (GO:0010467)|glomerular capillary formation (GO:0072104)|negative regulation of neuron differentiation (GO:0045665)|neuron fate commitment (GO:0048663)|Notch receptor processing (GO:0007220)|Notch signaling pathway (GO:0007219)|positive regulation of smooth muscle cell proliferation (GO:0048661)|regulation of transcription, DNA-templated (GO:0006355)|transcription initiation from RNA polymerase II promoter (GO:0006367)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)	p.L682I(1)		breast(4)|central_nervous_system(3)|endometrium(10)|kidney(3)|large_intestine(16)|liver(1)|lung(31)|ovary(8)|prostate(3)|skin(7)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(1)	93			OV - Ovarian serous cystadenocarcinoma(3;2.6e-20)|Epithelial(3;1.34e-16)|all cancers(3;5.13e-15)			GGCGGGCAGAGGCAGCGGAAG	0.642																																					p.L682I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C2044A	19						.						76.0	61.0	66.0					19																	15296398		2203	4300	6503	15157398	SO:0001583	missense	4854	exon13			U97669	CCDS12326.1	19p13.2-p13.1	2013-01-10	2010-06-24			ENSG00000074181		"""Ankyrin repeat domain containing"""	7883	protein-coding gene	gene with protein product		600276	"""Notch (Drosophila) homolog 3"", ""Notch homolog 3 (Drosophila)"""	CADASIL		7835890	Standard	NM_000435		Approved	CASIL	uc002nan.3	Q9UM47		ENST00000263388.2:c.2044C>A	19.37:g.15296398G>T	ENSP00000263388:p.Leu682Ile	Somatic		Capture	Illumina HiSeq	Phase_I	15157398	NM_000435	Q9UEB3|Q9UPL3|Q9Y6L8	Missense_Mutation	SNP	ENST00000263388.2	37	CCDS12326.1	.	.	.	.	.	.	.	.	.	.	G	16.57	3.160467	0.57368	.	.	ENSG00000074181	ENST00000263388;ENST00000539383	D	0.95342	-3.68	5.11	4.03	0.46877	EGF-like calcium-binding (1);Epidermal growth factor-like, type 3 (1);	0.000000	0.29579	N	0.011741	D	0.87712	0.6246	N	0.11892	0.195	0.33438	D	0.581985	B;B	0.27853	0.011;0.191	B;B	0.27796	0.017;0.083	D	0.88643	0.3177	10	0.36615	T	0.2	.	13.8447	0.63459	0.0:0.0:0.8466:0.1534	.	685;682	Q59FL3;Q9UM47	.;NOTC3_HUMAN	I	682;684	ENSP00000263388:L682I	ENSP00000263388:L682I	L	-	1	0	NOTCH3	15157398	1.000000	0.71417	1.000000	0.80357	0.962000	0.63368	1.208000	0.32345	2.388000	0.81334	0.655000	0.94253	CTC		0.642	NOTCH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465714.1	NM_000435	
TCF3	6929	broad.mit.edu	37	19	1623996	1623996	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr19:1623996G>A	ENST00000262965.5	-	8	847	c.503C>T	c.(502-504)aCg>aTg	p.T168M	TCF3_ENST00000395423.3_Missense_Mutation_p.T117M|TCF3_ENST00000588136.1_Missense_Mutation_p.T168M|TCF3_ENST00000344749.5_Missense_Mutation_p.T168M|TCF3_ENST00000453954.2_Missense_Mutation_p.T84M	NM_003200.3	NP_003191.1	Q9HCS4	TF7L1_HUMAN	transcription factor 3	0	Pro-rich.				anterior/posterior axis specification, embryo (GO:0008595)|axial mesoderm morphogenesis (GO:0048319)|brain development (GO:0007420)|canonical Wnt signaling pathway (GO:0060070)|chromatin organization (GO:0006325)|generation of neurons (GO:0048699)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription from RNA polymerase II promoter during mitosis (GO:0046022)|regulation of stem cell maintenance (GO:2000036)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|regulation of Wnt signaling pathway (GO:0030111)|skin development (GO:0043588)|somatic stem cell maintenance (GO:0035019)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)	p.T168M(1)		breast(2)|central_nervous_system(1)|kidney(2)|large_intestine(2)|lung(6)|ovary(1)|skin(2)	16		Acute lymphoblastic leukemia(61;5.94e-12)|all_hematologic(61;1.27e-07)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		CTTGGGCTGCGTGTCTGTTAG	0.612			T	"""PBX1, HLF, TFPT"""	pre B-ALL																																p.T168M			Dom	yes		19	19p13.3	6929	transcription factor 3 (E2A immunoglobulin enhancer binding factors E12/E47)		L	.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C503T	19						.						55.0	59.0	57.0					19																	1623996		2203	4299	6502	1574996	SO:0001583	missense	6929	exon7			M65214	CCDS12074.1, CCDS45899.1	19p13.3	2014-02-13	2013-02-26		ENSG00000071564	ENSG00000071564		"""Basic helix-loop-helix proteins"""	11633	protein-coding gene	gene with protein product	"""transcription factor E2-alpha"", ""immunoglobulin transcription factor 1"", ""kappa-E2-binding factor"", ""E2A immunoglobulin enhancer-binding factor E12/E47"", ""VDR interacting repressor"""	147141				2308859, 1967983	Standard	NM_003200		Approved	E2A, ITF1, MGC129647, MGC129648, bHLHb21, VDIR, E47	uc002ltt.4	P15923	OTTHUMG00000180031	ENST00000262965.5:c.503C>T	19.37:g.1623996G>A	ENSP00000262965:p.Thr168Met	Somatic		Capture	Illumina HiSeq	Phase_I	1574996	NM_001136139	Q53R97|Q6PD70|Q9NP00	Missense_Mutation	SNP	ENST00000262965.5	37	CCDS12074.1	.	.	.	.	.	.	.	.	.	.	G	14.23	2.473338	0.43942	.	.	ENSG00000071564	ENST00000262965;ENST00000344749;ENST00000453954;ENST00000395423	T;T;T	0.46819	0.86;0.86;0.86	4.12	3.03	0.35002	.	2.621480	0.01879	N	0.037713	T	0.56978	0.2022	L	0.50333	1.59	0.09310	N	1	D;D;D	0.67145	0.996;0.992;0.981	P;P;P	0.54270	0.747;0.475;0.66	T	0.42849	-0.9427	10	0.34782	T	0.22	-27.4212	9.0781	0.36534	0.0:0.3785:0.6215:0.0	.	168;168;117	P15923-2;P15923;Q2TB39	.;TFE2_HUMAN;.	M	168;168;168;117	ENSP00000262965:T168M;ENSP00000344375:T168M;ENSP00000378813:T117M	ENSP00000262965:T168M	T	-	2	0	TCF3	1574996	0.018000	0.18449	0.048000	0.18961	0.236000	0.25371	2.171000	0.42453	1.853000	0.53794	0.313000	0.20887	ACG		0.612	TCF3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000449367.1	NM_003200	
CYP4F22	126410	broad.mit.edu	37	19	15651382	15651382	+	Missense_Mutation	SNP	C	C	T	rs144569785		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr19:15651382C>T	ENST00000269703.3	+	8	992	c.793C>T	c.(793-795)Cgg>Tgg	p.R265W	CYP4F22_ENST00000601005.2_Missense_Mutation_p.R265W	NM_173483.3	NP_775754.2	Q6NT55	CP4FN_HUMAN	cytochrome P450, family 4, subfamily F, polypeptide 22	265						endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)	heme binding (GO:0020037)|iron ion binding (GO:0005506)|monooxygenase activity (GO:0004497)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen (GO:0016705)	p.R265W(1)		endometrium(6)|large_intestine(9)|lung(16)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|soft_tissue(1)	37						GCGGAGGTTCCGGCAGGCCTG	0.617													C|||	1	0.000199681	0.0008	0.0	5008	,	,		15644	0.0		0.0	False		,,,				2504	0.0				p.R265W												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C793T	19						.	C	TRP/ARG	0,4406		0,0,2203	71.0	67.0	68.0		793	3.1	1.0	19	dbSNP_134	68	1,8599	1.2+/-3.3	0,1,4299	no	missense	CYP4F22	NM_173483.3	101	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging	265/532	15651382	1,13005	2203	4300	6503	15512382	SO:0001583	missense	126410	exon8				CCDS12331.1	19p13.12	2013-11-11			ENSG00000171954	ENSG00000171954		"""Cytochrome P450s"""	26820	protein-coding gene	gene with protein product		611495				16436457	Standard	NM_173483		Approved	FLJ39501	uc002nbh.4	Q6NT55	OTTHUMG00000182451	ENST00000269703.3:c.793C>T	19.37:g.15651382C>T	ENSP00000269703:p.Arg265Trp	Somatic		Capture	Illumina HiSeq	Phase_I	15512382	NM_173483	Q8N8H4	Missense_Mutation	SNP	ENST00000269703.3	37	CCDS12331.1	.	.	.	.	.	.	.	.	.	.	C	15.12	2.740263	0.49045	0.0	1.16E-4	ENSG00000171954	ENST00000269703	T	0.69561	-0.41	5.39	3.07	0.35406	.	0.450603	0.24485	N	0.038118	T	0.76271	0.3964	M	0.75150	2.29	0.30214	N	0.797457	D	0.67145	0.996	P	0.62491	0.903	T	0.73817	-0.3863	10	0.59425	D	0.04	.	9.49	0.38953	0.1527:0.7607:0.0:0.0865	.	265	Q6NT55	CP4FN_HUMAN	W	265	ENSP00000269703:R265W	ENSP00000269703:R265W	R	+	1	2	CYP4F22	15512382	0.048000	0.20356	0.988000	0.46212	0.212000	0.24457	0.139000	0.16036	1.274000	0.44362	0.453000	0.30009	CGG		0.617	CYP4F22-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461338.2	NM_173483	
AP1M1	8907	broad.mit.edu	37	19	16344325	16344325	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr19:16344325C>T	ENST00000291439.3	+	10	1518	c.1069C>T	c.(1069-1071)Cgg>Tgg	p.R357W	AP1M1_ENST00000541844.1_Missense_Mutation_p.R285W|AP1M1_ENST00000444449.2_Missense_Mutation_p.R369W|AP1M1_ENST00000429941.2_Missense_Mutation_p.R304W|AP1M1_ENST00000590756.1_Missense_Mutation_p.R285W	NM_032493.3	NP_115882.1	Q9BXS5	AP1M1_HUMAN	adaptor-related protein complex 1, mu 1 subunit	357	MHD. {ECO:0000255|PROSITE- ProRule:PRU00404}.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|endosome to melanosome transport (GO:0035646)|intracellular protein transport (GO:0006886)|melanosome organization (GO:0032438)|membrane organization (GO:0061024)|post-Golgi vesicle-mediated transport (GO:0006892)|regulation of defense response to virus by virus (GO:0050690)|viral process (GO:0016032)	clathrin adaptor complex (GO:0030131)|cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|trans-Golgi network membrane (GO:0032588)		p.R357W(1)		breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(7)|ovary(3)|prostate(2)	21						GTACCTGATGCGGGCCCACTT	0.642																																					p.R369W												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1105T	19						.						37.0	35.0	35.0					19																	16344325		2198	4297	6495	16205325	SO:0001583	missense	8907	exon11				CCDS12342.1, CCDS46008.1	19p13.12	2008-05-23							13667	protein-coding gene	gene with protein product		603535				9653655, 17988225	Standard	NM_032493		Approved	AP47, CLAPM2	uc002ndv.2	Q9BXS5		ENST00000291439.3:c.1069C>T	19.37:g.16344325C>T	ENSP00000291439:p.Arg357Trp	Somatic		Capture	Illumina HiSeq	Phase_I	16205325	NM_001130524	Q4TTY5	Missense_Mutation	SNP	ENST00000291439.3	37	CCDS12342.1	.	.	.	.	.	.	.	.	.	.	C	18.23	3.578063	0.65878	.	.	ENSG00000072958	ENST00000444449;ENST00000291439;ENST00000541844;ENST00000429941	T;T;T;T	0.22134	1.97;1.97;1.97;2.01	3.73	1.37	0.22104	Clathrin adaptor, mu subunit, C-terminal (3);	0.000000	0.85682	D	0.000000	T	0.52419	0.1733	H	0.96889	3.9	0.58432	D	0.999996	D;D;D	0.89917	0.999;1.0;1.0	D;D;D	0.91635	0.93;0.999;0.999	T	0.54741	-0.8248	10	0.87932	D	0	-32.7484	4.7846	0.13219	0.3775:0.506:0.0:0.1164	.	304;369;357	E7ENJ6;Q4TTY5;Q9BXS5	.;.;AP1M1_HUMAN	W	369;357;285;304	ENSP00000388996:R369W;ENSP00000291439:R357W;ENSP00000445682:R285W;ENSP00000411498:R304W	ENSP00000291439:R357W	R	+	1	2	AP1M1	16205325	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	0.869000	0.27996	0.904000	0.36572	0.655000	0.94253	CGG		0.642	AP1M1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460492.1	NM_032493	
CHERP	10523	broad.mit.edu	37	19	16643469	16643469	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr19:16643469C>A	ENST00000198939.6	-	5	650	c.614G>T	c.(613-615)gGg>gTg	p.G205V	CHERP_ENST00000546361.2_Missense_Mutation_p.G205V|CTD-3222D19.2_ENST00000409035.1_Intron					calcium homeostasis endoplasmic reticulum protein									p.G205V(1)		endometrium(3)|kidney(2)|large_intestine(4)|lung(9)|ovary(2)|stomach(1)|urinary_tract(3)	24						GAAGTGTGCCCCATCAGCCGT	0.637																																					p.G205V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G614T	19						.																																			16504469	SO:0001583	missense	10523	exon5			U94836	CCDS42518.1	19p13.1	2013-01-28				ENSG00000085872		"""G patch domain containing"""	16930	protein-coding gene	gene with protein product						8896557, 10794731	Standard	NM_006387		Approved	ERPROT213-21, DAN16	uc002nei.1	Q8IWX8	OTTHUMG00000169304	ENST00000198939.6:c.614G>T	19.37:g.16643469C>A	ENSP00000198939:p.Gly205Val	Somatic		Capture	Illumina HiSeq	Phase_I	16504469	NM_006387		Missense_Mutation	SNP	ENST00000198939.6	37		.	.	.	.	.	.	.	.	.	.	C	14.27	2.484999	0.44147	.	.	ENSG00000085872	ENST00000546361;ENST00000198939	T;T	0.24723	1.84;1.86	4.94	4.94	0.65067	ENTH/VHS (1);RNA polymerase II, large subunit, CTD (2);	.	.	.	.	T	0.27384	0.0672	L	0.54323	1.7	0.80722	D	1	P	0.50943	0.94	B	0.39590	0.304	T	0.15206	-1.0445	9	0.62326	D	0.03	-24.2381	17.136	0.86739	0.0:1.0:0.0:0.0	.	205	Q8IWX8	CHERP_HUMAN	V	205	ENSP00000439856:G205V;ENSP00000198939:G205V	ENSP00000198939:G205V	G	-	2	0	CHERP	16504469	0.301000	0.24444	0.550000	0.28217	0.587000	0.36485	2.354000	0.44098	2.286000	0.76751	0.491000	0.48974	GGG		0.637	CHERP-003	NOVEL	not_organism_supported|basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000403372.1	NM_006387	
SIN3B	23309	broad.mit.edu	37	19	16976445	16976445	+	Silent	SNP	C	C	T	rs202186432	byFrequency	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr19:16976445C>T	ENST00000248054.5	+	11	1629	c.1608C>T	c.(1606-1608)ccC>ccT	p.P536P	SIN3B_ENST00000595541.1_Silent_p.P126P|SIN3B_ENST00000379803.1_Silent_p.P568P					SIN3 transcription regulator family member B									p.P568P(1)		endometrium(4)|kidney(2)|large_intestine(8)|lung(8)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	26						CCGCTGTCCCCGTTGTCCTGA	0.642													C|||	2	0.000399361	0.0008	0.0014	5008	,	,		9298	0.0		0.0	False		,,,				2504	0.0				p.P568P												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1704T	19						.						58.0	38.0	45.0					19																	16976445		2203	4300	6503	16837445	SO:0001819	synonymous_variant	23309	exon12			AB014600	CCDS32946.1, CCDS74308.1	19p13.12	2013-08-21	2013-08-21						19354	protein-coding gene	gene with protein product		607777	"""SIN3 homolog B, transcription regulator (yeast)"", ""SIN3 transcription regulator homolog B (yeast)"""			9734811	Standard	XM_005259832		Approved	KIAA0700	uc002ney.2	O75182		ENST00000248054.5:c.1608C>T	19.37:g.16976445C>T		Somatic		Capture	Illumina HiSeq	Phase_I	16837445	NM_015260		Silent	SNP	ENST00000248054.5	37																																																																																					0.642	SIN3B-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000462846.1	NM_015260	
FAM129C	199786	broad.mit.edu	37	19	17654145	17654145	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr19:17654145C>T	ENST00000335393.4	+	12	1580	c.1442C>T	c.(1441-1443)gCc>gTc	p.A481V	FAM129C_ENST00000449408.2_Missense_Mutation_p.A207V|FAM129C_ENST00000599124.1_Missense_Mutation_p.A450V|FAM129C_ENST00000352727.3_Missense_Mutation_p.A481V|FAM129C_ENST00000601861.1_Missense_Mutation_p.A450V|FAM129C_ENST00000599164.1_Missense_Mutation_p.A450V|FAM129C_ENST00000600871.1_Missense_Mutation_p.A427V|FAM129C_ENST00000300971.2_Missense_Mutation_p.A481V|FAM129C_ENST00000595684.1_Missense_Mutation_p.A481V|FAM129C_ENST00000332386.5_Missense_Mutation_p.A481V	NM_173544.4	NP_775815	Q86XR2	NIBL2_HUMAN	family with sequence similarity 129, member C	481								p.A481V(1)		autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(8)|liver(2)|lung(14)|ovary(1)|skin(3)|stomach(1)	33						GACGCCGTGGCCACCTTCCTG	0.647																																					p.A481V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1442T	19						.						71.0	74.0	73.0					19																	17654145		2203	4300	6503	17515145	SO:0001583	missense	199786	exon12			AY254198	CCDS12362.1, CCDS42521.1	19p13.11	2008-02-05				ENSG00000167483			24130	protein-coding gene	gene with protein product	B cell novel protein 1	609967				12886250	Standard	NM_173544		Approved	FLJ39802, BCNP1	uc021uqj.1	Q86XR2		ENST00000335393.4:c.1442C>T	19.37:g.17654145C>T	ENSP00000335040:p.Ala481Val	Somatic		Capture	Illumina HiSeq	Phase_I	17515145	NM_173544	B4DNU3|B4DVN7|Q7Z6H6|Q86XR3|Q86XR4|Q8TEQ3	Missense_Mutation	SNP	ENST00000335393.4	37	CCDS12362.1	.	.	.	.	.	.	.	.	.	.	c	12.43	1.935921	0.34189	.	.	ENSG00000167483	ENST00000335393;ENST00000332386;ENST00000352727;ENST00000300971;ENST00000449408;ENST00000435646	T;T;T;T;T	0.24151	2.21;2.22;1.93;1.93;1.87	4.87	3.73	0.42828	.	0.624901	0.15038	N	0.284049	T	0.23492	0.0568	L	0.57536	1.79	0.23743	N	0.996968	B;B;B;B;P;B	0.36909	0.211;0.211;0.211;0.211;0.573;0.211	B;B;B;B;B;B	0.33521	0.04;0.04;0.04;0.04;0.165;0.04	T	0.12192	-1.0557	10	0.44086	T	0.13	-17.579	9.1438	0.36919	0.2728:0.7272:0.0:0.0	.	427;481;481;481;207;481	E7ENP6;Q86XR2;Q86XR2-3;Q86XR2-4;B4DNU3;Q86XR2-2	.;NIBL2_HUMAN;.;.;.;.	V	481;481;481;481;207;427	ENSP00000335040:A481V;ENSP00000333447:A481V;ENSP00000341067:A481V;ENSP00000300971:A481V;ENSP00000394929:A207V	ENSP00000300971:A481V	A	+	2	0	FAM129C	17515145	0.963000	0.33076	0.982000	0.44146	0.872000	0.50106	2.511000	0.45476	2.421000	0.82119	0.486000	0.48141	GCC		0.647	FAM129C-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000464206.1	NM_173544	
COLGALT1	79709	broad.mit.edu	37	19	17670202	17670202	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr19:17670202G>A	ENST00000252599.4	+	2	463	c.343G>A	c.(343-345)Gtg>Atg	p.V115M		NM_024656.2	NP_078932.2	Q8NBJ5	GT251_HUMAN	collagen beta(1-O)galactosyltransferase 1	115					extracellular matrix organization (GO:0030198)|lipopolysaccharide biosynthetic process (GO:0009103)	endoplasmic reticulum lumen (GO:0005788)|membrane (GO:0016020)	procollagen galactosyltransferase activity (GO:0050211)	p.V115M(1)									GTACCATTCCGTGGAGTGGCG	0.592																																					p.V115M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G343A	19						.						120.0	91.0	101.0					19																	17670202		2147	4188	6335	17531202	SO:0001583	missense	79709	exon2			AK075541	CCDS12363.1	19p13.11	2013-02-27	2013-02-27	2013-02-27	ENSG00000130309	ENSG00000130309			26182	protein-coding gene	gene with protein product			"""glycosyltransferase 25 domain containing 1"""	GLT25D1		19075007	Standard	NM_024656		Approved	FLJ22329	uc002nhc.1	Q8NBJ5		ENST00000252599.4:c.343G>A	19.37:g.17670202G>A	ENSP00000252599:p.Val115Met	Somatic		Capture	Illumina HiSeq	Phase_I	17531202	NM_024656	Q8NC64	Missense_Mutation	SNP	ENST00000252599.4	37	CCDS12363.1	.	.	.	.	.	.	.	.	.	.	G	18.84	3.709356	0.68615	.	.	ENSG00000130309	ENST00000252599	D	0.86694	-2.16	3.8	3.8	0.43715	.	0.000000	0.85682	D	0.000000	D	0.93539	0.7938	M	0.87097	2.86	0.80722	D	1	D	0.89917	1.0	D	0.78314	0.991	D	0.94503	0.7711	10	0.72032	D	0.01	-19.0372	13.5576	0.61768	0.0:0.0:1.0:0.0	.	115	Q8NBJ5	GT251_HUMAN	M	115	ENSP00000252599:V115M	ENSP00000252599:V115M	V	+	1	0	GLT25D1	17531202	1.000000	0.71417	0.979000	0.43373	0.519000	0.34347	9.636000	0.98440	1.856000	0.53863	0.423000	0.28283	GTG		0.592	COLGALT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464216.1	NM_024656	
FCHO1	23149	broad.mit.edu	37	19	17881602	17881602	+	Splice_Site	SNP	C	C	T	rs144793428		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr19:17881602C>T	ENST00000596536.1	+	9	774	c.491C>T	c.(490-492)gCg>gTg	p.A164V	FCHO1_ENST00000252771.7_Splice_Site_p.A164V|FCHO1_ENST00000596951.1_Splice_Site_p.A164V|FCHO1_ENST00000597512.1_Splice_Site_p.A171V|FCHO1_ENST00000539407.1_Splice_Site_p.A164V|FCHO1_ENST00000595033.1_Splice_Site_p.A114V|FCHO1_ENST00000594202.1_Splice_Site_p.A164V|FCHO1_ENST00000389133.4_Splice_Site_p.A164V|FCHO1_ENST00000600676.1_Splice_Site_p.A164V	NM_015122.2	NP_055937.1	O14526	FCHO1_HUMAN	FCH domain only 1	164	Mediates membrane-binding.				clathrin coat assembly (GO:0048268)|clathrin-mediated endocytosis (GO:0072583)	coated pit (GO:0005905)|plasma membrane (GO:0005886)	AP-2 adaptor complex binding (GO:0035612)	p.A164V(1)		NS(2)|breast(1)|large_intestine(6)|liver(1)|lung(12)	22						GCTTTGTAGGCGGAGACTAAA	0.607																																					p.A114V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C341T	19						.	C	VAL/ALA,VAL/ALA,VAL/ALA,VAL/ALA	1,4405	2.1+/-5.4	0,1,2202	77.0	78.0	78.0		491,491,341,491	2.8	1.0	19	dbSNP_134	78	3,8597	3.0+/-9.4	0,3,4297	yes	missense-near-splice,missense-near-splice,missense-near-splice,missense-near-splice	FCHO1	NM_001161357.1,NM_001161358.1,NM_001161359.1,NM_015122.2	64,64,64,64	0,4,6499	TT,TC,CC		0.0349,0.0227,0.0308	probably-damaging,probably-damaging,probably-damaging,probably-damaging	164/892,164/890,114/840,164/890	17881602	4,13002	2203	4300	6503	17742602	SO:0001630	splice_region_variant	23149	exon7			AB006628	CCDS32955.1, CCDS59365.1, CCDS59366.1	19p13.12	2008-02-05				ENSG00000130475			29002	protein-coding gene	gene with protein product		613437				12477932	Standard	NM_001161357		Approved	KIAA0290	uc002nhg.3	O14526		ENST00000596536.1:c.490-1C>T	19.37:g.17881602C>T		Somatic		Capture	Illumina HiSeq	Phase_I	17742602	NM_001161359	A6NHE6|A8K5U5|B4E120|Q05C93|Q8IW22	Missense_Mutation	SNP	ENST00000596536.1	37	CCDS32955.1	.	.	.	.	.	.	.	.	.	.	C	13.02	2.112573	0.37242	2.27E-4	3.49E-4	ENSG00000130475	ENST00000252771;ENST00000389133;ENST00000539407	T;T;T	0.49139	0.79;0.79;0.79	3.87	2.84	0.33178	.	0.056555	0.64402	D	0.000002	T	0.33644	0.0870	M	0.73962	2.25	0.43021	D	0.994578	B;P;P	0.39748	0.075;0.616;0.686	B;B;B	0.23275	0.003;0.023;0.045	T	0.16748	-1.0392	10	0.15066	T	0.55	-15.0633	6.6561	0.22988	0.0:0.8704:0.0:0.1296	.	114;164;164	B4E120;O14526;O14526-2	.;FCHO1_HUMAN;.	V	164	ENSP00000252771:A164V;ENSP00000373785:A164V;ENSP00000437978:A164V	ENSP00000252771:A164V	A	+	2	0	FCHO1	17742602	1.000000	0.71417	0.998000	0.56505	0.464000	0.32679	4.821000	0.62679	2.167000	0.68274	0.491000	0.48974	GCG		0.607	FCHO1-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466946.2	NM_015122	Missense_Mutation
REXO1	57455	broad.mit.edu	37	19	1827903	1827903	+	Silent	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr19:1827903C>T	ENST00000170168.4	-	2	979	c.885G>A	c.(883-885)acG>acA	p.T295T	REXO1_ENST00000587524.1_5'UTR	NM_020695.3	NP_065746.3	Q8N1G1	REXO1_HUMAN	REX1, RNA exonuclease 1 homolog (S. cerevisiae)	295						nucleus (GO:0005634)	exonuclease activity (GO:0004527)|nucleic acid binding (GO:0003676)	p.T295T(1)		breast(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(5)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	16		Ovarian(11;1.78e-06)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		TACCTGGGACCGTGGCGGCCT	0.647																																					p.T295T												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G885A	19						.						44.0	46.0	45.0					19																	1827903		2203	4300	6503	1778903	SO:0001819	synonymous_variant	57455	exon2			AB032964	CCDS32866.1	19p13.3	2014-05-28	2005-08-22	2005-08-22	ENSG00000079313	ENSG00000079313			24616	protein-coding gene	gene with protein product	"""elongin A binding protein 1"""	609614	"""transcription elongation factor B polypeptide 3 binding protein 1"""	TCEB3BP1		10574461	Standard	NM_020695		Approved	EloA-BP1, KIAA1138	uc002lua.4	Q8N1G1	OTTHUMG00000179991	ENST00000170168.4:c.885G>A	19.37:g.1827903C>T		Somatic		Capture	Illumina HiSeq	Phase_I	1778903	NM_020695	Q9ULT2	Silent	SNP	ENST00000170168.4	37	CCDS32866.1																																																																																				0.647	REXO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449200.1	NM_020695	
FCHO1	23149	broad.mit.edu	37	19	17895541	17895541	+	Missense_Mutation	SNP	G	G	A	rs151277101		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr19:17895541G>A	ENST00000596536.1	+	26	2517	c.2234G>A	c.(2233-2235)cGc>cAc	p.R745H	FCHO1_ENST00000252771.7_Missense_Mutation_p.R745H|FCHO1_ENST00000596951.1_Missense_Mutation_p.R745H|FCHO1_ENST00000597512.1_Missense_Mutation_p.R752H|FCHO1_ENST00000539407.1_Missense_Mutation_p.R745H|FCHO1_ENST00000595033.1_Missense_Mutation_p.R695H|FCHO1_ENST00000594202.1_Missense_Mutation_p.R745H|FCHO1_ENST00000389133.4_Missense_Mutation_p.R745H|FCHO1_ENST00000600676.1_Missense_Mutation_p.R745H	NM_015122.2	NP_055937.1	O14526	FCHO1_HUMAN	FCH domain only 1	745	MHD. {ECO:0000255|PROSITE- ProRule:PRU00404}.|Mediates interaction with AGFG1, CALM, DAB2, EPS15, EPS15R, ITSN1 and clathrin.				clathrin coat assembly (GO:0048268)|clathrin-mediated endocytosis (GO:0072583)	coated pit (GO:0005905)|plasma membrane (GO:0005886)	AP-2 adaptor complex binding (GO:0035612)	p.R745H(1)		NS(2)|breast(1)|large_intestine(6)|liver(1)|lung(12)	22						TAGTTCTCCCGCCCGGGTCCC	0.612											OREG0025350	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	1	0.000199681	0.0	0.0	5008	,	,		17415	0.0		0.0	False		,,,				2504	0.001				p.R695H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2084A	19						.	G	HIS/ARG,HIS/ARG,HIS/ARG,HIS/ARG	1,4405	2.1+/-5.4	0,1,2202	130.0	110.0	117.0		2234,2234,2084,2234	2.6	1.0	19	dbSNP_134	117	0,8600		0,0,4300	no	missense,missense,missense,missense	FCHO1	NM_001161357.1,NM_001161358.1,NM_001161359.1,NM_015122.2	29,29,29,29	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	benign,benign,benign,benign	745/892,745/890,695/840,745/890	17895541	1,13005	2203	4300	6503	17756541	SO:0001583	missense	23149	exon24			AB006628	CCDS32955.1, CCDS59365.1, CCDS59366.1	19p13.12	2008-02-05				ENSG00000130475			29002	protein-coding gene	gene with protein product		613437				12477932	Standard	NM_001161357		Approved	KIAA0290	uc002nhg.3	O14526		ENST00000596536.1:c.2234G>A	19.37:g.17895541G>A	ENSP00000470731:p.Arg745His	Somatic	721	Capture	Illumina HiSeq	Phase_I	17756541	NM_001161359	A6NHE6|A8K5U5|B4E120|Q05C93|Q8IW22	Missense_Mutation	SNP	ENST00000596536.1	37	CCDS32955.1	.	.	.	.	.	.	.	.	.	.	G	12.87	2.068367	0.36470	2.27E-4	0.0	ENSG00000130475	ENST00000252771;ENST00000389133;ENST00000539407	T;T;T	0.42131	0.98;0.98;0.98	3.64	2.59	0.31030	Muniscin C-terminal mu homology domain (1);	0.391328	0.24640	N	0.036813	T	0.25382	0.0617	L	0.29908	0.895	0.36307	D	0.857401	B;B	0.06786	0.001;0.001	B;B	0.06405	0.002;0.001	T	0.18429	-1.0337	10	0.34782	T	0.22	-20.504	5.0272	0.14391	0.2485:0.0:0.7515:0.0	.	745;745	O14526;O14526-2	FCHO1_HUMAN;.	H	745	ENSP00000252771:R745H;ENSP00000373785:R745H;ENSP00000437978:R745H	ENSP00000252771:R745H	R	+	2	0	FCHO1	17756541	0.991000	0.36638	1.000000	0.80357	0.896000	0.52359	1.176000	0.31957	2.056000	0.61249	0.436000	0.28706	CGC		0.612	FCHO1-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466946.2	NM_015122	
JAK3	3718	broad.mit.edu	37	19	17945718	17945718	+	Silent	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr19:17945718C>T	ENST00000527670.1	-	15	2171	c.2142G>A	c.(2140-2142)acG>acA	p.T714T	JAK3_ENST00000534444.1_Silent_p.T714T|JAK3_ENST00000458235.1_Silent_p.T714T			P52333	JAK3_HUMAN	Janus kinase 3	714	Protein kinase 1. {ECO:0000255|PROSITE- ProRule:PRU00159}.				B cell differentiation (GO:0030183)|enzyme linked receptor protein signaling pathway (GO:0007167)|innate immune response (GO:0045087)|interleukin-4-mediated signaling pathway (GO:0035771)|intracellular signal transduction (GO:0035556)|JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)|negative regulation of dendritic cell cytokine production (GO:0002731)|negative regulation of FasL biosynthetic process (GO:0045221)|negative regulation of interleukin-10 production (GO:0032693)|negative regulation of interleukin-12 production (GO:0032695)|negative regulation of T cell activation (GO:0050868)|negative regulation of T-helper 1 cell differentiation (GO:0045626)|negative regulation of thymocyte apoptotic process (GO:0070244)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of dendritic cell apoptotic process (GO:2000670)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein phosphorylation (GO:0006468)|regulation of T cell apoptotic process (GO:0070232)|response to interleukin-15 (GO:0070672)|response to interleukin-2 (GO:0070669)|response to interleukin-4 (GO:0070670)|response to interleukin-9 (GO:0071104)|STAT protein import into nucleus (GO:0007262)|T cell homeostasis (GO:0043029)|tyrosine phosphorylation of STAT protein (GO:0007260)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|membrane (GO:0016020)	ATP binding (GO:0005524)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein phosphatase binding (GO:0019903)|protein tyrosine kinase activity (GO:0004713)	p.T714T(1)		breast(5)|endometrium(4)|haematopoietic_and_lymphoid_tissue(85)|kidney(4)|large_intestine(11)|lung(22)|ovary(3)|prostate(5)|skin(1)|stomach(2)|upper_aerodigestive_tract(5)	147					Tofacitinib(DB08895)	CTTCCCAGACCGTGGCGCCGA	0.632		2	Mis		"""acute megakaryocytic leukemia, ETP ALL"""																																p.T714T			Dom	yes		19	19p13.1	3718	Janus kinase 3		L	.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G2142A	19						.						72.0	77.0	76.0					19																	17945718		2203	4300	6503	17806718	SO:0001819	synonymous_variant	3718	exon16			U31601	CCDS12366.1	19p13-p12	2014-09-17	2009-04-23		ENSG00000105639	ENSG00000105639	2.7.10.1		6193	protein-coding gene	gene with protein product	"""tyrosine-protein kinase JAK3"", ""leukocyte Janus kinase"""	600173				8921370, 9226382	Standard	NM_000215		Approved	L-JAK, JAKL, LJAK, JAK3_HUMAN, JAK-3	uc002nhn.4	P52333	OTTHUMG00000165648	ENST00000527670.1:c.2142G>A	19.37:g.17945718C>T		Somatic		Capture	Illumina HiSeq	Phase_I	17806718	NM_000215	Q13259|Q13260|Q13611|Q8N1E8|Q99699|Q9Y6S2	Silent	SNP	ENST00000527670.1	37	CCDS12366.1																																																																																				0.632	JAK3-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385549.1	NM_000215	
SLC5A5	6528	broad.mit.edu	37	19	17986774	17986774	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr19:17986774C>A	ENST00000222248.3	+	5	904	c.557C>A	c.(556-558)gCt>gAt	p.A186D		NM_000453.2	NP_000444.1	Q92911	SC5A5_HUMAN	solute carrier family 5 (sodium/iodide cotransporter), member 5	186					cellular nitrogen compound metabolic process (GO:0034641)|cellular response to cAMP (GO:0071320)|cellular response to gonadotropin stimulus (GO:0071371)|iodide transport (GO:0015705)|ion transport (GO:0006811)|small molecule metabolic process (GO:0044281)|thyroid hormone generation (GO:0006590)|transmembrane transport (GO:0055085)|transport (GO:0006810)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|vesicle (GO:0031982)	iodide transmembrane transporter activity (GO:0015111)|sodium:iodide symporter activity (GO:0008507)	p.A186D(1)		NS(2)|biliary_tract(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|large_intestine(6)|lung(13)|ovary(1)|prostate(1)|skin(3)	31						GGCATGAAGGCTGTGGTCTGG	0.622																																					p.A186D	Melanoma(65;1008 1708 7910 46650)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C557A	19						.						319.0	229.0	259.0					19																	17986774		2203	4300	6503	17847774	SO:0001583	missense	6528	exon5				CCDS12368.1	19p13.11	2013-07-19	2013-07-19		ENSG00000105641	ENSG00000105641		"""Solute carriers"""	11040	protein-coding gene	gene with protein product		601843	"""solute carrier family 5 (sodium iodide symporter), member 5"""			9231811	Standard	NM_000453		Approved	NIS	uc002nhr.4	Q92911		ENST00000222248.3:c.557C>A	19.37:g.17986774C>A	ENSP00000222248:p.Ala186Asp	Somatic		Capture	Illumina HiSeq	Phase_I	17847774	NM_000453	O43702|Q2M335|Q9NYB6	Missense_Mutation	SNP	ENST00000222248.3	37	CCDS12368.1	.	.	.	.	.	.	.	.	.	.	C	25.3	4.626573	0.87560	.	.	ENSG00000105641	ENST00000222248	D	0.94138	-3.36	5.0	5.0	0.66597	Sodium/solute symporter, conserved site (1);	0.056142	0.64402	D	0.000001	D	0.98124	0.9381	H	0.98507	4.25	0.80722	D	1	D	0.76494	0.999	D	0.83275	0.996	D	0.99466	1.0944	10	0.87932	D	0	.	16.1536	0.81640	0.0:1.0:0.0:0.0	.	186	Q92911	SC5A5_HUMAN	D	186	ENSP00000222248:A186D	ENSP00000222248:A186D	A	+	2	0	SLC5A5	17847774	1.000000	0.71417	1.000000	0.80357	0.840000	0.47671	7.649000	0.83500	2.515000	0.84797	0.491000	0.48974	GCT		0.622	SLC5A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466690.1		
KCNN1	3780	broad.mit.edu	37	19	18092728	18092728	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr19:18092728C>T	ENST00000222249.9	+	5	1028	c.709C>T	c.(709-711)Cgc>Tgc	p.R237C		NM_002248.3	NP_002239.2	Q92952	KCNN1_HUMAN	potassium intermediate/small conductance calcium-activated channel, subfamily N, member 1	237					potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|synaptic transmission (GO:0007268)	neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	calcium-activated potassium channel activity (GO:0015269)|calmodulin binding (GO:0005516)|small conductance calcium-activated potassium channel activity (GO:0016286)	p.R254C(1)		endometrium(1)|kidney(1)|lung(5)|urinary_tract(1)	8					Miconazole(DB01110)|Procaine(DB00721)	CATGTTCCTGCGCCTCTACCT	0.647																																					p.R237C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C709T	19						.						40.0	41.0	41.0					19																	18092728		2203	4300	6503	17953728	SO:0001583	missense	3780	exon5			U69883	CCDS67611.1	19p13.1	2012-07-05				ENSG00000105642		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels, calcium-activated"""	6290	protein-coding gene	gene with protein product		602982				8781233, 10516439, 16382103	Standard	NM_002248		Approved	KCa2.1, hSK1	uc002nht.3	Q92952		ENST00000222249.9:c.709C>T	19.37:g.18092728C>T	ENSP00000476519:p.Arg237Cys	Somatic		Capture	Illumina HiSeq	Phase_I	17953728	NM_002248	Q5KR10|Q6DJU4	Missense_Mutation	SNP	ENST00000222249.9	37		.	.	.	.	.	.	.	.	.	.	C	22.7	4.329965	0.81690	.	.	ENSG00000105642	ENST00000222249;ENST00000536713	.	.	.	4.7	4.7	0.59300	.	0.000000	0.64402	D	0.000001	T	0.79753	0.4500	M	0.87456	2.885	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.82733	-0.0311	9	0.87932	D	0	-23.2761	10.4122	0.44301	0.1953:0.8047:0.0:0.0	.	237	Q92952	KCNN1_HUMAN	C	254;237	.	ENSP00000222249:R254C	R	+	1	0	KCNN1	17953728	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	2.887000	0.48586	2.168000	0.68352	0.561000	0.74099	CGC		0.647	KCNN1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000471896.2	NM_002248	
MAST3	23031	broad.mit.edu	37	19	18245670	18245670	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr19:18245670G>A	ENST00000262811.6	+	16	1661	c.1661G>A	c.(1660-1662)cGc>cAc	p.R554H		NM_015016.1	NP_055831.1	O60307	MAST3_HUMAN	microtubule associated serine/threonine kinase 3	554	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.						ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|protein serine/threonine kinase activity (GO:0004674)	p.R576H(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(8)|lung(6)|ovary(4)|pancreas(1)|stomach(1)	31						GTGATCTTCCGCCAGGGCTAT	0.632																																					p.R554H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1661A	19						.						84.0	88.0	87.0					19																	18245670		2023	4204	6227	18106670	SO:0001583	missense	23031	exon16			AB011133	CCDS46014.1	19p13	2008-02-05				ENSG00000099308			19036	protein-coding gene	gene with protein product		612258					Standard	NM_015016		Approved	KIAA0561	uc002nhz.4	O60307		ENST00000262811.6:c.1661G>A	19.37:g.18245670G>A	ENSP00000262811:p.Arg554His	Somatic		Capture	Illumina HiSeq	Phase_I	18106670	NM_015016	Q7LDZ8|Q9UPI0	Missense_Mutation	SNP	ENST00000262811.6	37	CCDS46014.1	.	.	.	.	.	.	.	.	.	.	G	17.16	3.317623	0.60524	.	.	ENSG00000099308	ENST00000262811	T	0.25250	1.81	4.87	4.87	0.63330	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.131252	0.56097	D	0.000035	T	0.18215	0.0437	L	0.31420	0.93	0.54753	D	0.999988	P	0.35363	0.497	B	0.29598	0.104	T	0.04870	-1.0921	10	0.62326	D	0.03	-23.5892	12.7161	0.57115	0.0:0.0:0.8239:0.1761	.	554	O60307	MAST3_HUMAN	H	554	ENSP00000262811:R554H	ENSP00000262811:R554H	R	+	2	0	MAST3	18106670	1.000000	0.71417	1.000000	0.80357	0.790000	0.44656	6.279000	0.72620	2.258000	0.74832	0.313000	0.20887	CGC		0.632	MAST3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466526.2	XM_038150	
CRTC1	23373	broad.mit.edu	37	19	18860639	18860639	+	Silent	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr19:18860639G>A	ENST00000321949.8	+	5	518	c.492G>A	c.(490-492)caG>caA	p.Q164Q	CRTC1_ENST00000601916.1_Silent_p.Q89Q|CRTC1_ENST00000594658.1_Silent_p.Q123Q|CRTC1_ENST00000338797.6_Silent_p.Q180Q	NM_015321.2	NP_056136.2			CREB regulated transcription coactivator 1									p.Q164Q(1)	CRTC1/MAML2(516)	NS(1)|breast(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(6)|ovary(1)|skin(1)	19						CGCCCACGCAGCCAGAATCCT	0.592																																					p.Q164Q												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G492A	19						.						115.0	93.0	100.0					19																	18860639		2203	4300	6503	18721639	SO:0001819	synonymous_variant	23373	exon5			AY040323	CCDS32963.1, CCDS42525.1	19p13	2012-07-31	2005-11-24	2005-11-24					16062	protein-coding gene	gene with protein product	"""transducer of regulated cAMP response element-binding protein"""	607536	"""mucoepidermoid carcinoma translocated 1"""	MECT1		12539049, 14536081, 14506290	Standard	NM_015321		Approved	KIAA0616, FLJ14027, TORC1	uc010ebv.3	Q6UUV9		ENST00000321949.8:c.492G>A	19.37:g.18860639G>A		Somatic		Capture	Illumina HiSeq	Phase_I	18721639	NM_015321		Silent	SNP	ENST00000321949.8	37	CCDS32963.1																																																																																				0.592	CRTC1-002	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465151.3	NM_025021	
COMP	1311	broad.mit.edu	37	19	18897428	18897428	+	Missense_Mutation	SNP	C	C	T	rs151050419		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr19:18897428C>T	ENST00000222271.2	-	11	1212	c.1168G>A	c.(1168-1170)Gta>Ata	p.V390I	COMP_ENST00000425807.1_Missense_Mutation_p.V337I|COMP_ENST00000542601.2_Missense_Mutation_p.V357I	NM_000095.2	NP_000086.2	P49747	COMP_HUMAN	cartilage oligomeric matrix protein	390					apoptotic process (GO:0006915)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|growth plate cartilage development (GO:0003417)|limb development (GO:0060173)|negative regulation of apoptotic process (GO:0043066)|organ morphogenesis (GO:0009887)|skeletal system development (GO:0001501)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|collagen binding (GO:0005518)|extracellular matrix structural constituent (GO:0005201)|heparan sulfate proteoglycan binding (GO:0043395)|heparin binding (GO:0008201)|protease binding (GO:0002020)	p.V390I(1)		breast(6)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(12)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	32						GAGTTGGGTACCCTAGGGCAG	0.577																																					p.V390I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1168A	19						.	C	ILE/VAL	0,4406		0,0,2203	149.0	110.0	123.0		1168	-0.4	0.7	19	dbSNP_134	123	1,8599	1.2+/-3.3	0,1,4299	no	missense	COMP	NM_000095.2	29	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	benign	390/758	18897428	1,13005	2203	4300	6503	18758428	SO:0001583	missense	1311	exon11			L32137	CCDS12385.1	19p13.1	2008-02-05				ENSG00000105664			2227	protein-coding gene	gene with protein product	"""thrombospondin-5"""	600310	"""cartilage oligomeric matrix protein (pseudoachondroplasia, epiphyseal dysplasia 1, multiple)"""	PSACH, EDM1, EPD1		7713493, 8307576	Standard	NM_000095		Approved	MED, THBS5	uc002nke.3	P49747	OTTHUMG00000169318	ENST00000222271.2:c.1168G>A	19.37:g.18897428C>T	ENSP00000222271:p.Val390Ile	Somatic		Capture	Illumina HiSeq	Phase_I	18758428	NM_000095	B4DKJ3|O14592|Q16388|Q16389|Q2NL86|Q8N4T2	Missense_Mutation	SNP	ENST00000222271.2	37	CCDS12385.1	.	.	.	.	.	.	.	.	.	.	C	8.877	0.950798	0.18431	0.0	1.16E-4	ENSG00000105664	ENST00000542601;ENST00000222271;ENST00000425807;ENST00000454701	D;D;D	0.98313	-4.86;-4.86;-4.86	3.35	-0.418	0.12344	.	0.084607	0.47455	N	0.000225	D	0.95101	0.8413	L	0.46157	1.445	0.21719	N	0.999579	B;B	0.09022	0.0;0.002	B;B	0.09377	0.004;0.004	D	0.89120	0.3502	10	0.46703	T	0.11	-12.8851	8.1266	0.31003	0.0:0.6873:0.1317:0.181	.	337;390	B4DKJ3;P49747	.;COMP_HUMAN	I	357;390;337;377	ENSP00000439156:V357I;ENSP00000222271:V390I;ENSP00000403792:V337I	ENSP00000222271:V390I	V	-	1	0	COMP	18758428	0.473000	0.25878	0.680000	0.29994	0.255000	0.26057	1.388000	0.34442	-0.142000	0.11354	-1.786000	0.00637	GTA		0.577	COMP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403457.1	NM_000095	
MKNK2	2872	broad.mit.edu	37	19	2043502	2043502	+	Splice_Site	SNP	C	C	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr19:2043502C>A	ENST00000591601.1	-	5	454	c.419G>T	c.(418-420)aGg>aTg	p.R140M	MKNK2_ENST00000588014.1_5'Flank|MKNK2_ENST00000591142.1_5'Flank|MKNK2_ENST00000541165.1_Splice_Site_p.R9M|MKNK2_ENST00000591588.1_5'Flank|MKNK2_ENST00000250896.3_Splice_Site_p.R140M|MKNK2_ENST00000309340.7_Splice_Site_p.R140M			Q9HBH9	MKNK2_HUMAN	MAP kinase interacting serine/threonine kinase 2	140	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cell surface receptor signaling pathway (GO:0007166)|cellular response to arsenic-containing substance (GO:0071243)|extrinsic apoptotic signaling pathway in absence of ligand (GO:0097192)|hemopoiesis (GO:0030097)|intracellular signal transduction (GO:0035556)|protein phosphorylation (GO:0006468)|regulation of translation (GO:0006417)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)	p.R140M(2)		breast(1)|kidney(3)|large_intestine(3)|lung(3)	10		Ovarian(11;2.11e-07)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		GCTCACCTACCTGTGTCCCTG	0.587																																					p.R140M												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G419T	19						.						142.0	98.0	113.0					19																	2043502		2203	4300	6503	1994502	SO:0001630	splice_region_variant	2872	exon6			AF125532	CCDS12079.1, CCDS12080.1	19p13.3	2012-12-20			ENSG00000099875	ENSG00000099875			7111	protein-coding gene	gene with protein product	"""Putative map kinase interacting kinase"""	605069	"""G protein-coupled receptor kinase 7"""	GPRK7		11013076	Standard	NM_199054		Approved	MNK2	uc002lus.2	Q9HBH9	OTTHUMG00000180020	ENST00000591601.1:c.419+1G>T	19.37:g.2043502C>A		Somatic		Capture	Illumina HiSeq	Phase_I	1994502	NM_017572	Q6GPI3|Q9HBH8|Q9UHR0|Q9Y2N6	Missense_Mutation	SNP	ENST00000591601.1	37	CCDS12080.1	.	.	.	.	.	.	.	.	.	.	C	27.4	4.825167	0.90955	.	.	ENSG00000099875	ENST00000309340;ENST00000250896;ENST00000541165;ENST00000545627	T;T;T	0.41065	1.01;1.01;1.01	4.47	4.47	0.54385	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.159851	0.53938	D	0.000041	T	0.56077	0.1961	L	0.49350	1.555	0.53688	D	0.999979	D;P	0.58970	0.984;0.905	D;P	0.67231	0.95;0.693	T	0.54410	-0.8298	9	.	.	.	-14.874	14.6262	0.68624	0.0:1.0:0.0:0.0	.	140;140	Q9HBH9;Q9HBH9-2	MKNK2_HUMAN;.	M	140;140;9;93	ENSP00000309485:R140M;ENSP00000250896:R140M;ENSP00000438904:R9M	.	R	-	2	0	MKNK2	1994502	1.000000	0.71417	0.997000	0.53966	0.934000	0.57294	2.093000	0.41710	2.009000	0.58944	0.561000	0.74099	AGG		0.587	MKNK2-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000449312.1	NM_199054	Missense_Mutation
AP3D1	8943	broad.mit.edu	37	19	2110171	2110171	+	Silent	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr19:2110171C>T	ENST00000345016.5	-	26	3273	c.3042G>A	c.(3040-3042)gcG>gcA	p.A1014A	AP3D1_ENST00000355272.6_Silent_p.A1076A|AP3D1_ENST00000356926.4_Silent_p.A973A|AP3D1_ENST00000350812.6_Silent_p.A845A	NM_003938.6	NP_003929.4	O14617	AP3D1_HUMAN	adaptor-related protein complex 3, delta 1 subunit	1014					anterograde axon cargo transport (GO:0008089)|anterograde synaptic vesicle transport (GO:0048490)|antigen processing and presentation, exogenous lipid antigen via MHC class Ib (GO:0048007)|endosome to melanosome transport (GO:0035646)|eye pigment biosynthetic process (GO:0006726)|intracellular protein transport (GO:0006886)|melanosome organization (GO:0032438)|positive regulation of NK T cell differentiation (GO:0051138)|protein localization to membrane (GO:0072657)|protein localization to organelle (GO:0033365)|regulation of sequestering of zinc ion (GO:0061088)|synaptic vesicle membrane organization (GO:0048499)	endosome membrane (GO:0010008)|Golgi apparatus (GO:0005794)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|membrane coat (GO:0030117)|terminal bouton (GO:0043195)	protein transporter activity (GO:0008565)|transporter activity (GO:0005215)	p.A1014A(2)		breast(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(23)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	37		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		TGAGCTTCTGCGCCATGACGA	0.637																																					p.A1014A												.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.G3042A	19						.						70.0	71.0	71.0					19																	2110171		2056	4181	6237	2061171	SO:0001819	synonymous_variant	8943	exon26			U91930	CCDS42459.1, CCDS58638.1	19p13.3	2014-09-04			ENSG00000065000	ENSG00000065000			568	protein-coding gene	gene with protein product		607246				9151686, 9303295	Standard	NM_003938		Approved	ADTD	uc002lva.4	O14617	OTTHUMG00000180354	ENST00000345016.5:c.3042G>A	19.37:g.2110171C>T		Somatic		Capture	Illumina HiSeq	Phase_I	2061171	NM_003938	O00202|O75262|Q59HF5|Q96G11|Q9H3C6	Silent	SNP	ENST00000345016.5	37	CCDS42459.1																																																																																				0.637	AP3D1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000450912.1		
SF3A2	8175	broad.mit.edu	37	19	2246936	2246936	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr19:2246936C>T	ENST00000221494.5	+	7	879	c.461C>T	c.(460-462)gCg>gTg	p.A154V	AMH_ENST00000221496.4_5'Flank	NM_007165.4	NP_009096.2	Q15428	SF3A2_HUMAN	splicing factor 3a, subunit 2, 66kDa	154					gene expression (GO:0010467)|mRNA 3'-splice site recognition (GO:0000389)|mRNA processing (GO:0006397)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)	catalytic step 2 spliceosome (GO:0071013)|nucleoplasm (GO:0005654)|small nuclear ribonucleoprotein complex (GO:0030532)|spliceosomal complex (GO:0005681)	poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)	p.A154V(1)		NS(1)|large_intestine(1)|lung(2)	4		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		TTCATGTCTGCGTACGAGCAG	0.647																																					p.A154V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C461T	19						.						66.0	58.0	61.0					19																	2246936		2203	4300	6503	2197936	SO:0001583	missense	8175	exon7			L21990	CCDS12084.1	19p13.3	2012-10-02	2002-08-29		ENSG00000104897	ENSG00000104897			10766	protein-coding gene	gene with protein product		600796	"""splicing factor 3a, subunit 2, 66kD"""			8211113, 8541848	Standard	NM_007165		Approved	SF3a66, SAP62, PRPF11, Prp11	uc002lvg.3	Q15428	OTTHUMG00000180414	ENST00000221494.5:c.461C>T	19.37:g.2246936C>T	ENSP00000221494:p.Ala154Val	Somatic		Capture	Illumina HiSeq	Phase_I	2197936	NM_007165	B2RBU1|D6W605|O75245	Missense_Mutation	SNP	ENST00000221494.5	37	CCDS12084.1	.	.	.	.	.	.	.	.	.	.	C	28.9	4.963236	0.92791	.	.	ENSG00000104897	ENST00000221494	D	0.88124	-2.34	5.04	4.01	0.46588	.	0.000000	0.85682	D	0.000000	D	0.93275	0.7857	M	0.86343	2.81	0.80722	D	1	D	0.89917	1.0	D	0.70716	0.97	D	0.93529	0.6868	10	0.62326	D	0.03	-17.4912	12.1449	0.54018	0.0:0.9175:0.0:0.0825	.	154	Q15428	SF3A2_HUMAN	V	154	ENSP00000221494:A154V	ENSP00000221494:A154V	A	+	2	0	SF3A2	2197936	1.000000	0.71417	0.929000	0.37066	0.757000	0.42996	7.004000	0.76317	1.109000	0.41680	0.555000	0.69702	GCG		0.647	SF3A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451268.3		
JSRP1	126306	broad.mit.edu	37	19	2254260	2254260	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr19:2254260G>T	ENST00000300961.6	-	4	252	c.188C>A	c.(187-189)cCc>cAc	p.P63H	JSRP1_ENST00000586471.2_Missense_Mutation_p.P63H	NM_144616.3	NP_653217.1	Q96MG2	JSPR1_HUMAN	junctional sarcoplasmic reticulum protein 1	63	Mediates interaction with CACNA1S. {ECO:0000250}.				protein localization to membrane (GO:0072657)|regulation of ryanodine-sensitive calcium-release channel activity (GO:0060314)|skeletal muscle contraction (GO:0003009)	membrane (GO:0016020)|sarcoplasmic reticulum (GO:0016529)		p.P63H(1)		haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(1)|pancreas(1)|urinary_tract(1)	6				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		CATCTTCTTGGGCCTGGTGTC	0.602											OREG0025137	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.P63H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C188A	19						.						93.0	94.0	93.0					19																	2254260		2203	4300	6503	2205260	SO:0001583	missense	126306	exon4			AK056978	CCDS12086.1	19p13.3	2010-03-23			ENSG00000167476	ENSG00000167476			24963	protein-coding gene	gene with protein product	"""homolog of mouse skeletal muscle sarcoplasmic reticulum protein JP-45"""	608743				12871958	Standard	NM_144616		Approved	JP-45, FLJ32416	uc002lvj.2	Q96MG2		ENST00000300961.6:c.188C>A	19.37:g.2254260G>T	ENSP00000300961:p.Pro63His	Somatic	602	Capture	Illumina HiSeq	Phase_I	2205260	NM_144616		Missense_Mutation	SNP	ENST00000300961.6	37	CCDS12086.1	.	.	.	.	.	.	.	.	.	.	G	14.90	2.671972	0.47781	.	.	ENSG00000167476	ENST00000300961	T	0.18338	2.22	2.88	-0.627	0.11541	.	0.918821	0.09037	N	0.857882	T	0.19644	0.0472	N	0.24115	0.695	0.09310	N	0.999999	D	0.76494	0.999	D	0.64237	0.923	T	0.17806	-1.0357	10	0.59425	D	0.04	-5.7075	2.9461	0.05846	0.2906:0.2435:0.4658:0.0	.	63	Q96MG2	JSPR1_HUMAN	H	63	ENSP00000300961:P63H	ENSP00000300961:P63H	P	-	2	0	JSRP1	2205260	0.079000	0.21365	0.264000	0.24511	0.918000	0.54935	0.231000	0.17872	-0.043000	0.13513	0.555000	0.69702	CCC		0.602	JSRP1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451266.2	NM_144616	
SPPL2B	56928	broad.mit.edu	37	19	2338839	2338839	+	RNA	SNP	C	C	T	rs201843729		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr19:2338839C>T	ENST00000452401.2	+	0	538							Q8TCT7	SPP2B_HUMAN	signal peptide peptidase like 2B						membrane protein ectodomain proteolysis (GO:0006509)|membrane protein intracellular domain proteolysis (GO:0031293)|regulation of immune response (GO:0050776)	endosome membrane (GO:0010008)|Golgi-associated vesicle membrane (GO:0030660)|integral component of cytoplasmic side of endoplasmic reticulum membrane (GO:0071458)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|lysosomal membrane (GO:0005765)|plasma membrane (GO:0005886)	aspartic endopeptidase activity, intramembrane cleaving (GO:0042500)|protein homodimerization activity (GO:0042803)	p.T153M(1)					Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		GACATCTTCACGGTAGGTCTG	0.642																																					p.T153M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C458T	19						.	G	MET/THR,MET/THR	0,4068		0,0,2034	33.0	36.0	35.0		458,458	2.4	1.0	19		35	1,8369		0,1,4184	yes	missense-near-splice,missense-near-splice	SPPL2B	NM_001077238.1,NM_152988.2	81,81	0,1,6218	TT,TC,CC		0.0119,0.0,0.0080	probably-damaging,probably-damaging	153/512,153/593	2338839	1,12437	2034	4185	6219	2289839			56928	exon4				CCDS74252.1, CCDS74253.1	19p13.3	2012-02-21			ENSG00000005206	ENSG00000005206			30627	protein-coding gene	gene with protein product	"""intramembrane protease 4"""	608239				10819331	Standard	NM_001077238		Approved	IMP4, PSL1, KIAA1532	uc002lvs.3	Q8TCT7			19.37:g.2338839C>T		Somatic		Capture	Illumina HiSeq	Phase_I	2289839	NM_001077238	D6W609|O60365|Q567S3|Q8IUH9|Q9BUY6|Q9H3M4|Q9NPN2|Q9P1Z6	Missense_Mutation	SNP	ENST00000452401.2	37		.	.	.	.	.	.	.	.	.	.	G	17.44	3.390404	0.62066	0.0	1.19E-4	ENSG00000005206	ENST00000452401;ENST00000382189	.	.	.	4.55	2.39	0.29439	.	0.193277	0.52532	D	0.000065	T	0.14874	0.0359	N	0.19112	0.55	0.09310	N	0.999995	B;P;P;P;P;P	0.42337	0.323;0.522;0.466;0.466;0.776;0.66	B;B;B;B;B;B	0.25506	0.047;0.061;0.036;0.036;0.061;0.061	T	0.19289	-1.0310	8	0.46703	T	0.11	-12.9534	5.0537	0.14522	0.6829:0.1838:0.1333:0.0	.	153;153;153;153;153;153	Q8TCT7-4;A6NFV1;Q8TCT7-3;Q8TCT7-2;Q8TCT7;C9JFE6	.;.;.;.;PSL1_HUMAN;.	M	153	.	ENSP00000371624:T153M	T	+	2	0	AC004410.1	2289839	1.000000	0.71417	0.957000	0.39632	0.470000	0.32858	3.128000	0.50492	0.008000	0.14787	-0.382000	0.06688	ACG		0.642	SPPL2B-202	KNOWN	basic	processed_transcript	processed_transcript		NM_020172	
SGTA	6449	broad.mit.edu	37	19	2763719	2763719	+	Silent	SNP	G	G	A	rs150298044		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr19:2763719G>A	ENST00000221566.2	-	6	590	c.429C>T	c.(427-429)ggC>ggT	p.G143G		NM_003021.3	NP_003012.1	O43765	SGTA_HUMAN	small glutamine-rich tetratricopeptide repeat (TPR)-containing, alpha	143					viral process (GO:0016032)	cytoplasm (GO:0005737)		p.G143G(1)		endometrium(2)|large_intestine(2)|lung(2)|ovary(1)	7		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		CCTGCACCGCGCCTGCGTAGT	0.662																																					p.G143G												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C429T	19						.	G		3,4403	6.2+/-15.9	0,3,2200	67.0	56.0	60.0		429	-8.1	0.0	19	dbSNP_134	60	0,8600		0,0,4300	no	coding-synonymous	SGTA	NM_003021.3		0,3,6500	AA,AG,GG		0.0,0.0681,0.0231		143/314	2763719	3,13003	2203	4300	6503	2714719	SO:0001819	synonymous_variant	6449	exon6			AJ223828	CCDS12094.1	19p13	2013-01-10	2003-11-24	2003-11-26		ENSG00000104969		"""Tetratricopeptide (TTC) repeat domain containing"""	10819	protein-coding gene	gene with protein product		603419	"""small glutamine-rich tetratricopeptide repeat (TPR)-containing"""	SGT		9740675, 12735788	Standard	NM_003021		Approved		uc002lwi.1	O43765		ENST00000221566.2:c.429C>T	19.37:g.2763719G>A		Somatic		Capture	Illumina HiSeq	Phase_I	2714719	NM_003021	D6W610|Q6FIA9|Q9BTZ9	Silent	SNP	ENST00000221566.2	37	CCDS12094.1																																																																																				0.662	SGTA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451448.2	NM_003021	
GNA15	2769	broad.mit.edu	37	19	3150197	3150197	+	Silent	SNP	G	G	A	rs375875879	byFrequency	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr19:3150197G>A	ENST00000262958.3	+	3	657	c.399G>A	c.(397-399)gcG>gcA	p.A133A	AC005264.2_ENST00000587587.1_RNA	NM_002068.2	NP_002059.2	P30679	GNA15_HUMAN	guanine nucleotide binding protein (G protein), alpha 15 (Gq class)	133					activation of phospholipase C activity (GO:0007202)|adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|blood coagulation (GO:0007596)|phospholipase C-activating dopamine receptor signaling pathway (GO:0060158)|phospholipase C-activating G-protein coupled acetylcholine receptor signaling pathway (GO:0007207)|platelet activation (GO:0030168)|positive regulation of cytosolic calcium ion concentration (GO:0007204)	heterotrimeric G-protein complex (GO:0005834)|plasma membrane (GO:0005886)	G-protein beta/gamma-subunit complex binding (GO:0031683)|G-protein coupled receptor binding (GO:0001664)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|metal ion binding (GO:0046872)|signal transducer activity (GO:0004871)	p.A133A(1)		large_intestine(5)|lung(3)|skin(7)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	18		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;7.04e-05)|OV - Ovarian serous cystadenocarcinoma(105;5.08e-113)|Epithelial(107;6.19e-111)|all cancers(105;6.19e-103)|BRCA - Breast invasive adenocarcinoma(158;0.00145)|STAD - Stomach adenocarcinoma(1328;0.184)		GCTACGCTGCGGCCATGCAGT	0.622													G|||	7	0.00139776	0.0	0.0	5008	,	,		15345	0.0		0.0	False		,,,				2504	0.0072				p.A133A												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G399A	19						.	G		0,4406		0,0,2203	85.0	84.0	84.0		399	-0.4	0.6	19		84	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	GNA15	NM_002068.2		0,1,6502	AA,AG,GG		0.0116,0.0,0.0077		133/375	3150197	1,13005	2203	4300	6503	3101197	SO:0001819	synonymous_variant	2769	exon3				CCDS12104.1	19p13.3	2008-07-16				ENSG00000060558			4383	protein-coding gene	gene with protein product		139314				1302014	Standard	NM_002068		Approved	GNA16	uc002lxf.2	P30679		ENST00000262958.3:c.399G>A	19.37:g.3150197G>A		Somatic		Capture	Illumina HiSeq	Phase_I	3101197	NM_002068	E9KL40|E9KL47|O75247|Q53XK2	Silent	SNP	ENST00000262958.3	37	CCDS12104.1																																																																																				0.622	GNA15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452320.2	NM_002068	
TJP3	27134	broad.mit.edu	37	19	3748060	3748060	+	Missense_Mutation	SNP	C	C	T	rs199978081	byFrequency	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr19:3748060C>T	ENST00000541714.2	+	19	3053	c.2591C>T	c.(2590-2592)tCg>tTg	p.S864L	TJP3_ENST00000262968.9_Missense_Mutation_p.S897L|TJP3_ENST00000587686.1_Missense_Mutation_p.S883L|TJP3_ENST00000382008.3_Missense_Mutation_p.S878L|TJP3_ENST00000539908.2_Missense_Mutation_p.S828L|TJP3_ENST00000589378.1_Missense_Mutation_p.S873L	NM_001267560.1	NP_001254489.1	O95049	ZO3_HUMAN	tight junction protein 3	864					regulation of G1/S transition of mitotic cell cycle (GO:2000045)	apical plasma membrane (GO:0016324)|nucleus (GO:0005634)|tight junction (GO:0005923)		p.S897L(1)		breast(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(2)|lung(10)|ovary(1)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)	26				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0118)|STAD - Stomach adenocarcinoma(1328;0.18)		GGGAGAATCTCGGCTCATCAG	0.682																																					p.S897L												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C2690T	19						.						7.0	9.0	8.0					19																	3748060		2158	4256	6414	3699060	SO:0001583	missense	27134	exon18			AC005954	CCDS32873.1, CCDS32873.2, CCDS59332.1	19p13.3	2012-07-12	2012-07-12			ENSG00000105289			11829	protein-coding gene	gene with protein product	"""zona occludens 3"""	612689					Standard	NM_001267560		Approved	ZO-3	uc010xhu.3	O95049		ENST00000541714.2:c.2591C>T	19.37:g.3748060C>T	ENSP00000439278:p.Ser864Leu	Somatic		Capture	Illumina HiSeq	Phase_I	3699060	NM_014428	A6NFP3|B3KR73|B3KXZ0|B4E2W6|F5H2X0|F5H4S9|K7EK22|Q32N01	Missense_Mutation	SNP	ENST00000541714.2	37	CCDS32873.2	.	.	.	.	.	.	.	.	.	.	C	7.911	0.736558	0.15574	.	.	ENSG00000105289	ENST00000541714;ENST00000539908;ENST00000382008;ENST00000262968	T;T;T;T	0.07800	3.16;3.33;3.16;3.25	4.26	2.05	0.26809	.	3.319140	0.01218	N	0.008002	T	0.08626	0.0214	L	0.31294	0.92	0.09310	N	1	B;B;B;B	0.19935	0.002;0.04;0.001;0.002	B;B;B;B	0.11329	0.002;0.006;0.001;0.002	T	0.44528	-0.9322	10	0.16420	T	0.52	.	10.9134	0.47122	0.0:0.8251:0.0:0.1749	.	883;897;878;864	O95049-3;O95049-2;O95049;F5H2X0	.;.;ZO3_HUMAN;.	L	864;828;878;897	ENSP00000439278:S864L;ENSP00000439991:S828L;ENSP00000371438:S878L;ENSP00000262968:S897L	ENSP00000262968:S897L	S	+	2	0	TJP3	3699060	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	0.974000	0.29436	-0.020000	0.14032	-1.134000	0.01955	TCG		0.682	TJP3-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000453434.1		
MATK	4145	broad.mit.edu	37	19	3779033	3779033	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr19:3779033C>T	ENST00000310132.6	-	12	1552	c.1154G>A	c.(1153-1155)cGg>cAg	p.R385Q	MATK_ENST00000585778.1_Missense_Mutation_p.R385Q|MATK_ENST00000395040.2_Missense_Mutation_p.R344Q|MATK_ENST00000395045.2_Missense_Mutation_p.R386Q	NM_139355.2	NP_647612.1	P42679	MATK_HUMAN	megakaryocyte-associated tyrosine kinase	385	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cell proliferation (GO:0008283)|mesoderm development (GO:0007498)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of cell proliferation (GO:0008284)|protein phosphorylation (GO:0006468)	cytosol (GO:0005829)|membrane (GO:0016020)	ATP binding (GO:0005524)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein tyrosine kinase activity (GO:0004713)	p.R385Q(1)		central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(13)|ovary(1)|skin(2)|stomach(2)|urinary_tract(1)	26		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.00461)|STAD - Stomach adenocarcinoma(1328;0.18)		GACGGGCAGCCGGCTTGAGTC	0.657																																					p.R344Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1031A	19						.						30.0	34.0	33.0					19																	3779033		2203	4300	6503	3730033	SO:0001583	missense	4145	exon11			L18974	CCDS12113.1, CCDS12114.1, CCDS42468.1	19p13.3	2013-02-14						"""SH2 domain containing"""	6906	protein-coding gene	gene with protein product	"""Csk-homologous kinase"", ""tyrosine-protein kinase CTK"", ""protein kinase HYL"", ""hematopoietic consensus tyrosine-lacking kinase"", ""tyrosylprotein kinase"", ""hydroxyaryl-protein kinase"", ""Csk-type protein tyrosine kinase"", ""HYL tyrosine kinase"", ""tyrosine kinase MATK"", ""leukocyte carboxyl-terminal src kinase related"""	600038				8288563, 7530249	Standard	NM_139355		Approved	HYLTK, CTK, HYL, Lsk, CHK, HHYLTK, DKFZp434N1212, MGC1708, MGC2101	uc002lyt.3	P42679		ENST00000310132.6:c.1154G>A	19.37:g.3779033C>T	ENSP00000308734:p.Arg385Gln	Somatic		Capture	Illumina HiSeq	Phase_I	3730033	NM_139354	B3KNZ9|Q9NST8	Missense_Mutation	SNP	ENST00000310132.6	37	CCDS12114.1	.	.	.	.	.	.	.	.	.	.	C	16.32	3.089578	0.55968	.	.	ENSG00000007264	ENST00000395045;ENST00000310132;ENST00000395040	T;T;T	0.62498	0.02;0.02;0.02	4.47	4.47	0.54385	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.164515	0.41938	D	0.000794	T	0.58977	0.2160	L	0.47190	1.495	0.29279	N	0.870151	D;D;D	0.60575	0.967;0.988;0.967	P;P;P	0.46362	0.514;0.514;0.514	T	0.63301	-0.6668	10	0.87932	D	0	-42.2188	12.3369	0.55073	0.1809:0.8191:0.0:0.0	.	385;386;385	F1T0G6;B3KNZ9;P42679	.;.;MATK_HUMAN	Q	386;385;344	ENSP00000378485:R386Q;ENSP00000308734:R385Q;ENSP00000378481:R344Q	ENSP00000308734:R385Q	R	-	2	0	MATK	3730033	1.000000	0.71417	1.000000	0.80357	0.152000	0.21847	2.987000	0.49378	2.225000	0.72522	0.478000	0.44815	CGG		0.657	MATK-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000453639.1	NM_139355	
MATK	4145	broad.mit.edu	37	19	3779422	3779422	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr19:3779422G>A	ENST00000310132.6	-	11	1353	c.955C>T	c.(955-957)Cgg>Tgg	p.R319W	MATK_ENST00000585778.1_Missense_Mutation_p.R319W|MATK_ENST00000395040.2_Missense_Mutation_p.R278W|MATK_ENST00000395045.2_Missense_Mutation_p.R320W	NM_139355.2	NP_647612.1	P42679	MATK_HUMAN	megakaryocyte-associated tyrosine kinase	319	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cell proliferation (GO:0008283)|mesoderm development (GO:0007498)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of cell proliferation (GO:0008284)|protein phosphorylation (GO:0006468)	cytosol (GO:0005829)|membrane (GO:0016020)	ATP binding (GO:0005524)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein tyrosine kinase activity (GO:0004713)	p.R319W(1)		central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(13)|ovary(1)|skin(2)|stomach(2)|urinary_tract(1)	26		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.00461)|STAD - Stomach adenocarcinoma(1328;0.18)		GCTCGACCCCGGGTCCGCAGA	0.682																																					p.R278W												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C832T	19						.						39.0	42.0	41.0					19																	3779422		2203	4300	6503	3730422	SO:0001583	missense	4145	exon10			L18974	CCDS12113.1, CCDS12114.1, CCDS42468.1	19p13.3	2013-02-14						"""SH2 domain containing"""	6906	protein-coding gene	gene with protein product	"""Csk-homologous kinase"", ""tyrosine-protein kinase CTK"", ""protein kinase HYL"", ""hematopoietic consensus tyrosine-lacking kinase"", ""tyrosylprotein kinase"", ""hydroxyaryl-protein kinase"", ""Csk-type protein tyrosine kinase"", ""HYL tyrosine kinase"", ""tyrosine kinase MATK"", ""leukocyte carboxyl-terminal src kinase related"""	600038				8288563, 7530249	Standard	NM_139355		Approved	HYLTK, CTK, HYL, Lsk, CHK, HHYLTK, DKFZp434N1212, MGC1708, MGC2101	uc002lyt.3	P42679		ENST00000310132.6:c.955C>T	19.37:g.3779422G>A	ENSP00000308734:p.Arg319Trp	Somatic		Capture	Illumina HiSeq	Phase_I	3730422	NM_139354	B3KNZ9|Q9NST8	Missense_Mutation	SNP	ENST00000310132.6	37	CCDS12114.1	.	.	.	.	.	.	.	.	.	.	G	17.64	3.439070	0.63067	.	.	ENSG00000007264	ENST00000395045;ENST00000310132;ENST00000395040	D;D;D	0.83506	-1.73;-1.73;-1.73	3.52	2.45	0.29901	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.218073	0.37809	N	0.001927	D	0.89291	0.6673	M	0.89658	3.05	0.53005	D	0.999965	D;D;D	0.89917	0.999;1.0;0.999	P;P;P	0.59171	0.69;0.853;0.69	D	0.88573	0.3131	10	0.72032	D	0.01	-18.2697	7.6842	0.28530	0.0:0.1811:0.632:0.1869	.	319;320;319	F1T0G6;B3KNZ9;P42679	.;.;MATK_HUMAN	W	320;319;278	ENSP00000378485:R320W;ENSP00000308734:R319W;ENSP00000378481:R278W	ENSP00000308734:R319W	R	-	1	2	MATK	3730422	0.989000	0.36119	0.668000	0.29813	0.939000	0.58152	2.306000	0.43673	0.808000	0.34231	0.306000	0.20318	CGG		0.682	MATK-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000453639.1	NM_139355	
GATAD2A	54815	broad.mit.edu	37	19	19606651	19606651	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr19:19606651C>T	ENST00000360315.3	+	6	1025	c.713C>T	c.(712-714)gCg>gTg	p.A238V	GATAD2A_ENST00000537887.1_Intron|GATAD2A_ENST00000358713.3_Missense_Mutation_p.A238V|GATAD2A_ENST00000252577.5_Missense_Mutation_p.A238V|GATAD2A_ENST00000429563.2_Missense_Mutation_p.A65V|GATAD2A_ENST00000404158.1_Missense_Mutation_p.A238V	NM_017660.3	NP_060130.3	Q86YP4	P66A_HUMAN	GATA zinc finger domain containing 2A	238					anterior neuropore closure (GO:0021506)|blood vessel development (GO:0001568)|DNA methylation (GO:0006306)|embryonic body morphogenesis (GO:0010172)|in utero embryonic development (GO:0001701)|negative regulation of transcription, DNA-templated (GO:0045892)|neural fold formation (GO:0001842)|programmed cell death (GO:0012501)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|NuRD complex (GO:0016581)	protein binding, bridging (GO:0030674)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)	p.A95V(1)		endometrium(2)|kidney(1)|large_intestine(2)|lung(6)|ovary(1)|urinary_tract(1)	13						GGGCCACAGGCGAGCTCACAG	0.657																																					p.A238V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C713T	19						.						49.0	43.0	45.0					19																	19606651		2203	4300	6503	19467651	SO:0001583	missense	54815	exon6			AL390164	CCDS12402.2	19p13.11	2013-01-25			ENSG00000167491	ENSG00000167491		"""GATA zinc finger domain containing"""	29989	protein-coding gene	gene with protein product	"""p66 alpha"""	614997				12183469	Standard	NM_017660		Approved	p66alpha	uc010xqt.2	Q86YP4	OTTHUMG00000152541	ENST00000360315.3:c.713C>T	19.37:g.19606651C>T	ENSP00000353463:p.Ala238Val	Somatic		Capture	Illumina HiSeq	Phase_I	19467651	NM_017660	B5MC40|Q7L3J2|Q96F28|Q9NPU2|Q9NXS1	Missense_Mutation	SNP	ENST00000360315.3	37	CCDS12402.2	.	.	.	.	.	.	.	.	.	.	C	13.43	2.235023	0.39498	.	.	ENSG00000167491	ENST00000360315;ENST00000252577;ENST00000404158;ENST00000358713;ENST00000429563	T;T;T;T	0.44881	1.49;1.47;1.49;0.91	4.93	2.47	0.30058	.	0.423303	0.27896	N	0.017407	T	0.17152	0.0412	N	0.08118	0	0.54753	D	0.999986	P;P;P	0.46987	0.797;0.888;0.797	B;B;B	0.32864	0.154;0.107;0.107	T	0.06373	-1.0830	10	0.56958	D	0.05	-8.0873	8.9108	0.35552	0.2219:0.6517:0.1264:0.0	.	65;257;238	B4DKZ7;B5MC40;Q86YP4	.;.;P66A_HUMAN	V	238;238;257;238;65	ENSP00000353463:A238V;ENSP00000252577:A238V;ENSP00000351552:A238V;ENSP00000388416:A65V	ENSP00000252577:A238V	A	+	2	0	GATAD2A	19467651	0.589000	0.26807	0.734000	0.30879	0.727000	0.41649	1.573000	0.36472	1.180000	0.42898	0.655000	0.94253	GCG		0.657	GATAD2A-202	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000326671.4	NM_017660	
ZFR2	23217	broad.mit.edu	37	19	3831779	3831779	+	Silent	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr19:3831779C>T	ENST00000262961.4	-	4	487	c.477G>A	c.(475-477)gcG>gcA	p.A159A	ZFR2_ENST00000591965.1_5'UTR	NM_015174.1	NP_055989.1	Q9UPR6	ZFR2_HUMAN	zinc finger RNA binding protein 2	159							nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)	p.A159A(1)		central_nervous_system(1)|kidney(3)|large_intestine(4)|lung(5)|pancreas(1)|prostate(1)|skin(1)	16				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.00514)|STAD - Stomach adenocarcinoma(1328;0.19)		ACAAGGTGCTCGCTGGCTGTC	0.672																																					p.A159A												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G477A	19						.						25.0	30.0	28.0					19																	3831779		2142	4242	6384	3782779	SO:0001819	synonymous_variant	23217	exon4			AB029009	CCDS45921.1, CCDS45922.1	19p13.3	2012-10-05	2008-03-25	2008-03-25	ENSG00000105278	ENSG00000105278			29189	protein-coding gene	gene with protein product			"""KIAA1086"""	KIAA1086		10470851	Standard	NM_015174		Approved		uc002lyw.2	Q9UPR6	OTTHUMG00000180918	ENST00000262961.4:c.477G>A	19.37:g.3831779C>T		Somatic		Capture	Illumina HiSeq	Phase_I	3782779	NM_015174		Silent	SNP	ENST00000262961.4	37	CCDS45921.1																																																																																				0.672	ZFR2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453648.2	NM_015174	
DPY19L3	147991	broad.mit.edu	37	19	32971457	32971457	+	Silent	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr19:32971457C>T	ENST00000342179.5	+	18	2198	c.1983C>T	c.(1981-1983)aaC>aaT	p.N661N	DPY19L3_ENST00000392250.2_Silent_p.N661N|DPY19L3_ENST00000586987.1_Silent_p.N661N	NM_207325.2	NP_997208.2	Q6ZPD9	D19L3_HUMAN	dpy-19-like 3 (C. elegans)	661						integral component of membrane (GO:0016021)	transferase activity, transferring glycosyl groups (GO:0016757)	p.N661N(1)		breast(1)|endometrium(1)|kidney(3)|large_intestine(5)|lung(17)|ovary(4)|pancreas(1)	32	Esophageal squamous(110;0.162)					ACATTGCCAACGGCCACGTGA	0.577																																					p.N661N												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1983T	19						.						31.0	32.0	32.0					19																	32971457		2203	4300	6503	37663297	SO:0001819	synonymous_variant	147991	exon18				CCDS12422.1	19q13.11	2008-02-05				ENSG00000178904			27120	protein-coding gene	gene with protein product		613894					Standard	NM_207325		Approved		uc002ntg.3	Q6ZPD9		ENST00000342179.5:c.1983C>T	19.37:g.32971457C>T		Somatic		Capture	Illumina HiSeq	Phase_I	37663297	NM_001172774	Q68DC7|Q6ZTB7|Q6ZTS2	Silent	SNP	ENST00000342179.5	37	CCDS12422.1																																																																																				0.577	DPY19L3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450311.1	NM_207325	
LSM14A	26065	broad.mit.edu	37	19	34706070	34706070	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr19:34706070A>G	ENST00000433627.5	+	5	655	c.580A>G	c.(580-582)Acc>Gcc	p.T194A	LSM14A_ENST00000540746.2_Missense_Mutation_p.T153A|LSM14A_ENST00000544216.3_Missense_Mutation_p.T194A	NM_001114093.1	NP_001107565.1	Q8ND56	LS14A_HUMAN	LSM14A, SCD6 homolog A (S. cerevisiae)	194					cytoplasmic mRNA processing body assembly (GO:0033962)|multicellular organismal development (GO:0007275)|positive regulation of type I interferon-mediated signaling pathway (GO:0060340)|regulation of translation (GO:0006417)|RIG-I signaling pathway (GO:0039529)	cytoplasm (GO:0005737)|cytoplasmic mRNA processing body (GO:0000932)|cytoplasmic stress granule (GO:0010494)|intracellular membrane-bounded organelle (GO:0043231)	double-stranded DNA binding (GO:0003690)|double-stranded RNA binding (GO:0003725)|poly(A) RNA binding (GO:0044822)|single-stranded RNA binding (GO:0003727)	p.T194A(1)		breast(1)|endometrium(4)|kidney(1)|large_intestine(8)|lung(7)|skin(1)	22	Esophageal squamous(110;0.162)					AAAAAGCCCAACCATGGAACA	0.483																																					p.T194A												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A580G	19						.						99.0	96.0	97.0					19																	34706070		2203	4300	6503	39397910	SO:0001583	missense	26065	exon5			AL834398	CCDS12435.1, CCDS46040.1	19q13.12	2010-01-27	2006-12-21	2006-01-24		ENSG00000257103			24489	protein-coding gene	gene with protein product		610677	"""chromosome 19 open reading frame 13"", ""family with sequence similarity 61, member A"", ""LSM14 homolog A (SCD6, S. cerevisiae)"""	C19orf13, FAM61A		12477932	Standard	NM_015578		Approved	DKFZP434D1335, RAP55A, RAP55	uc002nva.4	Q8ND56		ENST00000433627.5:c.580A>G	19.37:g.34706070A>G	ENSP00000413964:p.Thr194Ala	Somatic		Capture	Illumina HiSeq	Phase_I	39397910	NM_001114093	B4DTG6|Q76LX7|Q96AR3|Q96K73|Q96SN5|Q9UFR3	Missense_Mutation	SNP	ENST00000433627.5	37	CCDS46040.1	.	.	.	.	.	.	.	.	.	.	a	15.36	2.811202	0.50527	.	.	ENSG00000257103	ENST00000544216;ENST00000433627;ENST00000540746	T;T;T	0.33654	1.41;1.4;1.42	5.77	4.7	0.59300	.	0.089566	0.85682	D	0.000000	T	0.32793	0.0841	M	0.67953	2.075	0.58432	D	0.999999	B;B;B	0.31318	0.135;0.037;0.319	B;B;B	0.27796	0.08;0.013;0.083	T	0.08680	-1.0710	10	0.13853	T	0.58	-10.5603	12.1032	0.53796	0.8715:0.0:0.0:0.1285	.	153;194;194	B4DTG6;Q8ND56;Q8ND56-2	.;LS14A_HUMAN;.	A	194;194;153	ENSP00000446271:T194A;ENSP00000413964:T194A;ENSP00000446451:T153A	ENSP00000314768:T194A	T	+	1	0	LSM14A	39397910	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	2.652000	0.46682	2.326000	0.78906	0.533000	0.62120	ACC		0.483	LSM14A-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000451576.3	NM_015578	
GPI	2821	broad.mit.edu	37	19	34887520	34887520	+	Silent	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr19:34887520G>A	ENST00000356487.5	+	14	1468	c.1227G>A	c.(1225-1227)ccG>ccA	p.P409P	GPI_ENST00000415930.3_Silent_p.P420P|GPI_ENST00000586425.1_Silent_p.P409P	NM_000175.3	NP_000166.2	P06744	G6PI_HUMAN	glucose-6-phosphate isomerase	409					aldehyde catabolic process (GO:0046185)|angiogenesis (GO:0001525)|carbohydrate metabolic process (GO:0005975)|gluconeogenesis (GO:0006094)|glucose 6-phosphate metabolic process (GO:0051156)|glucose metabolic process (GO:0006006)|glycolytic process (GO:0006096)|hemostasis (GO:0007599)|humoral immune response (GO:0006959)|learning or memory (GO:0007611)|methylglyoxal biosynthetic process (GO:0019242)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of neuron apoptotic process (GO:0043524)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	glucose-6-phosphate isomerase activity (GO:0004347)|intramolecular transferase activity (GO:0016866)|monosaccharide binding (GO:0048029)	p.P409P(1)		breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(11)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	25	Esophageal squamous(110;0.162)					TCCTCATCCCGGTCCAGACCC	0.602																																					p.P409P												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G1227A	19						.						60.0	53.0	56.0					19																	34887520		2203	4300	6503	39579360	SO:0001819	synonymous_variant	2821	exon14			M61214	CCDS12437.1, CCDS54246.1	19q13.1	2012-10-02	2010-05-11			ENSG00000105220	5.3.1.9		4458	protein-coding gene	gene with protein product		172400	"""glucose phosphate isomerase"""			2387591, 8575767	Standard	NM_001184722		Approved	AMF, NLK	uc002nvg.2	P06744		ENST00000356487.5:c.1227G>A	19.37:g.34887520G>A		Somatic		Capture	Illumina HiSeq	Phase_I	39579360	NM_000175	B4DG39|Q9BRD3|Q9BSK5|Q9UHE6	Silent	SNP	ENST00000356487.5	37	CCDS12437.1																																																																																				0.602	GPI-006	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451693.3		
WTIP	126374	broad.mit.edu	37	19	34983947	34983947	+	Nonsense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr19:34983947C>T	ENST00000590071.2	+	3	1112	c.775C>T	c.(775-777)Cga>Tga	p.R259*	WTIP_ENST00000270288.6_Nonsense_Mutation_p.R483*	NM_001080436.1	NP_001073905.1	A6NIX2	WTIP_HUMAN	Wilms tumor 1 interacting protein	259	LIM zinc-binding 1. {ECO:0000255|PROSITE- ProRule:PRU00125}.				cytoskeleton organization (GO:0007010)|gene silencing by miRNA (GO:0035195)|negative regulation of hippo signaling (GO:0035331)|positive regulation of gene silencing by miRNA (GO:2000637)|regulation of cell morphogenesis (GO:0022604)|regulation of transcription, DNA-templated (GO:0006355)|response to hypoxia (GO:0001666)|transcription, DNA-templated (GO:0006351)	cell junction (GO:0030054)|cytoplasmic mRNA processing body (GO:0000932)|nucleus (GO:0005634)	transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)	p.R259*(1)		NS(1)|large_intestine(2)|lung(1)	4	all_lung(56;5.94e-07)|Lung NSC(56;9.35e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.211)			TGCAGGGAGACGACTCCGTGG	0.622																																					p.R259X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.C775T	19						.						114.0	118.0	117.0					19																	34983947		1998	4151	6149	39675787	SO:0001587	stop_gained	126374	exon3			AK130059	CCDS59375.1	19q13.11	2012-03-16			ENSG00000142279	ENSG00000142279			20964	protein-coding gene	gene with protein product	"""WT1-interacting protein"""	614790				14736876	Standard	NM_001080436		Approved		uc002nvm.3	A6NIX2		ENST00000590071.2:c.775C>T	19.37:g.34983947C>T	ENSP00000466953:p.Arg259*	Somatic		Capture	Illumina HiSeq	Phase_I	39675787	NM_001080436		Nonsense_Mutation	SNP	ENST00000590071.2	37	CCDS59375.1	.	.	.	.	.	.	.	.	.	.	C	26.0	4.693227	0.88735	.	.	ENSG00000142279	ENST00000270288	.	.	.	5.06	2.82	0.32997	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.08381	T	0.77	.	10.505	0.44828	0.4742:0.5258:0.0:0.0	.	.	.	.	X	483	.	ENSP00000270288:R483X	R	+	1	2	WTIP	39675787	1.000000	0.71417	1.000000	0.80357	0.614000	0.37383	3.699000	0.54778	1.351000	0.45789	-0.268000	0.10319	CGA		0.622	WTIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459381.3	XM_059037	
ZNF30	90075	broad.mit.edu	37	19	35434734	35434734	+	Silent	SNP	C	C	T	rs372239598		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr19:35434734C>T	ENST00000601142.1	+	5	1101	c.864C>T	c.(862-864)taC>taT	p.Y288Y	ZNF30_ENST00000303586.7_Silent_p.Y289Y|ZNF30_ENST00000439785.1_Silent_p.Y289Y|ZNF30_ENST00000601957.1_3'UTR|ZNF30_ENST00000426813.2_Silent_p.Y207Y			P17039	ZNF30_HUMAN	zinc finger protein 30	288					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.Y289Y(1)		breast(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(3)|ovary(1)|prostate(2)	16	all_lung(56;8.38e-08)|Lung NSC(56;1.31e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0849)	GBM - Glioblastoma multiforme(1328;0.0265)		AAAAACCTTACGAATGCAAAG	0.458																																					p.Y289Y												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C867T	19						.	C	,,	0,4384		0,0,2192	81.0	91.0	87.0		867,867,864	-0.2	0.0	19		87	5,8587	5.0+/-18.6	0,5,4291	no	coding-synonymous,coding-synonymous,coding-synonymous	ZNF30	NM_001099437.1,NM_001099438.1,NM_194325.2	,,	0,5,6483	TT,TC,CC		0.0582,0.0,0.0385	,,	289/625,289/625,288/624	35434734	5,12971	2192	4296	6488	40126574	SO:0001819	synonymous_variant	90075	exon5			X52359	CCDS46044.1, CCDS46045.1	19q13.13	2013-01-08	2006-05-10			ENSG00000168661		"""Zinc fingers, C2H2-type"", ""-"""	13090	protein-coding gene	gene with protein product			"""zinc finger protein 30 (KOX 28)"""				Standard	NM_001099437		Approved	KOX28, DKFZp686N19164, FLJ20562	uc010edq.1	P17039		ENST00000601142.1:c.864C>T	19.37:g.35434734C>T		Somatic		Capture	Illumina HiSeq	Phase_I	40126574	NM_001099437	A5PLP1|A8K320|B4DIC0|Q6N068	Silent	SNP	ENST00000601142.1	37	CCDS46045.1																																																																																				0.458	ZNF30-003	KNOWN	NAGNAG_splice_site|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000464432.1	NM_194325	
FXYD5	53827	broad.mit.edu	37	19	35657168	35657168	+	Missense_Mutation	SNP	C	C	T	rs200435409		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr19:35657168C>T	ENST00000342879.3	+	7	1205	c.427C>T	c.(427-429)Cgg>Tgg	p.R143W	FXYD5_ENST00000392217.3_Missense_Mutation_p.R72W|FXYD5_ENST00000392219.2_Missense_Mutation_p.R143W|FXYD5_ENST00000541435.2_Missense_Mutation_p.R143W|FXYD5_ENST00000543307.1_Missense_Mutation_p.R143W|FXYD5_ENST00000423817.3_Missense_Mutation_p.R143W|FXYD5_ENST00000590686.1_Missense_Mutation_p.R143W|FXYD5_ENST00000591716.2_3'UTR|FXYD5_ENST00000588699.1_Missense_Mutation_p.R143W			Q96DB9	FXYD5_HUMAN	FXYD domain containing ion transport regulator 5	143					microvillus assembly (GO:0030033)|negative regulation of calcium-dependent cell-cell adhesion (GO:0046588)	integral component of membrane (GO:0016021)	actin binding (GO:0003779)|cadherin binding (GO:0045296)|ion channel activity (GO:0005216)	p.R143W(1)		endometrium(2)|kidney(1)|large_intestine(3)|lung(3)	9	all_lung(56;9.4e-09)|Lung NSC(56;1.4e-08)|Esophageal squamous(110;0.162)		Epithelial(14;5.75e-22)|OV - Ovarian serous cystadenocarcinoma(14;3.17e-20)|all cancers(14;7.07e-19)|LUSC - Lung squamous cell carcinoma(66;0.0221)			ACACACCCTCCGGAAACGGGG	0.532																																					p.R143W												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C427T	19						.						200.0	205.0	203.0					19																	35657168		2203	4300	6503	40349008	SO:0001583	missense	53827	exon8			AF161462	CCDS12447.1	19q13.12	2008-02-05	2002-01-14		ENSG00000089327	ENSG00000089327			4029	protein-coding gene	gene with protein product	"""dysadherin"""	606669	"""FXYD domain-containing ion transport regulator 5"""				Standard	NM_144779		Approved	OIT2	uc002nyg.2	Q96DB9	OTTHUMG00000048092	ENST00000342879.3:c.427C>T	19.37:g.35657168C>T	ENSP00000344254:p.Arg143Trp	Somatic		Capture	Illumina HiSeq	Phase_I	40349008	NM_001164605	B7WNZ8|Q6UW44|Q9HC34|Q9P039	Missense_Mutation	SNP	ENST00000342879.3	37	CCDS12447.1	.	.	.	.	.	.	.	.	.	.	C	22.1	4.239451	0.79800	.	.	ENSG00000089327	ENST00000543307;ENST00000392219;ENST00000541435;ENST00000342879;ENST00000423817;ENST00000392217	T;T;T;T;T;T	0.76839	-1.05;-1.05;-1.05;-1.05;-1.05;-1.05	5.17	5.17	0.71159	.	0.000000	0.64402	D	0.000004	D	0.88959	0.6579	M	0.86805	2.84	0.43187	D	0.995019	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	D	0.90351	0.4366	10	0.87932	D	0	-18.3928	14.0344	0.64636	0.0:1.0:0.0:0.0	.	143;72;143	F5H4X8;Q96DB9-2;Q96DB9	.;.;FXYD5_HUMAN	W	143;143;143;143;143;72	ENSP00000444839:R143W;ENSP00000376053:R143W;ENSP00000443390:R143W;ENSP00000344254:R143W;ENSP00000393848:R143W;ENSP00000376051:R72W	ENSP00000344254:R143W	R	+	1	2	FXYD5	40349008	0.978000	0.34361	1.000000	0.80357	0.932000	0.56968	0.708000	0.25719	2.688000	0.91661	0.563000	0.77884	CGG		0.532	FXYD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109443.1	NM_014164	
GAPDHS	26330	broad.mit.edu	37	19	36033442	36033442	+	Silent	SNP	G	G	A	rs148996097		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr19:36033442G>A	ENST00000222286.4	+	6	707	c.591G>A	c.(589-591)ccG>ccA	p.P197P	AD000090.2_ENST00000589137.1_RNA|AD000090.2_ENST00000444728.1_RNA|AD000090.2_ENST00000588286.1_RNA|AD000090.2_ENST00000590717.1_RNA|AD000090.2_ENST00000590125.1_RNA	NM_014364.4	NP_055179.1	O14556	G3PT_HUMAN	glyceraldehyde-3-phosphate dehydrogenase, spermatogenic	197					carbohydrate metabolic process (GO:0005975)|gluconeogenesis (GO:0006094)|glucose metabolic process (GO:0006006)|glycolytic process (GO:0006096)|positive regulation of glycolytic process (GO:0045821)|small molecule metabolic process (GO:0044281)|sperm motility (GO:0030317)|spermatid development (GO:0007286)	cytosol (GO:0005829)|nucleus (GO:0005634)|sperm fibrous sheath (GO:0035686)|sperm principal piece (GO:0097228)	glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity (GO:0004365)|NAD binding (GO:0051287)|NADP binding (GO:0050661)	p.P197P(1)		endometrium(1)|kidney(1)|large_intestine(1)|lung(8)	11	all_lung(56;1.05e-07)|Lung NSC(56;1.63e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0724)			CGCCCTCACCGGATGCACCAA	0.552													G|||	1	0.000199681	0.0008	0.0	5008	,	,		22619	0.0		0.0	False		,,,				2504	0.0				p.P197P												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G591A	19						.	G		2,4404	4.2+/-10.8	0,2,2201	121.0	94.0	103.0		591	-10.0	0.0	19	dbSNP_134	103	0,8600		0,0,4300	no	coding-synonymous	GAPDHS	NM_014364.4		0,2,6501	AA,AG,GG		0.0,0.0454,0.0154		197/409	36033442	2,13004	2203	4300	6503	40725282	SO:0001819	synonymous_variant	26330	exon6			AJ005371	CCDS12465.1	19q13.1	2008-02-05		2005-05-06		ENSG00000105679			24864	protein-coding gene	gene with protein product		609169		GAPDS		10714828	Standard	NM_014364		Approved	GAPDH-2, GAPD2	uc002oaf.1	O14556		ENST00000222286.4:c.591G>A	19.37:g.36033442G>A		Somatic		Capture	Illumina HiSeq	Phase_I	40725282	NM_014364	B2RC82|O60823|Q6JTT9|Q9HCU6	Silent	SNP	ENST00000222286.4	37	CCDS12465.1																																																																																				0.552	GAPDHS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460423.1	NM_014364	
RBM42	79171	broad.mit.edu	37	19	36124005	36124005	+	Missense_Mutation	SNP	G	G	A	rs376033321		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr19:36124005G>A	ENST00000262633.4	+	6	640	c.535G>A	c.(535-537)Ggc>Agc	p.G179S	RBM42_ENST00000589559.1_Missense_Mutation_p.G150S|RBM42_ENST00000360475.4_Missense_Mutation_p.G150S|RBM42_ENST00000586618.1_Intron|RBM42_ENST00000589871.1_Missense_Mutation_p.G157S|RBM42_ENST00000592202.1_Missense_Mutation_p.G125S|RBM42_ENST00000588161.1_Missense_Mutation_p.G149S	NM_024321.3	NP_077297.2	Q9BTD8	RBM42_HUMAN	RNA binding motif protein 42	179						cytoplasm (GO:0005737)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)	p.G179S(1)		breast(1)|endometrium(3)|large_intestine(7)|lung(9)|prostate(1)	21	all_lung(56;1.58e-07)|Lung NSC(56;2.43e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0724)			TGCAGCAGCCGGCCCCCGCCC	0.682																																					p.G179S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G535A	19						.	G	SER/GLY	1,4405	2.1+/-5.4	0,1,2202	78.0	99.0	92.0		535	5.1	0.1	19		92	0,8600		0,0,4300	no	missense	RBM42	NM_024321.3	56	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	probably-damaging	179/481	36124005	1,13005	2203	4300	6503	40815845	SO:0001583	missense	79171	exon6			BC004204	CCDS12468.1	19q13.12	2013-02-12				ENSG00000126254		"""RNA binding motif (RRM) containing"""	28117	protein-coding gene	gene with protein product		613232				12477932	Standard	NM_024321		Approved	MGC10433	uc002oan.3	Q9BTD8		ENST00000262633.4:c.535G>A	19.37:g.36124005G>A	ENSP00000262633:p.Gly179Ser	Somatic		Capture	Illumina HiSeq	Phase_I	40815845	NM_024321	O00320|Q8N5R7|Q9BU66	Missense_Mutation	SNP	ENST00000262633.4	37	CCDS12468.1	.	.	.	.	.	.	.	.	.	.	G	16.90	3.249066	0.59103	2.27E-4	0.0	ENSG00000126254	ENST00000262633;ENST00000360475	T;T	0.12147	2.71;3.27	5.05	5.05	0.67936	.	0.244474	0.41097	D	0.000953	T	0.17704	0.0425	L	0.36672	1.1	0.34096	D	0.661266	P;P;D	0.67145	0.927;0.927;0.996	B;B;P	0.50352	0.39;0.39;0.638	T	0.08166	-1.0735	10	0.45353	T	0.12	-2.3771	13.7681	0.63008	0.0:0.0:1.0:0.0	.	150;149;179	Q9BTD8-3;Q9BTD8-2;Q9BTD8	.;.;RBM42_HUMAN	S	179;150	ENSP00000262633:G179S;ENSP00000353663:G150S	ENSP00000262633:G179S	G	+	1	0	RBM42	40815845	0.258000	0.24033	0.110000	0.21437	0.916000	0.54674	2.890000	0.48609	2.628000	0.89032	0.561000	0.74099	GGC		0.682	RBM42-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459057.2	NM_024321	
NPHS1	4868	broad.mit.edu	37	19	36322217	36322217	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr19:36322217C>T	ENST00000378910.5	-	26	3367	c.3368G>A	c.(3367-3369)cGg>cAg	p.R1123Q	NPHS1_ENST00000353632.6_Missense_Mutation_p.R1083Q	NM_004646.3	NP_004637.1	O60500	NPHN_HUMAN	nephrosis 1, congenital, Finnish type (nephrin)	1123					cell adhesion (GO:0007155)|excretion (GO:0007588)|glomerular basement membrane development (GO:0032836)|glomerular visceral epithelial cell development (GO:0072015)|JNK cascade (GO:0007254)|myoblast fusion (GO:0007520)|positive regulation of actin filament polymerization (GO:0030838)|regulation of excretion (GO:0044062)|skeletal muscle tissue development (GO:0007519)	cell projection (GO:0042995)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|slit diaphragm (GO:0036057)	myosin binding (GO:0017022)	p.R1123L(1)|p.R1123Q(1)		NS(2)|breast(1)|cervix(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(16)|liver(1)|lung(26)|ovary(5)|prostate(1)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	74	all_lung(56;7.14e-07)|Lung NSC(56;1.12e-06)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0515)			CTGAGTGTCCCGCTCTCCTGT	0.612																																					p.R1123Q												.	.	2	Substitution - Missense(2)	large_intestine(1)|lung(1)	c.G3368A	19						.						88.0	81.0	83.0					19																	36322217		2203	4300	6503	41014057	SO:0001583	missense	4868	exon26				CCDS32996.1	19q12-q13.1	2014-09-17				ENSG00000161270		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	7908	protein-coding gene	gene with protein product		602716				9915943, 9660941	Standard	NM_004646		Approved	CNF, NPHN	uc002oby.3	O60500		ENST00000378910.5:c.3368G>A	19.37:g.36322217C>T	ENSP00000368190:p.Arg1123Gln	Somatic		Capture	Illumina HiSeq	Phase_I	41014057	NM_004646	A6NDH2|C3RX61	Missense_Mutation	SNP	ENST00000378910.5	37	CCDS32996.1	.	.	.	.	.	.	.	.	.	.	C	0.371	-0.933879	0.02340	.	.	ENSG00000161270	ENST00000378910;ENST00000353632	T;T	0.75477	-0.94;-0.82	5.07	-0.945	0.10388	.	0.764374	0.12665	N	0.449249	T	0.49847	0.1581	N	0.17082	0.46	0.09310	N	1	B	0.13145	0.007	B	0.06405	0.002	T	0.24048	-1.0171	10	0.20519	T	0.43	-10.0484	4.0308	0.09708	0.1536:0.48:0.0:0.3664	.	1123	O60500	NPHN_HUMAN	Q	1123;1083	ENSP00000368190:R1123Q;ENSP00000343634:R1083Q	ENSP00000343634:R1083Q	R	-	2	0	NPHS1	41014057	0.000000	0.05858	0.300000	0.25030	0.004000	0.04260	-1.225000	0.02956	-0.219000	0.10003	-0.860000	0.03012	CGG		0.612	NPHS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452553.1		
NPHS1	4868	broad.mit.edu	37	19	36333319	36333319	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr19:36333319G>A	ENST00000378910.5	-	18	2467	c.2468C>T	c.(2467-2469)gCg>gTg	p.A823V	NPHS1_ENST00000353632.6_Missense_Mutation_p.A823V	NM_004646.3	NP_004637.1	O60500	NPHN_HUMAN	nephrosis 1, congenital, Finnish type (nephrin)	823	Ig-like C2-type 7.				cell adhesion (GO:0007155)|excretion (GO:0007588)|glomerular basement membrane development (GO:0032836)|glomerular visceral epithelial cell development (GO:0072015)|JNK cascade (GO:0007254)|myoblast fusion (GO:0007520)|positive regulation of actin filament polymerization (GO:0030838)|regulation of excretion (GO:0044062)|skeletal muscle tissue development (GO:0007519)	cell projection (GO:0042995)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|slit diaphragm (GO:0036057)	myosin binding (GO:0017022)	p.A823V(1)		NS(2)|breast(1)|cervix(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(16)|liver(1)|lung(26)|ovary(5)|prostate(1)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	74	all_lung(56;7.14e-07)|Lung NSC(56;1.12e-06)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0515)			TGCTGGAGGCGCCACCCCATT	0.582																																					p.A823V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C2468T	19						.						77.0	71.0	73.0					19																	36333319		2203	4300	6503	41025159	SO:0001583	missense	4868	exon18				CCDS32996.1	19q12-q13.1	2014-09-17				ENSG00000161270		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	7908	protein-coding gene	gene with protein product		602716				9915943, 9660941	Standard	NM_004646		Approved	CNF, NPHN	uc002oby.3	O60500		ENST00000378910.5:c.2468C>T	19.37:g.36333319G>A	ENSP00000368190:p.Ala823Val	Somatic		Capture	Illumina HiSeq	Phase_I	41025159	NM_004646	A6NDH2|C3RX61	Missense_Mutation	SNP	ENST00000378910.5	37	CCDS32996.1	.	.	.	.	.	.	.	.	.	.	G	16.89	3.247623	0.59103	.	.	ENSG00000161270	ENST00000378910;ENST00000353632	T;T	0.78707	-1.2;-1.2	4.57	3.51	0.40186	Immunoglobulin subtype (1);Immunoglobulin-like fold (1);	0.267907	0.36778	N	0.002413	T	0.78935	0.4362	L	0.48642	1.525	0.30789	N	0.7411	D	0.64830	0.994	P	0.56163	0.793	T	0.78231	-0.2284	10	0.54805	T	0.06	-3.9004	10.4424	0.44472	0.0:0.1977:0.8023:0.0	.	823	O60500	NPHN_HUMAN	V	823	ENSP00000368190:A823V;ENSP00000343634:A823V	ENSP00000343634:A823V	A	-	2	0	NPHS1	41025159	0.738000	0.28186	0.999000	0.59377	0.468000	0.32798	1.041000	0.30291	1.135000	0.42183	0.558000	0.71614	GCG		0.582	NPHS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452553.1		
WDR62	284403	broad.mit.edu	37	19	36573979	36573979	+	Silent	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr19:36573979C>T	ENST00000270301.7	+	11	1386	c.1386C>T	c.(1384-1386)gtC>gtT	p.V462V	WDR62_ENST00000401500.2_Silent_p.V462V			O43379	WDR62_HUMAN	WD repeat domain 62	462					cerebral cortex development (GO:0021987)|neurogenesis (GO:0022008)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|spindle pole (GO:0000922)		p.V462V(1)		cervix(1)|endometrium(8)|kidney(2)|large_intestine(8)|lung(15)|prostate(4)|stomach(2)|urinary_tract(3)	43	Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.06)			TGCTGAAGGTCGTGTACGTGG	0.587																																					p.V462V												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1386T	19						.						51.0	39.0	43.0					19																	36573979		2203	4300	6503	41265819	SO:0001819	synonymous_variant	284403	exon11			BX647726	CCDS33001.1, CCDS46059.1	19q13.12	2013-01-09	2005-05-09	2005-05-09	ENSG00000075702	ENSG00000075702		"""WD repeat domain containing"""	24502	protein-coding gene	gene with protein product		613583	"""chromosome 19 open reading frame 14"", ""microcephaly, primary autosomal recessive 2"""	C19orf14, MCPH2		19910486, 20729831, 20890278, 21496009	Standard	NM_001083961		Approved	DKFZP434J046, FLJ33298	uc002odd.2	O43379	OTTHUMG00000048139	ENST00000270301.7:c.1386C>T	19.37:g.36573979C>T		Somatic		Capture	Illumina HiSeq	Phase_I	41265819	NM_001083961	Q63HP9|Q659D7|Q8NBF7|Q96AD9	Silent	SNP	ENST00000270301.7	37	CCDS33001.1																																																																																				0.587	WDR62-006	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000457436.1	NM_015671	
ZNF529	57711	broad.mit.edu	37	19	37038163	37038163	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr19:37038163C>T	ENST00000591340.1	-	5	1455	c.1297G>A	c.(1297-1299)Gta>Ata	p.V433I	ZNF529_ENST00000334116.7_Missense_Mutation_p.V328I	NM_020951.4	NP_066002.3	Q6P280	ZN529_HUMAN	zinc finger protein 529	433					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.V433I(1)		breast(1)	1	Esophageal squamous(110;0.198)					TCACTACCTACTCCAAATGCT	0.373																																					p.V433I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1297A	19						.						102.0	110.0	107.0					19																	37038163		2138	4276	6414	41730003	SO:0001583	missense	57711	exon6			AK025110	CCDS54256.1	19q13.13	2014-08-22			ENSG00000186020	ENSG00000186020		"""Zinc fingers, C2H2-type"", ""-"""	29328	protein-coding gene	gene with protein product						10997877	Standard	NM_020951		Approved	KIAA1615	uc002oeh.4	Q6P280	OTTHUMG00000180714	ENST00000591340.1:c.1297G>A	19.37:g.37038163C>T	ENSP00000465578:p.Val433Ile	Somatic		Capture	Illumina HiSeq	Phase_I	41730003	NM_001145649	K7EKE1|Q9H731|Q9HCF7	Missense_Mutation	SNP	ENST00000591340.1	37	CCDS54256.1	.	.	.	.	.	.	.	.	.	.	C	8.762	0.923900	0.18056	.	.	ENSG00000186020	ENST00000334116	.	.	.	3.19	-2.35	0.06684	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.11623	0.0283	N	0.11818	0.18	0.09310	N	1	B;B	0.29552	0.248;0.16	B;B	0.26202	0.067;0.03	T	0.27640	-1.0068	8	0.21540	T	0.41	.	1.5047	0.02484	0.3273:0.2297:0.3229:0.1202	.	328;400	Q6P280-2;Q6P280	.;ZN529_HUMAN	I	433	.	ENSP00000334695:V433I	V	-	1	0	ZNF529	41730003	0.000000	0.05858	0.655000	0.29622	0.998000	0.95712	-1.968000	0.01507	0.048000	0.15891	0.591000	0.81541	GTA		0.373	ZNF529-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452730.1	NM_020951	
SH3GL1	6455	broad.mit.edu	37	19	4366964	4366964	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr19:4366964C>T	ENST00000269886.3	-	2	251	c.73G>A	c.(73-75)Gag>Aag	p.E25K	SH3GL1_ENST00000598564.1_Missense_Mutation_p.E25K|AC007292.6_ENST00000594444.1_RNA|SH3GL1_ENST00000417295.2_Missense_Mutation_p.E25K	NM_003025.3	NP_003016.1	Q99961	SH3G1_HUMAN	SH3-domain GRB2-like 1	25	BAR. {ECO:0000255|PROSITE- ProRule:PRU00361}.				central nervous system development (GO:0007417)|endocytosis (GO:0006897)|signal transduction (GO:0007165)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|endosome (GO:0005768)|membrane (GO:0016020)	identical protein binding (GO:0042802)|lipid binding (GO:0008289)	p.E25*(1)|p.E25K(1)		NS(1)|endometrium(2)|kidney(16)|large_intestine(3)|lung(2)|ovary(2)	26				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0152)|STAD - Stomach adenocarcinoma(1328;0.182)		TTGGTCCCCTCGGCCCCTCCG	0.602			T	MLL	AL																																p.E25K	NSCLC(94;1152 2133 30346 33362)		Dom	yes		19	19p13.3	6455	SH3-domain GRB2-like 1 (EEN)		L	.	.	2	Substitution - Nonsense(1)|Substitution - Missense(1)	large_intestine(1)|lung(1)	c.G73A	19						.						319.0	277.0	291.0					19																	4366964		2203	4300	6503	4317964	SO:0001583	missense	6455	exon2				CCDS32874.1, CCDS56076.1, CCDS59335.1	19p13.3	2008-07-22							10830	protein-coding gene	gene with protein product	"""extra 11-19 leukemia fusion"", ""fusion partner of MLL"", ""SH3-containing Grb-2-like 1 protein"", ""SH3-containing protein EEN"", ""SH3 domain GRB2-like 1"""	601768				9169142	Standard	NM_003025		Approved	SH3P8, SH3D2B, CNSA1, EEN, MGC111371	uc002maj.3	Q99961		ENST00000269886.3:c.73G>A	19.37:g.4366964C>T	ENSP00000269886:p.Glu25Lys	Somatic		Capture	Illumina HiSeq	Phase_I	4317964	NM_003025	B4DRA1|E7EVZ4|M0QZV5|Q99668	Missense_Mutation	SNP	ENST00000269886.3	37	CCDS32874.1	.	.	.	.	.	.	.	.	.	.	.	32	5.134613	0.94517	.	.	ENSG00000141985	ENST00000269886;ENST00000417295	T;T	0.40476	1.03;1.03	4.64	4.64	0.57946	BAR (3);	0.000000	0.85682	D	0.000000	T	0.63581	0.2523	M	0.69823	2.125	0.80722	D	1	D;D;D	0.89917	0.999;1.0;1.0	D;D;D	0.70016	0.954;0.967;0.967	T	0.69109	-0.5232	10	0.87932	D	0	-4.783	16.4683	0.84092	0.0:1.0:0.0:0.0	.	25;25;25	E7EVZ4;Q6FGM0;Q99961	.;.;SH3G1_HUMAN	K	25	ENSP00000269886:E25K;ENSP00000404568:E25K	ENSP00000269886:E25K	E	-	1	0	SH3GL1	4317964	1.000000	0.71417	0.817000	0.32601	0.962000	0.63368	7.761000	0.85260	2.113000	0.64589	0.561000	0.74099	GAG		0.602	SH3GL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458302.1	NM_003025	
ZNF607	84775	broad.mit.edu	37	19	38189846	38189846	+	Missense_Mutation	SNP	T	T	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr19:38189846T>A	ENST00000355202.4	-	5	1781	c.1186A>T	c.(1186-1188)Aac>Tac	p.N396Y	CTD-2528L19.4_ENST00000586606.2_Intron|ZNF607_ENST00000395835.3_Missense_Mutation_p.N395Y	NM_032689.4	NP_116078.4	Q96SK3	ZN607_HUMAN	zinc finger protein 607	396					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.N396Y(1)		cervix(1)|endometrium(3)|kidney(3)|large_intestine(11)|lung(8)|urinary_tract(1)	27			UCEC - Uterine corpus endometrioid carcinoma (49;0.0775)			CCACATTTGTTACATTCATAG	0.403																																					p.N396Y												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A1186T	19						.						86.0	86.0	86.0					19																	38189846		2203	4300	6503	42881686	SO:0001583	missense	84775	exon5			AK127464	CCDS33006.1, CCDS54259.1	19q13.1	2013-01-08				ENSG00000198182		"""Zinc fingers, C2H2-type"", ""-"""	28192	protein-coding gene	gene with protein product						14702039	Standard	NM_032689		Approved	MGC13071, FLJ14802	uc002ohc.2	Q96SK3		ENST00000355202.4:c.1186A>T	19.37:g.38189846T>A	ENSP00000347338:p.Asn396Tyr	Somatic		Capture	Illumina HiSeq	Phase_I	42881686	NM_032689	F5H141|Q6ZMN2|Q6ZMN4|Q96C40	Missense_Mutation	SNP	ENST00000355202.4	37	CCDS33006.1	.	.	.	.	.	.	.	.	.	.	T	13.05	2.120058	0.37436	.	.	ENSG00000198182	ENST00000355202;ENST00000395835	T;T	0.07688	3.17;3.17	1.77	-0.718	0.11205	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.16041	0.0386	L	0.50919	1.6	0.09310	N	1	D;D	0.63046	0.977;0.992	P;D	0.71184	0.515;0.972	T	0.16188	-1.0411	9	0.72032	D	0.01	.	2.4995	0.04630	0.2105:0.2881:0.0:0.5014	.	396;395	Q96SK3;F5H141	ZN607_HUMAN;.	Y	396;395	ENSP00000347338:N396Y;ENSP00000438015:N395Y	ENSP00000347338:N396Y	N	-	1	0	ZNF607	42881686	0.000000	0.05858	0.141000	0.22245	0.820000	0.46376	-0.795000	0.04580	-0.476000	0.06842	0.459000	0.35465	AAC		0.403	ZNF607-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000459502.2	NM_032689	
SPINT2	10653	broad.mit.edu	37	19	38778556	38778556	+	Silent	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr19:38778556G>A	ENST00000301244.7	+	3	753	c.318G>A	c.(316-318)gcG>gcA	p.A106A	CTB-102L5.4_ENST00000591889.1_5'Flank|SPINT2_ENST00000587090.1_Silent_p.A56A|SPINT2_ENST00000454580.3_Silent_p.A49A	NM_021102.3	NP_066925.1	O43291	SPIT2_HUMAN	serine peptidase inhibitor, Kunitz type, 2	106					cellular component movement (GO:0006928)|negative regulation of endopeptidase activity (GO:0010951)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)	endopeptidase inhibitor activity (GO:0004866)|serine-type endopeptidase inhibitor activity (GO:0004867)	p.A106A(1)		large_intestine(2)|lung(1)|ovary(1)	4	all_cancers(60;6.83e-07)		Lung(45;0.000246)|LUSC - Lung squamous cell carcinoma(53;0.000292)			GGAATGCAGCGGATTCCTCTG	0.532																																					p.A49A												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G147A	19						.						126.0	117.0	120.0					19																	38778556		2203	4300	6503	43470396	SO:0001819	synonymous_variant	10653	exon2			U78095	CCDS12510.1, CCDS54261.1	19q13.2	2010-05-12	2005-08-17		ENSG00000167642	ENSG00000167642			11247	protein-coding gene	gene with protein product	"""placental bikunin"""	605124	"""serine protease inhibitor, Kunitz type, 2"""			9115294, 9346890	Standard	NM_021102		Approved	Kop, HAI-2	uc002ohr.2	O43291		ENST00000301244.7:c.318G>A	19.37:g.38778556G>A		Somatic		Capture	Illumina HiSeq	Phase_I	43470396	NM_001166103	A8K667|B4DLU1|O00271|O14895|Q5TZQ3|Q969E0	Silent	SNP	ENST00000301244.7	37	CCDS12510.1																																																																																				0.532	SPINT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458151.2		
FAM98C	147965	broad.mit.edu	37	19	38896167	38896167	+	Silent	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr19:38896167G>A	ENST00000252530.5	+	6	661	c.642G>A	c.(640-642)ttG>ttA	p.L214L	FAM98C_ENST00000343358.7_Silent_p.L188L|FAM98C_ENST00000588262.1_Intron	NM_174905.3	NP_777565.3	Q17RN3	FA98C_HUMAN	family with sequence similarity 98, member C	214								p.L214L(1)		endometrium(2)|large_intestine(3)|lung(6)|pancreas(1)|prostate(1)|skin(1)|urinary_tract(1)	15	all_cancers(60;3.95e-06)		Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272)			AGGAAGCGTTGGAGTCTCTGT	0.567																																					p.L214L												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G642A	19						.						86.0	91.0	89.0					19																	38896167		2187	4284	6471	43588007	SO:0001819	synonymous_variant	147965	exon6				CCDS42562.1	19q13.2	2008-02-05				ENSG00000130244			27119	protein-coding gene	gene with protein product						12477932	Standard	NM_174905		Approved	FLJ44669	uc002oin.1	Q17RN3		ENST00000252530.5:c.642G>A	19.37:g.38896167G>A		Somatic		Capture	Illumina HiSeq	Phase_I	43588007	NM_174905	A6NMW3|Q66K45	Silent	SNP	ENST00000252530.5	37	CCDS42562.1																																																																																				0.567	FAM98C-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000459222.1	NM_174905	
RYR1	6261	broad.mit.edu	37	19	39037099	39037099	+	Silent	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr19:39037099C>T	ENST00000359596.3	+	88	12027	c.12027C>T	c.(12025-12027)atC>atT	p.I4009I	RYR1_ENST00000355481.4_Silent_p.I4004I|RYR1_ENST00000360985.3_Silent_p.I4004I			P21817	RYR1_HUMAN	ryanodine receptor 1 (skeletal)	4009					calcium ion transport (GO:0006816)|cellular response to caffeine (GO:0071313)|cytosolic calcium ion homeostasis (GO:0051480)|ion transmembrane transport (GO:0034220)|muscle contraction (GO:0006936)|ossification involved in bone maturation (GO:0043931)|outflow tract morphogenesis (GO:0003151)|release of sequestered calcium ion into cytosol (GO:0051209)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|skeletal muscle fiber development (GO:0048741)|skin development (GO:0043588)|transmembrane transport (GO:0055085)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|I band (GO:0031674)|integral component of plasma membrane (GO:0005887)|junctional membrane complex (GO:0030314)|junctional sarcoplasmic reticulum membrane (GO:0014701)|plasma membrane (GO:0005886)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|T-tubule (GO:0030315)|terminal cisterna (GO:0014802)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-release channel activity (GO:0015278)|calmodulin binding (GO:0005516)|ryanodine-sensitive calcium-release channel activity (GO:0005219)|voltage-gated calcium channel activity (GO:0005245)	p.I4009I(2)		NS(4)|autonomic_ganglia(2)|breast(3)|central_nervous_system(5)|endometrium(26)|haematopoietic_and_lymphoid_tissue(3)|kidney(34)|large_intestine(42)|liver(1)|lung(106)|ovary(11)|pancreas(5)|prostate(9)|skin(12)|stomach(11)|upper_aerodigestive_tract(4)|urinary_tract(7)	285	all_cancers(60;7.91e-06)		Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272)		Caffeine(DB00201)|Dantrolene(DB01219)|Suramin(DB04786)	CAAGCCAGATCGAGCTGCTGA	0.572																																					p.I4004I												.	.	2	Substitution - coding silent(2)	large_intestine(1)|lung(1)	c.C12012T	19						.						104.0	85.0	91.0					19																	39037099		2203	4300	6503	43728939	SO:0001819	synonymous_variant	6261	exon87			J05200	CCDS33011.1, CCDS42563.1	19q13.1	2014-09-17				ENSG00000196218		"""Ion channels / Ryanodine receptors"""	10483	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 137"""	180901	"""central core disease of muscle"""	MHS, MHS1, CCO		1862346, 16621918	Standard	NM_000540		Approved	RYR, PPP1R137	uc002oit.3	P21817		ENST00000359596.3:c.12027C>T	19.37:g.39037099C>T		Somatic		Capture	Illumina HiSeq	Phase_I	43728939	NM_001042723	Q16314|Q16368|Q9NPK1|Q9P1U4	Silent	SNP	ENST00000359596.3	37	CCDS33011.1																																																																																				0.572	RYR1-010	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000462137.1		
SAMD4B	55095	broad.mit.edu	37	19	39860434	39860434	+	Silent	SNP	A	A	G			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr19:39860434A>G	ENST00000314471.6	+	6	1371	c.336A>G	c.(334-336)tcA>tcG	p.S112S	SAMD4B_ENST00000596368.1_Silent_p.S112S|SAMD4B_ENST00000598913.1_Silent_p.S112S|RN7SL566P_ENST00000467650.2_RNA	NM_018028.2	NP_060498.2	Q5PRF9	SMAG2_HUMAN	sterile alpha motif domain containing 4B	112					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)	p.S112S(1)		autonomic_ganglia(1)|breast(1)|endometrium(5)|large_intestine(1)|lung(4)|skin(1)|urinary_tract(2)	15	all_cancers(60;2.5e-07)|all_lung(34;4.03e-08)|Lung NSC(34;4.66e-08)|all_epithelial(25;6.4e-07)|Ovarian(47;0.0512)		Epithelial(26;9.6e-28)|all cancers(26;9.14e-25)|Lung(45;0.000168)|LUSC - Lung squamous cell carcinoma(53;0.000199)			TGGCCTACTCAATCGAGAGCA	0.587																																					p.S112S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.A336G	19						.						75.0	57.0	63.0					19																	39860434		2203	4300	6503	44552274	SO:0001819	synonymous_variant	55095	exon6				CCDS33020.1	19q13.2	2013-01-10				ENSG00000179134		"""Sterile alpha motif (SAM) domain containing"""	25492	protein-coding gene	gene with protein product	"""smaug homolog B (Drosophila)"""					16221671	Standard	XM_005259029		Approved	FLJ10211, MGC99832, SMGB, hSmaug2	uc002olb.3	Q5PRF9		ENST00000314471.6:c.336A>G	19.37:g.39860434A>G		Somatic		Capture	Illumina HiSeq	Phase_I	44552274	NM_018028	A5Z0M6|Q6P194	Silent	SNP	ENST00000314471.6	37	CCDS33020.1																																																																																				0.587	SAMD4B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000464467.1	NM_018028	
PLEKHG2	64857	broad.mit.edu	37	19	39905887	39905887	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr19:39905887G>A	ENST00000409794.3	+	3	1215	c.365G>A	c.(364-366)cGc>cAc	p.R122H	PLEKHG2_ENST00000425673.1_Missense_Mutation_p.R122H|PLEKHG2_ENST00000409797.2_Missense_Mutation_p.R122H|PLEKHG2_ENST00000378550.1_Missense_Mutation_p.R122H|PLEKHG2_ENST00000458508.2_Missense_Mutation_p.R63H	NM_022835.2	NP_073746.2	Q9H7P9	PKHG2_HUMAN	pleckstrin homology domain containing, family G (with RhoGef domain) member 2	122	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.				apoptotic signaling pathway (GO:0097190)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)	p.R122H(1)|p.R80H(1)		breast(3)|central_nervous_system(1)|endometrium(8)|kidney(2)|large_intestine(2)|liver(1)|lung(13)|pancreas(1)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	40	all_cancers(60;3.08e-07)|all_lung(34;2.66e-08)|Lung NSC(34;3e-08)|all_epithelial(25;6.57e-07)|Ovarian(47;0.0569)		Epithelial(26;2.92e-26)|all cancers(26;2.01e-23)|Lung(45;0.000499)|LUSC - Lung squamous cell carcinoma(53;0.000657)			AGGGACCTCCGCAGCATCGTG	0.647																																					p.R122H												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G365A	19						.						37.0	34.0	35.0					19																	39905887		2198	4297	6495	44597727	SO:0001583	missense	64857	exon3			AK024429	CCDS33022.2	19q13.2	2013-01-11			ENSG00000090924	ENSG00000090924		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	29515	protein-coding gene	gene with protein product		611893				11839748, 18045877	Standard	NM_022835		Approved	CLG, FLJ00018, ARHGEF42	uc010xuz.2	Q9H7P9	OTTHUMG00000152570	ENST00000409794.3:c.365G>A	19.37:g.39905887G>A	ENSP00000386733:p.Arg122His	Somatic		Capture	Illumina HiSeq	Phase_I	44597727	NM_022835	B8ZZK6|C9J0Y4|Q6DHV6|Q96BU2|Q96D18|Q9H699	Missense_Mutation	SNP	ENST00000409794.3	37	CCDS33022.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	17.80|17.80	3.477943|3.477943	0.63849|0.63849	.|.	.|.	ENSG00000090924|ENSG00000090924	ENST00000205135|ENST00000409794;ENST00000425673;ENST00000378550;ENST00000458508;ENST00000438123;ENST00000409797;ENST00000451354	.|T;T;T;T;T;T;T	.|0.68903	.|-0.36;-0.36;-0.36;-0.36;1.52;-0.36;1.52	4.63|4.63	3.58|3.58	0.41010|0.41010	.|Dbl homology (DH) domain (5);	.|0.341520	.|0.21655	.|N	.|0.071102	T|T	0.74801|0.74801	0.3764|0.3764	L|L	0.50919|0.50919	1.6|1.6	0.30936|0.30936	N|N	0.72642|0.72642	.|D;D;D	.|0.89917	.|1.0;0.999;1.0	.|D;D;D	.|0.87578	.|0.998;0.976;0.975	T|T	0.74054|0.74054	-0.3788|-0.3788	5|10	.|0.66056	.|D	.|0.02	.|.	9.8666|9.8666	0.41148|0.41148	0.0:0.0:0.7956:0.2044|0.0:0.0:0.7956:0.2044	.|.	.|122;63;122	.|Q9H7P9;E7ESZ3;Q9H7P9-2	.|PKHG2_HUMAN;.;.	T|H	19|122;122;122;63;123;122;123	.|ENSP00000386733:R122H;ENSP00000392906:R122H;ENSP00000367812:R122H;ENSP00000408857:R63H;ENSP00000397615:R123H;ENSP00000386492:R122H;ENSP00000412818:R123H	.|ENSP00000367812:R122H	A|R	+|+	1|2	0|0	PLEKHG2|PLEKHG2	44597727|44597727	1.000000|1.000000	0.71417|0.71417	0.996000|0.996000	0.52242|0.52242	0.670000|0.670000	0.39368|0.39368	6.065000|6.065000	0.71176|0.71176	1.147000|1.147000	0.42369|0.42369	0.491000|0.491000	0.48974|0.48974	GCA|CGC		0.647	PLEKHG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326802.1	NM_022835	
FCGBP	8857	broad.mit.edu	37	19	40433368	40433368	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr19:40433368G>A	ENST00000221347.6	-	2	908	c.901C>T	c.(901-903)Cca>Tca	p.P301S		NM_003890.2	NP_003881.2	Q9Y6R7	FCGBP_HUMAN	Fc fragment of IgG binding protein	301	IgGFc-binding.					extracellular vesicular exosome (GO:0070062)		p.P301S(1)		NS(3)|autonomic_ganglia(1)|breast(7)|central_nervous_system(5)|endometrium(13)|kidney(9)|large_intestine(27)|lung(49)|ovary(8)|pancreas(3)|prostate(13)|skin(9)|stomach(9)|upper_aerodigestive_tract(6)|urinary_tract(3)	165	all_cancers(60;6.03e-06)|all_lung(34;5.58e-08)|Lung NSC(34;6.62e-08)|Ovarian(47;0.06)		Epithelial(26;6.25e-23)|all cancers(26;1.13e-20)			GGCCAGGATGGCCGGACCTCA	0.567																																					p.P301S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C901T	19						.						61.0	56.0	58.0					19																	40433368		2203	4300	6503	45125208	SO:0001583	missense	8857	exon2			D84239		19q13.2	2013-09-20			ENSG00000090920	ENSG00000275395			13572	protein-coding gene	gene with protein product	"""IgG Fc binding protein"", ""Human Fc gamma BP"""					9182547	Standard	NM_003890		Approved	FC(GAMMA)BP	uc002omp.4	Q9Y6R7	OTTHUMG00000182580	ENST00000221347.6:c.901C>T	19.37:g.40433368G>A	ENSP00000221347:p.Pro301Ser	Somatic		Capture	Illumina HiSeq	Phase_I	45125208	NM_003890	O95784	Missense_Mutation	SNP	ENST00000221347.6	37	CCDS12546.1	.	.	.	.	.	.	.	.	.	.	G	4.517	0.095996	0.08681	.	.	ENSG00000090920	ENST00000221347	T	0.13901	2.55	4.36	4.36	0.52297	.	0.436920	0.18570	N	0.137369	T	0.04092	0.0114	N	0.02315	-0.6	0.09310	N	1	B	0.25772	0.134	B	0.17979	0.02	T	0.42032	-0.9475	10	0.09338	T	0.73	.	6.6416	0.22913	0.1871:0.0:0.8129:0.0	.	301	Q9Y6R7	FCGBP_HUMAN	S	301	ENSP00000221347:P301S	ENSP00000221347:P301S	P	-	1	0	FCGBP	45125208	0.055000	0.20627	0.045000	0.18777	0.286000	0.27126	2.391000	0.44424	2.715000	0.92844	0.655000	0.94253	CCA		0.567	FCGBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462507.1	NM_003890	
AKT2	208	broad.mit.edu	37	19	40741244	40741244	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr19:40741244G>A	ENST00000392038.2	-	12	1487	c.1189C>T	c.(1189-1191)Ccc>Tcc	p.P397S	AKT2_ENST00000424901.1_Missense_Mutation_p.P397S|AKT2_ENST00000579047.1_Missense_Mutation_p.P335S|AKT2_ENST00000311278.6_Missense_Mutation_p.P354S	NM_001243027.1|NM_001243028.1|NM_001626.4	NP_001229956.1|NP_001229957.1|NP_001617.1	P31751	AKT2_HUMAN	v-akt murine thymoma viral oncogene homolog 2	397	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of Ral GTPase activity (GO:0032859)|apoptotic process (GO:0006915)|carbohydrate transport (GO:0008643)|cellular protein modification process (GO:0006464)|cellular response to insulin stimulus (GO:0032869)|fat cell differentiation (GO:0045444)|glucose metabolic process (GO:0006006)|glycogen biosynthetic process (GO:0005978)|insulin receptor signaling pathway (GO:0008286)|intracellular protein transmembrane transport (GO:0065002)|mammary gland epithelial cell differentiation (GO:0060644)|membrane organization (GO:0061024)|negative regulation of plasma membrane long-chain fatty acid transport (GO:0010748)|peripheral nervous system myelin maintenance (GO:0032287)|positive regulation of cell motility (GO:2000147)|positive regulation of fatty acid beta-oxidation (GO:0032000)|positive regulation of glucose import (GO:0046326)|positive regulation of glucose import in response to insulin stimulus (GO:2001275)|positive regulation of glucose metabolic process (GO:0010907)|positive regulation of glycogen biosynthetic process (GO:0045725)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of protein targeting to membrane (GO:0090314)|positive regulation of vesicle fusion (GO:0031340)|protein localization to plasma membrane (GO:0072659)|regulation of cell cycle arrest (GO:0071156)|regulation of cell migration (GO:0030334)|regulation of translation (GO:0006417)|signal transduction (GO:0007165)	cell cortex (GO:0005938)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)	ATP binding (GO:0005524)|kinase activity (GO:0016301)|protein serine/threonine kinase activity (GO:0004674)	p.P397S(1)		breast(1)|cervix(1)|kidney(3)|large_intestine(9)|lung(10)|prostate(2)|skin(1)	27			Lung(22;0.000499)			GCATCGCTGGGCCCCCCACCA	0.652			A		"""ovarian, pancreatic """																																p.P397S			Dom	yes		19	19q13.1-q13.2	208	v-akt murine thymoma viral oncogene homolog 2		E	.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1189T	19						.						67.0	60.0	63.0					19																	40741244		2203	4300	6503	45433084	SO:0001583	missense	208	exon12			M77198	CCDS12552.1	19q13.1-q13.2	2013-01-10			ENSG00000105221	ENSG00000105221	2.7.11.1	"""Pleckstrin homology (PH) domain containing"""	392	protein-coding gene	gene with protein product		164731				1409633	Standard	NM_001626		Approved		uc002onf.3	P31751	OTTHUMG00000137375	ENST00000392038.2:c.1189C>T	19.37:g.40741244G>A	ENSP00000375892:p.Pro397Ser	Somatic		Capture	Illumina HiSeq	Phase_I	45433084	NM_001626	B2RBD8|Q05BV0|Q0VAN0|Q0VAN1|Q68GC0	Missense_Mutation	SNP	ENST00000392038.2	37	CCDS12552.1	.	.	.	.	.	.	.	.	.	.	G	14.31	2.498439	0.44455	.	.	ENSG00000105221	ENST00000392038;ENST00000391844;ENST00000424901;ENST00000311278	T;T;T	0.73152	-0.72;-0.72;-0.72	5.39	4.36	0.52297	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.051089	0.85682	N	0.000000	T	0.50069	0.1594	N	0.05487	-0.04	0.80722	D	1	B;B;B	0.16603	0.008;0.011;0.018	B;B;B	0.21546	0.019;0.035;0.019	T	0.42916	-0.9423	10	0.22706	T	0.39	.	12.9122	0.58187	0.0788:0.0:0.9212:0.0	.	335;354;397	B4DG79;Q0VAN0;P31751	.;.;AKT2_HUMAN	S	397;298;397;354	ENSP00000375892:P397S;ENSP00000399532:P397S;ENSP00000309428:P354S	ENSP00000309428:P354S	P	-	1	0	AKT2	45433084	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	4.366000	0.59492	1.513000	0.48852	0.655000	0.94253	CCC		0.652	AKT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268029.1	NM_001626	
SERTAD3	29946	broad.mit.edu	37	19	40947494	40947494	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr19:40947494C>A	ENST00000322354.3	-	2	990	c.494G>T	c.(493-495)cGg>cTg	p.R165L	CTC-492K19.4_ENST00000599050.1_RNA|SERTAD3_ENST00000601217.1_5'Flank|SERTAD3_ENST00000392028.4_Missense_Mutation_p.R165L	NM_203344.2	NP_976219.1	Q9UJW9	SRTD3_HUMAN	SERTA domain containing 3	165					negative regulation of cell growth (GO:0030308)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)		p.R165L(1)		kidney(1)|large_intestine(4)|lung(2)	7			Lung(22;6.24e-05)|LUSC - Lung squamous cell carcinoma(20;0.000384)			TGGTGGGGCCCGTGCAGGCTC	0.532																																					p.R165L												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G494T	19						.						80.0	87.0	85.0					19																	40947494		2203	4300	6503	45639334	SO:0001583	missense	29946	exon2			AF192529	CCDS12558.1	19q13.2	2008-02-05				ENSG00000167565			17931	protein-coding gene	gene with protein product	"""RPA-binding trans-activator"""	612125				10982866, 11331592	Standard	NM_013368		Approved	RBT1	uc002onv.4	Q9UJW9		ENST00000322354.3:c.494G>T	19.37:g.40947494C>A	ENSP00000325414:p.Arg165Leu	Somatic		Capture	Illumina HiSeq	Phase_I	45639334	NM_203344	B3KQB3|Q96CQ2	Missense_Mutation	SNP	ENST00000322354.3	37	CCDS12558.1	.	.	.	.	.	.	.	.	.	.	C	1.699	-0.502094	0.04261	.	.	ENSG00000167565	ENST00000322354;ENST00000392028	.	.	.	6.0	-3.34	0.04943	.	0.767318	0.10848	N	0.627471	T	0.12646	0.0307	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.18840	-1.0324	9	0.27082	T	0.32	-13.6083	0.3676	0.00374	0.3258:0.1239:0.2127:0.3375	.	165	Q9UJW9	SRTD3_HUMAN	L	165	.	ENSP00000325414:R165L	R	-	2	0	SERTAD3	45639334	0.000000	0.05858	0.000000	0.03702	0.049000	0.14656	0.177000	0.16801	-0.679000	0.05217	-1.608000	0.00805	CGG		0.532	SERTAD3-001	KNOWN	upstream_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462573.1	NM_013368	
SPTBN4	57731	broad.mit.edu	37	19	40995993	40995993	+	Silent	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr19:40995993G>A	ENST00000352632.3	+	4	419	c.333G>A	c.(331-333)acG>acA	p.T111T	SPTBN4_ENST00000595535.1_Silent_p.T111T|SPTBN4_ENST00000598249.1_Silent_p.T111T|SPTBN4_ENST00000338932.3_Silent_p.T111T|SPTBN4_ENST00000344104.3_Silent_p.T111T			Q9H254	SPTN4_HUMAN	spectrin, beta, non-erythrocytic 4	111	Actin-binding.|CH 1. {ECO:0000255|PROSITE- ProRule:PRU00044}.				actin filament capping (GO:0051693)|adult walking behavior (GO:0007628)|axon guidance (GO:0007411)|axonogenesis (GO:0007409)|cardiac conduction (GO:0061337)|central nervous system projection neuron axonogenesis (GO:0021952)|clustering of voltage-gated sodium channels (GO:0045162)|cytoskeletal anchoring at plasma membrane (GO:0007016)|establishment of protein localization to plasma membrane (GO:0090002)|fertilization (GO:0009566)|negative regulation of heart rate (GO:0010459)|positive regulation of multicellular organism growth (GO:0040018)|regulation of peptidyl-serine phosphorylation (GO:0033135)|regulation of sodium ion transport (GO:0002028)|sensory perception of sound (GO:0007605)|transmission of nerve impulse (GO:0019226)|vesicle-mediated transport (GO:0016192)	adherens junction (GO:0005912)|axon hillock (GO:0043203)|axon initial segment (GO:0043194)|cell body fiber (GO:0070852)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|node of Ranvier (GO:0033268)|nuclear matrix (GO:0016363)|paranode region of axon (GO:0033270)|plasma membrane (GO:0005886)|PML body (GO:0016605)|spectrin (GO:0008091)	actin binding (GO:0003779)|ankyrin binding (GO:0030506)|phosphatase binding (GO:0019902)|phospholipid binding (GO:0005543)|spectrin binding (GO:0030507)|structural constituent of cytoskeleton (GO:0005200)	p.T111T(1)		breast(4)|central_nervous_system(1)|endometrium(6)|kidney(7)|large_intestine(9)|lung(32)|ovary(3)|prostate(2)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	73			Lung(22;0.000114)|LUSC - Lung squamous cell carcinoma(20;0.000384)			CCAGGCCCACGCGCGGCCGCA	0.667																																					p.T111T												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G333A	19						.						35.0	31.0	33.0					19																	40995993		2203	4300	6503	45687833	SO:0001819	synonymous_variant	57731	exon4			AF082075	CCDS12559.1, CCDS42569.1	19q13.13	2013-01-10				ENSG00000160460		"""Pleckstrin homology (PH) domain containing"""	14896	protein-coding gene	gene with protein product		606214				11086001	Standard	NM_020971		Approved	SPTBN3, KIAA1642	uc002onz.3	Q9H254		ENST00000352632.3:c.333G>A	19.37:g.40995993G>A		Somatic		Capture	Illumina HiSeq	Phase_I	45687833	NM_020971	E9PGQ5|Q9H1K7|Q9H1K8|Q9H1K9|Q9H253|Q9H3G8|Q9HCD0	Silent	SNP	ENST00000352632.3	37	CCDS12559.1																																																																																				0.667	SPTBN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462559.2		
DPP9	91039	broad.mit.edu	37	19	4704161	4704161	+	Silent	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr19:4704161G>A	ENST00000598800.1	-	7	1000	c.495C>T	c.(493-495)ggC>ggT	p.G165G	DPP9_ENST00000597849.1_Silent_p.G194G|DPP9_ENST00000262960.9_Silent_p.G194G|DPP9_ENST00000594671.1_Silent_p.G165G			Q86TI2	DPP9_HUMAN	dipeptidyl-peptidase 9	165						cytoplasm (GO:0005737)|membrane (GO:0016020)	aminopeptidase activity (GO:0004177)|identical protein binding (GO:0042802)|serine-type peptidase activity (GO:0008236)	p.G273G(1)		cervix(2)|endometrium(3)|kidney(3)|large_intestine(2)|lung(6)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	20		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.00884)		CGTTCTTGCCGCCGTCGCGGC	0.667																																					p.G194G												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C582T	19						.						37.0	45.0	42.0					19																	4704161		2034	4174	6208	4655161	SO:0001819	synonymous_variant	91039	exon6			AF452102	CCDS45928.1	19p13.3	2014-06-11	2006-01-12		ENSG00000142002	ENSG00000142002			18648	protein-coding gene	gene with protein product		608258	"""dipeptidylpeptidase 9"""				Standard	NM_139159		Approved		uc002mba.3	Q86TI2	OTTHUMG00000182040	ENST00000598800.1:c.495C>T	19.37:g.4704161G>A		Somatic		Capture	Illumina HiSeq	Phase_I	4655161	NM_139159	O75273|O75868|Q1ZZB8|Q6AI37|Q6UAL0|Q6ZMT2|Q6ZNJ5|Q8N2J7|Q8N3F5|Q8WXD8|Q96NT8|Q9BVR3	Silent	SNP	ENST00000598800.1	37																																																																																					0.667	DPP9-026	NOVEL	basic	protein_coding	protein_coding	OTTHUMT00000459343.2		
HNRNPUL1	11100	broad.mit.edu	37	19	41774165	41774165	+	Silent	SNP	C	C	T	rs374312400		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr19:41774165C>T	ENST00000392006.3	+	2	506	c.333C>T	c.(331-333)taC>taT	p.Y111Y	HNRNPUL1_ENST00000594207.1_3'UTR|HNRNPUL1_ENST00000595018.1_Silent_p.Y11Y|HNRNPUL1_ENST00000352456.3_Silent_p.Y11Y|HNRNPUL1_ENST00000593587.1_Silent_p.Y11Y|HNRNPUL1_ENST00000602130.1_Silent_p.Y111Y|HNRNPUL1_ENST00000263367.3_Silent_p.Y22Y|HNRNPUL1_ENST00000378215.4_Silent_p.Y68Y	NM_007040.3	NP_008971.2	Q9BUJ2	HNRL1_HUMAN	heterogeneous nuclear ribonucleoprotein U-like 1	111					gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|regulation of transcription, DNA-templated (GO:0006355)|response to virus (GO:0009615)|RNA processing (GO:0006396)|RNA splicing (GO:0008380)|transcription, DNA-templated (GO:0006351)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	enzyme binding (GO:0019899)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)	p.Y111Y(1)		breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(8)|prostate(1)|skin(1)|urinary_tract(1)	29						ACCAATTCTACGATACCCAAG	0.453																																					p.Y11Y												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C33T	19						.	C	,	0,4406		0,0,2203	119.0	96.0	104.0		333,33	0.3	1.0	19		104	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous	HNRNPUL1	NM_007040.3,NM_144732.2	,	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	,	111/857,11/757	41774165	1,13005	2203	4300	6503	46466005	SO:0001819	synonymous_variant	11100	exon2			AJ007509	CCDS12576.1, CCDS12577.1	19q13.2	2013-06-12		2008-04-18	ENSG00000105323	ENSG00000105323			17011	protein-coding gene	gene with protein product	"""E1B 55kDa associated protein 5"""	605800		HNRPUL1		9733834, 12489984	Standard	XM_005258459		Approved	E1B-AP5, E1BAP5, FLJ12944	uc002oqb.4	Q9BUJ2	OTTHUMG00000182740	ENST00000392006.3:c.333C>T	19.37:g.41774165C>T		Somatic		Capture	Illumina HiSeq	Phase_I	46466005	NM_144732	B3KMW7|O76022|Q6ZSZ0|Q7L8P4|Q8N6Z4|Q96G37|Q9HAL3|Q9UG75	Silent	SNP	ENST00000392006.3	37	CCDS12576.1																																																																																				0.453	HNRNPUL1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463406.1	NM_144732, NM_007040	
BCKDHA	593	broad.mit.edu	37	19	41931575	41931575	+	IGR	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr19:41931575C>T	ENST00000269980.2	+	0	2103				B3GNT8_ENST00000601379.1_5'Flank|CTC-435M10.6_ENST00000598887.1_RNA|B3GNT8_ENST00000321702.2_Missense_Mutation_p.R370H	NM_000709.3|NM_001164783.1	NP_000700.1|NP_001158255.1	P12694	ODBA_HUMAN	branched chain keto acid dehydrogenase E1, alpha polypeptide						branched-chain amino acid catabolic process (GO:0009083)|cellular nitrogen compound metabolic process (GO:0034641)|response to cAMP (GO:0051591)|response to glucocorticoid (GO:0051384)|response to nutrient (GO:0007584)|small molecule metabolic process (GO:0044281)	mitochondrial alpha-ketoglutarate dehydrogenase complex (GO:0005947)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	3-methyl-2-oxobutanoate dehydrogenase (2-methylpropanoyl-transferring) activity (GO:0003863)|alpha-ketoacid dehydrogenase activity (GO:0003826)|carboxy-lyase activity (GO:0016831)|metal ion binding (GO:0046872)	p.R370H(1)		central_nervous_system(1)|kidney(1)|large_intestine(3)|lung(4)|prostate(1)	10						CAGCAGGTTGCGGAAAGCACA	0.657																																					p.R370H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1109A	19						.																																			46623415	SO:0001628	intergenic_variant	374907	exon3			J04474	CCDS12581.1	19q13.1-q13.2	2008-07-09	2005-11-29		ENSG00000248098	ENSG00000248098			986	protein-coding gene	gene with protein product	"""maple syrup urine disease"""	608348	"""branched chain keto acid dehydrogenase E1, alpha polypeptide (maple syrup urine disease)"", ""2-oxoisovalerate dehydrogenase (lipoamide)"""	OVD1A			Standard	NM_000709		Approved	MSU	uc002oqq.3	P12694	OTTHUMG00000168128		19.37:g.41931575C>T		Somatic		Capture	Illumina HiSeq	Phase_I	46623415	NM_198540	B4DP47|E7EW46|Q16034|Q16472	Missense_Mutation	SNP	ENST00000269980.2	37	CCDS12581.1	.	.	.	.	.	.	.	.	.	.	C	6.727	0.502908	0.12822	.	.	ENSG00000177191	ENST00000321702	T	0.37752	1.18	3.81	-0.667	0.11395	.	0.403761	0.23250	N	0.050257	T	0.30103	0.0754	M	0.66506	2.035	0.09310	N	1	P	0.47604	0.898	B	0.39904	0.313	T	0.22382	-1.0218	10	0.44086	T	0.13	.	7.822	0.29292	0.0:0.5086:0.0:0.4914	.	370	Q7Z7M8	B3GN8_HUMAN	H	370	ENSP00000312700:R370H	ENSP00000312700:R370H	R	-	2	0	B3GNT8	46623415	0.525000	0.26290	0.001000	0.08648	0.228000	0.25075	0.970000	0.29383	0.081000	0.16988	0.655000	0.94253	CGC		0.657	BCKDHA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398313.3	NM_000709	
CIC	23152	broad.mit.edu	37	19	42793060	42793060	+	Missense_Mutation	SNP	G	G	A	rs376580917		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr19:42793060G>A	ENST00000575354.2	+	7	992	c.952G>A	c.(952-954)Gtt>Att	p.V318I	CIC_ENST00000160740.3_Missense_Mutation_p.V318I|CIC_ENST00000572681.2_Missense_Mutation_p.V1227I	NM_015125.3	NP_055940.3	Q96RK0	CIC_HUMAN	capicua transcriptional repressor	318					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)	p.V318I(1)		autonomic_ganglia(1)|breast(5)|central_nervous_system(32)|endometrium(10)|kidney(2)|large_intestine(7)|lung(9)|ovary(7)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	82		Prostate(69;0.00682)				GCTCCTGTCCGTTGCAGCCCA	0.582			"""Mis, F, S"""		oligodendroglioma																																p.V318I			Rec	yes		19	19q13.2	23152	capicua homolog		O	.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G952A	19						.	G	ILE/VAL	1,4405		0,1,2202	46.0	43.0	44.0		952	4.9	0.3	19		44	1,8599	1.2+/-3.3	0,1,4299	no	missense	CIC	NM_015125.3	29	0,2,6501	AA,AG,GG		0.0116,0.0227,0.0154	benign	318/1609	42793060	2,13004	2203	4300	6503	47484900	SO:0001583	missense	23152	exon7			AB002304	CCDS12601.1	19q13.2	2013-03-15	2013-03-15		ENSG00000079432	ENSG00000079432			14214	protein-coding gene	gene with protein product		612082	"""capicua (Drosophila) homolog"", ""capicua homolog (Drosophila)"""			12393275, 15981098	Standard	NM_015125		Approved	KIAA0306	uc002otf.1	Q96RK0		ENST00000575354.2:c.952G>A	19.37:g.42793060G>A	ENSP00000458663:p.Val318Ile	Somatic		Capture	Illumina HiSeq	Phase_I	47484900	NM_015125	Q7LGI1|Q9UEG5|Q9Y6T1	Missense_Mutation	SNP	ENST00000575354.2	37	CCDS12601.1	.	.	.	.	.	.	.	.	.	.	G	9.169	1.020566	0.19433	2.27E-4	1.16E-4	ENSG00000079432	ENST00000160740	.	.	.	4.88	4.88	0.63580	.	.	.	.	.	T	0.20129	0.0484	N	0.08118	0	0.19300	N	0.999979	B	0.30889	0.299	B	0.16289	0.015	T	0.14615	-1.0466	8	0.87932	D	0	-11.1809	13.3946	0.60843	0.0:0.0:1.0:0.0	.	318	Q96RK0	CIC_HUMAN	I	318	.	ENSP00000160740:V318I	V	+	1	0	CIC	47484900	0.517000	0.26226	0.282000	0.24776	0.250000	0.25880	3.653000	0.54446	2.546000	0.85860	0.555000	0.69702	GTT		0.582	CIC-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000438532.2		
PSG2	5670	broad.mit.edu	37	19	43585208	43585208	+	Silent	SNP	G	G	A	rs148293206	byFrequency	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr19:43585208G>A	ENST00000406487.1	-	2	353	c.255C>T	c.(253-255)gaC>gaT	p.D85D	PSG2_ENST00000491995.1_5'Flank	NM_031246.3	NP_112536.2	P11465	PSG2_HUMAN	pregnancy specific beta-1-glycoprotein 2	85	Ig-like V-type.				cell migration (GO:0016477)|female pregnancy (GO:0007565)	extracellular region (GO:0005576)		p.D85D(1)		central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(5)|lung(24)|ovary(1)|pancreas(2)|prostate(6)|stomach(2)|urinary_tract(2)	49		Prostate(69;0.00682)				TTATTTGACCGTCTACTACAT	0.443													G|||	5	0.000998403	0.0	0.0	5008	,	,		20886	0.002		0.003	False		,,,				2504	0.0				p.D85D												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C255T	19						.	G		0,4406		0,0,2203	199.0	202.0	201.0		255	-1.1	0.0	19	dbSNP_134	201	3,8593		0,3,4295	no	coding-synonymous	PSG2	NM_031246.3		0,3,6498	AA,AG,GG		0.0349,0.0,0.0231		85/336	43585208	3,12999	2203	4298	6501	48277048	SO:0001819	synonymous_variant	5675	exon2				CCDS12616.1	19q13.1-q13.2	2013-01-29			ENSG00000242221	ENSG00000242221		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	9519	protein-coding gene	gene with protein product	"""pregnancy-specific beta-1 glycoprotein"", ""pregnancy-specific beta-1-glycoprotein 7"", ""carcinoembryonic antigen SG8"""	176391		PSBG2		2377620	Standard	NM_031246		Approved	PSGGB, PSG1, CEA	uc002ovr.3	P11465	OTTHUMG00000151547	ENST00000406487.1:c.255C>T	19.37:g.43585208G>A		Somatic		Capture	Illumina HiSeq	Phase_I	48277048	NM_031246	Q8TCD9|Q9UEA4|Q9UQ78	Silent	SNP	ENST00000406487.1	37	CCDS12616.1																																																																																				0.443	PSG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323083.1	NM_031246	
CADM4	199731	broad.mit.edu	37	19	44127515	44127515	+	Silent	SNP	G	G	A	rs144737031		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr19:44127515G>A	ENST00000222374.2	-	9	1182	c.1134C>T	c.(1132-1134)gaC>gaT	p.D378D	CADM4_ENST00000593506.1_5'Flank	NM_145296.1	NP_660339.1	Q8NFZ8	CADM4_HUMAN	cell adhesion molecule 4	378					cell adhesion (GO:0007155)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)		p.D378D(1)		endometrium(2)|large_intestine(3)|lung(4)|prostate(1)|skin(2)	12		Prostate(69;0.0199)				TCTTGTGTCCGTCGCTGCCAT	0.612																																					p.D378D												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1134T	19						.	G		2,4404	4.2+/-10.8	0,2,2201	162.0	159.0	160.0		1134	-7.1	0.9	19	dbSNP_134	160	0,8600		0,0,4300	no	coding-synonymous	CADM4	NM_145296.1		0,2,6501	AA,AG,GG		0.0,0.0454,0.0154		378/389	44127515	2,13004	2203	4300	6503	48819355	SO:0001819	synonymous_variant	199731	exon9			AF363368	CCDS12627.1	19q13.32	2013-01-29	2007-02-07	2007-02-07		ENSG00000105767		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	30825	protein-coding gene	gene with protein product	"""nectin-like 4"""	609744	"""immunoglobulin superfamily, member 4C"""	IGSF4C		11536053	Standard	NM_145296		Approved	TSLL2, Necl-4, SynCAM4	uc002oxc.1	Q8NFZ8		ENST00000222374.2:c.1134C>T	19.37:g.44127515G>A		Somatic		Capture	Illumina HiSeq	Phase_I	48819355	NM_145296	B2R7L5|Q9Y4A4	Silent	SNP	ENST00000222374.2	37	CCDS12627.1																																																																																				0.612	CADM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463352.1	NM_145296	
SMG9	56006	broad.mit.edu	37	19	44251908	44251908	+	Missense_Mutation	SNP	C	C	T	rs568897261	byFrequency	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr19:44251908C>T	ENST00000270066.6	-	4	709	c.367G>A	c.(367-369)Gcc>Acc	p.A123T	SMG9_ENST00000601170.1_Missense_Mutation_p.A123T	NM_019108.2	NP_061981.2	Q9H0W8	SMG9_HUMAN	SMG9 nonsense mediated mRNA decay factor	123	Pro-rich.				gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|RNA metabolic process (GO:0016070)	cytosol (GO:0005829)|intracellular (GO:0005622)	identical protein binding (GO:0042802)	p.A123T(1)		kidney(1)|large_intestine(5)|liver(1)|lung(7)|pancreas(1)|prostate(2)|urinary_tract(2)	19						GGTGGTGGGGCGGTGCCCTCA	0.677													C|||	3	0.000599042	0.0	0.0	5008	,	,		11961	0.0		0.0	False		,,,				2504	0.0031				p.A123T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G367A	19						.						17.0	21.0	20.0					19																	44251908		2196	4298	6494	48943748	SO:0001583	missense	56006	exon4			BC008869	CCDS33043.2	19q13.31	2013-07-02	2013-07-02	2011-06-21	ENSG00000105771	ENSG00000105771			25763	protein-coding gene	gene with protein product		613176	"""chromosome 19 open reading frame 61"", ""smg-9 homolog, nonsense mediated mRNA decay factor (C. elegans)"""	C19orf61		11230166, 19417104	Standard	NM_019108		Approved	FLJ12886	uc002oxj.2	Q9H0W8	OTTHUMG00000150337	ENST00000270066.6:c.367G>A	19.37:g.44251908C>T	ENSP00000270066:p.Ala123Thr	Somatic		Capture	Illumina HiSeq	Phase_I	48943748	NM_019108	O60429|Q9H9A9	Missense_Mutation	SNP	ENST00000270066.6	37	CCDS33043.2	.	.	.	.	.	.	.	.	.	.	C	11.50	1.658575	0.29515	.	.	ENSG00000105771	ENST00000270066	.	.	.	5.3	0.25	0.15535	.	0.366667	0.26631	N	0.023314	T	0.20251	0.0487	N	0.14661	0.345	0.21627	N	0.999619	B;B	0.10296	0.003;0.001	B;B	0.04013	0.001;0.0	T	0.19386	-1.0307	9	0.18276	T	0.48	7.5896	8.0594	0.30625	0.0:0.5278:0.0:0.4722	.	123;123	Q9H0W8-2;Q9H0W8	.;SMG9_HUMAN	T	123	.	ENSP00000270066:A123T	A	-	1	0	SMG9	48943748	0.081000	0.21417	0.148000	0.22405	0.978000	0.69477	0.478000	0.22212	0.249000	0.21456	0.655000	0.94253	GCC		0.677	SMG9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317668.1	NM_019108	
ZNF227	7770	broad.mit.edu	37	19	44740580	44740580	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr19:44740580G>A	ENST00000313040.7	+	6	2202	c.1997G>A	c.(1996-1998)gGa>gAa	p.G666E	ZNF227_ENST00000589005.1_Missense_Mutation_p.G615E|ZNF227_ENST00000391961.2_Missense_Mutation_p.G615E|ZNF235_ENST00000589799.1_3'UTR	NM_182490.1	NP_872296.1	Q86WZ6	ZN227_HUMAN	zinc finger protein 227	666					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.G666E(1)		central_nervous_system(1)|kidney(3)|large_intestine(4)|lung(12)|ovary(2)|stomach(1)|urinary_tract(1)	24		Prostate(69;0.0435)				GATGTGTGTGGAAAGGGCTTT	0.463																																					p.G666E												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1997A	19						.						72.0	75.0	74.0					19																	44740580		2203	4300	6503	49432420	SO:0001583	missense	7770	exon6			AK092253	CCDS12636.1, CCDS74388.1	19q13.32	2013-01-08						"""Zinc fingers, C2H2-type"", ""-"""	13020	protein-coding gene	gene with protein product							Standard	XM_005259232		Approved		uc002oyu.3	Q86WZ6		ENST00000313040.7:c.1997G>A	19.37:g.44740580G>A	ENSP00000321049:p.Gly666Glu	Somatic		Capture	Illumina HiSeq	Phase_I	49432420	NM_182490	B3KRU7|B7Z5P9	Missense_Mutation	SNP	ENST00000313040.7	37	CCDS12636.1	.	.	.	.	.	.	.	.	.	.	G	16.11	3.029332	0.54790	.	.	ENSG00000131115	ENST00000313040;ENST00000328297;ENST00000391961;ENST00000418980;ENST00000377916	T;T	0.01005	5.45;5.45	3.68	3.68	0.42216	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.03520	0.0101	L	0.48362	1.52	0.80722	D	1	D;D;D;D	0.89917	0.997;1.0;1.0;0.997	P;D;D;P	0.97110	0.82;1.0;1.0;0.82	T	0.58025	-0.7709	9	0.59425	D	0.04	.	14.716	0.69269	0.0:0.0:1.0:0.0	.	587;645;618;666	B7Z6M2;Q658S5;Q9NS43;Q86WZ6	.;.;.;ZN227_HUMAN	E	666;623;615;645;305	ENSP00000321049:G666E;ENSP00000375823:G615E	ENSP00000321049:G666E	G	+	2	0	ZNF227	49432420	0.996000	0.38824	0.992000	0.48379	0.824000	0.46624	2.354000	0.44098	2.071000	0.62044	0.655000	0.94253	GGA		0.463	ZNF227-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460720.1	NM_182490	
EXOC3L2	90332	broad.mit.edu	37	19	45716536	45716536	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr19:45716536G>A	ENST00000252482.3	-	9	1048	c.1021C>T	c.(1021-1023)Cgg>Tgg	p.R341W	AC006126.3_ENST00000591569.1_Intron|EXOC3L2_ENST00000413988.1_Missense_Mutation_p.R341W			Q2M3D2	EX3L2_HUMAN	exocyst complex component 3-like 2	341					exocytosis (GO:0006887)	exocyst (GO:0000145)		p.R341W(1)		endometrium(1)|large_intestine(5)|lung(3)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	12		all_neural(266;0.224)|Ovarian(192;0.231)		OV - Ovarian serous cystadenocarcinoma(262;0.00883)		TCCAGGTCCCGGGCCACGGCC	0.657																																					p.R341W												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1021T	19						.						40.0	42.0	41.0					19																	45716536		2203	4300	6503	50408376	SO:0001583	missense	90332	exon10			AK093466	CCDS12657.1	19q13.32	2011-07-07			ENSG00000130201	ENSG00000130201			30162	protein-coding gene	gene with protein product						21566143	Standard	NM_138568		Approved	FLJ36147, XTP7	uc002pay.1	Q2M3D2	OTTHUMG00000155018	ENST00000252482.3:c.1021C>T	19.37:g.45716536G>A	ENSP00000252482:p.Arg341Trp	Somatic		Capture	Illumina HiSeq	Phase_I	50408376	NM_138568	Q8N9W2|Q96GV2	Missense_Mutation	SNP	ENST00000252482.3	37	CCDS12657.1	.	.	.	.	.	.	.	.	.	.	G	19.40	3.820602	0.71028	.	.	ENSG00000130201	ENST00000252482;ENST00000413988	T;T	0.08008	3.14;3.14	4.53	4.53	0.55603	.	0.181571	0.41938	D	0.000791	T	0.24699	0.0599	M	0.62723	1.935	0.33477	D	0.586931	D	0.89917	1.0	D	0.78314	0.991	T	0.28713	-1.0035	10	0.87932	D	0	.	12.7701	0.57415	0.0:0.0:1.0:0.0	.	341	Q2M3D2	EX3L2_HUMAN	W	341	ENSP00000252482:R341W;ENSP00000400713:R341W	ENSP00000252482:R341W	R	-	1	2	EXOC3L2	50408376	1.000000	0.71417	1.000000	0.80357	0.835000	0.47333	1.485000	0.35519	2.073000	0.62155	0.455000	0.32223	CGG		0.657	EXOC3L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338073.1	NM_138568	
CKM	1158	broad.mit.edu	37	19	45810118	45810118	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr19:45810118C>T	ENST00000221476.3	-	8	1210	c.1036G>A	c.(1036-1038)Gaa>Aaa	p.E346K		NM_001824.4	NP_001815.2	P06732	KCRM_HUMAN	creatine kinase, muscle	346	Phosphagen kinase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00843}.				cellular nitrogen compound metabolic process (GO:0034641)|creatine metabolic process (GO:0006600)|phosphocreatine biosynthetic process (GO:0046314)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	ATP binding (GO:0005524)|creatine kinase activity (GO:0004111)	p.E346K(1)		cervix(1)|endometrium(1)|large_intestine(8)|lung(3)|prostate(2)|skin(2)	17		Ovarian(192;0.0336)|all_neural(266;0.112)		OV - Ovarian serous cystadenocarcinoma(262;2.29e-44)|Epithelial(262;1.05e-38)|GBM - Glioblastoma multiforme(486;3.56e-07)	Creatine(DB00148)	TGTTCTACTTCGGACGAGCCC	0.582																																					p.E346K												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1036A	19						.						192.0	158.0	169.0					19																	45810118		2203	4300	6503	50501958	SO:0001583	missense	1158	exon8			M14780	CCDS12659.1	19q13.32	2012-10-02			ENSG00000104879	ENSG00000104879	2.7.3.2		1994	protein-coding gene	gene with protein product		123310		CKMM			Standard	NM_001824		Approved		uc002pbd.4	P06732		ENST00000221476.3:c.1036G>A	19.37:g.45810118C>T	ENSP00000221476:p.Glu346Lys	Somatic		Capture	Illumina HiSeq	Phase_I	50501958	NM_001824	Q96QL9	Missense_Mutation	SNP	ENST00000221476.3	37	CCDS12659.1	.	.	.	.	.	.	.	.	.	.	C	36	5.691287	0.96793	.	.	ENSG00000104879	ENST00000221476	T	0.58358	0.34	5.49	5.49	0.81192	ATP:guanido phosphotransferase, catalytic domain (2);Glutamine synthetase/guanido kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.81626	0.4862	H	0.98068	4.14	0.80722	D	1	D	0.65815	0.995	P	0.62491	0.903	D	0.88117	0.2829	10	0.62326	D	0.03	-50.6638	16.8714	0.86041	0.0:1.0:0.0:0.0	.	346	P06732	KCRM_HUMAN	K	346	ENSP00000221476:E346K	ENSP00000221476:E346K	E	-	1	0	CKM	50501958	1.000000	0.71417	0.999000	0.59377	0.962000	0.63368	7.459000	0.80802	2.594000	0.87642	0.561000	0.74099	GAA		0.582	CKM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457569.1		
ERCC1	2067	broad.mit.edu	37	19	45926585	45926585	+	Silent	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr19:45926585C>T	ENST00000300853.3	-	2	639	c.48G>A	c.(46-48)ccG>ccA	p.P16P	ERCC1_ENST00000013807.5_Silent_p.P16P|ERCC1_ENST00000423698.2_Silent_p.P16P|ERCC1_ENST00000340192.7_Silent_p.P16P|ERCC1_ENST00000591636.1_Silent_p.P16P|ERCC1_ENST00000589165.1_Silent_p.P16P	NM_001983.3	NP_001974.1	P07992	ERCC1_HUMAN	excision repair cross-complementation group 1	16					cell proliferation (GO:0008283)|chromosome organization (GO:0051276)|DNA catabolic process, endonucleolytic (GO:0000737)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|interstrand cross-link repair (GO:0036297)|isotype switching (GO:0045190)|male gonad development (GO:0008584)|mitotic recombination (GO:0006312)|multicellular organism growth (GO:0035264)|multicellular organismal aging (GO:0010259)|negative regulation of telomere maintenance (GO:0032205)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA damage removal (GO:0000718)|nucleotide-excision repair, DNA incision, 3'-to lesion (GO:0006295)|nucleotide-excision repair, DNA incision, 5'-to lesion (GO:0006296)|oogenesis (GO:0048477)|post-embryonic hemopoiesis (GO:0035166)|pyrimidine dimer repair by nucleotide-excision repair (GO:0000720)|replicative cell aging (GO:0001302)|response to nutrient (GO:0007584)|response to oxidative stress (GO:0006979)|response to sucrose (GO:0009744)|response to X-ray (GO:0010165)|spermatogenesis (GO:0007283)|syncytium formation (GO:0006949)|transcription-coupled nucleotide-excision repair (GO:0006283)|UV protection (GO:0009650)	cytoplasm (GO:0005737)|nuclear chromosome, telomeric region (GO:0000784)|nucleoplasm (GO:0005654)|nucleotide-excision repair complex (GO:0000109)|nucleus (GO:0005634)|transcription factor TFIID complex (GO:0005669)	damaged DNA binding (GO:0003684)|endonuclease activity (GO:0004519)|protein C-terminus binding (GO:0008022)|protein domain specific binding (GO:0019904)|single-stranded DNA binding (GO:0003697)	p.P16P(1)		central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(4)|lung(2)|ovary(2)|skin(1)	15		Ovarian(192;0.051)|all_neural(266;0.112)		OV - Ovarian serous cystadenocarcinoma(262;0.0247)		TCCTTGCTGGCGGCCCTGAGG	0.632								Nucleotide excision repair (NER)																													p.P16P												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G48A	19						.						69.0	60.0	63.0					19																	45926585		2203	4300	6503	50618425	SO:0001819	synonymous_variant	2067	exon2				CCDS12662.1, CCDS12663.1, CCDS54279.1	19q13.32	2014-03-07	2014-03-07			ENSG00000012061			3433	protein-coding gene	gene with protein product		126380	"""excision repair cross-complementing rodent repair deficiency, complementation group 1 (includes overlapping antisense sequence)"""			6462228	Standard	NM_001983		Approved	RAD10	uc002pbs.2	P07992		ENST00000300853.3:c.48G>A	19.37:g.45926585C>T		Somatic		Capture	Illumina HiSeq	Phase_I	50618425	NM_001983	B2RC01|B3KRR0|Q7Z7F5|Q96S40	Silent	SNP	ENST00000300853.3	37	CCDS12662.1																																																																																				0.632	ERCC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459542.1	NM_001983	
NOVA2	4858	broad.mit.edu	37	19	46444134	46444134	+	Missense_Mutation	SNP	C	C	T	rs200399286	byFrequency	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr19:46444134C>T	ENST00000263257.5	-	4	660	c.466G>A	c.(466-468)Gtg>Atg	p.V156M		NM_002516.2	NP_002507.1	Q9UNW9	NOVA2_HUMAN	neuro-oncological ventral antigen 2	156	KH 2. {ECO:0000255|PROSITE- ProRule:PRU00117}.				regulation of RNA metabolic process (GO:0051252)	nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)	p.V156M(1)		endometrium(3)|large_intestine(5)|lung(13)	21		all_neural(266;0.113)|Ovarian(192;0.127)		OV - Ovarian serous cystadenocarcinoma(262;0.00245)|GBM - Glioblastoma multiforme(486;0.0782)|Epithelial(262;0.179)		TGTTCCATCACGGCTTTCACC	0.642																																					p.V156M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G466A	19						.	C	MET/VAL	0,4406		0,0,2203	33.0	31.0	32.0		466	3.8	1.0	19		32	5,8595	4.3+/-15.6	0,5,4295	yes	missense	NOVA2	NM_002516.2	21	0,5,6498	TT,TC,CC		0.0581,0.0,0.0384	probably-damaging	156/493	46444134	5,13001	2203	4300	6503	51135974	SO:0001583	missense	4858	exon4			U70477	CCDS12679.1	19q13.3	2008-07-17				ENSG00000104967			7887	protein-coding gene	gene with protein product	"""neuro-oncological ventral antigen 3"""	601991		NOVA3		9344654, 10368286	Standard	NM_002516		Approved	ANOVA	uc002pdv.2	Q9UNW9		ENST00000263257.5:c.466G>A	19.37:g.46444134C>T	ENSP00000263257:p.Val156Met	Somatic		Capture	Illumina HiSeq	Phase_I	51135974	NM_002516	O43267|Q9UEA1	Missense_Mutation	SNP	ENST00000263257.5	37	CCDS12679.1	.	.	.	.	.	.	.	.	.	.	C	17.23	3.337550	0.60963	0.0	5.81E-4	ENSG00000104967	ENST00000263257	T	0.28666	1.6	3.82	3.82	0.43975	K Homology (1);K Homology, type 1, subgroup (1);K Homology, type 1 (1);	0.152129	0.43747	N	0.000528	T	0.20292	0.0488	N	0.02158	-0.66	0.41174	D	0.986182	D	0.69078	0.997	P	0.59357	0.856	T	0.10222	-1.0639	10	0.39692	T	0.17	-12.9484	7.15	0.25606	0.0:0.8781:0.0:0.1219	.	156	Q9UNW9	NOVA2_HUMAN	M	156	ENSP00000263257:V156M	ENSP00000263257:V156M	V	-	1	0	NOVA2	51135974	0.999000	0.42202	1.000000	0.80357	0.951000	0.60555	3.710000	0.54860	1.994000	0.58287	0.484000	0.47621	GTG		0.642	NOVA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437210.2	NM_002516	
CCDC61	729440	broad.mit.edu	37	19	46519603	46519603	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr19:46519603C>T	ENST00000595358.1	+	9	1092	c.1043C>T	c.(1042-1044)aCg>aTg	p.T348M	CCDC61_ENST00000263284.2_Missense_Mutation_p.T367M|MIR769_ENST00000390225.1_RNA|CCDC61_ENST00000536603.1_Intron|CCDC61_ENST00000594087.1_Intron	NM_001267723.1	NP_001254652.1	Q9Y6R9	CCD61_HUMAN	coiled-coil domain containing 61	348						centrosome (GO:0005813)		p.T367M(1)		endometrium(3)|kidney(3)|large_intestine(1)|lung(5)|ovary(1)	13		all_neural(266;0.113)|Ovarian(192;0.127)		OV - Ovarian serous cystadenocarcinoma(262;0.00221)|GBM - Glioblastoma multiforme(486;0.0233)|Epithelial(262;0.164)		TTCGACCCCACGGCCTTTGTG	0.667																																					p.T367M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1100T	19						.						72.0	87.0	82.0					19																	46519603		2016	4158	6174	51211443	SO:0001583	missense	729440	exon10				CCDS46120.1, CCDS46120.2	19q13.32	2014-09-04			ENSG00000104983	ENSG00000104983			33629	protein-coding gene	gene with protein product							Standard	NM_001267723		Approved		uc031rlj.1	Q9Y6R9	OTTHUMG00000182488	ENST00000595358.1:c.1043C>T	19.37:g.46519603C>T	ENSP00000471454:p.Thr348Met	Somatic		Capture	Illumina HiSeq	Phase_I	51211443	NM_001080402	C8CAP4|Q9HDB6	Missense_Mutation	SNP	ENST00000595358.1	37	CCDS46120.2	.	.	.	.	.	.	.	.	.	.	C	25.3	4.626920	0.87560	.	.	ENSG00000104983	ENST00000263284	.	.	.	4.19	4.19	0.49359	.	0.101452	0.64402	D	0.000002	T	0.70307	0.3209	L	0.57536	1.79	0.58432	D	0.999998	D	0.89917	1.0	D	0.85130	0.997	T	0.72846	-0.4169	9	0.66056	D	0.02	-3.651	11.948	0.52938	0.0:1.0:0.0:0.0	.	310	Q9Y6R9	CCD61_HUMAN	M	367	.	ENSP00000263284:T367M	T	+	2	0	CCDC61	51211443	0.999000	0.42202	1.000000	0.80357	0.935000	0.57460	3.722000	0.54948	2.174000	0.68829	0.544000	0.68410	ACG		0.667	CCDC61-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461689.1	NM_001080402	
NPAS1	4861	broad.mit.edu	37	19	47542319	47542319	+	Silent	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr19:47542319C>T	ENST00000602212.1	+	7	934	c.714C>T	c.(712-714)ccC>ccT	p.P238P	NPAS1_ENST00000439365.2_Silent_p.P62P|NPAS1_ENST00000449844.2_Silent_p.P238P|NPAS1_ENST00000602189.1_Silent_p.P62P			Q99742	NPAS1_HUMAN	neuronal PAS domain protein 1	238					central nervous system development (GO:0007417)|maternal behavior (GO:0042711)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|startle response (GO:0001964)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)	p.P238P(1)		endometrium(2)|kidney(1)|large_intestine(2)|lung(1)	6		all_cancers(25;4.31e-08)|all_epithelial(76;2.96e-06)|all_lung(116;7.86e-06)|Lung NSC(112;2.31e-05)|all_neural(266;0.026)|Ovarian(192;0.0392)|Breast(70;0.102)		all cancers(93;6.02e-05)|OV - Ovarian serous cystadenocarcinoma(262;7.35e-05)|Epithelial(262;0.00389)|GBM - Glioblastoma multiforme(486;0.0252)		AGGTGCCCCCCTCCTCCCTGG	0.607																																					p.P238P												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C714T	19						.						81.0	75.0	77.0					19																	47542319		2203	4300	6503	52234159	SO:0001819	synonymous_variant	4861	exon6			U77968	CCDS12694.1	19q13.2-q13.3	2013-05-21				ENSG00000130751		"""Basic helix-loop-helix proteins"""	7894	protein-coding gene	gene with protein product	"""neuronal PAS1"", ""member of PAS superfamily 5"""	603346				9012850, 9079689	Standard	NM_002517		Approved	MOP5, PASD5, bHLHe11	uc002pfy.3	Q99742		ENST00000602212.1:c.714C>T	19.37:g.47542319C>T		Somatic		Capture	Illumina HiSeq	Phase_I	52234159	NM_002517	B4DR69|Q99632|Q9BY83	Silent	SNP	ENST00000602212.1	37	CCDS12694.1																																																																																				0.607	NPAS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466658.1	NM_002517	
SAE1	10055	broad.mit.edu	37	19	47712419	47712419	+	Silent	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr19:47712419C>T	ENST00000270225.7	+	9	1020	c.952C>T	c.(952-954)Ctg>Ttg	p.L318L	SAE1_ENST00000413379.3_Missense_Mutation_p.P246L|SAE1_ENST00000540850.1_Silent_p.L144L|SAE1_ENST00000598840.1_Silent_p.L237L|SAE1_ENST00000392776.3_3'UTR	NM_005500.2	NP_005491.1	Q9UBE0	SAE1_HUMAN	SUMO1 activating enzyme subunit 1	318					cellular protein metabolic process (GO:0044267)|positive regulation of catalytic activity (GO:0043085)|post-translational protein modification (GO:0043687)|protein sumoylation (GO:0016925)|protein ubiquitination (GO:0016567)|regulation of mitotic cell cycle (GO:0007346)|SMT3-dependent protein catabolic process (GO:0019950)	cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP-dependent protein binding (GO:0043008)|enzyme activator activity (GO:0008047)|protein C-terminus binding (GO:0008022)|protein heterodimerization activity (GO:0046982)|ubiquitin activating enzyme activity (GO:0004839)	p.L318L(1)		endometrium(3)|large_intestine(5)|lung(4)|ovary(1)	13		all_cancers(25;1.13e-05)|all_lung(116;0.000192)|all_epithelial(76;0.000274)|Lung NSC(112;0.000446)|all_neural(266;0.0652)|Ovarian(192;0.15)		all cancers(93;0.00013)|OV - Ovarian serous cystadenocarcinoma(262;0.000146)|Epithelial(262;0.00697)|GBM - Glioblastoma multiforme(486;0.0278)		TCCCCAGGCCCTGTCTCAGCG	0.458																																					p.P246L												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C737T	19						.						90.0	87.0	88.0					19																	47712419		2203	4300	6503	52404259	SO:0001819	synonymous_variant	10055	exon7			BC018271	CCDS12696.1, CCDS54284.1, CCDS54285.1	19q13.32	2013-09-26				ENSG00000142230		"""Ubiquitin-like modifier activating enzymes"""	30660	protein-coding gene	gene with protein product	"""activator Of sumo 1"""	613294				10187858, 9920803, 10217437	Standard	NM_005500		Approved	AOS1, FLJ3091, Sua1	uc002pgc.3	Q9UBE0		ENST00000270225.7:c.952C>T	19.37:g.47712419C>T		Somatic		Capture	Illumina HiSeq	Phase_I	52404259	NM_001145713	B2RDP5|B3KMQ2|F5GXX7|G3XAK6|O95717|Q9P020	Missense_Mutation	SNP	ENST00000270225.7	37	CCDS12696.1	.	.	.	.	.	.	.	.	.	.	C	12.44	1.938532	0.34189	.	.	ENSG00000142230	ENST00000413379	T	0.69306	-0.39	6.07	6.07	0.98685	.	.	.	.	.	T	0.58850	0.2151	.	.	.	0.80722	D	1	B	0.30686	0.29	B	0.32864	0.154	T	0.53380	-0.8447	7	.	.	.	.	16.144	0.81551	0.0:1.0:0.0:0.0	.	246	G3XAK6	.	L	246	ENSP00000416557:P246L	.	P	+	2	0	SAE1	52404259	0.993000	0.37304	0.991000	0.47740	0.137000	0.21094	2.987000	0.49378	2.884000	0.98904	0.655000	0.94253	CCT		0.458	SAE1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466775.1	NM_005500	
SLC8A2	6543	broad.mit.edu	37	19	47941204	47941204	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr19:47941204C>T	ENST00000236877.6	-	7	2307	c.1912G>A	c.(1912-1914)Gag>Aag	p.E638K	SLC8A2_ENST00000542837.1_Missense_Mutation_p.E394K|SLC8A2_ENST00000539381.1_Missense_Mutation_p.E101K|SLC8A2_ENST00000601757.1_5'UTR	NM_015063.2	NP_055878.1	Q9UPR5	NAC2_HUMAN	solute carrier family 8 (sodium/calcium exchanger), member 2	638	Poly-Glu.				blood coagulation (GO:0007596)|cell communication (GO:0007154)|ion transport (GO:0006811)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium:sodium antiporter activity (GO:0005432)	p.E638K(1)		breast(1)|endometrium(4)|kidney(2)|large_intestine(4)|lung(10)|ovary(2)|prostate(2)|skin(5)|stomach(1)	31		all_cancers(25;3.05e-07)|all_lung(116;4.19e-06)|Lung NSC(112;7.16e-06)|all_epithelial(76;7.65e-06)|all_neural(266;0.0652)|Ovarian(192;0.086)|Breast(70;0.173)		OV - Ovarian serous cystadenocarcinoma(262;0.000501)|all cancers(93;0.00058)|Epithelial(262;0.0181)|GBM - Glioblastoma multiforme(486;0.0457)		TCCTCCTCCTCGGCTGTTAGC	0.562																																					p.E638K												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1912A	19						.						107.0	106.0	106.0					19																	47941204		2203	4300	6503	52633016	SO:0001583	missense	6543	exon7			AB029010	CCDS33065.1	19q13.32	2013-07-15	2008-09-02		ENSG00000118160	ENSG00000118160		"""Solute carriers"""	11069	protein-coding gene	gene with protein product		601901				8021246	Standard	NM_015063		Approved	NCX2, KIAA1087	uc002pgx.3	Q9UPR5	OTTHUMG00000183529	ENST00000236877.6:c.1912G>A	19.37:g.47941204C>T	ENSP00000236877:p.Glu638Lys	Somatic		Capture	Illumina HiSeq	Phase_I	52633016	NM_015063	B4DYQ9	Missense_Mutation	SNP	ENST00000236877.6	37	CCDS33065.1	.	.	.	.	.	.	.	.	.	.	C	8.876	0.950364	0.18431	.	.	ENSG00000118160	ENST00000391903;ENST00000236877;ENST00000539381;ENST00000542837	T;T;T	0.27890	1.64;1.64;1.64	2.54	1.5	0.22942	.	0.000000	0.64402	U	0.000003	T	0.18551	0.0445	N	0.13371	0.34	0.53005	D	0.999962	B;D	0.67145	0.006;0.996	B;P	0.48089	0.005;0.566	T	0.03566	-1.1024	10	0.13853	T	0.58	.	9.1717	0.37086	0.0:0.8807:0.0:0.1193	.	466;638	E9PGS7;Q9UPR5	.;NAC2_HUMAN	K	466;638;101;394	ENSP00000236877:E638K;ENSP00000440588:E101K;ENSP00000437536:E394K	ENSP00000236877:E638K	E	-	1	0	SLC8A2	52633016	0.932000	0.31603	0.939000	0.37840	0.678000	0.39670	2.049000	0.41288	0.649000	0.30751	-0.464000	0.05259	GAG		0.562	SLC8A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466997.1		
GRWD1	83743	broad.mit.edu	37	19	48956135	48956135	+	Silent	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr19:48956135C>T	ENST00000253237.5	+	7	1427	c.1194C>T	c.(1192-1194)ccC>ccT	p.P398P	KCNJ14_ENST00000342291.2_5'Flank	NM_031485.3	NP_113673.3	Q9BQ67	GRWD1_HUMAN	glutamate-rich WD repeat containing 1	398						cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)	p.P398P(2)		endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(3)|lung(10)|ovary(1)|stomach(1)	19		all_lung(116;0.000147)|Lung NSC(112;0.000251)|all_epithelial(76;0.000326)|all_neural(266;0.0506)|Ovarian(192;0.113)		OV - Ovarian serous cystadenocarcinoma(262;0.000206)|all cancers(93;0.000207)|Epithelial(262;0.0125)|GBM - Glioblastoma multiforme(486;0.0222)		AGGCCGACCCCGGACTGGCCG	0.692																																					p.P398P												.	.	2	Substitution - coding silent(2)	large_intestine(1)|lung(1)	c.C1194T	19						.						33.0	32.0	32.0					19																	48956135		2201	4298	6499	53647947	SO:0001819	synonymous_variant	83743	exon7			AF337808	CCDS12720.1	19q13.33	2013-05-21				ENSG00000105447		"""WD repeat domain containing"""	21270	protein-coding gene	gene with protein product	regulator of ribosome biogenesis 1 homolog (S. cerevisiae)	610597				15885502	Standard	NM_031485		Approved	WDR28, GRWD, RRB1	uc002pjd.2	Q9BQ67		ENST00000253237.5:c.1194C>T	19.37:g.48956135C>T		Somatic		Capture	Illumina HiSeq	Phase_I	53647947	NM_031485	Q8TF59	Silent	SNP	ENST00000253237.5	37	CCDS12720.1																																																																																				0.692	GRWD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466122.1	NM_031485	
FAM83E	54854	broad.mit.edu	37	19	49104398	49104398	+	Missense_Mutation	SNP	C	C	G			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	G	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr19:49104398C>G	ENST00000263266.3	-	5	1594	c.1405G>C	c.(1405-1407)Gcc>Ccc	p.A469P		NM_017708.3	NP_060178.2	Q2M2I3	FA83E_HUMAN	family with sequence similarity 83, member E	469								p.A469P(1)		NS(1)|endometrium(2)|large_intestine(1)|lung(3)|ovary(1)|urinary_tract(2)	10		all_epithelial(76;2.38e-06)|all_lung(116;4.89e-06)|Lung NSC(112;9.34e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		OV - Ovarian serous cystadenocarcinoma(262;0.000102)|all cancers(93;0.000117)|GBM - Glioblastoma multiforme(486;0.00627)|Epithelial(262;0.0158)		GCCCGGGGGGCCCAGTCTGAC	0.657																																					p.A469P												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1405C	19						.						29.0	31.0	30.0					19																	49104398		1911	4116	6027	53796210	SO:0001583	missense	54854	exon5			AK000207	CCDS42587.1	19q13.33	2013-10-24			ENSG00000105523	ENSG00000105523			25972	protein-coding gene	gene with protein product							Standard	NM_017708		Approved	FLJ20200	uc002pjn.2	Q2M2I3	OTTHUMG00000183315	ENST00000263266.3:c.1405G>C	19.37:g.49104398C>G	ENSP00000263266:p.Ala469Pro	Somatic		Capture	Illumina HiSeq	Phase_I	53796210	NM_017708	Q9NXK1	Missense_Mutation	SNP	ENST00000263266.3	37	CCDS42587.1	.	.	.	.	.	.	.	.	.	.	C	16.10	3.026589	0.54683	.	.	ENSG00000105523	ENST00000263266	T	0.13089	2.62	4.03	2.99	0.34606	.	655.221000	0.00166	U	0.000006	T	0.09818	0.0241	N	0.14661	0.345	0.20638	N	0.999875	P	0.37864	0.61	B	0.31869	0.137	T	0.28170	-1.0052	10	0.72032	D	0.01	-5.831	7.9018	0.29740	0.0:0.8801:0.0:0.1199	.	469	Q2M2I3	FA83E_HUMAN	P	469	ENSP00000263266:A469P	ENSP00000263266:A469P	A	-	1	0	FAM83E	53796210	0.139000	0.22563	0.308000	0.25141	0.032000	0.12392	0.262000	0.18460	0.829000	0.34733	0.549000	0.68633	GCC		0.657	FAM83E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466145.1	NM_017708	
IZUMO1	284359	broad.mit.edu	37	19	49247795	49247795	+	Splice_Site	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr19:49247795G>A	ENST00000332955.2	-	4	859	c.312C>T	c.(310-312)ggC>ggT	p.G104G		NM_182575.2	NP_872381.2	Q8IYV9	IZUM1_HUMAN	izumo sperm-egg fusion 1	104					cell adhesion (GO:0007155)|fusion of sperm to egg plasma membrane (GO:0007342)|multicellular organism reproduction (GO:0032504)|single fertilization (GO:0007338)|sperm-egg recognition (GO:0035036)	acrosomal membrane (GO:0002080)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)	p.G104G(1)		endometrium(4)|kidney(3)|large_intestine(4)|lung(2)|ovary(1)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)	17		all_lung(116;0.000156)|Lung NSC(112;0.000251)|all_epithelial(76;0.000761)|all_neural(266;0.0506)|Ovarian(192;0.113)		OV - Ovarian serous cystadenocarcinoma(262;0.000134)|all cancers(93;0.000348)|Epithelial(262;0.019)|GBM - Glioblastoma multiforme(486;0.022)		CGAAGAGATCGCCTGGGAAGA	0.498																																					p.G104G												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C312T	19						.						85.0	76.0	79.0					19																	49247795		2203	4300	6503	53939607	SO:0001630	splice_region_variant	284359	exon4			BC034769	CCDS12732.1	19q13.33	2014-07-23			ENSG00000182264	ENSG00000182264		"""-"""	28539	protein-coding gene	gene with protein product	"""oocyte binding/fusion factor"""	609278				15759005, 18952059, 19658160, 22957301	Standard	NM_182575		Approved	IZUMO, MGC34799, OBF	uc002pkj.3	Q8IYV9	OTTHUMG00000183324	ENST00000332955.2:c.311-1C>T	19.37:g.49247795G>A		Somatic		Capture	Illumina HiSeq	Phase_I	53939607	NM_182575	Q6Q8P6|Q6Q8P7	Silent	SNP	ENST00000332955.2	37	CCDS12732.1																																																																																				0.498	IZUMO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466189.1	NM_182575	Silent
BCAT2	587	broad.mit.edu	37	19	49303323	49303323	+	Missense_Mutation	SNP	C	C	T	rs549092161		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr19:49303323C>T	ENST00000316273.6	-	5	458	c.446G>A	c.(445-447)cGc>cAc	p.R149H	BCAT2_ENST00000598162.1_Missense_Mutation_p.R149H|BCAT2_ENST00000402551.1_Missense_Mutation_p.R109H|BCAT2_ENST00000599246.1_Missense_Mutation_p.R57H|BCAT2_ENST00000597011.1_Missense_Mutation_p.R109H|BCAT2_ENST00000545387.2_Missense_Mutation_p.R57H	NM_001190.3	NP_001181.2	O15382	BCAT2_HUMAN	branched chain amino-acid transaminase 2, mitochondrial	149					branched-chain amino acid biosynthetic process (GO:0009082)|branched-chain amino acid catabolic process (GO:0009083)|cellular nitrogen compound metabolic process (GO:0034641)|isoleucine catabolic process (GO:0006550)|leucine metabolic process (GO:0006551)|regulation of hormone levels (GO:0010817)|small molecule metabolic process (GO:0044281)|valine metabolic process (GO:0006573)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	branched-chain-amino-acid transaminase activity (GO:0004084)|L-isoleucine transaminase activity (GO:0052656)|L-leucine transaminase activity (GO:0052654)|L-valine transaminase activity (GO:0052655)	p.R149H(1)		endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(5)|ovary(2)|skin(1)	12		all_epithelial(76;7e-07)|all_lung(116;1.7e-06)|Lung NSC(112;3.55e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		OV - Ovarian serous cystadenocarcinoma(262;0.000138)|all cancers(93;0.000366)|Epithelial(262;0.0195)|GBM - Glioblastoma multiforme(486;0.0224)	L-Isoleucine(DB00167)|L-Leucine(DB00149)	GATGAGCCGGCGGATGCACTC	0.647													C|||	1	0.000199681	0.0	0.0014	5008	,	,		12418	0.0		0.0	False		,,,				2504	0.0				p.R57H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G170A	19						.						45.0	48.0	47.0					19																	49303323		2203	4300	6503	53995135	SO:0001583	missense	587	exon3			U68418	CCDS12735.1, CCDS54290.1, CCDS74416.1	19q13.33	2013-09-20	2010-05-07		ENSG00000105552	ENSG00000105552	2.6.1.42		977	protein-coding gene	gene with protein product		113530	"""branched chain aminotransferase 2, mitochondrial"""	BCT2		9165094	Standard	NM_001190		Approved	BCAM	uc002pkr.3	O15382	OTTHUMG00000183327	ENST00000316273.6:c.446G>A	19.37:g.49303323C>T	ENSP00000322991:p.Arg149His	Somatic		Capture	Illumina HiSeq	Phase_I	53995135	NM_001164773	B2RB87|O00269|Q96KG1|Q9BTB6|Q9BUU6	Missense_Mutation	SNP	ENST00000316273.6	37	CCDS12735.1	.	.	.	.	.	.	.	.	.	.	C	14.36	2.513626	0.44763	.	.	ENSG00000105552	ENST00000316273;ENST00000545387;ENST00000402551	T;T;T	0.21734	1.99;1.99;1.99	4.86	3.81	0.43845	.	0.245043	0.39146	N	0.001446	T	0.37732	0.1014	L	0.58101	1.795	0.41770	D	0.989766	D;D;D;D	0.71674	0.998;0.998;0.993;0.998	P;D;P;P	0.65010	0.899;0.931;0.704;0.899	T	0.15292	-1.0442	10	0.56958	D	0.05	-8.0067	11.1143	0.48252	0.0:0.9076:0.0:0.0924	.	109;149;57;149	B3KSI3;Q53EW7;O15382-2;O15382	.;.;.;BCAT2_HUMAN	H	149;57;109	ENSP00000322991:R149H;ENSP00000440973:R57H;ENSP00000385161:R109H	ENSP00000322991:R149H	R	-	2	0	BCAT2	53995135	0.642000	0.27260	0.941000	0.38009	0.710000	0.40934	1.158000	0.31737	1.157000	0.42530	0.561000	0.74099	CGC		0.647	BCAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466202.1		
ALDH16A1	126133	broad.mit.edu	37	19	49967724	49967724	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr19:49967724C>T	ENST00000293350.4	+	11	1545	c.1382C>T	c.(1381-1383)tCg>tTg	p.S461L	CTD-3148I10.9_ENST00000599536.1_Missense_Mutation_p.R51W|ALDH16A1_ENST00000433981.2_Missense_Mutation_p.S296L|ALDH16A1_ENST00000540132.1_Missense_Mutation_p.S298L|ALDH16A1_ENST00000455361.2_Missense_Mutation_p.S410L	NM_153329.3	NP_699160.2	Q8IZ83	A16A1_HUMAN	aldehyde dehydrogenase 16 family, member A1	461						extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor (GO:0016620)	p.S461L(1)		cervix(2)|endometrium(3)|kidney(2)|large_intestine(3)|lung(5)|skin(2)|urinary_tract(3)	20		all_lung(116;5.39e-06)|Lung NSC(112;1.97e-05)|all_neural(266;0.0966)|Ovarian(192;0.15)		OV - Ovarian serous cystadenocarcinoma(262;0.00156)|GBM - Glioblastoma multiforme(486;0.0251)		AGAGACCCTTCGGTGCCCACA	0.662																																					p.S461L												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1382T	19						.						25.0	32.0	30.0					19																	49967724		2202	4300	6502	54659536	SO:0001583	missense	126133	exon11			AY007096	CCDS12766.1, CCDS46141.1	19q13.33	2014-08-12			ENSG00000161618	ENSG00000161618		"""Aldehyde dehydrogenases"""	28114	protein-coding gene	gene with protein product		613358					Standard	NM_153329		Approved	MGC10204	uc002pnt.3	Q8IZ83	OTTHUMG00000183163	ENST00000293350.4:c.1382C>T	19.37:g.49967724C>T	ENSP00000293350:p.Ser461Leu	Somatic		Capture	Illumina HiSeq	Phase_I	54659536	NM_153329	B4DLQ1|C9JBH6|Q86YF0|Q8IYL4|Q8TEI8	Missense_Mutation	SNP	ENST00000293350.4	37	CCDS12766.1	.	.	.	.	.	.	.	.	.	.	C	13.42	2.233044	0.39498	.	.	ENSG00000161618	ENST00000293350;ENST00000455361;ENST00000540132;ENST00000433981	T;T;T;T	0.76839	-1.05;-1.05;-1.05;-1.05	5.27	-1.23	0.09465	Aldehyde dehydrogenase domain (1);Aldehyde dehydrogenase, C-terminal (1);Aldehyde/histidinol dehydrogenase (1);	1.727610	0.02843	N	0.128214	T	0.66237	0.2769	L	0.39020	1.185	0.09310	N	1	B;B;B	0.27166	0.141;0.139;0.17	B;B;B	0.19391	0.014;0.025;0.024	T	0.55431	-0.8142	10	0.87932	D	0	-23.6496	3.3782	0.07244	0.1209:0.4578:0.264:0.1573	.	298;410;461	F5H4B6;B4DLQ1;Q8IZ83	.;.;A16A1_HUMAN	L	461;410;298;296	ENSP00000293350:S461L;ENSP00000410142:S410L;ENSP00000445088:S298L;ENSP00000398675:S296L	ENSP00000293350:S461L	S	+	2	0	ALDH16A1	54659536	0.003000	0.15002	0.521000	0.27850	0.610000	0.37248	0.369000	0.20416	0.185000	0.20105	0.561000	0.74099	TCG		0.662	ALDH16A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465358.1	NM_153329	
AP2A1	160	broad.mit.edu	37	19	50285221	50285221	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr19:50285221G>T	ENST00000359032.5	+	3	154	c.154G>T	c.(154-156)Ggc>Tgc	p.G52C	AP2A1_ENST00000354293.5_Missense_Mutation_p.G52C|AP2A1_ENST00000600199.1_3'UTR	NM_014203.2	NP_055018.2	O95782	AP2A1_HUMAN	adaptor-related protein complex 2, alpha 1 subunit	52					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|axon guidance (GO:0007411)|endocytosis (GO:0006897)|epidermal growth factor receptor signaling pathway (GO:0007173)|Golgi to endosome transport (GO:0006895)|intracellular protein transport (GO:0006886)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of hyaluronan biosynthetic process (GO:1900126)|neurotrophin TRK receptor signaling pathway (GO:0048011)|regulation of defense response to virus by virus (GO:0050690)|synaptic transmission (GO:0007268)|viral process (GO:0016032)	AP-2 adaptor complex (GO:0030122)|apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|clathrin coat of trans-Golgi network vesicle (GO:0030130)|clathrin-coated endocytic vesicle membrane (GO:0030669)|cytosol (GO:0005829)|endocytic vesicle membrane (GO:0030666)|membrane (GO:0016020)|plasma membrane (GO:0005886)	protein kinase binding (GO:0019901)|protein transporter activity (GO:0008565)	p.G52C(1)		cervix(1)|endometrium(5)|kidney(1)|large_intestine(3)|lung(7)|ovary(2)	19		all_lung(116;3.24e-07)|Lung NSC(112;1.6e-06)|all_neural(266;0.0459)|Ovarian(192;0.0728)		OV - Ovarian serous cystadenocarcinoma(262;0.0023)|GBM - Glioblastoma multiforme(134;0.0157)		AGCCTTGGATGGCTACAGTAA	0.502																																					p.G52C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G154T	19						.						67.0	61.0	63.0					19																	50285221		1931	4149	6080	54977033	SO:0001583	missense	160	exon3			AA993745	CCDS46148.1, CCDS46149.1	19q13.3	2008-05-23				ENSG00000196961			561	protein-coding gene	gene with protein product		601026		CLAPA1, ADTAA		2564002	Standard	NM_014203		Approved		uc002ppn.3	O95782		ENST00000359032.5:c.154G>T	19.37:g.50285221G>T	ENSP00000351926:p.Gly52Cys	Somatic		Capture	Illumina HiSeq	Phase_I	54977033	NM_130787	Q96CI7|Q96PP6|Q96PP7|Q9H070	Missense_Mutation	SNP	ENST00000359032.5	37	CCDS46148.1	.	.	.	.	.	.	.	.	.	.	G	16.43	3.120142	0.56613	.	.	ENSG00000196961	ENST00000354293;ENST00000359032	T;T	0.26957	1.7;1.7	5.42	5.42	0.78866	Clathrin/coatomer adaptor, adaptin-like, N-terminal (1);Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.59662	0.2210	M	0.88979	2.995	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.67597	-0.5630	10	0.87932	D	0	.	17.9788	0.89134	0.0:0.0:1.0:0.0	.	52;52	O95782-2;O95782	.;AP2A1_HUMAN	C	52	ENSP00000346246:G52C;ENSP00000351926:G52C	ENSP00000346246:G52C	G	+	1	0	AP2A1	54977033	1.000000	0.71417	1.000000	0.80357	0.016000	0.09150	9.869000	0.99810	2.535000	0.85469	0.650000	0.86243	GGC		0.502	AP2A1-008	NOVEL	non_canonical_U12|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000465809.1		
NUP62	23636	broad.mit.edu	37	19	50412397	50412397	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr19:50412397G>T	ENST00000596217.1	-	2	2555	c.668C>A	c.(667-669)gCg>gAg	p.A223E	IL4I1_ENST00000341114.3_Intron|NUP62_ENST00000597029.1_Missense_Mutation_p.A223E|NUP62_ENST00000413454.1_Missense_Mutation_p.A223E|NUP62_ENST00000422090.2_Missense_Mutation_p.A223E|NUP62_ENST00000352066.3_Missense_Mutation_p.A223E|IL4I1_ENST00000595948.1_Intron|NUP62_ENST00000597723.1_Missense_Mutation_p.A223E|NUP62_ENST00000600583.1_5'Flank			P37198	NUP62_HUMAN	nucleoporin 62kDa	223	15 X 9 AA approximate repeats.|Ala-rich.|Thr-rich.				carbohydrate metabolic process (GO:0005975)|cell aging (GO:0007569)|cell death (GO:0008219)|cell surface receptor signaling pathway (GO:0007166)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|hormone-mediated signaling pathway (GO:0009755)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of programmed cell death (GO:0043069)|negative regulation of Ras protein signal transduction (GO:0046580)|nucleocytoplasmic transport (GO:0006913)|positive regulation of epidermal growth factor receptor signaling pathway (GO:0045742)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of transcription, DNA-templated (GO:0045893)|protein transport (GO:0015031)|regulation of glucose transport (GO:0010827)|regulation of Ras protein signal transduction (GO:0046578)|regulation of signal transduction (GO:0009966)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|intracellular membrane-bounded organelle (GO:0043231)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nuclear pore (GO:0005643)|nucleocytoplasmic shuttling complex (GO:0031074)|pore complex (GO:0046930)|ribonucleoprotein complex (GO:0030529)	chromatin binding (GO:0003682)|receptor signaling complex scaffold activity (GO:0030159)|SH2 domain binding (GO:0042169)|structural constituent of nuclear pore (GO:0017056)|thyroid hormone receptor binding (GO:0046966)|ubiquitin binding (GO:0043130)	p.A223E(1)		breast(2)|endometrium(1)|kidney(1)|large_intestine(4)|lung(8)|stomach(1)|urinary_tract(2)	19		all_lung(116;1.47e-05)|all_neural(266;0.0459)|Ovarian(192;0.0481)		GBM - Glioblastoma multiforme(134;0.00242)|OV - Ovarian serous cystadenocarcinoma(262;0.0177)		TGCTATTGACGCAAAGAGGCT	0.642																																					p.A223E												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C668A	19						.						93.0	86.0	89.0					19																	50412397		2203	4300	6503	55104209	SO:0001583	missense	23636	exon2			X58521	CCDS12788.1	19q13.33	2013-09-20	2002-08-29		ENSG00000213024	ENSG00000213024			8066	protein-coding gene	gene with protein product	"""nuclear pore glycoprotein p62"""	605815	"""nucleoporin 62kD"""			1915414	Standard	NM_016553		Approved	p62, DKFZp547L134, IBSN, SNDI, MGC841, FLJ20822, FLJ43869	uc002pqx.3	P37198	OTTHUMG00000183077	ENST00000596217.1:c.668C>A	19.37:g.50412397G>T	ENSP00000471191:p.Ala223Glu	Somatic		Capture	Illumina HiSeq	Phase_I	55104209	NM_012346	B3KWU5|Q503A4|Q6GTM2|Q96C43|Q9NSL1	Missense_Mutation	SNP	ENST00000596217.1	37	CCDS12788.1	.	.	.	.	.	.	.	.	.	.	G	18.94	3.730590	0.69074	.	.	ENSG00000213024	ENST00000352066;ENST00000422090;ENST00000413454	T;T;T	0.39406	1.08;1.08;1.08	5.18	4.14	0.48551	Nucleoporin, NSP1-like, C-terminal (1);	0.172871	0.35013	U	0.003517	T	0.38983	0.1061	M	0.62723	1.935	0.09310	N	1	P	0.52061	0.95	B	0.41510	0.359	T	0.37596	-0.9699	9	.	.	.	-11.5517	10.222	0.43203	0.0941:0.0:0.9059:0.0	.	223	P37198	NUP62_HUMAN	E	223	ENSP00000305503:A223E;ENSP00000407331:A223E;ENSP00000387991:A223E	.	A	-	2	0	NUP62	55104209	0.210000	0.23517	0.004000	0.12327	0.013000	0.08279	1.552000	0.36244	1.491000	0.48482	0.655000	0.94253	GCG		0.642	NUP62-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464991.1	NM_153719	
MYH14	79784	broad.mit.edu	37	19	50775819	50775819	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr19:50775819C>T	ENST00000596571.1	+	24	3175	c.3175C>T	c.(3175-3177)Cgc>Tgc	p.R1059C	MYH14_ENST00000440075.2_Missense_Mutation_p.R1100C|MYH14_ENST00000598205.1_Missense_Mutation_p.R1067C|MYH14_ENST00000262269.8_Missense_Mutation_p.R1100C|MYH14_ENST00000425460.1_Missense_Mutation_p.R1067C|MYH14_ENST00000376970.2_Missense_Mutation_p.R1092C|MYH14_ENST00000601313.1_Missense_Mutation_p.R1100C			Q7Z406	MYH14_HUMAN	myosin, heavy chain 14, non-muscle	1059					actin filament-based movement (GO:0030048)|actomyosin structure organization (GO:0031032)|ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|mitochondrion morphogenesis (GO:0070584)|neuronal action potential (GO:0019228)|regulation of cell shape (GO:0008360)|sensory perception of sound (GO:0007605)|skeletal muscle atrophy (GO:0014732)|skeletal muscle contraction (GO:0003009)|skeletal muscle tissue development (GO:0007519)|vocalization behavior (GO:0071625)	actomyosin (GO:0042641)|axon (GO:0030424)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|growth cone (GO:0030426)|membrane (GO:0016020)|myosin II complex (GO:0016460)|myosin II filament (GO:0097513)|stress fiber (GO:0001725)	actin-dependent ATPase activity (GO:0030898)|ATP binding (GO:0005524)|microfilament motor activity (GO:0000146)	p.R1059C(1)|p.R1100C(1)		central_nervous_system(1)|cervix(2)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(10)|ovary(1)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	46		all_neural(266;0.0571)|Ovarian(192;0.0728)		OV - Ovarian serous cystadenocarcinoma(262;0.00389)|GBM - Glioblastoma multiforme(134;0.0195)		GCCTCCAGACCGCCTACGGAA	0.627																																					p.R1067C												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.C3199T	19						.						8.0	10.0	9.0					19																	50775819		2082	4203	6285	55467631	SO:0001583	missense	79784	exon26			AY165122	CCDS46151.1, CCDS54295.1, CCDS59411.1	19q13.33	2011-09-27	2009-11-19			ENSG00000105357		"""Myosins / Myosin superfamily : Class II"""	23212	protein-coding gene	gene with protein product		608568	"""myosin, heavy polypeptide 14"", ""myosin, heavy chain 14"""	DFNA4		12909352, 15015131, 17940200	Standard	NM_024729		Approved	FLJ13881, KIAA2034, MHC16, MYH17	uc010enu.1	Q7Z406		ENST00000596571.1:c.3175C>T	19.37:g.50775819C>T	ENSP00000472819:p.Arg1059Cys	Somatic		Capture	Illumina HiSeq	Phase_I	55467631	NM_001077186	B0I1S2|C3TTN4|Q5CZ75|Q6XYE4|Q76B62|Q8WV23|Q96I22|Q9BT27|Q9BW35|Q9H882	Missense_Mutation	SNP	ENST00000596571.1	37	CCDS59411.1	.	.	.	.	.	.	.	.	.	.	C	16.00	2.999873	0.54147	.	.	ENSG00000105357	ENST00000301415;ENST00000440075;ENST00000376970;ENST00000425460;ENST00000376965;ENST00000262269	D;D;D;D	0.95272	-3.66;-3.66;-3.66;-3.66	3.06	3.06	0.35304	.	.	.	.	.	D	0.96420	0.8832	M	0.82517	2.595	0.58432	D	0.999999	D;P;D	0.89917	0.977;0.923;1.0	P;B;D	0.72075	0.514;0.198;0.976	D	0.95647	0.8703	9	0.66056	D	0.02	.	7.6324	0.28247	0.253:0.747:0.0:0.0	.	1100;1059;1067	Q7Z406-2;Q7Z406;Q7Z406-6	.;MYH14_HUMAN;.	C	1059;1100;1092;1067;1059;1100	ENSP00000406273:R1100C;ENSP00000366169:R1092C;ENSP00000407879:R1067C;ENSP00000262269:R1100C	ENSP00000262269:R1100C	R	+	1	0	MYH14	55467631	1.000000	0.71417	1.000000	0.80357	0.888000	0.51559	3.445000	0.52921	2.040000	0.60383	0.491000	0.48974	CGC		0.627	MYH14-008	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000464710.2	NM_024729	
MYH14	79784	broad.mit.edu	37	19	50781488	50781488	+	Missense_Mutation	SNP	G	G	A	rs201181045		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr19:50781488G>A	ENST00000596571.1	+	27	3851	c.3851G>A	c.(3850-3852)cGg>cAg	p.R1284Q	MYH14_ENST00000440075.2_Missense_Mutation_p.R1325Q|MYH14_ENST00000598205.1_Missense_Mutation_p.R1292Q|MYH14_ENST00000262269.8_Missense_Mutation_p.R1325Q|MYH14_ENST00000425460.1_Missense_Mutation_p.R1292Q|MYH14_ENST00000376970.2_Missense_Mutation_p.R1317Q|MYH14_ENST00000601313.1_Missense_Mutation_p.R1325Q			Q7Z406	MYH14_HUMAN	myosin, heavy chain 14, non-muscle	1284					actin filament-based movement (GO:0030048)|actomyosin structure organization (GO:0031032)|ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|mitochondrion morphogenesis (GO:0070584)|neuronal action potential (GO:0019228)|regulation of cell shape (GO:0008360)|sensory perception of sound (GO:0007605)|skeletal muscle atrophy (GO:0014732)|skeletal muscle contraction (GO:0003009)|skeletal muscle tissue development (GO:0007519)|vocalization behavior (GO:0071625)	actomyosin (GO:0042641)|axon (GO:0030424)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|growth cone (GO:0030426)|membrane (GO:0016020)|myosin II complex (GO:0016460)|myosin II filament (GO:0097513)|stress fiber (GO:0001725)	actin-dependent ATPase activity (GO:0030898)|ATP binding (GO:0005524)|microfilament motor activity (GO:0000146)	p.R1325Q(1)|p.R1284Q(1)		central_nervous_system(1)|cervix(2)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(10)|ovary(1)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	46		all_neural(266;0.0571)|Ovarian(192;0.0728)		OV - Ovarian serous cystadenocarcinoma(262;0.00389)|GBM - Glioblastoma multiforme(134;0.0195)		GTGCAGGGCCGGGCTGGTGAT	0.667													G|||	1	0.000199681	0.0	0.0	5008	,	,		16158	0.001		0.0	False		,,,				2504	0.0				p.R1292Q												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G3875A	19						.						19.0	26.0	24.0					19																	50781488		2070	4184	6254	55473300	SO:0001583	missense	79784	exon29			AY165122	CCDS46151.1, CCDS54295.1, CCDS59411.1	19q13.33	2011-09-27	2009-11-19			ENSG00000105357		"""Myosins / Myosin superfamily : Class II"""	23212	protein-coding gene	gene with protein product		608568	"""myosin, heavy polypeptide 14"", ""myosin, heavy chain 14"""	DFNA4		12909352, 15015131, 17940200	Standard	NM_024729		Approved	FLJ13881, KIAA2034, MHC16, MYH17	uc010enu.1	Q7Z406		ENST00000596571.1:c.3851G>A	19.37:g.50781488G>A	ENSP00000472819:p.Arg1284Gln	Somatic		Capture	Illumina HiSeq	Phase_I	55473300	NM_001077186	B0I1S2|C3TTN4|Q5CZ75|Q6XYE4|Q76B62|Q8WV23|Q96I22|Q9BT27|Q9BW35|Q9H882	Missense_Mutation	SNP	ENST00000596571.1	37	CCDS59411.1	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	G	22.3	4.267663	0.80469	.	.	ENSG00000105357	ENST00000301415;ENST00000440075;ENST00000376970;ENST00000425460;ENST00000376965;ENST00000262269	T;T;T;T	0.78595	-1.19;-1.19;-1.19;-1.19	3.78	3.78	0.43462	Myosin tail (1);	.	.	.	.	T	0.81664	0.4870	L	0.55990	1.75	0.37119	D	0.900738	D;D;D	0.69078	0.997;0.997;0.993	P;D;P	0.64877	0.884;0.93;0.847	D	0.84089	0.0389	9	0.87932	D	0	.	7.3752	0.26825	0.1192:0.0:0.8808:0.0	.	1325;1284;1292	Q7Z406-2;Q7Z406;Q7Z406-6	.;MYH14_HUMAN;.	Q	1284;1325;1317;1292;1284;1325	ENSP00000406273:R1325Q;ENSP00000366169:R1317Q;ENSP00000407879:R1292Q;ENSP00000262269:R1325Q	ENSP00000262269:R1325Q	R	+	2	0	MYH14	55473300	0.050000	0.20438	0.958000	0.39756	0.970000	0.65996	1.121000	0.31283	2.149000	0.67028	0.462000	0.41574	CGG		0.667	MYH14-008	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000464710.2	NM_024729	
MYBPC2	4606	broad.mit.edu	37	19	50939080	50939080	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr19:50939080G>A	ENST00000357701.5	+	3	208	c.157G>A	c.(157-159)Gtt>Att	p.V53I		NM_004533.3	NP_004524.3	Q14324	MYPC2_HUMAN	myosin binding protein C, fast type	53	Ig-like C2-type 1.				cell adhesion (GO:0007155)|muscle filament sliding (GO:0030049)	cytosol (GO:0005829)|myosin filament (GO:0032982)	structural constituent of muscle (GO:0008307)	p.V53I(1)		breast(1)	1		all_neural(266;0.057)		OV - Ovarian serous cystadenocarcinoma(262;0.0079)|GBM - Glioblastoma multiforme(134;0.0144)		GCCCACCGGCGTTTTCCTGAA	0.662																																					p.V53I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G157A	19						.						21.0	23.0	22.0					19																	50939080		1881	4102	5983	55630892	SO:0001583	missense	4606	exon3				CCDS46152.1	19q13.33	2013-02-11	2001-11-28		ENSG00000086967	ENSG00000086967		"""Myosin binding proteins"", ""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	7550	protein-coding gene	gene with protein product	"""fast-type muscle myosin-binding-protein C"""	160793	"""myosin-binding protein C, fast-type"""			8375400	Standard	NM_004533		Approved	MYBPCF, MYBPC, MGC163408	uc002psf.2	Q14324		ENST00000357701.5:c.157G>A	19.37:g.50939080G>A	ENSP00000350332:p.Val53Ile	Somatic		Capture	Illumina HiSeq	Phase_I	55630892	NM_004533	A1L4G9	Missense_Mutation	SNP	ENST00000357701.5	37	CCDS46152.1	.	.	.	.	.	.	.	.	.	.	.	6.567	0.472894	0.12461	.	.	ENSG00000086967	ENST00000357701	T	0.68903	-0.36	4.6	-9.19	0.00685	Immunoglobulin-like fold (1);	.	.	.	.	T	0.34803	0.0910	N	0.04508	-0.205	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.25745	-1.0123	9	0.25106	T	0.35	.	8.5286	0.33319	0.1909:0.4591:0.35:0.0	.	53	Q14324	MYPC2_HUMAN	I	53	ENSP00000350332:V53I	ENSP00000350332:V53I	V	+	1	0	MYBPC2	55630892	0.000000	0.05858	0.003000	0.11579	0.064000	0.16182	-2.122000	0.01321	-1.955000	0.01023	-0.483000	0.04790	GTT		0.662	MYBPC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464751.1	NM_004533	
MYBPC2	4606	broad.mit.edu	37	19	50946767	50946767	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr19:50946767G>A	ENST00000357701.5	+	10	970	c.919G>A	c.(919-921)Gtt>Att	p.V307I		NM_004533.3	NP_004524.3	Q14324	MYPC2_HUMAN	myosin binding protein C, fast type	307	Ig-like C2-type 2.				cell adhesion (GO:0007155)|muscle filament sliding (GO:0030049)	cytosol (GO:0005829)|myosin filament (GO:0032982)	structural constituent of muscle (GO:0008307)	p.V307I(1)		breast(1)	1		all_neural(266;0.057)		OV - Ovarian serous cystadenocarcinoma(262;0.0079)|GBM - Glioblastoma multiforme(134;0.0144)		GTTTGAGAACGTTGGTAAGAA	0.498																																					p.V307I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G919A	19						.						64.0	64.0	64.0					19																	50946767		2090	4228	6318	55638579	SO:0001583	missense	4606	exon10				CCDS46152.1	19q13.33	2013-02-11	2001-11-28		ENSG00000086967	ENSG00000086967		"""Myosin binding proteins"", ""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	7550	protein-coding gene	gene with protein product	"""fast-type muscle myosin-binding-protein C"""	160793	"""myosin-binding protein C, fast-type"""			8375400	Standard	NM_004533		Approved	MYBPCF, MYBPC, MGC163408	uc002psf.2	Q14324		ENST00000357701.5:c.919G>A	19.37:g.50946767G>A	ENSP00000350332:p.Val307Ile	Somatic		Capture	Illumina HiSeq	Phase_I	55638579	NM_004533	A1L4G9	Missense_Mutation	SNP	ENST00000357701.5	37	CCDS46152.1	.	.	.	.	.	.	.	.	.	.	g	8.992	0.977995	0.18812	.	.	ENSG00000086967	ENST00000357701	T	0.67523	-0.27	3.91	3.91	0.45181	Immunoglobulin subtype (1);Immunoglobulin I-set (1);Immunoglobulin-like fold (1);	0.218756	0.20796	U	0.085540	T	0.41465	0.1160	N	0.04508	-0.205	0.30649	N	0.755595	B	0.27910	0.193	B	0.28139	0.086	T	0.42632	-0.9440	10	0.30078	T	0.28	.	9.4786	0.38887	0.1042:0.0:0.8958:0.0	.	307	Q14324	MYPC2_HUMAN	I	307	ENSP00000350332:V307I	ENSP00000350332:V307I	V	+	1	0	MYBPC2	55638579	0.990000	0.36364	0.951000	0.38953	0.453000	0.32348	3.484000	0.53201	2.128000	0.65567	0.205000	0.17691	GTT		0.498	MYBPC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464751.1	NM_004533	
GPR32	2854	broad.mit.edu	37	19	51273896	51273896	+	Silent	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr19:51273896C>T	ENST00000270590.4	+	1	176	c.39C>T	c.(37-39)gaC>gaT	p.D13D		NM_001506.1	NP_001497.1	O75388	GPR32_HUMAN	G protein-coupled receptor 32	13					G-protein coupled receptor signaling pathway (GO:0007186)	integral component of plasma membrane (GO:0005887)	G-protein coupled receptor activity (GO:0004930)	p.D13D(1)		breast(4)|endometrium(4)|kidney(1)|large_intestine(3)|lung(12)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	29		all_neural(266;0.131)		OV - Ovarian serous cystadenocarcinoma(262;0.00641)|GBM - Glioblastoma multiforme(134;0.028)		GCTGCAGTGACAGGCAACCTG	0.502																																					p.D13D	Esophageal Squamous(113;152 1581 5732 15840 44398)											.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C39T	19						.						60.0	50.0	53.0					19																	51273896		2203	4300	6503	55965708	SO:0001819	synonymous_variant	2854	exon1			AF045764	CCDS12801.1	19q13.33	2012-08-20			ENSG00000142511	ENSG00000142511		"""GPCR / Class A : Resolvin receptors"""	4487	protein-coding gene	gene with protein product	"""resolvin D1 receptor"""	603195				9653656	Standard	NM_001506		Approved	RVDR1	uc010ycf.3	O75388		ENST00000270590.4:c.39C>T	19.37:g.51273896C>T		Somatic		Capture	Illumina HiSeq	Phase_I	55965708	NM_001506	Q502U7|Q6NWS5	Silent	SNP	ENST00000270590.4	37	CCDS12801.1																																																																																				0.502	GPR32-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465016.1		
CATSPERD	257062	broad.mit.edu	37	19	5745965	5745965	+	Silent	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr19:5745965C>T	ENST00000381624.3	+	9	760	c.699C>T	c.(697-699)ttC>ttT	p.F233F	CATSPERD_ENST00000381614.2_5'UTR	NM_152784.3	NP_689997.3	Q86XM0	CTSRD_HUMAN	catsper channel auxiliary subunit delta	233					multicellular organism reproduction (GO:0032504)|multicellular organismal development (GO:0007275)|single fertilization (GO:0007338)|sperm capacitation (GO:0048240)|sperm motility (GO:0030317)|sperm-egg recognition (GO:0035036)|spermatogenesis (GO:0007283)	CatSper complex (GO:0036128)|plasma membrane (GO:0005886)|sperm principal piece (GO:0097228)		p.F233F(3)									ACCGGAGTTTCGGGCTGTCTT	0.532																																					p.F233F												.	.	3	Substitution - coding silent(3)	large_intestine(3)	c.C699T	19						.						167.0	160.0	163.0					19																	5745965		1888	4121	6009	5696965	SO:0001819	synonymous_variant	257062	exon9			BC043005	CCDS12149.2	19p13.3	2013-10-11	2012-02-22	2012-02-22	ENSG00000174898	ENSG00000174898			28598	protein-coding gene	gene with protein product			"""transmembrane protein 146"""	TMEM146		21224844	Standard	NM_152784		Approved	MGC39581	uc002mda.3	Q86XM0	OTTHUMG00000143036	ENST00000381624.3:c.699C>T	19.37:g.5745965C>T		Somatic		Capture	Illumina HiSeq	Phase_I	5696965	NM_152784	Q6ZRP1	Silent	SNP	ENST00000381624.3	37	CCDS12149.2																																																																																				0.532	CATSPERD-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000286953.2	NM_152784	
KLK11	11012	broad.mit.edu	37	19	51525880	51525880	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr19:51525880G>A	ENST00000594768.1	-	6	955	c.770C>T	c.(769-771)gCg>gTg	p.A257V	KLK11_ENST00000391804.3_Missense_Mutation_p.A250V|KLK10_ENST00000309958.3_5'Flank|KLK11_ENST00000319720.7_Missense_Mutation_p.A225V|KLK10_ENST00000391805.1_5'Flank|KLK11_ENST00000600362.1_Missense_Mutation_p.A84V|KLK11_ENST00000594458.1_5'Flank|KLK11_ENST00000453757.3_Missense_Mutation_p.A225V|KLK10_ENST00000358789.3_5'Flank	NM_144947.1	NP_659196.1	Q9UBX7	KLK11_HUMAN	kallikrein-related peptidase 11	257	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.					extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)	serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)	p.A257V(1)		breast(1)|endometrium(2)|large_intestine(1)|lung(2)|skin(1)	7		all_neural(266;0.026)		OV - Ovarian serous cystadenocarcinoma(262;0.00327)|GBM - Glioblastoma multiforme(134;0.00878)		TCGGGTGATCGCACACGGATC	0.562																																					p.A225V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C674T	19						.						142.0	134.0	137.0					19																	51525880		2203	4300	6503	56217692	SO:0001583	missense	11012	exon6			AB012917	CCDS12818.1, CCDS12819.1, CCDS54297.1	19q13.33	2011-09-07	2006-10-27			ENSG00000167757		"""Kallikreins"", ""Serine peptidases / Serine peptidases"""	6359	protein-coding gene	gene with protein product		604434	"""kallikrein 11"""	PRSS20		9765601, 10662548, 16800724, 16800723	Standard	NM_006853		Approved	TLSP	uc002pvb.2	Q9UBX7		ENST00000594768.1:c.770C>T	19.37:g.51525880G>A	ENSP00000473047:p.Ala257Val	Somatic		Capture	Illumina HiSeq	Phase_I	56217692	NM_001136032	O75837|Q0WXX5|Q8IXD7|Q9NS65	Missense_Mutation	SNP	ENST00000594768.1	37	CCDS12818.1	.	.	.	.	.	.	.	.	.	.	g	25.8	4.671489	0.88348	.	.	ENSG00000167757	ENST00000391804;ENST00000319720;ENST00000453757;ENST00000319756	D;D;D	0.93906	-3.31;-3.31;-3.31	4.42	4.42	0.53409	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	0.000000	0.36591	U	0.002517	D	0.95996	0.8696	M	0.78223	2.4	0.49483	D	0.999793	D;D	0.71674	0.998;0.995	P;D	0.64877	0.821;0.93	D	0.96450	0.9333	10	0.87932	D	0	.	14.5583	0.68118	0.0:0.0:1.0:0.0	.	257;250	Q9UBX7;Q8IXD7	KLK11_HUMAN;.	V	250;225;225;257	ENSP00000375680:A250V;ENSP00000324269:A225V;ENSP00000413958:A225V	ENSP00000324269:A225V	A	-	2	0	KLK11	56217692	1.000000	0.71417	0.888000	0.34837	0.633000	0.38033	3.966000	0.56795	2.306000	0.77630	0.305000	0.20034	GCG		0.562	KLK11-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000464314.2	NM_006853	
DUS3L	56931	broad.mit.edu	37	19	5787321	5787321	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr19:5787321G>A	ENST00000309061.7	-	7	1360	c.1264C>T	c.(1264-1266)Cgt>Tgt	p.R422C	DUS3L_ENST00000320699.8_Missense_Mutation_p.R180C|DUS3L_ENST00000590681.1_5'Flank|CTB-54O9.9_ENST00000586012.1_5'Flank|PRR22_ENST00000419421.2_5'Flank	NM_020175.2	NP_064560.2	Q96G46	DUS3L_HUMAN	dihydrouridine synthase 3-like (S. cerevisiae)	422							flavin adenine dinucleotide binding (GO:0050660)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|tRNA dihydrouridine synthase activity (GO:0017150)	p.R422C(1)		endometrium(1)|kidney(1)|large_intestine(1)|lung(8)|prostate(1)|skin(2)	14						TTCATGCCACGGACGATCTGC	0.652																																					p.R180C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C538T	19						.						67.0	80.0	75.0					19																	5787321		2203	4300	6503	5738321	SO:0001583	missense	56931	exon6				CCDS32880.1, CCDS54202.1	19p13.3	2014-02-12			ENSG00000141994	ENSG00000141994			26920	protein-coding gene	gene with protein product						12477932	Standard	NM_020175		Approved	DUS3, FLJ13896	uc002mdc.3	Q96G46	OTTHUMG00000162311	ENST00000309061.7:c.1264C>T	19.37:g.5787321G>A	ENSP00000311977:p.Arg422Cys	Somatic		Capture	Illumina HiSeq	Phase_I	5738321	NM_001161619	Q96HM5|Q9BSU4|Q9H877|Q9NPR1	Missense_Mutation	SNP	ENST00000309061.7	37	CCDS32880.1	.	.	.	.	.	.	.	.	.	.	g	12.96	2.094273	0.36952	.	.	ENSG00000141994	ENST00000309061;ENST00000320699	T;T	0.25250	1.81;1.81	4.02	4.02	0.46733	Aldolase-type TIM barrel (1);	0.132210	0.48767	U	0.000170	T	0.47266	0.1436	M	0.81341	2.54	0.22127	N	0.999348	D;D	0.76494	0.998;0.999	P;D	0.65140	0.78;0.932	T	0.37549	-0.9701	10	0.87932	D	0	-1.6201	9.198	0.37240	0.0:0.0:0.7829:0.2171	.	180;422	Q96G46-3;Q96G46	.;DUS3L_HUMAN	C	422;180	ENSP00000311977:R422C;ENSP00000315558:R180C	ENSP00000311977:R422C	R	-	1	0	DUS3L	5738321	0.489000	0.26004	0.242000	0.24170	0.310000	0.27922	2.254000	0.43214	1.821000	0.53095	0.437000	0.28790	CGT		0.652	DUS3L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451870.2	NM_020175	
FPR3	2359	broad.mit.edu	37	19	52327714	52327714	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr19:52327714G>A	ENST00000339223.4	+	2	892	c.713G>A	c.(712-714)cGt>cAt	p.R238H	FPR3_ENST00000595991.1_Missense_Mutation_p.R238H	NM_002030.3	NP_002021.3	P25089	FPR3_HUMAN	formyl peptide receptor 3	238					cellular component movement (GO:0006928)|chemotaxis (GO:0006935)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	N-formyl peptide receptor activity (GO:0004982)	p.R238H(2)		NS(1)|breast(3)|endometrium(3)|kidney(1)|large_intestine(5)|lung(17)|ovary(1)|prostate(1)|skin(3)	35						AAATCCAGCCGTCCCTTACGT	0.458																																					p.R238H												.	.	2	Substitution - Missense(2)	large_intestine(1)|endometrium(1)	c.G713A	19						.						160.0	137.0	145.0					19																	52327714		2203	4300	6503	57019526	SO:0001583	missense	2359	exon2				CCDS12841.1	19q13.3-q13.4	2012-08-08	2008-04-17	2008-04-17		ENSG00000187474		"""GPCR / Class A : Formyl peptide receptors"""	3828	protein-coding gene	gene with protein product		136539	"""formyl peptide receptor-like 2"""	FPRL2		1612600, 8198572	Standard	NM_002030		Approved	FPRH1, FMLPY, RMLP-R-I	uc002pxt.1	P25089		ENST00000339223.4:c.713G>A	19.37:g.52327714G>A	ENSP00000341821:p.Arg238His	Somatic		Capture	Illumina HiSeq	Phase_I	57019526	NM_002030		Missense_Mutation	SNP	ENST00000339223.4	37	CCDS12841.1	.	.	.	.	.	.	.	.	.	.	.	11.11	1.543175	0.27563	.	.	ENSG00000187474	ENST00000339223	T	0.43688	0.94	2.34	1.24	0.21308	GPCR, rhodopsin-like superfamily (1);	0.166842	0.34555	N	0.003868	T	0.45597	0.1350	M	0.89287	3.02	0.22354	N	0.999179	P	0.35272	0.493	B	0.37780	0.258	T	0.47114	-0.9142	10	0.62326	D	0.03	.	4.5625	0.12166	0.3368:0.0:0.6632:0.0	.	238	P25089	FPR3_HUMAN	H	238	ENSP00000341821:R238H	ENSP00000341821:R238H	R	+	2	0	FPR3	57019526	0.000000	0.05858	0.044000	0.18714	0.515000	0.34225	0.832000	0.27490	0.327000	0.23409	0.467000	0.42956	CGT		0.458	FPR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466914.1	NM_002030	
PPP2R1A	5518	broad.mit.edu	37	19	52715982	52715982	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr19:52715982C>T	ENST00000322088.6	+	5	605	c.547C>T	c.(547-549)Cgg>Tgg	p.R183W	PPP2R1A_ENST00000444322.2_Missense_Mutation_p.R128W|PPP2R1A_ENST00000462990.1_Missense_Mutation_p.R4W	NM_014225.5	NP_055040.2	P30153	2AAA_HUMAN	protein phosphatase 2, regulatory subunit A, alpha	183	PP2A subunit B binding.|Polyoma small and medium T antigens Binding.|SV40 small T antigen binding.				apoptotic process (GO:0006915)|ceramide metabolic process (GO:0006672)|chromosome segregation (GO:0007059)|fibroblast growth factor receptor signaling pathway (GO:0008543)|G2/M transition of mitotic cell cycle (GO:0000086)|gene expression (GO:0010467)|inactivation of MAPK activity (GO:0000188)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope reassembly (GO:0007084)|mRNA metabolic process (GO:0016071)|negative regulation of cell growth (GO:0030308)|negative regulation of tyrosine phosphorylation of Stat3 protein (GO:0042518)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|peptidyl-serine dephosphorylation (GO:0070262)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)|protein complex assembly (GO:0006461)|protein dephosphorylation (GO:0006470)|regulation of cell adhesion (GO:0030155)|regulation of cell differentiation (GO:0045595)|regulation of DNA replication (GO:0006275)|regulation of growth (GO:0040008)|regulation of transcription, DNA-templated (GO:0006355)|regulation of Wnt signaling pathway (GO:0030111)|response to organic substance (GO:0010033)|RNA metabolic process (GO:0016070)|RNA splicing (GO:0008380)|second-messenger-mediated signaling (GO:0019932)	chromosome, centromeric region (GO:0000775)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|microtubule cytoskeleton (GO:0015630)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|protein phosphatase type 2A complex (GO:0000159)	antigen binding (GO:0003823)|protein heterodimerization activity (GO:0046982)|protein phosphatase type 2A regulator activity (GO:0008601)|protein serine/threonine phosphatase activity (GO:0004722)	p.R183W(22)|p.R183G(2)		NS(1)|breast(4)|cervix(2)|endometrium(62)|kidney(1)|large_intestine(7)|lung(21)|ovary(32)|pancreas(1)|prostate(2)|skin(1)|urinary_tract(1)	135				GBM - Glioblastoma multiforme(134;0.00456)|OV - Ovarian serous cystadenocarcinoma(262;0.015)		CATGGTGCGGCGGGCCGCAGC	0.617			Mis		clear cell ovarian carcinoma																																p.R183W			Dom?	yes		19	19q13.41	5518	"""protein phosphatase 2, regulatory subunit A, alpha"""		E	.	.	24	Substitution - Missense(24)	ovary(16)|endometrium(4)|large_intestine(3)|pancreas(1)	c.C547T	19						.						69.0	57.0	61.0					19																	52715982		2203	4300	6503	57407794	SO:0001583	missense	5518	exon5				CCDS12849.1	19q13	2010-06-18	2010-04-14		ENSG00000105568	ENSG00000105568	3.1.3.16	"""Serine/threonine phosphatases / Protein phosphatase 2, regulatory subunits"""	9302	protein-coding gene	gene with protein product	"""protein phosphatase 2A, regulatory subunit A, alpha isoform"", ""protein phosphatase 2, 65kDa regulatory subunit A"""	605983	"""protein phosphatase 2 (formerly 2A), regulatory subunit A (PR 65), alpha isoform"", ""protein phosphatase 2 (formerly 2A), regulatory subunit A, alpha isoform"""				Standard	NR_033500		Approved	PR65A, PP2A-Aalpha	uc002pyp.3	P30153	OTTHUMG00000137367	ENST00000322088.6:c.547C>T	19.37:g.52715982C>T	ENSP00000324804:p.Arg183Trp	Somatic		Capture	Illumina HiSeq	Phase_I	57407794	NM_014225	Q13773|Q6ICQ3|Q96DH3	Missense_Mutation	SNP	ENST00000322088.6	37	CCDS12849.1	.	.	.	.	.	.	.	.	.	.	C	23.0	4.360081	0.82353	.	.	ENSG00000105568	ENST00000423369;ENST00000391791;ENST00000322088;ENST00000444322	T;T	0.06528	3.29;3.29	4.5	4.5	0.54988	Armadillo-like helical (1);Armadillo-type fold (1);	0.114427	0.37136	N	0.002231	T	0.34193	0.0889	H	0.96333	3.805	0.58432	D	0.999999	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;0.997;0.997	T	0.40459	-0.9562	10	0.87932	D	0	-15.4468	10.2034	0.43099	0.1981:0.8019:0.0:0.0	.	128;183;183	F5H3X9;A8K7B7;P30153	.;.;2AAA_HUMAN	W	173;103;183;128	ENSP00000324804:R183W;ENSP00000415067:R128W	ENSP00000324804:R183W	R	+	1	2	PPP2R1A	57407794	1.000000	0.71417	1.000000	0.80357	1.000000	0.99986	4.933000	0.63484	2.503000	0.84419	0.655000	0.94253	CGG		0.617	PPP2R1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000267967.2	NM_014225	
ZNF808	388558	broad.mit.edu	37	19	53057130	53057130	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr19:53057130G>T	ENST00000359798.4	+	5	1141	c.961G>T	c.(961-963)Ggc>Tgc	p.G321C		NM_001039886.3	NP_001034975.2	Q8N4W9	ZN808_HUMAN	zinc finger protein 808	321					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(8)|kidney(3)|lung(12)|urinary_tract(1)	24				OV - Ovarian serous cystadenocarcinoma(262;0.00501)|GBM - Glioblastoma multiforme(134;0.0213)		TAATGAGTGTGGCAAGGTCTT	0.388																																					p.G321C												.	.	0			c.G961T	19						.						101.0	104.0	103.0					19																	53057130		2203	4300	6503	57748942	SO:0001583	missense	388558	exon5			CR749856	CCDS46167.1	19q13.41	2013-01-08			ENSG00000198482	ENSG00000198482		"""Zinc fingers, C2H2-type"", ""-"""	33230	protein-coding gene	gene with protein product							Standard	NM_001039886		Approved		uc010epq.1	Q8N4W9	OTTHUMG00000158230	ENST00000359798.4:c.961G>T	19.37:g.53057130G>T	ENSP00000352846:p.Gly321Cys	Somatic		Capture	Illumina HiSeq	Phase_I	57748942	NM_001039886	Q68CN7	Missense_Mutation	SNP	ENST00000359798.4	37	CCDS46167.1	.	.	.	.	.	.	.	.	.	.	.	11.33	1.605621	0.28623	.	.	ENSG00000198482	ENST00000359798	T	0.61742	0.08	1.57	-0.802	0.10889	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.80757	0.4684	H	0.97491	4.015	0.09310	N	1	D	0.89917	1.0	D	0.91635	0.999	T	0.67023	-0.5775	9	0.87932	D	0	.	6.8665	0.24096	0.3122:0.0:0.6878:0.0	.	321	Q8N4W9	ZN808_HUMAN	C	321	ENSP00000352846:G321C	ENSP00000352846:G321C	G	+	1	0	ZNF808	57748942	0.064000	0.20934	0.001000	0.08648	0.003000	0.03518	0.987000	0.29603	-0.004000	0.14419	-0.680000	0.03767	GGC		0.388	ZNF808-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350447.3	NM_001039886	
ZNF415	55786	broad.mit.edu	37	19	53611927	53611927	+	Silent	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr19:53611927G>A	ENST00000500065.4	-	4	1704	c.1371C>T	c.(1369-1371)acC>acT	p.T457T	ZNF415_ENST00000421033.1_Silent_p.T469T|ZNF415_ENST00000597503.1_3'UTR|ZNF415_ENST00000594011.1_3'UTR|ZNF415_ENST00000595193.1_3'UTR|ZNF415_ENST00000440291.1_Silent_p.T444T|ZNF415_ENST00000601493.1_Silent_p.T227T|ZNF415_ENST00000455735.2_Silent_p.T505T|ZNF415_ENST00000448501.1_Silent_p.T505T|ZNF415_ENST00000243643.4_Silent_p.T457T|ZNF415_ENST00000597748.1_3'UTR	NM_001136038.2	NP_001129510.2	Q09FC8	ZN415_HUMAN	zinc finger protein 415	505					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|microtubule cytoskeleton (GO:0015630)|nucleolus (GO:0005730)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.T457T(1)		breast(1)|kidney(3)|large_intestine(8)|lung(11)|ovary(2)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	31				GBM - Glioblastoma multiforme(134;0.0191)		TGACCTGATGGGTAGTTAAGT	0.438																																					p.T457T												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1371T	19						.						206.0	181.0	189.0					19																	53611927		2203	4300	6503	58303739	SO:0001819	synonymous_variant	55786	exon4			AK002053	CCDS12860.1, CCDS54313.1	19q13.42	2014-03-18			ENSG00000170954	ENSG00000170954		"""Zinc fingers, C2H2-type"", ""-"""	20636	protein-coding gene	gene with protein product						14702039	Standard	NM_001136038		Approved		uc002qaw.3	Q09FC8	OTTHUMG00000182865	ENST00000500065.4:c.1371C>T	19.37:g.53611927G>A		Somatic		Capture	Illumina HiSeq	Phase_I	58303739	NM_001136038	F5H287|Q09FC7|Q09FC9|Q09FD0|Q6NSZ2|Q6P3S0|Q9NUR2	Silent	SNP	ENST00000500065.4	37	CCDS54313.1																																																																																				0.438	ZNF415-025	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000464043.1	NM_018355	
ZNF761	388561	broad.mit.edu	37	19	53959586	53959586	+	RNA	SNP	A	A	G			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr19:53959586A>G	ENST00000454407.1	+	0	2278							Q86XN6	ZN761_HUMAN	zinc finger protein 761						regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.N555D(1)		endometrium(1)|kidney(2)|large_intestine(5)|lung(13)|ovary(1)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	30				GBM - Glioblastoma multiforme(134;0.00786)		TTACAAGTGTAATGAGTGTGG	0.393																																					p.X609X												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A1826G	19						.						131.0	134.0	133.0					19																	53959586		2203	4300	6503	58651398			388561	exon6			AB107355		19q13.42	2007-10-05	2006-08-11	2006-08-11	ENSG00000160336	ENSG00000160336		"""Zinc fingers, C2H2-type"""	23179	protein-coding gene	gene with protein product							Standard	NM_001008401		Approved	KIAA2033, FLJ16231, FLJ35333	uc010eqp.3	Q86XN6	OTTHUMG00000156999		19.37:g.53959586A>G		Somatic		Capture	Illumina HiSeq	Phase_I	58651398	NM_001008401	Q6ZNB9	Missense_Mutation	SNP	ENST00000454407.1	37																																																																																					0.393	ZNF761-203	KNOWN	basic	processed_transcript	processed_transcript		NM_001008401	
PRKCG	5582	broad.mit.edu	37	19	54401762	54401762	+	Silent	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr19:54401762C>T	ENST00000263431.3	+	11	1443	c.1161C>T	c.(1159-1161)atC>atT	p.I387I	PRKCG_ENST00000542049.1_Silent_p.I274I|PRKCG_ENST00000536044.1_3'UTR|PRKCG_ENST00000540413.1_Silent_p.I387I	NM_002739.3	NP_002730.1	P05129	KPCG_HUMAN	protein kinase C, gamma	387	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of phospholipase C activity (GO:0007202)|blood coagulation (GO:0007596)|cell death (GO:0008219)|chemosensory behavior (GO:0007635)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|innervation (GO:0060384)|intracellular signal transduction (GO:0035556)|learning or memory (GO:0007611)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of protein catabolic process (GO:0042177)|negative regulation of protein ubiquitination (GO:0031397)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphorylation (GO:0016310)|platelet activation (GO:0030168)|positive regulation of mismatch repair (GO:0032425)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|response to morphine (GO:0043278)|response to pain (GO:0048265)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)	cell-cell junction (GO:0005911)|cytosol (GO:0005829)|dendrite (GO:0030425)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|synaptic membrane (GO:0097060)	ATP binding (GO:0005524)|calcium-dependent protein kinase C activity (GO:0004698)|protein kinase activity (GO:0004672)|protein kinase C activity (GO:0004697)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|zinc ion binding (GO:0008270)	p.I387I(1)		large_intestine(1)|lung(4)|ovary(2)|pancreas(2)|skin(1)	10	all_cancers(19;0.0462)|all_epithelial(19;0.0258)|all_lung(19;0.185)|Ovarian(34;0.19)|Lung NSC(19;0.218)			GBM - Glioblastoma multiforme(134;0.0521)	Tamoxifen(DB00675)	AGGACGTGATCGTCCAGGACG	0.627																																					p.I387I												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1161T	19						.						58.0	52.0	54.0					19																	54401762		2203	4300	6503	59093574	SO:0001819	synonymous_variant	5582	exon11			M13977	CCDS12867.1	19q13.4	2014-09-17			ENSG00000126583	ENSG00000126583	2.7.11.1		9402	protein-coding gene	gene with protein product	"""PKC-gamma"""	176980		PKCG, SCA14		8432525, 3755548	Standard	NM_002739		Approved	PKCC, MGC57564	uc002qcq.1	P05129	OTTHUMG00000064846	ENST00000263431.3:c.1161C>T	19.37:g.54401762C>T		Somatic		Capture	Illumina HiSeq	Phase_I	59093574	NM_002739	B7Z8Q0	Silent	SNP	ENST00000263431.3	37	CCDS12867.1																																																																																				0.627	PRKCG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000139233.3	NM_002739	
TFPT	29844	broad.mit.edu	37	19	54611507	54611507	+	Silent	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr19:54611507C>T	ENST00000391759.1	-	5	873	c.468G>A	c.(466-468)gcG>gcA	p.A156A	TFPT_ENST00000391757.1_Missense_Mutation_p.R144Q|TFPT_ENST00000391758.1_Silent_p.A147A|NDUFA3_ENST00000391764.3_Intron	NM_013342.3	NP_037474.1	P0C1Z6	TFPT_HUMAN	TCF3 (E2A) fusion partner (in childhood Leukemia)	156					apoptotic signaling pathway (GO:0097190)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|positive regulation of apoptotic process (GO:0043065)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	actin filament (GO:0005884)|cytoplasm (GO:0005737)|Ino80 complex (GO:0031011)|nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA binding (GO:0003677)	p.A156A(1)		large_intestine(2)|lung(2)	4	all_cancers(19;0.004)|all_epithelial(19;0.00195)|all_lung(19;0.0193)|Lung NSC(19;0.0358)|Breast(117;0.137)|Ovarian(34;0.19)					GCTCATTCTCCGCATTGCCTG	0.682			T	TCF3	pre-B ALL																																p.A156A			Dom	yes		19	19q13	29844	TCF3 (E2A) fusion partner (in childhood Leukemia)		L	.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G468A	19						.						21.0	22.0	22.0					19																	54611507		2201	4299	6500	59303319	SO:0001819	synonymous_variant	29844	exon5			AF052052	CCDS12878.1	19q13	2011-07-06			ENSG00000105619	ENSG00000105619		"""INO80 complex subunits"""	13630	protein-coding gene	gene with protein product	"""amida, partner of the E2A"", ""INO80 complex subunit F"""	609519				10644725, 16230350	Standard	NM_013342		Approved	FB1, amida, INO80F	uc010yej.1	P0C1Z6	OTTHUMG00000065906	ENST00000391759.1:c.468G>A	19.37:g.54611507C>T		Somatic		Capture	Illumina HiSeq	Phase_I	59303319	NM_013342		Silent	SNP	ENST00000391759.1	37	CCDS12878.1	.	.	.	.	.	.	.	.	.	.	A	15.43	2.829829	0.50845	.	.	ENSG00000105619	ENST00000391757	.	.	.	5.04	-8.9	0.00782	.	.	.	.	.	T	0.11580	0.0282	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.20338	-1.0278	5	0.14656	T	0.56	-2.9054	0.6714	0.00859	0.2531:0.2541:0.2718:0.221	.	.	.	.	Q	144	.	ENSP00000375637:R144Q	R	-	2	0	TFPT	59303319	0.000000	0.05858	0.043000	0.18650	0.282000	0.26991	-2.217000	0.01220	-2.003000	0.00962	-0.986000	0.02555	CGG		0.682	TFPT-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000141215.4	NM_013342	
RFX2	5990	broad.mit.edu	37	19	6004288	6004288	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr19:6004288C>T	ENST00000303657.5	-	13	1573	c.1424G>A	c.(1423-1425)cGt>cAt	p.R475H	RFX2_ENST00000359161.3_Missense_Mutation_p.R475H|CTC-232P5.1_ENST00000587836.1_RNA|RFX2_ENST00000592546.1_Missense_Mutation_p.R450H	NM_000635.3	NP_000626.2	P48378	RFX2_HUMAN	regulatory factor X, 2 (influences HLA class II expression)	475					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)	p.R475H(1)		breast(4)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(4)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	21						GGCAAAGTTACGGATGGCCTG	0.542																																					p.R475H	Colon(38;171 817 19800 47433 48051)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1424A	19						.						169.0	144.0	153.0					19																	6004288		2203	4300	6503	5955288	SO:0001583	missense	5990	exon13				CCDS12157.1, CCDS12158.1	19p13.3	2011-11-23			ENSG00000087903	ENSG00000087903			9983	protein-coding gene	gene with protein product	"""trans-acting regulatory factor 2"", ""DNA binding protein RFX2"", ""HLA class II regulatory factor RFX2"""	142765				1505960	Standard	NM_000635		Approved	FLJ14226	uc002meb.3	P48378		ENST00000303657.5:c.1424G>A	19.37:g.6004288C>T	ENSP00000306335:p.Arg475His	Somatic		Capture	Illumina HiSeq	Phase_I	5955288	NM_000635	A8K581|B3KNC4|Q6IQ44|Q8SNA2	Missense_Mutation	SNP	ENST00000303657.5	37	CCDS12157.1	.	.	.	.	.	.	.	.	.	.	C	29.9	5.047174	0.93740	.	.	ENSG00000087903	ENST00000303657;ENST00000359161;ENST00000537791	T	0.09723	2.95	5.14	5.14	0.70334	.	0.000000	0.85682	D	0.000000	T	0.44435	0.1293	M	0.92833	3.35	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.999;1.0	T	0.57376	-0.7822	10	0.87932	D	0	-22.4824	17.5283	0.87807	0.0:1.0:0.0:0.0	.	450;475	P48378-2;P48378	.;RFX2_HUMAN	H	475;450;262	ENSP00000306335:R475H	ENSP00000306335:R475H	R	-	2	0	RFX2	5955288	1.000000	0.71417	0.876000	0.34364	0.885000	0.51271	7.616000	0.83018	2.544000	0.85801	0.655000	0.94253	CGT		0.542	RFX2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000452687.1	NM_000635	
LILRB2	10288	broad.mit.edu	37	19	54782801	54782801	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr19:54782801G>A	ENST00000391749.4	-	6	1092	c.821C>T	c.(820-822)gCt>gTt	p.A274V	LILRB2_ENST00000314446.5_Missense_Mutation_p.A274V|LILRB2_ENST00000391746.1_Missense_Mutation_p.A274V|LILRB2_ENST00000434421.1_Missense_Mutation_p.A158V|LILRB2_ENST00000471216.1_5'Flank|LILRB2_ENST00000391748.1_Missense_Mutation_p.A274V	NM_001278406.1	NP_001265335.1	Q8N423	LIRB2_HUMAN	leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 2	274	Ig-like C2-type 3.				cell surface receptor signaling pathway (GO:0007166)|cell-cell signaling (GO:0007267)|cellular defense response (GO:0006968)|cellular response to lipopolysaccharide (GO:0071222)|Fc receptor mediated inhibitory signaling pathway (GO:0002774)|heterotypic cell-cell adhesion (GO:0034113)|immune response (GO:0006955)|immune response-inhibiting cell surface receptor signaling pathway (GO:0002767)|negative regulation of antigen processing and presentation (GO:0002578)|negative regulation of calcium ion transport (GO:0051926)|negative regulation of T cell proliferation (GO:0042130)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of regulatory T cell differentiation (GO:0045591)|positive regulation of T cell proliferation (GO:0042102)|positive regulation of T cell tolerance induction (GO:0002666)|regulation of dendritic cell differentiation (GO:2001198)|regulation of immune response (GO:0050776)|signal transduction (GO:0007165)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	cell adhesion molecule binding (GO:0050839)|inhibitory MHC class I receptor activity (GO:0032396)|MHC class I protein binding (GO:0042288)|MHC class Ib protein binding (GO:0023029)|protein phosphatase 1 binding (GO:0008157)|receptor activity (GO:0004872)	p.A274V(1)		breast(2)|endometrium(3)|kidney(1)|large_intestine(4)|lung(30)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	44	Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.105)		GGAGAGCCCAGCCTGGGGCTG	0.622																																					p.A274V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C821T	19						.						51.0	54.0	53.0					19																	54782801		2203	4300	6503	59474613	SO:0001583	missense	10288	exon6			AF000574	CCDS12886.1, CCDS42612.1, CCDS62791.1, CCDS62792.1	19q13.4	2013-01-11			ENSG00000131042	ENSG00000131042		"""Leukocyte immunoglobulin-like receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6606	protein-coding gene	gene with protein product		604815				9151699, 9079806	Standard	XM_006722966		Approved	LIR-2, ILT4, MIR-10, LIR2, CD85d, MIR10	uc002qfb.3	Q8N423	OTTHUMG00000064896	ENST00000391749.4:c.821C>T	19.37:g.54782801G>A	ENSP00000375629:p.Ala274Val	Somatic		Capture	Illumina HiSeq	Phase_I	59474613	NM_001080978	A8MU67|C9JF29|O75017|Q8NHJ7|Q8NHJ8	Missense_Mutation	SNP	ENST00000391749.4	37	CCDS12886.1	.	.	.	.	.	.	.	.	.	.	G	16.29	3.080815	0.55753	.	.	ENSG00000131042	ENST00000391748;ENST00000314446;ENST00000391749;ENST00000391746;ENST00000434421	T;T;T;T;T	0.00745	5.75;5.75;5.75;5.75;5.75	2.44	1.29	0.21616	Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.896517	0.09282	N	0.823623	T	0.03827	0.0108	M	0.83483	2.645	0.09310	N	1	D;D;P	0.58970	0.984;0.972;0.806	D;D;P	0.67548	0.936;0.952;0.785	T	0.34079	-0.9843	10	0.62326	D	0.03	.	7.4367	0.27160	0.0:0.2728:0.7272:0.0	.	274;291;274	A8MU67;E7EVY1;Q8N423	.;.;LIRB2_HUMAN	V	274;274;274;274;158	ENSP00000375628:A274V;ENSP00000319960:A274V;ENSP00000375629:A274V;ENSP00000375626:A274V;ENSP00000410117:A158V	ENSP00000319960:A274V	A	-	2	0	LILRB2	59474613	0.000000	0.05858	0.001000	0.08648	0.403000	0.30841	0.147000	0.16202	0.299000	0.22661	0.449000	0.29647	GCT		0.622	LILRB2-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000139510.1		
KIR3DL1	3811	broad.mit.edu	37	19	55329874	55329874	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr19:55329874A>G	ENST00000391728.4	+	3	208	c.175A>G	c.(175-177)Atg>Gtg	p.M59V	KIR3DL1_ENST00000326542.7_Missense_Mutation_p.M59V|KIR3DL1_ENST00000541392.1_Missense_Mutation_p.M59V|KIR3DL1_ENST00000358178.4_Intron|KIR3DL1_ENST00000402254.2_Missense_Mutation_p.M59V|KIR3DL1_ENST00000538269.1_Missense_Mutation_p.M59V	NM_013289.2	NP_037421.2	P43629	KI3L1_HUMAN	killer cell immunoglobulin-like receptor, three domains, long cytoplasmic tail, 1	59	Ig-like C2-type 1.				immune response (GO:0006955)|regulation of immune response (GO:0050776)|signal transduction (GO:0007165)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	HLA-B specific inhibitory MHC class I receptor activity (GO:0030109)	p.M59V(2)		breast(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	11				GBM - Glioblastoma multiforme(193;0.0192)		TAACAATTTCATGCTATACAA	0.502																																					p.M59V												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.A175G	19						.						69.0	90.0	82.0					19																	55329874		2175	4123	6298	60021686	SO:0001583	missense	3811	exon3			L41269	CCDS42621.1	19q13.4	2014-05-22			ENSG00000167633	ENSG00000167633		"""Killer cell immunoglobulin-like receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6338	protein-coding gene	gene with protein product		604946		KIR		7716543, 7749980	Standard	NM_013289		Approved	cl-2, NKB1, cl-11, nkat3, NKB1B, AMB11, CD158e1/2, CD158E1, CD158e2		P43629	OTTHUMG00000065933	ENST00000391728.4:c.175A>G	19.37:g.55329874A>G	ENSP00000375608:p.Met59Val	Somatic		Capture	Illumina HiSeq	Phase_I	60021686	NM_013289	O43473|Q14946|Q16541	Missense_Mutation	SNP	ENST00000391728.4	37	CCDS42621.1	.	.	.	.	.	.	.	.	.	.	A	2.830	-0.242799	0.05906	.	.	ENSG00000167633	ENST00000402254;ENST00000538269;ENST00000541392;ENST00000355608;ENST00000391728;ENST00000326542	T;T;T;T;T	0.11712	2.75;2.75;2.75;2.75;2.75	1.25	-1.17	0.09648	Immunoglobulin subtype (1);Immunoglobulin (1);Immunoglobulin-like fold (1);	3.535310	0.02162	U	0.058865	T	0.04543	0.0124	N	0.01529	-0.815	0.09310	N	1	B;B;B	0.18461	0.002;0.028;0.012	B;B;B	0.22386	0.011;0.039;0.004	T	0.37079	-0.9721	10	0.87932	D	0	.	4.0245	0.09680	0.6376:0.0:0.3624:0.0	.	59;59;59	Q15702;F6QF33;P43629	.;.;KI3L1_HUMAN	V	59;59;59;37;59;59	ENSP00000384528:M59V;ENSP00000443350:M59V;ENSP00000442355:M59V;ENSP00000375608:M59V;ENSP00000326868:M59V	ENSP00000326868:M59V	M	+	1	0	KIR3DL1	60021686	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-3.120000	0.00595	-0.383000	0.07858	0.155000	0.16302	ATG		0.502	KIR3DL1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000141238.1	NM_013289	
NLRP7	199713	broad.mit.edu	37	19	55451568	55451568	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr19:55451568C>T	ENST00000590030.1	-	3	659	c.619G>A	c.(619-621)Gcg>Acg	p.A207T	NLRP7_ENST00000448121.2_Missense_Mutation_p.A207T|NLRP7_ENST00000588756.1_Missense_Mutation_p.A207T|NLRP7_ENST00000340844.2_Missense_Mutation_p.A207T|NLRP7_ENST00000446217.1_Missense_Mutation_p.A235T|NLRP7_ENST00000328092.5_Missense_Mutation_p.A207T|NLRP7_ENST00000592784.1_Missense_Mutation_p.A207T			Q8WX94	NALP7_HUMAN	NLR family, pyrin domain containing 7	207	NACHT. {ECO:0000255|PROSITE- ProRule:PRU00136}.						ATP binding (GO:0005524)	p.A207T(1)		autonomic_ganglia(1)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(17)|liver(1)|lung(33)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(3)	73				GBM - Glioblastoma multiforme(193;0.0325)		AGGTAGAACGCGTATCTGAGC	0.587																																					p.A207T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G619A	19						.						109.0	104.0	106.0					19																	55451568		2203	4300	6503	60143380	SO:0001583	missense	199713	exon4			AF464765	CCDS12912.1, CCDS33109.1, CCDS46183.1	19q13.42	2008-02-05	2006-12-08	2006-12-08		ENSG00000167634		"""Nucleotide-binding domain and leucine rich repeat containing"""	22947	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 7"""	609661	"""NACHT, leucine rich repeat and PYD containing 7"""	NALP7		12563287, 12019269	Standard	NM_139176		Approved	PYPAF3, NOD12, PAN7, CLR19.4	uc002qii.4	Q8WX94		ENST00000590030.1:c.619G>A	19.37:g.55451568C>T	ENSP00000465520:p.Ala207Thr	Somatic		Capture	Illumina HiSeq	Phase_I	60143380	NM_139176	E9PE16|Q32MH8|Q7RTR1	Missense_Mutation	SNP	ENST00000590030.1	37	CCDS33109.1	.	.	.	.	.	.	.	.	.	.	C	13.69	2.312333	0.40895	.	.	ENSG00000167634	ENST00000328092;ENST00000448121;ENST00000340844;ENST00000446217	T;T;T;T	0.78481	-1.18;-1.18;-1.18;-1.18	1.88	0.832	0.18867	NACHT nucleoside triphosphatase (1);	.	.	.	.	T	0.79347	0.4430	L	0.49455	1.56	0.09310	N	1	D;D;D;D	0.71674	0.998;0.998;0.998;0.997	P;P;P;P	0.62435	0.902;0.902;0.902;0.842	T	0.65615	-0.6125	9	0.33141	T	0.24	.	6.4788	0.22051	0.0:0.8342:0.0:0.1658	.	235;207;207;207	E7EPM2;Q32MH9;Q8WX94;Q8WX94-2	.;.;NALP7_HUMAN;.	T	207;207;207;235	ENSP00000329568:A207T;ENSP00000409137:A207T;ENSP00000339491:A207T;ENSP00000414273:A235T	ENSP00000329568:A207T	A	-	1	0	NLRP7	60143380	0.000000	0.05858	0.003000	0.11579	0.099000	0.18886	-0.092000	0.11129	0.361000	0.24292	0.462000	0.41574	GCG		0.587	NLRP7-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000451396.1	NM_139176	
NLRP2	55655	broad.mit.edu	37	19	55496562	55496562	+	Silent	SNP	C	C	T	rs150962178		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr19:55496562C>T	ENST00000543010.1	+	7	2321	c.2178C>T	c.(2176-2178)gaC>gaT	p.D726D	NLRP2_ENST00000391721.4_Silent_p.D702D|NLRP2_ENST00000339757.7_Silent_p.D704D|NLRP2_ENST00000448584.2_Silent_p.D726D|NLRP2_ENST00000427260.2_Silent_p.D703D|NLRP2_ENST00000263437.6_Silent_p.D723D|NLRP2_ENST00000538819.1_Silent_p.D702D|NLRP2_ENST00000537859.1_Silent_p.D704D	NM_001174081.1	NP_001167552.1	Q9NX02	NALP2_HUMAN	NLR family, pyrin domain containing 2	726					positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of interleukin-1 beta secretion (GO:0050718)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|Pyrin domain binding (GO:0032090)	p.D726D(2)		large_intestine(4)|liver(1)|ovary(1)|skin(2)|upper_aerodigestive_tract(3)	11			BRCA - Breast invasive adenocarcinoma(297;0.163)	GBM - Glioblastoma multiforme(193;0.028)		TAGCCTCTGACACCTGTCATC	0.398																																					p.D703D												.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.C2109T	19						.	C	,,,	0,4406		0,0,2203	145.0	129.0	134.0		2178,2112,2109,2178	-1.9	0.0	19	dbSNP_134	134	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	NLRP2	NM_001174081.1,NM_001174082.1,NM_001174083.1,NM_017852.3	,,,	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	,,,	726/1063,704/1041,703/1040,726/1063	55496562	1,13005	2203	4300	6503	60188374	SO:0001819	synonymous_variant	55655	exon8			AK000517	CCDS12913.1, CCDS54318.1, CCDS54319.1	19q13.42	2008-02-05	2006-12-08	2006-12-08	ENSG00000022556	ENSG00000022556		"""Nucleotide-binding domain and leucine rich repeat containing"""	22948	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 2"""	609364	"""NACHT, leucine rich repeat and PYD containing 2"""	NALP2		12563287, 11270363	Standard	NM_001174081		Approved	FLJ20510, PYPAF2, NBS1, PAN1, CLR19.9	uc021vbq.1	Q9NX02	OTTHUMG00000167763	ENST00000543010.1:c.2178C>T	19.37:g.55496562C>T		Somatic		Capture	Illumina HiSeq	Phase_I	60188374	NM_001174083	B4DZL7|I3L0G4|Q53FL5|Q59G09|Q8IXT0|Q9BVN5|Q9H6G6|Q9HAV9|Q9NWK3	Silent	SNP	ENST00000543010.1	37	CCDS12913.1																																																																																				0.398	NLRP2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000396152.1	NM_017852	
DNAAF3	352909	broad.mit.edu	37	19	55670727	55670727	+	Silent	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr19:55670727G>A	ENST00000524407.2	-	12	1362	c.1329C>T	c.(1327-1329)acC>acT	p.T443T	CTD-2587H24.4_ENST00000587871.1_Missense_Mutation_p.R105W|TNNI3_ENST00000344887.5_5'Flank|TNNI3_ENST00000590463.1_5'Flank|TNNI3_ENST00000588882.1_5'Flank|DNAAF3_ENST00000527223.2_Silent_p.T510T|DNAAF3_ENST00000587789.2_5'UTR|DNAAF3_ENST00000391720.4_Silent_p.T490T|DNAAF3_ENST00000455045.1_Silent_p.T389T|CTD-2587H24.5_ENST00000591665.1_RNA			Q8N9W5	DAAF3_HUMAN	dynein, axonemal, assembly factor 3	443					axonemal dynein complex assembly (GO:0070286)|motile cilium assembly (GO:0044458)	cytoplasm (GO:0005737)		p.T490T(1)									GCCTGGCCCCGGTCTGTGGAG	0.622																																					p.T490T												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1470T	19						.						45.0	51.0	49.0					19																	55670727		1966	4164	6130	60362539	SO:0001819	synonymous_variant	352909	exon12			AK097388	CCDS12918.2, CCDS58679.1, CCDS58680.1, CCDS59422.1	19q13.42	2012-10-05	2012-03-09	2012-03-09	ENSG00000167646	ENSG00000167646			30492	protein-coding gene	gene with protein product		614566	"""chromosome 19 open reading frame 51"", ""ciliary dyskinesia, primary 2"""	C19orf51, CILD2		22387996	Standard	NM_001256714		Approved	FLJ40069, FLJ36139, PF22, PCD	uc002qjl.2	Q8N9W5	OTTHUMG00000128547	ENST00000524407.2:c.1329C>T	19.37:g.55670727G>A		Somatic		Capture	Illumina HiSeq	Phase_I	60362539	NM_178837	A8MUY0|E3W9A1|E9PAX5|Q6P4F6|Q8N9W0|Q96AR2	Silent	SNP	ENST00000524407.2	37	CCDS59422.1																																																																																				0.622	DNAAF3-003	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000250388.5	NM_178837	
PPP6R1	22870	broad.mit.edu	37	19	55748152	55748152	+	Missense_Mutation	SNP	C	C	T	rs201425646		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr19:55748152C>T	ENST00000412770.2	-	17	2413	c.1847G>A	c.(1846-1848)cGc>cAc	p.R616H	AC010327.1_ENST00000581390.1_RNA|PPP6R1_ENST00000587283.1_Missense_Mutation_p.R616H	NM_014931.3	NP_055746.3	Q9UPN7	PP6R1_HUMAN	protein phosphatase 6, regulatory subunit 1	616					regulation of phosphoprotein phosphatase activity (GO:0043666)	cytoplasm (GO:0005737)	protein phosphatase binding (GO:0019903)	p.R616H(2)		breast(1)	1						CTGCTGGATGCGGTCCTTGTA	0.627													C|||	1	0.000199681	0.0	0.0	5008	,	,		17696	0.0		0.0	False		,,,				2504	0.001				p.R616H												.	.	2	Substitution - Missense(2)	large_intestine(1)|endometrium(1)	c.G1847A	19						.	C	HIS/ARG	2,4054		0,2,2026	91.0	91.0	91.0		1847	4.8	1.0	19		91	0,8372		0,0,4186	yes	missense	PPP6R1	NM_014931.3	29	0,2,6212	TT,TC,CC		0.0,0.0493,0.0161	possibly-damaging	616/882	55748152	2,12426	2028	4186	6214	60439964	SO:0001583	missense	22870	exon17			AB029038	CCDS46186.1	19q13.42	2012-04-17	2010-06-28	2010-06-28	ENSG00000105063	ENSG00000105063		"""Serine/threonine phosphatases / Protein phosphatase 6, regulatory subunits"""	29195	protein-coding gene	gene with protein product		610875	"""KIAA1115"", ""SAPS domain family, member 1"""	KIAA1115, SAPS1		16769727	Standard	NM_014931		Approved	SAP190	uc002qjw.4	Q9UPN7		ENST00000412770.2:c.1847G>A	19.37:g.55748152C>T	ENSP00000414202:p.Arg616His	Somatic		Capture	Illumina HiSeq	Phase_I	60439964	NM_014931	Q2M2H3|Q504V2|Q6NVJ6|Q9BU97	Missense_Mutation	SNP	ENST00000412770.2	37	CCDS46186.1	.	.	.	.	.	.	.	.	.	.	C	16.02	3.002951	0.54254	4.93E-4	0.0	ENSG00000105063	ENST00000412770	T	0.67523	-0.27	4.83	4.83	0.62350	.	0.108819	0.39834	N	0.001247	T	0.72095	0.3418	L	0.37561	1.115	0.34209	D	0.674079	D	0.76494	0.999	P	0.60886	0.88	T	0.78013	-0.2370	10	0.45353	T	0.12	-25.04	17.209	0.86926	0.0:1.0:0.0:0.0	.	616	Q9UPN7	PP6R1_HUMAN	H	616	ENSP00000414202:R616H	ENSP00000414202:R616H	R	-	2	0	PPP6R1	60439964	0.937000	0.31787	1.000000	0.80357	0.991000	0.79684	1.818000	0.39012	2.677000	0.91161	0.563000	0.77884	CGC		0.627	PPP6R1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452663.1	NM_014931	
NLRP9	338321	broad.mit.edu	37	19	56220323	56220323	+	Silent	SNP	T	T	C			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr19:56220323T>C	ENST00000332836.2	-	9	2958	c.2931A>G	c.(2929-2931)ggA>ggG	p.G977G	CTD-2611O12.8_ENST00000596293.1_RNA|CTD-2611O12.7_ENST00000597680.1_RNA|CTD-2611O12.6_ENST00000600582.1_RNA	NM_176820.2	NP_789790.2	Q7RTR0	NALP9_HUMAN	NLR family, pyrin domain containing 9	977						cytoplasm (GO:0005737)	ATP binding (GO:0005524)	p.G977G(1)		NS(2)|breast(5)|cervix(1)|endometrium(7)|kidney(8)|large_intestine(15)|lung(21)|ovary(2)|prostate(3)|skin(7)|urinary_tract(3)	74		Colorectal(82;0.000133)|Ovarian(87;0.133)		GBM - Glioblastoma multiforme(193;0.123)		CAATCCAAGGTCCATGTGAAA	0.473																																					p.G977G												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.A2931G	19						.						105.0	100.0	102.0					19																	56220323		2203	4300	6503	60912135	SO:0001819	synonymous_variant	338321	exon9			AY154464	CCDS12934.1	19q13.43	2006-12-08	2006-12-08	2006-12-08				"""Nucleotide-binding domain and leucine rich repeat containing"""	22941	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 9"""	609663	"""NACHT, leucine rich repeat and PYD containing 9"""	NALP9		12563287	Standard	NM_176820		Approved	NOD6, PAN12, CLR19.1	uc002qly.3	Q7RTR0		ENST00000332836.2:c.2931A>G	19.37:g.56220323T>C		Somatic		Capture	Illumina HiSeq	Phase_I	60912135	NM_176820	B2RN12|Q86W27	Silent	SNP	ENST00000332836.2	37	CCDS12934.1																																																																																				0.473	NLRP9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453653.1	NM_176820	
NLRP4	147945	broad.mit.edu	37	19	56379186	56379186	+	Silent	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr19:56379186C>T	ENST00000301295.6	+	6	2720	c.2298C>T	c.(2296-2298)ggC>ggT	p.G766G	NLRP4_ENST00000587891.1_Silent_p.G691G|NLRP4_ENST00000346986.5_Intron	NM_134444.4	NP_604393.2	Q96MN2	NALP4_HUMAN	NLR family, pyrin domain containing 4	766					inflammatory response (GO:0006954)|innate immune response (GO:0045087)|positive regulation of type I interferon production (GO:0032481)|regulation of type I interferon production (GO:0032479)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)	p.G766G(1)		breast(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(14)|lung(3)|ovary(6)|pancreas(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(8)	42		Colorectal(82;0.0002)|Ovarian(87;0.221)		GBM - Glioblastoma multiforme(193;0.0606)		TAGACACAGGCGTGCCCCTTT	0.542																																					p.G766G												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C2298T	19						.						172.0	141.0	151.0					19																	56379186		2203	4300	6503	61070998	SO:0001819	synonymous_variant	147945	exon6			AF479747	CCDS12936.1	19q13.43	2009-03-27	2006-12-08	2006-12-08				"""Nucleotide-binding domain and leucine rich repeat containing"""	22943	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 4"", ""cancer/testis antigen 58"""	609645	"""NACHT, leucine rich repeat and PYD containing 4"""	NALP4		12563287, 12019269	Standard	NM_134444		Approved	PYPAF4, FLJ32126, PAN2, RNH2, CLR19.5, CT58	uc002qmd.4	Q96MN2		ENST00000301295.6:c.2298C>T	19.37:g.56379186C>T		Somatic		Capture	Illumina HiSeq	Phase_I	61070998	NM_134444	Q86W87|Q96AY6	Silent	SNP	ENST00000301295.6	37	CCDS12936.1																																																																																				0.542	NLRP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457367.2	NM_134444	
NLRP5	126206	broad.mit.edu	37	19	56538996	56538996	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr19:56538996A>G	ENST00000390649.3	+	7	1397	c.1397A>G	c.(1396-1398)gAc>gGc	p.D466G		NM_153447.4	NP_703148.4	P59047	NALP5_HUMAN	NLR family, pyrin domain containing 5	466	NACHT. {ECO:0000255|PROSITE- ProRule:PRU00136}.				cellular protein complex assembly (GO:0043623)|cellular protein localization (GO:0034613)|embryo implantation (GO:0007566)|fertilization (GO:0009566)|in utero embryonic development (GO:0001701)|neuron death (GO:0070997)|organ morphogenesis (GO:0009887)|regulation of protein stability (GO:0031647)|regulation of RNA stability (GO:0043487)	apical cortex (GO:0045179)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|protein complex (GO:0043234)	ATP binding (GO:0005524)	p.D466G(1)		breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|ovary(5)|skin(2)|stomach(4)|upper_aerodigestive_tract(2)	25		Colorectal(82;3.46e-05)|Ovarian(87;0.0481)|Renal(1328;0.157)		GBM - Glioblastoma multiforme(193;0.0326)		GAGCTGCTCGACCAGTGCCAG	0.612																																					p.D466G												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A1397G	19						.						35.0	39.0	38.0					19																	56538996		2114	4232	6346	61230808	SO:0001583	missense	126206	exon7			AY154460	CCDS12938.1	19q13.43	2008-10-30	2006-12-08	2006-12-08	ENSG00000171487	ENSG00000171487		"""Nucleotide-binding domain and leucine rich repeat containing"""	21269	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 5"""	609658	"""NACHT, leucine rich repeat and PYD containing 5"""	NALP5		12563287, 11925379	Standard	NM_153447		Approved	PYPAF8, MATER, PAN11, CLR19.8	uc002qmj.3	P59047	OTTHUMG00000149887	ENST00000390649.3:c.1397A>G	19.37:g.56538996A>G	ENSP00000375063:p.Asp466Gly	Somatic		Capture	Illumina HiSeq	Phase_I	61230808	NM_153447	A8MTY4|Q86W29	Missense_Mutation	SNP	ENST00000390649.3	37	CCDS12938.1	.	.	.	.	.	.	.	.	.	.	A	12.93	2.086388	0.36855	.	.	ENSG00000171487	ENST00000390649	T	0.71341	-0.56	2.82	1.79	0.24919	.	0.619175	0.13406	N	0.390255	T	0.64305	0.2586	L	0.54323	1.7	0.09310	N	1	P	0.43352	0.804	B	0.44224	0.444	T	0.53920	-0.8370	10	0.42905	T	0.14	.	4.7959	0.13272	0.8515:0.0:0.1485:0.0	.	466	P59047	NALP5_HUMAN	G	466	ENSP00000375063:D466G	ENSP00000375063:D466G	D	+	2	0	NLRP5	61230808	0.006000	0.16342	0.003000	0.11579	0.002000	0.02628	0.519000	0.22862	0.471000	0.27319	-0.290000	0.09829	GAC		0.612	NLRP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313735.1	NM_153447	
ZNF667	63934	broad.mit.edu	37	19	56952755	56952755	+	Missense_Mutation	SNP	T	T	G			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr19:56952755T>G	ENST00000504904.3	-	7	2328	c.1609A>C	c.(1609-1611)Agt>Cgt	p.S537R	ZNF667_ENST00000342634.3_Missense_Mutation_p.S665R|ZNF667_ENST00000591790.1_3'UTR|ZNF667_ENST00000292069.6_Missense_Mutation_p.S537R			Q5HYK9	ZN667_HUMAN	zinc finger protein 667	537					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.S537R(1)		breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(11)|lung(18)|pancreas(1)|skin(1)|upper_aerodigestive_tract(3)	38		Colorectal(82;0.000256)|Ovarian(87;0.243)		GBM - Glioblastoma multiforme(193;0.0615)		GTGCGCTGACTAAAGGCCTTA	0.458																																					p.S537R												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A1609C	19						.						99.0	83.0	89.0					19																	56952755		2203	4300	6503	61644567	SO:0001583	missense	63934	exon5				CCDS12944.1	19q13.43	2013-01-08				ENSG00000198046		"""Zinc fingers, C2H2-type"", ""-"""	28854	protein-coding gene	gene with protein product		611024					Standard	NM_022103		Approved	FLJ14011	uc002qnd.3	Q5HYK9		ENST00000504904.3:c.1609A>C	19.37:g.56952755T>G	ENSP00000439402:p.Ser537Arg	Somatic		Capture	Illumina HiSeq	Phase_I	61644567	NM_022103	B2RMS6|B9EK36|Q6B093|Q9H807	Missense_Mutation	SNP	ENST00000504904.3	37	CCDS12944.1	.	.	.	.	.	.	.	.	.	.	T	4.824	0.153249	0.09185	.	.	ENSG00000198046	ENST00000342634;ENST00000504904;ENST00000292069;ENST00000452518;ENST00000360227	T;T;T	0.07567	3.18;3.18;3.18	4.66	2.51	0.30379	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.312957	0.23121	N	0.051681	T	0.04363	0.0120	N	0.20881	0.62	0.09310	N	1	P;P	0.39094	0.659;0.659	B;B	0.35278	0.199;0.199	T	0.38308	-0.9667	10	0.24483	T	0.36	-7.2712	4.1556	0.10260	0.0:0.1896:0.1751:0.6353	.	665;537	E7EPS0;Q5HYK9	.;ZN667_HUMAN	R	665;537;537;319;252	ENSP00000344699:S665R;ENSP00000439402:S537R;ENSP00000292069:S537R	ENSP00000292069:S537R	S	-	1	0	ZNF667	61644567	0.000000	0.05858	0.755000	0.31263	0.026000	0.11368	0.081000	0.14823	0.263000	0.21812	-0.250000	0.11733	AGT		0.458	ZNF667-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458394.1	NM_022103	
ZNF543	125919	broad.mit.edu	37	19	57840177	57840177	+	Missense_Mutation	SNP	A	A	C			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr19:57840177A>C	ENST00000321545.4	+	4	1692	c.1347A>C	c.(1345-1347)aaA>aaC	p.K449N		NM_213598.3	NP_998763.2	Q08ER8	ZN543_HUMAN	zinc finger protein 543	449					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.K449N(1)		breast(1)|kidney(2)|large_intestine(8)|lung(11)|pancreas(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)	28		Colorectal(82;0.000256)|all_neural(62;0.0577)|Ovarian(87;0.221)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0257)		CAGGAGAAAAACCCTATGAAT	0.478																																					p.K449N												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A1347C	19						.						64.0	66.0	65.0					19																	57840177		2203	4300	6503	62531989	SO:0001583	missense	125919	exon4			AL834534	CCDS33130.1	19q13.43	2013-01-08				ENSG00000178229		"""Zinc fingers, C2H2-type"", ""-"""	25281	protein-coding gene	gene with protein product							Standard	NM_213598		Approved	DKFZp434H055	uc002qoi.2	Q08ER8		ENST00000321545.4:c.1347A>C	19.37:g.57840177A>C	ENSP00000322545:p.Lys449Asn	Somatic		Capture	Illumina HiSeq	Phase_I	62531989	NM_213598	Q495U9|Q495V0|Q6ZMP4|Q8NCX4	Missense_Mutation	SNP	ENST00000321545.4	37	CCDS33130.1	.	.	.	.	.	.	.	.	.	.	A	16.45	3.125553	0.56721	.	.	ENSG00000178229	ENST00000321545	T	0.26067	1.76	3.0	3.0	0.34707	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.52175	0.1718	M	0.84948	2.725	0.27659	N	0.947127	D	0.89917	1.0	D	0.72982	0.979	T	0.43032	-0.9416	9	0.87932	D	0	.	10.5184	0.44903	1.0:0.0:0.0:0.0	.	449	Q08ER8	ZN543_HUMAN	N	449	ENSP00000322545:K449N	ENSP00000322545:K449N	K	+	3	2	ZNF543	62531989	0.013000	0.17824	0.992000	0.48379	0.949000	0.60115	-0.045000	0.12003	1.353000	0.45828	0.459000	0.35465	AAA		0.478	ZNF543-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465780.1	XM_064865	
VN1R1	57191	broad.mit.edu	37	19	57966866	57966866	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr19:57966866G>A	ENST00000321039.3	-	1	988	c.989C>T	c.(988-990)aCt>aTt	p.T330I	AC004076.9_ENST00000596831.1_Intron|AC004076.9_ENST00000415705.3_5'UTR	NM_020633.3	NP_065684.1	Q9GZP7	VN1R1_HUMAN	vomeronasal 1 receptor 1	330					response to pheromone (GO:0019236)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	pheromone receptor activity (GO:0016503)	p.T330I(1)		NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(8)|ovary(1)|pancreas(1)|skin(2)	19		Colorectal(82;5.46e-05)|all_neural(62;0.0218)|Ovarian(87;0.0694)|Renal(1328;0.157)|Breast(46;0.222)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0254)|Lung(386;0.171)		AGAGATATGAGTATCACTCAT	0.463																																					p.T330I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C989T	19						.						88.0	91.0	90.0					19																	57966866		2203	4300	6503	62658678	SO:0001583	missense	57191	exon1			AF255342	CCDS12951.1	19q13.4	2012-08-22	2003-01-15		ENSG00000178201	ENSG00000178201		"""Vomeronasal receptors / Type 1"", ""GPCR / Unclassified : Vomeronasal receptors, type 1"""	13548	protein-coding gene	gene with protein product		605234	"""vomeronasal olfactory receptor, (chromosome 19) subtype I, member 1"""	VNR19I1		10973240	Standard	NM_020633		Approved	V1RL1, ZVNR1, ZVNH1	uc002qos.2	Q9GZP7		ENST00000321039.3:c.989C>T	19.37:g.57966866G>A	ENSP00000322339:p.Thr330Ile	Somatic		Capture	Illumina HiSeq	Phase_I	62658678	NM_020633	B3KSV5|Q7Z5H8|Q7Z5H9	Missense_Mutation	SNP	ENST00000321039.3	37	CCDS12951.1	.	.	.	.	.	.	.	.	.	.	G	13.73	2.322976	0.41096	.	.	ENSG00000178201	ENST00000321039	T	0.09445	2.98	4.07	-5.31	0.02730	.	.	.	.	.	T	0.09423	0.0232	L	0.47716	1.5	0.09310	N	1	P	0.40144	0.704	B	0.42653	0.394	T	0.17048	-1.0382	9	0.52906	T	0.07	.	4.0324	0.09714	0.0803:0.3901:0.2843:0.2453	.	330	Q9GZP7	VN1R1_HUMAN	I	330	ENSP00000322339:T330I	ENSP00000322339:T330I	T	-	2	0	VN1R1	62658678	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.133000	0.10451	-0.858000	0.04110	-0.203000	0.12734	ACT		0.463	VN1R1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466464.1	NM_020633	
ABCA7	10347	broad.mit.edu	37	19	1043731	1043731	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr19:1043731G>A	ENST00000263094.6	+	10	1169	c.938G>A	c.(937-939)cGg>cAg	p.R313Q	ABCA7_ENST00000433129.1_Missense_Mutation_p.R313Q|ABCA7_ENST00000435683.2_Missense_Mutation_p.R175Q	NM_019112.3	NP_061985.2	Q8IZY2	ABCA7_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 7	313					apolipoprotein A-I-mediated signaling pathway (GO:0038027)|ATP catabolic process (GO:0006200)|cholesterol efflux (GO:0033344)|high-density lipoprotein particle assembly (GO:0034380)|memory (GO:0007613)|negative regulation of amyloid precursor protein biosynthetic process (GO:0042985)|negative regulation of ATPase activity (GO:0032780)|negative regulation of beta-amyloid formation (GO:1902430)|peptide cross-linking (GO:0018149)|phagocytosis (GO:0006909)|phospholipid efflux (GO:0033700)|phospholipid scrambling (GO:0017121)|positive regulation of ATPase activity (GO:0032781)|positive regulation of beta-amyloid clearance (GO:1900223)|positive regulation of cholesterol efflux (GO:0010875)|positive regulation of engulfment of apoptotic cell (GO:1901076)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of phagocytosis (GO:0050766)|positive regulation of phospholipid efflux (GO:1902995)|protein localization to nucleus (GO:0034504)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|ATP-binding cassette (ABC) transporter complex (GO:0043190)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|phagocytic cup (GO:0001891)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)	apolipoprotein A-I receptor activity (GO:0034188)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|phospholipid transporter activity (GO:0005548)|transporter activity (GO:0005215)	p.R313Q(1)		NS(1)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(7)|lung(22)|ovary(1)|pancreas(7)|prostate(4)|skin(3)|upper_aerodigestive_tract(1)	65		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;1.04e-05)|all_lung(49;1.53e-05)|Breast(49;9.42e-05)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		CAGGTGAACCGGACCTTCGAG	0.637																																					p.R313Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G938A	19						.						116.0	111.0	112.0					19																	1043731		2203	4300	6503	994731	SO:0001583	missense	10347	exon10			AF328787	CCDS12055.1	19p13.3	2012-03-14			ENSG00000064687	ENSG00000064687		"""ATP binding cassette transporters / subfamily A"""	37	protein-coding gene	gene with protein product		605414					Standard	NM_019112		Approved	ABCX	uc002lqw.4	Q8IZY2	OTTHUMG00000167547	ENST00000263094.6:c.938G>A	19.37:g.1043731G>A	ENSP00000263094:p.Arg313Gln	Somatic		Capture	Illumina HiSeq	Phase_I	994731	NM_019112	Q96S58|Q9BZC4|Q9NR73|Q9UKP8	Missense_Mutation	SNP	ENST00000263094.6	37	CCDS12055.1	.	.	.	.	.	.	.	.	.	.	G	6.405	0.442789	0.12164	.	.	ENSG00000064687	ENST00000263094;ENST00000433129	D;D	0.84516	-1.86;-1.86	4.47	-5.07	0.02938	.	.	.	.	.	T	0.67850	0.2937	N	0.05414	-0.055	0.28644	N	0.907038	B;B	0.19706	0.038;0.024	B;B	0.18561	0.022;0.003	T	0.50874	-0.8776	9	0.27082	T	0.32	.	13.1386	0.59423	0.8434:0.0:0.1566:0.0	.	175;313	Q8IZY2-2;Q8IZY2	.;ABCA7_HUMAN	Q	313	ENSP00000263094:R313Q;ENSP00000414062:R313Q	ENSP00000263094:R313Q	R	+	2	0	ABCA7	994731	0.001000	0.12720	0.924000	0.36721	0.232000	0.25224	-0.655000	0.05348	-0.954000	0.03640	-0.463000	0.05309	CGG		0.637	ABCA7-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000394993.1	NM_019112	
TUBB4A	10382	broad.mit.edu	37	19	6495277	6495277	+	Silent	SNP	G	G	A	rs138128036		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr19:6495277G>A	ENST00000264071.2	-	4	1604	c.1233C>T	c.(1231-1233)gcC>gcT	p.A411A	TUBB4A_ENST00000540257.1_Silent_p.A411A|CTD-2396E7.9_ENST00000599292.1_RNA|CTD-2396E7.10_ENST00000596027.1_RNA			P04350	TBB4A_HUMAN	tubulin, beta 4A class IVa	411					'de novo' posttranslational protein folding (GO:0051084)|cellular protein metabolic process (GO:0044267)|G2/M transition of mitotic cell cycle (GO:0000086)|microtubule-based process (GO:0007017)|mitotic cell cycle (GO:0000278)|protein folding (GO:0006457)|protein polymerization (GO:0051258)	cilium (GO:0005929)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|internode region of axon (GO:0033269)|microtubule (GO:0005874)|myelin sheath (GO:0043209)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|structural constituent of cytoskeleton (GO:0005200)	p.A411A(2)									TGTTGCTCTCGGCCTCGGTGA	0.622																																					p.A411A												.	.	2	Substitution - coding silent(2)	large_intestine(1)|lung(1)	c.C1233T	19						.	G		0,4406		0,0,2203	126.0	113.0	118.0		1233	0.8	1.0	19	dbSNP_134	118	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	TUBB4	NM_006087.2		0,1,6502	AA,AG,GG		0.0116,0.0,0.0077		411/445	6495277	1,13005	2203	4300	6503	6446277	SO:0001819	synonymous_variant	10382	exon4			AK075307	CCDS12168.1	19p13.3	2014-02-05	2011-10-11	2011-10-10	ENSG00000104833	ENSG00000104833		"""Tubulins"""	20774	protein-coding gene	gene with protein product	"""class IVa beta-tubulin"""	602662	"""tubulin, beta 4"", ""tubulin, beta 4 class IVa"", ""dystonia 4, torsion (autosomal dominant)"""	TUBB4, DYT4		6865944, 6462917, 23595291	Standard	NM_001289123		Approved	beta-5	uc002mfg.1	P04350		ENST00000264071.2:c.1233C>T	19.37:g.6495277G>A		Somatic		Capture	Illumina HiSeq	Phase_I	6446277	NM_006087	B3KQP4|Q969E5	Silent	SNP	ENST00000264071.2	37	CCDS12168.1																																																																																				0.622	TUBB4A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457841.1	NM_006087	
SH2D3A	10045	broad.mit.edu	37	19	6760878	6760878	+	Missense_Mutation	SNP	G	G	A	rs535033168		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr19:6760878G>A	ENST00000245908.6	-	3	459	c.190C>T	c.(190-192)Cgt>Tgt	p.R64C	SH2D3A_ENST00000599563.1_5'UTR|SH2D3A_ENST00000437152.3_Intron	NM_005490.2	NP_005481.2	Q9BRG2	SH23A_HUMAN	SH2 domain containing 3A	64	SH2. {ECO:0000255|PROSITE- ProRule:PRU00191}.				JNK cascade (GO:0007254)|positive regulation of signal transduction (GO:0009967)|small GTPase mediated signal transduction (GO:0007264)		guanyl-nucleotide exchange factor activity (GO:0005085)|SH3/SH2 adaptor activity (GO:0005070)	p.R64C(1)		breast(3)|endometrium(3)|kidney(1)|large_intestine(4)|lung(9)|skin(3)|urinary_tract(1)	24						AGGGCCACACGGAACACCTCA	0.627																																					p.R64C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C190T	19						.						43.0	43.0	43.0					19																	6760878		2203	4299	6502	6711878	SO:0001583	missense	10045	exon3			AF124249	CCDS12173.1	19p13.3	2013-02-14	2002-01-14			ENSG00000125731		"""SH2 domain containing"""	16885	protein-coding gene	gene with protein product		604721	"""SH2 domain-containing 3A"""			10187783	Standard	NM_005490		Approved	NSP1	uc002mft.3	Q9BRG2		ENST00000245908.6:c.190C>T	19.37:g.6760878G>A	ENSP00000245908:p.Arg64Cys	Somatic		Capture	Illumina HiSeq	Phase_I	6711878	NM_005490	A8K9R6|B4DRS7|Q9Y2X4	Missense_Mutation	SNP	ENST00000245908.6	37	CCDS12173.1	.	.	.	.	.	.	.	.	.	.	G	13.07	2.128636	0.37533	.	.	ENSG00000125731	ENST00000245908	D	0.89123	-2.47	4.97	2.86	0.33363	SH2 motif (4);	0.000000	0.43416	D	0.000564	D	0.83815	0.5336	L	0.60957	1.885	0.09310	N	0.999992	B	0.22346	0.068	B	0.17722	0.019	T	0.75918	-0.3148	10	0.87932	D	0	-2.8553	5.1445	0.14977	0.1828:0.1705:0.6467:0.0	.	64	Q9BRG2	SH23A_HUMAN	C	64	ENSP00000245908:R64C	ENSP00000245908:R64C	R	-	1	0	SH2D3A	6711878	0.198000	0.23374	0.832000	0.32986	0.801000	0.45260	1.142000	0.31540	0.707000	0.31934	0.555000	0.69702	CGT		0.627	SH2D3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458016.1	NM_005490	
VAV1	7409	broad.mit.edu	37	19	6822293	6822293	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr19:6822293G>A	ENST00000602142.1	+	5	593	c.511G>A	c.(511-513)Gac>Aac	p.D171N	VAV1_ENST00000539284.1_Missense_Mutation_p.D106N|VAV1_ENST00000596764.1_Missense_Mutation_p.D171N|VAV1_ENST00000599806.1_Missense_Mutation_p.D116N|VAV1_ENST00000304076.2_Missense_Mutation_p.D171N	NM_005428.3	NP_005419.2	P15498	VAV_HUMAN	vav 1 guanine nucleotide exchange factor	171					apoptotic signaling pathway (GO:0097190)|blood coagulation (GO:0007596)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|G-protein coupled receptor signaling pathway (GO:0007186)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|neurotrophin TRK receptor signaling pathway (GO:0048011)|neutrophil chemotaxis (GO:0030593)|phosphatidylinositol-mediated signaling (GO:0048015)|platelet activation (GO:0030168)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|reactive oxygen species metabolic process (GO:0072593)|regulation of Rac GTPase activity (GO:0032314)|regulation of small GTPase mediated signal transduction (GO:0051056)|regulation of transcription, DNA-templated (GO:0006355)|small GTPase mediated signal transduction (GO:0007264)|T cell activation (GO:0042110)|T cell costimulation (GO:0031295)	cell-cell junction (GO:0005911)|cytosol (GO:0005829)|plasma membrane (GO:0005886)	guanyl-nucleotide exchange factor activity (GO:0005085)|metal ion binding (GO:0046872)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.D171N(1)		biliary_tract(1)|breast(3)|central_nervous_system(2)|endometrium(3)|kidney(5)|large_intestine(16)|lung(18)|ovary(5)|prostate(2)|skin(5)|upper_aerodigestive_tract(2)	62						GGCGGAAGGCGACGAGATCTA	0.667																																					p.D171N												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G511A	19						.						111.0	81.0	91.0					19																	6822293		2201	4297	6498	6773293	SO:0001583	missense	7409	exon5				CCDS12174.1, CCDS59341.1, CCDS59342.1	19p13.2	2013-02-14	2007-07-25			ENSG00000141968		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"", ""SH2 domain containing"""	12657	protein-coding gene	gene with protein product		164875	"""vav 1 oncogene"""	VAV		9438848	Standard	NM_005428		Approved		uc010xjh.2	P15498		ENST00000602142.1:c.511G>A	19.37:g.6822293G>A	ENSP00000472929:p.Asp171Asn	Somatic		Capture	Illumina HiSeq	Phase_I	6773293	NM_005428	B4DVK9|M0QXX6|Q15860	Missense_Mutation	SNP	ENST00000602142.1	37	CCDS12174.1	.	.	.	.	.	.	.	.	.	.	G	14.70	2.613661	0.46631	.	.	ENSG00000141968	ENST00000304076;ENST00000539284	T;T	0.58210	1.31;0.35	4.17	4.17	0.49024	Dbl homology (DH) domain (1);Calponin homology domain (1);	0.065161	0.64402	D	0.000017	T	0.34366	0.0895	L	0.35854	1.095	0.49798	D	0.999823	P;B;B;B	0.37061	0.58;0.186;0.027;0.012	B;B;B;B	0.26094	0.066;0.047;0.04;0.024	T	0.21724	-1.0237	10	0.39692	T	0.17	.	8.0479	0.30559	0.1105:0.0:0.8895:0.0	.	106;171;116;171	F5H5P4;B2R8B5;Q96D37;P15498	.;.;.;VAV_HUMAN	N	171;106	ENSP00000302269:D171N;ENSP00000443242:D106N	ENSP00000302269:D171N	D	+	1	0	VAV1	6773293	1.000000	0.71417	0.730000	0.30809	0.927000	0.56198	6.276000	0.72601	2.323000	0.78572	0.563000	0.77884	GAC		0.667	VAV1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458475.1		
INSR	3643	broad.mit.edu	37	19	7267488	7267488	+	Silent	SNP	A	A	G			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr19:7267488A>G	ENST00000302850.5	-	2	662	c.520T>C	c.(520-522)Ttg>Ctg	p.L174L	INSR_ENST00000341500.5_Silent_p.L174L	NM_000208.2	NP_000199.2	P06213	INSR_HUMAN	insulin receptor	174	Leu-rich.				activation of MAPK activity (GO:0000187)|activation of protein kinase activity (GO:0032147)|activation of protein kinase B activity (GO:0032148)|carbohydrate metabolic process (GO:0005975)|cellular response to growth factor stimulus (GO:0071363)|cellular response to insulin stimulus (GO:0032869)|epidermis development (GO:0008544)|exocrine pancreas development (GO:0031017)|G-protein coupled receptor signaling pathway (GO:0007186)|glucose homeostasis (GO:0042593)|heart morphogenesis (GO:0003007)|insulin receptor signaling pathway (GO:0008286)|male sex determination (GO:0030238)|peptidyl-tyrosine autophosphorylation (GO:0038083)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of developmental growth (GO:0048639)|positive regulation of DNA replication (GO:0045740)|positive regulation of glucose import (GO:0046326)|positive regulation of glycogen biosynthetic process (GO:0045725)|positive regulation of glycolytic process (GO:0045821)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mitosis (GO:0045840)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of respiratory burst (GO:0060267)|protein autophosphorylation (GO:0046777)|protein heterotetramerization (GO:0051290)|regulation of embryonic development (GO:0045995)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction by phosphorylation (GO:0023014)|transformation of host cell by virus (GO:0019087)	caveola (GO:0005901)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|insulin receptor complex (GO:0005899)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|GTP binding (GO:0005525)|insulin binding (GO:0043559)|insulin receptor substrate binding (GO:0043560)|insulin-activated receptor activity (GO:0005009)|insulin-like growth factor I binding (GO:0031994)|insulin-like growth factor II binding (GO:0031995)|insulin-like growth factor receptor binding (GO:0005159)|phosphatidylinositol 3-kinase binding (GO:0043548)|protein tyrosine kinase activity (GO:0004713)|PTB domain binding (GO:0051425)|receptor signaling protein tyrosine kinase activity (GO:0004716)	p.L174L(1)		breast(1)|central_nervous_system(4)|endometrium(6)|kidney(2)|large_intestine(13)|lung(25)|ovary(4)|prostate(4)|skin(3)|stomach(2)|urinary_tract(2)	66					"""""""Insulin(DB00071)|""""Insulin(DB08914)|Insulin Aspart(DB01306)|Insulin Detemir(DB01307)|Insulin Glargine(DB00047)|Insulin Glulisine(DB01309)|Insulin Lispro(DB00046)|Insulin Regular(DB00030)|Mecasermin(DB01277)"""	TCTTTGTTCAACACGATGTAA	0.542																																					p.L174L												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.T520C	19						.						167.0	130.0	143.0					19																	7267488		2203	4300	6503	7218488	SO:0001819	synonymous_variant	3643	exon2			M10051	CCDS12176.1, CCDS42487.1	19p13.3-p13.2	2013-02-11				ENSG00000171105		"""CD molecules"", ""Fibronectin type III domain containing"""	6091	protein-coding gene	gene with protein product		147670				2983222	Standard	NM_000208		Approved	CD220	uc002mgd.1	P06213		ENST00000302850.5:c.520T>C	19.37:g.7267488A>G		Somatic		Capture	Illumina HiSeq	Phase_I	7218488	NM_000208	Q17RW0|Q59H98|Q9UCB7|Q9UCB8|Q9UCB9	Silent	SNP	ENST00000302850.5	37	CCDS12176.1																																																																																				0.542	INSR-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000458544.1		
ARHGEF18	23370	broad.mit.edu	37	19	7509252	7509252	+	Missense_Mutation	SNP	G	G	A	rs146605267		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr19:7509252G>A	ENST00000359920.6	+	4	1212	c.959G>A	c.(958-960)cGg>cAg	p.R320Q	ARHGEF18_ENST00000319670.9_Missense_Mutation_p.R162Q|CTD-2207O23.3_ENST00000593531.1_Missense_Mutation_p.G278S	NM_001130955.1	NP_001124427.1	Q6ZSZ5	ARHGI_HUMAN	Rho/Rac guanine nucleotide exchange factor (GEF) 18	320	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.				actin cytoskeleton organization (GO:0030036)|apoptotic signaling pathway (GO:0097190)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|regulation of cell shape (GO:0008360)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|transforming growth factor beta receptor signaling pathway (GO:0007179)	apical part of cell (GO:0045177)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytosol (GO:0005829)	guanyl-nucleotide exchange factor activity (GO:0005085)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)	p.R162Q(1)		central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(6)|lung(4)|ovary(2)|prostate(2)|stomach(1)|urinary_tract(1)	23		Renal(5;0.0902)				TTCCTCGCTCGGCTCAAGGAG	0.637																																					p.R162Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G485A	19						.	G	GLN/ARG,GLN/ARG	2,4404	4.2+/-10.8	0,2,2201	52.0	52.0	52.0		959,485	3.9	0.9	19	dbSNP_134	52	0,8600		0,0,4300	yes	missense,missense	ARHGEF18	NM_001130955.1,NM_015318.3	43,43	0,2,6501	AA,AG,GG		0.0,0.0454,0.0154	possibly-damaging,possibly-damaging	320/1174,162/1016	7509252	2,13004	2203	4300	6503	7415252	SO:0001583	missense	23370	exon5			AK074372	CCDS12177.1, CCDS45946.1	19p13.3	2013-01-10	2009-06-12			ENSG00000104880		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	17090	protein-coding gene	gene with protein product	"""Rho-specific guanine nucleotide exchange factor p114"""		"""rho/rac guanine nucleotide exchange factor (GEF) 18"""			9628581, 11318610	Standard	NM_015318		Approved	P114-RhoGEF, KIAA0521, MGC15913	uc002mgi.3	Q6ZSZ5		ENST00000359920.6:c.959G>A	19.37:g.7509252G>A	ENSP00000352995:p.Arg320Gln	Somatic		Capture	Illumina HiSeq	Phase_I	7415252	NM_015318	A8MV62|B5ME81|O60274|Q6DD92	Missense_Mutation	SNP	ENST00000359920.6	37	CCDS45946.1	.	.	.	.	.	.	.	.	.	.	G	13.63	2.294742	0.40594	4.54E-4	0.0	ENSG00000104880	ENST00000319670;ENST00000359920	T;T	0.62232	0.04;0.04	5.0	3.94	0.45596	Dbl homology (DH) domain (5);	0.247838	0.28828	N	0.014010	T	0.38506	0.1043	N	0.16233	0.39	0.52099	D	0.999944	P	0.38582	0.638	B	0.29785	0.107	T	0.19321	-1.0309	10	0.13108	T	0.6	-22.1011	12.4961	0.55929	0.0:0.0:0.8317:0.1683	.	320	Q6ZSZ5	ARHGI_HUMAN	Q	162;320	ENSP00000319200:R162Q;ENSP00000352995:R320Q	ENSP00000319200:R162Q	R	+	2	0	ARHGEF18	7415252	0.769000	0.28531	0.852000	0.33557	0.320000	0.28249	3.658000	0.54482	1.076000	0.40961	-0.314000	0.08810	CGG		0.637	ARHGEF18-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000436340.1	NM_015318	
MYO1F	4542	broad.mit.edu	37	19	8616651	8616651	+	Silent	SNP	G	G	A	rs201115094		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr19:8616651G>A	ENST00000338257.8	-	8	1011	c.744C>T	c.(742-744)gaC>gaT	p.D248D	AC092316.1_ENST00000598703.1_RNA	NM_012335.3	NP_036467.2	O00160	MYO1F_HUMAN	myosin IF	248	Myosin motor.				defense response to Gram-positive bacterium (GO:0050830)|negative regulation of cell adhesion (GO:0007162)|neutrophil degranulation (GO:0043312)|positive regulation of cell migration (GO:0030335)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of innate immune response (GO:0045088)	cortical actin cytoskeleton (GO:0030864)|filamentous actin (GO:0031941)|unconventional myosin complex (GO:0016461)	actin binding (GO:0003779)|ATP binding (GO:0005524)|motor activity (GO:0003774)	p.D248D(1)		breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(6)|large_intestine(7)|lung(13)|ovary(3)|prostate(3)|skin(3)|urinary_tract(1)	42						CGCTTCTGTCGTCCGTGCCGT	0.582													G|||	1	0.000199681	0.0	0.0	5008	,	,		17447	0.0		0.0	False		,,,				2504	0.001				p.D248D												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C744T	19						.	G		0,4126		0,0,2063	140.0	143.0	142.0		744	-0.7	1.0	19		142	5,8393		0,5,4194	no	coding-synonymous	MYO1F	NM_012335.3		0,5,6257	AA,AG,GG		0.0595,0.0,0.0399		248/1099	8616651	5,12519	2063	4199	6262	8522651	SO:0001819	synonymous_variant	4542	exon8			X98411	CCDS42494.1	19p13.3-p13.2	2011-09-27			ENSG00000142347	ENSG00000142347		"""Myosins / Myosin superfamily : Class I"""	7600	protein-coding gene	gene with protein product		601480				9119401, 8884266	Standard	NM_012335		Approved		uc002mkg.3	O00160	OTTHUMG00000156005	ENST00000338257.8:c.744C>T	19.37:g.8616651G>A		Somatic		Capture	Illumina HiSeq	Phase_I	8522651	NM_012335	Q8WWN7	Silent	SNP	ENST00000338257.8	37	CCDS42494.1																																																																																				0.582	MYO1F-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342716.2		
MUC16	94025	broad.mit.edu	37	19	9017354	9017354	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr19:9017354T>C	ENST00000397910.4	-	26	38173	c.37970A>G	c.(37969-37971)tAt>tGt	p.Y12657C		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	12659	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.Y12657C(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						ACCATTGACATAGAGACTGTT	0.572																																					p.Y12657C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A37970G	19						.						190.0	174.0	179.0					19																	9017354		1964	4159	6123	8878354	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.37970A>G	19.37:g.9017354T>C	ENSP00000381008:p.Tyr12657Cys	Somatic		Capture	Illumina HiSeq	Phase_I	8878354	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	.	.	.	.	.	.	.	.	.	.	.	2.977	-0.211259	0.06140	.	.	ENSG00000181143	ENST00000397910	T	0.23147	1.92	3.26	3.26	0.37387	.	.	.	.	.	T	0.47783	0.1464	M	0.79123	2.44	.	.	.	D	0.89917	1.0	D	0.78314	0.991	T	0.61628	-0.7024	8	0.87932	D	0	.	8.2502	0.31712	0.0:0.0:0.0:1.0	.	12657	B5ME49	.	C	12657	ENSP00000381008:Y12657C	ENSP00000381008:Y12657C	Y	-	2	0	MUC16	8878354	0.788000	0.28762	0.433000	0.26760	0.324000	0.28378	0.900000	0.28431	1.243000	0.43853	0.329000	0.21502	TAT		0.572	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
ZNF773	374928	broad.mit.edu	37	19	58018494	58018494	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr19:58018494C>A	ENST00000282292.4	+	4	1171	c.1031C>A	c.(1030-1032)tCc>tAc	p.S344Y	ZNF773_ENST00000599847.1_Intron|ZNF773_ENST00000593916.1_Intron|ZNF773_ENST00000598770.1_Missense_Mutation_p.S343Y	NM_198542.1	NP_940944.1	Q6PK81	ZN773_HUMAN	zinc finger protein 773	344					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.S344Y(1)		breast(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(6)|ovary(1)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	22		Colorectal(82;0.000256)|all_neural(62;0.0577)|Ovarian(87;0.221)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0254)		AGCCACAAGTCCAGCCTTATC	0.418																																					p.S344Y												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1031A	19						.						103.0	106.0	105.0					19																	58018494		2203	4300	6503	62710306	SO:0001583	missense	374928	exon4			BC005167	CCDS33134.1	19q13.43	2013-01-08	2006-12-15	2006-12-15		ENSG00000152439		"""Zinc fingers, C2H2-type"", ""-"""	30487	protein-coding gene	gene with protein product			"""zinc finger protein 419B"""	ZNF419B		12477932	Standard	NM_198542		Approved	MGC4728	uc002qox.3	Q6PK81		ENST00000282292.4:c.1031C>A	19.37:g.58018494C>A	ENSP00000282292:p.Ser344Tyr	Somatic		Capture	Illumina HiSeq	Phase_I	62710306	NM_198542	Q96DL8	Missense_Mutation	SNP	ENST00000282292.4	37	CCDS33134.1	.	.	.	.	.	.	.	.	.	.	C	11.73	1.727057	0.30593	.	.	ENSG00000152439	ENST00000282292	T	0.07567	3.18	1.24	1.24	0.21308	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.25121	0.0610	M	0.75085	2.285	0.09310	N	1	D;D	0.71674	0.997;0.998	D;D	0.78314	0.915;0.991	T	0.02925	-1.1093	9	0.54805	T	0.06	.	10.0353	0.42125	0.0:1.0:0.0:0.0	.	343;344	Q6PK81-2;Q6PK81	.;ZN773_HUMAN	Y	344	ENSP00000282292:S344Y	ENSP00000282292:S344Y	S	+	2	0	ZNF773	62710306	0.000000	0.05858	0.003000	0.11579	0.945000	0.59286	-2.781000	0.00773	0.987000	0.38709	0.305000	0.20034	TCC		0.418	ZNF773-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000466475.1	NM_198542	
RRAGC	64121	broad.mit.edu	37	1	39325151	39325152	+	Frame_Shift_Ins	INS	-	-	C			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	-	-					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr1:39325151_39325152insC	ENST00000373001.3	-	1	343_344	c.167_168insG	c.(166-168)ggcfs	p.G56fs	RP5-864K19.4_ENST00000433671.2_RNA|RP5-864K19.4_ENST00000456813.1_RNA	NM_022157.2	NP_071440.1			Ras-related GTP binding C									p.A57fs*2(1)		endometrium(1)|kidney(1)|large_intestine(5)|lung(2)|ovary(1)	10	Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0393)				AGCTGTCAGCGCCCCCCGGACC	0.718																																					p.G56fs												.	.	1	Insertion - Frameshift(1)	large_intestine(1)	c.168_169insG	1						.																																			39097739	SO:0001589	frameshift_variant	64121	exon1			AF323609	CCDS430.1	1p34	2008-02-05			ENSG00000116954	ENSG00000116954			19902	protein-coding gene	gene with protein product		608267				11073942	Standard	NM_022157		Approved	GTR2, FLJ13311	uc001ccq.3	Q9HB90	OTTHUMG00000000490	ENST00000373001.3:c.168dupG	1.37:g.39325157_39325157dupC	ENSP00000362092:p.Gly56fs	Somatic		Capture	Illumina HiSeq	Phase_I	39097738	NM_022157		Frame_Shift_Ins	INS	ENST00000373001.3	37	CCDS430.1																																																																																				0.718	RRAGC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001222.2	NM_022157	
EXTL2	2135	broad.mit.edu	37	1	101343115	101343115	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr1:101343115T>C	ENST00000370114.3	-	3	1786	c.350A>G	c.(349-351)cAc>cGc	p.H117R	EXTL2_ENST00000370113.3_Missense_Mutation_p.H117R|EXTL2_ENST00000535414.1_Missense_Mutation_p.H104R	NM_001033025.2|NM_001261440.1	NP_001028197.1|NP_001248369.1	Q9UBQ6	EXTL2_HUMAN	exostosin-like glycosyltransferase 2	117					heparan sulfate proteoglycan biosynthetic process (GO:0015012)|N-acetylglucosamine metabolic process (GO:0006044)|UDP-N-acetylgalactosamine metabolic process (GO:0019276)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|intrinsic component of endoplasmic reticulum membrane (GO:0031227)	alpha-1,4-N-acetylgalactosaminyltransferase activity (GO:0035248)|glucuronyl-galactosyl-proteoglycan 4-alpha-N-acetylglucosaminyltransferase activity (GO:0001888)|metal ion binding (GO:0046872)	p.H117R(1)|p.H125R(1)		haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(4)|skin(1)|urinary_tract(1)	14		all_epithelial(167;2.48e-06)|all_lung(203;0.000414)|Lung NSC(277;0.000946)		Epithelial(280;0.0425)|all cancers(265;0.0628)|COAD - Colon adenocarcinoma(174;0.148)|Colorectal(144;0.167)|Lung(183;0.195)		AGGGATAGGGTGGGGCCCTAG	0.438																																					p.H117R												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.A350G	1						.						114.0	114.0	114.0					1																	101343115		2203	4299	6502	101115703	SO:0001583	missense	2135	exon3			U76189	CCDS775.1, CCDS72831.1	1p21	2013-03-01	2013-03-01		ENSG00000162694	ENSG00000162694	2.4.1.223	"""Exostosin glycosyltransferase family"""	3516	protein-coding gene	gene with protein product	"""alpha-1,4-N-acteylhexosaminyltransferase"""	602411	"""exostoses (multiple)-like 2"""			9450183, 15831490	Standard	NM_001439		Approved		uc001dtk.2	Q9UBQ6	OTTHUMG00000011814	ENST00000370114.3:c.350A>G	1.37:g.101343115T>C	ENSP00000359132:p.His117Arg	Somatic		Capture	Illumina HiSeq	Phase_I	101115703	NM_001033025	B2R795|D3DT60	Missense_Mutation	SNP	ENST00000370114.3	37	CCDS775.1	.	.	.	.	.	.	.	.	.	.	T	25.4	4.631019	0.87660	.	.	ENSG00000162694	ENST00000370114;ENST00000370113;ENST00000535414;ENST00000450240;ENST00000416479	T;T;T;T;T	0.76578	-1.03;-1.03;-1.03;-1.03;-1.03	5.61	5.61	0.85477	EXTL2, alpha-1,4-N-acetylhexosaminyltransferase (1);	0.000000	0.85682	D	0.000000	T	0.81735	0.4885	L	0.49571	1.57	0.80722	D	1	D;D	0.89917	0.999;1.0	D;D	0.71414	0.973;0.973	D	0.83779	0.0224	10	0.62326	D	0.03	-25.7784	16.1025	0.81194	0.0:0.0:0.0:1.0	.	117;117	Q8N8F1;Q9UBQ6	.;EXTL2_HUMAN	R	117;117;104;125;104	ENSP00000359132:H117R;ENSP00000359131:H117R;ENSP00000444385:H104R;ENSP00000403363:H125R;ENSP00000392255:H104R	ENSP00000359131:H117R	H	-	2	0	EXTL2	101115703	1.000000	0.71417	1.000000	0.80357	0.931000	0.56810	7.655000	0.83696	2.254000	0.74563	0.533000	0.62120	CAC		0.438	EXTL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032705.1	NM_001439	
PRMT6	55170	broad.mit.edu	37	1	107600334	107600334	+	Nonsense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr1:107600334C>T	ENST00000370078.1	+	1	1034	c.997C>T	c.(997-999)Caa>Taa	p.Q333*	PRMT6_ENST00000361318.5_Nonsense_Mutation_p.Q274*			Q96LA8	ANM6_HUMAN	protein arginine methyltransferase 6	333	SAM-dependent MTase PRMT-type. {ECO:0000255|PROSITE-ProRule:PRU01015}.				base-excision repair (GO:0006284)|histone H3-R2 methylation (GO:0034970)|histone H4-R3 methylation (GO:0043985)|histone methylation (GO:0016571)|negative regulation of transcription, DNA-templated (GO:0045892)|peptidyl-arginine methylation, to asymmetrical-dimethyl arginine (GO:0019919)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	cytosol (GO:0005829)|nucleus (GO:0005634)	histone binding (GO:0042393)|histone methyltransferase activity (GO:0042054)|histone methyltransferase activity (H2A-R3 specific) (GO:0070612)|histone methyltransferase activity (H3-R2 specific) (GO:0070611)|histone methyltransferase activity (H4-R3 specific) (GO:0044020)|protein-arginine omega-N asymmetric methyltransferase activity (GO:0035242)|protein-arginine omega-N monomethyltransferase activity (GO:0035241)	p.Q274*(1)		biliary_tract(1)|breast(2)|kidney(1)|large_intestine(4)|lung(5)|urinary_tract(1)	14		all_epithelial(167;0.000429)|all_lung(203;0.00122)|Lung NSC(277;0.00185)		Lung(183;0.0305)|Epithelial(280;0.0765)|Colorectal(144;0.0998)|all cancers(265;0.14)|LUSC - Lung squamous cell carcinoma(189;0.173)|BRCA - Breast invasive adenocarcinoma(282;0.242)		GCAAGTGGAGCAAGACACGGA	0.632																																					p.Q333X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.C997T	1						.						38.0	42.0	41.0					1																	107600334		1993	4164	6157	107401857	SO:0001587	stop_gained	55170	exon1			AK001421	CCDS41360.1, CCDS41360.2	1p13.2	2008-02-05	2006-02-16	2006-02-16	ENSG00000198890	ENSG00000198890		"""Protein arginine methyltransferases"""	18241	protein-coding gene	gene with protein product		608274	"""HMT1 hnRNP methyltransferase-like 6 (S. cerevisiae)"""	HRMT1L6		11724789	Standard	NM_018137		Approved	FLJ10559	uc010ous.2	Q96LA8	OTTHUMG00000010964	ENST00000370078.1:c.997C>T	1.37:g.107600334C>T	ENSP00000359095:p.Gln333*	Somatic		Capture	Illumina HiSeq	Phase_I	107401857	NM_018137	A3KME1|B4DID8|Q5T5Y5|Q6DKI4|Q9NVR8	Nonsense_Mutation	SNP	ENST00000370078.1	37	CCDS41360.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	37|37	6.160008|6.160008	0.97334|0.97334	.|.	.|.	ENSG00000198890|ENSG00000198890	ENST00000540389|ENST00000361318;ENST00000370078	.|.	.|.	.|.	5.64|5.64	5.64|5.64	0.86602|0.86602	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	T|.	0.40222|.	0.1108|.	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|.	0.30357|.	-0.9981|.	5|.	0.87932|0.09590	D|T	0|0.72	-9.012|-9.012	17.1963|17.1963	0.86893|0.86893	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|.	.|.	.|.	V|X	226|274;333	.|.	ENSP00000440829:A226V|ENSP00000355145:Q274X	A|Q	+|+	2|1	0|0	PRMT6|PRMT6	107401857|107401857	1.000000|1.000000	0.71417|0.71417	0.995000|0.995000	0.50966|0.50966	0.873000|0.873000	0.50193|0.50193	4.659000|4.659000	0.61504|0.61504	2.653000|2.653000	0.90120|0.90120	0.542000|0.542000	0.68232|0.68232	GCA|CAA		0.632	PRMT6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030185.1	NM_018137	
C1orf127	148345	broad.mit.edu	37	1	11007855	11007855	+	Silent	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr1:11007855G>A	ENST00000377008.4	-	11	2282	c.1836C>T	c.(1834-1836)taC>taT	p.Y612Y	C1orf127_ENST00000377004.4_Silent_p.Y779Y			Q8N9H9	CA127_HUMAN	chromosome 1 open reading frame 127	612								p.Y612Y(1)		NS(2)|breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(7)|lung(9)|ovary(1)|prostate(2)|skin(5)	32	Ovarian(185;0.249)	Lung NSC(185;0.000226)|all_lung(284;0.000302)|Renal(390;0.000469)|Colorectal(325;0.0062)|Breast(348;0.0139)|Hepatocellular(190;0.0305)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0731)	STAD - Stomach adenocarcinoma(5;0.0224)	UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;3.71e-07)|COAD - Colon adenocarcinoma(227;7.79e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000305)|Kidney(185;0.000785)|KIRC - Kidney renal clear cell carcinoma(229;0.00262)|READ - Rectum adenocarcinoma(331;0.0509)		CCTGGAAGGGGTATTCAAGCT	0.632																																					p.Y779Y												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C2337T	1						.						28.0	29.0	29.0					1																	11007855		2203	4300	6503	10930442	SO:0001819	synonymous_variant	148345	exon12			AK094437	CCDS53267.1	1p36.22	2008-02-05			ENSG00000175262	ENSG00000175262			26730	protein-coding gene	gene with protein product						14702039	Standard	NM_001170754		Approved	FLJ37118	uc010oao.2	Q8N9H9	OTTHUMG00000002032	ENST00000377008.4:c.1836C>T	1.37:g.11007855G>A		Somatic		Capture	Illumina HiSeq	Phase_I	10930442	NM_001170754	A0AVG8|A6NKM7|Q5VXJ2	Silent	SNP	ENST00000377008.4	37		.	.	.	.	.	.	.	.	.	.	G	2.191	-0.385290	0.04966	.	.	ENSG00000175262	ENST00000418570;ENST00000520253	.	.	.	4.31	-3.71	0.04424	.	.	.	.	.	T	0.21761	0.0524	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.32955	-0.9887	4	.	.	.	0.1261	5.3846	0.16211	0.3283:0.4402:0.2315:0.0	.	.	.	.	I	614;731	.	.	T	-	2	0	C1orf127	10930442	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	-0.682000	0.05185	-0.472000	0.06881	-0.229000	0.12294	ACC		0.632	C1orf127-202	KNOWN	basic	protein_coding	protein_coding		NM_173507	
VAV3	10451	broad.mit.edu	37	1	108507337	108507337	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr1:108507337G>A	ENST00000370056.4	-	1	429	c.155C>T	c.(154-156)gCg>gTg	p.A52V	VAV3-AS1_ENST00000438318.1_RNA|VAV3_ENST00000371846.4_5'UTR|VAV3_ENST00000527011.1_Missense_Mutation_p.A52V	NM_006113.4	NP_006104.4	Q9UKW4	VAV3_HUMAN	vav 3 guanine nucleotide exchange factor	52	CH. {ECO:0000255|PROSITE- ProRule:PRU00044}.				angiogenesis (GO:0001525)|apoptotic signaling pathway (GO:0097190)|B cell receptor signaling pathway (GO:0050853)|blood coagulation (GO:0007596)|cellular response to DNA damage stimulus (GO:0006974)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|lamellipodium assembly (GO:0030032)|neurotrophin TRK receptor signaling pathway (GO:0048011)|neutrophil chemotaxis (GO:0030593)|platelet activation (GO:0030168)|positive regulation of apoptotic process (GO:0043065)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of cell adhesion (GO:0045785)|positive regulation of GTPase activity (GO:0043547)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of signal transduction (GO:0009967)|regulation of Rac GTPase activity (GO:0032314)|regulation of small GTPase mediated signal transduction (GO:0051056)|response to drug (GO:0042493)|small GTPase mediated signal transduction (GO:0007264)|vesicle fusion (GO:0006906)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	GTPase activator activity (GO:0005096)|guanyl-nucleotide exchange factor activity (GO:0005085)|metal ion binding (GO:0046872)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)|SH3/SH2 adaptor activity (GO:0005070)	p.A52V(1)		NS(2)|breast(5)|endometrium(4)|kidney(2)|large_intestine(14)|lung(20)|ovary(6)|prostate(3)|stomach(1)|urinary_tract(1)	58		all_epithelial(167;5.38e-05)|all_lung(203;0.000314)|Lung NSC(277;0.000594)		Colorectal(144;0.0331)|Lung(183;0.128)|Epithelial(280;0.204)		GATGGAGTGCGCCCGGAGGTT	0.647																																					p.A52V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C155T	1						.						51.0	51.0	51.0					1																	108507337		2203	4300	6503	108308860	SO:0001583	missense	10451	exon1			AF118886	CCDS785.1, CCDS44181.1	1p13.3	2013-02-14	2007-07-25		ENSG00000134215	ENSG00000134215		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"", ""SH2 domain containing"""	12659	protein-coding gene	gene with protein product		605541	"""vav 3 oncogene"""				Standard	NM_001079874		Approved		uc001dvk.1	Q9UKW4	OTTHUMG00000010995	ENST00000370056.4:c.155C>T	1.37:g.108507337G>A	ENSP00000359073:p.Ala52Val	Somatic		Capture	Illumina HiSeq	Phase_I	108308860	NM_006113	B1AMM0|B1APV5|B4E232|B7ZLR1|E9PQ97|O60498|O95230|Q9Y5X8	Missense_Mutation	SNP	ENST00000370056.4	37	CCDS785.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	19.02|19.02	3.746604|3.746604	0.69418|0.69418	.|.	.|.	ENSG00000134215|ENSG00000134215	ENST00000370056;ENST00000527011|ENST00000490388	T;T|.	0.59502|.	0.26;0.26|.	5.05|5.05	4.11|4.11	0.48088|0.48088	Calponin homology domain (5);|.	0.334636|.	0.27262|.	N|.	0.020177|.	T|T	0.49695|0.49695	0.1572|0.1572	L|L	0.51914|0.51914	1.62|1.62	0.80722|0.80722	D|D	1|1	B;B;B|.	0.24963|.	0.093;0.115;0.099|.	B;B;B|.	0.24006|.	0.011;0.025;0.05|.	T|T	0.47433|0.47433	-0.9118|-0.9118	10|5	0.87932|.	D|.	0|.	.|.	11.381|11.381	0.49757|0.49757	0.0:0.3893:0.6107:0.0|0.0:0.3893:0.6107:0.0	.|.	52;52;52|.	B7ZLR1;E9PQ97;Q9UKW4|.	.;.;VAV3_HUMAN|.	V|C	52|47	ENSP00000359073:A52V;ENSP00000432540:A52V|.	ENSP00000359073:A52V|.	A|R	-|-	2|1	0|0	VAV3|VAV3	108308860|108308860	0.906000|0.906000	0.30813|0.30813	1.000000|1.000000	0.80357|0.80357	0.992000|0.992000	0.81027|0.81027	1.699000|1.699000	0.37804|0.37804	2.388000|2.388000	0.81334|0.81334	0.456000|0.456000	0.33151|0.33151	GCG|CGC		0.647	VAV3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030242.2	NM_006113	
TAF13	6884	broad.mit.edu	37	1	109607295	109607295	+	Silent	SNP	A	A	G			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr1:109607295A>G	ENST00000338366.5	-	4	279	c.225T>C	c.(223-225)atT>atC	p.I75I		NM_005645.3	NP_005636.1	Q15543	TAF13_HUMAN	TAF13 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 18kDa	75					DNA-templated transcription, initiation (GO:0006352)|gene expression (GO:0010467)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor TFIID complex (GO:0005669)	DNA binding (GO:0003677)|protein C-terminus binding (GO:0008022)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.I75I(1)		endometrium(1)|large_intestine(1)|lung(1)	3		all_epithelial(167;0.000102)|all_lung(203;0.000321)|Lung NSC(277;0.000626)		Colorectal(144;0.0138)|Lung(183;0.0425)|COAD - Colon adenocarcinoma(174;0.113)|Epithelial(280;0.166)|all cancers(265;0.191)|LUSC - Lung squamous cell carcinoma(189;0.228)		CTTGTCTTCCAATTGACATTG	0.318																																					p.I75I												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.T225C	1						.						180.0	189.0	186.0					1																	109607295		2203	4296	6499	109408818	SO:0001819	synonymous_variant	6884	exon4			XM_496381	CCDS30788.1	1p13.3	2010-04-22	2002-08-29	2001-12-07	ENSG00000197780	ENSG00000197780			11546	protein-coding gene	gene with protein product		600774	"""TATA box binding protein (TBP)-associated factor, RNA polymerase II, K, 18kD"""	TAF2K		7729427	Standard	NM_005645		Approved	TAFII18	uc001dwm.1	Q15543	OTTHUMG00000042363	ENST00000338366.5:c.225T>C	1.37:g.109607295A>G		Somatic		Capture	Illumina HiSeq	Phase_I	109408818	NM_005645	B2R5E5|Q5TYV6	Silent	SNP	ENST00000338366.5	37	CCDS30788.1																																																																																				0.318	TAF13-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000100609.2	NM_005645	
SORT1	6272	broad.mit.edu	37	1	109870189	109870189	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr1:109870189G>A	ENST00000256637.6	-	12	1464	c.1406C>T	c.(1405-1407)tCc>tTc	p.S469F	SORT1_ENST00000538502.1_Missense_Mutation_p.S332F	NM_002959.5	NP_002950.3	Q99523	SORT_HUMAN	sortilin 1	469					endocytosis (GO:0006897)|endosome to lysosome transport (GO:0008333)|endosome transport via multivesicular body sorting pathway (GO:0032509)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|G-protein coupled receptor signaling pathway (GO:0007186)|glucose import (GO:0046323)|Golgi to endosome transport (GO:0006895)|multicellular organismal development (GO:0007275)|myotube differentiation (GO:0014902)|negative regulation of lipoprotein lipase activity (GO:0051005)|nerve growth factor signaling pathway (GO:0038180)|neuropeptide signaling pathway (GO:0007218)|neurotrophin TRK receptor signaling pathway (GO:0048011)|ossification (GO:0001503)|plasma membrane to endosome transport (GO:0048227)|regulation of gene expression (GO:0010468)|response to insulin (GO:0032868)|vesicle organization (GO:0016050)	cell surface (GO:0009986)|clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|cytoplasmic membrane-bounded vesicle (GO:0016023)|early endosome (GO:0005769)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|trans-Golgi network transport vesicle (GO:0030140)	enzyme binding (GO:0019899)|nerve growth factor binding (GO:0048406)|nerve growth factor receptor activity (GO:0010465)|neurotensin receptor activity, non-G-protein coupled (GO:0030379)	p.S469F(1)		NS(1)|breast(2)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(9)|lung(5)|ovary(2)|prostate(1)|skin(1)	26		all_epithelial(167;4.69e-05)|all_lung(203;0.00016)|Lung NSC(277;0.000318)|Breast(1374;0.244)		Lung(183;0.0529)|Colorectal(144;0.142)|Epithelial(280;0.145)|Kidney(133;0.169)|all cancers(265;0.184)		CAGTTTCTGGGAGATGCTGTA	0.433																																					p.S469F												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1406T	1						.						95.0	88.0	91.0					1																	109870189		2203	4300	6503	109671712	SO:0001583	missense	6272	exon12			BC023542	CCDS798.1, CCDS55618.1	1p13.3	2008-05-14			ENSG00000134243	ENSG00000134243			11186	protein-coding gene	gene with protein product		602458					Standard	NM_002959		Approved	Gp95, NT3	uc001dxm.2	Q99523	OTTHUMG00000011999	ENST00000256637.6:c.1406C>T	1.37:g.109870189G>A	ENSP00000256637:p.Ser469Phe	Somatic		Capture	Illumina HiSeq	Phase_I	109671712	NM_002959	B4DWI3|C0JYZ0|Q8IZ49	Missense_Mutation	SNP	ENST00000256637.6	37	CCDS798.1	.	.	.	.	.	.	.	.	.	.	G	17.86	3.492658	0.64074	.	.	ENSG00000134243	ENST00000256637;ENST00000538502	T;T	0.32023	1.47;1.47	5.62	5.62	0.85841	VPS10 (1);	0.121539	0.56097	D	0.000032	T	0.10594	0.0259	L	0.31926	0.97	0.58432	D	0.999999	B;P	0.46656	0.222;0.882	B;B	0.34346	0.048;0.18	T	0.07046	-1.0793	10	0.10111	T	0.7	-15.3372	18.4615	0.90739	0.0:0.0:1.0:0.0	.	332;469	B4DWI3;Q99523	.;SORT_HUMAN	F	469;332	ENSP00000256637:S469F;ENSP00000438597:S332F	ENSP00000256637:S469F	S	-	2	0	SORT1	109671712	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.045000	0.93812	2.648000	0.89879	0.650000	0.86243	TCC		0.433	SORT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033179.1	NM_002959	
AMIGO1	57463	broad.mit.edu	37	1	110051166	110051166	+	Silent	SNP	A	A	G			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr1:110051166A>G	ENST00000369864.4	-	2	718	c.369T>C	c.(367-369)cgT>cgC	p.R123R	AMIGO1_ENST00000369862.1_Silent_p.R123R					adhesion molecule with Ig-like domain 1									p.R123R(1)		autonomic_ganglia(1)|breast(2)|endometrium(1)|large_intestine(6)|lung(3)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	16		all_epithelial(167;2.83e-05)|all_lung(203;0.00016)|Lung NSC(277;0.000318)|Breast(1374;0.244)		Colorectal(144;0.0129)|Lung(183;0.0182)|Epithelial(280;0.046)|all cancers(265;0.0492)|READ - Rectum adenocarcinoma(129;0.0689)|LUSC - Lung squamous cell carcinoma(189;0.227)		CATCCAGTGTACGCAGCTGGT	0.572																																					p.R123R												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.T369C	1						.						97.0	91.0	93.0					1																	110051166		2203	4300	6503	109852689	SO:0001819	synonymous_variant	57463	exon2				CCDS30795.1	1p13.3	2013-01-11			ENSG00000181754	ENSG00000181754		"""Immunoglobulin superfamily / V-set domain containing"""	20824	protein-coding gene	gene with protein product	"""amphoterin-induced gene and open reading frame"""	615689				12629050	Standard	NM_020703		Approved	AMIGO, KIAA1163	uc001dxx.4	Q86WK6	OTTHUMG00000011653	ENST00000369864.4:c.369T>C	1.37:g.110051166A>G		Somatic		Capture	Illumina HiSeq	Phase_I	109852689	NM_020703		Silent	SNP	ENST00000369864.4	37	CCDS30795.1																																																																																				0.572	AMIGO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032247.1	NM_020703	
SRM	6723	broad.mit.edu	37	1	11116779	11116779	+	Silent	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr1:11116779G>A	ENST00000376957.2	-	4	497	c.417C>T	c.(415-417)ggC>ggT	p.G139G		NM_003132.2	NP_003123.2	P19623	SPEE_HUMAN	spermidine synthase	139	PABS.				cellular nitrogen compound metabolic process (GO:0034641)|polyamine metabolic process (GO:0006595)|small molecule metabolic process (GO:0044281)|spermidine biosynthetic process (GO:0008295)	cytosol (GO:0005829)	protein homodimerization activity (GO:0042803)|spermidine synthase activity (GO:0004766)	p.G139G(1)		large_intestine(1)|lung(1)|urinary_tract(1)	3	Ovarian(185;0.249)	Lung NSC(185;1.74e-05)|all_lung(284;2.05e-05)|Renal(390;0.000147)|Colorectal(325;0.00205)|Breast(348;0.00262)|Hepatocellular(190;0.00913)|Ovarian(437;0.00965)|Myeloproliferative disorder(586;0.0255)	STAD - Stomach adenocarcinoma(5;0.228)	UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;3.14e-07)|COAD - Colon adenocarcinoma(227;7.11e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000294)|Kidney(185;0.000728)|KIRC - Kidney renal clear cell carcinoma(229;0.00258)|READ - Rectum adenocarcinoma(331;0.0487)|STAD - Stomach adenocarcinoma(313;0.192)	S-Adenosylmethionine(DB00118)	CAATGGCCATGCCTGGCAGGA	0.567																																					p.G139G												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C417T	1						.						97.0	86.0	89.0					1																	11116779		2203	4300	6503	11039366	SO:0001819	synonymous_variant	6723	exon4			BC033106	CCDS125.1	1p36-p22	2010-11-08			ENSG00000116649	ENSG00000116649	2.5.1.16		11296	protein-coding gene	gene with protein product		182891		SRML1		2344393	Standard	NM_003132		Approved	SPS1	uc001arz.1	P19623	OTTHUMG00000002119	ENST00000376957.2:c.417C>T	1.37:g.11116779G>A		Somatic		Capture	Illumina HiSeq	Phase_I	11039366	NM_003132	B1AKP9|Q15511	Silent	SNP	ENST00000376957.2	37	CCDS125.1																																																																																				0.567	SRM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006056.1	NM_003132	
STRIP1	85369	broad.mit.edu	37	1	110582021	110582021	+	Silent	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr1:110582021G>A	ENST00000369795.3	+	5	487	c.465G>A	c.(463-465)acG>acA	p.T155T	STRIP1_ENST00000369794.2_Silent_p.T155T|STRIP1_ENST00000369796.1_Silent_p.T60T	NM_033088.3	NP_149079.2	Q5VSL9	STRP1_HUMAN	striatin interacting protein 1	155					cortical actin cytoskeleton organization (GO:0030866)|regulation of cell morphogenesis (GO:0022604)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)		p.T155T(1)									TTGCAGGCACGTTTGGGGAGT	0.587																																					p.T155T												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G465A	1						.						98.0	83.0	88.0					1																	110582021		2203	4300	6503	110383544	SO:0001819	synonymous_variant	85369	exon5			AK027649	CCDS30798.1, CCDS59197.1	1p13.3	2012-11-05	2012-11-05	2012-11-05	ENSG00000143093	ENSG00000143093			25916	protein-coding gene	gene with protein product	"""FAR11 factor arrest 11 homolog A (yeast)"""		"""family with sequence similarity 40, member A"""	FAM40A		11214970, 12588993, 22782902, 22298706, 18782753	Standard	NM_033088		Approved	FLJ14743, KIAA1761, FAR11A	uc001dza.2	Q5VSL9	OTTHUMG00000170607	ENST00000369795.3:c.465G>A	1.37:g.110582021G>A		Somatic		Capture	Illumina HiSeq	Phase_I	110383544	NM_033088	Q0V925|Q5VSL8|Q658K2|Q6ZV31|Q8N598|Q96SN2|Q9C0A2	Silent	SNP	ENST00000369795.3	37	CCDS30798.1																																																																																				0.587	STRIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032213.1	NM_033088	
CD53	963	broad.mit.edu	37	1	111435051	111435051	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr1:111435051C>A	ENST00000271324.5	+	3	260	c.148C>A	c.(148-150)Ctc>Atc	p.L50I	CD53_ENST00000429072.2_Missense_Mutation_p.L50I	NM_000560.3|NM_001040033.1	NP_000551.1|NP_001035122.1	P19397	CD53_HUMAN	CD53 molecule	50					positive regulation of myoblast fusion (GO:1901741)|signal transduction (GO:0007165)	cell surface (GO:0009986)|cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|immunological synapse (GO:0001772)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.L50I(1)		breast(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(6)	17		all_cancers(81;1.06e-05)|all_epithelial(167;1.95e-05)|all_lung(203;0.000199)|Lung NSC(277;0.000398)		Lung(183;0.0264)|Colorectal(144;0.0375)|all cancers(265;0.11)|Epithelial(280;0.114)|COAD - Colon adenocarcinoma(174;0.141)|LUSC - Lung squamous cell carcinoma(189;0.144)		CCTCCCCTCCCTCACGCTGGG	0.498																																					p.L50I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C148A	1						.						210.0	184.0	193.0					1																	111435051		2203	4300	6503	111236574	SO:0001583	missense	963	exon3			BC040693	CCDS829.1	1p13	2013-02-14	2006-03-28		ENSG00000143119	ENSG00000143119		"""CD molecules"", ""Tetraspanins"""	1686	protein-coding gene	gene with protein product		151525	"""CD53 antigen"""	MOX44		8319976	Standard	XM_006711053		Approved	TSPAN25	uc001dzw.3	P19397	OTTHUMG00000048020	ENST00000271324.5:c.148C>A	1.37:g.111435051C>A	ENSP00000271324:p.Leu50Ile	Somatic		Capture	Illumina HiSeq	Phase_I	111236574	NM_000560	B2R905|Q5U0D6	Missense_Mutation	SNP	ENST00000271324.5	37	CCDS829.1	.	.	.	.	.	.	.	.	.	.	C	17.42	3.385523	0.61956	.	.	ENSG00000143119	ENST00000429072;ENST00000271324	T;T	0.80214	-1.35;-1.35	5.93	5.93	0.95920	.	0.116963	0.34802	U	0.003666	T	0.80127	0.4566	L	0.46741	1.465	0.39421	D	0.966922	D;P	0.53619	0.961;0.91	P;P	0.52957	0.714;0.657	T	0.81807	-0.0763	10	0.66056	D	0.02	.	17.8477	0.88736	0.0:1.0:0.0:0.0	.	50;50	B4DQB5;P19397	.;CD53_HUMAN	I	50	ENSP00000412250:L50I;ENSP00000271324:L50I	ENSP00000271324:L50I	L	+	1	0	CD53	111236574	0.998000	0.40836	1.000000	0.80357	0.926000	0.56050	3.684000	0.54671	2.826000	0.97356	0.655000	0.94253	CTC		0.498	CD53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032931.1	NM_000560	
PTCHD2	57540	broad.mit.edu	37	1	11561078	11561078	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr1:11561078A>G	ENST00000294484.6	+	2	167	c.29A>G	c.(28-30)cAg>cGg	p.Q10R	PTCHD2_ENST00000389575.3_Missense_Mutation_p.Q10R	NM_020780.1	NP_065831.1	Q9P2K9	PTHD2_HUMAN	patched domain containing 2	10					cholesterol homeostasis (GO:0042632)|regulation of lipid transport (GO:0032368)|smoothened signaling pathway (GO:0007224)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|nuclear membrane (GO:0031965)	hedgehog receptor activity (GO:0008158)	p.Q227R(1)		NS(3)|breast(2)|endometrium(9)|kidney(4)|large_intestine(5)|lung(34)|ovary(3)|pancreas(1)|prostate(6)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(3)	76	Ovarian(185;0.249)	Lung NSC(185;4.16e-05)|all_lung(284;4.76e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00913)|Ovarian(437;0.00965)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;3.13e-07)|COAD - Colon adenocarcinoma(227;4.83e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000325)|Kidney(185;0.000877)|KIRC - Kidney renal clear cell carcinoma(229;0.00273)|STAD - Stomach adenocarcinoma(313;0.00766)|READ - Rectum adenocarcinoma(331;0.0549)		CCCTTGCTGCAGGATGTGTGG	0.612																																					p.Q10R												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A29G	1						.						54.0	59.0	57.0					1																	11561078		2015	4162	6177	11483665	SO:0001583	missense	57540	exon2			AB037758	CCDS41247.1	1p36.22	2010-02-17			ENSG00000204624	ENSG00000204624			29251	protein-coding gene	gene with protein product		611251				15738394	Standard	NM_020780		Approved	KIAA1337, DISP3	uc001ash.4	Q9P2K9	OTTHUMG00000002074	ENST00000294484.6:c.29A>G	1.37:g.11561078A>G	ENSP00000294484:p.Gln10Arg	Somatic		Capture	Illumina HiSeq	Phase_I	11483665	NM_020780	Q5VTU9|Q9UJD6	Missense_Mutation	SNP	ENST00000294484.6	37	CCDS41247.1	.	.	.	.	.	.	.	.	.	.	A	23.0	4.365632	0.82463	.	.	ENSG00000204624	ENST00000294484;ENST00000389575	T;T	0.25414	1.8;1.8	5.78	5.78	0.91487	.	0.343259	0.23413	U	0.048454	T	0.39091	0.1065	L	0.29908	0.895	0.54753	D	0.999981	D	0.60160	0.987	D	0.67725	0.953	T	0.21895	-1.0232	10	0.72032	D	0.01	-18.2547	15.2958	0.73906	1.0:0.0:0.0:0.0	.	10	Q9P2K9	PTHD2_HUMAN	R	10	ENSP00000294484:Q10R;ENSP00000374226:Q10R	ENSP00000294484:Q10R	Q	+	2	0	PTCHD2	11483665	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	6.972000	0.76110	2.200000	0.70718	0.460000	0.39030	CAG		0.612	PTCHD2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000005770.2	XM_052561	
DRAM2	128338	broad.mit.edu	37	1	111660804	111660804	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr1:111660804C>T	ENST00000286692.4	-	9	1396	c.779G>A	c.(778-780)cGg>cAg	p.R260Q	DRAM2_ENST00000539140.1_Missense_Mutation_p.R260Q|DRAM2_ENST00000484310.1_5'UTR			Q6UX65	DRAM2_HUMAN	DNA-damage regulated autophagy modulator 2	260					apoptotic process (GO:0006915)|regulation of autophagy (GO:0010506)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|lysosome (GO:0005764)|microtubule cytoskeleton (GO:0015630)		p.R260Q(1)		endometrium(1)|large_intestine(5)|lung(3)	9						GGAAAGTAGCCGTGTTCGTTC	0.373																																					p.R260Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G779A	1						.						134.0	139.0	137.0					1																	111660804		2203	4300	6503	111462327	SO:0001583	missense	128338	exon9			AY336747	CCDS30801.1	1p13.3	2010-07-08	2009-06-12	2009-06-12	ENSG00000156171	ENSG00000156171			28769	protein-coding gene	gene with protein product		613360	"""transmembrane protein 77"""	TMEM77		12975309	Standard	NM_178454		Approved	MGC54289, PRO180, WWFQ154, RP5-1180E21.1	uc001ead.4	Q6UX65	OTTHUMG00000011911	ENST00000286692.4:c.779G>A	1.37:g.111660804C>T	ENSP00000286692:p.Arg260Gln	Somatic		Capture	Illumina HiSeq	Phase_I	111462327	NM_178454	B3SUG9|Q4VWF6|Q86VD3|Q8NBQ4	Missense_Mutation	SNP	ENST00000286692.4	37	CCDS30801.1	.	.	.	.	.	.	.	.	.	.	C	12.18	1.860931	0.32884	.	.	ENSG00000156171	ENST00000286692;ENST00000539140	.	.	.	5.79	-6.8	0.01709	.	0.985758	0.08278	N	0.970438	T	0.03434	0.0099	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.33854	-0.9852	9	0.21014	T	0.42	-17.1438	0.7753	0.01031	0.1911:0.1891:0.2438:0.376	.	260	Q6UX65	DRAM2_HUMAN	Q	260	.	ENSP00000286692:R260Q	R	-	2	0	DRAM2	111462327	0.013000	0.17824	0.427000	0.26684	0.989000	0.77384	-0.450000	0.06803	-0.877000	0.04012	0.585000	0.79938	CGG		0.373	DRAM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032930.3	NM_178454	
DENND2C	163259	broad.mit.edu	37	1	115166211	115166211	+	Missense_Mutation	SNP	G	G	A	rs199921408		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr1:115166211G>A	ENST00000393274.1	-	5	1485	c.860C>T	c.(859-861)aCg>aTg	p.T287M	DENND2C_ENST00000393276.3_Missense_Mutation_p.T287M|DENND2C_ENST00000481894.1_5'UTR|DENND2C_ENST00000393277.1_Missense_Mutation_p.T287M	NM_001256404.1	NP_001243333.1	Q68D51	DEN2C_HUMAN	DENN/MADD domain containing 2C	287					positive regulation of Rab GTPase activity (GO:0032851)		Rab guanyl-nucleotide exchange factor activity (GO:0017112)	p.T287M(1)		NS(2)|breast(2)|cervix(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(10)|lung(10)|pancreas(1)|skin(3)	37	all_epithelial(7;9.54e-05)|all_lung(7;0.000179)|Lung NSC(6;0.00195)|Lung SC(450;0.211)	all_cancers(81;4.64e-07)|all_epithelial(167;4.2e-07)|all_lung(203;9.97e-06)|Lung NSC(69;1.74e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|all cancers(265;0.112)|Epithelial(280;0.124)|LUSC - Lung squamous cell carcinoma(189;0.133)		TTCACGAATCGTCTGTGAGTT	0.333																																					p.T287M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C860T	1						.						94.0	92.0	92.0					1																	115166211		2202	4300	6502	114967734	SO:0001583	missense	163259	exon3				CCDS875.1, CCDS58018.1	1p13.2-p13.1	2012-10-03			ENSG00000175984	ENSG00000175984		"""DENN/MADD domain containing"""	24748	protein-coding gene	gene with protein product							Standard	NM_198459		Approved	FLJ37099, DKFZp686G0351, DKFZp779P1149, dJ1156J9.1, RP5-1156J9.1	uc001efd.1	Q68D51	OTTHUMG00000011893	ENST00000393274.1:c.860C>T	1.37:g.115166211G>A	ENSP00000376955:p.Thr287Met	Somatic		Capture	Illumina HiSeq	Phase_I	114967734	NM_198459	B1AL26|Q5TCX6|Q6P3R3	Missense_Mutation	SNP	ENST00000393274.1	37	CCDS58018.1	.	.	.	.	.	.	.	.	.	.	G	9.339	1.062497	0.19987	.	.	ENSG00000175984	ENST00000393276;ENST00000393274;ENST00000369540;ENST00000393277	T;T;T	0.44482	3.72;3.7;0.92	6.06	3.76	0.43208	.	0.390390	0.29139	N	0.013021	T	0.11580	0.0282	N	0.19112	0.55	0.21064	N	0.999796	P;P	0.42556	0.783;0.773	B;B	0.39771	0.115;0.309	T	0.04481	-1.0948	10	0.59425	D	0.04	.	6.0577	0.19820	0.0:0.1977:0.133:0.6693	.	287;287	Q68D51;Q68D51-3	DEN2C_HUMAN;.	M	287	ENSP00000376957:T287M;ENSP00000376955:T287M;ENSP00000376958:T287M	ENSP00000358553:T287M	T	-	2	0	DENND2C	114967734	0.993000	0.37304	0.998000	0.56505	0.139000	0.21198	1.182000	0.32029	0.544000	0.28883	-1.085000	0.02201	ACG		0.333	DENND2C-005	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000314822.1	NM_198459	
CSDE1	7812	broad.mit.edu	37	1	115268950	115268950	+	Nonsense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr1:115268950G>A	ENST00000358528.4	-	14	1948	c.1522C>T	c.(1522-1524)Cga>Tga	p.R508*	Y_RNA_ENST00000365030.1_RNA|CSDE1_ENST00000534699.1_Nonsense_Mutation_p.R508*|CSDE1_ENST00000438362.2_Nonsense_Mutation_p.R554*|CSDE1_ENST00000369530.1_Nonsense_Mutation_p.R523*|CSDE1_ENST00000530886.1_Nonsense_Mutation_p.R378*|CSDE1_ENST00000261443.5_Nonsense_Mutation_p.R477*|CSDE1_ENST00000339438.6_Nonsense_Mutation_p.R477*	NM_001007553.2	NP_001007554.1	O75534	CSDE1_HUMAN	cold shock domain containing E1, RNA-binding	508					male gonad development (GO:0008584)|nuclear-transcribed mRNA catabolic process, no-go decay (GO:0070966)|regulation of transcription, DNA-templated (GO:0006355)	CRD-mediated mRNA stability complex (GO:0070937)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)	p.R508*(1)		NS(1)|breast(4)|endometrium(11)|kidney(2)|large_intestine(12)|lung(17)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	51	all_epithelial(7;5.11e-05)|all_lung(7;0.000179)|Lung NSC(6;0.00195)|Lung SC(450;0.211)	all_cancers(81;2.21e-07)|all_epithelial(167;4.2e-07)|all_lung(203;9.97e-06)|Lung NSC(69;1.74e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|all cancers(265;0.112)|Epithelial(280;0.124)|LUSC - Lung squamous cell carcinoma(189;0.133)		CCTAAAAGTCGCACACAAGTT	0.398																																					p.R523X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.C1567T	1						.						83.0	83.0	83.0					1																	115268950		2203	4300	6503	115070473	SO:0001587	stop_gained	7812	exon14				CCDS30811.1, CCDS30812.1, CCDS44197.1, CCDS55626.1	1p13.2	2011-11-02			ENSG00000009307	ENSG00000009307			29905	protein-coding gene	gene with protein product	"""upstream of NRAS"""	191510				2204029, 10048485	Standard	NM_007158		Approved	D1S155E, UNR	uc001efi.3	O75534	OTTHUMG00000012060	ENST00000358528.4:c.1522C>T	1.37:g.115268950G>A	ENSP00000351329:p.Arg508*	Somatic		Capture	Illumina HiSeq	Phase_I	115070473	NM_001130523	A8K281|E9PGZ0|G5E9Q2|O94961|Q5TF04|Q5TF05|Q68DF1|Q68DI9|Q9Y2S4	Nonsense_Mutation	SNP	ENST00000358528.4	37	CCDS30812.1	.	.	.	.	.	.	.	.	.	.	G	44	10.651004	0.99444	.	.	ENSG00000009307	ENST00000339438;ENST00000438362;ENST00000358528;ENST00000261443;ENST00000530886;ENST00000369530;ENST00000534699	.	.	.	5.85	2.74	0.32292	.	0.108957	0.64402	D	0.000012	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-6.0017	7.9765	0.30157	0.0789:0.0:0.4216:0.4995	.	.	.	.	X	477;554;508;477;378;523;508	.	ENSP00000261443:R477X	R	-	1	2	CSDE1	115070473	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	2.329000	0.43876	0.768000	0.33290	0.655000	0.94253	CGA		0.398	CSDE1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033397.1	NM_007158	
ATP1A1	476	broad.mit.edu	37	1	116936293	116936293	+	Silent	SNP	C	C	T	rs142766448		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr1:116936293C>T	ENST00000295598.5	+	12	1860	c.1608C>T	c.(1606-1608)gaC>gaT	p.D536D	ATP1A1_ENST00000369496.4_Silent_p.D505D|ATP1A1_ENST00000537345.1_Silent_p.D536D	NM_000701.7	NP_000692.2	P05023	AT1A1_HUMAN	ATPase, Na+/K+ transporting, alpha 1 polypeptide	536					ATP biosynthetic process (GO:0006754)|cardiac muscle contraction (GO:0060048)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cellular potassium ion homeostasis (GO:0030007)|cellular response to mechanical stimulus (GO:0071260)|cellular response to steroid hormone stimulus (GO:0071383)|cellular sodium ion homeostasis (GO:0006883)|ion transmembrane transport (GO:0034220)|membrane hyperpolarization (GO:0060081)|membrane repolarization (GO:0086009)|membrane repolarization during cardiac muscle cell action potential (GO:0086013)|negative regulation of glucocorticoid biosynthetic process (GO:0031947)|negative regulation of heart contraction (GO:0045822)|positive regulation of heart contraction (GO:0045823)|positive regulation of striated muscle contraction (GO:0045989)|potassium ion import (GO:0010107)|regulation of blood pressure (GO:0008217)|regulation of cardiac muscle cell contraction (GO:0086004)|regulation of sodium ion transport (GO:0002028)|regulation of the force of heart contraction (GO:0002026)|relaxation of cardiac muscle (GO:0055119)|response to drug (GO:0042493)|sodium ion export from cell (GO:0036376)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|caveola (GO:0005901)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|sarcolemma (GO:0042383)|sodium:potassium-exchanging ATPase complex (GO:0005890)|T-tubule (GO:0030315)|vesicle (GO:0031982)	ADP binding (GO:0043531)|ATP binding (GO:0005524)|chaperone binding (GO:0051087)|phosphatase activity (GO:0016791)|potassium ion binding (GO:0030955)|sodium ion binding (GO:0031402)|sodium:potassium-exchanging ATPase activity (GO:0005391)|steroid hormone binding (GO:1990239)	p.D536E(1)|p.D536D(1)		NS(2)|breast(2)|cervix(3)|endometrium(2)|kidney(5)|large_intestine(9)|lung(17)|ovary(1)|prostate(1)|skin(3)|stomach(1)|urinary_tract(1)	47	Lung SC(450;0.225)	all_cancers(81;1.28e-06)|all_epithelial(167;3.48e-07)|all_lung(203;2.64e-06)|Lung NSC(69;1.98e-05)		Lung(183;0.0164)|LUSC - Lung squamous cell carcinoma(189;0.0548)|Colorectal(144;0.0825)|COAD - Colon adenocarcinoma(174;0.127)|all cancers(265;0.24)	Acetyldigitoxin(DB00511)|Almitrine(DB01430)|Aluminium(DB01370)|Bepridil(DB01244)|Bretylium(DB01158)|Ciclopirox(DB01188)|Deslanoside(DB01078)|Diazoxide(DB01119)|Digitoxin(DB01396)|Digoxin(DB00390)|Ethacrynic acid(DB00903)|Hydroflumethiazide(DB00774)|Ouabain(DB01092)|Trichlormethiazide(DB01021)	AGCTGAAAGACGCCTTTCAGA	0.562													C|||	1	0.000199681	0.0008	0.0	5008	,	,		17859	0.0		0.0	False		,,,				2504	0.0				p.D536D												.	.	2	Substitution - Missense(1)|Substitution - coding silent(1)	large_intestine(1)|NS(1)	c.C1608T	1						.	C	,,	1,4405	2.1+/-5.4	0,1,2202	57.0	61.0	59.0		1608,1608,1515	-7.6	0.6	1	dbSNP_134	59	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous,coding-synonymous,coding-synonymous	ATP1A1	NM_000701.7,NM_001160233.1,NM_001160234.1	,,	0,3,6500	TT,TC,CC		0.0233,0.0227,0.0231	,,	536/1024,536/1024,505/993	116936293	3,13003	2203	4300	6503	116737816	SO:0001819	synonymous_variant	476	exon12			D00099	CCDS887.1, CCDS53351.1, CCDS53352.1	1p13	2012-10-22			ENSG00000163399	ENSG00000163399	3.6.3.9	"""ATPases / P-type"""	799	protein-coding gene	gene with protein product	"""sodium/potassium-transporting ATPase subunit alpha-1"", ""sodium pump subunit alpha-1"", ""sodium-potassium ATPase catalytic subunit alpha-1"""	182310					Standard	NM_000701		Approved		uc001ege.3	P05023	OTTHUMG00000012109	ENST00000295598.5:c.1608C>T	1.37:g.116936293C>T		Somatic		Capture	Illumina HiSeq	Phase_I	116737816	NM_000701	B2RBR6|B7Z2T5|B7Z3U6|F5H3A1|Q16689|Q6LDM4|Q9UCN1|Q9UJ20|Q9UJ21	Silent	SNP	ENST00000295598.5	37	CCDS887.1																																																																																				0.562	ATP1A1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000033481.5	NM_001160233	
PTGFRN	5738	broad.mit.edu	37	1	117487548	117487548	+	Silent	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr1:117487548C>T	ENST00000393203.2	+	3	813	c.666C>T	c.(664-666)ctC>ctT	p.L222L		NM_020440.2	NP_065173.2	Q9P2B2	FPRP_HUMAN	prostaglandin F2 receptor inhibitor	222	Ig-like C2-type 2.				lipid particle organization (GO:0034389)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)		p.L222L(1)		NS(1)|breast(1)|endometrium(4)|large_intestine(10)|liver(1)|lung(22)|ovary(1)|prostate(4)|stomach(1)|upper_aerodigestive_tract(1)	46	Lung SC(450;0.225)	all_cancers(81;0.00104)|all_lung(203;8.97e-05)|all_epithelial(167;0.000139)|Lung NSC(69;0.000446)		Lung(183;0.0704)|LUSC - Lung squamous cell carcinoma(189;0.227)|Colorectal(144;0.248)		ACGTGCGCCTCGACACCGTGG	0.711																																					p.L222L												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C666T	1						.						33.0	31.0	31.0					1																	117487548		2203	4300	6503	117289071	SO:0001819	synonymous_variant	5738	exon3			AB014734	CCDS890.1	1p13.1	2013-01-29	2013-01-25		ENSG00000134247	ENSG00000134247		"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	9601	protein-coding gene	gene with protein product		601204	"""prostaglandin F2 receptor negative regulator"""			8655148	Standard	NM_020440		Approved	FPRP, EWI-F, CD9P-1, FLJ11001, KIAA1436, SMAP-6, CD315	uc001egv.1	Q9P2B2	OTTHUMG00000012028	ENST00000393203.2:c.666C>T	1.37:g.117487548C>T		Somatic		Capture	Illumina HiSeq	Phase_I	117289071	NM_020440	Q5VVU9|Q8N2K6	Silent	SNP	ENST00000393203.2	37	CCDS890.1																																																																																				0.711	PTGFRN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033271.1	NM_020440	
TTF2	8458	broad.mit.edu	37	1	117618193	117618193	+	Silent	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr1:117618193G>A	ENST00000369466.4	+	5	1031	c.987G>A	c.(985-987)gcG>gcA	p.A329A		NM_003594.3	NP_003585.3	Q9UNY4	TTF2_HUMAN	transcription termination factor, RNA polymerase II	329					ATP catabolic process (GO:0006200)|DNA-templated transcription, termination (GO:0006353)|mRNA processing (GO:0006397)|regulation of transcription, DNA-templated (GO:0006355)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)	cytoplasm (GO:0005737)|spliceosomal complex (GO:0005681)|transcription elongation factor complex (GO:0008023)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|DNA binding (GO:0003677)|DNA-dependent ATPase activity (GO:0008094)|zinc ion binding (GO:0008270)	p.A329A(1)		NS(1)|autonomic_ganglia(1)|breast(1)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|liver(1)|lung(24)|ovary(1)|prostate(2)|skin(2)|urinary_tract(2)	50	Lung SC(450;0.225)	all_cancers(81;4.23e-06)|all_epithelial(167;3.65e-07)|all_lung(203;2.81e-06)|Lung NSC(69;1.98e-05)		Lung(183;0.0553)|Colorectal(144;0.179)|LUSC - Lung squamous cell carcinoma(189;0.19)		GAGGACCAGCGGCTCAGGCTG	0.602																																					p.A329A												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G987A	1						.						45.0	42.0	43.0					1																	117618193		2203	4300	6503	117419716	SO:0001819	synonymous_variant	8458	exon5			AF073771	CCDS892.1	1p13.1	2014-02-18			ENSG00000116830	ENSG00000116830			12398	protein-coding gene	gene with protein product	"""zinc finger, GRF-type containing 6"""	604718				9748214	Standard	NM_003594		Approved	HuF2, ZGRF6	uc001egy.3	Q9UNY4	OTTHUMG00000012030	ENST00000369466.4:c.987G>A	1.37:g.117618193G>A		Somatic		Capture	Illumina HiSeq	Phase_I	117419716	NM_003594	A8K4Q2|O75921|Q5T2K7|Q5VVU8|Q8N6I8	Silent	SNP	ENST00000369466.4	37	CCDS892.1																																																																																				0.602	TTF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033277.3		
DVL1	1855	broad.mit.edu	37	1	1275637	1275637	+	Silent	SNP	C	C	T	rs1140338	byFrequency	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr1:1275637C>T	ENST00000378888.5	-	7	1043	c.759G>A	c.(757-759)acG>acA	p.T253T	DVL1_ENST00000378891.5_Silent_p.T253T			O14640	DVL1_HUMAN	dishevelled segment polarity protein 1	253	PDZ. {ECO:0000255|PROSITE- ProRule:PRU00143}.				axon extension (GO:0048675)|axon guidance (GO:0007411)|canonical Wnt signaling pathway (GO:0060070)|cochlea morphogenesis (GO:0090103)|collateral sprouting (GO:0048668)|convergent extension (GO:0060026)|convergent extension involved in neural plate elongation (GO:0022007)|cytoplasmic microtubule organization (GO:0031122)|dendrite morphogenesis (GO:0048813)|intracellular signal transduction (GO:0035556)|negative regulation of protein binding (GO:0032091)|negative regulation of protein kinase activity (GO:0006469)|neural tube development (GO:0021915)|neuromuscular junction development (GO:0007528)|neurotransmitter secretion (GO:0007269)|planar cell polarity pathway involved in neural tube closure (GO:0090179)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of neuron projection development (GO:0010976)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of Wnt signaling pathway (GO:0030177)|prepulse inhibition (GO:0060134)|protein localization to microtubule (GO:0035372)|protein localization to nucleus (GO:0034504)|receptor clustering (GO:0043113)|regulation of neurotransmitter levels (GO:0001505)|skeletal muscle acetylcholine-gated channel clustering (GO:0071340)|social behavior (GO:0035176)|synapse organization (GO:0050808)|transcription from RNA polymerase II promoter (GO:0006366)|Wnt signaling pathway, planar cell polarity pathway (GO:0060071)	axon (GO:0030424)|cell cortex (GO:0005938)|clathrin-coated vesicle (GO:0030136)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytoplasmic vesicle (GO:0031410)|dendrite (GO:0030425)|growth cone (GO:0030426)|microtubule (GO:0005874)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|synapse (GO:0045202)	enzyme binding (GO:0019899)|frizzled binding (GO:0005109)|identical protein binding (GO:0042802)|protein kinase binding (GO:0019901)|Rac GTPase binding (GO:0048365)	p.T253T(1)		endometrium(1)|kidney(1)|large_intestine(2)|lung(5)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)	13	all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;8.75e-19)|all_lung(118;2.3e-08)|Lung NSC(185;2.38e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Lung SC(97;0.128)		Epithelial(90;2.83e-35)|OV - Ovarian serous cystadenocarcinoma(86;3.77e-21)|Colorectal(212;0.000155)|COAD - Colon adenocarcinoma(227;0.000193)|Kidney(185;0.00227)|BRCA - Breast invasive adenocarcinoma(365;0.0025)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0339)|Lung(427;0.145)		CCATGTTGAGCGTGACAGTGA	0.622																																					p.T253T												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G759A	1						.	C		5,4401	9.9+/-24.2	0,5,2198	122.0	108.0	113.0		759	-7.2	0.5	1	dbSNP_86	113	0,8592		0,0,4296	no	coding-synonymous	DVL1	NM_004421.2		0,5,6494	TT,TC,CC		0.0,0.1135,0.0385		253/671	1275637	5,12993	2203	4296	6499	1265500	SO:0001819	synonymous_variant	1855	exon7			AF006011	CCDS22.1	1p36	2013-05-22	2013-05-22		ENSG00000107404	ENSG00000107404		"""Dishevelled homologs"""	3084	protein-coding gene	gene with protein product		601365	"""dishevelled 1 (homologous to Drosophila dsh)"", ""dishevelled, dsh homolog 1 (Drosophila)"""			8817329	Standard	NM_004421		Approved		uc001aer.4	O14640	OTTHUMG00000003069	ENST00000378888.5:c.759G>A	1.37:g.1275637C>T		Somatic		Capture	Illumina HiSeq	Phase_I	1265500	NM_004421	Q5TA33|Q5TA35	Silent	SNP	ENST00000378888.5	37																																																																																					0.622	DVL1-004	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000008490.1	NM_004421	
MTHFR	4524	broad.mit.edu	37	1	11855293	11855293	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr1:11855293C>T	ENST00000376592.1	-	5	1021	c.893G>A	c.(892-894)gGc>gAc	p.G298D	MTHFR_ENST00000376585.1_Missense_Mutation_p.G339D|MTHFR_ENST00000376583.3_Missense_Mutation_p.G339D|MTHFR_ENST00000376590.3_Missense_Mutation_p.G298D			P42898	MTHR_HUMAN	methylenetetrahydrofolate reductase (NAD(P)H)	298					blood circulation (GO:0008015)|cellular amino acid metabolic process (GO:0006520)|folic acid metabolic process (GO:0046655)|homocysteine metabolic process (GO:0050667)|methionine biosynthetic process (GO:0009086)|response to drug (GO:0042493)|response to folic acid (GO:0051593)|response to hypoxia (GO:0001666)|response to interleukin-1 (GO:0070555)|response to vitamin B2 (GO:0033274)|S-adenosylmethionine metabolic process (GO:0046500)|small molecule metabolic process (GO:0044281)|tetrahydrofolate interconversion (GO:0035999)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|neuron projection (GO:0043005)	flavin adenine dinucleotide binding (GO:0050660)|methylenetetrahydrofolate reductase (NAD(P)H) activity (GO:0004489)|modified amino acid binding (GO:0072341)|NADP binding (GO:0050661)	p.G298D(1)		NS(4)|breast(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(9)|lung(6)|prostate(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	33	Ovarian(185;0.249)	Lung NSC(185;8.69e-05)|all_lung(284;9.87e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00826)|Ovarian(437;0.00965)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;5.66e-06)|COAD - Colon adenocarcinoma(227;0.000261)|BRCA - Breast invasive adenocarcinoma(304;0.000304)|Kidney(185;0.000777)|KIRC - Kidney renal clear cell carcinoma(229;0.00261)|STAD - Stomach adenocarcinoma(313;0.0073)|READ - Rectum adenocarcinoma(331;0.0649)	Benazepril(DB00542)|Cyanocobalamin(DB00115)|Fluorouracil(DB00544)|Folic Acid(DB00158)|L-Methionine(DB00134)|Menadione(DB00170)|Methotrexate(DB00563)|Riboflavin(DB00140)|Tetrahydrofolic acid(DB00116)	CAGCTCGATGCCATAGTTGCG	0.582																																					p.G298D												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G893A	1						.						100.0	95.0	96.0					1																	11855293		2203	4300	6503	11777880	SO:0001583	missense	4524	exon6			BC053509	CCDS137.1	1p36.3	2014-09-17	2010-05-04		ENSG00000177000	ENSG00000177000	1.5.1.20		7436	protein-coding gene	gene with protein product		607093	"""5,10-methylenetetrahydrofolate reductase (NADPH)"""			7920641	Standard	NM_005957		Approved		uc001atc.2	P42898	OTTHUMG00000002277	ENST00000376592.1:c.893G>A	1.37:g.11855293C>T	ENSP00000365777:p.Gly298Asp	Somatic		Capture	Illumina HiSeq	Phase_I	11777880	NM_005957	B2R7A6|Q5SNW6|Q5SNW9|Q7Z6M6|Q8IU73|Q9UQR2	Missense_Mutation	SNP	ENST00000376592.1	37	CCDS137.1	.	.	.	.	.	.	.	.	.	.	C	33	5.224136	0.95139	.	.	ENSG00000177000	ENST00000376592;ENST00000376583;ENST00000376590;ENST00000376585	D;D;D;D	0.95001	-3.58;-3.58;-3.58;-3.58	4.97	4.97	0.65823	.	0.093677	0.85682	D	0.000000	D	0.98501	0.9500	H	0.98295	4.195	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.999	D	0.99804	1.1037	10	0.87932	D	0	.	17.5883	0.87988	0.0:1.0:0.0:0.0	.	298;339	P42898;Q5SNW6	MTHR_HUMAN;.	D	298;339;298;339	ENSP00000365777:G298D;ENSP00000365767:G339D;ENSP00000365775:G298D;ENSP00000365770:G339D	ENSP00000365767:G339D	G	-	2	0	MTHFR	11777880	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	7.085000	0.76875	2.457000	0.83068	0.462000	0.41574	GGC		0.582	MTHFR-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000006538.1	NM_005957	
MFN2	9927	broad.mit.edu	37	1	12067173	12067173	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr1:12067173G>A	ENST00000235329.5	+	17	2258	c.1936G>A	c.(1936-1938)Gtc>Atc	p.V646I	MFN2_ENST00000444836.1_Missense_Mutation_p.V646I	NM_014874.3	NP_055689.1	O95140	MFN2_HUMAN	mitofusin 2	646					apoptotic process (GO:0006915)|autophagy (GO:0006914)|blastocyst formation (GO:0001825)|blood coagulation (GO:0007596)|camera-type eye morphogenesis (GO:0048593)|mitochondrial fusion (GO:0008053)|mitochondrial membrane organization (GO:0007006)|mitochondrion localization (GO:0051646)|negative regulation of Ras protein signal transduction (GO:0046580)|negative regulation of smooth muscle cell proliferation (GO:0048662)|protein localization to pre-autophagosomal structure (GO:0034497)|protein targeting to mitochondrion (GO:0006626)|response to unfolded protein (GO:0006986)	cytosol (GO:0005829)|integral component of membrane (GO:0016021)|intrinsic component of mitochondrial outer membrane (GO:0031306)|microtubule cytoskeleton (GO:0015630)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|ubiquitin protein ligase binding (GO:0031625)	p.V344I(1)|p.V646I(1)		endometrium(4)|kidney(1)|large_intestine(4)|liver(2)|lung(3)|ovary(1)|pancreas(1)|prostate(2)|skin(2)	20	Ovarian(185;0.249)	Lung NSC(185;8.69e-05)|all_lung(284;9.87e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Ovarian(437;0.00965)|Hepatocellular(190;0.0202)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;7.25e-06)|COAD - Colon adenocarcinoma(227;0.000302)|BRCA - Breast invasive adenocarcinoma(304;0.000329)|Kidney(185;0.000896)|KIRC - Kidney renal clear cell carcinoma(229;0.00274)|STAD - Stomach adenocarcinoma(313;0.00773)|READ - Rectum adenocarcinoma(331;0.0656)		CCTCCTCTACGTCTATGAGCG	0.597																																					p.V646I												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G1936A	1						.						115.0	103.0	107.0					1																	12067173		2203	4300	6503	11989760	SO:0001583	missense	9927	exon16			AF036536	CCDS30587.1	1p36.22	2014-09-17			ENSG00000116688	ENSG00000116688			16877	protein-coding gene	gene with protein product		608507				12499352, 11181170	Standard	NM_014874		Approved	CPRP1, KIAA0214, MARF, CMT2A2	uc009vni.3	O95140	OTTHUMG00000002392	ENST00000235329.5:c.1936G>A	1.37:g.12067173G>A	ENSP00000235329:p.Val646Ile	Somatic		Capture	Illumina HiSeq	Phase_I	11989760	NM_001127660	A8K1B3|O95572|Q5JXC3|Q5JXC4|Q9H131|Q9NSX8	Missense_Mutation	SNP	ENST00000235329.5	37	CCDS30587.1	.	.	.	.	.	.	.	.	.	.	G	13.16	2.154614	0.38021	.	.	ENSG00000116688	ENST00000444836;ENST00000235329;ENST00000376337	D;D	0.96396	-4.0;-4.0	4.47	4.47	0.54385	Fzo/mitofusin HR2 domain (1);	0.069349	0.56097	D	0.000024	D	0.93854	0.8034	L	0.44542	1.39	0.58432	D	0.999998	B	0.18166	0.026	B	0.18263	0.021	D	0.91616	0.5307	10	0.45353	T	0.12	-31.8727	16.3264	0.82983	0.0:0.0:1.0:0.0	.	646	O95140	MFN2_HUMAN	I	646;646;344	ENSP00000416338:V646I;ENSP00000235329:V646I	ENSP00000235329:V646I	V	+	1	0	MFN2	11989760	1.000000	0.71417	0.960000	0.40013	0.478000	0.33099	3.554000	0.53720	2.312000	0.78011	0.561000	0.74099	GTC		0.597	MFN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006859.2	NM_014874	
VPS13D	55187	broad.mit.edu	37	1	12337745	12337745	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr1:12337745C>T	ENST00000358136.3	+	19	4230	c.4100C>T	c.(4099-4101)tCg>tTg	p.S1367L	VPS13D_ENST00000356315.4_Missense_Mutation_p.S1367L	NM_015378.2	NP_056193.2			vacuolar protein sorting 13 homolog D (S. cerevisiae)									p.S1367L(2)		NS(1)|breast(6)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(13)|large_intestine(28)|lung(44)|ovary(5)|pancreas(1)|prostate(8)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(4)	130	Ovarian(185;0.249)	Lung NSC(185;4.08e-05)|all_lung(284;4.55e-05)|Renal(390;0.000147)|Colorectal(325;0.00058)|Breast(348;0.00093)|Ovarian(437;0.00965)|Hepatocellular(190;0.0202)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0327)|Colorectal(212;4.63e-06)|BRCA - Breast invasive adenocarcinoma(304;0.000289)|COAD - Colon adenocarcinoma(227;0.000801)|Kidney(185;0.00216)|KIRC - Kidney renal clear cell carcinoma(229;0.00544)|STAD - Stomach adenocarcinoma(313;0.012)|READ - Rectum adenocarcinoma(331;0.0476)|Lung(427;0.209)		GACCTAGCTTCGTCTCATTTG	0.443																																					p.S1367L												.	.	2	Substitution - Missense(2)	large_intestine(1)|endometrium(1)	c.C4100T	1						.						62.0	67.0	65.0					1																	12337745		2203	4300	6503	12260332	SO:0001583	missense	55187	exon19			AJ608774	CCDS30588.1, CCDS30589.1	1p36.21	2008-02-05	2006-04-04		ENSG00000048707	ENSG00000048707			23595	protein-coding gene	gene with protein product		608877	"""vacuolar protein sorting 13D (yeast)"""				Standard	NM_015378		Approved	FLJ10619, KIAA0453	uc001atv.3	Q5THJ4	OTTHUMG00000013155	ENST00000358136.3:c.4100C>T	1.37:g.12337745C>T	ENSP00000350854:p.Ser1367Leu	Somatic		Capture	Illumina HiSeq	Phase_I	12260332	NM_018156		Missense_Mutation	SNP	ENST00000358136.3	37	CCDS30588.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	2.127|2.127	-0.400063|-0.400063	0.04865|0.04865	.|.	.|.	ENSG00000048707|ENSG00000048707	ENST00000011700|ENST00000356315;ENST00000358136	.|T;T	.|0.55760	.|0.51;0.5	5.91|5.91	4.99|4.99	0.66335|0.66335	.|.	.|0.614327	.|0.16809	.|N	.|0.198643	T|T	0.37046|0.37046	0.0989|0.0989	N|N	0.14661|0.14661	0.345|0.345	0.20403|0.20403	N|N	0.999908|0.999908	.|B;B	.|0.24426	.|0.031;0.103	.|B;B	.|0.17098	.|0.014;0.017	T|T	0.14727|0.14727	-1.0462|-1.0462	5|10	.|0.27082	.|T	.|0.32	.|.	15.8295|15.8295	0.78741|0.78741	0.0:0.5971:0.4029:0.0|0.0:0.5971:0.4029:0.0	.|.	.|1367;1367	.|Q5THJ4-2;Q5THJ4	.|.;VP13D_HUMAN	C|L	190|1367	.|ENSP00000348666:S1367L;ENSP00000350854:S1367L	.|ENSP00000348666:S1367L	R|S	+|+	1|2	0|0	VPS13D|VPS13D	12260332|12260332	0.012000|0.012000	0.17670|0.17670	0.008000|0.008000	0.14137|0.14137	0.248000|0.248000	0.25809|0.25809	1.874000|1.874000	0.39568|0.39568	1.484000|1.484000	0.48361|0.48361	0.655000|0.655000	0.94253|0.94253	CGT|TCG		0.443	VPS13D-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000036897.2	NM_015378	
VPS13D	55187	broad.mit.edu	37	1	12418603	12418603	+	Nonsense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr1:12418603C>T	ENST00000358136.3	+	50	10217	c.10087C>T	c.(10087-10089)Cga>Tga	p.R3363*	VPS13D_ENST00000356315.4_Nonsense_Mutation_p.R3338*	NM_015378.2	NP_056193.2			vacuolar protein sorting 13 homolog D (S. cerevisiae)									p.R3363*(1)		NS(1)|breast(6)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(13)|large_intestine(28)|lung(44)|ovary(5)|pancreas(1)|prostate(8)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(4)	130	Ovarian(185;0.249)	Lung NSC(185;4.08e-05)|all_lung(284;4.55e-05)|Renal(390;0.000147)|Colorectal(325;0.00058)|Breast(348;0.00093)|Ovarian(437;0.00965)|Hepatocellular(190;0.0202)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0327)|Colorectal(212;4.63e-06)|BRCA - Breast invasive adenocarcinoma(304;0.000289)|COAD - Colon adenocarcinoma(227;0.000801)|Kidney(185;0.00216)|KIRC - Kidney renal clear cell carcinoma(229;0.00544)|STAD - Stomach adenocarcinoma(313;0.012)|READ - Rectum adenocarcinoma(331;0.0476)|Lung(427;0.209)		TAGTGGTGTCCGAGCTTTGAA	0.552																																					p.R3338X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.C10012T	1						.						125.0	119.0	121.0					1																	12418603		2203	4300	6503	12341190	SO:0001587	stop_gained	55187	exon49			AJ608774	CCDS30588.1, CCDS30589.1	1p36.21	2008-02-05	2006-04-04		ENSG00000048707	ENSG00000048707			23595	protein-coding gene	gene with protein product		608877	"""vacuolar protein sorting 13D (yeast)"""				Standard	NM_015378		Approved	FLJ10619, KIAA0453	uc001atv.3	Q5THJ4	OTTHUMG00000013155	ENST00000358136.3:c.10087C>T	1.37:g.12418603C>T	ENSP00000350854:p.Arg3363*	Somatic		Capture	Illumina HiSeq	Phase_I	12341190	NM_018156		Nonsense_Mutation	SNP	ENST00000358136.3	37	CCDS30588.1	.	.	.	.	.	.	.	.	.	.	C	52	19.215651	0.99916	.	.	ENSG00000048707	ENST00000356315;ENST00000358136	.	.	.	6.17	5.24	0.73138	.	0.062472	0.64402	D	0.000002	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.07813	T	0.8	.	12.9425	0.58352	0.3577:0.6423:0.0:0.0	.	.	.	.	X	3338;3363	.	ENSP00000348666:R3338X	R	+	1	2	VPS13D	12341190	0.991000	0.36638	1.000000	0.80357	0.997000	0.91878	1.847000	0.39299	1.582000	0.49881	0.655000	0.94253	CGA		0.552	VPS13D-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000036897.2	NM_015378	
PRAMEF14	729528	broad.mit.edu	37	1	13669060	13669060	+	Missense_Mutation	SNP	G	G	A	rs199937476		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr1:13669060G>A	ENST00000344998.3	-	4	1308	c.1126C>T	c.(1126-1128)Cgt>Tgt	p.R376C	PRAMEF14_ENST00000334600.6_Missense_Mutation_p.R424C|PRAMEF14_ENST00000602491.1_5'UTR			Q5SWL7	PRA14_HUMAN	PRAME family member 14	376					negative regulation of apoptotic process (GO:0043066)|negative regulation of cell differentiation (GO:0045596)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of cell proliferation (GO:0008284)			p.R376C(1)		large_intestine(1)|skin(1)|upper_aerodigestive_tract(1)	3	Ovarian(185;0.249)	Renal(390;0.000469)|Lung NSC(185;0.00143)|all_lung(284;0.00181)|Colorectal(325;0.00215)|Breast(348;0.00224)|Myeloproliferative disorder(586;0.0393)|Hepatocellular(190;0.0623)|Ovarian(437;0.0731)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00812)|Colorectal(212;4.88e-06)|Kidney(185;4.89e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.000194)|COAD - Colon adenocarcinoma(227;0.000241)|BRCA - Breast invasive adenocarcinoma(304;0.000293)|STAD - Stomach adenocarcinoma(313;0.0072)|READ - Rectum adenocarcinoma(331;0.0649)		CAATCGACACGAACCAAGGAA	0.557																																					p.R376C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1126T	1						.	G	CYS/ARG	0,4126		0,0,2063	13.0	15.0	15.0		1126	-2.0	0.0	1		15	6,8344		0,6,4169	no	missense	PRAMEF14	NM_001099854.1	180	0,6,6232	AA,AG,GG		0.0719,0.0,0.0481	benign	376/427	13669060	6,12470	2063	4175	6238	13541647	SO:0001583	missense	400736	exon4					1p36.21	2014-04-01			ENSG00000204481	ENSG00000204481		"""-"""	13576	other	unknown							Standard	NM_001024661		Approved	OTTHUMG00000007916		Q5SWL7	OTTHUMG00000007916	ENST00000344998.3:c.1126C>T	1.37:g.13669060G>A	ENSP00000341333:p.Arg376Cys	Somatic		Capture	Illumina HiSeq	Phase_I	13541647	NM_001099854		Missense_Mutation	SNP	ENST00000344998.3	37		.	.	.	.	.	.	.	.	.	.	G	7.375	0.627632	0.14257	0.0	7.19E-4	ENSG00000204481	ENST00000344998;ENST00000334600	T;T	0.47177	0.85;0.85	1.69	-1.95	0.07548	.	2.267370	0.01587	N	0.021351	T	0.39091	0.1065	L	0.38531	1.155	0.09310	N	1	P	0.52316	0.952	P	0.45794	0.493	T	0.23655	-1.0182	10	0.37606	T	0.19	.	2.7892	0.05383	0.0:0.3741:0.2583:0.3676	.	376	Q5SWL7	PRA14_HUMAN	C	376;424	ENSP00000341333:R376C;ENSP00000334410:R424C	ENSP00000334410:R424C	R	-	1	0	PRAMEF14	13541647	0.000000	0.05858	0.000000	0.03702	0.106000	0.19336	-1.550000	0.02180	-0.551000	0.06175	0.162000	0.16502	CGT		0.557	PRAMEF14-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_001099854	
PRDM2	7799	broad.mit.edu	37	1	14142933	14142933	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr1:14142933G>A	ENST00000235372.7	+	9	5904	c.5048G>A	c.(5047-5049)cGc>cAc	p.R1683H	PRDM2_ENST00000503842.1_Missense_Mutation_p.A11T|PRDM2_ENST00000376048.5_Missense_Mutation_p.A175T|PRDM2_ENST00000505823.1_Missense_Mutation_p.A11T	NM_012231.4	NP_036363.2	Q13029	PRDM2_HUMAN	PR domain containing 2, with ZNF domain	1683					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)	p.R1683H(2)		endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(16)|lung(20)|ovary(3)|prostate(3)|skin(1)|urinary_tract(2)	55	Ovarian(185;0.249)	all_lung(284;2.56e-05)|Lung NSC(185;4.94e-05)|Renal(390;0.000147)|Breast(348;0.000162)|Colorectal(325;0.00058)|Ovarian(437;0.00965)|Hepatocellular(190;0.0245)|Myeloproliferative disorder(586;0.0255)	GBM - Glioblastoma multiforme(2;0.00182)	UCEC - Uterine corpus endometrioid carcinoma (279;0.00224)|Colorectal(212;3.23e-08)|BRCA - Breast invasive adenocarcinoma(304;2.16e-05)|COAD - Colon adenocarcinoma(227;2.53e-05)|Kidney(185;0.000762)|KIRC - Kidney renal clear cell carcinoma(229;0.00258)|STAD - Stomach adenocarcinoma(313;0.00446)|READ - Rectum adenocarcinoma(331;0.0276)|Lung(427;0.145)		TACAGCCTCCGCTTGGCGTCC	0.597																																					p.R1683H												.	.	2	Substitution - Missense(2)	large_intestine(1)|lung(1)	c.G5048A	1						.						85.0	82.0	83.0					1																	14142933		2203	4300	6503	14015520	SO:0001583	missense	7799	exon9			U17838	CCDS150.1, CCDS151.1, CCDS30603.1, CCDS44061.1	1p36	2011-07-01			ENSG00000116731	ENSG00000116731		"""Chromatin-modifying enzymes / K-methyltransferases"""	9347	protein-coding gene	gene with protein product	"""retinoblastoma protein-binding zinc finger protein"", ""retinoblastoma protein-interacting zinc finger protein"", ""MTE-binding protein"", ""zinc-finger DNA-binding protein"", ""GATA-3 binding protein G3B"""	601196				7538672	Standard	NM_012231		Approved	RIZ, RIZ1, RIZ2, KMT8, MTB-ZF, HUMHOXY1	uc001avi.3	Q13029	OTTHUMG00000007917	ENST00000235372.7:c.5048G>A	1.37:g.14142933G>A	ENSP00000235372:p.Arg1683His	Somatic		Capture	Illumina HiSeq	Phase_I	14015520	NM_012231	B1AJZ4|B5MC68|Q13149|Q14550|Q5THJ1|Q5VUL9	Missense_Mutation	SNP	ENST00000235372.7	37	CCDS150.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	18.23|18.23	3.578359|3.578359	0.65878|0.65878	.|.	.|.	ENSG00000116731|ENSG00000116731	ENST00000376048;ENST00000503842;ENST00000505823|ENST00000235372	T|T	0.56611|0.01647	0.45|4.71	5.07|5.07	5.07|5.07	0.68467|0.68467	.|.	.|0.000000	.|0.64402	.|D	.|0.000018	T|T	0.03608|0.03608	0.0103|0.0103	N|N	0.08118|0.08118	0|0	0.80722|0.80722	D|D	1|1	D|D	0.76494|0.76494	0.999|0.999	D|D	0.75020|0.76071	0.985|0.987	T|T	0.63857|0.63857	-0.6542|-0.6542	9|10	0.14252|0.72032	T|D	0.57|0.01	.|.	13.8205|13.8205	0.63318|0.63318	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	175|1683	B1AJZ4|Q13029	.|PRDM2_HUMAN	T|H	175;11;11|1683	ENSP00000365216:A175T|ENSP00000235372:R1683H	ENSP00000365216:A175T|ENSP00000235372:R1683H	A|R	+|+	1|2	0|0	PRDM2|PRDM2	14015520|14015520	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.987000|0.987000	0.75469|0.75469	4.414000|4.414000	0.59802|0.59802	2.615000|2.615000	0.88500|0.88500	0.655000|0.655000	0.94253|0.94253	GCT|CGC		0.597	PRDM2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000021792.2	NM_012231	
TTF2	8458	broad.mit.edu	37	1	117618265	117618265	+	Silent	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr1:117618265C>T	ENST00000369466.4	+	5	1103	c.1059C>T	c.(1057-1059)gaC>gaT	p.D353D		NM_003594.3	NP_003585.3	Q9UNY4	TTF2_HUMAN	transcription termination factor, RNA polymerase II	353					ATP catabolic process (GO:0006200)|DNA-templated transcription, termination (GO:0006353)|mRNA processing (GO:0006397)|regulation of transcription, DNA-templated (GO:0006355)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)	cytoplasm (GO:0005737)|spliceosomal complex (GO:0005681)|transcription elongation factor complex (GO:0008023)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|DNA binding (GO:0003677)|DNA-dependent ATPase activity (GO:0008094)|zinc ion binding (GO:0008270)	p.D353D(1)		NS(1)|autonomic_ganglia(1)|breast(1)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|liver(1)|lung(24)|ovary(1)|prostate(2)|skin(2)|urinary_tract(2)	50	Lung SC(450;0.225)	all_cancers(81;4.23e-06)|all_epithelial(167;3.65e-07)|all_lung(203;2.81e-06)|Lung NSC(69;1.98e-05)		Lung(183;0.0553)|Colorectal(144;0.179)|LUSC - Lung squamous cell carcinoma(189;0.19)		GCAGTGACGACGAGGAGGAAG	0.567																																					p.D353D												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1059T	1						.						71.0	61.0	65.0					1																	117618265		2203	4300	6503	117419788	SO:0001819	synonymous_variant	8458	exon5			AF073771	CCDS892.1	1p13.1	2014-02-18			ENSG00000116830	ENSG00000116830			12398	protein-coding gene	gene with protein product	"""zinc finger, GRF-type containing 6"""	604718				9748214	Standard	NM_003594		Approved	HuF2, ZGRF6	uc001egy.3	Q9UNY4	OTTHUMG00000012030	ENST00000369466.4:c.1059C>T	1.37:g.117618265C>T		Somatic		Capture	Illumina HiSeq	Phase_I	117419788	NM_003594	A8K4Q2|O75921|Q5T2K7|Q5VVU8|Q8N6I8	Silent	SNP	ENST00000369466.4	37	CCDS892.1																																																																																				0.567	TTF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033277.3		
BCL9	607	broad.mit.edu	37	1	147091373	147091373	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr1:147091373C>T	ENST00000234739.3	+	8	2152	c.1412C>T	c.(1411-1413)gCg>gTg	p.A471V		NM_004326.2	NP_004317.2	O00512	BCL9_HUMAN	B-cell CLL/lymphoma 9	471	Pro-rich.				canonical Wnt signaling pathway (GO:0060070)|myotube differentiation involved in skeletal muscle regeneration (GO:0014908)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|skeletal muscle cell differentiation (GO:0035914)|somatic stem cell maintenance (GO:0035019)	cis-Golgi network (GO:0005801)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)		p.A471V(1)		breast(1)|large_intestine(2)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	7	all_hematologic(923;0.115)					GAGCAGATAGCGTGGCTGAAA	0.512			T	"""IGH@, IGL@"""	B-ALL																																p.A471V			Dom	yes		1	1q21	607	B-cell CLL/lymphoma 9		L	.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1412T	1						.						51.0	54.0	53.0					1																	147091373		2203	4300	6503	145557997	SO:0001583	missense	607	exon8			Y13620	CCDS30833.1	1q21	2008-02-05			ENSG00000116128	ENSG00000116128			1008	protein-coding gene	gene with protein product		602597				9490669	Standard	NM_004326		Approved		uc001epq.3	O00512	OTTHUMG00000014031	ENST00000234739.3:c.1412C>T	1.37:g.147091373C>T	ENSP00000234739:p.Ala471Val	Somatic		Capture	Illumina HiSeq	Phase_I	145557997	NM_004326	Q5T489	Missense_Mutation	SNP	ENST00000234739.3	37	CCDS30833.1	.	.	.	.	.	.	.	.	.	.	C	18.15	3.559504	0.65538	.	.	ENSG00000116128	ENST00000234739	T	0.79845	-1.31	5.51	3.66	0.41972	.	0.000000	0.85682	D	0.000000	T	0.62732	0.2452	L	0.49350	1.555	0.80722	D	1	B;B	0.30937	0.301;0.301	B;B	0.17979	0.02;0.02	T	0.65389	-0.6180	10	0.52906	T	0.07	-8.4766	14.6966	0.69126	0.0:0.9198:0.0:0.0802	.	471;471	Q1JQ81;O00512	.;BCL9_HUMAN	V	471	ENSP00000234739:A471V	ENSP00000234739:A471V	A	+	2	0	BCL9	145557997	1.000000	0.71417	0.575000	0.28536	0.989000	0.77384	7.651000	0.83577	0.904000	0.36572	0.561000	0.74099	GCG		0.512	BCL9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039468.1	NM_004326	
NBPF15	284565	broad.mit.edu	37	1	148591317	148591317	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr1:148591317G>A	ENST00000369187.3	+	15	1871	c.1382G>A	c.(1381-1383)aGc>aAc	p.S461N	NBPF15_ENST00000464336.2_3'UTR|NBPF15_ENST00000442702.2_Missense_Mutation_p.S461N	NM_173638.3	NP_775909.2	Q8N660	NBPFF_HUMAN	neuroblastoma breakpoint family, member 15	461	NBPF 4. {ECO:0000255|PROSITE- ProRule:PRU00647}.					cytoplasm (GO:0005737)		p.S461N(1)		NS(1)|cervix(1)|endometrium(1)|large_intestine(4)|lung(3)|skin(2)	12	all_hematologic(923;0.032)					CAGCCCTACAGCAGTGCTGTT	0.483																																					p.S461N												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1382A	1						.						31.0	38.0	36.0					1																	148591317		792	2039	2831	146857941	SO:0001583	missense	284565	exon12			BC023087	CCDS72852.1	1q21.1	2014-01-16			ENSG00000243452	ENSG00000266338		"""neuroblastoma breakpoint family"""	28791	protein-coding gene	gene with protein product		610414, 614005	"""neuroblastoma breakpoint family, member 16"""	NBPF16		16079250	Standard	NM_173638		Approved	MGC8902	uc001esc.2	Q8N660	OTTHUMG00000013634	ENST00000369187.3:c.1382G>A	1.37:g.148591317G>A	ENSP00000358188:p.Ser461Asn	Somatic		Capture	Illumina HiSeq	Phase_I	146857941	NM_001102663	Q3BBV9|Q8IX77	Missense_Mutation	SNP	ENST00000369187.3	37	CCDS932.1	.	.	.	.	.	.	.	.	.	.	.	4.090	0.014677	0.07959	.	.	ENSG00000243452	ENST00000442702;ENST00000369187	T;T	0.06933	3.24;3.24	0.514	0.514	0.17007	DUF1220 (2);	.	.	.	.	T	0.01870	0.0059	L	0.34521	1.04	0.09310	N	1	B	0.24317	0.101	B	0.31016	0.123	T	0.48186	-0.9057	8	0.13470	T	0.59	.	.	.	.	.	461	Q8N660	NBPFF_HUMAN	N	461	ENSP00000416864:S461N;ENSP00000358188:S461N	ENSP00000358188:S461N	S	+	2	0	NBPF15	146857941	0.003000	0.15002	0.004000	0.12327	0.017000	0.09413	1.413000	0.34725	0.554000	0.29061	0.152000	0.16155	AGC		0.483	NBPF15-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000038609.3	NM_173638	
MTMR11	10903	broad.mit.edu	37	1	149903217	149903217	+	Nonsense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr1:149903217G>A	ENST00000439741.2	-	13	1475	c.1225C>T	c.(1225-1227)Cga>Tga	p.R409*	MTMR11_ENST00000361405.6_Intron|MTMR11_ENST00000369140.3_Nonsense_Mutation_p.R337*|SF3B4_ENST00000271628.8_5'Flank|MTMR11_ENST00000406732.3_Intron|MTMR11_ENST00000492824.1_Intron	NM_001145862.1	NP_001139334.1	A4FU01	MTMRB_HUMAN	myotubularin related protein 11	409	Myotubularin phosphatase. {ECO:0000255|PROSITE-ProRule:PRU00669}.						phosphatase activity (GO:0016791)	p.R337*(1)		breast(2)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(3)|lung(13)|prostate(2)|stomach(1)|urinary_tract(4)	34	Breast(34;0.0009)|Ovarian(49;0.0377)|all_hematologic(923;0.0597)|Hepatocellular(266;0.161)|Colorectal(459;0.171)		LUSC - Lung squamous cell carcinoma(543;0.221)|STAD - Stomach adenocarcinoma(528;0.247)			ACCCACTCTCGCTGTACTAGT	0.577																																					p.R337X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.C1009T	1						.						80.0	77.0	78.0					1																	149903217		2203	4300	6503	148169841	SO:0001587	stop_gained	10903	exon12			AK097000	CCDS72901.1, CCDS72902.1	1q12-q21	2011-06-09			ENSG00000014914	ENSG00000014914		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Myotubularins"""	24307	protein-coding gene	gene with protein product	"""cisplatin resistance associated"""					12495846	Standard	NM_181873		Approved	CRA	uc001etl.4	A4FU01	OTTHUMG00000012207	ENST00000439741.2:c.1225C>T	1.37:g.149903217G>A	ENSP00000391668:p.Arg409*	Somatic		Capture	Illumina HiSeq	Phase_I	148169841	NM_181873	B3KUE4|B4DJI6|B4DQF5|B4E3Q6|Q3ZCP7|Q5SZ62|Q6P2Q8|Q99752|Q99753	Nonsense_Mutation	SNP	ENST00000439741.2	37	CCDS53360.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	37|37	6.494690|6.494690	0.97612|0.97612	.|.	.|.	ENSG00000014914|ENSG00000014914	ENST00000405710|ENST00000369140;ENST00000439741	.|.	.|.	.|.	6.17|6.17	5.24|5.24	0.73138|0.73138	.|.	.|0.074905	.|0.53938	.|D	.|0.000045	T|.	0.50701|.	0.1631|.	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	P|.	0.35774|.	0.519|.	B|.	0.27887|.	0.084|.	T|.	0.50996|.	-0.8761|.	7|.	0.26408|0.30078	T|T	0.33|0.28	.|.	13.3154|13.3154	0.60405|0.60405	0.0:0.0:0.7128:0.2872|0.0:0.0:0.7128:0.2872	.|.	235|.	F8W8W0|.	.|.	V|X	235|337;409	.|.	ENSP00000384228:A235V|ENSP00000358136:R337X	A|R	-|-	2|1	0|2	MTMR11|MTMR11	148169841|148169841	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.991000|0.991000	0.79684|0.79684	3.196000|3.196000	0.51020|0.51020	1.575000|1.575000	0.49775|0.49775	0.655000|0.655000	0.94253|0.94253	GCG|CGA		0.577	MTMR11-203	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_181873	
RPRD2	23248	broad.mit.edu	37	1	150416763	150416763	+	Missense_Mutation	SNP	C	C	T	rs201468730		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr1:150416763C>T	ENST00000369068.4	+	6	608	c.604C>T	c.(604-606)Cgc>Tgc	p.R202C	RPRD2_ENST00000539519.1_Missense_Mutation_p.R176C|RPRD2_ENST00000492220.1_3'UTR|RPRD2_ENST00000401000.4_Missense_Mutation_p.R176C	NM_015203.3	NP_056018.2	Q5VT52	RPRD2_HUMAN	regulation of nuclear pre-mRNA domain containing 2	202						DNA-directed RNA polymerase II, holoenzyme (GO:0016591)		p.R202C(1)		central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(4)|lung(20)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	37						GCTATACAAGCGCTCAGAAGA	0.393																																					p.R202C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C604T	1						.	C	CYS/ARG	1,3771		0,1,1885	102.0	98.0	99.0		604	5.6	1.0	1		99	8,8228		0,8,4110	yes	missense	RPRD2	NM_015203.3	180	0,9,5995	TT,TC,CC		0.0971,0.0265,0.075	probably-damaging	202/1462	150416763	9,11999	1886	4118	6004	148683387	SO:0001583	missense	23248	exon6			BX641025	CCDS44216.1, CCDS72907.1	1q21.2	2012-02-09	2008-08-15	2008-07-28	ENSG00000163125	ENSG00000163125			29039	protein-coding gene	gene with protein product		614695	"""KIAA0460"""	KIAA0460		22231121	Standard	XM_005245033		Approved	FLJ32145, HSPC099	uc009wlr.3	Q5VT52	OTTHUMG00000012808	ENST00000369068.4:c.604C>T	1.37:g.150416763C>T	ENSP00000358064:p.Arg202Cys	Somatic		Capture	Illumina HiSeq	Phase_I	148683387	NM_015203	A8K6N8|B3KPT1|B4E2Q6|O75048|Q5VT51|Q5VT53|Q6MZL4|Q86XD2|Q9P0D7	Missense_Mutation	SNP	ENST00000369068.4	37	CCDS44216.1	.	.	.	.	.	.	.	.	.	.	C	32	5.144381	0.94603	2.65E-4	9.71E-4	ENSG00000163125	ENST00000401000;ENST00000539519;ENST00000369068	T;T;T	0.51325	0.76;0.77;0.71	5.56	5.56	0.83823	.	0.157716	0.64402	D	0.000016	T	0.60637	0.2284	L	0.53249	1.67	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.77004	0.95;0.95;0.989	T	0.62923	-0.6751	10	0.87932	D	0	-7.7172	19.5261	0.95208	0.0:1.0:0.0:0.0	.	176;202;176	B4E2Q6;Q5VT52;Q5VT52-3	.;RPRD2_HUMAN;.	C	176;176;202	ENSP00000383785:R176C;ENSP00000445482:R176C;ENSP00000358064:R202C	ENSP00000358064:R202C	R	+	1	0	RPRD2	148683387	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.624000	0.67764	2.632000	0.89209	0.655000	0.94253	CGC		0.393	RPRD2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000035844.1	NM_015203	
BNIPL	149428	broad.mit.edu	37	1	151011326	151011326	+	Missense_Mutation	SNP	G	G	A	rs373344206|rs371326091		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr1:151011326G>A	ENST00000368931.3	+	4	413	c.257G>A	c.(256-258)cGt>cAt	p.R86H	BNIPL_ENST00000295294.7_Missense_Mutation_p.R4H	NM_138278.3	NP_612122.2	Q7Z465	BNIPL_HUMAN	BCL2/adenovirus E1B 19kD interacting protein like	86					apoptotic process (GO:0006915)|negative regulation of cell proliferation (GO:0008285)|regulation of growth rate (GO:0040009)	cytosol (GO:0005829)|nucleus (GO:0005634)	identical protein binding (GO:0042802)	p.R4H(1)		autonomic_ganglia(1)|endometrium(3)|large_intestine(1)|lung(4)|skin(1)	10	Lung SC(34;0.00471)|Ovarian(49;0.0167)|all_hematologic(923;0.0597)|Hepatocellular(266;0.0997)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0486)|LUSC - Lung squamous cell carcinoma(543;0.211)			ATGCGCAAGCGTCTTTCTGCC	0.577																																					p.R4H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G11A	1						.	A	HIS/ARG,HIS/ARG	0,4406		0,0,2203	68.0	66.0	67.0		11,257	3.3	1.0	1		67	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	BNIPL	NM_001159642.1,NM_138278.3	29,29	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	benign,benign	4/276,86/358	151011326	1,13005	2203	4300	6503	149277950	SO:0001583	missense	149428	exon4			AF193056	CCDS978.2, CCDS53362.1	1q21.2	2008-02-05			ENSG00000163141	ENSG00000163141			16976	protein-coding gene	gene with protein product		611275				12681488, 11741952	Standard	NM_138278		Approved	BNIPl-1, BNIPL-2, PP753	uc001ewl.2	Q7Z465	OTTHUMG00000035157	ENST00000368931.3:c.257G>A	1.37:g.151011326G>A	ENSP00000357927:p.Arg86His	Somatic		Capture	Illumina HiSeq	Phase_I	149277950	NM_001159642	Q6DK43|Q8TCY7|Q8WYG2	Missense_Mutation	SNP	ENST00000368931.3	37	CCDS978.2	.	.	.	.	.	.	.	.	.	.	g	18.17	3.564433	0.65651	0.0	1.16E-4	ENSG00000163141	ENST00000368931;ENST00000361277;ENST00000295294;ENST00000392802	T;T;T	0.57107	1.12;1.16;0.42	5.15	3.26	0.37387	.	0.386996	0.26669	N	0.023114	T	0.55513	0.1925	M	0.79805	2.47	0.28381	N	0.919546	D	0.89917	1.0	D	0.67231	0.95	T	0.53121	-0.8483	10	0.72032	D	0.01	.	6.3965	0.21614	0.0912:0.0:0.7291:0.1796	.	86	Q7Z465	BNIPL_HUMAN	H	86;84;4;4	ENSP00000357927:R86H;ENSP00000355333:R84H;ENSP00000295294:R4H	ENSP00000295294:R4H	R	+	2	0	BNIPL	149277950	0.998000	0.40836	0.974000	0.42286	0.857000	0.48899	2.439000	0.44846	0.737000	0.32582	-0.213000	0.12676	CGT		0.577	BNIPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085092.1	NM_138279	
CDC42SE1	56882	broad.mit.edu	37	1	151027510	151027510	+	Silent	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr1:151027510G>A	ENST00000439374.2	-	6	1031	c.147C>T	c.(145-147)gcC>gcT	p.A49A	CDC42SE1_ENST00000492796.1_5'UTR|CDC42SE1_ENST00000540998.1_Silent_p.A49A|CDC42SE1_ENST00000357235.5_Silent_p.A49A|MLLT11_ENST00000368921.3_5'Flank			Q9NRR8	C42S1_HUMAN	CDC42 small effector 1	49					negative regulation of catalytic activity (GO:0043086)|phagocytosis (GO:0006909)|regulation of cell shape (GO:0008360)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|plasma membrane (GO:0005886)	GTPase inhibitor activity (GO:0005095)	p.A49A(1)		large_intestine(1)|lung(2)|upper_aerodigestive_tract(1)	4	Lung SC(34;0.00471)|Ovarian(49;0.0167)|all_hematologic(923;0.0597)|Hepatocellular(266;0.0997)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0486)|LUSC - Lung squamous cell carcinoma(543;0.211)			GTCCATCTCCGGCCCCCATCT	0.493																																					p.A49A												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C147T	1						.						182.0	142.0	156.0					1																	151027510		2203	4300	6503	149294134	SO:0001819	synonymous_variant	56882	exon4			AF187845	CCDS981.1	1q21.1	2008-02-05			ENSG00000197622	ENSG00000197622			17719	protein-coding gene	gene with protein product						10816584	Standard	NM_001038707		Approved	SCIP1, SPEC1	uc001ewp.3	Q9NRR8	OTTHUMG00000035158	ENST00000439374.2:c.147C>T	1.37:g.151027510G>A		Somatic		Capture	Illumina HiSeq	Phase_I	149294134	NM_001038707	D3DV12|Q9HB17|Q9NQR2	Silent	SNP	ENST00000439374.2	37	CCDS981.1																																																																																				0.493	CDC42SE1-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085096.2	NM_020239	
SEMA6C	10500	broad.mit.edu	37	1	151108068	151108068	+	Splice_Site	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr1:151108068G>A	ENST00000341697.3	-	14	3123	c.1432C>T	c.(1432-1434)Cgg>Tgg	p.R478W	SEMA6C_ENST00000479820.1_5'Flank			Q9H3T2	SEM6C_HUMAN	sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6C	478	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				axon guidance (GO:0007411)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)	p.R478W(2)		central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(5)|lung(15)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	28	Lung SC(34;0.00471)|Ovarian(49;0.0147)|all_hematologic(923;0.0597)|Hepatocellular(266;0.0997)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0486)|LUSC - Lung squamous cell carcinoma(543;0.211)			AGGCCTCACCGGGCAGGGCTG	0.597																																					p.R478W												.	.	2	Substitution - Missense(2)	large_intestine(1)|lung(1)	c.C1432T	1						.						70.0	76.0	74.0					1																	151108068		2203	4299	6502	149374692	SO:0001630	splice_region_variant	10500	exon14			AF339154	CCDS984.1, CCDS53363.1, CCDS53364.1	1q21.2	2008-02-05			ENSG00000143434	ENSG00000143434		"""Semaphorins"""	10740	protein-coding gene	gene with protein product	"""m-Sema Y2"""	609294				12110693	Standard	NM_030913		Approved	KIAA1869	uc001ewv.3	Q9H3T2	OTTHUMG00000012261	ENST00000341697.3:c.1433+1C>T	1.37:g.151108068G>A		Somatic		Capture	Illumina HiSeq	Phase_I	149374692	NM_001178061	D3DV15|Q5JR71|Q5JR72|Q5JR73|Q8WXT8|Q8WXT9|Q8WXU0|Q96JF8	Missense_Mutation	SNP	ENST00000341697.3	37	CCDS984.1	.	.	.	.	.	.	.	.	.	.	G	13.95	2.388909	0.42308	.	.	ENSG00000143434	ENST00000368914;ENST00000368912;ENST00000368913;ENST00000341697	T;T;T;T	0.20332	2.08;2.31;2.11;2.08	4.77	-1.01	0.10169	WD40/YVTN repeat-like-containing domain (1);Semaphorin/CD100 antigen (3);	0.000000	0.39210	N	0.001432	T	0.24624	0.0597	M	0.71036	2.16	0.28922	N	0.892079	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.91635	0.999;0.995;0.988;0.998	T	0.06041	-1.0849	10	0.87932	D	0	.	8.4767	0.33018	0.0831:0.0:0.2447:0.6722	.	478;438;478;478	B4DZD4;Q9H3T2-2;Q9H3T2-3;Q9H3T2	.;.;.;SEM6C_HUMAN	W	478;438;478;478	ENSP00000357910:R478W;ENSP00000357908:R438W;ENSP00000357909:R478W;ENSP00000344148:R478W	ENSP00000344148:R478W	R	-	1	2	SEMA6C	149374692	0.001000	0.12720	0.941000	0.38009	0.204000	0.24138	0.339000	0.19875	-0.152000	0.11156	-1.157000	0.01802	CGG		0.597	SEMA6C-004	KNOWN	alternative_5_UTR|mRNA_start_NF|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000034074.1	NM_030913	Missense_Mutation
POGZ	23126	broad.mit.edu	37	1	151400826	151400826	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr1:151400826G>T	ENST00000271715.2	-	6	946	c.632C>A	c.(631-633)cCt>cAt	p.P211H	POGZ_ENST00000409503.1_Missense_Mutation_p.P211H|POGZ_ENST00000361398.3_Missense_Mutation_p.P158H|POGZ_ENST00000540984.1_Intron|POGZ_ENST00000531094.1_Missense_Mutation_p.P158H|POGZ_ENST00000392723.1_Missense_Mutation_p.P158H|POGZ_ENST00000368863.2_Missense_Mutation_p.P116H|POGZ_ENST00000491586.1_Missense_Mutation_p.P158H	NM_001194937.1|NM_015100.3	NP_001181866.1|NP_055915.2	Q7Z3K3	POGZ_HUMAN	pogo transposable element with ZNF domain	211					kinetochore assembly (GO:0051382)|mitotic sister chromatid cohesion (GO:0007064)	cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.P211H(1)		NS(1)|breast(1)|endometrium(10)|kidney(3)|large_intestine(10)|liver(2)|lung(11)|ovary(3)|prostate(2)|skin(3)|urinary_tract(1)	47	Lung SC(34;0.00471)|Ovarian(49;0.00672)|Hepatocellular(266;0.0997)|all_hematologic(923;0.127)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.112)|LUSC - Lung squamous cell carcinoma(543;0.181)			TGGCCTCACAGGGGTCATCTG	0.547																																					p.P116H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C347A	1						.						237.0	240.0	239.0					1																	151400826		2203	4300	6503	149667450	SO:0001583	missense	23126	exon4			AB007930	CCDS997.1, CCDS998.1, CCDS44222.1, CCDS44222.2, CCDS53365.1, CCDS53366.1	1q21.1	2013-07-22			ENSG00000143442	ENSG00000143442			18801	protein-coding gene	gene with protein product	"""zinc finger protein 280E"", ""putative protein product of Nbla00003"""	614787				10976766	Standard	NM_015100		Approved	KIAA0461, ZNF635m, ZNF280E	uc001eyd.2	Q7Z3K3	OTTHUMG00000012499	ENST00000271715.2:c.632C>A	1.37:g.151400826G>T	ENSP00000271715:p.Pro211His	Somatic		Capture	Illumina HiSeq	Phase_I	149667450	NM_145796	B4DTP8|B4DYL9|B7ZBY5|E9PM80|O75049|Q3LIC4|Q5SZS1|Q5SZS2|Q5SZS3|Q5SZS4|Q8TDZ7|Q9Y4X7	Missense_Mutation	SNP	ENST00000271715.2	37	CCDS997.1	.	.	.	.	.	.	.	.	.	.	G	15.08	2.728010	0.48833	.	.	ENSG00000143442	ENST00000392723;ENST00000271715;ENST00000361398;ENST00000368863;ENST00000409503;ENST00000531094;ENST00000491586;ENST00000437847	D;D;D;D;D;D;D	0.82344	-1.6;-1.6;-1.6;-1.6;-1.6;-1.6;-1.6	5.04	4.06	0.47325	.	0.084270	0.50627	D	0.000111	T	0.63177	0.2489	N	0.08118	0	0.80722	D	1	P;P;P;P;P;P;B	0.50943	0.468;0.664;0.755;0.94;0.773;0.571;0.257	B;B;P;P;B;B;B	0.48166	0.201;0.201;0.487;0.569;0.366;0.281;0.201	T	0.71520	-0.4568	10	0.56958	D	0.05	-11.4262	10.3465	0.43909	0.0:0.0:0.6756:0.3244	.	158;211;116;211;158;158;211	E9PM80;B7ZBY5;Q7Z3K3-5;Q7Z3K3-4;Q7Z3K3-3;Q7Z3K3-2;Q7Z3K3	.;.;.;.;.;.;POGZ_HUMAN	H	158;211;158;116;211;158;158;211	ENSP00000376484:P158H;ENSP00000271715:P211H;ENSP00000354467:P158H;ENSP00000357856:P116H;ENSP00000386836:P211H;ENSP00000431259:P158H;ENSP00000418408:P158H	ENSP00000271715:P211H	P	-	2	0	POGZ	149667450	1.000000	0.71417	0.995000	0.50966	0.983000	0.72400	4.625000	0.61262	2.615000	0.88500	0.467000	0.42956	CCT		0.547	POGZ-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000034915.2	NM_207171	
CGN	57530	broad.mit.edu	37	1	151497303	151497303	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr1:151497303C>T	ENST00000271636.7	+	8	1688	c.1555C>T	c.(1555-1557)Cgg>Tgg	p.R519W		NM_020770.2	NP_065821.1	Q9P2M7	CING_HUMAN	cingulin	513	Glu-rich.				transforming growth factor beta receptor signaling pathway (GO:0007179)	cell junction (GO:0030054)|myosin complex (GO:0016459)|tight junction (GO:0005923)	actin binding (GO:0003779)|motor activity (GO:0003774)	p.R519W(1)		NS(1)|central_nervous_system(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(8)|liver(1)|lung(14)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	45	Ovarian(49;0.0273)|Hepatocellular(266;0.0997)|all_hematologic(923;0.127)|Melanoma(130;0.185)		LUSC - Lung squamous cell carcinoma(543;0.181)			GGAACATGTCCGGCAGCAGTA	0.617																																					p.R519W												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1555T	1						.						51.0	44.0	47.0					1																	151497303		2203	4300	6503	149763927	SO:0001583	missense	57530	exon8			AB037740	CCDS999.1	1q21	2008-02-05			ENSG00000143375	ENSG00000143375			17429	protein-coding gene	gene with protein product		609473				11042084, 12529927	Standard	NM_020770		Approved	KIAA1319	uc009wmw.3	Q9P2M7	OTTHUMG00000012497	ENST00000271636.7:c.1555C>T	1.37:g.151497303C>T	ENSP00000271636:p.Arg519Trp	Somatic		Capture	Illumina HiSeq	Phase_I	149763927	NM_020770	A6H8L3|A7MD22|Q5T386|Q9NR25	Missense_Mutation	SNP	ENST00000271636.7	37	CCDS999.1	.	.	.	.	.	.	.	.	.	.	C	15.16	2.750150	0.49257	.	.	ENSG00000143375	ENST00000271636	T	0.72167	-0.63	4.57	2.64	0.31445	.	0.130193	0.52532	D	0.000075	T	0.75436	0.3849	M	0.76002	2.32	0.46542	D	0.999096	D	0.89917	1.0	D	0.73708	0.981	T	0.77905	-0.2413	10	0.87932	D	0	-30.813	10.4126	0.44303	0.5194:0.4806:0.0:0.0	.	513	Q9P2M7	CING_HUMAN	W	519	ENSP00000271636:R519W	ENSP00000271636:R519W	R	+	1	2	CGN	149763927	0.411000	0.25384	0.952000	0.39060	0.569000	0.35902	0.814000	0.27239	0.516000	0.28340	-0.309000	0.09137	CGG		0.617	CGN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034900.3	NM_020770	
HRNR	388697	broad.mit.edu	37	1	152192058	152192058	+	Missense_Mutation	SNP	C	C	T	rs532023619		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr1:152192058C>T	ENST00000368801.2	-	3	2122	c.2047G>A	c.(2047-2049)Ggt>Agt	p.G683S	FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000420707.1_RNA	NM_001009931.1	NP_001009931.1	Q86YZ3	HORN_HUMAN	hornerin	683					establishment of skin barrier (GO:0061436)|hematopoietic progenitor cell differentiation (GO:0002244)|keratinization (GO:0031424)	cornified envelope (GO:0001533)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)	p.G683S(1)		autonomic_ganglia(1)|breast(6)|central_nervous_system(2)|cervix(2)|endometrium(22)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(19)|liver(1)|lung(84)|ovary(5)|prostate(6)|skin(12)|stomach(9)|upper_aerodigestive_tract(5)|urinary_tract(6)	192	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			GAAGACCAACCGGAGCCAGAC	0.592													a|||	1	0.000199681	0.0	0.0	5008	,	,		20957	0.0		0.0	False		,,,				2504	0.001				p.G683S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2047A	1						.						129.0	143.0	138.0					1																	152192058		2203	4300	6503	150458682	SO:0001583	missense	388697	exon3			AB104446	CCDS30859.1	1q21.3	2013-01-10			ENSG00000197915	ENSG00000197915		"""EF-hand domain containing"""	20846	protein-coding gene	gene with protein product	"""filaggrin family member 3"""						Standard	NM_001009931		Approved	S100a18, S100A16, FLG3	uc001ezt.2	Q86YZ3	OTTHUMG00000012243	ENST00000368801.2:c.2047G>A	1.37:g.152192058C>T	ENSP00000357791:p.Gly683Ser	Somatic		Capture	Illumina HiSeq	Phase_I	150458682	NM_001009931	Q5DT20|Q5U1F4	Missense_Mutation	SNP	ENST00000368801.2	37	CCDS30859.1	.	.	.	.	.	.	.	.	.	.	-	13.87	2.366744	0.41902	.	.	ENSG00000197915	ENST00000368801	T	0.18810	2.19	3.13	-3.82	0.04281	.	.	.	.	.	T	0.01320	0.0043	N	0.12746	0.255	0.09310	N	1	P	0.48911	0.917	B	0.29598	0.104	T	0.39583	-0.9607	9	0.12103	T	0.63	.	1.4043	0.02277	0.1503:0.3402:0.2953:0.2142	.	683	Q86YZ3	HORN_HUMAN	S	683	ENSP00000357791:G683S	ENSP00000357791:G683S	G	-	1	0	HRNR	150458682	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.462000	0.00997	-0.968000	0.03578	-1.796000	0.00623	GGT		0.592	HRNR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034016.1	XM_373868	
FLG	2312	broad.mit.edu	37	1	152277643	152277643	+	Missense_Mutation	SNP	C	C	T	rs188183903	byFrequency	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr1:152277643C>T	ENST00000368799.1	-	3	9754	c.9719G>A	c.(9718-9720)cGt>cAt	p.R3240H	FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000420707.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	3240	Ser-rich.				establishment of skin barrier (GO:0061436)|keratinocyte differentiation (GO:0030216)|multicellular organismal development (GO:0007275)	cytoplasmic membrane-bounded vesicle (GO:0016023)|intermediate filament (GO:0005882)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|structural molecule activity (GO:0005198)	p.R3240H(2)		autonomic_ganglia(1)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(38)|haematopoietic_and_lymphoid_tissue(1)|kidney(16)|large_intestine(57)|lung(211)|ovary(13)|pancreas(1)|prostate(15)|skin(24)|stomach(5)|upper_aerodigestive_tract(10)|urinary_tract(12)	424	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			AACAGATCCACGATGGTTTCT	0.587									Ichthyosis				T|||	3	0.000599042	0.0	0.0	5008	,	,		19741	0.003		0.0	False		,,,				2504	0.0				p.R3240H												.	.	2	Substitution - Missense(2)	large_intestine(1)|prostate(1)	c.G9719A	1						.						209.0	216.0	214.0					1																	152277643		2203	4300	6503	150544267	SO:0001583	missense	2312	exon3	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	XM_048104	CCDS30860.1	1q21.3	2013-01-10			ENSG00000143631	ENSG00000143631		"""EF-hand domain containing"""	3748	protein-coding gene	gene with protein product		135940				2740331, 2248957, 16444271	Standard	NM_002016		Approved		uc001ezu.1	P20930	OTTHUMG00000012202	ENST00000368799.1:c.9719G>A	1.37:g.152277643C>T	ENSP00000357789:p.Arg3240His	Somatic		Capture	Illumina HiSeq	Phase_I	150544267	NM_002016	Q01720|Q5T583|Q9UC71	Missense_Mutation	SNP	ENST00000368799.1	37	CCDS30860.1	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	T	3.777	-0.046533	0.07407	.	.	ENSG00000143631	ENST00000368799;ENST00000368796	T	0.00816	5.66	3.23	-6.47	0.01902	.	.	.	.	.	T	0.00073	0.0002	N	0.03209	-0.39	0.09310	N	1	B	0.17465	0.022	B	0.08055	0.003	T	0.46569	-0.9182	9	0.02654	T	1	.	0.5789	0.00708	0.3237:0.2717:0.225:0.1796	.	3240	P20930	FILA_HUMAN	H	3240;178	ENSP00000357789:R3240H	ENSP00000357786:R178H	R	-	2	0	FLG	150544267	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.482000	0.06544	-2.877000	0.00320	-2.017000	0.00434	CGT		0.587	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016	
FLG	2312	broad.mit.edu	37	1	152285900	152285900	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr1:152285900T>C	ENST00000368799.1	-	3	1497	c.1462A>G	c.(1462-1464)Agc>Ggc	p.S488G	FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000392688.2_RNA|FLG-AS1_ENST00000420707.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	488	Ser-rich.				establishment of skin barrier (GO:0061436)|keratinocyte differentiation (GO:0030216)|multicellular organismal development (GO:0007275)	cytoplasmic membrane-bounded vesicle (GO:0016023)|intermediate filament (GO:0005882)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|structural molecule activity (GO:0005198)	p.S488G(1)		autonomic_ganglia(1)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(38)|haematopoietic_and_lymphoid_tissue(1)|kidney(16)|large_intestine(57)|lung(211)|ovary(13)|pancreas(1)|prostate(15)|skin(24)|stomach(5)|upper_aerodigestive_tract(10)|urinary_tract(12)	424	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			CCTCCAGTGCTGGTCCCGGTC	0.622									Ichthyosis																												p.S488G												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A1462G	1						.						243.0	229.0	234.0					1																	152285900		2203	4300	6503	150552524	SO:0001583	missense	2312	exon3	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	XM_048104	CCDS30860.1	1q21.3	2013-01-10			ENSG00000143631	ENSG00000143631		"""EF-hand domain containing"""	3748	protein-coding gene	gene with protein product		135940				2740331, 2248957, 16444271	Standard	NM_002016		Approved		uc001ezu.1	P20930	OTTHUMG00000012202	ENST00000368799.1:c.1462A>G	1.37:g.152285900T>C	ENSP00000357789:p.Ser488Gly	Somatic		Capture	Illumina HiSeq	Phase_I	150552524	NM_002016	Q01720|Q5T583|Q9UC71	Missense_Mutation	SNP	ENST00000368799.1	37	CCDS30860.1	.	.	.	.	.	.	.	.	.	.	-	11.18	1.561387	0.27915	.	.	ENSG00000143631	ENST00000368799;ENST00000392689	T	0.01725	4.67	3.8	-4.01	0.04045	.	.	.	.	.	T	0.00552	0.0018	L	0.45581	1.43	0.09310	N	1	B	0.15930	0.015	B	0.26969	0.075	T	0.44236	-0.9341	9	0.20046	T	0.44	.	4.5638	0.12173	0.1661:0.4482:0.0:0.3857	.	488	P20930	FILA_HUMAN	G	488;20	ENSP00000357789:S488G	ENSP00000357789:S488G	S	-	1	0	FLG	150552524	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.317000	0.08060	-0.464000	0.06963	-0.394000	0.06481	AGC		0.622	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016	
PGLYRP4	57115	broad.mit.edu	37	1	153313047	153313047	+	Missense_Mutation	SNP	C	C	T	rs200799317		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr1:153313047C>T	ENST00000359650.5	-	7	698	c.634G>A	c.(634-636)Ggc>Agc	p.G212S	PGLYRP4_ENST00000368739.3_Missense_Mutation_p.G208S	NM_020393.2	NP_065126.2	Q96LB8	PGRP4_HUMAN	peptidoglycan recognition protein 4	212					defense response to Gram-positive bacterium (GO:0050830)|detection of bacterium (GO:0016045)|growth of symbiont in host (GO:0044117)|innate immune response (GO:0045087)|negative regulation of interferon-gamma production (GO:0032689)|negative regulation of natural killer cell differentiation involved in immune response (GO:0032827)|pattern recognition receptor signaling pathway (GO:0002221)|peptidoglycan catabolic process (GO:0009253)	extracellular region (GO:0005576)|intracellular (GO:0005622)|membrane (GO:0016020)	N-acetylmuramoyl-L-alanine amidase activity (GO:0008745)|peptidoglycan binding (GO:0042834)|peptidoglycan receptor activity (GO:0016019)|zinc ion binding (GO:0008270)	p.G212S(1)		breast(2)|endometrium(1)|large_intestine(4)|lung(10)|ovary(3)|prostate(1)|skin(1)|stomach(1)	23	all_lung(78;2.81e-33)|Lung NSC(65;9.54e-32)|Hepatocellular(266;0.0877)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.171)			GGGACAACGCCGGGGCAAGCT	0.592																																					p.G212S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G634A	1						.						43.0	42.0	43.0					1																	153313047		2203	4300	6503	151579671	SO:0001583	missense	57115	exon7			AF242518	CCDS30871.1	1q21	2008-02-05			ENSG00000163218	ENSG00000163218			30015	protein-coding gene	gene with protein product	"""peptidoglycan recognition protein I beta precursor"""	608198				11461926	Standard	XR_241090		Approved	SBBI67, PGRPIB, PGLYRPIbeta, PGRP-Ibeta	uc001fbo.3	Q96LB8	OTTHUMG00000037057	ENST00000359650.5:c.634G>A	1.37:g.153313047C>T	ENSP00000352672:p.Gly212Ser	Somatic		Capture	Illumina HiSeq	Phase_I	151579671	NM_020393	A8K838|Q3B822|Q3B823|Q5SY63|Q5SY64|Q9HD75	Missense_Mutation	SNP	ENST00000359650.5	37	CCDS30871.1	.	.	.	.	.	.	.	.	.	.	T	0.005	-2.135912	0.00335	.	.	ENSG00000163218	ENST00000368739;ENST00000359650	T;T	0.22336	1.96;1.96	3.64	-3.85	0.04243	Peptidoglycan recognition protein family domain, metazoa/bacteria (1);N-acetylmuramoyl-L-alanine amidase domain (5);	2.004400	0.02142	N	0.057294	T	0.02807	0.0084	L	0.32530	0.975	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.20706	-1.0267	10	0.07813	T	0.8	-28.0156	1.4729	0.02420	0.1438:0.3078:0.3116:0.2368	.	208;212	Q96LB8-2;Q96LB8	.;PGRP4_HUMAN	S	208;212	ENSP00000357728:G208S;ENSP00000352672:G212S	ENSP00000352672:G212S	G	-	1	0	PGLYRP4	151579671	0.000000	0.05858	0.001000	0.08648	0.009000	0.06853	-1.328000	0.02680	-1.101000	0.03027	-1.062000	0.02293	GGC		0.592	PGLYRP4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000089978.1	NM_020393	
NPR1	4881	broad.mit.edu	37	1	153662433	153662433	+	Missense_Mutation	SNP	G	G	A	rs144189754		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr1:153662433G>A	ENST00000368680.3	+	19	3381	c.2909G>A	c.(2908-2910)cGc>cAc	p.R970H		NM_000906.3	NP_000897.3	P16066	ANPRA_HUMAN	natriuretic peptide receptor 1	970	Guanylate cyclase. {ECO:0000255|PROSITE- ProRule:PRU00099}.				body fluid secretion (GO:0007589)|cell surface receptor signaling pathway (GO:0007166)|cGMP biosynthetic process (GO:0006182)|dopamine metabolic process (GO:0042417)|G-protein coupled receptor signaling pathway (GO:0007186)|intracellular signal transduction (GO:0035556)|negative regulation of angiogenesis (GO:0016525)|negative regulation of cell growth (GO:0030308)|negative regulation of smooth muscle cell proliferation (GO:0048662)|positive regulation of cGMP biosynthetic process (GO:0030828)|positive regulation of renal sodium excretion (GO:0035815)|positive regulation of urine volume (GO:0035810)|receptor guanylyl cyclase signaling pathway (GO:0007168)|regulation of blood pressure (GO:0008217)|regulation of blood vessel size (GO:0050880)|regulation of vascular permeability (GO:0043114)|regulation of vasodilation (GO:0042312)	integral component of plasma membrane (GO:0005887)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|G-protein coupled peptide receptor activity (GO:0008528)|GTP binding (GO:0005525)|guanylate cyclase activity (GO:0004383)|hormone binding (GO:0042562)|natriuretic peptide receptor activity (GO:0016941)|peptide hormone binding (GO:0017046)|protein kinase activity (GO:0004672)	p.R970H(1)		NS(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(8)|liver(1)|lung(17)|ovary(4)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	42	all_lung(78;3.75e-32)|Lung NSC(65;1.37e-30)|Hepatocellular(266;0.0877)|Melanoma(130;0.199)		LUSC - Lung squamous cell carcinoma(543;0.151)		Amyl Nitrite(DB01612)|Erythrityl Tetranitrate(DB01613)|Isosorbide Dinitrate(DB00883)|Nesiritide(DB04899)|Nitroglycerin(DB00727)|Nitroprusside(DB00325)	GAGCAGCTGCGCTTGCGCATT	0.667																																					p.R970H	Pancreas(141;1349 1870 15144 15830 40702)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2909A	1						.	G	HIS/ARG	1,4295		0,1,2147	14.0	15.0	15.0		2909	2.9	1.0	1	dbSNP_134	15	0,8372		0,0,4186	no	missense	NPR1	NM_000906.3	29	0,1,6333	AA,AG,GG		0.0,0.0233,0.0079	probably-damaging	970/1062	153662433	1,12667	2148	4186	6334	151929057	SO:0001583	missense	4881	exon19			BC063304	CCDS1051.1	1q21-q22	2014-03-03	2014-03-03		ENSG00000169418	ENSG00000169418			7943	protein-coding gene	gene with protein product	"""guanylate cyclase A"""	108960	"""atrionatriuretic peptide receptor A"", ""natriuretic peptide receptor A"""	ANPRA, NPRA		1979052	Standard	NM_000906		Approved	GUCY2A, ANPa	uc001fcs.4	P16066	OTTHUMG00000037085	ENST00000368680.3:c.2909G>A	1.37:g.153662433G>A	ENSP00000357669:p.Arg970His	Somatic		Capture	Illumina HiSeq	Phase_I	151929057	NM_000906	B0ZBF0|Q5SR08|Q6P4Q3	Missense_Mutation	SNP	ENST00000368680.3	37	CCDS1051.1	.	.	.	.	.	.	.	.	.	.	G	16.60	3.168480	0.57584	2.33E-4	0.0	ENSG00000169418	ENST00000368680;ENST00000428723;ENST00000368677	D	0.81821	-1.54	2.87	2.87	0.33458	Adenylyl cyclase class-3/4/guanylyl cyclase (5);	0.082046	0.42053	D	0.000767	T	0.82121	0.4968	M	0.62016	1.91	0.45097	D	0.998119	D;P	0.58268	0.982;0.663	P;B	0.62491	0.903;0.176	D	0.83736	0.0201	10	0.62326	D	0.03	.	11.9439	0.52918	0.0:0.0:1.0:0.0	.	449;970	B7Z4Y7;P16066	.;ANPRA_HUMAN	H	970;449;151	ENSP00000357669:R970H	ENSP00000357666:R151H	R	+	2	0	NPR1	151929057	0.033000	0.19621	0.999000	0.59377	0.984000	0.73092	1.805000	0.38883	1.907000	0.55213	0.462000	0.41574	CGC		0.667	NPR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090034.1	NM_000906	
DENND4B	9909	broad.mit.edu	37	1	153912692	153912692	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr1:153912692G>A	ENST00000361217.4	-	11	1961	c.1543C>T	c.(1543-1545)Cgc>Tgc	p.R515C		NM_014856.2	NP_055671.2	O75064	DEN4B_HUMAN	DENN/MADD domain containing 4B	515					positive regulation of Rab GTPase activity (GO:0032851)|regulation of Rab protein signal transduction (GO:0032483)	Golgi apparatus (GO:0005794)|nucleus (GO:0005634)	Rab guanyl-nucleotide exchange factor activity (GO:0017112)	p.R403C(1)		NS(1)|breast(1)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(6)|lung(9)|ovary(1)|prostate(5)|skin(2)|urinary_tract(1)	36	all_lung(78;2.89e-32)|Lung NSC(65;2.27e-30)|Hepatocellular(266;0.0877)|Melanoma(130;0.199)		LUSC - Lung squamous cell carcinoma(543;0.151)			TAGGGTCTGCGGGGCAGGGTC	0.592																																					p.R515C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1543T	1						.						45.0	46.0	46.0					1																	153912692		1903	4122	6025	152179316	SO:0001583	missense	9909	exon11			AB007945	CCDS44228.1	1q21.3	2012-10-03	2006-01-27	2006-01-27	ENSG00000198837	ENSG00000198837		"""DENN/MADD domain containing"""	29044	protein-coding gene	gene with protein product			"""KIAA0476"""	KIAA0476		9455484, 12906859	Standard	NM_014856		Approved		uc001fdd.1	O75064	OTTHUMG00000037157	ENST00000361217.4:c.1543C>T	1.37:g.153912692G>A	ENSP00000354597:p.Arg515Cys	Somatic		Capture	Illumina HiSeq	Phase_I	152179316	NM_014856	Q5T4K0	Missense_Mutation	SNP	ENST00000361217.4	37	CCDS44228.1	.	.	.	.	.	.	.	.	.	.	G	22.4	4.281691	0.80692	.	.	ENSG00000198837	ENST00000361217;ENST00000368646	T;T	0.07800	3.16;3.16	4.72	4.72	0.59763	.	0.124816	0.50627	D	0.000105	T	0.15869	0.0382	L	0.50333	1.59	0.80722	D	1	D	0.89917	1.0	D	0.68483	0.958	T	0.00728	-1.1591	10	0.87932	D	0	-18.9799	16.6069	0.84832	0.0:0.0:1.0:0.0	.	515	O75064	DEN4B_HUMAN	C	515;526	ENSP00000354597:R515C;ENSP00000357635:R526C	ENSP00000354597:R515C	R	-	1	0	DENND4B	152179316	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	4.309000	0.59135	2.455000	0.83008	0.563000	0.77884	CGC		0.592	DENND4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090278.2	XM_375806	
CRTC2	200186	broad.mit.edu	37	1	153923813	153923813	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr1:153923813C>T	ENST00000368633.1	-	11	1454	c.1327G>A	c.(1327-1329)Gac>Aac	p.D443N	CRTC2_ENST00000476883.1_5'Flank|CRTC2_ENST00000368630.3_Missense_Mutation_p.D123N	NM_181715.2	NP_859066.1	Q53ET0	CRTC2_HUMAN	CREB regulated transcription coactivator 2	443					gluconeogenesis (GO:0006094)|glucose homeostasis (GO:0042593)|histone H3-K9 acetylation (GO:0043970)|positive regulation of CREB transcription factor activity (GO:0032793)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein homotetramerization (GO:0051289)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	cAMP response element binding protein binding (GO:0008140)	p.D443N(1)|p.D443Y(1)		NS(1)|breast(1)|cervix(2)|endometrium(4)|large_intestine(5)|lung(8)|ovary(3)|skin(1)|upper_aerodigestive_tract(2)	27	all_lung(78;3.05e-32)|Lung NSC(65;3.74e-30)|Hepatocellular(266;0.0877)|Melanoma(130;0.199)		LUSC - Lung squamous cell carcinoma(543;0.151)			CTTCTGGCGTCGGCTGGGCCC	0.637																																					p.D443N												.	.	2	Substitution - Missense(2)	large_intestine(1)|lung(1)	c.G1327A	1						.						47.0	39.0	42.0					1																	153923813		2203	4300	6503	152190437	SO:0001583	missense	200186	exon11			AY360172	CCDS30875.1	1q21.3	2008-02-05			ENSG00000160741	ENSG00000160741			27301	protein-coding gene	gene with protein product		608972				14506290, 14536081	Standard	NM_181715		Approved	TORC2	uc021pab.1	Q53ET0	OTTHUMG00000037156	ENST00000368633.1:c.1327G>A	1.37:g.153923813C>T	ENSP00000357622:p.Asp443Asn	Somatic		Capture	Illumina HiSeq	Phase_I	152190437	NM_181715	Q6UUV8|Q7Z3X7|Q8N332	Missense_Mutation	SNP	ENST00000368633.1	37	CCDS30875.1	.	.	.	.	.	.	.	.	.	.	C	20.4	3.990838	0.74703	.	.	ENSG00000160741	ENST00000368630;ENST00000368633	T;T	0.51325	0.71;2.68	4.99	4.99	0.66335	.	0.076408	0.51477	D	0.000099	T	0.38241	0.1033	L	0.57536	1.79	0.36373	D	0.861432	D	0.61697	0.99	P	0.47470	0.548	T	0.26780	-1.0093	10	0.33940	T	0.23	-18.2965	13.6478	0.62292	0.0:1.0:0.0:0.0	.	443	Q53ET0	CRTC2_HUMAN	N	123;443	ENSP00000357619:D123N;ENSP00000357622:D443N	ENSP00000357619:D123N	D	-	1	0	CRTC2	152190437	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.893000	0.75649	2.602000	0.87976	0.557000	0.71058	GAC		0.637	CRTC2-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090272.3	NM_181715	
CRTC2	200186	broad.mit.edu	37	1	153924004	153924004	+	Missense_Mutation	SNP	C	C	T	rs143226168		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr1:153924004C>T	ENST00000368633.1	-	11	1263	c.1136G>A	c.(1135-1137)cGc>cAc	p.R379H	CRTC2_ENST00000476883.1_5'Flank|CRTC2_ENST00000368630.3_Missense_Mutation_p.R59H	NM_181715.2	NP_859066.1	Q53ET0	CRTC2_HUMAN	CREB regulated transcription coactivator 2	379	Ser-rich.		R -> C (in dbSNP:rs150423770). {ECO:0000269|PubMed:14506290, ECO:0000269|PubMed:17950019}.		gluconeogenesis (GO:0006094)|glucose homeostasis (GO:0042593)|histone H3-K9 acetylation (GO:0043970)|positive regulation of CREB transcription factor activity (GO:0032793)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein homotetramerization (GO:0051289)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	cAMP response element binding protein binding (GO:0008140)	p.R379H(1)		NS(1)|breast(1)|cervix(2)|endometrium(4)|large_intestine(5)|lung(8)|ovary(3)|skin(1)|upper_aerodigestive_tract(2)	27	all_lung(78;3.05e-32)|Lung NSC(65;3.74e-30)|Hepatocellular(266;0.0877)|Melanoma(130;0.199)		LUSC - Lung squamous cell carcinoma(543;0.151)			CAGTACATGGCGGGCCAAGGA	0.637													C|||	1	0.000199681	0.0	0.0	5008	,	,		15494	0.0		0.001	False		,,,				2504	0.0				p.R379H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1136A	1						.	C	HIS/ARG	0,4406	2.1+/-5.4	0,0,2203	48.0	54.0	52.0		1136	0.9	0.3	1	dbSNP_134	52	2,8598	2.2+/-6.3	0,2,4298	yes	missense	CRTC2	NM_181715.2	29	0,2,6501	TT,TC,CC		0.0233,0.0,0.0154	possibly-damaging	379/694	153924004	2,13004	2203	4300	6503	152190628	SO:0001583	missense	200186	exon11			AY360172	CCDS30875.1	1q21.3	2008-02-05			ENSG00000160741	ENSG00000160741			27301	protein-coding gene	gene with protein product		608972				14506290, 14536081	Standard	NM_181715		Approved	TORC2	uc021pab.1	Q53ET0	OTTHUMG00000037156	ENST00000368633.1:c.1136G>A	1.37:g.153924004C>T	ENSP00000357622:p.Arg379His	Somatic		Capture	Illumina HiSeq	Phase_I	152190628	NM_181715	Q6UUV8|Q7Z3X7|Q8N332	Missense_Mutation	SNP	ENST00000368633.1	37	CCDS30875.1	0	0.0	0	0.0	0	0.0	0	0.0	0	0.0	C	4.157	0.027560	0.08054	0.0	2.33E-4	ENSG00000160741	ENST00000368630;ENST00000368633	T;T	0.44881	0.91;2.72	4.39	0.891	0.19224	.	0.672384	0.14840	N	0.295356	T	0.10594	0.0259	L	0.31294	0.92	0.23304	N	0.997944	B	0.06786	0.001	B	0.01281	0.0	T	0.31943	-0.9925	10	0.31617	T	0.26	0.0733	6.7599	0.23534	0.0:0.4628:0.0:0.5372	.	379	Q53ET0	CRTC2_HUMAN	H	59;379	ENSP00000357619:R59H;ENSP00000357622:R379H	ENSP00000357619:R59H	R	-	2	0	CRTC2	152190628	0.994000	0.37717	0.278000	0.24718	0.217000	0.24651	0.218000	0.17622	-0.016000	0.14127	-0.262000	0.10625	CGC		0.637	CRTC2-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090272.3	NM_181715	
TPM3	7170	broad.mit.edu	37	1	154131522	154131522	+	Missense_Mutation	SNP	G	G	A	rs542934206		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr1:154131522G>A	ENST00000368531.2	-	8	677	c.667C>T	c.(667-669)Cgt>Tgt	p.R223C	TPM3_ENST00000341372.3_Intron|TPM3_ENST00000302206.5_Intron|TPM3_ENST00000328159.4_Intron|TPM3_ENST00000271850.7_Intron|TPM3_ENST00000330188.9_Intron|TPM3_ENST00000341485.5_Intron|TPM3_ENST00000323144.7_Missense_Mutation_p.R223C|TPM3_ENST00000469717.1_Intron|TPM3_ENST00000368533.3_Intron			P06753	TPM3_HUMAN	tropomyosin 3	260					cellular component movement (GO:0006928)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|muscle thin filament tropomyosin (GO:0005862)|stress fiber (GO:0001725)		p.R223C(1)	TPM3/NTRK1_ENST00000392302(70)|TPM3/ALK(33)	breast(1)|endometrium(1)|large_intestine(2)|lung(4)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	11	all_lung(78;9.35e-31)|Lung NSC(65;1.33e-28)|Hepatocellular(266;0.0877)|Melanoma(130;0.128)					CTGTAGAGACGCTCTGCAGCA	0.493			T	"""NTRK1, ALK, ROS1"""	"""papillary thyroid, ALCL, NSCLC"""								G|||	1	0.000199681	0.0	0.0	5008	,	,		19253	0.001		0.0	False		,,,				2504	0.0				p.R223C			Dom	yes		1	1q22-q23	7170	tropomyosin 3		"""E, L"""	.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C667T	1						.						71.0	68.0	69.0					1																	154131522		1967	4146	6113	152398146	SO:0001583	missense	7170	exon8			BC008425	CCDS1060.1, CCDS41400.1, CCDS41401.1, CCDS41402.1, CCDS41403.1, CCDS60274.1, CCDS60275.1, CCDS72922.1	1q21.2	2014-09-17			ENSG00000143549	ENSG00000143549		"""Tropomyosins"""	12012	protein-coding gene	gene with protein product		191030		NEM1		1829807	Standard	NM_153649		Approved	TRK	uc001fec.2	P06753	OTTHUMG00000035853	ENST00000368531.2:c.667C>T	1.37:g.154131522G>A	ENSP00000357517:p.Arg223Cys	Somatic		Capture	Illumina HiSeq	Phase_I	152398146	NM_001043353	D3DV71|P12324|Q2QD06|Q5VU58|Q5VU63|Q5VU66|Q5VU71|Q5VU72|Q8TCG3|Q969Q2|Q9NQH8	Missense_Mutation	SNP	ENST00000368531.2	37	CCDS41402.1	.	.	.	.	.	.	.	.	.	.	G	18.40	3.615198	0.66672	.	.	ENSG00000143549	ENST00000368531;ENST00000323144	T;T	0.79247	-1.25;-1.25	5.43	4.51	0.55191	.	.	.	.	.	D	0.85208	0.5644	M	0.93197	3.39	0.80722	D	1	P;P	0.41080	0.638;0.737	B;P	0.51453	0.371;0.67	D	0.88502	0.3083	9	0.87932	D	0	.	14.019	0.64543	0.073:0.0:0.927:0.0	.	223;223	P06753-3;Q5VU72	.;.	C	223	ENSP00000357517:R223C;ENSP00000357518:R223C	ENSP00000357518:R223C	R	-	1	0	TPM3	152398146	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	2.845000	0.48254	1.279000	0.44446	0.462000	0.41574	CGT		0.493	TPM3-026	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000360306.1	NM_152263	
UBAP2L	9898	broad.mit.edu	37	1	154233433	154233433	+	Missense_Mutation	SNP	C	C	G			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	G	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr1:154233433C>G	ENST00000361546.2	+	22	2686	c.2644C>G	c.(2644-2646)Ccc>Gcc	p.P882A	UBAP2L_ENST00000428931.1_Missense_Mutation_p.P882A|UBAP2L_ENST00000343815.6_Missense_Mutation_p.P882A|SNORA58_ENST00000364259.1_RNA|UBAP2L_ENST00000271877.7_Missense_Mutation_p.P893A			Q14157	UBP2L_HUMAN	ubiquitin associated protein 2-like	882					binding of sperm to zona pellucida (GO:0007339)		poly(A) RNA binding (GO:0044822)	p.P882A(1)|p.P378A(1)		NS(2)|breast(7)|central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(8)|lung(20)|ovary(1)|prostate(1)|urinary_tract(2)	50	all_lung(78;1.09e-30)|Lung NSC(65;1.66e-28)|Hepatocellular(266;0.0877)		LUSC - Lung squamous cell carcinoma(543;0.185)			CTTGGCCCAACCCCAACAGAA	0.582																																					p.P882A												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.C2644G	1						.						79.0	78.0	78.0					1																	154233433		2203	4300	6503	152500057	SO:0001583	missense	9898	exon23			BC003170	CCDS1063.1, CCDS44229.1, CCDS72925.1	1q21.3	2008-02-05			ENSG00000143569	ENSG00000143569			29877	protein-coding gene	gene with protein product						8590280, 11230159	Standard	NM_014847		Approved	NICE-4, KIAA0144	uc001fep.4	Q14157	OTTHUMG00000035983	ENST00000361546.2:c.2644C>G	1.37:g.154233433C>G	ENSP00000355343:p.Pro882Ala	Somatic		Capture	Illumina HiSeq	Phase_I	152500057	NM_014847	B4E0U8|Q5VU75|Q5VU76|Q9BTU3|Q9UGL2|Q9UGL3|Q9UGL4|Q9UGL5	Missense_Mutation	SNP	ENST00000361546.2	37	CCDS1063.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	15.30|15.30	2.791503|2.791503	0.50102|0.50102	.|.	.|.	ENSG00000143569|ENSG00000143569	ENST00000343815;ENST00000428931;ENST00000456955;ENST00000433006;ENST00000271877;ENST00000361546|ENST00000433615;ENST00000428595	T;T;T;T|.	0.30448|.	1.53;1.53;1.53;1.53|.	5.23|5.23	5.23|5.23	0.72850|0.72850	.|.	0.054793|.	0.85682|.	D|.	0.000000|.	T|T	0.58666|0.58666	0.2138|0.2138	L|L	0.44542|0.44542	1.39|1.39	0.48975|0.48975	D|D	0.999739|0.999739	B;P;P;P;P;B;B|.	0.42692|.	0.374;0.612;0.759;0.759;0.787;0.143;0.23|.	B;B;B;B;B;B;B|.	0.42995|.	0.222;0.301;0.222;0.222;0.404;0.063;0.118|.	T|T	0.54437|0.54437	-0.8294|-0.8294	10|5	0.39692|.	T|.	0.17|.	-11.8593|-11.8593	17.9549|17.9549	0.89065|0.89065	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	796;893;875;882;378;882;882|.	B4DZJ6;F8W726;Q14157-4;Q14157-1;C9JD99;Q14157-3;Q14157|.	.;.;.;.;.;.;UBP2L_HUMAN|.	A|S	882;882;378;378;893;882|212;160	ENSP00000345308:P882A;ENSP00000389445:P882A;ENSP00000271877:P893A;ENSP00000355343:P882A|.	ENSP00000271877:P893A|.	P|T	+|+	1|2	0|0	UBAP2L|UBAP2L	152500057|152500057	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	5.672000|5.672000	0.68102|0.68102	2.715000|2.715000	0.92844|0.92844	0.555000|0.555000	0.69702|0.69702	CCC|ACC		0.582	UBAP2L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087673.1	NM_014847	
HAX1	10456	broad.mit.edu	37	1	154245954	154245954	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr1:154245954A>G	ENST00000328703.7	+	2	409	c.196A>G	c.(196-198)Agc>Ggc	p.S66G	HAX1_ENST00000532105.1_Intron|HAX1_ENST00000483970.2_Missense_Mutation_p.S66G|HAX1_ENST00000457918.2_Splice_Site	NM_006118.3	NP_006109.2	O00165	HAX1_HUMAN	HCLS1 associated protein X-1	66					cellular response to cytokine stimulus (GO:0071345)|positive regulation of actin cytoskeleton reorganization (GO:2000251)|positive regulation of granulocyte differentiation (GO:0030854)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of actin filament polymerization (GO:0030833)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrion degradation (GO:1903146)|regulation of protein targeting to mitochondrion (GO:1903214)	actin cytoskeleton (GO:0015629)|cytoplasmic vesicle (GO:0031410)|endoplasmic reticulum (GO:0005783)|lamellipodium (GO:0030027)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nuclear envelope (GO:0005635)|sarcoplasmic reticulum (GO:0016529)|transcription factor complex (GO:0005667)	interleukin-1 binding (GO:0019966)|protein N-terminus binding (GO:0047485)	p.S66G(1)		cervix(1)|endometrium(2)|large_intestine(2)|lung(8)|prostate(1)|upper_aerodigestive_tract(1)	15	all_lung(78;2.62e-30)|Lung NSC(65;3.94e-28)|Hepatocellular(266;0.0877)		LUSC - Lung squamous cell carcinoma(543;0.185)			CTTCGGCTTCAGCTTCAGCCC	0.532									Kostmann syndrome																												p.S66G												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A196G	1						.						77.0	72.0	74.0					1																	154245954		2203	4300	6503	152512578	SO:0001583	missense	10456	exon2	Familial Cancer Database	Kostmann Infantile Agranulocytosis, Severe Congenital Neutropenia, Congenital Agranulocytosis	U68566	CCDS1064.1, CCDS44230.1	1q21.3	2014-09-17			ENSG00000143575	ENSG00000143575			16915	protein-coding gene	gene with protein product	"""HCLS1 (and PKD2) associated protein"""	605998				9058808, 10760273	Standard	NM_006118		Approved	HS1BP1, HCLSBP1	uc001fes.3	O00165	OTTHUMG00000035978	ENST00000328703.7:c.196A>G	1.37:g.154245954A>G	ENSP00000329002:p.Ser66Gly	Somatic		Capture	Illumina HiSeq	Phase_I	152512578	NM_006118	A8W4W9|A8W4X0|B4DUJ7|Q5VYD5|Q5VYD7|Q96AU4|Q9BS80	Missense_Mutation	SNP	ENST00000328703.7	37	CCDS1064.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	18.59|18.59	3.657525|3.657525	0.67586|0.67586	.|.	.|.	ENSG00000143575|ENSG00000143575	ENST00000457918|ENST00000328703;ENST00000483970;ENST00000435087	.|T;T;T	.|0.46451	.|0.87;0.87;0.87	5.58|5.58	4.38|4.38	0.52667|0.52667	.|.	.|0.134060	.|0.64402	.|D	.|0.000003	.|T	.|0.26738	.|0.0654	M|M	0.66939|0.66939	2.045|2.045	0.80722|0.80722	D|D	1|1	.|B;B	.|0.06786	.|0.001;0.0	.|B;B	.|0.09377	.|0.004;0.001	.|T	.|0.29518	.|-1.0009	.|10	.|0.59425	.|D	.|0.04	.|-2.8408	10.3057|10.3057	0.43678|0.43678	0.835:0.165:0.0:0.0|0.835:0.165:0.0:0.0	.|.	.|66;66	.|O00165-2;O00165	.|.;HAX1_HUMAN	.|G	-1|66	.|ENSP00000329002:S66G;ENSP00000435088:S66G;ENSP00000394920:S66G	.|ENSP00000329002:S66G	.|S	+|+	.|1	.|0	HAX1|HAX1	152512578|152512578	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	1.991000|1.991000	0.40727|0.40727	2.240000|2.240000	0.73641|0.73641	0.533000|0.533000	0.62120|0.62120	.|AGC		0.532	HAX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087650.1	NM_006118	
KAZN	23254	broad.mit.edu	37	1	15441059	15441059	+	Silent	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr1:15441059C>T	ENST00000376030.2	+	15	2550	c.2256C>T	c.(2254-2256)gaC>gaT	p.D752D	TMEM51-AS1_ENST00000310916.3_RNA	NM_201628.2	NP_963922.2	Q674X7	KAZRN_HUMAN	kazrin, periplakin interacting protein	752					keratinization (GO:0031424)	cornified envelope (GO:0001533)|cytoplasm (GO:0005737)|desmosome (GO:0030057)|nucleus (GO:0005634)		p.D199D(1)|p.D752D(1)		central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(9)|liver(1)|lung(6)|ovary(1)|prostate(2)	25						ATTGCGGAGACGATGACCCCC	0.557																																					p.D752D												.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.C2256T	1						.						63.0	50.0	55.0					1																	15441059		2203	4300	6503	15313646	SO:0001819	synonymous_variant	23254	exon15			AY505119	CCDS30604.1, CCDS41267.1, CCDS152.2, CCDS41268.1	1p36.21	2014-02-12	2011-01-31		ENSG00000189337	ENSG00000189337		"""Sterile alpha motif (SAM) domain containing"""	29173	protein-coding gene	gene with protein product						15337775, 18840647	Standard	NM_015209		Approved	KIAA1026, KAZRIN, FLJ43806	uc001avm.4	Q674X7	OTTHUMG00000002042	ENST00000376030.2:c.2256C>T	1.37:g.15441059C>T		Somatic		Capture	Illumina HiSeq	Phase_I	15313646	NM_201628	B0QYQ0|B1AK78|Q5TGF1|Q674X4|Q674X6|Q6ZUD1|Q8IYN7|Q8N409|Q9UIL2|Q9UPX4	Silent	SNP	ENST00000376030.2	37	CCDS152.2																																																																																				0.557	KAZN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005690.2	NM_001017999	
KCNN3	3782	broad.mit.edu	37	1	154744848	154744848	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr1:154744848C>T	ENST00000271915.4	-	3	1366	c.1051G>A	c.(1051-1053)Gcg>Acg	p.A351T	KCNN3_ENST00000358505.2_Missense_Mutation_p.A38T|KCNN3_ENST00000361147.4_Missense_Mutation_p.A46T	NM_001204087.1|NM_002249.5	NP_001191016.1|NP_002240.3	Q9UGI6	KCNN3_HUMAN	potassium intermediate/small conductance calcium-activated channel, subfamily N, member 3	356					potassium ion transmembrane transport (GO:0071805)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	calmodulin binding (GO:0005516)|small conductance calcium-activated potassium channel activity (GO:0016286)	p.A351T(1)		cervix(1)|endometrium(3)|kidney(2)|large_intestine(6)|lung(11)|prostate(4)|skin(1)	28	all_lung(78;2.29e-27)|all_hematologic(923;0.088)|Hepatocellular(266;0.108)|all_neural(408;0.245)		BRCA - Breast invasive adenocarcinoma(34;0.00819)		Miconazole(DB01110)|Procaine(DB00721)	CAGTCATCCGCGCCATTGTCG	0.597																																					p.A46T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G136A	1						.						41.0	37.0	39.0					1																	154744848		2203	4300	6503	153011472	SO:0001583	missense	3782	exon3			AF031815	CCDS1072.1, CCDS30880.1, CCDS72928.1	1q21.3	2012-07-05			ENSG00000143603	ENSG00000143603		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels, calcium-activated"""	6292	protein-coding gene	gene with protein product		602983				9491810, 16382103	Standard	NM_002249		Approved	KCa2.3, hSK3, SKCA3	uc021pah.1	Q9UGI6	OTTHUMG00000037260	ENST00000271915.4:c.1051G>A	1.37:g.154744848C>T	ENSP00000271915:p.Ala351Thr	Somatic		Capture	Illumina HiSeq	Phase_I	153011472	NM_170782	B1ANX0|O43517|Q86VF9|Q8WXG7	Missense_Mutation	SNP	ENST00000271915.4	37	CCDS30880.1	.	.	.	.	.	.	.	.	.	.	C	28.0	4.883209	0.91740	.	.	ENSG00000143603	ENST00000361147;ENST00000271915;ENST00000358505	D;D;D	0.98822	-5.16;-4.03;-5.15	4.51	4.51	0.55191	Potassium channel, calcium-activated, SK, conserved region (1);	0.000000	0.52532	D	0.000069	D	0.99260	0.9742	M	0.90252	3.1	0.80722	D	1	D;D;D	0.89917	1.0;0.999;0.968	D;D;P	0.91635	0.999;0.996;0.726	D	0.99204	1.0874	10	0.87932	D	0	-5.3796	17.0243	0.86441	0.0:1.0:0.0:0.0	.	357;356;46	Q6JXY2;Q9UGI6;Q9UGI6-2	.;KCNN3_HUMAN;.	T	46;351;38	ENSP00000354764:A46T;ENSP00000271915:A351T;ENSP00000351295:A38T	ENSP00000271915:A351T	A	-	1	0	KCNN3	153011472	1.000000	0.71417	0.976000	0.42696	0.932000	0.56968	7.647000	0.83462	2.312000	0.78011	0.561000	0.74099	GCG		0.597	KCNN3-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090688.3	NM_002249	
DCST2	127579	broad.mit.edu	37	1	155003009	155003009	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr1:155003009C>A	ENST00000368424.3	-	6	976	c.918G>T	c.(916-918)atG>atT	p.M306I	DCST2_ENST00000295536.5_Missense_Mutation_p.M306I	NM_144622.2	NP_653223.2	Q5T1A1	DCST2_HUMAN	DC-STAMP domain containing 2	306						integral component of membrane (GO:0016021)		p.M306I(1)		breast(1)|central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(10)|lung(13)|ovary(3)|prostate(1)|skin(1)	38	all_epithelial(22;2.77e-30)|all_lung(78;4.1e-28)|all_hematologic(923;0.0359)|Hepatocellular(266;0.0877)		BRCA - Breast invasive adenocarcinoma(34;0.00034)			CGTGGAGGTCCATGGCTACCT	0.592																																					p.M306I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G918T	1						.						74.0	56.0	62.0					1																	155003009		2203	4300	6503	153269633	SO:0001583	missense	127579	exon6			AK057496	CCDS1082.2	1q22	2008-02-05		2005-08-09	ENSG00000163354	ENSG00000163354			26562	protein-coding gene	gene with protein product							Standard	NM_144622		Approved	FLJ32934	uc001fgm.3	Q5T1A1	OTTHUMG00000037371	ENST00000368424.3:c.918G>T	1.37:g.155003009C>A	ENSP00000357409:p.Met306Ile	Somatic		Capture	Illumina HiSeq	Phase_I	153269633	NM_144622	Q2M2R2|Q8N810|Q96M03	Missense_Mutation	SNP	ENST00000368424.3	37	CCDS1082.2	.	.	.	.	.	.	.	.	.	.	C	8.180	0.793542	0.16327	.	.	ENSG00000163354	ENST00000368424;ENST00000295536	T;T	0.22743	1.94;1.95	5.08	3.08	0.35506	.	0.411149	0.21629	N	0.071518	T	0.02533	0.0077	N	0.08118	0	0.24475	N	0.994377	B	0.09022	0.002	B	0.06405	0.002	T	0.42015	-0.9476	10	0.22109	T	0.4	-1.4425	4.5473	0.12087	0.1528:0.6077:0.1492:0.0903	.	306	Q5T1A1	DCST2_HUMAN	I	306	ENSP00000357409:M306I;ENSP00000295536:M306I	ENSP00000295536:M306I	M	-	3	0	DCST2	153269633	0.218000	0.23608	0.988000	0.46212	0.569000	0.35902	0.276000	0.18716	1.276000	0.44395	0.655000	0.94253	ATG		0.592	DCST2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090953.3	NM_144622	
SCAMP3	10067	broad.mit.edu	37	1	155230400	155230400	+	Silent	SNP	T	T	C			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr1:155230400T>C	ENST00000302631.3	-	3	302	c.195A>G	c.(193-195)tcA>tcG	p.S65S	SCAMP3_ENST00000472397.1_5'Flank|CLK2_ENST00000497188.1_5'Flank|SCAMP3_ENST00000355379.3_Silent_p.S39S	NM_005698.3	NP_005689.2	O14828	SCAM3_HUMAN	secretory carrier membrane protein 3	65					post-Golgi vesicle-mediated transport (GO:0006892)|protein transport (GO:0015031)|response to retinoic acid (GO:0032526)	extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	ubiquitin protein ligase binding (GO:0031625)	p.S65S(1)		breast(1)|endometrium(3)|large_intestine(3)|lung(7)|ovary(4)|urinary_tract(1)	19	all_lung(78;2.32e-23)|Hepatocellular(266;0.0877)|all_hematologic(923;0.088)		Epithelial(20;3.72e-10)|all cancers(21;1.19e-09)|BRCA - Breast invasive adenocarcinoma(34;0.000752)|LUSC - Lung squamous cell carcinoma(543;0.193)			AGGAGGGAGCTGAGGGTGGAG	0.562																																					p.S39S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.A117G	1						.						126.0	130.0	129.0					1																	155230400		2203	4300	6503	153497024	SO:0001819	synonymous_variant	10067	exon2			AF005039	CCDS1105.1, CCDS1106.1	1q21	2013-02-21			ENSG00000116521	ENSG00000116521		"""Secretory carrier membrane proteins"""	10565	protein-coding gene	gene with protein product	"""Propin 1"""	606913		C1orf3		9331372, 9658162	Standard	NM_005698		Approved		uc001fjs.3	O14828	OTTHUMG00000035874	ENST00000302631.3:c.195A>G	1.37:g.155230400T>C		Somatic		Capture	Illumina HiSeq	Phase_I	153497024	NM_052837	A9Z1W6|B1AVS6|O15128|Q96FR8|Q9BPY0	Silent	SNP	ENST00000302631.3	37	CCDS1105.1																																																																																				0.562	SCAMP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087399.1	NM_005698	
ASH1L	55870	broad.mit.edu	37	1	155308161	155308161	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr1:155308161C>T	ENST00000368346.3	-	27	9176	c.8537G>A	c.(8536-8538)cGc>cAc	p.R2846H	ASH1L_ENST00000392403.3_Missense_Mutation_p.R2841H			Q9NR48	ASH1L_HUMAN	ash1 (absent, small, or homeotic)-like (Drosophila)	2846					cell-cell signaling (GO:0007267)|DNA packaging (GO:0006323)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|tight junction (GO:0005923)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|zinc ion binding (GO:0008270)	p.R2841H(1)		autonomic_ganglia(1)|breast(4)|central_nervous_system(1)|endometrium(12)|kidney(13)|large_intestine(28)|lung(39)|ovary(2)|pancreas(1)|prostate(6)|skin(11)|upper_aerodigestive_tract(2)|urinary_tract(4)	124	Hepatocellular(266;0.0997)|all_neural(408;0.129)|all_hematologic(923;0.145)		Epithelial(20;1.74e-08)|all cancers(21;3.29e-08)|BRCA - Breast invasive adenocarcinoma(34;0.021)			TGGCTTTGAGCGCTCAGACTT	0.498																																					p.R2841H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G8522A	1						.						71.0	71.0	71.0					1																	155308161		2203	4300	6503	153574785	SO:0001583	missense	55870	exon27			AB037841	CCDS1113.2	1q22	2013-01-28			ENSG00000116539	ENSG00000116539		"""Chromatin-modifying enzymes / K-methyltransferases"", ""Zinc fingers, PHD-type"""	19088	protein-coding gene	gene with protein product		607999				10860993, 16545939	Standard	NM_018489		Approved	huASH1, ASH1, ASH1L1, KMT2H	uc001fkt.3	Q9NR48	OTTHUMG00000014011	ENST00000368346.3:c.8537G>A	1.37:g.155308161C>T	ENSP00000357330:p.Arg2846His	Somatic		Capture	Illumina HiSeq	Phase_I	153574785	NM_018489	Q59GP1|Q5T714|Q5T715|Q9P2C7	Missense_Mutation	SNP	ENST00000368346.3	37		.	.	.	.	.	.	.	.	.	.	C	18.90	3.721223	0.68959	.	.	ENSG00000116539	ENST00000368346;ENST00000392403	D;D	0.89415	-2.51;-2.51	5.5	5.5	0.81552	.	0.056004	0.64402	D	0.000001	D	0.91660	0.7364	L	0.50333	1.59	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.80764	0.987;0.994	D	0.91009	0.4848	10	0.51188	T	0.08	.	17.348	0.87315	0.0:1.0:0.0:0.0	.	2846;2841	Q9NR48;Q9NR48-2	ASH1L_HUMAN;.	H	2846;2841	ENSP00000357330:R2846H;ENSP00000376204:R2841H	ENSP00000357330:R2846H	R	-	2	0	ASH1L	153574785	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	5.481000	0.66826	2.861000	0.98227	0.655000	0.94253	CGC		0.498	ASH1L-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000039400.1	NM_018489	
IQGAP3	128239	broad.mit.edu	37	1	156517944	156517944	+	Missense_Mutation	SNP	C	C	T	rs371514554		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr1:156517944C>T	ENST00000361170.2	-	19	2235	c.2225G>A	c.(2224-2226)cGt>cAt	p.R742H		NM_178229.4	NP_839943.2	Q86VI3	IQGA3_HUMAN	IQ motif containing GTPase activating protein 3	742	IQ 1. {ECO:0000255|PROSITE- ProRule:PRU00116}.				activation of MAPK activity (GO:0000187)|cellular response to organic substance (GO:0071310)|ERK1 and ERK2 cascade (GO:0070371)|G1/S transition of mitotic cell cycle (GO:0000082)|negative regulation of gene expression (GO:0010629)|positive regulation of gene expression (GO:0010628)|positive regulation of mammary gland epithelial cell proliferation (GO:0033601)|Ras protein signal transduction (GO:0007265)|regulation of cell size (GO:0008361)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|lateral plasma membrane (GO:0016328)	Ras GTPase activator activity (GO:0005099)	p.R742H(1)		NS(1)|breast(2)|central_nervous_system(1)|endometrium(8)|kidney(2)|large_intestine(14)|lung(29)|ovary(5)|prostate(5)|skin(5)|urinary_tract(3)	75	all_hematologic(923;0.088)|Hepatocellular(266;0.158)					TAGGAAGCCACGGAGGCGGGC	0.577																																					p.R742H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2225A	1						.	C	HIS/ARG	0,4406		0,0,2203	37.0	37.0	37.0		2225	4.3	1.0	1		37	1,8599	1.2+/-3.3	0,1,4299	no	missense	IQGAP3	NM_178229.4	29	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging	742/1632	156517944	1,13005	2203	4300	6503	154784568	SO:0001583	missense	128239	exon19			AY253300	CCDS1144.1	1q21.3	2008-02-05			ENSG00000183856	ENSG00000183856			20669	protein-coding gene	gene with protein product							Standard	NM_178229		Approved		uc001fpf.3	Q86VI3	OTTHUMG00000033114	ENST00000361170.2:c.2225G>A	1.37:g.156517944C>T	ENSP00000354451:p.Arg742His	Somatic		Capture	Illumina HiSeq	Phase_I	154784568	NM_178229	Q5T3H8	Missense_Mutation	SNP	ENST00000361170.2	37	CCDS1144.1	.	.	.	.	.	.	.	.	.	.	C	27.0	4.794876	0.90453	0.0	1.16E-4	ENSG00000183856	ENST00000361170	D	0.84298	-1.83	4.32	4.32	0.51571	.	0.000000	0.85682	D	0.000000	D	0.92625	0.7657	M	0.90019	3.08	0.58432	D	0.999999	D	0.89917	1.0	D	0.87578	0.998	D	0.94090	0.7352	10	0.87932	D	0	-7.9961	15.549	0.76133	0.0:1.0:0.0:0.0	.	742	Q86VI3	IQGA3_HUMAN	H	742	ENSP00000354451:R742H	ENSP00000354451:R742H	R	-	2	0	IQGAP3	154784568	1.000000	0.71417	0.998000	0.56505	0.971000	0.66376	7.601000	0.82783	2.236000	0.73375	0.561000	0.74099	CGT		0.577	IQGAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080657.1	NM_178229	
TTC24	164118	broad.mit.edu	37	1	156555793	156555793	+	Silent	SNP	G	G	A	rs369172224		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr1:156555793G>A	ENST00000368237.3	+	9	1623	c.1623G>A	c.(1621-1623)gcG>gcA	p.A541A	AL365181.1_ENST00000581084.1_RNA|TTC24_ENST00000368236.3_Silent_p.A541A			A2A3L6	TTC24_HUMAN	tetratricopeptide repeat domain 24	541								p.A541A(1)		breast(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(10)|pancreas(1)|prostate(1)	20	all_hematologic(923;0.088)|Hepatocellular(266;0.158)					CTCCCAGAGCGGAGTACCCTA	0.537																																					p.A541A												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G1623A	1						.	G		1,3781		0,1,1890	39.0	39.0	39.0		1623	3.3	0.0	1		39	5,8245		0,5,4120	no	coding-synonymous	TTC24	NM_001105669.2		0,6,6010	AA,AG,GG		0.0606,0.0264,0.0499		541/583	156555793	6,12026	1891	4125	6016	154822417	SO:0001819	synonymous_variant	164118	exon10				CCDS53379.1	1q22	2013-01-10			ENSG00000187862	ENSG00000187862		"""Tetratricopeptide (TTC) repeat domain containing"""	32348	protein-coding gene	gene with protein product							Standard	NM_001105669		Approved		uc021pbf.1	A2A3L6	OTTHUMG00000033202	ENST00000368237.3:c.1623G>A	1.37:g.156555793G>A		Somatic		Capture	Illumina HiSeq	Phase_I	154822417	NM_001105669	Q5T3H7	Silent	SNP	ENST00000368237.3	37	CCDS53379.1	.	.	.	.	.	.	.	.	.	.	G	3.187	-0.166583	0.06461	2.64E-4	6.06E-4	ENSG00000187862	ENST00000340086	.	.	.	4.17	3.26	0.37387	.	.	.	.	.	T	0.17916	0.0430	.	.	.	0.18873	N	0.999983	.	.	.	.	.	.	T	0.14504	-1.0470	4	.	.	.	-4.391	8.0288	0.30453	0.113:0.0:0.887:0.0	.	.	.	.	Q	314	.	.	R	+	2	0	TTC24	154822417	0.001000	0.12720	0.002000	0.10522	0.002000	0.02628	0.917000	0.28665	1.114000	0.41781	-0.258000	0.10820	CGG		0.537	TTC24-006	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000158547.1	XM_089384	
NTRK1	4914	broad.mit.edu	37	1	156849016	156849016	+	Silent	SNP	G	G	A	rs17838192	byFrequency	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr1:156849016G>A	ENST00000524377.1	+	15	1949	c.1908G>A	c.(1906-1908)gcG>gcA	p.A636A	NTRK1_ENST00000392302.2_Silent_p.A600A|NTRK1_ENST00000358660.3_Silent_p.A633A|NTRK1_ENST00000368196.3_Silent_p.A630A	NM_002529.3	NP_002520.2	P04629	NTRK1_HUMAN	neurotrophic tyrosine kinase, receptor, type 1	636	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of adenylate cyclase activity (GO:0007190)|activation of MAPKK activity (GO:0000186)|activation of phospholipase C activity (GO:0007202)|aging (GO:0007568)|axon guidance (GO:0007411)|axonogenesis involved in innervation (GO:0060385)|B cell differentiation (GO:0030183)|cellular response to nerve growth factor stimulus (GO:1990090)|cellular response to nicotine (GO:0071316)|circadian rhythm (GO:0007623)|detection of mechanical stimulus involved in sensory perception of pain (GO:0050966)|detection of temperature stimulus involved in sensory perception of pain (GO:0050965)|developmental programmed cell death (GO:0010623)|learning or memory (GO:0007611)|mechanoreceptor differentiation (GO:0042490)|negative regulation of cell proliferation (GO:0008285)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|olfactory nerve development (GO:0021553)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of angiogenesis (GO:0045766)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of neuron projection development (GO:0010976)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of programmed cell death (GO:0043068)|positive regulation of Ras GTPase activity (GO:0032320)|positive regulation of Ras protein signal transduction (GO:0046579)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|Ras protein signal transduction (GO:0007265)|response to activity (GO:0014823)|response to axon injury (GO:0048678)|response to drug (GO:0042493)|response to electrical stimulus (GO:0051602)|response to ethanol (GO:0045471)|response to hydrostatic pressure (GO:0051599)|response to nutrient levels (GO:0031667)|response to radiation (GO:0009314)|Sertoli cell development (GO:0060009)|small GTPase mediated signal transduction (GO:0007264)|sympathetic nervous system development (GO:0048485)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	axon (GO:0030424)|cell surface (GO:0009986)|cytoplasmic vesicle (GO:0031410)|dendrite (GO:0030425)|early endosome (GO:0005769)|endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)|late endosome (GO:0005770)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|nerve growth factor binding (GO:0048406)|nerve growth factor receptor activity (GO:0010465)|neurotrophin binding (GO:0043121)|protein homodimerization activity (GO:0042803)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)	p.A636A(1)|p.A600A(1)		breast(3)|central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(7)|lung(35)|ovary(8)|prostate(2)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	74	all_hematologic(923;0.0839)|Hepatocellular(266;0.158)				Amitriptyline(DB00321)|Imatinib(DB00619)|Regorafenib(DB08896)	AGGTCGCTGCGGGGATGGTGT	0.642			T	"""TPM3, TPR, TFG"""	papillary thyroid					TSP Lung(10;0.080)			G|||	4	0.000798722	0.0	0.0043	5008	,	,		16039	0.0		0.001	False		,,,				2504	0.0				p.A630A			Dom	yes		1	1q21-q22	4914	"""neurotrophic tyrosine kinase, receptor, type 1"""		E	.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.G1890A	1						.	G	,,	4,4402	8.1+/-20.4	0,4,2199	40.0	39.0	39.0		1800,1890,1908	-8.7	0.1	1	dbSNP_123	39	11,8589	7.7+/-29.5	0,11,4289	no	coding-synonymous,coding-synonymous,coding-synonymous	NTRK1	NM_001007792.1,NM_001012331.1,NM_002529.3	,,	0,15,6488	AA,AG,GG		0.1279,0.0908,0.1153	,,	600/761,630/791,636/797	156849016	15,12991	2203	4300	6503	155115640	SO:0001819	synonymous_variant	4914	exon14			Y09028	CCDS1161.1, CCDS30890.1, CCDS30891.1	1q21-q22	2014-09-17			ENSG00000198400	ENSG00000198400	2.7.10.1	"""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	8031	protein-coding gene	gene with protein product	"""high affinity nerve growth factor receptor"""	191315				2869410	Standard	NM_001007792		Approved	TRK, TRKA, MTC	uc001fqh.1	P04629	OTTHUMG00000041304	ENST00000524377.1:c.1908G>A	1.37:g.156849016G>A		Somatic		Capture	Illumina HiSeq	Phase_I	155115640	NM_001012331	B2R6T5|B7ZM34|P08119|Q15655|Q15656|Q5D056|Q5VZS2|Q7Z5C3|Q9UIU7	Silent	SNP	ENST00000524377.1	37	CCDS1161.1																																																																																				0.642	NTRK1-007	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000392279.1	NM_002529	
LRRC71	149499	broad.mit.edu	37	1	156897411	156897411	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr1:156897411C>A	ENST00000337428.7	+	7	940	c.786C>A	c.(784-786)aaC>aaA	p.N262K	LRRC71_ENST00000490146.1_3'UTR	NM_144702.2	NP_653303.2	Q8N4P6	LRC71_HUMAN	leucine rich repeat containing 71	262								p.N262K(1)		endometrium(2)|large_intestine(3)|lung(5)|ovary(1)|stomach(1)	12						TGGGTTTCAACCACATCGGTG	0.677											OREG0013892	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.N262K												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C786A	1						.						17.0	20.0	19.0					1																	156897411		2077	4194	6271	155164035	SO:0001583	missense	149499	exon7			BC033790	CCDS44249.1	1q23.1	2011-02-14	2011-02-14	2011-02-14	ENSG00000160838	ENSG00000160838			26556	protein-coding gene	gene with protein product			"""chromosome 1 open reading frame 92"""	C1orf92		14702039	Standard	NM_144702		Approved	FLJ32884	uc001fqm.2	Q8N4P6	OTTHUMG00000041298	ENST00000337428.7:c.786C>A	1.37:g.156897411C>A	ENSP00000336661:p.Asn262Lys	Somatic	1782	Capture	Illumina HiSeq	Phase_I	155164035	NM_144702	Q96M24	Missense_Mutation	SNP	ENST00000337428.7	37	CCDS44249.1	.	.	.	.	.	.	.	.	.	.	C	18.86	3.712688	0.68730	.	.	ENSG00000160838	ENST00000337428	T	0.80393	-1.37	4.28	3.33	0.38152	.	0.137794	0.33127	N	0.005245	D	0.91068	0.7189	H	0.98048	4.135	0.39059	D	0.960495	D;D	0.76494	0.997;0.999	D;D	0.68621	0.947;0.959	D	0.92265	0.5820	10	0.87932	D	0	-27.413	9.8439	0.41015	0.0:0.8974:0.0:0.1026	.	262;47	Q8N4P6;Q8N4P6-2	LRC71_HUMAN;.	K	262	ENSP00000336661:N262K	ENSP00000336661:N262K	N	+	3	2	LRRC71	155164035	1.000000	0.71417	1.000000	0.80357	0.819000	0.46315	1.661000	0.37408	2.220000	0.72140	0.455000	0.32223	AAC		0.677	LRRC71-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098961.1	NM_144702	
FCRL4	83417	broad.mit.edu	37	1	157556159	157556159	+	Missense_Mutation	SNP	C	C	T	rs142198646		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr1:157556159C>T	ENST00000271532.1	-	6	1069	c.934G>A	c.(934-936)Gtg>Atg	p.V312M	FCRL4_ENST00000448509.2_5'UTR	NM_031282.2	NP_112572.1	Q96PJ5	FCRL4_HUMAN	Fc receptor-like 4	312	Ig-like C2-type 4.				immune system process (GO:0002376)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.V312M(2)		breast(2)|central_nervous_system(2)|endometrium(1)|kidney(3)|large_intestine(5)|lung(20)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	40	all_hematologic(112;0.0378)|Hepatocellular(266;0.178)	Prostate(1639;0.245)				CCTTCAGCCACGGAGCAGACA	0.592													C|||	1	0.000199681	0.0	0.0	5008	,	,		19102	0.0		0.0	False		,,,				2504	0.001				p.V312M												.	.	2	Substitution - Missense(2)	large_intestine(1)|lung(1)	c.G934A	1						.	C	MET/VAL	0,4406		0,0,2203	80.0	73.0	75.0		934	-1.5	0.0	1	dbSNP_134	75	5,8595	4.3+/-15.6	0,5,4295	yes	missense	FCRL4	NM_031282.2	21	0,5,6498	TT,TC,CC		0.0581,0.0,0.0384	possibly-damaging	312/516	157556159	5,13001	2203	4300	6503	155822783	SO:0001583	missense	83417	exon6			AF343661	CCDS1166.1	1q21	2013-01-14			ENSG00000163518	ENSG00000163518		"""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	18507	protein-coding gene	gene with protein product		605876				11290337, 11493702	Standard	NM_031282		Approved	FCRH4, IRTA1, IGFP2, CD307d	uc001fqw.3	Q96PJ5	OTTHUMG00000035488	ENST00000271532.1:c.934G>A	1.37:g.157556159C>T	ENSP00000271532:p.Val312Met	Somatic		Capture	Illumina HiSeq	Phase_I	155822783	NM_031282	Q96PJ3|Q96RE0	Missense_Mutation	SNP	ENST00000271532.1	37	CCDS1166.1	.	.	.	.	.	.	.	.	.	.	C	7.197	0.592667	0.13875	0.0	5.81E-4	ENSG00000163518	ENST00000271532	T	0.13901	2.55	4.12	-1.47	0.08772	Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin (1);Immunoglobulin-like fold (1);	0.264658	0.20324	N	0.094577	T	0.09335	0.0230	M	0.64260	1.97	0.09310	N	1	D	0.61697	0.99	P	0.56343	0.796	T	0.08534	-1.0717	10	0.56958	D	0.05	.	3.9234	0.09253	0.1583:0.4707:0.0:0.371	.	312	Q96PJ5	FCRL4_HUMAN	M	312	ENSP00000271532:V312M	ENSP00000271532:V312M	V	-	1	0	FCRL4	155822783	0.020000	0.18652	0.000000	0.03702	0.055000	0.15305	0.069000	0.14552	-0.406000	0.07588	-0.670000	0.03821	GTG		0.592	FCRL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086180.1	NM_031282	
FCRL4	83417	broad.mit.edu	37	1	157557187	157557187	+	Silent	SNP	C	C	T	rs142002574		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr1:157557187C>T	ENST00000271532.1	-	5	861	c.726G>A	c.(724-726)acG>acA	p.T242T	FCRL4_ENST00000448509.2_5'UTR	NM_031282.2	NP_112572.1	Q96PJ5	FCRL4_HUMAN	Fc receptor-like 4	242	Ig-like C2-type 3.				immune system process (GO:0002376)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.T242T(2)		breast(2)|central_nervous_system(2)|endometrium(1)|kidney(3)|large_intestine(5)|lung(20)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	40	all_hematologic(112;0.0378)|Hepatocellular(266;0.178)	Prostate(1639;0.245)				GTTCCGGGTACGTGCTCCAGT	0.537																																					p.T242T												.	.	2	Substitution - coding silent(2)	large_intestine(1)|central_nervous_system(1)	c.G726A	1						.	C		0,4406		0,0,2203	282.0	281.0	282.0		726	-5.4	0.0	1	dbSNP_134	282	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	FCRL4	NM_031282.2		0,2,6501	TT,TC,CC		0.0233,0.0,0.0154		242/516	157557187	2,13004	2203	4300	6503	155823811	SO:0001819	synonymous_variant	83417	exon5			AF343661	CCDS1166.1	1q21	2013-01-14			ENSG00000163518	ENSG00000163518		"""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	18507	protein-coding gene	gene with protein product		605876				11290337, 11493702	Standard	NM_031282		Approved	FCRH4, IRTA1, IGFP2, CD307d	uc001fqw.3	Q96PJ5	OTTHUMG00000035488	ENST00000271532.1:c.726G>A	1.37:g.157557187C>T		Somatic		Capture	Illumina HiSeq	Phase_I	155823811	NM_031282	Q96PJ3|Q96RE0	Silent	SNP	ENST00000271532.1	37	CCDS1166.1																																																																																				0.537	FCRL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086180.1	NM_031282	
CD1C	911	broad.mit.edu	37	1	158259914	158259914	+	Splice_Site	SNP	C	C	T	rs539975387		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr1:158259914C>T	ENST00000368170.3	+	1	339	c.60C>T	c.(58-60)gaC>gaT	p.D20D		NM_001765.2	NP_001756.2	P29017	CD1C_HUMAN	CD1c molecule	20					antigen processing and presentation (GO:0019882)|T cell activation involved in immune response (GO:0002286)	endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	endogenous lipid antigen binding (GO:0030883)|exogenous lipid antigen binding (GO:0030884)|glycolipid binding (GO:0051861)|lipopeptide binding (GO:0071723)	p.D20D(2)		NS(1)|endometrium(3)|large_intestine(4)|lung(21)|ovary(2)|pancreas(1)|prostate(1)|skin(4)|stomach(1)|urinary_tract(1)	39	all_hematologic(112;0.0378)					ACAATGCAGACGGTAAGAACA	0.473													C|||	1	0.000199681	0.0008	0.0	5008	,	,		22878	0.0		0.0	False		,,,				2504	0.0				p.D20D												.	.	2	Substitution - coding silent(2)	large_intestine(1)|endometrium(1)	c.C60T	1						.						156.0	131.0	140.0					1																	158259914		2203	4300	6503	156526538	SO:0001630	splice_region_variant	911	exon1			M28827	CCDS1175.1	1q23.1	2014-01-14	2006-03-28		ENSG00000158481	ENSG00000158481		"""CD molecules"", ""Immunoglobulin superfamily / C1-set domain containing"""	1636	protein-coding gene	gene with protein product		188340	"""CD1C antigen, c polypeptide"", ""CD1c antigen"""	CD1		2447586	Standard	NM_001765		Approved		uc001fru.3	P29017	OTTHUMG00000017514	ENST00000368170.3:c.61+1C>T	1.37:g.158259914C>T		Somatic		Capture	Illumina HiSeq	Phase_I	156526538	NM_001765	Q5TDJ7|Q6IAS4|Q9UMM0|Q9UN96	Silent	SNP	ENST00000368170.3	37	CCDS1175.1																																																																																				0.473	CD1C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046351.2	NM_001765	Silent
CD48	962	broad.mit.edu	37	1	160654942	160654942	+	Silent	SNP	G	G	A	rs576472449		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr1:160654942G>A	ENST00000368046.3	-	2	207	c.120C>T	c.(118-120)aaC>aaT	p.N40N	RP11-404F10.2_ENST00000598917.2_RNA|RP11-404F10.2_ENST00000588034.1_RNA|RP11-404F10.2_ENST00000443928.2_RNA|CD48_ENST00000368045.3_Silent_p.N40N	NM_001778.3	NP_001769.2	P09326	CD48_HUMAN	CD48 molecule	40	Ig-like C2-type 1.				blood coagulation (GO:0007596)|defense response (GO:0006952)|leukocyte migration (GO:0050900)|mast cell activation (GO:0045576)|signal transduction (GO:0007165)|T cell activation (GO:0042110)	anchored component of plasma membrane (GO:0046658)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	antigen binding (GO:0003823)|receptor activity (GO:0004872)	p.N40N(1)		breast(2)|endometrium(1)|large_intestine(2)|lung(2)|ovary(1)|prostate(1)|stomach(1)	10	all_cancers(52;2.18e-17)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.0175)			TCAGAGTCACGTTGCTGCCGG	0.493													G|||	1	0.000199681	0.0008	0.0	5008	,	,		19969	0.0		0.0	False		,,,				2504	0.0				p.N40N												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C120T	1						.						66.0	66.0	66.0					1																	160654942		2203	4300	6503	158921566	SO:0001819	synonymous_variant	962	exon2			BC016182	CCDS1208.1, CCDS72955.1	1q21.3-q22	2013-01-29	2006-03-31		ENSG00000117091	ENSG00000117091		"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	1683	protein-coding gene	gene with protein product		109530	"""CD48 antigen (B-cell membrane protein)"", ""CD48 molecule """	BCM1		2828034	Standard	NM_001256030		Approved	BLAST, mCD48, hCD48, SLAMF2	uc001fwo.2	P09326	OTTHUMG00000024009	ENST00000368046.3:c.120C>T	1.37:g.160654942G>A		Somatic		Capture	Illumina HiSeq	Phase_I	158921566	NM_001778	Q5U055|Q8MGR0	Silent	SNP	ENST00000368046.3	37	CCDS1208.1																																																																																				0.493	CD48-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060471.1	NM_001778	
SLC25A34	284723	broad.mit.edu	37	1	16064627	16064627	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr1:16064627G>T	ENST00000294454.5	+	3	565	c.484G>T	c.(484-486)Ggg>Tgg	p.G162W	SLC25A34_ENST00000489568.1_3'UTR|RP11-169K16.4_ENST00000418525.1_RNA|RP11-288I21.1_ENST00000453804.1_RNA	NM_207348.1	NP_997231.1	Q6PIV7	S2534_HUMAN	solute carrier family 25, member 34	162					transport (GO:0006810)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)		p.G162W(1)		NS(1)|breast(1)|endometrium(3)|large_intestine(1)|lung(2)|skin(1)	9		Colorectal(325;0.00108)|Renal(390;0.00145)|Breast(348;0.00224)|Lung NSC(340;0.00566)|all_lung(284;0.00831)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0798)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;5.96e-07)|COAD - Colon adenocarcinoma(227;3.56e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000115)|KIRC - Kidney renal clear cell carcinoma(229;0.00244)|STAD - Stomach adenocarcinoma(313;0.0072)|READ - Rectum adenocarcinoma(331;0.0649)		GCGGCAGCAAGGGCTCTTGGG	0.682																																					p.G162W												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G484T	1						.						56.0	65.0	62.0					1																	16064627		2203	4300	6503	15937214	SO:0001583	missense	284723	exon3			BC027998	CCDS162.1	1p36.13	2013-05-22			ENSG00000162461	ENSG00000162461		"""Solute carriers"""	27653	protein-coding gene	gene with protein product		610817					Standard	NM_207348		Approved	DKFZp781A10161	uc001axb.1	Q6PIV7	OTTHUMG00000003063	ENST00000294454.5:c.484G>T	1.37:g.16064627G>T	ENSP00000294454:p.Gly162Trp	Somatic		Capture	Illumina HiSeq	Phase_I	15937214	NM_207348	Q68DV0	Missense_Mutation	SNP	ENST00000294454.5	37	CCDS162.1	.	.	.	.	.	.	.	.	.	.	G	16.92	3.255784	0.59321	.	.	ENSG00000162461	ENST00000294454	D	0.95272	-3.66	5.28	5.28	0.74379	Mitochondrial carrier domain (2);	0.061122	0.64402	D	0.000004	D	0.98504	0.9501	H	0.97806	4.08	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.99780	1.1027	10	0.87932	D	0	.	18.9097	0.92477	0.0:0.0:1.0:0.0	.	162	Q6PIV7	S2534_HUMAN	W	162	ENSP00000294454:G162W	ENSP00000294454:G162W	G	+	1	0	SLC25A34	15937214	1.000000	0.71417	0.998000	0.56505	0.018000	0.09664	9.122000	0.94380	2.446000	0.82766	0.563000	0.77884	GGG		0.682	SLC25A34-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008467.1	NM_207348	
ITLN1	55600	broad.mit.edu	37	1	160851800	160851800	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr1:160851800C>T	ENST00000326245.3	-	4	467	c.352G>A	c.(352-354)Gcc>Acc	p.A118T	ITLN1_ENST00000487531.1_5'Flank	NM_017625.2	NP_060095.2	Q8WWA0	ITLN1_HUMAN	intelectin 1 (galactofuranose binding)	118	Fibrinogen C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00739}.				positive regulation of glucose import (GO:0046326)|positive regulation of protein phosphorylation (GO:0001934)|response to nematode (GO:0009624)	anchored component of membrane (GO:0031225)|brush border membrane (GO:0031526)|extracellular vesicular exosome (GO:0070062)|membrane raft (GO:0045121)|receptor complex (GO:0043235)	carbohydrate binding (GO:0030246)	p.A118T(1)		breast(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(1)|lung(6)|ovary(2)|pancreas(1)|skin(3)|upper_aerodigestive_tract(1)	21	all_cancers(52;2.99e-17)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00737)			TTGTAGTTGGCCCAGTTGCCG	0.602																																					p.A118T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G352A	1						.						175.0	150.0	158.0					1																	160851800		2203	4300	6503	159118424	SO:0001583	missense	55600	exon4			AB036706	CCDS1211.1	1q21.3	2008-02-05			ENSG00000179914	ENSG00000179914			18259	protein-coding gene	gene with protein product		609873				11313366, 11181563	Standard	NM_017625		Approved	ITLN, FLJ20022, LFR, HL-1, hIntL	uc001fxc.3	Q8WWA0	OTTHUMG00000028604	ENST00000326245.3:c.352G>A	1.37:g.160851800C>T	ENSP00000323587:p.Ala118Thr	Somatic		Capture	Illumina HiSeq	Phase_I	159118424	NM_017625	Q5IWS4|Q5VYI4|Q6YDJ3|Q9NP67	Missense_Mutation	SNP	ENST00000326245.3	37	CCDS1211.1	.	.	.	.	.	.	.	.	.	.	C	27.7	4.852482	0.91355	.	.	ENSG00000179914	ENST00000326245	T	0.26067	1.76	4.17	4.17	0.49024	Fibrinogen, alpha/beta/gamma chain, C-terminal globular (2);Fibrinogen, alpha/beta/gamma chain, C-terminal globular, subdomain 1 (1);	0.000000	0.64402	D	0.000009	T	0.39279	0.1072	M	0.82132	2.575	0.52501	D	0.999959	D	0.61697	0.99	P	0.59357	0.856	T	0.43458	-0.9390	10	0.66056	D	0.02	-15.8175	14.0049	0.64456	0.0:1.0:0.0:0.0	.	118	Q8WWA0	ITLN1_HUMAN	T	118	ENSP00000323587:A118T	ENSP00000323587:A118T	A	-	1	0	ITLN1	159118424	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.667000	0.46808	2.129000	0.65627	0.655000	0.94253	GCC		0.602	ITLN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071462.1	NM_017625	
USP21	27005	broad.mit.edu	37	1	161134865	161134865	+	Silent	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr1:161134865C>T	ENST00000289865.8	+	12	1760	c.1539C>T	c.(1537-1539)agC>agT	p.S513S	PPOX_ENST00000367999.4_5'Flank|USP21_ENST00000368002.3_Silent_p.S513S|PPOX_ENST00000535223.1_5'Flank|USP21_ENST00000493054.1_3'UTR|PPOX_ENST00000544598.1_5'Flank|USP21_ENST00000368001.1_Silent_p.S499S|PPOX_ENST00000432542.2_5'Flank|PPOX_ENST00000352210.5_5'Flank	NM_012475.4	NP_036607.3	Q9UK80	UBP21_HUMAN	ubiquitin specific peptidase 21	513	USP.				histone deubiquitination (GO:0016578)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	cysteine-type peptidase activity (GO:0008234)|metal ion binding (GO:0046872)|NEDD8-specific protease activity (GO:0019784)|transcription coactivator activity (GO:0003713)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)	p.S513S(1)		breast(1)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(5)|lung(10)|ovary(3)|prostate(3)	29	all_cancers(52;3.73e-19)|Breast(13;0.000577)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00275)			ACTCAGGCAGCGTCCACTATG	0.537																																					p.S513S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1539T	1						.						105.0	96.0	99.0					1																	161134865		2203	4300	6503	159401489	SO:0001819	synonymous_variant	27005	exon12			AF177758	CCDS30920.1	1q22	2008-04-11	2005-08-08		ENSG00000143258	ENSG00000143258		"""Ubiquitin-specific peptidases"""	12620	protein-coding gene	gene with protein product		604729	"""ubiquitin specific protease 21"""	USP23		12838346, 10799498	Standard	XM_006711273		Approved	USP16	uc010pkd.2	Q9UK80	OTTHUMG00000033154	ENST00000289865.8:c.1539C>T	1.37:g.161134865C>T		Somatic		Capture	Illumina HiSeq	Phase_I	159401489	NM_012475	Q59H60|Q5BKT5|Q5VTW9|Q5VTX0|Q9BTV1|Q9HBS2|Q9NYN4	Silent	SNP	ENST00000289865.8	37	CCDS30920.1																																																																																				0.537	USP21-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080801.1		
OLFML2B	25903	broad.mit.edu	37	1	161953499	161953499	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr1:161953499T>C	ENST00000294794.3	-	8	2642	c.2219A>G	c.(2218-2220)cAc>cGc	p.H740R	OLFML2B_ENST00000367938.1_Missense_Mutation_p.H223R|OLFML2B_ENST00000367940.2_Missense_Mutation_p.H741R	NM_015441.1	NP_056256.1	Q68BL8	OLM2B_HUMAN	olfactomedin-like 2B	740	Olfactomedin-like. {ECO:0000255|PROSITE- ProRule:PRU00446}.				extracellular matrix organization (GO:0030198)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)	extracellular matrix binding (GO:0050840)	p.H740R(1)		breast(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(11)|lung(22)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	48	all_hematologic(112;0.156)		BRCA - Breast invasive adenocarcinoma(70;0.0172)			AGTGACCTGGTGGCCATTGTC	0.542																																					p.H740R												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A2219G	1						.						220.0	194.0	203.0					1																	161953499		2203	4300	6503	160220123	SO:0001583	missense	25903	exon8			BX648975	CCDS1236.1, CCDS72966.1	1q23.1	2008-02-05			ENSG00000162745	ENSG00000162745			24558	protein-coding gene	gene with protein product							Standard	XM_005245075		Approved	DKFZP586L151	uc001gbu.3	Q68BL8	OTTHUMG00000024047	ENST00000294794.3:c.2219A>G	1.37:g.161953499T>C	ENSP00000294794:p.His740Arg	Somatic		Capture	Illumina HiSeq	Phase_I	160220123	NM_015441	B7ZA39|Q5VU96|Q6NX46|Q86X11|Q9Y3X6	Missense_Mutation	SNP	ENST00000294794.3	37	CCDS1236.1	.	.	.	.	.	.	.	.	.	.	T	20.6	4.016340	0.75161	.	.	ENSG00000162745	ENST00000294794;ENST00000367940;ENST00000367938	D;D;D	0.90133	-2.62;-2.62;-2.62	5.6	5.6	0.85130	Olfactomedin-like (3);	.	.	.	.	D	0.93585	0.7952	M	0.72118	2.19	0.43703	D	0.996167	D;D	0.89917	1.0;0.97	D;D	0.97110	1.0;0.945	D	0.94744	0.7921	8	0.87932	D	0	.	13.7335	0.62804	0.0:0.0:0.0:1.0	.	741;740	F2Z3N3;Q68BL8	.;OLM2B_HUMAN	R	740;741;223	ENSP00000294794:H740R;ENSP00000356917:H741R;ENSP00000356915:H223R	ENSP00000294794:H740R	H	-	2	0	OLFML2B	160220123	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	5.043000	0.64208	2.116000	0.64780	0.533000	0.62120	CAC		0.542	OLFML2B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000060552.2	NM_015441	
UHMK1	127933	broad.mit.edu	37	1	162469795	162469795	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr1:162469795C>T	ENST00000489294.1	+	2	477	c.319C>T	c.(319-321)Cgc>Tgc	p.R107C	UHMK1_ENST00000538489.1_Missense_Mutation_p.R107C|UHMK1_ENST00000282169.8_3'UTR|UHMK1_ENST00000545294.1_Missense_Mutation_p.R33C	NM_175866.4	NP_787062.1	Q8TAS1	UHMK1_HUMAN	U2AF homology motif (UHM) kinase 1	107	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159, ECO:0000305}.				cell cycle arrest (GO:0007050)|neuron projection development (GO:0031175)|peptidyl-serine phosphorylation (GO:0018105)|positive regulation of translational initiation (GO:0045948)|protein autophosphorylation (GO:0046777)|regulation of protein export from nucleus (GO:0046825)	axon (GO:0030424)|dendrite cytoplasm (GO:0032839)|neuronal ribonucleoprotein granule (GO:0071598)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)|ribonucleoprotein complex binding (GO:0043021)|RNA binding (GO:0003723)|transferase activity (GO:0016740)	p.R107C(1)		endometrium(1)|large_intestine(2)|lung(6)|prostate(2)	11	all_hematologic(112;0.115)		BRCA - Breast invasive adenocarcinoma(70;0.126)			TGTGCCATCACGCTGTCTGTT	0.403																																					p.R107C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C319T	1						.						216.0	195.0	202.0					1																	162469795		2203	4300	6503	160736419	SO:0001583	missense	127933	exon2			BC026046	CCDS1239.1, CCDS53423.1, CCDS53424.1	1q23.1	2013-02-12			ENSG00000152332	ENSG00000152332		"""RNA binding motif (RRM) containing"""	19683	protein-coding gene	gene with protein product		608849				12093740, 12782393	Standard	NM_175866		Approved	KIS, Kist	uc001gcc.2	Q8TAS1	OTTHUMG00000031373	ENST00000489294.1:c.319C>T	1.37:g.162469795C>T	ENSP00000420270:p.Arg107Cys	Somatic		Capture	Illumina HiSeq	Phase_I	160736419	NM_175866	A8K8K4|G3V1M1|Q96C22	Missense_Mutation	SNP	ENST00000489294.1	37	CCDS1239.1	.	.	.	.	.	.	.	.	.	.	C	27.6	4.845166	0.91197	.	.	ENSG00000152332	ENST00000545294;ENST00000538489;ENST00000489294	T;T;T	0.65178	-0.14;-0.14;-0.14	5.49	5.49	0.81192	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.170948	0.53938	N	0.000050	T	0.57272	0.2042	L	0.27975	0.815	.	.	.	D;D;D	0.76494	0.998;0.996;0.999	P;P;P	0.57960	0.796;0.83;0.796	T	0.63479	-0.6628	9	0.66056	D	0.02	-7.5541	16.4617	0.84056	0.0:1.0:0.0:0.0	.	107;107;33	Q8TAS1-2;Q8TAS1;G3V1M1	.;UHMK1_HUMAN;.	C	33;107;107	ENSP00000441226:R33C;ENSP00000446416:R107C;ENSP00000420270:R107C	ENSP00000420270:R107C	R	+	1	0	UHMK1	160736419	0.998000	0.40836	1.000000	0.80357	0.996000	0.88848	4.041000	0.57339	2.739000	0.93911	0.655000	0.94253	CGC		0.403	UHMK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076788.1	NM_175866	
FBXO42	54455	broad.mit.edu	37	1	16577872	16577872	+	Missense_Mutation	SNP	C	C	G			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	G	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr1:16577872C>G	ENST00000375592.3	-	10	1663	c.1447G>C	c.(1447-1449)Gcc>Ccc	p.A483P		NM_018994.1	NP_061867.1	Q6P3S6	FBX42_HUMAN	F-box protein 42	483								p.A483P(1)		autonomic_ganglia(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(7)|lung(4)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(3)	26		Colorectal(325;0.000147)|Renal(390;0.00145)|Breast(348;0.00224)|Lung NSC(340;0.00475)|all_lung(284;0.00671)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0646)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0193)|Colorectal(212;3.16e-07)|COAD - Colon adenocarcinoma(227;1.46e-05)|BRCA - Breast invasive adenocarcinoma(304;4.37e-05)|Kidney(64;0.000246)|KIRC - Kidney renal clear cell carcinoma(64;0.00336)|STAD - Stomach adenocarcinoma(313;0.0139)|READ - Rectum adenocarcinoma(331;0.0693)		CGTCGGGGGGCCAAAGAAAGT	0.483																																					p.A483P												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1447C	1						.						52.0	56.0	55.0					1																	16577872		2203	4300	6503	16450459	SO:0001583	missense	54455	exon10			BC063864	CCDS30613.1	1p36.23-p36.11	2008-02-05			ENSG00000037637	ENSG00000037637		"""F-boxes /  ""other"""""	29249	protein-coding gene	gene with protein product		609109				10718198	Standard	XM_006710698		Approved	KIAA1332, Fbx42	uc001ayg.3	Q6P3S6	OTTHUMG00000002218	ENST00000375592.3:c.1447G>C	1.37:g.16577872C>G	ENSP00000364742:p.Ala483Pro	Somatic		Capture	Illumina HiSeq	Phase_I	16450459	NM_018994	B3KP30|Q5TEU8|Q86XI0|Q8N3N4|Q8N5F8|Q9BRM0|Q9P2L4	Missense_Mutation	SNP	ENST00000375592.3	37	CCDS30613.1	.	.	.	.	.	.	.	.	.	.	C	11.28	1.593163	0.28357	.	.	ENSG00000037637	ENST00000375592;ENST00000456164;ENST00000444116	T;T;T	0.52057	3.66;0.68;0.68	5.51	4.32	0.51571	.	0.543859	0.18885	N	0.128476	T	0.26846	0.0657	N	0.08118	0	0.20703	N	0.999869	B	0.02656	0.0	B	0.01281	0.0	T	0.13737	-1.0498	10	0.30078	T	0.28	-1.3216	10.8612	0.46827	0.0:0.8978:0.0:0.1022	.	483	Q6P3S6	FBX42_HUMAN	P	483;201;201	ENSP00000364742:A483P;ENSP00000415663:A201P;ENSP00000412416:A201P	ENSP00000364742:A483P	A	-	1	0	FBXO42	16450459	0.005000	0.15991	0.029000	0.17559	0.936000	0.57629	0.656000	0.24948	1.332000	0.45431	0.650000	0.86243	GCC		0.483	FBXO42-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006285.1		
LRRC52	440699	broad.mit.edu	37	1	165513742	165513742	+	Missense_Mutation	SNP	C	C	T	rs376324521	byFrequency	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr1:165513742C>T	ENST00000294818.1	+	1	499	c.209C>T	c.(208-210)gCa>gTa	p.A70V	RP11-280O1.2_ENST00000421273.1_RNA|RP11-280O1.2_ENST00000416424.1_RNA|RP11-280O1.2_ENST00000438275.1_RNA	NM_001005214.3	NP_001005214.2	Q8N7C0	LRC52_HUMAN	leucine rich repeat containing 52	70					ion transport (GO:0006811)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.A70V(1)		NS(1)|central_nervous_system(1)|cervix(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(5)|ovary(1)	18	all_hematologic(923;0.0773)|Acute lymphoblastic leukemia(8;0.155)					AGTTTGCCAGCAATGCATCTA	0.483													C|||	2	0.000399361	0.0	0.0	5008	,	,		18160	0.002		0.0	False		,,,				2504	0.0				p.A70V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C209T	1						.						164.0	161.0	162.0					1																	165513742		2203	4300	6503	163780366	SO:0001583	missense	440699	exon1			AK098677	CCDS30930.1	1q23.3	2008-02-05			ENSG00000162763	ENSG00000162763			32156	protein-coding gene	gene with protein product		615218					Standard	NM_001005214		Approved	FLJ25811	uc001gde.2	Q8N7C0	OTTHUMG00000034625	ENST00000294818.1:c.209C>T	1.37:g.165513742C>T	ENSP00000294818:p.Ala70Val	Somatic		Capture	Illumina HiSeq	Phase_I	163780366	NM_001005214	A2RUN7|Q5T9K5	Missense_Mutation	SNP	ENST00000294818.1	37	CCDS30930.1	.	.	.	.	.	.	.	.	.	.	C	20.4	3.984796	0.74474	.	.	ENSG00000162763	ENST00000294818	T	0.02472	4.28	5.68	5.68	0.88126	.	0.222920	0.44902	D	0.000404	T	0.03520	0.0101	M	0.75777	2.31	0.32856	D	0.507310	B	0.29571	0.249	B	0.33690	0.168	T	0.20207	-1.0282	9	0.48119	T	0.1	.	17.2918	0.87159	0.0:1.0:0.0:0.0	.	70	Q8N7C0	LRC52_HUMAN	V	70	ENSP00000294818:A70V	ENSP00000294818:A70V	A	+	2	0	LRRC52	163780366	0.989000	0.36119	0.980000	0.43619	0.996000	0.88848	7.196000	0.77805	2.677000	0.91161	0.563000	0.77884	GCA		0.483	LRRC52-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083793.1	NM_001005214	
CD247	919	broad.mit.edu	37	1	167407839	167407839	+	Missense_Mutation	SNP	G	G	A	rs148513413		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr1:167407839G>A	ENST00000362089.5	-	4	340	c.268C>T	c.(268-270)Cgt>Tgt	p.R90C	CD247_ENST00000392122.3_Missense_Mutation_p.R90C|CD247_ENST00000483825.1_5'UTR			P20963	CD3Z_HUMAN	CD247 molecule	90					Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|regulation of defense response to virus by virus (GO:0050690)|regulation of immune response (GO:0050776)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|viral process (GO:0016032)	alpha-beta T cell receptor complex (GO:0042105)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|T cell receptor complex (GO:0042101)	identical protein binding (GO:0042802)|protein homodimerization activity (GO:0042803)|transmembrane signaling receptor activity (GO:0004888)	p.R90C(1)		central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(1)|skin(1)	6			LUSC - Lung squamous cell carcinoma(543;0.236)		Muromonab(DB00075)	TCCCGGCCACGTCTCTTGTCC	0.552													G|||	1	0.000199681	0.0	0.0	5008	,	,		17232	0.001		0.0	False		,,,				2504	0.0				p.R90C	Ovarian(192;1815 2869 36877 43334)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C268T	1						.						151.0	141.0	145.0					1																	167407839		2203	4300	6503	165674463	SO:0001583	missense	919	exon4			BC025703	CCDS1260.1, CCDS1261.1	1q24.2	2014-09-17	2006-03-28	2006-03-09	ENSG00000198821	ENSG00000198821		"""CD molecules"""	1677	protein-coding gene	gene with protein product		186780	"""CD3z antigen, zeta polypeptide (TiT3 complex)"", ""CD247 antigen"""	CD3Z		2974162	Standard	NM_198053		Approved	CD3H, CD3Q	uc001gei.4	P20963	OTTHUMG00000034593	ENST00000362089.5:c.268C>T	1.37:g.167407839G>A	ENSP00000354782:p.Arg90Cys	Somatic		Capture	Illumina HiSeq	Phase_I	165674463	NM_198053	B1AK49|Q5VX13|Q8TAX4	Missense_Mutation	SNP	ENST00000362089.5	37	CCDS1261.1	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	G	16.10	3.026161	0.54683	.	.	ENSG00000198821	ENST00000392122;ENST00000362089	.	.	.	4.52	2.45	0.29901	.	0.137776	0.28718	U	0.014364	T	0.54224	0.1845	M	0.64997	1.995	0.35719	D	0.816966	D;D;D	0.89917	1.0;0.998;0.997	D;P;P	0.74023	0.982;0.855;0.72	T	0.58978	-0.7540	8	0.72032	D	0.01	.	8.5233	0.33289	0.0:0.1632:0.6634:0.1734	.	90;90;90	Q6KAV0;P20963-3;P20963	.;.;CD3Z_HUMAN	C	90	.	ENSP00000354782:R90C	R	-	1	0	CD247	165674463	0.000000	0.05858	0.115000	0.21578	0.951000	0.60555	0.149000	0.16243	1.096000	0.41439	0.563000	0.77884	CGT		0.552	CD247-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000083707.1	NM_198053	
MPZL1	9019	broad.mit.edu	37	1	167734960	167734960	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr1:167734960C>T	ENST00000359523.2	+	2	434	c.232C>T	c.(232-234)Cca>Tca	p.P78S	MPZL1_ENST00000474859.1_Missense_Mutation_p.P78S|MPZL1_ENST00000392121.3_Missense_Mutation_p.P78S	NM_003953.5|NM_024569.4	NP_003944.1|NP_078845.3	O95297	MPZL1_HUMAN	myelin protein zero-like 1	78	Ig-like V-type.				cell-cell signaling (GO:0007267)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cell surface (GO:0009986)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)	structural molecule activity (GO:0005198)	p.P78S(1)		breast(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(4)|ovary(2)|prostate(2)	15	all_hematologic(923;0.215)					GAGCTTCCAGCCAGAGGGGGC	0.498																																					p.P78S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C232T	1						.						43.0	43.0	43.0					1																	167734960		2203	4300	6503	166001584	SO:0001583	missense	9019	exon2			AF087020	CCDS1264.1, CCDS44273.1, CCDS53425.1	1q24.2	2013-01-11			ENSG00000197965	ENSG00000197965		"""Immunoglobulin superfamily / V-set domain containing"""	7226	protein-coding gene	gene with protein product		604376				9792637	Standard	NM_003953		Approved	PZR, FLJ21047	uc001geo.3	O95297	OTTHUMG00000034571	ENST00000359523.2:c.232C>T	1.37:g.167734960C>T	ENSP00000352513:p.Pro78Ser	Somatic		Capture	Illumina HiSeq	Phase_I	166001584	NM_024569	B2REB9|B2REC0|Q5R332|Q8IX11|Q9BWZ3|Q9NYK4|Q9UL20	Missense_Mutation	SNP	ENST00000359523.2	37	CCDS1264.1	.	.	.	.	.	.	.	.	.	.	C	17.50	3.404847	0.62288	.	.	ENSG00000197965	ENST00000359523;ENST00000392121;ENST00000474859;ENST00000367853	D;D;D;D	0.94232	-3.38;-3.38;-3.38;-3.38	4.68	3.67	0.42095	Immunoglobulin V-set (1);Immunoglobulin-like (1);Immunoglobulin V-set, subgroup (1);Immunoglobulin-like fold (1);	0.180935	0.49916	D	0.000134	D	0.90328	0.6974	L	0.39514	1.22	0.37213	D	0.904896	P;D;P	0.54207	0.546;0.965;0.895	B;P;P	0.50659	0.135;0.647;0.629	D	0.90902	0.4769	9	0.54805	T	0.06	.	14.68	0.69009	0.0:0.7577:0.2423:0.0	.	78;78;78	B2REC0;O95297-3;O95297	.;.;MPZL1_HUMAN	S	78;78;78;52	ENSP00000352513:P78S;ENSP00000375968:P78S;ENSP00000420455:P78S;ENSP00000356827:P52S	ENSP00000352513:P78S	P	+	1	0	MPZL1	166001584	0.999000	0.42202	1.000000	0.80357	0.686000	0.39977	0.926000	0.28804	2.543000	0.85770	0.655000	0.94253	CCA		0.498	MPZL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083655.2	NM_024569	
NECAP2	55707	broad.mit.edu	37	1	16782333	16782333	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr1:16782333C>T	ENST00000337132.5	+	7	778	c.688C>T	c.(688-690)Cca>Tca	p.P230S	NECAP2_ENST00000504551.2_Missense_Mutation_p.P169S|NECAP2_ENST00000457722.2_Missense_Mutation_p.P204S|NECAP2_ENST00000443980.2_Intron|NECAP2_ENST00000406746.1_Missense_Mutation_p.P230S	NM_001145278.1|NM_018090.4	NP_001138750.1|NP_060560.1	Q9NVZ3	NECP2_HUMAN	NECAP endocytosis associated 2	230					endocytosis (GO:0006897)|protein transport (GO:0015031)	clathrin vesicle coat (GO:0030125)|coated pit (GO:0005905)|intracellular (GO:0005622)|plasma membrane (GO:0005886)		p.P230S(1)		endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	9		Colorectal(325;0.000147)|Renal(390;0.00145)|Lung NSC(340;0.00215)|Breast(348;0.00224)|all_lung(284;0.00351)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0646)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0182)|COAD - Colon adenocarcinoma(227;1.13e-05)|BRCA - Breast invasive adenocarcinoma(304;4.13e-05)|Kidney(64;0.000181)|KIRC - Kidney renal clear cell carcinoma(64;0.00268)|STAD - Stomach adenocarcinoma(196;0.012)|READ - Rectum adenocarcinoma(331;0.0649)		TGTACCCTGGCCACAGCCCAA	0.562																																					p.P230S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C688T	1						.						59.0	56.0	57.0					1																	16782333		2203	4300	6503	16654920	SO:0001583	missense	55707	exon7			AK021938	CCDS173.1, CCDS44066.1, CCDS44067.1	1p36.13	2008-02-05			ENSG00000157191	ENSG00000157191			25528	protein-coding gene	gene with protein product		611624				14555962, 15494011	Standard	NM_001145277		Approved	FLJ10420	uc001ayq.3	Q9NVZ3	OTTHUMG00000002313	ENST00000337132.5:c.688C>T	1.37:g.16782333C>T	ENSP00000338746:p.Pro230Ser	Somatic		Capture	Illumina HiSeq	Phase_I	16654920	NM_018090	B4DY19|E9PGQ8|Q5VSU4|Q5VSU5|Q9H7L1|Q9H8L1	Missense_Mutation	SNP	ENST00000337132.5	37	CCDS173.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	10.19|10.19	1.283132|1.283132	0.23392|0.23392	.|.	.|.	ENSG00000157191|ENSG00000157191	ENST00000263498|ENST00000337132;ENST00000504551;ENST00000457722;ENST00000406746;ENST00000492095	.|T;T;T;T;T	.|0.29917	.|1.62;1.55;1.6;1.62;1.62	5.84|5.84	5.84|5.84	0.93424|0.93424	.|.	.|.	.|.	.|.	.|.	T|T	0.33265|0.33265	0.0857|0.0857	L|L	0.57536|0.57536	1.79|1.79	0.40612|0.40612	D|D	0.981683|0.981683	.|B;B	.|0.23650	.|0.089;0.021	.|B;B	.|0.26310	.|0.068;0.017	T|T	0.06197|0.06197	-1.0840|-1.0840	6|9	0.34782|0.28530	T|T	0.22|0.3	.|.	15.6387|15.6387	0.76977|0.76977	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|204;230	.|Q9NVZ3-4;Q9NVZ3	.|.;NECP2_HUMAN	V|S	178|230;169;204;230;230	.|ENSP00000338746:P230S;ENSP00000424509:P169S;ENSP00000407091:P204S;ENSP00000383925:P230S;ENSP00000427620:P230S	ENSP00000263498:A178V|ENSP00000338746:P230S	A|P	+|+	2|1	0|0	NECAP2|NECAP2	16654920|16654920	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.279000|0.279000	0.26890|0.26890	3.205000|3.205000	0.51090|0.51090	2.767000|2.767000	0.95098|0.95098	0.561000|0.561000	0.74099|0.74099	GCC|CCA		0.562	NECAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006680.2	NM_018090	
GPR161	23432	broad.mit.edu	37	1	168074035	168074035	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr1:168074035C>A	ENST00000367838.1	-	4	367	c.54G>T	c.(52-54)gaG>gaT	p.E18D	GPR161_ENST00000271357.5_Missense_Mutation_p.E18D|GPR161_ENST00000367835.1_Missense_Mutation_p.E18D|GPR161_ENST00000546300.1_Intron|GPR161_ENST00000367836.1_Intron|GPR161_ENST00000361697.2_Missense_Mutation_p.E18D|GPR161_ENST00000539777.1_Intron|GPR161_ENST00000537209.1_Missense_Mutation_p.E38D	NM_001267611.1|NM_153832.2	NP_001254540.1|NP_722561.1	Q8N6U8	GP161_HUMAN	G protein-coupled receptor 161	18					G-protein coupled receptor signaling pathway (GO:0007186)|multicellular organismal development (GO:0007275)|negative regulation of smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:1901621)|positive regulation of cAMP biosynthetic process (GO:0030819)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|primary cilium (GO:0072372)|recycling endosome (GO:0055037)	G-protein coupled receptor activity (GO:0004930)	p.E18D(1)		breast(1)|endometrium(3)|large_intestine(8)|lung(10)|ovary(1)|prostate(2)|skin(1)	26	all_hematologic(923;0.215)					CACCCTCCTCCTCAGTGAGAT	0.577																																					p.E18D												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G54T	1						.						115.0	95.0	102.0					1																	168074035		2203	4300	6503	166340659	SO:0001583	missense	23432	exon4			AF091890	CCDS1268.1, CCDS58042.1, CCDS58043.1, CCDS58044.1, CCDS58045.1, CCDS72978.1	1q23.3	2012-08-21			ENSG00000143147	ENSG00000143147		"""GPCR / Class A : Orphans"""	23694	protein-coding gene	gene with protein product		612250				11959142	Standard	NM_153832		Approved	RE2	uc009wvo.4	Q8N6U8	OTTHUMG00000034651	ENST00000367838.1:c.54G>T	1.37:g.168074035C>A	ENSP00000356812:p.Glu18Asp	Somatic		Capture	Illumina HiSeq	Phase_I	166340659	NM_153832	B3KV34|B7Z5D7|B7Z5E8|B7Z5Z6|F5GXD6|F5H6J7|O75963|Q5TGK0|Q5TGK1|Q5TGK2	Missense_Mutation	SNP	ENST00000367838.1	37	CCDS1268.1	.	.	.	.	.	.	.	.	.	.	C	0.400	-0.918684	0.02396	.	.	ENSG00000143147	ENST00000367838;ENST00000271357;ENST00000367835;ENST00000537209;ENST00000361697	T;T;T;T;T	0.63744	-0.06;-0.06;-0.06;0.05;-0.06	5.1	-1.23	0.09465	.	0.671285	0.14009	N	0.347582	T	0.13670	0.0331	N	0.14661	0.345	0.21147	N	0.999772	B;B;B;B	0.14805	0.011;0.007;0.004;0.003	B;B;B;B	0.15870	0.014;0.006;0.013;0.004	T	0.10683	-1.0619	9	0.10902	T	0.67	-2.5681	3.387	0.07276	0.099:0.4584:0.2144:0.2282	.	38;38;18;18	F5GXD6;B7Z5Z6;Q8N6U8-2;Q8N6U8	.;.;.;GP161_HUMAN	D	18;18;18;38;18	ENSP00000356812:E18D;ENSP00000271357:E18D;ENSP00000356809:E18D;ENSP00000441039:E38D;ENSP00000355194:E18D	ENSP00000271357:E18D	E	-	3	2	GPR161	166340659	0.000000	0.05858	0.000000	0.03702	0.050000	0.14768	-2.634000	0.00869	-0.100000	0.12241	-0.367000	0.07326	GAG		0.577	GPR161-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083829.1	NM_007369	
MROH9	80133	broad.mit.edu	37	1	170967486	170967486	+	Missense_Mutation	SNP	A	A	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr1:170967486A>T	ENST00000367758.3	+	15	1766	c.1667A>T	c.(1666-1668)cAg>cTg	p.Q556L	MROH9_ENST00000367759.4_Intron	NM_025063.2	NP_079339.2	Q5TGP6	MROH9_HUMAN	maestro heat-like repeat family member 9	556								p.Q556L(1)									TCAAAATTCCAGTTTCTCGTA	0.388																																					p.Q556L												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A1667T	1						.						175.0	153.0	160.0					1																	170967486		1830	4086	5916	169234110	SO:0001583	missense	80133	exon15			AK027203	CCDS41436.1, CCDS53429.1	1q24.3	2012-12-19	2012-12-19	2012-12-19	ENSG00000117501	ENSG00000117501		"""maestro heat-like repeat containing"""	26287	protein-coding gene	gene with protein product			"""chromosome 1 open reading frame 129"""	C1orf129			Standard	NM_025063		Approved	FLJ23550, ARMC11	uc010plz.2	Q5TGP6	OTTHUMG00000041456	ENST00000367758.3:c.1667A>T	1.37:g.170967486A>T	ENSP00000356732:p.Gln556Leu	Somatic		Capture	Illumina HiSeq	Phase_I	169234110	NM_025063	A0PJM0|A0PJM2|F5GWX6|Q9H5D7	Missense_Mutation	SNP	ENST00000367758.3	37	CCDS41436.1	.	.	.	.	.	.	.	.	.	.	A	9.031	0.987226	0.18889	.	.	ENSG00000117501	ENST00000367758	T	0.15603	2.41	4.16	-0.875	0.10628	.	2.293460	0.01879	N	0.037708	T	0.02727	0.0082	N	0.08118	0	0.09310	N	1	P	0.42518	0.782	B	0.35353	0.201	T	0.27905	-1.0060	10	0.87932	D	0	1.5901	7.3049	0.26443	0.6094:0.0:0.3906:0.0	.	556	Q5TGP6	CA129_HUMAN	L	556	ENSP00000356732:Q556L	ENSP00000356732:Q556L	Q	+	2	0	C1orf129	169234110	0.001000	0.12720	0.000000	0.03702	0.010000	0.07245	0.924000	0.28777	-0.267000	0.09325	-0.490000	0.04691	CAG		0.388	MROH9-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000099327.1	NM_025063	
SDHB	6390	broad.mit.edu	37	1	17350484	17350484	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr1:17350484G>T	ENST00000375499.3	-	6	776	c.626C>A	c.(625-627)cCt>cAt	p.P209H		NM_003000.2	NP_002991.2	P21912	SDHB_HUMAN	succinate dehydrogenase complex, subunit B, iron sulfur (Ip)	209					aerobic respiration (GO:0009060)|cellular metabolic process (GO:0044237)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)|succinate metabolic process (GO:0006105)|tricarboxylic acid cycle (GO:0006099)	extracellular vesicular exosome (GO:0070062)|mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex II (GO:0005749)|mitochondrion (GO:0005739)	2 iron, 2 sulfur cluster binding (GO:0051537)|3 iron, 4 sulfur cluster binding (GO:0051538)|4 iron, 4 sulfur cluster binding (GO:0051539)|electron carrier activity (GO:0009055)|metal ion binding (GO:0046872)|succinate dehydrogenase (ubiquinone) activity (GO:0008177)|ubiquinone binding (GO:0048039)	p.P209H(1)		breast(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(4)	10		Colorectal(325;3.46e-05)|Breast(348;0.000162)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.00054)|Ovarian(437;0.00669)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0049)|COAD - Colon adenocarcinoma(227;1.18e-05)|BRCA - Breast invasive adenocarcinoma(304;2.41e-05)|Kidney(64;0.000188)|KIRC - Kidney renal clear cell carcinoma(64;0.00273)|STAD - Stomach adenocarcinoma(196;0.00656)|READ - Rectum adenocarcinoma(331;0.0656)|Lung(427;0.19)	Succinic acid(DB00139)	AAGAACTGCAGGCCCCAGATA	0.498			"""Mis, N, F"""			"""paraganglioma, pheochromocytoma"""			Familial Paragangliomas;Cowden syndrome;Carney-Stratakis syndrome																												p.P209H		yes	Rec		Familial paraganglioma	1	1p36.1-p35	6390	"""succinate dehydrogenase complex, subunit B, iron sulfur (Ip)"""		O	.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C626A	1						.						47.0	47.0	47.0					1																	17350484		2203	4300	6503	17223071	SO:0001583	missense	6390	exon6	Familial Cancer Database	Hereditary Glomus Tumors, Familial Paragangliomas, Hereditary Paragangliomas, type 1-3: PGL1, PGL2, PGL3, incl. Familial Carotid Body Paraganglioma and Sensorineural Hearing Loss;CS, Cowden disease, Multiple Hamartoma Syndrome, incl.: Lhermitte-Duclos; part of PTEN hamartoma tumour syndrome (PHTS) / PTEN-MATCHS, Cowden-like syndrome;Carney-Stratakis dyad, Paraganglioma-Gastric Stromal Sarcoma dyad	U17248	CCDS176.1	1p36.1-p35	2014-09-17			ENSG00000117118	ENSG00000117118	1.3.99.1	"""Mitochondrial respiratory chain complex / Complex II"""	10681	protein-coding gene	gene with protein product		185470		SDH1, SDH			Standard	NM_003000		Approved		uc001bae.3	P21912	OTTHUMG00000002289	ENST00000375499.3:c.626C>A	1.37:g.17350484G>T	ENSP00000364649:p.Pro209His	Somatic		Capture	Illumina HiSeq	Phase_I	17223071	NM_003000	B2R545|Q0QEY7|Q9NQ12	Missense_Mutation	SNP	ENST00000375499.3	37	CCDS176.1	.	.	.	.	.	.	.	.	.	.	G	25.7	4.666728	0.88251	.	.	ENSG00000117118	ENST00000375499	D	0.98178	-4.77	5.34	5.34	0.76211	Fumarate reductase, C-terminal (1);Alpha-helical ferredoxin (1);	0.000000	0.85682	D	0.000000	D	0.99573	0.9846	H	0.99919	4.95	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.97395	0.9992	10	0.87932	D	0	-13.9369	17.9626	0.89090	0.0:0.0:1.0:0.0	.	209	P21912	DHSB_HUMAN	H	209	ENSP00000364649:P209H	ENSP00000364649:P209H	P	-	2	0	SDHB	17223071	1.000000	0.71417	0.456000	0.27044	0.978000	0.69477	8.737000	0.91562	2.659000	0.90383	0.591000	0.81541	CCT		0.498	SDHB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006603.1	NM_003000	
PRRC2C	23215	broad.mit.edu	37	1	171505242	171505242	+	Silent	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr1:171505242G>A	ENST00000338920.4	+	14	2349	c.2112G>A	c.(2110-2112)ccG>ccA	p.P704P	PRRC2C_ENST00000426496.2_Silent_p.P704P|PRRC2C_ENST00000392078.3_Silent_p.P706P|PRRC2C_ENST00000367742.3_Silent_p.P706P	NM_015172.3	NP_055987.2	Q9Y520	PRC2C_HUMAN	proline-rich coiled-coil 2C	704	Pro-rich.				hematopoietic progenitor cell differentiation (GO:0002244)	membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)|protein C-terminus binding (GO:0008022)	p.P706P(1)									CTTCACAACCGTCCAGTAGTA	0.493																																					p.P704P												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G2112A	1						.						172.0	120.0	137.0					1																	171505242		2201	4295	6496	169771866	SO:0001819	synonymous_variant	23215	exon14			AL096857	CCDS1296.2	1q24.3	2012-07-18	2010-12-09	2010-12-09	ENSG00000117523	ENSG00000117523			24903	protein-coding gene	gene with protein product			"""BAT2 domain containing 1"", ""HLA-B associated transcript 2-like 2"""	BAT2D1, BAT2L2		10470851, 12443540	Standard	NM_015172		Approved	KIAA1096, XTP2	uc010pmg.2	Q9Y520	OTTHUMG00000034665	ENST00000338920.4:c.2112G>A	1.37:g.171505242G>A		Somatic		Capture	Illumina HiSeq	Phase_I	169771866	NM_015172	Q05DM8|Q49A39|Q6PD54|Q9H2N2|Q9HA05|Q9NSM8|Q9NXL3|Q9UF29|Q9UPQ6	Silent	SNP	ENST00000338920.4	37	CCDS1296.2																																																																																				0.493	PRRC2C-010	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000314826.4	NM_015172	
TNR	7143	broad.mit.edu	37	1	175299238	175299238	+	Silent	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr1:175299238G>A	ENST00000367674.2	-	21	4473	c.3765C>T	c.(3763-3765)ctC>ctT	p.L1255L	RP3-518E13.2_ENST00000569593.1_RNA|TNR_ENST00000263525.2_Silent_p.L1255L			Q92752	TENR_HUMAN	tenascin R	1255	Fibrinogen C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00739}.				associative learning (GO:0008306)|axon guidance (GO:0007411)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|locomotory exploration behavior (GO:0035641)|long-term synaptic potentiation (GO:0060291)|negative regulation of axon extension involved in regeneration (GO:0048692)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of synaptic transmission (GO:0050805)|neuromuscular process controlling balance (GO:0050885)|neuron cell-cell adhesion (GO:0007158)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|positive regulation of transmission of nerve impulse (GO:0051971)|synapse organization (GO:0050808)|telencephalon cell migration (GO:0022029)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|membrane raft (GO:0045121)|nucleus (GO:0005634)|perineuronal net (GO:0072534)|proteinaceous extracellular matrix (GO:0005578)		p.L1255L(1)		NS(3)|breast(7)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(29)|lung(98)|ovary(4)|pancreas(5)|prostate(4)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	177	Renal(580;0.146)					TTCCTATGCGGAGTTTGTACA	0.597																																					p.L1255L												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C3765T	1						.						94.0	77.0	83.0					1																	175299238		2203	4300	6503	173565861	SO:0001819	synonymous_variant	7143	exon21			X98085	CCDS1318.1	1q24	2013-02-11	2012-07-12		ENSG00000116147	ENSG00000116147		"""Fibrinogen C domain containing"", ""Fibronectin type III domain containing"""	11953	protein-coding gene	gene with protein product	"""restrictin"", ""janusin"""	601995				8626505, 8940128	Standard	NM_003285		Approved		uc009wwu.1	Q92752	OTTHUMG00000034876	ENST00000367674.2:c.3765C>T	1.37:g.175299238G>A		Somatic		Capture	Illumina HiSeq	Phase_I	173565861	NM_003285	C9J563|Q15568|Q5R3G0	Silent	SNP	ENST00000367674.2	37	CCDS1318.1																																																																																				0.597	TNR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084414.4	NM_003285	
RALGPS2	55103	broad.mit.edu	37	1	178846706	178846706	+	Silent	SNP	A	A	G			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr1:178846706A>G	ENST00000367635.3	+	9	1019	c.681A>G	c.(679-681)caA>caG	p.Q227Q	RALGPS2_ENST00000367634.2_Silent_p.Q227Q|RALGPS2_ENST00000477383.1_3'UTR	NM_152663.3	NP_689876.2	Q86X27	RGPS2_HUMAN	Ral GEF with PH domain and SH3 binding motif 2	227	Ras-GEF. {ECO:0000255|PROSITE- ProRule:PRU00168}.				small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	guanyl-nucleotide exchange factor activity (GO:0005085)	p.Q227Q(1)		breast(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(11)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	29						AAAATGAGCAAAGATCAAATT	0.323																																					p.Q227Q												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.A681G	1						.						82.0	82.0	82.0					1																	178846706		2203	4300	6503	177113329	SO:0001819	synonymous_variant	55103	exon9			AK098470	CCDS1325.1, CCDS65733.1	1q24	2013-01-11			ENSG00000116191	ENSG00000116191		"""Pleckstrin homology (PH) domain containing"""	30279	protein-coding gene	gene with protein product						10747847, 12102558	Standard	NM_152663		Approved	KIAA0351, FLJ10244, FLJ25604	uc001glz.3	Q86X27	OTTHUMG00000035076	ENST00000367635.3:c.681A>G	1.37:g.178846706A>G		Somatic		Capture	Illumina HiSeq	Phase_I	177113329	NM_152663	B7Z7B1|Q5T5Z1|Q5VZ67|Q9NW78	Silent	SNP	ENST00000367635.3	37	CCDS1325.1																																																																																				0.323	RALGPS2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084926.2	NM_152663	
ABL2	27	broad.mit.edu	37	1	179090856	179090856	+	Silent	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr1:179090856G>A	ENST00000502732.1	-	5	1037	c.834C>T	c.(832-834)caC>caT	p.H278H	ABL2_ENST00000511413.1_Silent_p.H278H|ABL2_ENST00000507173.1_Silent_p.H257H|ABL2_ENST00000392043.3_Silent_p.H257H|ABL2_ENST00000408940.3_Silent_p.H242H|ABL2_ENST00000512653.1_Silent_p.H263H|ABL2_ENST00000504405.1_Silent_p.H242H|ABL2_ENST00000344730.3_Silent_p.H263H|ABL2_ENST00000367623.4_Silent_p.H257H	NM_001168236.1|NM_001168237.1|NM_001168238.1|NM_007314.3	NP_001161708.1|NP_001161709.1|NP_001161710.1|NP_009298.1	P42684	ABL2_HUMAN	ABL proto-oncogene 2, non-receptor tyrosine kinase	278					actin filament bundle assembly (GO:0051017)|axon guidance (GO:0007411)|cell adhesion (GO:0007155)|cellular protein modification process (GO:0006464)|cellular response to retinoic acid (GO:0071300)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of neuron projection development (GO:0010976)|positive regulation of oxidoreductase activity (GO:0051353)|positive regulation of phospholipase C activity (GO:0010863)|regulation of actin cytoskeleton reorganization (GO:2000249)|regulation of autophagy (GO:0010506)|regulation of cell adhesion (GO:0030155)|regulation of cell motility (GO:2000145)|regulation of endocytosis (GO:0030100)|signal transduction (GO:0007165)	actin cytoskeleton (GO:0015629)|cytosol (GO:0005829)	actin filament binding (GO:0051015)|actin monomer binding (GO:0003785)|ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|manganese ion binding (GO:0030145)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein kinase activity (GO:0004672)|protein tyrosine kinase activity (GO:0004713)	p.H242H(1)		breast(8)|central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(9)|lung(32)|ovary(3)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	65					Adenosine triphosphate(DB00171)|Dasatinib(DB01254)	CCCATTTGTCGTGGATGGGGG	0.498			T	ETV6	AML																																p.H242H			Dom	yes		1	1q24-q25	27	v-abl Abelson murine leukemia viral oncogene homolog 2		L	.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C726T	1						.						170.0	139.0	149.0					1																	179090856		2203	4300	6503	177357479	SO:0001819	synonymous_variant	27	exon4			M14904	CCDS30947.1, CCDS41441.1, CCDS44282.1, CCDS44283.1, CCDS41441.2, CCDS53435.1, CCDS53436.1, CCDS53437.1, CCDS53438.1	1q25.2	2014-06-26	2014-06-26		ENSG00000143322	ENSG00000143322		"""SH2 domain containing"""	77	protein-coding gene	gene with protein product	"""Abelson-related gene"""	164690	"""v-abl Abelson murine leukemia viral oncogene homolog 2 (arg, Abelson-related gene)"", ""v-abl Abelson murine leukemia viral oncogene homolog 2"", ""c-abl oncogene 2, non-receptor tyrosine kinase"""	ABLL		3787260	Standard	NM_001136001		Approved	ARG	uc001gmi.4	P42684	OTTHUMG00000035199	ENST00000502732.1:c.834C>T	1.37:g.179090856G>A		Somatic		Capture	Illumina HiSeq	Phase_I	177357479	NM_001168239	A0M8X0|B7UEF2|B7UEF3|B7UEF4|B7UEF5|Q5T0X6|Q5W0C5|Q6NZY6|Q7Z301	Silent	SNP	ENST00000502732.1	37	CCDS30947.1																																																																																				0.498	ABL2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000085174.3	NM_005158	
XPR1	9213	broad.mit.edu	37	1	180794315	180794315	+	Silent	SNP	C	C	T	rs531488499	byFrequency	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr1:180794315C>T	ENST00000367590.4	+	9	1167	c.969C>T	c.(967-969)ctC>ctT	p.L323L	AL590085.1_ENST00000579998.1_RNA|XPR1_ENST00000367589.3_Silent_p.L323L	NM_004736.3	NP_004727.2	Q9UBH6	XPR1_HUMAN	xenotropic and polytropic retrovirus receptor 1	323					G-protein coupled receptor signaling pathway (GO:0007186)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|receptor activity (GO:0004872)|transmembrane signaling receptor activity (GO:0004888)|virus receptor activity (GO:0001618)	p.L323L(1)		breast(1)|endometrium(3)|kidney(2)|large_intestine(15)|lung(7)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(5)	35						CTGGATTCCTCGGGATATTGT	0.363													C|||	2	0.000399361	0.0	0.0	5008	,	,		19787	0.0		0.0	False		,,,				2504	0.002				p.L323L												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C969T	1						.						190.0	187.0	188.0					1																	180794315		2203	4300	6503	179060938	SO:0001819	synonymous_variant	9213	exon9			AF099082	CCDS1340.1, CCDS44284.1	1q25.1	2013-07-18	2010-04-23		ENSG00000143324	ENSG00000143324			12827	protein-coding gene	gene with protein product		605237	"""xenotropic and polytropic retrovirus receptor"""			9990033	Standard	NM_004736		Approved	SYG1, X3	uc001goi.3	Q9UBH6	OTTHUMG00000035116	ENST00000367590.4:c.969C>T	1.37:g.180794315C>T		Somatic		Capture	Illumina HiSeq	Phase_I	179060938	NM_001135669	O95719|Q7L8K9|Q8IW20|Q9NT19|Q9UFB9	Silent	SNP	ENST00000367590.4	37	CCDS1340.1																																																																																				0.363	XPR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084996.2	NM_004736	
CACNA1E	777	broad.mit.edu	37	1	181741277	181741277	+	Silent	SNP	C	C	T	rs377072842		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr1:181741277C>T	ENST00000367573.2	+	37	5049	c.5049C>T	c.(5047-5049)acC>acT	p.T1683T	CACNA1E_ENST00000367570.1_Silent_p.T1683T|CACNA1E_ENST00000367567.4_Silent_p.T1290T|CACNA1E_ENST00000526775.1_Silent_p.T1664T|RNA5SP70_ENST00000517168.1_RNA|CACNA1E_ENST00000360108.3_Silent_p.T1664T|CACNA1E_ENST00000357570.5_Silent_p.T1634T|CACNA1E_ENST00000358338.5_Silent_p.T1615T	NM_001205293.1	NP_001192222.1	Q15878	CAC1E_HUMAN	calcium channel, voltage-dependent, R type, alpha 1E subunit	1683					calcium ion import (GO:0070509)|energy reserve metabolic process (GO:0006112)|membrane depolarization (GO:0051899)|membrane depolarization during action potential (GO:0086010)|regulation of insulin secretion (GO:0050796)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transport (GO:0006810)	plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	calcium ion binding (GO:0005509)|high voltage-gated calcium channel activity (GO:0008331)|voltage-gated calcium channel activity (GO:0005245)	p.T1683T(1)		NS(2)|breast(9)|central_nervous_system(3)|cervix(1)|endometrium(22)|haematopoietic_and_lymphoid_tissue(6)|kidney(4)|large_intestine(34)|lung(99)|ovary(6)|pancreas(1)|prostate(9)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	204						CTGACACCACCGCACCATCAG	0.552													C|||	1	0.000199681	0.0008	0.0	5008	,	,		21698	0.0		0.0	False		,,,				2504	0.0				p.T1683T												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C5049T	1						.						165.0	167.0	166.0					1																	181741277		2194	4285	6479	180007900	SO:0001819	synonymous_variant	777	exon37			AK096563	CCDS53443.1, CCDS55664.1, CCDS55665.1	1q25.3	2013-01-10	2007-02-16		ENSG00000198216	ENSG00000198216		"""Calcium channel subunits"", ""Voltage-gated ion channels / Calcium channels"", ""EF-hand domain containing"""	1392	protein-coding gene	gene with protein product		601013		CACNL1A6		8388125, 16382099	Standard	NM_001205293		Approved	Cav2.3, BII, CACH6	uc009wxt.3	Q15878	OTTHUMG00000037301	ENST00000367573.2:c.5049C>T	1.37:g.181741277C>T		Somatic		Capture	Illumina HiSeq	Phase_I	180007900	NM_000721	B1AM12|B1AM13|B1AM14|Q14580|Q14581	Silent	SNP	ENST00000367573.2	37	CCDS55664.1																																																																																				0.552	CACNA1E-003	KNOWN	non_canonical_U12|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000090793.2	NM_000721	
CACNA1E	777	broad.mit.edu	37	1	181764120	181764120	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr1:181764120C>T	ENST00000367573.2	+	46	6148	c.6148C>T	c.(6148-6150)Cgt>Tgt	p.R2050C	CACNA1E_ENST00000367570.1_Missense_Mutation_p.R2007C|CACNA1E_ENST00000367567.4_Missense_Mutation_p.R1614C|CACNA1E_ENST00000526775.1_Missense_Mutation_p.R1988C|CACNA1E_ENST00000360108.3_Missense_Mutation_p.R2031C|CACNA1E_ENST00000357570.5_Missense_Mutation_p.R2001C|CACNA1E_ENST00000358338.5_Missense_Mutation_p.R1939C	NM_001205293.1	NP_001192222.1	Q15878	CAC1E_HUMAN	calcium channel, voltage-dependent, R type, alpha 1E subunit	2050					calcium ion import (GO:0070509)|energy reserve metabolic process (GO:0006112)|membrane depolarization (GO:0051899)|membrane depolarization during action potential (GO:0086010)|regulation of insulin secretion (GO:0050796)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transport (GO:0006810)	plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	calcium ion binding (GO:0005509)|high voltage-gated calcium channel activity (GO:0008331)|voltage-gated calcium channel activity (GO:0005245)	p.R2007C(1)		NS(2)|breast(9)|central_nervous_system(3)|cervix(1)|endometrium(22)|haematopoietic_and_lymphoid_tissue(6)|kidney(4)|large_intestine(34)|lung(99)|ovary(6)|pancreas(1)|prostate(9)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	204						CTACAAGTCCCGTCGCCGGAG	0.517																																					p.R2007C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C6019T	1						.						72.0	74.0	73.0					1																	181764120		1936	4136	6072	180030743	SO:0001583	missense	777	exon45			AK096563	CCDS53443.1, CCDS55664.1, CCDS55665.1	1q25.3	2013-01-10	2007-02-16		ENSG00000198216	ENSG00000198216		"""Calcium channel subunits"", ""Voltage-gated ion channels / Calcium channels"", ""EF-hand domain containing"""	1392	protein-coding gene	gene with protein product		601013		CACNL1A6		8388125, 16382099	Standard	NM_001205293		Approved	Cav2.3, BII, CACH6	uc009wxt.3	Q15878	OTTHUMG00000037301	ENST00000367573.2:c.6148C>T	1.37:g.181764120C>T	ENSP00000356545:p.Arg2050Cys	Somatic		Capture	Illumina HiSeq	Phase_I	180030743	NM_000721	B1AM12|B1AM13|B1AM14|Q14580|Q14581	Missense_Mutation	SNP	ENST00000367573.2	37	CCDS55664.1	.	.	.	.	.	.	.	.	.	.	C	24.4	4.529012	0.85706	.	.	ENSG00000198216	ENST00000367570;ENST00000526775;ENST00000357570;ENST00000358338;ENST00000367567;ENST00000360108;ENST00000367573	D;D;D;D;D;D;D	0.97710	-4.41;-4.4;-4.24;-4.4;-4.5;-4.24;-4.24	5.91	4.99	0.66335	.	0.640902	0.17184	N	0.183774	D	0.97548	0.9197	L	0.38175	1.15	0.80722	D	1	D;D	0.89917	0.998;1.0	P;P	0.62014	0.627;0.897	D	0.97952	1.0332	10	0.72032	D	0.01	.	16.217	0.82237	0.134:0.866:0.0:0.0	.	1988;2007	Q15878-2;Q15878-3	.;.	C	2007;1988;2001;1939;1614;2031;2050	ENSP00000356542:R2007C;ENSP00000434814:R1988C;ENSP00000350183:R2001C;ENSP00000351101:R1939C;ENSP00000356539:R1614C;ENSP00000353222:R2031C;ENSP00000356545:R2050C	ENSP00000350183:R2001C	R	+	1	0	CACNA1E	180030743	1.000000	0.71417	0.063000	0.19743	0.984000	0.73092	6.555000	0.73928	1.488000	0.48433	0.655000	0.94253	CGT		0.517	CACNA1E-003	KNOWN	non_canonical_U12|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000090793.2	NM_000721	
RGS16	6004	broad.mit.edu	37	1	182569455	182569455	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr1:182569455C>T	ENST00000367558.5	-	5	729	c.581G>A	c.(580-582)tGc>tAc	p.C194Y		NM_002928.3	NP_002919.3	O15492	RGS16_HUMAN	regulator of G-protein signaling 16	194					positive regulation of GTPase activity (GO:0043547)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|termination of G-protein coupled receptor signaling pathway (GO:0038032)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	calmodulin binding (GO:0005516)|GTPase activator activity (GO:0005096)	p.C194Y(1)		NS(1)|endometrium(3)|large_intestine(2)|lung(4)|ovary(1)	11						GTCCAGGCTGCAGCTGGACAG	0.642																																					p.C194Y												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G581A	1						.						71.0	74.0	73.0					1																	182569455		2203	4300	6503	180836078	SO:0001583	missense	6004	exon5			U70426	CCDS1348.1	1q25-q31	2008-02-05	2007-08-14		ENSG00000143333	ENSG00000143333		"""Regulators of G-protein signaling"""	9997	protein-coding gene	gene with protein product		602514	"""regulator of G-protein signalling 16"""			9469939	Standard	NM_002928		Approved	A28-RGS14, RGS-r	uc001gpl.4	O15492	OTTHUMG00000035212	ENST00000367558.5:c.581G>A	1.37:g.182569455C>T	ENSP00000356529:p.Cys194Tyr	Somatic		Capture	Illumina HiSeq	Phase_I	180836078	NM_002928	B2R4M4|Q5VYN9|Q99701	Missense_Mutation	SNP	ENST00000367558.5	37	CCDS1348.1	.	.	.	.	.	.	.	.	.	.	C	11.63	1.696233	0.30052	.	.	ENSG00000143333	ENST00000367558	T	0.55588	0.51	4.59	4.59	0.56863	.	2.550170	0.01013	N	0.003876	T	0.45418	0.1341	N	0.22421	0.69	0.24137	N	0.995746	B	0.19583	0.037	B	0.17979	0.02	T	0.31364	-0.9946	10	0.66056	D	0.02	.	9.9998	0.41922	0.0:0.9051:0.0:0.0949	.	194	O15492	RGS16_HUMAN	Y	194	ENSP00000356529:C194Y	ENSP00000356529:C194Y	C	-	2	0	RGS16	180836078	0.020000	0.18652	0.195000	0.23364	0.045000	0.14185	1.360000	0.34125	2.388000	0.81334	0.655000	0.94253	TGC		0.642	RGS16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085188.1	NM_002928	
RGL1	23179	broad.mit.edu	37	1	183867013	183867013	+	Silent	SNP	G	G	C			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	C	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr1:183867013G>C	ENST00000360851.3	+	10	1390	c.1212G>C	c.(1210-1212)ctG>ctC	p.L404L	RGL1_ENST00000536277.1_Silent_p.L402L|RGL1_ENST00000539189.1_Silent_p.L404L|RGL1_ENST00000304685.4_Silent_p.L439L			Q9NZL6	RGL1_HUMAN	ral guanine nucleotide dissociation stimulator-like 1	404	Ras-GEF. {ECO:0000255|PROSITE- ProRule:PRU00168}.				cellular lipid metabolic process (GO:0044255)|positive regulation of Ral GTPase activity (GO:0032852)|small GTPase mediated signal transduction (GO:0007264)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	Ral guanyl-nucleotide exchange factor activity (GO:0008321)	p.L439L(1)		breast(5)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(12)|liver(1)|lung(17)|ovary(4)|prostate(3)|stomach(1)	51						AGAGGCGGCTGCAGCTCCAGA	0.552																																					p.L439L												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G1317C	1						.						75.0	78.0	77.0					1																	183867013		2203	4300	6503	182133636	SO:0001819	synonymous_variant	23179	exon11			AF186780	CCDS1359.1, CCDS72992.1	1q25.2	2008-02-05			ENSG00000143344	ENSG00000143344			30281	protein-coding gene	gene with protein product		605667				10760592, 10231032	Standard	XM_005245010		Approved	RGL	uc001gqm.3	Q9NZL6	OTTHUMG00000035328	ENST00000360851.3:c.1212G>C	1.37:g.183867013G>C		Somatic		Capture	Illumina HiSeq	Phase_I	182133636	NM_015149	Q5SXQ2|Q5SXQ6|Q9HBY3|Q9HBY4|Q9NZL5|Q9UG43|Q9Y2G6	Silent	SNP	ENST00000360851.3	37																																																																																					0.552	RGL1-002	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000085742.1	NM_015149	
KLHDC7A	127707	broad.mit.edu	37	1	18809556	18809556	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr1:18809556G>A	ENST00000400664.1	+	1	2133	c.2081G>A	c.(2080-2082)cGc>cAc	p.R694H		NM_152375.2	NP_689588.2	Q5VTJ3	KLD7A_HUMAN	kelch domain containing 7A	694						integral component of membrane (GO:0016021)		p.R694H(1)		endometrium(1)|kidney(1)|large_intestine(4)|lung(11)|ovary(2)|skin(1)|upper_aerodigestive_tract(2)	22		Colorectal(325;3.46e-05)|all_lung(284;0.000152)|Lung NSC(340;0.000185)|Breast(348;0.00046)|Renal(390;0.000518)|Ovarian(437;0.0014)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00462)|BRCA - Breast invasive adenocarcinoma(304;1.41e-05)|Kidney(64;0.00017)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)		GCCGTGTACCGCTGCAGCGCC	0.667																																					p.R694H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2081A	1						.						73.0	63.0	67.0					1																	18809556		2203	4299	6502	18682143	SO:0001583	missense	127707	exon1			AK096072	CCDS185.2	1p36.13	2008-02-05			ENSG00000179023	ENSG00000179023			26791	protein-coding gene	gene with protein product							Standard	NM_152375		Approved	FLJ38753	uc001bax.3	Q5VTJ3	OTTHUMG00000002431	ENST00000400664.1:c.2081G>A	1.37:g.18809556G>A	ENSP00000383505:p.Arg694His	Somatic		Capture	Illumina HiSeq	Phase_I	18682143	NM_152375	Q8N8W6	Missense_Mutation	SNP	ENST00000400664.1	37	CCDS185.2	.	.	.	.	.	.	.	.	.	.	G	28.5	4.924682	0.92319	.	.	ENSG00000179023	ENST00000400664;ENST00000540290	T	0.25250	1.81	4.81	4.81	0.61882	Kelch-type beta propeller (1);	0.000000	0.85682	D	0.000000	T	0.53286	0.1787	M	0.78637	2.42	0.58432	D	0.999994	D;D	0.89917	1.0;1.0	D;D	0.85130	0.997;0.997	T	0.60068	-0.7335	10	0.87932	D	0	.	16.4503	0.83977	0.0:0.0:1.0:0.0	.	631;694	A7E2V3;Q5VTJ3	.;KLD7A_HUMAN	H	694;631	ENSP00000383505:R694H	ENSP00000383505:R694H	R	+	2	0	KLHDC7A	18682143	1.000000	0.71417	1.000000	0.80357	0.969000	0.65631	7.877000	0.87225	2.194000	0.70268	0.655000	0.94253	CGC		0.667	KLHDC7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006923.3	NM_152375	
TPR	7175	broad.mit.edu	37	1	186330029	186330029	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr1:186330029C>A	ENST00000367478.4	-	10	1263	c.967G>T	c.(967-969)Gca>Tca	p.A323S	TPR_ENST00000474852.1_5'UTR	NM_003292.2	NP_003283.2	P12270	TPR_HUMAN	translocated promoter region, nuclear basket protein	323					carbohydrate metabolic process (GO:0005975)|cellular response to heat (GO:0034605)|cellular response to interferon-alpha (GO:0035457)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|MAPK import into nucleus (GO:0000189)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic nuclear envelope disassembly (GO:0007077)|mitotic spindle assembly checkpoint (GO:0007094)|mRNA export from nucleus in response to heat stress (GO:0031990)|negative regulation of RNA export from nucleus (GO:0046832)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of translational initiation (GO:0045947)|nuclear pore organization (GO:0006999)|positive regulation of heterochromatin assembly (GO:0031453)|positive regulation of intracellular protein transport (GO:0090316)|positive regulation of mitotic cell cycle spindle assembly checkpoint (GO:0090267)|positive regulation of protein export from nucleus (GO:0046827)|positive regulation of protein import into nucleus (GO:0042307)|protein import into nucleus (GO:0006606)|regulation of glucose transport (GO:0010827)|regulation of mitotic sister chromatid separation (GO:0010965)|regulation of spindle assembly involved in mitosis (GO:1901673)|response to epidermal growth factor (GO:0070849)|RNA export from nucleus (GO:0006405)|RNA import into nucleus (GO:0006404)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytoplasmic dynein complex (GO:0005868)|extrinsic component of membrane (GO:0019898)|kinetochore (GO:0000776)|mitotic spindle (GO:0072686)|nuclear envelope (GO:0005635)|nuclear inclusion body (GO:0042405)|nuclear membrane (GO:0031965)|nuclear periphery (GO:0034399)|nuclear pore (GO:0005643)|nuclear pore nuclear basket (GO:0044615)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|dynein complex binding (GO:0070840)|heat shock protein binding (GO:0031072)|mitogen-activated protein kinase binding (GO:0051019)|mRNA binding (GO:0003729)|nucleocytoplasmic transporter activity (GO:0005487)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)|tubulin binding (GO:0015631)	p.A324S(1)		autonomic_ganglia(1)|breast(5)|central_nervous_system(4)|cervix(2)|endometrium(9)|kidney(12)|large_intestine(23)|liver(1)|lung(45)|ovary(2)|pancreas(1)|prostate(6)|skin(3)|stomach(1)|urinary_tract(8)	123		Breast(1374;0.000659)|Lung SC(1967;0.0262)|Prostate(1639;0.157)		Colorectal(1306;1.12e-05)|KIRC - Kidney renal clear cell carcinoma(1967;0.00553)		TCTTGTATTGCTTTGTTGGCT	0.338			T	NTRK1	papillary thyroid																																p.A323S			Dom	yes		1	1q25	7175	translocated promoter region		E	.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G967T	1						.						106.0	91.0	96.0					1																	186330029		1816	4068	5884	184596652	SO:0001583	missense	7175	exon10			U69668	CCDS41446.1	1q25	2012-03-13	2012-03-13		ENSG00000047410	ENSG00000047410			12017	protein-coding gene	gene with protein product		189940	"""translocated promoter region (to activated MET oncogene)"""			1611909, 15229283	Standard	NM_003292		Approved		uc001grv.3	P12270	OTTHUMG00000035580	ENST00000367478.4:c.967G>T	1.37:g.186330029C>A	ENSP00000356448:p.Ala323Ser	Somatic		Capture	Illumina HiSeq	Phase_I	184596652	NM_003292	Q15655|Q5SWY0|Q99968	Missense_Mutation	SNP	ENST00000367478.4	37	CCDS41446.1	.	.	.	.	.	.	.	.	.	.	C	10.34	1.323226	0.24080	.	.	ENSG00000047410	ENST00000367478	T	0.24538	1.85	5.59	3.7	0.42460	.	0.379284	0.28865	N	0.013885	T	0.13798	0.0334	L	0.27053	0.805	0.26497	N	0.974831	B;B	0.14438	0.002;0.01	B;B	0.11329	0.006;0.004	T	0.31110	-0.9955	10	0.10902	T	0.67	.	5.6942	0.17847	0.1565:0.6804:0.0:0.1631	.	323;323	Q15624;P12270	.;TPR_HUMAN	S	323	ENSP00000356448:A323S	ENSP00000356448:A323S	A	-	1	0	TPR	184596652	1.000000	0.71417	0.995000	0.50966	0.990000	0.78478	2.445000	0.44899	0.693000	0.31634	0.655000	0.94253	GCA		0.338	TPR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086353.2	NM_003292	
CDC73	79577	broad.mit.edu	37	1	193104564	193104564	+	Silent	SNP	T	T	C			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr1:193104564T>C	ENST00000367435.3	+	4	535	c.351T>C	c.(349-351)ggT>ggC	p.G117G	MIR1278_ENST00000408753.1_RNA	NM_024529.4	NP_078805.3	Q6P1J9	CDC73_HUMAN	cell division cycle 73	117					cell cycle (GO:0007049)|cellular response to lipopolysaccharide (GO:0071222)|endodermal cell fate commitment (GO:0001711)|histone H2B ubiquitination (GO:0033523)|histone monoubiquitination (GO:0010390)|mRNA polyadenylation (GO:0006378)|negative regulation of cell proliferation (GO:0008285)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of myeloid cell differentiation (GO:0045638)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of mRNA 3'-end processing (GO:0031442)|positive regulation of transcription elongation from RNA polymerase II promoter (GO:0032968)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of Wnt signaling pathway (GO:0030177)|protein destabilization (GO:0031648)|stem cell maintenance (GO:0019827)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	Cdc73/Paf1 complex (GO:0016593)|nucleus (GO:0005634)	RNA polymerase II core binding (GO:0000993)	p.G117G(1)		breast(2)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(8)|lung(14)|ovary(1)|pancreas(1)|parathyroid(51)|skin(1)|upper_aerodigestive_tract(1)	87						TAGAAATAGGTCTTCAGCGAT	0.333																																					p.G117G												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.T351C	1						.						99.0	95.0	96.0					1																	193104564		2203	4300	6503	191371187	SO:0001819	synonymous_variant	79577	exon4			AF312865	CCDS1382.1	1q25	2014-09-17	2013-01-17	2005-07-20	ENSG00000134371	ENSG00000134371			16783	protein-coding gene	gene with protein product	"""Paf1/RNA polymerase II complex component"""	607393	"""chromosome 1 open reading frame 28"", ""hyperparathyroidism 2 (with jaw tumor)"", ""cell division cycle 73, Paf1/RNA polymerase II complex component, homolog (S. cerevisiae)"", ""hyperparathyroidism 1"""	C1orf28, HRPT2, HRPT1		11318611, 15632063, 18755853	Standard	NM_024529		Approved	parafibromin, FIHP	uc001gtb.3	Q6P1J9	OTTHUMG00000035676	ENST00000367435.3:c.351T>C	1.37:g.193104564T>C		Somatic		Capture	Illumina HiSeq	Phase_I	191371187	NM_024529	A6NLZ8|B2RBR2|Q6PK51|Q96A07|Q9H245|Q9H5L7	Silent	SNP	ENST00000367435.3	37	CCDS1382.1																																																																																				0.333	CDC73-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086696.2	NM_024529	
CFH	3075	broad.mit.edu	37	1	196706042	196706042	+	Silent	SNP	A	A	G			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr1:196706042A>G	ENST00000367429.4	+	16	2742	c.2502A>G	c.(2500-2502)aaA>aaG	p.K834K		NM_000186.3	NP_000177.2	P08603	CFAH_HUMAN	complement factor H	834	Sushi 14. {ECO:0000255|PROSITE- ProRule:PRU00302}.				complement activation (GO:0006956)|complement activation, alternative pathway (GO:0006957)|innate immune response (GO:0045087)|regulation of complement activation (GO:0030449)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	heparan sulfate proteoglycan binding (GO:0043395)|heparin binding (GO:0008201)	p.K834K(1)		NS(3)|breast(4)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(24)|lung(33)|ovary(1)|prostate(5)|skin(9)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	101						ATGGAGAAAAAGTATCTGTTC	0.378																																					p.K834K												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.A2502G	1						.						76.0	73.0	74.0					1																	196706042		2203	4300	6503	194972665	SO:0001819	synonymous_variant	3075	exon16			Y00716	CCDS1385.1	1q32	2014-09-17	2004-08-09	2004-08-12	ENSG00000000971	ENSG00000000971		"""Complement system"""	4883	protein-coding gene	gene with protein product	"""beta-1H"", ""H factor 2 (complement)"", ""age-related maculopathy susceptibility 1"""	134370	"""H factor 1 (complement)"""	HF, HF1, HF2		2889480, 2963625	Standard	NM_000186		Approved	HUS, FHL1, ARMS1, ARMD4	uc001gtj.4	P08603	OTTHUMG00000035607	ENST00000367429.4:c.2502A>G	1.37:g.196706042A>G		Somatic		Capture	Illumina HiSeq	Phase_I	194972665	NM_000186	A5PL14|P78435|Q14570|Q2TAZ5|Q38G77|Q5TFM3|Q8N708|Q9NU86	Silent	SNP	ENST00000367429.4	37	CCDS1385.1																																																																																				0.378	CFH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086412.2	NM_000186	
CRB1	23418	broad.mit.edu	37	1	197411383	197411383	+	Silent	SNP	C	C	T	rs63749127		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr1:197411383C>T	ENST00000367400.3	+	11	4101	c.3966C>T	c.(3964-3966)ctC>ctT	p.L1322L	CRB1_ENST00000367397.1_3'UTR|CRB1_ENST00000544212.1_Silent_p.L803L|CRB1_ENST00000367399.2_Silent_p.L1210L|CRB1_ENST00000535699.1_Silent_p.L1298L|RP11-75C23.1_ENST00000422250.1_RNA|CRB1_ENST00000538660.1_Silent_p.L786L	NM_201253.2	NP_957705.1	P82279	CRUM1_HUMAN	crumbs family member 1, photoreceptor morphogenesis associated	1322	EGF-like 19; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				cell-cell signaling (GO:0007267)|establishment or maintenance of cell polarity (GO:0007163)|eye photoreceptor cell development (GO:0042462)|plasma membrane organization (GO:0007009)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|microvillus (GO:0005902)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.L1322L(1)		NS(1)|breast(4)|central_nervous_system(2)|cervix(3)|endometrium(13)|kidney(4)|large_intestine(21)|lung(58)|ovary(7)|prostate(3)|skin(10)|upper_aerodigestive_tract(4)|urinary_tract(2)	132						TCCAGTGCCTCTGTGATGTTG	0.468																																					p.L1322L												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C3966T	1						.						284.0	260.0	269.0					1																	197411383		2203	4300	6503	195678006	SO:0001819	synonymous_variant	23418	exon11				CCDS1390.1, CCDS53454.1, CCDS58052.1, CCDS58053.1	1q31-q32.1	2014-02-06	2014-02-06		ENSG00000134376	ENSG00000134376			2343	protein-coding gene	gene with protein product		604210	"""crumbs (Drosophila) homolog 1"", ""crumbs homolog 1 (Drosophila)"""	RP12		10373321, 10508521	Standard	NM_201253		Approved	LCA8	uc001gtz.3	P82279	OTTHUMG00000035663	ENST00000367400.3:c.3966C>T	1.37:g.197411383C>T		Somatic		Capture	Illumina HiSeq	Phase_I	195678006	NM_201253	A2A308|B7Z5T2|B9EG71|Q5K3A6|Q5TC28|Q5VUT1|Q6N027|Q8WWY0|Q8WWY1	Silent	SNP	ENST00000367400.3	37	CCDS1390.1																																																																																				0.468	CRB1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086565.2	NM_201253	
NR5A2	2494	broad.mit.edu	37	1	200080383	200080383	+	Silent	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr1:200080383C>T	ENST00000367362.3	+	6	1410	c.1164C>T	c.(1162-1164)ctC>ctT	p.L388L	NR5A2_ENST00000236914.3_Silent_p.L342L|NR5A2_ENST00000544748.1_Silent_p.L316L	NM_001276464.1|NM_205860.1	NP_001263393.1|NP_995582.1	O00482	NR5A2_HUMAN	nuclear receptor subfamily 5, group A, member 2	388	Ligand-binding.				bile acid metabolic process (GO:0008206)|cholesterol homeostasis (GO:0042632)|embryo development (GO:0009790)|endocrine pancreas development (GO:0031018)|gene expression (GO:0010467)|homeostatic process (GO:0042592)|intracellular receptor signaling pathway (GO:0030522)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of viral genome replication (GO:0045070)|regulation of cell proliferation (GO:0042127)|regulation of transcription, DNA-templated (GO:0006355)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|phospholipid binding (GO:0005543)|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)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid hormone receptor activity (GO:0003707)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)	p.L388L(1)		cervix(1)|endometrium(1)|kidney(3)|large_intestine(6)|lung(15)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	31	Prostate(682;0.19)					TCTTAATCCTCGACCACATTT	0.383																																					p.L388L	Melanoma(179;1138 2773 15678 26136)											.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1164T	1						.						97.0	92.0	94.0					1																	200080383		2203	4300	6503	198347006	SO:0001819	synonymous_variant	2494	exon6			U93553	CCDS1400.1, CCDS1401.1, CCDS60383.1	1q32.11	2013-01-16			ENSG00000116833	ENSG00000116833		"""Nuclear hormone receptors"""	7984	protein-coding gene	gene with protein product	"""liver receptor homolog-1"""	604453		FTF		9858833, 7680097	Standard	NM_205860		Approved	FTZ-F1beta, hB1F, LRH-1, FTZ-F1, hB1F-2, B1F2	uc001gvb.4	O00482	OTTHUMG00000035635	ENST00000367362.3:c.1164C>T	1.37:g.200080383C>T		Somatic		Capture	Illumina HiSeq	Phase_I	198347006	NM_205860	B4E2P3|O95642|Q147U3	Silent	SNP	ENST00000367362.3	37	CCDS1401.1																																																																																				0.383	NR5A2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000086497.2		
KIF14	9928	broad.mit.edu	37	1	200571040	200571040	+	Silent	SNP	G	G	A	rs145353826	byFrequency	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr1:200571040G>A	ENST00000367350.4	-	11	2574	c.2136C>T	c.(2134-2136)aaC>aaT	p.N712N		NM_014875.2	NP_055690.1	Q15058	KIF14_HUMAN	kinesin family member 14	712					ATP catabolic process (GO:0006200)|cytoskeleton-dependent intracellular transport (GO:0030705)|establishment of protein localization (GO:0045184)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|negative regulation of integrin activation (GO:0033624)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of Rap protein signal transduction (GO:0032487)|substrate adhesion-dependent cell spreading (GO:0034446)	cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|membrane (GO:0016020)|microtubule (GO:0005874)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|PDZ domain binding (GO:0030165)	p.N712N(1)		NS(1)|breast(5)|central_nervous_system(2)|endometrium(8)|kidney(8)|large_intestine(15)|lung(13)|ovary(3)|prostate(2)|skin(3)|urinary_tract(1)	61						TTAACTTAGCGTTCATATCTT	0.328																																					p.N712N												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C2136T	1						.	G		0,4404		0,0,2202	115.0	106.0	109.0		2136	-1.0	0.3	1	dbSNP_134	109	12,8584	9.1+/-34.3	0,12,4286	no	coding-synonymous	KIF14	NM_014875.2		0,12,6488	AA,AG,GG		0.1396,0.0,0.0923		712/1649	200571040	12,12988	2202	4298	6500	198837663	SO:0001819	synonymous_variant	9928	exon11			D26361	CCDS30963.1	1q32.1	2008-03-03			ENSG00000118193	ENSG00000118193		"""Kinesins"""	19181	protein-coding gene	gene with protein product		611279				7584044	Standard	NM_014875		Approved	KIAA0042	uc010ppk.1	Q15058	OTTHUMG00000035723	ENST00000367350.4:c.2136C>T	1.37:g.200571040G>A		Somatic		Capture	Illumina HiSeq	Phase_I	198837663	NM_014875	Q14CI8|Q4G0A5|Q5T1W3	Silent	SNP	ENST00000367350.4	37	CCDS30963.1																																																																																				0.328	KIF14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086878.1	NM_014875	
ATP2B4	493	broad.mit.edu	37	1	203677064	203677064	+	Silent	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr1:203677064C>T	ENST00000357681.5	+	10	2512	c.1389C>T	c.(1387-1389)tgC>tgT	p.C463C	ATP2B4_ENST00000367218.3_Silent_p.C463C|ATP2B4_ENST00000367219.3_Silent_p.C451C|ATP2B4_ENST00000341360.2_Silent_p.C463C|ATP2B4_ENST00000391954.2_Silent_p.C463C	NM_001684.4	NP_001675.3	P23634	AT2B4_HUMAN	ATPase, Ca++ transporting, plasma membrane 4	463					blood coagulation (GO:0007596)|calcium ion homeostasis (GO:0055074)|calcium ion import across plasma membrane (GO:0098703)|calcium ion transmembrane transport (GO:0070588)|cellular calcium ion homeostasis (GO:0006874)|cellular response to epinephrine stimulus (GO:0071872)|ion transmembrane transport (GO:0034220)|negative regulation of adrenergic receptor signaling pathway involved in heart process (GO:1901205)|negative regulation of arginine catabolic process (GO:1900082)|negative regulation of calcineurin-NFAT signaling cascade (GO:0070885)|negative regulation of cardiac muscle hypertrophy in response to stress (GO:1903243)|negative regulation of citrulline biosynthetic process (GO:1903249)|negative regulation of nitric oxide biosynthetic process (GO:0045019)|negative regulation of nitric oxide mediated signal transduction (GO:0010751)|negative regulation of nitric-oxide synthase activity (GO:0051001)|negative regulation of peptidyl-cysteine S-nitrosylation (GO:1902083)|negative regulation of the force of heart contraction (GO:0098736)|positive regulation of cAMP-dependent protein kinase activity (GO:2000481)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|regulation of sodium ion transmembrane transport (GO:1902305)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to hydrostatic pressure (GO:0051599)|transmembrane transport (GO:0055085)	caveola (GO:0005901)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|T-tubule (GO:0030315)|Z disc (GO:0030018)	ATP binding (GO:0005524)|calcium-transporting ATPase activity (GO:0005388)|calmodulin binding (GO:0005516)|metal ion binding (GO:0046872)|nitric-oxide synthase binding (GO:0050998)|protein phosphatase 2B binding (GO:0030346)|scaffold protein binding (GO:0097110)	p.C463C(2)		NS(1)|breast(1)|central_nervous_system(2)|cervix(2)|endometrium(5)|kidney(2)|large_intestine(10)|lung(20)|ovary(2)|prostate(6)|skin(1)|stomach(1)|urinary_tract(3)	56	all_cancers(21;0.071)|all_epithelial(62;0.228)		BRCA - Breast invasive adenocarcinoma(75;0.109)			CCGCCATCTGCTCTGATAAGA	0.478																																					p.C463C												.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.C1389T	1						.						150.0	132.0	138.0					1																	203677064		2203	4300	6503	201943687	SO:0001819	synonymous_variant	493	exon10			M25874	CCDS1440.1, CCDS30977.1	1q32.1	2010-04-20	2005-05-26		ENSG00000058668	ENSG00000058668	3.6.3.8	"""ATPases / P-type"""	817	protein-coding gene	gene with protein product	"""plasma membrane calcium-transporting ATPase 4"""	108732	"""matrix-remodelling associated 1"""	ATP2B2, MXRA1		1674727	Standard	NM_001001396		Approved	PMCA4	uc001gzw.3	P23634	OTTHUMG00000035906	ENST00000357681.5:c.1389C>T	1.37:g.203677064C>T		Somatic		Capture	Illumina HiSeq	Phase_I	201943687	NM_001001396	B1APW5|B1APW6|Q13450|Q13452|Q13455|Q16817|Q7Z3S1	Silent	SNP	ENST00000357681.5	37	CCDS1440.1																																																																																				0.478	ATP2B4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087462.1	NM_001001396	
PIK3C2B	5287	broad.mit.edu	37	1	204416639	204416639	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr1:204416639C>T	ENST00000367187.3	-	16	2970	c.2414G>A	c.(2413-2415)cGc>cAc	p.R805H	PIK3C2B_ENST00000424712.2_Missense_Mutation_p.R805H	NM_002646.3	NP_002637.3	O00750	P3C2B_HUMAN	phosphatidylinositol-4-phosphate 3-kinase, catalytic subunit type 2 beta	805	PIK helical. {ECO:0000255|PROSITE- ProRule:PRU00878}.				phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|protein kinase B signaling (GO:0043491)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|lipid kinase activity (GO:0001727)|phosphatidylinositol binding (GO:0035091)	p.R805H(1)		breast(3)|central_nervous_system(1)|cervix(2)|endometrium(4)|large_intestine(11)|lung(24)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	52	all_cancers(21;0.00347)|all_neural(3;0.0218)|Glioma(3;0.0382)|all_epithelial(62;0.171)|Breast(84;0.179)|Prostate(682;0.227)		GBM - Glioblastoma multiforme(2;2.69e-45)|all cancers(3;1.66e-30)|KIRC - Kidney renal clear cell carcinoma(13;0.0584)|Kidney(21;0.0934)|BRCA - Breast invasive adenocarcinoma(75;0.143)|Epithelial(59;0.193)			AAACTCATAGCGGGGGCTGAA	0.557																																					p.R805H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2414A	1						.						58.0	59.0	59.0					1																	204416639		2203	4300	6503	202683262	SO:0001583	missense	5287	exon16			Y11312	CCDS1446.1	1q32	2012-07-13	2012-07-13		ENSG00000133056	ENSG00000133056	2.7.1.154		8972	protein-coding gene	gene with protein product		602838	"""phosphoinositide-3-kinase, class 2, beta polypeptide"""			9144573, 9830063	Standard	NM_002646		Approved	C2-PI3K, PI3K-C2beta	uc001haw.3	O00750	OTTHUMG00000036101	ENST00000367187.3:c.2414G>A	1.37:g.204416639C>T	ENSP00000356155:p.Arg805His	Somatic		Capture	Illumina HiSeq	Phase_I	202683262	NM_002646	O95666|Q5SW99	Missense_Mutation	SNP	ENST00000367187.3	37	CCDS1446.1	.	.	.	.	.	.	.	.	.	.	C	13.34	2.208715	0.39003	.	.	ENSG00000133056	ENST00000367187;ENST00000424712	T;T	0.63580	-0.05;-0.05	5.08	4.15	0.48705	Phosphoinositide 3-kinase, accessory (PIK) domain (2);Armadillo-type fold (1);	0.532223	0.20622	N	0.088770	T	0.44664	0.1304	N	0.22421	0.69	0.27618	N	0.94844	B;B	0.27264	0.012;0.173	B;B	0.22880	0.006;0.042	T	0.34229	-0.9837	10	0.38643	T	0.18	.	9.9673	0.41732	0.0:0.8348:0.0:0.1652	.	805;805	F5GWN5;O00750	.;P3C2B_HUMAN	H	805	ENSP00000356155:R805H;ENSP00000400561:R805H	ENSP00000356155:R805H	R	-	2	0	PIK3C2B	202683262	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	2.299000	0.43611	2.526000	0.85167	0.462000	0.41574	CGC		0.557	PIK3C2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087965.1	NM_002646	
NFASC	23114	broad.mit.edu	37	1	204923461	204923461	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr1:204923461C>T	ENST00000401399.1	+	5	560	c.361C>T	c.(361-363)Cgc>Tgc	p.R121C	NFASC_ENST00000367172.4_Missense_Mutation_p.R121C|NFASC_ENST00000513543.1_Missense_Mutation_p.R115C|NFASC_ENST00000360049.4_Missense_Mutation_p.R115C|NFASC_ENST00000403080.1_Missense_Mutation_p.R121C|NFASC_ENST00000404907.1_Missense_Mutation_p.R115C|NFASC_ENST00000339876.6_Missense_Mutation_p.R121C|NFASC_ENST00000367170.4_Missense_Mutation_p.R121C|NFASC_ENST00000404076.1_Missense_Mutation_p.R115C|NFASC_ENST00000338586.6_Missense_Mutation_p.R121C|NFASC_ENST00000367169.4_Missense_Mutation_p.R121C|NFASC_ENST00000367171.4_Missense_Mutation_p.R121C|NFASC_ENST00000539706.1_Missense_Mutation_p.R115C|NFASC_ENST00000338515.6_Missense_Mutation_p.R121C			O94856	NFASC_HUMAN	neurofascin	121	Ig-like C2-type 1.				axon guidance (GO:0007411)|clustering of voltage-gated sodium channels (GO:0045162)|heterotypic cell-cell adhesion (GO:0034113)|myelination (GO:0042552)|paranodal junction assembly (GO:0030913)|peripheral nervous system development (GO:0007422)|protein localization to juxtaparanode region of axon (GO:0071205)|protein localization to paranode region of axon (GO:0002175)|synapse organization (GO:0050808)|transmission of nerve impulse (GO:0019226)	axon initial segment (GO:0043194)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|intracellular (GO:0005622)|node of Ranvier (GO:0033268)|paranodal junction (GO:0033010)|paranode region of axon (GO:0033270)|plasma membrane (GO:0005886)		p.R115C(1)		NS(1)|breast(4)|central_nervous_system(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(22)|liver(1)|lung(24)|ovary(3)|pancreas(1)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)	81	all_cancers(21;0.0375)|Breast(84;0.0437)|all_epithelial(62;0.171)|Prostate(682;0.19)		KIRC - Kidney renal clear cell carcinoma(13;0.0584)|Kidney(21;0.0934)|BRCA - Breast invasive adenocarcinoma(75;0.158)			GTGCTTCGCCCGCAACAAATT	0.607																																					p.R115C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C343T	1						.						48.0	51.0	50.0					1																	204923461		2203	4300	6503	203190084	SO:0001583	missense	23114	exon3			AK027553	CCDS30982.1, CCDS53460.1, CCDS53461.1, CCDS53462.1	1q32.1	2013-02-11	2010-06-24		ENSG00000163531	ENSG00000163531		"""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	29866	protein-coding gene	gene with protein product		609145	"""neurofascin homolog (chicken)"""			1377696, 8672144	Standard	NM_015090		Approved	NRCAML, KIAA0756, FLJ46866, NF	uc001hbj.3	O94856	OTTHUMG00000151697	ENST00000401399.1:c.361C>T	1.37:g.204923461C>T	ENSP00000385637:p.Arg121Cys	Somatic		Capture	Illumina HiSeq	Phase_I	203190084	NM_001160331	B2RNN8|B3KQZ1|B5MDP6|B5MDR6|B7ZMD8|Q149P5|Q5T2F0|Q5T2F1|Q5T2F2|Q5T2F3|Q5T2F4|Q5T2F5|Q5T2F6|Q5T2F7|Q5T2F9|Q5T2G0|Q5W9F8|Q68DH3|Q6ZQV6|Q7Z3K1|Q96HT1|Q96K50	Missense_Mutation	SNP	ENST00000401399.1	37	CCDS53460.1	.	.	.	.	.	.	.	.	.	.	C	22.7	4.326758	0.81690	.	.	ENSG00000163531	ENST00000367172;ENST00000367171;ENST00000367170;ENST00000338515;ENST00000339876;ENST00000338586;ENST00000295776;ENST00000539706;ENST00000360049;ENST00000367169;ENST00000446412;ENST00000403080;ENST00000404076;ENST00000401399;ENST00000505079;ENST00000404907;ENST00000513543;ENST00000430393	T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.68025	-0.3;-0.3;-0.3;-0.3;-0.3;-0.3;-0.3;-0.3;-0.3;-0.3;-0.3;-0.3;-0.3;-0.3;-0.3;-0.3;-0.3	5.37	5.37	0.77165	.	0.000000	0.53938	D	0.000050	D	0.86075	0.5846	M	0.92880	3.355	0.51767	D	0.999938	D;D;D;D;D;D	0.89917	1.0;1.0;0.999;0.999;1.0;0.995	D;D;D;D;D;P	0.71656	0.956;0.947;0.974;0.947;0.947;0.886	D	0.88860	0.3325	10	0.59425	D	0.04	.	18.6966	0.91603	0.0:1.0:0.0:0.0	.	115;115;217;121;115;121	O94856-11;O94856-8;B4DRH7;O94856-9;O94856-3;O94856-2	.;.;.;.;.;.	C	121;121;121;121;121;121;115;115;115;121;121;121;115;121;121;115;115;91	ENSP00000356140:R121C;ENSP00000356139:R121C;ENSP00000356138:R121C;ENSP00000342128:R121C;ENSP00000344786:R121C;ENSP00000343509:R121C;ENSP00000438614:R115C;ENSP00000353154:R115C;ENSP00000356137:R121C;ENSP00000412161:R121C;ENSP00000384875:R121C;ENSP00000385676:R115C;ENSP00000385637:R121C;ENSP00000427586:R121C;ENSP00000384061:R115C;ENSP00000425908:R115C;ENSP00000415031:R91C	ENSP00000295776:R115C	R	+	1	0	NFASC	203190084	0.753000	0.28349	1.000000	0.80357	0.994000	0.84299	1.772000	0.38552	2.516000	0.84829	0.655000	0.94253	CGC		0.607	NFASC-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000131237.1	NM_001005388	
PM20D1	148811	broad.mit.edu	37	1	205797787	205797787	+	Silent	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr1:205797787G>A	ENST00000367136.4	-	13	1514	c.1470C>T	c.(1468-1470)gaC>gaT	p.D490D	PM20D1_ENST00000460624.1_5'UTR	NM_152491.4	NP_689704.4	Q6GTS8	P20D1_HUMAN	peptidase M20 domain containing 1	490					negative regulation of neuron death (GO:1901215)|regulation of defense response to virus by host (GO:0050691)|regulation of viral process (GO:0050792)	extracellular vesicular exosome (GO:0070062)	metal ion binding (GO:0046872)|peptidase activity (GO:0008233)	p.D490D(1)		breast(2)|endometrium(2)|kidney(1)|large_intestine(6)|lung(9)|ovary(1)|pancreas(1)|prostate(1)|skin(4)|stomach(1)	28	Breast(84;0.201)		BRCA - Breast invasive adenocarcinoma(75;0.0252)			CCTGGTCTGTGTCAGCATTCT	0.517																																					p.D490D												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1470T	1						.						155.0	139.0	144.0					1																	205797787		2203	4300	6503	204064410	SO:0001819	synonymous_variant	148811	exon13				CCDS1460.1	1q32.1	2008-02-05			ENSG00000162877	ENSG00000162877			26518	protein-coding gene	gene with protein product							Standard	NM_152491		Approved	FLJ32569, Cps1	uc001hdj.3	Q6GTS8	OTTHUMG00000035999	ENST00000367136.4:c.1470C>T	1.37:g.205797787G>A		Somatic		Capture	Illumina HiSeq	Phase_I	204064410	NM_152491	Q6P4E3|Q96DM4	Silent	SNP	ENST00000367136.4	37	CCDS1460.1																																																																																				0.517	PM20D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087736.1	NM_152491	
AVPR1B	553	broad.mit.edu	37	1	206225273	206225273	+	Missense_Mutation	SNP	G	G	A	rs369649163		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr1:206225273G>A	ENST00000367126.4	+	1	1298	c.833G>A	c.(832-834)cGa>cAa	p.R278Q	RP11-38J22.3_ENST00000425896.1_RNA	NM_000707.3	NP_000698.1	P47901	V1BR_HUMAN	arginine vasopressin receptor 1B	278					activation of phospholipase C activity (GO:0007202)|G-protein coupled receptor signaling pathway (GO:0007186)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|regulation of systemic arterial blood pressure by vasopressin (GO:0001992)	endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	protein kinase C binding (GO:0005080)|vasopressin receptor activity (GO:0005000)	p.R278Q(1)		breast(1)|cervix(1)|endometrium(1)|large_intestine(5)|lung(6)|ovary(3)|prostate(1)|skin(2)	20			BRCA - Breast invasive adenocarcinoma(75;0.0312)		Desmopressin(DB00035)|Terlipressin(DB02638)|Vasopressin(DB00067)	GCCAAGATCCGAACAGTGAAG	0.582																																					p.R278Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G833A	1						.	G	GLN/ARG	2,4404	4.2+/-10.8	0,2,2201	80.0	75.0	77.0		833	4.4	1.0	1		77	0,8600		0,0,4300	no	missense	AVPR1B	NM_000707.3	43	0,2,6501	AA,AG,GG		0.0,0.0454,0.0154	benign	278/425	206225273	2,13004	2203	4300	6503	204391896	SO:0001583	missense	553	exon1			D31833	CCDS73015.1	1q32	2014-05-06			ENSG00000198049	ENSG00000198049		"""GPCR / Class A : Vasopressin and oxytocin receptors"""	896	protein-coding gene	gene with protein product		600264		AVPR3		7929452, 8586456	Standard	NM_000707		Approved		uc001hds.2	P47901	OTTHUMG00000184377	ENST00000367126.4:c.833G>A	1.37:g.206225273G>A	ENSP00000356094:p.Arg278Gln	Somatic		Capture	Illumina HiSeq	Phase_I	204391896	NM_000707	B0M0J6|Q5TZ00	Missense_Mutation	SNP	ENST00000367126.4	37	CCDS30994.1	.	.	.	.	.	.	.	.	.	.	G	23.1	4.375455	0.82682	4.54E-4	0.0	ENSG00000198049	ENST00000367126	T	0.40225	1.04	5.34	4.43	0.53597	GPCR, rhodopsin-like superfamily (1);	0.092850	0.44097	N	0.000491	T	0.50051	0.1593	M	0.66439	2.03	0.48901	D	0.999723	P	0.51351	0.944	P	0.48425	0.577	T	0.56414	-0.7983	10	0.72032	D	0.01	-5.9253	13.7976	0.63180	0.0749:0.0:0.9251:0.0	.	278	P47901	V1BR_HUMAN	Q	278	ENSP00000356094:R278Q	ENSP00000356094:R278Q	R	+	2	0	AVPR1B	204391896	1.000000	0.71417	0.996000	0.52242	0.901000	0.52897	6.719000	0.74718	1.251000	0.43983	0.462000	0.41574	CGA		0.582	AVPR1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087996.1	NM_000707	
SRGAP2	23380	broad.mit.edu	37	1	206611440	206611440	+	De_novo_Start_OutOfFrame	SNP	C	C	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr1:206611440C>A	ENST00000419187.2	+	0	1338				SRGAP2_ENST00000414007.1_Missense_Mutation_p.A447D			O75044	SRGP2_HUMAN	SLIT-ROBO Rho GTPase activating protein 2						actin filament severing (GO:0051014)|axon guidance (GO:0007411)|dendritic spine development (GO:0060996)|extension of a leading process involved in cell motility in cerebral cortex radial glia guided migration (GO:0021816)|filopodium assembly (GO:0046847)|lamellipodium assembly involved in ameboidal cell migration (GO:0003363)|negative regulation of neuron migration (GO:2001223)|neuron projection morphogenesis (GO:0048812)|positive regulation of Rac GTPase activity (GO:0032855)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|substrate adhesion-dependent cell spreading (GO:0034446)	cell junction (GO:0030054)|cytosol (GO:0005829)|dendritic spine head (GO:0044327)|lamellipodium (GO:0030027)|nucleus (GO:0005634)|phagocytic vesicle (GO:0045335)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)	protein homodimerization activity (GO:0042803)|Rac GTPase activator activity (GO:0030675)|Rac GTPase binding (GO:0048365)	p.A447D(1)		NS(1)|breast(1)|kidney(1)|lung(1)	4	Breast(84;0.137)					GACCTGATGGCCTGCGTCAGT	0.502																																					p.G499G												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1497A	1						.						68.0	67.0	67.0					1																	206611440		1924	4136	6060	204678063			23380	exon13			AB007925	CCDS73017.1	1q32.1	2014-08-13	2004-11-12	2004-11-12	ENSG00000163486	ENSG00000266028		"""Rho GTPase activating proteins"""	19751	protein-coding gene	gene with protein product		606524	"""formin binding protein 2"""	FNBP2		15046868, 11672528	Standard	XM_005277510		Approved	KIAA0456, ARHGAP34, SRGAP2A	uc001hdy.3	O75044	OTTHUMG00000184381	ENST00000419187.2:c.-326C>A	1.37:g.206611440C>A		Somatic		Capture	Illumina HiSeq	Phase_I	204678063	NM_001170637		Missense_Mutation	SNP	ENST00000419187.2	37		.	.	.	.	.	.	.	.	.	.	C	16.97	3.269400	0.59540	.	.	ENSG00000163486	ENST00000414359;ENST00000414007;ENST00000439126	T;T	0.18810	2.19;2.19	6.03	6.03	0.97812	Rho GTPase-activating protein domain (4);Rho GTPase activation protein (1);	0.160763	0.56097	D	0.000025	T	0.14356	0.0347	.	.	.	0.80722	D	1.000000	B;B	0.30563	0.285;0.044	B;B	0.28916	0.096;0.06	T	0.19095	-1.0316	8	0.13108	T	0.6	.	15.973	0.80034	0.0:0.8661:0.1339:0.0	.	434;587	B4DDU0;O75044	.;FNBP2_HUMAN	D	500;447;201	ENSP00000390898:A447D;ENSP00000403036:A201D	ENSP00000390898:A447D	A	+	2	0	SRGAP2	204678063	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	4.902000	0.63266	2.861000	0.98227	0.655000	0.94253	GCC		0.502	SRGAP2-202	KNOWN	basic	protein_coding	protein_coding		NM_015326	
IKBKE	9641	broad.mit.edu	37	1	206647748	206647748	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr1:206647748G>T	ENST00000367120.3	+	4	535	c.162G>T	c.(160-162)agG>agT	p.R54S	IKBKE_ENST00000463979.1_3'UTR|IKBKE_ENST00000537984.1_5'UTR	NM_001193322.1|NM_014002.3	NP_001180251.1|NP_054721.1	Q14164	IKKE_HUMAN	inhibitor of kappa light polypeptide gene enhancer in B-cells, kinase epsilon	54	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				immune response (GO:0006955)|innate immune response (GO:0045087)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of type I interferon production (GO:0032480)|NIK/NF-kappaB signaling (GO:0038061)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|protein phosphorylation (GO:0006468)|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)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endosome membrane (GO:0010008)|nucleus (GO:0005634)|PML body (GO:0016605)	ATP binding (GO:0005524)|IkappaB kinase activity (GO:0008384)|NF-kappaB-inducing kinase activity (GO:0004704)	p.R54S(1)		NS(1)|breast(1)|central_nervous_system(2)|endometrium(3)|kidney(1)|large_intestine(6)|lung(13)|ovary(3)|skin(2)	32	Breast(84;0.137)					TGCAAGTGAGGGAGTTTGAGG	0.572																																					p.R54S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G162T	1						.						84.0	64.0	71.0					1																	206647748		2203	4300	6503	204714371	SO:0001583	missense	9641	exon4			AB016590	CCDS30996.1, CCDS53464.1, CCDS73019.1	1q31	2014-05-06			ENSG00000143466				14552	protein-coding gene	gene with protein product		605048				10421793, 10882136	Standard	NM_001193321		Approved	IKKE, IKK-i, KIAA0151	uc001hdz.2	Q14164	OTTHUMG00000184613	ENST00000367120.3:c.162G>T	1.37:g.206647748G>T	ENSP00000356087:p.Arg54Ser	Somatic		Capture	Illumina HiSeq	Phase_I	204714371	NM_001193322	D3DT78|Q3B754|Q3KR43|Q5JTS6	Missense_Mutation	SNP	ENST00000367120.3	37	CCDS30996.1	.	.	.	.	.	.	.	.	.	.	G	18.86	3.713835	0.68730	.	.	ENSG00000143466	ENST00000367120	T	0.49139	0.79	5.25	3.39	0.38822	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.63581	0.2523	M	0.70595	2.14	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.63247	-0.6680	10	0.72032	D	0.01	-3.406	8.5595	0.33503	0.3622:0.0:0.6378:0.0	.	54	Q14164	IKKE_HUMAN	S	54	ENSP00000356087:R54S	ENSP00000356087:R54S	R	+	3	2	IKBKE	204714371	1.000000	0.71417	1.000000	0.80357	0.915000	0.54546	1.556000	0.36288	0.614000	0.30107	-0.258000	0.10820	AGG		0.572	IKBKE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088484.1		
IKBKE	9641	broad.mit.edu	37	1	206648328	206648328	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr1:206648328C>T	ENST00000367120.3	+	5	722	c.349C>T	c.(349-351)Cgc>Tgc	p.R117C	IKBKE_ENST00000463979.1_3'UTR|IKBKE_ENST00000537984.1_Missense_Mutation_p.R32C	NM_001193322.1|NM_014002.3	NP_001180251.1|NP_054721.1	Q14164	IKKE_HUMAN	inhibitor of kappa light polypeptide gene enhancer in B-cells, kinase epsilon	117	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				immune response (GO:0006955)|innate immune response (GO:0045087)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of type I interferon production (GO:0032480)|NIK/NF-kappaB signaling (GO:0038061)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|protein phosphorylation (GO:0006468)|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)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endosome membrane (GO:0010008)|nucleus (GO:0005634)|PML body (GO:0016605)	ATP binding (GO:0005524)|IkappaB kinase activity (GO:0008384)|NF-kappaB-inducing kinase activity (GO:0004704)	p.R117C(1)		NS(1)|breast(1)|central_nervous_system(2)|endometrium(3)|kidney(1)|large_intestine(6)|lung(13)|ovary(3)|skin(2)	32	Breast(84;0.137)					GGTGGTGCTGCGCTGTGTGGG	0.617																																					p.R117C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C349T	1						.						187.0	134.0	152.0					1																	206648328		2203	4300	6503	204714951	SO:0001583	missense	9641	exon5			AB016590	CCDS30996.1, CCDS53464.1, CCDS73019.1	1q31	2014-05-06			ENSG00000143466				14552	protein-coding gene	gene with protein product		605048				10421793, 10882136	Standard	NM_001193321		Approved	IKKE, IKK-i, KIAA0151	uc001hdz.2	Q14164	OTTHUMG00000184613	ENST00000367120.3:c.349C>T	1.37:g.206648328C>T	ENSP00000356087:p.Arg117Cys	Somatic		Capture	Illumina HiSeq	Phase_I	204714951	NM_001193322	D3DT78|Q3B754|Q3KR43|Q5JTS6	Missense_Mutation	SNP	ENST00000367120.3	37	CCDS30996.1	.	.	.	.	.	.	.	.	.	.	C	24.9	4.579292	0.86645	.	.	ENSG00000143466	ENST00000367120;ENST00000537984	T;T	0.46819	0.86;1.72	5.23	4.29	0.51040	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.343332	0.29286	N	0.012598	T	0.62514	0.2434	M	0.64676	1.99	0.46981	D	0.999273	D;D	0.89917	0.999;1.0	P;P	0.60609	0.877;0.873	T	0.66874	-0.5813	10	0.87932	D	0	.	14.7595	0.69596	0.0:0.8198:0.1802:0.0	.	32;117	Q3B754;Q14164	.;IKKE_HUMAN	C	117;32	ENSP00000356087:R117C;ENSP00000444529:R32C	ENSP00000356087:R117C	R	+	1	0	IKBKE	204714951	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	3.912000	0.56386	1.093000	0.41377	0.561000	0.74099	CGC		0.617	IKBKE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088484.1		
C4BPA	722	broad.mit.edu	37	1	207286467	207286467	+	Missense_Mutation	SNP	C	C	A	rs116810489	byFrequency	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr1:207286467C>A	ENST00000367070.3	+	2	291	c.97C>A	c.(97-99)Ctc>Atc	p.L33I		NM_000715.3	NP_000706.1	P04003	C4BPA_HUMAN	complement component 4 binding protein, alpha	33					complement activation, classical pathway (GO:0006958)|innate immune response (GO:0045087)|negative regulation of complement activation, classical pathway (GO:0045959)|positive regulation of protein catabolic process (GO:0045732)|regulation of complement activation (GO:0030449)|regulation of opsonization (GO:1903027)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|other organism cell (GO:0044216)|plasma membrane (GO:0005886)	poly(A) RNA binding (GO:0044822)	p.L33I(1)		breast(1)|central_nervous_system(2)|endometrium(1)|kidney(2)|large_intestine(10)|lung(7)|ovary(2)|skin(1)|urinary_tract(2)	28						TGATCCAATTCTCTTCCAAAT	0.488																																					p.L33I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C97A	1						.						136.0	125.0	129.0					1																	207286467		2203	4300	6503	205353090	SO:0001583	missense	722	exon2			M31452	CCDS1477.1	1q32	2010-09-24	2001-11-28		ENSG00000123838	ENSG00000123838			1325	protein-coding gene	gene with protein product		120830	"""complement component 4-binding protein, alpha"""	C4BP			Standard	XM_005273251		Approved		uc001hfo.3	P04003	OTTHUMG00000036173	ENST00000367070.3:c.97C>A	1.37:g.207286467C>A	ENSP00000356037:p.Leu33Ile	Somatic		Capture	Illumina HiSeq	Phase_I	205353090	NM_000715	Q5VVQ8	Missense_Mutation	SNP	ENST00000367070.3	37	CCDS1477.1	.	.	.	.	.	.	.	.	.	.	C	17.61	3.431208	0.62844	.	.	ENSG00000123838	ENST00000367070;ENST00000421786	T;T	0.33865	1.39;1.71	4.88	3.96	0.45880	.	0.000000	0.41097	D	0.000947	T	0.56140	0.1965	M	0.79475	2.455	0.25339	N	0.988967	D	0.89917	1.0	D	0.91635	0.999	T	0.47289	-0.9129	10	0.45353	T	0.12	.	8.4232	0.32714	0.0:0.8916:0.0:0.1084	.	33	P04003	C4BPA_HUMAN	I	33	ENSP00000356037:L33I;ENSP00000403386:L33I	ENSP00000356037:L33I	L	+	1	0	C4BPA	205353090	0.653000	0.27358	0.964000	0.40570	0.716000	0.41182	0.301000	0.19174	1.388000	0.46506	0.563000	0.77884	CTC		0.488	C4BPA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088089.3		
CR2	1380	broad.mit.edu	37	1	207642150	207642150	+	Missense_Mutation	SNP	C	C	T	rs201760344		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr1:207642150C>T	ENST00000367058.3	+	4	829	c.640C>T	c.(640-642)Cgc>Tgc	p.R214C	CR2_ENST00000367057.3_Missense_Mutation_p.R214C|CR2_ENST00000458541.2_Missense_Mutation_p.R214C|CR2_ENST00000485707.1_3'UTR|CR2_ENST00000367059.3_Missense_Mutation_p.R214C	NM_001877.4	NP_001868.2	P20023	CR2_HUMAN	complement component (3d/Epstein Barr virus) receptor 2	214	Sushi 4. {ECO:0000255|PROSITE- ProRule:PRU00302}.				B cell differentiation (GO:0030183)|B cell proliferation (GO:0042100)|complement activation, classical pathway (GO:0006958)|immune response (GO:0006955)|innate immune response (GO:0045087)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	complement binding (GO:0001848)|complement receptor activity (GO:0004875)|DNA binding (GO:0003677)|protein homodimerization activity (GO:0042803)|transmembrane signaling receptor activity (GO:0004888)	p.R214C(1)		NS(2)|breast(3)|endometrium(4)|kidney(3)|large_intestine(12)|lung(26)|ovary(1)|pancreas(1)|prostate(1)|skin(12)|upper_aerodigestive_tract(3)|urinary_tract(1)	69						TTTAGAGGCACGCTGTAAATC	0.408													C|||	1	0.000199681	0.0	0.0	5008	,	,		20288	0.001		0.0	False		,,,				2504	0.0				p.R214C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C640T	1						.						105.0	98.0	101.0					1																	207642150		2203	4300	6503	205708773	SO:0001583	missense	1380	exon4			M26004	CCDS1478.1, CCDS31007.1	1q32	2014-09-17			ENSG00000117322	ENSG00000117322		"""CD molecules"", ""Complement system"""	2336	protein-coding gene	gene with protein product		120650					Standard	NM_001006658		Approved	CD21	uc001hfv.3	P20023	OTTHUMG00000036307	ENST00000367058.3:c.640C>T	1.37:g.207642150C>T	ENSP00000356025:p.Arg214Cys	Somatic		Capture	Illumina HiSeq	Phase_I	205708773	NM_001006658	C9JHD2|Q13866|Q14212|Q53EL2|Q5BKT9|Q5SR46|Q5SR48	Missense_Mutation	SNP	ENST00000367058.3	37	CCDS1478.1	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	C	10.89	1.477443	0.26511	.	.	ENSG00000117322	ENST00000367058;ENST00000367057;ENST00000367059;ENST00000458541	T;T;T;T	0.25085	1.82;1.82;1.82;1.82	5.5	0.0595	0.14332	Complement control module (2);Sushi/SCR/CCP (1);	.	.	.	.	T	0.25938	0.0632	L	0.37750	1.13	0.09310	N	1	D;D;D	0.64830	0.966;0.991;0.994	P;P;P	0.55667	0.513;0.669;0.781	T	0.12243	-1.0555	9	0.49607	T	0.09	.	2.2654	0.04077	0.1418:0.3902:0.3031:0.1649	.	214;214;214	Q5SR47;P20023;P20023-3	.;CR2_HUMAN;.	C	214	ENSP00000356025:R214C;ENSP00000356024:R214C;ENSP00000356026:R214C;ENSP00000404222:R214C	ENSP00000356024:R214C	R	+	1	0	CR2	205708773	0.000000	0.05858	0.044000	0.18714	0.034000	0.12701	-1.699000	0.01906	0.267000	0.21916	-0.251000	0.11542	CGC		0.408	CR2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000088274.1	NM_001877	
PLXNA2	5362	broad.mit.edu	37	1	208212318	208212318	+	Silent	SNP	G	G	A	rs113860539		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr1:208212318G>A	ENST00000367033.3	-	25	5269	c.4512C>T	c.(4510-4512)tgC>tgT	p.C1504C		NM_025179.3	NP_079455.3	O75051	PLXA2_HUMAN	plexin A2	1504					axon guidance (GO:0007411)|centrosome localization (GO:0051642)|cerebellar granule cell precursor tangential migration (GO:0021935)|limb bud formation (GO:0060174)|neural tube development (GO:0021915)|pharyngeal system development (GO:0060037)|regulation of cell migration (GO:0030334)|semaphorin-plexin signaling pathway (GO:0071526)|somitogenesis (GO:0001756)	integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)|plasma membrane (GO:0005886)|semaphorin receptor complex (GO:0002116)	semaphorin receptor activity (GO:0017154)	p.C1504C(1)		NS(1)|breast(3)|central_nervous_system(5)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|liver(1)|lung(28)|ovary(3)|prostate(5)|skin(2)|upper_aerodigestive_tract(3)	80				OV - Ovarian serous cystadenocarcinoma(81;0.199)		CAGGGTTGACGCAGTTCAGGA	0.488																																					p.C1504C												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C4512T	1						.						130.0	113.0	118.0					1																	208212318		2203	4300	6503	206278941	SO:0001819	synonymous_variant	5362	exon25			X87831	CCDS31013.1	1q32.2	2008-07-18			ENSG00000076356	ENSG00000076356		"""Plexins"""	9100	protein-coding gene	gene with protein product	"""plexin 2"", ""plexin-A2"", ""semaphorin receptor OCT"", ""transmembrane protein OCT"""	601054		PLXN2		8570614	Standard	NM_025179		Approved	OCT, FLJ11751, FLJ30634, KIAA0463	uc001hgz.3	O75051	OTTHUMG00000036564	ENST00000367033.3:c.4512C>T	1.37:g.208212318G>A		Somatic		Capture	Illumina HiSeq	Phase_I	206278941	NM_025179	A2RTX9|B2RMX7|Q6UX61|Q96GN9|Q9BRL1|Q9UIW1	Silent	SNP	ENST00000367033.3	37	CCDS31013.1																																																																																				0.488	PLXNA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088932.6	NM_025179	
HHAT	55733	broad.mit.edu	37	1	210761368	210761368	+	Silent	SNP	G	G	A	rs567965731		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr1:210761368G>A	ENST00000367010.1	+	10	1397	c.1170G>A	c.(1168-1170)gcG>gcA	p.A390A	HHAT_ENST00000391905.3_Silent_p.A390A|HHAT_ENST00000537898.1_Silent_p.A325A|HHAT_ENST00000367009.1_Silent_p.A80A|HHAT_ENST00000541565.1_Silent_p.A253A|HHAT_ENST00000545154.1_Silent_p.A391A|HHAT_ENST00000261458.3_Silent_p.A390A|HHAT_ENST00000308852.6_Silent_p.A345A|HHAT_ENST00000413764.2_Silent_p.A390A|HHAT_ENST00000545781.1_Silent_p.A327A	NM_001170580.1	NP_001164051.1	Q5VTY9	HHAT_HUMAN	hedgehog acyltransferase	390					multicellular organismal development (GO:0007275)|protein palmitoylation (GO:0018345)|smoothened signaling pathway (GO:0007224)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	GTP binding (GO:0005525)|palmitoyltransferase activity (GO:0016409)	p.A390A(1)		breast(3)|central_nervous_system(1)|kidney(1)|large_intestine(6)|lung(8)|ovary(2)|prostate(1)|skin(1)|stomach(3)|upper_aerodigestive_tract(1)	27				OV - Ovarian serous cystadenocarcinoma(81;0.0136)|all cancers(67;0.161)|KIRC - Kidney renal clear cell carcinoma(1967;0.215)		GCTGGGCAGCGCTCAACTGGC	0.592													G|||	1	0.000199681	0.0	0.0014	5008	,	,		16305	0.0		0.0	False		,,,				2504	0.0				p.A390A												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G1170A	1						.						62.0	55.0	57.0					1																	210761368		2203	4300	6503	208827991	SO:0001819	synonymous_variant	55733	exon10			AK001586	CCDS1495.1, CCDS53471.1, CCDS53472.1, CCDS53473.1	1q32	2008-02-05			ENSG00000054392	ENSG00000054392			18270	protein-coding gene	gene with protein product		605743				11160356	Standard	NM_001170587		Approved	FLJ10724, MART-2, MART2, Skn, ski, rasp, sit, GUP2	uc009xcx.3	Q5VTY9	OTTHUMG00000036447	ENST00000367010.1:c.1170G>A	1.37:g.210761368G>A		Somatic		Capture	Illumina HiSeq	Phase_I	208827991	NM_018194	B7Z4D5|B7Z5I1|B7Z868|B7ZA75|D3DT91|F5H444|Q17RZ7|Q4G0K3|Q5CZ95|Q5TGI2|Q9NVH9|Q9Y3N8	Silent	SNP	ENST00000367010.1	37	CCDS1495.1																																																																																				0.592	HHAT-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088662.1	NM_018194	
HP1BP3	50809	broad.mit.edu	37	1	21071441	21071441	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr1:21071441G>A	ENST00000312239.5	-	13	1650	c.1511C>T	c.(1510-1512)aCg>aTg	p.T504M	RP5-930J4.4_ENST00000413451.1_RNA|HP1BP3_ENST00000375003.2_Missense_Mutation_p.T352M	NM_016287.3	NP_057371.2	Q5SSJ5	HP1B3_HUMAN	heterochromatin protein 1, binding protein 3	504	Lys-rich.				nucleosome assembly (GO:0006334)	nucleosome (GO:0000786)|nucleus (GO:0005634)	DNA binding (GO:0003677)	p.T504M(1)		central_nervous_system(1)|endometrium(1)|large_intestine(4)|lung(5)|prostate(2)|skin(2)|urinary_tract(1)	16		all_lung(284;6.55e-06)|Lung NSC(340;6.59e-06)|Colorectal(325;3.46e-05)|Renal(390;9.67e-05)|Breast(348;0.00179)|Ovarian(437;0.00327)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0182)|COAD - Colon adenocarcinoma(152;1.26e-05)|BRCA - Breast invasive adenocarcinoma(304;0.00015)|GBM - Glioblastoma multiforme(114;0.000521)|Kidney(64;0.000529)|STAD - Stomach adenocarcinoma(196;0.00311)|KIRC - Kidney renal clear cell carcinoma(64;0.00687)|READ - Rectum adenocarcinoma(331;0.0655)|Lung(427;0.201)		CTTGGCAGGCGTTTTGGCCTT	0.522																																					p.T504M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1511T	1						.						123.0	115.0	118.0					1																	21071441		2203	4300	6503	20944028	SO:0001583	missense	50809	exon13			BC053327	CCDS30621.1	1p36.12	2008-02-05			ENSG00000127483	ENSG00000127483			24973	protein-coding gene	gene with protein product						12477932	Standard	NM_016287		Approved	HP1-BP74	uc001bdw.1	Q5SSJ5	OTTHUMG00000002622	ENST00000312239.5:c.1511C>T	1.37:g.21071441G>A	ENSP00000312625:p.Thr504Met	Somatic		Capture	Illumina HiSeq	Phase_I	20944028	NM_016287	A6NI71|A8K5D7|B3KMZ8|B4E210|Q05BI0|Q5SSJ6|Q5SWC6|Q6PIM9|Q8NDF0|Q9UHY0	Missense_Mutation	SNP	ENST00000312239.5	37	CCDS30621.1	.	.	.	.	.	.	.	.	.	.	G	18.70	3.679893	0.68042	.	.	ENSG00000127483	ENST00000312239;ENST00000375004;ENST00000375003	T;T	0.52754	0.65;0.66	5.87	4.95	0.65309	.	0.233607	0.50627	D	0.000107	T	0.36386	0.0965	L	0.27053	0.805	0.80722	D	1	P	0.51933	0.949	B	0.43331	0.416	T	0.30937	-0.9961	10	0.87932	D	0	-3.2823	9.9133	0.41419	0.0718:0.1402:0.788:0.0	.	504	Q5SSJ5	HP1B3_HUMAN	M	504;466;352	ENSP00000312625:T504M;ENSP00000364142:T352M	ENSP00000312625:T504M	T	-	2	0	HP1BP3	20944028	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	3.470000	0.53100	1.612000	0.50221	0.655000	0.94253	ACG		0.522	HP1BP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007457.2	NM_016287	
KCNH1	3756	broad.mit.edu	37	1	211192388	211192388	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr1:211192388C>T	ENST00000271751.4	-	6	796	c.769G>A	c.(769-771)Gtg>Atg	p.V257M	KCNH1_ENST00000367007.4_Missense_Mutation_p.V257M			O95259	KCNH1_HUMAN	potassium voltage-gated channel, subfamily H (eag-related), member 1	257					myoblast fusion (GO:0007520)|potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|regulation of membrane potential (GO:0042391)|synaptic transmission (GO:0007268)	nucleus (GO:0005634)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|phosphorelay sensor kinase activity (GO:0000155)	p.V257M(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(13)|lung(35)|ovary(4)|prostate(4)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	68				OV - Ovarian serous cystadenocarcinoma(81;0.0109)|all cancers(67;0.141)|Epithelial(68;0.185)		ATAACATCCACGATGCTATCA	0.443																																					p.V257M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G769A	1						.						148.0	138.0	141.0					1																	211192388		2203	4300	6503	209259011	SO:0001583	missense	3756	exon6			AJ001366	CCDS1496.1, CCDS31015.1	1q32.2	2012-07-05			ENSG00000143473	ENSG00000143473		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	6250	protein-coding gene	gene with protein product		603305				9738473, 16382104	Standard	NM_172362		Approved	Kv10.1, eag, h-eag, eag1	uc001hib.2	O95259	OTTHUMG00000036309	ENST00000271751.4:c.769G>A	1.37:g.211192388C>T	ENSP00000271751:p.Val257Met	Somatic		Capture	Illumina HiSeq	Phase_I	209259011	NM_002238	B1AQ26|O76035|Q14CL3	Missense_Mutation	SNP	ENST00000271751.4	37	CCDS1496.1	.	.	.	.	.	.	.	.	.	.	C	15.12	2.737803	0.49045	.	.	ENSG00000143473	ENST00000271751;ENST00000367007	D;D	0.94897	-3.55;-3.55	5.09	5.09	0.68999	Ion transport (1);	0.000000	0.85682	D	0.000000	D	0.96839	0.8968	M	0.73372	2.23	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.72338	0.977;0.977	D	0.97468	1.0039	10	0.87932	D	0	.	17.4587	0.87614	0.0:1.0:0.0:0.0	.	257;257	Q14CL3;O95259	.;KCNH1_HUMAN	M	257	ENSP00000271751:V257M;ENSP00000355974:V257M	ENSP00000271751:V257M	V	-	1	0	KCNH1	209259011	1.000000	0.71417	1.000000	0.80357	0.051000	0.14879	7.474000	0.81024	2.366000	0.80165	0.462000	0.41574	GTG		0.443	KCNH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088332.1	NM_002238	
RD3	343035	broad.mit.edu	37	1	211652576	211652576	+	Silent	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr1:211652576C>T	ENST00000367002.4	-	3	1553	c.390G>A	c.(388-390)aaG>aaA	p.K130K	RD3_ENST00000484910.1_5'UTR	NM_001164688.1|NM_183059.2	NP_001158160.1|NP_898882.1	Q7Z3Z2	RD3_HUMAN	retinal degeneration 3	130			K -> M (in an individual with cone-rod dystrophy features). {ECO:0000269|PubMed:17186464}.		response to stimulus (GO:0050896)|retina development in camera-type eye (GO:0060041)|visual perception (GO:0007601)			p.K130K(1)		central_nervous_system(1)|large_intestine(3)|lung(4)|ovary(1)|prostate(1)	10				OV - Ovarian serous cystadenocarcinoma(81;0.00284)|all cancers(67;0.0279)|Epithelial(68;0.0689)		CCTCTTCCTGCTTCATCCTCT	0.701																																					p.K130K												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G390A	1						.						21.0	21.0	21.0					1																	211652576		2199	4300	6499	209719199	SO:0001819	synonymous_variant	343035	exon3			AY191519	CCDS1498.1	1q32.3	2008-02-05	2006-11-13	2006-11-13	ENSG00000198570	ENSG00000198570			19689	protein-coding gene	gene with protein product		180040	"""chromosome 1 open reading frame 36"""	C1orf36		12914764	Standard	NM_183059		Approved	LCA12	uc001hin.2	Q7Z3Z2	OTTHUMG00000037002	ENST00000367002.4:c.390G>A	1.37:g.211652576C>T		Somatic		Capture	Illumina HiSeq	Phase_I	209719199	NM_001164688	A8K595	Silent	SNP	ENST00000367002.4	37	CCDS1498.1																																																																																				0.701	RD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089837.1	NM_183059	
INTS7	25896	broad.mit.edu	37	1	212151747	212151747	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr1:212151747C>T	ENST00000366994.3	-	11	1441	c.1337G>A	c.(1336-1338)cGg>cAg	p.R446Q	INTS7_ENST00000366992.3_Missense_Mutation_p.R446Q|INTS7_ENST00000440600.2_Missense_Mutation_p.R397Q|INTS7_ENST00000366993.3_Missense_Mutation_p.R446Q|INTS7_ENST00000469606.1_5'UTR	NM_001199811.1|NM_001199812.1|NM_015434.3	NP_001186740.1|NP_001186741.1|NP_056249.1	Q9NVH2	INT7_HUMAN	integrator complex subunit 7	446					cellular response to ionizing radiation (GO:0071479)|DNA damage checkpoint (GO:0000077)|snRNA processing (GO:0016180)	chromosome (GO:0005694)|integrator complex (GO:0032039)		p.R446Q(1)		NS(1)|breast(1)|kidney(1)|large_intestine(8)|lung(6)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	20				OV - Ovarian serous cystadenocarcinoma(81;0.00584)|all cancers(67;0.0318)|Epithelial(68;0.0852)		CATCAAAATCCGGGCAGCGTC	0.532																																					p.R397Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1190A	1						.						109.0	101.0	104.0					1																	212151747		2203	4300	6503	210218370	SO:0001583	missense	25896	exon10			AK022509	CCDS1501.1, CCDS55684.1, CCDS55683.1, CCDS55685.1	1q32.3	2008-02-05	2006-03-15	2006-03-15	ENSG00000143493	ENSG00000143493			24484	protein-coding gene	gene with protein product		611350	"""chromosome 1 open reading frame 73"""	C1orf73		16239144	Standard	NM_015434		Approved	DKFZP434B168, INT7	uc001hiw.2	Q9NVH2	OTTHUMG00000037119	ENST00000366994.3:c.1337G>A	1.37:g.212151747C>T	ENSP00000355961:p.Arg446Gln	Somatic		Capture	Illumina HiSeq	Phase_I	210218370	NM_001199809	B4DLZ6|B7WNP6|B7WPB6|Q8N4K7|Q8WUH5|Q9H9V3|Q9NVU5|Q9UFC6|Q9UFM3	Missense_Mutation	SNP	ENST00000366994.3	37	CCDS1501.1	.	.	.	.	.	.	.	.	.	.	C	24.2	4.503796	0.85176	.	.	ENSG00000143493	ENST00000366994;ENST00000366993;ENST00000366992;ENST00000440600	T;T;T;T	0.34667	1.35;1.35;1.35;1.35	5.69	5.69	0.88448	Armadillo-like helical (1);Armadillo-type fold (1);	0.048767	0.85682	D	0.000000	T	0.39384	0.1076	N	0.17474	0.49	0.80722	D	1	D;D;D;D	0.76494	0.997;0.999;0.999;0.996	P;P;P;P	0.58266	0.658;0.836;0.771;0.661	T	0.08932	-1.0698	10	0.12766	T	0.61	-11.8738	19.8022	0.96513	0.0:1.0:0.0:0.0	.	397;446;446;446	B4DLZ6;Q9NVH2-3;Q9NVH2-2;Q9NVH2	.;.;.;INT7_HUMAN	Q	446;446;446;397	ENSP00000355961:R446Q;ENSP00000355960:R446Q;ENSP00000355959:R446Q;ENSP00000388908:R397Q	ENSP00000355959:R446Q	R	-	2	0	INTS7	210218370	1.000000	0.71417	0.605000	0.28930	0.995000	0.86356	5.805000	0.69143	2.674000	0.91012	0.650000	0.86243	CGG		0.532	INTS7-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090142.1	NM_015434	
PTPN14	5784	broad.mit.edu	37	1	214567075	214567075	+	Nonsense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr1:214567075G>A	ENST00000366956.5	-	10	1086	c.892C>T	c.(892-894)Cga>Tga	p.R298*	PTPN14_ENST00000543945.1_3'UTR	NM_005401.4	NP_005392.2	Q15678	PTN14_HUMAN	protein tyrosine phosphatase, non-receptor type 14	298	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.				lymphangiogenesis (GO:0001946)|negative regulation of cell proliferation (GO:0008285)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|regulation of protein export from nucleus (GO:0046825)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	protein tyrosine phosphatase activity (GO:0004725)|receptor tyrosine kinase binding (GO:0030971)|transcription cofactor activity (GO:0003712)	p.R298*(2)		NS(2)|breast(3)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(9)|liver(3)|lung(21)|ovary(1)|pancreas(1)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	58				OV - Ovarian serous cystadenocarcinoma(81;0.00181)|all cancers(67;0.00194)|Epithelial(68;0.0157)|GBM - Glioblastoma multiforme(131;0.155)		AACTTGTGTCGTGTGGCAAAC	0.333																																					p.R298X	Colon(92;557 1424 24372 34121 40073)											.	.	2	Substitution - Nonsense(2)	upper_aerodigestive_tract(1)|large_intestine(1)	c.C892T	1						.						85.0	90.0	88.0					1																	214567075		2203	4300	6503	212633698	SO:0001587	stop_gained	5784	exon10			X82676	CCDS1514.1	1q32.2	2011-06-09			ENSG00000152104	ENSG00000152104		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"""	9647	protein-coding gene	gene with protein product		603155				7733990	Standard	NM_005401		Approved	PEZ	uc001hkk.2	Q15678	OTTHUMG00000037039	ENST00000366956.5:c.892C>T	1.37:g.214567075G>A	ENSP00000355923:p.Arg298*	Somatic		Capture	Illumina HiSeq	Phase_I	212633698	NM_005401	Q5VSI0	Nonsense_Mutation	SNP	ENST00000366956.5	37	CCDS1514.1	.	.	.	.	.	.	.	.	.	.	G	38	6.791934	0.97841	.	.	ENSG00000152104	ENST00000366956	.	.	.	5.78	-2.2	0.06994	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	18.8493	0.92220	0.0:0.0:0.1596:0.8404	.	.	.	.	X	298	.	ENSP00000355923:R298X	R	-	1	2	PTPN14	212633698	0.999000	0.42202	0.337000	0.25536	0.879000	0.50718	1.878000	0.39608	-0.192000	0.10432	0.655000	0.94253	CGA		0.333	PTPN14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089918.2	NM_005401	
USH2A	7399	broad.mit.edu	37	1	215972340	215972340	+	Silent	SNP	G	G	A	rs145814426	byFrequency	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr1:215972340G>A	ENST00000307340.3	-	50	10253	c.9867C>T	c.(9865-9867)ggC>ggT	p.G3289G	USH2A_ENST00000366943.2_Silent_p.G3289G	NM_206933.2	NP_996816	O75445	USH2A_HUMAN	Usher syndrome 2A (autosomal recessive, mild)	3289					hair cell differentiation (GO:0035315)|inner ear receptor cell differentiation (GO:0060113)|maintenance of organ identity (GO:0048496)|photoreceptor cell maintenance (GO:0045494)|response to stimulus (GO:0050896)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	apical plasma membrane (GO:0016324)|basement membrane (GO:0005604)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|stereocilia ankle link complex (GO:0002142)|stereocilium bundle (GO:0032421)|stereocilium membrane (GO:0060171)	collagen binding (GO:0005518)|myosin binding (GO:0017022)	p.G3289G(1)		NS(7)|breast(20)|central_nervous_system(3)|cervix(2)|endometrium(32)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(71)|liver(2)|lung(282)|ovary(25)|pancreas(2)|prostate(12)|skin(22)|stomach(7)|upper_aerodigestive_tract(20)|urinary_tract(3)	527				OV - Ovarian serous cystadenocarcinoma(81;0.0547)|all cancers(67;0.0875)		TCTGGCCATGGCCATCATGAA	0.522										HNSCC(13;0.011)			G|||	4	0.000798722	0.003	0.0	5008	,	,		18199	0.0		0.0	False		,,,				2504	0.0				p.G3289G												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C9867T	1						.	G		4,4402	8.1+/-20.4	0,4,2199	147.0	125.0	132.0		9867	1.7	0.5	1	dbSNP_134	132	0,8600		0,0,4300	no	coding-synonymous	USH2A	NM_206933.2		0,4,6499	AA,AG,GG		0.0,0.0908,0.0308		3289/5203	215972340	4,13002	2203	4300	6503	214038963	SO:0001819	synonymous_variant	7399	exon50			AF055580	CCDS1516.1, CCDS31025.1	1q41	2013-02-11			ENSG00000042781	ENSG00000042781		"""Fibronectin type III domain containing"""	12601	protein-coding gene	gene with protein product	"""usherin"""	608400		USH2		9624053, 10729113	Standard	NM_007123		Approved	RP39	uc001hku.1	O75445	OTTHUMG00000037079	ENST00000307340.3:c.9867C>T	1.37:g.215972340G>A		Somatic		Capture	Illumina HiSeq	Phase_I	214038963	NM_206933	Q5VVM9|Q6S362|Q9NS27	Silent	SNP	ENST00000307340.3	37	CCDS31025.1																																																																																				0.522	USH2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128138.1	NM_007123	
SUSD4	55061	broad.mit.edu	37	1	223536703	223536703	+	Missense_Mutation	SNP	T	T	C	rs143929528	byFrequency	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr1:223536703T>C	ENST00000343846.3	-	1	698	c.65A>G	c.(64-66)cAa>cGa	p.Q22R	SUSD4_ENST00000484758.2_Missense_Mutation_p.Q22R|SUSD4_ENST00000366878.4_Missense_Mutation_p.Q22R|SUSD4_ENST00000478605.1_5'UTR|SUSD4_ENST00000344029.6_Missense_Mutation_p.Q22R|SUSD4_ENST00000366877.3_Missense_Mutation_p.Q22R|SUSD4_ENST00000454695.2_5'UTR|SUSD4_ENST00000494793.2_Missense_Mutation_p.Q22R			Q5VX71	SUSD4_HUMAN	sushi domain containing 4	22						integral component of membrane (GO:0016021)		p.Q22R(2)|p.Q22delQ(2)		cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(5)|liver(1)|lung(5)|skin(1)	17				GBM - Glioblastoma multiforme(131;0.0611)		GGACTGAGGTtgctgctgctg	0.572																																					p.Q22R												.	.	4	Substitution - Missense(2)|Deletion - In frame(2)	large_intestine(4)	c.A65G	1						.						32.0	31.0	31.0					1																	223536703		2200	4298	6498	221603326	SO:0001583	missense	55061	exon2			AK096265	CCDS31034.1, CCDS41471.1	1q41	2008-05-14			ENSG00000143502	ENSG00000143502			25470	protein-coding gene	gene with protein product		615827				12477932	Standard	NM_017982		Approved	FLJ10052	uc001hny.4	Q5VX71	OTTHUMG00000037936	ENST00000343846.3:c.65A>G	1.37:g.223536703T>C	ENSP00000344219:p.Gln22Arg	Somatic		Capture	Illumina HiSeq	Phase_I	221603326	NM_001037175	D3DTB9|Q6UX62|Q9BSR0|Q9NWG0	Missense_Mutation	SNP	ENST00000343846.3	37	CCDS41471.1	.	.	.	.	.	.	.	.	.	.	T	15.46	2.841105	0.51057	.	.	ENSG00000143502	ENST00000343846;ENST00000366878;ENST00000542750;ENST00000271787;ENST00000344029;ENST00000342943;ENST00000366877	T;T;T	0.44482	1.29;1.29;0.92	3.77	2.58	0.30949	.	.	.	.	.	T	0.39145	0.1067	N	0.08118	0	0.18873	N	0.999987	D;D;P	0.59357	0.985;0.962;0.671	P;D;B	0.66716	0.535;0.946;0.202	T	0.20371	-1.0277	9	0.54805	T	0.06	-9.6776	7.8481	0.29437	0.0:0.0:0.4179:0.5821	.	22;22;22	B7Z369;Q5VX71-3;Q5VX71	.;.;SUSD4_HUMAN	R	22	ENSP00000344219:Q22R;ENSP00000355843:Q22R;ENSP00000339926:Q22R	ENSP00000271787:Q22R	Q	-	2	0	SUSD4	221603326	0.998000	0.40836	0.994000	0.49952	0.975000	0.68041	0.465000	0.22004	0.314000	0.23086	0.342000	0.21767	CAA		0.572	SUSD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092592.2	NM_017982	
LBR	3930	broad.mit.edu	37	1	225600291	225600291	+	Missense_Mutation	SNP	C	C	T	rs532068854		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr1:225600291C>T	ENST00000338179.2	-	8	1074	c.949G>A	c.(949-951)Gta>Ata	p.V317I	LBR_ENST00000272163.4_Missense_Mutation_p.V317I|AC092811.1_ENST00000366845.2_5'Flank	NM_194442.2	NP_919424.1	Q14739	LBR_HUMAN	lamin B receptor	317					cholesterol biosynthetic process (GO:0006695)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|integral component of nuclear inner membrane (GO:0005639)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)	chromo shadow domain binding (GO:0070087)|DNA binding (GO:0003677)|lamin binding (GO:0005521)|oxidoreductase activity, acting on the CH-CH group of donors, NAD or NADP as acceptor (GO:0016628)|poly(A) RNA binding (GO:0044822)	p.V317I(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(5)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	22	Breast(184;0.165)			GBM - Glioblastoma multiforme(131;0.117)		TGAAACTCTACGCCCTGGAAG	0.378													C|||	1	0.000199681	0.0	0.0	5008	,	,		15937	0.0		0.0	False		,,,				2504	0.001				p.V317I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G949A	1						.						74.0	75.0	74.0					1																	225600291		2203	4300	6503	223666914	SO:0001583	missense	3930	exon8			L25931	CCDS1545.1	1q42.1	2013-01-23			ENSG00000143815	ENSG00000143815		"""Tudor domain containing"""	6518	protein-coding gene	gene with protein product	"""tudor domain containing 18"""	600024				8157663, 9878250	Standard	NM_194442		Approved	DHCR14B, TDRD18	uc001hoy.3	Q14739	OTTHUMG00000037520	ENST00000338179.2:c.949G>A	1.37:g.225600291C>T	ENSP00000339883:p.Val317Ile	Somatic		Capture	Illumina HiSeq	Phase_I	223666914	NM_194442	B2R5P3|Q14740|Q53GU7|Q59FE6	Missense_Mutation	SNP	ENST00000338179.2	37	CCDS1545.1	.	.	.	.	.	.	.	.	.	.	C	4.142	0.024789	0.08054	.	.	ENSG00000143815	ENST00000272163;ENST00000338179	D;D	0.97924	-4.61;-4.61	6.07	-5.33	0.02713	.	0.707775	0.13769	N	0.364009	D	0.88400	0.6426	N	0.12471	0.22	0.09310	N	1	B	0.09022	0.002	B	0.11329	0.006	D	0.83873	0.0275	10	0.05620	T	0.96	-2.8126	3.0754	0.06245	0.0932:0.2153:0.3376:0.3539	.	317	Q14739	LBR_HUMAN	I	317	ENSP00000272163:V317I;ENSP00000339883:V317I	ENSP00000272163:V317I	V	-	1	0	LBR	223666914	0.000000	0.05858	0.000000	0.03702	0.009000	0.06853	-0.480000	0.06559	-0.628000	0.05582	-0.136000	0.14681	GTA		0.378	LBR-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091398.1	NM_002296	
TMEM63A	9725	broad.mit.edu	37	1	226034785	226034785	+	Nonsense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr1:226034785G>A	ENST00000366835.3	-	24	2650	c.2380C>T	c.(2380-2382)Cag>Tag	p.Q794*	RP11-285F7.2_ENST00000424332.1_RNA	NM_014698.2	NP_055513.2	O94886	CSCL1_HUMAN	transmembrane protein 63A	794					ion transport (GO:0006811)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)	nucleotide binding (GO:0000166)	p.Q794*(2)		breast(2)|endometrium(3)|large_intestine(5)|lung(6)|ovary(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	24	Breast(184;0.197)					GTGGCGCTCTGCGCCAAGCAC	0.667																																					p.Q794X												.	.	2	Substitution - Nonsense(2)	ovary(1)|large_intestine(1)	c.C2380T	1						.						63.0	63.0	63.0					1																	226034785		2203	4300	6503	224101408	SO:0001587	stop_gained	9725	exon24				CCDS31042.1	1q42.12	2008-02-05	2005-07-25	2005-07-25	ENSG00000196187	ENSG00000196187			29118	protein-coding gene	gene with protein product			"""KIAA0792"""	KIAA0792		9872452, 9455484	Standard	NM_014698		Approved		uc001hpm.2	O94886	OTTHUMG00000037442	ENST00000366835.3:c.2380C>T	1.37:g.226034785G>A	ENSP00000355800:p.Gln794*	Somatic		Capture	Illumina HiSeq	Phase_I	224101408	NM_014698	Q53GI7|Q5TE96|Q8N2U2	Nonsense_Mutation	SNP	ENST00000366835.3	37	CCDS31042.1	.	.	.	.	.	.	.	.	.	.	G	37	6.237780	0.97403	.	.	ENSG00000196187	ENST00000366835	.	.	.	3.46	3.46	0.39613	.	0.710219	0.13253	N	0.401902	.	.	.	.	.	.	0.32765	N	0.504565	.	.	.	.	.	.	.	.	.	.	0.06365	T	0.9	-7.7796	10.6255	0.45506	0.0:0.0:1.0:0.0	.	.	.	.	X	794	.	ENSP00000355800:Q794X	Q	-	1	0	TMEM63A	224101408	0.002000	0.14202	0.005000	0.12908	0.002000	0.02628	1.216000	0.32443	1.954000	0.56735	0.448000	0.29417	CAG		0.667	TMEM63A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091154.2	NM_014698	
LIN9	286826	broad.mit.edu	37	1	226453982	226453982	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr1:226453982G>A	ENST00000328205.5	-	9	1461	c.916C>T	c.(916-918)Cgg>Tgg	p.R306W	LIN9_ENST00000366801.1_Missense_Mutation_p.R255W|LIN9_ENST00000481685.1_Missense_Mutation_p.R271W	NM_173083.3	NP_775106.2	Q5TKA1	LIN9_HUMAN	lin-9 DREAM MuvB core complex component	290					DNA replication (GO:0006260)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|regulation of cell cycle (GO:0051726)|transcription, DNA-templated (GO:0006351)	nucleoplasm (GO:0005654)|transcriptional repressor complex (GO:0017053)		p.R306W(4)		breast(3)|endometrium(4)|kidney(2)|large_intestine(6)|lung(9)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	28	Breast(184;0.158)			GBM - Glioblastoma multiforme(131;0.131)		CGAGAAGGCCGCTGTTTTTGT	0.338																																					p.R306W	Ovarian(197;1696 2974 11248 14117)											.	.	4	Substitution - Missense(4)	endometrium(2)|large_intestine(1)|prostate(1)	c.C916T	1						.						60.0	61.0	61.0					1																	226453982		2203	4300	6503	224520605	SO:0001583	missense	286826	exon9			AY166858	CCDS1553.1	1q42	2014-07-17	2014-07-17		ENSG00000183814	ENSG00000183814			30830	protein-coding gene	gene with protein product	"""TUDOR gene similar"", ""rb related pathway actor"""	609375	"""lin-9 homolog (C. elegans)"""			15538385, 23667535	Standard	NM_173083		Approved	TGS	uc001hqa.3	Q5TKA1	OTTHUMG00000037557	ENST00000328205.5:c.916C>T	1.37:g.226453982G>A	ENSP00000329102:p.Arg306Trp	Somatic		Capture	Illumina HiSeq	Phase_I	224520605	NM_173083	Q5U5L8|Q5U7E1|Q6PI55|Q6ZTV4|Q7Z3J1	Missense_Mutation	SNP	ENST00000328205.5	37	CCDS1553.1	.	.	.	.	.	.	.	.	.	.	G	17.07	3.294073	0.60086	.	.	ENSG00000183814	ENST00000460719;ENST00000328205;ENST00000366808;ENST00000366801;ENST00000481685;ENST00000366807	.	.	.	5.59	4.67	0.58626	.	0.054512	0.64402	D	0.000001	T	0.76644	0.4016	M	0.78049	2.395	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.87578	0.995;0.998;0.998	T	0.78362	-0.2233	9	0.72032	D	0.01	.	9.7233	0.40317	0.0713:0.0:0.7911:0.1375	.	271;290;440	C9J5J4;Q5TKA1;B1ANK3	.;LIN9_HUMAN;.	W	266;306;361;255;271;440	.	ENSP00000329102:R306W	R	-	1	2	LIN9	224520605	1.000000	0.71417	1.000000	0.80357	0.329000	0.28539	4.565000	0.60836	2.648000	0.89879	0.561000	0.74099	CGG		0.338	LIN9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091523.2	NM_173083	
PARP1	142	broad.mit.edu	37	1	226564978	226564978	+	Missense_Mutation	SNP	C	C	T	rs377397890		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr1:226564978C>T	ENST00000366794.5	-	13	1915	c.1772G>A	c.(1771-1773)cGt>cAt	p.R591H		NM_001618.3	NP_001609.2	P09874	PARP1_HUMAN	poly (ADP-ribose) polymerase 1	591					base-excision repair (GO:0006284)|cellular response to insulin stimulus (GO:0032869)|DNA damage response, detection of DNA damage (GO:0042769)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|gene expression (GO:0010467)|macrophage differentiation (GO:0030225)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of SMAD protein import into nucleus (GO:0060391)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription regulatory region DNA binding (GO:2000679)|protein ADP-ribosylation (GO:0006471)|protein autoprocessing (GO:0016540)|protein poly-ADP-ribosylation (GO:0070212)|regulation of growth rate (GO:0040009)|signal transduction involved in regulation of gene expression (GO:0023019)|telomere maintenance (GO:0000723)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	membrane (GO:0016020)|nuclear envelope (GO:0005635)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|NAD binding (GO:0051287)|NAD+ ADP-ribosyltransferase activity (GO:0003950)|poly(A) RNA binding (GO:0044822)|protein N-terminus binding (GO:0047485)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)	p.R591H(1)		breast(2)|endometrium(4)|kidney(4)|large_intestine(8)|lung(15)|ovary(3)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)	44	Breast(184;0.133)			GBM - Glioblastoma multiforme(131;0.0531)		CGTACCCACACGGCCCCAGGA	0.512								Poly(ADP-ribose) polymerase (PARP) enzymes that bind to DNA																													p.R591H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1772A	1						.	C	HIS/ARG	0,4406		0,0,2203	182.0	186.0	185.0		1772	5.3	1.0	1		185	1,8599	1.2+/-3.3	0,1,4299	no	missense	PARP1	NM_001618.3	29	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging	591/1015	226564978	1,13005	2203	4300	6503	224631601	SO:0001583	missense	142	exon13			BC037545	CCDS1554.1	1q41-q42	2010-02-16	2008-07-28	2004-08-26	ENSG00000143799	ENSG00000143799	2.4.2.30	"""Poly (ADP-ribose) polymerases"""	270	protein-coding gene	gene with protein product		173870	"""ADP-ribosyltransferase (NAD+; poly (ADP-ribose) polymerase)"", ""poly (ADP-ribose) polymerase family, member 1"""	PPOL, ADPRT		10964595	Standard	NM_001618		Approved	PARP	uc001hqd.4	P09874	OTTHUMG00000037556	ENST00000366794.5:c.1772G>A	1.37:g.226564978C>T	ENSP00000355759:p.Arg591His	Somatic		Capture	Illumina HiSeq	Phase_I	224631601	NM_001618	B1ANJ4|Q8IUZ9	Missense_Mutation	SNP	ENST00000366794.5	37	CCDS1554.1	.	.	.	.	.	.	.	.	.	.	C	29.4	5.006985	0.93287	0.0	1.16E-4	ENSG00000143799	ENST00000366794	T	0.49720	0.77	5.31	5.31	0.75309	WGR domain (4);	0.000000	0.85682	D	0.000000	T	0.80592	0.4652	H	0.96576	3.845	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.87103	0.2180	10	0.87932	D	0	.	19.3286	0.94275	0.0:1.0:0.0:0.0	.	591	P09874	PARP1_HUMAN	H	591	ENSP00000355759:R591H	ENSP00000355759:R591H	R	-	2	0	PARP1	224631601	1.000000	0.71417	0.960000	0.40013	0.798000	0.45092	5.752000	0.68728	2.645000	0.89757	0.650000	0.86243	CGT		0.512	PARP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091519.1	NM_001618	
CDC42BPA	8476	broad.mit.edu	37	1	227333286	227333286	+	Silent	SNP	A	A	G			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr1:227333286A>G	ENST00000366769.3	-	8	2338	c.1047T>C	c.(1045-1047)gaT>gaC	p.D349D	CDC42BPA_ENST00000366764.2_Silent_p.D349D|CDC42BPA_ENST00000366765.3_Silent_p.D349D|CDC42BPA_ENST00000366766.2_Silent_p.D349D|CDC42BPA_ENST00000366767.3_Silent_p.D349D|CDC42BPA_ENST00000334218.5_Silent_p.D349D|CDC42BPA_ENST00000535525.1_Silent_p.D349D	NM_003607.3	NP_003598.2			CDC42 binding protein kinase alpha (DMPK-like)									p.D349D(2)		NS(1)|breast(4)|cervix(1)|endometrium(8)|kidney(8)|large_intestine(12)|lung(32)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|stomach(3)|urinary_tract(2)	77		all_cancers(173;0.156)|Prostate(94;0.0792)				TCCGAATATTATCCCAATCAA	0.343																																					p.D349D												.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.T1047C	1						.						129.0	124.0	126.0					1																	227333286		2203	4300	6503	225399909	SO:0001819	synonymous_variant	8476	exon8			U59305	CCDS1558.1, CCDS1559.1	1q42.11	2011-11-23	2001-11-28		ENSG00000143776	ENSG00000143776			1737	protein-coding gene	gene with protein product	"""myotonic dystrophy kinase-related Cdc42-binding kinase"""	603412	"""CDC42-binding protein kinase alpha (DMPK-like)"""				Standard	NM_003607		Approved	MRCKA, PK428, FLJ23347, KIAA0451, MRCK	uc001hqr.3	Q5VT25	OTTHUMG00000037618	ENST00000366769.3:c.1047T>C	1.37:g.227333286A>G		Somatic		Capture	Illumina HiSeq	Phase_I	225399909	NM_014826		Silent	SNP	ENST00000366769.3	37	CCDS1558.1																																																																																				0.343	CDC42BPA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091696.1	NM_014826	
ACTA1	58	broad.mit.edu	37	1	229567638	229567638	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr1:229567638C>T	ENST00000366684.3	-	6	922	c.820G>A	c.(820-822)Gcg>Acg	p.A274T	ACTA1_ENST00000366683.2_Missense_Mutation_p.A186T	NM_001100.3	NP_001091.1	P68133	ACTS_HUMAN	actin, alpha 1, skeletal muscle	274			A -> E (in NEM3).		cell growth (GO:0016049)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|response to extracellular stimulus (GO:0009991)|response to lithium ion (GO:0010226)|response to mechanical stimulus (GO:0009612)|response to steroid hormone (GO:0048545)|skeletal muscle fiber adaptation (GO:0043503)|skeletal muscle fiber development (GO:0048741)|skeletal muscle thin filament assembly (GO:0030240)	actin cytoskeleton (GO:0015629)|actin filament (GO:0005884)|blood microparticle (GO:0072562)|cytosol (GO:0005829)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|sarcomere (GO:0030017)|stress fiber (GO:0001725)|striated muscle thin filament (GO:0005865)	ADP binding (GO:0043531)|ATP binding (GO:0005524)|myosin binding (GO:0017022)|structural constituent of cytoskeleton (GO:0005200)	p.A274T(1)		endometrium(4)|large_intestine(4)|lung(18)|prostate(1)|urinary_tract(1)	28	Breast(184;0.0858)|Ovarian(103;0.103)	Prostate(94;0.167)				TGAATGCCCGCCGACTCCATA	0.682																																					p.A274T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G820A	1						.						101.0	93.0	96.0					1																	229567638		2203	4300	6503	227634261	SO:0001583	missense	58	exon6			J00068	CCDS1578.1	1q42.13	2014-09-17			ENSG00000143632	ENSG00000143632			129	protein-coding gene	gene with protein product	"""nemaline myopathy type 3"""	102610		ACTA		10072583, 6865942	Standard	NM_001100		Approved	NEM3	uc001htm.3	P68133	OTTHUMG00000038006	ENST00000366684.3:c.820G>A	1.37:g.229567638C>T	ENSP00000355645:p.Ala274Thr	Somatic		Capture	Illumina HiSeq	Phase_I	227634261	NM_001100	P02568|P99020|Q5T8M9	Missense_Mutation	SNP	ENST00000366684.3	37	CCDS1578.1	.	.	.	.	.	.	.	.	.	.	C	9.483	1.098650	0.20552	.	.	ENSG00000143632	ENST00000366684;ENST00000308794;ENST00000366683;ENST00000366682	D;D	0.94723	-3.5;-3.5	4.46	3.55	0.40652	.	0.000000	0.85682	D	0.000000	D	0.89798	0.6819	L	0.29908	0.895	0.58432	D	0.999998	B	0.02656	0.0	B	0.06405	0.002	D	0.86154	0.1589	10	0.62326	D	0.03	.	12.4405	0.55621	0.0:0.9183:0.0:0.0817	.	274	P68133	ACTS_HUMAN	T	274;184;186;239	ENSP00000355645:A274T;ENSP00000355644:A186T	ENSP00000312351:A184T	A	-	1	0	ACTA1	227634261	1.000000	0.71417	0.935000	0.37517	0.405000	0.30901	5.716000	0.68437	1.097000	0.41459	-0.251000	0.11542	GCG		0.682	ACTA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092781.1	NM_001100	
NUP133	55746	broad.mit.edu	37	1	229600595	229600595	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr1:229600595G>A	ENST00000261396.3	-	18	2418	c.2327C>T	c.(2326-2328)aCg>aTg	p.T776M	NUP133_ENST00000537506.1_Missense_Mutation_p.T760M	NM_018230.2	NP_060700.2	Q8WUM0	NU133_HUMAN	nucleoporin 133kDa	776					carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA export from nucleus (GO:0006406)|nuclear pore organization (GO:0006999)|paraxial mesoderm development (GO:0048339)|protein transport (GO:0015031)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytosol (GO:0005829)|kinetochore (GO:0000776)|membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear pore (GO:0005643)|nuclear pore outer ring (GO:0031080)	nucleocytoplasmic transporter activity (GO:0005487)	p.T776M(1)		NS(1)|breast(7)|endometrium(1)|kidney(6)|large_intestine(9)|lung(20)|ovary(1)|pancreas(1)|prostate(3)|skin(3)|stomach(4)	56	Breast(184;0.104)|Ovarian(103;0.249)	Prostate(94;0.167)				TATTATTACCGTTCGGATGCC	0.458																																					p.T776M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C2327T	1						.						121.0	99.0	107.0					1																	229600595		2203	4300	6503	227667218	SO:0001583	missense	55746	exon18				CCDS1579.1	1q42.13	2008-02-05	2002-08-29		ENSG00000069248	ENSG00000069248			18016	protein-coding gene	gene with protein product		607613	"""nucleoporin 133kD"""			11684705	Standard	NM_018230		Approved	FLJ10814	uc001htn.3	Q8WUM0	OTTHUMG00000039462	ENST00000261396.3:c.2327C>T	1.37:g.229600595G>A	ENSP00000261396:p.Thr776Met	Somatic		Capture	Illumina HiSeq	Phase_I	227667218	NM_018230	B2RAZ8|Q5T8N0|Q9H9W2|Q9NV71|Q9NVC4	Missense_Mutation	SNP	ENST00000261396.3	37	CCDS1579.1	.	.	.	.	.	.	.	.	.	.	G	17.32	3.360619	0.61403	.	.	ENSG00000069248	ENST00000366681;ENST00000261396;ENST00000366679;ENST00000537506	T;T;T	0.25579	1.79;1.84;1.79	6.17	5.27	0.74061	Nucleoporin, Nup133/Nup155-like, C-terminal (1);	0.263259	0.43416	D	0.000568	T	0.38931	0.1059	L	0.59436	1.845	0.26906	N	0.967016	D	0.53462	0.96	P	0.52554	0.702	T	0.27673	-1.0067	10	0.45353	T	0.12	-4.5505	15.5517	0.76158	0.0655:0.0:0.9345:0.0	.	776	Q8WUM0	NU133_HUMAN	M	776;776;776;760	ENSP00000261396:T776M;ENSP00000355640:T776M;ENSP00000443496:T760M	ENSP00000261396:T776M	T	-	2	0	NUP133	227667218	1.000000	0.71417	0.923000	0.36655	0.720000	0.41350	5.412000	0.66392	1.635000	0.50512	0.655000	0.94253	ACG		0.458	NUP133-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095224.1	NM_018230	
TTC13	79573	broad.mit.edu	37	1	231090108	231090108	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr1:231090108C>T	ENST00000366661.4	-	4	491	c.484G>A	c.(484-486)Gca>Aca	p.A162T	TTC13_ENST00000366662.4_Missense_Mutation_p.A162T|TTC13_ENST00000414259.1_Missense_Mutation_p.A162T	NM_024525.4	NP_078801.3	Q8NBP0	TTC13_HUMAN	tetratricopeptide repeat domain 13	162								p.A162T(1)		central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(9)|lung(16)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	39	Breast(184;0.0871)|Ovarian(103;0.183)	Prostate(94;0.167)		COAD - Colon adenocarcinoma(196;0.243)		TGCCGTATTGCTTCATCATAC	0.299																																					p.A162T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G484A	1						.						57.0	56.0	57.0					1																	231090108		2203	4298	6501	229156731	SO:0001583	missense	79573	exon4				CCDS1588.1, CCDS44332.1, CCDS44332.2	1q42.2	2013-01-10			ENSG00000143643	ENSG00000143643		"""Tetratricopeptide (TTC) repeat domain containing"""	26204	protein-coding gene	gene with protein product							Standard	NM_024525		Approved	FLJ22584	uc001huf.4	Q8NBP0	OTTHUMG00000037788	ENST00000366661.4:c.484G>A	1.37:g.231090108C>T	ENSP00000355621:p.Ala162Thr	Somatic		Capture	Illumina HiSeq	Phase_I	229156731	NM_024525	B1AQI1|B1AQI2|Q8IVP8|Q8NBI0|Q8ND20	Missense_Mutation	SNP	ENST00000366661.4	37	CCDS1588.1	.	.	.	.	.	.	.	.	.	.	C	19.27	3.795295	0.70452	.	.	ENSG00000143643	ENST00000366661;ENST00000366662;ENST00000414259;ENST00000522399	T;T;T;D	0.94232	-1.25;0.58;0.56;-3.38	5.56	5.56	0.83823	Tetratricopeptide-like helical (1);Tetratricopeptide repeat-containing (1);	0.052226	0.85682	D	0.000000	D	0.89441	0.6716	N	0.24115	0.695	0.80722	D	1	B;B;B	0.16802	0.007;0.011;0.019	B;B;B	0.17098	0.004;0.007;0.017	D	0.85095	0.0954	10	0.87932	D	0	-0.1856	18.6822	0.91549	0.0:1.0:0.0:0.0	.	162;162;162	E9PGV4;Q8NBP0-2;Q8NBP0	.;.;TTC13_HUMAN	T	162;162;162;105	ENSP00000355621:A162T;ENSP00000355622:A162T;ENSP00000416631:A162T;ENSP00000428622:A105T	ENSP00000355621:A162T	A	-	1	0	TTC13	229156731	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	5.864000	0.69575	2.774000	0.95407	0.655000	0.94253	GCA		0.299	TTC13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092229.2	NM_024525	
TRIM67	440730	broad.mit.edu	37	1	231298739	231298739	+	Silent	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr1:231298739C>T	ENST00000366653.5	+	1	24	c.24C>T	c.(22-24)ccC>ccT	p.P8P	TRIM67_ENST00000449018.3_Silent_p.P8P|TRIM67_ENST00000444294.3_Silent_p.P8P|TRIM67_ENST00000366652.2_Silent_p.P8P			Q6ZTA4	TRI67_HUMAN	tripartite motif containing 67	8					negative regulation of Ras protein signal transduction (GO:0046580)|positive regulation of neuron projection development (GO:0010976)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	zinc ion binding (GO:0008270)	p.P8P(1)		breast(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(10)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	29	Breast(184;0.0871)	all_cancers(173;0.189)|Prostate(94;0.167)				TGAAGTGTCCCGTGTGCGGCT	0.667																																					p.P8P												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C24T	1						.						34.0	37.0	36.0					1																	231298739		2042	4202	6244	229365362	SO:0001819	synonymous_variant	440730	exon1			AK126782	CCDS44333.1, CCDS73048.1	1q42.2	2014-02-17	2011-01-25		ENSG00000119283	ENSG00000119283		"""Tripartite motif containing / Tripartite motif containing"", ""Fibronectin type III domain containing"", ""RING-type (C3HC4) zinc fingers"""	31859	protein-coding gene	gene with protein product		610584	"""tripartite motif-containing 67"""				Standard	NM_001004342		Approved	TNL	uc009xfn.1	Q6ZTA4	OTTHUMG00000037958	ENST00000366653.5:c.24C>T	1.37:g.231298739C>T		Somatic		Capture	Illumina HiSeq	Phase_I	229365362	NM_001004342	Q5TER7|Q5TER8|Q7Z4K7	Silent	SNP	ENST00000366653.5	37	CCDS44333.1																																																																																				0.667	TRIM67-001	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000092649.3	NM_001004342	
SIPA1L2	57568	broad.mit.edu	37	1	232561526	232561526	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr1:232561526C>A	ENST00000366630.1	-	17	4797	c.4439G>T	c.(4438-4440)aGg>aTg	p.R1480M	SIPA1L2_ENST00000308942.4_Missense_Mutation_p.R554M|SIPA1L2_ENST00000262861.4_Missense_Mutation_p.R1480M			Q9P2F8	SI1L2_HUMAN	signal-induced proliferation-associated 1 like 2	1480					regulation of small GTPase mediated signal transduction (GO:0051056)		GTPase activator activity (GO:0005096)	p.R1480M(1)		NS(1)|breast(5)|central_nervous_system(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(13)|lung(49)|ovary(2)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	103		all_cancers(173;0.00605)|Prostate(94;0.128)|all_epithelial(177;0.186)				AAGCGACCTCCTTGGAGACAG	0.537																																					p.R1480M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G4439T	1						.						55.0	64.0	61.0					1																	232561526		2126	4243	6369	230628149	SO:0001583	missense	57568	exon16			AB037810	CCDS41474.1	1q42.2	2008-02-05			ENSG00000116991	ENSG00000116991			23800	protein-coding gene	gene with protein product		611609					Standard	NM_020808		Approved	KIAA1389	uc001hvg.3	Q9P2F8	OTTHUMG00000037820	ENST00000366630.1:c.4439G>T	1.37:g.232561526C>A	ENSP00000355589:p.Arg1480Met	Somatic		Capture	Illumina HiSeq	Phase_I	230628149	NM_020808	Q2TV88|Q5VXR7|Q5VXR8|Q641Q4|Q8NA38|Q96DZ3|Q9H9F6	Missense_Mutation	SNP	ENST00000366630.1	37	CCDS41474.1	.	.	.	.	.	.	.	.	.	.	C	23.8	4.460514	0.84317	.	.	ENSG00000116991	ENST00000366630;ENST00000262861;ENST00000308942	T;T;T	0.43688	0.94;0.94;0.94	5.66	4.76	0.60689	.	0.223011	0.38005	N	0.001856	T	0.59770	0.2218	M	0.70595	2.14	0.47153	D	0.999332	P;D	0.63046	0.912;0.992	P;P	0.59761	0.714;0.863	T	0.65631	-0.6121	10	0.87932	D	0	-24.9692	14.7211	0.69308	0.0:0.9306:0.0:0.0694	.	1480;554	Q9P2F8;Q9P2F8-2	SI1L2_HUMAN;.	M	1480;1480;554	ENSP00000355589:R1480M;ENSP00000262861:R1480M;ENSP00000309102:R554M	ENSP00000262861:R1480M	R	-	2	0	SIPA1L2	230628149	0.906000	0.30813	0.111000	0.21465	0.894000	0.52154	5.744000	0.68664	1.537000	0.49254	0.650000	0.86243	AGG		0.537	SIPA1L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092318.1	XM_045839	
SIPA1L2	57568	broad.mit.edu	37	1	232601052	232601052	+	Missense_Mutation	SNP	A	A	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr1:232601052A>T	ENST00000366630.1	-	8	2712	c.2354T>A	c.(2353-2355)aTc>aAc	p.I785N	SIPA1L2_ENST00000308942.4_5'Flank|SIPA1L2_ENST00000262861.4_Missense_Mutation_p.I785N			Q9P2F8	SI1L2_HUMAN	signal-induced proliferation-associated 1 like 2	785	Rap-GAP. {ECO:0000255|PROSITE- ProRule:PRU00165}.				regulation of small GTPase mediated signal transduction (GO:0051056)		GTPase activator activity (GO:0005096)	p.I785N(1)		NS(1)|breast(5)|central_nervous_system(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(13)|lung(49)|ovary(2)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	103		all_cancers(173;0.00605)|Prostate(94;0.128)|all_epithelial(177;0.186)				TTCTGCATTGATTACTTTGGC	0.463																																					p.I785N												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T2354A	1						.						89.0	91.0	90.0					1																	232601052		1954	4189	6143	230667675	SO:0001583	missense	57568	exon7			AB037810	CCDS41474.1	1q42.2	2008-02-05			ENSG00000116991	ENSG00000116991			23800	protein-coding gene	gene with protein product		611609					Standard	NM_020808		Approved	KIAA1389	uc001hvg.3	Q9P2F8	OTTHUMG00000037820	ENST00000366630.1:c.2354T>A	1.37:g.232601052A>T	ENSP00000355589:p.Ile785Asn	Somatic		Capture	Illumina HiSeq	Phase_I	230667675	NM_020808	Q2TV88|Q5VXR7|Q5VXR8|Q641Q4|Q8NA38|Q96DZ3|Q9H9F6	Missense_Mutation	SNP	ENST00000366630.1	37	CCDS41474.1	.	.	.	.	.	.	.	.	.	.	A	25.2	4.610168	0.87258	.	.	ENSG00000116991	ENST00000366630;ENST00000262861	D;D	0.96554	-4.05;-4.05	5.8	5.8	0.92144	Rap/ran-GAP (2);	0.000000	0.85682	D	0.000000	D	0.98720	0.9570	H	0.95574	3.69	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.99737	1.1014	10	0.87932	D	0	-32.6428	16.143	0.81539	1.0:0.0:0.0:0.0	.	785	Q9P2F8	SI1L2_HUMAN	N	785	ENSP00000355589:I785N;ENSP00000262861:I785N	ENSP00000262861:I785N	I	-	2	0	SIPA1L2	230667675	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	9.339000	0.96797	2.206000	0.71126	0.528000	0.53228	ATC		0.463	SIPA1L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092318.1	XM_045839	
PCNXL2	80003	broad.mit.edu	37	1	233393964	233393964	+	Silent	SNP	A	A	G			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr1:233393964A>G	ENST00000258229.9	-	5	1878	c.1644T>C	c.(1642-1644)atT>atC	p.I548I	PCNXL2_ENST00000430153.1_5'UTR	NM_014801.3	NP_055616.3	A6NKB5	PCX2_HUMAN	pecanex-like 2 (Drosophila)	548						integral component of membrane (GO:0016021)		p.I548I(1)		NS(1)|autonomic_ganglia(1)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(16)|kidney(7)|large_intestine(19)|lung(30)|pancreas(1)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	86		all_cancers(173;0.0347)|Prostate(94;0.137)				TATCGTTAACAATTTCTGCAG	0.458																																					p.I548I												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.T1644C	1						.						112.0	109.0	110.0					1																	233393964		1984	4165	6149	231460587	SO:0001819	synonymous_variant	80003	exon5			AK055374	CCDS44335.1	1q42.2	2008-02-05	2001-11-28		ENSG00000135749	ENSG00000135749			8736	protein-coding gene	gene with protein product			"""pecanex (Drosophila)-like 2"""			12477932	Standard	NM_014801		Approved	KIAA0435, FLJ11383	uc001hvl.2	A6NKB5	OTTHUMG00000037824	ENST00000258229.9:c.1644T>C	1.37:g.233393964A>G		Somatic		Capture	Illumina HiSeq	Phase_I	231460587	NM_014801	O43162|Q5T9Z8|Q5TDF1|Q8TEP4|Q96HP9|Q9HAL8	Silent	SNP	ENST00000258229.9	37	CCDS44335.1																																																																																				0.458	PCNXL2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092480.3	NM_014801	
PCNXL2	80003	broad.mit.edu	37	1	233394783	233394783	+	Silent	SNP	C	C	T	rs371142631		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr1:233394783C>T	ENST00000258229.9	-	5	1059	c.825G>A	c.(823-825)ccG>ccA	p.P275P	PCNXL2_ENST00000430153.1_De_novo_Start_OutOfFrame	NM_014801.3	NP_055616.3	A6NKB5	PCX2_HUMAN	pecanex-like 2 (Drosophila)	275						integral component of membrane (GO:0016021)		p.P275P(2)		NS(1)|autonomic_ganglia(1)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(16)|kidney(7)|large_intestine(19)|lung(30)|pancreas(1)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	86		all_cancers(173;0.0347)|Prostate(94;0.137)				CACTCCCCCACGGCTGGAAAG	0.522																																					p.P275P												.	.	2	Substitution - coding silent(2)	large_intestine(1)|lung(1)	c.G825A	1						.	C		0,3856		0,0,1928	56.0	59.0	58.0		825	-9.2	0.0	1		58	1,8241		0,1,4120	no	coding-synonymous	PCNXL2	NM_014801.3		0,1,6048	TT,TC,CC		0.0121,0.0,0.0083		275/2138	233394783	1,12097	1928	4121	6049	231461406	SO:0001819	synonymous_variant	80003	exon5			AK055374	CCDS44335.1	1q42.2	2008-02-05	2001-11-28		ENSG00000135749	ENSG00000135749			8736	protein-coding gene	gene with protein product			"""pecanex (Drosophila)-like 2"""			12477932	Standard	NM_014801		Approved	KIAA0435, FLJ11383	uc001hvl.2	A6NKB5	OTTHUMG00000037824	ENST00000258229.9:c.825G>A	1.37:g.233394783C>T		Somatic		Capture	Illumina HiSeq	Phase_I	231461406	NM_014801	O43162|Q5T9Z8|Q5TDF1|Q8TEP4|Q96HP9|Q9HAL8	Silent	SNP	ENST00000258229.9	37	CCDS44335.1																																																																																				0.522	PCNXL2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092480.3	NM_014801	
SLC35F3	148641	broad.mit.edu	37	1	234367267	234367267	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr1:234367267G>T	ENST00000366617.3	+	2	409	c.181G>T	c.(181-183)Gcg>Tcg	p.A61S	SLC35F3_ENST00000366618.3_Missense_Mutation_p.A130S			Q8IY50	S35F3_HUMAN	solute carrier family 35, member F3	61					thiamine transport (GO:0015888)	integral component of membrane (GO:0016021)		p.A130S(1)		breast(2)|endometrium(3)|kidney(2)|large_intestine(7)|lung(13)|ovary(2)|skin(2)|urinary_tract(1)	32	Ovarian(103;0.0454)	all_cancers(173;0.145)|Prostate(94;0.0885)	OV - Ovarian serous cystadenocarcinoma(106;0.00531)			GTGCTCCCGGGCGCAACTCAA	0.731																																					p.A130S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G388T	1						.						86.0	76.0	79.0					1																	234367267		2203	4299	6502	232433890	SO:0001583	missense	148641	exon3				CCDS1600.1, CCDS73050.1	1q42.3	2013-05-22			ENSG00000183780	ENSG00000183780		"""Solute carriers"""	23616	protein-coding gene	gene with protein product							Standard	XM_005273070		Approved	FLJ37712	uc001hvy.1	Q8IY50	OTTHUMG00000037929	ENST00000366617.3:c.181G>T	1.37:g.234367267G>T	ENSP00000355576:p.Ala61Ser	Somatic		Capture	Illumina HiSeq	Phase_I	232433890	NM_173508	Q5TDD6|Q8N9C9	Missense_Mutation	SNP	ENST00000366617.3	37		.	.	.	.	.	.	.	.	.	.	G	3.473	-0.107449	0.06924	.	.	ENSG00000183780	ENST00000366618;ENST00000366617	T;T	0.41065	1.01;1.03	4.57	3.64	0.41730	.	0.741877	0.13597	N	0.376157	T	0.16085	0.0387	N	0.03608	-0.345	0.09310	N	1	B;B	0.14438	0.006;0.01	B;B	0.21151	0.006;0.033	T	0.32561	-0.9902	10	0.05833	T	0.94	-0.5031	5.6972	0.17863	0.172:0.1765:0.6515:0.0	.	61;130	Q8IY50;Q8IY50-2	S35F3_HUMAN;.	S	130;61	ENSP00000355577:A130S;ENSP00000355576:A61S	ENSP00000355576:A61S	A	+	1	0	SLC35F3	232433890	0.417000	0.25432	0.118000	0.21660	0.458000	0.32498	3.695000	0.54749	1.090000	0.41315	0.491000	0.48974	GCG		0.731	SLC35F3-002	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000128322.1	NM_173508	
MTR	4548	broad.mit.edu	37	1	237054552	237054552	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr1:237054552G>A	ENST00000366577.5	+	29	3521	c.3127G>A	c.(3127-3129)Gac>Aac	p.D1043N	MTR_ENST00000535889.1_Missense_Mutation_p.D992N	NM_000254.2	NP_000245.2	Q99707	METH_HUMAN	5-methyltetrahydrofolate-homocysteine methyltransferase	1043	AdoMet activation. {ECO:0000255|PROSITE- ProRule:PRU00346}.				cellular nitrogen compound metabolic process (GO:0034641)|cobalamin metabolic process (GO:0009235)|methylation (GO:0032259)|nervous system development (GO:0007399)|pteridine-containing compound metabolic process (GO:0042558)|small molecule metabolic process (GO:0044281)|sulfur amino acid metabolic process (GO:0000096)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)	cobalamin binding (GO:0031419)|methionine synthase activity (GO:0008705)|S-adenosylmethionine-homocysteine S-methyltransferase activity (GO:0008898)|zinc ion binding (GO:0008270)	p.D1043N(1)		breast(4)|central_nervous_system(1)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(8)|lung(30)|ovary(1)|pancreas(1)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	67	Ovarian(103;0.0634)|Breast(184;0.221)	all_cancers(173;2.79e-22)|all_epithelial(177;4.84e-14)|Breast(1374;0.00123)|Prostate(94;0.0181)|Lung SC(1967;0.0262)|Acute lymphoblastic leukemia(190;0.117)	OV - Ovarian serous cystadenocarcinoma(106;0.0106)	KIRC - Kidney renal clear cell carcinoma(1967;0.248)	Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)|L-Methionine(DB00134)|Tetrahydrofolic acid(DB00116)	TATCCAAGACGACATTCACCT	0.542																																					p.D1043N												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G3127A	1						.						123.0	121.0	122.0					1																	237054552		2203	4300	6503	235121175	SO:0001583	missense	4548	exon29			U73338	CCDS1614.1, CCDS73054.1	1q43	2011-05-12			ENSG00000116984	ENSG00000116984	2.1.1.13		7468	protein-coding gene	gene with protein product		156570				8968735	Standard	NM_000254		Approved	cblG	uc001hyi.4	Q99707	OTTHUMG00000040060	ENST00000366577.5:c.3127G>A	1.37:g.237054552G>A	ENSP00000355536:p.Asp1043Asn	Somatic		Capture	Illumina HiSeq	Phase_I	235121175	NM_000254	A1L4N8|A9Z1W4|B9EGF7|Q99713|Q99723	Missense_Mutation	SNP	ENST00000366577.5	37	CCDS1614.1	.	.	.	.	.	.	.	.	.	.	G	27.7	4.850674	0.91277	.	.	ENSG00000116984	ENST00000417743;ENST00000366577;ENST00000535889;ENST00000366576	T;T;T	0.79352	-1.26;-1.26;-1.26	5.48	5.48	0.80851	Vitamin B12-dependent methionine synthase, activation domain (3);	0.105697	0.64402	D	0.000007	D	0.88108	0.6348	M	0.71296	2.17	0.58432	D	0.999992	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	D	0.88903	0.3354	10	0.87932	D	0	-25.9126	19.3522	0.94393	0.0:0.0:1.0:0.0	.	1043;992;1043	B7ZLW8;B7ZLW7;Q99707	.;.;METH_HUMAN	N	897;1043;992;597	ENSP00000355536:D1043N;ENSP00000441845:D992N;ENSP00000355535:D597N	ENSP00000355535:D597N	D	+	1	0	MTR	235121175	1.000000	0.71417	0.550000	0.28217	0.615000	0.37417	8.893000	0.92498	2.566000	0.86566	0.561000	0.74099	GAC		0.542	MTR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096632.2	NM_000254	
RYR2	6262	broad.mit.edu	37	1	237494214	237494214	+	Silent	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr1:237494214C>T	ENST00000366574.2	+	3	522	c.205C>T	c.(205-207)Ctg>Ttg	p.L69L	RYR2_ENST00000360064.6_Silent_p.C66C|RYR2_ENST00000542537.1_Silent_p.L53L	NM_001035.2	NP_001026.2	Q92736	RYR2_HUMAN	ryanodine receptor 2 (cardiac)	69					BMP signaling pathway (GO:0030509)|calcium ion transport (GO:0006816)|calcium ion transport into cytosol (GO:0060402)|calcium-mediated signaling (GO:0019722)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle contraction (GO:0060048)|cardiac muscle hypertrophy (GO:0003300)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cellular calcium ion homeostasis (GO:0006874)|cellular response to caffeine (GO:0071313)|cellular response to epinephrine stimulus (GO:0071872)|cytosolic calcium ion homeostasis (GO:0051480)|detection of calcium ion (GO:0005513)|embryonic heart tube morphogenesis (GO:0003143)|establishment of protein localization to endoplasmic reticulum (GO:0072599)|ion transmembrane transport (GO:0034220)|left ventricular cardiac muscle tissue morphogenesis (GO:0003220)|positive regulation of calcium-transporting ATPase activity (GO:1901896)|positive regulation of heart rate (GO:0010460)|positive regulation of ryanodine-sensitive calcium-release channel activity by adrenergic receptor signaling pathway involved in positive regulation of cardiac muscle contraction (GO:0086094)|positive regulation of sequestering of calcium ion (GO:0051284)|Purkinje myocyte to ventricular cardiac muscle cell signaling (GO:0086029)|regulation of cardiac muscle contraction (GO:0055117)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of heart rate (GO:0002027)|release of sequestered calcium ion into cytosol (GO:0051209)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|response to redox state (GO:0051775)|sarcoplasmic reticulum calcium ion transport (GO:0070296)|transmembrane transport (GO:0055085)|type B pancreatic cell apoptotic process (GO:0097050)|ventricular cardiac muscle cell action potential (GO:0086005)	calcium channel complex (GO:0034704)|extracellular vesicular exosome (GO:0070062)|junctional sarcoplasmic reticulum membrane (GO:0014701)|membrane (GO:0016020)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|Z disc (GO:0030018)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-induced calcium release activity (GO:0048763)|calcium-release channel activity (GO:0015278)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|intracellular ligand-gated calcium channel activity (GO:0005218)|ion channel binding (GO:0044325)|protein kinase A catalytic subunit binding (GO:0034236)|protein kinase A regulatory subunit binding (GO:0034237)|ryanodine-sensitive calcium-release channel activity (GO:0005219)|suramin binding (GO:0043924)	p.C66C(1)		NS(4)|breast(8)|central_nervous_system(11)|cervix(2)|endometrium(39)|haematopoietic_and_lymphoid_tissue(5)|kidney(17)|large_intestine(83)|liver(4)|lung(353)|ovary(18)|pancreas(5)|prostate(12)|skin(8)|stomach(1)|upper_aerodigestive_tract(12)|urinary_tract(4)	586	Ovarian(103;0.103)	all_cancers(173;0.000368)|Melanoma(53;0.0179)|all_epithelial(177;0.0225)	OV - Ovarian serous cystadenocarcinoma(106;0.00606)			CACCTTTGTGCTGGAGCAGTC	0.522																																					p.L69L												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C205T	1						.						90.0	93.0	92.0					1																	237494214		2065	4239	6304	235560837	SO:0001819	synonymous_variant	6262	exon3			X91869	CCDS55691.1	1q43	2014-09-17			ENSG00000198626	ENSG00000198626		"""Ion channels / Ryanodine receptors"", ""EF-hand domain containing"""	10484	protein-coding gene	gene with protein product		180902	"""arrhythmogenic right ventricular dysplasia 2"""	ARVD2		2380170, 8406504, 11159936	Standard	NM_001035		Approved	ARVC2, VTSIP	uc001hyl.1	Q92736	OTTHUMG00000039543	ENST00000366574.2:c.205C>T	1.37:g.237494214C>T		Somatic		Capture	Illumina HiSeq	Phase_I	235560837	NM_001035	Q15411|Q546N8|Q5T3P2	Silent	SNP	ENST00000366574.2	37	CCDS55691.1																																																																																				0.522	RYR2-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095402.2	NM_001035	
CHRM3	1131	broad.mit.edu	37	1	240070951	240070951	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr1:240070951A>G	ENST00000255380.4	+	5	979	c.200A>G	c.(199-201)cAa>cGa	p.Q67R		NM_000740.2	NP_000731.1	P20309	ACM3_HUMAN	cholinergic receptor, muscarinic 3	67					cell proliferation (GO:0008283)|cellular protein modification process (GO:0006464)|energy reserve metabolic process (GO:0006112)|G-protein coupled acetylcholine receptor signaling pathway (GO:0007213)|G-protein coupled receptor signaling pathway (GO:0007186)|nervous system development (GO:0007399)|positive regulation of smooth muscle contraction (GO:0045987)|regulation of insulin secretion (GO:0050796)|regulation of vascular smooth muscle contraction (GO:0003056)|saliva secretion (GO:0046541)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|smooth muscle contraction (GO:0006939)	asymmetric synapse (GO:0032279)|axon terminus (GO:0043679)|cell junction (GO:0030054)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	acetylcholine binding (GO:0042166)|drug binding (GO:0008144)|G-protein coupled acetylcholine receptor activity (GO:0016907)|phosphatidylinositol phospholipase C activity (GO:0004435)|receptor activity (GO:0004872)	p.Q67R(1)		breast(3)|endometrium(5)|kidney(2)|large_intestine(4)|lung(19)|ovary(4)|prostate(1)|skin(12)|upper_aerodigestive_tract(1)	51	Ovarian(103;0.127)	all_cancers(173;0.00567)|all_neural(198;0.203)	OV - Ovarian serous cystadenocarcinoma(106;0.00989)		Aclidinium(DB08897)|Amitriptyline(DB00321)|Amoxapine(DB00543)|Anisotropine Methylbromide(DB00517)|Aripiprazole(DB01238)|Atropine(DB00572)|Brompheniramine(DB00835)|Cevimeline(DB00185)|Chlorpromazine(DB00477)|Chlorprothixene(DB01239)|Cinnarizine(DB00568)|Clozapine(DB00363)|Cryptenamine(DB00785)|Cyproheptadine(DB00434)|Darifenacin(DB00496)|Desipramine(DB01151)|Diphemanil Methylsulfate(DB00729)|Diphenidol(DB01231)|Disopyramide(DB00280)|Doxepin(DB01142)|Fesoterodine(DB06702)|Glycopyrrolate(DB00986)|Homatropine Methylbromide(DB00725)|Hyoscyamine(DB00424)|Imipramine(DB00458)|Ipratropium bromide(DB00332)|Isopropamide(DB01625)|Ketamine(DB01221)|Loxapine(DB00408)|Maprotiline(DB00934)|Mepenzolate(DB04843)|Methacholine(DB06709)|Methotrimeprazine(DB01403)|Methylscopolamine bromide(DB00462)|Metixene(DB00340)|Mivacurium(DB01226)|Nicardipine(DB00622)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Oxybutynin(DB01062)|Oxyphencyclimine(DB00383)|Pancuronium(DB01337)|Paroxetine(DB00715)|Pethidine(DB00454)|Pilocarpine(DB01085)|Pipecuronium(DB01338)|Procyclidine(DB00387)|Promazine(DB00420)|Promethazine(DB01069)|Propiomazine(DB00777)|Quetiapine(DB01224)|Scopolamine(DB00747)|Solifenacin(DB01591)|Succinylcholine(DB00202)|Tiotropium(DB01409)|Tolterodine(DB01036)|Tramadol(DB00193)|Trihexyphenidyl(DB00376)|Trimipramine(DB00726)|Tropicamide(DB00809)|Ziprasidone(DB00246)	ACCGTCTGGCAAGTGGTCTTC	0.512																																					p.Q67R												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A200G	1						.						140.0	122.0	128.0					1																	240070951		2203	4300	6503	238137574	SO:0001583	missense	1131	exon5			U29589	CCDS1616.1	1q43	2012-09-20			ENSG00000133019	ENSG00000133019		"""Cholinergic receptors"", ""GPCR / Class A : Cholinergic receptors, muscarinic"""	1952	protein-coding gene	gene with protein product	"""acetylcholine receptor, muscarinic 3"""	118494					Standard	XM_005273032		Approved		uc001hyp.3	P20309	OTTHUMG00000039649	ENST00000255380.4:c.200A>G	1.37:g.240070951A>G	ENSP00000255380:p.Gln67Arg	Somatic		Capture	Illumina HiSeq	Phase_I	238137574	NM_000740	Q0VAJ8|Q4QRI3|Q5VXY2|Q9HB60	Missense_Mutation	SNP	ENST00000255380.4	37	CCDS1616.1	.	.	.	.	.	.	.	.	.	.	A	16.18	3.050713	0.55218	.	.	ENSG00000133019	ENST00000255380;ENST00000448020	T;T	0.37058	1.22;1.22	5.6	5.6	0.85130	.	0.000000	0.85682	D	0.000000	T	0.50633	0.1627	L	0.54323	1.7	0.80722	D	1	P	0.51449	0.945	P	0.55545	0.778	T	0.52609	-0.8553	10	0.87932	D	0	-10.4801	16.0863	0.81056	1.0:0.0:0.0:0.0	.	67	P20309	ACM3_HUMAN	R	67	ENSP00000255380:Q67R;ENSP00000404764:Q67R	ENSP00000255380:Q67R	Q	+	2	0	CHRM3	238137574	1.000000	0.71417	0.894000	0.35097	0.681000	0.39784	9.287000	0.95975	2.251000	0.74343	0.528000	0.53228	CAA		0.512	CHRM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095644.2	NM_000740	
FMN2	56776	broad.mit.edu	37	1	240370926	240370926	+	Silent	SNP	C	C	T	rs71170718|rs562038978		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr1:240370926C>T	ENST00000319653.9	+	5	3044	c.2814C>T	c.(2812-2814)ccC>ccT	p.P938P		NM_020066.4	NP_064450.3	Q9NZ56	FMN2_HUMAN	formin 2	938	FH1.|Pro-rich.				cellular response to DNA damage stimulus (GO:0006974)|cellular response to hypoxia (GO:0071456)|establishment of meiotic spindle localization (GO:0051295)|formin-nucleated actin cable assembly (GO:0070649)|homologous chromosome movement towards spindle pole involved in homologous chromosome segregation (GO:0051758)|intracellular signal transduction (GO:0035556)|intracellular transport (GO:0046907)|multicellular organismal development (GO:0007275)|negative regulation of apoptotic process (GO:0043066)|negative regulation of protein catabolic process (GO:0042177)|oogenesis (GO:0048477)|polar body extrusion after meiotic divisions (GO:0040038)|protein transport (GO:0015031)|vesicle-mediated transport (GO:0016192)	cell cortex (GO:0005938)|cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|microvillus (GO:0005902)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)|spindle (GO:0005819)	actin binding (GO:0003779)	p.P1081P(1)		NS(1)|breast(7)|central_nervous_system(6)|cervix(1)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(13)|lung(87)|ovary(6)|pancreas(3)|prostate(12)|skin(7)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(2)	178	Ovarian(103;0.127)	all_cancers(173;0.013)	OV - Ovarian serous cystadenocarcinoma(106;0.0106)			CCCCTCTACCCGGAGCGGGAA	0.697																																					p.P938P												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C2814T	1						.						27.0	34.0	31.0					1																	240370926		2203	4299	6502	238437549	SO:0001819	synonymous_variant	56776	exon5			AF218942	CCDS31069.2	1q43	2008-02-05			ENSG00000155816	ENSG00000155816			14074	protein-coding gene	gene with protein product		606373				10781961	Standard	NM_020066		Approved		uc010pyd.2	Q9NZ56	OTTHUMG00000039883	ENST00000319653.9:c.2814C>T	1.37:g.240370926C>T		Somatic		Capture	Illumina HiSeq	Phase_I	238437549	NM_020066	B0QZA7|B4DP05|Q59GF6|Q5VU37|Q9NZ55	Silent	SNP	ENST00000319653.9	37	CCDS31069.2																																																																																				0.697	FMN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096217.2	XM_371352	
HMGCL	3155	broad.mit.edu	37	1	24134781	24134781	+	Silent	SNP	G	G	A	rs139799938	byFrequency	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr1:24134781G>A	ENST00000374490.3	-	7	637	c.594C>T	c.(592-594)taC>taT	p.Y198Y	HMGCL_ENST00000436439.2_Silent_p.Y127Y|HMGCL_ENST00000374483.4_Silent_p.Y173Y|HMGCL_ENST00000509389.1_Intron	NM_000191.2	NP_000182.2	P35914	HMGCL_HUMAN	3-hydroxymethyl-3-methylglutaryl-CoA lyase	198					acyl-CoA metabolic process (GO:0006637)|cellular ketone body metabolic process (GO:0046950)|cellular lipid metabolic process (GO:0044255)|ketone body biosynthetic process (GO:0046951)|leucine catabolic process (GO:0006552)|liver development (GO:0001889)|mitochondrion organization (GO:0007005)|protein tetramerization (GO:0051262)|response to fatty acid (GO:0070542)|response to nutrient (GO:0007584)|response to starvation (GO:0042594)|small molecule metabolic process (GO:0044281)	mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|peroxisome (GO:0005777)	carboxylic acid binding (GO:0031406)|fatty-acyl-CoA binding (GO:0000062)|hydroxymethylglutaryl-CoA lyase activity (GO:0004419)|magnesium ion binding (GO:0000287)|manganese ion binding (GO:0030145)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)	p.Y198Y(1)		central_nervous_system(1)|endometrium(2)|large_intestine(2)|lung(3)|ovary(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	12		Colorectal(325;3.46e-05)|Renal(390;0.000219)|Lung NSC(340;0.000233)|all_lung(284;0.000321)|Ovarian(437;0.00348)|Breast(348;0.0044)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|OV - Ovarian serous cystadenocarcinoma(117;2.38e-24)|Colorectal(126;5.58e-08)|COAD - Colon adenocarcinoma(152;3.12e-06)|GBM - Glioblastoma multiforme(114;4.9e-06)|BRCA - Breast invasive adenocarcinoma(304;0.000982)|KIRC - Kidney renal clear cell carcinoma(1967;0.0034)|STAD - Stomach adenocarcinoma(196;0.0128)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.0856)|LUSC - Lung squamous cell carcinoma(448;0.188)		GGGAGATCTCGTAGCAGCCCA	0.552													G|||	2	0.000399361	0.0	0.0	5008	,	,		23617	0.002		0.0	False		,,,				2504	0.0				p.Y127Y												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C381T	1						.	G	,	1,4405	2.1+/-5.4	0,1,2202	125.0	120.0	122.0		594,381	-5.7	0.8	1	dbSNP_134	122	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	HMGCL	NM_000191.2,NM_001166059.1	,	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	,	198/326,127/255	24134781	1,13005	2203	4300	6503	24007368	SO:0001819	synonymous_variant	3155	exon5			BC010570	CCDS243.1, CCDS53279.1	1p36.1-p35	2010-04-30	2010-04-30		ENSG00000117305	ENSG00000117305	4.1.3.4		5005	protein-coding gene	gene with protein product	"""hydroxymethylglutaricaciduria"""	613898	"""3-hydroxymethyl-3-methylglutaryl-Coenzyme A lyase"""			8102917, 8978493	Standard	NM_001166059		Approved	HL	uc001bib.3	P35914	OTTHUMG00000002963	ENST00000374490.3:c.594C>T	1.37:g.24134781G>A		Somatic		Capture	Illumina HiSeq	Phase_I	24007368	NM_001166059	B4DUP4|B7UCC6|D3Y5K7|Q6IBC0|Q96FP8	Silent	SNP	ENST00000374490.3	37	CCDS243.1	2	9.157509157509158E-4	0	0.0	0	0.0	2	0.0034965034965034965	0	0.0	G	8.628	0.892896	0.17613	2.27E-4	0.0	ENSG00000117305	ENST00000235958	.	.	.	5.65	-5.74	0.02391	.	.	.	.	.	T	0.65196	0.2668	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.67138	-0.5746	4	.	.	.	-10.3653	16.4818	0.84159	0.7559:0.0:0.2441:0.0	.	.	.	.	M	55	.	.	T	-	2	0	HMGCL	24007368	0.000000	0.05858	0.838000	0.33150	0.981000	0.71138	-2.273000	0.01164	-1.086000	0.03084	-0.880000	0.02959	ACG		0.552	HMGCL-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008253.2	NM_000191	
FH	2271	broad.mit.edu	37	1	241667497	241667497	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr1:241667497T>C	ENST00000366560.3	-	7	991	c.953A>G	c.(952-954)cAt>cGt	p.H318R		NM_000143.3	NP_000134.2	P07954	FUMH_HUMAN	fumarate hydratase	318					cellular metabolic process (GO:0044237)|fumarate metabolic process (GO:0006106)|homeostasis of number of cells within a tissue (GO:0048873)|small molecule metabolic process (GO:0044281)|tricarboxylic acid cycle (GO:0006099)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|tricarboxylic acid cycle enzyme complex (GO:0045239)	fumarate hydratase activity (GO:0004333)	p.H318R(1)		biliary_tract(1)|endometrium(5)|kidney(1)|large_intestine(5)|lung(11)|ovary(1)|skin(2)	26	Ovarian(103;0.103)	all_cancers(173;2.37e-314)|all_epithelial(177;5.17e-286)|Breast(1374;1.06e-10)|Acute lymphoblastic leukemia(190;4.93e-10)|all_neural(198;0.00118)	OV - Ovarian serous cystadenocarcinoma(106;0.0214)	Colorectal(1306;2.33e-53)|COAD - Colon adenocarcinoma(196;1.05e-44)|KIRC - Kidney renal clear cell carcinoma(1967;0.000109)		CAGAGCGTCATGAGCAGCCAG	0.423			"""Mis, N, F"""			"""lieomyomatosis, renal"""			Hereditary Leiomyomatosis and Renal Cell Cancer																												p.H318R	Melanoma(148;1573 2486 7381 46575)	yes	Rec		hereditary leiomyomatosis and renal cell cancer	1	1q42.1	2271	fumarate hydratase		"""E, M"""	.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A953G	1	GRCh37	CM061769	FH	M		.						66.0	60.0	62.0					1																	241667497		2203	4300	6503	239734120	SO:0001583	missense	2271	exon7	Familial Cancer Database	HLRCC, Reed syndrome, Hereditary Multiple Leiomyomata of Skin and Uterus	BC003108	CCDS1617.1	1q42.1	2014-09-17			ENSG00000091483	ENSG00000091483	4.2.1.2		3700	protein-coding gene	gene with protein product		136850					Standard	NM_000143		Approved	fumarase	uc001hyx.3	P07954	OTTHUMG00000039597	ENST00000366560.3:c.953A>G	1.37:g.241667497T>C	ENSP00000355518:p.His318Arg	Somatic		Capture	Illumina HiSeq	Phase_I	239734120	NM_000143	B1ANK7	Missense_Mutation	SNP	ENST00000366560.3	37	CCDS1617.1	.	.	.	.	.	.	.	.	.	.	T	19.47	3.833329	0.71258	.	.	ENSG00000091483	ENST00000366560	D	0.99422	-5.88	5.73	5.73	0.89815	Lyase 1, N-terminal (1);L-Aspartase-like (1);	0.139342	0.64402	D	0.000003	D	0.98251	0.9421	L	0.42686	1.345	0.80722	D	1	B	0.29716	0.255	B	0.34385	0.181	D	0.98614	1.0664	10	0.40728	T	0.16	0.4301	13.9704	0.64237	0.0:0.0:0.0:1.0	.	318	P07954	FUMH_HUMAN	R	318	ENSP00000355518:H318R	ENSP00000355518:H318R	H	-	2	0	FH	239734120	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	7.498000	0.81546	2.187000	0.69744	0.533000	0.62120	CAT		0.423	FH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095490.1	NM_000143	
ZNF496	84838	broad.mit.edu	37	1	247464071	247464071	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr1:247464071G>A	ENST00000294753.4	-	9	1978	c.1514C>T	c.(1513-1515)gCg>gTg	p.A505V	ZNF496_ENST00000462139.1_5'UTR|ZNF496_ENST00000366498.2_Missense_Mutation_p.A541V	NM_032752.1	NP_116141.1	Q96IT1	ZN496_HUMAN	zinc finger protein 496	505					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription from RNA polymerase II promoter (GO:0006366)	nuclear body (GO:0016604)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)	p.A505V(1)		NS(2)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(5)|lung(13)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	36	all_cancers(71;0.000136)|all_epithelial(71;2.62e-05)|Breast(184;0.0226)|Ovarian(71;0.0377)|all_lung(81;0.0607)|Lung NSC(105;0.0661)		OV - Ovarian serous cystadenocarcinoma(106;0.00703)			ACCCTTGTCCGCGTCCTCGGA	0.637																																					p.A505V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1514T	1						.						91.0	93.0	92.0					1																	247464071		2203	4300	6503	245530694	SO:0001583	missense	84838	exon9			BC007263	CCDS1631.1	1q44	2013-01-09			ENSG00000162714	ENSG00000162714		"""Zinc fingers, C2H2-type"", ""-"", ""-"", ""-"""	23713	protein-coding gene	gene with protein product		613911				12477932	Standard	NM_032752		Approved	ZKSCAN17, MGC15548, ZSCAN49	uc001ico.3	Q96IT1	OTTHUMG00000041164	ENST00000294753.4:c.1514C>T	1.37:g.247464071G>A	ENSP00000294753:p.Ala505Val	Somatic		Capture	Illumina HiSeq	Phase_I	245530694	NM_032752	Q8TBS2	Missense_Mutation	SNP	ENST00000294753.4	37	CCDS1631.1	.	.	.	.	.	.	.	.	.	.	G	7.348	0.622291	0.14193	.	.	ENSG00000162714	ENST00000294753;ENST00000366498	T;T	0.07908	3.16;3.15	3.7	-7.41	0.01392	.	2.017010	0.02699	N	0.111517	T	0.03348	0.0097	N	0.08118	0	0.09310	N	1	B;B	0.06786	0.0;0.001	B;B	0.04013	0.001;0.0	T	0.30880	-0.9963	10	0.29301	T	0.29	0.8793	0.6332	0.00798	0.3613:0.1433:0.3099:0.1855	.	541;505	Q96IT1-2;Q96IT1	.;ZN496_HUMAN	V	505;541	ENSP00000294753:A505V;ENSP00000355454:A541V	ENSP00000294753:A505V	A	-	2	0	ZNF496	245530694	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-2.380000	0.01066	-3.987000	0.00084	-0.254000	0.11334	GCG		0.637	ZNF496-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098655.2	NM_032752	
AGRN	375790	broad.mit.edu	37	1	989314	989314	+	Missense_Mutation	SNP	G	G	A	rs145079121		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr1:989314G>A	ENST00000379370.2	+	34	5883	c.5833G>A	c.(5833-5835)Gtg>Atg	p.V1945M	RP11-54O7.14_ENST00000418300.1_RNA	NM_198576.3	NP_940978.2	O00468	AGRIN_HUMAN	agrin	1967	Laminin G-like 3. {ECO:0000255|PROSITE- ProRule:PRU00122}.				axon guidance (GO:0007411)|carbohydrate metabolic process (GO:0005975)|chondroitin sulfate metabolic process (GO:0030204)|clustering of voltage-gated sodium channels (GO:0045162)|extracellular matrix organization (GO:0030198)|G-protein coupled acetylcholine receptor signaling pathway (GO:0007213)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|neuromuscular junction development (GO:0007528)|neurotransmitter receptor metabolic process (GO:0045213)|phototransduction, visible light (GO:0007603)|plasma membrane organization (GO:0007009)|positive regulation of filopodium assembly (GO:0051491)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of synaptic growth at neuromuscular junction (GO:0045887)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|receptor clustering (GO:0043113)|retinoid metabolic process (GO:0001523)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synapse organization (GO:0050808)	basal lamina (GO:0005605)|cell junction (GO:0030054)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|lysosomal lumen (GO:0043202)|plasma membrane (GO:0005886)|synapse (GO:0045202)	acetylcholine receptor regulator activity (GO:0030548)|calcium ion binding (GO:0005509)|chondroitin sulfate binding (GO:0035374)|dystroglycan binding (GO:0002162)|heparan sulfate proteoglycan binding (GO:0043395)|laminin binding (GO:0043236)|sialic acid binding (GO:0033691)|structural constituent of cytoskeleton (GO:0005200)	p.V1945M(1)		breast(1)|central_nervous_system(2)|endometrium(8)|kidney(3)|large_intestine(2)|lung(20)|ovary(1)|prostate(1)|skin(3)|urinary_tract(1)	42	all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;8.75e-19)|all_lung(118;2.3e-08)|Lung NSC(185;2.38e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Lung SC(97;0.128)		UCEC - Uterine corpus endometrioid carcinoma (11;0.00462)|Epithelial(90;5.98e-38)|OV - Ovarian serous cystadenocarcinoma(86;5.43e-23)|Colorectal(212;5.97e-05)|COAD - Colon adenocarcinoma(227;0.000201)|Kidney(185;0.0024)|BRCA - Breast invasive adenocarcinoma(365;0.00246)|STAD - Stomach adenocarcinoma(132;0.00645)|KIRC - Kidney renal clear cell carcinoma(229;0.0354)|Lung(427;0.201)		GCGTTCCACCGTGCCCGTCAA	0.647																																					p.V1945M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G5833A	1						.	G	MET/VAL	0,4398		0,0,2199	48.0	36.0	40.0		5833	3.5	0.8	1	dbSNP_134	40	1,8591		0,1,4295	no	missense	AGRN	NM_198576.3	21	0,1,6494	AA,AG,GG		0.0116,0.0,0.0077	benign	1945/2046	989314	1,12989	2199	4296	6495	979177	SO:0001583	missense	375790	exon34			XM_372195	CCDS30551.1	1p36.33	2014-09-17		2007-02-16	ENSG00000188157	ENSG00000188157		"""Proteoglycans / Extracellular Matrix : Other"""	329	protein-coding gene	gene with protein product	"""agrin proteoglycan"""	103320				1851019, 12270958	Standard	NM_198576		Approved	AGRIN	uc001ack.2	O00468	OTTHUMG00000040778	ENST00000379370.2:c.5833G>A	1.37:g.989314G>A	ENSP00000368678:p.Val1945Met	Somatic		Capture	Illumina HiSeq	Phase_I	979177	NM_198576	Q5SVA1|Q5SVA2|Q60FE1|Q7KYS8|Q8N4J5|Q96IC1|Q9BTD4	Missense_Mutation	SNP	ENST00000379370.2	37	CCDS30551.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	17.22|17.22	3.333353|3.333353	0.60853|0.60853	0.0|0.0	1.16E-4|1.16E-4	ENSG00000188157|ENSG00000188157	ENST00000419249|ENST00000379370;ENST00000379364	.|T	.|0.76316	.|-1.01	4.47|4.47	3.54|3.54	0.40534|0.40534	.|Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Laminin G domain (2);Laminin G, subdomain 1 (1);	.|0.212136	.|0.30519	.|N	.|0.009445	T|T	0.77239|0.77239	0.4101|0.4101	M|M	0.74467|0.74467	2.265|2.265	0.53688|0.53688	D|D	0.99997|0.99997	.|P	.|0.43938	.|0.822	.|B	.|0.40940	.|0.344	T|T	0.78122|0.78122	-0.2327|-0.2327	5|10	.|0.48119	.|T	.|0.1	-12.7997|-12.7997	13.9594|13.9594	0.64170|0.64170	0.0:0.1538:0.8462:0.0|0.0:0.1538:0.8462:0.0	.|.	.|1945	.|O00468	.|AGRIN_HUMAN	H|M	266|1945;307	.|ENSP00000368678:V1945M	.|ENSP00000368671:V307M	R|V	+|+	2|1	0|0	AGRN|AGRN	979177|979177	1.000000|1.000000	0.71417|0.71417	0.785000|0.785000	0.31869|0.31869	0.463000|0.463000	0.32649|0.32649	7.555000|7.555000	0.82223|0.82223	0.859000|0.859000	0.35456|0.35456	-0.502000|-0.502000	0.04539|0.04539	CGT|GTG		0.647	AGRN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097990.2	NM_198576	
PRDM16	63976	broad.mit.edu	37	1	3313156	3313156	+	Splice_Site	SNP	C	C	T	rs535076398		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr1:3313156C>T	ENST00000270722.5	+	5	724	c.675C>T	c.(673-675)gaC>gaT	p.D225D	PRDM16_ENST00000378391.2_Splice_Site_p.D225D|PRDM16_ENST00000442529.2_Splice_Site_p.D225D|PRDM16_ENST00000511072.1_Splice_Site_p.D226D|PRDM16_ENST00000514189.1_Splice_Site_p.D226D|PRDM16_ENST00000441472.2_Splice_Site_p.D225D|PRDM16_ENST00000378398.3_Splice_Site_p.D226D|PRDM16_ENST00000512462.1_3'UTR			Q9HAZ2	PRD16_HUMAN	PR domain containing 16	225					brown fat cell differentiation (GO:0050873)|negative regulation of granulocyte differentiation (GO:0030853)|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)|neurogenesis (GO:0022008)|palate development (GO:0060021)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cellular respiration (GO:0043457)|somatic stem cell maintenance (GO:0035019)|tongue development (GO:0043586)|transcription, DNA-templated (GO:0006351)|white fat cell differentiation (GO:0050872)	nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)|transcription coactivator activity (GO:0003713)	p.D225D(1)		breast(4)|central_nervous_system(1)|endometrium(5)|kidney(4)|large_intestine(7)|lung(22)|ovary(2)|pancreas(1)|prostate(2)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(3)	59	all_cancers(77;0.00208)|all_epithelial(69;0.000732)|Ovarian(185;0.0634)|Lung NSC(156;0.109)|all_lung(157;0.111)	all_epithelial(116;2.03e-21)|all_lung(118;7.55e-09)|Lung NSC(185;1.28e-06)|Breast(487;0.000792)|Renal(390;0.00137)|Hepatocellular(190;0.00515)|Myeloproliferative disorder(586;0.0267)|Ovarian(437;0.0365)|Lung SC(97;0.114)|Medulloblastoma(700;0.134)		Epithelial(90;5.59e-35)|OV - Ovarian serous cystadenocarcinoma(86;1.99e-20)|GBM - Glioblastoma multiforme(42;3.72e-11)|Colorectal(212;0.000425)|BRCA - Breast invasive adenocarcinoma(365;0.000946)|COAD - Colon adenocarcinoma(227;0.000968)|Kidney(185;0.00155)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0175)|Lung(427;0.137)		CCGGCCTGGACGGTAAGACCC	0.642			T	EVI1	"""MDS, AML"""								C|||	1	0.000199681	0.0	0.0014	5008	,	,		14665	0.0		0.0	False		,,,				2504	0.0				p.D225D			Dom	yes		1	1p36.23-p33	63976	PR domain containing 16		L	.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C675T	1						.						30.0	34.0	33.0					1																	3313156		1976	4149	6125	3303016	SO:0001630	splice_region_variant	63976	exon5			AF294278	CCDS41236.1, CCDS44048.1, CCDS41236.2, CCDS44048.2	1p36.23-p33	2013-01-08			ENSG00000142611	ENSG00000142611		"""Zinc fingers, C2H2-type"""	14000	protein-coding gene	gene with protein product	"""MDS1/EVI1-like"", ""PR-domain zinc finger protein 16"", ""transcription factor MEL1"""	605557				11050005	Standard	NM_199454		Approved	MEL1, PFM13, KIAA1675, MGC166915	uc001akf.3	Q9HAZ2	OTTHUMG00000000581	ENST00000270722.5:c.676+1C>T	1.37:g.3313156C>T		Somatic		Capture	Illumina HiSeq	Phase_I	3303016	NM_022114	A6NHQ8|B1AJP7|B1AJP8|B1AJP9|B1WB48|Q8WYJ9|Q9C0I8	De_novo_Start_OutOfFrame	SNP	ENST00000270722.5	37	CCDS41236.2																																																																																				0.642	PRDM16-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000001382.3	NM_022114	Silent
LRRC47	57470	broad.mit.edu	37	1	3703493	3703493	+	Missense_Mutation	SNP	G	G	A	rs377537674		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr1:3703493G>A	ENST00000378251.1	-	2	1024	c.997C>T	c.(997-999)Cgg>Tgg	p.R333W	RP1-286D6.5_ENST00000607459.1_RNA	NM_020710.2	NP_065761.1	Q8N1G4	LRC47_HUMAN	leucine rich repeat containing 47	333							phenylalanine-tRNA ligase activity (GO:0004826)|poly(A) RNA binding (GO:0044822)	p.R333W(2)		central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(5)|ovary(2)|prostate(1)|urinary_tract(1)	17	all_cancers(77;0.0375)|Ovarian(185;0.0634)|all_lung(157;0.208)|Lung NSC(156;0.21)	all_epithelial(116;1.34e-16)|all_lung(118;2.53e-06)|Lung NSC(185;0.00028)|Renal(390;0.00357)|Breast(487;0.00446)|Hepatocellular(190;0.0218)|Myeloproliferative disorder(586;0.0393)|Lung SC(97;0.0743)|Ovarian(437;0.127)		Epithelial(90;5.49e-39)|OV - Ovarian serous cystadenocarcinoma(86;1.43e-22)|GBM - Glioblastoma multiforme(42;3.69e-16)|Colorectal(212;1.21e-05)|COAD - Colon adenocarcinoma(227;5.87e-05)|Kidney(185;0.000367)|BRCA - Breast invasive adenocarcinoma(365;0.000704)|KIRC - Kidney renal clear cell carcinoma(229;0.00567)|STAD - Stomach adenocarcinoma(132;0.00645)|Lung(427;0.124)		ATGTAGGGCCGCACATCCCGG	0.667																																					p.R333W												.	.	2	Substitution - Missense(2)	large_intestine(1)|endometrium(1)	c.C997T	1						.	G	TRP/ARG	0,4396		0,0,2198	28.0	28.0	28.0		997	5.2	1.0	1		28	1,8597		0,1,4298	no	missense	LRRC47	NM_020710.2	101	0,1,6496	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging	333/584	3703493	1,12993	2198	4299	6497	3693353	SO:0001583	missense	57470	exon2			AB033011	CCDS51.1	1p36.32	2008-02-05			ENSG00000130764	ENSG00000130764			29207	protein-coding gene	gene with protein product						10574461	Standard	NM_020710		Approved	KIAA1185, RP1-286D6.3	uc001akx.1	Q8N1G4	OTTHUMG00000003506	ENST00000378251.1:c.997C>T	1.37:g.3703493G>A	ENSP00000367498:p.Arg333Trp	Somatic		Capture	Illumina HiSeq	Phase_I	3693353	NM_020710	Q9ULN5	Missense_Mutation	SNP	ENST00000378251.1	37	CCDS51.1	.	.	.	.	.	.	.	.	.	.	G	23.1	4.371555	0.82573	0.0	1.16E-4	ENSG00000130764	ENST00000378251	D	0.89681	-2.55	5.22	5.22	0.72569	B3/B4 tRNA-binding domain (1);	0.120839	0.64402	D	0.000019	D	0.96599	0.8890	H	0.96720	3.87	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.97996	1.0357	10	0.87932	D	0	-24.7838	17.8375	0.88704	0.0:0.0:1.0:0.0	.	333	Q8N1G4	LRC47_HUMAN	W	333	ENSP00000367498:R333W	ENSP00000367498:R333W	R	-	1	2	LRRC47	3693353	1.000000	0.71417	1.000000	0.80357	0.878000	0.50629	4.070000	0.57548	2.448000	0.82819	0.650000	0.86243	CGG		0.667	LRRC47-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000009744.1	NM_020710	
C1orf174	339448	broad.mit.edu	37	1	3806548	3806548	+	Silent	SNP	G	G	A	rs61737469	byFrequency	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr1:3806548G>A	ENST00000361605.3	-	4	806	c.708C>T	c.(706-708)gaC>gaT	p.D236D	C1orf174_ENST00000486765.1_5'UTR	NM_207356.2	NP_997239.2	Q8IYL3	CA174_HUMAN	chromosome 1 open reading frame 174	236	Poly-Asp.					nucleus (GO:0005634)		p.D236D(1)		endometrium(1)|large_intestine(5)|lung(4)|prostate(1)	11	all_cancers(77;0.0395)|Ovarian(185;0.0634)|all_lung(157;0.222)|Lung NSC(156;0.227)	all_cancers(23;5.09e-25)|all_epithelial(116;9.35e-17)|all_lung(118;1.09e-06)|Lung NSC(185;0.000139)|all_neural(13;0.00287)|Renal(390;0.00357)|Breast(487;0.00446)|Hepatocellular(190;0.0219)|all_hematologic(16;0.027)|Colorectal(325;0.0276)|Myeloproliferative disorder(586;0.0393)|Lung SC(97;0.0743)|Ovarian(437;0.127)		Epithelial(90;1.55e-39)|OV - Ovarian serous cystadenocarcinoma(86;5.99e-23)|GBM - Glioblastoma multiforme(42;2.22e-17)|Colorectal(212;1.08e-05)|COAD - Colon adenocarcinoma(227;5.49e-05)|Kidney(185;0.000342)|BRCA - Breast invasive adenocarcinoma(365;0.000365)|KIRC - Kidney renal clear cell carcinoma(229;0.00549)|STAD - Stomach adenocarcinoma(132;0.00644)|Lung(427;0.19)		catcgtcgtcgtcatcatcat	0.393													g|||	80	0.0159744	0.0567	0.0058	5008	,	,		20841	0.0		0.0	False		,,,				2504	0.001				p.D236D												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C708T	1						.	A		198,4208	124.1+/-161.4	3,192,2008	209.0	175.0	187.0		708	-10.8	0.0	1	dbSNP_129	187	4,8596	3.7+/-12.6	0,4,4296	no	coding-synonymous	C1orf174	NM_207356.2		3,196,6304	AA,AG,GG		0.0465,4.4939,1.5531		236/244	3806548	202,12804	2203	4300	6503	3796408	SO:0001819	synonymous_variant	339448	exon4			BC035643	CCDS53.1	1p36.32	2012-07-25			ENSG00000198912	ENSG00000198912			27915	protein-coding gene	gene with protein product						12477932	Standard	NM_207356		Approved	RP13-531C17.2	uc001alf.3	Q8IYL3	OTTHUMG00000003739	ENST00000361605.3:c.708C>T	1.37:g.3806548G>A		Somatic		Capture	Illumina HiSeq	Phase_I	3796408	NM_207356	A8K0C8|A8MUG9|Q5SR20|Q6NX36	Silent	SNP	ENST00000361605.3	37	CCDS53.1																																																																																				0.393	C1orf174-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000010539.1	NM_207356	
NPHP4	261734	broad.mit.edu	37	1	5965733	5965733	+	Silent	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr1:5965733C>T	ENST00000378156.4	-	14	1987	c.1722G>A	c.(1720-1722)acG>acA	p.T574T	NPHP4_ENST00000478423.2_5'UTR	NM_015102.3	NP_055917.1	O75161	NPHP4_HUMAN	nephronophthisis 4	574					actin cytoskeleton organization (GO:0030036)|hippo signaling (GO:0035329)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|retina development in camera-type eye (GO:0060041)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|visual behavior (GO:0007632)	cell-cell junction (GO:0005911)|centrosome (GO:0005813)|cytosol (GO:0005829)|membrane (GO:0016020)|nonmotile primary cilium (GO:0031513)|tight junction (GO:0005923)	structural molecule activity (GO:0005198)	p.T574T(1)		NS(1)|breast(2)|cervix(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(15)|ovary(2)|pancreas(1)|prostate(4)	47	Ovarian(185;0.0634)	all_cancers(23;7.53e-41)|all_epithelial(116;3.96e-23)|all_lung(118;5.12e-09)|all_hematologic(16;5.45e-07)|Lung NSC(185;5.49e-07)|all_neural(13;3.21e-06)|Acute lymphoblastic leukemia(12;3.44e-05)|Breast(487;0.000601)|Renal(390;0.0007)|Colorectal(325;0.00113)|Hepatocellular(190;0.00213)|Glioma(11;0.00223)|Myeloproliferative disorder(586;0.0256)|Ovarian(437;0.04)|Lung SC(97;0.128)|Medulloblastoma(700;0.213)		Epithelial(90;1.69e-36)|GBM - Glioblastoma multiforme(13;5.07e-29)|OV - Ovarian serous cystadenocarcinoma(86;1.05e-19)|Colorectal(212;4.54e-07)|COAD - Colon adenocarcinoma(227;3.14e-05)|Kidney(185;0.00012)|BRCA - Breast invasive adenocarcinoma(365;0.00102)|KIRC - Kidney renal clear cell carcinoma(229;0.00179)|STAD - Stomach adenocarcinoma(132;0.00472)|READ - Rectum adenocarcinoma(331;0.0649)		CATGCAAAGGCGTGAACGGCA	0.597																																					p.T574T												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G1722A	1						.						52.0	58.0	56.0					1																	5965733		2055	4187	6242	5888320	SO:0001819	synonymous_variant	261734	exon14			AB014573	CCDS44052.1	1p36	2010-03-26			ENSG00000131697	ENSG00000131697			19104	protein-coding gene	gene with protein product	"""nephroretinin"", ""nephrocystin-4"", ""POC10 centriolar protein homolog (Chlamydomonas)"""	607215				11920287, 12205563	Standard	XR_244787		Approved	SLSN4, KIAA0673, POC10	uc001alq.2	O75161	OTTHUMG00000000701	ENST00000378156.4:c.1722G>A	1.37:g.5965733C>T		Somatic		Capture	Illumina HiSeq	Phase_I	5888320	NM_015102	Q8IWC0	Silent	SNP	ENST00000378156.4	37	CCDS44052.1																																																																																				0.597	NPHP4-001	KNOWN	non_canonical_polymorphism|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001715.2		
GPR153	387509	broad.mit.edu	37	1	6310547	6310547	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr1:6310547G>A	ENST00000377893.2	-	5	1376	c.1117C>T	c.(1117-1119)Ctc>Ttc	p.L373F		NM_207370.2	NP_997253.2	Q6NV75	GP153_HUMAN	G protein-coupled receptor 153	373						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)	p.L373F(1)		endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(2)|liver(1)|lung(7)|skin(1)	14	Ovarian(185;0.0634)	all_cancers(23;8.07e-33)|all_epithelial(116;4.45e-18)|all_lung(118;1.09e-06)|all_neural(13;3.68e-06)|Lung NSC(185;1.52e-05)|all_hematologic(16;2.39e-05)|Acute lymphoblastic leukemia(12;0.000372)|Glioma(11;0.00127)|Renal(390;0.00188)|Colorectal(325;0.00342)|Breast(487;0.00475)|Hepatocellular(190;0.0218)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.15)		Epithelial(90;1.91e-37)|GBM - Glioblastoma multiforme(13;4.87e-29)|OV - Ovarian serous cystadenocarcinoma(86;3.03e-19)|Colorectal(212;1.33e-07)|COAD - Colon adenocarcinoma(227;1.36e-05)|Kidney(185;4.89e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.000911)|BRCA - Breast invasive adenocarcinoma(365;0.00109)|STAD - Stomach adenocarcinoma(132;0.00313)|READ - Rectum adenocarcinoma(331;0.0642)|Lung(427;0.246)		AGTGGGTAGAGCTGGGGCAGG	0.627																																					p.L373F												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1117T	1						.						33.0	29.0	31.0					1																	6310547		2199	4300	6499	6233134	SO:0001583	missense	387509	exon5			AY255529	CCDS64.1	1p36.31	2012-08-21			ENSG00000158292	ENSG00000158292		"""GPCR / Class A : Orphans"""	23618	protein-coding gene	gene with protein product		614269				12679517	Standard	NM_207370		Approved	PGR1	uc001amp.2	Q6NV75	OTTHUMG00000001272	ENST00000377893.2:c.1117C>T	1.37:g.6310547G>A	ENSP00000367125:p.Leu373Phe	Somatic		Capture	Illumina HiSeq	Phase_I	6233134	NM_207370	Q5TGR5|Q6AHW8|Q86SP8	Missense_Mutation	SNP	ENST00000377893.2	37	CCDS64.1	.	.	.	.	.	.	.	.	.	.	G	12.50	1.956934	0.34565	.	.	ENSG00000158292	ENST00000377893	T	0.25749	1.78	4.87	0.5	0.16919	.	0.630262	0.15164	N	0.276999	T	0.09158	0.0226	N	0.12182	0.205	0.29854	N	0.828168	B	0.09022	0.002	B	0.08055	0.003	T	0.31251	-0.9950	10	0.08599	T	0.76	-14.0077	1.5708	0.02614	0.2362:0.1603:0.441:0.1625	.	373	Q6NV75	GP153_HUMAN	F	373	ENSP00000367125:L373F	ENSP00000367125:L373F	L	-	1	0	GPR153	6233134	0.995000	0.38212	0.996000	0.52242	0.910000	0.53928	0.925000	0.28791	0.042000	0.15717	0.455000	0.32223	CTC		0.627	GPR153-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000003717.2		
DNAJC11	55735	broad.mit.edu	37	1	6727837	6727837	+	Nonsense_Mutation	SNP	G	G	A	rs267598695		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr1:6727837G>A	ENST00000377577.5	-	4	433	c.310C>T	c.(310-312)Cga>Tga	p.R104*	DNAJC11_ENST00000294401.7_Nonsense_Mutation_p.R104*|DNAJC11_ENST00000349363.6_Nonsense_Mutation_p.R66*|DNAJC11_ENST00000377573.5_Nonsense_Mutation_p.R14*|DNAJC11_ENST00000542246.1_Nonsense_Mutation_p.R66*	NM_018198.3	NP_060668.2	Q9NVH1	DJC11_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 11	104						extracellular vesicular exosome (GO:0070062)|mitochondrial inner membrane (GO:0005743)		p.R104*(1)		NS(1)|breast(2)|endometrium(4)|kidney(2)|large_intestine(11)|lung(8)|ovary(2)|skin(1)|urinary_tract(1)	32	Ovarian(185;0.0265)|all_lung(157;0.154)	all_cancers(23;1.97e-27)|all_epithelial(116;1.76e-17)|all_lung(118;2.27e-05)|Lung NSC(185;9.97e-05)|Renal(390;0.00188)|Breast(487;0.00289)|Colorectal(325;0.00342)|Hepatocellular(190;0.0218)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.156)		Colorectal(212;2.34e-07)|COAD - Colon adenocarcinoma(227;2.05e-05)|Kidney(185;7.67e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000639)|KIRC - Kidney renal clear cell carcinoma(229;0.00128)|STAD - Stomach adenocarcinoma(132;0.00179)|READ - Rectum adenocarcinoma(331;0.0649)		AACTCCTCTCGAATTTCAGCA	0.517																																					p.R104X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.C310T	1						.						65.0	62.0	63.0					1																	6727837		2203	4300	6503	6650424	SO:0001587	stop_gained	55735	exon4			AF306695	CCDS87.1	1p36.23	2011-09-02			ENSG00000007923	ENSG00000007923		"""Heat shock proteins / DNAJ (HSP40)"""	25570	protein-coding gene	gene with protein product		614827				12964007	Standard	NM_018198		Approved	FLJ10737	uc001aof.2	Q9NVH1	OTTHUMG00000001443	ENST00000377577.5:c.310C>T	1.37:g.6727837G>A	ENSP00000366800:p.Arg104*	Somatic		Capture	Illumina HiSeq	Phase_I	6650424	NM_018198	Q4VWF5|Q5VZN0|Q6PK20|Q6PK70|Q8NDM2|Q96CL7	Nonsense_Mutation	SNP	ENST00000377577.5	37	CCDS87.1	.	.	.	.	.	.	.	.	.	.	g	38	7.181086	0.98118	.	.	ENSG00000007923	ENST00000377577;ENST00000451196;ENST00000349363;ENST00000294401;ENST00000542246;ENST00000377573;ENST00000426784	.	.	.	5.71	3.44	0.39384	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-0.3421	12.0543	0.53524	0.0:0.0:0.3134:0.6866	.	.	.	.	X	104;80;66;104;66;14;104	.	ENSP00000294401:R104X	R	-	1	2	DNAJC11	6650424	1.000000	0.71417	0.915000	0.36163	0.985000	0.73830	2.360000	0.44151	0.472000	0.27344	0.651000	0.88453	CGA		0.517	DNAJC11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000004216.3	NM_018198	
PARK7	11315	broad.mit.edu	37	1	8025436	8025436	+	Missense_Mutation	SNP	G	G	A	rs145727915		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr1:8025436G>A	ENST00000493678.1	+	3	210	c.143G>A	c.(142-144)cGt>cAt	p.R48H	PARK7_ENST00000338639.5_Missense_Mutation_p.R48H|PARK7_ENST00000497113.1_3'UTR|PARK7_ENST00000377488.1_Missense_Mutation_p.R48H|PARK7_ENST00000377493.5_Missense_Mutation_p.R48H|PARK7_ENST00000377491.1_Missense_Mutation_p.R48H			Q99497	PARK7_HUMAN	parkinson protein 7	48					adult locomotory behavior (GO:0008344)|autophagy (GO:0006914)|cellular response to glyoxal (GO:0036471)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to oxidative stress (GO:0034599)|dopamine uptake involved in synaptic transmission (GO:0051583)|glycolate biosynthetic process (GO:0046295)|glyoxal catabolic process (GO:1903190)|hydrogen peroxide metabolic process (GO:0042743)|inflammatory response (GO:0006954)|lactate biosynthetic process (GO:0019249)|membrane depolarization (GO:0051899)|membrane hyperpolarization (GO:0060081)|methylglyoxal catabolic process to D-lactate (GO:0019243)|mitochondrion organization (GO:0007005)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell death (GO:0060548)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic signaling pathway (GO:2001268)|negative regulation of death-inducing signaling complex assembly (GO:1903073)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of gene expression (GO:0010629)|negative regulation of hydrogen peroxide-induced cell death (GO:1903206)|negative regulation of hydrogen peroxide-induced neuron death (GO:1903208)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of neuron death (GO:1901215)|negative regulation of oxidative stress-induced cell death (GO:1903202)|negative regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway (GO:1903377)|negative regulation of protein acetylation (GO:1901984)|negative regulation of protein binding (GO:0032091)|negative regulation of protein export from nucleus (GO:0046826)|negative regulation of protein K48-linked deubiquitination (GO:1903094)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of protein sumoylation (GO:0033234)|negative regulation of protein ubiquitination (GO:0031397)|negative regulation of TRAIL-activated apoptotic signaling pathway (GO:1903122)|negative regulation of ubiquitin-protein transferase activity (GO:0051444)|negative regulation of ubiquitin-specific protease activity (GO:2000157)|positive regulation of androgen receptor activity (GO:2000825)|positive regulation of dopamine biosynthetic process (GO:1903181)|positive regulation of interleukin-8 production (GO:0032757)|positive regulation of L-dopa biosynthetic process (GO:1903197)|positive regulation of L-dopa decarboxylase activity (GO:1903200)|positive regulation of mitochondrial electron transport, NADH to ubiquinone (GO:1902958)|positive regulation of oxidative phosphorylation uncoupler activity (GO:2000277)|positive regulation of protein homodimerization activity (GO:0090073)|positive regulation of protein localization to nucleus (GO:1900182)|positive regulation of pyrroline-5-carboxylate reductase activity (GO:1903168)|positive regulation of superoxide dismutase activity (GO:1901671)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tyrosine 3-monooxygenase activity (GO:1903178)|protein stabilization (GO:0050821)|regulation of androgen receptor signaling pathway (GO:0060765)|regulation of fibril organization (GO:1902903)|regulation of inflammatory response (GO:0050727)|regulation of mitochondrial membrane potential (GO:0051881)|regulation of neuron apoptotic process (GO:0043523)|single fertilization (GO:0007338)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|PML body (GO:0016605)	androgen receptor binding (GO:0050681)|cupric ion binding (GO:1903135)|cuprous ion binding (GO:1903136)|cytokine binding (GO:0019955)|enzyme binding (GO:0019899)|glyoxalase (glycolic acid-forming) activity (GO:1990422)|glyoxalase III activity (GO:0019172)|identical protein binding (GO:0042802)|L-dopa decarboxylase activator activity (GO:0036478)|mRNA binding (GO:0003729)|oxidoreductase activity, acting on peroxide as acceptor (GO:0016684)|peptidase activity (GO:0008233)|peroxidase activity (GO:0004601)|peroxiredoxin activity (GO:0051920)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)|repressing transcription factor binding (GO:0070491)|RNA binding (GO:0003723)|scaffold protein binding (GO:0097110)|small protein activating enzyme binding (GO:0044388)|small protein conjugating enzyme binding (GO:0044390)|superoxide dismutase copper chaperone activity (GO:0016532)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|tyrosine 3-monooxygenase activator activity (GO:0036470)|ubiquitin-specific protease binding (GO:1990381)	p.R48H(3)		large_intestine(1)	1	Ovarian(185;0.06)|all_lung(157;0.151)	all_epithelial(116;1.76e-16)|all_lung(118;3.66e-05)|Lung NSC(185;0.000163)|Renal(390;0.000469)|Colorectal(325;0.0033)|Breast(348;0.0044)|Hepatocellular(190;0.0228)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.11)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|all cancers(8;1.28e-70)|GBM - Glioblastoma multiforme(8;3.05e-36)|Colorectal(212;6.83e-08)|COAD - Colon adenocarcinoma(227;7.51e-06)|Kidney(185;5.22e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000414)|KIRC - Kidney renal clear cell carcinoma(229;0.000967)|STAD - Stomach adenocarcinoma(132;0.00102)|READ - Rectum adenocarcinoma(331;0.0649)		CAGTGTAGCCGTGATGTGGTC	0.398																																					p.R48H												.	.	3	Substitution - Missense(3)	large_intestine(2)|central_nervous_system(1)	c.G143A	1						.	G	HIS/ARG,HIS/ARG	0,4406		0,0,2203	141.0	141.0	141.0		143,143	5.6	1.0	1	dbSNP_134	141	3,8597	3.0+/-9.4	0,3,4297	no	missense,missense	PARK7	NM_001123377.1,NM_007262.4	29,29	0,3,6500	AA,AG,GG		0.0349,0.0,0.0231	probably-damaging,probably-damaging	48/190,48/190	8025436	3,13003	2203	4300	6503	7948023	SO:0001583	missense	11315	exon3			D61380	CCDS93.1	1p36.23	2014-04-11	2011-07-21		ENSG00000116288	ENSG00000116288		"""Parkinson disease"""	16369	protein-coding gene	gene with protein product			"""Parkinson disease (autosomal recessive, early onset) 7"""			11462174, 9070310	Standard	NM_007262		Approved	DJ-1, DJ1	uc001aox.4	Q99497	OTTHUMG00000001210	ENST00000493678.1:c.143G>A	1.37:g.8025436G>A	ENSP00000418770:p.Arg48His	Somatic		Capture	Illumina HiSeq	Phase_I	7948023	NM_007262	B2R4Z1|O14805|Q6DR95|Q7LFU2	Missense_Mutation	SNP	ENST00000493678.1	37	CCDS93.1	.	.	.	.	.	.	.	.	.	.	G	21.5	4.161244	0.78226	0.0	3.49E-4	ENSG00000116288	ENST00000338639;ENST00000493678;ENST00000377491;ENST00000377488	T;T;T;T	0.73363	-0.74;-0.74;-0.74;-0.74	5.62	5.62	0.85841	ThiJ/PfpI (1);	0.097942	0.64402	D	0.000002	T	0.68742	0.3034	L	0.41124	1.26	0.80722	D	1	D	0.59357	0.985	P	0.46585	0.521	T	0.64058	-0.6496	10	0.12766	T	0.61	.	15.5109	0.75782	0.0:0.0:1.0:0.0	.	48	Q99497	PARK7_HUMAN	H	48	ENSP00000340278:R48H;ENSP00000418770:R48H;ENSP00000366711:R48H;ENSP00000366708:R48H	ENSP00000340278:R48H	R	+	2	0	PARK7	7948023	1.000000	0.71417	1.000000	0.80357	0.754000	0.42855	8.126000	0.89592	2.801000	0.96364	0.650000	0.86243	CGT		0.398	PARK7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000003577.1	NM_007262	
UBXN11	91544	broad.mit.edu	37	1	26609406	26609406	+	Missense_Mutation	SNP	C	C	T	rs371990639		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr1:26609406C>T	ENST00000374222.1	-	14	1564	c.1100G>A	c.(1099-1101)cGg>cAg	p.R367Q	UBXN11_ENST00000374223.1_Missense_Mutation_p.R124Q|UBXN11_ENST00000374217.2_Missense_Mutation_p.R334Q|UBXN11_ENST00000374221.3_Missense_Mutation_p.R367Q|UBXN11_ENST00000314675.7_Missense_Mutation_p.R247Q|UBXN11_ENST00000357089.4_Missense_Mutation_p.R334Q			Q5T124	UBX11_HUMAN	UBX domain protein 11	367						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)		p.R367Q(1)		endometrium(3)|kidney(2)|large_intestine(4)|lung(6)|ovary(2)|prostate(3)|upper_aerodigestive_tract(3)	23						CTCCTGGATCCGGGCAGGCAA	0.627																																					p.R247Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G740A	1						.						64.0	72.0	70.0					1																	26609406		2076	4218	6294	26481993	SO:0001583	missense	91544	exon9			AF521017	CCDS41286.1, CCDS41287.1, CCDS41288.1	1p36.11	2008-07-25	2008-07-25	2008-07-25	ENSG00000158062	ENSG00000158062		"""UBX domain containing"""	30600	protein-coding gene	gene with protein product	"""socius"""	609151	"""UBX domain containing 5"""	UBXD5		11940653	Standard	NM_183008		Approved	SOC, SOCI	uc001blw.3	Q5T124	OTTHUMG00000003382	ENST00000374222.1:c.1100G>A	1.37:g.26609406C>T	ENSP00000363339:p.Arg367Gln	Somatic		Capture	Illumina HiSeq	Phase_I	26481993	NM_001077262	D3DPK6|Q5T117|Q5T120|Q5T125|Q5T126|Q5T129|Q5T131|Q5T133|Q63HM6|Q71RB3|Q8IY27|Q8N1L6|Q8N9M4|Q8NA18|Q8NFE3|Q8NFE4|Q8NFE6	Missense_Mutation	SNP	ENST00000374222.1	37	CCDS41288.1	.	.	.	.	.	.	.	.	.	.	C	7.397	0.632056	0.14322	.	.	ENSG00000158062	ENST00000314675;ENST00000374223;ENST00000357089;ENST00000374221;ENST00000374222;ENST00000374217	T;T;T;T;T;T	0.17213	2.29;2.3;2.54;2.54;2.54;2.54	3.87	-0.586	0.11694	.	0.687549	0.12794	N	0.438594	T	0.13798	0.0334	M	0.64997	1.995	0.26662	N	0.971883	B;B;B;B	0.29862	0.098;0.196;0.259;0.059	B;B;B;B	0.16722	0.008;0.011;0.016;0.003	T	0.29549	-1.0008	10	0.17832	T	0.49	-4.6826	8.5498	0.33444	0.0:0.4296:0.4788:0.0916	.	334;329;247;367	Q5T124-2;Q5T124-4;Q5T124-3;Q5T124	.;.;.;UBX11_HUMAN	Q	247;124;334;367;367;334	ENSP00000324721:R247Q;ENSP00000363340:R124Q;ENSP00000349601:R334Q;ENSP00000363338:R367Q;ENSP00000363339:R367Q;ENSP00000363334:R334Q	ENSP00000324721:R247Q	R	-	2	0	UBXN11	26481993	0.000000	0.05858	0.053000	0.19242	0.029000	0.11900	-0.590000	0.05760	-0.079000	0.12707	-0.211000	0.12701	CGG		0.627	UBXN11-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000009500.1	NM_145345	
LIN28A	79727	broad.mit.edu	37	1	26738031	26738031	+	Silent	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr1:26738031C>T	ENST00000326279.6	+	2	300	c.186C>T	c.(184-186)gcC>gcT	p.A62A	LIN28A_ENST00000254231.4_Silent_p.A62A	NM_024674.4	NP_078950.1	Q9H9Z2	LN28A_HUMAN	lin-28 homolog A (C. elegans)	62	CSD.				germ cell development (GO:0007281)|miRNA catabolic process (GO:0010587)|negative regulation of glial cell differentiation (GO:0045686)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of translation (GO:0045727)|pre-miRNA processing (GO:0031054)|regulation of gene silencing by miRNA (GO:0060964)|regulation of transcription, DNA-templated (GO:0006355)|RNA 3'-end processing (GO:0031123)|stem cell maintenance (GO:0019827)	cytoplasm (GO:0005737)|cytoplasmic mRNA processing body (GO:0000932)|cytoplasmic stress granule (GO:0010494)|nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA binding (GO:0003677)|miRNA binding (GO:0035198)|mRNA binding (GO:0003729)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)	p.A62A(1)		central_nervous_system(1)|cervix(1)|endometrium(1)|large_intestine(3)|lung(2)	8						CCGCCCGCGCCGGGGTCGCGC	0.657																																					p.A62A												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C186T	1						.						46.0	51.0	50.0					1																	26738031		2202	4299	6501	26610618	SO:0001819	synonymous_variant	79727	exon2			AF521099	CCDS280.1	1p35.3	2013-01-09	2010-04-06	2010-04-06	ENSG00000131914	ENSG00000131914		"""Zinc fingers, CCHC domain containing"""	15986	protein-coding gene	gene with protein product		611043	"""lin-28 homolog (C. elegans)"""	LIN28		12798299	Standard	XM_006710899		Approved	LIN-28, FLJ12457, ZCCHC1, CSDD1	uc001bmj.3	Q9H9Z2	OTTHUMG00000003550	ENST00000326279.6:c.186C>T	1.37:g.26738031C>T		Somatic		Capture	Illumina HiSeq	Phase_I	26610618	NM_024674		Silent	SNP	ENST00000326279.6	37	CCDS280.1																																																																																				0.657	LIN28A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000009891.2	NM_024674	
ARID1A	8289	broad.mit.edu	37	1	27087503	27087503	+	Nonsense_Mutation	SNP	C	C	T	rs555633429		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr1:27087503C>T	ENST00000324856.7	+	5	2448	c.2077C>T	c.(2077-2079)Cga>Tga	p.R693*	ARID1A_ENST00000374152.2_Nonsense_Mutation_p.R310*|RN7SL501P_ENST00000578818.1_RNA|ARID1A_ENST00000457599.2_Nonsense_Mutation_p.R693*	NM_006015.4	NP_006006.3	O14497	ARI1A_HUMAN	AT rich interactive domain 1A (SWI-like)	693					androgen receptor signaling pathway (GO:0030521)|ATP-dependent chromatin remodeling (GO:0043044)|cardiac chamber development (GO:0003205)|chromatin remodeling (GO:0006338)|chromatin-mediated maintenance of transcription (GO:0048096)|forebrain development (GO:0030900)|glucocorticoid receptor signaling pathway (GO:0042921)|intracellular estrogen receptor signaling pathway (GO:0030520)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural tube closure (GO:0001843)|nucleosome disassembly (GO:0006337)|nucleosome mobilization (GO:0042766)|optic cup formation involved in camera-type eye development (GO:0003408)|placenta blood vessel development (GO:0060674)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nBAF complex (GO:0071565)|npBAF complex (GO:0071564)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|SWI/SNF complex (GO:0016514)	DNA binding (GO:0003677)|ligand-dependent nuclear receptor binding (GO:0016922)|transcription coactivator activity (GO:0003713)	p.R693*(5)	ARID1A/MAST2_ENST00000361297(2)	NS(1)|autonomic_ganglia(1)|biliary_tract(1)|breast(13)|central_nervous_system(6)|cervix(2)|endometrium(56)|haematopoietic_and_lymphoid_tissue(8)|kidney(10)|large_intestine(41)|liver(31)|lung(34)|ovary(130)|pancreas(18)|prostate(8)|skin(9)|stomach(14)|upper_aerodigestive_tract(4)|urinary_tract(24)	411		all_cancers(24;6.36e-27)|all_epithelial(13;5.93e-24)|Colorectal(325;3.46e-05)|all_lung(284;4.76e-05)|Lung NSC(340;5.83e-05)|Breast(348;9.7e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|all cancers(4;2.61e-56)|Epithelial(14;7.53e-55)|OV - Ovarian serous cystadenocarcinoma(117;4.5e-30)|Colorectal(126;2.07e-09)|COAD - Colon adenocarcinoma(152;4.29e-07)|BRCA - Breast invasive adenocarcinoma(304;4.13e-05)|STAD - Stomach adenocarcinoma(196;0.000279)|KIRC - Kidney renal clear cell carcinoma(1967;0.000794)|GBM - Glioblastoma multiforme(114;0.0132)|READ - Rectum adenocarcinoma(331;0.0469)|Lung(427;0.167)|LUSC - Lung squamous cell carcinoma(448;0.242)		GCCTGGCATCCGAGGCCCTTC	0.602			"""Mis, N, F, S, D"""		"""clear cell ovarian carcinoma, RCC"""																																p.R693X			Rec	yes		1	1p35.3	8289	AT rich interactive domain 1A (SWI-like)		E	.	.	5	Substitution - Nonsense(5)	endometrium(4)|large_intestine(1)	c.C2077T	1						.						101.0	99.0	99.0					1																	27087503		2203	4300	6503	26960090	SO:0001587	stop_gained	8289	exon5			AB001895	CCDS285.1, CCDS44091.1	1p36.1-p35	2014-09-17	2006-11-08	2004-01-30	ENSG00000117713	ENSG00000117713		"""-"""	11110	protein-coding gene	gene with protein product		603024	"""SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily f, member 1"", ""AT rich interactive domain 1A (SWI- like)"""	C1orf4, SMARCF1		9630625, 9434167	Standard	NM_139135		Approved	B120, P270, C10rf4, BAF250, BAF250a	uc001bmv.1	O14497	OTTHUMG00000004004	ENST00000324856.7:c.2077C>T	1.37:g.27087503C>T	ENSP00000320485:p.Arg693*	Somatic		Capture	Illumina HiSeq	Phase_I	26960090	NM_006015	D3DPL1|Q53FK9|Q5T0W1|Q5T0W2|Q5T0W3|Q8NFD6|Q96T89|Q9BY33|Q9HBJ5|Q9UPZ1	Nonsense_Mutation	SNP	ENST00000324856.7	37	CCDS285.1	.	.	.	.	.	.	.	.	.	.	C	38	7.181875	0.98118	.	.	ENSG00000117713	ENST00000324856;ENST00000457599;ENST00000374152	.	.	.	5.95	5.95	0.96441	.	0.060823	0.64402	D	0.000004	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-6.2658	13.2963	0.60298	0.2598:0.7402:0.0:0.0	.	.	.	.	X	693;693;310	.	ENSP00000320485:R693X	R	+	1	2	ARID1A	26960090	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	4.464000	0.60134	2.824000	0.97209	0.655000	0.94253	CGA		0.602	ARID1A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000011437.2	NM_139135	
AHDC1	27245	broad.mit.edu	37	1	27875057	27875057	+	Silent	SNP	T	T	C			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr1:27875057T>C	ENST00000247087.5	-	5	4166	c.3570A>G	c.(3568-3570)tcA>tcG	p.S1190S	AHDC1_ENST00000374011.2_Silent_p.S1190S			Q5TGY3	AHDC1_HUMAN	AT hook, DNA binding motif, containing 1	1190							DNA binding (GO:0003677)	p.S1190S(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(8)|lung(20)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	42		all_lung(284;1.06e-05)|Lung NSC(340;1.86e-05)|Colorectal(325;3.46e-05)|Renal(390;0.0007)|Breast(348;0.0021)|Ovarian(437;0.00503)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0434)|OV - Ovarian serous cystadenocarcinoma(117;8.48e-25)|Colorectal(126;9.17e-09)|COAD - Colon adenocarcinoma(152;1.84e-06)|KIRC - Kidney renal clear cell carcinoma(1967;0.00192)|BRCA - Breast invasive adenocarcinoma(304;0.00259)|STAD - Stomach adenocarcinoma(196;0.00311)|READ - Rectum adenocarcinoma(331;0.0291)		CCTCACTACTTGAGGCCTCGC	0.607																																					p.S1190S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.A3570G	1						.						54.0	49.0	50.0					1																	27875057		2203	4300	6503	27747644	SO:0001819	synonymous_variant	27245	exon6			AK125431	CCDS30652.1	1p36.13	2008-02-05			ENSG00000126705	ENSG00000126705			25230	protein-coding gene	gene with protein product		615790				8619474, 9110174	Standard	XM_005245848		Approved	DJ159A19.3, RP1-159A19.1	uc009vsy.3	Q5TGY3	OTTHUMG00000003398	ENST00000247087.5:c.3570A>G	1.37:g.27875057T>C		Somatic		Capture	Illumina HiSeq	Phase_I	27747644	NM_001029882	Q5TGY4|Q6PJK1|Q6ZUQ6|Q99769|Q9NUF5	Silent	SNP	ENST00000247087.5	37	CCDS30652.1																																																																																				0.607	AHDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000009523.3		
COL16A1	1307	broad.mit.edu	37	1	32151695	32151695	+	Silent	SNP	C	C	T	rs368571697		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr1:32151695C>T	ENST00000373672.3	-	28	2397	c.1881G>A	c.(1879-1881)gcG>gcA	p.A627A	COL16A1_ENST00000271069.6_Silent_p.A626A|COL16A1_ENST00000373668.3_Silent_p.A627A	NM_001856.3	NP_001847.3	Q07092	COGA1_HUMAN	collagen, type XVI, alpha 1	627	Collagen-like 2.|Triple-helical region 7 (COL7) with 1 imperfection.				cell adhesion (GO:0007155)|cellular response to amino acid stimulus (GO:0071230)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|female pregnancy (GO:0007565)|integrin-mediated signaling pathway (GO:0007229)	collagen type XVI trimer (GO:0005597)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	integrin binding (GO:0005178)	p.A627A(1)		breast(4)|central_nervous_system(2)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(7)|lung(15)|ovary(8)|prostate(4)	48		Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0423)|all_neural(195;0.0837)|Breast(348;0.116)		STAD - Stomach adenocarcinoma(196;0.059)		GACTCACCTTCGCCCCTTTGA	0.597																																					p.A627A	Colon(143;498 1786 21362 25193 36625)											.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G1881A	1						.	C		0,4300		0,0,2150	95.0	109.0	104.0		1881	2.4	1.0	1		104	3,8451		0,3,4224	no	coding-synonymous	COL16A1	NM_001856.3		0,3,6374	TT,TC,CC		0.0355,0.0,0.0235		627/1605	32151695	3,12751	2150	4227	6377	31924282	SO:0001819	synonymous_variant	1307	exon28			M92642	CCDS41297.1	1p35-p34	2013-01-16			ENSG00000084636	ENSG00000084636		"""Collagens"""	2193	protein-coding gene	gene with protein product		120326				1631157	Standard	NM_001856		Approved		uc001btk.1	Q07092	OTTHUMG00000003883	ENST00000373672.3:c.1881G>A	1.37:g.32151695C>T		Somatic		Capture	Illumina HiSeq	Phase_I	31924282	NM_001856	Q16593|Q59F89|Q71RG9	Silent	SNP	ENST00000373672.3	37	CCDS41297.1																																																																																				0.597	COL16A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011057.2	NM_001856	
KHDRBS1	10657	broad.mit.edu	37	1	32498801	32498801	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr1:32498801C>T	ENST00000327300.7	+	4	804	c.637C>T	c.(637-639)Cgc>Tgc	p.R213C	KHDRBS1_ENST00000307714.8_3'UTR|KHDRBS1_ENST00000492989.1_Missense_Mutation_p.R174C	NM_006559.1	NP_006550.1			KH domain containing, RNA binding, signal transduction associated 1									p.R213C(1)		endometrium(4)|kidney(1)|large_intestine(3)|lung(5)|ovary(1)	14		Myeloproliferative disorder(586;0.0393)|all_neural(195;0.186)				GGAAGAGCTGCGCAAAGGTGG	0.463																																					p.R213C	Ovarian(173;401 1982 12359 31110 42403)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C637T	1						.						99.0	93.0	95.0					1																	32498801		2203	4300	6503	32271388	SO:0001583	missense	10657	exon4			U78971	CCDS350.1, CCDS60067.1	1p32	2008-07-18			ENSG00000121774	ENSG00000121774			18116	protein-coding gene	gene with protein product	"""GAP-associated tyrosine phosphoprotein p62 (Sam68)"""	602489				1374686, 10564820	Standard	NM_006559		Approved	Sam68, p62, FLJ34027	uc001bub.4	Q07666	OTTHUMG00000003921	ENST00000327300.7:c.637C>T	1.37:g.32498801C>T	ENSP00000313829:p.Arg213Cys	Somatic		Capture	Illumina HiSeq	Phase_I	32271388	NM_006559		Missense_Mutation	SNP	ENST00000327300.7	37	CCDS350.1	.	.	.	.	.	.	.	.	.	.	C	23.8	4.456704	0.84317	.	.	ENSG00000121774	ENST00000327300;ENST00000492989;ENST00000355201	T;T	0.19806	2.12;2.12	5.31	5.31	0.75309	K Homology (1);	0.000000	0.85682	D	0.000000	T	0.54870	0.1885	M	0.87758	2.905	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.998;0.999	T	0.61013	-0.7148	10	0.87932	D	0	.	19.4554	0.94886	0.0:1.0:0.0:0.0	.	213;174	Q07666;Q07666-3	KHDR1_HUMAN;.	C	213;174;189	ENSP00000313829:R213C;ENSP00000417731:R174C	ENSP00000313829:R213C	R	+	1	0	KHDRBS1	32271388	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	3.930000	0.56522	2.854000	0.98071	0.655000	0.94253	CGC		0.463	KHDRBS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011199.4	NM_006559	
YARS	8565	broad.mit.edu	37	1	33248074	33248074	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr1:33248074G>A	ENST00000373477.4	-	9	1881	c.973C>T	c.(973-975)Cgg>Tgg	p.R325W	YARS_ENST00000469100.1_5'Flank	NM_003680.3	NP_003671.1	P54577	SYYC_HUMAN	tyrosyl-tRNA synthetase	325					apoptotic process (GO:0006915)|gene expression (GO:0010467)|signal transduction (GO:0007165)|tRNA aminoacylation for protein translation (GO:0006418)|tyrosyl-tRNA aminoacylation (GO:0006437)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular space (GO:0005615)|nucleus (GO:0005634)	ATP binding (GO:0005524)|interleukin-8 receptor binding (GO:0005153)|poly(A) RNA binding (GO:0044822)|signal transducer activity (GO:0004871)|tRNA binding (GO:0000049)|tyrosine-tRNA ligase activity (GO:0004831)	p.R325W(1)		endometrium(2)|kidney(1)|large_intestine(3)|lung(6)|skin(2)|urinary_tract(1)	15		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0837)|Breast(348;0.244)			L-Tyrosine(DB00135)	AACTTTTCCCGGATTGGATCC	0.498																																					p.R325W												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C973T	1						.						113.0	109.0	110.0					1																	33248074		2203	4300	6503	33020661	SO:0001583	missense	8565	exon9			U89436	CCDS368.1	1p35.1	2014-09-17			ENSG00000134684	ENSG00000134684	6.1.1.1	"""Aminoacyl tRNA synthetases / Class I"""	12840	protein-coding gene	gene with protein product	"""tyrosine tRNA ligase 1, cytoplasmic"""	603623				8552597, 9162081	Standard	NM_003680		Approved	YTS, YRS, tyrRS	uc001bvy.1	P54577	OTTHUMG00000003933	ENST00000373477.4:c.973C>T	1.37:g.33248074G>A	ENSP00000362576:p.Arg325Trp	Somatic		Capture	Illumina HiSeq	Phase_I	33020661	NM_003680	B3KWK4|D3DPQ4|O43276|Q53EN1	Missense_Mutation	SNP	ENST00000373477.4	37	CCDS368.1	.	.	.	.	.	.	.	.	.	.	G	18.74	3.688930	0.68271	.	.	ENSG00000134684	ENST00000373477	T	0.75154	-0.91	4.78	1.71	0.24356	.	0.090855	0.85682	D	0.000000	D	0.84750	0.5541	M	0.78049	2.395	0.80722	D	1	D	0.89917	1.0	D	0.81914	0.995	D	0.85871	0.1416	10	0.87932	D	0	-14.2024	14.2692	0.66140	0.0:0.0:0.3225:0.6775	.	325	P54577	SYYC_HUMAN	W	325	ENSP00000362576:R325W	ENSP00000362576:R325W	R	-	1	2	YARS	33020661	1.000000	0.71417	1.000000	0.80357	0.764000	0.43329	3.506000	0.53364	0.267000	0.21916	0.655000	0.94253	CGG		0.498	YARS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011225.1	NM_003680	
HPCA	3208	broad.mit.edu	37	1	33354525	33354525	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr1:33354525G>A	ENST00000373467.3	+	2	128	c.26G>A	c.(25-27)cGg>cAg	p.R9Q	HPCA_ENST00000480118.1_3'UTR	NM_002143.2	NP_002134.2	P84074	HPCA_HUMAN	hippocalcin	9					inner ear development (GO:0048839)		actin binding (GO:0003779)|calcium ion binding (GO:0005509)	p.R9Q(1)		breast(1)|endometrium(1)|large_intestine(1)|lung(2)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	9		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0837)				AGCAAGCTGCGGCCCGAGATG	0.617																																					p.R9Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G26A	1						.						59.0	61.0	60.0					1																	33354525		2203	4300	6503	33127112	SO:0001583	missense	3208	exon2			BC001777	CCDS370.1	1p35-p34.2	2013-01-10			ENSG00000121905	ENSG00000121905		"""EF-hand domain containing"""	5144	protein-coding gene	gene with protein product		142622				8166736, 9931466	Standard	NM_002143		Approved		uc001bwh.3	P84074	OTTHUMG00000004017	ENST00000373467.3:c.26G>A	1.37:g.33354525G>A	ENSP00000362566:p.Arg9Gln	Somatic		Capture	Illumina HiSeq	Phase_I	33127112	NM_002143	B2R9T3|D3DPQ7|P32076|P41211|P70510	Missense_Mutation	SNP	ENST00000373467.3	37	CCDS370.1	.	.	.	.	.	.	.	.	.	.	G	22.8	4.341051	0.81911	.	.	ENSG00000121905	ENST00000373467	T	0.20881	2.04	5.22	5.22	0.72569	EF-hand-like domain (1);	0.000000	0.85682	D	0.000000	T	0.22085	0.0532	L	0.55017	1.72	0.80722	D	1	B	0.30851	0.297	B	0.16722	0.016	T	0.01844	-1.1262	10	0.40728	T	0.16	.	17.9008	0.88902	0.0:0.0:1.0:0.0	.	9	P84074	HPCA_HUMAN	Q	9	ENSP00000362566:R9Q	ENSP00000362566:R9Q	R	+	2	0	HPCA	33127112	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	9.565000	0.98154	2.894000	0.99253	0.655000	0.94253	CGG		0.617	HPCA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011480.1	NM_002143	
CSMD2	114784	broad.mit.edu	37	1	34033233	34033233	+	Silent	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr1:34033233C>T	ENST00000373381.4	-	53	8516	c.8340G>A	c.(8338-8340)caG>caA	p.Q2780Q		NM_001281956.1|NM_052896.3	NP_001268885.1|NP_443128.2	Q7Z408	CSMD2_HUMAN	CUB and Sushi multiple domains 2	2757	Sushi 19. {ECO:0000255|PROSITE- ProRule:PRU00302}.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.Q2757Q(1)		NS(5)|breast(5)|central_nervous_system(3)|cervix(2)|endometrium(20)|haematopoietic_and_lymphoid_tissue(4)|kidney(9)|large_intestine(43)|lung(114)|ovary(8)|pancreas(1)|prostate(6)|skin(20)|upper_aerodigestive_tract(5)|urinary_tract(1)	246		Myeloproliferative disorder(586;0.0294)|all_neural(195;0.249)				GATGATCCTGCTGGCAGATGC	0.547																																					p.Q2757Q												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G8271A	1						.						128.0	100.0	110.0					1																	34033233		2203	4300	6503	33805820	SO:0001819	synonymous_variant	114784	exon54			AY210418	CCDS380.1, CCDS60082.1	1p34.3	2014-01-28			ENSG00000121904	ENSG00000121904			19290	protein-coding gene	gene with protein product		608398				11472063, 11572484	Standard	NM_001281956		Approved	KIAA1884	uc001bxn.1	Q7Z408	OTTHUMG00000011135	ENST00000373381.4:c.8340G>A	1.37:g.34033233C>T		Somatic		Capture	Illumina HiSeq	Phase_I	33805820	NM_052896	B1AM50|E7EUA6|Q53TY4|Q5VT59|Q8N963|Q96Q03|Q9H4V7|Q9H4V8|Q9H4V9|Q9H4W0|Q9H4W1|Q9H4W2|Q9H4W3|Q9H4W4|Q9HCY5|Q9HCY6|Q9HCY7	Silent	SNP	ENST00000373381.4	37																																																																																					0.547	CSMD2-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_052896	
GJB4	127534	broad.mit.edu	37	1	35227066	35227066	+	Missense_Mutation	SNP	G	G	A	rs370587030		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr1:35227066G>A	ENST00000339480.1	+	2	581	c.211G>A	c.(211-213)Gtg>Atg	p.V71M	RP1-34M23.5_ENST00000542839.1_RNA	NM_153212.2	NP_694944.1	Q9NTQ9	CXB4_HUMAN	gap junction protein, beta 4, 30.3kDa	71					cell communication (GO:0007154)|olfactory behavior (GO:0042048)|sensory perception of smell (GO:0007608)	connexon complex (GO:0005922)|integral component of membrane (GO:0016021)		p.V71M(1)		breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(6)|ovary(2)|skin(1)	16		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.234)				GTTCTTCCCCGTGTCCCACGT	0.637																																					p.V71M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G211A	1						.	G	MET/VAL	0,4406		0,0,2203	146.0	107.0	120.0		211	2.6	1.0	1		120	1,8599	1.2+/-3.3	0,1,4299	no	missense	GJB4	NM_153212.2	21	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging	71/267	35227066	1,13005	2203	4300	6503	34999653	SO:0001583	missense	127534	exon2				CCDS383.1	1p35-p34	2008-05-14	2007-11-06		ENSG00000189433	ENSG00000189433		"""Ion channels / Gap junction proteins (connexins)"""	4286	protein-coding gene	gene with protein product	"""connexin 30.3"""	605425	"""gap junction protein, beta 4 (connexin 30.3)"", ""gap junction protein, beta 4"""				Standard	NM_153212		Approved	CX30.3	uc001bxv.1	Q9NTQ9	OTTHUMG00000004052	ENST00000339480.1:c.211G>A	1.37:g.35227066G>A	ENSP00000345868:p.Val71Met	Somatic		Capture	Illumina HiSeq	Phase_I	34999653	NM_153212	B3KQ82	Missense_Mutation	SNP	ENST00000339480.1	37	CCDS383.1	.	.	.	.	.	.	.	.	.	.	G	19.45	3.829325	0.71258	0.0	1.16E-4	ENSG00000189433	ENST00000339480	D	0.99287	-5.69	5.56	2.61	0.31194	Connexin, N-terminal (2);	0.155859	0.42420	D	0.000704	D	0.99111	0.9694	M	0.82323	2.585	0.30442	N	0.776061	D	0.71674	0.998	D	0.69307	0.963	D	0.96749	0.9552	10	0.87932	D	0	.	6.4465	0.21879	0.1731:0.1724:0.6544:0.0	.	71	Q9NTQ9	CXB4_HUMAN	M	71	ENSP00000345868:V71M	ENSP00000345868:V71M	V	+	1	0	GJB4	34999653	0.323000	0.24643	1.000000	0.80357	0.998000	0.95712	0.675000	0.25232	1.335000	0.45486	0.655000	0.94253	GTG		0.637	GJB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011560.1	NM_153212	
TEKT2	27285	broad.mit.edu	37	1	36552839	36552839	+	Missense_Mutation	SNP	C	C	T	rs41267269		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr1:36552839C>T	ENST00000207457.3	+	7	909	c.782C>T	c.(781-783)aCg>aTg	p.T261M	ADPRHL2_ENST00000373178.4_5'Flank	NM_014466.2	NP_055281.2	Q9UIF3	TEKT2_HUMAN	tektin 2 (testicular)	261					cell projection organization (GO:0030030)|inner dynein arm assembly (GO:0036159)|sperm motility (GO:0030317)	cytoplasm (GO:0005737)|microtubule (GO:0005874)|motile cilium (GO:0031514)|nucleus (GO:0005634)		p.T261M(1)		breast(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(1)|lung(2)|pancreas(1)|skin(2)	13		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.164)				AGAGTTGCAACGGAATTTGCC	0.532																																					p.T261M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C782T	1						.	C	MET/THR	0,4406		0,0,2203	69.0	71.0	71.0		782	4.6	0.2	1	dbSNP_127	71	1,8599	1.2+/-3.3	0,1,4299	no	missense	TEKT2	NM_014466.2	81	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging	261/431	36552839	1,13005	2203	4300	6503	36325426	SO:0001583	missense	27285	exon7			AB033823	CCDS401.1	1p34.3	2008-02-05			ENSG00000092850	ENSG00000092850			11725	protein-coding gene	gene with protein product		608953				12029069, 11751288	Standard	NM_014466		Approved	TEKTB1	uc001bzr.3	Q9UIF3	OTTHUMG00000007629	ENST00000207457.3:c.782C>T	1.37:g.36552839C>T	ENSP00000207457:p.Thr261Met	Somatic		Capture	Illumina HiSeq	Phase_I	36325426	NM_014466	A6NIS6|O60638	Missense_Mutation	SNP	ENST00000207457.3	37	CCDS401.1	.	.	.	.	.	.	.	.	.	.	C	15.92	2.973995	0.53720	0.0	1.16E-4	ENSG00000092850	ENST00000207457	T	0.03065	4.06	5.49	4.58	0.56647	.	0.318671	0.38605	N	0.001623	T	0.15955	0.0384	M	0.80982	2.52	0.19300	N	0.999975	D	0.76494	0.999	D	0.65874	0.939	T	0.03344	-1.1046	10	0.62326	D	0.03	.	10.6577	0.45684	0.0:0.8531:0.0:0.1469	rs41267269	261	Q9UIF3	TEKT2_HUMAN	M	261	ENSP00000207457:T261M	ENSP00000207457:T261M	T	+	2	0	TEKT2	36325426	0.637000	0.27216	0.173000	0.22940	0.972000	0.66771	2.963000	0.49184	1.323000	0.45263	-0.244000	0.11960	ACG		0.532	TEKT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000020200.1	NM_014466	
MACF1	23499	broad.mit.edu	37	1	39913120	39913120	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr1:39913120C>T	ENST00000372915.3	+	80	19406	c.19319C>T	c.(19318-19320)gCc>gTc	p.A6440V	MACF1_ENST00000567887.1_Missense_Mutation_p.A6578V|MACF1_ENST00000564288.1_Missense_Mutation_p.A6541V|MACF1_ENST00000289893.4_Missense_Mutation_p.A4984V|MACF1_ENST00000539005.1_Missense_Mutation_p.A4352V|MACF1_ENST00000545844.1_Missense_Mutation_p.A4482V|MACF1_ENST00000361689.2_Missense_Mutation_p.A4482V|MACF1_ENST00000317713.7_Missense_Mutation_p.A4482V			Q9UPN3	MACF1_HUMAN	microtubule-actin crosslinking factor 1	6440					ATP catabolic process (GO:0006200)|cell cycle arrest (GO:0007050)|Golgi to plasma membrane protein transport (GO:0043001)|positive regulation of Wnt signaling pathway (GO:0030177)|regulation of epithelial cell migration (GO:0010632)|regulation of focal adhesion assembly (GO:0051893)|regulation of microtubule-based process (GO:0032886)|Wnt signaling pathway (GO:0016055)|wound healing (GO:0042060)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|ATPase activity (GO:0016887)|calcium ion binding (GO:0005509)|poly(A) RNA binding (GO:0044822)	p.A4984V(1)|p.A4482V(1)		breast(11)|central_nervous_system(5)|endometrium(18)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(36)|lung(78)|ovary(12)|prostate(2)|skin(9)|stomach(2)|upper_aerodigestive_tract(8)|urinary_tract(10)	203	Lung NSC(20;5.57e-06)|Ovarian(52;0.00769)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;7.78e-19)|Epithelial(16;1.73e-17)|all cancers(16;2.49e-16)|LUSC - Lung squamous cell carcinoma(16;0.00146)|Lung(16;0.00204)			CTGGAAGAGGCCCTCAACTTG	0.428																																					p.A4482V												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.C13445T	1						.						76.0	79.0	78.0					1																	39913120		2203	4300	6503	39685707	SO:0001583	missense	23499	exon78			AB007934	CCDS435.1	1p32-p31	2013-01-10			ENSG00000127603	ENSG00000127603		"""EF-hand domain containing"""	13664	protein-coding gene	gene with protein product	"""actin cross-linking factor"", ""620 kDa actin binding protein"", ""macrophin 1"", ""trabeculin-alpha"", ""actin cross-linking family protein 7"""	608271				7635207, 10529403	Standard	NM_012090		Approved	KIAA0465, ACF7, ABP620, KIAA1251, MACF, FLJ45612, FLJ46776	uc031pmc.1	Q9UPN3	OTTHUMG00000007754	ENST00000372915.3:c.19319C>T	1.37:g.39913120C>T	ENSP00000362006:p.Ala6440Val	Somatic		Capture	Illumina HiSeq	Phase_I	39685707	NM_012090	B1ALC5|E9PJT0|O75053|Q5VW20|Q8WXY1|Q8WXY2|Q96PK2|Q9H540|Q9UKP0|Q9ULG9	Missense_Mutation	SNP	ENST00000372915.3	37		.	.	.	.	.	.	.	.	.	.	C	17.17	3.322119	0.60634	.	.	ENSG00000127603	ENST00000545844;ENST00000372915;ENST00000361689;ENST00000317713;ENST00000539005;ENST00000289893	T;T;T;T;T;T	0.57436	1.15;0.4;1.15;1.15;1.15;0.4	6.07	5.07	0.68467	.	0.195004	0.36101	N	0.002794	T	0.69708	0.3141	M	0.87269	2.87	0.80722	D	1	P;D	0.58268	0.942;0.982	P;P	0.55055	0.463;0.767	T	0.74362	-0.3690	10	0.59425	D	0.04	.	13.8409	0.63437	0.0:0.9015:0.0:0.0985	.	6440;4482	Q9UPN3;F8W8Q1	MACF1_HUMAN;.	V	4482;6440;4482;4482;4352;4984	ENSP00000439537:A4482V;ENSP00000362006:A6440V;ENSP00000354573:A4482V;ENSP00000313438:A4482V;ENSP00000444364:A4352V;ENSP00000289893:A4984V	ENSP00000289893:A4984V	A	+	2	0	MACF1	39685707	0.999000	0.42202	1.000000	0.80357	0.999000	0.98932	4.034000	0.57289	2.890000	0.99128	0.650000	0.86243	GCC		0.428	MACF1-028	NOVEL	not_organism_supported|basic|appris_candidate|exp_conf	protein_coding	protein_coding	OTTHUMT00000392096.1	NM_033044	
CCDC30	728621	broad.mit.edu	37	1	43110443	43110443	+	Nonsense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr1:43110443C>T	ENST00000340612.4	+	12	1855	c.1855C>T	c.(1855-1857)Cga>Tga	p.R619*	CCDC30_ENST00000390640.4_Nonsense_Mutation_p.R408*|CCDC30_ENST00000428554.2_Nonsense_Mutation_p.R619*|CCDC30_ENST00000507855.1_Nonsense_Mutation_p.R408*|CCDC30_ENST00000342022.4_Nonsense_Mutation_p.R619*			Q5VVM6	CCD30_HUMAN	coiled-coil domain containing 30	619						extracellular vesicular exosome (GO:0070062)		p.R619*(1)		endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|lung(11)|ovary(1)|pancreas(1)|prostate(1)|urinary_tract(2)	30						CTTCTTAGAGCGAATTATAAG	0.423																																					p.R619X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.C1855T	1						.						123.0	107.0	112.0					1																	43110443		2203	4300	6503	42883030	SO:0001587	stop_gained	728621	exon13			AY639646	CCDS30690.1	1p34.2	2009-07-09			ENSG00000186409	ENSG00000186409			26103	protein-coding gene	gene with protein product	"""prefoldin 6-like"""					16710767	Standard	NM_001080850		Approved	FLJ20972, PFD6L, LOC728621	uc009vwk.1	Q5VVM6	OTTHUMG00000007334	ENST00000340612.4:c.1855C>T	1.37:g.43110443C>T	ENSP00000340378:p.Arg619*	Somatic		Capture	Illumina HiSeq	Phase_I	42883030	NM_001080850	Q14F06|Q5VVM5	Nonsense_Mutation	SNP	ENST00000340612.4	37	CCDS30690.1	.	.	.	.	.	.	.	.	.	.	C	24.3	4.521085	0.85495	.	.	ENSG00000186409	ENST00000428554;ENST00000507855;ENST00000340612;ENST00000342022;ENST00000390640	.	.	.	5.5	3.6	0.41247	.	0.517808	0.19144	N	0.121626	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	11.4645	0.50230	0.3271:0.6729:0.0:0.0	.	.	.	.	X	619;408;619;619;408	.	ENSP00000340378:R619X	R	+	1	2	CCDC30	42883030	0.982000	0.34865	0.018000	0.16275	0.893000	0.52053	2.589000	0.46145	0.769000	0.33313	0.655000	0.94253	CGA		0.423	CCDC30-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019524.3	NM_025030	
TIE1	7075	broad.mit.edu	37	1	43779015	43779015	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr1:43779015C>T	ENST00000372476.3	+	13	2216	c.2137C>T	c.(2137-2139)Cgc>Tgc	p.R713C	TIE1_ENST00000433781.2_Missense_Mutation_p.R358C|TIE1_ENST00000473014.1_3'UTR	NM_001253357.1|NM_005424.4	NP_001240286.1|NP_005415.1	P35590	TIE1_HUMAN	tyrosine kinase with immunoglobulin-like and EGF-like domains 1	713	Fibronectin type-III 3. {ECO:0000255|PROSITE-ProRule:PRU00316}.				angiogenesis (GO:0001525)|in utero embryonic development (GO:0001701)|mesoderm development (GO:0007498)|negative regulation of angiogenesis (GO:0016525)|negative regulation of cell migration (GO:0030336)|peptidyl-tyrosine phosphorylation (GO:0018108)|plasma membrane fusion (GO:0045026)|response to retinoic acid (GO:0032526)|signal transduction (GO:0007165)|vasculogenesis (GO:0001570)	integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)	p.R713C(1)		breast(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(8)|lung(28)|ovary(3)|prostate(2)|salivary_gland(1)|skin(10)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(4)	70	Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0505)				CGCCAGCACGCGCTACCTCTT	0.647																																					p.R713C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C2137T	1						.						146.0	119.0	128.0					1																	43779015		2203	4300	6503	43551602	SO:0001583	missense	7075	exon13			BC038239	CCDS482.1	1p34-p33	2013-02-11	2004-12-13	2004-12-14	ENSG00000066056	ENSG00000066056	2.7.10.1	"""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	11809	protein-coding gene	gene with protein product		600222	"""tyrosine kinase with immunoglobulin and epidermal growth factor homology domains 1"""	TIE		1312667	Standard	NM_005424		Approved	JTK14	uc001ciu.3	P35590	OTTHUMG00000007282	ENST00000372476.3:c.2137C>T	1.37:g.43779015C>T	ENSP00000361554:p.Arg713Cys	Somatic		Capture	Illumina HiSeq	Phase_I	43551602	NM_005424	B5A949|B5A950	Missense_Mutation	SNP	ENST00000372476.3	37	CCDS482.1	.	.	.	.	.	.	.	.	.	.	C	8.995	0.978605	0.18812	.	.	ENSG00000066056	ENST00000372476;ENST00000372475;ENST00000433781	T;T	0.58060	0.36;0.36	5.57	3.6	0.41247	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.180201	0.27076	N	0.021059	T	0.41119	0.1145	L	0.50333	1.59	0.20403	N	0.999907	B;B;B;B;B	0.10296	0.0;0.001;0.001;0.001;0.003	B;B;B;B;B	0.06405	0.0;0.002;0.002;0.0;0.002	T	0.31696	-0.9934	10	0.45353	T	0.12	.	4.317	0.10998	0.1611:0.5091:0.0:0.3299	.	358;668;713;358;713	E9PG63;B4DTW8;B5A952;B4DKW0;P35590	.;.;.;.;TIE1_HUMAN	C	713;116;358	ENSP00000361554:R713C;ENSP00000411728:R358C	ENSP00000361553:R116C	R	+	1	0	TIE1	43551602	0.000000	0.05858	0.910000	0.35882	0.439000	0.31926	0.105000	0.15333	1.252000	0.44001	0.655000	0.94253	CGC		0.647	TIE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019011.1	NM_005424	
SLC6A9	6536	broad.mit.edu	37	1	44463274	44463274	+	Silent	SNP	C	C	T	rs201082592		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr1:44463274C>T	ENST00000360584.2	-	14	2255	c.2064G>A	c.(2062-2064)gcG>gcA	p.A688A	SLC6A9_ENST00000357730.2_Silent_p.A634A|SLC6A9_ENST00000372307.3_Intron|SLC6A9_ENST00000372310.3_Silent_p.A615A|SLC6A9_ENST00000372306.3_Intron|SLC6A9_ENST00000475075.2_Silent_p.A504A	NM_201649.3	NP_964012.2	P48067	SC6A9_HUMAN	solute carrier family 6 (neurotransmitter transporter, glycine), member 9	688					transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	glycine:sodium symporter activity (GO:0015375)|neurotransmitter:sodium symporter activity (GO:0005328)	p.A688A(1)|p.A615A(1)		endometrium(3)|large_intestine(8)|lung(7)|ovary(1)|skin(1)|urinary_tract(2)	22	Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0511)			Glycine(DB00145)	TGGGGATCTGCGCCTTGTCCG	0.692													C|||	1	0.000199681	0.0	0.0014	5008	,	,		16179	0.0		0.0	False		,,,				2504	0.0				p.A688A												.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.G2064A	1						.						66.0	78.0	74.0					1																	44463274		2203	4300	6503	44235861	SO:0001819	synonymous_variant	6536	exon14			S70609	CCDS30695.1, CCDS41316.1, CCDS41317.1	1p33	2013-05-22			ENSG00000196517	ENSG00000196517		"""Solute carriers"""	11056	protein-coding gene	gene with protein product		601019				8183239, 7587377	Standard	NM_006934		Approved	GLYT1	uc001cll.4	P48067	OTTHUMG00000008294	ENST00000360584.2:c.2064G>A	1.37:g.44463274C>T		Somatic		Capture	Illumina HiSeq	Phase_I	44235861	NM_201649	A6NDH1|A6NII2|A6NNZ8|Q5TAB8|Q5TAB9|Q5TAC0	Silent	SNP	ENST00000360584.2	37	CCDS41317.1																																																																																				0.692	SLC6A9-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000022825.2	NM_201649	
DMAP1	55929	broad.mit.edu	37	1	44684829	44684829	+	Silent	SNP	G	G	A	rs566877674	byFrequency	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr1:44684829G>A	ENST00000372289.2	+	6	1085	c.822G>A	c.(820-822)gcG>gcA	p.A274A	DMAP1_ENST00000361745.6_Silent_p.A274A|DMAP1_ENST00000315913.5_Silent_p.A274A|DMAP1_ENST00000488433.1_3'UTR	NM_019100.4	NP_061973.1	Q9NPF5	DMAP1_HUMAN	DNA methyltransferase 1 associated protein 1	274					chromatin organization (GO:0006325)|chromatin remodeling (GO:0006338)|DNA methylation (GO:0006306)|DNA repair (GO:0006281)|histone H2A acetylation (GO:0043968)|histone H4 acetylation (GO:0043967)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription factor import into nucleus (GO:0042993)|regulation of growth (GO:0040008)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|NuA4 histone acetyltransferase complex (GO:0035267)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|replication fork (GO:0005657)	chromatin binding (GO:0003682)|RNA polymerase II repressing transcription factor binding (GO:0001103)|transcription corepressor activity (GO:0003714)	p.A274A(1)		breast(1)|cervix(1)|endometrium(6)|large_intestine(1)|lung(4)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	16	Acute lymphoblastic leukemia(166;0.155)					TGATCACAGCGGCAGACACCA	0.617													G|||	3	0.000599042	0.0	0.0	5008	,	,		19266	0.0		0.001	False		,,,				2504	0.002				p.A274A												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G822A	1						.						54.0	56.0	55.0					1																	44684829		2203	4300	6503	44457416	SO:0001819	synonymous_variant	55929	exon7			AB037846	CCDS509.1	1p34	2009-07-13			ENSG00000178028	ENSG00000178028			18291	protein-coding gene	gene with protein product		605077				10888872, 10718198	Standard	XM_005271039		Approved	DNMAP1, FLJ11543, KIAA1425, DNMTAP1, EAF2, MEAF2, SWC4	uc001clq.1	Q9NPF5	OTTHUMG00000007577	ENST00000372289.2:c.822G>A	1.37:g.44684829G>A		Somatic		Capture	Illumina HiSeq	Phase_I	44457416	NM_001034023	A8K001|D3DPY8|Q0JSM4|Q5TG41|Q7Z3H7|Q9H0S8|Q9P2C2	Silent	SNP	ENST00000372289.2	37	CCDS509.1																																																																																				0.617	DMAP1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000020027.3	NM_019100	
HECTD3	79654	broad.mit.edu	37	1	45474833	45474833	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr1:45474833C>T	ENST00000372172.4	-	7	1126	c.1055G>A	c.(1054-1056)cGc>cAc	p.R352H	UROD_ENST00000246337.4_5'Flank|HECTD3_ENST00000372168.3_5'Flank	NM_024602.5	NP_078878.3	Q5T447	HECD3_HUMAN	HECT domain containing E3 ubiquitin protein ligase 3	352	DOC. {ECO:0000255|PROSITE- ProRule:PRU00614}.				proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)	p.R68H(1)|p.R352H(1)		breast(1)|central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(5)|lung(11)|prostate(1)|stomach(1)	28	Acute lymphoblastic leukemia(166;0.155)					CTCCACGATGCGGATCTCGAT	0.562																																					p.R352H												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G1055A	1						.						63.0	63.0	63.0					1																	45474833		1988	4158	6146	45247420	SO:0001583	missense	79654	exon7			BC019105	CCDS41318.1	1p34.1	2012-02-23	2012-02-23		ENSG00000126107	ENSG00000126107			26117	protein-coding gene	gene with protein product			"""HECT domain containing 3"""			12477932	Standard	NM_024602		Approved	FLJ21156	uc009vxk.3	Q5T447	OTTHUMG00000008587	ENST00000372172.4:c.1055G>A	1.37:g.45474833C>T	ENSP00000361245:p.Arg352His	Somatic		Capture	Illumina HiSeq	Phase_I	45247420	NM_024602	B3KPV7|B3KRH4|Q5T448|Q9H783	Missense_Mutation	SNP	ENST00000372172.4	37	CCDS41318.1	.	.	.	.	.	.	.	.	.	.	C	19.71	3.877551	0.72294	.	.	ENSG00000126107	ENST00000372172	T	0.72167	-0.63	4.08	4.08	0.47627	Anaphase-promoting complex, subunit 10/DOC domain (2);Galactose-binding domain-like (1);	0.000000	0.85682	D	0.000000	T	0.79179	0.4402	M	0.73962	2.25	0.80722	D	1	D	0.71674	0.998	P	0.60236	0.871	T	0.80103	-0.1522	10	0.51188	T	0.08	.	10.5277	0.44958	0.0:0.9106:0.0:0.0894	.	352	Q5T447	HECD3_HUMAN	H	352	ENSP00000361245:R352H	ENSP00000361245:R352H	R	-	2	0	HECTD3	45247420	1.000000	0.71417	1.000000	0.80357	0.683000	0.39861	5.219000	0.65262	2.273000	0.75805	0.655000	0.94253	CGC		0.562	HECTD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000023734.1	NM_024602	
RAD54L	8438	broad.mit.edu	37	1	46733194	46733194	+	Missense_Mutation	SNP	C	C	T	rs142375065	byFrequency	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr1:46733194C>T	ENST00000371975.4	+	9	1629	c.955C>T	c.(955-957)Cgg>Tgg	p.R319W	RAD54L_ENST00000442598.1_Missense_Mutation_p.R319W|RAD54L_ENST00000473251.1_3'UTR	NM_003579.3	NP_003570.2	Q92698	RAD54_HUMAN	RAD54-like (S. cerevisiae)	319	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				chromosome organization (GO:0051276)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|DNA strand renaturation (GO:0000733)|double-strand break repair via homologous recombination (GO:0000724)|meiotic nuclear division (GO:0007126)|response to drug (GO:0042493)|response to ionizing radiation (GO:0010212)	nucleus (GO:0005634)	annealing helicase activity (GO:0036310)|ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)	p.R319W(1)		breast(2)|cervix(1)|kidney(3)|large_intestine(5)|liver(1)|lung(6)|ovary(2)|skin(3)|upper_aerodigestive_tract(2)	25	Acute lymphoblastic leukemia(166;0.155)	Breast(1374;0.0634)		KIRC - Kidney renal clear cell carcinoma(1967;0.000896)		GAACACCAGCCGGCGGGTGCT	0.488								Direct reversal of damage;Homologous recombination					C|||	2	0.000399361	0.0008	0.0	5008	,	,		19643	0.001		0.0	False		,,,				2504	0.0				p.R319W												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C955T	1						.	C	TRP/ARG,TRP/ARG	1,4405	2.1+/-5.4	0,1,2202	82.0	81.0	81.0		955,955	4.4	1.0	1	dbSNP_134	81	0,8600		0,0,4300	no	missense,missense	RAD54L	NM_001142548.1,NM_003579.3	101,101	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	probably-damaging,probably-damaging	319/748,319/748	46733194	1,13005	2203	4300	6503	46505781	SO:0001583	missense	8438	exon10			X97795	CCDS532.1	1p32	2008-02-05	2001-11-28		ENSG00000085999	ENSG00000085999			9826	protein-coding gene	gene with protein product		603615	"""RAD54 (S.cerevisiae)-like"""			8805304	Standard	NM_003579		Approved	hHR54, hRAD54, RAD54A	uc009vye.2	Q92698	OTTHUMG00000007772	ENST00000371975.4:c.955C>T	1.37:g.46733194C>T	ENSP00000361043:p.Arg319Trp	Somatic		Capture	Illumina HiSeq	Phase_I	46505781	NM_001142548	Q5TE31|Q6IUY3	Missense_Mutation	SNP	ENST00000371975.4	37	CCDS532.1	.	.	.	.	.	.	.	.	.	.	C	21.3	4.134590	0.77662	2.27E-4	0.0	ENSG00000085999	ENST00000442598;ENST00000371975;ENST00000535499	D;D	0.93426	-3.22;-3.22	5.34	4.41	0.53225	DEAD-like helicase (2);SNF2-related (1);	0.000000	0.85682	D	0.000000	D	0.97256	0.9103	M	0.91354	3.2	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.999;1.0	D	0.98018	1.0369	10	0.87932	D	0	-14.8197	15.2305	0.73383	0.1417:0.8583:0.0:0.0	.	139;319	G3V1N0;Q92698	.;RAD54_HUMAN	W	319;319;139	ENSP00000396113:R319W;ENSP00000361043:R319W	ENSP00000361043:R319W	R	+	1	2	RAD54L	46505781	1.000000	0.71417	0.997000	0.53966	0.857000	0.48899	2.839000	0.48207	1.196000	0.43129	0.561000	0.74099	CGG		0.488	RAD54L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021272.1	NM_003579	
FAAH	2166	broad.mit.edu	37	1	46874247	46874247	+	Silent	SNP	G	G	T	rs45476901		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr1:46874247G>T	ENST00000243167.8	+	8	1152	c.1068G>T	c.(1066-1068)gcG>gcT	p.A356A	FAAH_ENST00000493735.1_3'UTR	NM_001441.2	NP_001432.2	O00519	FAAH1_HUMAN	fatty acid amide hydrolase	356					fatty acid catabolic process (GO:0009062)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|integral component of membrane (GO:0016021)|organelle membrane (GO:0031090)	acylglycerol lipase activity (GO:0047372)|carbon-nitrogen ligase activity, with glutamine as amido-N-donor (GO:0016884)|fatty acid amide hydrolase activity (GO:0017064)	p.A356A(1)		breast(3)|endometrium(4)|kidney(2)|large_intestine(3)|lung(7)|ovary(2)|skin(1)	22	Acute lymphoblastic leukemia(166;0.155)				Propofol(DB00818)|Thiopental(DB00599)	TTGAGGCTGCGGGGCACACGG	0.617																																					p.A356A												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G1068T	1						.						150.0	154.0	153.0					1																	46874247		2203	4300	6503	46646834	SO:0001819	synonymous_variant	2166	exon8			U82535	CCDS535.1	1p35-p34	2008-02-05			ENSG00000117480	ENSG00000117480			3553	protein-coding gene	gene with protein product		602935				9122178	Standard	NM_001441		Approved	FAAH-1	uc001cpu.2	O00519	OTTHUMG00000007811	ENST00000243167.8:c.1068G>T	1.37:g.46874247G>T		Somatic		Capture	Illumina HiSeq	Phase_I	46646834	NM_001441	D3DQ19|Q52M86|Q5TDF8	Silent	SNP	ENST00000243167.8	37	CCDS535.1																																																																																				0.617	FAAH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021443.1	NM_001441	
CDKN2C	1031	broad.mit.edu	37	1	51439665	51439665	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr1:51439665C>T	ENST00000262662.1	+	4	2264	c.230C>T	c.(229-231)gCg>gTg	p.A77V	CDKN2C_ENST00000371761.3_Missense_Mutation_p.A77V|CDKN2C_ENST00000396148.1_Missense_Mutation_p.A77V			P42773	CDN2C_HUMAN	cyclin-dependent kinase inhibitor 2C (p18, inhibits CDK4)	77					cell cycle arrest (GO:0007050)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of phosphorylation (GO:0042326)|negative regulation of protein serine/threonine kinase activity (GO:0071901)|oligodendrocyte differentiation (GO:0048709)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	cyclin-dependent protein serine/threonine kinase inhibitor activity (GO:0004861)|protein kinase binding (GO:0019901)	p.0?(11)|p.?(1)|p.A77V(1)		central_nervous_system(8)|haematopoietic_and_lymphoid_tissue(5)|kidney(2)|large_intestine(2)|lung(2)|ovary(2)|prostate(1)|thyroid(1)	23				GBM - Glioblastoma multiforme(3;3.61e-13)|all cancers(3;0.00151)		ATTCATGATGCGGCCAGAGCA	0.473			D		"""glioma, MM"""																																p.A77V	Melanoma(47;50 1155 4767 22863 47597)		Rec	yes		1	1p32	1031	"""cyclin-dependent kinase inhibitor 2C (p18, inhibits CDK4)"""		"""O, L"""	.	.	13	Whole gene deletion(11)|Substitution - Missense(1)|Unknown(1)	central_nervous_system(6)|haematopoietic_and_lymphoid_tissue(5)|thyroid(1)|large_intestine(1)	c.C230T	1						.						96.0	91.0	93.0					1																	51439665		2203	4300	6503	51212253	SO:0001583	missense	1031	exon2			BC000598	CCDS555.1	1p32.3	2013-01-10			ENSG00000123080	ENSG00000123080		"""Ankyrin repeat domain containing"""	1789	protein-coding gene	gene with protein product		603369				8001816, 9636670	Standard	NM_001262		Approved	INK4C, p18	uc001csg.3	P42773	OTTHUMG00000008046	ENST00000262662.1:c.230C>T	1.37:g.51439665C>T	ENSP00000262662:p.Ala77Val	Somatic		Capture	Illumina HiSeq	Phase_I	51212253	NM_078626	Q8TB83	Missense_Mutation	SNP	ENST00000262662.1	37	CCDS555.1	.	.	.	.	.	.	.	.	.	.	C	17.95	3.513765	0.64522	.	.	ENSG00000123080	ENST00000262662;ENST00000396148;ENST00000371761	D;D;D	0.81579	-1.51;-1.51;-1.51	5.31	5.31	0.75309	Ankyrin repeat-containing domain (3);	0.109616	0.64402	D	0.000008	D	0.83252	0.5214	M	0.91818	3.245	0.58432	D	0.999996	B	0.31077	0.307	B	0.26202	0.067	D	0.84569	0.0654	10	0.72032	D	0.01	-4.5328	12.8814	0.58020	0.0:0.9163:0.0:0.0837	.	77	P42773	CDN2C_HUMAN	V	77	ENSP00000262662:A77V;ENSP00000379452:A77V;ENSP00000360826:A77V	ENSP00000262662:A77V	A	+	2	0	CDKN2C	51212253	1.000000	0.71417	0.997000	0.53966	0.991000	0.79684	4.993000	0.63895	2.770000	0.95276	0.655000	0.94253	GCG		0.473	CDKN2C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022058.1	NM_001262	
ORC1	4998	broad.mit.edu	37	1	52854183	52854183	+	Silent	SNP	A	A	C			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr1:52854183A>C	ENST00000371568.3	-	8	1532	c.1314T>G	c.(1312-1314)acT>acG	p.T438T	ORC1_ENST00000371566.1_Silent_p.T438T	NM_001190818.1|NM_001190819.1|NM_004153.3	NP_001177747.1|NP_001177748.1|NP_004144.2	Q13415	ORC1_HUMAN	origin recognition complex, subunit 1	438					DNA replication (GO:0006260)|DNA replication initiation (GO:0006270)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear origin of replication recognition complex (GO:0005664)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|origin recognition complex (GO:0000808)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)	p.T438T(1)		breast(1)|cervix(2)|endometrium(4)|kidney(4)|large_intestine(9)|lung(9)|ovary(1)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	37						TCCTGGACACAGTTCTGGGTG	0.488																																					p.T438T												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.T1314G	1						.						240.0	216.0	224.0					1																	52854183		2203	4300	6503	52626771	SO:0001819	synonymous_variant	4998	exon8				CCDS566.1	1p32	2010-10-12	2010-10-12	2010-10-12	ENSG00000085840	ENSG00000085840		"""ATPases / AAA-type"""	8487	protein-coding gene	gene with protein product	"""origin recognition complex, subunit 1, S. cerevisiae, homolog-like"", ""origin recognition complex 1"", ""replication control protein 1"""	601902	"""origin recognition complex, subunit 1 (yeast homolog)-like"", ""origin recognition complex, subunit 1-like (yeast)"", ""origin recognition complex, subunit 1 homolog (S. cerevisiae)"""	ORC1L		8884289	Standard	NM_004153		Approved	HSORC1, PARC1	uc001ctu.3	Q13415	OTTHUMG00000008104	ENST00000371568.3:c.1314T>G	1.37:g.52854183A>C		Somatic		Capture	Illumina HiSeq	Phase_I	52626771	NM_001190818	D3DQ34|Q13471|Q5T0F5	Silent	SNP	ENST00000371568.3	37	CCDS566.1																																																																																				0.488	ORC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022202.1	NM_004153	
HSPB11	51668	broad.mit.edu	37	1	54387365	54387365	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr1:54387365C>T	ENST00000194214.5	-	6	783	c.394G>A	c.(394-396)Gtt>Att	p.V132I	HSPB11_ENST00000489675.1_5'UTR|HSPB11_ENST00000371378.2_Intron	NM_016126.2	NP_057210.2	Q9Y547	IFT25_HUMAN	heat shock protein family B (small), member 11	132					cell adhesion (GO:0007155)|heart development (GO:0007507)|left/right axis specification (GO:0070986)|lung development (GO:0030324)|protein transport (GO:0015031)|response to stress (GO:0006950)|skeletal system development (GO:0001501)|smoothened signaling pathway (GO:0007224)	centrosome (GO:0005813)|cilium (GO:0005929)|extracellular vesicular exosome (GO:0070062)|intraciliary transport particle B (GO:0030992)	metal ion binding (GO:0046872)	p.V132I(1)		breast(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(3)|prostate(1)|urinary_tract(1)	9						TCTGCAGAAACGCTATGCACA	0.343																																					p.V132I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G394A	1						.						121.0	113.0	115.0					1																	54387365		1869	4114	5983	54159953	SO:0001583	missense	51668	exon6			AF100747	CCDS41341.1	1p32	2014-02-21	2008-06-24	2008-06-24	ENSG00000081870	ENSG00000081870		"""Intraflagellar transport homologs"", ""Heat shock proteins / HSPB"""	25019	protein-coding gene	gene with protein product	"""intraflagellar transport 25 homolog (Chlamydomonas)"""		"""chromosome 1 open reading frame 41"""	C1orf41		11042152, 19253336	Standard	NM_016126		Approved	HSPCO34, PP25, IFT25	uc001cwh.3	Q9Y547	OTTHUMG00000008408	ENST00000194214.5:c.394G>A	1.37:g.54387365C>T	ENSP00000194214:p.Val132Ile	Somatic		Capture	Illumina HiSeq	Phase_I	54159953	NM_016126	A6NG57|D3DQ45|Q9Y684	Missense_Mutation	SNP	ENST00000194214.5	37	CCDS41341.1	.	.	.	.	.	.	.	.	.	.	C	7.166	0.586591	0.13749	.	.	ENSG00000081870	ENST00000194214;ENST00000371378	T;T	0.79749	-1.3;-1.3	5.27	-5.38	0.02673	Galactose-binding domain-like (1);	0.407785	0.24048	N	0.042031	T	0.60392	0.2265	N	0.11064	0.09	0.38206	D	0.94032	B	0.02656	0.0	B	0.15484	0.013	T	0.10590	-1.0623	10	0.33141	T	0.24	-5.8151	16.0243	0.80532	0.0:0.8564:0.0:0.1436	.	132	Q9Y547	HSB11_HUMAN	I	132	ENSP00000194214:V132I;ENSP00000360429:V132I	ENSP00000194214:V132I	V	-	1	0	HSPB11	54159953	0.000000	0.05858	0.095000	0.20976	0.561000	0.35649	-0.823000	0.04443	-1.471000	0.01886	-0.302000	0.09304	GTT		0.343	HSPB11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000023114.1	NM_016126	
DAB1	1600	broad.mit.edu	37	1	57476449	57476449	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr1:57476449C>A	ENST00000371231.1	-	15	1720	c.1686G>T	c.(1684-1686)caG>caT	p.Q562H	DAB1_ENST00000420954.2_Missense_Mutation_p.Q527H|DAB1_ENST00000439789.2_Missense_Mutation_p.Q443H|DAB1_ENST00000414851.2_Missense_Mutation_p.Q511H|DAB1_ENST00000371234.4_Missense_Mutation_p.Q529H|DAB1_ENST00000485760.1_5'UTR|DAB1_ENST00000371236.2_Missense_Mutation_p.Q529H			O75553	DAB1_HUMAN	Dab, reelin signal transducer, homolog 1 (Drosophila)	562					adult walking behavior (GO:0007628)|cell-cell adhesion involved in neuronal-glial interactions involved in cerebral cortex radial glia guided migration (GO:0021813)|cerebellum structural organization (GO:0021589)|dendrite development (GO:0016358)|Golgi localization (GO:0051645)|lateral motor column neuron migration (GO:0097477)|midgut development (GO:0007494)|negative regulation of astrocyte differentiation (GO:0048712)|negative regulation of axonogenesis (GO:0050771)|negative regulation of cell adhesion (GO:0007162)|negative regulation of JAK-STAT cascade (GO:0046426)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of protein kinase activity (GO:0045860)|radial glia guided migration of Purkinje cell (GO:0021942)|response to drug (GO:0042493)|small GTPase mediated signal transduction (GO:0007264)|ventral spinal cord development (GO:0021517)	apical part of cell (GO:0045177)|brush border (GO:0005903)|cytosol (GO:0005829)|membrane (GO:0016020)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|perinuclear region of cytoplasm (GO:0048471)|postsynaptic density (GO:0014069)		p.Q529H(1)|p.Q529Q(1)		central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(12)|lung(28)|ovary(3)|skin(4)|upper_aerodigestive_tract(5)|urinary_tract(5)	64						TGGATGAGGCCTGTGATCCAT	0.443																																					p.Q529H												.	.	2	Substitution - Missense(1)|Substitution - coding silent(1)	large_intestine(1)|lung(1)	c.G1587T	1						.						93.0	91.0	92.0					1																	57476449		2203	4300	6503	57249037	SO:0001583	missense	1600	exon16			BC067445	CCDS607.1	1p32-p31	2013-10-03	2013-10-03		ENSG00000173406	ENSG00000173406			2661	protein-coding gene	gene with protein product		603448	"""disabled (Drosophila) homolog 1"", ""disabled homolog 1 (Drosophila)"", ""Dab, reelin signal transducer, homolog 1 (Drosophila)"", ""Dab reelin signal transducer 1"""			9790777	Standard	NM_021080		Approved		uc001cys.1	O75553	OTTHUMG00000008391	ENST00000371231.1:c.1686G>T	1.37:g.57476449C>A	ENSP00000360275:p.Gln562His	Somatic		Capture	Illumina HiSeq	Phase_I	57249037	NM_021080	A4FU90|B3KTG3|Q4LE59|Q5T6M6|Q5T6M9|Q5T835|Q5T836|Q5T837|Q6NWS9|Q6NWT0|Q6NWT1|Q9NYA8	Missense_Mutation	SNP	ENST00000371231.1	37		.	.	.	.	.	.	.	.	.	.	C	18.71	3.683282	0.68157	.	.	ENSG00000173406	ENST00000371236;ENST00000371233;ENST00000371234;ENST00000420954;ENST00000414851;ENST00000439789;ENST00000371231	T;T;T;T;T;T	0.48201	0.84;0.84;0.83;0.82;1.81;0.83	4.96	4.96	0.65561	.	0.495394	0.23600	N	0.046457	T	0.58047	0.2095	L	0.36672	1.1	0.58432	D	0.999998	D;D;D;D;D	0.71674	0.991;0.997;0.989;0.986;0.998	P;P;P;P;D	0.63597	0.743;0.825;0.773;0.808;0.916	T	0.53322	-0.8455	10	0.35671	T	0.21	-16.5285	18.7658	0.91871	0.0:1.0:0.0:0.0	.	511;562;529;443;527	O75553-4;O75553;O75553-6;O75553-3;O75553-5	.;DAB1_HUMAN;.;.;.	H	529;529;529;527;511;443;562	ENSP00000360280:Q529H;ENSP00000360278:Q529H;ENSP00000395296:Q527H;ENSP00000387581:Q511H;ENSP00000409328:Q443H;ENSP00000360275:Q562H	ENSP00000360275:Q562H	Q	-	3	2	DAB1	57249037	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.060000	0.71141	2.728000	0.93425	0.561000	0.74099	CAG		0.443	DAB1-010	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000027962.1	NM_021080	
MYSM1	114803	broad.mit.edu	37	1	59139308	59139308	+	Silent	SNP	A	A	G			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr1:59139308A>G	ENST00000472487.1	-	11	1548	c.1509T>C	c.(1507-1509)cgT>cgC	p.R503R	MYSM1_ENST00000493821.1_5'UTR	NM_001085487.2	NP_001078956.1	Q5VVJ2	MYSM1_HUMAN	Myb-like, SWIRM and MPN domains 1	503					chromatin remodeling (GO:0006338)|monoubiquitinated histone H2A deubiquitination (GO:0035522)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|histone binding (GO:0042393)|metal ion binding (GO:0046872)|metallopeptidase activity (GO:0008237)|protein complex binding (GO:0032403)|transcription coactivator activity (GO:0003713)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)	p.R503R(1)		breast(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(6)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	24	all_cancers(7;9.36e-06)					CTCGGACCCTACGTCTCCTTG	0.393																																					p.R503R												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.T1509C	1						.						74.0	74.0	74.0					1																	59139308		1898	4121	6019	58911896	SO:0001819	synonymous_variant	114803	exon11			AB067502	CCDS41343.1	1p32.1	2009-02-11	2009-02-11		ENSG00000162601	ENSG00000162601			29401	protein-coding gene	gene with protein product		612176				11572484, 17428495, 17707232	Standard	NM_001085487		Approved	KIAA1915	uc009wab.2	Q5VVJ2	OTTHUMG00000009533	ENST00000472487.1:c.1509T>C	1.37:g.59139308A>G		Somatic		Capture	Illumina HiSeq	Phase_I	58911896	NM_001085487	A8KA54|B3KX65|Q68DD3|Q6AI53|Q7Z3G8|Q96PX3	Silent	SNP	ENST00000472487.1	37	CCDS41343.1																																																																																				0.393	MYSM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026343.2	XM_055481	
INADL	10207	broad.mit.edu	37	1	62329910	62329910	+	Splice_Site	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr1:62329910G>A	ENST00000371158.2	+	20	2554	c.2440G>A	c.(2440-2442)Gga>Aga	p.G814R	INADL_ENST00000316485.6_Splice_Site_p.G814R	NM_176877.2	NP_795352	Q8NI35	INADL_HUMAN	InaD-like (Drosophila)	814					cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|intracellular signal transduction (GO:0035556)|tight junction assembly (GO:0070830)	apical part of cell (GO:0045177)|extracellular vesicular exosome (GO:0070062)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|tight junction (GO:0005923)		p.G814R(1)		breast(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(8)|liver(1)|lung(51)|ovary(3)|pancreas(1)|prostate(7)|skin(5)|stomach(1)|upper_aerodigestive_tract(3)	103						TTATTTATAGGGATTTAGAGA	0.353																																					p.G814R												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2440A	1						.						42.0	46.0	45.0					1																	62329910		2203	4299	6502	62102498	SO:0001630	splice_region_variant	10207	exon20			AB044807	CCDS617.2	1p31	2008-02-05			ENSG00000132849	ENSG00000132849			28881	protein-coding gene	gene with protein product		603199				9280290, 11374908	Standard	NM_176877		Approved	Cipp, PATJ	uc001dab.3	Q8NI35	OTTHUMG00000008560	ENST00000371158.2:c.2440-1G>A	1.37:g.62329910G>A		Somatic		Capture	Illumina HiSeq	Phase_I	62102498	NM_176877	O15249|O43742|O60833|Q5VUA5|Q5VUA6|Q5VUA7|Q5VUA8|Q5VUA9|Q5VUB0|Q8WU78|Q9H3N9	Missense_Mutation	SNP	ENST00000371158.2	37	CCDS617.2	.	.	.	.	.	.	.	.	.	.	G	13.25	2.181200	0.38511	.	.	ENSG00000132849	ENST00000371158;ENST00000316485;ENST00000371156;ENST00000395513;ENST00000255202	T;T	0.13196	2.75;2.61	5.17	5.17	0.71159	.	0.665176	0.13857	N	0.357947	T	0.15522	0.0374	L	0.60455	1.87	0.80722	D	1	B;P;P	0.39737	0.101;0.454;0.685	B;B;B	0.36030	0.019;0.154;0.216	T	0.02868	-1.1100	9	.	.	.	.	12.0762	0.53644	0.0789:0.0:0.9211:0.0	.	814;814;814	F8W8T2;Q8NI35;Q8NI35-4	.;INADL_HUMAN;.	R	814	ENSP00000360200:G814R;ENSP00000326199:G814R	.	G	+	1	0	INADL	62102498	1.000000	0.71417	1.000000	0.80357	0.917000	0.54804	4.780000	0.62382	2.407000	0.81776	0.555000	0.69702	GGA		0.353	INADL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000023639.2	NM_170605	Missense_Mutation
ROR1	4919	broad.mit.edu	37	1	64644491	64644491	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr1:64644491G>T	ENST00000371079.1	+	9	3142	c.2767G>T	c.(2767-2769)Gcc>Tcc	p.A923S	ROR1_ENST00000545203.1_Missense_Mutation_p.A374S	NM_005012.3	NP_005003.2	Q01973	ROR1_HUMAN	receptor tyrosine kinase-like orphan receptor 1	923					peptidyl-tyrosine phosphorylation (GO:0018108)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|Wnt-protein binding (GO:0017147)	p.A923S(1)		breast(7)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(14)|lung(10)|ovary(6)|prostate(1)|skin(5)|stomach(2)|upper_aerodigestive_tract(1)	51						ACTAGGAGACGCCAATATTCA	0.393																																					p.A923S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2767T	1						.						95.0	92.0	93.0					1																	64644491		2203	4299	6502	64417079	SO:0001583	missense	4919	exon9			M97675	CCDS626.1, CCDS41344.1	1p32-p31	2013-01-11			ENSG00000185483	ENSG00000185483		"""Immunoglobulin superfamily / I-set domain containing"""	10256	protein-coding gene	gene with protein product		602336		NTRKR1		1334494, 8875995	Standard	NM_001083592		Approved		uc001dbj.3	Q01973	OTTHUMG00000009022	ENST00000371079.1:c.2767G>T	1.37:g.64644491G>T	ENSP00000360120:p.Ala923Ser	Somatic		Capture	Illumina HiSeq	Phase_I	64417079	NM_005012	Q5VVX6|Q66K77|Q92776	Missense_Mutation	SNP	ENST00000371079.1	37	CCDS626.1	.	.	.	.	.	.	.	.	.	.	G	0.009	-1.849342	0.00563	.	.	ENSG00000185483	ENST00000371079;ENST00000544776;ENST00000545203	T;T	0.75260	-0.78;-0.92	5.45	-3.43	0.04810	.	0.370230	0.19624	N	0.109832	T	0.14570	0.0352	N	0.02539	-0.55	0.26916	N	0.966778	B	0.02656	0.0	B	0.01281	0.0	T	0.39563	-0.9608	10	0.02654	T	1	.	7.7102	0.28673	0.0971:0.0572:0.5152:0.3306	.	923	Q01973	ROR1_HUMAN	S	923;926;374	ENSP00000360120:A923S;ENSP00000441637:A374S	ENSP00000360120:A923S	A	+	1	0	ROR1	64417079	0.224000	0.23674	0.929000	0.37066	0.431000	0.31685	-0.483000	0.06536	-0.788000	0.04504	-1.061000	0.02294	GCC		0.393	ROR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025002.1	NM_005012	
RAVER2	55225	broad.mit.edu	37	1	65243523	65243523	+	Silent	SNP	T	T	C	rs373913304		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr1:65243523T>C	ENST00000294428.3	+	3	612	c.534T>C	c.(532-534)gtT>gtC	p.V178V	RAVER2_ENST00000430964.2_5'Flank|RAVER2_ENST00000371072.4_Silent_p.V178V			Q9HCJ3	RAVR2_HUMAN	ribonucleoprotein, PTB-binding 2	178	RRM 2. {ECO:0000255|PROSITE- ProRule:PRU00176}.					cytoplasm (GO:0005737)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)	p.V178V(1)		breast(2)|endometrium(2)|kidney(1)|large_intestine(7)|lung(6)|prostate(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	24						ATAGTGAAGTTACTGGCCATT	0.408																																					p.V178V												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.T534C	1						.	T		1,3785		0,1,1892	239.0	216.0	223.0		534	-10.7	0.7	1		223	1,8221		0,1,4110	no	coding-synonymous	RAVER2	NM_018211.3		0,2,6002	CC,CT,TT		0.0122,0.0264,0.0167		178/679	65243523	2,12006	1893	4111	6004	65016111	SO:0001819	synonymous_variant	55225	exon3			AB046799	CCDS41345.1	1p31.3	2013-02-12			ENSG00000162437	ENSG00000162437		"""RNA binding motif (RRM) containing"""	25577	protein-coding gene	gene with protein product		609953				16051233	Standard	NM_018211		Approved	KIAA1579, FLJ10770	uc001dbs.2	Q9HCJ3	OTTHUMG00000009102	ENST00000294428.3:c.534T>C	1.37:g.65243523T>C		Somatic		Capture	Illumina HiSeq	Phase_I	65016111	NM_018211	Q6P141|Q9NPV7	Silent	SNP	ENST00000294428.3	37																																																																																					0.408	RAVER2-201	KNOWN	basic	protein_coding	protein_coding		NM_018211	
LEPR	3953	broad.mit.edu	37	1	66087082	66087082	+	Silent	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr1:66087082G>A	ENST00000349533.6	+	18	2723	c.2538G>A	c.(2536-2538)gtG>gtA	p.V846V	LEPR_ENST00000344610.8_Silent_p.V846V|LEPR_ENST00000371058.1_Silent_p.V846V|LEPR_ENST00000371059.3_Silent_p.V846V|LEPR_ENST00000406510.3_Intron|LEPR_ENST00000371060.3_Silent_p.V846V	NM_002303.5	NP_002294.2	O15243	OBRG_HUMAN	leptin receptor	0					negative regulation of growth hormone receptor signaling pathway (GO:0060400)|negative regulation of JAK-STAT cascade (GO:0046426)|negative regulation of protein localization to cell surface (GO:2000009)	endosome (GO:0005768)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	receptor binding (GO:0005102)	p.V846V(1)		breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(7)|lung(22)|skin(2)	36				OV - Ovarian serous cystadenocarcinoma(397;0.00722)|KIRC - Kidney renal clear cell carcinoma(1967;0.094)		ATGTAATTGTGCCAGTAATTA	0.313																																					p.V846V												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G2538A	1						.						168.0	156.0	160.0					1																	66087082		2203	4296	6499	65859670	SO:0001819	synonymous_variant	3953	exon18			U43168	CCDS631.1, CCDS30740.1, CCDS30741.1, CCDS55604.1	1p31	2014-09-17			ENSG00000116678	ENSG00000116678		"""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6554	protein-coding gene	gene with protein product		601007				8548812, 8812446	Standard	NM_001003680		Approved	OBR, CD295	uc001dci.3	P48357	OTTHUMG00000009115	ENST00000349533.6:c.2538G>A	1.37:g.66087082G>A		Somatic		Capture	Illumina HiSeq	Phase_I	65859670	NM_001003679	Q6FHL5	Silent	SNP	ENST00000349533.6	37	CCDS631.1																																																																																				0.313	LEPR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025275.1	NM_002303	
ELTD1	64123	broad.mit.edu	37	1	79357355	79357355	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr1:79357355C>T	ENST00000370742.3	-	14	1927	c.1864G>A	c.(1864-1866)Gct>Act	p.A622T		NM_022159.3	NP_071442.2	Q9HBW9	ELTD1_HUMAN	EGF, latrophilin and seven transmembrane domain containing 1	622					G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)	p.A622T(1)		NS(1)|breast(1)|endometrium(3)|kidney(2)|large_intestine(10)|lung(45)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	69				COAD - Colon adenocarcinoma(225;0.0905)|Colorectal(170;0.103)|all cancers(265;0.105)|Epithelial(280;0.148)		AACAGAAGAGCGAGGGCTCCT	0.458																																					p.A622T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1864A	1						.						62.0	62.0	62.0					1																	79357355		1965	4143	6108	79129943	SO:0001583	missense	64123	exon14			AF192403	CCDS41352.1	1p33-p32	2014-08-08			ENSG00000162618	ENSG00000162618		"""-"", ""GPCR / Class B : Orphans"""	20822	protein-coding gene	gene with protein product						11050079	Standard	NM_022159		Approved	ETL	uc001diq.4	Q9HBW9	OTTHUMG00000009738	ENST00000370742.3:c.1864G>A	1.37:g.79357355C>T	ENSP00000359778:p.Ala622Thr	Somatic		Capture	Illumina HiSeq	Phase_I	79129943	NM_022159	B1AR71|Q5KU34	Missense_Mutation	SNP	ENST00000370742.3	37	CCDS41352.1	.	.	.	.	.	.	.	.	.	.	C	23.6	4.433794	0.83776	.	.	ENSG00000162618	ENST00000370742;ENST00000401034	T;T	0.44881	0.91;0.91	5.59	5.59	0.84812	GPCR, family 2-like (1);	0.000000	0.85682	D	0.000000	T	0.24774	0.0601	L	0.43757	1.38	0.58432	D	0.999999	P	0.42757	0.789	B	0.43990	0.438	T	0.05162	-1.0902	9	.	.	.	.	8.7488	0.34602	0.1513:0.7738:0.0:0.0749	.	622	Q9HBW9	ELTD1_HUMAN	T	622;80	ENSP00000359778:A622T;ENSP00000383813:A80T	.	A	-	1	0	ELTD1	79129943	1.000000	0.71417	0.979000	0.43373	0.921000	0.55340	5.960000	0.70348	2.612000	0.88384	0.655000	0.94253	GCT		0.458	ELTD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026859.1	NM_022159	
LPHN2	23266	broad.mit.edu	37	1	82409238	82409238	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr1:82409238A>G	ENST00000370728.1	+	8	1628	c.983A>G	c.(982-984)tAt>tGt	p.Y328C	LPHN2_ENST00000335786.5_Missense_Mutation_p.Y328C|LPHN2_ENST00000370715.1_Missense_Mutation_p.Y328C|LPHN2_ENST00000370725.1_Missense_Mutation_p.Y328C|LPHN2_ENST00000370727.1_Missense_Mutation_p.Y328C|LPHN2_ENST00000469377.2_Intron|LPHN2_ENST00000370723.1_Missense_Mutation_p.Y328C|LPHN2_ENST00000271029.4_Missense_Mutation_p.Y328C|LPHN2_ENST00000370713.1_Missense_Mutation_p.Y328C|LPHN2_ENST00000370717.2_Missense_Mutation_p.Y328C|LPHN2_ENST00000370730.1_Missense_Mutation_p.Y328C|LPHN2_ENST00000370721.1_Missense_Mutation_p.Y332C|LPHN2_ENST00000359929.3_Missense_Mutation_p.Y328C|LPHN2_ENST00000394879.1_Missense_Mutation_p.Y328C|LPHN2_ENST00000319517.6_Missense_Mutation_p.Y328C			O95490	LPHN2_HUMAN	latrophilin 2	328	Olfactomedin-like. {ECO:0000255|PROSITE- ProRule:PRU00446}.				G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)|G-protein coupled receptor activity (GO:0004930)|latrotoxin receptor activity (GO:0016524)	p.Y328C(1)		NS(3)|breast(6)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(18)|liver(2)|lung(37)|ovary(3)|pancreas(1)|prostate(3)|skin(22)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(5)	119				all cancers(265;0.00142)|Epithelial(280;0.00829)|OV - Ovarian serous cystadenocarcinoma(397;0.077)|STAD - Stomach adenocarcinoma(256;0.248)		AGGTCAGTTTATCAAGACAAT	0.408																																					p.Y328C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A983G	1						.						126.0	125.0	126.0					1																	82409238		2203	4300	6503	82181826	SO:0001583	missense	23266	exon5			AJ131581	CCDS689.1, CCDS72811.1	1p31.1	2014-08-08	2003-03-17	2003-05-02	ENSG00000117114	ENSG00000117114		"""-"", ""GPCR / Class B : Orphans"""	18582	protein-coding gene	gene with protein product		607018	"""latrophilin 1"""	LPHH1		10760572	Standard	XR_248786		Approved	KIAA0786, LEC1	uc001diu.3	O95490	OTTHUMG00000009844	ENST00000370728.1:c.983A>G	1.37:g.82409238A>G	ENSP00000359763:p.Tyr328Cys	Somatic		Capture	Illumina HiSeq	Phase_I	82181826	NM_012302	A5XEI2|B1ALT8|B1ALT9|B1ALU0|B1ALU2|B1ALU4|B1ALU5|B1ALU6|O94882|Q5VX76|Q9UKY5|Q9UKY6	Missense_Mutation	SNP	ENST00000370728.1	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	16.50|16.50	3.141613|3.141613	0.57044|0.57044	.|.	.|.	ENSG00000117114|ENSG00000117114	ENST00000449420|ENST00000370721;ENST00000370728;ENST00000370730;ENST00000370727;ENST00000370725;ENST00000370723;ENST00000359929;ENST00000370715;ENST00000370713;ENST00000319517;ENST00000370717;ENST00000394879;ENST00000271029;ENST00000335786	.|D;D;D;D;D;D;D;D;D;D;D;D;D;D	.|0.88896	.|-2.44;-2.44;-2.44;-2.44;-2.44;-2.44;-2.44;-2.44;-2.44;-2.44;-2.44;-2.44;-2.44;-2.44	5.4|5.4	5.4|5.4	0.78164|0.78164	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	D|D	0.93739|0.93739	0.7999|0.7999	M|M	0.83953|0.83953	2.67|2.67	0.80722|0.80722	D|D	1|1	.|D;D;D	.|0.89917	.|1.0;1.0;1.0	.|D;D;D	.|0.79784	.|0.993;0.983;0.993	D|D	0.94799|0.94799	0.7969|0.7969	5|10	.|0.87932	.|D	.|0	.|.	15.4327|15.4327	0.75116|0.75116	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	.|328;328;328	.|O95490-3;O95490-4;O95490-2	.|.;.;.	V|C	196|332;328;328;328;328;328;328;328;328;328;328;328;328;328	.|ENSP00000359756:Y332C;ENSP00000359763:Y328C;ENSP00000359765:Y328C;ENSP00000359762:Y328C;ENSP00000359760:Y328C;ENSP00000359758:Y328C;ENSP00000353006:Y328C;ENSP00000359750:Y328C;ENSP00000359748:Y328C;ENSP00000322270:Y328C;ENSP00000359752:Y328C;ENSP00000378344:Y328C;ENSP00000271029:Y328C;ENSP00000337306:Y328C	.|ENSP00000271029:Y328C	I|Y	+|+	1|2	0|0	LPHN2|LPHN2	82181826|82181826	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.970000|0.970000	0.65996|0.65996	8.883000|8.883000	0.92426|0.92426	2.038000|2.038000	0.60285|0.60285	0.374000|0.374000	0.22700|0.22700	ATC|TAT		0.408	LPHN2-007	KNOWN	non_canonical_conserved|not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000027188.1	NM_012302	
LPAR3	23566	broad.mit.edu	37	1	85331167	85331167	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr1:85331167C>T	ENST00000440886.1	-	1	675	c.637G>A	c.(637-639)Gtc>Atc	p.V213I	LPAR3_ENST00000491034.1_5'UTR|LPAR3_ENST00000370611.3_Missense_Mutation_p.V213I			Q9UBY5	LPAR3_HUMAN	lysophosphatidic acid receptor 3	213					activation of MAPK activity (GO:0000187)|bleb assembly (GO:0032060)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|positive regulation of calcium ion transport (GO:0051928)|positive regulation of collateral sprouting (GO:0048672)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of cytosolic calcium ion concentration involved in phospholipase C-activating G-protein coupled signaling pathway (GO:0051482)|synaptic transmission (GO:0007268)	axon (GO:0030424)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|lipid binding (GO:0008289)|lysophosphatidic acid receptor activity (GO:0070915)|phospholipid binding (GO:0005543)	p.V213I(1)		central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(11)|ovary(2)|urinary_tract(1)	24						TTCCTCTTGACGTACACGTAG	0.522																																					p.V213I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G637A	1						.						118.0	98.0	105.0					1																	85331167		2203	4300	6503	85103755	SO:0001583	missense	23566	exon2			AF127138	CCDS700.1	1p22.3	2012-08-08	2008-04-11	2008-04-11	ENSG00000171517	ENSG00000171517		"""GPCR / Class A : Lysophospholipid receptors : Lysophosphatidic acid"""	14298	protein-coding gene	gene with protein product		605106	"""endothelial differentiation, lysophosphatidic acid G-protein-coupled receptor, 7"""	EDG7		10488122	Standard	NM_012152		Approved	LP-A3, Edg-7, RP4-678I3, HOFNH30, LPA3	uc009wcj.1	Q9UBY5	OTTHUMG00000009925	ENST00000440886.1:c.637G>A	1.37:g.85331167C>T	ENSP00000395389:p.Val213Ile	Somatic		Capture	Illumina HiSeq	Phase_I	85103755	NM_012152	A0AVA3	Missense_Mutation	SNP	ENST00000440886.1	37	CCDS700.1	.	.	.	.	.	.	.	.	.	.	C	25.3	4.623054	0.87460	.	.	ENSG00000171517	ENST00000440886;ENST00000370611	T;T	0.36699	1.24;1.24	5.2	5.2	0.72013	GPCR, rhodopsin-like superfamily (1);	0.000000	0.85682	D	0.000000	T	0.54565	0.1866	M	0.71036	2.16	0.52501	D	0.999951	D	0.76494	0.999	D	0.79784	0.993	T	0.59241	-0.7491	10	0.72032	D	0.01	.	18.7607	0.91849	0.0:1.0:0.0:0.0	.	213	Q9UBY5	LPAR3_HUMAN	I	213	ENSP00000395389:V213I;ENSP00000359643:V213I	ENSP00000359643:V213I	V	-	1	0	LPAR3	85103755	1.000000	0.71417	0.820000	0.32676	0.876000	0.50452	7.792000	0.85828	2.437000	0.82529	0.650000	0.86243	GTC		0.522	LPAR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027467.1	NM_012152	
COL24A1	255631	broad.mit.edu	37	1	86523622	86523622	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr1:86523622C>A	ENST00000370571.2	-	10	2209	c.1843G>T	c.(1843-1845)Ggt>Tgt	p.G615C	COL24A1_ENST00000436319.1_Missense_Mutation_p.G615C	NM_152890.5	NP_690850.2	Q17RW2	COOA1_HUMAN	collagen, type XXIV, alpha 1	615					extracellular matrix organization (GO:0030198)|hematopoietic progenitor cell differentiation (GO:0002244)	collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)	p.G615S(1)|p.G615C(1)		NS(3)|central_nervous_system(2)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(9)|liver(1)|lung(56)|ovary(4)|prostate(2)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	101				all cancers(265;0.0627)|Epithelial(280;0.0689)		ACTTGTGCACCTTTAGGACCT	0.338																																					p.G615C												.	.	2	Substitution - Missense(2)	large_intestine(1)|lung(1)	c.G1843T	1						.						99.0	94.0	96.0					1																	86523622		1885	4096	5981	86296210	SO:0001583	missense	255631	exon10			AF410793	CCDS41353.1	1p22.3-p22.2	2013-01-16			ENSG00000171502	ENSG00000171502		"""Collagens"""	20821	protein-coding gene	gene with protein product		610025					Standard	NM_152890		Approved		uc001dlj.3	Q17RW2	OTTHUMG00000010629	ENST00000370571.2:c.1843G>T	1.37:g.86523622C>A	ENSP00000359603:p.Gly615Cys	Somatic		Capture	Illumina HiSeq	Phase_I	86296210	NM_152890	C9J1X6|Q14BD7|Q59EX5|Q5VY50|Q7Z5L5	Missense_Mutation	SNP	ENST00000370571.2	37	CCDS41353.1	.	.	.	.	.	.	.	.	.	.	C	12.32	1.903777	0.33628	.	.	ENSG00000171502	ENST00000370571;ENST00000436319	D;D	0.99537	-6.11;-6.11	5.64	5.64	0.86602	.	0.000000	0.37393	N	0.002108	D	0.99862	0.9935	H	0.98802	4.335	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.96599	0.9443	10	0.87932	D	0	.	17.8979	0.88895	0.0:1.0:0.0:0.0	.	615;615	F8WDM8;Q17RW2	.;COOA1_HUMAN	C	615	ENSP00000359603:G615C;ENSP00000392531:G615C	ENSP00000359603:G615C	G	-	1	0	COL24A1	86296210	1.000000	0.71417	1.000000	0.80357	0.258000	0.26162	3.940000	0.56599	2.653000	0.90120	0.655000	0.94253	GGT		0.338	COL24A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029335.4	NM_152890	
PKN2	5586	broad.mit.edu	37	1	89299057	89299057	+	Nonsense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr1:89299057C>T	ENST00000370521.3	+	22	3240	c.2881C>T	c.(2881-2883)Cga>Tga	p.R961*	PKN2_ENST00000370513.5_Nonsense_Mutation_p.R913*|PKN2_ENST00000370505.3_Nonsense_Mutation_p.R804*|PKN2_ENST00000495119.1_3'UTR|PKN2_ENST00000544045.1_Nonsense_Mutation_p.R635*	NM_006256.2	NP_006247.1	Q16513	PKN2_HUMAN	protein kinase N2	961	AGC-kinase C-terminal.|Necessary for the catalytic activity.				apical junction assembly (GO:0043297)|apoptotic process (GO:0006915)|cell adhesion (GO:0007155)|cell cycle (GO:0007049)|cell division (GO:0051301)|epithelial cell migration (GO:0010631)|positive regulation of cytokinesis (GO:0032467)|positive regulation of mitotic cell cycle (GO:0045931)|protein phosphorylation (GO:0006468)|regulation of cell motility (GO:2000145)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)	apical junction complex (GO:0043296)|centrosome (GO:0005813)|cleavage furrow (GO:0032154)|cytoplasm (GO:0005737)|intermediate filament cytoskeleton (GO:0045111)|lamellipodium (GO:0030027)|membrane (GO:0016020)|midbody (GO:0030496)|nucleus (GO:0005634)	ATP binding (GO:0005524)|histone deacetylase binding (GO:0042826)|poly(A) RNA binding (GO:0044822)|protein kinase activity (GO:0004672)|protein kinase C activity (GO:0004697)|protein serine/threonine kinase activity (GO:0004674)	p.R961*(1)		breast(2)|endometrium(3)|kidney(3)|large_intestine(8)|lung(15)|prostate(1)|skin(1)	33		Lung NSC(277;0.123)		all cancers(265;0.0136)|Epithelial(280;0.0301)		GACTCCACCTCGAGAACCAAG	0.403																																					p.R961X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.C2881T	1						.						99.0	96.0	97.0					1																	89299057		1943	4118	6061	89071645	SO:0001587	stop_gained	5586	exon22			U33052	CCDS714.1	1p22	2014-04-23	2004-07-01	2004-07-01	ENSG00000065243	ENSG00000065243			9406	protein-coding gene	gene with protein product	"""cardiolipin-activated protein kinase Pak2"""	602549	"""protein kinase C-like 2"""	PRKCL2		7988719, 7851406	Standard	NM_006256		Approved	PRK2, Pak-2, STK7	uc001dmn.3	Q16513	OTTHUMG00000010074	ENST00000370521.3:c.2881C>T	1.37:g.89299057C>T	ENSP00000359552:p.Arg961*	Somatic		Capture	Illumina HiSeq	Phase_I	89071645	NM_006256	B4DQ21|B4DTP5|B4DVG1|D3DT24|Q08AF4|Q9H1W4	Nonsense_Mutation	SNP	ENST00000370521.3	37	CCDS714.1	.	.	.	.	.	.	.	.	.	.	C	38	7.219799	0.98143	.	.	ENSG00000065243	ENST00000370521;ENST00000370505;ENST00000370513;ENST00000544045	.	.	.	5.84	5.84	0.93424	.	0.000000	0.37577	U	0.002027	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	16.3881	0.83523	0.1322:0.8678:0.0:0.0	.	.	.	.	X	961;804;913;635	.	ENSP00000359536:R804X	R	+	1	2	PKN2	89071645	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	4.560000	0.60802	2.758000	0.94735	0.591000	0.81541	CGA		0.403	PKN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027828.3	NM_006256	
GBP5	115362	broad.mit.edu	37	1	89733128	89733128	+	Frame_Shift_Del	DEL	T	T	-			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	T	T	T	-	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr1:89733128delT	ENST00000370459.3	-	4	527	c.400delA	c.(400-402)attfs	p.I134fs	RP4-620F22.2_ENST00000437128.1_RNA|GBP5_ENST00000343435.5_Frame_Shift_Del_p.I134fs			Q96PP8	GBP5_HUMAN	guanylate binding protein 5	134	GB1/RHD3-type G.|GTPase domain (Globular). {ECO:0000250}.					cytoplasm (GO:0005737)|membrane (GO:0016020)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|identical protein binding (GO:0042802)	p.I134fs*12(1)		breast(1)|endometrium(1)|large_intestine(6)|lung(14)|ovary(1)|prostate(1)	24				all cancers(265;0.00784)|Epithelial(280;0.0286)		CCCTGATCAATTTTGTTCACA	0.443																																					p.I134fs												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.400delA	1						.						129.0	110.0	117.0					1																	89733128		2203	4300	6503	89505716	SO:0001589	frameshift_variant	115362	exon4			AF430642	CCDS722.1	1p22.2	2008-02-05			ENSG00000154451	ENSG00000154451			19895	protein-coding gene	gene with protein product		611467					Standard	NM_052942		Approved		uc001dnd.3	Q96PP8	OTTHUMG00000010006	ENST00000370459.3:c.400delA	1.37:g.89733128delT	ENSP00000359488:p.Ile134fs	Somatic		Capture	Illumina HiSeq	Phase_I	89505716	NM_001134486	B2RCE1|Q86TM5	Frame_Shift_Del	DEL	ENST00000370459.3	37	CCDS722.1																																																																																				0.443	GBP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027700.1	NM_052942	
PALMD	54873	broad.mit.edu	37	1	100154472	100154472	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr1:100154472C>T	ENST00000263174.4	+	7	1031	c.656C>T	c.(655-657)gCa>gTa	p.A219V	PALMD_ENST00000605497.1_Missense_Mutation_p.A219V	NM_017734.4	NP_060204.1	Q9NP74	PALMD_HUMAN	palmdelphin	219					regulation of cell shape (GO:0008360)	cytoplasm (GO:0005737)|dendritic spine (GO:0043197)|membrane (GO:0016020)		p.A219V(1)		central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(9)|lung(8)|ovary(6)|pancreas(1)|prostate(2)	31		all_epithelial(167;0.000813)|all_lung(203;0.0214)|Lung NSC(277;0.0216)		Epithelial(280;0.067)|all cancers(265;0.117)|COAD - Colon adenocarcinoma(174;0.142)|Lung(183;0.201)		TCAGTGTATGCAGTAAGTTCT	0.418																																					p.A219V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C656T	1						.						118.0	118.0	118.0					1																	100154472		2203	4300	6503	99927060	SO:0001583	missense	54873	exon7			AJ312214	CCDS758.1	1p22-p21	2008-07-18			ENSG00000099260	ENSG00000099260			15846	protein-coding gene	gene with protein product		610182		C1orf11		11478809	Standard	NM_017734		Approved	FLJ20271, PALML	uc001dsg.3	Q9NP74	OTTHUMG00000010764	ENST00000263174.4:c.656C>T	1.37:g.100154472C>T	ENSP00000263174:p.Ala219Val	Somatic		Capture	Illumina HiSeq	Phase_I	99927060	NM_017734	Q9H7E6|Q9NPM5|Q9NPM6|Q9NPS0	Missense_Mutation	SNP	ENST00000263174.4	37	CCDS758.1	.	.	.	.	.	.	.	.	.	.	C	17.27	3.346706	0.61073	.	.	ENSG00000099260	ENST00000263174	T	0.21734	1.99	5.68	3.74	0.42951	.	0.101991	0.64402	D	0.000003	T	0.34890	0.0913	M	0.79258	2.445	0.58432	D	0.999998	D;D	0.69078	0.997;0.996	D;D	0.67382	0.951;0.919	T	0.33879	-0.9851	10	0.62326	D	0.03	-14.8205	14.7317	0.69386	0.2644:0.7356:0.0:0.0	.	219;139	Q9NP74;Q9NP74-2	PALMD_HUMAN;.	V	219	ENSP00000263174:A219V	ENSP00000263174:A219V	A	+	2	0	PALMD	99927060	1.000000	0.71417	0.753000	0.31225	0.480000	0.33159	4.019000	0.57181	0.686000	0.31488	0.563000	0.77884	GCA		0.418	PALMD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029672.1	NM_017734	
OBSCN	84033	broad.mit.edu	37	1	228434468	228434468	+	Frame_Shift_Del	DEL	G	G	-	rs372487722		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	-	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr1:228434468delG	ENST00000422127.1	+	13	4041	c.3997delG	c.(3997-3999)gggfs	p.G1334fs	OBSCN_ENST00000366707.4_5'UTR|OBSCN_ENST00000570156.2_Frame_Shift_Del_p.G1426fs|OBSCN_ENST00000366709.4_5'UTR|OBSCN_ENST00000284548.11_Frame_Shift_Del_p.G1334fs	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	1334	Ig-like 13.				apoptotic signaling pathway (GO:0097190)|multicellular organismal development (GO:0007275)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|protein localization to M-band (GO:0036309)|regulation of small GTPase mediated signal transduction (GO:0051056)|sarcomere organization (GO:0045214)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|M band (GO:0031430)|myofibril (GO:0030016)|Z disc (GO:0030018)	ankyrin binding (GO:0030506)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|structural constituent of muscle (GO:0008307)|titin binding (GO:0031432)	p.G1334fs*37(2)		NS(2)|breast(7)|central_nervous_system(5)|cervix(2)|endometrium(30)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(37)|lung(89)|ovary(8)|pancreas(3)|prostate(13)|skin(6)|stomach(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	223		Prostate(94;0.0405)				CTGTGAGGCTGGGGGCCAGCG	0.592																																					p.G1333fs												.	.	2	Deletion - Frameshift(2)	large_intestine(2)	c.3997delG	1						.						71.0	80.0	77.0					1																	228434468		2004	4180	6184	226501091	SO:0001589	frameshift_variant	84033	exon13			AJ002535	CCDS1570.2, CCDS58065.1, CCDS59204.1	1q42	2014-09-17			ENSG00000154358	ENSG00000154358		"""Rho guanine nucleotide exchange factors"", ""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	15719	protein-coding gene	gene with protein product		608616				11448995, 11814696	Standard	NM_001098623		Approved	KIAA1556, UNC89, KIAA1639, ARHGEF30	uc001hsq.2	Q5VST9	OTTHUMG00000039772	ENST00000422127.1:c.3997delG	1.37:g.228434468delG	ENSP00000409493:p.Gly1334fs	Somatic		Capture	Illumina HiSeq	Phase_I	226501091	NM_052843	Q2A664|Q5T7G8|Q5T7G9|Q5VSU2|Q86YC7|Q8NHN0|Q8NHN1|Q8NHN2|Q8NHN3|Q8NHN4|Q8NHN5|Q8NHN6|Q8NHN7|Q8NHN8|Q8NHN9|Q96AA2|Q9HCD3|Q9HCL6	Frame_Shift_Del	DEL	ENST00000422127.1	37	CCDS58065.1																																																																																				0.592	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843	
RYR2	6262	broad.mit.edu	37	1	237777658	237777658	+	Frame_Shift_Del	DEL	A	A	-			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	A	A	A	-	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr1:237777658delA	ENST00000366574.2	+	37	5547	c.5230delA	c.(5230-5232)aaafs	p.K1745fs	RYR2_ENST00000360064.6_Frame_Shift_Del_p.K1743fs|RYR2_ENST00000542537.1_Frame_Shift_Del_p.K1729fs	NM_001035.2	NP_001026.2	Q92736	RYR2_HUMAN	ryanodine receptor 2 (cardiac)	1745	4 X approximate repeats.				BMP signaling pathway (GO:0030509)|calcium ion transport (GO:0006816)|calcium ion transport into cytosol (GO:0060402)|calcium-mediated signaling (GO:0019722)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle contraction (GO:0060048)|cardiac muscle hypertrophy (GO:0003300)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cellular calcium ion homeostasis (GO:0006874)|cellular response to caffeine (GO:0071313)|cellular response to epinephrine stimulus (GO:0071872)|cytosolic calcium ion homeostasis (GO:0051480)|detection of calcium ion (GO:0005513)|embryonic heart tube morphogenesis (GO:0003143)|establishment of protein localization to endoplasmic reticulum (GO:0072599)|ion transmembrane transport (GO:0034220)|left ventricular cardiac muscle tissue morphogenesis (GO:0003220)|positive regulation of calcium-transporting ATPase activity (GO:1901896)|positive regulation of heart rate (GO:0010460)|positive regulation of ryanodine-sensitive calcium-release channel activity by adrenergic receptor signaling pathway involved in positive regulation of cardiac muscle contraction (GO:0086094)|positive regulation of sequestering of calcium ion (GO:0051284)|Purkinje myocyte to ventricular cardiac muscle cell signaling (GO:0086029)|regulation of cardiac muscle contraction (GO:0055117)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of heart rate (GO:0002027)|release of sequestered calcium ion into cytosol (GO:0051209)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|response to redox state (GO:0051775)|sarcoplasmic reticulum calcium ion transport (GO:0070296)|transmembrane transport (GO:0055085)|type B pancreatic cell apoptotic process (GO:0097050)|ventricular cardiac muscle cell action potential (GO:0086005)	calcium channel complex (GO:0034704)|extracellular vesicular exosome (GO:0070062)|junctional sarcoplasmic reticulum membrane (GO:0014701)|membrane (GO:0016020)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|Z disc (GO:0030018)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-induced calcium release activity (GO:0048763)|calcium-release channel activity (GO:0015278)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|intracellular ligand-gated calcium channel activity (GO:0005218)|ion channel binding (GO:0044325)|protein kinase A catalytic subunit binding (GO:0034236)|protein kinase A regulatory subunit binding (GO:0034237)|ryanodine-sensitive calcium-release channel activity (GO:0005219)|suramin binding (GO:0043924)	p.K1743fs*25(1)		NS(4)|breast(8)|central_nervous_system(11)|cervix(2)|endometrium(39)|haematopoietic_and_lymphoid_tissue(5)|kidney(17)|large_intestine(83)|liver(4)|lung(353)|ovary(18)|pancreas(5)|prostate(12)|skin(8)|stomach(1)|upper_aerodigestive_tract(12)|urinary_tract(4)	586	Ovarian(103;0.103)	all_cancers(173;0.000368)|Melanoma(53;0.0179)|all_epithelial(177;0.0225)	OV - Ovarian serous cystadenocarcinoma(106;0.00606)			TGATGAGAACAAAAAACACGG	0.522																																					p.K1744fs												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.5230delA	1						.						65.0	65.0	65.0					1																	237777658		2046	4201	6247	235844281	SO:0001589	frameshift_variant	6262	exon37			X91869	CCDS55691.1	1q43	2014-09-17			ENSG00000198626	ENSG00000198626		"""Ion channels / Ryanodine receptors"", ""EF-hand domain containing"""	10484	protein-coding gene	gene with protein product		180902	"""arrhythmogenic right ventricular dysplasia 2"""	ARVD2		2380170, 8406504, 11159936	Standard	NM_001035		Approved	ARVC2, VTSIP	uc001hyl.1	Q92736	OTTHUMG00000039543	ENST00000366574.2:c.5230delA	1.37:g.237777658delA	ENSP00000355533:p.Lys1745fs	Somatic		Capture	Illumina HiSeq	Phase_I	235844281	NM_001035	Q15411|Q546N8|Q5T3P2	Frame_Shift_Del	DEL	ENST00000366574.2	37	CCDS55691.1																																																																																				0.522	RYR2-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095402.2	NM_001035	
OR2T8	343172	broad.mit.edu	37	1	248084904	248084904	+	Silent	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr1:248084904C>T	ENST00000319968.4	+	1	585	c.585C>T	c.(583-585)aaC>aaT	p.N195N		NM_001005522.1	NP_001005522.1	A6NH00	OR2T8_HUMAN	olfactory receptor, family 2, subfamily T, member 8	195						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.N195N(1)		central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(20)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	34	all_cancers(71;0.000139)|all_epithelial(71;1.58e-05)|Breast(184;0.0117)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)	all_cancers(173;0.0211)	OV - Ovarian serous cystadenocarcinoma(106;0.0319)			TCTTCGAAAACGCCATGTACA	0.532																																					p.N195N												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C585T	1						.						4.0	3.0	4.0					1																	248084904		1800	3487	5287	246151527	SO:0001819	synonymous_variant	343172	exon1				CCDS31100.1	1q44	2012-08-09		2004-03-10	ENSG00000177462	ENSG00000177462		"""GPCR / Class A : Olfactory receptors"""	15020	protein-coding gene	gene with protein product				OR2T8P			Standard	XM_005273117		Approved		uc010pzc.2	A6NH00	OTTHUMG00000040205	ENST00000319968.4:c.585C>T	1.37:g.248084904C>T		Somatic		Capture	Illumina HiSeq	Phase_I	246151527	NM_001005522		Silent	SNP	ENST00000319968.4	37	CCDS31100.1																																																																																				0.532	OR2T8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096862.1	NM_001005522	
PCSK2	5126	broad.mit.edu	37	20	17417497	17417497	+	Missense_Mutation	SNP	C	C	T	rs542607464		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr20:17417497C>T	ENST00000262545.2	+	8	1169	c.854C>T	c.(853-855)aCg>aTg	p.T285M	PCSK2_ENST00000377899.1_Missense_Mutation_p.T266M|PCSK2_ENST00000536609.1_Missense_Mutation_p.T250M	NM_002594.3	NP_002585.2	P16519	NEC2_HUMAN	proprotein convertase subtilisin/kexin type 2	285	Peptidase S8.				cellular protein metabolic process (GO:0044267)|embryo development (GO:0009790)|enkephalin processing (GO:0034230)|insulin processing (GO:0030070)|islet amyloid polypeptide processing (GO:0034231)|nervous system development (GO:0007399)|protein autoprocessing (GO:0016540)|proteolysis (GO:0006508)	dendrite (GO:0030425)|extracellular space (GO:0005615)|membrane (GO:0016020)|perikaryon (GO:0043204)|secretory granule lumen (GO:0034774)	serine-type endopeptidase activity (GO:0004252)	p.T285M(2)		breast(2)|central_nervous_system(2)|endometrium(5)|kidney(5)|large_intestine(7)|lung(17)|ovary(3)|pancreas(2)|prostate(3)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	53					"""""""Insulin(DB00071)|Insulin Regular(DB00030)"""	CGGGAGCTCACGCTGCAGGCC	0.637													C|||	1	0.000199681	0.0	0.0	5008	,	,		17371	0.0		0.0	False		,,,				2504	0.001				p.T285M												.	.	2	Substitution - Missense(2)	upper_aerodigestive_tract(1)|large_intestine(1)	c.C854T	20						.						34.0	32.0	32.0					20																	17417497		2203	4300	6503	17365497	SO:0001583	missense	5126	exon8			AK312341	CCDS13125.1, CCDS56179.1, CCDS56180.1	20p11.2	2008-08-01			ENSG00000125851	ENSG00000125851			8744	protein-coding gene	gene with protein product	"""neuroendocrine convertase 2"", ""KEX2-like endoprotease 2"""	162151		NEC2		1765368	Standard	NM_001201528		Approved	PC2, SPC2	uc002wpm.3	P16519	OTTHUMG00000031941	ENST00000262545.2:c.854C>T	20.37:g.17417497C>T	ENSP00000262545:p.Thr285Met	Somatic		Capture	Illumina HiSeq	Phase_I	17365497	NM_002594	B1ANH9|B4DFQ3|Q14927|Q5JYQ1|Q8IWA8|Q9NQG3|Q9NUG1|Q9UJC6	Missense_Mutation	SNP	ENST00000262545.2	37	CCDS13125.1	.	.	.	.	.	.	.	.	.	.	C	29.1	4.973271	0.92919	.	.	ENSG00000125851	ENST00000377899;ENST00000262545;ENST00000536609	D;D;D	0.88046	-2.33;-2.33;-2.33	5.38	5.38	0.77491	Peptidase S8/S53, subtilisin/kexin/sedolisin (3);	0.000000	0.85682	D	0.000000	D	0.92499	0.7618	M	0.65320	2	0.80722	D	1	D;D	0.89917	1.0;0.999	D;D	0.81914	0.995;0.969	D	0.93116	0.6521	10	0.87932	D	0	-18.6857	17.6879	0.88261	0.0:1.0:0.0:0.0	.	250;285	B4DFQ3;P16519	.;NEC2_HUMAN	M	266;285;250	ENSP00000367131:T266M;ENSP00000262545:T285M;ENSP00000437458:T250M	ENSP00000262545:T285M	T	+	2	0	PCSK2	17365497	1.000000	0.71417	0.952000	0.39060	0.978000	0.69477	7.440000	0.80464	2.519000	0.84933	0.655000	0.94253	ACG		0.637	PCSK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078120.2	NM_002594	
XRN2	22803	broad.mit.edu	37	20	21346263	21346263	+	Missense_Mutation	SNP	C	C	T	rs377677641		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr20:21346263C>T	ENST00000377191.3	+	26	2472	c.2377C>T	c.(2377-2379)Cgg>Tgg	p.R793W	XRN2_ENST00000539513.1_Missense_Mutation_p.R739W|XRN2_ENST00000430571.2_Missense_Mutation_p.R717W	NM_012255.3	NP_036387.2	Q9H0D6	XRN2_HUMAN	5'-3' exoribonuclease 2	793					cell growth (GO:0016049)|DNA catabolic process, exonucleolytic (GO:0000738)|DNA-templated transcription, termination (GO:0006353)|mRNA processing (GO:0006397)|regulation of transcription, DNA-templated (GO:0006355)|RNA catabolic process (GO:0006401)|RNA metabolic process (GO:0016070)|RNA phosphodiester bond hydrolysis, exonucleolytic (GO:0090503)|RNA processing (GO:0006396)|spermatogenesis (GO:0007283)	aggresome (GO:0016235)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	5'-3' exonuclease activity (GO:0008409)|5'-3' exoribonuclease activity (GO:0004534)|nuclease activity (GO:0004518)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)	p.R793W(1)		endometrium(5)|kidney(6)|large_intestine(10)|lung(12)|ovary(1)|skin(5)	39						CAGCAATGGACGGCAGTGGAA	0.483																																					p.R793W												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C2377T	20						.	C	TRP/ARG	0,4406		0,0,2203	101.0	102.0	102.0		2377	2.7	0.4	20		102	1,8599	1.2+/-3.3	0,1,4299	no	missense	XRN2	NM_012255.3	101	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	benign	793/951	21346263	1,13005	2203	4300	6503	21294263	SO:0001583	missense	22803	exon26			AF064257	CCDS13144.1	20p11.2-p11.1	2011-09-12			ENSG00000088930	ENSG00000088930	3.1.13.-		12836	protein-coding gene	gene with protein product		608851				10409438	Standard	NM_012255		Approved		uc002wsf.1	Q9H0D6	OTTHUMG00000032025	ENST00000377191.3:c.2377C>T	20.37:g.21346263C>T	ENSP00000366396:p.Arg793Trp	Somatic		Capture	Illumina HiSeq	Phase_I	21294263	NM_012255	Q3L8N4|Q6KGZ9|Q9BQL1|Q9NTW0|Q9NXS6|Q9UL53	Missense_Mutation	SNP	ENST00000377191.3	37	CCDS13144.1	.	.	.	.	.	.	.	.	.	.	C	20.6	4.020875	0.75275	0.0	1.16E-4	ENSG00000088930	ENST00000377191;ENST00000430571;ENST00000539513	T;T;T	0.35973	1.29;1.28;1.29	5.85	2.71	0.32032	.	0.095678	0.64402	D	0.000001	T	0.41096	0.1144	M	0.68593	2.085	0.47547	D	0.999452	D	0.76494	0.999	P	0.49502	0.613	T	0.36504	-0.9745	10	0.87932	D	0	-13.1347	7.8	0.29168	0.4976:0.4235:0.0:0.079	.	793	Q9H0D6	XRN2_HUMAN	W	793;717;739	ENSP00000366396:R793W;ENSP00000413548:R717W;ENSP00000441113:R739W	ENSP00000366396:R793W	R	+	1	2	XRN2	21294263	0.634000	0.27190	0.429000	0.26710	0.990000	0.78478	1.098000	0.31000	0.807000	0.34208	0.655000	0.94253	CGG		0.483	XRN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078273.2	NM_012255	
ACSS1	84532	broad.mit.edu	37	20	24989998	24989998	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr20:24989998C>T	ENST00000323482.4	-	13	1877	c.1798G>A	c.(1798-1800)Gat>Aat	p.D600N	ACSS1_ENST00000432802.2_Intron|ACSS1_ENST00000537502.1_Missense_Mutation_p.D517N|ACSS1_ENST00000542618.1_Missense_Mutation_p.D479N|ACSS1_ENST00000484396.1_5'UTR	NM_001252675.1|NM_032501.3	NP_001239604.1|NP_115890.2	Q9NUB1	ACS2L_HUMAN	acyl-CoA synthetase short-chain family member 1	600					acetate biosynthetic process (GO:0019413)|acetyl-CoA biosynthetic process (GO:0006085)|acetyl-CoA biosynthetic process from acetate (GO:0019427)|ethanol oxidation (GO:0006069)|propionate biosynthetic process (GO:0019542)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	mitochondrial matrix (GO:0005759)	acetate-CoA ligase activity (GO:0003987)|AMP binding (GO:0016208)|ATP binding (GO:0005524)	p.D600N(1)		NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(11)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	26					Adenosine monophosphate(DB00131)|Adenosine triphosphate(DB00171)	CCCGCACTATCTTTCACCACA	0.507																																					p.D600N												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1798A	20						.						209.0	194.0	199.0					20																	24989998		2203	4300	6503	24937998	SO:0001583	missense	84532	exon13				CCDS13167.1, CCDS58764.1, CCDS58765.1	20p11.23-p11.21	2012-07-13	2005-09-08	2005-09-08	ENSG00000154930	ENSG00000154930	6.2.1.1	"""Acyl-CoA synthetase family"""	16091	protein-coding gene	gene with protein product		614355	"""acetyl-Coenzyme A synthetase 2 (AMP forming)-like"""	ACAS2L			Standard	NM_032501		Approved	dJ568C11.3, AceCS2L, MGC33843	uc002wub.3	Q9NUB1	OTTHUMG00000032112	ENST00000323482.4:c.1798G>A	20.37:g.24989998C>T	ENSP00000316924:p.Asp600Asn	Somatic		Capture	Illumina HiSeq	Phase_I	24937998	NM_032501	B3KXL2|B4DJZ3|D3DW48|F5H6F4|F8W7Y1|Q5TF42|Q8IV99|Q8N234|Q96JI1|Q96JX6|Q9NU28	Missense_Mutation	SNP	ENST00000323482.4	37	CCDS13167.1	.	.	.	.	.	.	.	.	.	.	C	9.634	1.137111	0.21123	.	.	ENSG00000154930	ENST00000323482;ENST00000376727;ENST00000537502;ENST00000542618	T;T;T	0.51071	0.72;0.72;0.72	4.79	4.79	0.61399	.	0.217438	0.45867	D	0.000333	T	0.44498	0.1296	L	0.58101	1.795	0.51767	D	0.99993	P;B;B;B	0.47106	0.89;0.164;0.102;0.102	B;B;B;B	0.40901	0.343;0.149;0.071;0.071	T	0.39840	-0.9594	10	0.16896	T	0.51	-22.9209	16.4276	0.83824	0.0:1.0:0.0:0.0	.	395;598;600;517	E9PC79;Q9NUB1-2;Q9NUB1;Q6ZV30	.;.;ACS2L_HUMAN;.	N	600;395;517;479	ENSP00000316924:D600N;ENSP00000439304:D517N;ENSP00000437657:D479N	ENSP00000316924:D600N	D	-	1	0	ACSS1	24937998	1.000000	0.71417	0.711000	0.30485	0.011000	0.07611	2.548000	0.45794	2.220000	0.72140	0.561000	0.74099	GAT		0.507	ACSS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078386.2	NM_032501	
ACSS1	84532	broad.mit.edu	37	20	24993513	24993513	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr20:24993513G>A	ENST00000323482.4	-	11	1721	c.1642C>T	c.(1642-1644)Cgg>Tgg	p.R548W	ACSS1_ENST00000432802.2_Missense_Mutation_p.R548W|ACSS1_ENST00000537502.1_Missense_Mutation_p.R465W|ACSS1_ENST00000542618.1_Missense_Mutation_p.R427W|ACSS1_ENST00000484396.1_5'Flank	NM_001252675.1|NM_032501.3	NP_001239604.1|NP_115890.2	Q9NUB1	ACS2L_HUMAN	acyl-CoA synthetase short-chain family member 1	548					acetate biosynthetic process (GO:0019413)|acetyl-CoA biosynthetic process (GO:0006085)|acetyl-CoA biosynthetic process from acetate (GO:0019427)|ethanol oxidation (GO:0006069)|propionate biosynthetic process (GO:0019542)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	mitochondrial matrix (GO:0005759)	acetate-CoA ligase activity (GO:0003987)|AMP binding (GO:0016208)|ATP binding (GO:0005524)	p.R548W(1)		NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(11)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	26					Adenosine monophosphate(DB00131)|Adenosine triphosphate(DB00171)	TCATCCATCCGCCCTGTGATC	0.582																																					p.R548W												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1642T	20						.						171.0	149.0	156.0					20																	24993513		2203	4300	6503	24941513	SO:0001583	missense	84532	exon11				CCDS13167.1, CCDS58764.1, CCDS58765.1	20p11.23-p11.21	2012-07-13	2005-09-08	2005-09-08	ENSG00000154930	ENSG00000154930	6.2.1.1	"""Acyl-CoA synthetase family"""	16091	protein-coding gene	gene with protein product		614355	"""acetyl-Coenzyme A synthetase 2 (AMP forming)-like"""	ACAS2L			Standard	NM_032501		Approved	dJ568C11.3, AceCS2L, MGC33843	uc002wub.3	Q9NUB1	OTTHUMG00000032112	ENST00000323482.4:c.1642C>T	20.37:g.24993513G>A	ENSP00000316924:p.Arg548Trp	Somatic		Capture	Illumina HiSeq	Phase_I	24941513	NM_032501	B3KXL2|B4DJZ3|D3DW48|F5H6F4|F8W7Y1|Q5TF42|Q8IV99|Q8N234|Q96JI1|Q96JX6|Q9NU28	Missense_Mutation	SNP	ENST00000323482.4	37	CCDS13167.1	.	.	.	.	.	.	.	.	.	.	G	21.8	4.200873	0.79015	.	.	ENSG00000154930	ENST00000323482;ENST00000376727;ENST00000537502;ENST00000432802;ENST00000542618	D;D;D;D	0.83163	-1.69;-1.69;-1.69;-1.69	4.99	2.87	0.33458	AMP-dependent synthetase/ligase (1);	0.000000	0.85682	D	0.000000	D	0.94476	0.8222	H	0.99238	4.48	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	1.0;0.995;0.997;0.999	D	0.95590	0.8654	10	0.87932	D	0	-23.7396	12.5576	0.56263	0.0:0.0:0.6993:0.3007	.	343;546;548;465	E9PC79;Q9NUB1-2;Q9NUB1;Q6ZV30	.;.;ACS2L_HUMAN;.	W	548;343;465;548;427	ENSP00000316924:R548W;ENSP00000439304:R465W;ENSP00000388793:R548W;ENSP00000437657:R427W	ENSP00000316924:R548W	R	-	1	2	ACSS1	24941513	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	7.351000	0.79395	1.207000	0.43291	-0.169000	0.13324	CGG		0.582	ACSS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078386.2	NM_032501	
NRSN2	80023	broad.mit.edu	37	20	333980	333980	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr20:333980G>T	ENST00000382291.3	+	4	556	c.316G>T	c.(316-318)Gcc>Tcc	p.A106S	NRSN2_ENST00000608736.1_Intron|NRSN2_ENST00000382285.2_Missense_Mutation_p.A106S|NRSN2_ENST00000492242.1_3'UTR	NM_024958.2	NP_079234.1	Q9GZP1	NRSN2_HUMAN	neurensin 2	106						integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|transport vesicle (GO:0030133)		p.A106S(1)		endometrium(1)|large_intestine(2)|lung(4)|urinary_tract(1)	8		all_cancers(10;0.0834)				TCAGCGGGCAGCCGACTACAA	0.642																																					p.A106S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G316T	20						.						70.0	65.0	67.0					20																	333980		2203	4300	6503	281980	SO:0001583	missense	80023	exon4			AL136915	CCDS12996.1	20p13	2008-02-04	2006-07-04	2006-07-04	ENSG00000125841	ENSG00000125841			16229	protein-coding gene	gene with protein product		610666	"""chromosome 20 open reading frame 98"""	C20orf98		16527258	Standard	NM_024958		Approved	dJ1103G7.6	uc002wdi.4	Q9GZP1	OTTHUMG00000031628	ENST00000382291.3:c.316G>T	20.37:g.333980G>T	ENSP00000371728:p.Ala106Ser	Somatic		Capture	Illumina HiSeq	Phase_I	281980	NM_024958	A8K3B2|Q6FII5|Q9NUD3	Missense_Mutation	SNP	ENST00000382291.3	37	CCDS12996.1	.	.	.	.	.	.	.	.	.	.	G	23.1	4.373107	0.82573	.	.	ENSG00000125841	ENST00000382291;ENST00000382285	T;T	0.17691	2.26;2.26	4.76	4.76	0.60689	.	0.220334	0.40469	N	0.001099	T	0.33847	0.0877	L	0.45581	1.43	0.32193	N	0.578853	D	0.76494	0.999	D	0.83275	0.996	T	0.31166	-0.9953	10	0.62326	D	0.03	-29.8635	13.1471	0.59467	0.0:0.0:1.0:0.0	.	106	Q9GZP1	NRSN2_HUMAN	S	106	ENSP00000371728:A106S;ENSP00000371722:A106S	ENSP00000371722:A106S	A	+	1	0	NRSN2	281980	0.995000	0.38212	1.000000	0.80357	0.975000	0.68041	2.487000	0.45268	2.486000	0.83907	0.643000	0.83706	GCC		0.642	NRSN2-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077446.1	NM_024958	
ZNF337	26152	broad.mit.edu	37	20	25657018	25657018	+	Silent	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr20:25657018G>A	ENST00000376436.1	-	4	1445	c.906C>T	c.(904-906)aaC>aaT	p.N302N	RP4-694B14.5_ENST00000428254.1_RNA|RP4-694B14.5_ENST00000455791.1_RNA|ZNF337_ENST00000481610.1_5'Flank|RP4-694B14.5_ENST00000421829.1_RNA|ZNF337_ENST00000538750.1_Silent_p.N270N|RP4-694B14.5_ENST00000439498.1_RNA|ZNF337_ENST00000252979.5_Silent_p.N302N|RP4-694B14.5_ENST00000414393.1_RNA			Q9Y3M9	ZN337_HUMAN	zinc finger protein 337	302					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.N302N(1)		breast(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(8)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	32						AGGACTTATCGTTAAACCTTC	0.483																																					p.N302N												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C906T	20						.						165.0	160.0	162.0					20																	25657018		2203	4300	6503	25605018	SO:0001819	synonymous_variant	26152	exon5				CCDS13174.1	20p11.1	2013-09-20			ENSG00000130684	ENSG00000130684		"""Zinc fingers, C2H2-type"", ""-"""	15809	protein-coding gene	gene with protein product							Standard	XM_005260702		Approved	dJ694B14.1	uc002wuz.3	Q9Y3M9	OTTHUMG00000032131	ENST00000376436.1:c.906C>T	20.37:g.25657018G>A		Somatic		Capture	Illumina HiSeq	Phase_I	25605018	NM_015655	B4DSM2|Q9Y3Y5	Silent	SNP	ENST00000376436.1	37	CCDS13174.1																																																																																				0.483	ZNF337-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078454.1		
TTLL9	164395	broad.mit.edu	37	20	30496395	30496395	+	Splice_Site	SNP	G	G	A	rs564856380		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr20:30496395G>A	ENST00000375938.4	+	5	461	c.208G>A	c.(208-210)Gaa>Aaa	p.E70K	TTLL9_ENST00000375934.4_Splice_Site_p.E52K|TTLL9_ENST00000535842.1_Splice_Site_p.E70K|TTLL9_ENST00000375922.4_Splice_Site_p.E20K|TTLL9_ENST00000375921.2_Splice_Site_p.E20K|TTLL9_ENST00000310998.4_Splice_Site_p.E20K			Q3SXZ7	TTLL9_HUMAN	tubulin tyrosine ligase-like family, member 9	70	TTL. {ECO:0000255|PROSITE- ProRule:PRU00568}.				cellular protein modification process (GO:0006464)	cilium (GO:0005929)|cytoplasm (GO:0005737)|microtubule (GO:0005874)	ligase activity (GO:0016874)	p.E52K(1)|p.E70K(1)		breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(8)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	26			Colorectal(19;0.00306)|COAD - Colon adenocarcinoma(19;0.0347)			CACCCCCAGCGAAGGGGAGTG	0.612													G|||	1	0.000199681	0.0	0.0	5008	,	,		15533	0.001		0.0	False		,,,				2504	0.0				p.E70K												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G208A	20						.						32.0	32.0	32.0					20																	30496395		1917	4125	6042	29960056	SO:0001630	splice_region_variant	164395	exon5			AL031658	CCDS42863.1	20q11	2013-02-14	2005-07-28	2005-07-28		ENSG00000131044		"""Tubulin tyrosine ligase-like family"""	16118	protein-coding gene	gene with protein product			"""chromosome 20 open reading frame 125"""	C20orf125		15890843	Standard	NM_001008409		Approved	dJ310O13.1	uc010gdx.1	Q3SXZ7		ENST00000375938.4:c.207-1G>A	20.37:g.30496395G>A		Somatic		Capture	Illumina HiSeq	Phase_I	29960056	NM_001008409	A6NH06|A6NIS5|B3KSG8|Q3SXZ8|Q5JYS3|Q5JYS4	Missense_Mutation	SNP	ENST00000375938.4	37	CCDS42863.1	.	.	.	.	.	.	.	.	.	.	G	18.18	3.565887	0.65651	.	.	ENSG00000131044	ENST00000375938;ENST00000535842;ENST00000310998;ENST00000375921;ENST00000375935;ENST00000375934;ENST00000375922	T;T;T;T;T;T	0.10573	3.8;3.8;3.75;3.06;2.86;3.79	5.0	5.0	0.66597	.	0.223034	0.27473	U	0.019203	T	0.13243	0.0321	L	0.48218	1.51	0.47441	D	0.999428	P	0.47762	0.9	B	0.42282	0.382	T	0.01617	-1.1311	10	0.49607	T	0.09	.	15.3874	0.74711	0.0:0.0:1.0:0.0	.	70	Q3SXZ7	TTLL9_HUMAN	K	70;70;20;20;52;52;20	ENSP00000365105:E70K;ENSP00000442515:E70K;ENSP00000308980:E20K;ENSP00000365086:E20K;ENSP00000365100:E52K;ENSP00000365088:E20K	ENSP00000308980:E20K	E	+	1	0	TTLL9	29960056	1.000000	0.71417	0.997000	0.53966	0.887000	0.51463	5.269000	0.65542	2.480000	0.83734	0.561000	0.74099	GAA		0.612	TTLL9-205	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001008409	Missense_Mutation
CCM2L	140706	broad.mit.edu	37	20	30602741	30602741	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr20:30602741C>T	ENST00000300415.8	+	2	78	c.65C>T	c.(64-66)cCc>cTc	p.P22L	CCM2L_ENST00000262659.8_Missense_Mutation_p.P22L			Q9NUG4	CCM2L_HUMAN	cerebral cavernous malformation 2-like	22								p.P22L(1)									CTGGTGTTCCCCAAGGCCGGG	0.597																																					p.P22L												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C65T	20						.						73.0	79.0	77.0					20																	30602741		2202	4300	6502	30066402	SO:0001583	missense	140706	exon2			AL031658	CCDS13195.1	20q11.21	2012-10-30	2012-10-30	2012-10-30	ENSG00000101331	ENSG00000101331			16153	protein-coding gene	gene with protein product			"""chromosome 20 open reading frame 160"""	C20orf160			Standard	NM_080625		Approved	dJ310O13.5	uc002wxf.2	Q9NUG4	OTTHUMG00000032197	ENST00000300415.8:c.65C>T	20.37:g.30602741C>T	ENSP00000300415:p.Pro22Leu	Somatic		Capture	Illumina HiSeq	Phase_I	30066402	NM_080625	Q5JYR9|Q8N5F1|Q8N6G8|Q96MD5	Missense_Mutation	SNP	ENST00000300415.8	37		.	.	.	.	.	.	.	.	.	.	C	32	5.122826	0.94429	.	.	ENSG00000101331	ENST00000300415;ENST00000339619;ENST00000262659	T;T	0.48836	0.8;0.8	4.86	4.86	0.63082	.	0.057459	0.64402	D	0.000001	T	0.57902	0.2085	M	0.69823	2.125	0.80722	D	1	P	0.52316	0.952	P	0.49085	0.6	T	0.64702	-0.6345	10	0.66056	D	0.02	-36.5449	17.1529	0.86782	0.0:1.0:0.0:0.0	.	22	Q9NUG4-2	.	L	22	ENSP00000300415:P22L;ENSP00000262659:P22L	ENSP00000262659:P22L	P	+	2	0	C20orf160	30066402	0.999000	0.42202	1.000000	0.80357	0.982000	0.71751	4.261000	0.58841	2.524000	0.85096	0.655000	0.94253	CCC		0.597	CCM2L-201	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_080625	
LZTS3	9762	broad.mit.edu	37	20	3146855	3146855	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr20:3146855C>T	ENST00000329152.3	-	2	2008	c.611G>A	c.(610-612)cGg>cAg	p.R204Q	LZTS3_ENST00000360342.3_Missense_Mutation_p.R204Q|LZTS3_ENST00000337576.5_Missense_Mutation_p.R204Q			O60299	LZTS3_HUMAN		204						cell junction (GO:0030054)|cytoplasm (GO:0005737)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)		p.R204Q(1)									AGTCATGGTCCGAGACTTGTC	0.622																																					p.R204Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G611A	20						.						56.0	49.0	51.0					20																	3146855		2203	4300	6503	3094855	SO:0001583	missense	9762	exon2																														ENST00000329152.3:c.611G>A	20.37:g.3146855C>T	ENSP00000332123:p.Arg204Gln	Somatic		Capture	Illumina HiSeq	Phase_I	3094855	NM_014731	A2A2Q7|D3DVX6|Q8IXX8	Missense_Mutation	SNP	ENST00000329152.3	37	CCDS13049.1	.	.	.	.	.	.	.	.	.	.	C	15.37	2.813208	0.50527	.	.	ENSG00000088899	ENST00000329152;ENST00000360342;ENST00000337576	T;T;T	0.33654	1.41;1.4;1.4	5.26	5.26	0.73747	.	0.243209	0.40818	N	0.001013	T	0.42494	0.1205	L	0.36672	1.1	0.47698	D	0.999498	D;D	0.76494	0.999;0.998	P;P	0.54346	0.749;0.565	T	0.09164	-1.0687	10	0.16896	T	0.51	-26.6337	18.8648	0.92287	0.0:1.0:0.0:0.0	.	204;204	O60299-2;O60299	.;PRIP1_HUMAN	Q	204	ENSP00000332123:R204Q;ENSP00000353496:R204Q;ENSP00000338166:R204Q	ENSP00000332123:R204Q	R	-	2	0	RP5-1187M17.10	3094855	1.000000	0.71417	1.000000	0.80357	0.315000	0.28087	2.095000	0.41729	2.450000	0.82876	0.561000	0.74099	CGG		0.622	LZTS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077715.2		
SLC4A11	83959	broad.mit.edu	37	20	3214824	3214824	+	Missense_Mutation	SNP	A	A	C			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr20:3214824A>C	ENST00000380056.3	-	4	523	c.476T>G	c.(475-477)tTc>tGc	p.F159C	SLC4A11_ENST00000380059.3_Missense_Mutation_p.F186C|SLC4A11_ENST00000539553.2_Missense_Mutation_p.F143C	NM_032034.3	NP_114423.1	Q8NBS3	S4A11_HUMAN	solute carrier family 4, sodium borate transporter, member 11	159					bicarbonate transport (GO:0015701)|borate transmembrane transport (GO:0035445)|borate transport (GO:0046713)|cellular cation homeostasis (GO:0030003)|fluid transport (GO:0042044)|proton transport (GO:0015992)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	basolateral plasma membrane (GO:0016323)|integral component of membrane (GO:0016021)	bicarbonate transmembrane transporter activity (GO:0015106)|borate transmembrane transporter activity (GO:0046715)|hydrogen ion channel activity (GO:0015252)|inorganic anion exchanger activity (GO:0005452)|protein dimerization activity (GO:0046983)|sodium channel activity (GO:0005272)|symporter activity (GO:0015293)	p.F159C(1)		breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|liver(1)|lung(16)|ovary(2)|prostate(4)|soft_tissue(1)|urinary_tract(1)	40						GTCCCTGGCGAAGCGGCGAAG	0.637																																					p.F186C	NSCLC(190;922 2139 10266 10292 38692)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T557G	20						.						129.0	121.0	124.0					20																	3214824		2203	4300	6503	3162824	SO:0001583	missense	83959	exon5			AF336127	CCDS13052.1, CCDS54445.1, CCDS54446.1	20p13	2014-02-14	2007-08-03		ENSG00000088836	ENSG00000088836		"""Solute carriers"""	16438	protein-coding gene	gene with protein product		610206	"""corneal endothelial dystrophy 2 (autosomal recessive)"", ""solute carrier family 4, sodium bicarbonate transporter-like, member 11"", ""corneal dystrophy and perceptive deafness 1"""	CHED2, CDPD1		10843999, 11302728, 16767101	Standard	NM_001174089		Approved	dJ794I6.2, BTR1, NaBC1, FECD4	uc010zqe.2	Q8NBS3	OTTHUMG00000031740	ENST00000380056.3:c.476T>G	20.37:g.3214824A>C	ENSP00000369396:p.Phe159Cys	Somatic		Capture	Illumina HiSeq	Phase_I	3162824	NM_001174090	B4DKC8|B4DKX9|G3V1M3|Q2TB62|Q2TB63|Q9BXF4|Q9NTW9	Missense_Mutation	SNP	ENST00000380056.3	37	CCDS13052.1	.	.	.	.	.	.	.	.	.	.	A	15.38	2.816118	0.50527	.	.	ENSG00000088836	ENST00000380059;ENST00000380056;ENST00000539553;ENST00000437836	T;T;T;T	0.80123	-1.34;-1.34;-1.34;-1.34	5.06	5.06	0.68205	Phosphotransferase/anion transporter (1);	0.558539	0.17133	N	0.185748	D	0.82416	0.5032	L	0.47716	1.5	0.46586	D	0.999115	P;D;P	0.53151	0.923;0.958;0.925	P;P;P	0.52710	0.707;0.608;0.512	T	0.83310	-0.0023	10	0.59425	D	0.04	.	13.9951	0.64392	1.0:0.0:0.0:0.0	.	143;186;159	G3V1M3;B4DKC8;Q8NBS3	.;.;S4A11_HUMAN	C	186;159;143;143	ENSP00000369399:F186C;ENSP00000369396:F159C;ENSP00000441370:F143C;ENSP00000404271:F143C	ENSP00000369396:F159C	F	-	2	0	SLC4A11	3162824	1.000000	0.71417	0.095000	0.20976	0.004000	0.04260	8.893000	0.92498	1.895000	0.54865	0.533000	0.62120	TTC		0.637	SLC4A11-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000077728.1		
NOL4L	140688	broad.mit.edu	37	20	31040105	31040105	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr20:31040105C>T	ENST00000359676.5	-	7	1166	c.1024G>A	c.(1024-1026)Ggg>Agg	p.G342R	RP5-1184F4.5_ENST00000442179.1_RNA|C20orf112_ENST00000475781.1_5'Flank	NM_001256798.1|NM_080616.4	NP_001243727.1|NP_542183.2	Q96MY1	NOL4L_HUMAN		342						cytoplasm (GO:0005737)|nucleus (GO:0005634)		p.G342R(1)		endometrium(3)|kidney(2)|large_intestine(5)|lung(5)	15						GCCCCGTACCCGCGGTAACTG	0.642																																					p.G342R												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1024A	20						.						123.0	108.0	113.0					20																	31040105		2203	4300	6503	30503766	SO:0001583	missense	140688	exon7																														ENST00000359676.5:c.1024G>A	20.37:g.31040105C>T	ENSP00000352704:p.Gly342Arg	Somatic		Capture	Illumina HiSeq	Phase_I	30503766	NM_080616	Q5JYB7|Q6P0Y4|Q9BR34|Q9NQF6	Missense_Mutation	SNP	ENST00000359676.5	37	CCDS13202.1	.	.	.	.	.	.	.	.	.	.	C	17.97	3.518913	0.64634	.	.	ENSG00000197183	ENST00000359676;ENST00000397984	.	.	.	4.34	-0.364	0.12553	.	0.114465	0.64402	D	0.000018	T	0.47728	0.1461	L	0.54323	1.7	0.80722	D	1	P	0.47409	0.895	P	0.46339	0.513	T	0.40776	-0.9545	9	0.40728	T	0.16	.	9.6374	0.39817	0.0:0.4873:0.0:0.5127	.	342	Q96MY1	CT112_HUMAN	R	342	.	ENSP00000352704:G342R	G	-	1	0	C20orf112	30503766	0.462000	0.25791	0.535000	0.28026	0.920000	0.55202	1.046000	0.30354	-0.092000	0.12417	0.561000	0.74099	GGG		0.642	C20orf112-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000078628.2		
TRPC4AP	26133	broad.mit.edu	37	20	33632433	33632433	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr20:33632433C>T	ENST00000252015.2	-	7	829	c.740G>A	c.(739-741)cGg>cAg	p.R247Q	TRPC4AP_ENST00000451813.2_Missense_Mutation_p.R247Q|TRPC4AP_ENST00000432634.2_Missense_Mutation_p.R208Q			Q8TEL6	TP4AP_HUMAN	transient receptor potential cation channel, subfamily C, member 4 associated protein	247	Interaction with TNFRSF1A. {ECO:0000250}.				calcium ion transmembrane transport (GO:0070588)|ion transmembrane transport (GO:0034220)|protein ubiquitination (GO:0016567)|transmembrane transport (GO:0055085)|ubiquitin-dependent protein catabolic process (GO:0006511)	Cul4A-RING E3 ubiquitin ligase complex (GO:0031464)|plasma membrane (GO:0005886)	phosphatase binding (GO:0019902)	p.R247Q(1)		breast(3)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(13)|skin(1)|stomach(1)|urinary_tract(1)	32			BRCA - Breast invasive adenocarcinoma(18;0.00936)			AGCCAGAATCCGGCAGAAATT	0.448																																					p.R247Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G740A	20						.						124.0	121.0	122.0					20																	33632433		2203	4300	6503	33096094	SO:0001583	missense	26133	exon7			AF055022	CCDS13246.1, CCDS46591.1	20q11.23	2014-06-13	2003-10-06	2003-10-08	ENSG00000100991	ENSG00000100991			16181	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 158"""	608430	"""chromosome 20 open reading frame 188"""	C20orf188			Standard	NM_015638		Approved	DKFZP727M231, DKFZp586C1223, dJ756N5.2, TRRP4AP, PPP1R158	uc002xbk.3	Q8TEL6	OTTHUMG00000032319	ENST00000252015.2:c.740G>A	20.37:g.33632433C>T	ENSP00000252015:p.Arg247Gln	Somatic		Capture	Illumina HiSeq	Phase_I	33096094	NM_199368	E1P5Q0|E1P5Q1|Q96H82|Q9BVB8|Q9H429|Q9UFS6	Missense_Mutation	SNP	ENST00000252015.2	37	CCDS13246.1	.	.	.	.	.	.	.	.	.	.	C	34	5.397007	0.96009	.	.	ENSG00000100991	ENST00000252015;ENST00000451813;ENST00000432634;ENST00000541994	T;T;T	0.29917	1.55;1.55;1.55	5.6	4.66	0.58398	.	0.000000	0.85682	D	0.000000	T	0.52517	0.1739	M	0.63843	1.955	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.76575	0.988;0.944;0.944	T	0.56721	-0.7932	10	0.87932	D	0	.	14.5912	0.68365	0.0:0.9297:0.0:0.0703	.	208;247;247	B4E0Q1;E1P5Q0;Q8TEL6	.;.;TP4AP_HUMAN	Q	247;247;208;232	ENSP00000252015:R247Q;ENSP00000400614:R247Q;ENSP00000400497:R208Q	ENSP00000252015:R247Q	R	-	2	0	TRPC4AP	33096094	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.757000	0.85209	1.356000	0.45884	0.585000	0.79938	CGG		0.448	TRPC4AP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078832.2	NM_015638	
MMP24	10893	broad.mit.edu	37	20	33842534	33842534	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr20:33842534C>T	ENST00000246186.6	+	4	879	c.794C>T	c.(793-795)aCg>aTg	p.T265M	MMP24-AS1_ENST00000454184.1_RNA|EDEM2_ENST00000540582.1_Intron|MMP24-AS1_ENST00000456350.1_RNA|MMP24-AS1_ENST00000438751.1_RNA|MMP24-AS1_ENST00000433764.1_RNA|MMP24-AS1_ENST00000453892.1_RNA|MMP24-AS1_ENST00000566203.2_RNA	NM_006690.3	NP_006681.1	Q9Y5R2	MMP24_HUMAN	matrix metallopeptidase 24 (membrane-inserted)	265					cell-cell adhesion (GO:0098609)|cell-cell adhesion mediated by cadherin (GO:0044331)|detection of temperature stimulus involved in sensory perception of pain (GO:0050965)|glial cell differentiation (GO:0010001)|neuronal stem cell maintenance (GO:0097150)|positive regulation of catalytic activity (GO:0043085)|proteolysis (GO:0006508)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|proteinaceous extracellular matrix (GO:0005578)|trans-Golgi network membrane (GO:0032588)	calcium ion binding (GO:0005509)|enzyme activator activity (GO:0008047)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)	p.T265M(1)		NS(1)|endometrium(3)|large_intestine(1)|lung(2)|prostate(2)|skin(5)	14			BRCA - Breast invasive adenocarcinoma(18;0.00252)		Marimastat(DB00786)	GAGCCATGGACGCTAGGAAAT	0.557																																					p.T212M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C635T	20						.						94.0	95.0	94.0					20																	33842534		2198	4300	6498	33305950	SO:0001583	missense	10893	exon4			AF131284	CCDS46593.1	20q11.2	2008-07-16	2005-08-08		ENSG00000125966	ENSG00000125966			7172	protein-coding gene	gene with protein product	"""membrane-type 5 matrix metalloproteinase"""	604871	"""matrix metalloproteinase 24 (membrane-inserted)"""			10363975	Standard	NM_006690		Approved	MT5-MMP	uc002xbu.2	Q9Y5R2	OTTHUMG00000032330	ENST00000246186.6:c.794C>T	20.37:g.33842534C>T	ENSP00000246186:p.Thr265Met	Somatic		Capture	Illumina HiSeq	Phase_I	33305950	NM_006690	B7ZBG8|Q9H440	Missense_Mutation	SNP	ENST00000246186.6	37	CCDS46593.1	.	.	.	.	.	.	.	.	.	.	C	25.8	4.678217	0.88542	.	.	ENSG00000125966	ENST00000246186;ENST00000540655	T	0.25749	1.78	5.12	5.12	0.69794	Peptidase M10, metallopeptidase (1);Peptidase, metallopeptidase (1);Metallopeptidase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.69070	0.3070	H	0.98314	4.2	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.82348	-0.0502	10	0.87932	D	0	.	17.729	0.88372	0.0:1.0:0.0:0.0	.	265	Q9Y5R2	MMP24_HUMAN	M	265;213	ENSP00000246186:T265M	ENSP00000246186:T265M	T	+	2	0	MMP24	33305950	1.000000	0.71417	0.961000	0.40146	0.970000	0.65996	7.651000	0.83577	2.653000	0.90120	0.655000	0.94253	ACG		0.557	MMP24-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078851.4	NM_006690	
CEP250	11190	broad.mit.edu	37	20	34092442	34092442	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr20:34092442A>G	ENST00000397527.1	+	30	6965	c.6245A>G	c.(6244-6246)cAa>cGa	p.Q2082R	CEP250_ENST00000342580.4_Missense_Mutation_p.Q2026R	NM_007186.3	NP_009117.2	Q9BV73	CP250_HUMAN	centrosomal protein 250kDa	2082	Gln/Glu-rich.			Q -> L (in Ref. 1; AAC06349). {ECO:0000305}.	centriole-centriole cohesion (GO:0010457)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|protein localization (GO:0008104)|protein localization to organelle (GO:0033365)|regulation of centriole-centriole cohesion (GO:0030997)	centriole (GO:0005814)|centrosome (GO:0005813)|cilium (GO:0005929)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|microtubule organizing center (GO:0005815)|protein complex (GO:0043234)|spindle pole centrosome (GO:0031616)	protein C-terminus binding (GO:0008022)|protein domain specific binding (GO:0019904)|protein kinase binding (GO:0019901)	p.Q2082R(1)		NS(1)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(13)|lung(13)|ovary(4)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	45	Lung NSC(9;0.00156)|all_lung(11;0.00243)		BRCA - Breast invasive adenocarcinoma(18;0.0106)			AATCTGGGGCAAGAGAGAGAA	0.532																																					p.Q2082R												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A6245G	20						.						51.0	55.0	54.0					20																	34092442		2203	4300	6503	33555856	SO:0001583	missense	11190	exon30			AF022655	CCDS13255.1	20q11.22	2014-02-20	2006-01-11	2006-01-11	ENSG00000126001	ENSG00000126001			1859	protein-coding gene	gene with protein product		609689	"""centrosomal protein 2"""	CEP2		9506584, 9647649	Standard	NM_007186		Approved	C-NAP1	uc021wco.1	Q9BV73	OTTHUMG00000032343	ENST00000397527.1:c.6245A>G	20.37:g.34092442A>G	ENSP00000380661:p.Gln2082Arg	Somatic		Capture	Illumina HiSeq	Phase_I	33555856	NM_007186	E1P5Q3|O14812|O60588|Q9H450	Missense_Mutation	SNP	ENST00000397527.1	37	CCDS13255.1	.	.	.	.	.	.	.	.	.	.	A	1.898	-0.453746	0.04540	.	.	ENSG00000126001	ENST00000397527;ENST00000342580;ENST00000422671	T;T;T	0.46819	2.97;2.96;0.86	4.78	3.68	0.42216	.	0.610393	0.14520	N	0.314545	T	0.27559	0.0677	N	0.12182	0.205	0.09310	N	1	B	0.10296	0.003	B	0.09377	0.004	T	0.15321	-1.0441	10	0.11794	T	0.64	.	11.5577	0.50759	0.8499:0.1501:0.0:0.0	.	2082	Q9BV73	CP250_HUMAN	R	2082;2026;570	ENSP00000380661:Q2082R;ENSP00000341541:Q2026R;ENSP00000395992:Q570R	ENSP00000341541:Q2026R	Q	+	2	0	CEP250	33555856	0.000000	0.05858	0.278000	0.24718	0.020000	0.10135	0.117000	0.15583	0.857000	0.35407	-0.366000	0.07423	CAA		0.532	CEP250-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078877.7	NM_007186	
CEP250	11190	broad.mit.edu	37	20	34092665	34092665	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr20:34092665G>T	ENST00000397527.1	+	30	7188	c.6468G>T	c.(6466-6468)caG>caT	p.Q2156H	CEP250_ENST00000342580.4_Missense_Mutation_p.Q2100H	NM_007186.3	NP_009117.2	Q9BV73	CP250_HUMAN	centrosomal protein 250kDa	2156	Gln/Glu-rich.				centriole-centriole cohesion (GO:0010457)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|protein localization (GO:0008104)|protein localization to organelle (GO:0033365)|regulation of centriole-centriole cohesion (GO:0030997)	centriole (GO:0005814)|centrosome (GO:0005813)|cilium (GO:0005929)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|microtubule organizing center (GO:0005815)|protein complex (GO:0043234)|spindle pole centrosome (GO:0031616)	protein C-terminus binding (GO:0008022)|protein domain specific binding (GO:0019904)|protein kinase binding (GO:0019901)	p.Q2156H(1)		NS(1)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(13)|lung(13)|ovary(4)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	45	Lung NSC(9;0.00156)|all_lung(11;0.00243)		BRCA - Breast invasive adenocarcinoma(18;0.0106)			AGCGGCTACAGGCAGCCCTGA	0.572																																					p.Q2156H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G6468T	20						.						50.0	53.0	52.0					20																	34092665		2203	4300	6503	33556079	SO:0001583	missense	11190	exon30			AF022655	CCDS13255.1	20q11.22	2014-02-20	2006-01-11	2006-01-11	ENSG00000126001	ENSG00000126001			1859	protein-coding gene	gene with protein product		609689	"""centrosomal protein 2"""	CEP2		9506584, 9647649	Standard	NM_007186		Approved	C-NAP1	uc021wco.1	Q9BV73	OTTHUMG00000032343	ENST00000397527.1:c.6468G>T	20.37:g.34092665G>T	ENSP00000380661:p.Gln2156His	Somatic		Capture	Illumina HiSeq	Phase_I	33556079	NM_007186	E1P5Q3|O14812|O60588|Q9H450	Missense_Mutation	SNP	ENST00000397527.1	37	CCDS13255.1	.	.	.	.	.	.	.	.	.	.	G	12.10	1.837877	0.32513	.	.	ENSG00000126001	ENST00000397527;ENST00000342580;ENST00000422671	T;T;T	0.46819	2.89;2.88;0.86	5.01	4.07	0.47477	.	0.333194	0.25192	N	0.032457	T	0.57755	0.2075	M	0.71581	2.175	0.09310	N	1	D	0.65815	0.995	D	0.63381	0.914	T	0.51442	-0.8705	10	0.44086	T	0.13	.	3.7616	0.08606	0.2488:0.0:0.5765:0.1747	.	2156	Q9BV73	CP250_HUMAN	H	2156;2100;644	ENSP00000380661:Q2156H;ENSP00000341541:Q2100H;ENSP00000395992:Q644H	ENSP00000341541:Q2100H	Q	+	3	2	CEP250	33556079	0.027000	0.19231	0.581000	0.28614	0.923000	0.55619	1.428000	0.34892	1.351000	0.45789	0.655000	0.94253	CAG		0.572	CEP250-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078877.7	NM_007186	
NFS1	9054	broad.mit.edu	37	20	34263091	34263091	+	Missense_Mutation	SNP	C	C	T	rs148047173		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr20:34263091C>T	ENST00000374092.4	-	8	894	c.824G>A	c.(823-825)cGt>cAt	p.R275H	NFS1_ENST00000540053.1_Missense_Mutation_p.R73H|NFS1_ENST00000541387.1_Missense_Mutation_p.R224H|NFS1_ENST00000498084.1_5'Flank|NFS1_ENST00000374085.1_Missense_Mutation_p.R215H|NFS1_ENST00000397425.1_Missense_Mutation_p.R215H|RP1-309K20.6_ENST00000541176.2_5'Flank	NM_021100.4	NP_066923.3	Q9Y697	NFS1_HUMAN	NFS1 cysteine desulfurase	275					cysteine metabolic process (GO:0006534)|iron incorporation into metallo-sulfur cluster (GO:0018283)|Mo-molybdopterin cofactor biosynthetic process (GO:0006777)|molybdopterin cofactor biosynthetic process (GO:0032324)|protein complex assembly (GO:0006461)|small molecule metabolic process (GO:0044281)|sulfur amino acid metabolic process (GO:0000096)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	cysteine desulfurase activity (GO:0031071)|protein homodimerization activity (GO:0042803)|pyridoxal phosphate binding (GO:0030170)	p.R275H(1)		central_nervous_system(1)|kidney(2)|large_intestine(2)|lung(8)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	18	Lung NSC(9;0.00608)|all_lung(11;0.00918)		BRCA - Breast invasive adenocarcinoma(18;0.0886)		L-Alanine(DB00160)|L-Cysteine(DB00151)	CACACGCACACGGGGCCGGCG	0.547																																					p.R275H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G824A	20						.	C	HIS/ARG,HIS/ARG	1,4405	2.1+/-5.4	0,1,2202	21.0	24.0	23.0		671,824	5.0	1.0	20	dbSNP_134	23	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	NFS1	NM_001198989.1,NM_021100.4	29,29	0,2,6501	TT,TC,CC		0.0116,0.0227,0.0154	probably-damaging,probably-damaging	224/407,275/458	34263091	2,13004	2203	4300	6503	33726505	SO:0001583	missense	9054	exon8			AF097025	CCDS13262.1, CCDS56185.1	20q11.22	2013-08-06	2013-08-06		ENSG00000244005	ENSG00000244005	2.8.1.7		15910	protein-coding gene	gene with protein product		603485	"""nitrogen fixation 1 (S. cerevisiae, homolog)"", ""NFS1 nitrogen fixation 1 homolog (S. cerevisiae)"""			9885568, 16847322	Standard	NM_021100		Approved	NifS, IscS	uc002xdw.2	Q9Y697	OTTHUMG00000032361	ENST00000374092.4:c.824G>A	20.37:g.34263091C>T	ENSP00000363205:p.Arg275His	Somatic		Capture	Illumina HiSeq	Phase_I	33726505	NM_021100	B3KMA5|B4DXK9|E1P5R8|F5GYK5|Q6P0L8|Q9NTZ5|Q9Y481	Missense_Mutation	SNP	ENST00000374092.4	37	CCDS13262.1	.	.	.	.	.	.	.	.	.	.	C	34	5.376251	0.95945	2.27E-4	1.16E-4	ENSG00000244005	ENST00000374092;ENST00000374085;ENST00000397425;ENST00000540053;ENST00000541387	D;D;D;D;D	0.86769	-2.17;-2.17;-2.17;-2.17;-2.17	5.03	5.03	0.67393	Pyridoxal phosphate-dependent transferase, major region, subdomain 1 (1);Pyridoxal phosphate-dependent transferase, major domain (1);Aminotransferase, class V/Cysteine desulfurase (1);	0.050910	0.85682	D	0.000000	D	0.94162	0.8127	M	0.86178	2.8	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.79108	0.992;0.973	D	0.94845	0.8008	10	0.87932	D	0	-0.8161	18.5491	0.91057	0.0:1.0:0.0:0.0	.	224;275	F5GYK5;Q9Y697	.;NFS1_HUMAN	H	275;215;215;73;224	ENSP00000363205:R275H;ENSP00000363198:R215H;ENSP00000380570:R215H;ENSP00000438594:R73H;ENSP00000440897:R224H	ENSP00000363198:R215H	R	-	2	0	NFS1	33726505	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.561000	0.82288	2.614000	0.88457	0.462000	0.41574	CGT		0.547	NFS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078936.4	NM_021100	
SAMHD1	25939	broad.mit.edu	37	20	35545145	35545145	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr20:35545145G>A	ENST00000262878.4	-	9	1241	c.1042C>T	c.(1042-1044)Cgt>Tgt	p.R348C	SAMHD1_ENST00000373694.5_Missense_Mutation_p.R133C	NM_015474.3	NP_056289.2	Q9Y3Z3	SAMH1_HUMAN	SAM domain and HD domain 1	348					dATP catabolic process (GO:0046061)|defense response to virus (GO:0051607)|dGTP catabolic process (GO:0006203)|immune response (GO:0006955)|innate immune response (GO:0045087)|protein homotetramerization (GO:0051289)|regulation of innate immune response (GO:0045088)	intracellular (GO:0005622)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	dGTP binding (GO:0032567)|dGTPase activity (GO:0008832)|nucleic acid binding (GO:0003676)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)	p.R348C(1)		breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(8)|urinary_tract(1)	20		Myeloproliferative disorder(115;0.00878)				GCACAAATACGCAACTCATTG	0.383																																					p.R348C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1042T	20						.						204.0	221.0	215.0					20																	35545145		2203	4300	6503	34978559	SO:0001583	missense	25939	exon9			AF228421	CCDS13288.1	20q11.23	2014-09-17			ENSG00000101347	ENSG00000101347		"""Sterile alpha motif (SAM) domain containing"""	15925	protein-coding gene	gene with protein product	"""HD domain containing 1"", ""monocyte protein 5"", ""Aicardi-Goutieres syndrome 5"""	606754				11064105, 11230166	Standard	NM_015474		Approved	SBBI88, Mg11, HDDC1, MOP-5, AGS5	uc002xgh.2	Q9Y3Z3	OTTHUMG00000032402	ENST00000262878.4:c.1042C>T	20.37:g.35545145G>A	ENSP00000262878:p.Arg348Cys	Somatic		Capture	Illumina HiSeq	Phase_I	34978559	NM_015474	B4E2A5|E1P5V2|Q5JXG8|Q8N491|Q9H004|Q9H005|Q9H3U9	Missense_Mutation	SNP	ENST00000262878.4	37	CCDS13288.1	.	.	.	.	.	.	.	.	.	.	G	15.65	2.897650	0.52121	.	.	ENSG00000101347	ENST00000262878;ENST00000373694	D;D	0.95447	-3.71;-2.46	5.67	3.74	0.42951	HD domain (1);	0.442134	0.26959	N	0.021632	D	0.92149	0.7511	L	0.39898	1.24	0.49389	D	0.999788	P	0.44659	0.84	B	0.40741	0.339	D	0.90695	0.4616	10	0.72032	D	0.01	-2.3505	11.6988	0.51558	0.1438:0.0:0.8562:0.0	.	348	Q9Y3Z3	SAMH1_HUMAN	C	348;133	ENSP00000262878:R348C;ENSP00000362798:R133C	ENSP00000262878:R348C	R	-	1	0	SAMHD1	34978559	1.000000	0.71417	0.394000	0.26270	0.839000	0.47603	3.065000	0.49994	0.755000	0.32990	0.591000	0.81541	CGT		0.383	SAMHD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079062.2	NM_015474	
HSPA12B	116835	broad.mit.edu	37	20	3722951	3722951	+	Silent	SNP	C	C	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr20:3722951C>A	ENST00000254963.2	+	4	307	c.162C>A	c.(160-162)ccC>ccA	p.P54P	HSPA12B_ENST00000542646.1_Intron	NM_001197327.1|NM_052970.4	NP_001184256.1|NP_443202.3	Q96MM6	HS12B_HUMAN	heat shock 70kD protein 12B	54							ATP binding (GO:0005524)	p.P54P(1)		NS(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(5)|ovary(1)|prostate(1)|skin(1)	14						TCCGAGCCCCCCAGCAGGCCT	0.582																																					p.P54P												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C162A	20						.						54.0	55.0	55.0					20																	3722951		2203	4300	6503	3670951	SO:0001819	synonymous_variant	116835	exon4			AK056712	CCDS13061.1	20p13	2011-09-02	2003-04-10	2003-04-10	ENSG00000132622	ENSG00000132622		"""Heat shock proteins / HSP70"""	16193	protein-coding gene	gene with protein product		610702	"""chromosome 20 open reading frame 60"""	C20orf60		12552099	Standard	NM_052970		Approved	dJ1009E24.2	uc002wjd.3	Q96MM6	OTTHUMG00000031755	ENST00000254963.2:c.162C>A	20.37:g.3722951C>A		Somatic		Capture	Illumina HiSeq	Phase_I	3670951	NM_001197327	D3DVX7|Q2TAK3|Q9BR52	Silent	SNP	ENST00000254963.2	37	CCDS13061.1																																																																																				0.582	HSPA12B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077756.2	NM_052970	
KIAA1755	85449	broad.mit.edu	37	20	36867997	36867997	+	Silent	SNP	T	T	C			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr20:36867997T>C	ENST00000279024.4	-	4	1951	c.1680A>G	c.(1678-1680)ccA>ccG	p.P560P		NM_001029864.1	NP_001025035.1	Q5JYT7	K1755_HUMAN	KIAA1755	560								p.P560P(1)		breast(2)|endometrium(3)|kidney(1)|large_intestine(5)|lung(31)|ovary(5)|pancreas(2)|skin(4)|stomach(1)	54		Myeloproliferative disorder(115;0.00874)				GCTCAGGCCCTGGGGGCTCCT	0.627																																					p.P560P												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.A1680G	20						.						40.0	43.0	42.0					20																	36867997		2203	4300	6503	36301411	SO:0001819	synonymous_variant	85449	exon4			AB051542	CCDS33467.1	20q11.23	2007-12-07			ENSG00000149633	ENSG00000149633			29372	protein-coding gene	gene with protein product						11214970	Standard	NM_001029864		Approved	RP5-1054A22.3	uc002xhy.1	Q5JYT7	OTTHUMG00000032436	ENST00000279024.4:c.1680A>G	20.37:g.36867997T>C		Somatic		Capture	Illumina HiSeq	Phase_I	36301411	NM_001029864	Q9C0A8	Silent	SNP	ENST00000279024.4	37	CCDS33467.1																																																																																				0.627	KIAA1755-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079144.3	NM_001029864	
FAM83D	81610	broad.mit.edu	37	20	37580996	37580996	+	Missense_Mutation	SNP	C	C	T	rs147472094	byFrequency	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr20:37580996C>T	ENST00000217429.4	+	4	1722	c.1681C>T	c.(1681-1683)Cgg>Tgg	p.R561W		NM_030919.2	NP_112181.2	Q9H4H8	FA83D_HUMAN	family with sequence similarity 83, member D	531					mitotic nuclear division (GO:0007067)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)		p.R561W(1)		endometrium(2)|kidney(2)|large_intestine(7)|lung(12)|ovary(4)|stomach(1)	28		Myeloproliferative disorder(115;0.00878)				GAACAAAGAGCGGCAATTCCA	0.507													C|||	4	0.000798722	0.0	0.0	5008	,	,		20991	0.004		0.0	False		,,,				2504	0.0				p.R561W												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1681T	20						.						71.0	75.0	74.0					20																	37580996		1944	4128	6072	37014410	SO:0001583	missense	81610	exon4			AL023803	CCDS42872.1	20q11.23	2014-03-13	2006-03-23	2006-03-23	ENSG00000101447	ENSG00000101447			16122	protein-coding gene	gene with protein product			"""chromosome 20 open reading frame 129"""	C20orf129		23205133	Standard	NM_030919		Approved	dJ616B8.3	uc002xjg.3	Q9H4H8	OTTHUMG00000032462	ENST00000217429.4:c.1681C>T	20.37:g.37580996C>T	ENSP00000217429:p.Arg561Trp	Somatic		Capture	Illumina HiSeq	Phase_I	37014410	NM_030919	B4E1I7|Q5THR2|Q68EN1|Q6P457|Q7Z6H0|Q96DF5|Q96N89|Q9BVM8	Missense_Mutation	SNP	ENST00000217429.4	37	CCDS42872.1	4	0.0018315018315018315	0	0.0	0	0.0	4	0.006993006993006993	0	0.0	C	20.0	3.929981	0.73327	.	.	ENSG00000101447	ENST00000217429;ENST00000424027	T	0.32988	1.43	6.17	2.97	0.34412	.	0.000000	0.64402	D	0.000001	T	0.47857	0.1468	M	0.78916	2.43	0.49798	D	0.999823	D	0.89917	1.0	D	0.85130	0.997	T	0.58346	-0.7652	10	0.87932	D	0	.	14.5886	0.68347	0.7569:0.2431:0.0:0.0	.	531	Q9H4H8	FA83D_HUMAN	W	561;515	ENSP00000217429:R561W	ENSP00000217429:R561W	R	+	1	2	FAM83D	37014410	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	2.883000	0.48554	0.401000	0.25424	0.655000	0.94253	CGG		0.507	FAM83D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079211.1		
PLCG1	5335	broad.mit.edu	37	20	39798134	39798134	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr20:39798134G>A	ENST00000373271.1	+	23	3023	c.2618G>A	c.(2617-2619)cGg>cAg	p.R873Q	PLCG1_ENST00000244007.3_Missense_Mutation_p.R873Q|PLCG1_ENST00000373272.2_Missense_Mutation_p.R873Q	NM_182811.1	NP_877963.1	P19174	PLCG1_HUMAN	phospholipase C, gamma 1	873					activation of MAPKK activity (GO:0000186)|activation of phospholipase C activity (GO:0007202)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|calcium-mediated signaling (GO:0019722)|cell migration (GO:0016477)|cellular response to epidermal growth factor stimulus (GO:0071364)|cytokine-mediated signaling pathway (GO:0019221)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|inositol phosphate metabolic process (GO:0043647)|leukocyte migration (GO:0050900)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phospholipid catabolic process (GO:0009395)|positive regulation of angiogenesis (GO:0045766)|positive regulation of blood vessel endothelial cell migration (GO:0043536)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of release of sequestered calcium ion into cytosol (GO:0051281)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|T cell receptor signaling pathway (GO:0050852)|viral process (GO:0016032)	cell projection (GO:0042995)|cell-cell junction (GO:0005911)|COP9 signalosome (GO:0008180)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	calcium ion binding (GO:0005509)|neurotrophin TRKA receptor binding (GO:0005168)|phosphatidylinositol phospholipase C activity (GO:0004435)|phospholipase C activity (GO:0004629)|protein kinase binding (GO:0019901)|receptor signaling protein activity (GO:0005057)	p.R873Q(1)		breast(5)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(16)|skin(6)|urinary_tract(2)	46		Myeloproliferative disorder(115;0.00878)				GACTTGCTGCGGGGGGTCTTG	0.537																																					p.R873Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2618A	20						.						165.0	164.0	165.0					20																	39798134		2203	4300	6503	39231548	SO:0001583	missense	5335	exon23			M34667	CCDS13313.1, CCDS13314.1	20q12-q13.1	2013-02-14	2004-01-29		ENSG00000124181	ENSG00000124181	3.1.4.11	"""Pleckstrin homology (PH) domain containing"", ""EF-hand domain containing"", ""SH2 domain containing"""	9065	protein-coding gene	gene with protein product		172420	"""phospholipase C, gamma 1 (formerly subtype 148)"""	PLC1		2167438, 3254788	Standard	NM_182811		Approved	PLC148, PLC-II, PLCgamma1, NCKAP3	uc002xjo.1	P19174	OTTHUMG00000033082	ENST00000373271.1:c.2618G>A	20.37:g.39798134G>A	ENSP00000362368:p.Arg873Gln	Somatic		Capture	Illumina HiSeq	Phase_I	39231548	NM_002660	B7ZLY7|B9EGH4|E1P5W4|Q2V575	Missense_Mutation	SNP	ENST00000373271.1	37	CCDS13314.1	.	.	.	.	.	.	.	.	.	.	G	20.5	3.993821	0.74703	.	.	ENSG00000124181	ENST00000244007;ENST00000373271;ENST00000373272	T;T;T	0.65916	-0.18;-0.18;-0.18	5.66	5.66	0.87406	PLC-like phosphodiesterase, TIM beta/alpha-barrel domain (1);Pleckstrin homology domain (1);	0.163313	0.53938	D	0.000043	T	0.54647	0.1871	L	0.38838	1.175	0.50467	D	0.99987	B;P;B;B	0.40875	0.132;0.731;0.081;0.081	B;B;B;B	0.36186	0.039;0.219;0.012;0.017	T	0.56177	-0.8022	10	0.41790	T	0.15	.	19.7383	0.96217	0.0:0.0:1.0:0.0	.	873;449;873;873	P19174-2;B4DMA3;P19174;A2A284	.;.;PLCG1_HUMAN;.	Q	873	ENSP00000244007:R873Q;ENSP00000362368:R873Q;ENSP00000362369:R873Q	ENSP00000244007:R873Q	R	+	2	0	PLCG1	39231548	1.000000	0.71417	1.000000	0.80357	0.952000	0.60782	5.610000	0.67668	2.675000	0.91044	0.655000	0.94253	CGG		0.537	PLCG1-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000080514.3	NM_182811	
ZHX3	23051	broad.mit.edu	37	20	39830759	39830759	+	Missense_Mutation	SNP	C	C	T	rs372943167		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr20:39830759C>T	ENST00000309060.3	-	4	3213	c.2798G>A	c.(2797-2799)cGt>cAt	p.R933H	ZHX3_ENST00000540170.1_Missense_Mutation_p.R933H|ZHX3_ENST00000432768.2_Missense_Mutation_p.R933H|ZHX3_ENST00000558993.1_Intron|ZHX3_ENST00000560361.1_Missense_Mutation_p.R933H|ZHX3_ENST00000544979.2_Intron|ZHX3_ENST00000559234.1_Missense_Mutation_p.R933H|ZHX3_ENST00000557816.1_Intron			Q9H4I2	ZHX3_HUMAN	zinc fingers and homeoboxes 3	933					cell differentiation (GO:0030154)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of osteoblast differentiation (GO:0045669)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)	p.R933H(1)		endometrium(2)|kidney(5)|large_intestine(8)|lung(4)|ovary(1)|pancreas(1)|prostate(2)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(2)	31		Myeloproliferative disorder(115;0.00425)				CTCAGGGACACGGGGCTCCCA	0.602																																					p.R933H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2798A	20						.	C	HIS/ARG	0,4406		0,0,2203	88.0	80.0	82.0		2798	4.1	0.2	20		82	1,8599	1.2+/-3.3	0,1,4299	no	missense	ZHX3	NM_015035.3	29	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	benign	933/957	39830759	1,13005	2203	4300	6503	39264173	SO:0001583	missense	23051	exon3			AB007855	CCDS13315.1	20q12	2012-03-09	2004-01-29	2004-01-30	ENSG00000174306	ENSG00000174306		"""Zinc fingers, C2H2-type"", ""Homeoboxes / ZF class"""	15935	protein-coding gene	gene with protein product		609598	"""triple homeobox 1"""	TIX1		9455477	Standard	XM_005260343		Approved	KIAA0395	uc002xjs.1	Q9H4I2	OTTHUMG00000032481	ENST00000309060.3:c.2798G>A	20.37:g.39830759C>T	ENSP00000312222:p.Arg933His	Somatic		Capture	Illumina HiSeq	Phase_I	39264173	NM_015035	E1P5W5|F5H820|O43145|Q6NUJ7	Missense_Mutation	SNP	ENST00000309060.3	37	CCDS13315.1	.	.	.	.	.	.	.	.	.	.	C	12.03	1.814336	0.32053	0.0	1.16E-4	ENSG00000174306	ENST00000309060;ENST00000373263;ENST00000540170;ENST00000373262	T;T	0.10192	2.9;2.9	6.02	4.06	0.47325	.	1.070770	0.07293	N	0.872760	T	0.07593	0.0191	N	0.08118	0	0.09310	N	1	B;B	0.06786	0.001;0.001	B;B	0.01281	0.0;0.0	T	0.37407	-0.9707	10	0.72032	D	0.01	2.5672	10.4182	0.44335	0.0:0.6811:0.2524:0.0665	.	933;933	A8K8Q0;Q9H4I2	.;ZHX3_HUMAN	H	933;933;933;711	ENSP00000362360:R933H;ENSP00000442290:R933H	ENSP00000312222:R933H	R	-	2	0	ZHX3	39264173	0.002000	0.14202	0.211000	0.23655	0.942000	0.58702	1.115000	0.31209	0.847000	0.35167	0.655000	0.94253	CGT		0.602	ZHX3-010	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079262.3	NM_015035	
MYBL2	4605	broad.mit.edu	37	20	42331170	42331170	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr20:42331170C>A	ENST00000217026.4	+	8	1119	c.992C>A	c.(991-993)cCt>cAt	p.P331H	MYBL2_ENST00000396863.4_Missense_Mutation_p.P307H	NM_002466.2	NP_002457.1	P10244	MYBB_HUMAN	v-myb avian myeloblastosis viral oncogene homolog-like 2	331					G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of cell cycle (GO:0051726)|spindle assembly involved in mitosis (GO:0090307)	Myb complex (GO:0031523)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|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 transcription factor activity (GO:0003700)	p.P331H(1)		endometrium(6)|haematopoietic_and_lymphoid_tissue(4)|kidney(4)|large_intestine(7)|liver(2)|lung(18)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	46		Myeloproliferative disorder(115;0.00452)	COAD - Colon adenocarcinoma(18;0.0031)			TTTGACCTCCCTGAGGAACCA	0.527																																					p.P331H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C992A	20						.						163.0	163.0	163.0					20																	42331170		2203	4300	6503	41764584	SO:0001583	missense	4605	exon8				CCDS13322.1, CCDS63276.1	20q13.1	2013-07-09	2013-07-09		ENSG00000101057	ENSG00000101057			7548	protein-coding gene	gene with protein product		601415				8812502	Standard	NM_002466		Approved	BMYB, B-MYB	uc002xlb.1	P10244	OTTHUMG00000033062	ENST00000217026.4:c.992C>A	20.37:g.42331170C>A	ENSP00000217026:p.Pro331His	Somatic		Capture	Illumina HiSeq	Phase_I	41764584	NM_002466	B2RBS5|B7Z8D9|F8W6N6|Q53F07	Missense_Mutation	SNP	ENST00000217026.4	37	CCDS13322.1	.	.	.	.	.	.	.	.	.	.	C	18.61	3.661236	0.67700	.	.	ENSG00000101057	ENST00000396863;ENST00000217026	T;T	0.15834	2.39;2.41	5.12	5.12	0.69794	.	0.227351	0.46758	D	0.000278	T	0.24967	0.0606	N	0.14661	0.345	0.58432	D	0.999998	P;D	0.89917	0.849;1.0	P;D	0.71184	0.555;0.972	T	0.06338	-1.0832	10	0.45353	T	0.12	-17.1966	15.8628	0.79038	0.0:1.0:0.0:0.0	.	307;331	F8W6N6;P10244	.;MYBB_HUMAN	H	307;331	ENSP00000380072:P307H;ENSP00000217026:P331H	ENSP00000217026:P331H	P	+	2	0	MYBL2	41764584	0.908000	0.30866	0.936000	0.37596	0.622000	0.37654	4.786000	0.62425	2.557000	0.86248	0.561000	0.74099	CCT		0.527	MYBL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080408.1	NM_002466	
ZSWIM3	140831	broad.mit.edu	37	20	44507213	44507213	+	Silent	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr20:44507213C>T	ENST00000255152.2	+	2	2225	c.2016C>T	c.(2014-2016)ggC>ggT	p.G672G	ZSWIM1_ENST00000372523.1_5'Flank|ZSWIM1_ENST00000372520.1_5'Flank|ZSWIM3_ENST00000454862.2_Silent_p.G666G	NM_080752.3	NP_542790.2	Q96MP5	ZSWM3_HUMAN	zinc finger, SWIM-type containing 3	672							zinc ion binding (GO:0008270)	p.G672G(1)		endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(15)|ovary(2)|skin(1)|upper_aerodigestive_tract(2)	35		Myeloproliferative disorder(115;0.0122)				AGGACGTGGGCCGCCTCCCTT	0.552																																					p.G672G												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C2016T	20						.						82.0	87.0	85.0					20																	44507213		2203	4300	6503	43940620	SO:0001819	synonymous_variant	140831	exon2			AL008726	CCDS13381.1	20q13.12	2014-06-13	2003-12-17	2003-12-19	ENSG00000132801	ENSG00000132801		"""Zinc fingers, SWIM-type"""	16157	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 174"""		"""chromosome 20 open reading frame 164"""	C20orf164			Standard	NM_080752		Approved	dJ337O18.7, PPP1R174	uc002xqd.3	Q96MP5	OTTHUMG00000032627	ENST00000255152.2:c.2016C>T	20.37:g.44507213C>T		Somatic		Capture	Illumina HiSeq	Phase_I	43940620	NM_080752	Q9BR13	Silent	SNP	ENST00000255152.2	37	CCDS13381.1																																																																																				0.552	ZSWIM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079540.1	NM_080752	
ZNF335	63925	broad.mit.edu	37	20	44589331	44589331	+	Missense_Mutation	SNP	C	C	T	rs150978634		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr20:44589331C>T	ENST00000322927.2	-	12	1806	c.1706G>A	c.(1705-1707)cGt>cAt	p.R569H	ZNF335_ENST00000426788.1_Missense_Mutation_p.R414H	NM_022095.3	NP_071378.1	Q9H4Z2	ZN335_HUMAN	zinc finger protein 335	569					brain development (GO:0007420)|brain morphogenesis (GO:0048854)|cerebral cortex neuron differentiation (GO:0021895)|histone H3-K4 trimethylation (GO:0080182)|in utero embryonic development (GO:0001701)|neuron projection morphogenesis (GO:0048812)|positive regulation of lymphocyte proliferation (GO:0050671)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of neurogenesis (GO:0050769)|regulation of gene expression, epigenetic (GO:0040029)|regulation of histone H3-K4 methylation (GO:0051569)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|transcription regulatory region DNA binding (GO:0044212)	p.R569H(1)		NS(1)|breast(2)|endometrium(3)|kidney(1)|large_intestine(13)|lung(17)|ovary(2)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	51		Myeloproliferative disorder(115;0.0122)				GGGGTACACACGGCCACACAC	0.567																																					p.R569H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1706A	20						.	C	HIS/ARG	0,4406		0,0,2203	98.0	104.0	102.0		1706	5.2	1.0	20	dbSNP_134	102	1,8599	1.2+/-3.3	0,1,4299	no	missense	ZNF335	NM_022095.3	29	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging	569/1343	44589331	1,13005	2203	4300	6503	44022738	SO:0001583	missense	63925	exon12			AK026157	CCDS13389.1	20q13.12	2011-09-12			ENSG00000198026	ENSG00000198026		"""Zinc fingers, C2H2-type"""	15807	protein-coding gene	gene with protein product	"""NRC-interacting factor 1"""	610827				12215545, 19131338	Standard	NM_022095		Approved	bA465L10.2, NIF-1	uc002xqw.3	Q9H4Z2	OTTHUMG00000032637	ENST00000322927.2:c.1706G>A	20.37:g.44589331C>T	ENSP00000325326:p.Arg569His	Somatic		Capture	Illumina HiSeq	Phase_I	44022738	NM_022095	B4DLG7|Q548D0|Q9H684	Missense_Mutation	SNP	ENST00000322927.2	37	CCDS13389.1	.	.	.	.	.	.	.	.	.	.	C	26.0	4.696515	0.88830	0.0	1.16E-4	ENSG00000198026	ENST00000322927;ENST00000243961;ENST00000426788	T;T	0.29655	1.56;1.56	5.24	5.24	0.73138	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.061403	0.64402	D	0.000016	T	0.44030	0.1274	L	0.27053	0.805	0.52099	D	0.999942	D;D	0.89917	1.0;1.0	D;D	0.74023	0.982;0.959	T	0.33240	-0.9876	10	0.52906	T	0.07	-14.8925	18.0038	0.89204	0.0:1.0:0.0:0.0	.	414;569	Q9H4Z2-2;Q9H4Z2	.;ZN335_HUMAN	H	569;346;414	ENSP00000325326:R569H;ENSP00000397098:R414H	ENSP00000243961:R346H	R	-	2	0	ZNF335	44022738	0.997000	0.39634	0.994000	0.49952	0.998000	0.95712	3.553000	0.53713	2.740000	0.93945	0.557000	0.71058	CGT		0.567	ZNF335-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079553.1	NM_022095	
SLC12A5	57468	broad.mit.edu	37	20	44665950	44665950	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr20:44665950G>A	ENST00000454036.2	+	6	656	c.607G>A	c.(607-609)Gtg>Atg	p.V203M	SLC12A5_ENST00000372315.1_Missense_Mutation_p.V180M|SLC12A5_ENST00000243964.3_Missense_Mutation_p.V180M	NM_001134771.1	NP_001128243.1	Q9H2X9	S12A5_HUMAN	solute carrier family 12 (potassium/chloride transporter), member 5	203					cellular ion homeostasis (GO:0006873)|chloride transmembrane transport (GO:1902476)|ion transport (GO:0006811)|learning (GO:0007612)|multicellular organism growth (GO:0035264)|potassium ion transport (GO:0006813)|response to drug (GO:0042493)|synaptic transmission (GO:0007268)|thermosensory behavior (GO:0040040)|transmembrane transport (GO:0055085)|transport (GO:0006810)	dendritic shaft (GO:0043198)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	potassium:chloride symporter activity (GO:0015379)|protein kinase binding (GO:0019901)	p.V180M(1)		NS(2)|breast(1)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(14)|liver(1)|lung(38)|ovary(3)|prostate(2)|skin(5)|upper_aerodigestive_tract(1)	80		Myeloproliferative disorder(115;0.0122)			Bumetanide(DB00887)|Potassium Chloride(DB00761)	TGGGGGTGCCGTGGGCCTCTG	0.592																																					p.V180M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G538A	20						.						83.0	72.0	76.0					20																	44665950		2203	4300	6503	44099357	SO:0001583	missense	57468	exon6			AB033002	CCDS13391.1, CCDS46610.1	20q13.12	2013-05-22	2010-04-20		ENSG00000124140	ENSG00000124140		"""Solute carriers"""	13818	protein-coding gene	gene with protein product		606726					Standard	NM_020708		Approved	KIAA1176, KCC2	uc010zxl.1	Q9H2X9	OTTHUMG00000032638	ENST00000454036.2:c.607G>A	20.37:g.44665950G>A	ENSP00000387694:p.Val203Met	Somatic		Capture	Illumina HiSeq	Phase_I	44099357	NM_020708	A2RTX2|Q5VZ41|Q9H4Z0|Q9ULP4	Missense_Mutation	SNP	ENST00000454036.2	37	CCDS46610.1	.	.	.	.	.	.	.	.	.	.	G	26.1	4.705426	0.89018	.	.	ENSG00000124140	ENST00000454036;ENST00000372315;ENST00000243964	D;D;D	0.98835	-5.17;-5.17;-5.17	4.79	4.79	0.61399	Amino acid permease domain (1);	0.070462	0.56097	D	0.000027	D	0.99321	0.9762	M	0.92268	3.29	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.999;0.999	D	0.98824	1.0748	10	0.87932	D	0	.	17.0107	0.86405	0.0:0.0:1.0:0.0	.	203;180;180	Q9H2X9;Q9H2X9-2;A8K143	S12A5_HUMAN;.;.	M	203;180;180	ENSP00000387694:V203M;ENSP00000361389:V180M;ENSP00000243964:V180M	ENSP00000243964:V180M	V	+	1	0	SLC12A5	44099357	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.657000	0.98554	2.492000	0.84095	0.655000	0.94253	GTG		0.592	SLC12A5-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000471538.1		
SLC35C2	51006	broad.mit.edu	37	20	44979101	44979101	+	Missense_Mutation	SNP	G	G	A	rs202041610		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr20:44979101G>A	ENST00000372227.1	-	10	1570	c.1030C>T	c.(1030-1032)Cgg>Tgg	p.R344W	SLC35C2_ENST00000317734.8_Missense_Mutation_p.R323W|SLC35C2_ENST00000243896.2_Missense_Mutation_p.R344W|SLC35C2_ENST00000372229.1_Missense_Mutation_p.R211W|SLC35C2_ENST00000543605.1_Missense_Mutation_p.R373W|SLC35C2_ENST00000372230.5_Missense_Mutation_p.R344W|SLC35C2_ENST00000493599.1_5'UTR	NM_001281458.1|NM_001281460.1	NP_001268387.1|NP_001268389.1	Q9NQQ7	S35C2_HUMAN	solute carrier family 35 (GDP-fucose transporter), member C2	344					negative regulation of gene expression (GO:0010629)|positive regulation of Notch signaling pathway (GO:0045747)|protein O-linked fucosylation (GO:0036066)|transport (GO:0006810)	cis-Golgi network (GO:0005801)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)		p.R344W(1)		cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(4)|ovary(2)|prostate(1)	16		Myeloproliferative disorder(115;0.0122)				TGGCTGCTCCGGAGCAGCAGC	0.627																																					p.R323W												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C967T	20						.						48.0	45.0	46.0					20																	44979101		2203	4300	6503	44412508	SO:0001583	missense	51006	exon10				CCDS13396.1, CCDS13397.1, CCDS63292.1	20q13.12	2013-07-17	2013-07-17	2003-10-10	ENSG00000080189	ENSG00000080189		"""Solute carriers"""	17117	protein-coding gene	gene with protein product			"""ovarian cancer overexpressed 1"", ""solute carrier family 35, member C2"""	C20orf5, OVCOV1		10810093, 11549316	Standard	NM_173179		Approved	CGI-15, bA394O2.1	uc002xrq.3	Q9NQQ7	OTTHUMG00000033050	ENST00000372227.1:c.1030C>T	20.37:g.44979101G>A	ENSP00000361301:p.Arg344Trp	Somatic		Capture	Illumina HiSeq	Phase_I	44412508	NM_173073	B7Z6V6|E1P5T0|Q53GK3|Q5JW05|Q96CJ8|Q9Y304	Missense_Mutation	SNP	ENST00000372227.1	37	CCDS13396.1	.	.	.	.	.	.	.	.	.	.	G	26.1	4.704969	0.88924	.	.	ENSG00000080189	ENST00000317734;ENST00000243896;ENST00000372227;ENST00000372229;ENST00000372230;ENST00000372225;ENST00000543605	T;T	0.78707	-1.2;0.79	4.48	4.48	0.54585	.	0.328929	0.24089	N	0.041649	T	0.71187	0.3310	L	0.27053	0.805	0.38509	D	0.948433	D;P;P;P	0.59767	0.986;0.916;0.95;0.916	P;B;B;B	0.47015	0.534;0.165;0.312;0.165	T	0.77848	-0.2435	10	0.66056	D	0.02	-10.2403	14.5002	0.67716	0.0:0.0:1.0:0.0	.	373;209;323;344	F5H4T9;B7Z6R4;Q9NQQ7-2;Q9NQQ7	.;.;.;S35C2_HUMAN	W	323;344;344;211;344;212;373	ENSP00000318960:R323W;ENSP00000361303:R211W	ENSP00000243896:R344W	R	-	1	2	SLC35C2	44412508	0.886000	0.30341	1.000000	0.80357	0.995000	0.86356	2.916000	0.48813	2.331000	0.79229	0.655000	0.94253	CGG		0.627	SLC35C2-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080363.1	NM_015945	
PREX1	57580	broad.mit.edu	37	20	47266108	47266108	+	Missense_Mutation	SNP	A	A	C			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr20:47266108A>C	ENST00000371941.3	-	25	3057	c.3035T>G	c.(3034-3036)cTg>cGg	p.L1012R	PREX1_ENST00000396220.1_Missense_Mutation_p.L1012R	NM_020820.3	NP_065871	Q8TCU6	PREX1_HUMAN	phosphatidylinositol-3,4,5-trisphosphate-dependent Rac exchange factor 1	1012					actin filament polymerization (GO:0030041)|G-protein coupled receptor signaling pathway (GO:0007186)|intracellular signal transduction (GO:0035556)|neutrophil activation (GO:0042119)|neutrophil chemotaxis (GO:0030593)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|regulation of actin filament polymerization (GO:0030833)|regulation of dendrite development (GO:0050773)|superoxide metabolic process (GO:0006801)|T cell differentiation (GO:0030217)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|growth cone (GO:0030426)|intracellular membrane-bounded organelle (GO:0043231)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	enzyme binding (GO:0019899)|phospholipid binding (GO:0005543)|Rho GTPase activator activity (GO:0005100)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)	p.L1012R(2)		breast(3)|central_nervous_system(1)|endometrium(4)|kidney(6)|large_intestine(27)|lung(53)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|stomach(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	110			BRCA - Breast invasive adenocarcinoma(12;0.0135)|Colorectal(8;0.198)			CATGGGGTTCAGGTGGCCTGC	0.587																																					p.L1012R												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.T3035G	20						.						51.0	39.0	43.0					20																	47266108		2201	4296	6497	46699515	SO:0001583	missense	57580	exon25			AB037836	CCDS13410.1	20q13.13	2013-01-10	2008-09-15		ENSG00000124126	ENSG00000124126		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	32594	protein-coding gene	gene with protein product		606905				11955434, 15545267, 16301320	Standard	NM_020820		Approved	KIAA1415, P-REX1	uc002xtw.1	Q8TCU6	OTTHUMG00000032685	ENST00000371941.3:c.3035T>G	20.37:g.47266108A>C	ENSP00000361009:p.Leu1012Arg	Somatic		Capture	Illumina HiSeq	Phase_I	46699515	NM_020820	E1P5X9|Q5JS95|Q5JS96|Q69YL2|Q7Z2L9|Q9BQH0|Q9BX55|Q9H4Q6|Q9P2D2|Q9UGQ4	Missense_Mutation	SNP	ENST00000371941.3	37	CCDS13410.1	.	.	.	.	.	.	.	.	.	.	A	20.5	3.996983	0.74818	.	.	ENSG00000124126	ENST00000371941;ENST00000396220	T;T	0.52295	0.67;0.67	4.6	4.6	0.57074	.	0.533482	0.15438	U	0.262340	T	0.61924	0.2386	L	0.52573	1.65	0.52501	D	0.999952	D;D	0.71674	0.998;0.997	D;D	0.68943	0.95;0.961	T	0.63449	-0.6635	10	0.87932	D	0	.	13.2042	0.59787	1.0:0.0:0.0:0.0	.	1012;309	Q8TCU6;Q8TCU6-2	PREX1_HUMAN;.	R	1012	ENSP00000361009:L1012R;ENSP00000379522:L1012R	ENSP00000361009:L1012R	L	-	2	0	PREX1	46699515	1.000000	0.71417	1.000000	0.80357	0.829000	0.46940	9.110000	0.94302	1.707000	0.51288	0.459000	0.35465	CTG		0.587	PREX1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079623.1	NM_020820	
PREX1	57580	broad.mit.edu	37	20	47269910	47269910	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr20:47269910C>T	ENST00000371941.3	-	20	2357	c.2335G>A	c.(2335-2337)Gaa>Aaa	p.E779K	PREX1_ENST00000396220.1_Missense_Mutation_p.E779K	NM_020820.3	NP_065871	Q8TCU6	PREX1_HUMAN	phosphatidylinositol-3,4,5-trisphosphate-dependent Rac exchange factor 1	779					actin filament polymerization (GO:0030041)|G-protein coupled receptor signaling pathway (GO:0007186)|intracellular signal transduction (GO:0035556)|neutrophil activation (GO:0042119)|neutrophil chemotaxis (GO:0030593)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|regulation of actin filament polymerization (GO:0030833)|regulation of dendrite development (GO:0050773)|superoxide metabolic process (GO:0006801)|T cell differentiation (GO:0030217)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|growth cone (GO:0030426)|intracellular membrane-bounded organelle (GO:0043231)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	enzyme binding (GO:0019899)|phospholipid binding (GO:0005543)|Rho GTPase activator activity (GO:0005100)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)	p.E779K(2)		breast(3)|central_nervous_system(1)|endometrium(4)|kidney(6)|large_intestine(27)|lung(53)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|stomach(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	110			BRCA - Breast invasive adenocarcinoma(12;0.0135)|Colorectal(8;0.198)			AGGGCCTCTTCGCGCCGACTC	0.577																																					p.E779K												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G2335A	20						.						77.0	81.0	80.0					20																	47269910		2203	4300	6503	46703317	SO:0001583	missense	57580	exon20			AB037836	CCDS13410.1	20q13.13	2013-01-10	2008-09-15		ENSG00000124126	ENSG00000124126		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	32594	protein-coding gene	gene with protein product		606905				11955434, 15545267, 16301320	Standard	NM_020820		Approved	KIAA1415, P-REX1	uc002xtw.1	Q8TCU6	OTTHUMG00000032685	ENST00000371941.3:c.2335G>A	20.37:g.47269910C>T	ENSP00000361009:p.Glu779Lys	Somatic		Capture	Illumina HiSeq	Phase_I	46703317	NM_020820	E1P5X9|Q5JS95|Q5JS96|Q69YL2|Q7Z2L9|Q9BQH0|Q9BX55|Q9H4Q6|Q9P2D2|Q9UGQ4	Missense_Mutation	SNP	ENST00000371941.3	37	CCDS13410.1	.	.	.	.	.	.	.	.	.	.	C	13.45	2.241167	0.39598	.	.	ENSG00000124126	ENST00000371941;ENST00000396220	T;T	0.37915	1.17;1.17	5.12	3.08	0.35506	PDZ/DHR/GLGF (1);	0.113477	0.37669	U	0.001995	T	0.20333	0.0489	N	0.08118	0	0.42504	D	0.99294	P;P	0.50369	0.454;0.934	B;B	0.43082	0.075;0.407	T	0.03739	-1.1008	10	0.26408	T	0.33	.	12.9594	0.58449	0.0:0.3937:0.6063:0.0	.	779;76	Q8TCU6;Q8TCU6-2	PREX1_HUMAN;.	K	779	ENSP00000361009:E779K;ENSP00000379522:E779K	ENSP00000361009:E779K	E	-	1	0	PREX1	46703317	0.998000	0.40836	0.408000	0.26446	0.130000	0.20726	3.543000	0.53633	1.124000	0.41980	0.462000	0.41574	GAA		0.577	PREX1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079623.1	NM_020820	
ARFGEF2	10564	broad.mit.edu	37	20	47630126	47630126	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr20:47630126A>G	ENST00000371917.4	+	29	3944	c.3944A>G	c.(3943-3945)gAc>gGc	p.D1315G		NM_006420.2	NP_006411.2	Q9Y6D5	BIG2_HUMAN	ADP-ribosylation factor guanine nucleotide-exchange factor 2 (brefeldin A-inhibited)	1315					endomembrane system organization (GO:0010256)|endosome organization (GO:0007032)|exocytosis (GO:0006887)|Golgi to plasma membrane transport (GO:0006893)|intracellular signal transduction (GO:0035556)|positive regulation of GTPase activity (GO:0043547)|positive regulation of tumor necrosis factor production (GO:0032760)|protein transport (GO:0015031)|receptor recycling (GO:0001881)|regulation of ARF protein signal transduction (GO:0032012)|vesicle-mediated transport (GO:0016192)	asymmetric synapse (GO:0032279)|axonemal microtubule (GO:0005879)|cell junction (GO:0030054)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|Golgi membrane (GO:0000139)|membrane (GO:0016020)|microtubule organizing center (GO:0005815)|recycling endosome (GO:0055037)|symmetric synapse (GO:0032280)|trans-Golgi network (GO:0005802)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)|GABA receptor binding (GO:0050811)|guanyl-nucleotide exchange factor activity (GO:0005085)|protein kinase A regulatory subunit binding (GO:0034237)	p.D1315G(1)		breast(7)|cervix(2)|endometrium(8)|kidney(4)|large_intestine(11)|lung(19)|ovary(1)|prostate(3)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	63			BRCA - Breast invasive adenocarcinoma(12;0.00148)|Colorectal(8;0.198)			ACAAGTGATGACATGAATGTA	0.428																																					p.D1315G	Esophageal Squamous(176;1738 1974 26285 33069 35354)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A3944G	20						.						136.0	133.0	134.0					20																	47630126		2203	4300	6503	47063533	SO:0001583	missense	10564	exon29			AF084521	CCDS13411.1	20q13.13	2010-08-20			ENSG00000124198	ENSG00000124198		"""A-kinase anchor proteins"""	15853	protein-coding gene	gene with protein product	"""Brefeldin A-inhibited guanine nucleotide-exchange protein 2"""	605371				10212200	Standard	NM_006420		Approved	BIG2	uc002xtx.4	Q9Y6D5	OTTHUMG00000032687	ENST00000371917.4:c.3944A>G	20.37:g.47630126A>G	ENSP00000360985:p.Asp1315Gly	Somatic		Capture	Illumina HiSeq	Phase_I	47063533	NM_006420	Q5TFT9|Q9NTS1	Missense_Mutation	SNP	ENST00000371917.4	37	CCDS13411.1	.	.	.	.	.	.	.	.	.	.	A	27.1	4.800066	0.90538	.	.	ENSG00000124198	ENST00000371917	T	0.54675	0.56	5.7	5.7	0.88788	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.49133	0.1539	L	0.47716	1.5	0.80722	D	1	B	0.18166	0.026	B	0.17979	0.02	T	0.43925	-0.9361	10	0.52906	T	0.07	.	15.9571	0.79896	1.0:0.0:0.0:0.0	.	1315	Q9Y6D5	BIG2_HUMAN	G	1315	ENSP00000360985:D1315G	ENSP00000360985:D1315G	D	+	2	0	ARFGEF2	47063533	1.000000	0.71417	0.998000	0.56505	0.997000	0.91878	9.339000	0.96797	2.172000	0.68678	0.402000	0.26972	GAC		0.428	ARFGEF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079627.1	NM_006420	
SPATA2	9825	broad.mit.edu	37	20	48522746	48522746	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr20:48522746G>A	ENST00000422556.1	-	3	1322	c.973C>T	c.(973-975)Cgc>Tgc	p.R325C	SPATA2_ENST00000543716.1_Missense_Mutation_p.R188C|SPATA2_ENST00000289431.5_Missense_Mutation_p.R325C	NM_001135773.1	NP_001129245.1	Q9UM82	SPAT2_HUMAN	spermatogenesis associated 2	325					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)		p.R325C(1)		central_nervous_system(1)|endometrium(2)|large_intestine(3)|lung(11)|ovary(1)|prostate(1)|skin(1)	20	Hepatocellular(150;0.133)		BRCA - Breast invasive adenocarcinoma(9;4.03e-06)			TAGGTACCGCGCAGCAGGGCC	0.667																																					p.R325C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C973T	20						.						47.0	52.0	50.0					20																	48522746		2201	4300	6501	47956153	SO:0001583	missense	9825	exon3			AB018300	CCDS13422.1	20q13.13	2014-06-13			ENSG00000158480	ENSG00000158480			14681	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 145"""	607662					Standard	NM_001135773		Approved	KIAA0757, PD1, tamo, PPP1R145	uc002xuw.3	Q9UM82	OTTHUMG00000032704	ENST00000422556.1:c.973C>T	20.37:g.48522746G>A	ENSP00000416799:p.Arg325Cys	Somatic		Capture	Illumina HiSeq	Phase_I	47956153	NM_001135773	E1P626|O94857	Missense_Mutation	SNP	ENST00000422556.1	37	CCDS13422.1	.	.	.	.	.	.	.	.	.	.	G	11.61	1.690266	0.29962	.	.	ENSG00000158480	ENST00000289431;ENST00000422556;ENST00000543716	T;T;T	0.47528	0.85;0.85;0.84	4.38	2.27	0.28462	.	0.562862	0.15764	N	0.245797	T	0.38081	0.1027	L	0.53249	1.67	0.09310	N	0.999999	B	0.17465	0.022	B	0.12156	0.007	T	0.37820	-0.9689	10	0.72032	D	0.01	-35.2928	4.1882	0.10409	0.4922:0.0:0.5078:0.0	.	325	Q9UM82	SPAT2_HUMAN	C	325;325;188	ENSP00000289431:R325C;ENSP00000416799:R325C;ENSP00000438855:R188C	ENSP00000289431:R325C	R	-	1	0	SPATA2	47956153	1.000000	0.71417	0.203000	0.23512	0.168000	0.22595	4.301000	0.59086	1.050000	0.40346	0.505000	0.49811	CGC		0.667	SPATA2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079658.1	NM_006038	
ADNP	23394	broad.mit.edu	37	20	49510791	49510791	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr20:49510791G>A	ENST00000396029.3	-	5	1027	c.460C>T	c.(460-462)Cct>Tct	p.P154S	ADNP_ENST00000396032.3_Missense_Mutation_p.P154S|ADNP_ENST00000371602.4_Missense_Mutation_p.P154S|ADNP_ENST00000349014.3_Missense_Mutation_p.P154S	NM_001282531.1|NM_015339.2	NP_001269460.1|NP_056154.1	Q9H2P0	ADNP_HUMAN	activity-dependent neuroprotector homeobox	154					negative regulation of neuron apoptotic process (GO:0043524)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	extracellular space (GO:0005615)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.P154S(1)		NS(1)|breast(4)|endometrium(7)|kidney(1)|large_intestine(13)|lung(7)|ovary(2)|prostate(2)|skin(2)	39						GCCTGCTTAGGTTTAAGGCCA	0.403																																					p.P154S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C460T	20						.						198.0	191.0	193.0					20																	49510791		2203	4300	6503	48944198	SO:0001583	missense	23394	exon5			AF250860	CCDS13433.1	20q13.13	2011-06-20	2007-07-17		ENSG00000101126	ENSG00000101126		"""Homeoboxes / ZF class"""	15766	protein-coding gene	gene with protein product	"""ADNP homeobox 1"""	611386	"""activity-dependent neuroprotector"""			9872452, 11013255	Standard	NM_015339		Approved	KIAA0784, ADNP1	uc002xvu.1	Q9H2P0	OTTHUMG00000032737	ENST00000396029.3:c.460C>T	20.37:g.49510791G>A	ENSP00000379346:p.Pro154Ser	Somatic		Capture	Illumina HiSeq	Phase_I	48944198	NM_015339	E1P5Y2|O94881|Q5BKU2|Q9UG34	Missense_Mutation	SNP	ENST00000396029.3	37	CCDS13433.1	.	.	.	.	.	.	.	.	.	.	G	9.303	1.053670	0.19907	.	.	ENSG00000101126	ENST00000371602;ENST00000349014;ENST00000396029;ENST00000396032;ENST00000534467	T;T;T;T;T	0.69175	-0.38;-0.38;-0.38;-0.38;-0.38	5.87	4.92	0.64577	.	0.168848	0.56097	D	0.000039	T	0.51822	0.1697	L	0.29908	0.895	0.44862	D	0.997877	B	0.02656	0.0	B	0.04013	0.001	T	0.47249	-0.9132	10	0.07813	T	0.8	-19.1784	14.9197	0.70829	0.0686:0.0:0.9314:0.0	.	154	Q9H2P0	ADNP_HUMAN	S	154	ENSP00000360662:P154S;ENSP00000342905:P154S;ENSP00000379346:P154S;ENSP00000379349:P154S;ENSP00000436181:P154S	ENSP00000342905:P154S	P	-	1	0	ADNP	48944198	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	6.322000	0.72886	1.487000	0.48415	0.655000	0.94253	CCT		0.403	ADNP-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079705.2	NM_181442	
ATP9A	10079	broad.mit.edu	37	20	50287791	50287791	+	Missense_Mutation	SNP	C	C	T	rs539931418		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr20:50287791C>T	ENST00000338821.5	-	12	1307	c.1043G>A	c.(1042-1044)cGt>cAt	p.R348H	ATP9A_ENST00000311637.5_Missense_Mutation_p.R212H|ATP9A_ENST00000402822.1_Missense_Mutation_p.R227H	NM_006045.1	NP_006036.1	O75110	ATP9A_HUMAN	ATPase, class II, type 9A	348					phospholipid translocation (GO:0045332)	early endosome (GO:0005769)|integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)|recycling endosome (GO:0055037)|trans-Golgi network (GO:0005802)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)	p.R348H(1)		breast(2)|cervix(2)|endometrium(6)|kidney(1)|large_intestine(10)|lung(18)|ovary(5)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	48						CAGGTTCACACGCAAACTAGG	0.502													C|||	1	0.000199681	0.0	0.0	5008	,	,		20703	0.0		0.0	False		,,,				2504	0.001				p.R348H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1043A	20						.						77.0	65.0	69.0					20																	50287791		2203	4300	6503	49721198	SO:0001583	missense	10079	exon12			AB014511	CCDS33489.1	20q13.2	2010-04-20	2007-09-19		ENSG00000054793	ENSG00000054793		"""ATPases / P-type"""	13540	protein-coding gene	gene with protein product		609126	"""ATPase, Class II, type 9A"""			9734811, 11015572	Standard	NM_006045		Approved	KIAA0611, ATPIIA	uc002xwg.1	O75110	OTTHUMG00000032751	ENST00000338821.5:c.1043G>A	20.37:g.50287791C>T	ENSP00000342481:p.Arg348His	Somatic		Capture	Illumina HiSeq	Phase_I	49721198	NM_006045	E1P5Y3|E1P5Y4|Q5TFW5|Q5TFW6|Q5TFW9|Q6ZMF3|Q9NQK6|Q9NQK7	Missense_Mutation	SNP	ENST00000338821.5	37	CCDS33489.1	.	.	.	.	.	.	.	.	.	.	C	20.6	4.012942	0.75161	.	.	ENSG00000054793	ENST00000311637;ENST00000338821;ENST00000402822	D;D;D	0.88664	-2.41;-2.41;-2.41	5.33	5.33	0.75918	ATPase, P-type, ATPase-associated domain (1);	0.000000	0.85682	D	0.000000	D	0.95862	0.8653	M	0.91354	3.2	0.80722	D	1	D;D	0.89917	0.999;1.0	D;D	0.97110	0.99;1.0	D	0.96608	0.9450	10	0.87932	D	0	-16.8871	18.985	0.92766	0.0:1.0:0.0:0.0	.	227;348	O75110-2;O75110	.;ATP9A_HUMAN	H	212;348;227	ENSP00000309086:R212H;ENSP00000342481:R348H;ENSP00000385875:R227H	ENSP00000309086:R212H	R	-	2	0	ATP9A	49721198	1.000000	0.71417	0.976000	0.42696	0.270000	0.26580	7.436000	0.80404	2.478000	0.83669	0.313000	0.20887	CGT		0.502	ATP9A-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000106494.1	NM_006045	
GPCPD1	56261	broad.mit.edu	37	20	5559069	5559069	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr20:5559069G>A	ENST00000379019.4	-	8	874	c.662C>T	c.(661-663)aCg>aTg	p.T221M	GPCPD1_ENST00000481038.1_5'UTR	NM_019593.3	NP_062539.1	Q9NPB8	GPCP1_HUMAN	glycerophosphocholine phosphodiesterase GDE1 homolog (S. cerevisiae)	221					glycerophospholipid biosynthetic process (GO:0046474)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)	glycerophosphocholine phosphodiesterase activity (GO:0047389)|starch binding (GO:2001070)	p.T221M(2)		breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(4)|ovary(2)|skin(1)	16						TGGTTCCATCGTCTGTATGCT	0.433																																					p.T221M												.	.	2	Substitution - Missense(2)	large_intestine(1)|endometrium(1)	c.C662T	20						.						115.0	106.0	109.0					20																	5559069		2203	4300	6503	5507069	SO:0001583	missense	56261	exon8				CCDS13090.1	20p12.3	2011-01-25			ENSG00000125772	ENSG00000125772			26957	protein-coding gene	gene with protein product		614124				10718198, 20576599	Standard	NM_019593		Approved	KIAA1434, GDE5, GDPD6	uc002wme.4	Q9NPB8	OTTHUMG00000031806	ENST00000379019.4:c.662C>T	20.37:g.5559069G>A	ENSP00000368305:p.Thr221Met	Somatic		Capture	Illumina HiSeq	Phase_I	5507069	NM_019593	D3DW06|Q9BQL8|Q9NUX0	Missense_Mutation	SNP	ENST00000379019.4	37	CCDS13090.1	.	.	.	.	.	.	.	.	.	.	G	22.8	4.331039	0.81690	.	.	ENSG00000125772	ENST00000379019	T	0.49139	0.79	5.26	5.26	0.73747	.	0.050453	0.85682	D	0.000000	T	0.59059	0.2166	L	0.29908	0.895	0.80722	D	1	D	0.89917	1.0	D	0.71656	0.974	T	0.61744	-0.7000	10	0.62326	D	0.03	-21.7794	19.2282	0.93825	0.0:0.0:1.0:0.0	.	221	Q9NPB8	GPCP1_HUMAN	M	221	ENSP00000368305:T221M	ENSP00000368305:T221M	T	-	2	0	GPCPD1	5507069	1.000000	0.71417	1.000000	0.80357	0.951000	0.60555	7.908000	0.87438	2.621000	0.88768	0.591000	0.81541	ACG		0.433	GPCPD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077869.1	NM_019593	
SALL4	57167	broad.mit.edu	37	20	50406576	50406576	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr20:50406576G>A	ENST00000217086.4	-	2	2557	c.2446C>T	c.(2446-2448)Cgc>Tgc	p.R816C	SALL4_ENST00000483130.1_5'Flank|SALL4_ENST00000395997.3_Intron|SALL4_ENST00000371539.3_Intron	NM_020436.3	NP_065169.1	Q9UJQ4	SALL4_HUMAN	spalt-like transcription factor 4	816					embryonic limb morphogenesis (GO:0030326)|inner cell mass cell proliferation (GO:0001833)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural tube closure (GO:0001843)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|stem cell maintenance (GO:0019827)|transcription, DNA-templated (GO:0006351)|ventricular septum development (GO:0003281)	cytoplasm (GO:0005737)|heterochromatin (GO:0000792)|nucleus (GO:0005634)|protein complex (GO:0043234)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.R816C(1)		endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(27)|ovary(5)|prostate(2)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	63						ATCTCAGTGCGGCTGTTCTCG	0.498																																					p.R816C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C2446T	20						.						75.0	78.0	77.0					20																	50406576		2203	4300	6503	49839983	SO:0001583	missense	57167	exon2			AK001666	CCDS13438.1	20q13.2	2014-09-17	2013-10-17		ENSG00000101115	ENSG00000101115		"""Zinc fingers, C2H2-type"""	15924	protein-coding gene	gene with protein product		607343	"""sal (Drosophila)-like 4"", ""sal-like 4 (Drosophila)"""				Standard	NM_020436		Approved	dJ1112F19.1, ZNF797	uc002xwh.4	Q9UJQ4	OTTHUMG00000032752	ENST00000217086.4:c.2446C>T	20.37:g.50406576G>A	ENSP00000217086:p.Arg816Cys	Somatic		Capture	Illumina HiSeq	Phase_I	49839983	NM_020436	A2A2D8|Q540H3|Q6Y8G6	Missense_Mutation	SNP	ENST00000217086.4	37	CCDS13438.1	.	.	.	.	.	.	.	.	.	.	G	12.71	2.018980	0.35606	.	.	ENSG00000101115	ENST00000217086	T	0.10668	2.85	5.56	4.57	0.56435	.	0.000000	0.41938	D	0.000795	T	0.09818	0.0241	L	0.43152	1.355	0.20196	N	0.99993	D	0.65815	0.995	B	0.44315	0.446	T	0.26780	-1.0093	10	0.37606	T	0.19	-13.4327	5.8769	0.18834	0.0729:0.1376:0.6468:0.1427	.	816	Q9UJQ4	SALL4_HUMAN	C	816	ENSP00000217086:R816C	ENSP00000217086:R816C	R	-	1	0	SALL4	49839983	0.387000	0.25188	0.986000	0.45419	0.998000	0.95712	1.723000	0.38053	2.589000	0.87451	0.655000	0.94253	CGC		0.498	SALL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079738.3		
CTCFL	140690	broad.mit.edu	37	20	56099084	56099084	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr20:56099084C>T	ENST00000608263.1	-	1	839	c.178G>A	c.(178-180)Gtc>Atc	p.V60I	CTCFL_ENST00000608158.1_Missense_Mutation_p.V60I|CTCFL_ENST00000429804.3_Missense_Mutation_p.V60I|CTCFL_ENST00000609232.1_Missense_Mutation_p.V60I|CTCFL_ENST00000423479.3_Missense_Mutation_p.V60I|CTCFL_ENST00000502686.2_Intron|CTCFL_ENST00000608858.1_Intron|CTCFL_ENST00000608425.1_Missense_Mutation_p.V60I|CTCFL_ENST00000433949.3_Intron|CTCFL_ENST00000243914.3_Missense_Mutation_p.V60I|CTCFL_ENST00000371196.2_Missense_Mutation_p.V60I|CTCFL_ENST00000608903.1_Intron|CTCFL_ENST00000481655.2_Missense_Mutation_p.V60I|CTCFL_ENST00000608440.1_Missense_Mutation_p.V60I|CTCFL_ENST00000422869.2_Missense_Mutation_p.V60I|CTCFL_ENST00000539382.1_Intron|CTCFL_ENST00000432255.2_Missense_Mutation_p.V60I	NM_001269041.1	NP_001255970.1	Q8NI51	CTCFL_HUMAN	CCCTC-binding factor (zinc finger protein)-like	60					cell cycle (GO:0007049)|DNA methylation involved in gamete generation (GO:0043046)|histone methylation (GO:0016571)|positive regulation of gene expression (GO:0010628)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of gene expression by genetic imprinting (GO:0006349)|regulation of histone H3-K4 methylation (GO:0051569)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone binding (GO:0042393)|metal ion binding (GO:0046872)|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)|transcription regulatory region DNA binding (GO:0044212)	p.V60I(1)		NS(1)|breast(1)|cervix(2)|endometrium(6)|kidney(4)|large_intestine(9)|lung(28)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	58	Lung NSC(12;0.00132)|all_lung(29;0.00433)|Melanoma(10;0.242)		BRCA - Breast invasive adenocarcinoma(13;3.95e-12)|Epithelial(14;3.41e-08)|all cancers(14;2.09e-07)			TCCTCCAGGACGCTGTCCTGG	0.592																																					p.V60I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G178A	20						.						123.0	132.0	129.0					20																	56099084		2203	4300	6503	55532490	SO:0001583	missense	140690	exon2				CCDS13459.1, CCDS58776.1, CCDS58777.1, CCDS58778.1, CCDS58779.1, CCDS58780.1, CCDS58781.1, CCDS58782.1, CCDS68161.1, CCDS68162.1, CCDS68163.1, CCDS68164.1	20q13.31	2013-01-08			ENSG00000124092	ENSG00000124092		"""Zinc fingers, C2H2-type"""	16234	protein-coding gene	gene with protein product	"""cancer/testis antigen 27"""	607022					Standard	NM_001269040		Approved	dJ579F20.2, BORIS, CT27	uc010giw.1	Q8NI51	OTTHUMG00000032829	ENST00000608263.1:c.178G>A	20.37:g.56099084C>T	ENSP00000476783:p.Val60Ile	Somatic		Capture	Illumina HiSeq	Phase_I	55532490	NM_080618	A0S6W1|A1L4C6|A6XGL8|A6XGM2|A6XGM3|A6XGM8|A6XGN0|A6XGN1|A6XGN2|A6XGN3|A6XGN4|E7EQ27|E7EUE3|E9PBA9|Q5JUG4|Q9BZ30|Q9NQJ3	Missense_Mutation	SNP	ENST00000608263.1	37	CCDS13459.1	.	.	.	.	.	.	.	.	.	.	C	1.575	-0.533060	0.04112	.	.	ENSG00000124092	ENST00000423479;ENST00000243914;ENST00000371196;ENST00000429804;ENST00000433949;ENST00000422109;ENST00000426658;ENST00000432255;ENST00000422869	T;T;T;T;T;T;T;T;T	0.09911	2.93;2.97;2.97;3.17;2.99;3.34;3.0;3.65;2.98	4.45	-6.78	0.01721	.	1.595540	0.04239	N	0.336521	T	0.02649	0.0080	N	0.02539	-0.55	0.09310	N	1	B;B;B;B;B;B;B;B	0.29716	0.002;0.002;0.001;0.255;0.01;0.003;0.003;0.001	B;B;B;B;B;B;B;B	0.15484	0.0;0.0;0.0;0.013;0.0;0.0;0.0;0.0	T	0.36696	-0.9737	10	0.19147	T	0.46	-2.1788	2.5013	0.04634	0.1116:0.3409:0.2983:0.2492	.	60;60;60;60;60;60;60;60	A6XGM3;A6XGM0;A6XGM9;A6XGM8;A6XGM2;E7EUE3;A6XGL8;Q8NI51	.;.;.;.;.;.;.;CTCFL_HUMAN	I	60	ENSP00000415579:V60I;ENSP00000243914:V60I;ENSP00000360239:V60I;ENSP00000415329:V60I;ENSP00000392034:V60I;ENSP00000413713:V60I;ENSP00000403369:V60I;ENSP00000409344:V60I;ENSP00000399061:V60I	ENSP00000243914:V60I	V	-	1	0	CTCFL	55532490	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.474000	0.06607	-1.040000	0.03271	-0.904000	0.02843	GTC		0.592	CTCFL-019	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000472040.1	NM_080618	
ZBP1	81030	broad.mit.edu	37	20	56185392	56185392	+	Silent	SNP	C	C	T	rs374383138		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr20:56185392C>T	ENST00000371173.3	-	7	1083	c.906G>A	c.(904-906)tcG>tcA	p.S302S	ZBP1_ENST00000340462.4_Silent_p.S279S|ZBP1_ENST00000343535.4_Silent_p.S302S|ZBP1_ENST00000395822.3_Silent_p.S227S	NM_001160417.1|NM_030776.2	NP_001153889.1|NP_110403.2	Q9H171	ZBP1_HUMAN	Z-DNA binding protein 1	302					innate immune response (GO:0045087)|positive regulation of type I interferon production (GO:0032481)|positive regulation of type I interferon-mediated signaling pathway (GO:0060340)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	DNA binding (GO:0003677)|double-stranded RNA adenosine deaminase activity (GO:0003726)|left-handed Z-DNA binding (GO:0003692)|RNA binding (GO:0003723)	p.S302S(1)		large_intestine(11)|lung(8)|ovary(4)|prostate(1)|skin(2)|urinary_tract(1)	27	Lung NSC(12;0.000545)|all_lung(29;0.00195)|Melanoma(10;0.242)		BRCA - Breast invasive adenocarcinoma(13;7.87e-13)|Epithelial(14;3.26e-09)|all cancers(14;3.62e-08)			TTGCTTCAAACGAAGCTTCTG	0.607																																					p.S301S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G903A	20						.	C	,,	1,4405	2.1+/-5.4	0,1,2202	127.0	140.0	135.0		903,681,906	-8.0	0.0	20		135	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous,coding-synonymous	ZBP1	NM_001160417.1,NM_001160418.1,NM_030776.2	,,	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	,,	301/429,227/355,302/430	56185392	1,13005	2203	4300	6503	55618798	SO:0001819	synonymous_variant	81030	exon7			AJ300575	CCDS13461.1, CCDS54477.1, CCDS54478.1	20q13.31	2009-08-21	2002-07-25	2002-07-26	ENSG00000124256	ENSG00000124256			16176	protein-coding gene	gene with protein product	"""DNA-dependent activator of IRFs"""	606750	"""chromosome 20 open reading frame 183"""	C20orf183		11842111	Standard	NM_030776		Approved	dJ718J7.3, DLM1, DLM-1, DAI	uc002xyo.3	Q9H171	OTTHUMG00000032824	ENST00000371173.3:c.906G>A	20.37:g.56185392C>T		Somatic		Capture	Illumina HiSeq	Phase_I	55618798	NM_001160417	A2A2F7|B3KVA1|F5GYT1|Q5JY39|Q9BYW4	Silent	SNP	ENST00000371173.3	37	CCDS13461.1																																																																																				0.607	ZBP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079849.1	NM_030776	
NPEPL1	79716	broad.mit.edu	37	20	57269550	57269550	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr20:57269550C>T	ENST00000356091.6	+	3	697	c.409C>T	c.(409-411)Cgc>Tgc	p.R137C	STX16-NPEPL1_ENST00000530122.1_3'UTR|NPEPL1_ENST00000525967.1_Missense_Mutation_p.R109C|NPEPL1_ENST00000525817.1_Missense_Mutation_p.R89C	NM_024663.3	NP_078939.3	Q8NDH3	PEPL1_HUMAN	aminopeptidase-like 1	137						cytoplasm (GO:0005737)|nucleus (GO:0005634)	aminopeptidase activity (GO:0004177)|manganese ion binding (GO:0030145)|metalloexopeptidase activity (GO:0008235)	p.R137C(1)		endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(7)|prostate(1)	14	all_lung(29;0.0175)		BRCA - Breast invasive adenocarcinoma(13;2.88e-09)|Colorectal(105;0.109)			GTTCACCCACCGCTCAGGTGC	0.637																																					p.P137L												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C410T	20						.						54.0	59.0	57.0					20																	57269550		1998	4165	6163	56702957	SO:0001583	missense	79716	exon3			AK021645	CCDS46621.1, CCDS56200.1, CCDS56201.1	20q13.32	2008-07-02			ENSG00000215440	ENSG00000215440			16244	protein-coding gene	gene with protein product						14702039	Standard	NM_001204872		Approved	FLJ11583, bA261P9.2	uc010zzs.1	Q8NDH3	OTTHUMG00000033060	ENST00000356091.6:c.409C>T	20.37:g.57269550C>T	ENSP00000348395:p.Arg137Cys	Somatic		Capture	Illumina HiSeq	Phase_I	56702957	NM_024663	A6NGZ0|B4DMW7|B7ZBN0|E9PN47|G5EA34|Q53G37|Q5W083|Q8TF28|Q8WUI2|Q9H1T6|Q9HAI5	Missense_Mutation	SNP	ENST00000356091.6	37	CCDS46621.1	.	.	.	.	.	.	.	.	.	.	C	22.2	4.252174	0.80135	.	.	ENSG00000215440	ENST00000525967;ENST00000525817;ENST00000356091	T;T;T	0.34667	1.35;1.36;1.35	4.62	3.66	0.41972	.	0.049953	0.85682	D	0.000000	T	0.55609	0.1931	M	0.67953	2.075	0.80722	D	1	D;D;D;D	0.89917	0.999;0.999;0.999;1.0	P;P;P;D	0.69142	0.856;0.827;0.899;0.962	T	0.59747	-0.7396	10	0.87932	D	0	-26.74	13.1398	0.59428	0.1611:0.8389:0.0:0.0	.	137;89;109;137	Q8NDH3;G5EA34;E9PN47;Q8NDH3-3	PEPL1_HUMAN;.;.;.	C	109;89;137	ENSP00000434810:R109C;ENSP00000437112:R89C;ENSP00000348395:R137C	ENSP00000348395:R137C	R	+	1	0	NPEPL1	56702957	1.000000	0.71417	1.000000	0.80357	0.785000	0.44390	7.440000	0.80464	0.931000	0.37242	-0.320000	0.08662	CGC		0.637	NPEPL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080402.6	NM_024663	
FAM217B	63939	broad.mit.edu	37	20	58519584	58519584	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr20:58519584G>A	ENST00000358293.3	+	5	1001	c.586G>A	c.(586-588)Gta>Ata	p.V196I	FAM217B_ENST00000360816.3_Missense_Mutation_p.V196I|FAM217B_ENST00000469084.1_3'UTR	NM_001190826.1	NP_001177755.1	Q9NTX9	F217B_HUMAN	family with sequence similarity 217, member B	196								p.V196I(1)									AGTCCAGACTGTACAGTGTGA	0.537																																					p.V196I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G586A	20						.						36.0	41.0	39.0					20																	58519584		2203	4300	6503	57952979	SO:0001583	missense	63939	exon5			AL109928	CCDS13484.1	20q13.33	2012-02-07	2012-02-07	2012-02-07	ENSG00000196227	ENSG00000196227			16170	protein-coding gene	gene with protein product			"""chromosome 20 open reading frame 177"""	C20orf177			Standard	NM_022106		Approved	dJ551D2.5	uc002ybc.3	Q9NTX9	OTTHUMG00000032873	ENST00000358293.3:c.586G>A	20.37:g.58519584G>A	ENSP00000351040:p.Val196Ile	Somatic		Capture	Illumina HiSeq	Phase_I	57952979	NM_001190826	B3KWH1|Q9NTA3	Missense_Mutation	SNP	ENST00000358293.3	37	CCDS13484.1	.	.	.	.	.	.	.	.	.	.	G	12.15	1.851887	0.32699	.	.	ENSG00000196227	ENST00000358293;ENST00000360816	T;T	0.18810	2.19;2.19	5.8	-2.28	0.06826	.	0.370264	0.23593	N	0.046526	T	0.07098	0.0180	N	0.04335	-0.225	0.09310	N	1	B	0.24043	0.096	B	0.22152	0.038	T	0.39941	-0.9589	10	0.08179	T	0.78	-9.8718	11.0874	0.48095	0.4584:0.0:0.5416:0.0	.	196	Q9NTX9	CT177_HUMAN	I	196	ENSP00000351040:V196I;ENSP00000354056:V196I	ENSP00000351040:V196I	V	+	1	0	C20orf177	57952979	0.757000	0.28394	0.000000	0.03702	0.226000	0.24999	0.901000	0.28445	-0.400000	0.07656	-0.345000	0.07892	GTA		0.537	FAM217B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268139.1	NM_022106	
CDH26	60437	broad.mit.edu	37	20	58559834	58559834	+	Nonsense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr20:58559834C>T	ENST00000244047.5	+	6	993	c.682C>T	c.(682-684)Cga>Tga	p.R228*	CDH26_ENST00000348616.4_Nonsense_Mutation_p.R228*			Q8IXH8	CAD26_HUMAN	cadherin 26	228	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.R228*(2)		breast(1)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(11)|lung(14)|ovary(4)|pancreas(2)|prostate(2)|skin(2)|urinary_tract(1)	44	all_lung(29;0.00963)		BRCA - Breast invasive adenocarcinoma(7;5.58e-09)			TGGAGAAATACGACTCTCTGG	0.388																																					p.R228X												.	.	2	Substitution - Nonsense(2)	large_intestine(2)	c.C682T	20						.						139.0	138.0	139.0					20																	58559834		2203	4300	6503	57993229	SO:0001587	stop_gained	60437	exon6			AF169690, AK055202	CCDS13485.1, CCDS13486.1	20q13.33	2010-01-26	2009-11-20		ENSG00000124215	ENSG00000124215		"""Cadherins / Major cadherins"""	15902	protein-coding gene	gene with protein product			"""cadherin-like 26"""				Standard	NM_177980		Approved	VR20	uc002ybe.3	Q8IXH8	OTTHUMG00000032874	ENST00000244047.5:c.682C>T	20.37:g.58559834C>T	ENSP00000244047:p.Arg228*	Somatic		Capture	Illumina HiSeq	Phase_I	57993229	NM_177980	A2A2M5|B3KNX3|Q6P5Y6|Q8TCH3|Q9BQN4|Q9NRU1	Nonsense_Mutation	SNP	ENST00000244047.5	37		.	.	.	.	.	.	.	.	.	.	C	19.03	3.748516	0.69533	.	.	ENSG00000124215	ENST00000244047;ENST00000348616	.	.	.	4.43	-3.19	0.05171	.	1.159350	0.06321	N	0.704444	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.12766	T	0.61	.	0.6398	0.00809	0.2726:0.3485:0.133:0.2459	.	.	.	.	X	228	.	ENSP00000244047:R228X	R	+	1	2	CDH26	57993229	0.000000	0.05858	0.000000	0.03702	0.023000	0.10783	-0.167000	0.09940	-0.572000	0.06006	-0.169000	0.13324	CGA		0.388	CDH26-201	KNOWN	basic	protein_coding	protein_coding		NM_177980	
CDH4	1002	broad.mit.edu	37	20	60448839	60448839	+	Silent	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr20:60448839C>T	ENST00000360469.5	+	7	1021	c.933C>T	c.(931-933)aaC>aaT	p.N311N	CDH4_ENST00000543233.1_Silent_p.N237N	NM_001794.3	NP_001785.2	P55283	CADH4_HUMAN	cadherin 4, type 1, R-cadherin (retinal)	311	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				adherens junction organization (GO:0034332)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.N311N(1)		NS(2)|breast(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(17)|liver(2)|lung(25)|ovary(2)|prostate(1)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	74			BRCA - Breast invasive adenocarcinoma(19;2.36e-08)			CCACGGCCAACGGGATGGTGC	0.607																																					p.N311N												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C933T	20						.						155.0	121.0	132.0					20																	60448839		2203	4300	6503	59882234	SO:0001819	synonymous_variant	1002	exon7			L34059	CCDS13488.1, CCDS58784.1	20q13.3	2010-01-26			ENSG00000179242	ENSG00000179242		"""Cadherins / Major cadherins"""	1763	protein-coding gene	gene with protein product	"""R-Cadherin"""	603006				10191097, 10516427	Standard	NM_001794		Approved		uc002ybn.2	P55283	OTTHUMG00000032890	ENST00000360469.5:c.933C>T	20.37:g.60448839C>T		Somatic		Capture	Illumina HiSeq	Phase_I	59882234	NM_001794	B3KWB8|G3V1P8|Q2M208|Q5VZ44|Q9BZ05	Silent	SNP	ENST00000360469.5	37	CCDS13488.1																																																																																				0.607	CDH4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079965.2	NM_001794	
RBBP8NL	140893	broad.mit.edu	37	20	60990844	60990844	+	Splice_Site	SNP	C	C	A	rs6121579		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr20:60990844C>A	ENST00000252998.1	-	7	700	c.544G>T	c.(544-546)Gaa>Taa	p.E182*		NM_080833.2	NP_543023.2	Q8NC74	RB8NL_HUMAN	RBBP8 N-terminal like	182						extracellular space (GO:0005615)		p.E182*(1)									CCCACAGCACCTTCTCCCCGT	0.716																																					p.E182X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.G544T	20						.						32.0	35.0	34.0					20																	60990844		2202	4299	6501	60424239	SO:0001630	splice_region_variant	140893	exon7			AL121832	CCDS13498.1	20q13.33	2012-10-30	2012-10-30	2012-10-30	ENSG00000130701	ENSG00000130701			16144	protein-coding gene	gene with protein product	"""hypothetical protein LOC140893"""		"""chromosome 20 open reading frame 151"""	C20orf151		11780052	Standard	NM_080833		Approved	dJ908M14.3	uc002ycw.2	Q8NC74	OTTHUMG00000032913	ENST00000252998.1:c.544+1G>T	20.37:g.60990844C>A		Somatic		Capture	Illumina HiSeq	Phase_I	60424239	NM_080833	B2RP98|Q8N4Z9|Q9BR75|Q9H0Y9	Nonsense_Mutation	SNP	ENST00000252998.1	37	CCDS13498.1	.	.	.	.	.	.	.	.	.	.	C	29.9	5.045808	0.93685	.	.	ENSG00000130701	ENST00000252998	.	.	.	3.81	3.81	0.43845	.	0.599062	0.16226	N	0.223824	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.1239	0.59342	0.0:1.0:0.0:0.0	.	.	.	.	X	182	.	.	E	-	1	0	C20orf151	60424239	0.005000	0.15991	0.037000	0.18230	0.012000	0.07955	1.482000	0.35486	2.144000	0.66660	0.555000	0.69702	GAA		0.716	RBBP8NL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080029.1	NM_080833	Nonsense_Mutation
SLC52A3	113278	broad.mit.edu	37	20	745857	745857	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr20:745857C>T	ENST00000217254.7	-	2	803	c.562G>A	c.(562-564)Gca>Aca	p.A188T	SLC52A3_ENST00000473664.1_5'UTR|SLC52A3_ENST00000381944.3_Missense_Mutation_p.A188T	NM_033409.3	NP_212134.3	Q9NQ40	S52A3_HUMAN	solute carrier family 52 (riboflavin transporter), member 3	188					cellular response to heat (GO:0034605)|riboflavin metabolic process (GO:0006771)|riboflavin transport (GO:0032218)|sensory perception of sound (GO:0007605)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	riboflavin transporter activity (GO:0032217)	p.A188T(1)									GGTACCTGTGCGATGTCAGTC	0.547																																					p.A188T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G562A	20						.						69.0	63.0	65.0					20																	745857		2202	4299	6501	693857	SO:0001583	missense	113278	exon2			AL118502	CCDS13007.1	20p13	2013-07-17	2013-07-17	2012-02-29	ENSG00000101276	ENSG00000101276		"""Solute carriers"""	16187	protein-coding gene	gene with protein product	"""hypothetical protein LOC113278"""	613350	"""chromosome 20 open reading frame 54"""	C20orf54		11780052, 19122205	Standard	NM_033409		Approved	bA371L19.1, hRFT2, RFVT3	uc002wed.4	Q9NQ40	OTTHUMG00000031647	ENST00000217254.7:c.562G>A	20.37:g.745857C>T	ENSP00000217254:p.Ala188Thr	Somatic		Capture	Illumina HiSeq	Phase_I	693857	NM_033409	A8K6P1|Q5W1A0|Q5W1A1|Q8NCL7|Q96GD5	Missense_Mutation	SNP	ENST00000217254.7	37	CCDS13007.1	.	.	.	.	.	.	.	.	.	.	C	3.400	-0.122391	0.06795	.	.	ENSG00000101276	ENST00000217254;ENST00000381944	T;T	0.72615	-0.67;-0.67	5.01	-5.92	0.02261	.	0.754623	0.11411	N	0.566805	T	0.31358	0.0794	N	0.02011	-0.69	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.38993	-0.9635	10	0.10111	T	0.7	4.0611	5.1846	0.15178	0.0863:0.084:0.2034:0.6264	.	188;188	Q9NQ40-2;Q9NQ40	.;RFT2_HUMAN	T	188	ENSP00000217254:A188T;ENSP00000371370:A188T	ENSP00000217254:A188T	A	-	1	0	C20orf54	693857	0.036000	0.19791	0.032000	0.17829	0.182000	0.23217	-0.227000	0.09126	-0.721000	0.04929	-0.459000	0.05422	GCA		0.547	SLC52A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077482.2	NM_033409	
DIDO1	11083	broad.mit.edu	37	20	61538606	61538606	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr20:61538606C>T	ENST00000266070.4	-	5	1592	c.1267G>A	c.(1267-1269)Gca>Aca	p.A423T	DIDO1_ENST00000354665.4_Missense_Mutation_p.A423T|DIDO1_ENST00000395335.2_Missense_Mutation_p.A423T|DIDO1_ENST00000266071.5_Missense_Mutation_p.A423T|DIDO1_ENST00000370366.1_Missense_Mutation_p.A423T|DIDO1_ENST00000395340.1_Missense_Mutation_p.A423T|DIDO1_ENST00000395343.1_Missense_Mutation_p.A423T|DIDO1_ENST00000370368.1_Missense_Mutation_p.A423T|DIDO1_ENST00000370371.4_Missense_Mutation_p.A423T	NM_033081.2	NP_149072.2	Q9BTC0	DIDO1_HUMAN	death inducer-obliterator 1	423					apoptotic signaling pathway (GO:0097190)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)	p.A423T(1)		NS(6)|breast(5)|central_nervous_system(1)|cervix(3)|endometrium(6)|kidney(1)|large_intestine(17)|lung(39)|ovary(8)|prostate(3)|skin(7)|stomach(2)|upper_aerodigestive_tract(1)	99	Breast(26;5.68e-08)					ATTGTCGCTGCGGCGTGTTTG	0.522																																					p.A423T	Melanoma(25;381 482 3385 5362 7955 17159 17174 40604 47095)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1267A	20						.						218.0	211.0	213.0					20																	61538606		2203	4300	6503	61009051	SO:0001583	missense	11083	exon5			AB002331	CCDS13508.2, CCDS13509.1, CCDS33506.1	20q13.33	2013-01-28	2005-11-11	2005-11-11	ENSG00000101191	ENSG00000101191		"""Zinc fingers, PHD-type"""	2680	protein-coding gene	gene with protein product		604140	"""chromosome 20 open reading frame 158"", ""death associated transcription factor 1"""	C20orf158, DATF1		10393935	Standard	NM_033081		Approved	DIO1, dJ885L7.8, FLJ11265, KIAA0333, DIO-1, BYE1	uc002ydr.2	Q9BTC0	OTTHUMG00000032945	ENST00000266070.4:c.1267G>A	20.37:g.61538606C>T	ENSP00000266070:p.Ala423Thr	Somatic		Capture	Illumina HiSeq	Phase_I	61009051	NM_022105	A8MY65|B9EH82|E1P5I1|O15043|Q3ZTL7|Q3ZTL8|Q4VXS1|Q4VXS2|Q4VXV8|Q4VXV9|Q96D72|Q9BQW0|Q9BW03|Q9H4G6|Q9H4G7|Q9NTU8|Q9NUM8|Q9UFB6	Missense_Mutation	SNP	ENST00000266070.4	37	CCDS33506.1	.	.	.	.	.	.	.	.	.	.	C	21.4	4.136914	0.77662	.	.	ENSG00000101191	ENST00000266070;ENST00000395343;ENST00000395340;ENST00000395335;ENST00000370371;ENST00000370368;ENST00000354665;ENST00000370366;ENST00000266071	T;T;T;T;T;T;T;T;T	0.23348	2.77;2.77;2.41;2.41;1.91;1.91;1.91;1.92;1.92	4.96	4.96	0.65561	.	0.000000	0.42821	D	0.000654	T	0.44705	0.1306	L	0.41079	1.255	0.80722	D	1	D;D;D;P	0.89917	0.999;0.999;1.0;0.774	D;D;D;B	0.97110	0.939;0.939;1.0;0.051	T	0.39941	-0.9589	10	0.66056	D	0.02	-27.938	18.5732	0.91144	0.0:1.0:0.0:0.0	.	423;423;423;423	Q9BTC0-2;Q9BTC0-3;Q9BTC0-1;Q9BTC0	.;.;.;DIDO1_HUMAN	T	423	ENSP00000266070:A423T;ENSP00000378752:A423T;ENSP00000378749:A423T;ENSP00000378744:A423T;ENSP00000359397:A423T;ENSP00000359394:A423T;ENSP00000346692:A423T;ENSP00000359391:A423T;ENSP00000266071:A423T	ENSP00000266070:A423T	A	-	1	0	DIDO1	61009051	1.000000	0.71417	0.324000	0.25361	0.087000	0.18053	7.666000	0.83877	2.472000	0.83506	0.561000	0.74099	GCA		0.522	DIDO1-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000080091.2	NM_080796	
LTN1	26046	broad.mit.edu	37	21	30339395	30339395	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr21:30339395G>A	ENST00000361371.5	-	10	1497	c.1418C>T	c.(1417-1419)aCg>aTg	p.T473M	LTN1_ENST00000389194.2_Missense_Mutation_p.T519M|LTN1_ENST00000389195.2_Missense_Mutation_p.T519M			O94822	LTN1_HUMAN	listerin E3 ubiquitin protein ligase 1	473					protein ubiquitination (GO:0016567)		ligase activity (GO:0016874)|zinc ion binding (GO:0008270)	p.T473M(1)		NS(1)|central_nervous_system(1)|endometrium(4)|kidney(5)|large_intestine(12)|lung(19)|ovary(5)|pancreas(1)|prostate(2)|skin(6)|stomach(2)|upper_aerodigestive_tract(2)	60						ATCTTTTTCCGTGTCTGCTTT	0.423																																					p.T519M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1556T	21						.						159.0	140.0	146.0					21																	30339395		2203	4300	6503	29261266	SO:0001583	missense	26046	exon10			AK001915	CCDS33527.1, CCDS33527.2	21q21.3	2013-01-09	2010-09-17	2010-09-17	ENSG00000198862	ENSG00000198862		"""RING-type (C3HC4) zinc fingers"""	13082	protein-coding gene	gene with protein product	"""listerin"""	613083	"""chromosome 21 open reading frame 98"", ""zinc finger protein 294"", ""ring finger protein 160"""	C21orf98, C21orf10, ZNF294, RNF160		20835226, 19196968	Standard	NM_015565		Approved	KIAA0714, FLJ11053, LISTERIN	uc002ymr.2	O94822	OTTHUMG00000078803	ENST00000361371.5:c.1418C>T	21.37:g.30339395G>A	ENSP00000354977:p.Thr473Met	Somatic		Capture	Illumina HiSeq	Phase_I	29261266	NM_015565	A6NL41|A7E2D0|B2RTS0|C9J7U3|J3KPL4|Q05C47|Q9H8M4|Q9NUY5|Q9P0E9	Missense_Mutation	SNP	ENST00000361371.5	37		.	.	.	.	.	.	.	.	.	.	g	8.149	0.786935	0.16189	.	.	ENSG00000198862	ENST00000389194;ENST00000361371;ENST00000446611;ENST00000389195	T;T;T	0.23348	2.25;2.26;1.91	5.02	-7.2	0.01495	Armadillo-type fold (1);	1.743810	0.02090	N	0.053088	T	0.13543	0.0328	N	0.19112	0.55	0.09310	N	1	B	0.11235	0.004	B	0.06405	0.002	T	0.14172	-1.0482	10	0.45353	T	0.12	.	3.2572	0.06836	0.4266:0.0838:0.3251:0.1645	.	473	O94822	LTN1_HUMAN	M	519;473;475;519	ENSP00000373846:T519M;ENSP00000354977:T473M;ENSP00000373847:T519M	ENSP00000354977:T473M	T	-	2	0	LTN1	29261266	0.000000	0.05858	0.000000	0.03702	0.495000	0.33615	-0.826000	0.04429	-1.729000	0.01364	-2.135000	0.00341	ACG		0.423	LTN1-008	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000472108.1	NM_015565	
LTN1	26046	broad.mit.edu	37	21	30359089	30359089	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr21:30359089C>T	ENST00000361371.5	-	2	288	c.209G>A	c.(208-210)cGg>cAg	p.R70Q	LTN1_ENST00000389194.2_Missense_Mutation_p.R116Q|LTN1_ENST00000389195.2_Missense_Mutation_p.R116Q			O94822	LTN1_HUMAN	listerin E3 ubiquitin protein ligase 1	70					protein ubiquitination (GO:0016567)		ligase activity (GO:0016874)|zinc ion binding (GO:0008270)	p.R70Q(1)		NS(1)|central_nervous_system(1)|endometrium(4)|kidney(5)|large_intestine(12)|lung(19)|ovary(5)|pancreas(1)|prostate(2)|skin(6)|stomach(2)|upper_aerodigestive_tract(2)	60						TGAAAGTTTCCGCAGCACCAT	0.343																																					p.R116Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G347A	21						.						84.0	87.0	86.0					21																	30359089		2203	4300	6503	29280960	SO:0001583	missense	26046	exon2			AK001915	CCDS33527.1, CCDS33527.2	21q21.3	2013-01-09	2010-09-17	2010-09-17	ENSG00000198862	ENSG00000198862		"""RING-type (C3HC4) zinc fingers"""	13082	protein-coding gene	gene with protein product	"""listerin"""	613083	"""chromosome 21 open reading frame 98"", ""zinc finger protein 294"", ""ring finger protein 160"""	C21orf98, C21orf10, ZNF294, RNF160		20835226, 19196968	Standard	NM_015565		Approved	KIAA0714, FLJ11053, LISTERIN	uc002ymr.2	O94822	OTTHUMG00000078803	ENST00000361371.5:c.209G>A	21.37:g.30359089C>T	ENSP00000354977:p.Arg70Gln	Somatic		Capture	Illumina HiSeq	Phase_I	29280960	NM_015565	A6NL41|A7E2D0|B2RTS0|C9J7U3|J3KPL4|Q05C47|Q9H8M4|Q9NUY5|Q9P0E9	Missense_Mutation	SNP	ENST00000361371.5	37		.	.	.	.	.	.	.	.	.	.	C	34	5.314322	0.95655	.	.	ENSG00000198862	ENST00000389194;ENST00000361371;ENST00000446611;ENST00000389195	T;T;T	0.64991	3.6;3.6;-0.13	4.83	4.83	0.62350	Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.77831	0.4189	M	0.66378	2.025	0.80722	D	1	D	0.89917	1.0	D	0.80764	0.994	T	0.78732	-0.2089	10	0.51188	T	0.08	.	18.1275	0.89590	0.0:1.0:0.0:0.0	.	70	O94822	LTN1_HUMAN	Q	116;70;70;116	ENSP00000373846:R116Q;ENSP00000354977:R70Q;ENSP00000373847:R116Q	ENSP00000354977:R70Q	R	-	2	0	LTN1	29280960	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.257000	0.78362	2.514000	0.84764	0.561000	0.74099	CGG		0.343	LTN1-008	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000472108.1	NM_015565	
TIAM1	7074	broad.mit.edu	37	21	32624446	32624446	+	Silent	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr21:32624446G>A	ENST00000286827.3	-	6	1494	c.1023C>T	c.(1021-1023)acC>acT	p.T341T	TIAM1_ENST00000469412.1_5'UTR|TIAM1_ENST00000541036.1_Silent_p.T341T	NM_003253.2	NP_003244.2	Q13009	TIAM1_HUMAN	T-cell lymphoma invasion and metastasis 1	341					apoptotic signaling pathway (GO:0097190)|cell migration (GO:0016477)|cell-matrix adhesion (GO:0007160)|ephrin receptor signaling pathway (GO:0048013)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of axonogenesis (GO:0050772)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of Rho GTPase activity (GO:0032321)|Rac protein signal transduction (GO:0016601)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cell-cell contact zone (GO:0044291)|cell-cell junction (GO:0005911)|cytosol (GO:0005829)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)	phospholipid binding (GO:0005543)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)|receptor signaling protein activity (GO:0005057)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)	p.T341T(2)		autonomic_ganglia(3)|breast(7)|central_nervous_system(2)|endometrium(13)|kidney(4)|large_intestine(33)|lung(44)|ovary(2)|prostate(3)|skin(2)|urinary_tract(2)	115						GGTCCGTGTCGGTAGTGGCCC	0.587																																					p.T341T												.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.C1023T	21						.						180.0	189.0	186.0					21																	32624446		2203	4300	6503	31546317	SO:0001819	synonymous_variant	7074	exon6				CCDS13609.1	21q22.1	2013-01-10			ENSG00000156299	ENSG00000156299		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	11805	protein-coding gene	gene with protein product		600687				8595894, 15340013	Standard	NM_003253		Approved		uc002yow.1	Q13009	OTTHUMG00000084869	ENST00000286827.3:c.1023C>T	21.37:g.32624446G>A		Somatic		Capture	Illumina HiSeq	Phase_I	31546317	NM_003253	B7ZLR6|F5GZ53|Q17RT7	Silent	SNP	ENST00000286827.3	37	CCDS13609.1																																																																																				0.587	TIAM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000192552.1	NM_003253	
PAXBP1	94104	broad.mit.edu	37	21	34123489	34123489	+	Silent	SNP	G	G	A	rs372686133		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr21:34123489G>A	ENST00000331923.4	-	9	1737	c.1548C>T	c.(1546-1548)cgC>cgT	p.R516R	PAXBP1_ENST00000290178.4_Silent_p.R516R	NM_016631.3	NP_057715.2	Q9Y5B6	PAXB1_HUMAN	PAX3 and PAX7 binding protein 1	516	Necessary and sufficient for interaction with PAX7. {ECO:0000250}.				muscle organ development (GO:0007517)|positive regulation of histone methylation (GO:0031062)|positive regulation of myoblast proliferation (GO:2000288)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of satellite cell proliferation (GO:0014842)|transcription, DNA-templated (GO:0006351)	cytosol (GO:0005829)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.R516R(1)									GTGCCCGATCGCGTCCAAAGG	0.458																																					p.R516R												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1548T	21						.	G	,	2,4404	4.2+/-10.8	0,2,2201	113.0	93.0	100.0		1548,1548	-9.9	0.7	21		100	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	GCFC1	NM_013329.3,NM_016631.3	,	0,2,6501	AA,AG,GG		0.0,0.0454,0.0154	,	516/816,516/918	34123489	2,13004	2203	4300	6503	33045360	SO:0001819	synonymous_variant	94104	exon9			AF231920	CCDS13619.1, CCDS33541.1	21q22.11	2014-01-23	2013-01-08	2013-01-08	ENSG00000159086	ENSG00000159086			13579	protein-coding gene	gene with protein product	"""functional spliceosome-associated protein 105"", ""GC-rich sequence DNA-binding factor candidate"""		"""chromosome 21 open reading frame 66"", ""GC-rich sequence DNA-binding factor 1"""	C21orf66, GCFC1		11707072, 22862948	Standard	NM_016631		Approved	GCFC, fSAP105	uc002yqn.3	Q9Y5B6	OTTHUMG00000064980	ENST00000331923.4:c.1548C>T	21.37:g.34123489G>A		Somatic		Capture	Illumina HiSeq	Phase_I	33045360	NM_013329	D3DSE7|Q96DU8|Q9NYQ0	Silent	SNP	ENST00000331923.4	37	CCDS13619.1																																																																																				0.458	PAXBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000139563.1	NM_013329	
ATP5O	539	broad.mit.edu	37	21	35279670	35279670	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr21:35279670A>G	ENST00000290299.2	-	5	632	c.416T>C	c.(415-417)gTa>gCa	p.V139A	AP000304.12_ENST00000429238.1_Silent_p.G87G	NM_001697.2	NP_001688.1	P48047	ATPO_HUMAN	ATP synthase, H+ transporting, mitochondrial F1 complex, O subunit	139					ATP biosynthetic process (GO:0006754)|ATP catabolic process (GO:0006200)|cellular metabolic process (GO:0044237)|mitochondrial ATP synthesis coupled proton transport (GO:0042776)|proton transport (GO:0015992)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|mitochondrial inner membrane (GO:0005743)|mitochondrial proton-transporting ATP synthase complex (GO:0005753)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	drug binding (GO:0008144)|proton-transporting ATP synthase activity, rotational mechanism (GO:0046933)|transmembrane transporter activity (GO:0022857)|transporter activity (GO:0005215)	p.V139A(1)		large_intestine(2)|lung(1)|ovary(1)|urinary_tract(1)	5						TGTGCAAGGTACCTCTCCGCG	0.453																																					p.V139A												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T416C	21						.						217.0	201.0	206.0					21																	35279670		2203	4300	6503	34201540	SO:0001583	missense	539	exon5			AF088071	CCDS13634.1	21q22	2012-10-12	2008-07-31		ENSG00000241837	ENSG00000241837	3.6.3.14	"""Mitochondrial respiratory chain complex / Complex V"", ""ATPases / F-type"""	850	protein-coding gene	gene with protein product	"""oligomycin sensitivity conferring protein"""	600828				7490082	Standard	NM_001697		Approved	OSCP, ATPO		P48047	OTTHUMG00000065186	ENST00000290299.2:c.416T>C	21.37:g.35279670A>G	ENSP00000290299:p.Val139Ala	Somatic		Capture	Illumina HiSeq	Phase_I	34201540	NM_001697	B2R4E2|Q5U042|Q6IBI2	Missense_Mutation	SNP	ENST00000290299.2	37	CCDS13634.1	.	.	.	.	.	.	.	.	.	.	A	14.81	2.646555	0.47258	.	.	ENSG00000241837	ENST00000290299	T	0.46819	0.86	5.38	5.38	0.77491	.	0.000000	0.85682	D	0.000000	T	0.58708	0.2141	M	0.81614	2.55	0.80722	D	1	P	0.39376	0.67	P	0.45119	0.47	T	0.65344	-0.6191	10	0.87932	D	0	-25.219	13.622	0.62143	1.0:0.0:0.0:0.0	.	139	P48047	ATPO_HUMAN	A	139	ENSP00000290299:V139A	ENSP00000290299:V139A	V	-	2	0	ATP5O	34201540	1.000000	0.71417	0.439000	0.26833	0.381000	0.30169	8.545000	0.90657	2.028000	0.59812	0.460000	0.39030	GTA		0.453	ATP5O-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000139907.1	NM_001697	
DSCAM	1826	broad.mit.edu	37	21	41447080	41447080	+	Missense_Mutation	SNP	T	T	G			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr21:41447080T>G	ENST00000400454.1	-	27	5249	c.4772A>C	c.(4771-4773)gAg>gCg	p.E1591A		NM_001271534.1|NM_001389.3	NP_001258463.1|NP_001380.2	O60469	DSCAM_HUMAN	Down syndrome cell adhesion molecule	1591					cell adhesion (GO:0007155)|dendrite morphogenesis (GO:0048813)|dendrite self-avoidance (GO:0070593)|locomotory behavior (GO:0007626)|negative regulation of cell adhesion (GO:0007162)|nervous system development (GO:0007399)|positive regulation of axon extension involved in axon guidance (GO:0048842)|positive regulation of phosphorylation (GO:0042327)|post-embryonic retina morphogenesis in camera-type eye (GO:0060060)	axon (GO:0030424)|extracellular region (GO:0005576)|growth cone (GO:0030426)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)		p.E1591A(1)		NS(2)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(22)|haematopoietic_and_lymphoid_tissue(4)|kidney(6)|large_intestine(22)|lung(47)|ovary(7)|pancreas(2)|prostate(3)|skin(14)|upper_aerodigestive_tract(6)|urinary_tract(4)	142		all_cancers(19;0.186)|Prostate(19;1.15e-05)|all_epithelial(19;0.0103)				CTTGAGCCCCTCGTTGGTCGT	0.547																																					p.E1591A	Melanoma(134;970 1778 1785 21664 32388)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A4772C	21						.						124.0	129.0	127.0					21																	41447080		2070	4206	6276	40368950	SO:0001583	missense	1826	exon27			AF023449	CCDS42929.1	21q22.2-q22.3	2013-02-11			ENSG00000171587	ENSG00000171587		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	3039	protein-coding gene	gene with protein product		602523				9426258	Standard	NM_001271534		Approved	CHD2-42, CHD2-52	uc002yyq.1	O60469	OTTHUMG00000086732	ENST00000400454.1:c.4772A>C	21.37:g.41447080T>G	ENSP00000383303:p.Glu1591Ala	Somatic		Capture	Illumina HiSeq	Phase_I	40368950	NM_001389	O60468	Missense_Mutation	SNP	ENST00000400454.1	37	CCDS42929.1	.	.	.	.	.	.	.	.	.	.	T	13.19	2.163892	0.38217	.	.	ENSG00000171587	ENST00000400454;ENST00000404019	T;T	0.58940	0.3;0.41	5.69	4.52	0.55395	.	0.115267	0.56097	D	0.000026	T	0.39145	0.1067	N	0.24115	0.695	0.36141	D	0.846824	B	0.27229	0.172	B	0.22386	0.039	T	0.35375	-0.9791	10	0.08837	T	0.75	.	12.932	0.58292	0.0:0.0:0.1356:0.8644	.	1591	O60469	DSCAM_HUMAN	A	1591;1343	ENSP00000383303:E1591A;ENSP00000385342:E1343A	ENSP00000383303:E1591A	E	-	2	0	DSCAM	40368950	1.000000	0.71417	0.949000	0.38748	0.996000	0.88848	2.905000	0.48727	0.957000	0.37930	0.533000	0.62120	GAG		0.547	DSCAM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195029.1	NM_001389	
MX2	4600	broad.mit.edu	37	21	42767625	42767625	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr21:42767625G>A	ENST00000330714.3	+	7	1167	c.983G>A	c.(982-984)cGg>cAg	p.R328Q	MX2_ENST00000496774.1_3'UTR|MX2_ENST00000543692.1_3'UTR	NM_002463.1	NP_002454.1	P20592	MX2_HUMAN	MX dynamin-like GTPase 2	328	Dynamin-type G.				cytokine-mediated signaling pathway (GO:0019221)|defense response (GO:0006952)|defense response to virus (GO:0051607)|GTP catabolic process (GO:0006184)|mRNA transport (GO:0051028)|protein transport (GO:0015031)|regulation of cell cycle (GO:0051726)|regulation of nucleocytoplasmic transport (GO:0046822)|response to interferon-alpha (GO:0035455)|response to virus (GO:0009615)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear pore (GO:0005643)|nucleus (GO:0005634)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)	p.R328Q(1)		breast(2)|endometrium(3)|large_intestine(6)|lung(12)|ovary(2)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(3)	34		Prostate(19;1.57e-07)|all_epithelial(19;0.0222)				GTGAAGTGCCGGGGCCAGCAG	0.483																																					p.R328Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G983A	21						.						109.0	99.0	102.0					21																	42767625		2203	4300	6503	41689495	SO:0001583	missense	4600	exon7				CCDS13672.1	21q22.3	2014-07-15	2014-07-15		ENSG00000183486	ENSG00000183486			7533	protein-coding gene	gene with protein product	"""interferon-regulated resistance GTP-binding protein MXB"", ""second interferon-induced protein p78"""	147890	"""myxovirus (influenza) resistance 2, homolog of murine"", ""myxovirus (influenza virus) resistance 2 (mouse)"""			2481229, 8798556	Standard	NM_002463		Approved	MXB	uc002yzf.1	P20592	OTTHUMG00000086753	ENST00000330714.3:c.983G>A	21.37:g.42767625G>A	ENSP00000333657:p.Arg328Gln	Somatic		Capture	Illumina HiSeq	Phase_I	41689495	NM_002463	B7Z5D3|D3DSI7	Missense_Mutation	SNP	ENST00000330714.3	37	CCDS13672.1	.	.	.	.	.	.	.	.	.	.	G	25.4	4.638998	0.87760	.	.	ENSG00000183486	ENST00000330714	D	0.88818	-2.43	3.5	3.5	0.40072	Dynamin, GTPase domain (1);Dynamin central domain (1);	0.125171	0.49916	U	0.000123	D	0.95010	0.8385	M	0.89715	3.055	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.95932	0.8939	10	0.72032	D	0.01	-27.3892	14.4855	0.67614	0.0:0.0:1.0:0.0	.	328	P20592	MX2_HUMAN	Q	328	ENSP00000333657:R328Q	ENSP00000333657:R328Q	R	+	2	0	MX2	41689495	1.000000	0.71417	0.979000	0.43373	0.725000	0.41563	6.056000	0.71111	1.907000	0.55213	0.467000	0.42956	CGG		0.483	MX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195147.1	NM_002463	
MX1	4599	broad.mit.edu	37	21	42807880	42807880	+	Silent	SNP	C	C	T	rs200861936		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr21:42807880C>T	ENST00000398600.2	+	8	1247	c.222C>T	c.(220-222)gcC>gcT	p.A74A	MX1_ENST00000288383.6_Silent_p.A74A|MX1_ENST00000398598.3_Silent_p.A74A|MX1_ENST00000455164.2_Silent_p.A74A	NM_001144925.1	NP_001138397.1	P20591	MX1_HUMAN	MX dynamin-like GTPase 1	74	Dynamin-type G.|GTPase domain (Globular).				apoptotic process (GO:0006915)|cytokine-mediated signaling pathway (GO:0019221)|defense response (GO:0006952)|defense response to virus (GO:0051607)|innate immune response (GO:0045087)|negative regulation of viral genome replication (GO:0045071)|response to type I interferon (GO:0034340)|response to virus (GO:0009615)|signal transduction (GO:0007165)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)	p.A74A(1)		breast(1)|central_nervous_system(1)|endometrium(4)|large_intestine(9)|lung(5)|ovary(1)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	27		Prostate(19;3.18e-07)|all_epithelial(19;0.0277)				CAGCCATCGCCGTCATCGGGG	0.607																																					p.A74A												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C222T	21						.	C	,,	1,4405	2.1+/-5.4	0,1,2202	80.0	80.0	80.0		222,222,222	-6.4	0.7	21		80	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous,coding-synonymous	MX1	NM_001144925.1,NM_001178046.1,NM_002462.3	,,	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	,,	74/663,74/663,74/663	42807880	1,13005	2203	4300	6503	41729750	SO:0001819	synonymous_variant	4599	exon8				CCDS13673.1, CCDS74796.1	21q22.3	2014-07-15	2014-07-15		ENSG00000157601	ENSG00000157601			7532	protein-coding gene	gene with protein product	"""interferon-inducible protein p78"""	147150	"""myxovirus (influenza) resistance 1, homolog of murine (interferon-inducible protein p78)"", ""myxovirus (influenza virus) resistance 1, interferon-inducible protein p78 (mouse)"""			17570575	Standard	XM_005260979		Approved	IFI-78K, MxA	uc010goq.3	P20591	OTTHUMG00000086755	ENST00000398600.2:c.222C>T	21.37:g.42807880C>T		Somatic		Capture	Illumina HiSeq	Phase_I	41729750	NM_001144925	B2RDA5|B3KU10|C9IYV7|C9J8D6|C9JN19|C9JN88|C9JUL1|C9JZS6|D3DSI8|Q86YP5|Q96CI3	Silent	SNP	ENST00000398600.2	37	CCDS13673.1																																																																																				0.607	MX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195161.2		
C2CD2	25966	broad.mit.edu	37	21	43327878	43327878	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr21:43327878G>A	ENST00000380486.3	-	9	1275	c.1034C>T	c.(1033-1035)gCg>gTg	p.A345V	C2CD2_ENST00000329623.7_Missense_Mutation_p.A190V	NM_015500.1	NP_056315.1	Q9Y426	CU025_HUMAN	C2 calcium-dependent domain containing 2	345	C2.					cytosol (GO:0005829)|extracellular region (GO:0005576)|nucleus (GO:0005634)		p.A345V(1)		endometrium(2)|kidney(1)|large_intestine(4)|lung(3)|ovary(3)|prostate(1)|stomach(1)	15						AGGAACTGTCGCCGTCGCCAG	0.627																																					p.A190V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C569T	21						.						34.0	38.0	37.0					21																	43327878		2203	4300	6503	42200947	SO:0001583	missense	25966	exon8			AB047784	CCDS13677.1, CCDS42933.1	21q22.3	2008-11-24	2007-10-17	2007-10-17	ENSG00000157617	ENSG00000157617			1266	protein-coding gene	gene with protein product	"""TMEM24-like"""		"""chromosome 21 open reading frame 25"""	C21orf25		15289880	Standard	NM_015500		Approved	TMEM24L, DKFZP586F0422, C21orf258	uc002yzw.3	Q9Y426	OTTHUMG00000086779	ENST00000380486.3:c.1034C>T	21.37:g.43327878G>A	ENSP00000369853:p.Ala345Val	Somatic		Capture	Illumina HiSeq	Phase_I	42200947	NM_199050	Q5R2V7|Q6AHX8|Q9NSE6	Missense_Mutation	SNP	ENST00000380486.3	37	CCDS42933.1	.	.	.	.	.	.	.	.	.	.	G	11.62	1.692473	0.30052	.	.	ENSG00000157617	ENST00000329623;ENST00000380486	T;T	0.68765	-0.35;-0.35	5.51	4.63	0.57726	C2 calcium-dependent membrane targeting (1);C2 calcium/lipid-binding domain, CaLB (1);	0.501510	0.21703	N	0.070397	T	0.52581	0.1743	L	0.40543	1.245	0.09310	N	1	B;P	0.36086	0.214;0.536	B;B	0.31245	0.088;0.126	T	0.42050	-0.9474	10	0.28530	T	0.3	-6.5489	10.0797	0.42381	0.1586:0.0:0.8414:0.0	.	190;345	Q6P6D1;Q9Y426	.;CU025_HUMAN	V	190;345	ENSP00000329302:A190V;ENSP00000369853:A345V	ENSP00000329302:A190V	A	-	2	0	C2CD2	42200947	0.422000	0.25473	0.002000	0.10522	0.001000	0.01503	3.835000	0.55805	1.328000	0.45358	0.650000	0.86243	GCG		0.627	C2CD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195228.2	NM_015500	
UBASH3A	53347	broad.mit.edu	37	21	43863428	43863428	+	Silent	SNP	G	G	A	rs147514329		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr21:43863428G>A	ENST00000319294.6	+	13	1669	c.1638G>A	c.(1636-1638)gcG>gcA	p.A546A	UBASH3A_ENST00000291535.6_Silent_p.A508A|UBASH3A_ENST00000398367.1_Intron	NM_018961.3	NP_061834.1	P57075	UBS3A_HUMAN	ubiquitin associated and SH3 domain containing A	546	Phosphatase-like.				negative regulation of T cell receptor signaling pathway (GO:0050860)|regulation of cytokine production (GO:0001817)	cytosol (GO:0005829)|nucleus (GO:0005634)	catalytic activity (GO:0003824)	p.A546A(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(1)|large_intestine(9)|lung(12)|ovary(3)	28						CCAGGCCCGCGTTTCCCCTGT	0.592													G|||	1	0.000199681	0.0	0.0	5008	,	,		19484	0.0		0.001	False		,,,				2504	0.0				p.A508A												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G1524A	21						.	G	,	2,4404	4.2+/-10.8	0,2,2201	64.0	49.0	54.0		1524,1638	-6.2	0.0	21	dbSNP_134	54	6,8594	5.0+/-18.6	0,6,4294	no	coding-synonymous,coding-synonymous	UBASH3A	NM_001001895.2,NM_018961.3	,	0,8,6495	AA,AG,GG		0.0698,0.0454,0.0615	,	508/624,546/662	43863428	8,12998	2203	4300	6503	42736497	SO:0001819	synonymous_variant	53347	exon12			AJ277750	CCDS13687.1, CCDS33566.1, CCDS58791.1	21q22.3	2010-04-28	2010-04-28		ENSG00000160185	ENSG00000160185			12462	protein-coding gene	gene with protein product		605736				11281453	Standard	NM_018961		Approved	STS-2, TULA, CLIP4	uc002zbf.3	P57075	OTTHUMG00000086805	ENST00000319294.6:c.1638G>A	21.37:g.43863428G>A		Somatic		Capture	Illumina HiSeq	Phase_I	42736497	NM_001001895	G5E9E4|Q6HA34|Q6HA35|Q6ISI6|Q6ISK3|Q6ISS9	Silent	SNP	ENST00000319294.6	37	CCDS13687.1																																																																																				0.592	UBASH3A-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000195382.1	NM_001001895	
WDR4	10785	broad.mit.edu	37	21	44279795	44279795	+	Missense_Mutation	SNP	C	C	T	rs543569485		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr21:44279795C>T	ENST00000398208.2	-	6	663	c.604G>A	c.(604-606)Ggg>Agg	p.G202R	WDR4_ENST00000492742.1_5'UTR|WDR4_ENST00000330317.2_Missense_Mutation_p.G202R	NM_001260474.1|NM_001260475.1|NM_001260476.1|NM_018669.5	NP_001247403.1|NP_001247404.1|NP_001247405.1|NP_061139.2			WD repeat domain 4									p.G202R(1)		haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(3)|ovary(2)	11				Colorectal(79;0.0165)|Lung(125;0.0484)|STAD - Stomach adenocarcinoma(101;0.0624)|COAD - Colon adenocarcinoma(84;0.128)|LUSC - Lung squamous cell carcinoma(216;0.244)		AGAAGCAGCCCGGGCTGAGTT	0.662													C|||	1	0.000199681	0.0008	0.0	5008	,	,		14456	0.0		0.0	False		,,,				2504	0.0				p.G202R												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G604A	21						.						56.0	43.0	48.0					21																	44279795		2186	4262	6448	43152864	SO:0001583	missense	10785	exon6			AJ243912	CCDS13691.1	21q22.3	2013-01-09			ENSG00000160193	ENSG00000160193		"""WD repeat domain containing"""	12756	protein-coding gene	gene with protein product	"""TRM82 tRNA methyltransferase 82 homolog (S. cerevisiae)"""	605924				12403464	Standard	NM_018669		Approved	TRM82, TRMT82	uc002zci.4	P57081	OTTHUMG00000086826	ENST00000398208.2:c.604G>A	21.37:g.44279795C>T	ENSP00000381266:p.Gly202Arg	Somatic		Capture	Illumina HiSeq	Phase_I	43152864	NM_033661		Missense_Mutation	SNP	ENST00000398208.2	37	CCDS13691.1	.	.	.	.	.	.	.	.	.	.	C	3.252	-0.153070	0.06585	.	.	ENSG00000160193	ENST00000330317;ENST00000398208	T;T	0.59502	0.26;0.26	4.39	3.49	0.39957	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.652417	0.14634	N	0.307636	T	0.35248	0.0925	N	0.12746	0.255	0.19300	N	0.99997	B;B	0.27117	0.033;0.168	B;B	0.18263	0.006;0.021	T	0.11717	-1.0576	10	0.16420	T	0.52	-12.9328	11.5184	0.50536	0.0:0.8179:0.1821:0.0	.	202;202	P57081-2;P57081	.;WDR4_HUMAN	R	202	ENSP00000328671:G202R;ENSP00000381266:G202R	ENSP00000328671:G202R	G	-	1	0	WDR4	43152864	0.297000	0.24408	0.174000	0.22961	0.076000	0.17211	0.893000	0.28336	0.831000	0.34780	0.313000	0.20887	GGG		0.662	WDR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195479.1		
SIK1	150094	broad.mit.edu	37	21	44841560	44841560	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr21:44841560C>T	ENST00000270162.6	-	5	589	c.457G>A	c.(457-459)Gag>Aag	p.E153K		NM_173354.3	NP_775490.2	P57059	SIK1_HUMAN	salt-inducible kinase 1	153	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cardiac muscle cell differentiation (GO:0055007)|cell cycle (GO:0007049)|entrainment of circadian clock by photoperiod (GO:0043153)|intracellular signal transduction (GO:0035556)|negative regulation of CREB transcription factor activity (GO:0032792)|negative regulation of gluconeogenesis (GO:0045721)|negative regulation of triglyceride biosynthetic process (GO:0010868)|positive regulation of anoikis (GO:2000210)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of cell differentiation (GO:0045595)|regulation of mitotic cell cycle (GO:0007346)|regulation of myotube differentiation (GO:0010830)|regulation of sodium ion transport (GO:0002028)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	14-3-3 protein binding (GO:0071889)|ATP binding (GO:0005524)|cAMP response element binding protein binding (GO:0008140)|magnesium ion binding (GO:0000287)|protein kinase binding (GO:0019901)|protein serine/threonine kinase activity (GO:0004674)	p.E153K(1)		breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(6)|ovary(1)|prostate(1)|skin(2)|testis(2)|urinary_tract(1)	21					Dabrafenib(DB08912)	AGGAGGTTCTCGGTCTTGAGG	0.617																																					p.E153K												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G457A	21						.						87.0	73.0	78.0					21																	44841560		2203	4300	6503	43665988	SO:0001583	missense	150094	exon5			BC038504	CCDS33575.1	21q22.3	2008-12-23	2008-12-23	2008-12-23	ENSG00000142178	ENSG00000142178			11142	protein-coding gene	gene with protein product	"""myocardial SNF1-like kinase"""	605705	"""SNF1-like kinase"""	SNF1LK		7893599	Standard	NM_173354		Approved	msk	uc002zdf.2	P57059	OTTHUMG00000086874	ENST00000270162.6:c.457G>A	21.37:g.44841560C>T	ENSP00000270162:p.Glu153Lys	Somatic		Capture	Illumina HiSeq	Phase_I	43665988	NM_173354	A6NC84|Q5R2V5|Q6ZNL8|Q86YJ2	Missense_Mutation	SNP	ENST00000270162.6	37	CCDS33575.1	.	.	.	.	.	.	.	.	.	.	C	35	5.498249	0.96355	.	.	ENSG00000142178	ENST00000270162	T	0.28895	1.59	5.26	4.38	0.52667	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.053245	0.64402	N	0.000001	T	0.62865	0.2463	M	0.92026	3.265	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.72124	-0.4385	10	0.87932	D	0	.	13.4523	0.61178	0.0:0.9248:0.0:0.0752	.	153	P57059	SIK1_HUMAN	K	153	ENSP00000270162:E153K	ENSP00000270162:E153K	E	-	1	0	SIK1	43665988	1.000000	0.71417	0.983000	0.44433	0.922000	0.55478	7.382000	0.79729	1.218000	0.43458	0.561000	0.74099	GAG		0.617	SIK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195654.1	NM_173354	
C21orf33	8209	broad.mit.edu	37	21	45564756	45564756	+	Silent	SNP	C	C	T	rs372249793		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr21:45564756C>T	ENST00000291577.6	+	7	825	c.732C>T	c.(730-732)tgC>tgT	p.C244C	C21orf33_ENST00000348499.5_Silent_p.C213C	NM_004649.6	NP_004640	P30042	ES1_HUMAN	chromosome 21 open reading frame 33	244						mitochondrion (GO:0005739)		p.C244C(1)		NS(1)|endometrium(1)|large_intestine(1)|lung(3)|ovary(1)|skin(1)	8				STAD - Stomach adenocarcinoma(101;0.168)|Colorectal(79;0.191)		CCTTCATGTGCGAGACGGCAC	0.582													C|||	1	0.000199681	0.0	0.0014	5008	,	,		16654	0.0		0.0	False		,,,				2504	0.0				p.C213C												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C639T	21						.	C	,	0,4406		0,0,2203	104.0	73.0	84.0		732,639	-8.8	0.1	21		84	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous,coding-synonymous	C21orf33	NM_004649.6,NM_198155.3	,	0,2,6501	TT,TC,CC		0.0233,0.0,0.0154	,	244/269,213/238	45564756	2,13004	2203	4300	6503	44389184	SO:0001819	synonymous_variant	8209	exon6			Y07572	CCDS33580.1, CCDS33581.1	21q22.3	2008-07-29			ENSG00000160221	ENSG00000160221			1273	protein-coding gene	gene with protein product		601659				9150728, 8975701	Standard	NM_004649		Approved	KNP-Ia, GT335, ES1, HES1, D21S2048E, KNPI, KNPH, KNP-I	uc002zec.4	P30042	OTTHUMG00000086916	ENST00000291577.6:c.732C>T	21.37:g.45564756C>T		Somatic		Capture	Illumina HiSeq	Phase_I	44389184	NM_198155	A6NFJ6|A6NJY7|O00650|O00660|O15011|O15012|P55346|P78474|Q92505|Q92507	Silent	SNP	ENST00000291577.6	37	CCDS33580.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	1.238|1.238	-0.622115|-0.622115	0.03636|0.03636	0.0|0.0	2.33E-4|2.33E-4	ENSG00000160221|ENSG00000160221	ENST00000419699|ENST00000449622	.|.	.|.	.|.	4.48|4.48	-8.83|-8.83	0.00806|0.00806	.|.	.|.	.|.	.|.	.|.	T|.	0.66416|.	0.2787|.	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|.	0.73892|.	-0.3839|.	4|.	.|.	.|.	.|.	-13.1485|-13.1485	20.1759|20.1759	0.98177|0.98177	0.0:0.1038:0.0:0.8962|0.0:0.1038:0.0:0.8962	.|.	.|.	.|.	.|.	V|X	160|233	.|.	.|.	A|R	+|+	2|1	0|2	C21orf33|C21orf33	44389184|44389184	0.010000|0.010000	0.17322|0.17322	0.056000|0.056000	0.19401|0.19401	0.108000|0.108000	0.19459|0.19459	-1.166000|-1.166000	0.03129|0.03129	-2.100000|-2.100000	0.00848|0.00848	-0.794000|-0.794000	0.03295|0.03295	GCG|CGA		0.582	C21orf33-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000195824.1	NM_004649	
TRPM2	7226	broad.mit.edu	37	21	45838422	45838422	+	Missense_Mutation	SNP	G	G	A	rs202159569		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr21:45838422G>A	ENST00000397928.1	+	22	3890	c.3445G>A	c.(3445-3447)Gag>Aag	p.E1149K	TRPM2_ENST00000300482.5_Missense_Mutation_p.E1149K|AP001065.2_ENST00000456880.1_RNA|TRPM2_ENST00000498430.1_3'UTR|TRPM2_ENST00000397932.2_Missense_Mutation_p.E1149K|TRPM2_ENST00000300481.9_Missense_Mutation_p.E1129K|AP001065.2_ENST00000423310.1_RNA	NM_003307.3	NP_003298	O94759	TRPM2_HUMAN	transient receptor potential cation channel, subfamily M, member 2	1149					calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|ion transmembrane transport (GO:0034220)|response to hydroperoxide (GO:0033194)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ADP-ribose diphosphatase activity (GO:0047631)|calcium channel activity (GO:0005262)|manganese ion transmembrane transporter activity (GO:0005384)|sodium channel activity (GO:0005272)	p.E1149K(1)		breast(3)|central_nervous_system(2)|endometrium(4)|kidney(3)|large_intestine(15)|lung(29)|ovary(3)|pancreas(1)|prostate(5)|skin(7)|upper_aerodigestive_tract(3)|urinary_tract(1)	76						GCAGAAGATCGAGGACATCAG	0.607													G|||	1	0.000199681	0.0	0.0	5008	,	,		17757	0.0		0.001	False		,,,				2504	0.0				p.E1149K												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G3445A	21						.	G	LYS/GLU	1,4405	2.1+/-5.4	0,1,2202	117.0	126.0	123.0		3445	2.5	0.5	21		123	0,8600		0,0,4300	no	missense	TRPM2	NM_003307.3	56	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	benign	1149/1504	45838422	1,13005	2203	4300	6503	44662850	SO:0001583	missense	7226	exon22			AB001535	CCDS13710.1	21q22.3	2011-12-14		2002-01-18	ENSG00000142185	ENSG00000142185		"""Voltage-gated ion channels / Transient receptor potential cation channels"", ""Nudix motif containing"""	12339	protein-coding gene	gene with protein product		603749		TRPC7		9806837, 11385575, 16382100	Standard	NR_038257		Approved	KNP3, LTRPC2, NUDT9L1, NUDT9H, EREG1	uc002zew.1	O94759	OTTHUMG00000040840	ENST00000397928.1:c.3445G>A	21.37:g.45838422G>A	ENSP00000381023:p.Glu1149Lys	Somatic		Capture	Illumina HiSeq	Phase_I	44662850	NM_003307	D3DSL6|Q5KTC2|Q6J3P5|Q96KN6|Q96Q93	Missense_Mutation	SNP	ENST00000397928.1	37	CCDS13710.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	G	2.108	-0.404493	0.04832	2.27E-4	0.0	ENSG00000142185	ENST00000300482;ENST00000397928;ENST00000300481;ENST00000397932	T;T;T;T	0.75477	-0.94;-0.94;-0.94;-0.94	4.42	2.46	0.29980	.	0.546885	0.17290	N	0.179695	T	0.35913	0.0948	N	0.00272	-1.73	0.24965	N	0.991701	B;B;B	0.17465	0.01;0.022;0.01	B;B;B	0.08055	0.003;0.002;0.001	T	0.37430	-0.9706	10	0.27082	T	0.32	-3.7275	9.5487	0.39297	0.1348:0.551:0.3142:0.0	.	1149;935;1149	E9PGK7;Q5KTC1;O94759	.;.;TRPM2_HUMAN	K	1149;1149;1129;1149	ENSP00000300482:E1149K;ENSP00000381023:E1149K;ENSP00000300481:E1129K;ENSP00000381026:E1149K	ENSP00000300481:E1129K	E	+	1	0	TRPM2	44662850	0.709000	0.27886	0.486000	0.27416	0.555000	0.35460	0.806000	0.27126	0.998000	0.38996	0.514000	0.50259	GAG		0.607	TRPM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098086.1	NM_003307	
KRTAP10-7	386675	broad.mit.edu	37	21	46021398	46021398	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr21:46021398T>C	ENST00000380102.2	+	1	902	c.877T>C	c.(877-879)Tgc>Cgc	p.C293R	TSPEAR_ENST00000323084.4_Intron	NM_198689.2	NP_941962.1	P60409	KR107_HUMAN	keratin associated protein 10-7	293	30 X 5 AA repeats of C-C-X(3).					keratin filament (GO:0045095)		p.C293R(1)		breast(1)|large_intestine(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	8						CAGTTCATGCTGCCAGCAGTC	0.652																																					p.C288R												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T862C	21						.						100.0	92.0	94.0					21																	46021398		2203	4298	6501	44845826	SO:0001583	missense	386675	exon2			AJ566385	CCDS74803.1	21q22.3	2014-04-10			ENSG00000205441	ENSG00000272804		"""Keratin associated proteins"""	22970	protein-coding gene	gene with protein product				KRTAP18-7			Standard	NM_198689		Approved	KAP10.7, KAP18.7	uc002zfn.4	P60409	OTTHUMG00000188307	ENST00000380102.2:c.877T>C	21.37:g.46021398T>C	ENSP00000369445:p.Cys293Arg	Somatic		Capture	Illumina HiSeq	Phase_I	44845826	NM_198689	Q0VDJ8|Q70LJ2	Missense_Mutation	SNP	ENST00000380102.2	37		.	.	.	.	.	.	.	.	.	.	t	11.14	1.551264	0.27739	.	.	ENSG00000205441	ENST00000380102	T	0.02812	4.15	1.15	1.15	0.20763	.	.	.	.	.	T	0.13756	0.0333	M	0.90705	3.14	0.50813	D	0.999891	D	0.62365	0.991	D	0.68039	0.955	T	0.01001	-1.1485	9	0.66056	D	0.02	.	6.4321	0.21803	0.0:0.0:0.0:1.0	.	288	P60409-2	.	R	293	ENSP00000369445:C293R	ENSP00000369445:C293R	C	+	1	0	KRTAP10-7	44845826	0.941000	0.31946	0.989000	0.46669	0.882000	0.50991	2.682000	0.46934	0.803000	0.34113	0.383000	0.25322	TGC		0.652	KRTAP10-7-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000128038.1	NM_198689	
COL18A1	80781	broad.mit.edu	37	21	46907403	46907403	+	Nonsense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr21:46907403C>T	ENST00000359759.4	+	16	3142	c.3121C>T	c.(3121-3123)Cga>Tga	p.R1041*	COL18A1_ENST00000400337.2_Nonsense_Mutation_p.R626*|COL18A1_ENST00000355480.5_Nonsense_Mutation_p.R806*			P39060	COIA1_HUMAN	collagen, type XVIII, alpha 1	1041	Nonhelical region 4 (NC4).				angiogenesis (GO:0001525)|cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|endothelial cell morphogenesis (GO:0001886)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|negative regulation of cell proliferation (GO:0008285)|organ morphogenesis (GO:0009887)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of endothelial cell apoptotic process (GO:2000353)|response to drug (GO:0042493)|response to hydrostatic pressure (GO:0051599)|visual perception (GO:0007601)	basement membrane (GO:0005604)|collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|structural molecule activity (GO:0005198)	p.R806*(2)		breast(1)|central_nervous_system(2)|endometrium(4)|kidney(2)|large_intestine(4)|lung(8)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	25				Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929)		GTCAACAGCCCGAAGCGCTGA	0.632																																					p.R806X												.	.	2	Substitution - Nonsense(2)	large_intestine(1)|endometrium(1)	c.C2416T	21						.						51.0	57.0	55.0					21																	46907403		1993	4161	6154	45731831	SO:0001587	stop_gained	80781	exon16				CCDS42971.1, CCDS42972.1	21q22.3	2013-01-16			ENSG00000182871	ENSG00000182871		"""Collagens"""	2195	protein-coding gene	gene with protein product	"""endostatin"""	120328	"""Knobloch syndrome, type 1"""	KNO		8188291, 8776601, 10942434, 17546652	Standard	NM_130445		Approved	KS, KNO1	uc002zhi.3	P39060	OTTHUMG00000090407	ENST00000359759.4:c.3121C>T	21.37:g.46907403C>T	ENSP00000352798:p.Arg1041*	Somatic		Capture	Illumina HiSeq	Phase_I	45731831	NM_030582	A8MVI4|Q58EX6|Q6RZ39|Q6RZ40|Q6RZ41|Q8N4S4|Q8WXI5|Q96T70|Q9UK38|Q9Y6Q7|Q9Y6Q8	Nonsense_Mutation	SNP	ENST00000359759.4	37		.	.	.	.	.	.	.	.	.	.	C	38	7.281946	0.98186	.	.	ENSG00000182871	ENST00000400337;ENST00000400347;ENST00000355480;ENST00000359759;ENST00000539645	.	.	.	3.77	3.77	0.43336	.	1.295700	0.06336	U	0.707065	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.11182	T	0.66	.	11.3059	0.49334	0.0:1.0:0.0:0.0	.	.	.	.	X	626;626;806;1041;1041	.	ENSP00000347665:R806X	R	+	1	2	COL18A1	45731831	0.000000	0.05858	0.003000	0.11579	0.006000	0.05464	0.411000	0.21115	2.136000	0.66102	0.561000	0.74099	CGA		0.632	COL18A1-201	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000206827.1		
LSS	4047	broad.mit.edu	37	21	47642586	47642586	+	Missense_Mutation	SNP	C	C	T	rs200708561		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr21:47642586C>T	ENST00000397728.3	-	4	464	c.386G>A	c.(385-387)cGg>cAg	p.R129Q	LSS_ENST00000457828.2_Missense_Mutation_p.R49Q|LSS_ENST00000356396.4_Missense_Mutation_p.R129Q|LSS_ENST00000522411.1_Missense_Mutation_p.R129Q|AP001469.5_ENST00000418029.1_RNA|LSS_ENST00000464357.1_5'UTR	NM_001145436.1|NM_002340.5	NP_001138908.1|NP_002331.3	P48449	ERG7_HUMAN	lanosterol synthase (2,3-oxidosqualene-lanosterol cyclase)	129					cholesterol biosynthetic process (GO:0006695)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)	endoplasmic reticulum membrane (GO:0005789)|lipid particle (GO:0005811)|membrane (GO:0016020)	lanosterol synthase activity (GO:0000250)	p.R129Q(1)		cervix(1)|endometrium(6)|kidney(1)|large_intestine(3)|liver(1)|lung(7)|skin(1)|urinary_tract(1)	21	Breast(49;0.214)					CCGCAGGTACCGCACAATCTC	0.592																																					p.R49Q	Pancreas(114;955 2313 34923 50507)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G146A	21						.						132.0	101.0	111.0					21																	47642586		2203	4300	6503	46467014	SO:0001583	missense	4047	exon3			U22526	CCDS13733.1, CCDS46654.1, CCDS54489.1	21q22.3	1998-05-07			ENSG00000160285	ENSG00000160285	5.4.99.7		6708	protein-coding gene	gene with protein product		600909				7639730, 8655142	Standard	NM_001001438		Approved	OSC	uc002zij.3	P48449	OTTHUMG00000090633	ENST00000397728.3:c.386G>A	21.37:g.47642586C>T	ENSP00000380837:p.Arg129Gln	Somatic		Capture	Illumina HiSeq	Phase_I	46467014	NM_001145437	B4DJZ9|D3DSN0|E9PEI9|G5E9Q9|Q8IYL6|Q9UEZ1	Missense_Mutation	SNP	ENST00000397728.3	37	CCDS13733.1	.	.	.	.	.	.	.	.	.	.	C	36	5.969216	0.97156	.	.	ENSG00000160285	ENST00000356396;ENST00000457828;ENST00000397728;ENST00000522411;ENST00000450351	T;T;T;T;T	0.39229	1.09;1.09;1.09;1.09;1.09	5.07	5.07	0.68467	Terpenoid cylases/protein prenyltransferase alpha-alpha toroid (1);	0.000000	0.85682	D	0.000000	T	0.72859	0.3513	M	0.91663	3.23	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.79904	-0.1606	10	0.72032	D	0.01	.	18.4016	0.90518	0.0:1.0:0.0:0.0	.	129;129	E9PEI9;P48449	.;ERG7_HUMAN	Q	129;49;129;129;130	ENSP00000348762:R129Q;ENSP00000409191:R49Q;ENSP00000380837:R129Q;ENSP00000429133:R129Q;ENSP00000391368:R130Q	ENSP00000348762:R129Q	R	-	2	0	LSS	46467014	1.000000	0.71417	0.992000	0.48379	0.997000	0.91878	7.463000	0.80869	2.512000	0.84698	0.609000	0.83330	CGG		0.592	LSS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207274.2		
MCM3AP	8888	broad.mit.edu	37	21	47685882	47685882	+	Silent	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr21:47685882C>T	ENST00000397708.1	-	12	3242	c.2988G>A	c.(2986-2988)gcG>gcA	p.A996A	MCM3AP_ENST00000291688.1_Silent_p.A996A			O60318	GANP_HUMAN	minichromosome maintenance complex component 3 associated protein	996					DNA replication (GO:0006260)|immune system process (GO:0002376)|mRNA transport (GO:0051028)|protein import into nucleus (GO:0006606)	cytosol (GO:0005829)|nuclear pore (GO:0005643)|nucleus (GO:0005634)	DNA binding (GO:0003677)|transferase activity, transferring acyl groups (GO:0016746)	p.A996A(1)		NS(1)|breast(2)|central_nervous_system(1)|endometrium(10)|kidney(5)|large_intestine(17)|lung(24)|ovary(4)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	72	Breast(49;0.112)					CGGGCAGCTCCGCGGCCAGGC	0.617																																					p.A996A												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G2988A	21						.						90.0	98.0	96.0					21																	47685882		2203	4300	6503	46510310	SO:0001819	synonymous_variant	8888	exon11			AB005543	CCDS13734.1	21q22.3	2012-12-19	2007-04-04		ENSG00000160294	ENSG00000160294			6946	protein-coding gene	gene with protein product	"""germinal-centre associated nuclear protein"""	603294	"""minichromosome maintenance deficient (S. cerevisiae) 3-associated protein"", ""MCM3 minichromosome maintenance deficient 3 (S. cerevisiae) associated protein"""			9712829, 16914116, 21195085	Standard	XM_005261205		Approved	Map80, KIAA0572, GANP, SAC3	uc002zir.1	O60318	OTTHUMG00000090630	ENST00000397708.1:c.2988G>A	21.37:g.47685882C>T		Somatic		Capture	Illumina HiSeq	Phase_I	46510310	NM_003906	C9JL56|Q2M3C1|Q6PJP6|Q9BSY5|Q9UMT4	Silent	SNP	ENST00000397708.1	37	CCDS13734.1																																																																																				0.617	MCM3AP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207254.1	NM_003906	
PCNT	5116	broad.mit.edu	37	21	47850066	47850066	+	Silent	SNP	C	C	T	rs139227909	byFrequency	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr21:47850066C>T	ENST00000359568.5	+	36	7940	c.7833C>T	c.(7831-7833)tcC>tcT	p.S2611S	PCNT_ENST00000480896.1_3'UTR	NM_006031.5	NP_006022.3	O95613	PCNT_HUMAN	pericentrin	2611					brain morphogenesis (GO:0048854)|cerebellar cortex morphogenesis (GO:0021696)|cilium assembly (GO:0042384)|G2/M transition of mitotic cell cycle (GO:0000086)|in utero embryonic development (GO:0001701)|limb morphogenesis (GO:0035108)|microtubule cytoskeleton organization (GO:0000226)|mitotic cell cycle (GO:0000278)|multicellular organism growth (GO:0035264)|negative regulation of apoptotic process (GO:0043066)|neural precursor cell proliferation (GO:0061351)|neuron migration (GO:0001764)|olfactory bulb development (GO:0021772)|positive regulation of intracellular protein transport (GO:0090316)|spindle organization (GO:0007051)	centriolar satellite (GO:0034451)|centriole (GO:0005814)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|intercellular bridge (GO:0045171)|membrane (GO:0016020)|microtubule (GO:0005874)|motile cilium (GO:0031514)|pericentriolar material (GO:0000242)		p.S2611S(1)		NS(1)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(15)|liver(2)|lung(41)|ovary(5)|pancreas(3)|prostate(3)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(2)	104	Breast(49;0.112)					ATTTGAAGTCCGACCTCTGTG	0.602													C|||	2	0.000399361	0.0	0.0	5008	,	,		18499	0.0		0.002	False		,,,				2504	0.0				p.S2611S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C7833T	21						.	C		1,4405	2.1+/-5.4	0,1,2202	98.0	92.0	94.0		7833	-8.4	0.0	21	dbSNP_134	94	9,8591	7.1+/-27.0	0,9,4291	no	coding-synonymous	PCNT	NM_006031.5		0,10,6493	TT,TC,CC		0.1047,0.0227,0.0769		2611/3337	47850066	10,12996	2203	4300	6503	46674494	SO:0001819	synonymous_variant	5116	exon36			AB007862	CCDS33592.1	21q22.3	2014-02-20	2008-01-30	2005-11-03	ENSG00000160299	ENSG00000160299			16068	protein-coding gene	gene with protein product	"""kendrin"", ""Seckel syndrome 4"""	605925	"""pericentrin 2 (kendrin)"""	PCNT2		8812505, 9455477	Standard	NM_006031		Approved	KEN, KIAA0402, PCN, PCNTB, SCKL4	uc002zji.4	O95613	OTTHUMG00000090665	ENST00000359568.5:c.7833C>T	21.37:g.47850066C>T		Somatic		Capture	Illumina HiSeq	Phase_I	46674494	NM_006031	O43152|Q7Z7C9	Silent	SNP	ENST00000359568.5	37	CCDS33592.1																																																																																				0.602	PCNT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207336.1	NM_006031	
TPTE	7179	broad.mit.edu	37	21	10951369	10951369	+	Missense_Mutation	SNP	A	A	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr21:10951369A>T	ENST00000361285.4	-	10	672	c.343T>A	c.(343-345)Ttc>Atc	p.F115I	TPTE_ENST00000415664.2_5'UTR|TPTE_ENST00000342420.5_Missense_Mutation_p.F77I|TPTE_ENST00000298232.7_Missense_Mutation_p.F97I	NM_199261.2	NP_954870	P56180	TPTE_HUMAN	transmembrane phosphatase with tensin homology	115					peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)	ion channel activity (GO:0005216)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)	p.F97L(1)|p.F97I(1)		NS(1)|breast(1)|central_nervous_system(2)|cervix(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(19)|lung(76)|ovary(2)|prostate(2)|skin(8)|urinary_tract(1)	130			Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)		CTGTCAGTGAAAATTAGGTCG	0.318																																					p.F97I												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.T289A	21						.						119.0	127.0	124.0					21																	10951369		2203	4300	6503	9973240	SO:0001583	missense	7179	exon9			AF007118	CCDS74771.1, CCDS74772.1, CCDS74773.1	21p11	2011-06-09			ENSG00000166157	ENSG00000274391		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs"""	12023	protein-coding gene	gene with protein product	"""PTEN-related tyrosine phosphatase"", ""cancer/testis antigen 44"""	604336				10830953, 14659893	Standard	NM_001290224		Approved	PTEN2, CT44	uc002yip.1	P56180	OTTHUMG00000074127	ENST00000361285.4:c.343T>A	21.37:g.10951369A>T	ENSP00000355208:p.Phe115Ile	Somatic		Capture	Illumina HiSeq	Phase_I	9973240	NM_199259	B2RAP7|C9J6D6|C9JKK8|Q6XPS4|Q6XPS5|Q71JA8|Q8NCS8	Missense_Mutation	SNP	ENST00000361285.4	37	CCDS13560.2	.	.	.	.	.	.	.	.	.	.	.	1.923	-0.447801	0.04572	.	.	ENSG00000166157	ENST00000298232;ENST00000361285;ENST00000342420;ENST00000328758	D;D;D	0.97480	-4.4;-4.4;-4.4	1.8	-1.84	0.07809	.	0.777811	0.11419	N	0.565967	D	0.90587	0.7049	L	0.29908	0.895	0.09310	N	1	B;B;B	0.19445	0.035;0.035;0.036	B;B;B	0.16722	0.016;0.016;0.013	T	0.80464	-0.1371	10	0.13470	T	0.59	-0.0044	2.6918	0.05123	0.3612:0.4089:0.0:0.2299	.	77;97;115	P56180-3;P56180-2;P56180	.;.;TPTE_HUMAN	I	97;115;77;97	ENSP00000298232:F97I;ENSP00000355208:F115I;ENSP00000344441:F77I	ENSP00000298232:F97I	F	-	1	0	TPTE	9973240	0.000000	0.05858	0.001000	0.08648	0.057000	0.15508	-3.983000	0.00320	-0.359000	0.08150	0.163000	0.16589	TTC		0.318	TPTE-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000157413.1		
BRWD1	54014	broad.mit.edu	37	21	40667674	40667675	+	Frame_Shift_Del	DEL	AG	AG	-			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	AG	AG	AG	-	AG	AG	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr21:40667674_40667675delAG	ENST00000333229.2	-	7	930_931	c.603_604delCT	c.(601-606)atctttfs	p.F202fs	BRWD1_ENST00000470108.1_5'Flank|BRWD1_ENST00000342449.3_Frame_Shift_Del_p.F202fs|BRWD1_ENST00000380800.3_Frame_Shift_Del_p.F202fs	NM_018963.4	NP_061836.2	Q9NSI6	BRWD1_HUMAN	bromodomain and WD repeat domain containing 1	202					cytoskeleton organization (GO:0007010)|regulation of cell shape (GO:0008360)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)		p.F202fs*5(2)|p.I201I(2)		cervix(2)|endometrium(6)|kidney(8)|large_intestine(14)|liver(2)|lung(13)|ovary(1)|pancreas(1)|prostate(2)|skin(7)|urinary_tract(2)	58		Prostate(19;8.44e-08)|all_epithelial(19;0.223)				CTCACTGTAAAGATTCTATGTC	0.351																																					p.201_202del	Melanoma(170;988 1986 4794 16843 39731)											.	.	4	Deletion - Frameshift(2)|Substitution - coding silent(2)	large_intestine(4)	c.603_604del	21						.																																			39589545	SO:0001589	frameshift_variant	54014	exon7			AJ002572	CCDS13662.1, CCDS13663.1, CCDS33557.1	21q22.2	2013-05-21	2005-05-13	2005-05-13	ENSG00000185658	ENSG00000185658		"""WD repeat domain containing"""	12760	protein-coding gene	gene with protein product			"""chromosome 21 open reading frame 107"", ""WD repeat domain 9"""	C21orf107, WDR9			Standard	NM_033656		Approved	FLJ11315, N143	uc002yxk.2	Q9NSI6	OTTHUMG00000066030	ENST00000333229.2:c.603_604delCT	21.37:g.40667674_40667675delAG	ENSP00000330753:p.Phe202fs	Somatic		Capture	Illumina HiSeq	Phase_I	39589544	NM_033656	C9JK25|O43721|Q5R2V0|Q5R2V1|Q6P2D1|Q8TCV3|Q96QG9|Q96QH0|Q9NUK1	Frame_Shift_Del	DEL	ENST00000333229.2	37	CCDS13662.1																																																																																				0.351	BRWD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000141398.3	NM_033656	
DIP2A	23181	broad.mit.edu	37	21	47971612	47971612	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr21:47971612G>A	ENST00000417564.2	+	24	2926	c.2905G>A	c.(2905-2907)Ggg>Agg	p.G969R	DIP2A_ENST00000318711.7_Missense_Mutation_p.G970R|DIP2A_ENST00000427143.2_Missense_Mutation_p.G905R|DIP2A_ENST00000400274.1_Missense_Mutation_p.G965R			Q14689	DIP2A_HUMAN	DIP2 disco-interacting protein 2 homolog A (Drosophila)	969					multicellular organismal development (GO:0007275)|negative regulation of gene expression (GO:0010629)|regulation of apoptotic process (GO:0042981)	cell surface (GO:0009986)|nucleus (GO:0005634)	catalytic activity (GO:0003824)	p.G969R(1)		cervix(1)|endometrium(7)|kidney(2)|large_intestine(6)|lung(22)|ovary(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	43	Breast(49;0.0933)			Epithelial(3;3.12e-06)|OV - Ovarian serous cystadenocarcinoma(3;5.68e-06)|all cancers(3;4.08e-05)|Colorectal(79;0.0129)|COAD - Colon adenocarcinoma(84;0.0824)		TCAGGCTTCCGGGAGAGAGCT	0.627																																					p.G905R												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2713A	21						.						36.0	39.0	38.0					21																	47971612		2053	4218	6271	46796040	SO:0001583	missense	23181	exon22			AF490768	CCDS46655.1, CCDS46656.1, CCDS46657.1, CCDS54490.1, CCDS54491.1	21q22.3	2010-08-20	2006-01-13	2006-01-13	ENSG00000160305	ENSG00000160305			17217	protein-coding gene	gene with protein product		607711	"""chromosome 21 open reading frame 106"""	C21orf106			Standard	NM_015151		Approved	Dip2, KIAA0184	uc002zjo.2	Q14689	OTTHUMG00000090717	ENST00000417564.2:c.2905G>A	21.37:g.47971612G>A	ENSP00000392066:p.Gly969Arg	Somatic		Capture	Illumina HiSeq	Phase_I	46796040	NM_001146114	A6P4T3|B4E0F0|E7EMA5|Q8IVA3|Q8N4S2|Q8TD89|Q96ML9	Missense_Mutation	SNP	ENST00000417564.2	37	CCDS46655.1	.	.	.	.	.	.	.	.	.	.	G	33	5.226674	0.95173	.	.	ENSG00000160305	ENST00000400274;ENST00000427143;ENST00000318711;ENST00000417564	T;T;T;T	0.26373	1.74;1.74;1.74;1.74	5.34	5.34	0.76211	.	0.000000	0.85682	D	0.000000	T	0.56470	0.1987	M	0.83953	2.67	0.80722	D	1	D;D;D	0.89917	1.0;0.998;0.999	D;P;D	0.97110	1.0;0.773;0.975	T	0.61584	-0.7033	10	0.62326	D	0.03	-27.5363	18.0294	0.89278	0.0:0.0:1.0:0.0	.	970;905;969	E9PER1;E7EMA5;Q14689	.;.;DIP2A_HUMAN	R	965;905;970;969	ENSP00000383133:G965R;ENSP00000400528:G905R;ENSP00000323633:G970R;ENSP00000392066:G969R	ENSP00000323633:G970R	G	+	1	0	DIP2A	46796040	1.000000	0.71417	0.927000	0.36925	0.910000	0.53928	9.689000	0.98673	2.489000	0.83994	0.655000	0.94253	GGG		0.627	DIP2A-012	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000376736.1	NM_015151	
TBX1	6899	broad.mit.edu	37	22	19766797	19766798	+	Frame_Shift_Ins	INS	-	-	AG	rs150417730	byFrequency	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	-	-					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr22:19766797_19766798insAG	ENST00000329705.7	+	9	1193_1194	c.1064_1065insAG	c.(1063-1068)ccagagfs	p.PE355fs	TBX1_ENST00000359500.3_Intron	NM_080646.1	NP_542377.1	O43435	TBX1_HUMAN	T-box 1	355					angiogenesis (GO:0001525)|anterior/posterior pattern specification (GO:0009952)|aorta morphogenesis (GO:0035909)|artery morphogenesis (GO:0048844)|blood vessel development (GO:0001568)|blood vessel morphogenesis (GO:0048514)|blood vessel remodeling (GO:0001974)|cell fate specification (GO:0001708)|cell proliferation (GO:0008283)|cellular response to fibroblast growth factor stimulus (GO:0044344)|cellular response to retinoic acid (GO:0071300)|cochlea morphogenesis (GO:0090103)|coronary artery morphogenesis (GO:0060982)|determination of left/right symmetry (GO:0007368)|ear morphogenesis (GO:0042471)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic viscerocranium morphogenesis (GO:0048703)|enamel mineralization (GO:0070166)|epithelial cell differentiation (GO:0030855)|face morphogenesis (GO:0060325)|heart development (GO:0007507)|heart morphogenesis (GO:0003007)|inner ear morphogenesis (GO:0042472)|lymph vessel development (GO:0001945)|mesenchymal cell apoptotic process (GO:0097152)|mesoderm development (GO:0007498)|middle ear morphogenesis (GO:0042474)|muscle cell fate commitment (GO:0042693)|muscle organ development (GO:0007517)|muscle organ morphogenesis (GO:0048644)|muscle tissue morphogenesis (GO:0060415)|negative regulation of cell differentiation (GO:0045596)|negative regulation of mesenchymal cell apoptotic process (GO:2001054)|neural crest cell migration (GO:0001755)|odontogenesis of dentin-containing tooth (GO:0042475)|otic vesicle morphogenesis (GO:0071600)|outer ear morphogenesis (GO:0042473)|outflow tract morphogenesis (GO:0003151)|outflow tract septum morphogenesis (GO:0003148)|parathyroid gland development (GO:0060017)|pattern specification process (GO:0007389)|pharyngeal system development (GO:0060037)|positive regulation of cell proliferation (GO:0008284)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of secondary heart field cardioblast proliferation (GO:0072513)|positive regulation of tongue muscle cell differentiation (GO:2001037)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of organ morphogenesis (GO:2000027)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|retinoic acid receptor signaling pathway (GO:0048384)|semicircular canal morphogenesis (GO:0048752)|sensory perception of sound (GO:0007605)|social behavior (GO:0035176)|soft palate development (GO:0060023)|thymus development (GO:0048538)|thyroid gland development (GO:0030878)|tongue morphogenesis (GO:0043587)|transcription, DNA-templated (GO:0006351)|vagus nerve morphogenesis (GO:0021644)	nucleus (GO:0005634)	DNA binding (GO:0003677)|protein dimerization activity (GO:0046983)|protein homodimerization activity (GO:0042803)|sequence-specific DNA binding (GO:0043565)	p.V359fs*5(1)		breast(2)|central_nervous_system(1)|lung(3)|ovary(2)	8	Colorectal(54;0.0993)	all_lung(157;3.05e-06)				AGGAACACACCAGAGAGAGAAG	0.564																																					p.P355fs												.	.	1	Insertion - Frameshift(1)	large_intestine(1)	c.1064_1065insAG	22						.																																			18146798	SO:0001589	frameshift_variant	6899	exon9			AF012131	CCDS13765.1, CCDS13766.1, CCDS13767.1	22q11.21	2014-09-17			ENSG00000184058	ENSG00000184058		"""T-boxes"""	11592	protein-coding gene	gene with protein product		602054	"""velocardiofacial syndrome"""	VCF		9268629, 23000736	Standard	NM_080646		Approved	CATCH22	uc002zqa.1	O43435	OTTHUMG00000150421	ENST00000329705.7:c.1071_1072dupAG	22.37:g.19766804_19766805dupAG	ENSP00000331176:p.Pro355fs	Somatic		Capture	Illumina HiSeq	Phase_I	18146797	NM_080646	C6G493|C6G494|O43436|Q96RJ2	Frame_Shift_Ins	INS	ENST00000329705.7	37	CCDS13766.1																																																																																				0.564	TBX1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318033.1	NM_080647	
CECR2	27443	broad.mit.edu	37	22	18021577	18021577	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr22:18021577C>T	ENST00000400585.2	+	15	1883	c.1445C>T	c.(1444-1446)gCc>gTc	p.A482V	CECR2_ENST00000262608.8_Missense_Mutation_p.A624V|CECR2_ENST00000400573.5_Missense_Mutation_p.A623V			Q9BXF3	CECR2_HUMAN	cat eye syndrome chromosome region, candidate 2	665	Bromo. {ECO:0000255|PROSITE- ProRule:PRU00035}.				apoptotic DNA fragmentation (GO:0006309)|ATP-dependent chromatin remodeling (GO:0043044)|cytokinesis (GO:0000910)|cytoskeleton organization (GO:0007010)|execution phase of apoptosis (GO:0097194)|neural tube development (GO:0021915)|vesicle-mediated transport (GO:0016192)	CERF complex (GO:0090537)|nucleus (GO:0005634)		p.A623V(1)		NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(22)|ovary(1)|pancreas(1)|prostate(2)|skin(5)|stomach(1)|urinary_tract(1)	59		all_epithelial(15;0.139)		Lung(27;0.146)		TCAGATCCTGCCACCTTGTAT	0.567																																					p.P624S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1870T	22						.						46.0	49.0	48.0					22																	18021577		1934	4149	6083	16401577	SO:0001583	missense	27443	exon14			AF336133		22q11.2	2012-04-19			ENSG00000099954	ENSG00000099954			1840	protein-coding gene	gene with protein product		607576				11381032	Standard	XM_006724077		Approved	KIAA1740	uc002zml.2	Q9BXF3	OTTHUMG00000150072	ENST00000400585.2:c.1445C>T	22.37:g.18021577C>T	ENSP00000383428:p.Ala482Val	Somatic		Capture	Illumina HiSeq	Phase_I	16401577	NM_031413	A8MS90|A8MX16|Q658Z4|Q96P58|Q9C0C3	Missense_Mutation	SNP	ENST00000400585.2	37		.	.	.	.	.	.	.	.	.	.	C	8.634	0.894438	0.17613	.	.	ENSG00000099954	ENST00000400585;ENST00000400573;ENST00000262608	T;T;T	0.25250	1.93;1.93;1.81	5.65	1.82	0.25136	.	0.926155	0.09006	N	0.862352	T	0.17066	0.0410	L	0.29908	0.895	0.09310	N	1	B;B;B	0.10296	0.003;0.002;0.001	B;B;B	0.08055	0.003;0.002;0.002	T	0.30119	-0.9989	10	0.23891	T	0.37	-0.9706	6.6433	0.22921	0.1197:0.574:0.2336:0.0727	.	665;482;623	Q9BXF3;B7WPH3;E2QRE6	CECR2_HUMAN;.;.	V	482;623;624	ENSP00000383428:A482V;ENSP00000383417:A623V;ENSP00000262608:A624V	ENSP00000262608:A624V	A	+	2	0	CECR2	16401577	0.013000	0.17824	0.040000	0.18447	0.228000	0.25075	0.540000	0.23191	0.683000	0.31428	0.591000	0.81541	GCC		0.567	CECR2-002	NOVEL	basic|appris_candidate|exp_conf	protein_coding	protein_coding	OTTHUMT00000316226.2	NM_031413	
MICAL3	57553	broad.mit.edu	37	22	18304842	18304842	+	Silent	SNP	C	C	T	rs368949279		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr22:18304842C>T	ENST00000441493.2	-	24	3754	c.3402G>A	c.(3400-3402)tcG>tcA	p.S1134S		NM_015241.2	NP_056056.2	Q7RTP6	MICA3_HUMAN	microtubule associated monooxygenase, calponin and LIM domain containing 3	1134	Glu-rich.				actin filament depolymerization (GO:0030042)|cytoskeleton organization (GO:0007010)|exocytosis (GO:0006887)|oxidation-reduction process (GO:0055114)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	actin binding (GO:0003779)|FAD binding (GO:0071949)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen (GO:0016709)|zinc ion binding (GO:0008270)	p.S1134S(1)		large_intestine(1)|lung(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	4		all_epithelial(15;0.198)		Lung(27;0.0427)		CCTCATCTTCCGACACCCTCA	0.577																																					p.S1134S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G3402A	22						.	C		0,4250		0,0,2125	97.0	109.0	105.0		3402	-8.5	0.0	22		105	1,8445		0,1,4222	no	coding-synonymous	MICAL3	NM_015241.2		0,1,6347	TT,TC,CC		0.0118,0.0,0.0079		1134/2003	18304842	1,12695	2125	4223	6348	16684842	SO:0001819	synonymous_variant	57553	exon24			AB037785	CCDS46659.1, CCDS46660.1, CCDS46661.1	22q11.21	2013-03-26	2013-03-26		ENSG00000243156	ENSG00000243156			24694	protein-coding gene	gene with protein product		608882				12110185	Standard	NM_015241		Approved	KIAA0819	uc002zng.4	Q7RTP6	OTTHUMG00000150067	ENST00000441493.2:c.3402G>A	22.37:g.18304842C>T		Somatic		Capture	Illumina HiSeq	Phase_I	16684842	NM_015241	B2RXJ5|E9PEF0|O94909|Q5U4P4|Q6ICK4|Q96DF2|Q9P2I3	Silent	SNP	ENST00000441493.2	37	CCDS46659.1	.	.	.	.	.	.	.	.	.	.	C	5.022	0.189775	0.09547	0.0	1.18E-4	ENSG00000093100	ENST00000252134	.	.	.	4.27	-8.54	0.00912	.	.	.	.	.	T	0.17492	0.0420	.	.	.	0.26000	N	0.982129	.	.	.	.	.	.	T	0.18272	-1.0342	4	.	.	.	.	4.1869	0.10402	0.109:0.4356:0.2741:0.1813	.	.	.	.	Q	116	.	.	R	-	2	0	XXbac-B461K10.4	16684842	0.005000	0.15991	0.000000	0.03702	0.018000	0.09664	-2.782000	0.00772	-2.027000	0.00932	-0.351000	0.07748	CGG		0.577	MICAL3-010	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447351.1		
PPIL2	23759	broad.mit.edu	37	22	22041233	22041233	+	Silent	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr22:22041233C>T	ENST00000335025.8	+	12	934	c.843C>T	c.(841-843)taC>taT	p.Y281Y	PPIL2_ENST00000406385.1_Silent_p.Y281Y|PPIL2_ENST00000412327.1_Silent_p.Y281Y|PPIL2_ENST00000446951.1_3'UTR|PPIL2_ENST00000492445.2_Silent_p.Y281Y|PPIL2_ENST00000456792.2_Silent_p.Y260Y|PPIL2_ENST00000398831.3_Silent_p.Y281Y					peptidylprolyl isomerase (cyclophilin)-like 2									p.Y281Y(1)		endometrium(4)|kidney(2)|large_intestine(4)|lung(3)|ovary(2)|skin(2)	17	Colorectal(54;0.105)					AGAAGGGCTACGTGCGGCTGC	0.632																																					p.Y281Y												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C843T	22						.						136.0	121.0	126.0					22																	22041233		2203	4300	6503	20371233	SO:0001819	synonymous_variant	23759	exon12				CCDS13793.1	22q11.21	2013-01-29			ENSG00000100023	ENSG00000100023		"""U-box domain containing"""	9261	protein-coding gene	gene with protein product	"""U-box domain containing 7"""	607588				10591208	Standard	NM_014337		Approved	UBOX7, CYC4, Cyp-60	uc002zvh.4	Q13356	OTTHUMG00000030174	ENST00000335025.8:c.843C>T	22.37:g.22041233C>T		Somatic		Capture	Illumina HiSeq	Phase_I	20371233	NM_148176		Silent	SNP	ENST00000335025.8	37	CCDS13793.1																																																																																				0.632	PPIL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075028.4		
CHCHD10	400916	broad.mit.edu	37	22	24108331	24108331	+	Silent	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr22:24108331C>T	ENST00000484558.2	-	3	961	c.393G>A	c.(391-393)caG>caA	p.Q131Q	CHCHD10_ENST00000401675.3_Silent_p.Q138Q|CHCHD10_ENST00000520222.1_3'UTR			Q8WYQ3	CHC10_HUMAN	coiled-coil-helix-coiled-coil-helix domain containing 10	131	CHCH.				ATP biosynthetic process (GO:0006754)|negative regulation of ATP citrate synthase activity (GO:2000984)|oxidative phosphorylation (GO:0006119)	mitochondrion (GO:0005739)		p.Q131Q(1)		large_intestine(2)|lung(1)	3						AGTACTTGCACTGCTTCAGGG	0.627																																					p.Q131Q												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G393A	22						.						60.0	42.0	48.0					22																	24108331		2203	4299	6502	22438331	SO:0001819	synonymous_variant	400916	exon3			AB050774	CCDS13815.1	22q11.23	2011-03-28	2008-06-13	2008-06-13	ENSG00000250479	ENSG00000250479		"""Coiled-coil-helix-coiled-coil-helix domain containing"""	15559	protein-coding gene	gene with protein product		615903	"""chromosome 22 open reading frame 16"""	C22orf16			Standard	XM_006724241		Approved	N27C7-4	uc002zxw.3	Q8WYQ3	OTTHUMG00000150736	ENST00000484558.2:c.393G>A	22.37:g.24108331C>T		Somatic		Capture	Illumina HiSeq	Phase_I	22438331	NM_213720	A8K0J5	Silent	SNP	ENST00000484558.2	37	CCDS13815.1	.	.	.	.	.	.	.	.	.	.	C	8.258	0.810616	0.16537	.	.	ENSG00000250479	ENST00000521886	.	.	.	4.3	2.11	0.27256	.	.	.	.	.	T	0.56321	0.1977	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.48917	-0.8992	4	.	.	.	-15.613	8.3588	0.32346	0.0:0.7857:0.0:0.2143	.	.	.	.	M	80	.	.	V	-	1	0	CHCHD10	22438331	1.000000	0.71417	1.000000	0.80357	0.964000	0.63967	2.363000	0.44178	0.485000	0.27652	0.485000	0.47835	GTG		0.627	CHCHD10-001	KNOWN	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000319870.2	NM_213720	
MMP11	4320	broad.mit.edu	37	22	24125612	24125612	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr22:24125612C>A	ENST00000215743.3	+	8	1400	c.1348C>A	c.(1348-1350)Ctg>Atg	p.L450M	AP000349.1_ENST00000598975.1_Missense_Mutation_p.Q178H	NM_005940.3	NP_005931.2	P24347	MMP11_HUMAN	matrix metallopeptidase 11 (stromelysin 3)	450					basement membrane organization (GO:0071711)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|multicellular organismal development (GO:0007275)|negative regulation of fat cell differentiation (GO:0045599)|proteolysis (GO:0006508)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|Golgi lumen (GO:0005796)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)	p.L450M(1)		central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(7)|liver(2)|lung(5)|prostate(1)|skin(7)|upper_aerodigestive_tract(1)	27		Medulloblastoma(6;9.86e-08)|all_neural(6;0.000318)			Marimastat(DB00786)	TGCCTACTTCCTGCGCGGCCG	0.617																																					p.L450M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1348A	22						.						92.0	75.0	81.0					22																	24125612		2203	4300	6503	22455612	SO:0001583	missense	4320	exon8				CCDS13816.1	22q11.23	2008-06-11	2005-08-08		ENSG00000099953	ENSG00000099953			7157	protein-coding gene	gene with protein product		185261	"""matrix metalloproteinase 11 (stromelysin 3)"""	STMY3		1639418, 7657606, 12006591	Standard	NM_005940		Approved		uc002zxx.3	P24347	OTTHUMG00000150742	ENST00000215743.3:c.1348C>A	22.37:g.24125612C>A	ENSP00000215743:p.Leu450Met	Somatic		Capture	Illumina HiSeq	Phase_I	22455612	NM_005940	Q5FX24|Q6PEZ6|Q9UC26	Missense_Mutation	SNP	ENST00000215743.3	37	CCDS13816.1	.	.	.	.	.	.	.	.	.	.	C	17.21	3.331307	0.60853	.	.	ENSG00000099953	ENST00000215743	T	0.02498	4.27	4.73	3.71	0.42584	Hemopexin/matrixin (2);	0.294039	0.33457	N	0.004889	T	0.10078	0.0247	L	0.59436	1.845	0.44417	D	0.997338	D	0.89917	1.0	D	0.76575	0.988	T	0.01202	-1.1420	10	0.87932	D	0	.	8.3407	0.32241	0.0:0.7613:0.1555:0.0832	.	450	P24347	MMP11_HUMAN	M	450	ENSP00000215743:L450M	ENSP00000215743:L450M	L	+	1	2	MMP11	22455612	0.999000	0.42202	1.000000	0.80357	0.994000	0.84299	0.751000	0.26348	1.382000	0.46385	0.650000	0.86243	CTG		0.617	MMP11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319891.2	NM_005940	
CABIN1	23523	broad.mit.edu	37	22	24456510	24456510	+	Missense_Mutation	SNP	C	C	T	rs567361031	byFrequency	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr22:24456510C>T	ENST00000398319.2	+	12	1908	c.1523C>T	c.(1522-1524)gCg>gTg	p.A508V	CABIN1_ENST00000263119.5_Missense_Mutation_p.A508V|CABIN1_ENST00000405822.2_Missense_Mutation_p.A458V	NM_001199281.1	NP_001186210.1	Q9Y6J0	CABIN_HUMAN	calcineurin binding protein 1	508					cell surface receptor signaling pathway (GO:0007166)|chromatin modification (GO:0016568)|DNA replication-independent nucleosome assembly (GO:0006336)|negative regulation of catalytic activity (GO:0043086)	aggresome (GO:0016235)|cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	protein phosphatase inhibitor activity (GO:0004864)	p.A508V(1)		breast(2)|central_nervous_system(2)|endometrium(6)|kidney(6)|large_intestine(13)|liver(1)|lung(18)|ovary(5)|pancreas(3)|prostate(1)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	65						CCAGGCTTGGCGGAGGTCGTG	0.602													C|||	15	0.00299521	0.0	0.0	5008	,	,		20293	0.0		0.0	False		,,,				2504	0.0153				p.A508V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1523T	22						.						89.0	71.0	77.0					22																	24456510		2203	4300	6503	22786510	SO:0001583	missense	23523	exon12			AF072441	CCDS13823.1, CCDS74830.1	22q11.23	2008-09-16			ENSG00000099991	ENSG00000099991			24187	protein-coding gene	gene with protein product		604251				9655484, 9205841	Standard	NM_001199281		Approved	KIAA0330, PPP3IN	uc002zzi.1	Q9Y6J0	OTTHUMG00000150797	ENST00000398319.2:c.1523C>T	22.37:g.24456510C>T	ENSP00000381364:p.Ala508Val	Somatic		Capture	Illumina HiSeq	Phase_I	22786510	NM_001199281	G5E9F3|Q6PHY0|Q9Y460	Missense_Mutation	SNP	ENST00000398319.2	37	CCDS13823.1	.	.	.	.	.	.	.	.	.	.	C	15.57	2.873679	0.51695	.	.	ENSG00000099991	ENST00000263119;ENST00000405822;ENST00000398319	T;T;T	0.71341	-0.56;-0.56;-0.56	5.33	4.25	0.50352	.	0.384218	0.28927	N	0.013686	T	0.50326	0.1609	N	0.14661	0.345	0.80722	D	1	B;B	0.31100	0.308;0.205	B;B	0.24974	0.057;0.015	T	0.49447	-0.8939	10	0.11182	T	0.66	.	16.2486	0.82467	0.0:0.7881:0.2118:0.0	.	458;508	G5E9F3;Q9Y6J0	.;CABIN_HUMAN	V	508;458;508	ENSP00000263119:A508V;ENSP00000384694:A458V;ENSP00000381364:A508V	ENSP00000263119:A508V	A	+	2	0	CABIN1	22786510	0.916000	0.31088	0.963000	0.40424	0.729000	0.41735	4.788000	0.62439	2.673000	0.90976	0.551000	0.68910	GCG		0.602	CABIN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320161.2	NM_012295	
CABIN1	23523	broad.mit.edu	37	22	24491942	24491942	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr22:24491942G>A	ENST00000398319.2	+	25	4220	c.3835G>A	c.(3835-3837)Gat>Aat	p.D1279N	CABIN1_ENST00000263119.5_Missense_Mutation_p.D1279N|CABIN1_ENST00000405822.2_Missense_Mutation_p.D1229N	NM_001199281.1	NP_001186210.1	Q9Y6J0	CABIN_HUMAN	calcineurin binding protein 1	1279					cell surface receptor signaling pathway (GO:0007166)|chromatin modification (GO:0016568)|DNA replication-independent nucleosome assembly (GO:0006336)|negative regulation of catalytic activity (GO:0043086)	aggresome (GO:0016235)|cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	protein phosphatase inhibitor activity (GO:0004864)	p.D1279N(1)		breast(2)|central_nervous_system(2)|endometrium(6)|kidney(6)|large_intestine(13)|liver(1)|lung(18)|ovary(5)|pancreas(3)|prostate(1)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	65						GGGGAAGCCCGATTCTGGGGT	0.542																																					p.D1279N												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G3835A	22						.						129.0	132.0	131.0					22																	24491942		2203	4300	6503	22821942	SO:0001583	missense	23523	exon25			AF072441	CCDS13823.1, CCDS74830.1	22q11.23	2008-09-16			ENSG00000099991	ENSG00000099991			24187	protein-coding gene	gene with protein product		604251				9655484, 9205841	Standard	NM_001199281		Approved	KIAA0330, PPP3IN	uc002zzi.1	Q9Y6J0	OTTHUMG00000150797	ENST00000398319.2:c.3835G>A	22.37:g.24491942G>A	ENSP00000381364:p.Asp1279Asn	Somatic		Capture	Illumina HiSeq	Phase_I	22821942	NM_001199281	G5E9F3|Q6PHY0|Q9Y460	Missense_Mutation	SNP	ENST00000398319.2	37	CCDS13823.1	.	.	.	.	.	.	.	.	.	.	G	17.89	3.499612	0.64298	.	.	ENSG00000099991	ENST00000263119;ENST00000405822;ENST00000398319	T;T;T	0.63255	0.17;-0.03;0.17	4.91	3.87	0.44632	Tetratricopeptide-like helical (1);	0.253396	0.39407	N	0.001361	T	0.60209	0.2251	L	0.29908	0.895	0.80722	D	1	D;D	0.67145	0.996;0.992	P;P	0.53861	0.736;0.549	T	0.61158	-0.7119	10	0.44086	T	0.13	.	13.3883	0.60809	0.0812:0.0:0.9188:0.0	.	1229;1279	G5E9F3;Q9Y6J0	.;CABIN_HUMAN	N	1279;1229;1279	ENSP00000263119:D1279N;ENSP00000384694:D1229N;ENSP00000381364:D1279N	ENSP00000263119:D1279N	D	+	1	0	CABIN1	22821942	1.000000	0.71417	0.118000	0.21660	0.954000	0.61252	6.777000	0.75028	2.468000	0.83385	0.650000	0.86243	GAT		0.542	CABIN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320161.2	NM_012295	
MYO18B	84700	broad.mit.edu	37	22	26168327	26168327	+	Silent	SNP	C	C	T	rs371193611		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr22:26168327C>T	ENST00000407587.2	+	7	1888	c.1719C>T	c.(1717-1719)gtC>gtT	p.V573V	MYO18B_ENST00000335473.7_Silent_p.V573V|MYO18B_ENST00000536101.1_Silent_p.V573V			Q8IUG5	MY18B_HUMAN	myosin XVIIIB	573	Myosin motor.					cytoplasm (GO:0005737)|nucleus (GO:0005634)|unconventional myosin complex (GO:0016461)	ATP binding (GO:0005524)|motor activity (GO:0003774)	p.V573V(1)		NS(2)|breast(6)|central_nervous_system(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(4)|kidney(5)|large_intestine(27)|liver(2)|lung(60)|ovary(7)|prostate(8)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(2)	146						TGGACCAGGTCGAGGACCTGG	0.627																																					p.V573V												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1719T	22						.						106.0	104.0	105.0					22																	26168327		1984	4156	6140	24498327	SO:0001819	synonymous_variant	84700	exon7			AJ310931	CCDS54507.1	22q12.1	2011-09-27			ENSG00000133454	ENSG00000133454		"""Myosins / Myosin superfamily : Class XVIII"""	18150	protein-coding gene	gene with protein product		607295				12209013, 12547197	Standard	NM_032608		Approved	BK125H2.1	uc003abz.1	Q8IUG5	OTTHUMG00000151129	ENST00000407587.2:c.1719C>T	22.37:g.26168327C>T		Somatic		Capture	Illumina HiSeq	Phase_I	24498327	NM_032608	B2RWP3|F5GYU7|Q8NDI8|Q8TE65|Q8WWS0|Q96KH2|Q96KR8|Q96KR9	Silent	SNP	ENST00000407587.2	37																																																																																					0.627	MYO18B-006	NOVEL	non_canonical_conserved|basic|appris_candidate_longest|exp_conf	protein_coding	protein_coding	OTTHUMT00000400691.1	NM_032608	
MYO18B	84700	broad.mit.edu	37	22	26173603	26173603	+	Silent	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr22:26173603G>A	ENST00000407587.2	+	8	2092	c.1923G>A	c.(1921-1923)caG>caA	p.Q641Q	MYO18B_ENST00000335473.7_Silent_p.Q641Q|MYO18B_ENST00000536101.1_Silent_p.Q641Q			Q8IUG5	MY18B_HUMAN	myosin XVIIIB	641	Myosin motor.					cytoplasm (GO:0005737)|nucleus (GO:0005634)|unconventional myosin complex (GO:0016461)	ATP binding (GO:0005524)|motor activity (GO:0003774)	p.Q641Q(1)		NS(2)|breast(6)|central_nervous_system(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(4)|kidney(5)|large_intestine(27)|liver(2)|lung(60)|ovary(7)|prostate(8)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(2)	146						CCATGGCACAGCGGGCATACT	0.647																																					p.Q641Q												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G1923A	22						.						39.0	44.0	42.0					22																	26173603		2043	4199	6242	24503603	SO:0001819	synonymous_variant	84700	exon8			AJ310931	CCDS54507.1	22q12.1	2011-09-27			ENSG00000133454	ENSG00000133454		"""Myosins / Myosin superfamily : Class XVIII"""	18150	protein-coding gene	gene with protein product		607295				12209013, 12547197	Standard	NM_032608		Approved	BK125H2.1	uc003abz.1	Q8IUG5	OTTHUMG00000151129	ENST00000407587.2:c.1923G>A	22.37:g.26173603G>A		Somatic		Capture	Illumina HiSeq	Phase_I	24503603	NM_032608	B2RWP3|F5GYU7|Q8NDI8|Q8TE65|Q8WWS0|Q96KH2|Q96KR8|Q96KR9	Silent	SNP	ENST00000407587.2	37																																																																																					0.647	MYO18B-006	NOVEL	non_canonical_conserved|basic|appris_candidate_longest|exp_conf	protein_coding	protein_coding	OTTHUMT00000400691.1	NM_032608	
ASPHD2	57168	broad.mit.edu	37	22	26830455	26830455	+	Nonsense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr22:26830455C>T	ENST00000215906.5	+	2	1312	c.874C>T	c.(874-876)Cga>Tga	p.R292*		NM_020437.4	NP_065170.2	Q6ICH7	ASPH2_HUMAN	aspartate beta-hydroxylase domain containing 2	292	2-oxoglutarate binding. {ECO:0000250}.				peptidyl-amino acid modification (GO:0018193)	integral component of membrane (GO:0016021)|membrane (GO:0016020)	dioxygenase activity (GO:0051213)|metal ion binding (GO:0046872)	p.R266*(1)		endometrium(3)|large_intestine(3)|lung(4)|ovary(1)|prostate(4)|urinary_tract(1)	16						CATCCGCATCCGATGCCATTT	0.522																																					p.R292X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.C874T	22						.						139.0	140.0	140.0					22																	26830455		2203	4300	6503	25160455	SO:0001587	stop_gained	57168	exon2			AK097157	CCDS13834.2	22q12.1	2006-02-02			ENSG00000128203	ENSG00000128203			30437	protein-coding gene	gene with protein product							Standard	NM_020437		Approved	FLJ39838	uc003acg.2	Q6ICH7	OTTHUMG00000150884	ENST00000215906.5:c.874C>T	22.37:g.26830455C>T	ENSP00000215906:p.Arg292*	Somatic		Capture	Illumina HiSeq	Phase_I	25160455	NM_020437	B2RCH3|Q7L0W3|Q9NSN3	Nonsense_Mutation	SNP	ENST00000215906.5	37	CCDS13834.2	.	.	.	.	.	.	.	.	.	.	C	41	8.594547	0.98877	.	.	ENSG00000128203	ENST00000215906	.	.	.	4.69	4.69	0.59074	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-11.5555	11.9794	0.53111	0.1728:0.8271:0.0:0.0	.	.	.	.	X	292	.	ENSP00000215906:R292X	R	+	1	2	ASPHD2	25160455	1.000000	0.71417	0.999000	0.59377	0.875000	0.50365	5.131000	0.64751	2.434000	0.82447	0.460000	0.39030	CGA		0.522	ASPHD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320422.1	NM_020437	
NF2	4771	broad.mit.edu	37	22	30067836	30067836	+	Nonsense_Mutation	SNP	C	C	T	rs74315499		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr22:30067836C>T	ENST00000338641.4	+	11	1462	c.1021C>T	c.(1021-1023)Cga>Tga	p.R341*	NF2_ENST00000413209.2_Intron|NF2_ENST00000361676.4_Nonsense_Mutation_p.R299*|NF2_ENST00000361166.4_Nonsense_Mutation_p.R341*|NF2_ENST00000347330.5_Intron|NF2_ENST00000403435.1_Intron|NF2_ENST00000403999.3_Nonsense_Mutation_p.R341*|NF2_ENST00000361452.4_Nonsense_Mutation_p.R300*|NF2_ENST00000397789.3_Nonsense_Mutation_p.R341*|NF2_ENST00000353887.4_Nonsense_Mutation_p.R258*|NF2_ENST00000334961.7_Nonsense_Mutation_p.R258*	NM_000268.3|NM_016418.5|NM_181832.2	NP_000259.1|NP_057502.2|NP_861970.1	P35240	MERL_HUMAN	neurofibromin 2 (merlin)	341	Glu-rich.				actin cytoskeleton organization (GO:0030036)|cell-cell junction organization (GO:0045216)|ectoderm development (GO:0007398)|hippocampus development (GO:0021766)|lens fiber cell differentiation (GO:0070306)|mesoderm formation (GO:0001707)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of DNA replication (GO:0008156)|negative regulation of JAK-STAT cascade (GO:0046426)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of tyrosine phosphorylation of Stat3 protein (GO:0042518)|negative regulation of tyrosine phosphorylation of Stat5 protein (GO:0042524)|odontogenesis of dentin-containing tooth (GO:0042475)|positive regulation of cell differentiation (GO:0045597)|positive regulation of stress fiber assembly (GO:0051496)|regulation of hippo signaling (GO:0035330)|regulation of neural precursor cell proliferation (GO:2000177)|regulation of protein localization to nucleus (GO:1900180)|regulation of protein stability (GO:0031647)|Schwann cell proliferation (GO:0014010)	adherens junction (GO:0005912)|apical part of cell (GO:0045177)|cleavage furrow (GO:0032154)|cortical actin cytoskeleton (GO:0030864)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|early endosome (GO:0005769)|extrinsic component of membrane (GO:0019898)|filopodium (GO:0030175)|lamellipodium (GO:0030027)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|ruffle (GO:0001726)		p.R341*(22)|p.?(3)|p.M334fs*4(1)|p.M334_Q362del(1)		NS(1)|bone(2)|breast(5)|central_nervous_system(21)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(17)|large_intestine(9)|liver(1)|lung(9)|meninges(372)|ovary(2)|pituitary(1)|pleura(9)|prostate(1)|skin(7)|soft_tissue(303)|stomach(2)|thyroid(2)|upper_aerodigestive_tract(1)|urinary_tract(4)	776						GCGCCTCGCTCGAGAGAAGCA	0.567			"""D, Mis, N, F, S, O"""		"""meningioma, acoustic neuroma, renal """	"""meningioma, acoustic neuroma"""			Neurofibromatosis, type 2																												p.R341X		yes	Rec	yes	Neurofibromatosis type 2	22	22q12.2	4771	neurofibromatosis type 2 gene		O	NF2,soft_tissue,nerve_sheath,Substitution - Nonsense,0 	.	27	Substitution - Nonsense(22)|Unknown(3)|Deletion - In frame(1)|Deletion - Frameshift(1)	meninges(12)|soft_tissue(6)|large_intestine(2)|pleura(2)|kidney(2)|central_nervous_system(1)|skin(1)|stomach(1)	c.C1021T	22	GRCh37	CM930516	NF2	M	rs74315499	.						83.0	75.0	78.0					22																	30067836		2203	4300	6503	28397836	SO:0001587	stop_gained	4771	exon11	Familial Cancer Database	NF2, Central Neurofibromatosis, Bilateral Acoustic Neurofibromatosis	L11353	CCDS13861.1, CCDS13862.1, CCDS13863.1, CCDS13864.1, CCDS13865.1, CCDS54516.1	22q12.2	2014-09-17	2007-12-17		ENSG00000186575	ENSG00000186575		"""A-kinase anchor proteins"""	7773	protein-coding gene	gene with protein product	"""moesin-ezrin-radixin like"", ""schwannomin"""	607379	"""neurofibromin 2 (bilateral acoustic neuroma)"""			10591208	Standard	NM_000268		Approved	merlin	uc003age.4	P35240	OTTHUMG00000030727	ENST00000338641.4:c.1021C>T	22.37:g.30067836C>T	ENSP00000344666:p.Arg341*	Somatic		Capture	Illumina HiSeq	Phase_I	28397836	NM_000268	O95683|Q8WUJ2|Q969N0|Q969Q3|Q96T30|Q96T31|Q96T32|Q96T33|Q9BTW3|Q9UNG9|Q9UNH3|Q9UNH4	Nonsense_Mutation	SNP	ENST00000338641.4	37	CCDS13861.1	.	.	.	.	.	.	.	.	.	.	C	33	5.258801	0.95368	.	.	ENSG00000186575	ENST00000338641;ENST00000361452;ENST00000397822;ENST00000403999;ENST00000334961;ENST00000353887;ENST00000397789;ENST00000361676;ENST00000361166	.	.	.	5.66	3.38	0.38709	.	0.055487	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.8185	0.70052	0.2339:0.7661:0.0:0.0	.	.	.	.	X	341;300;341;341;258;258;341;299;341	.	.	R	+	1	2	NF2	28397836	0.749000	0.28305	0.842000	0.33263	0.994000	0.84299	1.510000	0.35790	2.681000	0.91329	0.462000	0.41574	CGA		0.567	NF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075615.3	NM_000268	
SEC14L4	284904	broad.mit.edu	37	22	30887872	30887872	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr22:30887872C>T	ENST00000255858.7	-	10	943	c.860G>A	c.(859-861)gGc>gAc	p.G287D	RP4-539M6.14_ENST00000442126.1_RNA|SEC14L4_ENST00000540456.1_Missense_Mutation_p.G272D|SEC14L4_ENST00000392772.2_Missense_Mutation_p.G233D|SEC14L4_ENST00000381982.3_Missense_Mutation_p.G287D|RP4-539M6.14_ENST00000610156.1_RNA	NM_001161368.1|NM_174977.3	NP_001154840.1|NP_777637.1	Q9UDX3	S14L4_HUMAN	SEC14-like 4 (S. cerevisiae)	287	GOLD. {ECO:0000255|PROSITE- ProRule:PRU00096}.					integral component of membrane (GO:0016021)|intracellular (GO:0005622)	lipid binding (GO:0008289)|transporter activity (GO:0005215)	p.G287D(1)		breast(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(5)|pancreas(1)|skin(1)	21					Vitamin E(DB00163)	CAGGGAGGAGCCGCGGCCCAC	0.627																																					p.G287D												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G860A	22						.						27.0	24.0	25.0					22																	30887872		2203	4298	6501	29217872	SO:0001583	missense	284904	exon10			AY158085	CCDS13878.1, CCDS54517.1	22q12.1	2003-03-10			ENSG00000133488	ENSG00000133488			20627	protein-coding gene	gene with protein product		612825					Standard	NM_174977		Approved	TAP3, dJ130H16.5	uc003aid.2	Q9UDX3	OTTHUMG00000151258	ENST00000255858.7:c.860G>A	22.37:g.30887872C>T	ENSP00000255858:p.Gly287Asp	Somatic		Capture	Illumina HiSeq	Phase_I	29217872	NM_001161368	A5D6W7|A6NCV4	Missense_Mutation	SNP	ENST00000255858.7	37	CCDS13878.1	.	.	.	.	.	.	.	.	.	.	C	14.29	2.491731	0.44249	.	.	ENSG00000133488	ENST00000255858;ENST00000540456;ENST00000392772;ENST00000381982	T;T;T;T	0.52983	0.64;0.64;0.64;0.64	4.12	3.1	0.35709	GOLD (2);	0.058703	0.64402	D	0.000002	T	0.51550	0.1681	M	0.88512	2.96	0.80722	D	1	P;P;B	0.39737	0.594;0.685;0.441	B;B;B	0.35278	0.199;0.188;0.144	T	0.62374	-0.6868	10	0.62326	D	0.03	-17.6889	11.8521	0.52417	0.0:0.9132:0.0:0.0868	.	233;272;287	B3KSF0;G3V1L4;Q9UDX3	.;.;S14L4_HUMAN	D	287;272;233;287	ENSP00000255858:G287D;ENSP00000440848:G272D;ENSP00000376525:G233D;ENSP00000371412:G287D	ENSP00000255858:G287D	G	-	2	0	SEC14L4	29217872	1.000000	0.71417	0.985000	0.45067	0.683000	0.39861	2.740000	0.47418	1.085000	0.41206	0.591000	0.81541	GGC		0.627	SEC14L4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321946.1	NM_174977	
DEPDC5	9681	broad.mit.edu	37	22	32289604	32289604	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr22:32289604A>G	ENST00000382112.3	+	38	4113	c.4043A>G	c.(4042-4044)gAt>gGt	p.D1348G	DEPDC5_ENST00000400248.2_Missense_Mutation_p.D1326G|DEPDC5_ENST00000382105.2_3'UTR|DEPDC5_ENST00000539165.1_Missense_Mutation_p.D174G|DEPDC5_ENST00000266091.3_Missense_Mutation_p.D1335G|DEPDC5_ENST00000400249.2_Missense_Mutation_p.D1326G|DEPDC5_ENST00000535622.1_Missense_Mutation_p.D1257G|DEPDC5_ENST00000382111.2_Missense_Mutation_p.D1357G|DEPDC5_ENST00000400246.1_Missense_Mutation_p.D1357G	NM_001136029.2|NM_001242896.1	NP_001129501.1|NP_001229825.1	O75140	DEPD5_HUMAN	DEP domain containing 5	1357					intracellular signal transduction (GO:0035556)	cytosol (GO:0005829)|lysosomal membrane (GO:0005765)|perinuclear region of cytoplasm (GO:0048471)	GTPase activator activity (GO:0005096)	p.D1326G(1)		breast(1)|central_nervous_system(5)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|lung(24)|ovary(5)|pancreas(2)|prostate(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	63						GTGACCCTGGATGTTGACGTG	0.527																																					p.D1326G												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A3977G	22						.						89.0	94.0	93.0					22																	32289604		2024	4191	6215	30619604	SO:0001583	missense	9681	exon38			AB014545	CCDS43006.1, CCDS43007.1, CCDS46692.1, CCDS56229.1, CCDS74849.1	22q12.3	2013-04-29			ENSG00000100150	ENSG00000100150			18423	protein-coding gene	gene with protein product		614191				23542697, 23542701	Standard	NM_001242896		Approved	KIAA0645, DEP.5	uc011alu.2	O75140	OTTHUMG00000030926	ENST00000382112.3:c.4043A>G	22.37:g.32289604A>G	ENSP00000371546:p.Asp1348Gly	Somatic		Capture	Illumina HiSeq	Phase_I	30619604	NM_014662	A6H8V6|A8MPX9|B4DH93|B9EGN9|Q5K3V5|Q5THY9|Q5THZ0|Q5THZ1|Q5THZ3|Q68DR1|Q6MZX3|Q6PEZ1|Q9UGV8|Q9UH13	Missense_Mutation	SNP	ENST00000382112.3	37	CCDS46692.1	.	.	.	.	.	.	.	.	.	.	A	24.7	4.559696	0.86335	.	.	ENSG00000100150	ENST00000535622;ENST00000266091;ENST00000400249;ENST00000382109;ENST00000400246;ENST00000382112;ENST00000382111;ENST00000400248;ENST00000539165	T;T;T;T;T;T;T	0.56275	0.47;0.9;0.91;0.96;0.9;0.96;0.91	4.99	4.99	0.66335	.	0.000000	0.85682	D	0.000000	T	0.69993	0.3173	M	0.65975	2.015	0.80722	D	1	D;D;D;D;D;D	0.76494	0.998;0.999;0.999;0.998;0.997;0.997	D;D;D;D;D;D	0.87578	0.992;0.995;0.998;0.995;0.989;0.989	T	0.73895	-0.3838	10	0.87932	D	0	.	13.8902	0.63733	1.0:0.0:0.0:0.0	.	1357;1257;743;1335;1348;1326	B9EGN9;B4DH93;O75140-7;O75140-4;A8MPX9;O75140	.;.;.;.;.;DEPD5_HUMAN	G	1257;1335;1326;1257;1357;1348;1357;1326;174	ENSP00000440210:D1257G;ENSP00000266091:D1335G;ENSP00000383108:D1326G;ENSP00000383105:D1357G;ENSP00000371546:D1348G;ENSP00000371545:D1357G;ENSP00000383107:D1326G	ENSP00000266091:D1335G	D	+	2	0	DEPDC5	30619604	1.000000	0.71417	0.923000	0.36655	0.984000	0.73092	8.870000	0.92336	1.874000	0.54306	0.460000	0.39030	GAT		0.527	DEPDC5-006	NOVEL	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000129087.1	NM_014662	
SLC5A4	6527	broad.mit.edu	37	22	32621682	32621682	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr22:32621682A>G	ENST00000266086.4	-	12	1420	c.1409T>C	c.(1408-1410)gTc>gCc	p.V470A	RP1-90G24.10_ENST00000434942.1_RNA	NM_014227.2	NP_055042.1	Q9NY91	SC5A4_HUMAN	solute carrier family 5 (glucose activated ion channel), member 4	470					carbohydrate transport (GO:0008643)|sodium ion transport (GO:0006814)	integral component of membrane (GO:0016021)	symporter activity (GO:0015293)	p.V470A(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(15)|pancreas(2)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	36						AAGCACAAAGACAGCTGCAAT	0.403																																					p.V470A												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T1409C	22						.						108.0	109.0	109.0					22																	32621682		2203	4300	6503	30951682	SO:0001583	missense	6527	exon12			U41897	CCDS13903.1	22q12.3	2013-07-19	2013-07-19		ENSG00000100191	ENSG00000100191		"""Solute carriers"""	11039	protein-coding gene	gene with protein product			"""solute carrier family 5 (low affinity glucose cotransporter), member 4"""			9501190, 12354616	Standard	NM_014227		Approved	SAAT1, SGLT3, DJ90G24.4	uc003ami.3	Q9NY91	OTTHUMG00000150007	ENST00000266086.4:c.1409T>C	22.37:g.32621682A>G	ENSP00000266086:p.Val470Ala	Somatic		Capture	Illumina HiSeq	Phase_I	30951682	NM_014227	O15279	Missense_Mutation	SNP	ENST00000266086.4	37	CCDS13903.1	.	.	.	.	.	.	.	.	.	.	A	15.81	2.944639	0.53079	.	.	ENSG00000100191	ENST00000266086	D	0.90788	-2.73	5.16	5.16	0.70880	.	0.000000	0.85682	D	0.000000	D	0.92906	0.7743	M	0.79475	2.455	0.80722	D	1	P	0.42961	0.795	P	0.50440	0.641	D	0.93678	0.6996	10	0.87932	D	0	.	12.9864	0.58594	1.0:0.0:0.0:0.0	.	470	Q9NY91	SC5A4_HUMAN	A	470	ENSP00000266086:V470A	ENSP00000266086:V470A	V	-	2	0	SLC5A4	30951682	1.000000	0.71417	1.000000	0.80357	0.006000	0.05464	7.216000	0.77974	2.165000	0.68154	0.477000	0.44152	GTC		0.403	SLC5A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315724.1	NM_014227	
SLC5A4	6527	broad.mit.edu	37	22	32626992	32626992	+	Silent	SNP	G	G	A	rs536135729		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr22:32626992G>A	ENST00000266086.4	-	10	1103	c.1092C>T	c.(1090-1092)taC>taT	p.Y364Y	RP1-90G24.10_ENST00000434942.1_RNA	NM_014227.2	NP_055042.1	Q9NY91	SC5A4_HUMAN	solute carrier family 5 (glucose activated ion channel), member 4	364					carbohydrate transport (GO:0008643)|sodium ion transport (GO:0006814)	integral component of membrane (GO:0016021)	symporter activity (GO:0015293)	p.Y364Y(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(15)|pancreas(2)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	36						TGGGGTATGCGTAGTTGGTGC	0.542													G|||	1	0.000199681	0.0	0.0	5008	,	,		19730	0.0		0.0	False		,,,				2504	0.001				p.Y364Y												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1092T	22						.						127.0	94.0	105.0					22																	32626992		2203	4300	6503	30956992	SO:0001819	synonymous_variant	6527	exon10			U41897	CCDS13903.1	22q12.3	2013-07-19	2013-07-19		ENSG00000100191	ENSG00000100191		"""Solute carriers"""	11039	protein-coding gene	gene with protein product			"""solute carrier family 5 (low affinity glucose cotransporter), member 4"""			9501190, 12354616	Standard	NM_014227		Approved	SAAT1, SGLT3, DJ90G24.4	uc003ami.3	Q9NY91	OTTHUMG00000150007	ENST00000266086.4:c.1092C>T	22.37:g.32626992G>A		Somatic		Capture	Illumina HiSeq	Phase_I	30956992	NM_014227	O15279	Silent	SNP	ENST00000266086.4	37	CCDS13903.1																																																																																				0.542	SLC5A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315724.1	NM_014227	
MYH9	4627	broad.mit.edu	37	22	36710222	36710222	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr22:36710222G>T	ENST00000216181.5	-	13	1752	c.1522C>A	c.(1522-1524)Ctg>Atg	p.L508M	RN7SL349P_ENST00000582364.1_RNA	NM_002473.4	NP_002464.1	P35579	MYH9_HUMAN	myosin, heavy chain 9, non-muscle	508	Myosin motor.				actin cytoskeleton reorganization (GO:0031532)|actin filament-based movement (GO:0030048)|actomyosin structure organization (GO:0031032)|angiogenesis (GO:0001525)|ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|blood vessel endothelial cell migration (GO:0043534)|cytokinesis (GO:0000910)|establishment of meiotic spindle localization (GO:0051295)|establishment of T cell polarity (GO:0001768)|in utero embryonic development (GO:0001701)|integrin-mediated signaling pathway (GO:0007229)|leukocyte migration (GO:0050900)|meiotic spindle organization (GO:0000212)|membrane protein ectodomain proteolysis (GO:0006509)|monocyte differentiation (GO:0030224)|myoblast fusion (GO:0007520)|platelet aggregation (GO:0070527)|platelet formation (GO:0030220)|protein transport (GO:0015031)|regulation of cell shape (GO:0008360)|termination of G-protein coupled receptor signaling pathway (GO:0038032)|uropod organization (GO:0032796)	actin cytoskeleton (GO:0015629)|actomyosin (GO:0042641)|actomyosin contractile ring (GO:0005826)|cell leading edge (GO:0031252)|cell-cell adherens junction (GO:0005913)|cleavage furrow (GO:0032154)|cortical cytoskeleton (GO:0030863)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|immunological synapse (GO:0001772)|membrane (GO:0016020)|myosin II complex (GO:0016460)|myosin II filament (GO:0097513)|neuromuscular junction (GO:0031594)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|ruffle (GO:0001726)|spindle (GO:0005819)|stress fiber (GO:0001725)|uropod (GO:0001931)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|actin-dependent ATPase activity (GO:0030898)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microfilament motor activity (GO:0000146)|motor activity (GO:0003774)|poly(A) RNA binding (GO:0044822)|protein anchor (GO:0043495)|protein homodimerization activity (GO:0042803)	p.L508M(1)		NS(1)|breast(8)|central_nervous_system(3)|cervix(2)|endometrium(5)|kidney(4)|large_intestine(16)|lung(29)|ovary(4)|pancreas(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(6)|urinary_tract(3)	86						CAGGGCTGCAGGTCGAGGCCA	0.587			T	ALK	ALCL		"""Deafness, autosomal dominant 17, Epstein syndrome, Fechtner syndrome, May-Hegglin anomaly, Sebastian syndrome"""		Hereditary Macrothrombocytopenia, MYH9-associated																												p.L508M			Dom	yes		22	22q13.1	4627	"""myosin, heavy polypeptide 9, non-muscle"""	yes	L	.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1522A	22						.						169.0	127.0	142.0					22																	36710222		2203	4300	6503	35040168	SO:0001583	missense	4627	exon13	Familial Cancer Database	MYHIIA syndrome, incl. Fechtner Syndrome, FTNS, and May-Hegglin Anomaly, MHA		CCDS13927.1	22q13.1	2014-09-17	2006-09-29		ENSG00000100345	ENSG00000100345		"""Myosins / Myosin superfamily : Class II"""	7579	protein-coding gene	gene with protein product	"""nonmuscle myosin heavy chain II-A"""	160775	"""myosin, heavy polypeptide 9, non-muscle"""	DFNA17		1860190, 11023810	Standard	NM_002473		Approved	NMMHCA, NMHC-II-A, MHA, FTNS, EPSTS	uc003apg.3	P35579	OTTHUMG00000030429	ENST00000216181.5:c.1522C>A	22.37:g.36710222G>T	ENSP00000216181:p.Leu508Met	Somatic		Capture	Illumina HiSeq	Phase_I	35040168	NM_002473	A8K6E4|O60805|Q60FE2|Q86T83	Missense_Mutation	SNP	ENST00000216181.5	37	CCDS13927.1	.	.	.	.	.	.	.	.	.	.	G	26.7	4.761367	0.89932	.	.	ENSG00000100345	ENST00000337818;ENST00000216181	T	0.73152	-0.72	5.05	5.05	0.67936	Myosin head, motor domain (3);	0.000000	0.64402	D	0.000001	D	0.89368	0.6695	H	0.98426	4.23	0.80722	D	1	P	0.51933	0.949	P	0.58077	0.832	D	0.93547	0.6883	10	0.87932	D	0	.	18.4598	0.90735	0.0:0.0:1.0:0.0	.	508	P35579	MYH9_HUMAN	M	372;508	ENSP00000216181:L508M	ENSP00000216181:L508M	L	-	1	2	MYH9	35040168	1.000000	0.71417	1.000000	0.80357	0.967000	0.64934	5.735000	0.68587	2.524000	0.85096	0.558000	0.71614	CTG		0.587	MYH9-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000259110.3	NM_002473	
TST	7263	broad.mit.edu	37	22	37407100	37407100	+	Missense_Mutation	SNP	G	G	A	rs148918180		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr22:37407100G>A	ENST00000403892.3	-	2	1596	c.862C>T	c.(862-864)Cgt>Tgt	p.R288C	TST_ENST00000249042.3_Missense_Mutation_p.R288C|Y_RNA_ENST00000516603.1_RNA	NM_001270483.1	NP_001257412.1	Q16762	THTR_HUMAN	thiosulfate sulfurtransferase (rhodanese)	288	Rhodanese 2. {ECO:0000255|PROSITE- ProRule:PRU00173}.				cellular nitrogen compound metabolic process (GO:0034641)|cyanate catabolic process (GO:0009440)|epithelial cell differentiation (GO:0030855)|rRNA import into mitochondrion (GO:0035928)|rRNA transport (GO:0051029)|small molecule metabolic process (GO:0044281)|sulfide oxidation, using sulfide:quinone oxidoreductase (GO:0070221)|sulfur amino acid catabolic process (GO:0000098)|sulfur amino acid metabolic process (GO:0000096)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	5S rRNA binding (GO:0008097)|thiosulfate sulfurtransferase activity (GO:0004792)	p.R288C(1)		kidney(1)|large_intestine(1)|lung(2)|prostate(1)|skin(1)|urinary_tract(1)	7						TGGGACACACGGCTCTCTGGG	0.617													G|||	1	0.000199681	0.0	0.0	5008	,	,		16277	0.001		0.0	False		,,,				2504	0.0				p.R288C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C862T	22						.	G	CYS/ARG	0,4404		0,0,2202	54.0	59.0	57.0		862	1.9	0.4	22	dbSNP_134	57	2,8594		0,2,4296	no	missense	TST	NM_003312.4	180	0,2,6498	AA,AG,GG		0.0233,0.0,0.0154	probably-damaging	288/298	37407100	2,12998	2202	4298	6500	35737046	SO:0001583	missense	7263	exon3			Z73420	CCDS13938.1	22q13.1	2002-02-05			ENSG00000128311	ENSG00000128311	2.8.1.1		12388	protein-coding gene	gene with protein product		180370				1953758	Standard	NM_003312		Approved	RDS	uc003aqh.4	Q16762	OTTHUMG00000150533	ENST00000403892.3:c.862C>T	22.37:g.37407100G>A	ENSP00000385828:p.Arg288Cys	Somatic		Capture	Illumina HiSeq	Phase_I	35737046	NM_003312	B3KRM1|Q6IB06	Missense_Mutation	SNP	ENST00000403892.3	37	CCDS13938.1	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	G	12.14	1.848173	0.32699	0.0	2.33E-4	ENSG00000128311	ENST00000403892;ENST00000249042;ENST00000413912	T;T	0.31769	1.48;1.48	5.08	1.85	0.25348	Rhodanese-like (2);	0.411052	0.24185	N	0.040762	T	0.17365	0.0417	N	0.24115	0.695	0.09310	N	1	P	0.44659	0.84	B	0.42522	0.39	T	0.10965	-1.0607	10	0.54805	T	0.06	-1.7964	1.7689	0.03008	0.1658:0.1183:0.4431:0.2728	.	288	Q16762	THTR_HUMAN	C	288;288;235	ENSP00000385828:R288C;ENSP00000249042:R288C	ENSP00000249042:R288C	R	-	1	0	TST	35737046	0.002000	0.14202	0.430000	0.26722	0.255000	0.26057	0.904000	0.28491	0.313000	0.23062	-0.136000	0.14681	CGT		0.617	TST-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318790.1		
ELFN2	114794	broad.mit.edu	37	22	37770540	37770540	+	Silent	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr22:37770540G>A	ENST00000402918.2	-	3	1820	c.1035C>T	c.(1033-1035)atC>atT	p.I345I	RP1-63G5.8_ENST00000609322.1_RNA|ELFN2_ENST00000435824.1_5'Flank|RP1-63G5.5_ENST00000430883.1_RNA	NM_052906.3	NP_443138.2	Q5R3F8	PPR29_HUMAN	extracellular leucine-rich repeat and fibronectin type III domain containing 2	345	Fibronectin type-III.				negative regulation of phosphatase activity (GO:0010923)	extracellular space (GO:0005615)|integral component of membrane (GO:0016021)	phosphatase binding (GO:0019902)|protein phosphatase inhibitor activity (GO:0004864)	p.I345I(1)		NS(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(13)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	35	Melanoma(58;0.0574)					CCAGCGTCACGATCTCCTTCT	0.557																																					p.I345I												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1035T	22						.						271.0	251.0	258.0					22																	37770540		2203	4300	6503	36100486	SO:0001819	synonymous_variant	114794	exon3			BC041596	CCDS33642.1	22q13.1	2013-02-11	2011-10-27	2011-10-27	ENSG00000166897	ENSG00000166897		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"", ""Fibronectin type III domain containing"""	29396	protein-coding gene	gene with protein product			"""leucine rich repeat containing 62"", ""extracellular leucine-rich repeat and fibronectin type III containing 2"", ""extracellular leucine-rich repeat and fibronectin type III domain containing 2"", ""protein phosphatase 1, regulatory subunit 29"""	LRRC62, PPP1R29		17868438	Standard	XR_244427		Approved	dJ63G5.3, KIAA1904	uc003asq.4	Q5R3F8	OTTHUMG00000150558	ENST00000402918.2:c.1035C>T	22.37:g.37770540G>A		Somatic		Capture	Illumina HiSeq	Phase_I	36100486	NM_052906	Q96PY3	Silent	SNP	ENST00000402918.2	37	CCDS33642.1																																																																																				0.557	ELFN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318900.2	NM_052906	
SOX10	6663	broad.mit.edu	37	22	38369885	38369885	+	Missense_Mutation	SNP	C	C	T	rs549034055		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr22:38369885C>T	ENST00000396884.2	-	4	1300	c.1018G>A	c.(1018-1020)Gtg>Atg	p.V340M	POLR2F_ENST00000405557.1_Intron|POLR2F_ENST00000407936.1_Intron|SOX10_ENST00000360880.2_Missense_Mutation_p.V340M	NM_006941.3	NP_008872.1	P56693	SOX10_HUMAN	SRY (sex determining region Y)-box 10	340					anatomical structure morphogenesis (GO:0009653)|cell maturation (GO:0048469)|developmental growth (GO:0048589)|digestive tract morphogenesis (GO:0048546)|enteric nervous system development (GO:0048484)|in utero embryonic development (GO:0001701)|melanocyte differentiation (GO:0030318)|negative regulation of apoptotic process (GO:0043066)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of transcription, DNA-templated (GO:0045892)|neural crest cell migration (GO:0001755)|oligodendrocyte differentiation (GO:0048709)|peripheral nervous system development (GO:0007422)|positive regulation of gliogenesis (GO:0014015)|positive regulation of neuroblast proliferation (GO:0002052)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	extrinsic component of mitochondrial outer membrane (GO:0031315)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|identical protein binding (GO:0042802)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|RNA polymerase II transcription factor binding transcription factor activity involved in positive regulation of transcription (GO:0001190)|transcription coactivator activity (GO:0003713)	p.V340M(1)		NS(6)|breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(4)|skin(2)	20	Melanoma(58;0.045)					GGCAGAGCCACGCCTGGTGGC	0.682													C|||	1	0.000199681	0.0	0.0	5008	,	,		14205	0.001		0.0	False		,,,				2504	0.0				p.V340M	Melanoma(39;342 1098 6220 32775 40068)|GBM(21;140 497 5227 16059 19275)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1018A	22						.						41.0	43.0	43.0					22																	38369885		2203	4300	6503	36699831	SO:0001583	missense	6663	exon4				CCDS13964.1	22q13.1	2014-09-17			ENSG00000100146	ENSG00000100146		"""SRY (sex determining region Y)-boxes"""	11190	protein-coding gene	gene with protein product	"""dominant megacolon, mouse, human homolog of"""	602229				9462749, 10441344, 12944398	Standard	NM_006941		Approved	DOM, WS4, WS2E	uc003aun.1	P56693	OTTHUMG00000149913	ENST00000396884.2:c.1018G>A	22.37:g.38369885C>T	ENSP00000380093:p.Val340Met	Somatic		Capture	Illumina HiSeq	Phase_I	36699831	NM_006941	B4DV62|Q6FHW7	Missense_Mutation	SNP	ENST00000396884.2	37	CCDS13964.1	.	.	.	.	.	.	.	.	.	.	C	10.77	1.444435	0.25987	.	.	ENSG00000100146	ENST00000396884;ENST00000360880	D;D	0.98455	-4.94;-4.94	4.87	4.87	0.63330	.	0.500491	0.20787	N	0.085690	D	0.96506	0.8860	N	0.25647	0.755	0.30687	N	0.75178	D	0.60575	0.988	P	0.49799	0.622	D	0.94588	0.7785	10	0.32370	T	0.25	.	16.1971	0.82040	0.0:1.0:0.0:0.0	.	340	P56693	SOX10_HUMAN	M	340	ENSP00000380093:V340M;ENSP00000354130:V340M	ENSP00000354130:V340M	V	-	1	0	SOX10	36699831	1.000000	0.71417	0.945000	0.38365	0.043000	0.13939	5.654000	0.67974	2.249000	0.74217	0.455000	0.32223	GTG		0.682	SOX10-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313875.1	NM_006941	
SLC16A8	23539	broad.mit.edu	37	22	38474456	38474456	+	Missense_Mutation	SNP	C	C	T	rs140740838	byFrequency	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr22:38474456C>T	ENST00000320521.5	-	5	1562	c.1454G>A	c.(1453-1455)cGg>cAg	p.R485Q	SLC16A8_ENST00000469516.1_5'UTR	NM_013356.2	NP_037488.2	O95907	MOT3_HUMAN	solute carrier family 16 (monocarboxylate transporter), member 8	485					blood coagulation (GO:0007596)|cellular metabolic process (GO:0044237)|lactate transmembrane transport (GO:0035873)|lactate transport (GO:0015727)|leukocyte migration (GO:0050900)|pyruvate metabolic process (GO:0006090)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	lactate transmembrane transporter activity (GO:0015129)|secondary active monocarboxylate transmembrane transporter activity (GO:0015355)|symporter activity (GO:0015293)	p.R485Q(1)		kidney(1)|large_intestine(1)|prostate(1)	3	Melanoma(58;0.045)				Pyruvic acid(DB00119)	GGGCTCGCCCCGGGCGCTGAG	0.642																																					p.R485Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1454A	22						.						46.0	52.0	50.0					22																	38474456		2203	4300	6503	36804402	SO:0001583	missense	23539	exon5			AF132610	CCDS13966.1	22q12.3-q13.2	2013-07-18	2013-07-18		ENSG00000100156	ENSG00000100156		"""Solute carriers"""	16270	protein-coding gene	gene with protein product	"""monocarboxylate transporter 3"""	610409	"""solute carrier 16 (monocarboxylic acid transporters), member 8"""			10493836	Standard	NM_013356		Approved	MCT3, REMP	uc003auu.3	O95907	OTTHUMG00000151196	ENST00000320521.5:c.1454G>A	22.37:g.38474456C>T	ENSP00000321735:p.Arg485Gln	Somatic		Capture	Illumina HiSeq	Phase_I	36804402	NM_013356	Q9UBE2	Missense_Mutation	SNP	ENST00000320521.5	37	CCDS13966.1	.	.	.	.	.	.	.	.	.	.	C	5.676	0.309273	0.10733	.	.	ENSG00000100156	ENST00000320521	T	0.19532	2.14	4.17	-0.0116	0.13991	.	11.475900	0.00728	N	0.000930	T	0.10294	0.0252	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.18053	-1.0349	10	0.17832	T	0.49	.	3.5017	0.07676	0.1808:0.4793:0.0:0.3398	.	485	O95907	MOT3_HUMAN	Q	485	ENSP00000321735:R485Q	ENSP00000321735:R485Q	R	-	2	0	SLC16A8	36804402	0.000000	0.05858	0.003000	0.11579	0.024000	0.10985	0.360000	0.20250	0.074000	0.16767	-0.591000	0.04113	CGG		0.642	SLC16A8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321724.1	NM_013356	
JOSD1	9929	broad.mit.edu	37	22	39083943	39083943	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr22:39083943C>A	ENST00000216039.5	-	4	1252	c.573G>T	c.(571-573)gaG>gaT	p.E191D		NM_014876.5	NP_055691.1	Q15040	JOS1_HUMAN	Josephin domain containing 1	191	Josephin. {ECO:0000255|PROSITE- ProRule:PRU00331}.					cytoplasm (GO:0005737)|membrane (GO:0016020)|plasma membrane (GO:0005886)	omega peptidase activity (GO:0008242)	p.E191D(1)		large_intestine(1)|lung(1)|ovary(2)|pancreas(1)	5	Melanoma(58;0.04)					GAGCCTCTACCTCTTCTGGTA	0.493																																					p.E191D												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G573T	22						.						140.0	103.0	116.0					22																	39083943		2203	4300	6503	37413889	SO:0001583	missense	9929	exon4				CCDS13976.1	22q13.1	2005-11-10			ENSG00000100221	ENSG00000100221			28953	protein-coding gene	gene with protein product		615323				7584044	Standard	NM_014876		Approved	KIAA0063	uc003awf.3	Q15040	OTTHUMG00000151030	ENST00000216039.5:c.573G>T	22.37:g.39083943C>A	ENSP00000216039:p.Glu191Asp	Somatic		Capture	Illumina HiSeq	Phase_I	37413889	NM_014876	A8K712	Missense_Mutation	SNP	ENST00000216039.5	37	CCDS13976.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	13.35|13.35	2.211691|2.211691	0.39102|0.39102	.|.	.|.	ENSG00000100221|ENSG00000100221	ENST00000216039|ENST00000545590	T|.	0.50001|.	0.76|.	5.28|5.28	3.18|3.18	0.36537|0.36537	.|.	0.196100|.	0.52532|.	D|.	0.000063|.	T|T	0.42154|0.42154	0.1190|0.1190	N|N	0.25144|0.25144	0.715|0.715	0.80722|0.80722	D|D	1|1	B|.	0.17852|.	0.024|.	B|.	0.12837|.	0.008|.	T|T	0.12218|0.12218	-1.0556|-1.0556	10|5	0.28530|.	T|.	0.3|.	-4.4093|-4.4093	10.2274|10.2274	0.43233|0.43233	0.0:0.7743:0.0:0.2257|0.0:0.7743:0.0:0.2257	.|.	191|.	Q15040|.	JOS1_HUMAN|.	D|C	191|143	ENSP00000216039:E191D|.	ENSP00000216039:E191D|.	E|G	-|-	3|1	2|0	JOSD1|JOSD1	37413889|37413889	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.945000|0.945000	0.59286|0.59286	0.805000|0.805000	0.27112|0.27112	0.597000|0.597000	0.29811|0.29811	-0.150000|-0.150000	0.13652|0.13652	GAG|GGT		0.493	JOSD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321047.1	NM_014876	
APOBEC3C	27350	broad.mit.edu	37	22	39411671	39411671	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr22:39411671G>A	ENST00000361441.4	+	2	369	c.89G>A	c.(88-90)cGg>cAg	p.R30Q	APOBEC3D_ENST00000381568.4_Intron	NM_014508.2	NP_055323.2	Q9NRW3	ABC3C_HUMAN	apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like 3C	30					cytidine deamination (GO:0009972)|defense response to virus (GO:0051607)|DNA demethylation (GO:0080111)|innate immune response (GO:0045087)|negative regulation of transposition (GO:0010529)|negative regulation of viral genome replication (GO:0045071)|viral process (GO:0016032)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amidines (GO:0016814)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)	p.R30Q(1)		endometrium(1)|large_intestine(3)|lung(1)|skin(1)	6	Melanoma(58;0.04)					GCCAACGATCGGAACGAAACT	0.502																																					p.R30Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G89A	22						.						114.0	111.0	112.0					22																	39411671		2203	4300	6503	37741617	SO:0001583	missense	27350	exon2			AF165520	CCDS13983.1	22q13.1-q13.2	2014-01-28			ENSG00000244509	ENSG00000244509		"""Apolipoprotein B mRNA editing enzymes"""	17353	protein-coding gene	gene with protein product		607750				11863358	Standard	NM_014508		Approved	APOBEC1L, PBI, bK150C2.3, ARDC2, ARDC4, ARP5	uc003awr.3	Q9NRW3	OTTHUMG00000151087	ENST00000361441.4:c.89G>A	22.37:g.39411671G>A	ENSP00000355340:p.Arg30Gln	Somatic		Capture	Illumina HiSeq	Phase_I	37741617	NM_014508	B2R884|Q5JZ92|Q7Z2N7|Q96F12	Missense_Mutation	SNP	ENST00000361441.4	37	CCDS13983.1	.	.	.	.	.	.	.	.	.	.	.	13.97	2.396935	0.42512	.	.	ENSG00000244509	ENST00000361441	T	0.73047	-0.71	1.86	-0.598	0.11649	APOBEC-like, N-terminal (1);	.	.	.	.	T	0.65101	0.2659	M	0.68728	2.09	0.09310	N	1	P	0.50528	0.936	B	0.43916	0.436	T	0.57791	-0.7750	9	0.72032	D	0.01	.	4.2453	0.10669	0.4429:0.0:0.5571:0.0	.	30	Q9NRW3	ABC3C_HUMAN	Q	30	ENSP00000355340:R30Q	ENSP00000355340:R30Q	R	+	2	0	APOBEC3C	37741617	0.002000	0.14202	0.000000	0.03702	0.001000	0.01503	0.520000	0.22878	-0.093000	0.12396	-0.451000	0.05528	CGG		0.502	APOBEC3C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321241.2	NM_014508	
APOBEC3C	27350	broad.mit.edu	37	22	39413961	39413961	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr22:39413961G>A	ENST00000361441.4	+	3	645	c.365G>A	c.(364-366)cGc>cAc	p.R122H	APOBEC3D_ENST00000381568.4_Intron	NM_014508.2	NP_055323.2	Q9NRW3	ABC3C_HUMAN	apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like 3C	122					cytidine deamination (GO:0009972)|defense response to virus (GO:0051607)|DNA demethylation (GO:0080111)|innate immune response (GO:0045087)|negative regulation of transposition (GO:0010529)|negative regulation of viral genome replication (GO:0045071)|viral process (GO:0016032)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amidines (GO:0016814)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)	p.R122H(1)		endometrium(1)|large_intestine(3)|lung(1)|skin(1)	6	Melanoma(58;0.04)					TTCACCGCCCGCCTCTACTAC	0.587																																					p.R122H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G365A	22						.						116.0	122.0	120.0					22																	39413961		2203	4300	6503	37743907	SO:0001583	missense	27350	exon3			AF165520	CCDS13983.1	22q13.1-q13.2	2014-01-28			ENSG00000244509	ENSG00000244509		"""Apolipoprotein B mRNA editing enzymes"""	17353	protein-coding gene	gene with protein product		607750				11863358	Standard	NM_014508		Approved	APOBEC1L, PBI, bK150C2.3, ARDC2, ARDC4, ARP5	uc003awr.3	Q9NRW3	OTTHUMG00000151087	ENST00000361441.4:c.365G>A	22.37:g.39413961G>A	ENSP00000355340:p.Arg122His	Somatic		Capture	Illumina HiSeq	Phase_I	37743907	NM_014508	B2R884|Q5JZ92|Q7Z2N7|Q96F12	Missense_Mutation	SNP	ENST00000361441.4	37	CCDS13983.1	.	.	.	.	.	.	.	.	.	.	.	17.25	3.342785	0.61073	.	.	ENSG00000244509	ENST00000361441	T	0.66815	-0.23	2.01	2.01	0.26516	APOBEC-like, N-terminal (1);Cytidine deaminase-like (1);	.	.	.	.	T	0.80534	0.4641	M	0.87827	2.91	0.80722	D	1	D	0.76494	0.999	D	0.66979	0.948	T	0.82894	-0.0231	9	0.87932	D	0	.	10.1132	0.42574	0.0:0.0:1.0:0.0	.	122	Q9NRW3	ABC3C_HUMAN	H	122	ENSP00000355340:R122H	ENSP00000355340:R122H	R	+	2	0	APOBEC3C	37743907	1.000000	0.71417	0.527000	0.27925	0.087000	0.18053	4.205000	0.58466	1.450000	0.47717	0.479000	0.44913	CGC		0.587	APOBEC3C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321241.2	NM_014508	
CBX7	23492	broad.mit.edu	37	22	39534655	39534655	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr22:39534655G>A	ENST00000216133.5	-	4	437	c.232C>T	c.(232-234)Cgg>Tgg	p.R78W	CBX7_ENST00000401405.3_Missense_Mutation_p.R78W|CBX7_ENST00000475962.1_Intron	NM_175709.3	NP_783640.1	O95931	CBX7_HUMAN	chromobox homolog 7	78					chromatin modification (GO:0016568)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|sebaceous gland development (GO:0048733)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|heterochromatin (GO:0000792)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|PcG protein complex (GO:0031519)|PRC1 complex (GO:0035102)	chromatin binding (GO:0003682)|single-stranded RNA binding (GO:0003727)	p.R78W(1)		endometrium(1)|large_intestine(2)|lung(2)|ovary(1)|skin(1)	7	Melanoma(58;0.04)					AGCAGAAGCCGCTTGGGTTTC	0.582																																					p.R78W	GBM(46;845 904 3560 9866 23971)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C232T	22						.						182.0	152.0	162.0					22																	39534655		2203	4300	6503	37864601	SO:0001583	missense	23492	exon4				CCDS13986.1	22q13.1	2010-07-06			ENSG00000100307	ENSG00000100307			1557	protein-coding gene	gene with protein product		608457					Standard	NM_175709		Approved		uc003axb.3	O95931	OTTHUMG00000150418	ENST00000216133.5:c.232C>T	22.37:g.39534655G>A	ENSP00000216133:p.Arg78Trp	Somatic		Capture	Illumina HiSeq	Phase_I	37864601	NM_175709	Q86T17	Missense_Mutation	SNP	ENST00000216133.5	37	CCDS13986.1	.	.	.	.	.	.	.	.	.	.	G	21.6	4.166534	0.78339	.	.	ENSG00000100307	ENST00000216133;ENST00000401405;ENST00000434260	T;T;T	0.61980	0.06;0.06;0.06	4.79	4.79	0.61399	.	0.122470	0.53938	D	0.000049	T	0.73705	0.3621	L	0.47716	1.5	0.58432	D	0.999999	D;D	0.89917	1.0;1.0	D;D	0.69654	0.965;0.952	T	0.76719	-0.2856	10	0.72032	D	0.01	.	17.818	0.88640	0.0:0.0:1.0:0.0	.	78;78	B0QYP2;O95931	.;CBX7_HUMAN	W	78;78;56	ENSP00000216133:R78W;ENSP00000384035:R78W;ENSP00000410896:R56W	ENSP00000216133:R78W	R	-	1	2	CBX7	37864601	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.691000	0.61738	2.387000	0.81309	0.549000	0.68633	CGG		0.582	CBX7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318020.1	NM_175709	
TNRC6B	23112	broad.mit.edu	37	22	40657951	40657951	+	Silent	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr22:40657951C>T	ENST00000454349.2	+	4	442	c.231C>T	c.(229-231)aaC>aaT	p.N77N	TNRC6B_ENST00000301923.9_Silent_p.N113N|TNRC6B_ENST00000402203.1_Silent_p.N113N|TNRC6B_ENST00000335727.9_Silent_p.N77N	NM_001162501.1	NP_001155973.1	Q9UPQ9	TNR6B_HUMAN	trinucleotide repeat containing 6B	77	Interaction with argonaute proteins.				epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|gene expression (GO:0010467)|gene silencing by RNA (GO:0031047)|innate immune response (GO:0045087)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch signaling pathway (GO:0007219)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:1900153)|positive regulation of nuclear-transcribed mRNA poly(A) tail shortening (GO:0060213)|regulation of translation (GO:0006417)	cytosol (GO:0005829)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)	p.N91N(1)		breast(1)	1						CAGTGCCGAACGGACAACCGC	0.607																																					p.N77N												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C231T	22						.						20.0	25.0	24.0					22																	40657951		1978	4146	6124	38987897	SO:0001819	synonymous_variant	23112	exon4			AB029016	CCDS46712.1, CCDS46713.1, CCDS54533.1	22q13	2006-08-22			ENSG00000100354	ENSG00000100354		"""Trinucleotide (CAG) repeat containing"""	29190	protein-coding gene	gene with protein product		610740					Standard	NM_015088		Approved	KIAA1093	uc011aor.2	Q9UPQ9	OTTHUMG00000151114	ENST00000454349.2:c.231C>T	22.37:g.40657951C>T		Somatic		Capture	Illumina HiSeq	Phase_I	38987897	NM_015088	B0QY73|B0QY78|B4DGC0|Q5TH52|Q8TBX2	Silent	SNP	ENST00000454349.2	37	CCDS54533.1																																																																																				0.607	TNRC6B-202	KNOWN	basic|CCDS	protein_coding	protein_coding			
MKL1	57591	broad.mit.edu	37	22	40831511	40831511	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr22:40831511G>A	ENST00000355630.3	-	5	645	c.55C>T	c.(55-57)Cgg>Tgg	p.R19W	MKL1_ENST00000402042.1_Missense_Mutation_p.R19W|MKL1_ENST00000396617.3_Missense_Mutation_p.R19W|MKL1_ENST00000407029.1_Missense_Mutation_p.R19W|MKL1_ENST00000402630.1_Missense_Mutation_p.R19W	NM_020831.3	NP_065882.1	Q969V6	MKL1_HUMAN	megakaryoblastic leukemia (translocation) 1	19	Mediates interaction with SCAI and ACTB. {ECO:0000250}.				negative regulation of apoptotic signaling pathway (GO:2001234)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription via serum response element binding (GO:0010735)|smooth muscle cell differentiation (GO:0051145)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	actin binding (GO:0003779)|actin monomer binding (GO:0003785)|leucine zipper domain binding (GO:0043522)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription regulatory region sequence-specific DNA binding (GO:0000976)	p.R19W(3)		breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(3)|lung(13)|ovary(4)|skin(1)|stomach(1)|urinary_tract(1)	30						ACCCTGGCCCGCTCCAAGCTC	0.448			T	RBM15	acute megakaryocytic leukemia																																p.R19W			Dom	yes		22	22q13	57591	megakaryoblastic leukemia (translocation) 1		L	.	.	3	Substitution - Missense(3)	kidney(2)|large_intestine(1)	c.C55T	22						.						110.0	106.0	108.0					22																	40831511		2203	4300	6503	39161457	SO:0001583	missense	57591	exon5			AB037859	CCDS14003.1, CCDS74865.1, CCDS74866.1	22q13	2008-06-12			ENSG00000196588	ENSG00000196588			14334	protein-coding gene	gene with protein product	"""megakaryocytic acute leukemia"", ""myocardin-related transcription factor A"", ""basic, SAP and coiled-coil domain"""	606078				11431691, 12019265, 14970199	Standard	XM_005261692		Approved	KIAA1438, MAL, MRTF-A, BSAC	uc003ayw.1	Q969V6	OTTHUMG00000151146	ENST00000355630.3:c.55C>T	22.37:g.40831511G>A	ENSP00000347847:p.Arg19Trp	Somatic		Capture	Illumina HiSeq	Phase_I	39161457	NM_020831	Q8TCL1|Q96SC5|Q96SC6|Q9P2B0	Missense_Mutation	SNP	ENST00000355630.3	37	CCDS14003.1	.	.	.	.	.	.	.	.	.	.	G	20.6	4.016253	0.75161	.	.	ENSG00000196588	ENST00000355630;ENST00000396617;ENST00000402042;ENST00000407029;ENST00000402630;ENST00000422851	D;D;D;D;D;D	0.99859	-7.24;-7.24;-7.24;-7.24;-7.24;-7.24	5.18	5.18	0.71444	.	0.000000	0.85682	D	0.000000	D	0.99837	0.9926	M	0.84082	2.675	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.993;0.993	D	0.96485	0.9359	10	0.87932	D	0	-42.8267	13.9724	0.64250	0.0:0.0:0.8483:0.1516	.	19;19;19	B0QY83;E7ER32;Q969V6	.;.;MKL1_HUMAN	W	19;19;19;19;19;46	ENSP00000347847:R19W;ENSP00000379861:R19W;ENSP00000385584:R19W;ENSP00000385835:R19W;ENSP00000385076:R19W;ENSP00000398478:R46W	ENSP00000347847:R19W	R	-	1	2	MKL1	39161457	1.000000	0.71417	1.000000	0.80357	0.821000	0.46438	2.071000	0.41500	2.594000	0.87642	0.555000	0.69702	CGG		0.448	MKL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321522.1	NM_020831	
RANGAP1	5905	broad.mit.edu	37	22	41645346	41645346	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr22:41645346G>A	ENST00000455915.2	-	14	3151	c.1682C>T	c.(1681-1683)gCg>gTg	p.A561V	RANGAP1_ENST00000405486.1_Missense_Mutation_p.A561V|RANGAP1_ENST00000407260.4_Missense_Mutation_p.A506V|RANGAP1_ENST00000356244.3_Missense_Mutation_p.A561V			P46060	RAGP1_HUMAN	Ran GTPase activating protein 1	561					mitotic cell cycle (GO:0000278)|negative regulation of protein export from nucleus (GO:0046826)|positive regulation of Ran GTPase activity (GO:0032853)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|kinetochore (GO:0000776)|nuclear pore (GO:0005643)|perinuclear region of cytoplasm (GO:0048471)	Ran GTPase activator activity (GO:0005098)	p.A561V(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	19						GGTCACGAACGCCAGCAGCAG	0.642																																					p.A561V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1682T	22						.						66.0	54.0	58.0					22																	41645346		2203	4300	6503	39975292	SO:0001583	missense	5905	exon15			X82260	CCDS14012.1	22q13	2013-01-17			ENSG00000100401	ENSG00000100401			9854	protein-coding gene	gene with protein product		602362	"""segregation distorter homolog (Drosophila)"""	SD		7878053	Standard	NM_002883		Approved	Fug1, KIAA1835	uc003azu.3	P46060	OTTHUMG00000150940	ENST00000455915.2:c.1682C>T	22.37:g.41645346G>A	ENSP00000401470:p.Ala561Val	Somatic		Capture	Illumina HiSeq	Phase_I	39975292	NM_002883	Q96JJ2	Missense_Mutation	SNP	ENST00000455915.2	37	CCDS14012.1	.	.	.	.	.	.	.	.	.	.	G	20.7	4.034584	0.75617	.	.	ENSG00000100401	ENST00000405486;ENST00000356244;ENST00000405383;ENST00000455915;ENST00000407260	T;T;T;T	0.39787	1.06;1.06;1.06;1.06	5.4	5.4	0.78164	Ran-GTPase activating protein 1, C-terminal (3);	0.104899	0.64402	D	0.000005	T	0.58395	0.2119	L	0.53249	1.67	0.58432	D	0.999992	D;D	0.89917	0.999;1.0	P;P	0.61328	0.549;0.887	T	0.54450	-0.8292	10	0.38643	T	0.18	-14.1197	19.186	0.93644	0.0:0.0:1.0:0.0	.	506;561	F8W7I9;P46060	.;RAGP1_HUMAN	V	561;561;561;561;506	ENSP00000385866:A561V;ENSP00000348577:A561V;ENSP00000401470:A561V;ENSP00000385354:A506V	ENSP00000348577:A561V	A	-	2	0	RANGAP1	39975292	1.000000	0.71417	0.951000	0.38953	0.651000	0.38670	3.773000	0.55333	2.515000	0.84797	0.467000	0.42956	GCG		0.642	RANGAP1-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320606.1	NM_002883	
POLDIP3	84271	broad.mit.edu	37	22	42981828	42981828	+	Missense_Mutation	SNP	G	G	A	rs113566870	byFrequency	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr22:42981828G>A	ENST00000252115.5	-	9	1339	c.1235C>T	c.(1234-1236)aCg>aTg	p.T412M	POLDIP3_ENST00000339677.6_Intron|POLDIP3_ENST00000451060.2_3'UTR|POLDIP3_ENST00000491021.1_5'Flank|POLDIP3_ENST00000348657.2_Missense_Mutation_p.T383M	NM_032311.3	NP_115687.2	Q9BY77	PDIP3_HUMAN	polymerase (DNA-directed), delta interacting protein 3	412					poly(A)+ mRNA export from nucleus (GO:0016973)|positive regulation of translation (GO:0045727)	cytoplasm (GO:0005737)|nuclear speck (GO:0016607)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)	p.T412M(1)		biliary_tract(1)|endometrium(5)|kidney(1)|large_intestine(5)|lung(3)|upper_aerodigestive_tract(1)	16						TGTGGGCTGCGTGGTCACAGA	0.587																																					p.T383M	Ovarian(52;967 1128 5875 19997 42537)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1148T	22						.						116.0	116.0	116.0					22																	42981828		2203	4300	6503	41311772	SO:0001583	missense	84271	exon8				CCDS14038.1, CCDS14039.1, CCDS74873.1	22q13.31	2013-02-12			ENSG00000100227	ENSG00000100227		"""RNA binding motif (RRM) containing"""	23782	protein-coding gene	gene with protein product		611520				12522211	Standard	NM_032311		Approved	PDIP46, KIAA1649	uc003bcu.3	Q9BY77	OTTHUMG00000150887	ENST00000252115.5:c.1235C>T	22.37:g.42981828G>A	ENSP00000252115:p.Thr412Met	Somatic		Capture	Illumina HiSeq	Phase_I	41311772	NM_178136	A8K6F8|A8K6V9|Q009A7|Q5H972|Q6PGN6|Q7Z6Z0|Q9NSP5|Q9NSP6	Missense_Mutation	SNP	ENST00000252115.5	37	CCDS14038.1	.	.	.	.	.	.	.	.	.	.	G	23.2	4.385390	0.82792	.	.	ENSG00000100227	ENST00000348657;ENST00000252115	.	.	.	5.66	4.58	0.56647	.	0.299365	0.36444	N	0.002581	T	0.39572	0.1083	N	0.14661	0.345	0.80722	D	1	D;D;D	0.69078	0.99;0.997;0.99	P;P;P	0.58013	0.603;0.831;0.58	T	0.37454	-0.9705	9	0.59425	D	0.04	-15.526	3.7016	0.08384	0.3399:0.0:0.6601:0.0	.	429;383;412	B4E0L0;Q9BY77-2;Q9BY77	.;.;PDIP3_HUMAN	M	383;412	.	ENSP00000252115:T412M	T	-	2	0	POLDIP3	41311772	1.000000	0.71417	0.988000	0.46212	0.991000	0.79684	4.312000	0.59154	2.671000	0.90904	0.555000	0.69702	ACG		0.587	POLDIP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320433.1	NM_032311	
PACSIN2	11252	broad.mit.edu	37	22	43289531	43289531	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr22:43289531C>T	ENST00000263246.3	-	3	350	c.149G>A	c.(148-150)cGc>cAc	p.R50H	PACSIN2_ENST00000402229.1_Missense_Mutation_p.R50H|PACSIN2_ENST00000407585.1_Missense_Mutation_p.R50H|PACSIN2_ENST00000403744.3_Missense_Mutation_p.R50H|PACSIN2_ENST00000337959.4_Missense_Mutation_p.R50H	NM_001184970.1	NP_001171899.1	Q9UNF0	PACN2_HUMAN	protein kinase C and casein kinase substrate in neurons 2	50	F-BAR domain.|FCH. {ECO:0000255|PROSITE- ProRule:PRU00083}.				actin cytoskeleton organization (GO:0030036)|caveola assembly (GO:0070836)|caveolin-mediated endocytosis (GO:0072584)|cell projection morphogenesis (GO:0048858)|membrane tubulation (GO:0097320)|negative regulation of endocytosis (GO:0045806)|protein localization to endosome (GO:0036010)	caveola (GO:0005901)|cell projection (GO:0042995)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|focal adhesion (GO:0005925)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)|recycling endosome membrane (GO:0055038)	identical protein binding (GO:0042802)|phosphatidic acid binding (GO:0070300)|transporter activity (GO:0005215)	p.R50H(1)		NS(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(6)|lung(3)|prostate(2)|upper_aerodigestive_tract(1)	19		Glioma(61;0.222)				CTTCTCGATGCGCGCCCGCTC	0.647																																					p.R50H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G149A	22						.						38.0	43.0	42.0					22																	43289531		2173	4289	6462	41619475	SO:0001583	missense	11252	exon3			AF128536	CCDS43023.1, CCDS54536.1	22q13.2-q13.33	2009-05-08			ENSG00000100266	ENSG00000100266			8571	protein-coding gene	gene with protein product	"""syndapin II"""	604960				10431838, 11082044	Standard	NM_007229		Approved	SDPII	uc003bdg.4	Q9UNF0	OTTHUMG00000150701	ENST00000263246.3:c.149G>A	22.37:g.43289531C>T	ENSP00000263246:p.Arg50His	Somatic		Capture	Illumina HiSeq	Phase_I	41619475	NM_001184971	O95921|Q96HV9|Q9H0D3|Q9NPN1|Q9Y4V2	Missense_Mutation	SNP	ENST00000263246.3	37	CCDS43023.1	.	.	.	.	.	.	.	.	.	.	C	31	5.078841	0.94050	.	.	ENSG00000100266	ENST00000263246;ENST00000337959;ENST00000407585;ENST00000403744;ENST00000402229;ENST00000453643;ENST00000418133;ENST00000422336	T;T;T;T;T;T;T;T	0.43294	2.27;2.27;2.27;2.27;2.27;0.95;0.95;0.95	4.49	4.49	0.54785	Fps/Fes/Fer/CIP4 homology (3);	0.161948	0.56097	D	0.000031	T	0.49064	0.1535	L	0.39898	1.24	0.80722	D	1	P;D	0.63880	0.955;0.993	P;P	0.60949	0.799;0.881	T	0.33979	-0.9847	10	0.41790	T	0.15	0.0609	11.928	0.52831	0.0:0.9189:0.0:0.081	.	50;50	Q6FIA3;Q9UNF0	.;PACN2_HUMAN	H	50	ENSP00000263246:R50H;ENSP00000338379:R50H;ENSP00000385952:R50H;ENSP00000385372:R50H;ENSP00000385040:R50H;ENSP00000398573:R50H;ENSP00000396816:R50H;ENSP00000403435:R50H	ENSP00000263246:R50H	R	-	2	0	PACSIN2	41619475	0.864000	0.29904	0.998000	0.56505	0.925000	0.55904	1.590000	0.36654	2.784000	0.95788	0.551000	0.68910	CGC		0.647	PACSIN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319665.1	NM_007229	
KIAA0930	23313	broad.mit.edu	37	22	45601757	45601757	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr22:45601757G>A	ENST00000336156.5	-	3	318	c.253C>T	c.(253-255)Cgg>Tgg	p.R85W	KIAA0930_ENST00000251993.7_Missense_Mutation_p.R90W|KIAA0930_ENST00000391627.2_Missense_Mutation_p.R51W|KIAA0930_ENST00000443310.3_Missense_Mutation_p.R67W	NM_001009880.1	NP_001009880.1	Q6ICG6	K0930_HUMAN	KIAA0930	85								p.R90W(1)		endometrium(1)|kidney(4)|large_intestine(2)|lung(7)|urinary_tract(1)	15						TTGGAGTCCCGCCGGTACACC	0.627																																					p.R90W												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C268T	22						.						58.0	55.0	56.0					22																	45601757		2203	4300	6503	43980421	SO:0001583	missense	23313	exon3			AK025608	CCDS33665.1, CCDS33666.1	22q13.31	2011-02-23	2011-02-23	2011-02-23	ENSG00000100364	ENSG00000100364			1314	protein-coding gene	gene with protein product			"""chromosome 22 open reading frame 9"""	C22orf9		10231032	Standard	NM_015264		Approved	bK268H5.C22.1	uc003bfw.1	Q6ICG6	OTTHUMG00000151263	ENST00000336156.5:c.253C>T	22.37:g.45601757G>A	ENSP00000336720:p.Arg85Trp	Somatic		Capture	Illumina HiSeq	Phase_I	43980421	NM_015264	B0QY17|B0QY19|B3KT48|Q6ZVE5|Q7Z6K9|Q8IZ76|Q9Y2E2	Missense_Mutation	SNP	ENST00000336156.5	37	CCDS33665.1	.	.	.	.	.	.	.	.	.	.	G	24.2	4.499792	0.85176	.	.	ENSG00000100364	ENST00000336156;ENST00000251993;ENST00000391627;ENST00000443310;ENST00000414854;ENST00000424508	.	.	.	4.22	0.422	0.16457	.	0.156057	0.56097	D	0.000038	T	0.76033	0.3931	M	0.80332	2.49	0.58432	D	0.999994	D;D;D;D	0.76494	0.995;0.998;0.998;0.999	P;P;P;D	0.68765	0.879;0.907;0.903;0.96	T	0.78790	-0.2066	9	0.87932	D	0	-9.8678	12.4481	0.55662	0.0:0.0:0.2828:0.7172	.	67;85;90;156	B0AZU2;Q6ICG6;Q6ICG6-2;Q8IUY4	.;K0930_HUMAN;.;.	W	85;90;51;67;51;67	.	ENSP00000251993:R90W	R	-	1	2	KIAA0930	43980421	1.000000	0.71417	0.995000	0.50966	0.991000	0.79684	1.626000	0.37039	0.316000	0.23135	0.561000	0.74099	CGG		0.627	KIAA0930-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321975.2	NM_001009880	
ZBED4	9889	broad.mit.edu	37	22	50278253	50278253	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr22:50278253C>T	ENST00000216268.5	+	2	1420	c.943C>T	c.(943-945)Cgg>Tgg	p.R315W		NM_014838.2	NP_055653.2	O75132	ZBED4_HUMAN	zinc finger, BED-type containing 4	315						cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.R315W(1)		breast(2)|endometrium(3)|kidney(2)|large_intestine(11)|lung(20)|ovary(2)|skin(3)|upper_aerodigestive_tract(1)	44		all_cancers(38;8.58e-10)|all_epithelial(38;1.15e-08)|all_lung(38;0.000109)|Lung NSC(38;0.0018)|Breast(42;0.00191)|Ovarian(80;0.0164)|Lung SC(80;0.164)		UCEC - Uterine corpus endometrioid carcinoma (28;0.168)|BRCA - Breast invasive adenocarcinoma(115;0.2)|LUAD - Lung adenocarcinoma(64;0.247)		CGAGTTCAGCCGGGGGAAGAA	0.602																																					p.R315W												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C943T	22						.						81.0	85.0	83.0					22																	50278253		2203	4300	6503	48664257	SO:0001583	missense	9889	exon2			AB014537	CCDS33677.1	22q13.33	2013-05-03			ENSG00000100426	ENSG00000100426		"""Zinc fingers, BED-type"""	20721	protein-coding gene	gene with protein product		612552				23533661	Standard	NM_014838		Approved	KIAA0637	uc003bix.2	O75132	OTTHUMG00000150291	ENST00000216268.5:c.943C>T	22.37:g.50278253C>T	ENSP00000216268:p.Arg315Trp	Somatic		Capture	Illumina HiSeq	Phase_I	48664257	NM_014838	B2RZH1|Q1ECU0|Q9UGG8	Missense_Mutation	SNP	ENST00000216268.5	37	CCDS33677.1	.	.	.	.	.	.	.	.	.	.	C	14.87	2.665643	0.47677	.	.	ENSG00000100426	ENST00000216268	T	0.54479	0.57	5.41	-10.8	0.00216	Zinc finger, BED-type predicted (3);	0.000000	0.85682	D	0.000000	T	0.66587	0.2804	M	0.72894	2.215	0.29226	N	0.873627	D	0.89917	1.0	D	0.97110	1.0	T	0.81872	-0.0733	10	0.87932	D	0	-33.7528	22.3715	0.99970	0.8453:0.104:0.0:0.0507	.	315	O75132	ZBED4_HUMAN	W	315	ENSP00000216268:R315W	ENSP00000216268:R315W	R	+	1	2	ZBED4	48664257	0.013000	0.17824	0.002000	0.10522	0.637000	0.38172	-0.075000	0.11431	-2.923000	0.00303	-1.036000	0.02392	CGG		0.602	ZBED4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317408.2	NM_014838	
MLC1	23209	broad.mit.edu	37	22	50523256	50523256	+	Missense_Mutation	SNP	C	C	T	rs201522059	byFrequency	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr22:50523256C>T	ENST00000311597.5	-	2	682	c.76G>A	c.(76-78)Gcc>Acc	p.A26T	MLC1_ENST00000535444.1_Intron|MLC1_ENST00000431262.2_Missense_Mutation_p.A26T|MLC1_ENST00000538737.1_Missense_Mutation_p.A26T|MLC1_ENST00000395876.2_Missense_Mutation_p.A26T|MLC1_ENST00000450140.2_Missense_Mutation_p.A26T	NM_015166.3	NP_055981.1	Q15049	MLC1_HUMAN	megalencephalic leukoencephalopathy with subcortical cysts 1	26					caveolin-mediated endocytosis (GO:0072584)|cellular response to cholesterol (GO:0071397)|ion transport (GO:0006811)|positive regulation of intracellular transport (GO:0032388)|protein oligomerization (GO:0051259)|regulation of response to osmotic stress (GO:0047484)|transport (GO:0006810)|vesicle-mediated transport (GO:0016192)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|caveola (GO:0005901)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|early endosome (GO:0005769)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)|membrane raft (GO:0045121)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|recycling endosome (GO:0055037)	protein complex binding (GO:0032403)|protein transporter activity (GO:0008565)|transporter activity (GO:0005215)	p.A26T(1)		endometrium(1)|kidney(1)|large_intestine(5)|lung(7)|pancreas(1)|prostate(3)	18		all_cancers(38;7.69e-11)|all_epithelial(38;9.52e-10)|all_lung(38;3.67e-05)|Breast(42;0.000776)|Lung NSC(38;0.000946)|Ovarian(80;0.0365)|Lung SC(80;0.113)		READ - Rectum adenocarcinoma(2;0.000669)|Colorectal(2;0.00242)|LUAD - Lung adenocarcinoma(64;0.0695)|BRCA - Breast invasive adenocarcinoma(115;0.216)		GCATAGCTGGCGGGGTCTTGC	0.647													C|||	2	0.000399361	0.0008	0.0014	5008	,	,		14863	0.0		0.0	False		,,,				2504	0.0				p.A26T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G76A	22						.						44.0	42.0	43.0					22																	50523256		2203	4300	6503	48865383	SO:0001583	missense	23209	exon2			D25217	CCDS14083.1	22q13.33	2007-03-20			ENSG00000100427	ENSG00000100427			17082	protein-coding gene	gene with protein product		605908				7584026, 7584028	Standard	XR_430476		Approved	MLC, KIAA0027, LVM, VL	uc003bjg.1	Q15049	OTTHUMG00000150236	ENST00000311597.5:c.76G>A	22.37:g.50523256C>T	ENSP00000310375:p.Ala26Thr	Somatic		Capture	Illumina HiSeq	Phase_I	48865383	NM_015166	B3KW61|B7Z659|Q5JZ83|Q8TAG4|Q96RP5|Q9UGY8	Missense_Mutation	SNP	ENST00000311597.5	37	CCDS14083.1	2	9.157509157509158E-4	1	0.0020325203252032522	1	0.0027624309392265192	0	0.0	0	0.0	C	5.785	0.329184	0.10956	.	.	ENSG00000100427	ENST00000395876;ENST00000311597;ENST00000538737;ENST00000431262;ENST00000450140;ENST00000442311	D;D;D;D;D;D	0.91351	-2.83;-2.83;-2.83;-2.83;-2.83;-2.83	5.54	2.31	0.28768	.	0.626684	0.17646	N	0.166855	T	0.80859	0.4704	N	0.22421	0.69	0.22280	N	0.999232	B;B;B;B	0.10296	0.003;0.003;0.003;0.001	B;B;B;B	0.06405	0.002;0.002;0.002;0.002	T	0.65651	-0.6116	10	0.29301	T	0.29	-22.773	6.313	0.21174	0.0:0.6289:0.1475:0.2237	.	26;26;26;26	F5H1B9;B7Z659;B7Z1X1;Q15049	.;.;.;MLC1_HUMAN	T	26	ENSP00000379216:A26T;ENSP00000310375:A26T;ENSP00000445805:A26T;ENSP00000415877:A26T;ENSP00000412448:A26T;ENSP00000401385:A26T	ENSP00000310375:A26T	A	-	1	0	MLC1	48865383	0.001000	0.12720	0.000000	0.03702	0.007000	0.05969	1.547000	0.36190	0.306000	0.22856	-0.812000	0.03155	GCC		0.647	MLC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316979.2	NM_015166	
CPT1B	1375	broad.mit.edu	37	22	51012968	51012968	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr22:51012968G>A	ENST00000360719.2	-	8	976	c.839C>T	c.(838-840)gCc>gTc	p.A280V	CPT1B_ENST00000405237.3_Missense_Mutation_p.A280V|CPT1B_ENST00000434492.2_Missense_Mutation_p.A77V|CPT1B_ENST00000312108.7_Missense_Mutation_p.A280V|CPT1B_ENST00000457250.1_Missense_Mutation_p.A246V|CPT1B_ENST00000395650.2_Missense_Mutation_p.A280V|CHKB-CPT1B_ENST00000453634.1_3'UTR|CPT1B_ENST00000440709.1_Missense_Mutation_p.A280V	NM_001145135.1|NM_152245.2	NP_001138607.1|NP_689451.1	Q92523	CPT1B_HUMAN	carnitine palmitoyltransferase 1B (muscle)	280					carnitine shuttle (GO:0006853)|cellular lipid metabolic process (GO:0044255)|fatty acid beta-oxidation (GO:0006635)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)	carnitine O-palmitoyltransferase activity (GO:0004095)	p.A280V(1)		central_nervous_system(1)|endometrium(2)|large_intestine(5)|lung(7)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	22		all_cancers(38;8.8e-15)|all_epithelial(38;1.12e-12)|all_lung(38;3.07e-05)|Breast(42;6.27e-05)|Lung NSC(38;0.000813)|Ovarian(80;0.0221)|Hepatocellular(38;0.0691)|Lung SC(80;0.113)		all cancers(3;3.56e-77)|OV - Ovarian serous cystadenocarcinoma(4;5.39e-74)|Epithelial(4;5.58e-70)|GBM - Glioblastoma multiforme(4;5.59e-08)|LUAD - Lung adenocarcinoma(64;0.0016)|Lung(4;0.00942)|BRCA - Breast invasive adenocarcinoma(115;0.207)		CATGATCATGGCGTGGATGAT	0.577																																					p.A280V	Esophageal Squamous(170;988 1933 25577 30295 48163)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C839T	22						.						209.0	183.0	192.0					22																	51012968		2203	4300	6503	49359834	SO:0001583	missense	1375	exon8			U62733	CCDS14098.1, CCDS46734.1	22q13.33	2007-07-26			ENSG00000205560	ENSG00000205560			2329	protein-coding gene	gene with protein product		601987				9070950	Standard	NM_152245		Approved	M-CPT1, CPT1-M	uc003bmm.3	Q92523	OTTHUMG00000137390	ENST00000360719.2:c.839C>T	22.37:g.51012968G>A	ENSP00000353945:p.Ala280Val	Somatic		Capture	Illumina HiSeq	Phase_I	49359834	NM_152246	B7Z4U4|B7Z5T8|E9PCP2|Q13389|Q99655|Q9BY90	Missense_Mutation	SNP	ENST00000360719.2	37	CCDS14098.1	.	.	.	.	.	.	.	.	.	.	G	34	5.305901	0.95629	.	.	ENSG00000205560	ENST00000405237;ENST00000312108;ENST00000360719;ENST00000457250;ENST00000440709;ENST00000434492;ENST00000395650	D;D;D;D;D;D;D	0.90385	-2.66;-2.66;-2.66;-1.52;-2.66;-1.52;-2.66	4.81	4.81	0.61882	.	0.051727	0.85682	D	0.000000	D	0.96658	0.8909	H	0.95645	3.7	0.80722	D	1	D;P;D;D	0.89917	0.999;0.939;1.0;1.0	D;P;D;D	0.87578	0.998;0.864;0.99;0.992	D	0.97504	1.0062	10	0.66056	D	0.02	-16.0967	15.3912	0.74744	0.0:0.0:1.0:0.0	.	280;246;77;280	E9PCP2;B7Z4U4;A2RRE8;Q92523	.;.;.;CPT1B_HUMAN	V	280;280;280;246;280;77;280	ENSP00000385486:A280V;ENSP00000312189:A280V;ENSP00000353945:A280V;ENSP00000409342:A246V;ENSP00000414713:A280V;ENSP00000410966:A77V;ENSP00000379011:A280V	ENSP00000312189:A280V	A	-	2	0	CPT1B	49359834	1.000000	0.71417	0.941000	0.38009	0.930000	0.56654	9.059000	0.93902	2.503000	0.84419	0.561000	0.74099	GCC		0.577	CPT1B-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317264.5	NM_152246	
SHANK3	85358	broad.mit.edu	37	22	51117070	51117070	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr22:51117070C>T	ENST00000414786.2	+	4	624	c.397C>T	c.(397-399)Cgc>Tgc	p.R133C	SHANK3_ENST00000262795.3_Missense_Mutation_p.R133C|SHANK3_ENST00000445220.2_Missense_Mutation_p.R133C			Q9BYB0	SHAN3_HUMAN	SH3 and multiple ankyrin repeat domains 3	133					adult behavior (GO:0030534)|alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor clustering (GO:0097113)|brain morphogenesis (GO:0048854)|dendritic spine morphogenesis (GO:0060997)|guanylate kinase-associated protein clustering (GO:0097117)|learning (GO:0007612)|MAPK cascade (GO:0000165)|memory (GO:0007613)|N-methyl-D-aspartate receptor clustering (GO:0097114)|negative regulation of actin filament bundle assembly (GO:0032232)|negative regulation of cell volume (GO:0045794)|positive regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000969)|positive regulation of dendritic spine development (GO:0060999)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of glutamate receptor signaling pathway (GO:1900451)|positive regulation of long-term neuronal synaptic plasticity (GO:0048170)|positive regulation of synapse structural plasticity (GO:0051835)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|postsynaptic density assembly (GO:0097107)|regulation of dendritic spine morphogenesis (GO:0061001)|regulation of long term synaptic depression (GO:1900452)|regulation of long-term synaptic potentiation (GO:1900271)|social behavior (GO:0035176)|striatal medium spiny neuron differentiation (GO:0021773)|synapse assembly (GO:0007416)|vocal learning (GO:0042297)|vocalization behavior (GO:0071625)	cell junction (GO:0030054)|ciliary membrane (GO:0060170)|cytoplasm (GO:0005737)|neuron projection (GO:0043005)|neuron spine (GO:0044309)|neuronal postsynaptic density (GO:0097481)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	GKAP/Homer scaffold activity (GO:0030160)|identical protein binding (GO:0042802)|ionotropic glutamate receptor binding (GO:0035255)|protein C-terminus binding (GO:0008022)|scaffold protein binding (GO:0097110)|SH3 domain binding (GO:0017124)|zinc ion binding (GO:0008270)	p.R133C(1)		central_nervous_system(1)|endometrium(1)|kidney(1)|lung(5)	8		all_cancers(38;3.75e-11)|all_epithelial(38;1.82e-09)|Breast(42;0.000448)|all_lung(38;0.000665)|Lung NSC(38;0.0104)|Ovarian(80;0.104)|Lung SC(80;0.162)|Hepatocellular(38;0.178)		BRCA - Breast invasive adenocarcinoma(115;0.22)		CAAGGTGGCACGCCTGTTGGA	0.627																																					p.R133C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C397T	22						.						57.0	62.0	61.0					22																	51117070		2194	4296	6490	49463936	SO:0001583	missense	85358	exon4			AB051437		22q13.3	2013-11-14			ENSG00000251322	ENSG00000251322		"""Sterile alpha motif (SAM) domain containing"", ""Ankyrin repeat domain containing"""	14294	protein-coding gene	gene with protein product	"""proline rich synapse associated protein 2"", ""shank postsynaptic density protein"""	606230				11258795, 11431708, 10806096, 17173049	Standard	NM_033517		Approved	SPANK-2, prosap2, KIAA1650, PSAP2	uc031ryd.1	Q9BYB0	OTTHUMG00000150169	ENST00000414786.2:c.397C>T	22.37:g.51117070C>T	ENSP00000464552:p.Arg133Cys	Somatic		Capture	Illumina HiSeq	Phase_I	49463936	NM_001080420	D7UT47|Q8TET3	Missense_Mutation	SNP	ENST00000414786.2	37		.	.	.	.	.	.	.	.	.	.	C	19.70	3.876361	0.72180	.	.	ENSG00000251322	ENST00000262795;ENST00000445220	T;T	0.17854	2.25;2.25	4.83	3.74	0.42951	.	.	.	.	.	T	0.27098	0.0664	L	0.28400	0.85	0.33231	D	0.555882	D	0.89917	1.0	D	0.76071	0.987	T	0.25398	-1.0133	9	0.87932	D	0	.	9.6038	0.39622	0.3381:0.6619:0.0:0.0	.	133	F2Z3L0	.	C	133	ENSP00000442518:R133C;ENSP00000446078:R133C	ENSP00000442518:R133C	R	+	1	0	SHANK3	49463936	0.030000	0.19436	1.000000	0.80357	0.977000	0.68977	0.766000	0.26560	2.231000	0.72958	0.557000	0.71058	CGC		0.627	SHANK3-001	KNOWN	non_canonical_polymorphism|basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000316674.2	NM_001080420	
MN1	4330	broad.mit.edu	37	22	28196403	28196403	+	Frame_Shift_Del	DEL	C	C	-	rs369362515		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	-	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr22:28196403delC	ENST00000302326.4	-	1	1083	c.129delG	c.(127-129)gggfs	p.G43fs		NM_002430.2	NP_002421.3	Q10571	MN1_HUMAN	meningioma (disrupted in balanced translocation) 1	43					intramembranous ossification (GO:0001957)			p.P45fs*8(1)		NS(1)|breast(2)|central_nervous_system(3)|endometrium(4)|kidney(3)|large_intestine(6)|lung(15)|ovary(3)|prostate(4)|skin(3)|upper_aerodigestive_tract(1)	45						GGCCAGGGGGCCCCCCAGTGT	0.642			T	ETV6	"""AML, meningioma"""																																p.G43fs			Dom	yes		22	22q13	4330	meningioma (disrupted in balanced translocation) 1		"""L, O"""	.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.129delG	22						.						58.0	65.0	63.0					22																	28196403		1901	4106	6007	26526403	SO:0001589	frameshift_variant	4330	exon1			X82209	CCDS42998.1	22q12.1	2010-09-29			ENSG00000169184	ENSG00000169184			7180	protein-coding gene	gene with protein product	"""probable tumor suppressor protein MN1"""	156100	"""meningioma chromosome region"""	MGCR		7731706, 12569362	Standard	NM_002430		Approved	MGCR1-PEN, MGCR1	uc003adj.3	Q10571	OTTHUMG00000150975	ENST00000302326.4:c.129delG	22.37:g.28196403delC	ENSP00000304956:p.Gly43fs	Somatic		Capture	Illumina HiSeq	Phase_I	26526403	NM_002430	A9Z1V9	Frame_Shift_Del	DEL	ENST00000302326.4	37	CCDS42998.1																																																																																				0.642	MN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320737.1	NM_002430	
SHANK3	85358	broad.mit.edu	37	22	51117813	51117813	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr22:51117813C>T	ENST00000414786.2	+	7	1069	c.842C>T	c.(841-843)gCc>gTc	p.A281V	SHANK3_ENST00000262795.3_Missense_Mutation_p.A281V|SHANK3_ENST00000445220.2_Missense_Mutation_p.A281V			Q9BYB0	SHAN3_HUMAN	SH3 and multiple ankyrin repeat domains 3	281					adult behavior (GO:0030534)|alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor clustering (GO:0097113)|brain morphogenesis (GO:0048854)|dendritic spine morphogenesis (GO:0060997)|guanylate kinase-associated protein clustering (GO:0097117)|learning (GO:0007612)|MAPK cascade (GO:0000165)|memory (GO:0007613)|N-methyl-D-aspartate receptor clustering (GO:0097114)|negative regulation of actin filament bundle assembly (GO:0032232)|negative regulation of cell volume (GO:0045794)|positive regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000969)|positive regulation of dendritic spine development (GO:0060999)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of glutamate receptor signaling pathway (GO:1900451)|positive regulation of long-term neuronal synaptic plasticity (GO:0048170)|positive regulation of synapse structural plasticity (GO:0051835)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|postsynaptic density assembly (GO:0097107)|regulation of dendritic spine morphogenesis (GO:0061001)|regulation of long term synaptic depression (GO:1900452)|regulation of long-term synaptic potentiation (GO:1900271)|social behavior (GO:0035176)|striatal medium spiny neuron differentiation (GO:0021773)|synapse assembly (GO:0007416)|vocal learning (GO:0042297)|vocalization behavior (GO:0071625)	cell junction (GO:0030054)|ciliary membrane (GO:0060170)|cytoplasm (GO:0005737)|neuron projection (GO:0043005)|neuron spine (GO:0044309)|neuronal postsynaptic density (GO:0097481)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	GKAP/Homer scaffold activity (GO:0030160)|identical protein binding (GO:0042802)|ionotropic glutamate receptor binding (GO:0035255)|protein C-terminus binding (GO:0008022)|scaffold protein binding (GO:0097110)|SH3 domain binding (GO:0017124)|zinc ion binding (GO:0008270)	p.A281V(1)		central_nervous_system(1)|endometrium(1)|kidney(1)|lung(5)	8		all_cancers(38;3.75e-11)|all_epithelial(38;1.82e-09)|Breast(42;0.000448)|all_lung(38;0.000665)|Lung NSC(38;0.0104)|Ovarian(80;0.104)|Lung SC(80;0.162)|Hepatocellular(38;0.178)		BRCA - Breast invasive adenocarcinoma(115;0.22)		GCCCAGAACGCCTCGGGGAAC	0.612																																					p.A281V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C842T	22						.						44.0	53.0	50.0					22																	51117813		2195	4295	6490	49464679	SO:0001583	missense	85358	exon7			AB051437		22q13.3	2013-11-14			ENSG00000251322	ENSG00000251322		"""Sterile alpha motif (SAM) domain containing"", ""Ankyrin repeat domain containing"""	14294	protein-coding gene	gene with protein product	"""proline rich synapse associated protein 2"", ""shank postsynaptic density protein"""	606230				11258795, 11431708, 10806096, 17173049	Standard	NM_033517		Approved	SPANK-2, prosap2, KIAA1650, PSAP2	uc031ryd.1	Q9BYB0	OTTHUMG00000150169	ENST00000414786.2:c.842C>T	22.37:g.51117813C>T	ENSP00000464552:p.Ala281Val	Somatic		Capture	Illumina HiSeq	Phase_I	49464679	NM_001080420	D7UT47|Q8TET3	Missense_Mutation	SNP	ENST00000414786.2	37		.	.	.	.	.	.	.	.	.	.	C	28.8	4.955685	0.92726	.	.	ENSG00000251322	ENST00000262795;ENST00000445220	T;T	0.65549	-0.16;-0.16	5.34	5.34	0.76211	.	.	.	.	.	T	0.67804	0.2932	N	0.20304	0.555	0.37434	D	0.914156	D	0.76494	0.999	D	0.77004	0.989	T	0.75491	-0.3299	9	0.87932	D	0	.	16.5572	0.84488	0.0:1.0:0.0:0.0	.	281	F2Z3L0	.	V	281	ENSP00000442518:A281V;ENSP00000446078:A281V	ENSP00000442518:A281V	A	+	2	0	SHANK3	49464679	1.000000	0.71417	0.998000	0.56505	0.877000	0.50540	5.900000	0.69853	2.500000	0.84329	0.651000	0.88453	GCC		0.612	SHANK3-001	KNOWN	non_canonical_polymorphism|basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000316674.2	NM_001080420	
NPAS2	4862	broad.mit.edu	37	2	101594247	101594247	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr2:101594247G>A	ENST00000335681.5	+	15	1753	c.1468G>A	c.(1468-1470)Gct>Act	p.A490T	AC016738.3_ENST00000446644.1_RNA|AC016738.3_ENST00000439150.1_RNA|AC016738.3_ENST00000433012.1_RNA|NPAS2_ENST00000542504.1_Missense_Mutation_p.A555T	NM_002518.3	NP_002509.2	Q99743	NPAS2_HUMAN	neuronal PAS domain protein 2	490					cellular lipid metabolic process (GO:0044255)|cellular response to DNA damage stimulus (GO:0006974)|central nervous system development (GO:0007417)|circadian regulation of gene expression (GO:0032922)|circadian sleep/wake cycle (GO:0042745)|locomotor rhythm (GO:0045475)|negative regulation of cell death (GO:0060548)|positive regulation of DNA repair (GO:0045739)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of response to DNA damage stimulus (GO:2001020)|response to redox state (GO:0051775)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	cytosol (GO:0005829)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	core promoter binding (GO:0001047)|DNA binding (GO:0003677)|Hsp90 protein binding (GO:0051879)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)	p.A490T(1)		cervix(1)|endometrium(3)|large_intestine(7)|lung(9)|ovary(3)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29						GAGCACGCCCGCTCCCATGGC	0.617																																					p.A490T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1468A	2						.						80.0	79.0	79.0					2																	101594247		2203	4300	6503	100960679	SO:0001583	missense	4862	exon15			U77970	CCDS2048.1	2q11.2	2013-05-21			ENSG00000170485	ENSG00000170485		"""Basic helix-loop-helix proteins"""	7895	protein-coding gene	gene with protein product		603347				9012850, 9079689	Standard	NM_002518		Approved	MOP4, PASD4, bHLHe9	uc002tap.1	Q99743	OTTHUMG00000130675	ENST00000335681.5:c.1468G>A	2.37:g.101594247G>A	ENSP00000338283:p.Ala490Thr	Somatic		Capture	Illumina HiSeq	Phase_I	100960679	NM_002518	Q4ZFV9|Q53SQ3|Q86V96|Q99629	Missense_Mutation	SNP	ENST00000335681.5	37	CCDS2048.1	.	.	.	.	.	.	.	.	.	.	G	4.875	0.162667	0.09287	.	.	ENSG00000170485	ENST00000335681;ENST00000542504;ENST00000450763	T;T;T	0.31510	3.52;3.5;1.49	5.69	-0.362	0.12560	.	1.904440	0.02606	N	0.101579	T	0.30634	0.0771	L	0.57536	1.79	0.09310	N	1	B;B;B	0.26363	0.147;0.002;0.018	B;B;B	0.20767	0.031;0.001;0.005	T	0.23511	-1.0186	10	0.20046	T	0.44	.	10.005	0.41951	0.4527:0.0:0.5473:0.0	.	555;490;490	F5H027;A0PJF9;Q99743	.;.;NPAS2_HUMAN	T	490;555;89	ENSP00000338283:A490T;ENSP00000438428:A555T;ENSP00000392125:A89T	ENSP00000338283:A490T	A	+	1	0	NPAS2	100960679	0.087000	0.21565	0.002000	0.10522	0.061000	0.15899	0.781000	0.26774	-0.013000	0.14199	-0.768000	0.03414	GCT		0.617	NPAS2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253168.3		
ODC1	4953	broad.mit.edu	37	2	10581946	10581946	+	Silent	SNP	T	T	C			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr2:10581946T>C	ENST00000234111.4	-	10	1533	c.1023A>G	c.(1021-1023)caA>caG	p.Q341Q	ODC1_ENST00000446285.1_5'Flank|ODC1_ENST00000405333.1_Silent_p.Q341Q	NM_002539.1	NP_002530.1	P11926	DCOR_HUMAN	ornithine decarboxylase 1	341					cellular nitrogen compound metabolic process (GO:0034641)|kidney development (GO:0001822)|polyamine metabolic process (GO:0006595)|positive regulation of cell proliferation (GO:0008284)|putrescine biosynthetic process from ornithine (GO:0033387)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of protein catabolic process (GO:0042176)|response to virus (GO:0009615)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)	ornithine decarboxylase activity (GO:0004586)|protein homodimerization activity (GO:0042803)	p.Q341Q(1)		NS(1)|central_nervous_system(1)|large_intestine(7)|lung(5)|ovary(1)|prostate(1)|skin(3)	19	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.11)|OV - Ovarian serous cystadenocarcinoma(76;0.161)	Spermine(DB00127)	AAATTACCTTTTGCAGAAGGG	0.388																																					p.Q341Q												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.A1023G	2						.						128.0	130.0	130.0					2																	10581946		2203	4300	6503	10499397	SO:0001819	synonymous_variant	4953	exon10				CCDS1672.1	2p25	2012-10-02			ENSG00000115758	ENSG00000115758	4.1.1.17		8109	protein-coding gene	gene with protein product		165640					Standard	NM_002539		Approved	ODC	uc002rao.1	P11926	OTTHUMG00000090450	ENST00000234111.4:c.1023A>G	2.37:g.10581946T>C		Somatic		Capture	Illumina HiSeq	Phase_I	10499397	NM_002539	Q53TU3|Q6LDS9	Silent	SNP	ENST00000234111.4	37	CCDS1672.1																																																																																				0.388	ODC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206896.2		
TBC1D8	11138	broad.mit.edu	37	2	101650217	101650217	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr2:101650217G>A	ENST00000376840.4	-	10	1561	c.1562C>T	c.(1561-1563)gCg>gTg	p.A521V	TBC1D8_ENST00000409318.1_Missense_Mutation_p.A536V			O95759	TBCD8_HUMAN	TBC1 domain family, member 8 (with GRAM domain)	521	Rab-GAP TBC. {ECO:0000255|PROSITE- ProRule:PRU00163}.				blood circulation (GO:0008015)|positive regulation of cell proliferation (GO:0008284)	membrane (GO:0016020)	calcium ion binding (GO:0005509)|Rab GTPase activator activity (GO:0005097)	p.A521V(1)		breast(1)|cervix(1)|endometrium(8)|kidney(3)|large_intestine(2)|lung(12)|ovary(3)|prostate(1)|upper_aerodigestive_tract(1)	32						ATCCGTCACCGCATCTGAGTT	0.522																																					p.A521V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1562T	2						.						55.0	60.0	59.0					2																	101650217		2141	4272	6413	101016649	SO:0001583	missense	11138	exon10			AB024057	CCDS46375.1	2q12.1	2011-11-30			ENSG00000204634	ENSG00000204634			17791	protein-coding gene	gene with protein product	"""BUB2-like protein 1"", ""vascular Rab-GAP/TBC-containing protein"""					10373574	Standard	NM_001102426		Approved	HBLP1, VRP, AD3	uc010fiv.3	O95759	OTTHUMG00000153040	ENST00000376840.4:c.1562C>T	2.37:g.101650217G>A	ENSP00000366036:p.Ala521Val	Somatic		Capture	Illumina HiSeq	Phase_I	101016649	NM_001102426	A6NDL4|A8K9W1|B9A6K4|Q53SQ4|Q9UQ32	Missense_Mutation	SNP	ENST00000376840.4	37	CCDS46375.1	.	.	.	.	.	.	.	.	.	.	G	18.92	3.726322	0.69074	.	.	ENSG00000204634	ENST00000376840;ENST00000409318	T;T	0.03889	3.77;3.77	4.97	4.97	0.65823	Rab-GAP/TBC domain (4);	0.000000	0.64402	D	0.000015	T	0.23886	0.0578	M	0.77486	2.375	0.80722	D	1	D;D	0.89917	0.999;1.0	D;D	0.97110	0.987;1.0	T	0.01316	-1.1387	10	0.87932	D	0	-17.9327	18.2557	0.90019	0.0:0.0:1.0:0.0	.	536;521	B7Z6L4;O95759	.;TBCD8_HUMAN	V	521;536	ENSP00000366036:A521V;ENSP00000386856:A536V	ENSP00000366036:A521V	A	-	2	0	TBC1D8	101016649	1.000000	0.71417	0.948000	0.38648	0.084000	0.17831	9.553000	0.98118	2.295000	0.77249	0.655000	0.94253	GCG		0.522	TBC1D8-011	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376092.1	NM_007063	
GPR45	11250	broad.mit.edu	37	2	105859199	105859199	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr2:105859199G>A	ENST00000258456.1	+	1	1000	c.884G>A	c.(883-885)cGc>cAc	p.R295H		NM_007227.3	NP_009158.3	Q9Y5Y3	GPR45_HUMAN	G protein-coupled receptor 45	295						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)	p.R295H(1)		breast(1)|central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(8)|lung(10)|ovary(1)|prostate(1)|stomach(1)|urinary_tract(1)	28						TTTAGCCAGCGCTTTTACTGC	0.572																																					p.R295H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G884A	2						.						168.0	161.0	164.0					2																	105859199		2203	4300	6503	105225631	SO:0001583	missense	11250	exon1			AF118266	CCDS2066.1	2q11.1-q12	2012-08-21			ENSG00000135973	ENSG00000135973		"""GPCR / Class A : Orphans"""	4503	protein-coding gene	gene with protein product		604838				10036181	Standard	NM_007227		Approved	PSP24, PSP24A	uc002tco.1	Q9Y5Y3	OTTHUMG00000130805	ENST00000258456.1:c.884G>A	2.37:g.105859199G>A	ENSP00000258456:p.Arg295His	Somatic		Capture	Illumina HiSeq	Phase_I	105225631	NM_007227	Q6NWS4|Q6NXU6	Missense_Mutation	SNP	ENST00000258456.1	37	CCDS2066.1	.	.	.	.	.	.	.	.	.	.	G	4.376	0.069273	0.08436	.	.	ENSG00000135973	ENST00000258456	T	0.71934	-0.61	4.25	2.41	0.29592	GPCR, rhodopsin-like superfamily (1);	0.680368	0.12699	N	0.446515	T	0.43590	0.1254	N	0.04355	-0.22	0.09310	N	1	B	0.15719	0.014	B	0.12156	0.007	T	0.24905	-1.0147	10	0.36615	T	0.2	-4.9186	4.5406	0.12056	0.159:0.4488:0.3922:0.0	.	295	Q9Y5Y3	GPR45_HUMAN	H	295	ENSP00000258456:R295H	ENSP00000258456:R295H	R	+	2	0	GPR45	105225631	0.000000	0.05858	0.092000	0.20876	0.629000	0.37895	0.514000	0.22786	1.127000	0.42034	0.462000	0.41574	CGC		0.572	GPR45-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253348.1	NM_007227	
UXS1	80146	broad.mit.edu	37	2	106761671	106761671	+	Silent	SNP	G	G	A	rs375468394		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr2:106761671G>A	ENST00000409501.3	-	6	489	c.432C>T	c.(430-432)gaC>gaT	p.D144D	UXS1_ENST00000428048.2_Intron|UXS1_ENST00000540130.1_Silent_p.D87D|UXS1_ENST00000283148.7_Silent_p.D149D|UXS1_ENST00000479621.1_5'UTR			Q8NBZ7	UXS1_HUMAN	UDP-glucuronate decarboxylase 1	144					protein tetramerization (GO:0051262)|UDP-D-xylose biosynthetic process (GO:0033320)	extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)	NAD+ binding (GO:0070403)|protein homodimerization activity (GO:0042803)|UDP-glucuronate decarboxylase activity (GO:0048040)	p.D144D(1)		cervix(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(7)|ovary(2)	17						GCTCCACCACGTCGTGGTTAA	0.547																																					p.D144D												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C432T	2						.	G		0,3934		0,0,1967	88.0	87.0	87.0		432	-7.2	0.8	2		87	1,8263		0,1,4131	no	coding-synonymous	UXS1	NM_025076.3		0,1,6098	AA,AG,GG		0.0121,0.0,0.0082		144/421	106761671	1,12197	1967	4132	6099	106128103	SO:0001819	synonymous_variant	80146	exon6			AK027244	CCDS46378.1, CCDS58720.1, CCDS58721.1	2q12.2	2012-02-22			ENSG00000115652	ENSG00000115652	4.1.1.35	"""Short chain dehydrogenase/reductase superfamily / Extended SDR fold"""	17729	protein-coding gene	gene with protein product	"""short chain dehydrogenase/reductase family 6E, member 12"""	609749				19027726	Standard	NM_001253875		Approved	FLJ23591, UGD, SDR6E1	uc002tdn.3	Q8NBZ7	OTTHUMG00000153150	ENST00000409501.3:c.432C>T	2.37:g.106761671G>A		Somatic		Capture	Illumina HiSeq	Phase_I	106128103	NM_025076	Q8NBX3|Q9H5C2	Silent	SNP	ENST00000409501.3	37	CCDS46378.1																																																																																				0.547	UXS1-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000329778.1	NM_025076.3	
RANBP2	5903	broad.mit.edu	37	2	109383653	109383653	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr2:109383653C>T	ENST00000283195.6	+	20	6784	c.6658C>T	c.(6658-6660)Ccc>Tcc	p.P2220S		NM_006267.4	NP_006258.3	P49792	RBP2_HUMAN	RAN binding protein 2	2220					carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|negative regulation of glucokinase activity (GO:0033132)|protein folding (GO:0006457)|protein import into nucleus (GO:0006606)|protein sumoylation (GO:0016925)|regulation of gluconeogenesis involved in cellular glucose homeostasis (GO:0090526)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytosol (GO:0005829)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nuclear inclusion body (GO:0042405)|nuclear membrane (GO:0031965)|nuclear pore (GO:0005643)|nuclear pore nuclear basket (GO:0044615)	ligase activity (GO:0016874)|peptidyl-prolyl cis-trans isomerase activity (GO:0003755)|Ran GTPase binding (GO:0008536)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)	p.P2220S(2)	RANBP2/ALK(34)	NS(1)|biliary_tract(1)|breast(3)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(21)|large_intestine(19)|lung(51)|pancreas(1)|prostate(8)|skin(7)|upper_aerodigestive_tract(2)|urinary_tract(1)	129						AAACACTGGGCCCACATTAGA	0.443																																					p.P2220S												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.C6658T	2						.						61.0	67.0	65.0					2																	109383653		2200	4290	6490	108750085	SO:0001583	missense	5903	exon20			D42063	CCDS2079.1	2q13	2013-11-14			ENSG00000153201	ENSG00000153201		"""Tetratricopeptide (TTC) repeat domain containing"""	9848	protein-coding gene	gene with protein product		601181	"""acute necrotizing encephalopathy 1 (autosomal dominant)"""	ANE1		7724562, 19118815	Standard	NM_006267		Approved	NUP358, ADANE	uc002tem.4	P49792	OTTHUMG00000130981	ENST00000283195.6:c.6658C>T	2.37:g.109383653C>T	ENSP00000283195:p.Pro2220Ser	Somatic		Capture	Illumina HiSeq	Phase_I	108750085	NM_006267	Q13074|Q15280|Q53TE2|Q59FH7	Missense_Mutation	SNP	ENST00000283195.6	37	CCDS2079.1	.	.	.	.	.	.	.	.	.	.	C	14.68	2.607677	0.46527	.	.	ENSG00000153201	ENST00000409491;ENST00000283195	T	0.33865	1.39	5.4	4.52	0.55395	.	.	.	.	.	T	0.45337	0.1337	L	0.32530	0.975	0.36268	D	0.854998	D	0.65815	0.995	P	0.59424	0.857	T	0.56860	-0.7909	9	0.56958	D	0.05	-3.4708	15.2179	0.73285	0.1418:0.8581:0.0:0.0	.	2220	P49792	RBP2_HUMAN	S	1244;2220	ENSP00000283195:P2220S	ENSP00000283195:P2220S	P	+	1	0	RANBP2	108750085	1.000000	0.71417	0.853000	0.33588	0.772000	0.43724	3.883000	0.56168	1.265000	0.44215	0.455000	0.32223	CCC		0.443	RANBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253594.1	NM_006267	
SH3RF3	344558	broad.mit.edu	37	2	109964226	109964226	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr2:109964226C>T	ENST00000309415.6	+	2	670	c.670C>T	c.(670-672)Cgg>Tgg	p.R224W		NM_001099289.1	NP_001092759.1	Q8TEJ3	SH3R3_HUMAN	SH3 domain containing ring finger 3	224	SH3 1. {ECO:0000255|PROSITE- ProRule:PRU00192}.						zinc ion binding (GO:0008270)	p.R224W(1)		endometrium(2)|kidney(1)|large_intestine(6)|liver(2)|lung(5)|ovary(2)	18						CATCGTCCTGCGGCGCAAGGT	0.602																																					p.R224W												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C670T	2						.						63.0	68.0	66.0					2																	109964226		2157	4253	6410	109330658	SO:0001583	missense	344558	exon2			AK074131	CCDS74557.1	2q13	2013-01-11	2008-05-14	2008-05-14	ENSG00000172985	ENSG00000172985		"""RING-type (C3HC4) zinc fingers"""	24699	protein-coding gene	gene with protein product			"""SH3 multiple domains 4"""	SH3MD4		16374509	Standard	XM_006712493		Approved	FLJ00204, POSH2	uc010ywt.1	Q8TEJ3	OTTHUMG00000153439	ENST00000309415.6:c.670C>T	2.37:g.109964226C>T	ENSP00000309186:p.Arg224Trp	Somatic		Capture	Illumina HiSeq	Phase_I	109330658	NM_001099289	A0SDZ7|A8MPR1|Q8NDU1	Missense_Mutation	SNP	ENST00000309415.6	37		.	.	.	.	.	.	.	.	.	.	C	18.16	3.561461	0.65538	.	.	ENSG00000172985	ENST00000418513;ENST00000309415	T;T	0.30182	1.54;1.54	5.07	3.18	0.36537	Src homology-3 domain (4);	.	.	.	.	T	0.52613	0.1745	.	.	.	0.48975	D	0.999734	D	0.76494	0.999	D	0.70487	0.969	T	0.51340	-0.8718	8	0.42905	T	0.14	.	13.5303	0.61617	0.2932:0.7068:0.0:0.0	.	224	Q8TEJ3	SH3R3_HUMAN	W	224	ENSP00000414997:R224W;ENSP00000309186:R224W	ENSP00000309186:R224W	R	+	1	2	SH3RF3	109330658	1.000000	0.71417	0.839000	0.33178	0.519000	0.34347	2.627000	0.46469	0.456000	0.26937	0.484000	0.47621	CGG		0.602	SH3RF3-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_001099289	
POLR1B	84172	broad.mit.edu	37	2	113332592	113332592	+	Silent	SNP	G	G	A	rs149946383	byFrequency	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr2:113332592G>A	ENST00000263331.5	+	15	3274	c.2694G>A	c.(2692-2694)ccG>ccA	p.P898P	POLR1B_ENST00000537335.1_Silent_p.P687P|POLR1B_ENST00000541869.1_Silent_p.P936P|POLR1B_ENST00000409894.3_Silent_p.P715P|POLR1B_ENST00000417433.2_Silent_p.P842P	NM_019014.4	NP_061887.2	Q9H9Y6	RPA2_HUMAN	polymerase (RNA) I polypeptide B, 128kDa	898					gene expression (GO:0010467)|termination of RNA polymerase I transcription (GO:0006363)|transcription elongation from RNA polymerase I promoter (GO:0006362)|transcription from RNA polymerase I promoter (GO:0006360)|transcription initiation from RNA polymerase I promoter (GO:0006361)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|DNA-directed RNA polymerase activity (GO:0003899)|metal ion binding (GO:0046872)|ribonucleoside binding (GO:0032549)	p.P898P(1)		breast(3)|endometrium(9)|kidney(2)|large_intestine(9)|lung(14)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	42						GATTGTGGCCGGCTGAGGACA	0.488													G|||	2	0.000399361	0.0	0.0	5008	,	,		18652	0.0		0.001	False		,,,				2504	0.001				p.P842P	Ovarian(16;256 576 9537 23969 41147)											.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G2526A	2						.	G	,	0,4406		0,0,2203	134.0	132.0	133.0		2526,2694	-11.8	0.0	2	dbSNP_134	133	4,8596	3.7+/-12.6	0,4,4296	no	coding-synonymous,coding-synonymous	POLR1B	NM_001137604.1,NM_019014.4	,	0,4,6499	AA,AG,GG		0.0465,0.0,0.0308	,	842/1080,898/1136	113332592	4,13002	2203	4300	6503	113049063	SO:0001819	synonymous_variant	84172	exon14			AK001678	CCDS2097.1, CCDS46395.1, CCDS62988.1, CCDS62989.1, CCDS62990.1	2q13	2013-01-21			ENSG00000125630	ENSG00000125630		"""RNA polymerase subunits"""	20454	protein-coding gene	gene with protein product		602000					Standard	NM_001137604		Approved	Rpo1-2, FLJ21921, FLJ10816, RPA2	uc002thw.2	Q9H9Y6	OTTHUMG00000131314	ENST00000263331.5:c.2694G>A	2.37:g.113332592G>A		Somatic		Capture	Illumina HiSeq	Phase_I	113049063	NM_001137604	B7Z6Y7|B7Z823|F5GZX4|F8W898|Q2TAM4|Q585T5|Q6ZRR2|Q9H9D3	Silent	SNP	ENST00000263331.5	37	CCDS2097.1																																																																																				0.488	POLR1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254083.1	NM_019014	
PSD4	23550	broad.mit.edu	37	2	113950879	113950879	+	Missense_Mutation	SNP	G	G	A	rs149806578		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr2:113950879G>A	ENST00000245796.6	+	8	2159	c.1964G>A	c.(1963-1965)cGg>cAg	p.R655Q	PSD4_ENST00000441564.3_Missense_Mutation_p.R627Q	NM_012455.2	NP_036587.2	Q8NDX1	PSD4_HUMAN	pleckstrin and Sec7 domain containing 4	655	SEC7. {ECO:0000255|PROSITE- ProRule:PRU00189}.				neuron differentiation (GO:0030182)|positive regulation of GTPase activity (GO:0043547)|regulation of ARF protein signal transduction (GO:0032012)	cell junction (GO:0030054)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)|phospholipid binding (GO:0005543)	p.R655Q(1)		cervix(1)|endometrium(2)|large_intestine(4)|lung(13)|ovary(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29						ACTCAGGAACGGGAGCGAATC	0.602																																					p.R655Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1964A	2						.						66.0	70.0	69.0					2																	113950879		2203	4300	6503	113667350	SO:0001583	missense	23550	exon8			U63127	CCDS33276.1	2q13	2013-01-10			ENSG00000125637	ENSG00000125637		"""Pleckstrin homology (PH) domain containing"""	19096	protein-coding gene	gene with protein product		614442				12082148	Standard	XM_005263634		Approved	TIC, EFA6B	uc002tjc.3	Q8NDX1	OTTHUMG00000153339	ENST00000245796.6:c.1964G>A	2.37:g.113950879G>A	ENSP00000245796:p.Arg655Gln	Somatic		Capture	Illumina HiSeq	Phase_I	113667350	NM_012455	A6NEG7|A8K1Y0|O95621|Q4ZG34|Q6GPH8|Q8IYP4	Missense_Mutation	SNP	ENST00000245796.6	37	CCDS33276.1	.	.	.	.	.	.	.	.	.	.	G	35	5.516906	0.96416	.	.	ENSG00000125637	ENST00000245796;ENST00000441564	T;T	0.54675	0.56;0.56	5.28	5.28	0.74379	SEC7-like, alpha orthogonal bundle (1);SEC7-like (4);	0.000000	0.85682	D	0.000000	T	0.77928	0.4204	M	0.90542	3.125	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.87578	0.998;0.996;0.998	T	0.82912	-0.0222	10	0.87932	D	0	.	16.4071	0.83684	0.0:0.0:1.0:0.0	.	313;627;655	Q59HG0;Q8NDX1-2;Q8NDX1	.;.;PSD4_HUMAN	Q	655;627	ENSP00000245796:R655Q;ENSP00000413997:R627Q	ENSP00000245796:R655Q	R	+	2	0	PSD4	113667350	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	8.506000	0.90518	2.481000	0.83766	0.655000	0.94253	CGG		0.602	PSD4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000330789.1	NM_012455	
ACTR3	10096	broad.mit.edu	37	2	114709344	114709344	+	Silent	SNP	T	T	C			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr2:114709344T>C	ENST00000263238.2	+	10	1319	c.999T>C	c.(997-999)cgT>cgC	p.R333R	ACTR3_ENST00000535589.2_Silent_p.R282R|ACTR3_ENST00000536059.1_Silent_p.R271R	NM_001277140.1|NM_005721.3	NP_001264069.1|NP_005712.1	P61158	ARP3_HUMAN	ARP3 actin-related protein 3 homolog (yeast)	333					Arp2/3 complex-mediated actin nucleation (GO:0034314)|asymmetric cell division (GO:0008356)|cellular component movement (GO:0006928)|cilium morphogenesis (GO:0060271)|establishment or maintenance of cell polarity (GO:0007163)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|meiotic chromosome movement towards spindle pole (GO:0016344)|meiotic cytokinesis (GO:0033206)|positive regulation of dendrite morphogenesis (GO:0050775)|positive regulation of filopodium assembly (GO:0051491)|positive regulation of lamellipodium assembly (GO:0010592)|positive regulation of neuron differentiation (GO:0045666)|regulation of myosin II filament organization (GO:0043519)|response to antibiotic (GO:0046677)|response to carbohydrate (GO:0009743)|spindle localization (GO:0051653)	actin cytoskeleton (GO:0015629)|Arp2/3 protein complex (GO:0005885)|cell-cell junction (GO:0005911)|cytosol (GO:0005829)|excitatory synapse (GO:0060076)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi membrane (GO:0000139)|hemidesmosome (GO:0030056)|lamellipodium (GO:0030027)|membrane (GO:0016020)|podosome (GO:0002102)	ATP binding (GO:0005524)|structural constituent of cytoskeleton (GO:0005200)	p.R333R(1)		autonomic_ganglia(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(6)|skin(2)	15						ACTTTGGACGTCGCTTGCAAA	0.363																																					p.R333R												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.T999C	2						.						71.0	71.0	71.0					2																	114709344		2203	4300	6503	114425814	SO:0001819	synonymous_variant	10096	exon10			AF006083	CCDS33277.1, CCDS63000.1	2q14.1	2010-07-20	2001-11-28		ENSG00000115091	ENSG00000115091			170	protein-coding gene	gene with protein product		604222	"""ARP3 (actin-related protein 3, yeast) homolog"""			9230079	Standard	NM_005721		Approved	ARP3	uc002tkx.2	P61158	OTTHUMG00000153497	ENST00000263238.2:c.999T>C	2.37:g.114709344T>C		Somatic		Capture	Illumina HiSeq	Phase_I	114425814	NM_005721	P32391|Q53QM2	Silent	SNP	ENST00000263238.2	37	CCDS33277.1																																																																																				0.363	ACTR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331366.2	NM_005721	
GREB1	9687	broad.mit.edu	37	2	11767167	11767167	+	Silent	SNP	G	G	A	rs541354837		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr2:11767167G>A	ENST00000381486.2	+	25	4686	c.4386G>A	c.(4384-4386)gcG>gcA	p.A1462A	GREB1_ENST00000396123.1_Silent_p.A460A|GREB1_ENST00000234142.5_Silent_p.A1462A	NM_014668.3	NP_055483.2	Q4ZG55	GREB1_HUMAN	growth regulation by estrogen in breast cancer 1	1462						integral component of membrane (GO:0016021)		p.A1462A(1)		breast(3)|central_nervous_system(2)|endometrium(2)|kidney(4)|large_intestine(9)|lung(9)|ovary(1)	30	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.115)|OV - Ovarian serous cystadenocarcinoma(76;0.186)		AGTACGCAGCGTACAACACTT	0.587													G|||	1	0.000199681	0.0	0.0	5008	,	,		20049	0.0		0.0	False		,,,				2504	0.001				p.A1462A	Ovarian(39;850 945 2785 23371 33093)											.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G4386A	2						.						81.0	89.0	87.0					2																	11767167		2137	4245	6382	11684618	SO:0001819	synonymous_variant	9687	exon25				CCDS33146.1, CCDS33147.1, CCDS42655.1	2p25.1	2010-02-17	2009-09-10		ENSG00000196208	ENSG00000196208			24885	protein-coding gene	gene with protein product	"""gene regulated by estrogen in breast cancer"""	611736				11103799	Standard	NM_014668		Approved	KIAA0575	uc002rbk.1	Q4ZG55	OTTHUMG00000141276	ENST00000381486.2:c.4386G>A	2.37:g.11767167G>A		Somatic		Capture	Illumina HiSeq	Phase_I	11684618	NM_014668	A6NHD0|A6NKN0|B5MDA9|O60321|Q7Z5S2|Q9H2Q6|Q9H2Q7|Q9H2Q8	Silent	SNP	ENST00000381486.2	37	CCDS42655.1																																																																																				0.587	GREB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000280490.1	NM_014668	
DPP10	57628	broad.mit.edu	37	2	116525901	116525901	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr2:116525901G>A	ENST00000410059.1	+	13	1622	c.1142G>A	c.(1141-1143)gGc>gAc	p.G381D	DPP10_ENST00000310323.8_Missense_Mutation_p.G374D|DPP10_ENST00000409163.1_Missense_Mutation_p.G331D|DPP10_ENST00000393147.2_Missense_Mutation_p.G385D	NM_001178037.1|NM_020868.3	NP_001171508.1|NP_065919	Q8N608	DPP10_HUMAN	dipeptidyl-peptidase 10 (non-functional)	381						integral component of membrane (GO:0016021)|membrane (GO:0016020)	serine-type peptidase activity (GO:0008236)	p.G374D(1)		breast(4)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(24)|liver(2)|lung(48)|ovary(6)|prostate(1)|skin(5)|soft_tissue(1)	101						TCTAGAGACGGCAGCAAATTC	0.448																																					p.G331D												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G992A	2						.						140.0	134.0	136.0					2																	116525901		2203	4300	6503	116242371	SO:0001583	missense	57628	exon14			AY172661	CCDS33278.1, CCDS46400.1, CCDS54388.1, CCDS54389.1	2q14.1	2010-05-04	2010-05-04		ENSG00000175497	ENSG00000175497			20823	protein-coding gene	gene with protein product		608209	"""dipeptidylpeptidase 10"", ""dipeptidyl-peptidase 10"""			10819331, 12662155	Standard	NM_020868		Approved	DPRP3	uc002tle.3	Q8N608	OTTHUMG00000153294	ENST00000410059.1:c.1142G>A	2.37:g.116525901G>A	ENSP00000386565:p.Gly381Asp	Somatic		Capture	Illumina HiSeq	Phase_I	116242371	NM_001178036	A8K1Q2|J3KPP2|J3KQ46|Q0GLB8|Q53QT3|Q53S86|Q53SL8|Q53SS4|Q6TTV4|Q86YR9|Q9P236	Missense_Mutation	SNP	ENST00000410059.1	37	CCDS46400.1	.	.	.	.	.	.	.	.	.	.	G	29.3	4.997130	0.93167	.	.	ENSG00000175497	ENST00000410059;ENST00000409163;ENST00000393147;ENST00000310323;ENST00000476155	T;T;T;T	0.54479	0.57;0.57;0.57;0.57	5.25	5.25	0.73442	Peptidase S9B, dipeptidylpeptidase IV N-terminal (1);	0.107337	0.64402	D	0.000006	T	0.69797	0.3151	M	0.72576	2.205	0.58432	D	0.999999	P;P;D;D	0.56521	0.949;0.806;0.976;0.959	P;B;P;P	0.61132	0.747;0.366;0.884;0.836	T	0.72931	-0.4142	10	0.87932	D	0	-17.025	17.5891	0.87991	0.0:0.0:1.0:0.0	.	374;385;377;381	Q8N608-2;Q0GLB8;Q0GLB9;Q8N608	.;.;.;DPP10_HUMAN	D	381;331;385;374;331	ENSP00000386565:G381D;ENSP00000387038:G331D;ENSP00000376855:G385D;ENSP00000309066:G374D	ENSP00000309066:G374D	G	+	2	0	DPP10	116242371	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	5.400000	0.66320	2.724000	0.93272	0.655000	0.94253	GGC		0.448	DPP10-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000330580.4	NM_020868	
SCTR	6344	broad.mit.edu	37	2	120194496	120194496	+	IGR	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr2:120194496G>A	ENST00000019103.5	-	0	1865				TMEM37_ENST00000465296.1_3'UTR|TMEM37_ENST00000306406.4_Missense_Mutation_p.R18H|TMEM37_ENST00000409826.1_Missense_Mutation_p.R30H	NM_002980.2	NP_002971.2	P47872	SCTR_HUMAN	secretin receptor						digestion (GO:0007586)|excretion (GO:0007588)|G-protein coupled receptor signaling pathway (GO:0007186)	cytoplasmic microtubule (GO:0005881)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	secretin receptor activity (GO:0015055)	p.R18H(1)		central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(3)|lung(7)|ovary(1)|prostate(1)|skin(3)	19					Secretin(DB00021)	AGGCAGCCCCGCCGGTCCTTC	0.617																																					p.R18H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G53A	2						.						49.0	51.0	50.0					2																	120194496		2203	4300	6503	119910966	SO:0001628	intergenic_variant	140738	exon2				CCDS2127.1	2q14.1	2012-08-10			ENSG00000080293	ENSG00000080293		"""GPCR / Class B : Glucagon receptors"""	10608	protein-coding gene	gene with protein product		182098				1646711	Standard	NM_002980		Approved		uc002tma.3	P47872	OTTHUMG00000131407		2.37:g.120194496G>A		Somatic		Capture	Illumina HiSeq	Phase_I	119910966	NM_183240	Q12961|Q13213|Q53T00	Missense_Mutation	SNP	ENST00000019103.5	37	CCDS2127.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	0.046|0.046	-1.265586|-1.265586	0.01433|0.01433	.|.	.|.	ENSG00000171227|ENSG00000171227	ENST00000417645|ENST00000409826;ENST00000306406	.|.	.|.	.|.	4.93|4.93	-8.04|-8.04	0.01110|0.01110	.|.	.|1.223480	.|0.05613	.|N	.|0.578383	T|T	0.09730|0.09730	0.0239|0.0239	N|N	0.00368|0.00368	-1.59|-1.59	0.09310|0.09310	N|N	1|1	.|B	.|0.10296	.|0.003	.|B	.|0.01281	.|0.0	T|T	0.42999|0.42999	-0.9418|-0.9418	6|9	0.87932|0.21540	D|T	0|0.41	-7.4281|-7.4281	14.2166|14.2166	0.65797|0.65797	0.7778:0.0965:0.1257:0.0|0.7778:0.0965:0.1257:0.0	.|.	.|18	.|Q8WXS4	.|CCGL_HUMAN	T|H	24|30;18	.|.	ENSP00000400770:A24T|ENSP00000303148:R18H	A|R	+|+	1|2	0|0	TMEM37|TMEM37	119910966|119910966	0.000000|0.000000	0.05858|0.05858	0.350000|0.350000	0.25708|0.25708	0.357000|0.357000	0.29423|0.29423	-1.046000|-1.046000	0.03525|0.03525	-1.531000|-1.531000	0.01749|0.01749	-0.126000|-0.126000	0.14955|0.14955	GCC|CGC		0.617	SCTR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254198.2		
PTPN4	5775	broad.mit.edu	37	2	120692413	120692413	+	Nonsense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr2:120692413C>T	ENST00000263708.2	+	15	2005	c.1234C>T	c.(1234-1236)Cga>Tga	p.R412*	PTPN4_ENST00000544261.1_Nonsense_Mutation_p.R45*	NM_002830.3	NP_002821.1	P29074	PTN4_HUMAN	protein tyrosine phosphatase, non-receptor type 4 (megakaryocyte)	412					peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)	cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytoskeleton (GO:0005856)	non-membrane spanning protein tyrosine phosphatase activity (GO:0004726)	p.R412*(1)		endometrium(3)|kidney(2)|large_intestine(7)|lung(15)|ovary(2)|urinary_tract(1)	30					Alendronate(DB00630)	AACCCGGTTACGACCATCTTC	0.378																																					p.R412X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.C1234T	2						.						123.0	111.0	115.0					2																	120692413		2203	4300	6503	120408883	SO:0001587	stop_gained	5775	exon15				CCDS2129.1	2q14.2	2011-06-09			ENSG00000088179	ENSG00000088179		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"""	9656	protein-coding gene	gene with protein product		176878				1648233	Standard	NM_002830		Approved	PTPMEG	uc002tmf.2	P29074	OTTHUMG00000131436	ENST00000263708.2:c.1234C>T	2.37:g.120692413C>T	ENSP00000263708:p.Arg412*	Somatic		Capture	Illumina HiSeq	Phase_I	120408883	NM_002830	B2RBV8|Q9UDA7	Nonsense_Mutation	SNP	ENST00000263708.2	37	CCDS2129.1	.	.	.	.	.	.	.	.	.	.	C	36	5.665814	0.96745	.	.	ENSG00000088179	ENST00000263708;ENST00000544261;ENST00000431283	.	.	.	5.75	5.75	0.90469	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	20.3046	0.98621	0.0:1.0:0.0:0.0	.	.	.	.	X	412;45;38	.	ENSP00000263708:R412X	R	+	1	2	PTPN4	120408883	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	5.196000	0.65136	2.878000	0.98634	0.650000	0.86243	CGA		0.378	PTPN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254233.2		
EPB41L5	57669	broad.mit.edu	37	2	120836117	120836117	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr2:120836117C>A	ENST00000263713.5	+	10	977	c.763C>A	c.(763-765)Ctt>Att	p.L255I	EPB41L5_ENST00000443902.2_Missense_Mutation_p.L255I|EPB41L5_ENST00000443124.1_Missense_Mutation_p.L255I|EPB41L5_ENST00000331393.4_Missense_Mutation_p.L255I|EPB41L5_ENST00000452780.1_Missense_Mutation_p.L255I	NM_020909.3	NP_065960.2	Q9HCM4	E41L5_HUMAN	erythrocyte membrane protein band 4.1 like 5	255	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.				actomyosin structure organization (GO:0031032)|apical constriction (GO:0003383)|axial mesoderm morphogenesis (GO:0048319)|cellular response to transforming growth factor beta stimulus (GO:0071560)|ectoderm development (GO:0007398)|embryonic foregut morphogenesis (GO:0048617)|endoderm development (GO:0007492)|epithelial to mesenchymal transition (GO:0001837)|in utero embryonic development (GO:0001701)|left/right axis specification (GO:0070986)|mesoderm migration involved in gastrulation (GO:0007509)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of protein binding (GO:0032091)|neural plate morphogenesis (GO:0001839)|paraxial mesoderm development (GO:0048339)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of focal adhesion assembly (GO:0051894)|positive regulation of protein binding (GO:0032092)|posttranscriptional regulation of gene expression (GO:0010608)|regulation of establishment of protein localization (GO:0070201)|somite rostral/caudal axis specification (GO:0032525)|substrate-dependent cell migration, cell attachment to substrate (GO:0006931)|unidimensional cell growth (GO:0009826)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extrinsic component of membrane (GO:0019898)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)		p.L255I(1)		breast(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(5)|lung(12)|ovary(1)	26						AACAGGAGTCCTTGTTTTTGA	0.328																																					p.L255I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C763A	2						.						123.0	123.0	123.0					2																	120836117		2203	4299	6502	120552587	SO:0001583	missense	57669	exon10			AK023019	CCDS2130.1, CCDS54392.1, CCDS54393.1	2q14.2	2009-07-28			ENSG00000115109	ENSG00000115109			19819	protein-coding gene	gene with protein product		611730					Standard	NM_001184937		Approved	KIAA1548, FLJ12957, BE37, YMO1	uc002tmg.3	Q9HCM4	OTTHUMG00000131433	ENST00000263713.5:c.763C>A	2.37:g.120836117C>A	ENSP00000263713:p.Leu255Ile	Somatic		Capture	Illumina HiSeq	Phase_I	120552587	NM_001184937	Q7Z5S1|Q8IZ12|Q9H975	Missense_Mutation	SNP	ENST00000263713.5	37	CCDS2130.1	.	.	.	.	.	.	.	.	.	.	C	20.2	3.943931	0.73672	.	.	ENSG00000115109	ENST00000263713;ENST00000443902;ENST00000331393;ENST00000443124;ENST00000452780	D;D;D;D;D	0.87334	-2.24;-2.24;-2.24;-2.24;-2.24	4.83	4.83	0.62350	FERM, C-terminal PH-like domain (1);FERM domain (1);Pleckstrin homology-type (1);	0.000000	0.64402	D	0.000001	D	0.93229	0.7843	M	0.76328	2.33	0.80722	D	1	P;D;D;D	0.89917	0.849;1.0;0.985;1.0	P;D;D;D	0.91635	0.673;0.999;0.918;0.999	D	0.94073	0.7337	10	0.87932	D	0	.	17.891	0.88872	0.0:1.0:0.0:0.0	.	255;255;255;255	Q9HCM4-3;Q9HCM4-4;Q9HCM4-2;Q9HCM4	.;.;.;E41L5_HUMAN	I	255	ENSP00000263713:L255I;ENSP00000393856:L255I;ENSP00000329687:L255I;ENSP00000393722:L255I;ENSP00000390439:L255I	ENSP00000263713:L255I	L	+	1	0	EPB41L5	120552587	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	2.909000	0.48758	2.403000	0.81681	0.561000	0.74099	CTT		0.328	EPB41L5-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000254230.2	NM_020909	
CNTNAP5	129684	broad.mit.edu	37	2	124999867	124999867	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr2:124999867C>T	ENST00000431078.1	+	3	642	c.278C>T	c.(277-279)aCg>aTg	p.T93M		NM_130773.2	NP_570129.1	Q8WYK1	CNTP5_HUMAN	contactin associated protein-like 5	93	F5/8 type C. {ECO:0000255|PROSITE- ProRule:PRU00081}.				cell adhesion (GO:0007155)	integral component of membrane (GO:0016021)		p.T93M(1)		NS(1)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(24)|lung(100)|ovary(10)|prostate(12)|skin(4)|upper_aerodigestive_tract(3)	176				BRCA - Breast invasive adenocarcinoma(221;0.248)		GCAGTGGCCACGCAGGGAAGA	0.527																																					p.T93M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C278T	2						.						69.0	74.0	73.0					2																	124999867		2050	4199	6249	124716337	SO:0001583	missense	129684	exon3			AB077881	CCDS46401.1	2q14.1	2008-02-05			ENSG00000155052	ENSG00000155052			18748	protein-coding gene	gene with protein product		610519					Standard	NM_130773		Approved	caspr5, FLJ31966	uc002tno.3	Q8WYK1	OTTHUMG00000153356	ENST00000431078.1:c.278C>T	2.37:g.124999867C>T	ENSP00000399013:p.Thr93Met	Somatic		Capture	Illumina HiSeq	Phase_I	124716337	NM_130773	Q4ZFW2|Q4ZG21|Q53R09|Q53RX1|Q53SG3|Q584P3|Q96MS7	Missense_Mutation	SNP	ENST00000431078.1	37	CCDS46401.1	.	.	.	.	.	.	.	.	.	.	C	25.8	4.678496	0.88542	.	.	ENSG00000155052	ENST00000431078	D	0.98585	-5.01	5.83	5.83	0.93111	Coagulation factor 5/8 C-terminal type domain (3);Galactose-binding domain-like (1);	0.000000	0.52532	D	0.000072	D	0.99468	0.9811	H	0.98612	4.28	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.98221	1.0478	10	0.87932	D	0	.	19.1032	0.93282	0.0:1.0:0.0:0.0	.	93	Q8WYK1	CNTP5_HUMAN	M	93	ENSP00000399013:T93M	ENSP00000399013:T93M	T	+	2	0	CNTNAP5	124716337	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.705000	0.84606	2.761000	0.94854	0.650000	0.86243	ACG		0.527	CNTNAP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330864.3		
TRIB2	28951	broad.mit.edu	37	2	12880482	12880482	+	Silent	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr2:12880482C>T	ENST00000155926.4	+	3	2013	c.594C>T	c.(592-594)gaC>gaT	p.D198D	TRIB2_ENST00000381465.2_Silent_p.D62D|MIR3125_ENST00000579927.1_RNA	NM_021643.3	NP_067675.1			tribbles pseudokinase 2									p.D198D(1)		breast(1)|cervix(1)|endometrium(1)|large_intestine(8)|lung(5)|prostate(1)|skin(1)|stomach(1)	19	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)					GCCTGGAAGACGCCTACATTC	0.537																																					p.D198D												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C594T	2						.						88.0	87.0	87.0					2																	12880482		2203	4300	6503	12797933	SO:0001819	synonymous_variant	28951	exon3			AY245544	CCDS1683.1	2p25.1	2013-10-03	2013-10-03		ENSG00000071575	ENSG00000071575			30809	protein-coding gene	gene with protein product		609462	"""tribbles homolog 2 (Drosophila)"""			12736262, 17097562, 16715410	Standard	NM_021643		Approved	TRB2, GS3955	uc002rbv.4	Q92519	OTTHUMG00000090575	ENST00000155926.4:c.594C>T	2.37:g.12880482C>T		Somatic		Capture	Illumina HiSeq	Phase_I	12797933	NM_021643		Silent	SNP	ENST00000155926.4	37	CCDS1683.1																																																																																				0.537	TRIB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207114.2	NM_021643	
CYP27C1	339761	broad.mit.edu	37	2	127950678	127950678	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr2:127950678C>T	ENST00000335247.7	-	7	1124	c.994G>A	c.(994-996)Gtg>Atg	p.V332M	CYP27C1_ENST00000409327.1_Missense_Mutation_p.V332M	NM_001001665.3	NP_001001665.3	Q4G0S4	C27C1_HUMAN	cytochrome P450, family 27, subfamily C, polypeptide 1	332						membrane (GO:0016020)	heme binding (GO:0020037)|iron ion binding (GO:0005506)|monooxygenase activity (GO:0004497)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen (GO:0016705)	p.V332M(1)		central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(5)|prostate(1)|stomach(1)	16	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.071)		ACCTGGATCACGACGAGGTGA	0.507																																					p.V332M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G994A	2						.						71.0	70.0	70.0					2																	127950678		2203	4300	6503	127667148	SO:0001583	missense	339761	exon7			AC027142	CCDS33285.1	2q14.3	2008-05-14	2007-05-18		ENSG00000186684	ENSG00000186684		"""Cytochrome P450s"""	33480	protein-coding gene	gene with protein product							Standard	NM_001001665		Approved	FLJ16008	uc002tod.2	Q4G0S4	OTTHUMG00000153400	ENST00000335247.7:c.994G>A	2.37:g.127950678C>T	ENSP00000334128:p.Val332Met	Somatic		Capture	Illumina HiSeq	Phase_I	127667148	NM_001001665	Q6ZNI7	Missense_Mutation	SNP	ENST00000335247.7	37	CCDS33285.1	.	.	.	.	.	.	.	.	.	.	C	5.471	0.271903	0.10349	.	.	ENSG00000186684	ENST00000335247;ENST00000409327	T;T	0.68479	-0.33;-0.33	4.11	-7.09	0.01553	.	0.575258	0.16185	N	0.225659	T	0.36826	0.0981	N	0.11892	0.195	0.18873	N	0.999989	B	0.15930	0.015	B	0.17098	0.017	T	0.08785	-1.0705	10	0.52906	T	0.07	-1.9336	4.5119	0.11915	0.086:0.126:0.2812:0.5069	.	332	Q4G0S4	C27C1_HUMAN	M	332	ENSP00000334128:V332M;ENSP00000387198:V332M	ENSP00000334128:V332M	V	-	1	0	CYP27C1	127667148	0.005000	0.15991	0.001000	0.08648	0.004000	0.04260	-0.059000	0.11731	-1.564000	0.01678	-0.350000	0.07774	GTG		0.507	CYP27C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331046.1	NM_001001665	
WDR33	55339	broad.mit.edu	37	2	128482658	128482658	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr2:128482658C>T	ENST00000322313.4	-	9	1141	c.983G>A	c.(982-984)cGa>cAa	p.R328Q		NM_018383.4	NP_060853.3	Q9C0J8	WDR33_HUMAN	WD repeat domain 33	328					mRNA processing (GO:0006397)|postreplication repair (GO:0006301)|spermatogenesis (GO:0007283)	collagen trimer (GO:0005581)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)	p.R328Q(1)		NS(1)|breast(3)|endometrium(2)|kidney(2)|large_intestine(9)|lung(17)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	39	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.0695)		CTTATGACCTCGGAAGACTTG	0.398																																					p.R328Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G983A	2						.						82.0	81.0	81.0					2																	128482658		2203	4300	6503	128199128	SO:0001583	missense	55339	exon9				CCDS2150.1, CCDS42746.1, CCDS46407.1	2q21.1	2013-01-09			ENSG00000136709	ENSG00000136709		"""WD repeat domain containing"""	25651	protein-coding gene	gene with protein product						11162572	Standard	NM_001006622		Approved	FLJ11294, WDC146, NET14	uc002tpg.2	Q9C0J8	OTTHUMG00000131534	ENST00000322313.4:c.983G>A	2.37:g.128482658C>T	ENSP00000325377:p.Arg328Gln	Somatic		Capture	Illumina HiSeq	Phase_I	128199128	NM_018383	Q05DP8|Q53FG9|Q587J1|Q69YF7|Q6NUQ0|Q9NUL1	Missense_Mutation	SNP	ENST00000322313.4	37	CCDS2150.1	.	.	.	.	.	.	.	.	.	.	C	28.3	4.908701	0.92107	.	.	ENSG00000136709	ENST00000322313	T	0.60672	0.17	5.54	5.54	0.83059	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.000000	0.85682	D	0.000000	T	0.72211	0.3432	L	0.46741	1.465	0.80722	D	1	D	0.71674	0.998	D	0.79108	0.992	T	0.73959	-0.3818	10	0.87932	D	0	-10.0267	19.4772	0.94994	0.0:1.0:0.0:0.0	.	328	Q9C0J8	WDR33_HUMAN	Q	328	ENSP00000325377:R328Q	ENSP00000325377:R328Q	R	-	2	0	WDR33	128199128	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.629000	0.83207	2.602000	0.87976	0.563000	0.77884	CGA		0.398	WDR33-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331141.2	NM_018383	
AMMECR1L	83607	broad.mit.edu	37	2	128628468	128628468	+	Nonsense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr2:128628468G>A	ENST00000272647.5	-	5	813	c.553C>T	c.(553-555)Cga>Tga	p.R185*	AMMECR1L_ENST00000393001.1_Nonsense_Mutation_p.R185*	NM_001199140.1	NP_001186069.1	Q6DCA0	AMERL_HUMAN	AMMECR1-like	185	AMMECR1. {ECO:0000255|PROSITE- ProRule:PRU00467}.							p.R185*(1)		central_nervous_system(1)|kidney(1)|large_intestine(3)|lung(3)|prostate(1)	9	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.07)		AGCTCCTCTCGGGTCAGGGGG	0.532																																					p.R185X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.C553T	2						.						46.0	44.0	45.0					2																	128628468		2203	4300	6503	128344938	SO:0001587	stop_gained	83607	exon5				CCDS2152.1	2q21	2012-11-15	2012-11-15		ENSG00000144233	ENSG00000144233			28658	protein-coding gene	gene with protein product			"""AMME chromosomal region gene 1-like"""				Standard	NM_001199140		Approved	MGC4268	uc002tpl.3	Q6DCA0	OTTHUMG00000131535	ENST00000272647.5:c.553C>T	2.37:g.128628468G>A	ENSP00000272647:p.Arg185*	Somatic		Capture	Illumina HiSeq	Phase_I	128344938	NM_001199140	B4E276	Nonsense_Mutation	SNP	ENST00000272647.5	37	CCDS2152.1	.	.	.	.	.	.	.	.	.	.	G	38	6.945291	0.97952	.	.	ENSG00000144233	ENST00000272647;ENST00000393001	.	.	.	5.46	4.55	0.56014	.	0.000000	0.64402	D	0.000002	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-11.5901	15.6522	0.77108	0.0:0.0:0.8617:0.1383	.	.	.	.	X	185	.	ENSP00000272647:R185X	R	-	1	2	AMMECR1L	128344938	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.765000	0.68834	1.377000	0.46286	0.655000	0.94253	CGA		0.532	AMMECR1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254392.1	NM_031445	
TUBA3D	113457	broad.mit.edu	37	2	132240254	132240254	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr2:132240254G>A	ENST00000321253.6	+	5	1293	c.1186G>A	c.(1186-1188)Gat>Aat	p.D396N	MZT2A_ENST00000410036.2_5'Flank	NM_080386.3	NP_525125.2	Q13748	TBA3C_HUMAN	tubulin, alpha 3d	396					'de novo' posttranslational protein folding (GO:0051084)|cellular protein metabolic process (GO:0044267)|microtubule-based process (GO:0007017)|protein folding (GO:0006457)|protein polymerization (GO:0051258)	cytoplasm (GO:0005737)|microtubule (GO:0005874)|nucleus (GO:0005634)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|structural constituent of cytoskeleton (GO:0005200)	p.D396N(1)		breast(2)|endometrium(1)|kidney(1)|large_intestine(3)|lung(18)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)	32				BRCA - Breast invasive adenocarcinoma(221;0.13)		CCATAAGTTCGATCTCATGTA	0.642																																					p.D396N	Ovarian(137;2059 2432 35543 39401)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1186A	2						.						129.0	128.0	128.0					2																	132240254		2203	4300	6503	131956724	SO:0001583	missense	113457	exon5			K03460	CCDS33290.1	2q21.1	2007-03-16			ENSG00000075886	ENSG00000075886		"""Tubulins"""	24071	protein-coding gene	gene with protein product	"""alpha-tubulin isotype H2-alpha"""					3785200	Standard	NM_080386		Approved	H2-ALPHA	uc002tsu.4	Q13748	OTTHUMG00000153600	ENST00000321253.6:c.1186G>A	2.37:g.132240254G>A	ENSP00000326042:p.Asp396Asn	Somatic		Capture	Illumina HiSeq	Phase_I	131956724	NM_080386	A6NJQ0|Q5W099|Q6PEY3|Q96F18	Missense_Mutation	SNP	ENST00000321253.6	37	CCDS33290.1	.	.	.	.	.	.	.	.	.	.	g	10.94	1.493688	0.26774	.	.	ENSG00000075886	ENST00000321253	D	0.85955	-2.05	2.41	1.5	0.22942	Tubulin, C-terminal (1);Tubulin/FtsZ, C-terminal (1);	0.000000	0.47455	U	0.000234	D	0.87935	0.6303	H	0.95004	3.61	0.39019	D	0.959716	B	0.16396	0.017	B	0.29077	0.098	D	0.84366	0.0541	10	0.87932	D	0	.	7.0778	0.25213	0.152:0.0:0.848:0.0	.	396	Q13748	TBA3C_HUMAN	N	396	ENSP00000326042:D396N	ENSP00000326042:D396N	D	+	1	0	TUBA3D	131956724	1.000000	0.71417	0.978000	0.43139	0.844000	0.47949	4.051000	0.57412	0.332000	0.23536	0.194000	0.17425	GAT		0.642	TUBA3D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331800.2	NM_080386	
NCKAP5	344148	broad.mit.edu	37	2	133539951	133539951	+	Nonsense_Mutation	SNP	A	A	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr2:133539951A>T	ENST00000409261.1	-	14	4806	c.4433T>A	c.(4432-4434)tTg>tAg	p.L1478*	NCKAP5_ENST00000405974.3_Intron|NCKAP5_ENST00000473859.1_5'Flank|NCKAP5_ENST00000409213.1_Intron|NCKAP5_ENST00000317721.6_Nonsense_Mutation_p.L1478*	NM_207363.2	NP_997246.2	O14513	NCKP5_HUMAN	NCK-associated protein 5	1478								p.L1478*(1)		NS(4)|autonomic_ganglia(1)|breast(5)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(29)|lung(51)|prostate(5)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	118						CTGAATGCACAACATGACCTT	0.512																																					p.L1478X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.T4433A	2						.						74.0	71.0	72.0					2																	133539951		1908	4131	6039	133256421	SO:0001587	stop_gained	344148	exon14			AB005217	CCDS46417.1, CCDS46418.1	2q21.2	2010-02-17			ENSG00000176771	ENSG00000176771			29847	protein-coding gene	gene with protein product	"""Nck associated protein 5"", ""peripheral clock protein"""	608789				9344857	Standard	NM_207363		Approved	NAP5, ERIH1, ERIH2	uc002ttp.3	O14513	OTTHUMG00000153573	ENST00000409261.1:c.4433T>A	2.37:g.133539951A>T	ENSP00000387128:p.Leu1478*	Somatic		Capture	Illumina HiSeq	Phase_I	133256421	NM_207363	B8ZZL0|Q29SS9|Q29ST0|Q2NL90|Q6ZVE2|Q8NAS3	Nonsense_Mutation	SNP	ENST00000409261.1	37	CCDS46418.1	.	.	.	.	.	.	.	.	.	.	A	48	14.025238	0.99775	.	.	ENSG00000176771	ENST00000409261;ENST00000317721	.	.	.	5.65	5.65	0.86999	.	0.000000	0.28371	U	0.015594	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.20519	T	0.43	.	14.6007	0.68438	1.0:0.0:0.0:0.0	.	.	.	.	X	1478	.	ENSP00000380603:L1478X	L	-	2	0	NCKAP5	133256421	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.855000	0.86950	2.371000	0.80710	0.533000	0.62120	TTG		0.512	NCKAP5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000331663.1	NM_207481	
NCKAP5	344148	broad.mit.edu	37	2	133547741	133547741	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr2:133547741G>T	ENST00000409261.1	-	13	1320	c.947C>A	c.(946-948)cCt>cAt	p.P316H	NCKAP5_ENST00000405974.3_Missense_Mutation_p.P316H|NCKAP5_ENST00000409213.1_Missense_Mutation_p.P316H|NCKAP5_ENST00000317721.6_Missense_Mutation_p.P316H	NM_207363.2	NP_997246.2	O14513	NCKP5_HUMAN	NCK-associated protein 5	316								p.P155H(1)|p.P316H(1)		NS(4)|autonomic_ganglia(1)|breast(5)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(29)|lung(51)|prostate(5)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	118						CCCCAAGCCAGGGCATTTCAA	0.493																																					p.P316H												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.C947A	2						.						78.0	84.0	82.0					2																	133547741		1984	4157	6141	133264211	SO:0001583	missense	344148	exon13			AB005217	CCDS46417.1, CCDS46418.1	2q21.2	2010-02-17			ENSG00000176771	ENSG00000176771			29847	protein-coding gene	gene with protein product	"""Nck associated protein 5"", ""peripheral clock protein"""	608789				9344857	Standard	NM_207363		Approved	NAP5, ERIH1, ERIH2	uc002ttp.3	O14513	OTTHUMG00000153573	ENST00000409261.1:c.947C>A	2.37:g.133547741G>T	ENSP00000387128:p.Pro316His	Somatic		Capture	Illumina HiSeq	Phase_I	133264211	NM_207481	B8ZZL0|Q29SS9|Q29ST0|Q2NL90|Q6ZVE2|Q8NAS3	Missense_Mutation	SNP	ENST00000409261.1	37	CCDS46418.1	.	.	.	.	.	.	.	.	.	.	G	15.24	2.773568	0.49786	.	.	ENSG00000176771	ENST00000409261;ENST00000409213;ENST00000317721;ENST00000405974;ENST00000537661	T;T;T;T	0.42900	2.97;0.96;2.97;0.96	5.23	4.32	0.51571	.	1.055640	0.07643	U	0.930545	T	0.30324	0.0761	N	0.19112	0.55	0.22034	N	0.999401	B;B	0.17667	0.004;0.023	B;B	0.16289	0.004;0.015	T	0.19160	-1.0314	10	0.22109	T	0.4	.	11.2168	0.48831	0.0:0.0:0.5881:0.4119	.	316;316	O14513-2;O14513	.;NCKP5_HUMAN	H	316	ENSP00000387128:P316H;ENSP00000386952:P316H;ENSP00000380603:P316H;ENSP00000385692:P316H	ENSP00000380603:P316H	P	-	2	0	NCKAP5	133264211	1.000000	0.71417	0.916000	0.36221	0.943000	0.58893	1.700000	0.37815	1.368000	0.46115	0.650000	0.86243	CCT		0.493	NCKAP5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000331663.1	NM_207481	
LCT	3938	broad.mit.edu	37	2	136561516	136561516	+	Silent	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr2:136561516G>A	ENST00000264162.2	-	11	4657	c.4647C>T	c.(4645-4647)taC>taT	p.Y1549Y		NM_002299.2	NP_002290.2	P09848	LPH_HUMAN	lactase	1549	4 X approximate repeats.				carbohydrate metabolic process (GO:0005975)|polysaccharide digestion (GO:0044245)|small molecule metabolic process (GO:0044281)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	glycosylceramidase activity (GO:0017042)|lactase activity (GO:0000016)	p.Y1549Y(1)		breast(6)|central_nervous_system(3)|cervix(1)|endometrium(8)|kidney(2)|large_intestine(26)|lung(57)|ovary(7)|pancreas(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(4)	124				BRCA - Breast invasive adenocarcinoma(221;0.169)	Vitamin C(DB00126)	CTGCTGTTCCGTAGCCATAGC	0.507																																					p.Y1549Y												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C4647T	2						.						96.0	73.0	81.0					2																	136561516		2203	4300	6503	136277986	SO:0001819	synonymous_variant	3938	exon11			X07994	CCDS2178.1	2q21	2014-09-17			ENSG00000115850	ENSG00000115850	3.2.1.108, 3.2.1.62		6530	protein-coding gene	gene with protein product		603202					Standard	NM_002299		Approved		uc002tuu.1	P09848	OTTHUMG00000131738	ENST00000264162.2:c.4647C>T	2.37:g.136561516G>A		Somatic		Capture	Illumina HiSeq	Phase_I	136277986	NM_002299	Q4ZG58	Silent	SNP	ENST00000264162.2	37	CCDS2178.1																																																																																				0.507	LCT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254657.1	NM_002299	
LCT	3938	broad.mit.edu	37	2	136570445	136570445	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr2:136570445C>T	ENST00000264162.2	-	7	1799	c.1789G>A	c.(1789-1791)Gtg>Atg	p.V597M	Y_RNA_ENST00000363794.1_RNA	NM_002299.2	NP_002290.2	P09848	LPH_HUMAN	lactase	597	4 X approximate repeats.				carbohydrate metabolic process (GO:0005975)|polysaccharide digestion (GO:0044245)|small molecule metabolic process (GO:0044281)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	glycosylceramidase activity (GO:0017042)|lactase activity (GO:0000016)	p.V597M(1)		breast(6)|central_nervous_system(3)|cervix(1)|endometrium(8)|kidney(2)|large_intestine(26)|lung(57)|ovary(7)|pancreas(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(4)	124				BRCA - Breast invasive adenocarcinoma(221;0.169)	Vitamin C(DB00126)	ACAATGCCCACGTGCCCCTGC	0.567																																					p.V597M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1789A	2						.						60.0	52.0	55.0					2																	136570445		2203	4300	6503	136286915	SO:0001583	missense	3938	exon7			X07994	CCDS2178.1	2q21	2014-09-17			ENSG00000115850	ENSG00000115850	3.2.1.108, 3.2.1.62		6530	protein-coding gene	gene with protein product		603202					Standard	NM_002299		Approved		uc002tuu.1	P09848	OTTHUMG00000131738	ENST00000264162.2:c.1789G>A	2.37:g.136570445C>T	ENSP00000264162:p.Val597Met	Somatic		Capture	Illumina HiSeq	Phase_I	136286915	NM_002299	Q4ZG58	Missense_Mutation	SNP	ENST00000264162.2	37	CCDS2178.1	.	.	.	.	.	.	.	.	.	.	C	20.2	3.951085	0.73787	.	.	ENSG00000115850	ENST00000264162;ENST00000455227	T	0.38077	1.16	5.49	5.49	0.81192	Glycoside hydrolase, subgroup, catalytic domain (1);Glycoside hydrolase, superfamily (1);	0.214951	0.40385	N	0.001108	T	0.69296	0.3095	M	0.89601	3.045	0.54753	D	0.999984	D	0.89917	1.0	D	0.87578	0.998	T	0.76110	-0.3079	10	0.87932	D	0	-20.0506	19.3929	0.94592	0.0:1.0:0.0:0.0	.	597	P09848	LPH_HUMAN	M	597;29	ENSP00000264162:V597M	ENSP00000264162:V597M	V	-	1	0	LCT	136286915	1.000000	0.71417	0.948000	0.38648	0.734000	0.41952	6.004000	0.70709	2.583000	0.87209	0.655000	0.94253	GTG		0.567	LCT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254657.1	NM_002299	
MCM6	4175	broad.mit.edu	37	2	136620271	136620271	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr2:136620271C>T	ENST00000264156.2	-	8	1186	c.1126G>A	c.(1126-1128)Gtt>Att	p.V376I	MCM6_ENST00000492091.1_5'UTR	NM_005915.5	NP_005906.2	Q14566	MCM6_HUMAN	minichromosome maintenance complex component 6	376	MCM.				DNA replication (GO:0006260)|DNA replication initiation (GO:0006270)|DNA strand elongation involved in DNA replication (GO:0006271)|DNA unwinding involved in DNA replication (GO:0006268)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)	MCM complex (GO:0042555)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA helicase activity (GO:0003678)|identical protein binding (GO:0042802)|single-stranded DNA binding (GO:0003697)	p.V376I(1)		breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(5)|liver(1)|lung(15)|prostate(2)|skin(1)	29				BRCA - Breast invasive adenocarcinoma(221;0.166)		GTCTTTGGAACGCCACCAAAG	0.418																																					p.V376I	Ovarian(196;141 2104 8848 24991 25939)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1126A	2						.						120.0	112.0	114.0					2																	136620271		2203	4300	6503	136336741	SO:0001583	missense	4175	exon8				CCDS2179.1	2q14-q21	2008-02-05	2007-04-04		ENSG00000076003	ENSG00000076003			6949	protein-coding gene	gene with protein product	"""MIS5 homolog (S.pombe)"""	601806	"""minichromosome maintenance deficient (mis5, S. pombe) 6"", ""MCM6 minichromosome maintenance deficient 6 (MIS5 homolog, S. pombe) (S. cerevisiae)"", ""minichromosome maintenance deficient 6 homolog (S. cerevisiae)"""				Standard	NM_005915		Approved	Mis5	uc002tuw.4	Q14566	OTTHUMG00000131739	ENST00000264156.2:c.1126G>A	2.37:g.136620271C>T	ENSP00000264156:p.Val376Ile	Somatic		Capture	Illumina HiSeq	Phase_I	136336741	NM_005915	B2R6H2|Q13504|Q99859	Missense_Mutation	SNP	ENST00000264156.2	37	CCDS2179.1	.	.	.	.	.	.	.	.	.	.	C	33	5.268754	0.95429	.	.	ENSG00000076003	ENST00000264156	T	0.08282	3.11	5.07	5.07	0.68467	.	0.000000	0.85682	D	0.000000	T	0.33265	0.0857	M	0.80746	2.51	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.13899	-1.0492	10	0.72032	D	0.01	-19.5415	18.4659	0.90755	0.0:1.0:0.0:0.0	.	376	Q14566	MCM6_HUMAN	I	376	ENSP00000264156:V376I	ENSP00000264156:V376I	V	-	1	0	MCM6	136336741	1.000000	0.71417	0.996000	0.52242	0.981000	0.71138	7.382000	0.79729	2.329000	0.79093	0.655000	0.94253	GTT		0.418	MCM6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254658.1	NM_005915	
TPO	7173	broad.mit.edu	37	2	1500436	1500436	+	Missense_Mutation	SNP	G	G	A	rs139734552		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr2:1500436G>A	ENST00000345913.4	+	13	2376	c.2285G>A	c.(2284-2286)cGc>cAc	p.R762H	TPO_ENST00000329066.4_Missense_Mutation_p.R762H|TPO_ENST00000382198.1_Missense_Mutation_p.R589H|TPO_ENST00000346956.3_Missense_Mutation_p.R762H|TPO_ENST00000382201.3_Missense_Mutation_p.R705H|TPO_ENST00000497517.2_Intron|TPO_ENST00000349624.3_Missense_Mutation_p.R589H|TPO_ENST00000337415.3_Missense_Mutation_p.R762H	NM_000547.5	NP_000538.3	P07202	PERT_HUMAN	thyroid peroxidase	762	Sushi. {ECO:0000255|PROSITE- ProRule:PRU00302}.				cellular nitrogen compound metabolic process (GO:0034641)|embryonic hemopoiesis (GO:0035162)|hormone biosynthetic process (GO:0042446)|hydrogen peroxide catabolic process (GO:0042744)|small molecule metabolic process (GO:0044281)|thyroid hormone generation (GO:0006590)	extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|heme binding (GO:0020037)|iodide peroxidase activity (GO:0004447)|peroxidase activity (GO:0004601)	p.R762H(1)		breast(1)|central_nervous_system(3)|endometrium(8)|kidney(4)|large_intestine(14)|liver(2)|lung(33)|ovary(8)|pancreas(6)|prostate(4)|skin(7)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	95	all_hematologic(175;0.0487)|Acute lymphoblastic leukemia(172;0.0627)	all_cancers(51;0.0338)		all cancers(51;0.0356)|OV - Ovarian serous cystadenocarcinoma(76;0.0748)|Epithelial(75;0.12)	Carbimazole(DB00389)|Dextrothyroxine(DB00509)|Methimazole(DB00763)|Propylthiouracil(DB00550)	TCTGGGAGGCGCGTGCTGGTG	0.572																																					p.R762H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2285A	2						.	G	HIS/ARG,HIS/ARG,HIS/ARG,HIS/ARG,HIS/ARG,HIS/ARG	1,4405	2.1+/-5.4	0,1,2202	160.0	153.0	156.0		2285,2285,2114,2114,2285,1766	1.8	0.0	2	dbSNP_134	156	0,8600		0,0,4300	no	missense,missense,missense,missense,missense,missense	TPO	NM_000547.5,NM_001206744.1,NM_001206745.1,NM_175719.3,NM_175721.3,NM_175722.3	29,29,29,29,29,29	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	benign,benign,benign,benign,benign,benign	762/934,762/934,705/877,705/877,762/890,589/761	1500436	1,13005	2203	4300	6503	1479443	SO:0001583	missense	7173	exon12				CCDS1643.1, CCDS1644.1, CCDS1646.1	2p25	2008-02-05			ENSG00000115705	ENSG00000115705	1.11.1.7		12015	protein-coding gene	gene with protein product		606765					Standard	NM_175722		Approved	TPX	uc002qww.3	P07202	OTTHUMG00000090271	ENST00000345913.4:c.2285G>A	2.37:g.1500436G>A	ENSP00000318820:p.Arg762His	Somatic		Capture	Illumina HiSeq	Phase_I	1479443	NM_175721	P09934|P09935|Q8IUL0|Q8NF94|Q8NF95|Q8NF96|Q8NF97|Q8TCI9	Missense_Mutation	SNP	ENST00000345913.4	37	CCDS1643.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	3.807|3.807	-0.040492|-0.040492	0.07497|0.07497	2.27E-4|2.27E-4	0.0|0.0	ENSG00000115705|ENSG00000115705	ENST00000446278|ENST00000337415;ENST00000345913;ENST00000346956;ENST00000349624;ENST00000329066;ENST00000382201;ENST00000382198;ENST00000422464;ENST00000469607	.|T;T;T;T;T;T;T;T;T	.|0.76448	.|-1.02;-1.02;-0.12;-0.12;-1.02;1.87;-0.12;-0.12;-0.12	4.9|4.9	1.79|1.79	0.24919|0.24919	.|Complement control module (2);Sushi/SCR/CCP (2);	.|0.420915	.|0.24039	.|N	.|0.042103	T|T	0.49253|0.49253	0.1546|0.1546	N|N	0.12182|0.12182	0.205|0.205	0.19300|0.19300	N|N	0.999975|0.999975	.|B;P;B;B	.|0.38535	.|0.066;0.635;0.066;0.039	.|B;B;B;B	.|0.27715	.|0.016;0.082;0.016;0.007	T|T	0.40098|0.40098	-0.9581|-0.9581	5|10	.|0.22706	.|T	.|0.39	-15.7217|-15.7217	6.3797|6.3797	0.21527|0.21527	0.0:0.2558:0.4141:0.33|0.0:0.2558:0.4141:0.33	.|.	.|762;589;705;762	.|P07202-4;P07202-5;P07202-2;P07202	.|.;.;.;PERT_HUMAN	T|H	237|762;762;762;589;762;705;589;691;236	.|ENSP00000337263:R762H;ENSP00000318820:R762H;ENSP00000263886:R762H;ENSP00000332044:R589H;ENSP00000329869:R762H;ENSP00000371636:R705H;ENSP00000371633:R589H;ENSP00000405788:R691H;ENSP00000419461:R236H	.|ENSP00000329869:R762H	A|R	+|+	1|2	0|0	TPO|TPO	1479443|1479443	0.000000|0.000000	0.05858|0.05858	0.026000|0.026000	0.17262|0.17262	0.024000|0.024000	0.10985|0.10985	0.166000|0.166000	0.16583|0.16583	1.131000|1.131000	0.42111|0.42111	0.591000|0.591000	0.81541|0.81541	GCG|CGC		0.572	TPO-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000206594.2	NM_000547	
LRP1B	53353	broad.mit.edu	37	2	141093272	141093272	+	Missense_Mutation	SNP	C	C	T	rs267598907		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr2:141093272C>T	ENST00000389484.3	-	78	12999	c.12028G>A	c.(12028-12030)Gta>Ata	p.V4010I		NM_018557.2	NP_061027.2	Q9NZR2	LRP1B_HUMAN	low density lipoprotein receptor-related protein 1B	4010					protein transport (GO:0015031)|receptor-mediated endocytosis (GO:0006898)	integral component of membrane (GO:0016021)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)|low-density lipoprotein receptor activity (GO:0005041)	p.V4010I(1)		NS(5)|autonomic_ganglia(1)|biliary_tract(1)|breast(3)|central_nervous_system(7)|endometrium(25)|haematopoietic_and_lymphoid_tissue(10)|kidney(27)|large_intestine(98)|liver(4)|lung(337)|ovary(15)|pancreas(6)|prostate(11)|skin(30)|stomach(2)|upper_aerodigestive_tract(19)|urinary_tract(5)	606		all_cancers(3;1.1e-60)|all_epithelial(3;1.94e-59)|all_lung(3;1.09e-24)|Lung NSC(3;5.65e-24)|Esophageal squamous(3;5.41e-13)|Renal(3;0.000147)|Breast(3;0.000527)|Hepatocellular(3;0.011)|all_neural(3;0.014)|Colorectal(150;0.101)		UCEC - Uterine corpus endometrioid carcinoma (2;0.00139)|Epithelial(1;1.25e-24)|all cancers(1;8.86e-24)|OV - Ovarian serous cystadenocarcinoma(1;2.45e-12)|LUSC - Lung squamous cell carcinoma(1;2.97e-10)|Lung(1;6.05e-09)|BRCA - Breast invasive adenocarcinoma(221;0.0103)		AGCTGCCCTACGTTGATAGAG	0.453										TSP Lung(27;0.18)																											p.V4010I	Colon(99;50 2074 2507 20106)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G12028A	2						.						146.0	140.0	142.0					2																	141093272		2203	4300	6503	140809742	SO:0001583	missense	53353	exon78			AF176832	CCDS2182.1	2q21.2	2013-05-29	2010-01-26		ENSG00000168702	ENSG00000168702		"""Low density lipoprotein receptors"""	6693	protein-coding gene	gene with protein product	"""LRP-deleted in tumors"""	608766				10766186	Standard	NM_018557		Approved	LRP-DIT, LRPDIT	uc002tvj.1	Q9NZR2	OTTHUMG00000131799	ENST00000389484.3:c.12028G>A	2.37:g.141093272C>T	ENSP00000374135:p.Val4010Ile	Somatic		Capture	Illumina HiSeq	Phase_I	140809742	NM_018557	Q8WY29|Q8WY30|Q8WY31	Missense_Mutation	SNP	ENST00000389484.3	37	CCDS2182.1	.	.	.	.	.	.	.	.	.	.	C	17.75	3.466935	0.63625	.	.	ENSG00000168702	ENST00000389484;ENST00000544579	D	0.95001	-3.58	5.49	5.49	0.81192	Six-bladed beta-propeller, TolB-like (1);Growth factor, receptor (1);	0.162448	0.39985	N	0.001219	D	0.94159	0.8126	M	0.75150	2.29	0.44918	D	0.99793	P	0.51240	0.943	B	0.40410	0.328	D	0.94886	0.8043	10	0.72032	D	0.01	.	19.7341	0.96195	0.0:1.0:0.0:0.0	.	4010	Q9NZR2	LRP1B_HUMAN	I	4010;3948	ENSP00000374135:V4010I	ENSP00000374135:V4010I	V	-	1	0	LRP1B	140809742	1.000000	0.71417	0.225000	0.23894	0.566000	0.35808	7.356000	0.79445	2.732000	0.93576	0.585000	0.79938	GTA		0.453	LRP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254736.2	NM_018557	
MBD5	55777	broad.mit.edu	37	2	149226675	149226675	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr2:149226675A>G	ENST00000407073.1	+	9	2160	c.1163A>G	c.(1162-1164)cAg>cGg	p.Q388R	MBD5_ENST00000404807.1_Missense_Mutation_p.Q388R	NM_018328.4	NP_060798.2	Q9P267	MBD5_HUMAN	methyl-CpG binding domain protein 5	388	Pro-rich.				glucose homeostasis (GO:0042593)|nervous system development (GO:0007399)|positive regulation of growth hormone receptor signaling pathway (GO:0060399)|regulation of multicellular organism growth (GO:0040014)|single-organism behavior (GO:0044708)	chromocenter (GO:0010369)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	chromatin binding (GO:0003682)	p.Q388R(1)		NS(1)|breast(4)|central_nervous_system(1)|endometrium(8)|kidney(1)|large_intestine(16)|lung(22)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(3)	62				BRCA - Breast invasive adenocarcinoma(221;0.0569)		GTCCACTCTCAGGTACCTATG	0.423																																					p.Q388R												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A1163G	2						.						206.0	205.0	205.0					2																	149226675		2203	4300	6503	148943145	SO:0001583	missense	55777	exon9			AB040894	CCDS33302.1	2q23.2	2009-04-17			ENSG00000204406	ENSG00000204406			20444	protein-coding gene	gene with protein product		611472				12529184	Standard	NM_018328		Approved	FLJ11113, KIAA1461	uc002twm.4	Q9P267	OTTHUMG00000150440	ENST00000407073.1:c.1163A>G	2.37:g.149226675A>G	ENSP00000386049:p.Gln388Arg	Somatic		Capture	Illumina HiSeq	Phase_I	148943145	NM_018328	A5HMQ4|A7E2B1|Q53SR1|Q9NUV6	Missense_Mutation	SNP	ENST00000407073.1	37	CCDS33302.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	15.00|15.00	2.701889|2.701889	0.48307|0.48307	.|.	.|.	ENSG00000204406|ENSG00000204406	ENST00000407073;ENST00000404807|ENST00000416015	T;T|.	0.33654|.	1.4;1.4|.	5.35|5.35	5.35|5.35	0.76521|0.76521	.|.	0.000000|.	0.56097|.	D|.	0.000024|.	T|T	0.51176|0.51176	0.1659|0.1659	N|N	0.19112|0.19112	0.55|0.55	0.58432|0.58432	D|D	0.999996|0.999996	D|.	0.61080|.	0.989|.	D|.	0.72982|.	0.979|.	T|T	0.48293|0.48293	-0.9048|-0.9048	10|5	0.45353|.	T|.	0.12|.	-2.6805|-2.6805	15.642|15.642	0.77012|0.77012	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	388|.	Q9P267|.	MBD5_HUMAN|.	R|G	388|128	ENSP00000386049:Q388R;ENSP00000384672:Q388R|.	ENSP00000384672:Q388R|.	Q|R	+|+	2|1	0|2	MBD5|MBD5	148943145|148943145	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.999000|0.999000	0.98932|0.98932	7.256000|7.256000	0.78350|0.78350	2.163000|2.163000	0.67991|0.67991	0.533000|0.533000	0.62120|0.62120	CAG|AGG		0.423	MBD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318111.2		
NEB	4703	broad.mit.edu	37	2	152371377	152371377	+	Silent	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr2:152371377C>T	ENST00000172853.10	-	130	18015	c.17868G>A	c.(17866-17868)acG>acA	p.T5956T	NEB_ENST00000603639.1_Silent_p.T7657T|NEB_ENST00000604864.1_Silent_p.T7657T|NEB_ENST00000397345.3_Silent_p.T7657T|NEB_ENST00000409198.1_Silent_p.T5956T|NEB_ENST00000427231.2_Silent_p.T7657T			P20929	NEBU_HUMAN	nebulin	5956					muscle filament sliding (GO:0030049)|muscle organ development (GO:0007517)|regulation of actin filament length (GO:0030832)|somatic muscle development (GO:0007525)	actin cytoskeleton (GO:0015629)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Z disc (GO:0030018)	structural constituent of muscle (GO:0008307)	p.T5956T(2)|p.T7657T(1)		NS(5)|autonomic_ganglia(3)|breast(9)|central_nervous_system(5)|cervix(3)|endometrium(35)|kidney(16)|large_intestine(77)|liver(1)|lung(99)|ovary(9)|pancreas(3)|prostate(13)|skin(7)|stomach(8)|upper_aerodigestive_tract(6)|urinary_tract(2)	301				BRCA - Breast invasive adenocarcinoma(221;0.219)		ACAAAGCTGGCGTGACCTCCA	0.383																																					p.T7657T												.	.	3	Substitution - coding silent(3)	endometrium(2)|large_intestine(1)	c.G22971A	2						.						61.0	61.0	61.0					2																	152371377		1868	4113	5981	152079623	SO:0001819	synonymous_variant	4703	exon158			X83957	CCDS46424.1, CCDS54407.1, CCDS54408.1, CCDS74588.1	2q22	2014-09-17			ENSG00000183091	ENSG00000183091			7720	protein-coding gene	gene with protein product	"""nemaline myopathy type 2"""	161650		NEM2		10051637, 9359044	Standard	NM_001164507		Approved	NEB177D	uc010fnx.3	P20929	OTTHUMG00000153784	ENST00000172853.10:c.17868G>A	2.37:g.152371377C>T		Somatic		Capture	Illumina HiSeq	Phase_I	152079623	NM_001164507	F8WCL5|F8WCP0|Q15346|Q53QQ2|Q53TG8	Silent	SNP	ENST00000172853.10	37																																																																																					0.383	NEB-201	KNOWN	basic	protein_coding	protein_coding		NM_004543	
NEB	4703	broad.mit.edu	37	2	152396866	152396866	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr2:152396866C>T	ENST00000172853.10	-	110	15928	c.15781G>A	c.(15781-15783)Gcc>Acc	p.A5261T	NEB_ENST00000603639.1_Missense_Mutation_p.A6962T|NEB_ENST00000604864.1_Missense_Mutation_p.A6962T|NEB_ENST00000397345.3_Missense_Mutation_p.A6962T|NEB_ENST00000409198.1_Missense_Mutation_p.A5261T|NEB_ENST00000427231.2_Missense_Mutation_p.A6962T			P20929	NEBU_HUMAN	nebulin	5261					muscle filament sliding (GO:0030049)|muscle organ development (GO:0007517)|regulation of actin filament length (GO:0030832)|somatic muscle development (GO:0007525)	actin cytoskeleton (GO:0015629)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Z disc (GO:0030018)	structural constituent of muscle (GO:0008307)	p.A5261T(1)		NS(5)|autonomic_ganglia(3)|breast(9)|central_nervous_system(5)|cervix(3)|endometrium(35)|kidney(16)|large_intestine(77)|liver(1)|lung(99)|ovary(9)|pancreas(3)|prostate(13)|skin(7)|stomach(8)|upper_aerodigestive_tract(6)|urinary_tract(2)	301				BRCA - Breast invasive adenocarcinoma(221;0.219)		ACATCACTGGCATTCCAGTAA	0.413																																					p.A6962T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G20884A	2						.						135.0	124.0	128.0					2																	152396866		1896	4130	6026	152105112	SO:0001583	missense	4703	exon138			X83957	CCDS46424.1, CCDS54407.1, CCDS54408.1, CCDS74588.1	2q22	2014-09-17			ENSG00000183091	ENSG00000183091			7720	protein-coding gene	gene with protein product	"""nemaline myopathy type 2"""	161650		NEM2		10051637, 9359044	Standard	NM_001164507		Approved	NEB177D	uc010fnx.3	P20929	OTTHUMG00000153784	ENST00000172853.10:c.15781G>A	2.37:g.152396866C>T	ENSP00000172853:p.Ala5261Thr	Somatic		Capture	Illumina HiSeq	Phase_I	152105112	NM_001164507	F8WCL5|F8WCP0|Q15346|Q53QQ2|Q53TG8	Missense_Mutation	SNP	ENST00000172853.10	37		.	.	.	.	.	.	.	.	.	.	C	22.8	4.340775	0.81911	.	.	ENSG00000183091	ENST00000409198;ENST00000397345;ENST00000427231;ENST00000397342;ENST00000413693;ENST00000172853;ENST00000420924	T;T;T;T;T;T	0.49432	0.78;0.78;0.78;0.78;0.78;0.78	5.44	5.44	0.79542	.	0.050958	0.85682	D	0.000000	T	0.54935	0.1889	N	0.19112	0.55	0.80722	D	1	D;D	0.65815	0.993;0.995	D;D	0.77004	0.93;0.989	T	0.50792	-0.8786	10	0.24483	T	0.36	.	19.2708	0.94008	0.0:1.0:0.0:0.0	.	5261;1692	P20929;Q14215	NEBU_HUMAN;.	T	5261;6962;6962;1310;1692;5261;50	ENSP00000386259:A5261T;ENSP00000380505:A6962T;ENSP00000416578:A6962T;ENSP00000410961:A1692T;ENSP00000172853:A5261T;ENSP00000405167:A50T	ENSP00000172853:A5261T	A	-	1	0	NEB	152105112	1.000000	0.71417	0.988000	0.46212	0.835000	0.47333	4.607000	0.61133	2.560000	0.86352	0.460000	0.39030	GCC		0.413	NEB-201	KNOWN	basic	protein_coding	protein_coding		NM_004543	
CACNB4	785	broad.mit.edu	37	2	152727063	152727063	+	Silent	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr2:152727063C>T	ENST00000539935.1	-	8	748	c.681G>A	c.(679-681)ccG>ccA	p.P227P	CACNB4_ENST00000534999.1_Silent_p.P193P|CACNB4_ENST00000360283.6_Silent_p.P194P|CACNB4_ENST00000427385.1_Silent_p.P209P|CACNB4_ENST00000201943.5_Silent_p.P227P|CACNB4_ENST00000397327.2_Silent_p.P180P	NM_000726.3|NM_001145798.1	NP_000717.2|NP_001139270.1	O00305	CACB4_HUMAN	calcium channel, voltage-dependent, beta 4 subunit	227					adult walking behavior (GO:0007628)|axon guidance (GO:0007411)|calcium ion transmembrane transport (GO:0070588)|cAMP metabolic process (GO:0046058)|cellular calcium ion homeostasis (GO:0006874)|detection of light stimulus involved in visual perception (GO:0050908)|gamma-aminobutyric acid secretion (GO:0014051)|gamma-aminobutyric acid signaling pathway (GO:0007214)|membrane depolarization (GO:0051899)|muscle fiber development (GO:0048747)|neuromuscular junction development (GO:0007528)|neuronal action potential propagation (GO:0019227)|Peyer's patch development (GO:0048541)|regulation of voltage-gated calcium channel activity (GO:1901385)|spleen development (GO:0048536)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|T cell receptor signaling pathway (GO:0050852)|thymus development (GO:0048538)|transport (GO:0006810)	cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|plasma membrane (GO:0005886)|synapse (GO:0045202)|voltage-gated calcium channel complex (GO:0005891)	voltage-gated calcium channel activity (GO:0005245)	p.P227P(3)		endometrium(1)|kidney(1)|large_intestine(3)|lung(4)|ovary(2)	11				BRCA - Breast invasive adenocarcinoma(221;0.156)	Dronedarone(DB04855)|Nimodipine(DB00393)|Spironolactone(DB00421)|Verapamil(DB00661)	CTTTCAGTGACGGCCCCACTA	0.498																																					p.P227P												.	.	3	Substitution - coding silent(3)	large_intestine(3)	c.G681A	2						.						87.0	87.0	87.0					2																	152727063		2082	4208	6290	152435309	SO:0001819	synonymous_variant	785	exon8			AF038852	CCDS46426.1, CCDS46427.1, CCDS46428.1, CCDS54409.1	2q22-q23	2009-09-04			ENSG00000182389	ENSG00000182389		"""Calcium channel subunits"""	1404	protein-coding gene	gene with protein product		601949				9628818	Standard	NM_000726		Approved	EJM4	uc002tya.3	O00305	OTTHUMG00000155091	ENST00000539935.1:c.681G>A	2.37:g.152727063C>T		Somatic		Capture	Illumina HiSeq	Phase_I	152435309	NM_001145798	A7BJ74|A8K1Y4|B4DG40|O60515|Q6B000|Q96L40	Silent	SNP	ENST00000539935.1	37	CCDS46426.1																																																																																				0.498	CACNB4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000338385.4	NM_000726.3	
GALNT5	11227	broad.mit.edu	37	2	158115922	158115922	+	Missense_Mutation	SNP	G	G	A	rs150434278		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr2:158115922G>A	ENST00000259056.4	+	1	1813	c.1328G>A	c.(1327-1329)cGt>cAt	p.R443H		NM_014568.1	NP_055383.1	Q7Z7M9	GALT5_HUMAN	polypeptide N-acetylgalactosaminyltransferase 5	443					cellular protein metabolic process (GO:0044267)|glycosaminoglycan biosynthetic process (GO:0006024)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)|polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)	p.R443H(1)		breast(4)|central_nervous_system(3)|endometrium(6)|kidney(3)|large_intestine(12)|lung(20)|prostate(1)|skin(4)|stomach(1)|urinary_tract(2)	56						CAGTTTGGGCGTCCTGTAGTT	0.473													G|||	1	0.000199681	0.0	0.0	5008	,	,		18919	0.0		0.0	False		,,,				2504	0.001				p.R443H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1328A	2						.	G	HIS/ARG	2,4404	4.2+/-10.8	0,2,2201	74.0	72.0	72.0		1328	2.9	0.7	2	dbSNP_134	72	4,8596	3.7+/-12.6	0,4,4296	yes	missense	GALNT5	NM_014568.1	29	0,6,6497	AA,AG,GG		0.0465,0.0454,0.0461	benign	443/941	158115922	6,13000	2203	4300	6503	157824168	SO:0001583	missense	11227	exon1			AJ245539	CCDS2203.1	2q24.1	2014-03-13	2014-03-13		ENSG00000136542	ENSG00000136542	2.4.1.41	"""Glycosyltransferase family 2 domain containing"""	4127	protein-coding gene	gene with protein product	"""polypeptide GalNAc transferase 5"""	615129	"""UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 5 (GalNAc-T5)"""			10545594	Standard	NM_014568		Approved	GalNAc-T5	uc002tzg.3	Q7Z7M9	OTTHUMG00000131965	ENST00000259056.4:c.1328G>A	2.37:g.158115922G>A	ENSP00000259056:p.Arg443His	Somatic		Capture	Illumina HiSeq	Phase_I	157824168	NM_014568	A5PKZ1|Q9UGK7|Q9UHL6	Missense_Mutation	SNP	ENST00000259056.4	37	CCDS2203.1	.	.	.	.	.	.	.	.	.	.	G	7.371	0.626900	0.14257	4.54E-4	4.65E-4	ENSG00000136542	ENST00000259056	T	0.58506	0.33	6.05	2.87	0.33458	.	0.977622	0.08417	N	0.948895	T	0.50205	0.1602	L	0.49640	1.575	0.09310	N	0.999999	B	0.14438	0.01	B	0.06405	0.002	T	0.40346	-0.9568	10	0.40728	T	0.16	.	7.4621	0.27302	0.1067:0.0:0.603:0.2904	.	443	Q7Z7M9	GALT5_HUMAN	H	443	ENSP00000259056:R443H	ENSP00000259056:R443H	R	+	2	0	GALNT5	157824168	0.985000	0.35326	0.700000	0.30305	0.030000	0.12068	2.895000	0.48648	0.861000	0.35504	-0.175000	0.13238	CGT		0.473	GALNT5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254925.2	NM_014568	
TANC1	85461	broad.mit.edu	37	2	160035154	160035154	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr2:160035154G>A	ENST00000263635.6	+	14	2227	c.1990G>A	c.(1990-1992)Gtc>Atc	p.V664I	TANC1_ENST00000454300.1_Missense_Mutation_p.V558I	NM_001145909.1|NM_033394.2	NP_001139381.1|NP_203752.2	Q9C0D5	TANC1_HUMAN	tetratricopeptide repeat, ankyrin repeat and coiled-coil containing 1	664					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.V664I(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						GCACGCCTACGTCCAGCACAG	0.527																																					p.V664I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1990A	2						.						56.0	59.0	58.0					2																	160035154		2166	4262	6428	159743400	SO:0001583	missense	85461	exon14			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.1990G>A	2.37:g.160035154G>A	ENSP00000263635:p.Val664Ile	Somatic		Capture	Illumina HiSeq	Phase_I	159743400	NM_033394	C9JD88|Q49AI8	Missense_Mutation	SNP	ENST00000263635.6	37	CCDS42766.1	.	.	.	.	.	.	.	.	.	.	G	6.056	0.378650	0.11466	.	.	ENSG00000115183	ENST00000454300;ENST00000263635	T;T	0.60040	0.22;0.26	5.91	5.03	0.67393	.	0.054467	0.64402	D	0.000001	T	0.17789	0.0427	N	0.00471	-1.455	0.38268	D	0.942078	B;B;B	0.13145	0.003;0.005;0.007	B;B;B	0.11329	0.002;0.004;0.006	T	0.43702	-0.9375	10	0.02654	T	1	.	5.6832	0.17788	0.2557:0.0:0.7443:0.0	.	656;558;664	B9EK39;Q9C0D5-2;Q9C0D5	.;.;TANC1_HUMAN	I	558;664	ENSP00000396339:V558I;ENSP00000263635:V664I	ENSP00000263635:V664I	V	+	1	0	TANC1	159743400	1.000000	0.71417	1.000000	0.80357	0.928000	0.56348	4.361000	0.59461	2.813000	0.96785	0.655000	0.94253	GTC		0.527	TANC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333135.1		
LY75	4065	broad.mit.edu	37	2	160734962	160734962	+	Missense_Mutation	SNP	A	A	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr2:160734962A>T	ENST00000263636.4	-	11	1674	c.1647T>A	c.(1645-1647)gaT>gaA	p.D549E	LY75_ENST00000554112.1_Missense_Mutation_p.D549E|LY75-CD302_ENST00000504764.1_Missense_Mutation_p.D549E|LY75-CD302_ENST00000505052.1_Missense_Mutation_p.D549E|LY75_ENST00000553424.1_Missense_Mutation_p.D549E	NM_002349.3	NP_002340.2	O60449	LY75_HUMAN	lymphocyte antigen 75	549	C-type lectin 3. {ECO:0000255|PROSITE- ProRule:PRU00040}.				endocytosis (GO:0006897)|immune response (GO:0006955)|inflammatory response (GO:0006954)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	carbohydrate binding (GO:0030246)|receptor activity (GO:0004872)	p.D549E(1)		NS(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(22)|prostate(7)|skin(6)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	59				COAD - Colon adenocarcinoma(177;0.132)		TTAGAGATTTATCATACTTTT	0.373																																					p.D549E												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T1647A	2						.						89.0	90.0	89.0					2																	160734962		2203	4300	6503	160443208	SO:0001583	missense	4065	exon11			AF011333	CCDS2211.1	2q24	2011-08-30			ENSG00000054219	ENSG00000054219		"""CD molecules"", ""C-type lectin domain containing"""	6729	protein-coding gene	gene with protein product		604524				9553150	Standard	NM_002349		Approved	DEC-205, CLEC13B, CD205		O60449	OTTHUMG00000132025	ENST00000263636.4:c.1647T>A	2.37:g.160734962A>T	ENSP00000263636:p.Asp549Glu	Somatic		Capture	Illumina HiSeq	Phase_I	160443208	NM_001198760	O75913|Q53R46|Q53TF5|Q7Z575|Q7Z577	Missense_Mutation	SNP	ENST00000263636.4	37	CCDS2211.1	.	.	.	.	.	.	.	.	.	.	A	13.46	2.243318	0.39697	.	.	ENSG00000054219;ENSG00000054219;ENSG00000054219;ENSG00000248672;ENSG00000248672	ENST00000554112;ENST00000553424;ENST00000263636;ENST00000504764;ENST00000505052	T;T;T;T;T	0.09350	3.02;3.02;2.99;3.02;3.02	5.82	0.811	0.18739	C-type lectin fold (1);C-type lectin-like (1);C-type lectin (3);	0.971401	0.08337	N	0.961375	T	0.06645	0.0170	L	0.27053	0.805	0.26002	N	0.982102	B;B;P;B	0.35872	0.151;0.332;0.525;0.417	B;B;B;B	0.34590	0.158;0.167;0.186;0.085	T	0.39292	-0.9621	10	0.12430	T	0.62	-10.0101	5.6453	0.17586	0.4679:0.1515:0.3805:0.0	.	167;549;549;549	Q59H44;O60449-3;O60449;O60449-2	.;.;LY75_HUMAN;.	E	549	ENSP00000451511:D549E;ENSP00000451446:D549E;ENSP00000263636:D549E;ENSP00000423463:D549E;ENSP00000421035:D549E	ENSP00000423463:D549E	D	-	3	2	LY75;LY75-CD302	160443208	0.582000	0.26749	0.874000	0.34290	0.881000	0.50899	0.252000	0.18278	0.119000	0.18210	0.459000	0.35465	GAT		0.373	LY75-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000255035.1		
TBR1	10716	broad.mit.edu	37	2	162273121	162273121	+	Missense_Mutation	SNP	A	A	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr2:162273121A>T	ENST00000389554.3	+	1	517	c.200A>T	c.(199-201)aAt>aTt	p.N67I	TBR1_ENST00000410035.1_5'Flank	NM_006593.2	NP_006584.1	Q16650	TBR1_HUMAN	T-box, brain, 1	67					axon guidance (GO:0007411)|brain development (GO:0007420)|hindbrain development (GO:0030902)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of neuron projection development (GO:0010975)|specification of organ identity (GO:0010092)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.N67I(1)		central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(6)|lung(15)|ovary(1)|prostate(1)|skin(3)	30						GATACAGACAATTTTCCTGAC	0.483																																					p.N67I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A200T	2						.						80.0	88.0	85.0					2																	162273121		2203	4300	6503	161981367	SO:0001583	missense	10716	exon1			U49250	CCDS33310.1	2q24.2	2011-06-13			ENSG00000136535	ENSG00000136535		"""T-boxes"""	11590	protein-coding gene	gene with protein product		604616				7619531	Standard	NM_006593		Approved		uc002ubw.1	Q16650	OTTHUMG00000153888	ENST00000389554.3:c.200A>T	2.37:g.162273121A>T	ENSP00000374205:p.Asn67Ile	Somatic		Capture	Illumina HiSeq	Phase_I	161981367	NM_006593	B0AZS4|B2R6G5|Q14DC5|Q53TH0|Q56A81	Missense_Mutation	SNP	ENST00000389554.3	37	CCDS33310.1	.	.	.	.	.	.	.	.	.	.	A	10.06	1.246206	0.22796	.	.	ENSG00000136535	ENST00000389554	D	0.87179	-2.22	5.15	5.15	0.70609	.	0.060584	0.64402	D	0.000006	T	0.79684	0.4488	L	0.40543	1.245	0.80722	D	1	P	0.37864	0.61	B	0.33042	0.157	T	0.80870	-0.1189	10	0.72032	D	0.01	.	8.5663	0.33543	0.9138:0.0:0.0862:0.0	.	67	Q16650	TBR1_HUMAN	I	67	ENSP00000374205:N67I	ENSP00000374205:N67I	N	+	2	0	TBR1	161981367	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	3.726000	0.54977	2.171000	0.68590	0.533000	0.62120	AAT		0.483	TBR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000332845.1	NM_006593	
SLC4A10	57282	broad.mit.edu	37	2	162757512	162757512	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr2:162757512G>A	ENST00000446997.1	+	12	1526	c.1433G>A	c.(1432-1434)cGa>cAa	p.R478Q	SLC4A10_ENST00000421911.1_Missense_Mutation_p.R478Q|SLC4A10_ENST00000415876.2_Missense_Mutation_p.R448Q|SLC4A10_ENST00000272716.5_Missense_Mutation_p.R448Q|SLC4A10_ENST00000493021.1_3'UTR|SLC4A10_ENST00000375514.5_Missense_Mutation_p.R459Q|SLC4A10_ENST00000535165.1_3'UTR	NM_001178015.1	NP_001171486.1	Q6U841	S4A10_HUMAN	solute carrier family 4, sodium bicarbonate transporter, member 10	478					bicarbonate transport (GO:0015701)|chloride transport (GO:0006821)|ion transport (GO:0006811)|regulation of pH (GO:0006885)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	inorganic anion exchanger activity (GO:0005452)|symporter activity (GO:0015293)	p.R448Q(1)		endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(9)|lung(35)|ovary(2)|pancreas(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	60					Sodium bicarbonate(DB01390)	GAACTCCAGCGAACTGGAAGG	0.453																																					p.R459Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1376A	2						.						47.0	53.0	51.0					2																	162757512		1935	4123	6058	162465758	SO:0001583	missense	57282	exon12				CCDS46438.1, CCDS54411.1, CCDS54412.1	2q24.2	2013-05-22	2008-09-15		ENSG00000144290	ENSG00000144290		"""Solute carriers"""	13811	protein-coding gene	gene with protein product		605556	"""solute carrier family 4, sodium bicarbonate transporter-like, member 10"""			10964153, 18319254	Standard	NM_022058		Approved	NBCn2, NCBE	uc002ubx.4	Q6U841	OTTHUMG00000153938	ENST00000446997.1:c.1433G>A	2.37:g.162757512G>A	ENSP00000393066:p.Arg478Gln	Somatic		Capture	Illumina HiSeq	Phase_I	162465758	NM_001178016	B7Z1R0|B7Z2J0|B7ZLC5|B9EG69|F8W675|Q4ZFX6|Q8TCP2|Q9HCQ6	Missense_Mutation	SNP	ENST00000446997.1	37	CCDS54411.1	.	.	.	.	.	.	.	.	.	.	G	28.8	4.953262	0.92660	.	.	ENSG00000144290	ENST00000375514;ENST00000415876;ENST00000272716;ENST00000449513;ENST00000446997;ENST00000421911;ENST00000415711	T;T;T;T;T	0.81247	-1.47;-1.47;-1.47;-1.47;-1.47	5.27	5.27	0.74061	Bicarbonate transporter, C-terminal (1);	0.000000	0.85682	D	0.000000	D	0.92361	0.7576	M	0.92412	3.305	0.80722	D	1	D;D;D;D	0.89917	0.997;1.0;0.997;0.999	D;D;D;D	0.80764	0.944;0.994;0.944;0.969	D	0.93845	0.7140	10	0.87932	D	0	.	19.2477	0.93909	0.0:0.0:1.0:0.0	.	459;478;448;478	F8W675;E7EW28;Q6U841-2;Q6U841	.;.;.;S4A10_HUMAN	Q	459;448;448;447;478;478;477	ENSP00000364664:R459Q;ENSP00000395797:R448Q;ENSP00000272716:R448Q;ENSP00000393066:R478Q;ENSP00000404486:R478Q	ENSP00000272716:R448Q	R	+	2	0	SLC4A10	162465758	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	9.813000	0.99286	2.628000	0.89032	0.655000	0.94253	CGA		0.453	SLC4A10-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000333090.1	NM_022058	
KCNH7	90134	broad.mit.edu	37	2	163279905	163279905	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr2:163279905G>A	ENST00000332142.5	-	9	2194	c.2095C>T	c.(2095-2097)Cgt>Tgt	p.R699C	KCNH7_ENST00000328032.4_Missense_Mutation_p.R692C	NM_033272.3	NP_150375.2	Q9NS40	KCNH7_HUMAN	potassium voltage-gated channel, subfamily H (eag-related), member 7	699					circadian rhythm (GO:0007623)|potassium ion transmembrane transport (GO:0071805)|protein heterooligomerization (GO:0051291)|regulation of membrane potential (GO:0042391)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	inward rectifier potassium channel activity (GO:0005242)|signal transducer activity (GO:0004871)|voltage-gated potassium channel activity (GO:0005249)	p.R699C(1)		NS(1)|biliary_tract(1)|breast(4)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(22)|lung(53)|ovary(3)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(3)	108					Doxazosin(DB00590)|Ibutilide(DB00308)|Miconazole(DB01110)|Prazosin(DB00457)|Terazosin(DB01162)	TCTTCAAGACGTTGCCTCAGA	0.453																																					p.R692C	GBM(196;1492 2208 17507 24132 45496)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C2074T	2						.						255.0	237.0	243.0					2																	163279905		2203	4300	6503	162988151	SO:0001583	missense	90134	exon8			AF032897	CCDS2219.1, CCDS2220.1	2q24.3	2012-07-05			ENSG00000184611	ENSG00000184611		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	18863	protein-coding gene	gene with protein product		608169				16382104	Standard	NM_173162		Approved	Kv11.3, HERG3, erg3	uc002uch.2	Q9NS40	OTTHUMG00000132069	ENST00000332142.5:c.2095C>T	2.37:g.163279905G>A	ENSP00000331727:p.Arg699Cys	Somatic		Capture	Illumina HiSeq	Phase_I	162988151	NM_173162	Q53QU4|Q53TB7|Q53TP9|Q8IV15	Missense_Mutation	SNP	ENST00000332142.5	37	CCDS2219.1	.	.	.	.	.	.	.	.	.	.	G	21.8	4.198249	0.79015	.	.	ENSG00000184611	ENST00000332142;ENST00000328032	D;D	0.97480	-4.4;-4.4	5.95	5.02	0.67125	Cyclic nucleotide-binding-like (1);	0.000000	0.85682	D	0.000000	D	0.98676	0.9556	M	0.92970	3.365	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.999	D	0.98903	1.0777	10	0.87932	D	0	.	13.796	0.63171	0.0:0.0:0.7319:0.2681	.	692;699	Q9NS40-2;Q9NS40	.;KCNH7_HUMAN	C	699;692	ENSP00000331727:R699C;ENSP00000333781:R692C	ENSP00000333781:R692C	R	-	1	0	KCNH7	162988151	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.494000	0.53273	2.824000	0.97209	0.655000	0.94253	CGT		0.453	KCNH7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255093.1	NM_033272	
KCNH7	90134	broad.mit.edu	37	2	163360976	163360976	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr2:163360976T>C	ENST00000332142.5	-	6	1204	c.1105A>G	c.(1105-1107)Aat>Gat	p.N369D	KCNH7_ENST00000328032.4_Missense_Mutation_p.N362D|KCNH7_ENST00000477019.1_5'UTR	NM_033272.3	NP_150375.2	Q9NS40	KCNH7_HUMAN	potassium voltage-gated channel, subfamily H (eag-related), member 7	369					circadian rhythm (GO:0007623)|potassium ion transmembrane transport (GO:0071805)|protein heterooligomerization (GO:0051291)|regulation of membrane potential (GO:0042391)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	inward rectifier potassium channel activity (GO:0005242)|signal transducer activity (GO:0004871)|voltage-gated potassium channel activity (GO:0005249)	p.N369D(1)		NS(1)|biliary_tract(1)|breast(4)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(22)|lung(53)|ovary(3)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(3)	108					Doxazosin(DB00590)|Ibutilide(DB00308)|Miconazole(DB01110)|Prazosin(DB00457)|Terazosin(DB01162)	TCAGTCACATTGTGTGTTCGA	0.353																																					p.N362D	GBM(196;1492 2208 17507 24132 45496)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A1084G	2						.						172.0	168.0	170.0					2																	163360976		2203	4300	6503	163069222	SO:0001583	missense	90134	exon5			AF032897	CCDS2219.1, CCDS2220.1	2q24.3	2012-07-05			ENSG00000184611	ENSG00000184611		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	18863	protein-coding gene	gene with protein product		608169				16382104	Standard	NM_173162		Approved	Kv11.3, HERG3, erg3	uc002uch.2	Q9NS40	OTTHUMG00000132069	ENST00000332142.5:c.1105A>G	2.37:g.163360976T>C	ENSP00000331727:p.Asn369Asp	Somatic		Capture	Illumina HiSeq	Phase_I	163069222	NM_173162	Q53QU4|Q53TB7|Q53TP9|Q8IV15	Missense_Mutation	SNP	ENST00000332142.5	37	CCDS2219.1	.	.	.	.	.	.	.	.	.	.	T	17.42	3.384004	0.61845	.	.	ENSG00000184611	ENST00000332142;ENST00000328032	D;D	0.93247	-3.19;-3.19	5.8	5.8	0.92144	.	0.000000	0.85682	D	0.000000	D	0.94696	0.8289	M	0.65975	2.015	0.54753	D	0.999983	B;D	0.55605	0.096;0.972	B;P	0.53006	0.073;0.715	D	0.94719	0.7899	10	0.54805	T	0.06	.	16.1611	0.81712	0.0:0.0:0.0:1.0	.	362;369	Q9NS40-2;Q9NS40	.;KCNH7_HUMAN	D	369;362	ENSP00000331727:N369D;ENSP00000333781:N362D	ENSP00000333781:N362D	N	-	1	0	KCNH7	163069222	1.000000	0.71417	1.000000	0.80357	0.911000	0.54048	6.165000	0.71891	2.213000	0.71641	0.477000	0.44152	AAT		0.353	KCNH7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255093.1	NM_033272	
SLC38A11	151258	broad.mit.edu	37	2	165771691	165771691	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr2:165771691C>T	ENST00000409149.3	-	8	904	c.613G>A	c.(613-615)Gtg>Atg	p.V205M	SLC38A11_ENST00000303735.4_Missense_Mutation_p.V183M|SLC38A11_ENST00000493887.1_5'UTR|SLC38A11_ENST00000409058.1_Missense_Mutation_p.V236M|SLC38A11_ENST00000409662.1_Missense_Mutation_p.V205M	NM_001199148.1	NP_001186077.1	Q08AI6	S38AB_HUMAN	solute carrier family 38, member 11	205					amino acid transport (GO:0006865)|sodium ion transport (GO:0006814)	integral component of membrane (GO:0016021)		p.V183M(1)		endometrium(2)|large_intestine(4)|lung(8)|ovary(1)	15						ACAGAAATCACGATGGACATA	0.378																																					p.V183M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G547A	2						.						118.0	113.0	114.0					2																	165771691		2203	4300	6503	165479937	SO:0001583	missense	151258	exon7				CCDS2224.1, CCDS56142.1	2q24.3	2013-05-22			ENSG00000169507	ENSG00000169507		"""Solute carriers"""	26836	protein-coding gene	gene with protein product							Standard	NM_173512		Approved	FLJ39822, AVT2	uc002ucw.2	Q08AI6	OTTHUMG00000132144	ENST00000409149.3:c.613G>A	2.37:g.165771691C>T	ENSP00000386272:p.Val205Met	Somatic		Capture	Illumina HiSeq	Phase_I	165479937	NM_173512	B4DF99|Q8N887	Missense_Mutation	SNP	ENST00000409149.3	37	CCDS56142.1	.	.	.	.	.	.	.	.	.	.	C	4.346	0.063719	0.08388	.	.	ENSG00000169507	ENST00000303735;ENST00000409149;ENST00000409058;ENST00000409662	T;T;T;T	0.02421	4.3;4.3;4.3;4.3	5.98	-1.09	0.09904	.	0.746306	0.13465	N	0.385839	T	0.01730	0.0055	N	0.11560	0.145	0.09310	N	1	B;B	0.23854	0.092;0.041	B;B	0.22880	0.042;0.025	T	0.46884	-0.9159	10	0.34782	T	0.22	0.4164	8.6632	0.34106	0.5199:0.354:0.1261:0.0	.	205;183	Q08AI6;Q08AI6-2	S38AB_HUMAN;.	M	183;205;236;205	ENSP00000306178:V183M;ENSP00000386272:V205M;ENSP00000387345:V236M;ENSP00000386774:V205M	ENSP00000306178:V183M	V	-	1	0	SLC38A11	165479937	0.419000	0.25449	0.004000	0.12327	0.119000	0.20118	0.942000	0.29017	-0.048000	0.13401	0.655000	0.94253	GTG		0.378	SLC38A11-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000333390.1	NM_173512	
SCN2A	6326	broad.mit.edu	37	2	166170146	166170146	+	Missense_Mutation	SNP	T	T	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr2:166170146T>A	ENST00000375437.2	+	9	1341	c.1051T>A	c.(1051-1053)Tac>Aac	p.Y351N	SCN2A_ENST00000283256.6_Missense_Mutation_p.Y351N|SCN2A_ENST00000357398.3_Missense_Mutation_p.Y351N|SCN2A_ENST00000375427.2_Missense_Mutation_p.Y351N	NM_001040142.1	NP_001035232.1	Q99250	SCN2A_HUMAN	sodium channel, voltage-gated, type II, alpha subunit	351					intrinsic apoptotic signaling pathway in response to osmotic stress (GO:0008627)|membrane depolarization during action potential (GO:0086010)|myelination (GO:0042552)|neuron apoptotic process (GO:0051402)|neuronal action potential (GO:0019228)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	axon (GO:0030424)|integral component of plasma membrane (GO:0005887)|intercalated disc (GO:0014704)|intrinsic component of plasma membrane (GO:0031226)|node of Ranvier (GO:0033268)|paranode region of axon (GO:0033270)|plasma membrane (GO:0005886)|sodium channel complex (GO:0034706)|T-tubule (GO:0030315)|voltage-gated sodium channel complex (GO:0001518)	voltage-gated sodium channel activity (GO:0005248)	p.Y351N(1)		NS(1)|breast(7)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(27)|liver(2)|lung(49)|ovary(6)|pancreas(1)|prostate(2)|skin(8)|upper_aerodigestive_tract(1)|urinary_tract(2)	118					Lamotrigine(DB00555)|Propofol(DB00818)|Valproic Acid(DB00313)|Zonisamide(DB00909)	TCCTGAAGGATACATCTGTGT	0.413																																					p.Y351N												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T1051A	2						.						139.0	133.0	135.0					2																	166170146		2203	4300	6503	165878392	SO:0001583	missense	6326	exon8			AB208888	CCDS33313.1, CCDS33314.1	2q24.3	2012-02-26	2007-01-23	2007-01-23	ENSG00000136531	ENSG00000136531		"""Sodium channels"", ""Voltage-gated ion channels / Sodium channels"""	10588	protein-coding gene	gene with protein product		182390	"""sodium channel, voltage-gated, type II, alpha 2 polypeptide"", ""sodium channel, voltage-gated, type II, alpha 1 polypeptide"""	SCN2A1, SCN2A2		1317301, 16382098	Standard	XM_005246753		Approved	Nav1.2, HBSCII, HBSCI	uc002ude.3	Q99250	OTTHUMG00000044172	ENST00000375437.2:c.1051T>A	2.37:g.166170146T>A	ENSP00000364586:p.Tyr351Asn	Somatic		Capture	Illumina HiSeq	Phase_I	165878392	NM_001040143	A6NC14|A6NIQ5|Q14472|Q53T77|Q9BZC9|Q9BZD0	Missense_Mutation	SNP	ENST00000375437.2	37	CCDS33314.1	.	.	.	.	.	.	.	.	.	.	T	25.3	4.628836	0.87560	.	.	ENSG00000136531	ENST00000424833;ENST00000375437;ENST00000357398;ENST00000283256;ENST00000375427	D;D;D;D;D	0.97089	-4.24;-4.22;-4.21;-4.22;-4.21	5.77	5.77	0.91146	Ion transport (1);	0.204155	0.34932	N	0.003580	D	0.98520	0.9506	M	0.86028	2.79	0.49582	D	0.999808	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	D	0.99694	1.1002	10	0.87932	D	0	.	16.3948	0.83586	0.0:0.0:0.0:1.0	.	351;351	Q99250-2;Q99250	.;SCN2A_HUMAN	N	351	ENSP00000406454:Y351N;ENSP00000364586:Y351N;ENSP00000349973:Y351N;ENSP00000283256:Y351N;ENSP00000364576:Y351N	ENSP00000283256:Y351N	Y	+	1	0	SCN2A	165878392	1.000000	0.71417	0.979000	0.43373	0.933000	0.57130	8.040000	0.89188	2.326000	0.78906	0.533000	0.62120	TAC		0.413	SCN2A-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000102659.2	NM_021007	
SCN2A	6326	broad.mit.edu	37	2	166201167	166201167	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr2:166201167G>A	ENST00000375437.2	+	16	2955	c.2665G>A	c.(2665-2667)Gcc>Acc	p.A889T	SCN2A_ENST00000283256.6_Missense_Mutation_p.A889T|SCN2A_ENST00000357398.3_Missense_Mutation_p.A889T|SCN2A_ENST00000375427.2_Missense_Mutation_p.A889T	NM_001040142.1	NP_001035232.1	Q99250	SCN2A_HUMAN	sodium channel, voltage-gated, type II, alpha subunit	889					intrinsic apoptotic signaling pathway in response to osmotic stress (GO:0008627)|membrane depolarization during action potential (GO:0086010)|myelination (GO:0042552)|neuron apoptotic process (GO:0051402)|neuronal action potential (GO:0019228)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	axon (GO:0030424)|integral component of plasma membrane (GO:0005887)|intercalated disc (GO:0014704)|intrinsic component of plasma membrane (GO:0031226)|node of Ranvier (GO:0033268)|paranode region of axon (GO:0033270)|plasma membrane (GO:0005886)|sodium channel complex (GO:0034706)|T-tubule (GO:0030315)|voltage-gated sodium channel complex (GO:0001518)	voltage-gated sodium channel activity (GO:0005248)	p.A889T(1)		NS(1)|breast(7)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(27)|liver(2)|lung(49)|ovary(6)|pancreas(1)|prostate(2)|skin(8)|upper_aerodigestive_tract(1)|urinary_tract(2)	118					Lamotrigine(DB00555)|Propofol(DB00818)|Valproic Acid(DB00313)|Zonisamide(DB00909)	CTTGGTATTGGCCATCATCGT	0.438																																					p.A889T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2665A	2						.						148.0	141.0	144.0					2																	166201167		2203	4300	6503	165909413	SO:0001583	missense	6326	exon15			AB208888	CCDS33313.1, CCDS33314.1	2q24.3	2012-02-26	2007-01-23	2007-01-23	ENSG00000136531	ENSG00000136531		"""Sodium channels"", ""Voltage-gated ion channels / Sodium channels"""	10588	protein-coding gene	gene with protein product		182390	"""sodium channel, voltage-gated, type II, alpha 2 polypeptide"", ""sodium channel, voltage-gated, type II, alpha 1 polypeptide"""	SCN2A1, SCN2A2		1317301, 16382098	Standard	XM_005246753		Approved	Nav1.2, HBSCII, HBSCI	uc002ude.3	Q99250	OTTHUMG00000044172	ENST00000375437.2:c.2665G>A	2.37:g.166201167G>A	ENSP00000364586:p.Ala889Thr	Somatic		Capture	Illumina HiSeq	Phase_I	165909413	NM_001040143	A6NC14|A6NIQ5|Q14472|Q53T77|Q9BZC9|Q9BZD0	Missense_Mutation	SNP	ENST00000375437.2	37	CCDS33314.1	.	.	.	.	.	.	.	.	.	.	G	34	5.294233	0.95546	.	.	ENSG00000136531	ENST00000375437;ENST00000357398;ENST00000283256;ENST00000375427	D;D;D;D	0.97505	-4.41;-4.41;-4.41;-4.41	5.53	5.53	0.82687	Ion transport (1);	0.000000	0.64402	D	0.000004	D	0.98150	0.9389	L	0.61387	1.9	0.80722	D	1	D;D	0.71674	0.994;0.998	D;D	0.91635	0.942;0.999	D	0.99194	1.0871	10	0.87932	D	0	.	19.4755	0.94985	0.0:0.0:1.0:0.0	.	889;889	Q99250-2;Q99250	.;SCN2A_HUMAN	T	889	ENSP00000364586:A889T;ENSP00000349973:A889T;ENSP00000283256:A889T;ENSP00000364576:A889T	ENSP00000283256:A889T	A	+	1	0	SCN2A	165909413	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	9.735000	0.98825	2.605000	0.88082	0.650000	0.86243	GCC		0.438	SCN2A-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000102659.2	NM_021007	
CSRNP3	80034	broad.mit.edu	37	2	166535654	166535654	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr2:166535654G>T	ENST00000342316.4	+	5	1421	c.1149G>T	c.(1147-1149)gaG>gaT	p.E383D	CSRNP3_ENST00000314499.7_Missense_Mutation_p.E383D|CSRNP3_ENST00000409420.1_Missense_Mutation_p.E415D	NM_024969.3	NP_079245.2	Q8WYN3	CSRN3_HUMAN	cysteine-serine-rich nuclear protein 3	383	Glu-rich.				apoptotic process (GO:0006915)|negative regulation of phosphatase activity (GO:0010923)|positive regulation of apoptotic process (GO:0043065)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	nucleus (GO:0005634)	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 (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.E383D(1)		breast(2)|cervix(1)|endometrium(1)|large_intestine(9)|lung(15)|ovary(3)|skin(2)	33						aggaggaggaggaTGACGATG	0.522																																					p.E383D												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1149T	2						.						118.0	106.0	110.0					2																	166535654		2203	4300	6503	166243900	SO:0001583	missense	80034	exon7			AB063300	CCDS2225.1	2q24.3	2012-04-17	2009-01-07	2009-01-07	ENSG00000178662	ENSG00000178662		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	30729	protein-coding gene	gene with protein product	"""TGF beta induced apotosis protein 2"", ""protein phosphatase 1, regulatory subunit 73"""		"""family with sequence similarity 130, member A2"""	FAM130A2		17726538	Standard	NM_024969		Approved	FLJ32093, TAIP-2, PPP1R73	uc002udg.3	Q8WYN3	OTTHUMG00000132145	ENST00000342316.4:c.1149G>T	2.37:g.166535654G>T	ENSP00000344042:p.Glu383Asp	Somatic		Capture	Illumina HiSeq	Phase_I	166243900	NM_001172173	B3KPR4|Q53SG0|Q6ZTX3|Q9HAF9	Missense_Mutation	SNP	ENST00000342316.4	37	CCDS2225.1	.	.	.	.	.	.	.	.	.	.	G	1.937	-0.444651	0.04604	.	.	ENSG00000178662	ENST00000421875;ENST00000431452;ENST00000314499;ENST00000342316;ENST00000409420	T	0.06528	3.29	5.79	-10.7	0.00240	.	0.515600	0.22125	N	0.064265	T	0.02649	0.0080	L	0.34521	1.04	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.30327	-0.9982	10	0.16896	T	0.51	-5.2459	4.9236	0.13882	0.5722:0.2258:0.124:0.078	.	383	Q8WYN3	CSRN3_HUMAN	D	383;390;383;383;415	ENSP00000412081:E383D	ENSP00000318258:E383D	E	+	3	2	CSRNP3	166243900	0.000000	0.05858	0.003000	0.11579	0.029000	0.11900	-2.509000	0.00960	-2.013000	0.00949	-0.136000	0.14681	GAG		0.522	CSRNP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255191.2	NM_024969	
XIRP2	129446	broad.mit.edu	37	2	168102643	168102643	+	Nonsense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr2:168102643C>T	ENST00000409195.1	+	9	4830	c.4741C>T	c.(4741-4743)Cga>Tga	p.R1581*	XIRP2_ENST00000409756.2_Intron|XIRP2_ENST00000409605.1_Intron|XIRP2_ENST00000409728.1_Intron|XIRP2_ENST00000420519.1_Intron|XIRP2_ENST00000409043.1_Intron|XIRP2_ENST00000409273.1_Nonsense_Mutation_p.R1359*|XIRP2_ENST00000295237.9_Nonsense_Mutation_p.R1581*	NM_152381.5	NP_689594.4	A4UGR9	XIRP2_HUMAN	xin actin-binding repeat containing 2	1406					actin cytoskeleton organization (GO:0030036)|cardiac muscle tissue morphogenesis (GO:0055008)|cell-cell junction organization (GO:0045216)|ventricular septum development (GO:0003281)	cell junction (GO:0030054)|Z disc (GO:0030018)		p.R1581*(2)		NS(3)|biliary_tract(2)|breast(5)|cervix(3)|endometrium(16)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(51)|lung(160)|ovary(7)|pancreas(3)|prostate(11)|skin(14)|stomach(5)|upper_aerodigestive_tract(8)|urinary_tract(7)	315						AGGGGATGTTCGAATGGCAAA	0.378																																					p.R1359X												.	.	2	Substitution - Nonsense(2)	large_intestine(2)	c.C4075T	2						.						45.0	42.0	43.0					2																	168102643		1835	4092	5927	167810889	SO:0001587	stop_gained	129446	exon7			AK056582	CCDS42768.1, CCDS42769.1, CCDS56143.1, CCDS56144.1, CCDS56145.1	2q31.1	2013-10-25	2007-06-27	2007-06-27	ENSG00000163092	ENSG00000163092			14303	protein-coding gene	gene with protein product	"""myomaxin"""	609778	"""cardiomyopathy associated 3"""	CMYA3		17046827, 12203715, 15454575	Standard	NM_001079810		Approved		uc002udx.3	A4UGR9	OTTHUMG00000154027	ENST00000409195.1:c.4741C>T	2.37:g.168102643C>T	ENSP00000386840:p.Arg1581*	Somatic		Capture	Illumina HiSeq	Phase_I	167810889	NM_001199144	A0PJ94|B2BBS0|B2BBS1|B2BBS4|B3KVH0|J3KNB1|Q53R52|Q5MJ67|Q702N7|Q86T36|Q86T38|Q86T46|Q86T51|Q86T53|Q86T55|Q86T79|Q86TB6|Q8N1M9|Q8N3R5|Q8TBV6	Nonsense_Mutation	SNP	ENST00000409195.1	37	CCDS42769.1	.	.	.	.	.	.	.	.	.	.	C	44	11.107693	0.99517	.	.	ENSG00000163092	ENST00000409195;ENST00000295237;ENST00000409273	.	.	.	5.56	4.66	0.58398	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-12.2102	12.7599	0.57359	0.3068:0.6932:0.0:0.0	.	.	.	.	X	1581;1581;1359	.	ENSP00000295237:R1581X	R	+	1	2	XIRP2	167810889	0.338000	0.24775	0.999000	0.59377	0.993000	0.82548	0.929000	0.28844	1.295000	0.44724	0.563000	0.77884	CGA		0.378	XIRP2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000333547.1	NM_152381	
LRP2	4036	broad.mit.edu	37	2	170090031	170090031	+	Missense_Mutation	SNP	C	C	T	rs200766881		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr2:170090031C>T	ENST00000263816.3	-	30	5273	c.4988G>A	c.(4987-4989)cGt>cAt	p.R1663H		NM_004525.2	NP_004516.2	P98164	LRP2_HUMAN	low density lipoprotein receptor-related protein 2	1663					cell proliferation (GO:0008283)|endocytosis (GO:0006897)|forebrain development (GO:0030900)|lipid metabolic process (GO:0006629)|phototransduction, visible light (GO:0007603)|protein glycosylation (GO:0006486)|receptor-mediated endocytosis (GO:0006898)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|vitamin D metabolic process (GO:0042359)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|coated pit (GO:0005905)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)	p.R1663H(1)		biliary_tract(1)|breast(16)|central_nervous_system(6)|cervix(2)|endometrium(24)|haematopoietic_and_lymphoid_tissue(2)|kidney(17)|large_intestine(70)|liver(1)|lung(117)|ovary(19)|pancreas(1)|prostate(2)|skin(17)|upper_aerodigestive_tract(7)|urinary_tract(13)	315				STAD - Stomach adenocarcinoma(1183;0.000766)|COAD - Colon adenocarcinoma(177;0.0101)	"""""""Insulin(DB00071)|Gentamicin(DB00798)|Insulin Regular(DB00030)|Urokinase(DB00013)"""	CATAACCCGACGAGTAGCACG	0.488																																					p.R1663H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G4988A	2						.						86.0	79.0	81.0					2																	170090031		2203	4300	6503	169798277	SO:0001583	missense	4036	exon30				CCDS2232.1	2q31.1	2013-05-28	2010-01-26		ENSG00000081479	ENSG00000081479		"""Low density lipoprotein receptors"""	6694	protein-coding gene	gene with protein product	"""megalin"""	600073				7959795	Standard	NM_004525		Approved	gp330, DBS	uc002ues.3	P98164	OTTHUMG00000132179	ENST00000263816.3:c.4988G>A	2.37:g.170090031C>T	ENSP00000263816:p.Arg1663His	Somatic		Capture	Illumina HiSeq	Phase_I	169798277	NM_004525	O00711|Q16215	Missense_Mutation	SNP	ENST00000263816.3	37	CCDS2232.1	.	.	.	.	.	.	.	.	.	.	C	10.73	1.431378	0.25813	.	.	ENSG00000081479	ENST00000263816	D	0.90955	-2.76	5.16	0.46	0.16684	Six-bladed beta-propeller, TolB-like (1);Growth factor, receptor (1);	0.815055	0.11488	N	0.559055	T	0.75258	0.3825	N	0.02266	-0.62	0.09310	N	1	B	0.06786	0.001	B	0.01281	0.0	T	0.62210	-0.6902	10	0.33141	T	0.24	.	9.335	0.38045	0.0:0.2974:0.0:0.7026	.	1663	P98164	LRP2_HUMAN	H	1663	ENSP00000263816:R1663H	ENSP00000263816:R1663H	R	-	2	0	LRP2	169798277	0.840000	0.29493	0.000000	0.03702	0.041000	0.13682	1.384000	0.34396	-0.092000	0.12417	-0.262000	0.10625	CGT		0.488	LRP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255231.2	NM_004525	
LRP2	4036	broad.mit.edu	37	2	170101288	170101288	+	Silent	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr2:170101288G>A	ENST00000263816.3	-	22	3630	c.3345C>T	c.(3343-3345)acC>acT	p.T1115T	LRP2_ENST00000443831.1_Silent_p.T978T	NM_004525.2	NP_004516.2	P98164	LRP2_HUMAN	low density lipoprotein receptor-related protein 2	1115	LDL-receptor class A 10. {ECO:0000255|PROSITE-ProRule:PRU00124}.				cell proliferation (GO:0008283)|endocytosis (GO:0006897)|forebrain development (GO:0030900)|lipid metabolic process (GO:0006629)|phototransduction, visible light (GO:0007603)|protein glycosylation (GO:0006486)|receptor-mediated endocytosis (GO:0006898)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|vitamin D metabolic process (GO:0042359)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|coated pit (GO:0005905)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)	p.T1115T(1)		biliary_tract(1)|breast(16)|central_nervous_system(6)|cervix(2)|endometrium(24)|haematopoietic_and_lymphoid_tissue(2)|kidney(17)|large_intestine(70)|liver(1)|lung(117)|ovary(19)|pancreas(1)|prostate(2)|skin(17)|upper_aerodigestive_tract(7)|urinary_tract(13)	315				STAD - Stomach adenocarcinoma(1183;0.000766)|COAD - Colon adenocarcinoma(177;0.0101)	"""""""Insulin(DB00071)|Gentamicin(DB00798)|Insulin Regular(DB00030)|Urokinase(DB00013)"""	GATTATCACAGGTGTATTGGG	0.502																																					p.T1115T												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C3345T	2						.						218.0	177.0	191.0					2																	170101288		2203	4300	6503	169809534	SO:0001819	synonymous_variant	4036	exon22				CCDS2232.1	2q31.1	2013-05-28	2010-01-26		ENSG00000081479	ENSG00000081479		"""Low density lipoprotein receptors"""	6694	protein-coding gene	gene with protein product	"""megalin"""	600073				7959795	Standard	NM_004525		Approved	gp330, DBS	uc002ues.3	P98164	OTTHUMG00000132179	ENST00000263816.3:c.3345C>T	2.37:g.170101288G>A		Somatic		Capture	Illumina HiSeq	Phase_I	169809534	NM_004525	O00711|Q16215	Silent	SNP	ENST00000263816.3	37	CCDS2232.1																																																																																				0.502	LRP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255231.2	NM_004525	
LRP2	4036	broad.mit.edu	37	2	170147494	170147494	+	Silent	SNP	A	A	G			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr2:170147494A>G	ENST00000263816.3	-	8	1068	c.783T>C	c.(781-783)caT>caC	p.H261H	LRP2_ENST00000443831.1_Silent_p.H261H	NM_004525.2	NP_004516.2	P98164	LRP2_HUMAN	low density lipoprotein receptor-related protein 2	261					cell proliferation (GO:0008283)|endocytosis (GO:0006897)|forebrain development (GO:0030900)|lipid metabolic process (GO:0006629)|phototransduction, visible light (GO:0007603)|protein glycosylation (GO:0006486)|receptor-mediated endocytosis (GO:0006898)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|vitamin D metabolic process (GO:0042359)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|coated pit (GO:0005905)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)	p.H261H(1)		biliary_tract(1)|breast(16)|central_nervous_system(6)|cervix(2)|endometrium(24)|haematopoietic_and_lymphoid_tissue(2)|kidney(17)|large_intestine(70)|liver(1)|lung(117)|ovary(19)|pancreas(1)|prostate(2)|skin(17)|upper_aerodigestive_tract(7)|urinary_tract(13)	315				STAD - Stomach adenocarcinoma(1183;0.000766)|COAD - Colon adenocarcinoma(177;0.0101)	"""""""Insulin(DB00071)|Gentamicin(DB00798)|Insulin Regular(DB00030)|Urokinase(DB00013)"""	TATGAACATCATGAGGACCGC	0.463																																					p.H261H												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.T783C	2						.						103.0	102.0	102.0					2																	170147494		2203	4300	6503	169855740	SO:0001819	synonymous_variant	4036	exon8				CCDS2232.1	2q31.1	2013-05-28	2010-01-26		ENSG00000081479	ENSG00000081479		"""Low density lipoprotein receptors"""	6694	protein-coding gene	gene with protein product	"""megalin"""	600073				7959795	Standard	NM_004525		Approved	gp330, DBS	uc002ues.3	P98164	OTTHUMG00000132179	ENST00000263816.3:c.783T>C	2.37:g.170147494A>G		Somatic		Capture	Illumina HiSeq	Phase_I	169855740	NM_004525	O00711|Q16215	Silent	SNP	ENST00000263816.3	37	CCDS2232.1																																																																																				0.463	LRP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255231.2	NM_004525	
KLHL41	10324	broad.mit.edu	37	2	170371185	170371185	+	Silent	SNP	A	A	G			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr2:170371185A>G	ENST00000284669.1	+	2	1289	c.1212A>G	c.(1210-1212)gcA>gcG	p.A404A	KLHL41_ENST00000463400.1_3'UTR|RP11-724O16.1_ENST00000513963.1_Silent_p.A342A|BBS5_ENST00000554017.1_Silent_p.A342A	NM_006063.2	NP_006054.2	O60662	KLH41_HUMAN	kelch-like family member 41	404					myofibril assembly (GO:0030239)|protein ubiquitination (GO:0016567)|regulation of lateral pseudopodium assembly (GO:0031275)|regulation of myoblast differentiation (GO:0045661)|regulation of myoblast proliferation (GO:2000291)|regulation of skeletal muscle cell differentiation (GO:2001014)|skeletal muscle cell differentiation (GO:0035914)|striated muscle contraction (GO:0006941)	Cul3-RING ubiquitin ligase complex (GO:0031463)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|M band (GO:0031430)|pseudopodium (GO:0031143)		p.A404A(1)									ATGTAGTTGCAGGCAAAGACC	0.448																																					p.A404A												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.A1212G	2						.						148.0	142.0	145.0					2																	170371185		2203	4300	6503	170079431	SO:0001819	synonymous_variant	10324	exon2			AF056929	CCDS2234.1	2q31.1	2013-02-22	2013-02-22	2013-01-08	ENSG00000239474	ENSG00000239474		"""Kelch-like"", ""BTB/POZ domain containing"""	16905	protein-coding gene	gene with protein product	"""sarcomeric muscle protein"""	607701	"""kelch repeat and BTB (POZ) domain containing 10"", ""kelch-like 41 (Drosophila)"""	KBTBD10		9655184	Standard	NM_006063		Approved	SARCOSIN, Krp1	uc002ueu.1	O60662	OTTHUMG00000132205	ENST00000284669.1:c.1212A>G	2.37:g.170371185A>G		Somatic		Capture	Illumina HiSeq	Phase_I	170079431	NM_006063	Q53R42	Silent	SNP	ENST00000284669.1	37	CCDS2234.1																																																																																				0.448	KLHL41-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255263.1	NM_006063	
METAP1D	254042	broad.mit.edu	37	2	172928559	172928559	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr2:172928559G>A	ENST00000315796.4	+	3	706	c.319G>A	c.(319-321)Gtc>Atc	p.V107I	METAP1D_ENST00000488581.1_3'UTR	NM_199227.1	NP_954697.1	Q6UB28	MAP12_HUMAN	methionyl aminopeptidase type 1D (mitochondrial)	107					N-terminal protein amino acid modification (GO:0031365)|peptidyl-methionine modification (GO:0018206)|protein initiator methionine removal (GO:0070084)	mitochondrion (GO:0005739)	aminopeptidase activity (GO:0004177)|metal ion binding (GO:0046872)|metalloaminopeptidase activity (GO:0070006)|metalloexopeptidase activity (GO:0008235)	p.V107I(1)		NS(1)|endometrium(1)|large_intestine(2)|lung(3)|skin(1)	8						GGCCCGCCACGTCCTCCTCTT	0.498																																					p.V107I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G319A	2						.						69.0	61.0	64.0					2																	172928559		2203	4300	6503	172636805	SO:0001583	missense	254042	exon3			AY374142, BC029123	CCDS2246.1	2q31.1	2010-09-21			ENSG00000172878	ENSG00000172878			32583	protein-coding gene	gene with protein product	"""methionine aminopeptidase 1D"""	610267				14532271, 16568094	Standard	NM_199227		Approved	MAP1D, Metap1l	uc002uhk.3	Q6UB28	OTTHUMG00000132283	ENST00000315796.4:c.319G>A	2.37:g.172928559G>A	ENSP00000315152:p.Val107Ile	Somatic		Capture	Illumina HiSeq	Phase_I	172636805	NM_199227	Q1WNX3	Missense_Mutation	SNP	ENST00000315796.4	37	CCDS2246.1	.	.	.	.	.	.	.	.	.	.	G	11.92	1.782781	0.31502	.	.	ENSG00000172878	ENST00000315796	T	0.79141	-1.24	5.67	5.67	0.87782	Peptidase M24, structural domain (3);	0.115539	0.64402	D	0.000015	T	0.59595	0.2205	N	0.10916	0.065	0.43489	D	0.995723	B	0.12630	0.006	B	0.15052	0.012	T	0.56038	-0.8045	10	0.39692	T	0.17	-2.6266	10.5471	0.45066	0.1434:0.0:0.8566:0.0	.	107	Q6UB28	AMP1D_HUMAN	I	107	ENSP00000315152:V107I	ENSP00000315152:V107I	V	+	1	0	METAP1D	172636805	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	3.652000	0.54439	2.836000	0.97738	0.655000	0.94253	GTC		0.498	METAP1D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255378.2	NM_199227	
SP3	6670	broad.mit.edu	37	2	174783367	174783367	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr2:174783367G>A	ENST00000310015.6	-	5	2316	c.1786C>T	c.(1786-1788)Cgg>Tgg	p.R596W	SP3_ENST00000455789.2_Missense_Mutation_p.R543W|SP3_ENST00000418194.2_Missense_Mutation_p.R528W	NM_001172712.1|NM_003111.4	NP_001166183.1|NP_003102.1	Q02447	SP3_HUMAN	Sp3 transcription factor	596	Repressor domain.				B cell differentiation (GO:0030183)|definitive hemopoiesis (GO:0060216)|embryonic camera-type eye morphogenesis (GO:0048596)|embryonic placenta development (GO:0001892)|embryonic process involved in female pregnancy (GO:0060136)|embryonic skeletal system development (GO:0048706)|enucleate erythrocyte differentiation (GO:0043353)|granulocyte differentiation (GO:0030851)|liver development (GO:0001889)|lung development (GO:0030324)|megakaryocyte differentiation (GO:0030219)|monocyte differentiation (GO:0030224)|natural killer cell differentiation (GO:0001779)|negative regulation of transcription, DNA-templated (GO:0045892)|ossification (GO:0001503)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|T cell differentiation (GO:0030217)|trophectodermal cell differentiation (GO:0001829)	nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	chromatin binding (GO:0003682)|core promoter proximal region sequence-specific DNA binding (GO:0000987)|double-stranded DNA binding (GO:0003690)|metal ion binding (GO:0046872)|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 sequence-specific DNA binding (GO:0000979)	p.R596W(1)	EWSR1/SP3(3)	NS(2)|large_intestine(3)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	9			OV - Ovarian serous cystadenocarcinoma(117;0.185)			GCTACCCTCCGAAGTCTTTTT	0.403																																					p.R593W												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1777T	2						.						188.0	168.0	175.0					2																	174783367		2203	4300	6503	174491613	SO:0001583	missense	6670	exon5			M97191	CCDS2254.1, CCDS46452.1	2q31	2013-01-08			ENSG00000172845	ENSG00000172845		"""Specificity protein transcription factors"", ""Zinc fingers, C2H2-type"""	11208	protein-coding gene	gene with protein product		601804				1341900, 1454515	Standard	NM_003111		Approved	SPR-2	uc002uig.3	Q02447	OTTHUMG00000132333	ENST00000310015.6:c.1786C>T	2.37:g.174783367G>A	ENSP00000310301:p.Arg596Trp	Somatic		Capture	Illumina HiSeq	Phase_I	174491613	NM_001172712	A0AVL9|B4E2B7|Q69B26|Q69B27|Q8TD56|Q8WWU4|Q9BQR1	Missense_Mutation	SNP	ENST00000310015.6	37	CCDS2254.1	.	.	.	.	.	.	.	.	.	.	G	17.33	3.362700	0.61403	.	.	ENSG00000172845	ENST00000310015;ENST00000455789;ENST00000418194	T;T;T	0.09630	2.96;2.98;2.98	5.5	5.5	0.81552	.	0.000000	0.85682	D	0.000000	T	0.36580	0.0972	M	0.83774	2.66	0.80722	D	1	B;P;D	0.89917	0.241;0.945;1.0	B;P;D	0.97110	0.066;0.461;1.0	T	0.10941	-1.0608	10	0.87932	D	0	.	14.5794	0.68274	0.0:0.0:0.8539:0.1461	.	593;596;543	B7ZLN9;Q02447;Q02447-6	.;SP3_HUMAN;.	W	596;543;528	ENSP00000310301:R596W;ENSP00000388903:R543W;ENSP00000406140:R528W	ENSP00000310301:R596W	R	-	1	2	SP3	174491613	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	6.476000	0.73587	2.745000	0.94114	0.491000	0.48974	CGG		0.403	SP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255452.1	NM_003111	
SCRN3	79634	broad.mit.edu	37	2	175268839	175268839	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr2:175268839C>T	ENST00000272732.6	+	5	632	c.550C>T	c.(550-552)Cgt>Tgt	p.R184C	SCRN3_ENST00000409673.3_Missense_Mutation_p.R177C	NM_001193528.1|NM_024583.4	NP_001180457.1|NP_078859.2	Q0VDG4	SCRN3_HUMAN	secernin 3	184							dipeptidase activity (GO:0016805)	p.R184C(1)		endometrium(1)|kidney(1)|large_intestine(1)|lung(6)|ovary(1)|urinary_tract(3)	13			OV - Ovarian serous cystadenocarcinoma(117;0.229)			AGAGGGAGTTCGTAATATTTC	0.363																																					p.R184C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C550T	2						.						52.0	50.0	51.0					2																	175268839		2203	4300	6503	174977085	SO:0001583	missense	79634	exon5			AF279776	CCDS2258.1, CCDS54420.1	2q31	2008-02-05			ENSG00000144306	ENSG00000144306			30382	protein-coding gene	gene with protein product		614967				12221138	Standard	NM_024583		Approved	FLJ23142	uc002uiq.3	Q0VDG4	OTTHUMG00000132332	ENST00000272732.6:c.550C>T	2.37:g.175268839C>T	ENSP00000272732:p.Arg184Cys	Somatic		Capture	Illumina HiSeq	Phase_I	174977085	NM_024583	B4DI11|C9JPC1|D3DPE0|Q7L1C5|Q9H5R5	Missense_Mutation	SNP	ENST00000272732.6	37	CCDS2258.1	.	.	.	.	.	.	.	.	.	.	C	17.66	3.444972	0.63178	.	.	ENSG00000144306	ENST00000458563;ENST00000409673;ENST00000272732;ENST00000548031	T;T;T;T	0.21932	1.98;1.98;1.98;1.98	5.29	5.29	0.74685	.	0.000000	0.85682	D	0.000000	T	0.46580	0.1400	M	0.79475	2.455	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.999	T	0.44605	-0.9317	10	0.56958	D	0.05	-12.9538	12.6104	0.56547	0.2901:0.7099:0.0:0.0	.	177;184	B4DI11;Q0VDG4	.;SCRN3_HUMAN	C	184;177;184;184	ENSP00000396884:R184C;ENSP00000387142:R177C;ENSP00000272732:R184C;ENSP00000446727:R184C	ENSP00000272732:R184C	R	+	1	0	SCRN3	174977085	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	2.890000	0.48609	2.451000	0.82905	0.462000	0.41574	CGT		0.363	SCRN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255451.2	NM_024583	
TTN	7273	broad.mit.edu	37	2	179396154	179396154	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr2:179396154G>T	ENST00000591111.1	-	308	100489	c.100265C>A	c.(100264-100266)gCt>gAt	p.A33422D	TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000589434.1_RNA|TTN-AS1_ENST00000450692.2_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000586707.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.A26123D|TTN_ENST00000460472.2_Missense_Mutation_p.A25998D|TTN-AS1_ENST00000442329.2_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.A35063D|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000589391.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN-AS1_ENST00000588244.1_RNA|TTN-AS1_ENST00000589842.1_RNA|TTN-AS1_ENST00000588804.1_RNA|TTN-AS1_ENST00000431259.2_RNA|TTN-AS1_ENST00000591867.1_RNA|TTN-AS1_ENST00000586831.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.A32495D|TTN-AS1_ENST00000585487.1_RNA|TTN-AS1_ENST00000604571.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000585625.1_RNA|TTN-AS1_ENST00000585358.1_RNA|TTN-AS1_ENST00000592182.1_RNA|TTN-AS1_ENST00000589355.1_RNA|TTN-AS1_ENST00000591466.1_RNA|TTN-AS1_ENST00000588257.1_RNA|TTN-AS1_ENST00000587944.1_RNA|TTN-AS1_ENST00000590040.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN-AS1_ENST00000591332.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.A26190D|TTN-AS1_ENST00000587568.1_RNA|TTN-AS1_ENST00000588716.1_RNA|TTN-AS1_ENST00000592836.1_RNA|TTN-AS1_ENST00000592600.1_RNA			Q8WZ42	TITIN_HUMAN	titin	33422					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.A26190D(1)|p.A25998D(1)|p.A32493D(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)			TGATGAAACAGCATACGCCTC	0.468																																					p.L25998M												.	.	3	Substitution - Missense(3)	large_intestine(3)	c.C77992A	2						.						116.0	116.0	116.0					2																	179396154		1909	4131	6040	179104400	SO:0001583	missense	7273	exon186			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.100265C>A	2.37:g.179396154G>T	ENSP00000465570:p.Ala33422Asp	Somatic		Capture	Illumina HiSeq	Phase_I	179104400	NM_003319	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	16.71	3.197968	0.58126	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.63417	-0.04;0.2;0.18;0.17	5.45	5.45	0.79879	Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);	.	.	.	.	T	0.53818	0.1820	N	0.24115	0.695	0.47214	D	0.999354	P;P;P;P	0.50272	0.933;0.933;0.933;0.93	P;P;P;B	0.44860	0.462;0.462;0.462;0.273	T	0.61153	-0.7120	9	0.87932	D	0	.	15.6335	0.76929	0.0:0.1375:0.8625:0.0	.	25998;26123;26190;33422	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	D	32495;25998;26190;26123;25995	ENSP00000343764:A32495D;ENSP00000434586:A25998D;ENSP00000340554:A26190D;ENSP00000352154:A26123D	ENSP00000340554:A26190D	A	-	2	0	TTN	179104400	1.000000	0.71417	0.950000	0.38849	0.682000	0.39822	4.279000	0.58953	2.558000	0.86282	0.650000	0.86243	GCT		0.468	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
TTN	7273	broad.mit.edu	37	2	179421585	179421585	+	Silent	SNP	G	G	A	rs370287542		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr2:179421585G>A	ENST00000591111.1	-	280	83597	c.83373C>T	c.(83371-83373)atC>atT	p.I27791I	TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000586707.1_RNA|TTN_ENST00000359218.5_Silent_p.I20492I|TTN_ENST00000460472.2_Silent_p.I20367I|TTN_ENST00000589042.1_Silent_p.I29432I|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN-AS1_ENST00000590932.1_RNA|TTN-AS1_ENST00000586831.1_RNA|TTN_ENST00000342992.6_Silent_p.I26864I|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN-AS1_ENST00000591332.1_RNA|TTN_ENST00000342175.6_Silent_p.I20559I|TTN-AS1_ENST00000438095.1_RNA|TTN-AS1_ENST00000592600.1_RNA			Q8WZ42	TITIN_HUMAN	titin	27791	Fibronectin type-III 102. {ECO:0000255|PROSITE-ProRule:PRU00316}.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)	p.I26862I(1)|p.I20559I(1)|p.I20367I(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)			CATAAGAATCGATGCAAGTAA	0.393																																					p.S20367L												.	.	3	Substitution - coding silent(3)	large_intestine(3)	c.C61100T	2						.	G	,,,	1,3795		0,1,1897	81.0	78.0	79.0		61101,80592,61476,61677	-6.4	0.8	2		79	0,8260		0,0,4130	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	TTN	NM_003319.4,NM_133378.4,NM_133432.3,NM_133437.3	,,,	0,1,6027	AA,AG,GG		0.0,0.0263,0.0083	,,,	20367/26927,26864/33424,20492/27052,20559/27119	179421585	1,12055	1898	4130	6028	179129831	SO:0001819	synonymous_variant	7273	exon158			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.83373C>T	2.37:g.179421585G>A		Somatic		Capture	Illumina HiSeq	Phase_I	179129831	NM_003319	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	Silent	SNP	ENST00000591111.1	37																																																																																					0.393	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
TTN	7273	broad.mit.edu	37	2	179449081	179449081	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr2:179449081T>C	ENST00000591111.1	-	261	60498	c.60274A>G	c.(60274-60276)Aga>Gga	p.R20092G	TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000586707.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.R12793G|TTN_ENST00000460472.2_Missense_Mutation_p.R12668G|TTN_ENST00000589042.1_Missense_Mutation_p.R21733G|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN-AS1_ENST00000590932.1_RNA|TTN-AS1_ENST00000586831.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.R19165G|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000589907.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN-AS1_ENST00000591332.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.R12860G|TTN-AS1_ENST00000438095.1_RNA|TTN-AS1_ENST00000590743.1_RNA|TTN-AS1_ENST00000592600.1_RNA			Q8WZ42	TITIN_HUMAN	titin	20092	Fibronectin type-III 45. {ECO:0000255|PROSITE-ProRule:PRU00316}.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)	p.R19163G(1)|p.R12860G(1)|p.R12668G(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)			GCATAGATTCTGAATGAATAC	0.433																																					p.S12667S												.	.	3	Substitution - Missense(3)	large_intestine(3)	c.A38001G	2						.						115.0	114.0	114.0					2																	179449081		1910	4129	6039	179157327	SO:0001583	missense	7273	exon139			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.60274A>G	2.37:g.179449081T>C	ENSP00000465570:p.Arg20092Gly	Somatic		Capture	Illumina HiSeq	Phase_I	179157327	NM_003319	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		.	.	.	.	.	.	.	.	.	.	T	11.72	1.723497	0.30593	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.60797	0.16;0.16;0.16;0.16	5.97	3.44	0.39384	Fibronectin, type III (4);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.79845	0.4516	H	0.98218	4.175	0.51012	D	0.999909	P;P;P;P	0.43938	0.822;0.822;0.822;0.822	P;P;P;P	0.51055	0.657;0.657;0.657;0.657	D	0.86889	0.2047	9	0.87932	D	0	.	14.2604	0.66080	0.0:0.0:0.2445:0.7555	.	12668;12793;12860;20092	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	G	19165;12668;12860;12793;12666	ENSP00000343764:R19165G;ENSP00000434586:R12668G;ENSP00000340554:R12860G;ENSP00000352154:R12793G	ENSP00000340554:R12860G	R	-	1	2	TTN	179157327	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	3.448000	0.52943	1.068000	0.40764	-0.291000	0.09656	AGA		0.433	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
TTN	7273	broad.mit.edu	37	2	179471892	179471892	+	Nonsense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr2:179471892G>A	ENST00000591111.1	-	228	48738	c.48514C>T	c.(48514-48516)Caa>Taa	p.Q16172*	TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000589487.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN_ENST00000359218.5_Nonsense_Mutation_p.Q8873*|TTN_ENST00000460472.2_Nonsense_Mutation_p.Q8748*|TTN_ENST00000589042.1_Nonsense_Mutation_p.Q17813*|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000342992.6_Nonsense_Mutation_p.Q15245*|TTN-AS1_ENST00000589830.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000589907.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN-AS1_ENST00000589234.1_RNA|TTN_ENST00000342175.6_Nonsense_Mutation_p.Q8940*			Q8WZ42	TITIN_HUMAN	titin	16172	Fibronectin type-III 17. {ECO:0000255|PROSITE-ProRule:PRU00316}.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)	p.Q8940*(1)|p.Q8748*(1)|p.Q15245*(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)			TCTATTGGTTGTCTCCAAGTA	0.403																																					p.Q8748X												.	.	3	Substitution - Nonsense(3)	large_intestine(3)	c.C26242T	2						.						243.0	230.0	234.0					2																	179471892		1886	4135	6021	179180137	SO:0001587	stop_gained	7273	exon106			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.48514C>T	2.37:g.179471892G>A	ENSP00000465570:p.Gln16172*	Somatic		Capture	Illumina HiSeq	Phase_I	179180137	NM_003319	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Nonsense_Mutation	SNP	ENST00000591111.1	37		.	.	.	.	.	.	.	.	.	.	G	60	42.413048	0.99986	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	.	.	.	5.84	5.84	0.93424	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	14.3205	0.66484	0.0704:0.0:0.9296:0.0	.	.	.	.	X	15245;8748;8940;8873;8748	.	ENSP00000340554:Q8940X	Q	-	1	0	TTN	179180137	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.606000	0.67641	2.760000	0.94817	0.655000	0.94253	CAA		0.403	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
KCNS3	3790	broad.mit.edu	37	2	18112959	18112959	+	Silent	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr2:18112959G>A	ENST00000403915.1	+	3	1135	c.684G>A	c.(682-684)gcG>gcA	p.A228A	KCNS3_ENST00000465292.1_Intron|KCNS3_ENST00000304101.4_Silent_p.A228A	NM_001282428.1	NP_001269357.1	Q9BQ31	KCNS3_HUMAN	potassium voltage-gated channel, delayed-rectifier, subfamily S, member 3	228					energy reserve metabolic process (GO:0006112)|potassium ion transport (GO:0006813)|protein homooligomerization (GO:0051260)|regulation of insulin secretion (GO:0050796)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|potassium channel regulator activity (GO:0015459)	p.A228A(1)		endometrium(5)|kidney(1)|large_intestine(7)|lung(11)|ovary(4)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	32	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.158)					TGGAGATCGCGTGCATTGCCT	0.547																																					p.A228A												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G684A	2						.						81.0	79.0	80.0					2																	18112959		2203	4300	6503	17976440	SO:0001819	synonymous_variant	3790	exon3			AF043472	CCDS1692.1	2p24	2011-07-05			ENSG00000170745	ENSG00000170745		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	6302	protein-coding gene	gene with protein product		603888				10484328, 16382104	Standard	NM_002252		Approved	Kv9.3	uc002rcw.3	Q9BQ31	OTTHUMG00000044150	ENST00000403915.1:c.684G>A	2.37:g.18112959G>A		Somatic		Capture	Illumina HiSeq	Phase_I	17976440	NM_002252	D6W520|O43651|Q4ZFY1|Q96B56	Silent	SNP	ENST00000403915.1	37	CCDS1692.1																																																																																				0.547	KCNS3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323808.1	NM_002252	
NT5C1B	93034	broad.mit.edu	37	2	18765920	18765920	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr2:18765920C>T	ENST00000359846.2	-	5	840	c.763G>A	c.(763-765)Gcc>Acc	p.A255T	NT5C1B_ENST00000600945.1_Missense_Mutation_p.A255T|NT5C1B-RDH14_ENST00000532967.1_Missense_Mutation_p.A255T|NT5C1B_ENST00000304081.4_Missense_Mutation_p.A195T|NT5C1B_ENST00000460052.1_5'Flank|RNU6-1215P_ENST00000384441.1_RNA	NM_001002006.2|NM_001199086.1|NM_001199087.1|NM_001199088.1	NP_001002006.1|NP_001186015.1|NP_001186016.1|NP_001186017.1	Q96P26	5NT1B_HUMAN	5'-nucleotidase, cytosolic IB	255					nucleobase-containing small molecule metabolic process (GO:0055086)|purine nucleobase metabolic process (GO:0006144)|purine nucleotide catabolic process (GO:0006195)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|nucleus (GO:0005634)	5'-nucleotidase activity (GO:0008253)|magnesium ion binding (GO:0000287)|nucleotide binding (GO:0000166)	p.A255T(1)		endometrium(2)|kidney(2)|large_intestine(10)|lung(8)|ovary(1)|pancreas(1)|prostate(1)|skin(3)|urinary_tract(1)	29	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.177)	Ovarian(717;0.208)				TGGGTGGAGGCGGGGTAGATC	0.667																																					p.A195T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G583A	2						.						21.0	23.0	23.0					2																	18765920		2203	4299	6502	18629401	SO:0001583	missense	93034	exon4			AF356185	CCDS33149.1, CCDS33150.1	2p24.2	2010-08-13			ENSG00000185013	ENSG00000185013	3.1.3.5		17818	protein-coding gene	gene with protein product		610526				11690631	Standard	NM_033253		Approved	AIRP, CN-IB		Q96P26	OTTHUMG00000151765	ENST00000359846.2:c.763G>A	2.37:g.18765920C>T	ENSP00000352904:p.Ala255Thr	Somatic		Capture	Illumina HiSeq	Phase_I	18629401	NM_033253	B5MCR0|B7ZVX7|Q53RX2|Q8N9W3|Q8NA26|Q96DU5|Q96KE6|Q96M25|Q96SA3	Missense_Mutation	SNP	ENST00000359846.2	37	CCDS33150.1	.	.	.	.	.	.	.	.	.	.	C	10.06	1.246475	0.22796	.	.	ENSG00000250741;ENSG00000250741;ENSG00000185013;ENSG00000185013	ENST00000532967;ENST00000444297;ENST00000304081;ENST00000359846	D	0.88741	-2.42	4.09	-5.96	0.02234	.	3.679170	0.00628	N	0.000464	T	0.67795	0.2931	N	0.03608	-0.345	0.09310	N	1	B;B;B;B;B;B;B;B;B	0.26547	0.005;0.02;0.152;0.005;0.001;0.004;0.143;0.088;0.143	B;B;B;B;B;B;B;B;B	0.15052	0.001;0.003;0.005;0.001;0.001;0.006;0.011;0.005;0.012	T	0.64922	-0.6293	10	0.15952	T	0.53	-32.0467	1.5529	0.02578	0.1751:0.3856:0.093:0.3463	.	238;272;195;238;197;47;195;255;255	E7EXB7;B4DZ86;B4DXQ9;B4DXZ9;C9J2C7;Q96P26-3;Q96P26-2;Q96P26;Q96P26-4	.;.;.;.;.;.;.;5NT1B_HUMAN;.	T	255;197;195;255	ENSP00000412639:A197T	ENSP00000305979:A195T	A	-	1	0	NT5C1B-RDH14;NT5C1B	18629401	0.000000	0.05858	0.000000	0.03702	0.015000	0.08874	-1.926000	0.01562	-1.049000	0.03234	0.313000	0.20887	GCC		0.667	NT5C1B-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000323822.1		
TTN	7273	broad.mit.edu	37	2	179587192	179587192	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr2:179587192C>T	ENST00000591111.1	-	75	21595	c.21371G>A	c.(21370-21372)cGa>cAa	p.R7124Q	TTN_ENST00000359218.5_Intron|TTN_ENST00000460472.2_Intron|TTN_ENST00000589042.1_Missense_Mutation_p.R7441Q|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.R6197Q|RP11-171I2.1_ENST00000590024.1_RNA|TTN_ENST00000342175.6_Intron			Q8WZ42	TITIN_HUMAN	titin	12700	Ig-like 53.				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.R6197Q(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)			GCCATTTAATCGACAAGTGAG	0.418																																					p.R6197Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G18590A	2						.						93.0	90.0	91.0					2																	179587192		1868	4122	5990	179295437	SO:0001583	missense	7273	exon74			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.21371G>A	2.37:g.179587192C>T	ENSP00000465570:p.Arg7124Gln	Somatic		Capture	Illumina HiSeq	Phase_I	179295437	NM_133378	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		.	.	.	.	.	.	.	.	.	.	C	13.36	2.214394	0.39102	.	.	ENSG00000155657	ENST00000342992	T	0.66280	-0.2	5.95	5.95	0.96441	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.72550	0.3474	L	0.37897	1.145	0.80722	D	1	D	0.89917	1.0	D	0.64410	0.925	T	0.73569	-0.3941	9	0.87932	D	0	.	20.3812	0.98933	0.0:1.0:0.0:0.0	.	7124	Q8WZ42	TITIN_HUMAN	Q	6197	ENSP00000343764:R6197Q	ENSP00000343764:R6197Q	R	-	2	0	TTN	179295437	0.997000	0.39634	0.999000	0.59377	0.995000	0.86356	3.779000	0.55379	2.821000	0.97095	0.650000	0.86243	CGA		0.418	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
MYT1L	23040	broad.mit.edu	37	2	1946986	1946986	+	Silent	SNP	G	G	A	rs575777422	byFrequency	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr2:1946986G>A	ENST00000399161.2	-	9	1020	c.273C>T	c.(271-273)gaC>gaT	p.D91D	MYT1L_ENST00000428368.2_Silent_p.D91D	NM_015025.2	NP_055840.2	Q9UL68	MYT1L_HUMAN	myelin transcription factor 1-like	91					cell differentiation (GO:0030154)|nervous system development (GO:0007399)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)	p.D91D(1)		breast(1)|central_nervous_system(1)|cervix(2)|endometrium(5)|kidney(6)|large_intestine(16)|lung(50)|ovary(5)|prostate(2)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(2)	97	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.0797)	all_cancers(51;0.037)|all_epithelial(98;0.241)		OV - Ovarian serous cystadenocarcinoma(76;0.169)|all cancers(51;0.244)		CATCACTGTCGTCACACTCAT	0.522													G|||	15	0.00299521	0.0	0.0	5008	,	,		18303	0.001		0.0	False		,,,				2504	0.0143				p.D91D												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C273T	2						.						98.0	95.0	96.0					2																	1946986		2120	4188	6308	1925993	SO:0001819	synonymous_variant	23040	exon9			AF036943	CCDS46222.1	2p25.3	2013-01-10			ENSG00000186487	ENSG00000186487		"""Zinc fingers, C2HC-type containing"""	7623	protein-coding gene	gene with protein product	"""neural zinc finger transcription factor 1"""	613084				9373037	Standard	XM_006711862		Approved	KIAA1106, NZF1, ZC2HC4B	uc002qxd.3	Q9UL68	OTTHUMG00000151407	ENST00000399161.2:c.273C>T	2.37:g.1946986G>A		Somatic		Capture	Illumina HiSeq	Phase_I	1925993	NM_015025	A7E2C7|B2RP54|Q6IQ17|Q9UPP6	Silent	SNP	ENST00000399161.2	37																																																																																					0.522	MYT1L-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000322493.1	NM_015025	
STAT1	6772	broad.mit.edu	37	2	191845365	191845365	+	Missense_Mutation	SNP	G	G	A	rs1803838		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr2:191845365G>A	ENST00000361099.3	-	19	2000	c.1613C>T	c.(1612-1614)cCg>cTg	p.P538L	STAT1_ENST00000392322.3_Missense_Mutation_p.P538L|STAT1_ENST00000540176.1_3'UTR|STAT1_ENST00000409465.1_Missense_Mutation_p.P538L|STAT1_ENST00000392323.2_Missense_Mutation_p.P540L	NM_007315.3	NP_009330.1	P42224	STAT1_HUMAN	signal transducer and activator of transcription 1, 91kDa	538					apoptotic process (GO:0006915)|blood circulation (GO:0008015)|cellular response to insulin stimulus (GO:0032869)|cellular response to interferon-beta (GO:0035458)|cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|interferon-gamma-mediated signaling pathway (GO:0060333)|JAK-STAT cascade (GO:0007259)|JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)|lipopolysaccharide-mediated signaling pathway (GO:0031663)|metanephric mesenchymal cell differentiation (GO:0072162)|metanephric mesenchymal cell proliferation involved in metanephros development (GO:0072136)|negative regulation of angiogenesis (GO:0016525)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of macrophage fusion (GO:0034240)|negative regulation of mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003340)|negative regulation of metanephric nephron tubule epithelial cell differentiation (GO:0072308)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of apoptotic process (GO:0042981)|regulation of interferon-gamma-mediated signaling pathway (GO:0060334)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|renal tubule development (GO:0061326)|response to cAMP (GO:0051591)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to exogenous dsRNA (GO:0043330)|response to hydrogen peroxide (GO:0042542)|response to mechanical stimulus (GO:0009612)|response to nutrient (GO:0007584)|response to peptide hormone (GO:0043434)|transcription from RNA polymerase II promoter (GO:0006366)|tumor necrosis factor-mediated signaling pathway (GO:0033209)|type I interferon signaling pathway (GO:0060337)|viral process (GO:0016032)	axon (GO:0030424)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendrite (GO:0030425)|nuclear chromatin (GO:0000790)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|double-stranded DNA binding (GO:0003690)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|protein homodimerization activity (GO:0042803)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II core promoter sequence-specific DNA binding transcription factor activity (GO:0000983)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|tumor necrosis factor receptor binding (GO:0005164)	p.P538L(1)		autonomic_ganglia(1)|breast(3)|central_nervous_system(2)|cervix(2)|endometrium(5)|kidney(2)|large_intestine(6)|lung(13)|ovary(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	39			OV - Ovarian serous cystadenocarcinoma(117;0.00434)|Epithelial(96;0.0555)|all cancers(119;0.141)			CCTCGTCCACGGAATGAGACC	0.433																																					p.P538L												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1613T	2						.						135.0	123.0	127.0					2																	191845365		2203	4300	6503	191553610	SO:0001583	missense	6772	exon19				CCDS2309.1, CCDS42793.1	2q32.2-q32.3	2014-09-17	2002-08-29		ENSG00000115415	ENSG00000115415		"""SH2 domain containing"""	11362	protein-coding gene	gene with protein product	"""transcription factor ISGF-3 components p91/p84"""	600555	"""signal transducer and activator of transcription 1, 91kD"""			7885841	Standard	NM_139266		Approved	STAT91, ISGF-3	uc002usj.2	P42224	OTTHUMG00000132699	ENST00000361099.3:c.1613C>T	2.37:g.191845365G>A	ENSP00000354394:p.Pro538Leu	Somatic		Capture	Illumina HiSeq	Phase_I	191553610	NM_007315	A8K989|B2RCA0|D2KFR8|D3DPI7|Q53S88|Q53XW4|Q68D00|Q9UDL5	Missense_Mutation	SNP	ENST00000361099.3	37	CCDS2309.1	.	.	.	.	.	.	.	.	.	.	G	16.09	3.023449	0.54683	.	.	ENSG00000115415	ENST00000361099;ENST00000409465;ENST00000392322;ENST00000392323	D;D;D;D	0.87412	-2.25;-2.25;-2.25;-2.25	5.13	5.13	0.70059	STAT transcription factor, DNA-binding (1);p53-like transcription factor, DNA-binding (1);EF-hand-like domain (1);	0.000000	0.85682	D	0.000000	D	0.89853	0.6835	M	0.71581	2.175	0.80722	D	1	D;P	0.58970	0.984;0.588	P;B	0.48677	0.586;0.147	D	0.91152	0.4954	10	0.87932	D	0	-22.3279	19.1279	0.93393	0.0:0.0:1.0:0.0	rs1803838	538;538	P42224-2;P42224	.;STAT1_HUMAN	L	538;538;538;540	ENSP00000354394:P538L;ENSP00000386244:P538L;ENSP00000376136:P538L;ENSP00000376137:P540L	ENSP00000354394:P538L	P	-	2	0	STAT1	191553610	1.000000	0.71417	0.910000	0.35882	0.272000	0.26649	3.982000	0.56909	2.824000	0.97209	0.655000	0.94253	CCG		0.433	STAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255997.3	NM_007315	
HSPD1	3329	broad.mit.edu	37	2	198358153	198358153	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr2:198358153T>C	ENST00000388968.3	-	7	1031	c.764A>G	c.(763-765)cAg>cGg	p.Q255R	HSPD1_ENST00000345042.2_Missense_Mutation_p.Q255R	NM_002156.4	NP_002147.2	P10809	CH60_HUMAN	heat shock 60kDa protein 1 (chaperonin)	255					'de novo' protein folding (GO:0006458)|activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|ATP catabolic process (GO:0006200)|B cell activation (GO:0042113)|B cell cytokine production (GO:0002368)|B cell proliferation (GO:0042100)|chaperone-mediated protein complex assembly (GO:0051131)|isotype switching to IgG isotypes (GO:0048291)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|negative regulation of apoptotic process (GO:0043066)|positive regulation of apoptotic process (GO:0043065)|positive regulation of interferon-alpha production (GO:0032727)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interleukin-10 production (GO:0032733)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of macrophage activation (GO:0043032)|positive regulation of T cell activation (GO:0050870)|positive regulation of T cell mediated immune response to tumor cell (GO:0002842)|protein maturation (GO:0051604)|protein refolding (GO:0042026)|protein stabilization (GO:0050821)|response to unfolded protein (GO:0006986)|T cell activation (GO:0042110)|viral process (GO:0016032)	cell surface (GO:0009986)|coated pit (GO:0005905)|coated vesicle (GO:0030135)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|early endosome (GO:0005769)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|lipopolysaccharide receptor complex (GO:0046696)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|secretory granule (GO:0030141)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|chaperone binding (GO:0051087)|DNA replication origin binding (GO:0003688)|double-stranded RNA binding (GO:0003725)|lipopolysaccharide binding (GO:0001530)|p53 binding (GO:0002039)|poly(A) RNA binding (GO:0044822)|single-stranded DNA binding (GO:0003697)|unfolded protein binding (GO:0051082)	p.Q255R(1)		NS(1)|breast(3)|endometrium(2)|large_intestine(3)|lung(7)|skin(1)	17			Epithelial(96;0.225)			TACAATGGACTGGATACTAGA	0.368																																					p.Q255R												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A764G	2						.						77.0	77.0	77.0					2																	198358153		2203	4300	6503	198066398	SO:0001583	missense	3329	exon7			M34664	CCDS33357.1	2q33.1	2011-09-02	2002-08-29		ENSG00000144381	ENSG00000144381		"""Heat Shock Proteins / Chaperonins"""	5261	protein-coding gene	gene with protein product		118190	"""heat shock 60kD protein 1 (chaperonin)"", ""spastic paraplegia 13 (autosomal dominant)"""	SPG13		1980192, 11898127	Standard	NM_002156		Approved	GROEL, HSP60	uc002uui.3	P10809	OTTHUMG00000154463	ENST00000388968.3:c.764A>G	2.37:g.198358153T>C	ENSP00000373620:p.Gln255Arg	Somatic		Capture	Illumina HiSeq	Phase_I	198066398	NM_002156	B2R5M6|B7Z712|Q38L19|Q9UCR6	Missense_Mutation	SNP	ENST00000388968.3	37	CCDS33357.1	.	.	.	.	.	.	.	.	.	.	T	20.3	3.970818	0.74246	.	.	ENSG00000144381	ENST00000388968;ENST00000345042;ENST00000536745	T;T	0.78924	-1.22;-1.22	5.42	5.42	0.78866	.	0.000000	0.85682	D	0.000000	T	0.78310	0.4263	M	0.67953	2.075	0.80722	D	1	B;B;B	0.18013	0.025;0.014;0.014	B;B;B	0.26770	0.073;0.073;0.019	T	0.76790	-0.2829	10	0.87932	D	0	-2.9182	15.7532	0.78005	0.0:0.0:0.0:1.0	.	246;255;255	B7Z597;B3GQS7;P10809	.;.;CH60_HUMAN	R	255;255;111	ENSP00000373620:Q255R;ENSP00000340019:Q255R	ENSP00000340019:Q255R	Q	-	2	0	HSPD1	198066398	1.000000	0.71417	1.000000	0.80357	0.962000	0.63368	7.932000	0.87634	2.176000	0.68965	0.528000	0.53228	CAG		0.368	HSPD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335324.2	NM_002156	
PUM2	23369	broad.mit.edu	37	2	20478422	20478422	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr2:20478422G>A	ENST00000361078.2	-	12	1901	c.1879C>T	c.(1879-1881)Cca>Tca	p.P627S	PUM2_ENST00000403432.1_Missense_Mutation_p.P627S|PUM2_ENST00000319801.5_Intron|PUM2_ENST00000536417.1_Missense_Mutation_p.P571S|PUM2_ENST00000338086.5_Missense_Mutation_p.P627S			Q8TB72	PUM2_HUMAN	pumilio RNA-binding family member 2	627	Ser-rich.				regulation of translation (GO:0006417)|stress granule assembly (GO:0034063)	cytoplasm (GO:0005737)|cytoplasmic stress granule (GO:0010494)|nuclear membrane (GO:0031965)|perinuclear region of cytoplasm (GO:0048471)	poly(A) RNA binding (GO:0044822)	p.P627S(1)		breast(2)|central_nervous_system(1)|endometrium(6)|kidney(4)|large_intestine(7)|lung(13)|ovary(2)|prostate(4)|urinary_tract(3)	42	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					GTTTGGCTTGGCAGAGGCATG	0.448																																					p.P627S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1879T	2						.						142.0	137.0	138.0					2																	20478422		2203	4299	6502	20341903	SO:0001583	missense	23369	exon12			AF315591	CCDS1698.1, CCDS74486.1, CCDS74487.1	2p22-p21	2013-09-02	2013-09-02		ENSG00000055917	ENSG00000055917			14958	protein-coding gene	gene with protein product		607205	"""pumilio (Drosphila) homolog 2"", ""pumilio homolog 2 (Drosophila)"""			9039502, 12459267, 12511597	Standard	XM_005262607		Approved	PUMH2, KIAA0235	uc002rds.1	Q8TB72	OTTHUMG00000122098	ENST00000361078.2:c.1879C>T	2.37:g.20478422G>A	ENSP00000354370:p.Pro627Ser	Somatic		Capture	Illumina HiSeq	Phase_I	20341903	NM_015317	B3KSL0|B4E2B6|D6W527|O00234|Q53TV7|Q8WY43|Q9HAN2	Missense_Mutation	SNP	ENST00000361078.2	37		.	.	.	.	.	.	.	.	.	.	G	18.22	3.575033	0.65878	.	.	ENSG00000055917	ENST00000338086;ENST00000361078;ENST00000403432;ENST00000536417	T;T;T;T	0.19250	2.18;2.46;2.18;2.16	5.73	4.86	0.63082	.	0.000000	0.64402	D	0.000001	T	0.37433	0.1003	L	0.46157	1.445	0.43133	D	0.994878	D;D;D	0.89917	1.0;1.0;0.98	D;D;P	0.91635	0.999;0.999;0.857	T	0.08472	-1.0720	10	0.19147	T	0.46	-8.0943	14.9125	0.70770	0.0688:0.0:0.9312:0.0	.	571;627;627	B4E2B6;Q8TB72-3;Q8TB72	.;.;PUM2_HUMAN	S	627;627;627;571	ENSP00000338173:P627S;ENSP00000354370:P627S;ENSP00000385992:P627S;ENSP00000440093:P571S	ENSP00000338173:P627S	P	-	1	0	PUM2	20341903	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.569000	0.82380	1.444000	0.47605	0.650000	0.86243	CCA		0.448	PUM2-202	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_015317	
HSPD1	3329	broad.mit.edu	37	2	198361985	198361985	+	Silent	SNP	G	G	T	rs527339486		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr2:198361985G>T	ENST00000388968.3	-	3	573	c.306C>A	c.(304-306)gcC>gcA	p.A102A	HSPE1_ENST00000233893.5_5'Flank|HSPD1_ENST00000544407.1_Silent_p.A102A|HSPE1_ENST00000409729.1_5'Flank|HSPD1_ENST00000345042.2_Silent_p.A102A	NM_002156.4	NP_002147.2	P10809	CH60_HUMAN	heat shock 60kDa protein 1 (chaperonin)	102					'de novo' protein folding (GO:0006458)|activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|ATP catabolic process (GO:0006200)|B cell activation (GO:0042113)|B cell cytokine production (GO:0002368)|B cell proliferation (GO:0042100)|chaperone-mediated protein complex assembly (GO:0051131)|isotype switching to IgG isotypes (GO:0048291)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|negative regulation of apoptotic process (GO:0043066)|positive regulation of apoptotic process (GO:0043065)|positive regulation of interferon-alpha production (GO:0032727)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interleukin-10 production (GO:0032733)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of macrophage activation (GO:0043032)|positive regulation of T cell activation (GO:0050870)|positive regulation of T cell mediated immune response to tumor cell (GO:0002842)|protein maturation (GO:0051604)|protein refolding (GO:0042026)|protein stabilization (GO:0050821)|response to unfolded protein (GO:0006986)|T cell activation (GO:0042110)|viral process (GO:0016032)	cell surface (GO:0009986)|coated pit (GO:0005905)|coated vesicle (GO:0030135)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|early endosome (GO:0005769)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|lipopolysaccharide receptor complex (GO:0046696)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|secretory granule (GO:0030141)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|chaperone binding (GO:0051087)|DNA replication origin binding (GO:0003688)|double-stranded RNA binding (GO:0003725)|lipopolysaccharide binding (GO:0001530)|p53 binding (GO:0002039)|poly(A) RNA binding (GO:0044822)|single-stranded DNA binding (GO:0003697)|unfolded protein binding (GO:0051082)	p.A102A(1)		NS(1)|breast(3)|endometrium(2)|large_intestine(3)|lung(7)|skin(1)	17			Epithelial(96;0.225)			TTGTGTTATTGGCAACATCTT	0.408																																					p.A102A												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C306A	2						.						115.0	108.0	111.0					2																	198361985		2203	4300	6503	198070230	SO:0001819	synonymous_variant	3329	exon3			M34664	CCDS33357.1	2q33.1	2011-09-02	2002-08-29		ENSG00000144381	ENSG00000144381		"""Heat Shock Proteins / Chaperonins"""	5261	protein-coding gene	gene with protein product		118190	"""heat shock 60kD protein 1 (chaperonin)"", ""spastic paraplegia 13 (autosomal dominant)"""	SPG13		1980192, 11898127	Standard	NM_002156		Approved	GROEL, HSP60	uc002uui.3	P10809	OTTHUMG00000154463	ENST00000388968.3:c.306C>A	2.37:g.198361985G>T		Somatic		Capture	Illumina HiSeq	Phase_I	198070230	NM_002156	B2R5M6|B7Z712|Q38L19|Q9UCR6	Silent	SNP	ENST00000388968.3	37	CCDS33357.1																																																																																				0.408	HSPD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335324.2	NM_002156	
PARD3B	117583	broad.mit.edu	37	2	205986516	205986516	+	Silent	SNP	C	C	T	rs369314488		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr2:205986516C>T	ENST00000406610.2	+	8	1215	c.1008C>T	c.(1006-1008)acC>acT	p.T336T	PARD3B_ENST00000462231.1_Silent_p.T336T|PARD3B_ENST00000351153.1_Silent_p.T336T|PARD3B_ENST00000349953.3_Silent_p.T336T|PARD3B_ENST00000358768.2_Silent_p.T336T	NM_057177.6|NM_152526.5|NM_205863.3	NP_476518.4|NP_689739.4|NP_995585.2	Q8TEW8	PAR3L_HUMAN	par-3 family cell polarity regulator beta	336					cell cycle (GO:0007049)|cell division (GO:0051301)	membrane (GO:0016020)|tight junction (GO:0005923)		p.T337T(1)		breast(1)|endometrium(9)|kidney(2)|large_intestine(6)|liver(4)|lung(33)|ovary(1)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)	65		all_cancers(1;2.88e-06)|all_epithelial(1;3.23e-06)		Epithelial(149;0.0739)		TCACAGGAACCGATAGTCCTG	0.478																																					p.T336T												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1008T	2						.	C	,,	0,3830		0,0,1915	118.0	110.0	113.0		1008,1008,1008	-5.5	0.0	2		113	1,8271		0,1,4135	no	coding-synonymous,coding-synonymous,coding-synonymous	PARD3B	NM_057177.6,NM_152526.5,NM_205863.3	,,	0,1,6050	TT,TC,CC		0.0121,0.0,0.0083	,,	336/1137,336/1144,336/1105	205986516	1,12101	1915	4136	6051	205694761	SO:0001819	synonymous_variant	117583	exon8			AB053321	CCDS42804.1, CCDS42805.1, CCDS42806.1	2q33.3	2013-08-28	2013-08-28	2006-09-28	ENSG00000116117	ENSG00000116117			14446	protein-coding gene	gene with protein product			"""amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 19"", ""par-3 partitioning defective 3 homolog B (C. elegans)"""	ALS2CR19		11586298, 12459187	Standard	NM_057177		Approved	Par3L, PAR3beta	uc002vap.2	Q8TEW8	OTTHUMG00000154562	ENST00000406610.2:c.1008C>T	2.37:g.205986516C>T		Somatic		Capture	Illumina HiSeq	Phase_I	205694761	NM_057177	E9PE87|Q8IUC7|Q8IUC9|Q96DK9|Q96N09|Q96NX6|Q96NX7|Q96Q29	Silent	SNP	ENST00000406610.2	37																																																																																					0.478	PARD3B-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000335992.1	NM_057177	
HS1BP3	64342	broad.mit.edu	37	2	20824597	20824597	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr2:20824597G>A	ENST00000304031.3	-	5	704	c.679C>T	c.(679-681)Cgg>Tgg	p.R227W		NM_022460.3	NP_071905.3	Q53T59	H1BP3_HUMAN	HCLS1 binding protein 3	227	Pro-rich.						phosphatidylinositol binding (GO:0035091)	p.R227W(1)		endometrium(4)|large_intestine(1)|lung(7)|ovary(1)|skin(2)	15	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					ATGGTGAGCCGGGGCGAGGGC	0.582																																					p.R227W												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C679T	2						.						86.0	90.0	88.0					2																	20824597		2203	4300	6503	20688078	SO:0001583	missense	64342	exon5				CCDS1700.1	2p24.1	2006-08-15			ENSG00000118960	ENSG00000118960			24979	protein-coding gene	gene with protein product		609359				10590261, 15699368	Standard	NM_022460		Approved	HS1-BP3,FLJ14249	uc002rdw.1	Q53T59	OTTHUMG00000122099	ENST00000304031.3:c.679C>T	2.37:g.20824597G>A	ENSP00000305193:p.Arg227Trp	Somatic		Capture	Illumina HiSeq	Phase_I	20688078	NM_022460	B2RAW2|D6W529|Q86VC2|Q8N367	Missense_Mutation	SNP	ENST00000304031.3	37	CCDS1700.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	19.05|19.05	3.752874|3.752874	0.69648|0.69648	.|.	.|.	ENSG00000118960|ENSG00000118960	ENST00000445102|ENST00000304031;ENST00000458740	T|T;T	0.36340|0.37915	1.26|1.94;1.17	4.7|4.7	2.72|2.72	0.32119|0.32119	.|.	.|0.099079	.|0.38058	.|N	.|0.001840	T|T	0.50051|0.50051	0.1593|0.1593	M|M	0.64997|0.64997	1.995|1.995	0.80722|0.80722	D|D	1|1	.|D	.|0.89917	.|1.0	.|D	.|0.87578	.|0.998	T|T	0.50294|0.50294	-0.8845|-0.8845	7|10	0.72032|0.87932	D|D	0.01|0	-12.0353|-12.0353	5.2373|5.2373	0.15452|0.15452	0.1056:0.0:0.6806:0.2138|0.1056:0.0:0.6806:0.2138	.|.	.|227	.|Q53T59	.|H1BP3_HUMAN	L|W	19|227;46	ENSP00000397546:P19L|ENSP00000305193:R227W;ENSP00000392203:R46W	ENSP00000397546:P19L|ENSP00000305193:R227W	P|R	-|-	2|1	0|2	HS1BP3|HS1BP3	20688078|20688078	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.943000|0.943000	0.58893|0.58893	1.201000|1.201000	0.32259|0.32259	1.185000|1.185000	0.42971|0.42971	0.655000|0.655000	0.94253|0.94253	CCG|CGG		0.582	HS1BP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000242863.1	NM_022460	
GPR1	2825	broad.mit.edu	37	2	207041182	207041182	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr2:207041182G>T	ENST00000407325.2	-	3	1152	c.790C>A	c.(790-792)Ctg>Atg	p.L264M	GPR1_ENST00000437420.1_Missense_Mutation_p.L264M	NM_001098199.1|NM_001261452.1|NM_001261453.1|NM_001261454.1|NM_001261455.1|NM_005279.3	NP_001091669.1|NP_001248381.1|NP_001248382.1|NP_001248383.1|NP_001248384.1|NP_005270.2	P46091	GPR1_HUMAN	G protein-coupled receptor 1	264					G-protein coupled receptor signaling pathway (GO:0007186)	integral component of plasma membrane (GO:0005887)	G-protein coupled receptor activity (GO:0004930)	p.L264M(1)		breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(7)|skin(1)	18		Lung NSC(271;7.93e-06)|Renal(323;0.000147)|Hepatocellular(293;0.000888)		UCEC - Uterine corpus endometrioid carcinoma (47;0.000241)|Epithelial(149;1.91e-37)|STAD - Stomach adenocarcinoma(1183;0.00178)|Lung(261;0.111)|LUSC - Lung squamous cell carcinoma(261;0.184)		ATGCTAAACAGGTGATAAGGA	0.488																																					p.L264M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C790A	2						.						99.0	97.0	98.0					2																	207041182		2203	4300	6503	206749427	SO:0001583	missense	2825	exon3				CCDS2368.1	2q33.3	2014-01-30			ENSG00000183671	ENSG00000183671		"""GPCR / Class A : Orphans"""	4463	protein-coding gene	gene with protein product		600239				7851889	Standard	NM_005279		Approved		uc031rqv.1	P46091	OTTHUMG00000132894	ENST00000407325.2:c.790C>A	2.37:g.207041182G>T	ENSP00000384345:p.Leu264Met	Somatic		Capture	Illumina HiSeq	Phase_I	206749427	NM_001098199	A5JUU6|A8K4L1|Q53TR9|Q6NVX4	Missense_Mutation	SNP	ENST00000407325.2	37	CCDS2368.1	.	.	.	.	.	.	.	.	.	.	G	16.20	3.055892	0.55325	.	.	ENSG00000183671	ENST00000407325;ENST00000437420	T;T	0.73575	-0.76;-0.76	5.7	3.77	0.43336	GPCR, rhodopsin-like superfamily (1);	0.453747	0.19694	N	0.108191	T	0.77096	0.4080	M	0.62723	1.935	0.29214	N	0.874364	P	0.45634	0.863	P	0.52758	0.708	T	0.72207	-0.4360	10	0.52906	T	0.07	.	7.5862	0.27993	0.0784:0.0:0.4373:0.4843	.	264	P46091	GPR1_HUMAN	M	264	ENSP00000384345:L264M;ENSP00000397535:L264M	ENSP00000384345:L264M	L	-	1	2	GPR1	206749427	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	1.676000	0.37565	1.385000	0.46445	0.655000	0.94253	CTG		0.488	GPR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256394.2	NM_001098199	
ZDBF2	57683	broad.mit.edu	37	2	207174321	207174321	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr2:207174321G>A	ENST00000374423.3	+	5	5455	c.5069G>A	c.(5068-5070)cGg>cAg	p.R1690Q		NM_020923.1	NP_065974.1	Q9HCK1	ZDBF2_HUMAN	zinc finger, DBF-type containing 2	1690							nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)	p.R1690Q(1)		endometrium(4)|kidney(5)|large_intestine(28)|lung(50)|ovary(4)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	95						GCCAGTCTTCGGAAGGATCCA	0.458																																					p.R1690Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G5069A	2						.						81.0	81.0	81.0					2																	207174321		1932	4122	6054	206882566	SO:0001583	missense	57683	exon5			AB046791	CCDS46501.1, CCDS74637.1	2q33.3	2013-01-10			ENSG00000204186	ENSG00000204186		"""Zinc fingers, DBF-type"""	29313	protein-coding gene	gene with protein product						10997877	Standard	XM_005246711		Approved	FLJ45338, KIAA1571	uc002vbp.2	Q9HCK1	OTTHUMG00000154648	ENST00000374423.3:c.5069G>A	2.37:g.207174321G>A	ENSP00000363545:p.Arg1690Gln	Somatic		Capture	Illumina HiSeq	Phase_I	206882566	NM_020923	Q6ZNP7|Q6ZSN8	Missense_Mutation	SNP	ENST00000374423.3	37	CCDS46501.1	.	.	.	.	.	.	.	.	.	.	G	9.529	1.110244	0.20714	.	.	ENSG00000204186	ENST00000374423	T	0.47177	0.85	4.06	-0.356	0.12583	.	.	.	.	.	T	0.31009	0.0783	L	0.34521	1.04	0.09310	N	1	B	0.17038	0.02	B	0.09377	0.004	T	0.20240	-1.0281	9	0.24483	T	0.36	.	6.7146	0.23296	0.5158:0.0:0.4842:0.0	.	1690	Q9HCK1	ZDBF2_HUMAN	Q	1690	ENSP00000363545:R1690Q	ENSP00000363545:R1690Q	R	+	2	0	ZDBF2	206882566	0.000000	0.05858	0.001000	0.08648	0.065000	0.16274	-0.177000	0.09796	-0.072000	0.12864	0.655000	0.94253	CGG		0.458	ZDBF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336458.1	NM_020923	
KLF7	8609	broad.mit.edu	37	2	207953263	207953263	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr2:207953263C>T	ENST00000309446.6	-	3	1152	c.776G>A	c.(775-777)cGt>cAt	p.R259H	KLF7_ENST00000423015.1_Missense_Mutation_p.V192I|KLF7_ENST00000467833.1_5'UTR|KLF7_ENST00000412414.2_Missense_Mutation_p.R231H|KLF7_ENST00000421199.1_Missense_Mutation_p.R226H|KLF7_ENST00000458272.1_Missense_Mutation_p.R69H	NM_003709.3	NP_003700.1	O75840	KLF7_HUMAN	Kruppel-like factor 7 (ubiquitous)	259					axon guidance (GO:0007411)|dendrite morphogenesis (GO:0048813)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|zinc ion binding (GO:0008270)	p.R259H(1)		breast(1)|central_nervous_system(1)|large_intestine(3)|liver(1)|lung(4)|skin(1)	11				LUSC - Lung squamous cell carcinoma(261;0.0856)|Lung(261;0.166)|Epithelial(149;0.173)		TCGTGCAAAACGCCACTCACA	0.502																																					p.R259H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G776A	2						.						148.0	116.0	127.0					2																	207953263		2203	4300	6503	207661508	SO:0001583	missense	8609	exon3			AB015132	CCDS2373.1, CCDS59438.1, CCDS59439.1, CCDS59440.1	2q32	2013-01-08			ENSG00000118263	ENSG00000118263		"""Kruppel-like transcription factors"", ""Zinc fingers, C2H2-type"""	6350	protein-coding gene	gene with protein product		604865				9774444	Standard	NM_003709		Approved	UKLF	uc010zix.2	O75840	OTTHUMG00000132935	ENST00000309446.6:c.776G>A	2.37:g.207953263C>T	ENSP00000309570:p.Arg259His	Somatic		Capture	Illumina HiSeq	Phase_I	207661508	NM_003709	B2RB03|B7Z4F7|C9JF04|E7EWH1|L0R4P2|Q7Z3H8|Q96E51	Missense_Mutation	SNP	ENST00000309446.6	37	CCDS2373.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	36|36	5.637103|5.637103	0.96693|0.96693	.|.	.|.	ENSG00000118263|ENSG00000118263	ENST00000309446;ENST00000421199;ENST00000412414;ENST00000458272|ENST00000423015	T;T;T;T|.	0.53640|.	0.61;0.61;0.61;2.38|.	5.95|5.95	5.95|5.95	0.96441|0.96441	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.59266|0.59266	0.2181|0.2181	L|L	0.54965|0.54965	1.715|1.715	0.80722|0.80722	D|D	1|1	D;D|P	0.89917|0.34780	1.0;1.0|0.468	D;D|B	0.79784|0.28232	0.993;0.993|0.087	T|T	0.58098|0.58098	-0.7696|-0.7696	10|8	0.87932|0.40728	D|T	0|0.16	.|.	20.3932|20.3932	0.98965|0.98965	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	231;259|192	B7Z4F7;O75840|Q96E51	.;KLF7_HUMAN|.	H|I	259;226;231;69|192	ENSP00000309570:R259H;ENSP00000387510:R226H;ENSP00000403284:R231H;ENSP00000393268:R69H|.	ENSP00000309570:R259H|ENSP00000398572:V192I	R|V	-|-	2|1	0|0	KLF7|KLF7	207661508|207661508	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.996000|0.996000	0.88848|0.88848	7.818000|7.818000	0.86416|0.86416	2.824000|2.824000	0.97209|0.97209	0.655000|0.655000	0.94253|0.94253	CGT|GTT		0.502	KLF7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256466.2	NM_003709	
APOB	338	broad.mit.edu	37	2	21230680	21230680	+	Silent	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr2:21230680C>T	ENST00000233242.1	-	26	9187	c.9060G>A	c.(9058-9060)agG>agA	p.R3020R		NM_000384.2	NP_000375	P04114	APOB_HUMAN	apolipoprotein B	3020					artery morphogenesis (GO:0048844)|blood coagulation (GO:0007596)|cellular response to prostaglandin stimulus (GO:0071379)|cellular response to tumor necrosis factor (GO:0071356)|cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|cholesterol transport (GO:0030301)|fertilization (GO:0009566)|in utero embryonic development (GO:0001701)|leukocyte migration (GO:0050900)|lipoprotein biosynthetic process (GO:0042158)|lipoprotein catabolic process (GO:0042159)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|low-density lipoprotein particle clearance (GO:0034383)|low-density lipoprotein particle remodeling (GO:0034374)|nervous system development (GO:0007399)|phototransduction, visible light (GO:0007603)|positive regulation of cholesterol storage (GO:0010886)|positive regulation of lipid storage (GO:0010884)|positive regulation of macrophage derived foam cell differentiation (GO:0010744)|post-embryonic development (GO:0009791)|receptor-mediated endocytosis (GO:0006898)|regulation of cholesterol biosynthetic process (GO:0045540)|response to carbohydrate (GO:0009743)|response to lipopolysaccharide (GO:0032496)|response to selenium ion (GO:0010269)|response to virus (GO:0009615)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)|triglyceride catabolic process (GO:0019433)|triglyceride mobilization (GO:0006642)|very-low-density lipoprotein particle assembly (GO:0034379)	actin cytoskeleton (GO:0015629)|chylomicron (GO:0042627)|chylomicron remnant (GO:0034360)|clathrin-coated endocytic vesicle membrane (GO:0030669)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|early endosome (GO:0005769)|endocytic vesicle lumen (GO:0071682)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum membrane (GO:0005789)|endosome lumen (GO:0031904)|endosome membrane (GO:0010008)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|intermediate-density lipoprotein particle (GO:0034363)|intracellular membrane-bounded organelle (GO:0043231)|low-density lipoprotein particle (GO:0034362)|mature chylomicron (GO:0034359)|plasma membrane (GO:0005886)|very-low-density lipoprotein particle (GO:0034361)	cholesterol transporter activity (GO:0017127)|heparin binding (GO:0008201)|lipase binding (GO:0035473)|low-density lipoprotein particle receptor binding (GO:0050750)|phospholipid binding (GO:0005543)	p.R3020R(1)		NS(5)|autonomic_ganglia(1)|breast(6)|central_nervous_system(4)|cervix(3)|endometrium(19)|kidney(10)|large_intestine(63)|liver(5)|lung(125)|ovary(16)|pancreas(1)|prostate(5)|skin(31)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(6)	305	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					GAGCATCATGCCTCCCAGTAA	0.428																																					p.R3020R												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G9060A	2						.						60.0	64.0	63.0					2																	21230680		2203	4300	6503	21084185	SO:0001819	synonymous_variant	338	exon26			M14162	CCDS1703.1	2p24-p23	2013-05-29	2013-05-29		ENSG00000084674	ENSG00000084674		"""Apolipoproteins"""	603	protein-coding gene	gene with protein product		107730	"""apolipoprotein B (including Ag(x) antigen)"""				Standard	NM_000384		Approved		uc002red.3	P04114	OTTHUMG00000090785	ENST00000233242.1:c.9060G>A	2.37:g.21230680C>T		Somatic		Capture	Illumina HiSeq	Phase_I	21084185	NM_000384	O00502|P78479|P78480|P78481|Q13779|Q13785|Q13786|Q13787|Q13788|Q4ZG63|Q53QC8|Q7Z600|Q9UMN0	Silent	SNP	ENST00000233242.1	37	CCDS1703.1																																																																																				0.428	APOB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207571.1		
PLEKHM3	389072	broad.mit.edu	37	2	208841726	208841726	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr2:208841726C>T	ENST00000427836.2	-	3	1684	c.1195G>A	c.(1195-1197)Gag>Aag	p.E399K	PLEKHM3_ENST00000389247.4_Missense_Mutation_p.E399K|PLEKHM3_ENST00000457206.1_Missense_Mutation_p.E399K	NM_001080475.2	NP_001073944.1	Q6ZWE6	PKHM3_HUMAN	pleckstrin homology domain containing, family M, member 3	399	PH 2. {ECO:0000255|PROSITE- ProRule:PRU00145}.				intracellular signal transduction (GO:0035556)		metal ion binding (GO:0046872)	p.E399K(1)		central_nervous_system(1)|cervix(1)|endometrium(2)|large_intestine(1)|lung(9)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	19						AGTGGATCCTCGTCTAGCTTG	0.512																																					p.E399K												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1195A	2						.						58.0	61.0	60.0					2																	208841726		2026	4186	6212	208549971	SO:0001583	missense	389072	exon3			AK057612	CCDS42808.1	2q33.3	2013-01-10	2008-04-03	2008-04-03	ENSG00000178385	ENSG00000178385		"""Pleckstrin homology (PH) domain containing"""	34006	protein-coding gene	gene with protein product	"""differentiation associated protein"""		"""pleckstrin homology domain containing, family M, member 1-like"""	PLEKHM1L		19028694	Standard	NM_001080475		Approved	DAPR	uc002vcl.2	Q6ZWE6	OTTHUMG00000154781	ENST00000427836.2:c.1195G>A	2.37:g.208841726C>T	ENSP00000417003:p.Glu399Lys	Somatic		Capture	Illumina HiSeq	Phase_I	208549971	NM_001080475	B9EKV2|Q8WW68	Missense_Mutation	SNP	ENST00000427836.2	37	CCDS42808.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	12.16|12.16	1.856078|1.856078	0.32791|0.32791	.|.	.|.	ENSG00000178385|ENSG00000178385	ENST00000427836;ENST00000389247;ENST00000457206|ENST00000447645	T;T;T|.	0.10477|.	2.87;2.87;2.87|.	5.82|5.82	5.82|5.82	0.92795|0.92795	Pleckstrin homology-type (1);Pleckstrin homology domain (3);|.	0.294052|.	0.38005|.	N|.	0.001853|.	T|T	0.56891|0.56891	0.2016|0.2016	N|N	0.22421|0.22421	0.69|0.69	0.51767|0.51767	D|D	0.99993|0.99993	D;P|.	0.53151|.	0.958;0.873|.	B;B|.	0.43990|.	0.438;0.355|.	T|T	0.49234|0.49234	-0.8961|-0.8961	10|5	0.07482|.	T|.	0.82|.	.|.	20.0991|20.0991	0.97865|0.97865	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	399;399|.	C9J119;Q6ZWE6|.	.;PKHM3_HUMAN|.	K|Q	399|150	ENSP00000417003:E399K;ENSP00000373899:E399K;ENSP00000400150:E399K|.	ENSP00000373899:E399K|.	E|R	-|-	1|2	0|0	PLEKHM3|PLEKHM3	208549971|208549971	0.979000|0.979000	0.34478|0.34478	0.975000|0.975000	0.42487|0.42487	0.388000|0.388000	0.30384|0.30384	2.275000|2.275000	0.43399|0.43399	2.752000|2.752000	0.94435|0.94435	0.655000|0.655000	0.94253|0.94253	GAG|CGA		0.512	PLEKHM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337036.1	NM_001080475	
ATIC	471	broad.mit.edu	37	2	216190751	216190751	+	Nonsense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr2:216190751C>T	ENST00000236959.9	+	6	747	c.421C>T	c.(421-423)Cga>Tga	p.R141*	ATIC_ENST00000435675.1_Nonsense_Mutation_p.R140*|ATIC_ENST00000540518.1_Nonsense_Mutation_p.R82*	NM_004044.6	NP_004035.2	P31939	PUR9_HUMAN	5-aminoimidazole-4-carboxamide ribonucleotide formyltransferase/IMP cyclohydrolase	141					'de novo' IMP biosynthetic process (GO:0006189)|brainstem development (GO:0003360)|cerebellum development (GO:0021549)|cerebral cortex development (GO:0021987)|dihydrofolate metabolic process (GO:0046452)|nucleobase-containing compound metabolic process (GO:0006139)|nucleobase-containing small molecule metabolic process (GO:0055086)|nucleoside metabolic process (GO:0009116)|organ regeneration (GO:0031100)|purine nucleobase metabolic process (GO:0006144)|purine ribonucleoside monophosphate biosynthetic process (GO:0009168)|response to inorganic substance (GO:0010035)|small molecule metabolic process (GO:0044281)|tetrahydrofolate biosynthetic process (GO:0046654)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrion (GO:0005739)	IMP cyclohydrolase activity (GO:0003937)|phosphoribosylaminoimidazolecarboxamide formyltransferase activity (GO:0004643)|protein homodimerization activity (GO:0042803)	p.R141*(1)	ATIC/ALK(24)	large_intestine(2)|lung(2)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	8		Renal(323;0.229)		Epithelial(149;2.02e-06)|all cancers(144;0.000316)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.0097)	Methotrexate(DB00563)|Pemetrexed(DB00642)|Tetrahydrofolic acid(DB00116)	AAACCACGCTCGAGTGACAGT	0.483			T	ALK	ALCL																																p.R141X			Dom	yes		2	2q35	471	5-aminoimidazole-4-carboxamide ribonucleotide formyltransferase/IMP cyclohydrolase		L	.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.C421T	2						.						102.0	93.0	96.0					2																	216190751		2203	4300	6503	215898996	SO:0001587	stop_gained	471	exon6				CCDS2398.1	2q35	2010-04-27			ENSG00000138363	ENSG00000138363	2.1.2.3, 3.5.4.10		794	protein-coding gene	gene with protein product	"""phosphoribosylaminoimidazolecarboxamide formyltransferase/IMP cyclohydrolase"""	601731				8567683, 9378707	Standard	NM_004044		Approved	PURH, AICARFT, IMPCHASE	uc002vex.4	P31939	OTTHUMG00000133023	ENST00000236959.9:c.421C>T	2.37:g.216190751C>T	ENSP00000236959:p.Arg141*	Somatic		Capture	Illumina HiSeq	Phase_I	215898996	NM_004044	A8K202|E9PBU3|Q13856|Q53S28	Nonsense_Mutation	SNP	ENST00000236959.9	37	CCDS2398.1	.	.	.	.	.	.	.	.	.	.	C	39	7.764280	0.98477	.	.	ENSG00000138363	ENST00000236959;ENST00000540518;ENST00000435675;ENST00000413174	.	.	.	5.84	5.84	0.93424	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-13.3536	19.7332	0.96192	0.0:1.0:0.0:0.0	.	.	.	.	X	141;82;140;82	.	ENSP00000236959:R141X	R	+	1	2	ATIC	215898996	1.000000	0.71417	0.961000	0.40146	0.812000	0.45895	7.147000	0.77382	2.763000	0.94921	0.650000	0.86243	CGA		0.483	ATIC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256610.1	NM_004044	
FN1	2335	broad.mit.edu	37	2	216256429	216256429	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr2:216256429T>C	ENST00000359671.1	-	25	4170	c.3905A>G	c.(3904-3906)tAc>tGc	p.Y1302C	FN1_ENST00000357009.2_Missense_Mutation_p.Y1302C|FN1_ENST00000356005.4_Missense_Mutation_p.Y1302C|FN1_ENST00000421182.1_Missense_Mutation_p.Y1302C|FN1_ENST00000336916.4_Missense_Mutation_p.Y1302C|FN1_ENST00000432072.2_Missense_Mutation_p.Y1393C|FN1_ENST00000323926.6_Missense_Mutation_p.Y1393C|FN1_ENST00000354785.4_Missense_Mutation_p.Y1393C|FN1_ENST00000446046.1_Missense_Mutation_p.Y1302C|FN1_ENST00000345488.5_Missense_Mutation_p.Y1302C|FN1_ENST00000443816.1_Missense_Mutation_p.Y1302C|FN1_ENST00000346544.3_Missense_Mutation_p.Y1302C|FN1_ENST00000357867.4_Missense_Mutation_p.Y1302C			P02751	FINC_HUMAN	fibronectin 1	1302	Cell-attachment.|Fibronectin type-III 8. {ECO:0000255|PROSITE-ProRule:PRU00316, ECO:0000255|PROSITE-ProRule:PRU00478, ECO:0000255|PROSITE-ProRule:PRU00479}.				acute-phase response (GO:0006953)|angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|calcium-independent cell-matrix adhesion (GO:0007161)|cell adhesion (GO:0007155)|cell-substrate junction assembly (GO:0007044)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|integrin activation (GO:0033622)|leukocyte migration (GO:0050900)|peptide cross-linking (GO:0018149)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of axon extension (GO:0045773)|regulation of cell shape (GO:0008360)|response to wounding (GO:0009611)|substrate adhesion-dependent cell spreading (GO:0034446)	apical plasma membrane (GO:0016324)|basal lamina (GO:0005605)|blood microparticle (GO:0072562)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|fibrinogen complex (GO:0005577)|platelet alpha granule lumen (GO:0031093)	collagen binding (GO:0005518)|heparin binding (GO:0008201)|integrin binding (GO:0005178)|peptidase activator activity (GO:0016504)|protease binding (GO:0002020)	p.Y1302C(1)	FN1/ALK(2)	NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(7)|endometrium(9)|kidney(8)|large_intestine(33)|lung(38)|ovary(1)|pancreas(1)|prostate(3)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)	109		Renal(323;0.127)		Epithelial(149;9.59e-07)|all cancers(144;0.000174)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00948)	Ocriplasmin(DB08888)	CACAGGTGAGTAACGCACCAG	0.473																																					p.Y1302C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A3905G	2						.						128.0	120.0	123.0					2																	216256429		2203	4300	6503	215964674	SO:0001583	missense	2335	exon25				CCDS2399.1, CCDS2400.1, CCDS42813.1, CCDS42814.1, CCDS46510.1, CCDS46512.1	2q34	2014-01-30			ENSG00000115414	ENSG00000115414		"""Fibronectin type III domain containing"", ""Endogenous ligands"""	3778	protein-coding gene	gene with protein product	"""migration-stimulating factor"", ""cold-insoluble globulin"""	135600				2992939, 3003095	Standard	NM_054034		Approved	MSF, CIG, LETS, GFND2, FINC	uc002vfa.3	P02751	OTTHUMG00000133054	ENST00000359671.1:c.3905A>G	2.37:g.216256429T>C	ENSP00000352696:p.Tyr1302Cys	Somatic		Capture	Illumina HiSeq	Phase_I	215964674	NM_212476	B7ZLF0|E9PE77|E9PG29|O95609|O95610|Q14312|Q14325|Q14326|Q17RV7|Q564H7|Q585T2|Q59EH1|Q60FE4|Q68DP8|Q68DP9|Q68DT4|Q6LDP6|Q6MZS0|Q6MZU5|Q6N025|Q6N0A6|Q7Z391|Q86T27|Q8IVI8|Q96KP7|Q96KP8|Q96KP9|Q9H1B8|Q9HAP3|Q9UMK2	Missense_Mutation	SNP	ENST00000359671.1	37		.	.	.	.	.	.	.	.	.	.	T	15.85	2.953713	0.53293	.	.	ENSG00000115414	ENST00000421182;ENST00000323926;ENST00000336916;ENST00000357867;ENST00000354785;ENST00000359671;ENST00000346544;ENST00000345488;ENST00000357009;ENST00000446046;ENST00000443816;ENST00000432072;ENST00000356005;ENST00000456923	T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.61274	0.12;0.12;0.12;0.12;0.12;0.12;0.12;0.12;0.12;0.12;0.12;0.12;0.12;0.12	5.62	4.47	0.54385	.	0.000000	0.64402	D	0.000014	T	0.72463	0.3463	M	0.77313	2.365	0.25121	N	0.990645	D;D;D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D;D;D;D	0.97110	1.0;0.995;0.999;0.995;1.0;0.998;1.0;1.0;0.984	T	0.64757	-0.6332	10	0.72032	D	0.01	.	7.2249	0.26010	0.1298:0.0706:0.0:0.7996	.	1393;1393;1302;1302;1302;1302;1302;1302;1393	P02751-13;P02751-7;P02751-10;P02751-8;E9PE77;P02751-3;P02751-9;P02751-14;P02751-15	.;.;.;.;.;.;.;.;.	C	1302;1393;1302;1302;1393;1302;1302;1302;1302;1302;1302;1393;1302;109	ENSP00000394423:Y1302C;ENSP00000323534:Y1393C;ENSP00000338200:Y1302C;ENSP00000350534:Y1302C;ENSP00000346839:Y1393C;ENSP00000352696:Y1302C;ENSP00000265312:Y1302C;ENSP00000273049:Y1302C;ENSP00000349509:Y1302C;ENSP00000410422:Y1302C;ENSP00000415018:Y1302C;ENSP00000399538:Y1393C;ENSP00000348285:Y1302C;ENSP00000416139:Y109C	ENSP00000323534:Y1393C	Y	-	2	0	FN1	215964674	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	5.463000	0.66712	0.968000	0.38212	0.533000	0.62120	TAC		0.473	FN1-204	KNOWN	basic	protein_coding	protein_coding		NM_212476	
CCDC108	255101	broad.mit.edu	37	2	219892386	219892386	+	Missense_Mutation	SNP	A	A	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr2:219892386A>T	ENST00000341552.5	-	13	2280	c.2197T>A	c.(2197-2199)Ttc>Atc	p.F733I	CCDC108_ENST00000409865.3_Missense_Mutation_p.F722I|CCDC108_ENST00000410037.1_Missense_Mutation_p.F668I|CCDC108_ENST00000453220.1_Missense_Mutation_p.F733I|CCDC108_ENST00000441968.1_Missense_Mutation_p.F733I	NM_194302.2	NP_919278.2	Q6ZU64	CC108_HUMAN	coiled-coil domain containing 108	733						integral component of membrane (GO:0016021)	poly(A) RNA binding (GO:0044822)|structural molecule activity (GO:0005198)	p.F733I(1)		autonomic_ganglia(1)|breast(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(18)|liver(1)|lung(34)|ovary(2)|pancreas(1)|prostate(6)|skin(5)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	80		Renal(207;0.0915)		Epithelial(149;1.12e-06)|all cancers(144;0.000196)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		TAGATGGCGAAGGCTTCGAGC	0.617																																					p.F733I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T2197A	2						.						83.0	85.0	84.0					2																	219892386		2203	4300	6503	219600630	SO:0001583	missense	255101	exon13			NM_194302, AL833882, AK127189	CCDS2430.2, CCDS2431.2, CCDS63125.1, CCDS63126.1	2q35	2008-02-05			ENSG00000181378	ENSG00000181378			25325	protein-coding gene	gene with protein product		614270				12477932	Standard	NM_194302		Approved	DKFZp434O0527, MGC35338	uc002vjl.2	Q6ZU64	OTTHUMG00000133013	ENST00000341552.5:c.2197T>A	2.37:g.219892386A>T	ENSP00000340776:p.Phe733Ile	Somatic		Capture	Illumina HiSeq	Phase_I	219600630	NM_194302	A2BDD8|E9PCR1|E9PG25|E9PG72|Q6ZSR8|Q8N0T4|Q8NDJ3	Missense_Mutation	SNP	ENST00000341552.5	37	CCDS2430.2	.	.	.	.	.	.	.	.	.	.	A	20.6	4.018290	0.75275	.	.	ENSG00000181378	ENST00000341552;ENST00000441968;ENST00000453220;ENST00000545086;ENST00000409865;ENST00000410037;ENST00000441164	T;T;T;T;T	0.15603	3.11;3.11;3.11;2.41;2.42	5.18	5.18	0.71444	.	0.000000	0.48286	D	0.000190	T	0.41096	0.1144	M	0.71581	2.175	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.80764	0.989;0.982;0.994	T	0.19778	-1.0295	10	0.46703	T	0.11	-19.4997	15.1942	0.73071	1.0:0.0:0.0:0.0	.	722;667;733	E9PG25;B4DYZ8;Q6ZU64	.;.;CC108_HUMAN	I	733;733;733;209;722;668;667	ENSP00000340776:F733I;ENSP00000413377:F733I;ENSP00000409117:F733I;ENSP00000386945:F722I;ENSP00000386258:F668I	ENSP00000340776:F733I	F	-	1	0	CCDC108	219600630	1.000000	0.71417	0.994000	0.49952	0.371000	0.29859	7.197000	0.77814	2.172000	0.68678	0.533000	0.62120	TTC		0.617	CCDC108-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256598.4	NM_194302	
PTPRN	5798	broad.mit.edu	37	2	220162130	220162130	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr2:220162130G>A	ENST00000295718.2	-	14	2153	c.1913C>T	c.(1912-1914)aCg>aTg	p.T638M	AC114803.3_ENST00000417355.1_RNA|PTPRN_ENST00000423636.2_Missense_Mutation_p.T548M|PTPRN_ENST00000409251.3_Missense_Mutation_p.T609M|PTPRN_ENST00000497977.1_5'Flank	NM_002846.3	NP_002837.1	Q16849	PTPRN_HUMAN	protein tyrosine phosphatase, receptor type, N	638					cytokine-mediated signaling pathway (GO:0019221)|peptidyl-tyrosine dephosphorylation (GO:0035335)|response to cAMP (GO:0051591)|response to estrogen (GO:0043627)|response to glucose (GO:0009749)|response to insulin (GO:0032868)|response to reactive oxygen species (GO:0000302)	integral component of plasma membrane (GO:0005887)	spectrin binding (GO:0030507)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)	p.T638M(1)		breast(3)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(28)|ovary(3)|prostate(4)|skin(11)|upper_aerodigestive_tract(1)|urinary_tract(1)	65		Renal(207;0.0474)		Epithelial(149;4.22e-07)|all cancers(144;8.82e-05)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)|STAD - Stomach adenocarcinoma(1183;0.0875)		CAAGGACTTCGTGGCCATGTG	0.622																																					p.T548M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1643T	2						.						52.0	54.0	53.0					2																	220162130		2203	4300	6503	219870374	SO:0001583	missense	5798	exon14				CCDS2440.1, CCDS56167.1, CCDS56168.1	2q35-q36.1	2011-06-09			ENSG00000054356	ENSG00000054356		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"""	9676	protein-coding gene	gene with protein product		601773				8024693	Standard	NM_001199763		Approved	IA-2	uc002vkz.3	Q16849	OTTHUMG00000133129	ENST00000295718.2:c.1913C>T	2.37:g.220162130G>A	ENSP00000295718:p.Thr638Met	Somatic		Capture	Illumina HiSeq	Phase_I	219870374	NM_001199764	B4DK12|F5GZS3|Q08319|Q53QD6|Q6NSL1	Missense_Mutation	SNP	ENST00000295718.2	37	CCDS2440.1	.	.	.	.	.	.	.	.	.	.	G	13.26	2.182968	0.38511	.	.	ENSG00000054356	ENST00000409251;ENST00000295718;ENST00000539342;ENST00000537666	T;T;T	0.03635	3.91;3.86;3.86	4.22	3.29	0.37713	.	0.352783	0.26321	N	0.025049	T	0.02610	0.0079	N	0.14661	0.345	0.26705	N	0.971097	P;B	0.49358	0.923;0.045	B;B	0.38327	0.271;0.018	T	0.45775	-0.9238	10	0.72032	D	0.01	.	12.5786	0.56378	0.0:0.311:0.689:0.0	.	609;638	Q6NSL1;Q16849	.;PTPRN_HUMAN	M	609;638;609;548	ENSP00000386638:T609M;ENSP00000295718:T638M;ENSP00000444244:T548M	ENSP00000295718:T638M	T	-	2	0	PTPRN	219870374	0.502000	0.26107	0.996000	0.52242	0.866000	0.49608	2.662000	0.46766	2.180000	0.69256	0.561000	0.74099	ACG		0.622	PTPRN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256819.2		
TMEM198	130612	broad.mit.edu	37	2	220414496	220414496	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr2:220414496G>A	ENST00000344458.2	+	6	1588	c.1003G>A	c.(1003-1005)Gcc>Acc	p.A335T	RP11-256I23.1_ENST00000596829.1_RNA|MIR3132_ENST00000581997.1_RNA|TMEM198_ENST00000373883.3_Missense_Mutation_p.A335T			Q66K66	TM198_HUMAN	transmembrane protein 198	335					multicellular organismal development (GO:0007275)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|Wnt signaling pathway (GO:0016055)	cytoplasmic membrane-bounded vesicle (GO:0016023)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.A335T(2)		NS(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(2)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	16		Renal(207;0.0376)		Epithelial(149;6.49e-08)|all cancers(144;6.45e-06)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00802)		CTCCTTCATGGCCTCACCCAC	0.597																																					p.A335T												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G1003A	2						.						53.0	58.0	56.0					2																	220414496		2203	4300	6503	220122740	SO:0001583	missense	130612	exon5			BC068567	CCDS33385.1	2q35	2011-12-06			ENSG00000188760	ENSG00000188760			33704	protein-coding gene	gene with protein product							Standard	NM_001005209		Approved	MGC99813, TMEM198A	uc002vmf.3	Q66K66	OTTHUMG00000059156	ENST00000344458.2:c.1003G>A	2.37:g.220414496G>A	ENSP00000343507:p.Ala335Thr	Somatic		Capture	Illumina HiSeq	Phase_I	220122740	NM_001005209		Missense_Mutation	SNP	ENST00000344458.2	37	CCDS33385.1	.	.	.	.	.	.	.	.	.	.	G	10.58	1.389024	0.25118	.	.	ENSG00000188760	ENST00000344458;ENST00000373883	.	.	.	5.1	2.2	0.27929	.	0.349704	0.27922	N	0.017310	T	0.15435	0.0372	N	0.03608	-0.345	0.31206	N	0.699253	B	0.11235	0.004	B	0.11329	0.006	T	0.20773	-1.0265	9	0.11485	T	0.65	-8.6206	5.6922	0.17835	0.2312:0.14:0.6289:0.0	.	335	Q66K66	TM198_HUMAN	T	335	.	ENSP00000343507:A335T	A	+	1	0	TMEM198	220122740	0.038000	0.19896	1.000000	0.80357	0.981000	0.71138	1.336000	0.33850	0.373000	0.24621	-0.176000	0.13171	GCC		0.597	TMEM198-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131063.1	NM_001005209	
OBSL1	23363	broad.mit.edu	37	2	220431579	220431579	+	Nonsense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr2:220431579G>A	ENST00000404537.1	-	5	2163	c.2107C>T	c.(2107-2109)Cag>Tag	p.Q703*	OBSL1_ENST00000603926.1_Nonsense_Mutation_p.Q703*|OBSL1_ENST00000373873.4_Nonsense_Mutation_p.Q703*|OBSL1_ENST00000373876.1_Nonsense_Mutation_p.Q703*|OBSL1_ENST00000289656.3_Nonsense_Mutation_p.Q290*|OBSL1_ENST00000265318.4_Nonsense_Mutation_p.Q703*	NM_015311.2	NP_056126.1	O75147	OBSL1_HUMAN	obscurin-like 1	703					cardiac myofibril assembly (GO:0055003)|cytoskeleton organization (GO:0007010)|Golgi organization (GO:0007030)|microtubule cytoskeleton organization (GO:0000226)|positive regulation of dendrite morphogenesis (GO:0050775)|protein localization to Golgi apparatus (GO:0034067)|regulation of mitosis (GO:0007088)	3M complex (GO:1990393)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|intercalated disc (GO:0014704)|M band (GO:0031430)|perinuclear region of cytoplasm (GO:0048471)|Z disc (GO:0030018)	cytoskeletal adaptor activity (GO:0008093)	p.Q703*(1)					Renal(207;0.0376)		Epithelial(149;2.02e-07)|all cancers(144;1.68e-05)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00834)		GCTGAGTCCTGCACGCCGGGG	0.597																																					p.Q703X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.C2107T	2						.						54.0	58.0	57.0					2																	220431579		2070	4211	6281	220139823	SO:0001587	stop_gained	23363	exon5			BC007201	CCDS46520.1, CCDS54433.1, CCDS63134.1	2q35	2013-01-29			ENSG00000124006	ENSG00000124006		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	29092	protein-coding gene	gene with protein product		610991				9734811	Standard	NM_015311		Approved	KIAA0657	uc010fwk.3	O75147	OTTHUMG00000059157	ENST00000404537.1:c.2107C>T	2.37:g.220431579G>A	ENSP00000385636:p.Gln703*	Somatic		Capture	Illumina HiSeq	Phase_I	220139823	NM_001173431	A4KVA4|A4KVA5|Q96IW3|S4R3M6	Nonsense_Mutation	SNP	ENST00000404537.1	37	CCDS46520.1	.	.	.	.	.	.	.	.	.	.	G	38	6.945129	0.97952	.	.	ENSG00000124006	ENST00000265318;ENST00000404537;ENST00000373876;ENST00000373873;ENST00000289656	.	.	.	5.23	5.23	0.72850	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.06099	T	0.92	.	16.1116	0.81266	0.0:0.0:1.0:0.0	.	.	.	.	X	703;703;703;703;290	.	ENSP00000265318:Q703X	Q	-	1	0	OBSL1	220139823	1.000000	0.71417	1.000000	0.80357	0.789000	0.44602	2.821000	0.48065	2.736000	0.93811	0.655000	0.94253	CAG		0.597	OBSL1-014	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322012.1		
SLC4A3	6508	broad.mit.edu	37	2	220504357	220504357	+	Silent	SNP	G	G	A	rs138004203		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr2:220504357G>A	ENST00000358055.3	+	20	3689	c.3177G>A	c.(3175-3177)gcG>gcA	p.A1059A	SLC4A3_ENST00000373760.2_Silent_p.A1059A|SLC4A3_ENST00000373762.3_Silent_p.A1086A|SLC4A3_ENST00000273063.6_Silent_p.A1086A|SLC4A3_ENST00000317151.3_Silent_p.A1059A			P48751	B3A3_HUMAN	solute carrier family 4 (anion exchanger), member 3	1059	Membrane (anion exchange).				bicarbonate transport (GO:0015701)|ion transport (GO:0006811)|regulation of intracellular pH (GO:0051453)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	inorganic anion exchanger activity (GO:0005452)	p.A1086A(1)		breast(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(13)|lung(20)|ovary(3)|prostate(3)|skin(3)|upper_aerodigestive_tract(2)	51		Renal(207;0.0183)		Epithelial(149;2.53e-07)|all cancers(144;5.57e-05)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		ATGTCAATGCGTTGACAGTGA	0.652																																					p.A1059A												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G3177A	2						.	G	,	0,4406		0,0,2203	72.0	62.0	65.0		3177,3258	-5.2	0.0	2	dbSNP_134	65	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous	SLC4A3	NM_005070.3,NM_201574.2	,	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	,	1059/1233,1086/1260	220504357	1,13005	2203	4300	6503	220212601	SO:0001819	synonymous_variant	6508	exon20				CCDS2445.1, CCDS2446.1	2q35	2013-07-19	2013-07-19		ENSG00000114923	ENSG00000114923		"""Solute carriers"""	11029	protein-coding gene	gene with protein product	"""Anion exchanger 3, neuronal"""	106195	"""solute carrier family 4, anion exchanger, member 3"""			8001971	Standard	NM_005070		Approved	AE3, SLC2C	uc002vmo.4	P48751	OTTHUMG00000059238	ENST00000358055.3:c.3177G>A	2.37:g.220504357G>A		Somatic		Capture	Illumina HiSeq	Phase_I	220212601	NM_005070	A6H8L2|A8K1Q9|B7ZVX6|B9EGD1|Q6YIQ9	Silent	SNP	ENST00000358055.3	37	CCDS2445.1																																																																																				0.652	SLC4A3-009	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316472.1	NM_005070	
SERPINE2	5270	broad.mit.edu	37	2	224849483	224849483	+	Silent	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr2:224849483C>T	ENST00000258405.4	-	5	1112	c.870G>A	c.(868-870)caG>caA	p.Q290Q	SERPINE2_ENST00000447280.2_Silent_p.Q302Q|SERPINE2_ENST00000409840.3_Silent_p.Q290Q|SERPINE2_ENST00000409304.1_Silent_p.Q290Q	NM_001136528.1|NM_006216.3	NP_001130000.1|NP_006207.1	P07093	GDN_HUMAN	serpin peptidase inhibitor, clade E (nexin, plasminogen activator inhibitor type 1), member 2	290					blood coagulation (GO:0007596)|cerebellar granular layer morphogenesis (GO:0021683)|detection of mechanical stimulus involved in sensory perception (GO:0050974)|innervation (GO:0060384)|long-term synaptic potentiation (GO:0060291)|mating plug formation (GO:0042628)|negative regulation of blood coagulation (GO:0030195)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of phosphatidylinositol 3-kinase signaling (GO:0014067)|negative regulation of plasminogen activation (GO:0010757)|negative regulation of platelet activation (GO:0010544)|negative regulation of platelet aggregation (GO:0090331)|negative regulation of protein catabolic process (GO:0042177)|negative regulation of protein processing (GO:0010955)|negative regulation of proteolysis (GO:0045861)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of sodium ion transport (GO:0010766)|positive regulation of astrocyte differentiation (GO:0048711)|regulation of cell migration (GO:0030334)|regulation of synaptic transmission, glutamatergic (GO:0051966)|regulation of timing of cell differentiation (GO:0048505)|secretion by cell (GO:0032940)|secretory granule organization (GO:0033363)|seminal vesicle epithelium development (GO:0061108)	cytosol (GO:0005829)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extrinsic component of external side of plasma membrane (GO:0031232)|neuromuscular junction (GO:0031594)|platelet alpha granule (GO:0031091)|vesicle (GO:0031982)	glycosaminoglycan binding (GO:0005539)|heparin binding (GO:0008201)|receptor binding (GO:0005102)|serine-type endopeptidase inhibitor activity (GO:0004867)	p.Q290Q(1)		breast(2)|central_nervous_system(1)|cervix(1)|kidney(1)|large_intestine(7)|lung(4)|ovary(1)	17		Renal(207;0.025)|all_lung(227;0.0586)|Lung NSC(271;0.0682)|all_hematologic(139;0.0797)		Epithelial(121;5.68e-10)|all cancers(144;1.9e-07)|Lung(261;0.0088)|LUSC - Lung squamous cell carcinoma(224;0.00902)		GCAGGATCACCTGCACCCTCT	0.532																																					p.Q302Q												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G906A	2						.						93.0	78.0	83.0					2																	224849483		2203	4300	6503	224557727	SO:0001819	synonymous_variant	5270	exon5			M17783	CCDS2460.1, CCDS46525.1, CCDS46526.1	2q36.1	2014-02-18	2005-08-18		ENSG00000135919	ENSG00000135919		"""Serine (or cysteine) peptidase inhibitors"""	8951	protein-coding gene	gene with protein product	"""glial-derived nexin 1"""	177010	"""serine (or cysteine) proteinase inhibitor, clade E (nexin, plasminogen activator inhibitor type 1), member 2"""	PI7		7665170, 24172014	Standard	NM_006216		Approved	PN1, GDN, PNI, nexin	uc002vnu.2	P07093	OTTHUMG00000133163	ENST00000258405.4:c.870G>A	2.37:g.224849483C>T		Somatic		Capture	Illumina HiSeq	Phase_I	224557727	NM_001136530	B2R6A4|B4DIF2|Q53S15|Q5D0C4	Silent	SNP	ENST00000258405.4	37	CCDS2460.1																																																																																				0.532	SERPINE2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256865.2	NM_006216	
NYAP2	57624	broad.mit.edu	37	2	226447266	226447266	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr2:226447266C>T	ENST00000272907.6	+	4	1546	c.1133C>T	c.(1132-1134)gCg>gTg	p.A378V	NYAP2_ENST00000409269.2_Intron	NM_020864.1	NP_065915.1	Q9P242	NYAP2_HUMAN	neuronal tyrosine-phosphorylated phosphoinositide-3-kinase adaptor 2	378	Pro-rich.				neuron projection morphogenesis (GO:0048812)|phosphatidylinositol 3-kinase signaling (GO:0014065)			p.A378V(1)									CCAGCCGGGGCGTCGCCCTCC	0.662																																					p.A378V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1133T	2						.						14.0	18.0	17.0					2																	226447266		1981	4144	6125	226155510	SO:0001583	missense	57624	exon4			AB040919	CCDS46529.1	2q36.3	2011-11-30	2011-11-30	2011-11-30	ENSG00000144460	ENSG00000144460			29291	protein-coding gene	gene with protein product		615478	"""KIAA1486"""	KIAA1486		10819331, 21946561	Standard	NM_020864		Approved		uc002voe.2	Q9P242	OTTHUMG00000153450	ENST00000272907.6:c.1133C>T	2.37:g.226447266C>T	ENSP00000272907:p.Ala378Val	Somatic		Capture	Illumina HiSeq	Phase_I	226155510	NM_020864	A2RRN4|Q96NL2	Missense_Mutation	SNP	ENST00000272907.6	37	CCDS46529.1	.	.	.	.	.	.	.	.	.	.	C	10.45	1.354859	0.24512	.	.	ENSG00000144460	ENST00000272907	T	0.44482	0.92	5.16	5.16	0.70880	.	0.270316	0.35262	N	0.003337	T	0.43188	0.1236	M	0.65975	2.015	0.80722	D	1	B	0.19583	0.037	B	0.11329	0.006	T	0.39143	-0.9628	10	0.54805	T	0.06	-13.7231	13.9544	0.64137	0.0:0.9251:0.0:0.0749	.	378	Q9P242	K1486_HUMAN	V	378	ENSP00000272907:A378V	ENSP00000272907:A378V	A	+	2	0	KIAA1486	226155510	0.036000	0.19791	0.019000	0.16419	0.028000	0.11728	2.272000	0.43373	2.399000	0.81585	0.650000	0.86243	GCG		0.662	NYAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331258.1	NM_020864	
TRIP12	9320	broad.mit.edu	37	2	230650571	230650571	+	Splice_Site	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr2:230650571G>A	ENST00000283943.5	-	33	4949	c.4771C>T	c.(4771-4773)Cgt>Tgt	p.R1591C	TRIP12_ENST00000389045.3_Splice_Site_p.R1321C|TRIP12_ENST00000389044.4_Splice_Site_p.R1639C	NM_001284214.1|NM_004238.1	NP_001271143.1|NP_004229.1	Q14669	TRIPC_HUMAN	thyroid hormone receptor interactor 12	1591					cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|embryo development (GO:0009790)|negative regulation of double-strand break repair (GO:2000780)|negative regulation of histone H2A K63-linked ubiquitination (GO:1901315)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ligase activity (GO:0016874)|thyroid hormone receptor binding (GO:0046966)|ubiquitin-protein transferase activity (GO:0004842)	p.R1591C(1)		breast(2)|central_nervous_system(4)|cervix(1)|endometrium(5)|kidney(6)|large_intestine(19)|lung(32)|ovary(5)|prostate(4)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	87		Renal(207;0.025)|all_hematologic(139;0.122)|all_lung(227;0.126)|Acute lymphoblastic leukemia(138;0.164)		Epithelial(121;4.76e-13)|all cancers(144;4.34e-10)|LUSC - Lung squamous cell carcinoma(224;0.00864)|Lung(119;0.0116)		TTCACAGTACGCTACAAAGAA	0.443																																					p.R1591C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C4771T	2						.						79.0	81.0	80.0					2																	230650571		2203	4300	6503	230358815	SO:0001630	splice_region_variant	9320	exon33			L40383	CCDS33391.1, CCDS63145.1, CCDS63146.1	2q36.3	2008-05-27			ENSG00000153827	ENSG00000153827			12306	protein-coding gene	gene with protein product		604506				7776974	Standard	XM_005246961		Approved	KIAA0045	uc002vpw.1	Q14669	OTTHUMG00000153623	ENST00000283943.5:c.4771-1C>T	2.37:g.230650571G>A		Somatic		Capture	Illumina HiSeq	Phase_I	230358815	NM_004238	D4HL82|Q14CA3|Q14CF1|Q15644|Q53R87|Q53TE7	Missense_Mutation	SNP	ENST00000283943.5	37	CCDS33391.1	.	.	.	.	.	.	.	.	.	.	G	23.0	4.363590	0.82353	.	.	ENSG00000153827	ENST00000283943;ENST00000389045;ENST00000389044	T;T;T	0.42900	0.96;0.96;0.96	5.66	5.66	0.87406	HECT (1);	0.000000	0.85682	D	0.000000	T	0.58337	0.2115	L	0.41492	1.28	0.80722	D	1	D;D;D	0.89917	0.99;1.0;0.99	P;D;P	0.76575	0.556;0.988;0.556	T	0.55101	-0.8193	10	0.46703	T	0.11	.	19.7491	0.96260	0.0:0.0:1.0:0.0	.	1321;1639;1591	Q14CF1;Q14CA3;Q14669	.;.;TRIPC_HUMAN	C	1591;1321;1639	ENSP00000283943:R1591C;ENSP00000373697:R1321C;ENSP00000373696:R1639C	ENSP00000283943:R1591C	R	-	1	0	TRIP12	230358815	1.000000	0.71417	1.000000	0.80357	0.878000	0.50629	6.898000	0.75676	2.661000	0.90470	0.585000	0.79938	CGT		0.443	TRIP12-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000331861.3	NM_004238	Missense_Mutation
COPS7B	64708	broad.mit.edu	37	2	232672230	232672230	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr2:232672230G>A	ENST00000350033.3	+	7	811	c.670G>A	c.(670-672)Gca>Aca	p.A224T	COPS7B_ENST00000409295.1_Missense_Mutation_p.A190T|COPS7B_ENST00000409091.1_Missense_Mutation_p.A117T|COPS7B_ENST00000410024.1_Missense_Mutation_p.A224T|COPS7B_ENST00000373608.3_Silent_p.P241P|COPS7B_ENST00000410017.1_Silent_p.P246P|RP11-690I21.2_ENST00000563949.1_RNA	NM_001282949.1|NM_022730.1	NP_001269878.1|NP_073567.1	Q9H9Q2	CSN7B_HUMAN	COP9 signalosome subunit 7B	224					cullin deneddylation (GO:0010388)	COP9 signalosome (GO:0008180)|cytoplasm (GO:0005737)|nucleus (GO:0005634)		p.A224T(1)		large_intestine(1)|liver(1)|lung(4)|ovary(1)|skin(1)	8		all_hematologic(139;0.0123)|Acute lymphoblastic leukemia(138;0.0182)|Renal(207;0.025)		Epithelial(121;1.36e-12)|BRCA - Breast invasive adenocarcinoma(100;0.00136)|LUSC - Lung squamous cell carcinoma(224;0.0115)|Lung(119;0.0142)		CAAAGCCACCGCATCCTCCTC	0.537																																					p.A224T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G670A	2						.						68.0	52.0	58.0					2																	232672230		2203	4300	6503	232380474	SO:0001583	missense	64708	exon7			AK022674	CCDS2488.1, CCDS63152.1, CCDS63153.1, CCDS63154.1, CCDS74668.1	2q37.1	2013-03-14	2013-03-14		ENSG00000144524	ENSG00000144524			16760	protein-coding gene	gene with protein product			"""COP9 (constitutive photomorphogenic, Arabidopsis, homolog) subunit 7B"", ""COP9 constitutive photomorphogenic homolog subunit 7B (Arabidopsis)"""			9707402	Standard	NM_001282950		Approved	CSN7B	uc002vsg.1	Q9H9Q2	OTTHUMG00000133228	ENST00000350033.3:c.670G>A	2.37:g.232672230G>A	ENSP00000272995:p.Ala224Thr	Somatic		Capture	Illumina HiSeq	Phase_I	232380474	NM_022730	Q53S22|Q5BJG3|Q9H7V6	Missense_Mutation	SNP	ENST00000350033.3	37	CCDS2488.1	.	.	.	.	.	.	.	.	.	.	G	17.22	3.333857	0.60853	.	.	ENSG00000144524	ENST00000410024;ENST00000409295;ENST00000409091;ENST00000350033;ENST00000537799;ENST00000449174	T;T;T;T;T	0.47528	0.84;0.84;0.84;0.84;0.84	5.69	5.69	0.88448	.	.	.	.	.	T	0.33206	0.0855	L	0.35288	1.05	0.80722	D	1	P	0.42993	0.797	B	0.23419	0.046	T	0.16453	-1.0402	9	0.26408	T	0.33	0.0065	19.8116	0.96549	0.0:0.0:1.0:0.0	.	224	Q9H9Q2	CSN7B_HUMAN	T	224;190;117;224;117;88	ENSP00000386567:A224T;ENSP00000386438:A190T;ENSP00000386527:A117T;ENSP00000272995:A224T;ENSP00000403300:A88T	ENSP00000272995:A224T	A	+	1	0	COPS7B	232380474	1.000000	0.71417	0.257000	0.24404	0.969000	0.65631	6.737000	0.74816	2.674000	0.91012	0.655000	0.94253	GCA		0.537	COPS7B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256964.2	NM_022730	
DIS3L2	129563	broad.mit.edu	37	2	233195473	233195473	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr2:233195473C>T	ENST00000409307.1	+	15	1997	c.1997C>T	c.(1996-1998)tCc>tTc	p.S666F	DIS3L2_ENST00000325385.7_Missense_Mutation_p.S666F|DIS3L2_ENST00000273009.6_Intron					DIS3 like 3'-5' exoribonuclease 2									p.S666F(1)		breast(2)|central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(7)|lung(18)|ovary(1)|prostate(2)|urinary_tract(1)	40		all_hematologic(139;0.00809)|Renal(207;0.0113)|Acute lymphoblastic leukemia(138;0.0195)|all_lung(227;0.0465)|Lung NSC(271;0.136)		Epithelial(121;1.6e-13)|BRCA - Breast invasive adenocarcinoma(100;0.00104)|LUSC - Lung squamous cell carcinoma(224;0.0109)|Lung(119;0.0149)		AACATGTGCTCCCGGCCCATG	0.597																																					p.S666F												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1997T	2						.						120.0	131.0	128.0					2																	233195473		1957	4147	6104	232903717	SO:0001583	missense	129563	exon16			BC026166	CCDS42834.1, CCDS58752.1, CCDS58753.1	2q37.1	2014-09-17	2014-03-05		ENSG00000144535	ENSG00000144535			28648	protein-coding gene	gene with protein product		614184	"""family with sequence similarity 6, member A"", ""DIS3 mitotic control homolog (S. cerevisiae)-like 2"""	FAM6A		22306653, 23503588	Standard	NM_152383		Approved	FLJ36974, MGC42174	uc010fxz.3	Q8IYB7	OTTHUMG00000153385	ENST00000409307.1:c.1997C>T	2.37:g.233195473C>T	ENSP00000386799:p.Ser666Phe	Somatic		Capture	Illumina HiSeq	Phase_I	232903717	NM_152383		Missense_Mutation	SNP	ENST00000409307.1	37	CCDS42834.1	.	.	.	.	.	.	.	.	.	.	N	17.25	3.340970	0.60963	.	.	ENSG00000144535	ENST00000325385;ENST00000431466;ENST00000409307;ENST00000424049	T;T;T	0.37584	1.19;1.19;1.19	5.06	5.06	0.68205	Ribonuclease II/R (2);	0.000000	0.85682	D	0.000000	T	0.43322	0.1242	L	0.49350	1.555	0.80722	D	1	B	0.22800	0.075	B	0.36186	0.219	T	0.41431	-0.9509	10	0.56958	D	0.05	-26.419	18.0995	0.89501	0.0:1.0:0.0:0.0	.	666	Q8IYB7	DI3L2_HUMAN	F	666;666;666;301	ENSP00000315569:S666F;ENSP00000386799:S666F;ENSP00000415419:S301F	ENSP00000315569:S666F	S	+	2	0	DIS3L2	232903717	1.000000	0.71417	0.999000	0.59377	0.989000	0.77384	7.236000	0.78154	2.348000	0.79779	0.644000	0.83932	TCC		0.597	DIS3L2-015	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330988.1	NM_152383	
ALPI	248	broad.mit.edu	37	2	233322351	233322351	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr2:233322351A>G	ENST00000295463.3	+	6	802	c.725A>G	c.(724-726)cAg>cGg	p.Q242R		NM_001631.3	NP_001622.2	P09923	PPBI_HUMAN	alkaline phosphatase, intestinal	242					dephosphorylation (GO:0016311)	anchored component of membrane (GO:0031225)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	alkaline phosphatase activity (GO:0004035)|magnesium ion binding (GO:0000287)|protease binding (GO:0002020)|zinc ion binding (GO:0008270)	p.Q242R(1)		NS(1)|breast(1)|central_nervous_system(2)|endometrium(3)|kidney(2)|large_intestine(2)|lung(10)|prostate(2)|upper_aerodigestive_tract(1)	24		all_hematologic(139;0.00793)|Renal(207;0.0112)|Acute lymphoblastic leukemia(138;0.0182)|all_lung(227;0.0449)|Lung NSC(271;0.132)		Epithelial(121;1.64e-16)|Kidney(3;9.71e-08)|KIRC - Kidney renal clear cell carcinoma(3;2.74e-06)|BRCA - Breast invasive adenocarcinoma(100;0.000763)|Lung(119;0.00564)|LUSC - Lung squamous cell carcinoma(224;0.00746)		GATGCCAGCCAGAATGGAATC	0.622																																					p.Q242R												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A725G	2						.						61.0	63.0	62.0					2																	233322351		2203	4300	6503	233030595	SO:0001583	missense	248	exon6			M15694	CCDS2492.1	2q37.1	2008-02-05			ENSG00000163295	ENSG00000163295	3.1.3.1		437	protein-coding gene	gene with protein product		171740				3468508, 3469665	Standard	NM_001631		Approved		uc002vst.4	P09923	OTTHUMG00000133258	ENST00000295463.3:c.725A>G	2.37:g.233322351A>G	ENSP00000295463:p.Gln242Arg	Somatic		Capture	Illumina HiSeq	Phase_I	233030595	NM_001631	B2R7Y4|Q53S80|Q9UBV5|Q9UCL2	Missense_Mutation	SNP	ENST00000295463.3	37	CCDS2492.1	.	.	.	.	.	.	.	.	.	.	A	5.513	0.279572	0.10458	.	.	ENSG00000163295	ENST00000295463	D	0.96651	-4.08	4.22	0.301	0.15781	Alkaline phosphatase-like, alpha/beta/alpha (1);Alkaline-phosphatase-like, core domain (1);	0.718068	0.14360	N	0.324469	D	0.91523	0.7323	L	0.41632	1.29	0.09310	N	1	B	0.11235	0.004	B	0.26614	0.071	T	0.80286	-0.1446	10	0.20046	T	0.44	.	4.6258	0.12477	0.6934:0.0:0.165:0.1416	.	242	P09923	PPBI_HUMAN	R	242	ENSP00000295463:Q242R	ENSP00000295463:Q242R	Q	+	2	0	ALPI	233030595	0.000000	0.05858	0.000000	0.03702	0.009000	0.06853	0.779000	0.26746	-0.030000	0.13804	0.459000	0.35465	CAG		0.622	ALPI-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257035.2	NM_001631	
TRPM8	79054	broad.mit.edu	37	2	234858740	234858740	+	Missense_Mutation	SNP	C	C	T	rs372873712		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr2:234858740C>T	ENST00000324695.4	+	9	1130	c.1090C>T	c.(1090-1092)Cgc>Tgc	p.R364C	AC005538.5_ENST00000455991.1_RNA|TRPM8_ENST00000433712.2_Missense_Mutation_p.R52C	NM_024080.4	NP_076985.4	Q7Z2W7	TRPM8_HUMAN	transient receptor potential cation channel, subfamily M, member 8	364					calcium ion transmembrane transport (GO:0070588)|cellular calcium ion homeostasis (GO:0006874)|detection of temperature stimulus (GO:0016048)|ion transmembrane transport (GO:0034220)|protein homotetramerization (GO:0051289)|protein homotrimerization (GO:0070207)|response to cold (GO:0009409)|thermoception (GO:0050955)|transmembrane transport (GO:0055085)	endoplasmic reticulum (GO:0005783)|external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)	p.R364C(1)		breast(5)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(15)|liver(2)|lung(27)|prostate(2)|skin(7)|stomach(2)	66		Breast(86;0.00205)|Renal(207;0.00694)|all_lung(227;0.0129)|Lung NSC(271;0.0408)|all_hematologic(139;0.0753)|Acute lymphoblastic leukemia(138;0.224)		Epithelial(121;1.19e-17)|BRCA - Breast invasive adenocarcinoma(100;0.000139)|Lung(119;0.00758)|LUSC - Lung squamous cell carcinoma(224;0.0108)	Menthol(DB00825)	CTTTTTACCCCGCACGGTGTC	0.562																																					p.R364C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1090T	2						.	C	CYS/ARG	1,4405	2.1+/-5.4	0,1,2202	62.0	60.0	61.0		1090	5.4	1.0	2		61	0,8600		0,0,4300	no	missense	TRPM8	NM_024080.4	180	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	probably-damaging	364/1105	234858740	1,13005	2203	4300	6503	234523479	SO:0001583	missense	79054	exon9			AC005538	CCDS33407.1	2q37	2011-12-14			ENSG00000144481	ENSG00000144481		"""Voltage-gated ion channels / Transient receptor potential cation channels"""	17961	protein-coding gene	gene with protein product		606678				16382100	Standard	NM_024080		Approved		uc002vvh.3	Q7Z2W7	OTTHUMG00000059129	ENST00000324695.4:c.1090C>T	2.37:g.234858740C>T	ENSP00000323926:p.Arg364Cys	Somatic		Capture	Illumina HiSeq	Phase_I	234523479	NM_024080	A0AVG2|Q3YFM7|Q6QNH9|Q8TAC3|Q8TDX8|Q9BVK1	Missense_Mutation	SNP	ENST00000324695.4	37	CCDS33407.1	.	.	.	.	.	.	.	.	.	.	C	23.5	4.425450	0.83667	2.27E-4	0.0	ENSG00000144481	ENST00000324695;ENST00000433712	T;T	0.36340	1.26;1.26	5.43	5.43	0.79202	.	0.150053	0.48286	D	0.000199	T	0.58552	0.2130	M	0.68593	2.085	0.58432	D	0.999998	D;D	0.89917	0.999;1.0	D;P	0.66602	0.945;0.828	T	0.60692	-0.7213	10	0.66056	D	0.02	-21.8859	17.8142	0.88625	0.0:1.0:0.0:0.0	.	52;364	A0AVG2;Q7Z2W7	.;TRPM8_HUMAN	C	364;52	ENSP00000323926:R364C;ENSP00000404423:R52C	ENSP00000323926:R364C	R	+	1	0	TRPM8	234523479	0.999000	0.42202	1.000000	0.80357	0.964000	0.63967	5.314000	0.65804	2.548000	0.85928	0.557000	0.71058	CGC		0.562	TRPM8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131005.4	NM_024080	
TRPM8	79054	broad.mit.edu	37	2	234869591	234869591	+	Missense_Mutation	SNP	G	G	A	rs200884995		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr2:234869591G>A	ENST00000324695.4	+	12	1574	c.1534G>A	c.(1534-1536)Gcc>Acc	p.A512T	TRPM8_ENST00000433712.2_Missense_Mutation_p.A200T	NM_024080.4	NP_076985.4	Q7Z2W7	TRPM8_HUMAN	transient receptor potential cation channel, subfamily M, member 8	512					calcium ion transmembrane transport (GO:0070588)|cellular calcium ion homeostasis (GO:0006874)|detection of temperature stimulus (GO:0016048)|ion transmembrane transport (GO:0034220)|protein homotetramerization (GO:0051289)|protein homotrimerization (GO:0070207)|response to cold (GO:0009409)|thermoception (GO:0050955)|transmembrane transport (GO:0055085)	endoplasmic reticulum (GO:0005783)|external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)	p.A512T(1)		breast(5)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(15)|liver(2)|lung(27)|prostate(2)|skin(7)|stomach(2)	66		Breast(86;0.00205)|Renal(207;0.00694)|all_lung(227;0.0129)|Lung NSC(271;0.0408)|all_hematologic(139;0.0753)|Acute lymphoblastic leukemia(138;0.224)		Epithelial(121;1.19e-17)|BRCA - Breast invasive adenocarcinoma(100;0.000139)|Lung(119;0.00758)|LUSC - Lung squamous cell carcinoma(224;0.0108)	Menthol(DB00825)	TCTGCAGATCGCCAAGAATTC	0.507																																					p.A512T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1534A	2						.						115.0	98.0	103.0					2																	234869591		2203	4300	6503	234534330	SO:0001583	missense	79054	exon12			AC005538	CCDS33407.1	2q37	2011-12-14			ENSG00000144481	ENSG00000144481		"""Voltage-gated ion channels / Transient receptor potential cation channels"""	17961	protein-coding gene	gene with protein product		606678				16382100	Standard	NM_024080		Approved		uc002vvh.3	Q7Z2W7	OTTHUMG00000059129	ENST00000324695.4:c.1534G>A	2.37:g.234869591G>A	ENSP00000323926:p.Ala512Thr	Somatic		Capture	Illumina HiSeq	Phase_I	234534330	NM_024080	A0AVG2|Q3YFM7|Q6QNH9|Q8TAC3|Q8TDX8|Q9BVK1	Missense_Mutation	SNP	ENST00000324695.4	37	CCDS33407.1	.	.	.	.	.	.	.	.	.	.	G	30	5.056896	0.93846	.	.	ENSG00000144481	ENST00000324695;ENST00000433712	T;T	0.59364	0.27;0.32	5.8	5.8	0.92144	.	0.000000	0.64402	D	0.000003	T	0.71921	0.3397	L	0.54323	1.7	0.50313	D	0.999863	D;D	0.76494	0.999;0.999	D;P	0.68621	0.959;0.825	T	0.68368	-0.5427	10	0.38643	T	0.18	-29.8559	18.6269	0.91344	0.0:0.0:1.0:0.0	.	200;512	A0AVG2;Q7Z2W7	.;TRPM8_HUMAN	T	512;200	ENSP00000323926:A512T;ENSP00000404423:A200T	ENSP00000323926:A512T	A	+	1	0	TRPM8	234534330	1.000000	0.71417	0.971000	0.41717	0.987000	0.75469	6.673000	0.74482	2.735000	0.93741	0.655000	0.94253	GCC		0.507	TRPM8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131005.4	NM_024080	
COL6A3	1293	broad.mit.edu	37	2	238253701	238253701	+	Splice_Site	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr2:238253701G>A	ENST00000295550.4	-	34	7614	c.7162C>T	c.(7162-7164)Cct>Tct	p.P2388S	COL6A3_ENST00000409809.1_Splice_Site_p.P2182S|COL6A3_ENST00000353578.4_Splice_Site_p.P2182S|COL6A3_ENST00000346358.4_Splice_Site_p.P2188S|COL6A3_ENST00000347401.3_Splice_Site_p.P2187S|COL6A3_ENST00000472056.1_Splice_Site_p.P1781S	NM_004369.3	NP_004360.2	P12111	CO6A3_HUMAN	collagen, type VI, alpha 3	2388	Nonhelical region.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|muscle organ development (GO:0007517)|response to glucose (GO:0009749)	collagen type VI trimer (GO:0005589)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)|sarcolemma (GO:0042383)|vesicle (GO:0031982)	serine-type endopeptidase inhibitor activity (GO:0004867)	p.P2388S(1)		breast(6)|central_nervous_system(7)|cervix(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(13)|large_intestine(64)|lung(62)|ovary(14)|pancreas(2)|prostate(11)|skin(14)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(4)	217		Breast(86;0.000301)|Renal(207;0.000966)|all_hematologic(139;0.067)|Ovarian(221;0.0694)|all_lung(227;0.0943)|Melanoma(123;0.203)		Epithelial(121;1.23e-21)|OV - Ovarian serous cystadenocarcinoma(60;1.34e-10)|Kidney(56;5.71e-09)|KIRC - Kidney renal clear cell carcinoma(57;1.51e-07)|BRCA - Breast invasive adenocarcinoma(100;0.00025)|Lung(119;0.0142)|LUSC - Lung squamous cell carcinoma(224;0.034)		ATGTACTTACGGCATTTATCT	0.348																																					p.P1781S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C5341T	2						.						114.0	108.0	110.0					2																	238253701		2203	4300	6503	237918440	SO:0001630	splice_region_variant	1293	exon31			X52022	CCDS33409.1, CCDS33410.1, CCDS33411.1, CCDS33412.1, CCDS33410.2, CCDS33411.2, CCDS54439.1	2q37	2014-09-17			ENSG00000163359	ENSG00000163359		"""Collagens"""	2213	protein-coding gene	gene with protein product		120250				1339440, 11992252	Standard	NM_004369		Approved		uc002vwl.2	P12111	OTTHUMG00000150020	ENST00000295550.4:c.7162+1C>T	2.37:g.238253701G>A		Somatic		Capture	Illumina HiSeq	Phase_I	237918440	NM_057166	A8MT30|B4E3U5|B7ZMJ7|E9PFQ6|E9PGQ9|Q16501|Q53QF4|Q53QF6	Missense_Mutation	SNP	ENST00000295550.4	37	CCDS33412.1	.	.	.	.	.	.	.	.	.	.	G	13.67	2.306713	0.40795	.	.	ENSG00000163359	ENST00000295550;ENST00000347401;ENST00000353578;ENST00000472056;ENST00000409809;ENST00000346358	D;D;D;D;D;D	0.96802	-4.13;-4.13;-4.13;-4.13;-4.13;-4.13	5.31	5.31	0.75309	.	0.244160	0.28659	N	0.014567	D	0.98182	0.9399	M	0.82323	2.585	0.80722	D	1	D;D;D;D	0.89917	0.999;0.996;0.999;1.0	P;P;D;D	0.76071	0.822;0.73;0.914;0.987	D	0.98476	1.0603	9	.	.	.	.	19.0167	0.92897	0.0:0.0:1.0:0.0	.	1781;1781;2182;2388	E9PFQ6;B7ZMJ7;P12111-2;P12111	.;.;.;CO6A3_HUMAN	S	2388;2187;2182;1781;2182;2188	ENSP00000295550:P2388S;ENSP00000315609:P2187S;ENSP00000315873:P2182S;ENSP00000418285:P1781S;ENSP00000386844:P2182S;ENSP00000295546:P2188S	.	P	-	1	0	COL6A3	237918440	1.000000	0.71417	0.998000	0.56505	0.815000	0.46073	7.851000	0.86920	2.484000	0.83849	0.655000	0.94253	CCT		0.348	COL6A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315790.2	NM_004369	Missense_Mutation
RAMP1	10267	broad.mit.edu	37	2	238785934	238785934	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr2:238785934C>A	ENST00000254661.4	+	2	253	c.121C>A	c.(121-123)Ctc>Atc	p.L41I	RAMP1_ENST00000403885.1_Missense_Mutation_p.L19I|RAMP1_ENST00000404910.2_Missense_Mutation_p.L19I|RAMP1_ENST00000409726.1_Missense_Mutation_p.L19I	NM_005855.2	NP_005846.1	O60894	RAMP1_HUMAN	receptor (G protein-coupled) activity modifying protein 1	41					angiogenesis (GO:0001525)|calcium ion transport (GO:0006816)|intracellular protein transport (GO:0006886)|positive regulation of cAMP biosynthetic process (GO:0030819)|positive regulation of protein glycosylation (GO:0060050)|protein localization to plasma membrane (GO:0072659)|protein transport (GO:0015031)|receptor internalization (GO:0031623)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)	cell surface (GO:0009986)|extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcitonin receptor activity (GO:0004948)|calcitonin receptor binding (GO:0031716)|coreceptor activity (GO:0015026)|protein transporter activity (GO:0008565)|receptor activity (GO:0004872)	p.L41I(1)		kidney(1)|large_intestine(1)|lung(2)	4		Breast(86;0.000596)|Renal(207;0.00183)|Ovarian(221;0.0481)|all_hematologic(139;0.158)|all_lung(227;0.198)|Melanoma(123;0.203)|Hepatocellular(293;0.244)		Epithelial(121;9.56e-23)|OV - Ovarian serous cystadenocarcinoma(60;2.49e-11)|Kidney(56;3.21e-09)|KIRC - Kidney renal clear cell carcinoma(57;8.49e-08)|BRCA - Breast invasive adenocarcinoma(100;0.00013)|Lung(119;0.0119)|LUSC - Lung squamous cell carcinoma(224;0.0288)	Pramlintide(DB01278)	GGAGCTCTGCCTCACCCAGTT	0.627																																					p.L41I	NSCLC(177;211 2889 43936 50767)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C121A	2						.						96.0	90.0	92.0					2																	238785934		2203	4300	6503	238450673	SO:0001583	missense	10267	exon2			AJ001014	CCDS2522.1	2q36-q37.1	2008-02-05	2006-11-21		ENSG00000132329	ENSG00000132329		"""Receptor (G protein-coupled) activity modifying proteins"""	9843	protein-coding gene	gene with protein product		605153	"""receptor activity modifying protein 1"", ""receptor (calcitonin) activity modifying protein 1"""				Standard	NM_005855		Approved		uc002vxj.3	O60894	OTTHUMG00000133337	ENST00000254661.4:c.121C>A	2.37:g.238785934C>A	ENSP00000254661:p.Leu41Ile	Somatic		Capture	Illumina HiSeq	Phase_I	238450673	NM_005855	Q6FGS5	Missense_Mutation	SNP	ENST00000254661.4	37	CCDS2522.1	.	.	.	.	.	.	.	.	.	.	C	12.41	1.930299	0.34096	.	.	ENSG00000132329	ENST00000404910;ENST00000254661;ENST00000409726;ENST00000403885	T;T;T;T	0.48522	0.81;0.81;0.81;0.81	4.84	4.84	0.62591	.	0.000000	0.64402	D	0.000001	T	0.66858	0.2832	M	0.80183	2.485	0.40470	D	0.980339	D	0.76494	0.999	D	0.71184	0.972	T	0.66540	-0.5898	10	0.29301	T	0.29	-47.4539	13.3096	0.60371	0.0:1.0:0.0:0.0	.	41	O60894	RAMP1_HUMAN	I	19;41;19;19	ENSP00000384688:L19I;ENSP00000254661:L41I;ENSP00000386720:L19I;ENSP00000386046:L19I	ENSP00000254661:L41I	L	+	1	0	RAMP1	238450673	0.986000	0.35501	0.981000	0.43875	0.045000	0.14185	1.657000	0.37366	2.512000	0.84698	0.561000	0.74099	CTC		0.627	RAMP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257166.2	NM_005855	
MFSD2B	388931	broad.mit.edu	37	2	24245737	24245737	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr2:24245737C>T	ENST00000406420.3	+	10	1040	c.1024C>T	c.(1024-1026)Cgc>Tgc	p.R342C	MFSD2B_ENST00000338315.4_Missense_Mutation_p.R342C	NM_001080473.1	NP_001073942.1	A6NFX1	MFS2B_HUMAN	major facilitator superfamily domain containing 2B	342					transport (GO:0006810)	integral component of membrane (GO:0016021)		p.R342C(1)		cervix(2)|endometrium(1)|large_intestine(2)|lung(3)|ovary(2)	10						GGTTCTCCAGCGCTTTGGGAA	0.632																																					p.R342C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1024T	2						.						51.0	54.0	53.0					2																	24245737		1982	4161	6143	24099241	SO:0001583	missense	388931	exon10				CCDS46228.1	2p23.3	2010-05-11			ENSG00000205639	ENSG00000205639			37207	protein-coding gene	gene with protein product						18694395	Standard	NM_001080473		Approved		uc002reo.2	A6NFX1	OTTHUMG00000090819	ENST00000406420.3:c.1024C>T	2.37:g.24245737C>T	ENSP00000385527:p.Arg342Cys	Somatic		Capture	Illumina HiSeq	Phase_I	24099241	NM_001080473	B5MC32	Missense_Mutation	SNP	ENST00000406420.3	37	CCDS46228.1	.	.	.	.	.	.	.	.	.	.	C	17.31	3.357541	0.61293	.	.	ENSG00000205639	ENST00000406420;ENST00000338315	D;D	0.85088	-1.94;-1.94	5.39	3.29	0.37713	Major facilitator superfamily domain, general substrate transporter (1);	0.278211	0.37053	N	0.002269	D	0.89812	0.6823	M	0.68317	2.08	0.52099	D	0.99994	D	0.89917	1.0	D	0.81914	0.995	D	0.89234	0.3579	10	0.49607	T	0.09	-12.3684	10.8524	0.46777	0.5013:0.4987:0.0:0.0	.	342	A6NFX1	MFS2B_HUMAN	C	342	ENSP00000385527:R342C;ENSP00000342501:R342C	ENSP00000342501:R342C	R	+	1	0	MFSD2B	24099241	0.021000	0.18746	0.948000	0.38648	0.464000	0.32679	1.265000	0.33027	1.393000	0.46605	0.561000	0.74099	CGC		0.632	MFSD2B-001	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000324307.1	NM_001080473	
NDUFA10	4705	broad.mit.edu	37	2	240960787	240960787	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr2:240960787C>A	ENST00000252711.2	-	3	387	c.287G>T	c.(286-288)aGt>aTt	p.S96I	NDUFA10_ENST00000307300.4_Missense_Mutation_p.S96I|NDUFA10_ENST00000404554.1_Missense_Mutation_p.S96I|NDUFA10_ENST00000407129.3_Missense_Mutation_p.S96I	NM_004544.3	NP_004535.1	O95299	NDUAA_HUMAN	NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 10, 42kDa	96					cellular metabolic process (GO:0044237)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|respiratory electron transport chain (GO:0022904)|response to drug (GO:0042493)|small molecule metabolic process (GO:0044281)	mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex I (GO:0005747)	ATP binding (GO:0005524)|NADH dehydrogenase (ubiquinone) activity (GO:0008137)|nucleoside kinase activity (GO:0019206)	p.S96I(1)		central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(8)	16		all_epithelial(40;4.26e-15)|Breast(86;4.4e-05)|Renal(207;0.00183)|Ovarian(221;0.0228)|all_lung(227;0.0396)|Lung NSC(271;0.128)|all_hematologic(139;0.158)|Melanoma(123;0.16)|Hepatocellular(293;0.244)		Epithelial(121;7.82e-28)|OV - Ovarian serous cystadenocarcinoma(60;1.5e-13)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;6.5e-08)|BRCA - Breast invasive adenocarcinoma(100;2.39e-05)|Lung(119;0.00519)|LUSC - Lung squamous cell carcinoma(224;0.0202)		TCCTGTGGTACTGTCTGGATA	0.493											OREG0015348	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.S96I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G287T	2						.						76.0	76.0	76.0					2																	240960787		2203	4300	6503	240609460	SO:0001583	missense	4705	exon3			AF087661	CCDS2531.1	2q37.3	2011-07-04	2002-08-29		ENSG00000130414	ENSG00000130414		"""Mitochondrial respiratory chain complex / Complex I"""	7684	protein-coding gene	gene with protein product	"""complex I 42kDa subunit"""	603835	"""NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 10 (42kD)"""			9878551	Standard	NM_004544		Approved	CI-42k	uc002vyn.3	O95299	OTTHUMG00000133350	ENST00000252711.2:c.287G>T	2.37:g.240960787C>A	ENSP00000252711:p.Ser96Ile	Somatic	2423	Capture	Illumina HiSeq	Phase_I	240609460	NM_004544	Q8WXC9	Missense_Mutation	SNP	ENST00000252711.2	37	CCDS2531.1	.	.	.	.	.	.	.	.	.	.	C	11.78	1.739282	0.30774	.	.	ENSG00000130414	ENST00000252711;ENST00000404554;ENST00000422018;ENST00000443626;ENST00000307300;ENST00000407129	T;T;T;T;T	0.77877	-1.1;-1.11;-1.09;-1.13;-1.1	4.25	2.38	0.29361	.	0.369676	0.33382	N	0.004975	T	0.68458	0.3003	M	0.63843	1.955	0.22389	N	0.999145	B;P;B;B	0.34977	0.38;0.478;0.28;0.394	B;B;B;B	0.36666	0.23;0.161;0.129;0.115	T	0.54370	-0.8304	10	0.22706	T	0.39	-13.79	3.6241	0.08107	0.1738:0.5628:0.1683:0.0951	.	96;96;101;96	Q8WXC9;Q8N1B9;Q59FM0;O95299	.;.;.;NDUAA_HUMAN	I	96	ENSP00000252711:S96I;ENSP00000385697:S96I;ENSP00000411527:S96I;ENSP00000302321:S96I;ENSP00000383975:S96I	ENSP00000252711:S96I	S	-	2	0	NDUFA10	240609460	0.275000	0.24201	0.000000	0.03702	0.017000	0.09413	0.690000	0.25451	0.479000	0.27511	-0.261000	0.10672	AGT		0.493	NDUFA10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257180.2	NM_004544	
SNED1	25992	broad.mit.edu	37	2	241973253	241973253	+	Silent	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr2:241973253C>T	ENST00000310397.8	+	3	603	c.603C>T	c.(601-603)agC>agT	p.S201S	SNED1_ENST00000405547.3_Silent_p.S201S|AC005237.4_ENST00000458377.1_RNA|SNED1_ENST00000342631.6_Silent_p.S201S|SNED1_ENST00000401884.1_Silent_p.S201S	NM_001080437.1	NP_001073906.1	Q8TER0	SNED1_HUMAN	sushi, nidogen and EGF-like domains 1	201	NIDO. {ECO:0000255|PROSITE- ProRule:PRU00570}.				cell-matrix adhesion (GO:0007160)	extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)	p.S201S(1)		NS(1)|breast(1)|central_nervous_system(3)|kidney(2)|large_intestine(6)|lung(4)|ovary(3)|prostate(3)|upper_aerodigestive_tract(1)	24		all_cancers(19;7.48e-31)|all_epithelial(40;1.35e-12)|Breast(86;0.000148)|Renal(207;0.00528)|Ovarian(221;0.104)|Esophageal squamous(248;0.131)|all_lung(227;0.17)|all_hematologic(139;0.182)|Melanoma(123;0.238)		Epithelial(32;6.46e-32)|all cancers(36;6.23e-29)|OV - Ovarian serous cystadenocarcinoma(60;2.1e-14)|Kidney(56;6.35e-09)|KIRC - Kidney renal clear cell carcinoma(57;5.98e-08)|BRCA - Breast invasive adenocarcinoma(100;3.66e-06)|Lung(119;0.00072)|LUSC - Lung squamous cell carcinoma(224;0.00553)|Colorectal(34;0.0162)|COAD - Colon adenocarcinoma(134;0.109)		ACGCCAGCAGCGGGGGCAACG	0.607																																					p.S201S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C603T	2						.						44.0	46.0	45.0					2																	241973253		2129	4224	6353	241621926	SO:0001819	synonymous_variant	25992	exon3			AK074062	CCDS46562.1	2q37.3	2014-01-28			ENSG00000162804	ENSG00000162804		"""Fibronectin type III domain containing"""	24696	protein-coding gene	gene with protein product						12477932	Standard	NM_001080437		Approved	FLJ00133, SST3, Snep	uc002wah.1	Q8TER0	OTTHUMG00000151803	ENST00000310397.8:c.603C>T	2.37:g.241973253C>T		Somatic		Capture	Illumina HiSeq	Phase_I	241621926	NM_001080437	B5MDC3|B7WNK6|B7WPM0|Q336F4|Q336F5|Q8N369|Q8TEP7	Silent	SNP	ENST00000310397.8	37	CCDS46562.1																																																																																				0.607	SNED1-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323935.2	XM_059482	
HDLBP	3069	broad.mit.edu	37	2	242170238	242170238	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr2:242170238C>T	ENST00000391975.1	-	25	3637	c.3410G>A	c.(3409-3411)cGc>cAc	p.R1137H	HDLBP_ENST00000391976.2_Missense_Mutation_p.R1137H|HDLBP_ENST00000310931.4_Missense_Mutation_p.R1137H|HDLBP_ENST00000427183.2_Missense_Mutation_p.R1104H	NM_203346.3	NP_976221	Q00341	VIGLN_HUMAN	high density lipoprotein binding protein	1137	KH 14. {ECO:0000255|PROSITE- ProRule:PRU00117}.				cholesterol metabolic process (GO:0008203)|lipid transport (GO:0006869)	cytoplasm (GO:0005737)|high-density lipoprotein particle (GO:0034364)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	lipid binding (GO:0008289)|poly(A) RNA binding (GO:0044822)	p.R1137H(1)		breast(7)|cervix(1)|endometrium(8)|kidney(1)|large_intestine(11)|lung(8)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	44		all_cancers(19;7.77e-41)|all_epithelial(40;1.74e-18)|Breast(86;1.53e-05)|Renal(207;0.00179)|all_lung(227;0.00338)|Ovarian(221;0.00556)|Lung NSC(271;0.0121)|Esophageal squamous(248;0.129)|all_hematologic(139;0.158)|Melanoma(123;0.16)|all_neural(83;0.243)|Hepatocellular(293;0.244)		Epithelial(32;8.13e-34)|all cancers(36;4.71e-31)|OV - Ovarian serous cystadenocarcinoma(60;2.34e-15)|Kidney(56;3.72e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.76e-08)|BRCA - Breast invasive adenocarcinoma(100;3.38e-06)|Lung(119;0.000109)|LUSC - Lung squamous cell carcinoma(224;0.000964)|Colorectal(34;0.0132)|COAD - Colon adenocarcinoma(134;0.0928)		GGCGTGAACGCGGTGGTCCAG	0.547																																					p.R1137H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G3410A	2						.						146.0	114.0	125.0					2																	242170238		2203	4300	6503	241818911	SO:0001583	missense	3069	exon25				CCDS2547.1, CCDS58760.1	2q37.3	2008-07-18	2008-07-18		ENSG00000115677	ENSG00000115677			4857	protein-coding gene	gene with protein product		142695	"""vigilin"""	VGL		1318310, 8390966	Standard	NM_005336		Approved	HBP	uc002waz.3	Q00341	OTTHUMG00000133391	ENST00000391975.1:c.3410G>A	2.37:g.242170238C>T	ENSP00000375836:p.Arg1137His	Somatic		Capture	Illumina HiSeq	Phase_I	241818911	NM_005336	B4DTQ2|E7EM71|Q53QU2|Q9UCY3	Missense_Mutation	SNP	ENST00000391975.1	37	CCDS2547.1	.	.	.	.	.	.	.	.	.	.	C	15.93	2.978747	0.53720	.	.	ENSG00000115677	ENST00000391975;ENST00000391976;ENST00000310931;ENST00000427183;ENST00000442730	T;T;T;T	0.30714	1.52;1.52;1.52;1.52	5.53	2.7	0.31948	K Homology (1);K Homology, type 1, subgroup (1);K Homology, type 1 (1);	0.045449	0.85682	D	0.000000	T	0.49167	0.1541	M	0.64997	1.995	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.967;0.998	T	0.42899	-0.9424	10	0.72032	D	0.01	-3.331	10.4504	0.44518	0.0:0.7824:0.0:0.2176	.	1104;1137	E7EM71;Q00341	.;VIGLN_HUMAN	H	1137;1137;1137;1104;1	ENSP00000375836:R1137H;ENSP00000375837:R1137H;ENSP00000312042:R1137H;ENSP00000399139:R1104H	ENSP00000312042:R1137H	R	-	2	0	HDLBP	241818911	1.000000	0.71417	0.068000	0.19968	0.002000	0.02628	7.613000	0.82986	0.278000	0.22164	-0.156000	0.13503	CGC		0.547	HDLBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257245.5	NM_203346	
HDLBP	3069	broad.mit.edu	37	2	242173274	242173274	+	Silent	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr2:242173274G>A	ENST00000391975.1	-	24	3476	c.3249C>T	c.(3247-3249)gaC>gaT	p.D1083D	HDLBP_ENST00000391976.2_Silent_p.D1083D|HDLBP_ENST00000310931.4_Silent_p.D1083D|HDLBP_ENST00000427183.2_Silent_p.D1050D	NM_203346.3	NP_976221	Q00341	VIGLN_HUMAN	high density lipoprotein binding protein	1083	KH 13. {ECO:0000255|PROSITE- ProRule:PRU00117}.				cholesterol metabolic process (GO:0008203)|lipid transport (GO:0006869)	cytoplasm (GO:0005737)|high-density lipoprotein particle (GO:0034364)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	lipid binding (GO:0008289)|poly(A) RNA binding (GO:0044822)	p.D1083D(1)		breast(7)|cervix(1)|endometrium(8)|kidney(1)|large_intestine(11)|lung(8)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	44		all_cancers(19;7.77e-41)|all_epithelial(40;1.74e-18)|Breast(86;1.53e-05)|Renal(207;0.00179)|all_lung(227;0.00338)|Ovarian(221;0.00556)|Lung NSC(271;0.0121)|Esophageal squamous(248;0.129)|all_hematologic(139;0.158)|Melanoma(123;0.16)|all_neural(83;0.243)|Hepatocellular(293;0.244)		Epithelial(32;8.13e-34)|all cancers(36;4.71e-31)|OV - Ovarian serous cystadenocarcinoma(60;2.34e-15)|Kidney(56;3.72e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.76e-08)|BRCA - Breast invasive adenocarcinoma(100;3.38e-06)|Lung(119;0.000109)|LUSC - Lung squamous cell carcinoma(224;0.000964)|Colorectal(34;0.0132)|COAD - Colon adenocarcinoma(134;0.0928)		GGATGTTCACGTCATGCTCCA	0.507																																					p.D1083D												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C3249T	2						.						181.0	159.0	166.0					2																	242173274		2203	4300	6503	241821947	SO:0001819	synonymous_variant	3069	exon24				CCDS2547.1, CCDS58760.1	2q37.3	2008-07-18	2008-07-18		ENSG00000115677	ENSG00000115677			4857	protein-coding gene	gene with protein product		142695	"""vigilin"""	VGL		1318310, 8390966	Standard	NM_005336		Approved	HBP	uc002waz.3	Q00341	OTTHUMG00000133391	ENST00000391975.1:c.3249C>T	2.37:g.242173274G>A		Somatic		Capture	Illumina HiSeq	Phase_I	241821947	NM_005336	B4DTQ2|E7EM71|Q53QU2|Q9UCY3	Silent	SNP	ENST00000391975.1	37	CCDS2547.1	.	.	.	.	.	.	.	.	.	.	G	3.888	-0.024674	0.07589	.	.	ENSG00000115677	ENST00000373292	.	.	.	5.29	-10.6	0.00265	.	.	.	.	.	T	0.32823	0.0842	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.42137	-0.9469	4	.	.	.	-30.622	2.8567	0.05574	0.5774:0.0725:0.1076:0.2426	.	.	.	.	C	892	.	.	R	-	1	0	HDLBP	241821947	0.001000	0.12720	0.751000	0.31187	0.473000	0.32948	-1.576000	0.02129	-1.561000	0.01684	-0.251000	0.11542	CGT		0.507	HDLBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257245.5	NM_203346	
THAP4	51078	broad.mit.edu	37	2	242573366	242573366	+	Missense_Mutation	SNP	A	A	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr2:242573366A>T	ENST00000407315.1	-	2	637	c.206T>A	c.(205-207)cTg>cAg	p.L69Q		NM_015963.5	NP_057047.4	Q8WY91	THAP4_HUMAN	THAP domain containing 4	69							DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.L69Q(1)		kidney(1)|large_intestine(3)|lung(2)|ovary(2)|prostate(1)	9		all_cancers(19;2.09e-34)|all_epithelial(40;2.09e-14)|Breast(86;0.000141)|Renal(207;0.0143)|all_lung(227;0.0344)|Ovarian(221;0.069)|Lung NSC(271;0.0886)|Esophageal squamous(248;0.131)|all_hematologic(139;0.182)|Melanoma(123;0.2)		Epithelial(32;2.3e-33)|all cancers(36;8.99e-31)|OV - Ovarian serous cystadenocarcinoma(60;3.68e-15)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;1.65e-06)|Lung(119;0.000152)|LUSC - Lung squamous cell carcinoma(224;0.00154)|Colorectal(34;0.0129)|COAD - Colon adenocarcinoma(134;0.0844)		CTGGTCCTCCAGCCTCTTGGA	0.547																																					p.L69Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T206A	2						.						95.0	106.0	102.0					2																	242573366		2203	4296	6499	242222039	SO:0001583	missense	51078	exon2			AF258556	CCDS2551.1, CCDS54440.1	2q37.3	2013-01-25			ENSG00000176946	ENSG00000176946		"""THAP (C2CH-type zinc finger) domain containing"""	23187	protein-coding gene	gene with protein product		612533				12575992, 10810093	Standard	NM_015963		Approved	CGI-36	uc002wbt.3	Q8WY91	OTTHUMG00000133410	ENST00000407315.1:c.206T>A	2.37:g.242573366A>T	ENSP00000385006:p.Leu69Gln	Somatic		Capture	Illumina HiSeq	Phase_I	242222039	NM_015963	Q53NU7|Q6GRN0|Q6IPJ3|Q9NW26|Q9Y325	Missense_Mutation	SNP	ENST00000407315.1	37	CCDS2551.1	.	.	.	.	.	.	.	.	.	.	A	20.5	3.998265	0.74818	.	.	ENSG00000176946	ENST00000407315	D	0.96011	-3.88	4.8	4.8	0.61643	Zinc finger, C2CH-type (4);	0.759894	0.10707	N	0.643284	D	0.95999	0.8697	L	0.28556	0.865	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.93985	0.7261	10	0.66056	D	0.02	-24.9798	13.235	0.59965	1.0:0.0:0.0:0.0	.	69	Q8WY91	THAP4_HUMAN	Q	69	ENSP00000385006:L69Q	ENSP00000385006:L69Q	L	-	2	0	THAP4	242222039	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	3.615000	0.54167	1.919000	0.55581	0.533000	0.62120	CTG		0.547	THAP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257267.3	NM_015963	
KIDINS220	57498	broad.mit.edu	37	2	8925926	8925926	+	Missense_Mutation	SNP	C	C	T	rs572569622		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr2:8925926C>T	ENST00000256707.3	-	17	2355	c.2174G>A	c.(2173-2175)cGc>cAc	p.R725H	KIDINS220_ENST00000427284.1_Missense_Mutation_p.R725H|KIDINS220_ENST00000473731.1_Missense_Mutation_p.R725H|KIDINS220_ENST00000319688.5_Missense_Mutation_p.R726H|KIDINS220_ENST00000418530.1_Missense_Mutation_p.R683H	NM_020738.2	NP_065789.1	Q9ULH0	KDIS_HUMAN	kinase D-interacting substrate, 220kDa	725	KAP NTPase.				activation of MAPKK activity (GO:0000186)|cellular response to nerve growth factor stimulus (GO:1990090)|cytoplasmic transport (GO:0016482)|dendrite morphogenesis (GO:0048813)|in utero embryonic development (GO:0001701)|nerve growth factor signaling pathway (GO:0038180)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of neuron projection development (GO:0010976)	cytosol (GO:0005829)|integral component of membrane (GO:0016021)|late endosome (GO:0005770)|membrane (GO:0016020)|protein complex (GO:0043234)	PDZ domain binding (GO:0030165)	p.R725H(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(11)|lung(25)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	60	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)					ATTATGGAGGCGTTTTCTTTG	0.418																																					p.R725H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2174A	2						.						122.0	115.0	117.0					2																	8925926		1945	4156	6101	8843377	SO:0001583	missense	57498	exon17			AK025528	CCDS42650.1	2p24	2013-01-10			ENSG00000134313	ENSG00000134313		"""Ankyrin repeat domain containing"""	29508	protein-coding gene	gene with protein product	"""ankyrin repeat-rich membrane-spanning protein"""	615759				10998417, 10574462	Standard	NM_020738		Approved	ARMS	uc002qzc.2	Q9ULH0	OTTHUMG00000151658	ENST00000256707.3:c.2174G>A	2.37:g.8925926C>T	ENSP00000256707:p.Arg725His	Somatic		Capture	Illumina HiSeq	Phase_I	8843377	NM_020738	A1L4N4|Q4VC08|Q6MZU2|Q9H889|Q9H9E4|Q9NT37|Q9UF42	Missense_Mutation	SNP	ENST00000256707.3	37	CCDS42650.1	.	.	.	.	.	.	.	.	.	.	C	20.8	4.052946	0.75960	.	.	ENSG00000134313	ENST00000496383;ENST00000541927;ENST00000256707;ENST00000427284;ENST00000418530;ENST00000473731;ENST00000489024;ENST00000319688	T;T;T;T;T;T;T	0.68765	0.8;-0.35;-0.31;-0.23;-0.31;-0.27;-0.26	5.37	5.37	0.77165	KAP P-loop (1);	0.047096	0.85682	D	0.000000	T	0.76407	0.3983	L	0.45422	1.42	0.80722	D	1	D;B;P;P	0.89917	1.0;0.016;0.769;0.69	D;B;P;P	0.85130	0.997;0.009;0.511;0.643	T	0.73487	-0.3967	10	0.34782	T	0.22	.	17.6439	0.88144	0.0:1.0:0.0:0.0	.	726;726;683;725	B4DK94;E9PH70;Q9ULH0-2;Q9ULH0	.;.;.;KDIS_HUMAN	H	472;409;725;725;683;725;726;726	ENSP00000420364:R472H;ENSP00000256707:R725H;ENSP00000411849:R725H;ENSP00000414923:R683H;ENSP00000418974:R725H;ENSP00000419964:R726H;ENSP00000319947:R726H	ENSP00000256707:R725H	R	-	2	0	KIDINS220	8843377	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.667000	0.83888	2.654000	0.90174	0.655000	0.94253	CGC		0.418	KIDINS220-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323408.2	NM_020738	
NCOA1	8648	broad.mit.edu	37	2	24952627	24952627	+	Silent	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr2:24952627G>A	ENST00000406961.1	+	17	3796	c.3144G>A	c.(3142-3144)ccG>ccA	p.P1048P	NCOA1_ENST00000407230.1_Silent_p.P897P|NCOA1_ENST00000348332.3_Silent_p.P1048P|NCOA1_ENST00000395856.3_Silent_p.P1048P|NCOA1_ENST00000538539.1_Silent_p.P1048P|NCOA1_ENST00000288599.5_Silent_p.P1048P|NCOA1_ENST00000405141.1_Silent_p.P1048P			Q15788	NCOA1_HUMAN	nuclear receptor coactivator 1	1048					androgen receptor signaling pathway (GO:0030521)|cellular lipid metabolic process (GO:0044255)|cellular response to hormone stimulus (GO:0032870)|cerebellum development (GO:0021549)|cerebral cortex development (GO:0021987)|estrous cycle phase (GO:0060206)|hippocampus development (GO:0021766)|histone H4 acetylation (GO:0043967)|hypothalamus development (GO:0021854)|labyrinthine layer morphogenesis (GO:0060713)|lactation (GO:0007595)|male gonad development (GO:0008584)|male mating behavior (GO:0060179)|ovulation cycle (GO:0042698)|positive regulation of apoptotic process (GO:0043065)|positive regulation of female receptivity (GO:0045925)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase II promoter by galactose (GO:0000435)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cellular response to drug (GO:2001038)|response to estradiol (GO:0032355)|response to progesterone (GO:0032570)|response to retinoic acid (GO:0032526)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|neuron projection (GO:0043005)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)	androgen receptor binding (GO:0050681)|chromatin binding (GO:0003682)|enzyme binding (GO:0019899)|histone acetyltransferase activity (GO:0004402)|ligand-dependent nuclear receptor binding (GO:0016922)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|nuclear hormone receptor binding (GO:0035257)|protein N-terminus binding (GO:0047485)|RNA polymerase II regulatory region DNA binding (GO:0001012)|RNA polymerase II transcription coactivator activity (GO:0001105)|signal transducer activity (GO:0004871)|transcription coactivator activity (GO:0003713)	p.P1048P(2)	PAX3/NCOA1(8)	breast(3)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(13)|lung(26)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	53	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					ACAGACCTCCGGCTGCACCTA	0.488			T	PAX3	alveolar rhadomyosarcoma																																p.P1048P			Dom	yes		2	2p23	8648	nuclear receptor coactivator 1		M	.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.G3144A	2						.						101.0	101.0	101.0					2																	24952627		2203	4300	6503	24806131	SO:0001819	synonymous_variant	8648	exon15			U40396	CCDS1712.1, CCDS1713.1, CCDS42660.1	2p23	2011-07-01			ENSG00000084676	ENSG00000084676		"""Chromatin-modifying enzymes / K-acetyltransferases"", ""Basic helix-loop-helix proteins"""	7668	protein-coding gene	gene with protein product		602691				7481822, 9575154	Standard	XM_005264625		Approved	SRC1, F-SRC-1, NCoA-1, KAT13A, RIP160, bHLHe74	uc002rfk.3	Q15788	OTTHUMG00000125523	ENST00000406961.1:c.3144G>A	2.37:g.24952627G>A		Somatic		Capture	Illumina HiSeq	Phase_I	24806131	NM_003743	O00150|O43792|O43793|Q13071|Q13420|Q2T9G5|Q53SX3|Q6GVI5|Q7KYV3	Silent	SNP	ENST00000406961.1	37	CCDS1712.1																																																																																				0.488	NCOA1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000246852.3	NM_147223	
NCOA1	8648	broad.mit.edu	37	2	24964907	24964907	+	Silent	SNP	G	G	A	rs531091549		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr2:24964907G>A	ENST00000406961.1	+	19	4210	c.3558G>A	c.(3556-3558)ccG>ccA	p.P1186P	NCOA1_ENST00000407230.1_Silent_p.P1035P|NCOA1_ENST00000348332.3_Silent_p.P1186P|NCOA1_ENST00000395856.3_Silent_p.P1186P|NCOA1_ENST00000538539.1_Silent_p.P1186P|NCOA1_ENST00000288599.5_Silent_p.P1186P|NCOA1_ENST00000405141.1_Silent_p.P1186P			Q15788	NCOA1_HUMAN	nuclear receptor coactivator 1	1186					androgen receptor signaling pathway (GO:0030521)|cellular lipid metabolic process (GO:0044255)|cellular response to hormone stimulus (GO:0032870)|cerebellum development (GO:0021549)|cerebral cortex development (GO:0021987)|estrous cycle phase (GO:0060206)|hippocampus development (GO:0021766)|histone H4 acetylation (GO:0043967)|hypothalamus development (GO:0021854)|labyrinthine layer morphogenesis (GO:0060713)|lactation (GO:0007595)|male gonad development (GO:0008584)|male mating behavior (GO:0060179)|ovulation cycle (GO:0042698)|positive regulation of apoptotic process (GO:0043065)|positive regulation of female receptivity (GO:0045925)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase II promoter by galactose (GO:0000435)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cellular response to drug (GO:2001038)|response to estradiol (GO:0032355)|response to progesterone (GO:0032570)|response to retinoic acid (GO:0032526)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|neuron projection (GO:0043005)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)	androgen receptor binding (GO:0050681)|chromatin binding (GO:0003682)|enzyme binding (GO:0019899)|histone acetyltransferase activity (GO:0004402)|ligand-dependent nuclear receptor binding (GO:0016922)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|nuclear hormone receptor binding (GO:0035257)|protein N-terminus binding (GO:0047485)|RNA polymerase II regulatory region DNA binding (GO:0001012)|RNA polymerase II transcription coactivator activity (GO:0001105)|signal transducer activity (GO:0004871)|transcription coactivator activity (GO:0003713)	p.P1186P(2)	PAX3/NCOA1(8)	breast(3)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(13)|lung(26)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	53	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					CTACCAGCCCGTTTTCACAAC	0.527			T	PAX3	alveolar rhadomyosarcoma								G|||	1	0.000199681	0.0	0.0014	5008	,	,		22478	0.0		0.0	False		,,,				2504	0.0				p.P1186P			Dom	yes		2	2p23	8648	nuclear receptor coactivator 1		M	.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.G3558A	2						.						129.0	122.0	124.0					2																	24964907		2203	4300	6503	24818411	SO:0001819	synonymous_variant	8648	exon17			U40396	CCDS1712.1, CCDS1713.1, CCDS42660.1	2p23	2011-07-01			ENSG00000084676	ENSG00000084676		"""Chromatin-modifying enzymes / K-acetyltransferases"", ""Basic helix-loop-helix proteins"""	7668	protein-coding gene	gene with protein product		602691				7481822, 9575154	Standard	XM_005264625		Approved	SRC1, F-SRC-1, NCoA-1, KAT13A, RIP160, bHLHe74	uc002rfk.3	Q15788	OTTHUMG00000125523	ENST00000406961.1:c.3558G>A	2.37:g.24964907G>A		Somatic		Capture	Illumina HiSeq	Phase_I	24818411	NM_003743	O00150|O43792|O43793|Q13071|Q13420|Q2T9G5|Q53SX3|Q6GVI5|Q7KYV3	Silent	SNP	ENST00000406961.1	37	CCDS1712.1																																																																																				0.527	NCOA1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000246852.3	NM_147223	
KIF3C	3797	broad.mit.edu	37	2	26203965	26203965	+	Silent	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr2:26203965G>A	ENST00000264712.3	-	1	1401	c.822C>T	c.(820-822)ggC>ggT	p.G274G	KIF3C_ENST00000405914.1_Silent_p.G274G	NM_002254.6	NP_002245	O14782	KIF3C_HUMAN	kinesin family member 3C	274	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.|Poly-Gly.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|ATP catabolic process (GO:0006200)|blood coagulation (GO:0007596)|cytoskeleton-dependent intracellular transport (GO:0030705)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|organelle transport along microtubule (GO:0072384)	cytosol (GO:0005829)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|motor activity (GO:0003774)	p.G274G(1)		breast(3)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(8)|ovary(4)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	29	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					tgcctccaccgccaccaccgc	0.632																																					p.G274G												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C822T	2						.						34.0	34.0	34.0					2																	26203965		2203	4298	6501	26057469	SO:0001819	synonymous_variant	3797	exon1				CCDS1719.1	2p23	2008-02-05			ENSG00000084731	ENSG00000084731		"""Kinesins"""	6321	protein-coding gene	gene with protein product		602845				9480755	Standard	NM_002254		Approved		uc002rgu.2	O14782	OTTHUMG00000094797	ENST00000264712.3:c.822C>T	2.37:g.26203965G>A		Somatic		Capture	Illumina HiSeq	Phase_I	26057469	NM_002254	O43544|Q4ZG18|Q53SX5|Q562F7	Silent	SNP	ENST00000264712.3	37	CCDS1719.1																																																																																				0.632	KIF3C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000211611.1		
OTOF	9381	broad.mit.edu	37	2	26696038	26696038	+	Missense_Mutation	SNP	C	C	T	rs371588016		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr2:26696038C>T	ENST00000272371.2	-	29	3821	c.3695G>A	c.(3694-3696)cGg>cAg	p.R1232Q	OTOF_ENST00000402415.3_Missense_Mutation_p.R542Q|OTOF_ENST00000403946.3_Missense_Mutation_p.R1232Q|OTOF_ENST00000339598.3_Missense_Mutation_p.R485Q|OTOF_ENST00000338581.6_Missense_Mutation_p.R485Q	NM_194248.2	NP_919224.1	Q9HC10	OTOF_HUMAN	otoferlin	1232					membrane fusion (GO:0061025)|sensory perception of sound (GO:0007605)|synaptic vesicle exocytosis (GO:0016079)	cell junction (GO:0030054)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|synaptic vesicle membrane (GO:0030672)	calcium ion binding (GO:0005509)	p.R485Q(1)|p.R1232Q(1)		NS(1)|autonomic_ganglia(1)|breast(9)|central_nervous_system(4)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(14)|lung(35)|ovary(8)|pancreas(1)|prostate(5)|skin(5)|stomach(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	106	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					GTCTGGGGGCCGGTAGATGAA	0.687													C|||	1	0.000199681	0.0	0.0014	5008	,	,		14438	0.0		0.0	False		,,,				2504	0.0				p.R485Q	GBM(102;732 1451 20652 24062 31372)											.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G1454A	2						.						37.0	42.0	40.0					2																	26696038		2203	4299	6502	26549542	SO:0001583	missense	9381	exon12			AF107403	CCDS1724.1, CCDS1725.1, CCDS1726.1, CCDS46241.1, CCDS74497.1	2p23.1	2014-06-27			ENSG00000115155	ENSG00000115155			8515	protein-coding gene	gene with protein product	"""fer-1-like family member 2"""	603681		DFNB9		10192385, 18381613	Standard	NM_194248		Approved	FER1L2, DFNB6	uc002rhk.3	Q9HC10	OTTHUMG00000096977	ENST00000272371.2:c.3695G>A	2.37:g.26696038C>T	ENSP00000272371:p.Arg1232Gln	Somatic		Capture	Illumina HiSeq	Phase_I	26549542	NM_194323	B4DJX0|B5MCC1|B9A0H6|Q53R90|Q9HC08|Q9HC09|Q9Y650	Missense_Mutation	SNP	ENST00000272371.2	37	CCDS1725.1	.	.	.	.	.	.	.	.	.	.	C	18.88	3.718351	0.68844	.	.	ENSG00000115155	ENST00000338581;ENST00000339598;ENST00000402415;ENST00000272371;ENST00000403946	T;T;T;T;T	0.77750	-1.12;-1.12;-1.09;-0.18;-0.18	4.58	4.58	0.56647	C2 calcium/lipid-binding domain, CaLB (1);	0.272711	0.33515	N	0.004823	T	0.77089	0.4079	L	0.56396	1.775	0.33444	D	0.582809	D;P;D;P	0.65815	0.995;0.538;0.978;0.538	P;B;P;B	0.48063	0.56;0.062;0.565;0.062	T	0.80101	-0.1523	10	0.16896	T	0.51	-21.3079	15.955	0.79880	0.0:1.0:0.0:0.0	.	1232;485;542;485	Q9HC10;Q9HC10-2;Q9HC10-3;Q9HC10-4	OTOF_HUMAN;.;.;.	Q	485;485;542;1232;1232	ENSP00000345137:R485Q;ENSP00000344521:R485Q;ENSP00000383906:R542Q;ENSP00000272371:R1232Q;ENSP00000385255:R1232Q	ENSP00000272371:R1232Q	R	-	2	0	OTOF	26549542	0.994000	0.37717	0.996000	0.52242	0.942000	0.58702	1.618000	0.36954	2.103000	0.63969	0.484000	0.47621	CGG		0.687	OTOF-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000214047.3		
MAPRE3	22924	broad.mit.edu	37	2	27249157	27249157	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr2:27249157G>A	ENST00000233121.2	+	7	985	c.787G>A	c.(787-789)Gca>Aca	p.A263T	MAPRE3_ENST00000402218.1_Missense_Mutation_p.A248T|MAPRE3_ENST00000405074.3_Missense_Mutation_p.A248T			Q9UPY8	MARE3_HUMAN	microtubule-associated protein, RP/EB family, member 3	263	DCTN1-binding.|EB1 C-terminal. {ECO:0000255|PROSITE- ProRule:PRU00576}.				mitotic nuclear division (GO:0007067)|positive regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045737)|positive regulation of microtubule plus-end binding (GO:1903033)|positive regulation of transcription, DNA-templated (GO:0045893)	cytoplasm (GO:0005737)|microtubule cytoskeleton (GO:0015630)|microtubule plus-end (GO:0035371)|midbody (GO:0030496)|perinuclear region of cytoplasm (GO:0048471)	microtubule binding (GO:0008017)	p.A263T(1)		endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(3)|ovary(3)|upper_aerodigestive_tract(1)	13	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					GGAAGGATTCGCACCCCCTGA	0.602																																					p.A263T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G787A	2						.						92.0	81.0	85.0					2																	27249157		2203	4300	6503	27102661	SO:0001583	missense	22924	exon7			Y11174	CCDS1731.1	2p23.3-p23.1	2008-06-04			ENSG00000084764	ENSG00000084764			6892	protein-coding gene	gene with protein product		605788				9233623	Standard	NM_012326		Approved	RP3, EB3	uc002rhw.3	Q9UPY8	OTTHUMG00000097067	ENST00000233121.2:c.787G>A	2.37:g.27249157G>A	ENSP00000233121:p.Ala263Thr	Somatic		Capture	Illumina HiSeq	Phase_I	27102661	NM_012326	B7WPK5|O00265|Q6FHB0|Q6FI15|Q9BZP7|Q9BZP8	Missense_Mutation	SNP	ENST00000233121.2	37	CCDS1731.1	.	.	.	.	.	.	.	.	.	.	g	23.2	4.384820	0.82792	.	.	ENSG00000084764	ENST00000233121;ENST00000405074;ENST00000402218	T;T;T	0.46451	0.87;0.89;0.89	4.86	4.86	0.63082	EB1, C-terminal (1);	0.000000	0.85682	D	0.000000	T	0.54398	0.1856	M	0.82517	2.595	0.80722	D	1	D;P	0.55800	0.973;0.955	P;B	0.46940	0.532;0.284	T	0.63541	-0.6614	10	0.48119	T	0.1	-8.0571	16.7569	0.85502	0.0:0.0:1.0:0.0	.	248;263	Q9UPY8-2;Q9UPY8	.;MARE3_HUMAN	T	263;248;248	ENSP00000233121:A263T;ENSP00000383915:A248T;ENSP00000385715:A248T	ENSP00000233121:A263T	A	+	1	0	MAPRE3	27102661	1.000000	0.71417	1.000000	0.80357	0.943000	0.58893	8.959000	0.93110	2.254000	0.74563	0.457000	0.33378	GCA		0.602	MAPRE3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214183.1	NM_012326	
TMEM214	54867	broad.mit.edu	37	2	27263267	27263267	+	Silent	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr2:27263267C>T	ENST00000238788.9	+	16	1908	c.1846C>T	c.(1846-1848)Ctg>Ttg	p.L616L	TMEM214_ENST00000404032.3_Silent_p.L571L	NM_017727.4	NP_060197.4	Q6NUQ4	TM214_HUMAN	transmembrane protein 214	616					apoptotic process (GO:0006915)	cytoplasmic microtubule (GO:0005881)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)		p.L616L(1)		kidney(1)|large_intestine(5)|lung(9)|prostate(1)|skin(2)	18						TCTGAGAGAGCTGCCCCTGCT	0.587																																					p.L571L												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1711T	2						.						91.0	96.0	95.0					2																	27263267		2038	4178	6216	27116771	SO:0001819	synonymous_variant	54867	exon15				CCDS42664.1, CCDS46242.1	2p23.3	2013-06-19			ENSG00000119777	ENSG00000119777			25983	protein-coding gene	gene with protein product						23661706	Standard	NM_001083590		Approved	FLJ20254	uc002ria.4	Q6NUQ4	OTTHUMG00000151999	ENST00000238788.9:c.1846C>T	2.37:g.27263267C>T		Somatic		Capture	Illumina HiSeq	Phase_I	27116771	NM_001083590	A6NNF2|B3KUI9|B5MCD8|D6W547|Q53SW1|Q69YH4|Q8NC45|Q8WZ37|Q9NXH2	Silent	SNP	ENST00000238788.9	37	CCDS42664.1																																																																																				0.587	TMEM214-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324748.1	NM_017727	
IFT172	26160	broad.mit.edu	37	2	27685972	27685972	+	Missense_Mutation	SNP	G	G	A	rs201921339	byFrequency	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr2:27685972G>A	ENST00000260570.3	-	19	2117	c.2014C>T	c.(2014-2016)Cgg>Tgg	p.R672W		NM_015662.1	NP_056477.1	Q9UG01	IF172_HUMAN	intraflagellar transport 172	672					bone development (GO:0060348)|brain development (GO:0007420)|cilium assembly (GO:0042384)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|epidermis development (GO:0008544)|heart looping (GO:0001947)|hindgut development (GO:0061525)|left/right axis specification (GO:0070986)|limb development (GO:0060173)|negative regulation of epithelial cell proliferation (GO:0050680)|neural tube closure (GO:0001843)|Notch signaling pathway (GO:0007219)|palate development (GO:0060021)|positive regulation of smoothened signaling pathway (GO:0045880)|protein processing (GO:0016485)|smoothened signaling pathway (GO:0007224)|spinal cord motor neuron differentiation (GO:0021522)	axoneme (GO:0005930)|ciliary basal body (GO:0036064)|cilium (GO:0005929)|intraciliary transport particle B (GO:0030992)|sperm midpiece (GO:0097225)|sperm principal piece (GO:0097228)|vesicle (GO:0031982)		p.R672W(1)		central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(17)|lung(17)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)	43	Acute lymphoblastic leukemia(172;0.155)					GCATATTCCCGGGATACTTGA	0.448													G|||	2	0.000399361	0.0008	0.0	5008	,	,		17811	0.001		0.0	False		,,,				2504	0.0				p.R672W												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C2014T	2						.						124.0	119.0	121.0					2																	27685972		2203	4300	6503	27539476	SO:0001583	missense	26160	exon19			AB033005	CCDS1755.1	2p23.3	2014-07-03	2014-07-03		ENSG00000138002	ENSG00000138002		"""Intraflagellar transport homologs"", ""WD repeat domain containing"""	30391	protein-coding gene	gene with protein product	"""wimple homolog"""	607386	"""intraflagellar transport 172 homolog (Chlamydomonas)"""			10788441, 10574461, 24140113	Standard	XM_005264254		Approved	SLB, wim, osm-1, NPHP17	uc002rku.3	Q9UG01	OTTHUMG00000128425	ENST00000260570.3:c.2014C>T	2.37:g.27685972G>A	ENSP00000260570:p.Arg672Trp	Somatic		Capture	Illumina HiSeq	Phase_I	27539476	NM_015662	A5PKZ0|B2RNU5|Q86X44|Q96HW4|Q9UFJ9|Q9ULP1	Missense_Mutation	SNP	ENST00000260570.3	37	CCDS1755.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	G	15.77	2.930792	0.52866	.	.	ENSG00000138002	ENST00000260570	T	0.63744	-0.06	5.54	0.568	0.17333	.	0.447542	0.25299	N	0.031677	T	0.55893	0.1949	L	0.39898	1.24	0.44927	D	0.997949	D	0.65815	0.995	P	0.49047	0.599	T	0.56282	-0.8005	10	0.66056	D	0.02	-1.0181	9.6221	0.39727	0.0742:0.0:0.4134:0.5124	.	672	Q9UG01	IF172_HUMAN	W	672	ENSP00000260570:R672W	ENSP00000260570:R672W	R	-	1	2	IFT172	27539476	1.000000	0.71417	0.979000	0.43373	0.937000	0.57800	1.733000	0.38156	0.159000	0.19401	0.655000	0.94253	CGG		0.448	IFT172-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250213.2	NM_015662	
PLB1	151056	broad.mit.edu	37	2	28764630	28764630	+	Silent	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr2:28764630C>T	ENST00000327757.5	+	13	875	c.831C>T	c.(829-831)acC>acT	p.T277T	PLB1_ENST00000422425.2_Silent_p.T288T	NM_153021.4	NP_694566.4	Q6P1J6	PLB1_HUMAN	phospholipase B1	277	4 X 308-326 AA approximate repeats.				glycerophospholipid biosynthetic process (GO:0046474)|lipid catabolic process (GO:0016042)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phospholipid metabolic process (GO:0006644)|phototransduction, visible light (GO:0007603)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	lysophospholipase activity (GO:0004622)|phospholipase A2 activity (GO:0004623)	p.T277T(2)|p.T288T(1)		NS(2)|breast(1)|central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(10)|lung(31)|ovary(6)|prostate(1)|skin(7)|stomach(2)	69	Acute lymphoblastic leukemia(172;0.155)					AGTCCTTCACCGTGGTTTTCC	0.587																																					p.T288T												.	.	3	Substitution - coding silent(3)	lung(2)|large_intestine(1)	c.C864T	2						.						68.0	64.0	66.0					2																	28764630		2203	4300	6503	28618134	SO:0001819	synonymous_variant	151056	exon13				CCDS33168.1, CCDS54340.1	2p23.3	2014-03-14			ENSG00000163803	ENSG00000163803	3.1.1.4, 3.1.1.5		30041	protein-coding gene	gene with protein product		610179				12150957	Standard	NM_153021		Approved	PLB, FLJ30866	uc002rmb.2	Q6P1J6	OTTHUMG00000152014	ENST00000327757.5:c.831C>T	2.37:g.28764630C>T		Somatic		Capture	Illumina HiSeq	Phase_I	28618134	NM_001170585	A8KAX2|Q53S03|Q8IUP7|Q96DP9	Silent	SNP	ENST00000327757.5	37	CCDS33168.1	.	.	.	.	.	.	.	.	.	.	c	1.731	-0.494172	0.04322	.	.	ENSG00000163803	ENST00000404858	.	.	.	5.6	-11.2	0.00127	.	.	.	.	.	T	0.19005	0.0456	.	.	.	0.28921	N	0.892132	.	.	.	.	.	.	T	0.33163	-0.9879	4	.	.	.	-1.8207	3.0389	0.06132	0.4404:0.2504:0.0719:0.2373	.	.	.	.	L	287	.	.	P	+	2	0	PLB1	28618134	0.000000	0.05858	0.000000	0.03702	0.438000	0.31896	-8.201000	0.00023	-6.146000	0.00006	-2.599000	0.00162	CCG		0.587	PLB1-012	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000353348.2		
FAM179A	165186	broad.mit.edu	37	2	29226424	29226424	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr2:29226424G>A	ENST00000379558.4	+	6	1057	c.706G>A	c.(706-708)Gtg>Atg	p.V236M	FAM179A_ENST00000403861.2_Missense_Mutation_p.V236M	NM_199280.2	NP_954974.2	Q6ZUX3	F179A_HUMAN	family with sequence similarity 179, member A	236								p.V236M(1)		breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(5)|lung(9)|ovary(3)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	26						GGGCGCCATCGTGATCCCACC	0.637																																					p.V236M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G706A	2						.						40.0	47.0	45.0					2																	29226424		2065	4182	6247	29079928	SO:0001583	missense	165186	exon6			AK125239, AK125744	CCDS1769.2	2p23.2	2008-10-30			ENSG00000189350	ENSG00000189350			33715	protein-coding gene	gene with protein product						16344560	Standard	NM_199280		Approved	FLJ43249, LOC165186	uc010ezl.3	Q6ZUX3	OTTHUMG00000128432	ENST00000379558.4:c.706G>A	2.37:g.29226424G>A	ENSP00000368876:p.Val236Met	Somatic		Capture	Illumina HiSeq	Phase_I	29079928	NM_199280	Q6ZUF5	Missense_Mutation	SNP	ENST00000379558.4	37	CCDS1769.2	.	.	.	.	.	.	.	.	.	.	G	4.068	0.010533	0.07912	.	.	ENSG00000189350	ENST00000379558;ENST00000403861	T;T	0.13901	2.78;2.55	4.86	1.74	0.24563	.	.	.	.	.	T	0.08447	0.0210	L	0.27053	0.805	0.09310	N	0.999996	B;B	0.22003	0.063;0.017	B;B	0.15484	0.013;0.009	T	0.32771	-0.9894	9	0.35671	T	0.21	.	4.7897	0.13243	0.2054:0.2252:0.5695:0.0	.	236;236	F8W8E4;Q6ZUX3	.;F179A_HUMAN	M	236	ENSP00000368876:V236M;ENSP00000384699:V236M	ENSP00000368876:V236M	V	+	1	0	FAM179A	29079928	0.418000	0.25440	0.505000	0.27651	0.000000	0.00434	0.523000	0.22925	0.588000	0.29660	-1.430000	0.01095	GTG		0.637	FAM179A-003	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317848.4	NM_199280	
ALK	238	broad.mit.edu	37	2	29606679	29606679	+	Nonsense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr2:29606679G>A	ENST00000389048.3	-	5	2107	c.1201C>T	c.(1201-1203)Cga>Tga	p.R401*	ALK_ENST00000431873.1_Intron	NM_004304.4	NP_004295.2	Q9UM73	ALK_HUMAN	anaplastic lymphoma receptor tyrosine kinase	401	MAM 1. {ECO:0000255|PROSITE- ProRule:PRU00128}.				activation of MAPK activity (GO:0000187)|cell proliferation (GO:0008283)|neuron development (GO:0048666)|NIK/NF-kappaB signaling (GO:0038061)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphorylation (GO:0016310)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|protein autophosphorylation (GO:0046777)|regulation of apoptotic process (GO:0042981)|signal transduction (GO:0007165)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|protein complex (GO:0043234)	ATP binding (GO:0005524)|NF-kappaB-inducing kinase activity (GO:0004704)|protein tyrosine kinase activity (GO:0004713)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)	p.R401*(3)	ATIC/ALK(24)|FN1/ALK(2)|C2orf44/ALK(2)|TPM3/ALK(33)|KLC1/ALK(2)|VCL/ALK(4)|TPM4/ALK(12)|KIF5B/ALK(8)|RANBP2/ALK(34)|SQSTM1/ALK(2)|EML4/ALK(543)|PPFIBP1/ALK(3)|SEC31A/ALK(3)|NPM1/ALK(632)|CLTC/ALK(44)|CARS/ALK(5)|MSN/ALK(6)|TFG/ALK(9)	NS(2)|autonomic_ganglia(198)|breast(8)|central_nervous_system(2)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(7)|kidney(4)|large_intestine(25)|lung(61)|ovary(6)|pancreas(1)|prostate(2)|skin(5)|soft_tissue(3)|stomach(2)|thyroid(2)	340	Acute lymphoblastic leukemia(172;0.155)				Adenosine triphosphate(DB00171)|Crizotinib(DB08865)	AGGGCCACTCGAAATGGGTTG	0.483			"""T, Mis, A"""	"""NPM1, TPM3, TFG, TPM4, ATIC, CLTC, MSN, ALO17, CARS, EML4, KIF5B, C2orf22"""	"""ALCL, NSCLC, Neuroblastoma"""	neuroblastoma			Neuroblastoma, Familial Clustering of;Congenital Central Hypoventilation Syndrome																												p.R401X		yes	Dom	yes	Familial neuroblastoma	2	2p23	238	anaplastic lymphoma kinase (Ki-1)		"""L, E, M"""	ALK,ovary,NS,Substitution - Nonsense,0 	.	3	Substitution - Nonsense(3)	large_intestine(2)|ovary(1)	c.C1201T	2						.						120.0	113.0	115.0					2																	29606679		2203	4300	6503	29460183	SO:0001587	stop_gained	238	exon5	Familial Cancer Database	Familial Neuroblastoma;CCHS, Ondine Curse, incl. Ondine-Hirschsprung Disease	D45915	CCDS33172.1	2p23	2014-09-17	2008-01-23		ENSG00000171094	ENSG00000171094		"""CD molecules"""	427	protein-coding gene	gene with protein product		105590	"""anaplastic lymphoma kinase (Ki-1)"""			8122112	Standard	NM_004304		Approved	CD246	uc002rmy.3	Q9UM73	OTTHUMG00000152034	ENST00000389048.3:c.1201C>T	2.37:g.29606679G>A	ENSP00000373700:p.Arg401*	Somatic		Capture	Illumina HiSeq	Phase_I	29460183	NM_004304	Q4ZFX9|Q53QQ6|Q53RZ4|Q59FI3|Q9Y4K6	Nonsense_Mutation	SNP	ENST00000389048.3	37	CCDS33172.1	.	.	.	.	.	.	.	.	.	.	G	46	12.444284	0.99668	.	.	ENSG00000171094	ENST00000389048	.	.	.	6.02	6.02	0.97574	.	0.000000	0.29980	N	0.010702	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	17.6932	0.88275	0.0:0.0:1.0:0.0	.	.	.	.	X	401	.	.	R	-	1	2	ALK	29460183	1.000000	0.71417	0.998000	0.56505	0.459000	0.32528	4.361000	0.59461	2.857000	0.98124	0.650000	0.86243	CGA		0.483	ALK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324994.1	NM_004304	
EHD3	30845	broad.mit.edu	37	2	31489172	31489172	+	Missense_Mutation	SNP	C	C	T	rs183394828	byFrequency	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr2:31489172C>T	ENST00000322054.5	+	6	1495	c.1210C>T	c.(1210-1212)Cgg>Tgg	p.R404W	EHD3_ENST00000541626.1_3'UTR	NM_014600.2	NP_055415.1	Q9NZN3	EHD3_HUMAN	EH-domain containing 3	404					blood coagulation (GO:0007596)|endocytic recycling (GO:0032456)|protein homooligomerization (GO:0051260)|protein targeting to plasma membrane (GO:0072661)|regulation of cardiac muscle cell membrane potential (GO:0086036)	cytoplasm (GO:0005737)|endocytic vesicle (GO:0030139)|endosome membrane (GO:0010008)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|recycling endosome membrane (GO:0055038)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|nucleic acid binding (GO:0003676)	p.R404W(2)		NS(1)|breast(2)|endometrium(2)|kidney(1)|large_intestine(11)|lung(12)|ovary(1)|skin(3)	33	Acute lymphoblastic leukemia(172;0.155)					GGAGTCACAGCGGCCCATCCA	0.627													C|||	2	0.000399361	0.0015	0.0	5008	,	,		19658	0.0		0.0	False		,,,				2504	0.0				p.R404W												.	.	2	Substitution - Missense(2)	large_intestine(1)|lung(1)	c.C1210T	2						.						62.0	59.0	60.0					2																	31489172		2203	4300	6503	31342676	SO:0001583	missense	30845	exon6			AF181264	CCDS1774.1	2p21	2013-01-10			ENSG00000013016	ENSG00000013016		"""EF-hand domain containing"""	3244	protein-coding gene	gene with protein product		605891		PAST3		10673336	Standard	NM_014600		Approved		uc002rnu.3	Q9NZN3	OTTHUMG00000099365	ENST00000322054.5:c.1210C>T	2.37:g.31489172C>T	ENSP00000327116:p.Arg404Trp	Somatic		Capture	Illumina HiSeq	Phase_I	31342676	NM_014600	B4DFR5|D6W574|Q8N514|Q9NZB3	Missense_Mutation	SNP	ENST00000322054.5	37	CCDS1774.1	3	0.0013736263736263737	3	0.006097560975609756	0	0.0	0	0.0	0	0.0	C	15.34	2.805695	0.50315	.	.	ENSG00000013016	ENST00000322054	T	0.18502	2.21	5.84	2.94	0.34122	.	0.224665	0.46145	N	0.000305	T	0.06554	0.0168	N	0.19112	0.55	0.80722	D	1	B	0.33379	0.41	B	0.25140	0.058	T	0.17684	-1.0361	10	0.66056	D	0.02	-18.5698	9.2477	0.37536	0.4743:0.4603:0.0:0.0655	.	404	Q9NZN3	EHD3_HUMAN	W	404	ENSP00000327116:R404W	ENSP00000327116:R404W	R	+	1	2	EHD3	31342676	0.892000	0.30473	0.997000	0.53966	0.974000	0.67602	0.495000	0.22483	0.790000	0.33803	0.561000	0.74099	CGG		0.627	EHD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216810.1	NM_014600	
LTBP1	4052	broad.mit.edu	37	2	33622300	33622300	+	Silent	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr2:33622300C>T	ENST00000404816.2	+	33	5288	c.4935C>T	c.(4933-4935)tgC>tgT	p.C1645C	LTBP1_ENST00000404525.1_Silent_p.C1266C|LTBP1_ENST00000402934.1_Silent_p.C1264C|LTBP1_ENST00000390003.4_Silent_p.C1320C|LTBP1_ENST00000354476.3_Silent_p.C1646C|LTBP1_ENST00000272273.5_Silent_p.C543C|LTBP1_ENST00000418533.2_Silent_p.C1277C|LTBP1_ENST00000407925.1_Silent_p.C1319C			Q14766	LTBP1_HUMAN	latent transforming growth factor beta binding protein 1	1645	EGF-like 17. {ECO:0000255|PROSITE- ProRule:PRU00076}.				extracellular matrix organization (GO:0030198)|sequestering of TGFbeta in extracellular matrix (GO:0035583)|transmembrane receptor protein serine/threonine kinase signaling pathway (GO:0007178)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|transforming growth factor beta binding (GO:0050431)|transforming growth factor beta-activated receptor activity (GO:0005024)	p.C1646C(1)		breast(2)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(13)|lung(60)|ovary(4)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(3)	108	all_hematologic(175;0.115)	Medulloblastoma(90;0.215)				GTTACACCTGCGATTGCTTTG	0.463																																					p.C1319C												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C3957T	2						.						212.0	184.0	194.0					2																	33622300		2203	4300	6503	33475804	SO:0001819	synonymous_variant	4052	exon29				CCDS33177.1, CCDS33178.1, CCDS33177.2, CCDS33178.2, CCDS54344.1, CCDS54345.1	2p22-p21	2008-05-23			ENSG00000049323	ENSG00000049323		"""Latent transforming growth factor, beta binding proteins"""	6714	protein-coding gene	gene with protein product	"""TGF-beta1-BP-1"""	150390				2350783, 11104663	Standard	NM_206943		Approved		uc021vft.1	Q14766	OTTHUMG00000152118	ENST00000404816.2:c.4935C>T	2.37:g.33622300C>T		Somatic		Capture	Illumina HiSeq	Phase_I	33475804	NM_000627	A1L3V1|P22064|Q53SD8|Q53SF3|Q53SG1|Q59HF7|Q8TD95	Silent	SNP	ENST00000404816.2	37	CCDS33177.2																																																																																				0.463	LTBP1-014	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000326227.2	NM_206943	
RASGRP3	25780	broad.mit.edu	37	2	33764177	33764177	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr2:33764177C>T	ENST00000403687.3	+	12	1918	c.1178C>T	c.(1177-1179)aCg>aTg	p.T393M	RASGRP3_ENST00000407811.1_Missense_Mutation_p.T392M|RASGRP3_ENST00000402538.3_Missense_Mutation_p.T393M	NM_001139488.1	NP_001132960.1	Q8IV61	GRP3_HUMAN	RAS guanyl releasing protein 3 (calcium and DAG-regulated)	393			T -> A (in dbSNP:rs13388394).		MAPK cascade (GO:0000165)|positive regulation of GTPase activity (GO:0043547)|positive regulation of Rap GTPase activity (GO:0032854)|Ras protein signal transduction (GO:0007265)|small GTPase mediated signal transduction (GO:0007264)	guanyl-nucleotide exchange factor complex (GO:0032045)|integral component of plasma membrane (GO:0005887)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|diacylglycerol binding (GO:0019992)|guanyl-nucleotide exchange factor activity (GO:0005085)|Rap GTPase activator activity (GO:0046582)|Ras guanyl-nucleotide exchange factor activity (GO:0005088)|signal transducer activity (GO:0004871)	p.T393M(1)		large_intestine(3)|lung(3)|ovary(2)|pancreas(1)|stomach(2)	11	all_hematologic(175;0.115)					ACCTCCCCTACGACGCCCAAC	0.463																																					p.T393M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1178T	2						.						36.0	33.0	34.0					2																	33764177		1840	4091	5931	33617681	SO:0001583	missense	25780	exon13			AB020653	CCDS46256.1, CCDS54346.1	2p25.1-p24.1	2013-01-10			ENSG00000152689	ENSG00000152689		"""EF-hand domain containing"""	14545	protein-coding gene	gene with protein product		609531				10048485, 10934204	Standard	NM_170672		Approved	KIAA0846, GRP3	uc002roy.3	Q8IV61	OTTHUMG00000152124	ENST00000403687.3:c.1178C>T	2.37:g.33764177C>T	ENSP00000384192:p.Thr393Met	Somatic		Capture	Illumina HiSeq	Phase_I	33617681	NM_170672	D6W583|O94931|Q53SD7	Missense_Mutation	SNP	ENST00000403687.3	37	CCDS46256.1	.	.	.	.	.	.	.	.	.	.	C	15.40	2.823459	0.50739	.	.	ENSG00000152689	ENST00000402538;ENST00000403687;ENST00000407811	T;T;T	0.46819	0.86;0.86;0.86	5.8	5.8	0.92144	Ras guanine nucleotide exchange factor, domain (1);	0.000000	0.85682	D	0.000000	T	0.64516	0.2605	L	0.50333	1.59	0.47659	D	0.999487	D;D	0.89917	1.0;0.997	D;D	0.71184	0.972;0.945	T	0.57963	-0.7720	10	0.34782	T	0.22	-11.41	20.0503	0.97624	0.0:1.0:0.0:0.0	.	392;393	D6W583;Q8IV61	.;GRP3_HUMAN	M	393;393;392	ENSP00000385886:T393M;ENSP00000384192:T393M;ENSP00000383917:T392M	ENSP00000385886:T393M	T	+	2	0	RASGRP3	33617681	0.965000	0.33210	0.473000	0.27253	0.556000	0.35491	2.316000	0.43761	2.736000	0.93811	0.591000	0.81541	ACG		0.463	RASGRP3-006	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000325462.2	NM_015376	
QPCT	25797	broad.mit.edu	37	2	37599963	37599963	+	Missense_Mutation	SNP	A	A	G	rs4670696	byFrequency	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr2:37599963A>G	ENST00000338415.3	+	7	1237	c.1079A>G	c.(1078-1080)cAt>cGt	p.H360R	QPCT_ENST00000537448.1_Missense_Mutation_p.H311R	NM_012413.3	NP_036545.1	Q16769	QPCT_HUMAN	glutaminyl-peptide cyclotransferase	360			H -> P (in dbSNP:rs4670696). {ECO:0000269|PubMed:15489334}.		cellular protein modification process (GO:0006464)|peptidyl-pyroglutamic acid biosynthetic process, using glutaminyl-peptide cyclotransferase (GO:0017186)	extracellular vesicular exosome (GO:0070062)	glutaminyl-peptide cyclotransferase activity (GO:0016603)|zinc ion binding (GO:0008270)	p.H360R(1)		central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(4)|lung(3)|prostate(1)|stomach(2)	17		Ovarian(717;0.051)|all_hematologic(82;0.21)				GAATATCTTCATTTGTAATAC	0.318																																					p.H360R												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A1079G	2						.						70.0	66.0	67.0					2																	37599963		2203	4300	6503	37453467	SO:0001583	missense	25797	exon7			X71125	CCDS1790.1	2p22	2008-07-31	2008-07-31		ENSG00000115828	ENSG00000115828	2.3.2.5		9753	protein-coding gene	gene with protein product	"""glutaminyl cyclase"""	607065				7999256	Standard	NM_012413		Approved	QC, GCT	uc002rqg.3	Q16769	OTTHUMG00000100963	ENST00000338415.3:c.1079A>G	2.37:g.37599963A>G	ENSP00000344829:p.His360Arg	Somatic		Capture	Illumina HiSeq	Phase_I	37453467	NM_012413	Q16770|Q3KRG6|Q53TR4	Missense_Mutation	SNP	ENST00000338415.3	37	CCDS1790.1	.	.	.	.	.	.	.	.	.	.	A	15.26	2.779396	0.49891	.	.	ENSG00000115828	ENST00000338415;ENST00000537448	T;T	0.29142	2.31;1.58	5.96	5.96	0.96718	.	0.093684	0.64402	D	0.000001	T	0.22399	0.0540	N	0.20530	0.585	0.25619	P	0.9864227	P;B	0.40250	0.709;0.432	B;B	0.36885	0.235;0.083	T	0.26849	-1.0091	9	0.42905	T	0.14	0.5586	16.1181	0.81324	1.0:0.0:0.0:0.0	.	311;360	Q16769-2;Q16769	.;QPCT_HUMAN	R	360;311	ENSP00000344829:H360R;ENSP00000441606:H311R	ENSP00000344829:H360R	H	+	2	0	QPCT	37453467	1.000000	0.71417	1.000000	0.80357	0.860000	0.49131	3.941000	0.56607	2.284000	0.76573	0.528000	0.53228	CAT		0.318	QPCT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000218572.2		
DHX57	90957	broad.mit.edu	37	2	39089429	39089429	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr2:39089429T>C	ENST00000295373.6	-	4	556	c.430A>G	c.(430-432)Aac>Gac	p.N144D	AC018693.6_ENST00000442829.1_RNA|DHX57_ENST00000479345.2_5'UTR	NM_198963.1	NP_945314.1	Q6P158	DHX57_HUMAN	DEAH (Asp-Glu-Ala-Asp/His) box polypeptide 57	144							ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)	p.N144D(1)		NS(2)|breast(3)|central_nervous_system(1)|endometrium(9)|kidney(2)|large_intestine(15)|lung(20)|ovary(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	62		all_hematologic(82;0.248)				CGCTCATCGTTACAGCAATCA	0.468																																					p.N144D	Melanoma(191;1090 2095 4375 23729 47341)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A430G	2						.						98.0	86.0	90.0					2																	39089429		2203	4300	6503	38942933	SO:0001583	missense	90957	exon4			AF070590	CCDS1800.1	2p22.3	2008-02-05			ENSG00000163214	ENSG00000163214		"""DEAH-boxes"""	20086	protein-coding gene	gene with protein product							Standard	NM_198963		Approved	DDX57	uc002rrf.3	Q6P158	OTTHUMG00000102103	ENST00000295373.6:c.430A>G	2.37:g.39089429T>C	ENSP00000295373:p.Asn144Asp	Somatic		Capture	Illumina HiSeq	Phase_I	38942933	NM_198963	A2RRC7|Q53SI4|Q6P9G1|Q7Z6H3|Q8NG17|Q96M33	Missense_Mutation	SNP	ENST00000295373.6	37	CCDS1800.1	.	.	.	.	.	.	.	.	.	.	T	6.695	0.496835	0.12762	.	.	ENSG00000163214	ENST00000295373;ENST00000355320;ENST00000417233	T	0.02446	4.29	5.37	4.48	0.54585	.	0.326590	0.25929	N	0.027396	T	0.01421	0.0046	N	0.02539	-0.55	0.33648	D	0.608054	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.37865	-0.9687	10	0.12103	T	0.63	.	11.8591	0.52454	0.0:0.9174:0.0:0.0826	.	144;144	Q6P158-2;Q6P158	.;DHX57_HUMAN	D	144;42;42	ENSP00000295373:N144D	ENSP00000295373:N144D	N	-	1	0	DHX57	38942933	1.000000	0.71417	0.034000	0.17996	0.913000	0.54294	5.045000	0.64220	1.371000	0.46172	-0.366000	0.07423	AAC		0.468	DHX57-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219940.2	NM_145646	
HAAO	23498	broad.mit.edu	37	2	43010506	43010506	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr2:43010506C>T	ENST00000294973.6	-	4	353	c.298G>A	c.(298-300)Gtg>Atg	p.V100M		NM_012205.2	NP_036337.2			3-hydroxyanthranilate 3,4-dioxygenase									p.V100M(1)		breast(2)|cervix(1)|large_intestine(2)|lung(2)|ovary(1)|prostate(1)|urinary_tract(2)	11						ACCAGCCCCACGGTGTTGGCA	0.582																																					p.V100M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G298A	2						.						42.0	38.0	39.0					2																	43010506		2202	4300	6502	42864010	SO:0001583	missense	23498	exon4			Z29481	CCDS33187.1	2p	2008-02-05			ENSG00000162882	ENSG00000162882	1.13.11.6		4796	protein-coding gene	gene with protein product		604521				7514594	Standard	NM_012205		Approved		uc002rst.4	P46952	OTTHUMG00000152348	ENST00000294973.6:c.298G>A	2.37:g.43010506C>T	ENSP00000294973:p.Val100Met	Somatic		Capture	Illumina HiSeq	Phase_I	42864010	NM_012205		Missense_Mutation	SNP	ENST00000294973.6	37	CCDS33187.1	.	.	.	.	.	.	.	.	.	.	C	14.24	2.475346	0.43942	.	.	ENSG00000162882	ENST00000294973;ENST00000431905	T;T	0.39229	1.09;1.09	4.69	0.303	0.15791	Cupin, RmlC-type (1);	0.080716	0.48767	N	0.000165	T	0.37571	0.1008	M	0.70108	2.13	0.29327	N	0.866968	P	0.45044	0.849	B	0.41412	0.356	T	0.33777	-0.9855	10	0.44086	T	0.13	.	6.8303	0.23907	0.0:0.4325:0.0:0.5675	.	100	P46952	3HAO_HUMAN	M	100;66	ENSP00000294973:V100M;ENSP00000412601:V66M	ENSP00000294973:V100M	V	-	1	0	HAAO	42864010	0.627000	0.27129	0.477000	0.27303	0.875000	0.50365	0.646000	0.24797	-0.106000	0.12110	-0.384000	0.06662	GTG		0.582	HAAO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325948.2		
PLEKHH2	130271	broad.mit.edu	37	2	43989479	43989479	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr2:43989479T>C	ENST00000282406.4	+	28	4218	c.4108T>C	c.(4108-4110)Tgg>Cgg	p.W1370R		NM_172069.3	NP_742066.2	Q8IVE3	PKHH2_HUMAN	pleckstrin homology domain containing, family H (with MyTH4 domain) member 2	1370	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.				negative regulation of actin filament depolymerization (GO:0030835)	cortical actin cytoskeleton (GO:0030864)|cytoplasm (GO:0005737)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)	actin binding (GO:0003779)	p.W1370R(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(4)|large_intestine(12)|lung(24)|pancreas(1)|prostate(1)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	56		all_hematologic(82;0.166)|Acute lymphoblastic leukemia(82;0.17)				TACTTTCTTGTGGCTGGCTGT	0.358																																					p.W1370R												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T4108C	2						.						148.0	136.0	140.0					2																	43989479		2203	4300	6503	43842983	SO:0001583	missense	130271	exon28			AB095948	CCDS1812.1	2p22	2013-01-10			ENSG00000152527	ENSG00000152527		"""Pleckstrin homology (PH) domain containing"""	30506	protein-coding gene	gene with protein product		612723					Standard	NM_172069		Approved	KIAA2028, PLEKHH1L	uc010yny.2	Q8IVE3	OTTHUMG00000128657	ENST00000282406.4:c.4108T>C	2.37:g.43989479T>C	ENSP00000282406:p.Trp1370Arg	Somatic		Capture	Illumina HiSeq	Phase_I	43842983	NM_172069	Q5JPJ6|Q6P4Q1|Q8N3Q3	Missense_Mutation	SNP	ENST00000282406.4	37	CCDS1812.1	.	.	.	.	.	.	.	.	.	.	T	19.92	3.917087	0.73098	.	.	ENSG00000152527	ENST00000282406	T	0.77750	-1.12	5.19	5.19	0.71726	FERM domain (1);	0.000000	0.85682	D	0.000000	D	0.88239	0.6383	M	0.81112	2.525	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	D	0.89996	0.4111	10	0.87932	D	0	-0.8758	15.0711	0.72037	0.0:0.0:0.0:1.0	.	1370	Q8IVE3	PKHH2_HUMAN	R	1370	ENSP00000282406:W1370R	ENSP00000282406:W1370R	W	+	1	0	PLEKHH2	43842983	1.000000	0.71417	0.904000	0.35570	0.894000	0.52154	7.293000	0.78740	1.944000	0.56390	0.533000	0.62120	TGG		0.358	PLEKHH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250537.1	NM_172069	
LRPPRC	10128	broad.mit.edu	37	2	44132916	44132916	+	Silent	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr2:44132916C>T	ENST00000260665.7	-	31	3336	c.3279G>A	c.(3277-3279)gcG>gcA	p.A1093A		NM_133259.3	NP_573566.2	P42704	LPPRC_HUMAN	leucine-rich pentatricopeptide repeat containing	1093					mitochondrion transport along microtubule (GO:0047497)|mRNA transport (GO:0051028)|negative regulation of mitochondrial RNA catabolic process (GO:0000961)|regulation of mitochondrial translation (GO:0070129)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	condensed nuclear chromosome (GO:0000794)|cytoskeleton (GO:0005856)|membrane (GO:0016020)|microtubule (GO:0005874)|mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|ribonucleoprotein complex (GO:0030529)	beta-tubulin binding (GO:0048487)|microtubule binding (GO:0008017)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|single-stranded DNA binding (GO:0003697)	p.A1093A(1)		breast(3)|endometrium(3)|kidney(5)|large_intestine(9)|lung(15)|ovary(2)|prostate(2)|skin(2)	41		all_hematologic(82;0.166)|Acute lymphoblastic leukemia(82;0.17)				TGTGGGTCTCCGCGCTAAAAG	0.423																																					p.A1093A												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G3279A	2						.						109.0	95.0	100.0					2																	44132916		2203	4300	6503	43986420	SO:0001819	synonymous_variant	10128	exon31			M92439	CCDS33189.1	2p21	2012-02-24	2012-02-24		ENSG00000138095	ENSG00000138095			15714	protein-coding gene	gene with protein product		607544	"""Leigh syndrome, French-Canadian type (cytochrome oxidase deficiency)"""	LSFC		8012652, 8619474, 22045337	Standard	NM_133259		Approved	GP130, LRP130	uc002rtr.2	P42704	OTTHUMG00000152782	ENST00000260665.7:c.3279G>A	2.37:g.44132916C>T		Somatic		Capture	Illumina HiSeq	Phase_I	43986420	NM_133259	A0PJE3|A8K1V1|Q53PC0|Q53QN7|Q6ZUD8|Q7Z7A6|Q96D84	Silent	SNP	ENST00000260665.7	37	CCDS33189.1																																																																																				0.423	LRPPRC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327823.1	NM_133259	
SLC3A1	6519	broad.mit.edu	37	2	44502985	44502985	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr2:44502985C>T	ENST00000260649.6	+	1	387	c.311C>T	c.(310-312)aCc>aTc	p.T104I	SLC3A1_ENST00000410056.3_Missense_Mutation_p.T104I|SLC3A1_ENST00000409387.1_Missense_Mutation_p.T104I|SLC3A1_ENST00000409741.1_Missense_Mutation_p.T104I|SLC3A1_ENST00000409229.3_Missense_Mutation_p.T104I	NM_000341.3	NP_000332.2	Q07837	SLC31_HUMAN	solute carrier family 3 (amino acid transporter heavy chain), member 1	104					amino acid transmembrane transport (GO:0003333)|amino acid transport (GO:0006865)|basic amino acid transport (GO:0015802)|carbohydrate metabolic process (GO:0005975)|cellular amino acid metabolic process (GO:0006520)|ion transport (GO:0006811)|L-cystine transport (GO:0015811)|transmembrane transport (GO:0055085)	brush border membrane (GO:0031526)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)|plasma membrane (GO:0005886)|vacuolar membrane (GO:0005774)	amino acid transmembrane transporter activity (GO:0015171)|basic amino acid transmembrane transporter activity (GO:0015174)|catalytic activity (GO:0003824)|cation binding (GO:0043169)|L-cystine transmembrane transporter activity (GO:0015184)	p.T104I(1)		breast(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(11)|prostate(1)|skin(3)	26		all_hematologic(82;0.166)|Acute lymphoblastic leukemia(82;0.17)			L-Cystine(DB00138)	ATCGCGGCCACCATAGCCATC	0.572																																					p.T104I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C311T	2						.						64.0	62.0	63.0					2																	44502985		2203	4300	6503	44356489	SO:0001583	missense	6519	exon1				CCDS1819.1	2p16.3	2013-07-19	2013-07-19		ENSG00000138079	ENSG00000138079		"""Solute carriers"""	11025	protein-coding gene	gene with protein product		104614	"""solute carrier family 3 (cystine, dibasic and neutral amino acid transporters, activator of cystine, dibasic and neutral amino acid transport), member 1"""			8486766, 9186880	Standard	NM_000341		Approved	CSNU1, D2H, RBAT, ATR1, NBAT	uc002ruc.4	Q07837	OTTHUMG00000128759	ENST00000260649.6:c.311C>T	2.37:g.44502985C>T	ENSP00000260649:p.Thr104Ile	Somatic		Capture	Illumina HiSeq	Phase_I	44356489	NM_000341	A8K0S1|O00658|Q15295|Q4J6B4|Q4J6B5|Q4J6B6|Q4J6B7|Q4J6B8|Q4J6B9|Q52M92|Q52M94	Missense_Mutation	SNP	ENST00000260649.6	37	CCDS1819.1	.	.	.	.	.	.	.	.	.	.	C	18.90	3.721499	0.68959	.	.	ENSG00000138079	ENST00000260649;ENST00000409387;ENST00000540334;ENST00000410056;ENST00000409741;ENST00000409229;ENST00000541289	D;D;D;D;D	0.99511	-5.44;-6.05;-5.4;-5.91;-6.05	5.64	5.64	0.86602	.	0.000000	0.85682	D	0.000000	D	0.99507	0.9824	M	0.80183	2.485	0.80722	D	1	D;D;D;D;D	0.76494	0.995;0.998;0.999;0.996;0.998	P;P;D;D;D	0.68353	0.854;0.854;0.94;0.94;0.957	D	0.98863	1.0763	10	0.66056	D	0.02	-25.961	19.7174	0.96129	0.0:1.0:0.0:0.0	.	104;104;104;104;104	Q07837;B8ZZK1;Q4J6B5;Q4J6B6;Q4J6B8	SLC31_HUMAN;.;.;.;.	I	104;104;40;104;104;104;104	ENSP00000260649:T104I;ENSP00000387308:T104I;ENSP00000387337:T104I;ENSP00000386954:T104I;ENSP00000386620:T104I	ENSP00000260649:T104I	T	+	2	0	SLC3A1	44356489	1.000000	0.71417	0.687000	0.30102	0.015000	0.08874	7.699000	0.84547	2.653000	0.90120	0.655000	0.94253	ACC		0.572	SLC3A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250676.1	NM_000341	
NRXN1	9378	broad.mit.edu	37	2	51255121	51255121	+	Silent	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr2:51255121G>A	ENST00000406316.2	-	2	1767	c.291C>T	c.(289-291)tgC>tgT	p.C97C	NRXN1_ENST00000402717.3_Silent_p.C97C|NRXN1_ENST00000406859.3_Silent_p.C97C|NRXN1_ENST00000405472.3_Silent_p.C97C|NRXN1_ENST00000404971.1_Silent_p.C97C|NRXN1_ENST00000405581.1_Silent_p.C97C|NRXN1_ENST00000401669.2_Silent_p.C97C	NM_004801.4	NP_004792.1	Q9ULB1	NRX1A_HUMAN	neurexin 1	97	Laminin G-like 1. {ECO:0000255|PROSITE- ProRule:PRU00122}.				adult behavior (GO:0030534)|axon guidance (GO:0007411)|calcium-dependent cell-cell adhesion (GO:0016339)|cerebellar granule cell differentiation (GO:0021707)|establishment of protein localization (GO:0045184)|extracellular matrix organization (GO:0030198)|gamma-aminobutyric acid receptor clustering (GO:0097112)|gephyrin clustering (GO:0097116)|guanylate kinase-associated protein clustering (GO:0097117)|heterophilic cell-cell adhesion (GO:0007157)|learning (GO:0007612)|N-methyl-D-aspartate receptor clustering (GO:0097114)|negative regulation of filopodium assembly (GO:0051490)|neuroligin clustering (GO:0097118)|neuromuscular process controlling balance (GO:0050885)|neuron cell-cell adhesion (GO:0007158)|neuron maturation (GO:0042551)|neurotransmitter secretion (GO:0007269)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of synapse assembly (GO:0051965)|positive regulation of synapse maturation (GO:0090129)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|postsynaptic density protein 95 clustering (GO:0097119)|postsynaptic membrane assembly (GO:0097104)|presynaptic membrane assembly (GO:0097105)|receptor localization to synapse (GO:0097120)|regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000311)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|social behavior (GO:0035176)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)|synaptic vesicle clustering (GO:0097091)|vocal learning (GO:0042297)|vocalization behavior (GO:0071625)	axonal growth cone (GO:0044295)|cell junction (GO:0030054)|cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|presynaptic membrane (GO:0042734)	acetylcholine receptor binding (GO:0033130)|calcium channel regulator activity (GO:0005246)|calcium ion binding (GO:0005509)|cell adhesion molecule binding (GO:0050839)|neuroligin family protein binding (GO:0097109)|receptor activity (GO:0004872)	p.C97C(1)		breast(1)|endometrium(3)|kidney(3)|large_intestine(10)|lung(33)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	58		all_hematologic(82;0.152)|Acute lymphoblastic leukemia(82;0.192)	Lung(47;0.0813)|LUSC - Lung squamous cell carcinoma(58;0.116)			CAGGCTCAGCGCAGAAGATGG	0.667																																					p.C97C												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C291T	2						.						16.0	20.0	19.0					2																	51255121		2026	4177	6203	51108625	SO:0001819	synonymous_variant	9378	exon2			AB011150	CCDS1845.1, CCDS46282.1, CCDS54360.1	2p16.3	2008-05-15			ENSG00000179915	ENSG00000179915			8008	protein-coding gene	gene with protein product		600565					Standard	NM_001135659		Approved	KIAA0578, Hs.22998	uc021vhj.1	P58400	OTTHUMG00000129263	ENST00000406316.2:c.291C>T	2.37:g.51255121G>A		Somatic		Capture	Illumina HiSeq	Phase_I	51108625	NM_001135659	A7KRL9|O60323|Q53TJ9|Q53TQ1|Q9C079|Q9C080|Q9C081|Q9H3M2|Q9UDM6	Silent	SNP	ENST00000406316.2	37	CCDS54360.1																																																																																				0.667	NRXN1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000325291.2		
TSPYL6	388951	broad.mit.edu	37	2	54482285	54482285	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr2:54482285C>T	ENST00000317802.7	-	1	1124	c.1004G>A	c.(1003-1005)gGa>gAa	p.G335E	ACYP2_ENST00000607452.1_Intron|ACYP2_ENST00000606865.1_Intron|ACYP2_ENST00000394666.3_Intron|ACYP2_ENST00000303536.4_Intron	NM_001003937.2	NP_001003937.2	Q8N831	TSYL6_HUMAN	TSPY-like 6	335					nucleosome assembly (GO:0006334)	nucleus (GO:0005634)		p.G335E(1)		NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(5)|lung(1)|ovary(1)|skin(1)|stomach(2)	20						GGACTGGGGTCCATGGCCCCG	0.498																																					p.G335E												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1004A	2						.						76.0	79.0	78.0					2																	54482285		2116	4273	6389	54335789	SO:0001583	missense	388951	exon1			AK097417	CCDS42682.1	2p16.3	2007-10-22			ENSG00000178021	ENSG00000178021			14521	protein-coding gene	gene with protein product							Standard	NM_001003937		Approved		uc002rxr.2	Q8N831	OTTHUMG00000151823	ENST00000317802.7:c.1004G>A	2.37:g.54482285C>T	ENSP00000417919:p.Gly335Glu	Somatic		Capture	Illumina HiSeq	Phase_I	54335789	NM_001003937	Q6NUJ3	Missense_Mutation	SNP	ENST00000317802.7	37	CCDS42682.1	.	.	.	.	.	.	.	.	.	.	C	0.012	-1.658587	0.00779	.	.	ENSG00000178021	ENST00000317802	T	0.22945	1.93	1.67	0.482	0.16815	.	.	.	.	.	T	0.06735	0.0172	N	0.02120	-0.675	0.09310	N	1	B	0.09022	0.002	B	0.17098	0.017	T	0.38757	-0.9646	9	0.02654	T	1	.	3.2295	0.06744	0.0:0.2676:0.0:0.7324	.	335	Q8N831	TSYL6_HUMAN	E	335	ENSP00000417919:G335E	ENSP00000417919:G335E	G	-	2	0	TSPYL6	54335789	0.973000	0.33851	0.005000	0.12908	0.173000	0.22820	1.124000	0.31320	0.121000	0.18284	-0.373000	0.07131	GGA		0.498	TSPYL6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324069.3	XM_371494	
SPTBN1	6711	broad.mit.edu	37	2	54849604	54849604	+	Silent	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr2:54849604C>T	ENST00000356805.4	+	9	1325	c.1044C>T	c.(1042-1044)cgC>cgT	p.R348R	SPTBN1_ENST00000333896.5_Silent_p.R335R	NM_003128.2	NP_003119.2	Q01082	SPTB2_HUMAN	spectrin, beta, non-erythrocytic 1	348					actin filament capping (GO:0051693)|axon guidance (GO:0007411)|Golgi to plasma membrane protein transport (GO:0043001)|membrane assembly (GO:0071709)|mitotic cytokinesis (GO:0000281)|plasma membrane organization (GO:0007009)|protein targeting to plasma membrane (GO:0072661)	axolemma (GO:0030673)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleolus (GO:0005730)|protein complex (GO:0043234)|spectrin (GO:0008091)|spectrin-associated cytoskeleton (GO:0014731)	actin binding (GO:0003779)|ankyrin binding (GO:0030506)|phospholipid binding (GO:0005543)|poly(A) RNA binding (GO:0044822)|structural constituent of cytoskeleton (GO:0005200)	p.R348R(1)		NS(1)|breast(8)|central_nervous_system(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(11)|lung(27)|ovary(4)|prostate(2)|skin(5)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	82			Lung(47;0.24)			ACACTTACCGCACTGTGGAGA	0.418																																					p.R348R												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1044T	2						.						126.0	120.0	122.0					2																	54849604		2203	4300	6503	54703108	SO:0001819	synonymous_variant	6711	exon9				CCDS33198.1, CCDS33199.1	2p21	2013-01-10			ENSG00000115306	ENSG00000115306		"""Pleckstrin homology (PH) domain containing"""	11275	protein-coding gene	gene with protein product		182790					Standard	NM_003128		Approved		uc002rxu.3	Q01082	OTTHUMG00000133746	ENST00000356805.4:c.1044C>T	2.37:g.54849604C>T		Somatic		Capture	Illumina HiSeq	Phase_I	54703108	NM_003128	B2RP63|O60837|Q16057|Q53R99|Q59ER3|Q8IX99	Silent	SNP	ENST00000356805.4	37	CCDS33198.1																																																																																				0.418	SPTBN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258115.3		
MTIF2	4528	broad.mit.edu	37	2	55479717	55479717	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr2:55479717G>A	ENST00000263629.4	-	8	1052	c.737C>T	c.(736-738)gCc>gTc	p.A246V	MTIF2_ENST00000394600.3_Missense_Mutation_p.A246V|MTIF2_ENST00000403721.1_Missense_Mutation_p.A246V|MTIF2_ENST00000446660.1_5'Flank	NM_002453.2	NP_002444.2	P46199	IF2M_HUMAN	mitochondrial translational initiation factor 2	246	tr-type G.				formation of translation initiation complex (GO:0001732)|regulation of translational initiation (GO:0006446)|ribosome disassembly (GO:0032790)	mitochondrion (GO:0005739)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|poly(A) RNA binding (GO:0044822)|ribosomal small subunit binding (GO:0043024)|translation factor activity, nucleic acid binding (GO:0008135)|translation initiation factor activity (GO:0003743)	p.A246V(1)		breast(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(5)|ovary(1)|prostate(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)	24						AGCACCTCTGGCTCTCATTGC	0.433																																					p.A246V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C737T	2						.						119.0	105.0	110.0					2																	55479717		2203	4300	6503	55333221	SO:0001583	missense	4528	exon9			L34600	CCDS1853.1	2p16.1	2008-02-05			ENSG00000085760	ENSG00000085760			7441	protein-coding gene	gene with protein product		603766				9925935, 7829522	Standard	XM_005264335		Approved	IF-2mt	uc002ryo.3	P46199	OTTHUMG00000129338	ENST00000263629.4:c.737C>T	2.37:g.55479717G>A	ENSP00000263629:p.Ala246Val	Somatic		Capture	Illumina HiSeq	Phase_I	55333221	NM_001005369	D6W5D0	Missense_Mutation	SNP	ENST00000263629.4	37	CCDS1853.1	.	.	.	.	.	.	.	.	.	.	G	35	5.539050	0.96474	.	.	ENSG00000085760	ENST00000403721;ENST00000263629;ENST00000394600;ENST00000535023	T;T;T	0.70869	-0.52;-0.52;-0.52	6.07	6.07	0.98685	Small GTP-binding protein domain (1);Protein synthesis factor, GTP-binding (1);	0.000000	0.85682	D	0.000000	T	0.74928	0.3781	L	0.33093	0.98	0.80722	D	1	P	0.51351	0.944	P	0.59056	0.851	T	0.76369	-0.2984	10	0.87932	D	0	-10.0258	15.3849	0.74691	0.0:0.0:0.8607:0.1393	.	246	P46199	IF2M_HUMAN	V	246	ENSP00000384481:A246V;ENSP00000263629:A246V;ENSP00000378099:A246V	ENSP00000263629:A246V	A	-	2	0	MTIF2	55333221	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	7.327000	0.79147	2.885000	0.99019	0.655000	0.94253	GCC		0.433	MTIF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251486.4	NM_002453	
PAPOLG	64895	broad.mit.edu	37	2	60998723	60998723	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr2:60998723C>T	ENST00000238714.3	+	7	811	c.562C>T	c.(562-564)Cgc>Tgc	p.R188C		NM_022894.3	NP_075045.2	Q9BWT3	PAPOG_HUMAN	poly(A) polymerase gamma	188					mRNA polyadenylation (GO:0006378)|RNA polyadenylation (GO:0043631)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|polynucleotide adenylyltransferase activity (GO:0004652)|RNA binding (GO:0003723)	p.R188C(1)		breast(2)|central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(6)|liver(1)|lung(11)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	35	all_hematologic(2;0.0797)		LUSC - Lung squamous cell carcinoma(5;1.19e-07)|Lung(5;2.86e-06)|Epithelial(17;0.0768)			AGACGACTCTCGCCTGAGAAG	0.343																																					p.R188C	GBM(183;1497 2932 21839 46797)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C562T	2						.						83.0	86.0	85.0					2																	60998723		2203	4300	6503	60852227	SO:0001583	missense	64895	exon7			AC012498	CCDS1863.1	2p16.1	2008-02-08			ENSG00000115421	ENSG00000115421	2.7.7.19		14982	protein-coding gene	gene with protein product							Standard	NM_022894		Approved	FLJ12972	uc002sai.3	Q9BWT3	OTTHUMG00000129419	ENST00000238714.3:c.562C>T	2.37:g.60998723C>T	ENSP00000238714:p.Arg188Cys	Somatic		Capture	Illumina HiSeq	Phase_I	60852227	NM_022894	B2RBH4|Q59G05|Q969N1|Q9H8L2|Q9HAD0	Missense_Mutation	SNP	ENST00000238714.3	37	CCDS1863.1	.	.	.	.	.	.	.	.	.	.	C	16.49	3.136850	0.56936	.	.	ENSG00000115421	ENST00000238714	.	.	.	5.38	5.38	0.77491	Poly(A) polymerase, central domain (1);	0.106321	0.64402	D	0.000003	T	0.53948	0.1828	L	0.36672	1.1	0.58432	D	0.999999	B	0.13145	0.007	B	0.15484	0.013	T	0.51980	-0.8636	9	0.59425	D	0.04	-16.58	14.851	0.70297	0.1445:0.8555:0.0:0.0	.	188	Q9BWT3	PAPOG_HUMAN	C	188	.	ENSP00000238714:R188C	R	+	1	0	PAPOLG	60852227	0.991000	0.36638	1.000000	0.80357	0.990000	0.78478	3.052000	0.49893	2.694000	0.91930	0.586000	0.80456	CGC		0.343	PAPOLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251577.3	NM_022894	
USP34	9736	broad.mit.edu	37	2	61544864	61544864	+	Silent	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr2:61544864G>A	ENST00000398571.2	-	23	3283	c.3207C>T	c.(3205-3207)ggC>ggT	p.G1069G		NM_014709.3	NP_055524.3	Q70CQ2	UBP34_HUMAN	ubiquitin specific peptidase 34	1069					positive regulation of canonical Wnt signaling pathway (GO:0090263)|protein deubiquitination (GO:0016579)|protein K48-linked deubiquitination (GO:0071108)|ubiquitin-dependent protein catabolic process (GO:0006511)|Wnt signaling pathway (GO:0016055)		cysteine-type endopeptidase activity (GO:0004197)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)	p.G1069G(1)		autonomic_ganglia(1)|breast(14)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(24)|lung(52)|ovary(8)|prostate(10)|skin(6)|urinary_tract(2)	138			Epithelial(17;0.229)			ACAGGTTTAAGCCAGTCATGC	0.388																																					p.G1069G												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C3207T	2						.						104.0	99.0	101.0					2																	61544864		1857	4112	5969	61398368	SO:0001819	synonymous_variant	9736	exon23			AB011142	CCDS42686.1	2p16.1-p15	2005-08-08	2005-08-08		ENSG00000115464	ENSG00000115464		"""Ubiquitin-specific peptidases"""	20066	protein-coding gene	gene with protein product		615295	"""ubiquitin specific protease 34"""			12838346	Standard	NM_014709		Approved	KIAA0570, KIAA0729	uc002sbe.3	Q70CQ2	OTTHUMG00000152265	ENST00000398571.2:c.3207C>T	2.37:g.61544864G>A		Somatic		Capture	Illumina HiSeq	Phase_I	61398368	NM_014709	A8MWD0|B3KWU9|O60316|O94834|Q3B777|Q6P6C9|Q7L8P6|Q8N3T9|Q8TBW2|Q9UGA1	Silent	SNP	ENST00000398571.2	37	CCDS42686.1																																																																																				0.388	USP34-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325650.4		
SLC1A4	6509	broad.mit.edu	37	2	65243671	65243671	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr2:65243671G>A	ENST00000234256.3	+	5	1141	c.898G>A	c.(898-900)Gca>Aca	p.A300T	SLC1A4_ENST00000493121.1_3'UTR|SLC1A4_ENST00000531327.1_Intron	NM_003038.4	NP_003029.2	P43007	SATT_HUMAN	solute carrier family 1 (glutamate/neutral amino acid transporter), member 4	300					amino acid transport (GO:0006865)|chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|cognition (GO:0050890)|glutamine transport (GO:0006868)|hydroxyproline transport (GO:0034589)|ion transport (GO:0006811)|L-alanine transport (GO:0015808)|L-cystine transport (GO:0015811)|L-serine transport (GO:0015825)|proline transmembrane transport (GO:0035524)|proline transport (GO:0015824)|synaptic transmission, glutamatergic (GO:0035249)|threonine transport (GO:0015826)|transmembrane transport (GO:0055085)	cell surface (GO:0009986)|centrosome (GO:0005813)|dendrite (GO:0030425)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|intermediate filament (GO:0005882)|membrane (GO:0016020)|microtubule organizing center (GO:0005815)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	chloride channel activity (GO:0005254)|L-alanine transmembrane transporter activity (GO:0015180)|L-cystine transmembrane transporter activity (GO:0015184)|L-glutamine transmembrane transporter activity (GO:0015186)|L-hydroxyproline transmembrane transporter activity (GO:0034590)|L-proline transmembrane transporter activity (GO:0015193)|L-serine transmembrane transporter activity (GO:0015194)|L-threonine transmembrane transporter activity (GO:0015195)|sodium:dicarboxylate symporter activity (GO:0017153)	p.A300T(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(3)|pancreas(1)|prostate(1)|urinary_tract(1)	13					L-Alanine(DB00160)	ATACATCTTCGCATCTATATT	0.443																																					p.A300T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G898A	2						.						188.0	180.0	183.0					2																	65243671		2203	4300	6503	65097175	SO:0001583	missense	6509	exon5				CCDS1879.1, CCDS54362.1	2p15-p13	2013-05-22			ENSG00000115902	ENSG00000115902		"""Solute carriers"""	10942	protein-coding gene	gene with protein product	"""alanine/serine/cysteine/threonine transporter"""	600229				7896285, 8910405	Standard	NM_003038		Approved	SATT, ASCT1	uc010yqa.2	P43007	OTTHUMG00000129537	ENST00000234256.3:c.898G>A	2.37:g.65243671G>A	ENSP00000234256:p.Ala300Thr	Somatic		Capture	Illumina HiSeq	Phase_I	65097175	NM_003038	B7Z3C0|D6W5F0	Missense_Mutation	SNP	ENST00000234256.3	37	CCDS1879.1	.	.	.	.	.	.	.	.	.	.	G	9.546	1.114542	0.20795	.	.	ENSG00000115902	ENST00000448784;ENST00000234256	T	0.57273	0.41	5.87	4.95	0.65309	.	0.090091	0.85682	N	0.000000	T	0.23249	0.0562	N	0.02403	-0.565	0.58432	D	0.999999	B;B	0.12630	0.006;0.006	B;B	0.12837	0.004;0.008	T	0.20306	-1.0279	10	0.02654	T	1	-19.9133	11.9239	0.52808	0.0904:0.0:0.9096:0.0	.	300;300	P43007;B2R7N6	SATT_HUMAN;.	T	220;300	ENSP00000234256:A300T	ENSP00000234256:A300T	A	+	1	0	SLC1A4	65097175	1.000000	0.71417	0.866000	0.34008	0.988000	0.76386	5.503000	0.66962	1.490000	0.48466	0.655000	0.94253	GCA		0.443	SLC1A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251726.2	NM_003038	
SPRED2	200734	broad.mit.edu	37	2	65540997	65540997	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr2:65540997G>A	ENST00000356388.4	-	6	1084	c.895C>T	c.(895-897)Cgg>Tgg	p.R299W	SPRED2_ENST00000474228.1_5'Flank|SPRED2_ENST00000443619.2_Missense_Mutation_p.R296W	NM_181784.2	NP_861449.2	Q7Z698	SPRE2_HUMAN	sprouty-related, EVH1 domain containing 2	299					inactivation of MAPK activity (GO:0000188)|multicellular organismal development (GO:0007275)|negative regulation of peptidyl-threonine phosphorylation (GO:0010801)|positive regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043517)|regulation of protein deacetylation (GO:0090311)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	protein kinase binding (GO:0019901)|protein serine/threonine kinase inhibitor activity (GO:0030291)|stem cell factor receptor binding (GO:0005173)	p.R299W(1)		breast(2)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(11)|lung(7)|ovary(2)|upper_aerodigestive_tract(3)	34						TCCTTCCGCCGCCGCGACTTG	0.687																																					p.R299W												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C895T	2						.						45.0	51.0	49.0					2																	65540997		2202	4296	6498	65394501	SO:0001583	missense	200734	exon6			AF052178	CCDS33211.1, CCDS46308.1	2p14	2003-06-02			ENSG00000198369	ENSG00000198369			17722	protein-coding gene	gene with protein product		609292					Standard	NM_181784		Approved	Spred-2, FLJ21897, FLJ31917	uc002sdr.4	Q7Z698	OTTHUMG00000152737	ENST00000356388.4:c.895C>T	2.37:g.65540997G>A	ENSP00000348753:p.Arg299Trp	Somatic		Capture	Illumina HiSeq	Phase_I	65394501	NM_181784	A1L3V4|B7Z5K7|D6W5F7|E9PEP0|Q2NKX6	Missense_Mutation	SNP	ENST00000356388.4	37	CCDS33211.1	.	.	.	.	.	.	.	.	.	.	G	19.35	3.810082	0.70797	.	.	ENSG00000198369	ENST00000356388;ENST00000443619;ENST00000452315;ENST00000421087	T;T;T;T	0.79033	-1.22;-1.21;-1.23;-0.24	5.75	1.89	0.25635	.	0.050619	0.85682	N	0.000000	D	0.85177	0.5637	M	0.83012	2.62	0.53688	D	0.999977	D;D	0.89917	0.999;1.0	P;D	0.69142	0.886;0.962	T	0.82384	-0.0484	10	0.72032	D	0.01	-2.1522	6.58	0.22588	0.1302:0.0:0.5102:0.3596	.	296;299	E9PEP0;Q7Z698	.;SPRE2_HUMAN	W	299;296;314;181	ENSP00000348753:R299W;ENSP00000393697:R296W;ENSP00000390595:R314W;ENSP00000407627:R181W	ENSP00000348753:R299W	R	-	1	2	SPRED2	65394501	0.911000	0.30947	0.965000	0.40720	0.991000	0.79684	0.891000	0.28309	0.066000	0.16515	0.655000	0.94253	CGG		0.687	SPRED2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000327632.1		
PNO1	56902	broad.mit.edu	37	2	68385659	68385659	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr2:68385659A>G	ENST00000263657.2	+	2	446	c.355A>G	c.(355-357)Agg>Ggg	p.R119G	WDR92_ENST00000492039.2_5'Flank|RP11-474G23.1_ENST00000406334.3_Intron|WDR92_ENST00000409164.1_5'Flank|WDR92_ENST00000295121.6_5'Flank|WDR92_ENST00000406245.2_5'Flank	NM_020143.2	NP_064528.1	Q9NRX1	PNO1_HUMAN	partner of NOB1 homolog (S. cerevisiae)	119						nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)	p.R119G(1)		endometrium(1)|large_intestine(1)|lung(2)	4						TGTAGAAATCAGGGTAAGGAA	0.373																																					p.R119G	NSCLC(83;642 1410 13044 32832 40058)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A355G	2						.						81.0	82.0	82.0					2																	68385659		2203	4300	6503	68239163	SO:0001583	missense	56902	exon2			AF164799	CCDS1885.1	2p14	2010-07-06			ENSG00000115946	ENSG00000115946			32790	protein-coding gene	gene with protein product	"""RNA binding protein"""		"""KH-type RNA binding protein 1"", ""KH-type RNA-binding protein 1"""	KHRBP1		15497447	Standard	NM_020143		Approved	RRP20	uc002seh.3	Q9NRX1	OTTHUMG00000129563	ENST00000263657.2:c.355A>G	2.37:g.68385659A>G	ENSP00000263657:p.Arg119Gly	Somatic		Capture	Illumina HiSeq	Phase_I	68239163	NM_020143	A8K6Q0|Q53G13|Q8WVB8	Missense_Mutation	SNP	ENST00000263657.2	37	CCDS1885.1	.	.	.	.	.	.	.	.	.	.	A	29.5	5.010032	0.93346	.	.	ENSG00000115946	ENST00000263657	T	0.44482	0.92	6.02	6.02	0.97574	.	0.039211	0.85682	D	0.000000	T	0.61185	0.2327	M	0.82433	2.59	0.80722	D	1	P	0.49358	0.923	P	0.52159	0.691	T	0.67503	-0.5654	10	0.87932	D	0	-0.6572	16.542	0.84395	1.0:0.0:0.0:0.0	.	119	Q9NRX1	PNO1_HUMAN	G	119	ENSP00000263657:R119G	ENSP00000263657:R119G	R	+	1	2	PNO1	68239163	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	9.148000	0.94652	2.304000	0.77564	0.528000	0.53228	AGG		0.373	PNO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251756.1	NM_020143	
PROKR1	10887	broad.mit.edu	37	2	68882574	68882574	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr2:68882574G>A	ENST00000303786.3	+	3	1468	c.1048G>A	c.(1048-1050)Gtc>Atc	p.V350I	PROKR1_ENST00000394342.2_Missense_Mutation_p.V350I			Q8TCW9	PKR1_HUMAN	prokineticin receptor 1	350					negative regulation of apoptotic process (GO:0043066)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	neuropeptide Y receptor activity (GO:0004983)	p.V350I(1)		endometrium(3)|kidney(2)|large_intestine(14)|lung(9)|ovary(1)|prostate(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	35						GAACGACACCGTCAAGTACTT	0.507																																					p.V350I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1048A	2						.						150.0	115.0	127.0					2																	68882574		2203	4300	6503	68736078	SO:0001583	missense	10887	exon2			AF506287	CCDS1889.1	2p14	2012-08-08	2006-02-15	2006-02-15	ENSG00000169618	ENSG00000169618		"""GPCR / Class A : Prokineticin receptors"""	4524	protein-coding gene	gene with protein product		607122	"""G protein-coupled receptor 73"""	GPR73		10760605	Standard	NM_138964		Approved	PKR1, ZAQ, GPR73a	uc010yqj.2	Q8TCW9	OTTHUMG00000129567	ENST00000303786.3:c.1048G>A	2.37:g.68882574G>A	ENSP00000303775:p.Val350Ile	Somatic		Capture	Illumina HiSeq	Phase_I	68736078	NM_138964	A5JUU2|Q53QT9|Q8NFJ7	Missense_Mutation	SNP	ENST00000303786.3	37	CCDS1889.1	.	.	.	.	.	.	.	.	.	.	G	0.166	-1.076235	0.01903	.	.	ENSG00000169618	ENST00000303786;ENST00000394342	T;T	0.36699	1.24;1.24	4.68	0.881	0.19166	.	0.263355	0.49305	N	0.000146	T	0.11836	0.0288	N	0.02539	-0.55	0.22017	N	0.999413	B	0.02656	0.0	B	0.01281	0.0	T	0.14615	-1.0466	10	0.56958	D	0.05	.	2.35	0.04281	0.5999:0.1579:0.0901:0.1521	.	350	Q8TCW9	PKR1_HUMAN	I	350	ENSP00000303775:V350I;ENSP00000377874:V350I	ENSP00000303775:V350I	V	+	1	0	PROKR1	68736078	1.000000	0.71417	0.994000	0.49952	0.021000	0.10359	3.086000	0.50159	0.146000	0.19002	-0.302000	0.09304	GTC		0.507	PROKR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251760.2		
ARHGAP25	9938	broad.mit.edu	37	2	69002484	69002484	+	Nonsense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr2:69002484C>T	ENST00000295381.3	+	2	612	c.193C>T	c.(193-195)Cag>Tag	p.Q65*	ARHGAP25_ENST00000409220.1_Nonsense_Mutation_p.Q58*|ARHGAP25_ENST00000409202.3_Nonsense_Mutation_p.Q65*|ARHGAP25_ENST00000497079.1_Nonsense_Mutation_p.Q58*|ARHGAP25_ENST00000409030.3_Nonsense_Mutation_p.Q58*|ARHGAP25_ENST00000456116.2_3'UTR|ARHGAP25_ENST00000467265.1_Nonsense_Mutation_p.Q65*|ARHGAP25_ENST00000544262.1_Nonsense_Mutation_p.Q39*	NM_001007231.2	NP_001007232.2	P42331	RHG25_HUMAN	Rho GTPase activating protein 25	65	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	GTPase activator activity (GO:0005096)	p.Q58*(1)		breast(3)|endometrium(5)|kidney(2)|large_intestine(11)|lung(20)|ovary(3)|prostate(1)|skin(5)|stomach(1)|urinary_tract(1)	52						GAACTGGCAGCAGAGGTACTT	0.572																																					p.Q58X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.C172T	2						.						140.0	148.0	145.0					2																	69002484		2203	4300	6503	68855988	SO:0001587	stop_gained	9938	exon1			D29642	CCDS33214.1, CCDS46312.1, CCDS33214.2, CCDS54363.1, CCDS54364.1	2p13.3	2013-01-10			ENSG00000163219	ENSG00000163219		"""Rho GTPase activating proteins"", ""Pleckstrin homology (PH) domain containing"""	28951	protein-coding gene	gene with protein product		610587				7584044	Standard	NM_001007231		Approved	KIAA0053	uc010fdg.3	P42331	OTTHUMG00000152621	ENST00000295381.3:c.193C>T	2.37:g.69002484C>T	ENSP00000295381:p.Gln65*	Somatic		Capture	Illumina HiSeq	Phase_I	68855988	NM_001166276	A8K2Y1|B7Z498|E9PFQ7|G5E9G2|Q8IXQ2	Nonsense_Mutation	SNP	ENST00000295381.3	37		.	.	.	.	.	.	.	.	.	.	C	40	8.105975	0.98657	.	.	ENSG00000163219	ENST00000544262;ENST00000295381;ENST00000409202;ENST00000467265;ENST00000409030;ENST00000409220;ENST00000482106;ENST00000497079;ENST00000543533	.	.	.	5.58	5.58	0.84498	.	0.063052	0.64402	D	0.000004	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.19147	T	0.46	.	18.1318	0.89604	0.0:1.0:0.0:0.0	.	.	.	.	X	39;65;65;65;58;58;58;58;58	.	ENSP00000295381:Q65X	Q	+	1	0	ARHGAP25	68855988	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	5.696000	0.68287	2.613000	0.88420	0.563000	0.77884	CAG		0.572	ARHGAP25-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_014882	
ARHGAP25	9938	broad.mit.edu	37	2	69053261	69053261	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr2:69053261A>G	ENST00000295381.3	+	11	2292	c.1873A>G	c.(1873-1875)Aag>Gag	p.K625E	ARHGAP25_ENST00000479844.1_Missense_Mutation_p.K319E|ARHGAP25_ENST00000409220.1_Missense_Mutation_p.K619E|ARHGAP25_ENST00000409202.3_Missense_Mutation_p.K626E|ARHGAP25_ENST00000409030.3_Missense_Mutation_p.K618E|ARHGAP25_ENST00000467265.1_Missense_Mutation_p.K586E	NM_001007231.2	NP_001007232.2	P42331	RHG25_HUMAN	Rho GTPase activating protein 25	625					regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	GTPase activator activity (GO:0005096)	p.K619E(1)		breast(3)|endometrium(5)|kidney(2)|large_intestine(11)|lung(20)|ovary(3)|prostate(1)|skin(5)|stomach(1)|urinary_tract(1)	52						GAAGAGGAACAAGGCCTTGGA	0.522																																					p.K619E												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A1855G	2						.						105.0	110.0	108.0					2																	69053261		2203	4300	6503	68906765	SO:0001583	missense	9938	exon10			D29642	CCDS33214.1, CCDS46312.1, CCDS33214.2, CCDS54363.1, CCDS54364.1	2p13.3	2013-01-10			ENSG00000163219	ENSG00000163219		"""Rho GTPase activating proteins"", ""Pleckstrin homology (PH) domain containing"""	28951	protein-coding gene	gene with protein product		610587				7584044	Standard	NM_001007231		Approved	KIAA0053	uc010fdg.3	P42331	OTTHUMG00000152621	ENST00000295381.3:c.1873A>G	2.37:g.69053261A>G	ENSP00000295381:p.Lys625Glu	Somatic		Capture	Illumina HiSeq	Phase_I	68906765	NM_001166276	A8K2Y1|B7Z498|E9PFQ7|G5E9G2|Q8IXQ2	Missense_Mutation	SNP	ENST00000295381.3	37		.	.	.	.	.	.	.	.	.	.	A	12.45	1.942963	0.34283	.	.	ENSG00000163219	ENST00000295381;ENST00000409202;ENST00000467265;ENST00000409030;ENST00000409220;ENST00000543533;ENST00000479844	T;T;T;T;T;T	0.58060	0.36;0.36;0.36;0.36;0.36;0.36	5.95	4.81	0.61882	.	0.298666	0.41823	N	0.000814	T	0.37598	0.1009	N	0.25890	0.77	0.80722	D	1	B;B;B;B;B	0.22800	0.001;0.075;0.075;0.075;0.015	B;B;B;B;B	0.19946	0.002;0.017;0.027;0.027;0.007	T	0.12400	-1.0549	10	0.22109	T	0.4	.	11.0478	0.47870	0.9283:0.0:0.0717:0.0	.	586;626;619;618;625	E9PFQ7;P42331-4;G5E9G2;P42331-3;P42331	.;.;.;.;RHG25_HUMAN	E	625;626;586;618;619;610;319	ENSP00000295381:K625E;ENSP00000386911:K626E;ENSP00000420583:K586E;ENSP00000386863:K618E;ENSP00000386241:K619E;ENSP00000417467:K319E	ENSP00000295381:K625E	K	+	1	0	ARHGAP25	68906765	1.000000	0.71417	0.998000	0.56505	0.996000	0.88848	2.521000	0.45563	1.089000	0.41292	0.533000	0.62120	AAG		0.522	ARHGAP25-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_014882	
C2orf78	388960	broad.mit.edu	37	2	74043619	74043619	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr2:74043619A>G	ENST00000409561.1	+	3	2390	c.2269A>G	c.(2269-2271)Act>Gct	p.T757A		NM_001080474.1	NP_001073943.1	A6NCI8	CB078_HUMAN	chromosome 2 open reading frame 78	757								p.T727A(1)		cervix(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(21)|ovary(2)|prostate(2)|soft_tissue(1)|urinary_tract(1)	34						ACCTGATTCTACTAACTCAGC	0.542																																					p.T757A												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A2269G	2						.						137.0	144.0	142.0					2																	74043619		2117	4230	6347	73897127	SO:0001583	missense	388960	exon3			AC092653, AC136006, AK125975	CCDS46338.1	2p13.2	2008-07-18			ENSG00000187833	ENSG00000187833			34349	protein-coding gene	gene with protein product							Standard	NM_001080474		Approved	FLJ43987, hCG1989538, COG5373	uc002sjr.1	A6NCI8	OTTHUMG00000152819	ENST00000409561.1:c.2269A>G	2.37:g.74043619A>G	ENSP00000387124:p.Thr757Ala	Somatic		Capture	Illumina HiSeq	Phase_I	73897127	NM_001080474		Missense_Mutation	SNP	ENST00000409561.1	37	CCDS46338.1	.	.	.	.	.	.	.	.	.	.	A	13.30	2.196086	0.38806	.	.	ENSG00000187833	ENST00000409561;ENST00000342345	T	0.44083	0.93	4.92	-0.905	0.10527	.	0.470598	0.15215	N	0.274231	T	0.36331	0.0963	L	0.57536	1.79	0.09310	N	1	P	0.46912	0.886	P	0.46275	0.51	T	0.18903	-1.0322	10	0.40728	T	0.16	-4.5794	3.2753	0.06896	0.4442:0.0:0.3665:0.1893	.	757	A6NCI8	CB078_HUMAN	A	757;727	ENSP00000387124:T757A	ENSP00000340692:T727A	T	+	1	0	C2orf78	73897127	0.000000	0.05858	0.004000	0.12327	0.031000	0.12232	0.232000	0.17891	0.001000	0.14605	0.460000	0.39030	ACT		0.542	C2orf78-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000328083.1	NM_001080474	
PCGF1	84759	broad.mit.edu	37	2	74733181	74733181	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr2:74733181G>T	ENST00000233630.6	-	5	1339	c.428C>A	c.(427-429)cCa>cAa	p.P143Q	LBX2_ENST00000550249.1_5'Flank|PCGF1_ENST00000480844.2_5'UTR|LBX2-AS1_ENST00000603175.1_RNA|LBX2_ENST00000460508.3_5'Flank|LBX2-AS1_ENST00000548978.2_RNA	NM_032673.2	NP_116062.2	Q9BSM1	PCGF1_HUMAN	polycomb group ring finger 1	143	Required for repressor activity.				histone H2A monoubiquitination (GO:0035518)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|PcG protein complex (GO:0031519)	protein C-terminus binding (GO:0008022)|zinc ion binding (GO:0008270)	p.P131Q(1)		endometrium(3)|kidney(1)|large_intestine(2)|lung(3)|ovary(1)|skin(2)	12						GCTCAGTGCTGGCTCTGAGAA	0.542																																					p.P143Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C428A	2						.						129.0	130.0	129.0					2																	74733181		2203	4300	6503	74586689	SO:0001583	missense	84759	exon5			AF087884	CCDS1946.2	2p13.1	2013-01-09			ENSG00000115289	ENSG00000115289		"""RING-type (C3HC4) zinc fingers"", ""Polycomb group ring fingers"""	17615	protein-coding gene	gene with protein product		610231				11287196	Standard	NM_032673		Approved	NSPC1, RNF68, MGC10882	uc002slz.3	Q9BSM1	OTTHUMG00000129954	ENST00000233630.6:c.428C>A	2.37:g.74733181G>T	ENSP00000233630:p.Pro143Gln	Somatic		Capture	Illumina HiSeq	Phase_I	74586689	NM_032673	Q7Z506	Missense_Mutation	SNP	ENST00000233630.6	37	CCDS1946.2	.	.	.	.	.	.	.	.	.	.	G	13.34	2.207945	0.39003	.	.	ENSG00000115289	ENST00000233630	T	0.24151	1.87	4.98	4.98	0.66077	.	0.635768	0.14612	N	0.308990	T	0.19248	0.0462	L	0.28192	0.835	0.40894	D	0.98409	B	0.24533	0.105	B	0.26770	0.073	T	0.05989	-1.0852	10	0.13470	T	0.59	-7.1981	14.1244	0.65210	0.0:0.0:1.0:0.0	.	143	Q9BSM1	PCGF1_HUMAN	Q	143	ENSP00000233630:P143Q	ENSP00000233630:P143Q	P	-	2	0	PCGF1	74586689	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	5.026000	0.64103	2.469000	0.83416	0.655000	0.94253	CCA		0.542	PCGF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252216.1	NM_032673	
REG1A	5967	broad.mit.edu	37	2	79350057	79350057	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr2:79350057G>A	ENST00000233735.1	+	5	515	c.412G>A	c.(412-414)Gtg>Atg	p.V138M		NM_002909.4	NP_002900.2	P05451	REG1A_HUMAN	regenerating islet-derived 1 alpha	138	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.V138M(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						TGGCTACTGTGTGAGCCTGAC	0.572																																					p.V138M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G412A	2						.						101.0	95.0	97.0					2																	79350057		2203	4300	6503	79203565	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.412G>A	2.37:g.79350057G>A	ENSP00000233735:p.Val138Met	Somatic		Capture	Illumina HiSeq	Phase_I	79203565	NM_002909	P11379|Q4ZG28	Missense_Mutation	SNP	ENST00000233735.1	37	CCDS1964.1	.	.	.	.	.	.	.	.	.	.	g	18.28	3.589749	0.66105	.	.	ENSG00000115386	ENST00000233735	T	0.11385	2.78	3.15	3.15	0.36227	C-type lectin fold (1);C-type lectin, conserved site (1);C-type lectin-like (1);C-type lectin (3);	0.467854	0.15758	N	0.246049	T	0.30166	0.0756	M	0.90542	3.125	0.33455	D	0.584175	D	0.53151	0.958	P	0.54544	0.755	T	0.51896	-0.8647	10	0.59425	D	0.04	.	9.9324	0.41530	0.0:0.0:1.0:0.0	.	138	P05451	REG1A_HUMAN	M	138	ENSP00000233735:V138M	ENSP00000233735:V138M	V	+	1	0	REG1A	79203565	0.950000	0.32346	0.725000	0.30721	0.402000	0.30811	1.907000	0.39897	1.765000	0.52091	0.557000	0.71058	GTG		0.572	REG1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252289.1	NM_002909	
KANSL3	55683	broad.mit.edu	37	2	97267997	97267997	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr2:97267997T>C	ENST00000431828.1	-	19	2414	c.2338A>G	c.(2338-2340)Att>Gtt	p.I780V	KANSL3_ENST00000599854.1_Missense_Mutation_p.I693V|KANSL3_ENST00000440133.1_Missense_Mutation_p.I600V|KANSL3_ENST00000441706.2_Intron|KANSL3_ENST00000487070.1_Intron			Q9P2N6	KANL3_HUMAN	KAT8 regulatory NSL complex subunit 3	806					chromatin organization (GO:0006325)|histone H4-K16 acetylation (GO:0043984)|histone H4-K5 acetylation (GO:0043981)|histone H4-K8 acetylation (GO:0043982)	histone acetyltransferase complex (GO:0000123)|intracellular membrane-bounded organelle (GO:0043231)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)		p.I780V(1)									GCCACAGGAATGGTACGGACA	0.632																																					p.I780V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A2338G	2						.						40.0	42.0	41.0					2																	97267997		2078	4215	6293	96631724	SO:0001583	missense	55683	exon19			BC063792	CCDS46361.1	2q11.2	2011-10-31	2011-10-31	2011-10-31	ENSG00000114982	ENSG00000114982			25473	protein-coding gene	gene with protein product			"""KIAA1310"""	KIAA1310			Standard	NM_001115016		Approved	FLJ10081, Rcd1, NSL3	uc002swn.5	Q9P2N6	OTTHUMG00000155249	ENST00000431828.1:c.2338A>G	2.37:g.97267997T>C	ENSP00000396749:p.Ile780Val	Somatic		Capture	Illumina HiSeq	Phase_I	96631724	NM_001115016	A1L184|D3DXH3|D3DXH4|Q05BU4|Q6P3X2|Q6PJH6|Q86T19|Q96L64|Q9H0C9|Q9H8C9|Q9HAP8|Q9NWE5	Missense_Mutation	SNP	ENST00000431828.1	37	CCDS46361.1	.	.	.	.	.	.	.	.	.	.	T	13.53	2.265557	0.40095	.	.	ENSG00000114982	ENST00000354204;ENST00000447759;ENST00000431828;ENST00000440133;ENST00000444759	T;T	0.49139	0.79;0.82	5.81	4.66	0.58398	.	0.165197	0.53938	N	0.000060	T	0.24699	0.0599	N	0.08118	0	0.80722	D	1	B;B;B;B;B	0.09022	0.0;0.002;0.0;0.0;0.0	B;B;B;B;B	0.09377	0.001;0.004;0.001;0.001;0.001	T	0.05937	-1.0855	10	0.13470	T	0.59	.	10.0576	0.42255	0.0:0.0795:0.0:0.9204	.	574;806;780;691;666	B4E1W4;Q9P2N6;Q9P2N6-3;Q9P2N6-5;Q9P2N6-6	.;K1310_HUMAN;.;.;.	V	693;666;780;600;574	ENSP00000396749:I780V;ENSP00000406207:I600V	ENSP00000346144:I693V	I	-	1	0	KIAA1310	96631724	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	2.566000	0.45948	1.019000	0.39547	0.533000	0.62120	ATT		0.632	KANSL3-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339040.2	NM_017991	
FER1L5	90342	broad.mit.edu	37	2	97365733	97365733	+	RNA	SNP	C	C	T	rs368260119		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr2:97365733C>T	ENST00000457909.1	+	0	4349							A0AVI2	FR1L5_HUMAN	fer-1-like family member 5							integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.R1643W(1)		NS(1)|autonomic_ganglia(1)|breast(4)|cervix(1)|endometrium(9)|large_intestine(9)|lung(6)|ovary(2)|prostate(2)|skin(1)|urinary_tract(2)	38						CTATGCCAAGCGGAAAGGGCT	0.532																																					p.R1643W												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C4927T	2						.	C	TRP/ARG	1,3861		0,1,1930	54.0	56.0	56.0		4927	2.0	0.1	2		56	0,8274		0,0,4137	no	missense	FER1L5	NM_001113382.1	101	0,1,6067	TT,TC,CC		0.0,0.0259,0.0082	probably-damaging	1643/2094	97365733	1,12135	1931	4137	6068	96729460			90342	exon43			BC126368		2q11.2	2014-06-27	2014-06-27		ENSG00000249715	ENSG00000249715			19044	protein-coding gene	gene with protein product			"""fer-1-like 5 (C. elegans)"""				Standard	XM_006712826		Approved	DKFZp434I0121	uc010fia.3	A0AVI2	OTTHUMG00000154929		2.37:g.97365733C>T		Somatic		Capture	Illumina HiSeq	Phase_I	96729460	NM_001113382	Q17RH2|Q6ZU24	Missense_Mutation	SNP	ENST00000457909.1	37		.	.	.	.	.	.	.	.	.	.	C	1.310	-0.602326	0.03744	2.59E-4	0.0	ENSG00000214272	ENST00000414152;ENST00000436930;ENST00000397978	.	.	.	5.19	2.02	0.26589	.	0.620479	0.12804	U	0.437764	T	0.45836	0.1362	M	0.63843	1.955	.	.	.	D;D;D	0.76494	0.998;0.999;0.999	P;P;P	0.53861	0.549;0.549;0.736	T	0.51426	-0.8707	8	0.41790	T	0.15	-4.4064	3.0031	0.06020	0.4381:0.3438:0.1263:0.0917	.	360;1643;361	B7ZLI3;A0AVI2;A0AVI2-2	.;FR1L5_HUMAN;.	W	1643;1656;361	.	ENSP00000442027:R361W	R	+	1	2	FER1L5	96729460	0.005000	0.15991	0.133000	0.22050	0.107000	0.19398	0.569000	0.23638	0.564000	0.29238	-0.152000	0.13540	CGG		0.532	FER1L5-001	KNOWN	basic|exp_conf	retained_intron	pseudogene	OTTHUMT00000339030.1	NM_001077400	
ZAP70	7535	broad.mit.edu	37	2	98354277	98354277	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr2:98354277C>T	ENST00000264972.5	+	12	1755	c.1540C>T	c.(1540-1542)Cgc>Tgc	p.R514C	ZAP70_ENST00000442208.1_Missense_Mutation_p.R388C|ZAP70_ENST00000451498.2_Missense_Mutation_p.R207C|ZAP70_ENST00000463643.1_3'UTR	NM_001079.3	NP_001070.2	P43403	ZAP70_HUMAN	zeta-chain (TCR) associated protein kinase 70kDa	514	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				adaptive immune response (GO:0002250)|B cell activation (GO:0042113)|beta selection (GO:0043366)|immune response (GO:0006955)|intracellular signal transduction (GO:0035556)|negative thymic T cell selection (GO:0045060)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of alpha-beta T cell differentiation (GO:0046638)|positive regulation of alpha-beta T cell proliferation (GO:0046641)|positive regulation of calcium-mediated signaling (GO:0050850)|positive regulation of T cell differentiation (GO:0045582)|positive thymic T cell selection (GO:0045059)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|T cell activation (GO:0042110)|T cell aggregation (GO:0070489)|T cell differentiation (GO:0030217)|T cell migration (GO:0072678)|T cell receptor signaling pathway (GO:0050852)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|immunological synapse (GO:0001772)|plasma membrane (GO:0005886)|T cell receptor complex (GO:0042101)	ATP binding (GO:0005524)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein tyrosine kinase activity (GO:0004713)	p.R514C(1)		breast(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(15)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	29						CATCAACTTCCGCAAGTTCTC	0.642																																					p.R207C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C619T	2						.						120.0	129.0	126.0					2																	98354277		2203	4300	6503	97720709	SO:0001583	missense	7535	exon4			L05148	CCDS33254.1, CCDS33255.1	2q11-q13	2014-09-17	2002-08-29		ENSG00000115085	ENSG00000115085		"""SH2 domain containing"""	12858	protein-coding gene	gene with protein product		176947	"""zeta-chain (TCR) associated protein kinase (70 kD)"""	SRK		1423621	Standard	NM_001079		Approved	ZAP-70, STD	uc002syd.1	P43403	OTTHUMG00000153060	ENST00000264972.5:c.1540C>T	2.37:g.98354277C>T	ENSP00000264972:p.Arg514Cys	Somatic		Capture	Illumina HiSeq	Phase_I	97720709	NM_207519	A6NFP4|Q6PIA4|Q8IXD6|Q9UBS6	Missense_Mutation	SNP	ENST00000264972.5	37	CCDS33254.1	.	.	.	.	.	.	.	.	.	.	C	24.0	4.486868	0.84854	.	.	ENSG00000115085	ENST00000264972;ENST00000442208;ENST00000451498	D;D;D	0.83075	-1.68;-1.68;-1.68	5.2	5.2	0.72013	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.140072	0.32736	N	0.005703	D	0.90154	0.6923	M	0.75777	2.31	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.70227	0.951;0.968	D	0.89377	0.3679	10	0.40728	T	0.16	.	16.6148	0.84904	0.0:1.0:0.0:0.0	.	388;514	P43403-3;P43403	.;ZAP70_HUMAN	C	514;388;207	ENSP00000264972:R514C;ENSP00000411141:R388C;ENSP00000400475:R207C	ENSP00000264972:R514C	R	+	1	0	ZAP70	97720709	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	3.340000	0.52143	2.610000	0.88304	0.655000	0.94253	CGC		0.642	ZAP70-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329278.1		
VWA3B	200403	broad.mit.edu	37	2	98779407	98779407	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr2:98779407C>A	ENST00000477737.1	+	8	1286	c.1082C>A	c.(1081-1083)cCt>cAt	p.P361H	VWA3B_ENST00000435344.1_Missense_Mutation_p.P361H|VWA3B_ENST00000451075.2_Missense_Mutation_p.P211H	NM_144992.4	NP_659429.4	Q502W6	VWA3B_HUMAN	von Willebrand factor A domain containing 3B	361								p.P361H(1)		NS(3)|breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(10)|lung(33)|ovary(3)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	70						GTGGCCGAGCCTCCCAAGCCC	0.567																																					p.P361H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1082A	2						.						50.0	59.0	56.0					2																	98779407		2068	4216	6284	98145839	SO:0001583	missense	200403	exon8			AL832761	CCDS42718.1	2q11.2	2008-02-05			ENSG00000168658	ENSG00000168658			28385	protein-coding gene	gene with protein product						12477932	Standard	NM_144992		Approved	DKFZp686F2227, MGC26733	uc002syo.3	Q502W6	OTTHUMG00000153104	ENST00000477737.1:c.1082C>A	2.37:g.98779407C>A	ENSP00000417955:p.Pro361His	Somatic		Capture	Illumina HiSeq	Phase_I	98145839	NM_144992	B9EK71|Q86T73|Q8N2D0|Q8N770|Q8NA79|Q8ND63|Q8ND65|Q8WW02	Missense_Mutation	SNP	ENST00000477737.1	37	CCDS42718.1	.	.	.	.	.	.	.	.	.	.	C	7.541	0.660666	0.14645	.	.	ENSG00000168658	ENST00000435344;ENST00000477737;ENST00000451075	T;T;T	0.22134	1.97;3.41;2.5	4.68	-1.07	0.09968	.	1.167020	0.06266	N	0.694825	T	0.11665	0.0284	N	0.22421	0.69	0.09310	N	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.06405	0.0;0.0;0.002	T	0.35574	-0.9783	10	0.15499	T	0.54	.	4.405	0.11406	0.1485:0.5014:0.0:0.3501	.	211;361;361	B7Z7Q7;Q502W6;Q502W6-8	.;VWA3B_HUMAN;.	H	361;361;211	ENSP00000401959:P361H;ENSP00000417955:P361H;ENSP00000389463:P211H	ENSP00000411168:P361H	P	+	2	0	VWA3B	98145839	0.000000	0.05858	0.000000	0.03702	0.442000	0.32017	-0.607000	0.05648	-0.470000	0.06901	-0.158000	0.13435	CCT		0.567	VWA3B-020	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353469.2	NM_144992	
INPP4A	3631	broad.mit.edu	37	2	99170757	99170757	+	Silent	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr2:99170757C>T	ENST00000523221.1	+	14	1386	c.1386C>T	c.(1384-1386)tgC>tgT	p.C462C	INPP4A_ENST00000409851.3_Silent_p.C457C|INPP4A_ENST00000409540.3_Silent_p.C462C|INPP4A_ENST00000409463.1_Intron|INPP4A_ENST00000074304.5_Silent_p.C462C|INPP4A_ENST00000545415.1_Silent_p.C462C|INPP4A_ENST00000409016.4_Silent_p.C462C			Q96PE3	INP4A_HUMAN	inositol polyphosphate-4-phosphatase, type I, 107kDa	462					inositol phosphate metabolic process (GO:0043647)|phosphatidylinositol biosynthetic process (GO:0006661)|phospholipid metabolic process (GO:0006644)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	phosphatidylinositol-3,4-bisphosphate 4-phosphatase activity (GO:0016316)|phosphatidylinositol-4,5-bisphosphate 4-phosphatase activity (GO:0034597)	p.C462C(1)		breast(1)|endometrium(9)|kidney(2)|large_intestine(5)|lung(16)|ovary(2)|prostate(4)|upper_aerodigestive_tract(4)	43						TCACGGTCTGCGACTGCAAGC	0.622																																					p.C457C												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1371T	2						.						24.0	27.0	26.0					2																	99170757		2165	4271	6436	98537189	SO:0001819	synonymous_variant	3631	exon15			U26398	CCDS46369.1, CCDS46370.1, CCDS46371.1, CCDS46372.1	2q11.2	2008-05-27	2002-08-29		ENSG00000040933	ENSG00000040933			6074	protein-coding gene	gene with protein product		600916	"""inositol polyphosphate-4-phosphatase, type I, 107kD"""	INPP4		7608176, 9295334	Standard	NM_004027		Approved		uc002syy.3	Q96PE3	OTTHUMG00000153106	ENST00000523221.1:c.1386C>T	2.37:g.99170757C>T		Somatic		Capture	Illumina HiSeq	Phase_I	98537189	NM_001134225	O15326|Q13187|Q53TD8|Q8TC02	Silent	SNP	ENST00000523221.1	37	CCDS46369.1																																																																																				0.622	INPP4A-009	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000376095.1	NM_001566	
LYG1	129530	broad.mit.edu	37	2	99907878	99907878	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr2:99907878C>T	ENST00000409448.1	-	6	471	c.155G>A	c.(154-156)cGt>cAt	p.R52H	LYG1_ENST00000308528.4_Missense_Mutation_p.R52H			Q8N1E2	LYG1_HUMAN	lysozyme G-like 1	52					cell wall macromolecule catabolic process (GO:0016998)|peptidoglycan catabolic process (GO:0009253)	extracellular region (GO:0005576)	lysozyme activity (GO:0003796)	p.R52H(1)		endometrium(2)|kidney(1)|large_intestine(3)|lung(1)	7						TTCAGAAGCACGAACTCCTAA	0.463																																					p.R52H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G155A	2						.						116.0	94.0	101.0					2																	99907878		2203	4300	6503	99274310	SO:0001583	missense	129530	exon5			BC029126	CCDS2043.1	2q11.2	2008-02-05			ENSG00000144214	ENSG00000144214			27014	protein-coding gene	gene with protein product						12574869	Standard	NM_174898		Approved	SALW1939	uc002szy.3	Q8N1E2	OTTHUMG00000130639	ENST00000409448.1:c.155G>A	2.37:g.99907878C>T	ENSP00000386923:p.Arg52His	Somatic		Capture	Illumina HiSeq	Phase_I	99274310	NM_174898	Q53RV9	Missense_Mutation	SNP	ENST00000409448.1	37	CCDS2043.1	.	.	.	.	.	.	.	.	.	.	C	9.859	1.195650	0.22037	.	.	ENSG00000144214	ENST00000308528;ENST00000409448	.	.	.	4.82	3.04	0.35103	Lysozyme-like domain (1);	0.100557	0.44902	N	0.000409	T	0.35770	0.0943	L	0.34521	1.04	0.35333	D	0.785804	B	0.25169	0.119	B	0.20384	0.029	T	0.33369	-0.9871	8	.	.	.	-11.7141	7.7726	0.29017	0.0:0.8099:0.0:0.1901	.	52	Q8N1E2	LYG1_HUMAN	H	52	.	.	R	-	2	0	LYG1	99274310	0.015000	0.18098	0.871000	0.34182	0.329000	0.28539	-0.509000	0.06336	0.780000	0.33566	-0.124000	0.14976	CGT		0.463	LYG1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330315.1	NM_174898	
CCDC141	285025	broad.mit.edu	37	2	179720989	179720989	+	Frame_Shift_Del	DEL	T	T	-			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	T	T	T	-	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr2:179720989delT	ENST00000420890.2	-	18	2977	c.2860delA	c.(2860-2862)atgfs	p.M954fs	CCDC141_ENST00000295723.5_Frame_Shift_Del_p.M379fs	NM_173648.3	NP_775919.3	Q6ZP82	CC141_HUMAN	coiled-coil domain containing 141	954								p.M379fs*4(1)		NS(2)|breast(1)|endometrium(5)|kidney(1)|large_intestine(17)|lung(37)|ovary(8)|pancreas(2)|skin(4)|upper_aerodigestive_tract(1)	78			OV - Ovarian serous cystadenocarcinoma(117;0.0274)|Epithelial(96;0.0531)|all cancers(119;0.147)			GTTACCTGCATTTTTTCAGCA	0.299																																					p.M954fs												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.2860delA	2						.						115.0	109.0	111.0					2																	179720989		2202	4297	6499	179429234	SO:0001589	frameshift_variant	285025	exon18			AK096821		2q31.2	2013-01-14			ENSG00000163492	ENSG00000163492		"""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	26821	protein-coding gene	gene with protein product	"""coiled-coil protein associated with myosin II and DISC1"""					20956536	Standard	NM_173648		Approved	FLJ39502, CAMDI	uc002une.2	Q6ZP82	OTTHUMG00000132578	ENST00000420890.2:c.2860delA	2.37:g.179720989delT	ENSP00000395995:p.Met954fs	Somatic		Capture	Illumina HiSeq	Phase_I	179429234	NM_173648	H7C0P1|J3KNW6|Q8N8H3	Frame_Shift_Del	DEL	ENST00000420890.2	37																																																																																					0.299	CCDC141-202	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_173648	
FSIP2	401024	broad.mit.edu	37	2	186673611	186673611	+	Frame_Shift_Del	DEL	A	A	-			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	A	A	A	-	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr2:186673611delA	ENST00000424728.1	+	17	19578	c.19578delA	c.(19576-19578)ggafs	p.G6526fs	FSIP2_ENST00000343098.5_Frame_Shift_Del_p.G6615fs			Q5CZC0	FSIP2_HUMAN	fibrous sheath interacting protein 2	6526				G -> E (in Ref. 2; CAI46017). {ECO:0000305}.				p.K1226fs*5(2)		NS(1)|autonomic_ganglia(1)|breast(2)|endometrium(4)|kidney(1)|large_intestine(11)|lung(46)|pancreas(1)|urinary_tract(2)	69						CACATGTTGGAAAAAAACCAG	0.303																																					p.G6615fs												.	.	2	Deletion - Frameshift(2)	large_intestine(2)	c.19845delA	2						.			8,3456		1,6,1725	44.0	43.0	43.0			4.5	0.0	2		44	9,7773		2,5,3884	no	frameshift	FSIP2	NM_173651.2		3,11,5609	A1A1,A1R,RR		0.1157,0.2309,0.1512			186673611	17,11229	1788	4058	5846	186381856	SO:0001589	frameshift_variant	401024	exon17			AK092099	CCDS54426.1	2q32.1	2010-06-18			ENSG00000188738	ENSG00000188738			21675	protein-coding gene	gene with protein product		615796				14702039	Standard	NM_173651		Approved	FLJ34780	uc002upl.3	Q5CZC0	OTTHUMG00000153874	ENST00000424728.1:c.19578delA	2.37:g.186673611delA	ENSP00000401306:p.Gly6526fs	Somatic		Capture	Illumina HiSeq	Phase_I	186381856	NM_173651	Q53TL3|Q53TN5|Q5HYH2|Q6ZTZ5|Q6ZU14|Q6ZU21	Frame_Shift_Del	DEL	ENST00000424728.1	37																																																																																					0.303	FSIP2-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000332778.3	NM_173651	
ING5	84289	broad.mit.edu	37	2	242651431	242651431	+	Nonsense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr2:242651431C>T	ENST00000313552.6	+	5	453	c.427C>T	c.(427-429)Cga>Tga	p.R143*	ING5_ENST00000482774.1_3'UTR|ING5_ENST00000406941.1_Nonsense_Mutation_p.R143*	NM_032329.4	NP_115705.2	Q8WYH8	ING5_HUMAN	inhibitor of growth family, member 5	143					chromatin organization (GO:0006325)|DNA replication (GO:0006260)|histone H3 acetylation (GO:0043966)|negative regulation of cell proliferation (GO:0008285)|negative regulation of growth (GO:0045926)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of transcription, DNA-templated (GO:0045893)|protein acetylation (GO:0006473)|transcription, DNA-templated (GO:0006351)	MOZ/MORF histone acetyltransferase complex (GO:0070776)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|methylated histone binding (GO:0035064)|zinc ion binding (GO:0008270)	p.R143*(1)		large_intestine(1)|lung(1)|skin(1)	3		all_cancers(19;1.09e-40)|all_epithelial(40;2.03e-18)|Breast(86;1.53e-05)|all_lung(227;0.00338)|Renal(207;0.00502)|Ovarian(221;0.00716)|Lung NSC(271;0.012)|Esophageal squamous(248;0.129)|Melanoma(123;0.144)|all_hematologic(139;0.158)|all_neural(83;0.243)|Hepatocellular(293;0.244)		Epithelial(32;2.16e-33)|all cancers(36;4.99e-31)|OV - Ovarian serous cystadenocarcinoma(60;3.6e-15)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;1.65e-06)|Lung(119;0.000152)|LUSC - Lung squamous cell carcinoma(224;0.00154)|Colorectal(34;0.0129)|COAD - Colon adenocarcinoma(134;0.0839)		GTCCCGGGGCCGAGGCAGGAG	0.428																																					p.R143X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.C427T	2						.						76.0	75.0	76.0					2																	242651431		2189	4284	6473	242300104	SO:0001587	stop_gained	84289	exon5			AF189286	CCDS33425.1	2q37.3	2013-01-28			ENSG00000168395	ENSG00000168395		"""Zinc fingers, PHD-type"""	19421	protein-coding gene	gene with protein product		608525				12750254	Standard	NM_032329		Approved	FLJ23842, p28ING5	uc002wcd.3	Q8WYH8	OTTHUMG00000151501	ENST00000313552.6:c.427C>T	2.37:g.242651431C>T	ENSP00000322142:p.Arg143*	Somatic		Capture	Illumina HiSeq	Phase_I	242300104	NM_032329	A8K1P3|Q53NU6|Q57Z54|Q9BS30	Nonsense_Mutation	SNP	ENST00000313552.6	37	CCDS33425.1	.	.	.	.	.	.	.	.	.	.	C	34	5.351935	0.95830	.	.	ENSG00000168395	ENST00000313552;ENST00000406941	.	.	.	6.07	6.07	0.98685	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.05436	T	0.98	-1.7462	16.1648	0.81747	0.1339:0.8661:0.0:0.0	.	.	.	.	X	143	.	ENSP00000322142:R143X	R	+	1	2	ING5	242300104	0.917000	0.31117	0.735000	0.30896	0.993000	0.82548	1.717000	0.37991	2.884000	0.98904	0.655000	0.94253	CGA		0.428	ING5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322901.3	NM_032329	
TOMM70A	9868	broad.mit.edu	37	3	100105110	100105110	+	Missense_Mutation	SNP	G	G	A	rs9833995		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr3:100105110G>A	ENST00000284320.5	-	3	1025	c.577C>T	c.(577-579)Cgt>Tgt	p.R193C		NM_014820.4	NP_055635.3	O94826	TOM70_HUMAN	translocase of outer mitochondrial membrane 70 homolog A (S. cerevisiae)	193					cellular protein metabolic process (GO:0044267)|protein targeting to mitochondrion (GO:0006626)|protein transmembrane transport (GO:0071806)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrial outer membrane translocase complex (GO:0005742)|mitochondrion (GO:0005739)	protein transmembrane transporter activity (GO:0008320)	p.R193C(1)		endometrium(11)|large_intestine(5)|lung(10)|ovary(2)|skin(2)|upper_aerodigestive_tract(2)	32						GCTTTTGCACGTCTAAAGAGA	0.323													G|||	1	0.000199681	0.0	0.0	5008	,	,		18494	0.0		0.001	False		,,,				2504	0.0				p.R193C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C577T	3						.						166.0	162.0	163.0					3																	100105110		2203	4300	6503	101587800	SO:0001583	missense	9868	exon3			AB018262	CCDS33807.1	3q12.2	2013-01-10	2006-04-04		ENSG00000154174	ENSG00000154174		"""Tetratricopeptide (TTC) repeat domain containing"""	11985	protein-coding gene	gene with protein product		606081	"""translocase of outer mitochondrial membrane 70 (yeast) homolog A"", ""translocase of outer mitochondrial membrane 70 homolog A (yeast)"""			10582581	Standard	NM_014820		Approved	KIAA0719	uc003dtw.3	O94826	OTTHUMG00000159065	ENST00000284320.5:c.577C>T	3.37:g.100105110G>A	ENSP00000284320:p.Arg193Cys	Somatic		Capture	Illumina HiSeq	Phase_I	101587800	NM_014820	D3DN48	Missense_Mutation	SNP	ENST00000284320.5	37	CCDS33807.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	G	23.8	4.456649	0.84317	.	.	ENSG00000154174	ENST00000284320;ENST00000544924	T	0.76448	-1.02	6.07	6.07	0.98685	Tetratricopeptide-like helical (1);Tetratricopeptide repeat-containing (1);	0.000000	0.85682	D	0.000000	D	0.90469	0.7015	M	0.87269	2.87	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.90759	0.4663	10	0.87932	D	0	-9.6723	20.6593	0.99626	0.0:0.0:1.0:0.0	rs9833995;rs9833995	193	O94826	TOM70_HUMAN	C	193;86	ENSP00000284320:R193C	ENSP00000284320:R193C	R	-	1	0	TOMM70A	101587800	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	3.785000	0.55424	2.885000	0.99019	0.655000	0.94253	CGT		0.323	TOMM70A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353141.2		
LNP1	348801	broad.mit.edu	37	3	100174741	100174741	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr3:100174741G>T	ENST00000383693.3	+	4	1788	c.508G>T	c.(508-510)Gct>Tct	p.A170S	LNP1_ENST00000489752.1_Missense_Mutation_p.A183S	NM_001085451.1	NP_001078920.1	A1A4G5	LNP1_HUMAN	leukemia NUP98 fusion partner 1	170								p.A170S(1)		cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(1)	6						AGCACACATGGCTCCCCTGTT	0.428																																					p.A170S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G508T	3						.						126.0	127.0	127.0					3																	100174741		1883	4109	5992	101657431	SO:0001583	missense	348801	exon4				CCDS43120.1	3q12.2	2014-05-12			ENSG00000206535	ENSG00000206535			28014	protein-coding gene	gene with protein product						16467868	Standard	NM_001085451		Approved	NP3	uc003dtx.4	A1A4G5	OTTHUMG00000159082	ENST00000383693.3:c.508G>T	3.37:g.100174741G>T	ENSP00000373191:p.Ala170Ser	Somatic		Capture	Illumina HiSeq	Phase_I	101657431	NM_001085451	B7ZLT3	Missense_Mutation	SNP	ENST00000383693.3	37	CCDS43120.1	.	.	.	.	.	.	.	.	.	.	G	17.72	3.460099	0.63401	.	.	ENSG00000206535	ENST00000383693;ENST00000489752	.	.	.	5.54	-2.6	0.06190	.	0.976256	0.08378	N	0.955034	T	0.22475	0.0542	N	0.19112	0.55	0.09310	N	1	B	0.15141	0.012	B	0.16289	0.015	T	0.22765	-1.0207	9	0.22706	T	0.39	1.1396	5.1484	0.14996	0.1465:0.3:0.4605:0.0931	.	170	A1A4G5	LNP1_HUMAN	S	170;183	.	ENSP00000373191:A170S	A	+	1	0	LNP1	101657431	0.000000	0.05858	0.000000	0.03702	0.786000	0.44442	0.102000	0.15272	-0.564000	0.06070	0.655000	0.94253	GCT		0.428	LNP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353232.1		
IRAK2	3656	broad.mit.edu	37	3	10251350	10251350	+	Missense_Mutation	SNP	G	G	A	rs141312230		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr3:10251350G>A	ENST00000256458.4	+	4	592	c.502G>A	c.(502-504)Gac>Aac	p.D168N		NM_001570.3	NP_001561.3	O43187	IRAK2_HUMAN	interleukin-1 receptor-associated kinase 2	168					activation of MAPK activity (GO:0000187)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|interleukin-1-mediated signaling pathway (GO:0070498)|JNK cascade (GO:0007254)|lipopolysaccharide-mediated signaling pathway (GO:0031663)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|protein phosphorylation (GO:0006468)|regulation of cytokine-mediated signaling pathway (GO:0001959)|response to interleukin-1 (GO:0070555)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytosol (GO:0005829)|endosome membrane (GO:0010008)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|protein kinase activity (GO:0004672)	p.D168N(2)		breast(4)|large_intestine(8)|lung(11)|prostate(1)|stomach(1)	25						CTTGAGAAGCGACCTCCCCAC	0.567													G|||	1	0.000199681	0.0	0.0	5008	,	,		15668	0.001		0.0	False		,,,				2504	0.0				p.D168N												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G502A	3						.	G	ASN/ASP	0,4406		0,0,2203	134.0	136.0	135.0		502	-8.6	0.0	3	dbSNP_134	135	2,8598	2.2+/-6.3	0,2,4298	no	missense	IRAK2	NM_001570.3	23	0,2,6501	AA,AG,GG		0.0233,0.0,0.0154	benign	168/626	10251350	2,13004	2203	4300	6503	10226350	SO:0001583	missense	3656	exon4			AF026273	CCDS33697.1	3p25.2	2008-08-18			ENSG00000134070	ENSG00000134070			6113	protein-coding gene	gene with protein product		603304				9374458	Standard	XR_245126		Approved		uc003bve.1	O43187	OTTHUMG00000155358	ENST00000256458.4:c.502G>A	3.37:g.10251350G>A	ENSP00000256458:p.Asp168Asn	Somatic		Capture	Illumina HiSeq	Phase_I	10226350	NM_001570	B4DQZ6|Q08AG6|Q5K546	Missense_Mutation	SNP	ENST00000256458.4	37	CCDS33697.1	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	G	0.918	-0.716808	0.03206	0.0	2.33E-4	ENSG00000134070	ENST00000256458	T	0.51574	0.7	4.32	-8.64	0.00874	.	1.689760	0.03581	N	0.230196	T	0.21718	0.0523	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.17471	-1.0368	10	0.12766	T	0.61	-0.0133	7.8253	0.29311	0.5086:0.2807:0.2107:0.0	.	168	O43187	IRAK2_HUMAN	N	168	ENSP00000256458:D168N	ENSP00000256458:D168N	D	+	1	0	IRAK2	10226350	0.000000	0.05858	0.000000	0.03702	0.018000	0.09664	-2.358000	0.01085	-3.273000	0.00199	-2.236000	0.00289	GAC		0.567	IRAK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339623.1		
ABI3BP	25890	broad.mit.edu	37	3	100566448	100566448	+	Missense_Mutation	SNP	G	G	A	rs372669157		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr3:100566448G>A	ENST00000284322.5	-	17	1629	c.1520C>T	c.(1519-1521)cCg>cTg	p.P507L	ABI3BP_ENST00000495063.1_Missense_Mutation_p.P556L|ABI3BP_ENST00000383691.4_5'Flank|ABI3BP_ENST00000471714.1_Missense_Mutation_p.P556L	NM_015429.3	NP_056244.2	Q7Z7G0	TARSH_HUMAN	ABI family, member 3 (NESH) binding protein	507	Pro-rich.				extracellular matrix organization (GO:0030198)|positive regulation of cell-substrate adhesion (GO:0010811)	extracellular space (GO:0005615)|interstitial matrix (GO:0005614)	heparin binding (GO:0008201)	p.P556Q(1)|p.P508L(1)|p.P508Q(1)		central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(13)|lung(18)|ovary(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	50						ATTATTACCCGGTGTTGTCCA	0.373																																					p.P507L												.	.	3	Substitution - Missense(3)	lung(2)|large_intestine(1)	c.C1520T	3						.	G	LEU/PRO	0,3706		0,0,1853	277.0	265.0	269.0		1520	3.7	0.4	3		269	1,8187		0,1,4093	no	missense	ABI3BP	NM_015429.3	98	0,1,5946	AA,AG,GG		0.0122,0.0,0.0084	benign	507/1076	100566448	1,11893	1853	4094	5947	102049138	SO:0001583	missense	25890	exon17			AB056106	CCDS46880.1	3q12.2	2013-02-11	2008-09-12		ENSG00000154175	ENSG00000154175		"""Fibronectin type III domain containing"""	17265	protein-coding gene	gene with protein product	"""target of Nesh-SH3"""	606279				11501947	Standard	NM_015429		Approved	NESHBP, DKFZP586L2024, TARSH	uc003dun.3	Q7Z7G0	OTTHUMG00000159094	ENST00000284322.5:c.1520C>T	3.37:g.100566448G>A	ENSP00000284322:p.Pro507Leu	Somatic		Capture	Illumina HiSeq	Phase_I	102049138	NM_015429	B3KSL4|Q6ZW20|Q6ZW22|Q9C082|Q9UFI6	Missense_Mutation	SNP	ENST00000284322.5	37	CCDS46880.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	9.059|9.059	0.993986|0.993986	0.19043|0.19043	0.0|0.0	1.22E-4|1.22E-4	ENSG00000154175|ENSG00000154175	ENST00000471714;ENST00000284322;ENST00000495063|ENST00000528490;ENST00000533855	T;T;T|.	0.55760|.	0.5;0.5;0.5|.	4.88|4.88	3.73|3.73	0.42828|0.42828	.|.	1.185830|.	0.06378|.	N|.	0.714707|.	T|T	0.18882|0.18882	0.0453|0.0453	N|N	0.02315|0.02315	-0.6|-0.6	0.80722|0.80722	D|D	1|1	B;B|.	0.02656|.	0.0;0.0|.	B;B|.	0.01281|.	0.0;0.0|.	T|T	0.04017|0.04017	-1.0984|-1.0984	10|5	0.28530|.	T|.	0.3|.	0.2462|0.2462	4.3662|4.3662	0.11225|0.11225	0.7264:0.0:0.0995:0.1741|0.7264:0.0:0.0995:0.1741	.|.	556;507|.	Q5JPC9;Q7Z7G0|.	.;TARSH_HUMAN|.	L|W	556;507;556|24;185	ENSP00000420524:P556L;ENSP00000284322:P507L;ENSP00000433993:P556L|.	ENSP00000284322:P507L|.	P|R	-|-	2|1	0|2	ABI3BP|ABI3BP	102049138|102049138	0.988000|0.988000	0.35896|0.35896	0.362000|0.362000	0.25862|0.25862	0.858000|0.858000	0.48976|0.48976	1.440000|1.440000	0.35024|0.35024	0.976000|0.976000	0.38417|0.38417	-0.469000|-0.469000	0.05056|0.05056	CCG|CGG		0.373	ABI3BP-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000353260.1		
CCDC80	151887	broad.mit.edu	37	3	112324501	112324501	+	Silent	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr3:112324501G>A	ENST00000206423.3	-	8	3569	c.2616C>T	c.(2614-2616)gaC>gaT	p.D872D	CCDC80_ENST00000439685.2_Silent_p.D872D	NM_199511.1|NM_199512.1	NP_955805.1|NP_955806.1	Q76M96	CCD80_HUMAN	coiled-coil domain containing 80	872					extracellular matrix organization (GO:0030198)|positive regulation of cell-substrate adhesion (GO:0010811)	basement membrane (GO:0005604)|interstitial matrix (GO:0005614)	heparin binding (GO:0008201)	p.D872D(1)		breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(13)|liver(1)|lung(21)|ovary(3)|pancreas(2)|prostate(4)	51						TGACATTTCCGTCTTTTCCGA	0.448																																					p.D872D												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C2616T	3						.						110.0	96.0	101.0					3																	112324501		2203	4300	6503	113807191	SO:0001819	synonymous_variant	151887	exon8			AY333429	CCDS2968.1	3q13.2	2010-12-24			ENSG00000091986	ENSG00000091986			30649	protein-coding gene	gene with protein product	"""steroid sensitive gene 1"""	608298				15325258, 18178152	Standard	XM_005247135		Approved	URB, SSG1, DRO1	uc003dzf.3	Q76M96	OTTHUMG00000159265	ENST00000206423.3:c.2616C>T	3.37:g.112324501G>A		Somatic		Capture	Illumina HiSeq	Phase_I	113807191	NM_199511	D3DN67|Q5PR20|Q6GPG9|Q8IVT6|Q8NBV1|Q8NHY8	Silent	SNP	ENST00000206423.3	37	CCDS2968.1	.	.	.	.	.	.	.	.	.	.	G	7.390	0.630548	0.14322	.	.	ENSG00000091986	ENST00000461431	.	.	.	5.83	-1.48	0.08745	.	.	.	.	.	T	0.58509	0.2127	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.56372	-0.7990	4	.	.	.	-22.8347	12.1586	0.54091	0.5281:0.0:0.4719:0.0	.	.	.	.	W	243	.	.	R	-	1	2	CCDC80	113807191	0.473000	0.25878	0.997000	0.53966	0.994000	0.84299	-0.058000	0.11750	-0.178000	0.10672	-0.225000	0.12378	CGG		0.448	CCDC80-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354219.1	NM_199511	
CCDC80	151887	broad.mit.edu	37	3	112326062	112326062	+	Nonsense_Mutation	SNP	C	C	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr3:112326062C>A	ENST00000206423.3	-	7	3420	c.2467G>T	c.(2467-2469)Gag>Tag	p.E823*	CCDC80_ENST00000439685.2_Nonsense_Mutation_p.E823*	NM_199511.1|NM_199512.1	NP_955805.1|NP_955806.1	Q76M96	CCD80_HUMAN	coiled-coil domain containing 80	823					extracellular matrix organization (GO:0030198)|positive regulation of cell-substrate adhesion (GO:0010811)	basement membrane (GO:0005604)|interstitial matrix (GO:0005614)	heparin binding (GO:0008201)	p.E823*(1)		breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(13)|liver(1)|lung(21)|ovary(3)|pancreas(2)|prostate(4)	51						CCAACTTCCTCTCCAACGCCT	0.358																																					p.E823X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.G2467T	3						.						110.0	100.0	103.0					3																	112326062		2203	4300	6503	113808752	SO:0001587	stop_gained	151887	exon7			AY333429	CCDS2968.1	3q13.2	2010-12-24			ENSG00000091986	ENSG00000091986			30649	protein-coding gene	gene with protein product	"""steroid sensitive gene 1"""	608298				15325258, 18178152	Standard	XM_005247135		Approved	URB, SSG1, DRO1	uc003dzf.3	Q76M96	OTTHUMG00000159265	ENST00000206423.3:c.2467G>T	3.37:g.112326062C>A	ENSP00000206423:p.Glu823*	Somatic		Capture	Illumina HiSeq	Phase_I	113808752	NM_199511	D3DN67|Q5PR20|Q6GPG9|Q8IVT6|Q8NBV1|Q8NHY8	Nonsense_Mutation	SNP	ENST00000206423.3	37	CCDS2968.1	.	.	.	.	.	.	.	.	.	.	C	32	5.107403	0.94292	.	.	ENSG00000091986	ENST00000206423;ENST00000439685;ENST00000479368	.	.	.	5.76	5.76	0.90799	.	0.312106	0.34245	N	0.004134	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.09084	T	0.74	-16.1107	19.976	0.97309	0.0:1.0:0.0:0.0	.	.	.	.	X	823;823;101	.	ENSP00000206423:E823X	E	-	1	0	CCDC80	113808752	0.965000	0.33210	0.999000	0.59377	0.894000	0.52154	2.011000	0.40922	2.713000	0.92767	0.655000	0.94253	GAG		0.358	CCDC80-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354219.1	NM_199511	
CCDC80	151887	broad.mit.edu	37	3	112358139	112358139	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr3:112358139C>T	ENST00000206423.3	-	2	1567	c.614G>A	c.(613-615)aGc>aAc	p.S205N	CCDC80_ENST00000439685.2_Missense_Mutation_p.S205N|CCDC80_ENST00000475181.1_5'Flank	NM_199511.1|NM_199512.1	NP_955805.1|NP_955806.1	Q76M96	CCD80_HUMAN	coiled-coil domain containing 80	205					extracellular matrix organization (GO:0030198)|positive regulation of cell-substrate adhesion (GO:0010811)	basement membrane (GO:0005604)|interstitial matrix (GO:0005614)	heparin binding (GO:0008201)	p.S205N(1)		breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(13)|liver(1)|lung(21)|ovary(3)|pancreas(2)|prostate(4)	51						CTGGCCCTCGCTGGTGATCCT	0.577																																					p.S205N												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G614A	3						.						101.0	86.0	91.0					3																	112358139		2203	4300	6503	113840829	SO:0001583	missense	151887	exon2			AY333429	CCDS2968.1	3q13.2	2010-12-24			ENSG00000091986	ENSG00000091986			30649	protein-coding gene	gene with protein product	"""steroid sensitive gene 1"""	608298				15325258, 18178152	Standard	XM_005247135		Approved	URB, SSG1, DRO1	uc003dzf.3	Q76M96	OTTHUMG00000159265	ENST00000206423.3:c.614G>A	3.37:g.112358139C>T	ENSP00000206423:p.Ser205Asn	Somatic		Capture	Illumina HiSeq	Phase_I	113840829	NM_199511	D3DN67|Q5PR20|Q6GPG9|Q8IVT6|Q8NBV1|Q8NHY8	Missense_Mutation	SNP	ENST00000206423.3	37	CCDS2968.1	.	.	.	.	.	.	.	.	.	.	C	7.352	0.623077	0.14193	.	.	ENSG00000091986	ENST00000206423;ENST00000439685	T;T	0.40225	1.04;1.04	5.55	1.11	0.20524	.	0.267246	0.42172	N	0.000752	T	0.14056	0.0340	N	0.02011	-0.69	0.21627	N	0.999611	B;B;B	0.06786	0.001;0.001;0.001	B;B;B	0.08055	0.001;0.003;0.002	T	0.20371	-1.0277	10	0.25106	T	0.35	-11.3913	6.0833	0.19952	0.0:0.3512:0.3235:0.3253	.	216;205;205	Q76M96-2;A3KC71;Q76M96	.;.;CCD80_HUMAN	N	205	ENSP00000206423:S205N;ENSP00000411814:S205N	ENSP00000206423:S205N	S	-	2	0	CCDC80	113840829	0.063000	0.20901	0.906000	0.35671	0.927000	0.56198	0.332000	0.19751	0.282000	0.22254	0.650000	0.86243	AGC		0.577	CCDC80-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354219.1	NM_199511	
VGLL4	9686	broad.mit.edu	37	3	11744445	11744445	+	Splice_Site	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr3:11744445G>A	ENST00000273038.3	-	2	429	c.64C>T	c.(64-66)Cgc>Tgc	p.R22C	VGLL4_ENST00000404339.1_5'UTR	NM_001284391.1|NM_014667.2	NP_001271320.1|NP_055482.2	Q14135	VGLL4_HUMAN	vestigial-like family member 4	22					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)		p.R22C(1)		NS(1)|endometrium(1)|large_intestine(1)|ovary(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	10				LUSC - Lung squamous cell carcinoma(1;0.089)|Lung(1;0.111)		CCTCACTTACGTTTTTCGTCA	0.418																																					p.R22C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C64T	3						.						62.0	62.0	62.0					3																	11744445		2203	4300	6503	11719445	SO:0001630	splice_region_variant	9686	exon2			D50911	CCDS2606.1, CCDS46754.1, CCDS46755.1, CCDS46756.1, CCDS68342.1, CCDS68343.1	3p25.2	2014-03-03	2014-03-03		ENSG00000144560	ENSG00000144560			28966	protein-coding gene	gene with protein product			"""vestigial like 4 (Drosophila)"""			8590280, 15140898	Standard	NM_001284390		Approved	KIAA0121	uc010hdx.1	Q14135	OTTHUMG00000129739	ENST00000273038.3:c.64+1C>T	3.37:g.11744445G>A		Somatic		Capture	Illumina HiSeq	Phase_I	11719445	NM_014667	B4DTS7|J3KN68|Q7L5V0|Q9BQ78	Missense_Mutation	SNP	ENST00000273038.3	37	CCDS2606.1	.	.	.	.	.	.	.	.	.	.	G	13.18	2.158946	0.38119	.	.	ENSG00000144560	ENST00000273038;ENST00000445411;ENST00000418000;ENST00000417206;ENST00000419541	T;T;T;T;T	0.43688	0.94;0.94;0.94;0.94;0.94	5.28	5.28	0.74379	.	0.127189	0.33753	N	0.004593	T	0.49115	0.1538	N	0.22421	0.69	0.80722	D	1	D	0.89917	1.0	D	0.76575	0.988	T	0.39057	-0.9632	9	.	.	.	.	14.7724	0.69691	0.0:0.0:1.0:0.0	.	22	Q14135	VGLL4_HUMAN	C	22	ENSP00000273038:R22C;ENSP00000412923:R22C;ENSP00000394439:R22C;ENSP00000391932:R22C;ENSP00000395557:R22C	.	R	-	1	0	VGLL4	11719445	1.000000	0.71417	1.000000	0.80357	0.841000	0.47740	6.827000	0.75303	2.635000	0.89317	0.462000	0.41574	CGC		0.418	VGLL4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000251950.2	NM_014667	Missense_Mutation
KIAA1407	57577	broad.mit.edu	37	3	113697176	113697176	+	Silent	SNP	G	G	A	rs145896589	byFrequency	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr3:113697176G>A	ENST00000295878.3	-	16	2609	c.2463C>T	c.(2461-2463)taC>taT	p.Y821Y	KIAA1407_ENST00000545063.1_3'UTR	NM_020817.1	NP_065868.1	Q8NCU4	K1407_HUMAN	KIAA1407	821								p.Y821Y(1)		endometrium(9)|large_intestine(7)|lung(19)|ovary(2)|pancreas(1)|prostate(1)|urinary_tract(1)	40						GATCAATCACGTACTGGGGAT	0.353													G|||	2	0.000399361	0.0	0.0	5008	,	,		20877	0.0		0.0	False		,,,				2504	0.002				p.Y821Y												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C2463T	3						.	G		1,4405	2.1+/-5.4	0,1,2202	55.0	55.0	55.0		2463	-0.9	0.0	3	dbSNP_134	55	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	KIAA1407	NM_020817.1		0,2,6501	AA,AG,GG		0.0116,0.0227,0.0154		821/937	113697176	2,13004	2203	4300	6503	115179866	SO:0001819	synonymous_variant	57577	exon16			AF509494	CCDS2977.1	3q13.31	2005-01-10			ENSG00000163617	ENSG00000163617			29272	protein-coding gene	gene with protein product						10718198	Standard	NM_020817		Approved		uc003eax.3	Q8NCU4	OTTHUMG00000159337	ENST00000295878.3:c.2463C>T	3.37:g.113697176G>A		Somatic		Capture	Illumina HiSeq	Phase_I	115179866	NM_020817	B4DYL1|Q9P2E0	Silent	SNP	ENST00000295878.3	37	CCDS2977.1																																																																																				0.353	KIAA1407-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354724.2	NM_020817	
TIMP4	7079	broad.mit.edu	37	3	12195178	12195178	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr3:12195178G>A	ENST00000287814.4	-	5	1022	c.512C>T	c.(511-513)tCg>tTg	p.S171L	SYN2_ENST00000432424.2_RNA	NM_003256.3	NP_003247.1	Q99727	TIMP4_HUMAN	TIMP metallopeptidase inhibitor 4	171					central nervous system development (GO:0007417)|negative regulation of endopeptidase activity (GO:0010951)|ovulation cycle (GO:0042698)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to lipopolysaccharide (GO:0032496)|response to peptide hormone (GO:0043434)	extracellular space (GO:0005615)|sarcomere (GO:0030017)	metal ion binding (GO:0046872)|metalloendopeptidase inhibitor activity (GO:0008191)	p.S171L(1)		central_nervous_system(1)|kidney(1)|large_intestine(2)|lung(5)|skin(1)|upper_aerodigestive_tract(1)	11						GTTAGGGGCCGAGATGGTACA	0.498																																					p.S171L	Melanoma(199;1446 2144 30617 38794 51714)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C512T	3						.						134.0	125.0	128.0					3																	12195178		2203	4300	6503	12170178	SO:0001583	missense	7079	exon5			U76456	CCDS2608.1	3p25	2005-10-31	2005-08-08		ENSG00000157150	ENSG00000157150			11823	protein-coding gene	gene with protein product		601915	"""tissue inhibitor of metalloproteinase 4"""			8939999, 9693046	Standard	NM_003256		Approved		uc003bwo.3	Q99727	OTTHUMG00000129763	ENST00000287814.4:c.512C>T	3.37:g.12195178G>A	ENSP00000287814:p.Ser171Leu	Somatic		Capture	Illumina HiSeq	Phase_I	12170178	NM_003256	B2R7K6	Missense_Mutation	SNP	ENST00000287814.4	37	CCDS2608.1	.	.	.	.	.	.	.	.	.	.	G	12.96	2.093989	0.36952	.	.	ENSG00000157150	ENST00000287814	D	0.93604	-3.25	4.88	4.01	0.46588	Tissue inhibitor of metalloproteinases-like, OB-fold (1);	0.292508	0.31685	N	0.007234	D	0.89322	0.6682	M	0.68952	2.095	0.33561	D	0.597301	P	0.37330	0.59	B	0.27796	0.083	D	0.90575	0.4525	10	0.46703	T	0.11	.	8.5834	0.33644	0.0765:0.0:0.7732:0.1503	.	171	Q99727	TIMP4_HUMAN	L	171	ENSP00000287814:S171L	ENSP00000287814:S171L	S	-	2	0	TIMP4	12170178	1.000000	0.71417	0.926000	0.36857	0.337000	0.28794	5.328000	0.65887	1.296000	0.44742	-0.333000	0.08304	TCG		0.498	TIMP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251978.1	NM_003256	
PLA1A	51365	broad.mit.edu	37	3	119336940	119336940	+	Silent	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr3:119336940C>T	ENST00000273371.4	+	7	901	c.829C>T	c.(829-831)Ctg>Ttg	p.L277L	PLA1A_ENST00000488919.1_Silent_p.L104L|PLA1A_ENST00000495992.1_Silent_p.L261L|PLA1A_ENST00000494440.1_Silent_p.L261L	NM_015900.3	NP_056984.1	Q53H76	PLA1A_HUMAN	phospholipase A1 member A	277					lipid catabolic process (GO:0016042)|lipid metabolic process (GO:0006629)|phosphatidylserine metabolic process (GO:0006658)	extracellular vesicular exosome (GO:0070062)	phosphatidylcholine 1-acylhydrolase activity (GO:0008970)	p.L277L(1)		NS(1)|central_nervous_system(1)|endometrium(2)|large_intestine(6)|lung(16)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	30						TTCCTGTCCACTGATGGCCTT	0.488																																					p.L277L												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C829T	3						.						296.0	286.0	290.0					3																	119336940		2203	4300	6503	120819630	SO:0001819	synonymous_variant	51365	exon7			AF035268	CCDS2991.1, CCDS56268.1, CCDS56269.1	3q13.13-q13.2	2002-11-28			ENSG00000144837	ENSG00000144837			17661	protein-coding gene	gene with protein product		607460				10196188	Standard	NM_015900		Approved	ps-PLA1	uc003ecu.3	Q53H76	OTTHUMG00000159425	ENST00000273371.4:c.829C>T	3.37:g.119336940C>T		Somatic		Capture	Illumina HiSeq	Phase_I	120819630	NM_015900	B2R8V2|B4DXA2|O95991|Q86WX6|Q9UPD2	Silent	SNP	ENST00000273371.4	37	CCDS2991.1																																																																																				0.488	PLA1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355252.2		
KPNA1	3836	broad.mit.edu	37	3	122168454	122168454	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr3:122168454G>A	ENST00000344337.6	-	9	1060	c.884C>T	c.(883-885)gCg>gTg	p.A295V	KPNA1_ENST00000466923.1_5'UTR	NM_002264.3	NP_002255.3	P52294	IMA5_HUMAN	karyopherin alpha 1 (importin alpha 5)	295	Binding to RAG1.				apoptotic DNA fragmentation (GO:0006309)|apoptotic process (GO:0006915)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cytokine-mediated signaling pathway (GO:0019221)|intracellular transport of virus (GO:0075733)|NLS-bearing protein import into nucleus (GO:0006607)|positive regulation of protein import into nucleus (GO:0042307)|regulation of DNA recombination (GO:0000018)|viral life cycle (GO:0019058)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendrite (GO:0030425)|nuclear pore (GO:0005643)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	nuclear localization sequence binding (GO:0008139)|protein transporter activity (GO:0008565)	p.A295V(1)		NS(1)|breast(1)|cervix(2)|endometrium(2)|kidney(1)|large_intestine(7)|lung(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	21				GBM - Glioblastoma multiforme(114;0.0898)		ACATACTCCCGCATCGATGAC	0.443																																					p.A295V	Melanoma(12;340 801 11196 19797)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C884T	3						.						87.0	80.0	83.0					3																	122168454		2203	4300	6503	123651144	SO:0001583	missense	3836	exon9			S75295	CCDS3013.1	3q21	2013-02-14			ENSG00000114030	ENSG00000114030		"""Importins"", ""Armadillo repeat containing"""	6394	protein-coding gene	gene with protein product		600686				8052633	Standard	NM_002264		Approved	SRP1, RCH2, NPI-1, IPOA5	uc003efe.2	P52294	OTTHUMG00000159487	ENST00000344337.6:c.884C>T	3.37:g.122168454G>A	ENSP00000343701:p.Ala295Val	Somatic		Capture	Illumina HiSeq	Phase_I	123651144	NM_002264	D3DN93|Q6IBQ9|Q9BQ56	Missense_Mutation	SNP	ENST00000344337.6	37	CCDS3013.1	.	.	.	.	.	.	.	.	.	.	G	19.48	3.835619	0.71373	.	.	ENSG00000114030	ENST00000344337;ENST00000465882	T;T	0.71698	-0.59;-0.59	5.1	5.1	0.69264	Armadillo-like helical (1);Armadillo-type fold (1);	0.054505	0.85682	D	0.000000	T	0.64382	0.2593	L	0.58925	1.835	0.80722	D	1	P	0.40197	0.706	B	0.28139	0.086	T	0.70392	-0.4884	10	0.51188	T	0.08	-14.792	17.703	0.88301	0.0:0.0:1.0:0.0	.	295	P52294	IMA1_HUMAN	V	295	ENSP00000343701:A295V;ENSP00000419890:A295V	ENSP00000343701:A295V	A	-	2	0	KPNA1	123651144	1.000000	0.71417	1.000000	0.80357	0.849000	0.48306	9.263000	0.95617	2.644000	0.89710	0.563000	0.77884	GCG		0.443	KPNA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355740.1	NM_002264	
MYLK	4638	broad.mit.edu	37	3	123452975	123452975	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr3:123452975C>T	ENST00000475616.1	-	7	867	c.868G>A	c.(868-870)Gct>Act	p.A290T	MYLK_ENST00000360304.3_Missense_Mutation_p.A290T|MYLK_ENST00000360772.3_Missense_Mutation_p.A290T|MYLK_ENST00000346322.5_Missense_Mutation_p.A290T|MYLK_ENST00000359169.1_Missense_Mutation_p.A290T			Q15746	MYLK_HUMAN	myosin light chain kinase	290					actin filament organization (GO:0007015)|aorta smooth muscle tissue morphogenesis (GO:0060414)|bleb assembly (GO:0032060)|cellular hypotonic response (GO:0071476)|muscle contraction (GO:0006936)|positive regulation of calcium ion transport (GO:0051928)|positive regulation of cell migration (GO:0030335)|positive regulation of wound healing (GO:0090303)|protein phosphorylation (GO:0006468)|smooth muscle contraction (GO:0006939)|tonic smooth muscle contraction (GO:0014820)	cell-cell junction (GO:0005911)|cleavage furrow (GO:0032154)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|lamellipodium (GO:0030027)|stress fiber (GO:0001725)	ATP binding (GO:0005524)|calmodulin-dependent protein kinase activity (GO:0004683)|metal ion binding (GO:0046872)|myosin light chain kinase activity (GO:0004687)	p.A290T(1)		NS(2)|breast(4)|central_nervous_system(1)|endometrium(24)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(17)|lung(37)|ovary(7)|prostate(3)|skin(5)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	113		Lung NSC(201;0.0496)		GBM - Glioblastoma multiforme(114;0.0736)		TTGGCTGCAGCCTCCAGACTG	0.547																																					p.A290T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G868A	3						.						66.0	63.0	64.0					3																	123452975		2203	4300	6503	124935665	SO:0001583	missense	4638	exon10			X85337	CCDS3023.1, CCDS43141.1, CCDS46896.1, CCDS46897.1, CCDS58849.1	3q21	2013-02-11	2008-01-23		ENSG00000065534	ENSG00000065534	2.7.11.18	"""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	7590	protein-coding gene	gene with protein product	"""smooth muscle myosin light chain kinase"""	600922	"""myosin, light polypeptide kinase"""			8575746	Standard	NM_053026		Approved	MLCK, smMLCK, MYLK1, MLCK1	uc003ego.3	Q15746	OTTHUMG00000141304	ENST00000475616.1:c.868G>A	3.37:g.123452975C>T	ENSP00000418335:p.Ala290Thr	Somatic		Capture	Illumina HiSeq	Phase_I	124935665	NM_053025	B4DUE3|D3DN97|O95796|O95797|O95798|O95799|Q14844|Q16794|Q17S15|Q3ZCP9|Q5MY99|Q5MYA0|Q6P2N0|Q7Z4J0|Q9C0L5|Q9UBG5|Q9UBY6|Q9UIT9	Missense_Mutation	SNP	ENST00000475616.1	37	CCDS46896.1	.	.	.	.	.	.	.	.	.	.	C	3.115	-0.181853	0.06340	.	.	ENSG00000065534	ENST00000360772;ENST00000360304;ENST00000359169;ENST00000346322;ENST00000475616	T;T;T;T;T	0.65732	-0.17;-0.12;-0.17;-0.09;-0.12	5.43	-3.53	0.04667	.	.	.	.	.	T	0.32971	0.0847	N	0.14661	0.345	0.09310	N	1	B;B;B;B;B	0.02656	0.0;0.0;0.0;0.0;0.0	B;B;B;B;B	0.06405	0.002;0.0;0.002;0.0;0.001	T	0.21965	-1.0230	9	0.10377	T	0.69	.	3.4156	0.07375	0.387:0.2451:0.0:0.3679	.	290;290;290;290;290	Q15746-6;Q15746-4;Q15746-3;Q15746-2;Q15746	.;.;.;.;MYLK_HUMAN	T	290	ENSP00000354004:A290T;ENSP00000353452:A290T;ENSP00000352088:A290T;ENSP00000320622:A290T;ENSP00000418335:A290T	ENSP00000320622:A290T	A	-	1	0	MYLK	124935665	0.000000	0.05858	0.000000	0.03702	0.160000	0.22226	-0.292000	0.08332	-0.792000	0.04480	-0.302000	0.09304	GCT		0.547	MYLK-004	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356464.1	NM_053025	
MUC13	56667	broad.mit.edu	37	3	124629311	124629311	+	Missense_Mutation	SNP	C	C	T	rs142060793		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr3:124629311C>T	ENST00000311075.3	-	10	1323	c.1285G>A	c.(1285-1287)Gct>Act	p.A429T		NM_033049.3	NP_149038	Q9H3R2	MUC13_HUMAN	mucin 13, cell surface associated	430					cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	apical plasma membrane (GO:0016324)|cytosol (GO:0005829)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)	protein homodimerization activity (GO:0042803)	p.A429T(1)		breast(1)|central_nervous_system(1)|cervix(1)|kidney(1)|large_intestine(6)|lung(5)|prostate(1)|skin(1)|stomach(1)	18						ACAATGCCAGCGATGGTGCCC	0.408																																					p.A429T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1285A	3						.	C	THR/ALA	1,4405	2.1+/-5.4	0,1,2202	82.0	78.0	79.0		1285	3.4	0.0	3	dbSNP_134	79	0,8600		0,0,4300	no	missense	MUC13	NM_033049.3	58	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	probably-damaging	429/512	124629311	1,13005	2203	4300	6503	126112001	SO:0001583	missense	56667	exon10			AF286113		3q21.2	2007-01-17	2006-03-14		ENSG00000173702	ENSG00000173702		"""Mucins"""	7511	protein-coding gene	gene with protein product		612181	"""down-regulated in colon cancer 1"", ""mucin 13, epithelial transmembrane"""	DRCC1		11278439	Standard	NM_033049		Approved		uc003ehq.2	Q9H3R2	OTTHUMG00000159484	ENST00000311075.3:c.1285G>A	3.37:g.124629311C>T	ENSP00000312235:p.Ala429Thr	Somatic		Capture	Illumina HiSeq	Phase_I	126112001	NM_033049	Q6UWD9|Q9NXT5	Missense_Mutation	SNP	ENST00000311075.3	37		.	.	.	.	.	.	.	.	.	.	C	17.08	3.297839	0.60086	2.27E-4	0.0	ENSG00000173702	ENST00000311075	T	0.15718	2.4	5.19	3.37	0.38596	.	0.590904	0.15394	N	0.264656	T	0.27454	0.0674	L	0.55481	1.735	0.09310	N	1	D	0.76494	0.999	P	0.58970	0.849	T	0.05835	-1.0861	10	0.45353	T	0.12	-26.3194	6.3853	0.21558	0.1812:0.7274:0.0:0.0914	.	429	Q9H3R2	MUC13_HUMAN	T	429	ENSP00000312235:A429T	ENSP00000312235:A429T	A	-	1	0	MUC13	126112001	0.007000	0.16637	0.003000	0.11579	0.014000	0.08584	1.178000	0.31981	0.864000	0.35578	0.563000	0.77884	GCT		0.408	MUC13-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000355714.1	NM_033049	
ALDH1L1	10840	broad.mit.edu	37	3	125824614	125824614	+	Missense_Mutation	SNP	C	C	T	rs200290145		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr3:125824614C>T	ENST00000393434.2	-	22	2957	c.2608G>A	c.(2608-2610)Gct>Act	p.A870T	ALDH1L1_ENST00000472186.1_Missense_Mutation_p.A870T|ALDH1L1_ENST00000273450.3_Missense_Mutation_p.A880T|ALDH1L1_ENST00000452905.2_Missense_Mutation_p.A769T|ALDH1L1_ENST00000393431.2_3'UTR|ALDH1L1-AS1_ENST00000512384.1_RNA	NM_012190.3	NP_036322.2	O75891	AL1L1_HUMAN	aldehyde dehydrogenase 1 family, member L1	870	Aldehyde dehydrogenase.				10-formyltetrahydrofolate catabolic process (GO:0009258)|biosynthetic process (GO:0009058)|one-carbon metabolic process (GO:0006730)	extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	catalytic activity (GO:0003824)|formyltetrahydrofolate dehydrogenase activity (GO:0016155)|hydroxymethyl-, formyl- and related transferase activity (GO:0016742)|methyltransferase activity (GO:0008168)|oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor (GO:0016620)	p.A870T(2)		NS(1)|breast(2)|central_nervous_system(3)|endometrium(2)|kidney(5)|large_intestine(10)|lung(22)|ovary(3)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	52				GBM - Glioblastoma multiforme(114;0.0462)	Tetrahydrofolic acid(DB00116)	CCGAAGGGAGCGGCCACGTCG	0.493													C|||	1	0.000199681	0.0	0.0	5008	,	,		18443	0.001		0.0	False		,,,				2504	0.0				p.A870T												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G2608A	3						.						193.0	184.0	187.0					3																	125824614		2203	4300	6503	127307304	SO:0001583	missense	10840	exon22			AF052732	CCDS3034.1, CCDS58850.1, CCDS58851.1	3q21.2	2010-07-19		2005-01-27	ENSG00000144908	ENSG00000144908	1.5.1.6	"""Aldehyde dehydrogenases"""	3978	protein-coding gene	gene with protein product	"""cytosolic 10-formyltetrahydrofolate dehydrogenase"""	600249	"""formyltetrahydrofolate dehydrogenase"""	FTHFD			Standard	NM_012190		Approved	10-fTHF	uc031sbp.1	O75891	OTTHUMG00000125551	ENST00000393434.2:c.2608G>A	3.37:g.125824614C>T	ENSP00000377083:p.Ala870Thr	Somatic		Capture	Illumina HiSeq	Phase_I	127307304	NM_012190	B4DG36|E9PBX3|Q68CS1	Missense_Mutation	SNP	ENST00000393434.2	37	CCDS3034.1	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	C	19.67	3.871783	0.72180	.	.	ENSG00000144908	ENST00000273450;ENST00000472186;ENST00000452905;ENST00000393434	T;T;T;T	0.08634	3.07;3.07;3.07;3.07	4.53	4.53	0.55603	Aldehyde dehydrogenase domain (1);Aldehyde dehydrogenase, C-terminal (1);Aldehyde/histidinol dehydrogenase (1);	0.132430	0.49916	D	0.000126	T	0.21022	0.0506	L	0.45051	1.395	0.80722	D	1	D;D;D	0.89917	0.999;1.0;0.996	D;D;P	0.77004	0.973;0.989;0.905	T	0.00448	-1.1733	10	0.52906	T	0.07	.	14.7775	0.69740	0.0:1.0:0.0:0.0	.	769;405;870	E9PBX3;Q6ZV71;O75891	.;.;AL1L1_HUMAN	T	880;870;769;870	ENSP00000273450:A880T;ENSP00000420293:A870T;ENSP00000395881:A769T;ENSP00000377083:A870T	ENSP00000273450:A880T	A	-	1	0	ALDH1L1	127307304	0.859000	0.29813	0.813000	0.32504	0.875000	0.50365	1.695000	0.37763	2.329000	0.79093	0.591000	0.81541	GCT		0.493	ALDH1L1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354391.1	NM_012190	
ZXDC	79364	broad.mit.edu	37	3	126160629	126160629	+	Silent	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr3:126160629G>A	ENST00000389709.3	-	8	2426	c.2373C>T	c.(2371-2373)ggC>ggT	p.G791G		NM_025112.4	NP_079388.3	Q2QGD7	ZXDC_HUMAN	ZXD family zinc finger C	791	Interaction with CIITA.				positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	C2H2 zinc finger domain binding (GO:0070742)|LRR domain binding (GO:0030275)|metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.G791G(1)		endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(9)|ovary(1)	17				GBM - Glioblastoma multiforme(114;0.155)		GGACCTGGACGCCCTGCGCCC	0.672																																					p.G791G												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C2373T	3						.						31.0	38.0	36.0					3																	126160629		2097	4212	6309	127643319	SO:0001819	synonymous_variant	79364	exon8			AK023923	CCDS43145.1, CCDS43146.1	3q21.3	2014-02-12			ENSG00000070476	ENSG00000070476		"""Zinc fingers, C2H2-type"""	28160	protein-coding gene	gene with protein product		615746				8619474, 9110174	Standard	XM_005247757		Approved	MGC11349, FLJ13861	uc003eiv.3	Q2QGD7	OTTHUMG00000162754	ENST00000389709.3:c.2373C>T	3.37:g.126160629G>A		Somatic		Capture	Illumina HiSeq	Phase_I	127643319	NM_025112	C5J0H9|Q6DKI8|Q7L3L1|Q8NAU2	Silent	SNP	ENST00000389709.3	37	CCDS43145.1																																																																																				0.672	ZXDC-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000370327.2	NM_025112	
CAND2	23066	broad.mit.edu	37	3	12858669	12858669	+	Silent	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr3:12858669G>A	ENST00000456430.2	+	10	2279	c.2238G>A	c.(2236-2238)tcG>tcA	p.S746S	CAND2_ENST00000295989.5_Silent_p.S653S	NM_001162499.1	NP_001155971.1	O75155	CAND2_HUMAN	cullin-associated and neddylation-dissociated 2 (putative)	746					positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	intracellular (GO:0005622)|nucleus (GO:0005634)		p.S653S(1)		breast(3)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(10)|lung(8)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	37						TGCTGCGTTCGCCCCTGTTGC	0.647																																					p.S746S	GBM(43;676 868 1633 6395 37496)											.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G2238A	3						.						21.0	24.0	23.0					3																	12858669		2107	4243	6350	12833669	SO:0001819	synonymous_variant	23066	exon10				CCDS43053.1, CCDS54554.1	3p25.2	2008-02-05			ENSG00000144712	ENSG00000144712			30689	protein-coding gene	gene with protein product	"""TBP interacting protein"""	610403				9734811, 10441524	Standard	NM_012298		Approved	TIP120B, KIAA0667, Tp120b	uc003bxk.2	O75155	OTTHUMG00000155397	ENST00000456430.2:c.2238G>A	3.37:g.12858669G>A		Somatic		Capture	Illumina HiSeq	Phase_I	12833669	NM_001162499	B9EGM9|E9KL24	Silent	SNP	ENST00000456430.2	37	CCDS54554.1																																																																																				0.647	CAND2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339856.4	XM_371617	
PLXNA1	5361	broad.mit.edu	37	3	126736304	126736304	+	Missense_Mutation	SNP	C	C	T	rs376747849		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr3:126736304C>T	ENST00000393409.2	+	17	3313	c.3313C>T	c.(3313-3315)Cgc>Tgc	p.R1105C	PLXNA1_ENST00000251772.4_Missense_Mutation_p.R1082C	NM_032242.3	NP_115618.3	Q9UIW2	PLXA1_HUMAN	plexin A1	1105	IPT/TIG 3.				axon guidance (GO:0007411)|dichotomous subdivision of terminal units involved in salivary gland branching (GO:0060666)|multicellular organismal development (GO:0007275)|regulation of smooth muscle cell migration (GO:0014910)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|semaphorin receptor complex (GO:0002116)	receptor activity (GO:0004872)|semaphorin receptor activity (GO:0017154)	p.R1082C(1)		breast(3)|central_nervous_system(5)|endometrium(10)|kidney(5)|large_intestine(4)|lung(32)|ovary(2)|pancreas(1)|prostate(2)|skin(3)	67				GBM - Glioblastoma multiforme(114;0.155)		CATGGTATGCCGCGCCCCGTC	0.677																																					p.R1105C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C3313T	3						.	C	CYS/ARG	1,4405	2.1+/-5.4	0,1,2202	48.0	49.0	48.0		3313	4.2	0.9	3		48	0,8598		0,0,4299	no	missense	PLXNA1	NM_032242.3	180	0,1,6501	TT,TC,CC		0.0,0.0227,0.0077	possibly-damaging	1105/1897	126736304	1,13003	2203	4299	6502	128218994	SO:0001583	missense	5361	exon17			X87832	CCDS33847.1, CCDS33847.2	3q21.2	2006-12-19				ENSG00000114554		"""Plexins"""	9099	protein-coding gene	gene with protein product		601055		PLXN1		8570614	Standard	NM_032242		Approved	NOV	uc003ejg.3	Q9UIW2		ENST00000393409.2:c.3313C>T	3.37:g.126736304C>T	ENSP00000377061:p.Arg1105Cys	Somatic		Capture	Illumina HiSeq	Phase_I	128218994	NM_032242		Missense_Mutation	SNP	ENST00000393409.2	37	CCDS33847.2	.	.	.	.	.	.	.	.	.	.	C	16.52	3.146308	0.57044	2.27E-4	0.0	ENSG00000114554	ENST00000393409;ENST00000251772	T;T	0.77098	-1.07;-1.07	4.24	4.24	0.50183	Cell surface receptor IPT/TIG (2);Immunoglobulin E-set (1);Immunoglobulin-like fold (1);	0.733200	0.12383	N	0.473752	T	0.75613	0.3873	L	0.47190	1.495	0.46185	D	0.998919	P	0.43542	0.81	P	0.50109	0.631	T	0.72427	-0.4297	10	0.38643	T	0.18	.	5.0118	0.14317	0.0:0.7349:0.0:0.2651	.	1105	Q9UIW2	PLXA1_HUMAN	C	1105;1082	ENSP00000377061:R1105C;ENSP00000251772:R1082C	ENSP00000251772:R1082C	R	+	1	0	PLXNA1	128218994	0.979000	0.34478	0.942000	0.38095	0.975000	0.68041	1.791000	0.38744	2.191000	0.70037	0.467000	0.42956	CGC		0.677	PLXNA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356451.1	NM_032242	
GATA2	2624	broad.mit.edu	37	3	128200118	128200118	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr3:128200118C>T	ENST00000341105.2	-	6	1518	c.1187G>A	c.(1186-1188)cGg>cAg	p.R396Q	GATA2_ENST00000489987.1_5'UTR|GATA2_ENST00000487848.1_Missense_Mutation_p.R396Q|GATA2_ENST00000430265.2_Missense_Mutation_p.R382Q	NM_032638.4	NP_116027.2	P23769	GATA2_HUMAN	GATA binding protein 2	396					blood coagulation (GO:0007596)|cell differentiation in hindbrain (GO:0021533)|cell fate determination (GO:0001709)|cell maturation (GO:0048469)|central nervous system neuron development (GO:0021954)|commitment of neuronal cell to specific neuron type in forebrain (GO:0021902)|definitive hemopoiesis (GO:0060216)|embryonic placenta development (GO:0001892)|eosinophil fate commitment (GO:0035854)|GABAergic neuron differentiation (GO:0097154)|homeostasis of number of cells within a tissue (GO:0048873)|inner ear morphogenesis (GO:0042472)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of fat cell proliferation (GO:0070345)|negative regulation of macrophage differentiation (GO:0045650)|negative regulation of neural precursor cell proliferation (GO:2000178)|negative regulation of Notch signaling pathway (GO:0045746)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|phagocytosis (GO:0006909)|pituitary gland development (GO:0021983)|positive regulation of angiogenesis (GO:0045766)|positive regulation of erythrocyte differentiation (GO:0045648)|positive regulation of megakaryocyte differentiation (GO:0045654)|positive regulation of phagocytosis (GO:0050766)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of forebrain neuron differentiation (GO:2000977)|regulation of histone acetylation (GO:0035065)|semicircular canal development (GO:0060872)|somatic stem cell maintenance (GO:0035019)|transcription, DNA-templated (GO:0006351)|urogenital system development (GO:0001655)|ventral spinal cord interneuron differentiation (GO:0021514)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)	C2H2 zinc finger domain binding (GO:0070742)|chromatin binding (GO:0003682)|enhancer sequence-specific DNA binding (GO:0001158)|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 distal enhancer sequence-specific DNA binding (GO:0000980)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)	p.R396Q(1)		central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(58)|kidney(2)|large_intestine(3)|lung(9)|prostate(3)|skin(1)|urinary_tract(1)	79				GBM - Glioblastoma multiforme(114;0.173)		CTTCCGGTTCCGAGTCTGGAT	0.532			Mis		AML(CML blast transformation)																																p.R396Q			Dom	yes		3	3q21.3	2624	GATA binding protein 2		L	.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1187A	3						.						116.0	114.0	115.0					3																	128200118		2203	4300	6503	129682808	SO:0001583	missense	2624	exon6			AF169253	CCDS3049.1, CCDS46903.1	3q21	2014-09-17	2001-11-28		ENSG00000179348	ENSG00000179348		"""GATA zinc finger domain containing"""	4171	protein-coding gene	gene with protein product		137295	"""GATA-binding protein 2"""			1714909	Standard	NM_032638		Approved	NFE1B	uc003eko.2	P23769	OTTHUMG00000159689	ENST00000341105.2:c.1187G>A	3.37:g.128200118C>T	ENSP00000345681:p.Arg396Gln	Somatic		Capture	Illumina HiSeq	Phase_I	129682808	NM_032638	D3DNB3|Q53YE0|Q96BH0|Q96BH8|Q9BUJ6	Missense_Mutation	SNP	ENST00000341105.2	37	CCDS3049.1	.	.	.	.	.	.	.	.	.	.	C	35	5.459443	0.96240	.	.	ENSG00000179348	ENST00000341105;ENST00000430265;ENST00000487848	D;D;D	0.99701	-6.44;-6.45;-6.44	4.77	4.77	0.60923	Zinc finger, NHR/GATA-type (1);Zinc finger, GATA-type (1);	0.000000	0.85682	D	0.000000	D	0.99829	0.9923	H	0.95950	3.745	0.80722	D	1	D;D	0.89917	0.999;1.0	D;D	0.91635	0.99;0.999	D	0.96647	0.9478	10	0.87932	D	0	-22.6912	18.1584	0.89701	0.0:1.0:0.0:0.0	.	382;396	P23769-2;P23769	.;GATA2_HUMAN	Q	396;382;396	ENSP00000345681:R396Q;ENSP00000400259:R382Q;ENSP00000417074:R396Q	ENSP00000345681:R396Q	R	-	2	0	GATA2	129682808	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	7.726000	0.84824	2.355000	0.79922	0.491000	0.48974	CGG		0.532	GATA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356925.1	NM_032638	
RHO	6010	broad.mit.edu	37	3	129251142	129251142	+	Silent	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr3:129251142G>A	ENST00000296271.3	+	3	673	c.579G>A	c.(577-579)acG>acA	p.T193T		NM_000539.3	NP_000530.1	P08100	OPSD_HUMAN	rhodopsin	193					G-protein coupled receptor signaling pathway (GO:0007186)|phototransduction, visible light (GO:0007603)|protein phosphorylation (GO:0006468)|protein-chromophore linkage (GO:0018298)|red, far-red light phototransduction (GO:0009585)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|retina development in camera-type eye (GO:0060041)|retinoid metabolic process (GO:0001523)|rhodopsin mediated signaling pathway (GO:0016056)|visual perception (GO:0007601)	cell-cell junction (GO:0005911)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|photoreceptor disc membrane (GO:0097381)|photoreceptor inner segment (GO:0001917)|photoreceptor inner segment membrane (GO:0060342)|photoreceptor outer segment (GO:0001750)|photoreceptor outer segment membrane (GO:0042622)|plasma membrane (GO:0005886)|rough endoplasmic reticulum membrane (GO:0030867)	G-protein coupled receptor activity (GO:0004930)|metal ion binding (GO:0046872)|photoreceptor activity (GO:0009881)|retinal binding (GO:0016918)	p.T193T(2)		breast(1)|endometrium(1)|large_intestine(10)|lung(6)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)	22		all_neural(597;0.0227)|Myeloproliferative disorder(1037;0.0255)|Prostate(884;0.183)		GBM - Glioblastoma multiforme(114;2.58e-05)|Lung(219;0.0234)	Halothane(DB01159)	ACTACTACACGCTCAAGCCGG	0.547																																					p.T193T	Esophageal Squamous(118;214 1623 30842 43234 46940)											.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.G579A	3						.						275.0	217.0	236.0					3																	129251142		2203	4300	6503	130733832	SO:0001819	synonymous_variant	6010	exon3			AB065668	CCDS3063.1	3q21-q24	2014-01-28	2008-04-16		ENSG00000163914	ENSG00000163914		"""GPCR / Class A : Opsin receptors"""	10012	protein-coding gene	gene with protein product	"""opsin 2, rod pigment"""	180380	"""retinitis pigmentosa 4, autosomal dominant"""	RP4		2016091	Standard	NM_000539		Approved	OPN2, CSNBAD1	uc003emt.3	P08100	OTTHUMG00000159542	ENST00000296271.3:c.579G>A	3.37:g.129251142G>A		Somatic		Capture	Illumina HiSeq	Phase_I	130733832	NM_000539	Q16414|Q2M249	Silent	SNP	ENST00000296271.3	37	CCDS3063.1																																																																																				0.547	RHO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356101.1	NM_000539	
RHO	6010	broad.mit.edu	37	3	129252483	129252483	+	Silent	SNP	C	C	T	rs142771862		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr3:129252483C>T	ENST00000296271.3	+	5	1063	c.969C>T	c.(967-969)tgC>tgT	p.C323C		NM_000539.3	NP_000530.1	P08100	OPSD_HUMAN	rhodopsin	323					G-protein coupled receptor signaling pathway (GO:0007186)|phototransduction, visible light (GO:0007603)|protein phosphorylation (GO:0006468)|protein-chromophore linkage (GO:0018298)|red, far-red light phototransduction (GO:0009585)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|retina development in camera-type eye (GO:0060041)|retinoid metabolic process (GO:0001523)|rhodopsin mediated signaling pathway (GO:0016056)|visual perception (GO:0007601)	cell-cell junction (GO:0005911)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|photoreceptor disc membrane (GO:0097381)|photoreceptor inner segment (GO:0001917)|photoreceptor inner segment membrane (GO:0060342)|photoreceptor outer segment (GO:0001750)|photoreceptor outer segment membrane (GO:0042622)|plasma membrane (GO:0005886)|rough endoplasmic reticulum membrane (GO:0030867)	G-protein coupled receptor activity (GO:0004930)|metal ion binding (GO:0046872)|photoreceptor activity (GO:0009881)|retinal binding (GO:0016918)	p.C323C(1)		breast(1)|endometrium(1)|large_intestine(10)|lung(6)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)	22		all_neural(597;0.0227)|Myeloproliferative disorder(1037;0.0255)|Prostate(884;0.183)		GBM - Glioblastoma multiforme(114;2.58e-05)|Lung(219;0.0234)	Halothane(DB01159)	CCATCTGCTGCGGCAAGAACC	0.617													C|||	1	0.000199681	0.0	0.0	5008	,	,		16142	0.0		0.001	False		,,,				2504	0.0				p.C323C	Esophageal Squamous(118;214 1623 30842 43234 46940)											.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C969T	3						.	C		1,4405	2.1+/-5.4	0,1,2202	168.0	149.0	155.0		969	-2.1	1.0	3	dbSNP_134	155	16,8584	11.9+/-42.8	0,16,4284	no	coding-synonymous	RHO	NM_000539.3		0,17,6486	TT,TC,CC		0.186,0.0227,0.1307		323/349	129252483	17,12989	2203	4300	6503	130735173	SO:0001819	synonymous_variant	6010	exon5			AB065668	CCDS3063.1	3q21-q24	2014-01-28	2008-04-16		ENSG00000163914	ENSG00000163914		"""GPCR / Class A : Opsin receptors"""	10012	protein-coding gene	gene with protein product	"""opsin 2, rod pigment"""	180380	"""retinitis pigmentosa 4, autosomal dominant"""	RP4		2016091	Standard	NM_000539		Approved	OPN2, CSNBAD1	uc003emt.3	P08100	OTTHUMG00000159542	ENST00000296271.3:c.969C>T	3.37:g.129252483C>T		Somatic		Capture	Illumina HiSeq	Phase_I	130735173	NM_000539	Q16414|Q2M249	Silent	SNP	ENST00000296271.3	37	CCDS3063.1																																																																																				0.617	RHO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356101.1	NM_000539	
TMCC1	23023	broad.mit.edu	37	3	129373835	129373835	+	Silent	SNP	G	G	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr3:129373835G>T	ENST00000393238.3	-	5	1963	c.1623C>A	c.(1621-1623)tcC>tcA	p.S541S	TMCC1_ENST00000426664.2_Silent_p.S427S|TMCC1_ENST00000329333.5_Silent_p.S362S|TMCC1_ENST00000432054.2_Silent_p.S217S	NM_001017395.3	NP_001017395.2	O94876	TMCC1_HUMAN	transmembrane and coiled-coil domain family 1	541						endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)		p.S541S(2)	PLXND1/TMCC1(4)	breast(1)|endometrium(3)|large_intestine(8)|lung(12)|skin(1)	25						CCCGTTCATAGGACTGATACG	0.423																																					p.S541S												.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.C1623A	3						.						152.0	152.0	152.0					3																	129373835		2203	4300	6503	130856525	SO:0001819	synonymous_variant	23023	exon5			AB018322	CCDS33855.1	3q21.3	2010-04-19	2005-07-13		ENSG00000172765	ENSG00000172765		"""Transmembrane and coiled-coil domain containing"""	29116	protein-coding gene	gene with protein product			"""transmembrane and coiled-coil domains 1"""			9872452	Standard	NR_033361		Approved	KIAA0779	uc021xdy.1	O94876	OTTHUMG00000159579	ENST00000393238.3:c.1623C>A	3.37:g.129373835G>T		Somatic		Capture	Illumina HiSeq	Phase_I	130856525	NM_001017395	A8K5Y3|B4DE04|Q68E06|Q8IXM8	Silent	SNP	ENST00000393238.3	37	CCDS33855.1																																																																																				0.423	TMCC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356418.2	NM_015008	
COL6A5	256076	broad.mit.edu	37	3	130159520	130159520	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr3:130159520T>C	ENST00000432398.2	+	35	6832	c.6338T>C	c.(6337-6339)gTg>gCg	p.V2113A	COL6A5_ENST00000265379.6_Missense_Mutation_p.V2113A	NM_153264.5	NP_694996.5	A8TX70	CO6A5_HUMAN	collagen, type VI, alpha 5	2113	Nonhelical region.|VWFA 9. {ECO:0000255|PROSITE- ProRule:PRU00219}.				cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)	collagen trimer (GO:0005581)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)		p.V2113A(1)|p.V152A(1)		endometrium(6)|kidney(4)|large_intestine(8)|lung(19)|pancreas(2)|prostate(3)|stomach(1)|urinary_tract(1)	44						GTCATATTTGTGATTTCTCTG	0.418																																					p.V2113A												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.T6338C	3						.						114.0	109.0	111.0					3																	130159520		1925	4136	6061	131642210	SO:0001583	missense	256076	exon35			AK093199		3q21.3	2013-01-16	2010-05-24	2010-05-24	ENSG00000172752	ENSG00000172752		"""Collagens"""	26674	protein-coding gene	gene with protein product	"""von Willebrand factor A domain containing 4"""	611916	"""collagen, type XXIX, alpha 1"""	COL29A1		17850181	Standard	NM_153264		Approved	FLJ35880, VWA4	uc010htk.2	A8TX70	OTTHUMG00000159712	ENST00000432398.2:c.6338T>C	3.37:g.130159520T>C	ENSP00000390895:p.Val2113Ala	Somatic		Capture	Illumina HiSeq	Phase_I	131642210	NM_153264	A9J6L2|A9J6L4|A9J6L6|A9J6L7|A9J6M0|A9J6M1|A9J6M2|B5MEA7|Q6ZW26|Q8NA36	Missense_Mutation	SNP	ENST00000432398.2	37		.	.	.	.	.	.	.	.	.	.	T	12.42	1.931638	0.34096	.	.	ENSG00000172752	ENST00000432398;ENST00000265379;ENST00000373157	T;T;T	0.80738	-1.41;-1.41;2.58	5.87	5.87	0.94306	von Willebrand factor, type A (3);	0.000000	0.47852	D	0.000205	D	0.84261	0.5433	L	0.41632	1.29	0.25640	N	0.986211	D;D	0.89917	1.0;0.999	D;D	0.87578	0.998;0.984	T	0.75351	-0.3348	10	0.15499	T	0.54	.	15.2502	0.73539	0.0:0.0:0.0:1.0	.	2113;2113	A8TX70;A8TX70-2	CO6A5_HUMAN;.	A	2113;2113;56	ENSP00000390895:V2113A;ENSP00000265379:V2113A;ENSP00000362250:V56A	ENSP00000265379:V2113A	V	+	2	0	COL6A5	131642210	0.996000	0.38824	1.000000	0.80357	0.276000	0.26787	1.918000	0.40006	2.243000	0.73865	0.533000	0.62120	GTG		0.418	COL6A5-202	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_153264	
COL6A6	131873	broad.mit.edu	37	3	130285973	130285973	+	Silent	SNP	C	C	T	rs373317743		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr3:130285973C>T	ENST00000358511.6	+	4	1741	c.1710C>T	c.(1708-1710)atC>atT	p.I570I	COL6A6_ENST00000453409.2_Silent_p.I570I	NM_001102608.1	NP_001096078.1	A6NMZ7	CO6A6_HUMAN	collagen, type VI, alpha 6	570	Nonhelical region.|VWFA 3. {ECO:0000255|PROSITE- ProRule:PRU00219}.				cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)	collagen trimer (GO:0005581)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)		p.I570I(1)		NS(2)|breast(5)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(30)|lung(57)|ovary(8)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	134						TTTATGCTATCGGGATCAAGG	0.453																																					p.I570I												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1710T	3						.	C		3,3937		0,3,1967	112.0	112.0	112.0		1710	-7.6	0.0	3		112	0,8332		0,0,4166	no	coding-synonymous	COL6A6	NM_001102608.1		0,3,6133	TT,TC,CC		0.0,0.0761,0.0244		570/2264	130285973	3,12269	1970	4166	6136	131768663	SO:0001819	synonymous_variant	131873	exon4			AL713792	CCDS46911.1	3q22.1	2013-01-16			ENSG00000206384	ENSG00000206384		"""Collagens"""	27023	protein-coding gene	gene with protein product							Standard	NM_001102608		Approved		uc010htl.3	A6NMZ7	OTTHUMG00000159653	ENST00000358511.6:c.1710C>T	3.37:g.130285973C>T		Somatic		Capture	Illumina HiSeq	Phase_I	131768663	NM_001102608	A7DZQ0|A7DZQ1|A7DZQ2|Q69YT0	Silent	SNP	ENST00000358511.6	37	CCDS46911.1																																																																																				0.453	COL6A6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000356705.5	NM_001102608	
NUP210	23225	broad.mit.edu	37	3	13379370	13379370	+	Silent	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr3:13379370G>A	ENST00000254508.5	-	26	3601	c.3519C>T	c.(3517-3519)cgC>cgT	p.R1173R	NUP210_ENST00000485755.1_Intron	NM_024923.2	NP_079199.2	Q8TEM1	PO210_HUMAN	nucleoporin 210kDa	1173					carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|protein transport (GO:0015031)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear pore (GO:0005643)		p.R1173R(1)		NS(1)|biliary_tract(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(9)|kidney(2)|large_intestine(10)|liver(1)|lung(16)|ovary(7)|pancreas(1)|prostate(1)|skin(8)|upper_aerodigestive_tract(3)|urinary_tract(2)	66	all_neural(104;0.187)					TGATGGGGGCGCGGATCCTCA	0.647																																					p.R1173R												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C3519T	3						.						49.0	43.0	45.0					3																	13379370		2203	4300	6503	13354370	SO:0001819	synonymous_variant	23225	exon26			AB020713	CCDS33704.1	3p25	2008-02-05			ENSG00000132182	ENSG00000132182			30052	protein-coding gene	gene with protein product		607703				2184032, 7504063	Standard	NM_024923		Approved	GP210, POM210, FLJ22389, KIAA0906	uc003bxv.1	Q8TEM1	OTTHUMG00000157268	ENST00000254508.5:c.3519C>T	3.37:g.13379370G>A		Somatic		Capture	Illumina HiSeq	Phase_I	13354370	NM_024923	A6NN56|O94980|Q6NXG6|Q8NBJ1|Q9H6C8|Q9UFP3	Silent	SNP	ENST00000254508.5	37	CCDS33704.1																																																																																				0.647	NUP210-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340085.1	NM_024923	
NUP210	23225	broad.mit.edu	37	3	13438917	13438917	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr3:13438917G>A	ENST00000254508.5	-	3	458	c.376C>T	c.(376-378)Cgc>Tgc	p.R126C		NM_024923.2	NP_079199.2	Q8TEM1	PO210_HUMAN	nucleoporin 210kDa	126					carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|protein transport (GO:0015031)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear pore (GO:0005643)		p.R126C(1)		NS(1)|biliary_tract(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(9)|kidney(2)|large_intestine(10)|liver(1)|lung(16)|ovary(7)|pancreas(1)|prostate(1)|skin(8)|upper_aerodigestive_tract(3)|urinary_tract(2)	66	all_neural(104;0.187)					TAGAGCTCGCGGGTGGTGGAG	0.617																																					p.R126C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C376T	3						.						86.0	77.0	80.0					3																	13438917		2203	4300	6503	13413917	SO:0001583	missense	23225	exon3			AB020713	CCDS33704.1	3p25	2008-02-05			ENSG00000132182	ENSG00000132182			30052	protein-coding gene	gene with protein product		607703				2184032, 7504063	Standard	NM_024923		Approved	GP210, POM210, FLJ22389, KIAA0906	uc003bxv.1	Q8TEM1	OTTHUMG00000157268	ENST00000254508.5:c.376C>T	3.37:g.13438917G>A	ENSP00000254508:p.Arg126Cys	Somatic		Capture	Illumina HiSeq	Phase_I	13413917	NM_024923	A6NN56|O94980|Q6NXG6|Q8NBJ1|Q9H6C8|Q9UFP3	Missense_Mutation	SNP	ENST00000254508.5	37	CCDS33704.1	.	.	.	.	.	.	.	.	.	.	G	17.46	3.394007	0.62066	.	.	ENSG00000132182	ENST00000254508	T	0.10099	2.91	4.0	3.12	0.35913	.	0.231599	0.43747	D	0.000528	T	0.29256	0.0728	M	0.83483	2.645	0.58432	D	0.999999	D	0.89917	1.0	D	0.69654	0.965	T	0.02015	-1.1229	10	0.62326	D	0.03	-25.0499	6.6725	0.23076	0.0986:0.0:0.7244:0.177	.	126	Q8TEM1	PO210_HUMAN	C	126	ENSP00000254508:R126C	ENSP00000254508:R126C	R	-	1	0	NUP210	13413917	1.000000	0.71417	0.989000	0.46669	0.979000	0.70002	2.060000	0.41394	1.032000	0.39892	0.561000	0.74099	CGC		0.617	NUP210-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340085.1	NM_024923	
NEK11	79858	broad.mit.edu	37	3	130871280	130871280	+	Silent	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr3:130871280C>T	ENST00000383366.4	+	8	989	c.696C>T	c.(694-696)ttC>ttT	p.F232F	NEK11_ENST00000508196.1_Silent_p.F232F|NEK11_ENST00000426022.2_3'UTR|NEK11_ENST00000507910.1_Silent_p.F232F|NEK11_ENST00000412440.2_Silent_p.F84F|NEK11_ENST00000510769.1_Intron|NEK11_ENST00000510688.1_Silent_p.F232F|NEK11_ENST00000429253.2_Silent_p.F232F|NEK11_ENST00000356918.4_Silent_p.F232F|NEK11_ENST00000511262.1_Silent_p.F232F	NM_024800.4	NP_079076.3			NIMA-related kinase 11									p.F232F(1)		breast(2)|central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(8)|lung(14)|stomach(1)|urinary_tract(2)	33						ATCATGCATTCGCTGGCTCCA	0.353																																					p.F232F												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C696T	3						.						104.0	109.0	107.0					3																	130871280		2203	4300	6503	132353970	SO:0001819	synonymous_variant	79858	exon8			AK027148	CCDS3069.1, CCDS46915.1, CCDS54639.1	3q22.1	2012-11-15	2012-11-15		ENSG00000114670	ENSG00000114670			18593	protein-coding gene	gene with protein product		609779	"""NIMA (never in mitosis gene a)- related kinase 11"""				Standard	NM_024800		Approved	FLJ23495	uc003eny.3	Q8NG66	OTTHUMG00000159654	ENST00000383366.4:c.696C>T	3.37:g.130871280C>T		Somatic		Capture	Illumina HiSeq	Phase_I	132353970	NM_024800		Silent	SNP	ENST00000383366.4	37	CCDS3069.1																																																																																				0.353	NEK11-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000356755.1	NM_024800	
EPHB1	2047	broad.mit.edu	37	3	134968251	134968251	+	Missense_Mutation	SNP	G	G	A	rs373797543		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr3:134968251G>A	ENST00000398015.3	+	15	3134	c.2764G>A	c.(2764-2766)Gcc>Acc	p.A922T	EPHB1_ENST00000493838.1_Missense_Mutation_p.A483T	NM_004441.4	NP_004432.1	P54762	EPHB1_HUMAN	EPH receptor B1	922	SAM. {ECO:0000255|PROSITE- ProRule:PRU00184}.				angiogenesis (GO:0001525)|axon guidance (GO:0007411)|camera-type eye morphogenesis (GO:0048593)|cell chemotaxis (GO:0060326)|cell-substrate adhesion (GO:0031589)|central nervous system projection neuron axonogenesis (GO:0021952)|dendritic spine development (GO:0060996)|dendritic spine morphogenesis (GO:0060997)|detection of temperature stimulus involved in sensory perception of pain (GO:0050965)|ephrin receptor signaling pathway (GO:0048013)|establishment of cell polarity (GO:0030010)|neural precursor cell proliferation (GO:0061351)|neurogenesis (GO:0022008)|optic nerve morphogenesis (GO:0021631)|positive regulation of synapse assembly (GO:0051965)|protein autophosphorylation (GO:0046777)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of JNK cascade (GO:0046328)|retinal ganglion cell axon guidance (GO:0031290)	axon (GO:0030424)|early endosome membrane (GO:0031901)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)	ATP binding (GO:0005524)|axon guidance receptor activity (GO:0008046)|transmembrane-ephrin receptor activity (GO:0005005)	p.A922T(2)		NS(1)|breast(3)|central_nervous_system(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(13)|lung(63)|ovary(8)|pancreas(2)|prostate(8)|skin(7)|stomach(4)|upper_aerodigestive_tract(4)|urinary_tract(2)	130						CTGGCTCAGCGCCATCAAAAT	0.577																																					p.A922T												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G2764A	3						.	G	THR/ALA	0,4186		0,0,2093	95.0	97.0	96.0		2764	5.4	1.0	3		96	1,8451		0,1,4225	no	missense	EPHB1	NM_004441.4	58	0,1,6318	AA,AG,GG		0.0118,0.0,0.0079	probably-damaging	922/985	134968251	1,12637	2093	4226	6319	136450941	SO:0001583	missense	2047	exon15			L40636	CCDS46921.1	3q21-q23	2013-02-11	2004-10-28			ENSG00000154928		"""EPH receptors"", ""Sterile alpha motif (SAM) domain containing"", ""Fibronectin type III domain containing"""	3392	protein-coding gene	gene with protein product		600600	"""EphB1"""	EPHT2		8666391	Standard	NM_004441		Approved	Hek6	uc003eqt.3	P54762		ENST00000398015.3:c.2764G>A	3.37:g.134968251G>A	ENSP00000381097:p.Ala922Thr	Somatic		Capture	Illumina HiSeq	Phase_I	136450941	NM_004441	A8K593|B3KTB2|B5A969|O43569|O95142|O95143|Q0VG87	Missense_Mutation	SNP	ENST00000398015.3	37	CCDS46921.1	.	.	.	.	.	.	.	.	.	.	G	35	5.563692	0.96527	0.0	1.18E-4	ENSG00000154928	ENST00000398015;ENST00000493838	T;T	0.52295	0.67;0.67	5.43	5.43	0.79202	Sterile alpha motif domain (2);Sterile alpha motif/pointed domain (2);Sterile alpha motif, type 1 (1);	0.000000	0.85682	D	0.000000	T	0.68238	0.2979	M	0.64997	1.995	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.68689	-0.5342	10	0.66056	D	0.02	.	19.4372	0.94801	0.0:0.0:1.0:0.0	.	922	P54762	EPHB1_HUMAN	T	922;483	ENSP00000381097:A922T;ENSP00000419574:A483T	ENSP00000381097:A922T	A	+	1	0	EPHB1	136450941	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.601000	0.98297	2.827000	0.97445	0.650000	0.86243	GCC		0.577	EPHB1-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357671.1	NM_004441	
XPC	7508	broad.mit.edu	37	3	14190420	14190420	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr3:14190420C>T	ENST00000285021.7	-	12	2358	c.2144G>A	c.(2143-2145)cGg>cAg	p.R715Q	AC093495.4_ENST00000420253.1_RNA|XPC_ENST00000449060.2_Missense_Mutation_p.R678Q|AC093495.4_ENST00000428681.3_RNA	NM_001145769.1|NM_004628.4	NP_001139241.1|NP_004619.3	Q01831	XPC_HUMAN	xeroderma pigmentosum, complementation group C	715	DNA-binding; preference for heteroduplex DNA.|Interaction with RAD23B.|Minimal sensor domain involved in damage recognition.				DNA repair (GO:0006281)|intra-S DNA damage checkpoint (GO:0031573)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA damage recognition (GO:0000715)|nucleotide-excision repair, DNA damage removal (GO:0000718)|regulation of mitotic cell cycle phase transition (GO:1901990)|response to drug (GO:0042493)|response to UV-B (GO:0010224)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|XPC complex (GO:0071942)	bubble DNA binding (GO:0000405)|damaged DNA binding (GO:0003684)|heteroduplex DNA loop binding (GO:0000404)|single-stranded DNA binding (GO:0003697)	p.R715Q(1)		NS(1)|breast(2)|endometrium(1)|kidney(3)|large_intestine(4)|lung(5)|ovary(3)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	22						TCGGGCTTTCCGAGCACGGTT	0.592			"""Mis, N, F, S"""			"""skin basal cell, skin squamous cell, melanoma"""		Nucleotide excision repair (NER)	Xeroderma Pigmentosum																												p.R679Q		yes	Rec		Xeroderma pigmentosum (C)	3	3p25	7508	"""xeroderma pigmentosum, complementation group C"""		E	.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2036A	3						.						69.0	73.0	71.0					3																	14190420		1993	4168	6161	14165421	SO:0001583	missense	7508	exon12	Familial Cancer Database	incl. XPA, XPB, XPC, XPD, XPE, XPF, XPG, XP Variant, XPV		CCDS46763.1	3p25.1	2014-09-17			ENSG00000154767	ENSG00000154767			12816	protein-coding gene	gene with protein product	"""xeroderma pigmentosum group C protein"""	613208				1522891	Standard	NM_004628		Approved	XPCC, RAD4	uc011ave.2	Q01831	OTTHUMG00000155526	ENST00000285021.7:c.2144G>A	3.37:g.14190420C>T	ENSP00000285021:p.Arg715Gln	Somatic		Capture	Illumina HiSeq	Phase_I	14165421	NM_001145769	B4DIP3|E9PB96|E9PH69|Q53GT7|Q96AX0	Missense_Mutation	SNP	ENST00000285021.7	37	CCDS46763.1	.	.	.	.	.	.	.	.	.	.	C	27.0	4.791583	0.90367	.	.	ENSG00000154767	ENST00000285021;ENST00000449060	T;T	0.74526	-0.85;-0.85	5.69	5.69	0.88448	DNA repair protein Rad4, DNA-binding domain 2 (1);	0.000000	0.85682	D	0.000000	D	0.86506	0.5949	M	0.79475	2.455	0.80722	D	1	D;D	0.89917	1.0;0.975	D;P	0.73380	0.98;0.817	D	0.84419	0.0570	10	0.34782	T	0.22	-22.9546	19.8047	0.96525	0.0:1.0:0.0:0.0	.	678;715	E9PH69;Q01831	.;XPC_HUMAN	Q	715;678	ENSP00000285021:R715Q;ENSP00000404002:R678Q	ENSP00000285021:R715Q	R	-	2	0	XPC	14165421	1.000000	0.71417	0.997000	0.53966	0.178000	0.23041	7.629000	0.83207	2.692000	0.91855	0.563000	0.77884	CGG		0.592	XPC-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000340517.3	NM_004628	
CEP70	80321	broad.mit.edu	37	3	138256129	138256129	+	Nonsense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr3:138256129G>A	ENST00000264982.3	-	7	792	c.526C>T	c.(526-528)Caa>Taa	p.Q176*	CEP70_ENST00000478673.1_5'UTR|CEP70_ENST00000481834.1_Nonsense_Mutation_p.Q176*|CEP70_ENST00000484888.1_Nonsense_Mutation_p.Q176*|CEP70_ENST00000464035.1_Nonsense_Mutation_p.Q176*|CEP70_ENST00000542237.1_Nonsense_Mutation_p.Q156*|CEP70_ENST00000489254.1_Nonsense_Mutation_p.Q24*	NM_024491.2	NP_077817.2	Q8NHQ1	CEP70_HUMAN	centrosomal protein 70kDa	176					G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)		p.Q176*(1)		breast(2)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(9)|lung(6)|skin(3)	24						ACTTCCATTTGCAAAGAAGCA	0.348																																					p.Q176X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.C526T	3						.						125.0	112.0	116.0					3																	138256129		2203	4300	6503	139738819	SO:0001587	stop_gained	80321	exon7			AF202146	CCDS3102.1, CCDS75022.1, CCDS75023.1, CCDS75024.1	3q22.3	2014-02-20			ENSG00000114107	ENSG00000114107			29972	protein-coding gene	gene with protein product		614310				14654843	Standard	XM_005247802		Approved	BITE, FLJ13036	uc003esl.3	Q8NHQ1	OTTHUMG00000159891	ENST00000264982.3:c.526C>T	3.37:g.138256129G>A	ENSP00000264982:p.Gln176*	Somatic		Capture	Illumina HiSeq	Phase_I	139738819	NM_024491	B7Z5I8|B7Z7E8|D3DNE9|F5GZX8|Q96B31|Q9H2C3|Q9H2Z1|Q9H940	Nonsense_Mutation	SNP	ENST00000264982.3	37	CCDS3102.1	.	.	.	.	.	.	.	.	.	.	G	16.93	3.256956	0.59321	.	.	ENSG00000114107	ENST00000264982;ENST00000542237;ENST00000489254;ENST00000484888;ENST00000474781;ENST00000481834;ENST00000468900;ENST00000462419;ENST00000464035	.	.	.	4.72	4.72	0.59763	.	0.134244	0.51477	D	0.000090	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.23891	T	0.37	-11.6973	13.0477	0.58937	0.0:0.0:1.0:0.0	.	.	.	.	X	176;156;24;176;158;176;155;156;176	.	ENSP00000264982:Q176X	Q	-	1	0	CEP70	139738819	1.000000	0.71417	1.000000	0.80357	0.133000	0.20885	4.947000	0.63583	2.452000	0.82932	0.655000	0.94253	CAA		0.348	CEP70-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000358001.1	NM_024491	
PAQR9	344838	broad.mit.edu	37	3	142681379	142681379	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr3:142681379C>T	ENST00000340634.3	-	1	799	c.800G>A	c.(799-801)cGt>cAt	p.R267H	RP11-372E1.6_ENST00000595774.1_RNA|RP11-372E1.6_ENST00000493825.1_RNA|RP11-372E1.6_ENST00000497652.1_RNA|RP11-372E1.6_ENST00000608349.1_RNA|RP11-372E1.6_ENST00000595248.1_RNA|RP11-372E1.6_ENST00000607937.1_RNA|RP11-372E1.6_ENST00000594095.1_RNA|RP11-372E1.6_ENST00000593321.1_RNA|RP11-372E1.6_ENST00000598139.1_RNA|RP11-372E1.6_ENST00000608686.1_RNA|RP11-372E1.6_ENST00000478823.1_RNA|RP11-372E1.6_ENST00000598787.1_RNA	NM_198504.2	NP_940906.1	Q6ZVX9	PAQR9_HUMAN	progestin and adipoQ receptor family member IX	267						integral component of membrane (GO:0016021)	receptor activity (GO:0004872)	p.R267H(1)		endometrium(2)|large_intestine(7)|lung(12)|prostate(1)	22						GTTCTCCCCACGCAGGTCGAA	0.617																																					p.R267H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G800A	3						.						67.0	68.0	68.0					3																	142681379		2203	4300	6503	144164069	SO:0001583	missense	344838	exon1			AY424287	CCDS3128.1	3q23	2008-05-02			ENSG00000188582	ENSG00000188582			30131	protein-coding gene	gene with protein product		614580					Standard	NM_198504		Approved	FLJ41938	uc003evg.3	Q6ZVX9	OTTHUMG00000159313	ENST00000340634.3:c.800G>A	3.37:g.142681379C>T	ENSP00000341564:p.Arg267His	Somatic		Capture	Illumina HiSeq	Phase_I	144164069	NM_198504	Q147T6	Missense_Mutation	SNP	ENST00000340634.3	37	CCDS3128.1	.	.	.	.	.	.	.	.	.	.	C	22.1	4.247685	0.80024	.	.	ENSG00000188582	ENST00000340634	T	0.28454	1.61	5.63	5.63	0.86233	.	0.268720	0.28382	N	0.015544	T	0.26702	0.0653	L	0.27053	0.805	0.40708	D	0.982546	P	0.44195	0.828	B	0.39738	0.308	T	0.02781	-1.1111	10	0.39692	T	0.17	-9.8554	19.7096	0.96089	0.0:1.0:0.0:0.0	.	267	Q6ZVX9	PAQR9_HUMAN	H	267	ENSP00000341564:R267H	ENSP00000341564:R267H	R	-	2	0	PAQR9	144164069	1.000000	0.71417	0.801000	0.32222	0.960000	0.62799	4.868000	0.63021	2.652000	0.90054	0.655000	0.94253	CGT		0.617	PAQR9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354538.1	NM_198504	
GRIP2	80852	broad.mit.edu	37	3	14551449	14551449	+	RNA	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr3:14551449C>T	ENST00000273083.3	-	0	2021							Q9C0E4	GRIP2_HUMAN	glutamate receptor interacting protein 2						synaptic transmission (GO:0007268)	cytosol (GO:0005829)|plasma membrane (GO:0005886)		p.V654I(1)		endometrium(5)|large_intestine(4)|lung(8)|ovary(1)|pancreas(1)|prostate(5)|skin(1)	25						GTGTAACTGACGGCACCTGTG	0.612																																					p.P749P												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2247A	3						.						26.0	31.0	29.0					3																	14551449		1927	4108	6035	14526453			80852	exon18			AB051506		3p24-p23	2012-02-08			ENSG00000144596	ENSG00000144596			23841	protein-coding gene	gene with protein product							Standard	NM_001080423		Approved	KIAA1719	uc021wtn.1	Q9C0E4	OTTHUMG00000155544		3.37:g.14551449C>T		Somatic		Capture	Illumina HiSeq	Phase_I	14526453	NM_001080423	Q8TEH9|Q9H7H3	Missense_Mutation	SNP	ENST00000273083.3	37																																																																																					0.612	GRIP2-001	KNOWN	basic	processed_transcript	processed_transcript	OTTHUMT00000340582.2	NM_001080423	
SLC9A9	285195	broad.mit.edu	37	3	143186026	143186026	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr3:143186026C>T	ENST00000316549.6	-	12	1530	c.1322G>A	c.(1321-1323)cGa>cAa	p.R441Q		NM_173653.3	NP_775924.1	Q8IVB4	SL9A9_HUMAN	solute carrier family 9, subfamily A (NHE9, cation proton antiporter 9), member 9	441					ion transport (GO:0006811)|regulation of pH (GO:0006885)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|late endosome membrane (GO:0031902)|recycling endosome (GO:0055037)	sodium:proton antiporter activity (GO:0015385)	p.R441Q(1)		breast(2)|endometrium(5)|kidney(2)|large_intestine(13)|lung(29)|ovary(2)|skin(3)|stomach(1)	57						GATCGCTCCTCGCAAACCTTG	0.413																																					p.R441Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1322A	3						.						90.0	79.0	83.0					3																	143186026		2203	4300	6503	144668716	SO:0001583	missense	285195	exon12			AY254100	CCDS33872.1	3q23-q24	2014-01-28	2012-03-22		ENSG00000181804	ENSG00000181804		"""Solute carriers"""	20653	protein-coding gene	gene with protein product		608396	"""solute carrier family 9 (sodium/hydrogen exchanger), isoform 9"", ""solute carrier family 9 (sodium/hydrogen exchanger), member 9"""			14569117	Standard	NM_173653		Approved	FLJ35613, NHE9	uc003evn.3	Q8IVB4	OTTHUMG00000159373	ENST00000316549.6:c.1322G>A	3.37:g.143186026C>T	ENSP00000320246:p.Arg441Gln	Somatic		Capture	Illumina HiSeq	Phase_I	144668716	NM_173653	A6NMQ9|Q3LIC2|Q5JPI6|Q5WA58|Q8NAB9	Missense_Mutation	SNP	ENST00000316549.6	37	CCDS33872.1	.	.	.	.	.	.	.	.	.	.	C	36	5.740028	0.96873	.	.	ENSG00000181804	ENST00000316549	T	0.22539	1.95	5.95	5.95	0.96441	Cation/H+ exchanger (1);	0.000000	0.64402	D	0.000004	T	0.65312	0.2679	H	0.97465	4.01	0.80722	D	1	D	0.76494	0.999	D	0.80764	0.994	T	0.77504	-0.2563	10	0.87932	D	0	.	20.3932	0.98965	0.0:1.0:0.0:0.0	.	441	Q8IVB4	SL9A9_HUMAN	Q	441	ENSP00000320246:R441Q	ENSP00000320246:R441Q	R	-	2	0	SLC9A9	144668716	1.000000	0.71417	1.000000	0.80357	0.952000	0.60782	7.429000	0.80309	2.824000	0.97209	0.655000	0.94253	CGA		0.413	SLC9A9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354994.1	NM_173653	
MRPS25	64432	broad.mit.edu	37	3	15106694	15106694	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr3:15106694A>G	ENST00000253686.2	-	1	148	c.8T>C	c.(7-9)aTg>aCg	p.M3T	MRPS25_ENST00000444840.2_Missense_Mutation_p.M3T|MRPS25_ENST00000449354.2_Missense_Mutation_p.M3T	NM_022497.3	NP_071942.1	P82663	RT25_HUMAN	mitochondrial ribosomal protein S25	3						mitochondrion (GO:0005739)|ribosome (GO:0005840)		p.M3T(1)		large_intestine(1)|lung(1)	2						GCGGCCCTTCATGGGCATGGC	0.642																																					p.M3T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T8C	3						.						35.0	27.0	30.0					3																	15106694		2200	4296	6496	15081698	SO:0001583	missense	64432	exon1			AB061208	CCDS2622.1	3p25	2012-09-13			ENSG00000131368	ENSG00000131368		"""Mitochondrial ribosomal proteins / small subunits"""	14511	protein-coding gene	gene with protein product	"""mitochondrial 28S ribosomal protein S25"""	611987				11279123	Standard	NM_022497		Approved	MRP-S25, FLJ00023, DKFZp313H0817, RPMS25	uc003bzl.3	P82663	OTTHUMG00000129836	ENST00000253686.2:c.8T>C	3.37:g.15106694A>G	ENSP00000253686:p.Met3Thr	Somatic		Capture	Illumina HiSeq	Phase_I	15081698	NM_022497	B4DFJ5|B4DQG6|Q9H7P5	Missense_Mutation	SNP	ENST00000253686.2	37	CCDS2622.1	.	.	.	.	.	.	.	.	.	.	A	16.83	3.232027	0.58777	.	.	ENSG00000131368	ENST00000253686;ENST00000449354;ENST00000444840	.	.	.	4.85	4.85	0.62838	.	0.000000	0.85682	D	0.000000	T	0.79845	0.4516	M	0.86953	2.85	0.80722	D	1	D;D;D	0.76494	0.999;0.985;0.981	D;P;P	0.63488	0.915;0.715;0.69	D	0.84168	0.0432	9	0.87932	D	0	-54.6026	14.1306	0.65250	1.0:0.0:0.0:0.0	.	3;3;3	B4DFJ5;B4DQG6;P82663	.;.;RT25_HUMAN	T	3	.	ENSP00000253686:M3T	M	-	2	0	MRPS25	15081698	1.000000	0.71417	1.000000	0.80357	0.126000	0.20510	8.683000	0.91236	1.811000	0.52892	0.260000	0.18958	ATG		0.642	MRPS25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252076.2	NM_022497	
ZIC4	84107	broad.mit.edu	37	3	147108853	147108853	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr3:147108853C>T	ENST00000383075.3	-	4	1381	c.869G>A	c.(868-870)cGc>cAc	p.R290H	ZIC4_ENST00000425731.3_Missense_Mutation_p.R328H|ZIC4_ENST00000525172.2_Missense_Mutation_p.R340H|ZIC4_ENST00000491672.1_Missense_Mutation_p.R84H|ZIC4_ENST00000484399.1_Missense_Mutation_p.R290H|ZIC4_ENST00000473123.1_Missense_Mutation_p.R290H|ZIC4_ENST00000472749.2_5'UTR	NM_032153.5	NP_115529.2	Q8N9L1	ZIC4_HUMAN	Zic family member 4	290						nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.R290H(1)		breast(2)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(9)|lung(34)|upper_aerodigestive_tract(4)	57						CGGCGGCGAGCGCCCGTGCAC	0.667																																					p.R340H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1019A	3						.						31.0	39.0	36.0					3																	147108853		2187	4290	6477	148591543	SO:0001583	missense	84107	exon4			AF332509	CCDS43160.1, CCDS54652.1, CCDS54653.1, CCDS58857.1	3q24	2013-01-08	2003-02-21		ENSG00000174963	ENSG00000174963		"""Zinc fingers, C2H2-type"""	20393	protein-coding gene	gene with protein product		608948	"""zinc finger protein of the cerebellum 4"""				Standard	NM_001168378		Approved		uc011bno.2	Q8N9L1	OTTHUMG00000037281	ENST00000383075.3:c.869G>A	3.37:g.147108853C>T	ENSP00000372553:p.Arg290His	Somatic		Capture	Illumina HiSeq	Phase_I	148591543	NM_001168378	A0AVA2|B2RMQ8|B4DF89|B7Z2L2|C9J7D5|J3KQG1|Q4G157|Q9BZ94	Missense_Mutation	SNP	ENST00000383075.3	37	CCDS43160.1	.	.	.	.	.	.	.	.	.	.	C	29.1	4.976316	0.92982	.	.	ENSG00000174963	ENST00000383075;ENST00000425731;ENST00000525172;ENST00000484399;ENST00000473123;ENST00000491672	T;T;T;T;T;T	0.53640	2.41;2.41;2.41;2.41;2.41;0.61	5.05	4.04	0.47022	Zinc finger, C2H2 (1);	0.221422	0.23515	N	0.047350	T	0.46658	0.1404	L	0.44542	1.39	0.33648	D	0.608101	D;D	0.63046	0.992;0.99	P;P	0.55222	0.771;0.508	T	0.59963	-0.7355	9	0.72032	D	0.01	.	3.2819	0.06918	0.0:0.5982:0.0:0.4018	.	340;290	B7Z2L2;Q8N9L1	.;ZIC4_HUMAN	H	290;328;340;290;290;84	ENSP00000372553:R290H;ENSP00000397695:R328H;ENSP00000435509:R340H;ENSP00000417855:R290H;ENSP00000420775:R290H;ENSP00000418277:R84H	ENSP00000372553:R290H	R	-	2	0	ZIC4	148591543	1.000000	0.71417	1.000000	0.80357	0.936000	0.57629	2.731000	0.47343	2.337000	0.79520	0.462000	0.41574	CGC		0.667	ZIC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355504.1		
IGSF10	285313	broad.mit.edu	37	3	151155382	151155382	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr3:151155382C>T	ENST00000282466.3	-	6	6966	c.6967G>A	c.(6967-6969)Gtg>Atg	p.V2323M	IGSF10_ENST00000495443.1_5'UTR	NM_001178145.1|NM_001178146.1|NM_178822.4	NP_001171616.1|NP_001171617.1|NP_849144.2	Q6WRI0	IGS10_HUMAN	immunoglobulin superfamily, member 10	2323	Ig-like C2-type 9.				cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|ossification (GO:0001503)	extracellular region (GO:0005576)		p.V2323M(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(24)|liver(4)|lung(43)|ovary(8)|prostate(4)|skin(9)|stomach(1)|urinary_tract(3)	116			LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0517)			ACTACCAACACGCTCTCTCCA	0.423																																					p.V350M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1048A	3						.						145.0	143.0	144.0					3																	151155382		2203	4300	6503	152638072	SO:0001583	missense	285313	exon2			AY273815	CCDS3160.1	3q25.1	2013-01-11			ENSG00000152580	ENSG00000152580		"""Immunoglobulin superfamily / I-set domain containing"""	26384	protein-coding gene	gene with protein product						12477932	Standard	NM_178822		Approved	FLJ25972, CMF608	uc011bod.2	Q6WRI0	OTTHUMG00000159856	ENST00000282466.3:c.6967G>A	3.37:g.151155382C>T	ENSP00000282466:p.Val2323Met	Somatic		Capture	Illumina HiSeq	Phase_I	152638072	NM_001178145	Q86YJ9|Q8N772|Q8NA84	Missense_Mutation	SNP	ENST00000282466.3	37	CCDS3160.1	.	.	.	.	.	.	.	.	.	.	C	11.22	1.575821	0.28092	.	.	ENSG00000152580	ENST00000282466	T	0.66995	-0.24	5.77	-0.231	0.13086	Immunoglobulin subtype (1);Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.178608	0.26149	N	0.026049	T	0.58821	0.2149	L	0.49455	1.56	0.09310	N	1	P;P	0.49447	0.924;0.508	B;B	0.43990	0.438;0.197	T	0.55945	-0.8060	10	0.42905	T	0.14	.	11.0795	0.48051	0.0:0.4779:0.0:0.5221	.	2323;350	Q6WRI0;Q6WRI0-2	IGS10_HUMAN;.	M	2323	ENSP00000282466:V2323M	ENSP00000282466:V2323M	V	-	1	0	IGSF10	152638072	0.000000	0.05858	0.132000	0.22025	0.995000	0.86356	-0.172000	0.09868	-0.099000	0.12263	0.591000	0.81541	GTG		0.423	IGSF10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357782.1	NM_178822	
ARHGEF26	26084	broad.mit.edu	37	3	153840505	153840505	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr3:153840505G>A	ENST00000356448.4	+	2	1008	c.724G>A	c.(724-726)Gcc>Acc	p.A242T	ARHGEF26-AS1_ENST00000467912.1_RNA|ARHGEF26-AS1_ENST00000480639.1_RNA|ARHGEF26_ENST00000465817.1_Missense_Mutation_p.A242T|ARHGEF26-AS1_ENST00000479270.1_RNA|ARHGEF26_ENST00000465093.1_Missense_Mutation_p.A242T|ARHGEF26-AS1_ENST00000491862.1_RNA	NM_001251962.1	NP_001238891.1	Q96DR7	ARHGQ_HUMAN	Rho guanine nucleotide exchange factor (GEF) 26	242					endothelial cell morphogenesis (GO:0001886)|ruffle assembly (GO:0097178)	cell projection (GO:0042995)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)	p.A242T(1)		endometrium(4)|kidney(1)|large_intestine(7)|lung(8)|ovary(1)|pancreas(1)|urinary_tract(1)	23						CAGCCCCGCCGCCCTCAAAGT	0.502																																					p.A242T	GBM(163;191 2003 24758 29593 48540)|Ovarian(152;631 1885 20165 22910 51013)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G724A	3						.						15.0	17.0	17.0					3																	153840505		1852	4097	5949	155323195	SO:0001583	missense	26084	exon2			BC016628	CCDS46938.1, CCDS58858.1	3q25.2	2013-01-10			ENSG00000114790	ENSG00000114790		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	24490	protein-coding gene	gene with protein product	"""Src homology 3 domain-containing guanine nucleotide exchange factor"""					15133129, 12697679	Standard	NM_015595		Approved	DKFZP434D146, SGEF	uc021xgc.1	Q96DR7	OTTHUMG00000159098	ENST00000356448.4:c.724G>A	3.37:g.153840505G>A	ENSP00000348828:p.Ala242Thr	Somatic		Capture	Illumina HiSeq	Phase_I	155323195	NM_015595	B3KVP8|E9PBD0|Q68CL1|Q6AZ96|Q6Q8Q8|Q96AW8|Q96DR6|Q9H9D7|Q9H9R2|Q9UFW5	Missense_Mutation	SNP	ENST00000356448.4	37	CCDS46938.1	.	.	.	.	.	.	.	.	.	.	G	31	5.068120	0.93950	.	.	ENSG00000114790	ENST00000356448;ENST00000465093;ENST00000465817	T;T;T	0.72282	-0.64;-0.64;0.86	5.04	5.04	0.67666	.	0.107759	0.64402	D	0.000007	T	0.73666	0.3616	L	0.29908	0.895	0.58432	D	0.999997	D;D	0.76494	0.999;0.997	P;P	0.57911	0.829;0.735	T	0.76233	-0.3034	10	0.52906	T	0.07	-17.0122	17.981	0.89141	0.0:0.0:1.0:0.0	.	242;242	E9PBD0;Q96DR7	.;ARHGQ_HUMAN	T	242	ENSP00000348828:A242T;ENSP00000423418:A242T;ENSP00000423295:A242T	ENSP00000348828:A242T	A	+	1	0	ARHGEF26	155323195	1.000000	0.71417	0.952000	0.39060	0.829000	0.46940	6.509000	0.73725	2.316000	0.78162	0.655000	0.94253	GCC		0.502	ARHGEF26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353287.3	NM_015595	
PLCH1	23007	broad.mit.edu	37	3	155205891	155205891	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr3:155205891G>A	ENST00000340059.7	-	20	2508	c.2509C>T	c.(2509-2511)Cgg>Tgg	p.R837W	PLCH1_ENST00000447496.2_Missense_Mutation_p.R837W|PLCH1_ENST00000334686.6_Missense_Mutation_p.R819W|PLCH1_ENST00000460012.1_Missense_Mutation_p.R819W|PLCH1-AS2_ENST00000472913.1_RNA|PLCH1_ENST00000414191.1_Missense_Mutation_p.R819W|PLCH1_ENST00000494598.1_Missense_Mutation_p.R837W	NM_001130960.1	NP_001124432.1	Q4KWH8	PLCH1_HUMAN	phospholipase C, eta 1	837					inositol phosphate metabolic process (GO:0043647)|lipid catabolic process (GO:0016042)|phosphatidylinositol-mediated signaling (GO:0048015)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|calcium-dependent phospholipase C activity (GO:0050429)|phosphatidylinositol phospholipase C activity (GO:0004435)|signal transducer activity (GO:0004871)	p.R819W(1)		NS(3)|breast(3)|endometrium(9)|kidney(4)|large_intestine(20)|lung(45)|ovary(2)|prostate(5)|skin(8)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(4)	107			Lung(72;0.11)|LUSC - Lung squamous cell carcinoma(72;0.114)			TAGACATGCCGGTAGCCTGAT	0.368																																					p.R837W												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C2509T	3						.						112.0	108.0	110.0					3																	155205891		2203	4300	6503	156688585	SO:0001583	missense	23007	exon20			AB028992	CCDS33881.1, CCDS46939.1, CCDS46940.1	3q25	2013-01-10	2006-03-16	2006-03-16	ENSG00000114805	ENSG00000114805	3.1.4.11	"""EF-hand domain containing"""	29185	protein-coding gene	gene with protein product		612835	"""phospholipase C-like 3"""	PLCL3		15702972	Standard	NM_014996		Approved	KIAA1069, MGC117152, DKFZp434C1372, PLCeta1	uc021xge.1	Q4KWH8	OTTHUMG00000158477	ENST00000340059.7:c.2509C>T	3.37:g.155205891G>A	ENSP00000345988:p.Arg837Trp	Somatic		Capture	Illumina HiSeq	Phase_I	156688585	NM_001130960	Q29RV9|Q4KWH9|Q68CN0|Q86XK4|Q9H9U2|Q9UPT3	Missense_Mutation	SNP	ENST00000340059.7	37	CCDS46939.1	.	.	.	.	.	.	.	.	.	.	G	18.17	3.564833	0.65651	.	.	ENSG00000114805	ENST00000494598;ENST00000460012;ENST00000447496;ENST00000340059;ENST00000334686;ENST00000414191	T;T;T;T;T;T	0.16597	2.33;2.33;2.33;2.33;2.33;2.33	5.18	5.18	0.71444	C2 calcium-dependent membrane targeting (1);C2 calcium/lipid-binding domain, CaLB (1);	0.000000	0.85682	D	0.000000	T	0.45175	0.1329	M	0.73962	2.25	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	T	0.46373	-0.9196	10	0.87932	D	0	.	18.697	0.91604	0.0:0.0:1.0:0.0	.	819;837;837	Q4KWH8-2;Q4KWH8;Q4KWH8-3	.;PLCH1_HUMAN;.	W	837;819;837;837;819;819	ENSP00000419100:R837W;ENSP00000417502:R819W;ENSP00000402759:R837W;ENSP00000345988:R837W;ENSP00000335469:R819W;ENSP00000412977:R819W	ENSP00000335469:R819W	R	-	1	2	PLCH1	156688585	1.000000	0.71417	1.000000	0.80357	0.427000	0.31564	5.579000	0.67457	2.403000	0.81681	0.655000	0.94253	CGG		0.368	PLCH1-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000351125.1	NM_014996	
GALNT15	117248	broad.mit.edu	37	3	16250164	16250164	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr3:16250164A>G	ENST00000339732.5	+	4	1569	c.1066A>G	c.(1066-1068)Ata>Gta	p.I356V	GALNT15_ENST00000437509.1_Missense_Mutation_p.I356V	NM_054110.4	NP_473451.3	Q8N3T1	GLT15_HUMAN	polypeptide N-acetylgalactosaminyltransferase 15	356					cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|transport vesicle (GO:0030133)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)|polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)	p.I356V(1)									CCAGTCCCCCATAAGCCCCAT	0.577																																					p.I356V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A1066G	3						.						107.0	99.0	102.0					3																	16250164		2203	4300	6503	16225168	SO:0001583	missense	117248	exon4			AY358443	CCDS33711.1	3p25.1	2014-03-13	2014-03-13	2013-01-25	ENSG00000131386	ENSG00000131386	2.4.1.41	"""Glycosyltransferase family 2 domain containing"""	21531	protein-coding gene	gene with protein product	"""polypeptide GalNAc transferase 15"""	615131	"""UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase-like 2"", ""UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 15"""	GALNTL2		12975309, 14702039, 15147861	Standard	NM_054110		Approved	GALNT7, pp-GalNAc-T15	uc003car.4	Q8N3T1	OTTHUMG00000156893	ENST00000339732.5:c.1066A>G	3.37:g.16250164A>G	ENSP00000344260:p.Ile356Val	Somatic		Capture	Illumina HiSeq	Phase_I	16225168	NM_054110	A6NMN1|B2R638|F1LIP6|Q86T60|Q96C46|Q96DJ5	Missense_Mutation	SNP	ENST00000339732.5	37	CCDS33711.1	.	.	.	.	.	.	.	.	.	.	A	4.643	0.119587	0.08881	.	.	ENSG00000131386	ENST00000339732;ENST00000437509	T;T	0.58652	0.32;0.32	5.69	2.01	0.26516	.	0.536240	0.20639	N	0.088432	T	0.38692	0.1050	N	0.25286	0.73	0.26671	N	0.971725	B	0.06786	0.001	B	0.09377	0.004	T	0.18808	-1.0325	10	0.25751	T	0.34	.	9.2958	0.37815	0.7289:0.0:0.2711:0.0	.	356	Q8N3T1	GLTL2_HUMAN	V	356	ENSP00000344260:I356V;ENSP00000395873:I356V	ENSP00000344260:I356V	I	+	1	0	GALNTL2	16225168	1.000000	0.71417	0.986000	0.45419	0.127000	0.20565	2.497000	0.45354	0.108000	0.17862	-0.379000	0.06801	ATA		0.577	GALNT15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346483.2	NM_054110	
PLCL2	23228	broad.mit.edu	37	3	17052001	17052001	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr3:17052001A>G	ENST00000418129.2	+	2	1250	c.785A>G	c.(784-786)tAt>tGt	p.Y262C	PLCL2_ENST00000396755.2_Missense_Mutation_p.Y262C|PLCL2_ENST00000432376.1_Missense_Mutation_p.Y262C|PLCL2_ENST00000460467.1_Intron	NM_001144382.1	NP_001137854.1	Q9UPR0	PLCL2_HUMAN	phospholipase C-like 2	388					B cell proliferation involved in immune response (GO:0002322)|B-1a B cell differentiation (GO:0002337)|gamma-aminobutyric acid signaling pathway (GO:0007214)|intracellular signal transduction (GO:0035556)|lipid metabolic process (GO:0006629)|negative regulation of B cell receptor signaling pathway (GO:0050859)|positive regulation of receptor binding (GO:1900122)|regulation of peptidyl-serine phosphorylation (GO:0033135)|regulation of synaptic transmission, GABAergic (GO:0032228)	cytoplasm (GO:0005737)	calcium ion binding (GO:0005509)|GABA receptor binding (GO:0050811)|phosphatidylinositol phospholipase C activity (GO:0004435)|signal transducer activity (GO:0004871)	p.Y262C(1)		breast(4)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(9)|lung(13)|ovary(1)|prostate(2)|skin(7)|urinary_tract(1)	43						ATTCACAAATATGAACCATCC	0.398																																					p.M382V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A1144G	3						.						65.0	66.0	66.0					3																	17052001		2203	4300	6503	17027005	SO:0001583	missense	23228	exon3			AB029015	CCDS33713.1, CCDS74911.1	3p25.3-p25.1	2008-03-18	2002-02-18	2002-02-22	ENSG00000154822	ENSG00000154822			9064	protein-coding gene	gene with protein product		614276	"""phospholipase C, epsilon 2"""	PLCE2		10470851	Standard	NM_015184		Approved	KIAA1092	uc011awd.2	Q9UPR0	OTTHUMG00000155467	ENST00000418129.2:c.785A>G	3.37:g.17052001A>G	ENSP00000409637:p.Tyr262Cys	Somatic		Capture	Illumina HiSeq	Phase_I	17027005	NM_001144382	A8K5V4|Q8N498|Q9H8L0|Q9UFP9	Missense_Mutation	SNP	ENST00000418129.2	37	CCDS33713.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	0.515|0.515	-0.864609|-0.864609	0.02590|0.02590	.|.	.|.	ENSG00000154822|ENSG00000154822	ENST00000419842|ENST00000418129;ENST00000285094;ENST00000396755;ENST00000432376	.|T;T;T	.|0.25749	.|1.78;1.78;1.78	5.68|5.68	4.51|4.51	0.55191|0.55191	.|Phospholipase C, phosphoinositol-specific, EF-hand-like (1);EF-hand-like domain (1);	.|0.111167	.|0.64402	.|D	.|0.000005	T|T	0.24586|0.24586	0.0596|0.0596	.|.	.|.	.|.	0.53688|0.53688	D|D	0.999977|0.999977	.|B	.|0.22080	.|0.064	.|B	.|0.29077	.|0.098	T|T	0.03662|0.03662	-1.1015|-1.1015	4|9	.|0.52906	.|T	.|0.07	.|.	10.6089|10.6089	0.45410|0.45410	0.7436:0.0:0.0:0.2564|0.7436:0.0:0.0:0.2564	.|.	.|388	.|Q9UPR0	.|PLCL2_HUMAN	V|C	6|262;389;262;262	.|ENSP00000409637:Y262C;ENSP00000379979:Y262C;ENSP00000412836:Y262C	.|ENSP00000285094:Y389C	M|Y	+|+	1|2	0|0	PLCL2|PLCL2	17027005|17027005	1.000000|1.000000	0.71417|0.71417	0.715000|0.715000	0.30552|0.30552	0.051000|0.051000	0.14879|0.14879	7.396000|7.396000	0.79891|0.79891	0.964000|0.964000	0.38108|0.38108	-0.490000|-0.490000	0.04691|0.04691	ATG|TAT		0.398	PLCL2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340250.3		
RARRES1	5918	broad.mit.edu	37	3	158428698	158428698	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr3:158428698G>A	ENST00000237696.5	-	3	644	c.364C>T	c.(364-366)Cgt>Tgt	p.R122C	RARRES1_ENST00000498640.1_Intron|RARRES1_ENST00000479756.1_Missense_Mutation_p.R122C	NM_206963.1	NP_996846.1	P49788	TIG1_HUMAN	retinoic acid receptor responder (tazarotene induced) 1	122					negative regulation of cell proliferation (GO:0008285)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)		p.R122C(1)		NS(1)|central_nervous_system(2)|kidney(2)|large_intestine(2)|lung(1)|ovary(1)	9			Lung(72;0.00309)|LUSC - Lung squamous cell carcinoma(72;0.0043)		Tretinoin(DB00755)	TTCCCCAAACGTCCCTCACCT	0.443																																					p.R122C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C364T	3						.						173.0	159.0	164.0					3																	158428698		2203	4300	6503	159911392	SO:0001583	missense	5918	exon3			U27185	CCDS3184.1, CCDS54665.1	3q25.32	2013-07-29			ENSG00000118849	ENSG00000118849			9867	protein-coding gene	gene with protein product	"""latexin-like"""	605090				8601727, 9270552	Standard	NM_002888		Approved	TIG1, LXNL	uc003fci.3	P49788	OTTHUMG00000158834	ENST00000237696.5:c.364C>T	3.37:g.158428698G>A	ENSP00000237696:p.Arg122Cys	Somatic		Capture	Illumina HiSeq	Phase_I	159911392	NM_002888	Q8N1D7	Missense_Mutation	SNP	ENST00000237696.5	37	CCDS3184.1	.	.	.	.	.	.	.	.	.	.	G	15.55	2.867595	0.51588	.	.	ENSG00000118849	ENST00000237696;ENST00000479756	T;T	0.25414	1.8;1.8	5.7	1.89	0.25635	.	0.798454	0.10730	N	0.640701	T	0.32376	0.0827	L	0.44542	1.39	0.09310	N	1	D;D	0.76494	0.999;0.999	P;P	0.60541	0.804;0.876	T	0.17349	-1.0372	10	0.72032	D	0.01	7.7519	1.9324	0.03330	0.1713:0.1615:0.4998:0.1673	.	122;122	P49788-2;P49788	.;TIG1_HUMAN	C	122	ENSP00000237696:R122C;ENSP00000418556:R122C	ENSP00000237696:R122C	R	-	1	0	RARRES1	159911392	0.021000	0.18746	0.000000	0.03702	0.016000	0.09150	1.135000	0.31454	0.332000	0.23536	-0.176000	0.13171	CGT		0.443	RARRES1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352358.1		
SLC2A2	6514	broad.mit.edu	37	3	170723136	170723136	+	Nonsense_Mutation	SNP	G	G	A	rs121909743		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr3:170723136G>A	ENST00000314251.3	-	7	980	c.901C>T	c.(901-903)Cga>Tga	p.R301*	SLC2A2_ENST00000382808.4_Nonsense_Mutation_p.R182*	NM_000340.1	NP_000331.1	P11168	GTR2_HUMAN	solute carrier family 2 (facilitated glucose transporter), member 2	301					carbohydrate metabolic process (GO:0005975)|endocrine pancreas development (GO:0031018)|energy reserve metabolic process (GO:0006112)|glucose transport (GO:0015758)|hexose transmembrane transport (GO:0035428)|hexose transport (GO:0008645)|regulation of insulin secretion (GO:0050796)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	brush border (GO:0005903)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	D-glucose transmembrane transporter activity (GO:0055056)|dehydroascorbic acid transporter activity (GO:0033300)|glucose transmembrane transporter activity (GO:0005355)|hexose transmembrane transporter activity (GO:0015149)	p.R301*(1)		central_nervous_system(1)|endometrium(2)|large_intestine(9)|lung(9)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	24	all_cancers(22;1.41e-19)|all_lung(20;1.59e-15)|Lung NSC(18;7.08e-15)|Ovarian(172;0.00197)|Breast(254;0.122)		LUSC - Lung squamous cell carcinoma(14;1.1e-14)|Lung(28;2.99e-14)		Streptozocin(DB00428)	ATAGGCTGTCGGTAGCTGGAA	0.418																																					p.R301X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.C901T	3	GRCh37	CM971382	SLC2A2	M	rs121909743	.						201.0	182.0	189.0					3																	170723136		2203	4300	6503	172205830	SO:0001587	stop_gained	6514	exon7			J03810	CCDS3215.1	3q26.2-q27	2013-05-22			ENSG00000163581	ENSG00000163581		"""Solute carriers"""	11006	protein-coding gene	gene with protein product		138160		GLUT2		1852621	Standard	NM_000340		Approved		uc003fhe.1	P11168	OTTHUMG00000158997	ENST00000314251.3:c.901C>T	3.37:g.170723136G>A	ENSP00000323568:p.Arg301*	Somatic		Capture	Illumina HiSeq	Phase_I	172205830	NM_000340	A8K481|B2R936|B7Z547|F8W8V8|Q9UCW9	Nonsense_Mutation	SNP	ENST00000314251.3	37	CCDS3215.1	.	.	.	.	.	.	.	.	.	.	G	15.77	2.930078	0.52759	.	.	ENSG00000163581	ENST00000314251;ENST00000382808	.	.	.	5.53	2.71	0.32032	.	0.053497	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	9.9913	0.41872	0.0638:0.0:0.5056:0.4306	.	.	.	.	X	301;182	.	ENSP00000323568:R301X	R	-	1	2	SLC2A2	172205830	1.000000	0.71417	0.209000	0.23619	0.110000	0.19582	1.608000	0.36847	0.357000	0.24183	0.591000	0.81541	CGA		0.418	SLC2A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352834.1	NM_000340	
MCF2L2	23101	broad.mit.edu	37	3	182910862	182910862	+	Missense_Mutation	SNP	C	C	T	rs146776367	byFrequency	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr3:182910862C>T	ENST00000328913.3	-	27	3238	c.2941G>A	c.(2941-2943)Gga>Aga	p.G981R	MCF2L2_ENST00000468976.1_5'UTR|MCF2L2_ENST00000473233.1_Missense_Mutation_p.G981R	NM_015078.2	NP_055893	Q86YR7	MF2L2_HUMAN	MCF.2 cell line derived transforming sequence-like 2	981							Rho guanyl-nucleotide exchange factor activity (GO:0005089)	p.G981R(1)		breast(2)|endometrium(5)|kidney(4)|large_intestine(22)|lung(25)|ovary(3)|prostate(4)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	72	all_cancers(143;1.26e-12)|Ovarian(172;0.0355)		all cancers(12;3.35e-44)|Epithelial(37;6.48e-38)|LUSC - Lung squamous cell carcinoma(7;7.12e-25)|Lung(8;6.39e-23)|OV - Ovarian serous cystadenocarcinoma(80;6.75e-21)			ATCCATGGTCCGGATCCTGCT	0.502													C|||	4	0.000798722	0.003	0.0	5008	,	,		19094	0.0		0.0	False		,,,				2504	0.0				p.G981R												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2941A	3						.	C	ARG/GLY	14,4392	22.3+/-47.3	0,14,2189	204.0	179.0	188.0		2941	2.1	0.0	3	dbSNP_134	188	1,8599	1.2+/-3.3	0,1,4299	yes	missense	MCF2L2	NM_015078.2	125	0,15,6488	TT,TC,CC		0.0116,0.3177,0.1153	benign	981/1115	182910862	15,12991	2203	4300	6503	184393556	SO:0001583	missense	23101	exon27			AB020668	CCDS3243.1	3q27	2012-07-24			ENSG00000053524	ENSG00000053524		"""Rho guanine nucleotide exchange factors"""	30319	protein-coding gene	gene with protein product							Standard	NM_015078		Approved	KIAA0861, ARHGEF22	uc003fli.1	Q86YR7	OTTHUMG00000158388	ENST00000328913.3:c.2941G>A	3.37:g.182910862C>T	ENSP00000328118:p.Gly981Arg	Somatic		Capture	Illumina HiSeq	Phase_I	184393556	NM_015078	O94942|Q6P2B8|Q6ZVJ5|Q8N318	Missense_Mutation	SNP	ENST00000328913.3	37	CCDS3243.1	3	0.0013736263736263737	3	0.006097560975609756	0	0.0	0	0.0	0	0.0	C	1.709	-0.499545	0.04291	0.003177	1.16E-4	ENSG00000053524	ENST00000328913;ENST00000473233	T;T	0.32023	1.47;1.47	2.97	2.09	0.27110	.	1.989150	0.02922	N	0.138024	T	0.07458	0.0188	N	0.04508	-0.205	0.09310	N	0.999999	P	0.42296	0.775	B	0.25884	0.064	T	0.17806	-1.0357	10	0.11485	T	0.65	.	5.7818	0.18310	0.0:0.8524:0.0:0.1476	.	981	Q86YR7	MF2L2_HUMAN	R	981	ENSP00000328118:G981R;ENSP00000420070:G981R	ENSP00000328118:G981R	G	-	1	0	MCF2L2	184393556	0.002000	0.14202	0.001000	0.08648	0.001000	0.01503	1.013000	0.29937	0.805000	0.34159	0.467000	0.42956	GGA		0.502	MCF2L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350868.1	NM_015078	
YEATS2	55689	broad.mit.edu	37	3	183474383	183474383	+	Silent	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr3:183474383G>A	ENST00000305135.5	+	12	1653	c.1458G>A	c.(1456-1458)gtG>gtA	p.V486V		NM_018023.4	NP_060493.3	Q9ULM3	YETS2_HUMAN	YEATS domain containing 2	486					chromatin organization (GO:0006325)|histone H3 acetylation (GO:0043966)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)	Ada2/Gcn5/Ada3 transcription activator complex (GO:0005671)|mitotic spindle (GO:0072686)	TBP-class protein binding (GO:0017025)	p.V486V(1)		NS(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(24)|ovary(3)|prostate(2)|skin(3)	49	all_cancers(143;6.55e-10)|Ovarian(172;0.0303)		all cancers(12;2.38e-42)|Epithelial(37;1.9e-36)|OV - Ovarian serous cystadenocarcinoma(80;6.48e-22)			CAGTCCACGTGAAGCAAGGCA	0.473																																					p.V486V												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G1458A	3						.						104.0	107.0	106.0					3																	183474383		1927	4126	6053	184957077	SO:0001819	synonymous_variant	55689	exon12			AB033023	CCDS43175.1	3q27.3	2004-08-18			ENSG00000163872	ENSG00000163872			25489	protein-coding gene	gene with protein product		613373				10574462	Standard	NM_018023		Approved	FLJ10201, FLJ12841, FLJ13308, KIAA1197	uc003fly.2	Q9ULM3	OTTHUMG00000156898	ENST00000305135.5:c.1458G>A	3.37:g.183474383G>A		Somatic		Capture	Illumina HiSeq	Phase_I	184957077	NM_018023	A7E2B9|D3DNS9|Q641P6|Q9NW96	Silent	SNP	ENST00000305135.5	37	CCDS43175.1																																																																																				0.473	YEATS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346507.2	NM_018023	
YEATS2	55689	broad.mit.edu	37	3	183479892	183479892	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr3:183479892T>C	ENST00000305135.5	+	15	1967	c.1772T>C	c.(1771-1773)aTc>aCc	p.I591T		NM_018023.4	NP_060493.3	Q9ULM3	YETS2_HUMAN	YEATS domain containing 2	591					chromatin organization (GO:0006325)|histone H3 acetylation (GO:0043966)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)	Ada2/Gcn5/Ada3 transcription activator complex (GO:0005671)|mitotic spindle (GO:0072686)	TBP-class protein binding (GO:0017025)	p.I591T(1)		NS(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(24)|ovary(3)|prostate(2)|skin(3)	49	all_cancers(143;6.55e-10)|Ovarian(172;0.0303)		all cancers(12;2.38e-42)|Epithelial(37;1.9e-36)|OV - Ovarian serous cystadenocarcinoma(80;6.48e-22)			AAGGTGATCATCAAACAGGAA	0.468																																					p.I591T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T1772C	3						.						78.0	82.0	81.0					3																	183479892		1949	4148	6097	184962586	SO:0001583	missense	55689	exon15			AB033023	CCDS43175.1	3q27.3	2004-08-18			ENSG00000163872	ENSG00000163872			25489	protein-coding gene	gene with protein product		613373				10574462	Standard	NM_018023		Approved	FLJ10201, FLJ12841, FLJ13308, KIAA1197	uc003fly.2	Q9ULM3	OTTHUMG00000156898	ENST00000305135.5:c.1772T>C	3.37:g.183479892T>C	ENSP00000306983:p.Ile591Thr	Somatic		Capture	Illumina HiSeq	Phase_I	184962586	NM_018023	A7E2B9|D3DNS9|Q641P6|Q9NW96	Missense_Mutation	SNP	ENST00000305135.5	37	CCDS43175.1	.	.	.	.	.	.	.	.	.	.	T	23.3	4.404109	0.83230	.	.	ENSG00000163872	ENST00000421660;ENST00000305135	T	0.29142	1.58	5.77	5.77	0.91146	.	0.000000	0.85682	D	0.000000	T	0.45094	0.1325	L	0.32530	0.975	0.58432	D	0.999998	D	0.76494	0.999	D	0.78314	0.991	T	0.27365	-1.0076	10	0.38643	T	0.18	-20.0434	16.0977	0.81139	0.0:0.0:0.0:1.0	.	591	Q9ULM3	YETS2_HUMAN	T	591	ENSP00000306983:I591T	ENSP00000306983:I591T	I	+	2	0	YEATS2	184962586	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.222000	0.78025	2.216000	0.71823	0.528000	0.53228	ATC		0.468	YEATS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346507.2	NM_018023	
ABCC5	10057	broad.mit.edu	37	3	183679308	183679308	+	Silent	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr3:183679308C>T	ENST00000334444.6	-	16	2610	c.2370G>A	c.(2368-2370)ccG>ccA	p.P790P	ABCC5_ENST00000265586.6_Silent_p.P790P	NM_005688.2	NP_005679.2	O15440	MRP5_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 5	790					carbohydrate metabolic process (GO:0005975)|glycosaminoglycan metabolic process (GO:0030203)|hyaluronan biosynthetic process (GO:0030213)|hyaluronan metabolic process (GO:0030212)|organic anion transport (GO:0015711)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|organic anion transmembrane transporter activity (GO:0008514)	p.P790P(1)		NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(9)|lung(32)|ovary(3)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	62	all_cancers(143;1.85e-10)|Ovarian(172;0.0303)		Epithelial(37;1.74e-35)|OV - Ovarian serous cystadenocarcinoma(80;6.48e-22)		Adefovir Dipivoxil(DB00718)|Alprostadil(DB00770)|Atorvastatin(DB01076)|Cisplatin(DB00515)|Dinoprostone(DB00917)|Dipyridamole(DB00975)|Fluorouracil(DB00544)|Glutathione(DB00143)|Mercaptopurine(DB01033)|Probenecid(DB01032)|Rifampicin(DB01045)|Sildenafil(DB00203)|Sulfinpyrazone(DB01138)|Zidovudine(DB00495)	CCTCAACTGGCGGTGTCTCTC	0.483																																					p.P790P												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G2370A	3						.						67.0	72.0	70.0					3																	183679308		2109	4233	6342	185162002	SO:0001819	synonymous_variant	10057	exon16			AF104942	CCDS33898.1, CCDS43176.1	3q27	2012-03-14			ENSG00000114770	ENSG00000114770		"""ATP binding cassette transporters / subfamily C"""	56	protein-coding gene	gene with protein product		605251				8894702, 9827529	Standard	XM_005247058		Approved	MRP5, SMRP, EST277145, MOAT-C	uc003fmg.3	O15440	OTTHUMG00000156871	ENST00000334444.6:c.2370G>A	3.37:g.183679308C>T		Somatic		Capture	Illumina HiSeq	Phase_I	185162002	NM_005688	B9EIQ2|O14517|Q29ZA9|Q29ZB1|Q86UX3|Q86W30|Q9UN85|Q9UNP5|Q9UQC3	Silent	SNP	ENST00000334444.6	37	CCDS43176.1																																																																																				0.483	ABCC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346350.1	NM_005688	
HTR3C	170572	broad.mit.edu	37	3	183770910	183770910	+	Silent	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr3:183770910C>T	ENST00000318351.1	+	1	76	c.42C>T	c.(40-42)tgC>tgT	p.C14C		NM_130770.2	NP_570126.2	Q8WXA8	5HT3C_HUMAN	5-hydroxytryptamine (serotonin) receptor 3C, ionotropic	14					ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	extracellular ligand-gated ion channel activity (GO:0005230)	p.C14C(1)		central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(14)|ovary(1)|prostate(1)|skin(2)|stomach(2)	32	all_cancers(143;2.33e-10)|Ovarian(172;0.0303)		Epithelial(37;1.74e-35)|OV - Ovarian serous cystadenocarcinoma(80;3.11e-22)		Ergoloid mesylate(DB01049)	CCCTCCTCTGCCTCACTGTCA	0.552																																					p.C14C												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C42T	3						.						121.0	102.0	109.0					3																	183770910		2203	4300	6503	185253604	SO:0001819	synonymous_variant	170572	exon1			AF459285	CCDS3250.1	3q27	2012-05-22	2012-02-03		ENSG00000178084	ENSG00000178084		"""5-HT (serotonin) receptors"", ""Ligand-gated ion channels / 5-HT (serotonin) receptors, ionotropic"""	24003	protein-coding gene	gene with protein product		610121	"""5-hydroxytryptamine (serotonin) receptor 3, family member C"""			12801637, 15157181	Standard	NM_130770		Approved		uc003fmk.3	Q8WXA8	OTTHUMG00000156862	ENST00000318351.1:c.42C>T	3.37:g.183770910C>T		Somatic		Capture	Illumina HiSeq	Phase_I	185253604	NM_130770	A2RRR5	Silent	SNP	ENST00000318351.1	37	CCDS3250.1																																																																																				0.552	HTR3C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346296.1	NM_130770	
HTR3E	285242	broad.mit.edu	37	3	183824082	183824082	+	Silent	SNP	G	G	A	rs374233648		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr3:183824082G>A	ENST00000415389.2	+	8	1558	c.1092G>A	c.(1090-1092)gcG>gcA	p.A364A	HTR3E-AS1_ENST00000431427.1_RNA|HTR3E_ENST00000425359.2_Silent_p.A349A|HTR3E_ENST00000440596.2_Silent_p.A390A|HTR3E_ENST00000436361.2_Silent_p.A364A|HTR3E_ENST00000335304.2_Silent_p.A379A	NM_001256613.1|NM_198313.2	NP_001243542.1|NP_938055.1	A5X5Y0	5HT3E_HUMAN	5-hydroxytryptamine (serotonin) receptor 3E, ionotropic	364					ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	extracellular ligand-gated ion channel activity (GO:0005230)	p.A379A(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(8)|lung(20)|ovary(1)|skin(2)|upper_aerodigestive_tract(2)	40	all_cancers(143;1.46e-10)|Ovarian(172;0.0303)		Epithelial(37;7.06e-36)|OV - Ovarian serous cystadenocarcinoma(80;3.11e-22)		Ergoloid mesylate(DB01049)	GTCCCACTGCGCCCCAGAAGG	0.667																																					p.A379A	Melanoma(7;227 727 6634 44770)											.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G1137A	3						.	G		1,4405	2.1+/-5.4	0,1,2202	29.0	33.0	31.0		1137	-6.4	0.0	3		31	0,8600		0,0,4300	no	coding-synonymous	HTR3E	NM_182589.2		0,1,6502	AA,AG,GG		0.0,0.0227,0.0077		379/472	183824082	1,13005	2203	4300	6503	185306776	SO:0001819	synonymous_variant	285242	exon7			AY159813	CCDS3251.1, CCDS58868.1, CCDS58869.1, CCDS58870.1, CCDS58871.1	3q27	2012-05-22	2012-02-03		ENSG00000186038	ENSG00000186038		"""5-HT (serotonin) receptors"", ""Ligand-gated ion channels / 5-HT (serotonin) receptors, ionotropic"""	24005	protein-coding gene	gene with protein product		610123	"""5-hydroxytryptamine (serotonin) receptor 3, family member E"""			12801637, 15157181	Standard	NM_001256613		Approved		uc010hxr.3	A5X5Y0	OTTHUMG00000156857	ENST00000415389.2:c.1092G>A	3.37:g.183824082G>A		Somatic		Capture	Illumina HiSeq	Phase_I	185306776	NM_182589	A8IKD7|E9PGF1|Q495G1|Q495G3|Q6V706|Q6V707|Q7Z6B2	Silent	SNP	ENST00000415389.2	37	CCDS58868.1																																																																																				0.667	HTR3E-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000346284.1	NM_182589	
AP2M1	1173	broad.mit.edu	37	3	183897972	183897972	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr3:183897972G>A	ENST00000292807.5	+	4	504	c.356G>A	c.(355-357)gGc>gAc	p.G119D	AP2M1_ENST00000439647.1_Missense_Mutation_p.G119D|AP2M1_ENST00000382456.3_Missense_Mutation_p.G119D|EIF2B5_ENST00000444495.1_Intron|AP2M1_ENST00000411763.2_Missense_Mutation_p.G144D	NM_004068.3	NP_004059.2	Q96CW1	AP2M1_HUMAN	adaptor-related protein complex 2, mu 1 subunit	119					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|axon guidance (GO:0007411)|endocytosis (GO:0006897)|epidermal growth factor receptor signaling pathway (GO:0007173)|intracellular protein transport (GO:0006886)|membrane organization (GO:0061024)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of protein localization to plasma membrane (GO:1903077)|neurotrophin TRK receptor signaling pathway (GO:0048011)|regulation of defense response to virus by virus (GO:0050690)|synaptic transmission (GO:0007268)|viral process (GO:0016032)	clathrin adaptor complex (GO:0030131)|clathrin-coated endocytic vesicle membrane (GO:0030669)|coated pit (GO:0005905)|cytosol (GO:0005829)|endocytic vesicle membrane (GO:0030666)|extracellular vesicular exosome (GO:0070062)|lysosomal membrane (GO:0005765)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	lipid binding (GO:0008289)|transporter activity (GO:0005215)	p.G119D(1)		endometrium(1)|large_intestine(4)|lung(10)|prostate(1)|skin(1)|urinary_tract(1)	18	all_cancers(143;1.12e-10)|Ovarian(172;0.0339)		Epithelial(37;2.92e-34)|OV - Ovarian serous cystadenocarcinoma(80;2.72e-22)			CTAGACTTTGGCTACCCACAG	0.522																																					p.G119D												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G356A	3						.						62.0	62.0	62.0					3																	183897972		1945	4138	6083	185380666	SO:0001583	missense	1173	exon4			U36188	CCDS43177.1, CCDS43178.1	3q28	2008-07-18			ENSG00000161203	ENSG00000161203			564	protein-coding gene	gene with protein product	"""clathrin-associated/assembly/adaptor protein, medium 1"", ""plasma membrane adaptor AP-2 50kDA protein"", ""clathrin coat adaptor protein AP50"", ""clathrin adaptor complex AP2, mu subunit"", ""HA2 50 kDA subunit"", ""clathrin assembly protein complex 2 medium chain"", ""AP-2 mu 2 chain"""	601024		CLAPM1		8595912	Standard	NM_004068		Approved	AP50, mu2	uc003fmw.3	Q96CW1	OTTHUMG00000156822	ENST00000292807.5:c.356G>A	3.37:g.183897972G>A	ENSP00000292807:p.Gly119Asp	Somatic		Capture	Illumina HiSeq	Phase_I	185380666	NM_001025205	A6NE12|D3DNT1|P20172|P53679	Missense_Mutation	SNP	ENST00000292807.5	37	CCDS43177.1	.	.	.	.	.	.	.	.	.	.	G	24.4	4.524334	0.85600	.	.	ENSG00000161203	ENST00000382456;ENST00000411763;ENST00000292807;ENST00000540821;ENST00000539646;ENST00000448139;ENST00000439647;ENST00000432591;ENST00000431779	D;D;D;D	0.85258	-1.88;-1.96;-1.87;-1.88	5.38	5.38	0.77491	Longin-like (1);AP complex, mu/sigma subunit (1);	0.000000	0.85682	D	0.000000	D	0.95736	0.8613	H	0.98111	4.15	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	D	0.96984	0.9717	10	0.87932	D	0	.	19.3311	0.94288	0.0:0.0:1.0:0.0	.	119;144;119	Q96CW1;E9PFW3;Q96CW1-2	AP2M1_HUMAN;.;.	D	119;144;119;59;106;121;119;119;119	ENSP00000371894:G119D;ENSP00000403362:G144D;ENSP00000292807:G119D;ENSP00000409081:G119D	ENSP00000292807:G119D	G	+	2	0	AP2M1	185380666	1.000000	0.71417	1.000000	0.80357	0.601000	0.36947	8.996000	0.93539	2.813000	0.96785	0.655000	0.94253	GGC		0.522	AP2M1-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000346013.1	NM_004068	
ECE2	9718	broad.mit.edu	37	3	184009965	184009965	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr3:184009965G>T	ENST00000402825.3	+	19	2591	c.2591G>T	c.(2590-2592)cGg>cTg	p.R864L	ECE2_ENST00000359140.4_Missense_Mutation_p.R717L|ECE2_ENST00000404464.3_Missense_Mutation_p.R746L|EIF2B5_ENST00000444495.1_Intron|ECE2_ENST00000357474.5_Missense_Mutation_p.R792L	NM_014693.3	NP_055508.3	O60344	ECE2_HUMAN	endothelin converting enzyme 2	864	Endothelin-converting enzyme 2 region.				brain development (GO:0007420)|cardioblast differentiation (GO:0010002)|cell-cell signaling (GO:0007267)|heart development (GO:0007507)|peptide hormone processing (GO:0016486)	cytoplasmic vesicle membrane (GO:0030659)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)|methyltransferase activity (GO:0008168)	p.R717L(1)		breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(11)|lung(13)|ovary(3)|prostate(1)|skin(4)|upper_aerodigestive_tract(4)|urinary_tract(4)	49	all_cancers(143;1.39e-10)|Ovarian(172;0.0339)		Epithelial(37;8.28e-34)|OV - Ovarian serous cystadenocarcinoma(80;2.72e-22)			GACTTCCTGCGGCACTTCGGC	0.657																																					p.R864L												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2591T	3						.						47.0	48.0	48.0					3																	184009965		2203	4300	6503	185492659	SO:0001583	missense	9718	exon19			AF428263	CCDS3255.1, CCDS33899.1, CCDS3256.2, CCDS43179.1, CCDS46969.1	3q27.1	2007-07-26			ENSG00000145194	ENSG00000145194			13275	protein-coding gene	gene with protein product		610145				11718899	Standard	NM_032331		Approved	KIAA0604, MGC2408	uc003fni.4	O60344	OTTHUMG00000150551	ENST00000402825.3:c.2591G>T	3.37:g.184009965G>T	ENSP00000384223:p.Arg864Leu	Somatic		Capture	Illumina HiSeq	Phase_I	185492659	NM_014693	A5PLK8|Q6NTG7|Q6UW36|Q8NFD7|Q96NX3|Q96NX4|Q9BRZ8	Missense_Mutation	SNP	ENST00000402825.3	37	CCDS3256.2	.	.	.	.	.	.	.	.	.	.	G	14.83	2.651169	0.47362	.	.	ENSG00000145194	ENST00000402825;ENST00000359140;ENST00000404464;ENST00000357474	D;D;D;D	0.82803	-1.65;-1.65;-1.65;-1.65	5.47	1.47	0.22746	Peptidase M13, neprilysin, C-terminal (1);Metallopeptidase, catalytic domain (1);	0.420791	0.24136	N	0.041203	T	0.76615	0.4012	L	0.60455	1.87	0.30270	N	0.79236	P;B;P;B	0.42203	0.773;0.298;0.564;0.09	B;B;B;B	0.39562	0.303;0.168;0.222;0.112	T	0.74426	-0.3669	10	0.66056	D	0.02	-16.078	7.1832	0.25784	0.462:0.0:0.538:0.0	.	746;792;717;864	O60344-2;O60344-5;O60344-3;O60344	.;.;.;ECE2_HUMAN	L	864;717;746;792	ENSP00000384223:R864L;ENSP00000352052:R717L;ENSP00000385846:R746L;ENSP00000350066:R792L	ENSP00000350066:R792L	R	+	2	0	ECE2	185492659	0.675000	0.27558	0.955000	0.39395	0.849000	0.48306	1.384000	0.34396	0.606000	0.29965	-0.367000	0.07326	CGG		0.657	ECE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318874.3	NM_014693	
LPP	4026	broad.mit.edu	37	3	188242500	188242500	+	Silent	SNP	C	C	T	rs146490639		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr3:188242500C>T	ENST00000312675.4	+	5	600	c.354C>T	c.(352-354)gaC>gaT	p.D118D	LPP_ENST00000543006.1_Silent_p.D118D|LPP_ENST00000448637.1_Silent_p.D118D	NM_001167672.1|NM_005578.3	NP_001161144.1|NP_005569.1	Q93052	LPP_HUMAN	LIM domain containing preferred translocation partner in lipoma	118	Pro-rich.				cell adhesion (GO:0007155)	cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	zinc ion binding (GO:0008270)	p.D118D(1)	HMGA2/LPP(161)	NS(1)|breast(1)|large_intestine(3)|lung(2)|ovary(1)|upper_aerodigestive_tract(2)	10	all_cancers(143;1.37e-09)|all_hematologic(3;0.0429)|Ovarian(172;0.088)	all_lung(153;0.00139)|Lung NSC(153;0.00202)		GBM - Glioblastoma multiforme(93;0.00602)		CCAGCCTGGACGCTGAGATTG	0.527			T	"""HMGA2, MLL, C12orf9"""	"""lipoma, leukemia"""																																p.D118D			Dom	yes		3	3q28	4026	LIM domain containing preferred translocation partner in lipoma		"""L, M"""	.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C354T	3						.	C	,,	1,4405	2.1+/-5.4	0,1,2202	126.0	120.0	122.0		354,354,354	-1.6	1.0	3	dbSNP_134	122	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous,coding-synonymous	LPP	NM_001167671.1,NM_001167672.1,NM_005578.3	,,	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	,,	118/613,118/466,118/613	188242500	1,13005	2203	4300	6503	189725194	SO:0001819	synonymous_variant	4026	exon5			AL833171	CCDS3291.1	3q27-q28	2004-03-02	2002-01-14		ENSG00000145012	ENSG00000145012			6679	protein-coding gene	gene with protein product		600700	"""LIM domain-containing preferred translocation partner in lipoma"""			8812423	Standard	XM_005247453		Approved		uc003frs.2	Q93052	OTTHUMG00000156387	ENST00000312675.4:c.354C>T	3.37:g.188242500C>T		Somatic		Capture	Illumina HiSeq	Phase_I	189725194	NM_001167671	A1L4L6|D3DNV6|Q8NFX5	Silent	SNP	ENST00000312675.4	37	CCDS3291.1																																																																																				0.527	LPP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344030.1	NM_005578	
TP63	8626	broad.mit.edu	37	3	189456541	189456541	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr3:189456541C>T	ENST00000264731.3	+	3	391	c.302C>T	c.(301-303)tCg>tTg	p.S101L	TP63_ENST00000440651.2_Missense_Mutation_p.S101L|TP63_ENST00000418709.2_Missense_Mutation_p.S101L|TP63_ENST00000382063.4_Missense_Mutation_p.S101L|TP63_ENST00000320472.5_Missense_Mutation_p.S101L|TP63_ENST00000392460.3_Missense_Mutation_p.S101L	NM_001114978.1|NM_003722.4	NP_001108450.1|NP_003713.3	Q9H3D4	P63_HUMAN	tumor protein p63	101	Transcription activation.				apoptotic process (GO:0006915)|cell aging (GO:0007569)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to UV (GO:0034644)|chromatin remodeling (GO:0006338)|cloacal septation (GO:0060197)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|ectoderm and mesoderm interaction (GO:0007499)|embryonic limb morphogenesis (GO:0030326)|epidermal cell division (GO:0010481)|epithelial cell development (GO:0002064)|establishment of planar polarity (GO:0001736)|establishment of skin barrier (GO:0061436)|female genitalia morphogenesis (GO:0048807)|hair follicle morphogenesis (GO:0031069)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|keratinocyte differentiation (GO:0030216)|keratinocyte proliferation (GO:0043616)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organismal aging (GO:0010259)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cellular senescence (GO:2000773)|negative regulation of keratinocyte differentiation (GO:0045617)|negative regulation of mesoderm development (GO:2000381)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|odontogenesis of dentin-containing tooth (GO:0042475)|polarized epithelial cell differentiation (GO:0030859)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of cell cycle G1/S phase transition (GO:1902808)|positive regulation of fibroblast apoptotic process (GO:2000271)|positive regulation of keratinocyte proliferation (GO:0010838)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of Notch signaling pathway (GO:0045747)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|post-anal tail morphogenesis (GO:0036342)|prostatic bud formation (GO:0060513)|protein homotetramerization (GO:0051289)|proximal/distal pattern formation (GO:0009954)|regulation of epidermal cell division (GO:0010482)|regulation of neuron apoptotic process (GO:0043523)|response to gamma radiation (GO:0010332)|response to X-ray (GO:0010165)|skeletal system development (GO:0001501)|smooth muscle tissue development (GO:0048745)|squamous basal epithelial stem cell differentiation involved in prostate gland acinus development (GO:0060529)|sympathetic nervous system development (GO:0048485)|urinary bladder development (GO:0060157)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendrite (GO:0030425)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|double-stranded DNA binding (GO:0003690)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|p53 binding (GO:0002039)|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)|transcription factor binding transcription factor activity (GO:0000989)|transcription regulatory region DNA binding (GO:0044212)|WW domain binding (GO:0050699)	p.S101L(1)		breast(2)|central_nervous_system(2)|cervix(1)|endometrium(7)|kidney(5)|large_intestine(12)|lung(15)|ovary(2)|skin(9)|upper_aerodigestive_tract(6)	61	all_cancers(143;3.35e-10)|Ovarian(172;0.0925)		Lung(62;3.33e-05)	GBM - Glioblastoma multiforme(93;0.0227)		ATGCAGGACTCGGACCTGAGT	0.473										HNSCC(45;0.13)																											p.S101L												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C302T	3						.						114.0	103.0	107.0					3																	189456541		2203	4300	6503	190939235	SO:0001583	missense	8626	exon3			AB010153	CCDS3293.1, CCDS46976.1, CCDS46977.1, CCDS46978.1, CCDS46979.1, CCDS46980.1	3q27-q29	2014-09-17			ENSG00000073282	ENSG00000073282			15979	protein-coding gene	gene with protein product		603273	"""tumor protein p73-like"", ""tumor protein p53-like"", ""tumor protein p53-competing protein"""	TP73L, TP53L, TP53CP		9774969, 9662378, 11181441, 11181451	Standard	NM_003722		Approved	p51, SHFM4, EEC3, p63, p73L, OFC8, KET, p73H, NBP, p53CP	uc003fry.2	Q9H3D4	OTTHUMG00000156313	ENST00000264731.3:c.302C>T	3.37:g.189456541C>T	ENSP00000264731:p.Ser101Leu	Somatic		Capture	Illumina HiSeq	Phase_I	190939235	NM_001114979	O75080|O75195|O75922|O76078|Q6VEG2|Q6VEG3|Q6VEG4|Q6VFJ1|Q6VFJ2|Q6VFJ3|Q6VH20|Q7LDI3|Q7LDI4|Q7LDI5|Q96KR0|Q9H3D2|Q9H3D3|Q9H3P8|Q9NPH7|Q9P1B4|Q9P1B5|Q9P1B6|Q9P1B7|Q9UBV9|Q9UE10|Q9UP26|Q9UP27|Q9UP28|Q9UP74	Missense_Mutation	SNP	ENST00000264731.3	37	CCDS3293.1	.	.	.	.	.	.	.	.	.	.	C	15.98	2.992906	0.54041	.	.	ENSG00000073282	ENST00000264731;ENST00000418709;ENST00000320472;ENST00000392460;ENST00000440651;ENST00000382063	D;D;D;D;D;D	0.99735	-5.98;-6.26;-6.22;-6.22;-5.98;-6.58	5.57	5.57	0.84162	.	0.348394	0.26642	N	0.023241	D	0.97607	0.9216	N	0.08118	0	0.80722	D	1	B;B;B;B	0.19073	0.033;0.007;0.004;0.032	B;B;B;B	0.14578	0.005;0.011;0.002;0.001	D	0.98018	1.0369	9	.	.	.	-2.5029	14.1839	0.65592	0.0:0.8505:0.1495:0.0	.	101;101;101;101	Q9H3D4-7;Q9H3D4-3;Q9H3D4;Q9H3D4-5	.;.;P63_HUMAN;.	L	101	ENSP00000264731:S101L;ENSP00000407144:S101L;ENSP00000317510:S101L;ENSP00000376253:S101L;ENSP00000394337:S101L;ENSP00000371495:S101L	.	S	+	2	0	TP63	190939235	0.961000	0.32948	0.996000	0.52242	0.937000	0.57800	4.051000	0.57412	2.619000	0.88677	0.561000	0.74099	TCG		0.473	TP63-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000343865.1	NM_003722	
TMEM207	131920	broad.mit.edu	37	3	190159254	190159254	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr3:190159254T>C	ENST00000354905.2	-	3	197	c.131A>G	c.(130-132)gAc>gGc	p.D44G		NM_207316.1	NP_997199.1	Q6UWW9	TM207_HUMAN	transmembrane protein 207	44						integral component of membrane (GO:0016021)		p.D44G(1)		endometrium(1)|large_intestine(2)|lung(4)	7	all_cancers(143;3.61e-10)|Ovarian(172;0.0991)		Lung(62;2.23e-05)|LUSC - Lung squamous cell carcinoma(58;3.15e-05)	GBM - Glioblastoma multiforme(93;0.0176)		AGGGTGTTGGTCATTATAATT	0.373																																					p.D44G												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A131G	3						.						113.0	103.0	107.0					3																	190159254		2203	4300	6503	191641948	SO:0001583	missense	131920	exon3			BC071780	CCDS3297.1	3q28	2008-02-18			ENSG00000198398	ENSG00000198398			33705	protein-coding gene	gene with protein product		614786					Standard	NM_207316		Approved		uc003fsj.2	Q6UWW9	OTTHUMG00000156213	ENST00000354905.2:c.131A>G	3.37:g.190159254T>C	ENSP00000346981:p.Asp44Gly	Somatic		Capture	Illumina HiSeq	Phase_I	191641948	NM_207316		Missense_Mutation	SNP	ENST00000354905.2	37	CCDS3297.1	.	.	.	.	.	.	.	.	.	.	T	13.18	2.159400	0.38119	.	.	ENSG00000198398	ENST00000354905	T	0.10573	2.86	5.94	0.498	0.16908	.	0.979776	0.08334	N	0.961813	T	0.10380	0.0254	L	0.40543	1.245	0.09310	N	1	B	0.11235	0.004	B	0.11329	0.006	T	0.36553	-0.9743	10	0.72032	D	0.01	-0.1135	8.2648	0.31808	0.0:0.3508:0.0:0.6492	.	44	Q6UWW9	TM207_HUMAN	G	44	ENSP00000346981:D44G	ENSP00000346981:D44G	D	-	2	0	TMEM207	191641948	0.000000	0.05858	0.000000	0.03702	0.100000	0.18952	0.358000	0.20216	-0.114000	0.11936	-0.379000	0.06801	GAC		0.373	TMEM207-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343515.1	NM_207316	
OXTR	5021	broad.mit.edu	37	3	8809219	8809219	+	Missense_Mutation	SNP	A	A	C			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr3:8809219A>C	ENST00000316793.3	-	3	1279	c.655T>G	c.(655-657)Tgc>Ggc	p.C219G	CAV3_ENST00000472766.1_Intron	NM_000916.3	NP_000907.2	P30559	OXYR_HUMAN	oxytocin receptor	219					cell surface receptor signaling pathway (GO:0007166)|digestive tract development (GO:0048565)|eating behavior (GO:0042755)|ERK1 and ERK2 cascade (GO:0070371)|estrous cycle phase (GO:0060206)|female pregnancy (GO:0007565)|heart development (GO:0007507)|lactation (GO:0007595)|maternal behavior (GO:0042711)|maternal process involved in parturition (GO:0060137)|memory (GO:0007613)|muscle contraction (GO:0006936)|negative regulation of gastric acid secretion (GO:0060455)|positive regulation of blood pressure (GO:0045777)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of norepinephrine secretion (GO:0010701)|positive regulation of penile erection (GO:0060406)|positive regulation of synapse assembly (GO:0051965)|positive regulation of synaptic transmission, GABAergic (GO:0032230)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|positive regulation of uterine smooth muscle contraction (GO:0070474)|response to amphetamine (GO:0001975)|response to anoxia (GO:0034059)|response to cocaine (GO:0042220)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to peptide hormone (GO:0043434)|response to progesterone (GO:0032570)|sleep (GO:0030431)|social behavior (GO:0035176)|sperm ejaculation (GO:0042713)|suckling behavior (GO:0001967)|telencephalon development (GO:0021537)	apical plasma membrane (GO:0016324)|cell-cell adherens junction (GO:0005913)|integral component of plasma membrane (GO:0005887)|microvillus (GO:0005902)|plasma membrane (GO:0005886)	oxytocin receptor activity (GO:0004990)|peptide hormone binding (GO:0017046)|vasopressin receptor activity (GO:0005000)	p.C219G(1)		NS(1)|endometrium(2)|large_intestine(4)|lung(5)|urinary_tract(1)	13				OV - Ovarian serous cystadenocarcinoma(96;0.15)	Carbetocin(DB01282)|Oxytocin(DB00107)	AGGCCGTAGCAGGCAGCGAGC	0.652																																					p.C219G												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T655G	3						.						35.0	34.0	35.0					3																	8809219		2203	4299	6502	8784219	SO:0001583	missense	5021	exon3				CCDS2570.1	3p25	2012-08-08			ENSG00000180914	ENSG00000180914		"""GPCR / Class A : Vasopressin and oxytocin receptors"""	8529	protein-coding gene	gene with protein product		167055				1313946	Standard	NM_000916		Approved		uc003brc.3	P30559	OTTHUMG00000090537	ENST00000316793.3:c.655T>G	3.37:g.8809219A>C	ENSP00000324270:p.Cys219Gly	Somatic		Capture	Illumina HiSeq	Phase_I	8784219	NM_000916	Q15071	Missense_Mutation	SNP	ENST00000316793.3	37	CCDS2570.1	.	.	.	.	.	.	.	.	.	.	A	24.7	4.564663	0.86439	.	.	ENSG00000180914	ENST00000316793	T	0.42513	0.97	5.27	5.27	0.74061	GPCR, rhodopsin-like superfamily (1);	0.000000	0.85682	D	0.000000	T	0.74673	0.3747	H	0.96269	3.795	0.80722	D	1	D	0.71674	0.998	D	0.81914	0.995	D	0.83404	0.0024	10	0.87932	D	0	-47.6959	14.0417	0.64678	1.0:0.0:0.0:0.0	.	219	P30559	OXYR_HUMAN	G	219	ENSP00000324270:C219G	ENSP00000324270:C219G	C	-	1	0	OXTR	8784219	1.000000	0.71417	1.000000	0.80357	0.924000	0.55760	9.254000	0.95512	1.997000	0.58415	0.459000	0.35465	TGC		0.652	OXTR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207061.2		
TTLL3	26140	broad.mit.edu	37	3	9870828	9870828	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr3:9870828G>A	ENST00000547186.1	+	10	1519	c.1303G>A	c.(1303-1305)Gca>Aca	p.A435T	TTLL3_ENST00000397241.1_Missense_Mutation_p.A223T|TTLL3_ENST00000426895.4_Missense_Mutation_p.A578T|TTLL3_ENST00000430793.1_Missense_Mutation_p.A223T|TTLL3_ENST00000455274.1_Missense_Mutation_p.A223T|TTLL3_ENST00000427853.3_Missense_Mutation_p.A223T|TTLL3_ENST00000383827.1_Missense_Mutation_p.A223T|ARPC4-TTLL3_ENST00000397256.1_Missense_Mutation_p.A496T|TTLL3_ENST00000466245.1_3'UTR	NM_001025930.3	NP_001021100.3	Q9Y4R7	TTLL3_HUMAN	tubulin tyrosine ligase-like family, member 3	435	TTL. {ECO:0000255|PROSITE- ProRule:PRU00568}.				axoneme assembly (GO:0035082)|cilium assembly (GO:0042384)|protein polyglycylation (GO:0018094)	axoneme (GO:0005930)|cilium (GO:0005929)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)	protein-glycine ligase activity (GO:0070735)|protein-glycine ligase activity, initiating (GO:0070736)	p.A435T(1)		central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(10)|ovary(1)|prostate(2)|skin(1)	26	Medulloblastoma(99;0.227)					TGTGATCCACGCACTTCAGAC	0.597																																					p.A578T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1732A	3						.						132.0	102.0	112.0					3																	9870828		2203	4300	6503	9845828	SO:0001583	missense	26140	exon10				CCDS43048.1, CCDS43048.2	3p25.3	2013-02-14			ENSG00000214021	ENSG00000214021		"""Tubulin tyrosine ligase-like family"""	24483	protein-coding gene	gene with protein product						11054573	Standard	NR_037162		Approved	DKFZP434B103, HOTTL	uc003btg.4	Q9Y4R7	OTTHUMG00000128439	ENST00000547186.1:c.1303G>A	3.37:g.9870828G>A	ENSP00000446659:p.Ala435Thr	Somatic		Capture	Illumina HiSeq	Phase_I	9845828	NM_001025930	Q4KMS8|Q6AWA3|Q6ZU95|Q8NDN8|Q96GG8|Q9H876|Q9UI99	Missense_Mutation	SNP	ENST00000547186.1	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	12.98|12.98	2.099328|2.099328	0.37048|0.37048	.|.	.|.	ENSG00000250151;ENSG00000214021;ENSG00000214021;ENSG00000214021;ENSG00000214021;ENSG00000214021;ENSG00000214021;ENSG00000214021;ENSG00000214021|ENSG00000214021	ENST00000397256;ENST00000426895;ENST00000547186;ENST00000397241;ENST00000427853;ENST00000443148;ENST00000383827;ENST00000455274;ENST00000430793|ENST00000310252	T;T;T;T;T;T;T;T;T|.	0.09723|.	2.95;2.95;2.95;2.95;2.95;2.95;2.95;2.95;2.95|.	4.93|4.93	3.09|3.09	0.35607|0.35607	.|.	0.248149|.	0.33813|.	U|.	0.004530|.	T|T	0.21631|0.21631	0.0521|0.0521	N|N	0.11651|0.11651	0.15|0.15	0.20764|0.20764	N|N	0.99986|0.99986	B;B;B;B;B;B|.	0.28512|.	0.085;0.025;0.052;0.195;0.214;0.064|.	B;B;B;B;B;B|.	0.31495|.	0.075;0.014;0.014;0.131;0.018;0.024|.	T|T	0.12967|0.12967	-1.0527|-1.0527	10|5	0.09590|.	T|.	0.72|.	.|.	10.3607|10.3607	0.43991|0.43991	0.1865:0.0:0.8135:0.0|0.1865:0.0:0.8135:0.0	.|.	374;223;223;435;496;223|.	B4DM47;Q9Y4R7-2;Q9Y4R7-5;Q9Y4R7;E7ETI0;C9JSD3|.	.;.;.;TTLL3_HUMAN;.;.|.	T|H	496;578;435;223;223;373;223;223;223|390	ENSP00000380427:A496T;ENSP00000392549:A578T;ENSP00000446659:A435T;ENSP00000380416:A223T;ENSP00000394462:A223T;ENSP00000398097:A373T;ENSP00000373338:A223T;ENSP00000409632:A223T;ENSP00000403874:A223T|.	ENSP00000380416:A223T|.	A|R	+|+	1|2	0|0	ARPC4-TTLL3;TTLL3|TTLL3	9845828|9845828	0.379000|0.379000	0.25123|0.25123	0.284000|0.284000	0.24805|0.24805	0.620000|0.620000	0.37586|0.37586	1.232000|1.232000	0.32636|0.32636	2.285000|2.285000	0.76669|0.76669	0.563000|0.563000	0.77884|0.77884	GCA|CGC		0.597	TTLL3-203	KNOWN	basic	protein_coding	protein_coding		NM_001025930.2	
UBE2E2	7325	broad.mit.edu	37	3	23631283	23631283	+	Silent	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr3:23631283C>T	ENST00000396703.1	+	6	747	c.567C>T	c.(565-567)gaC>gaT	p.D189D	UBE2E2_ENST00000425792.1_Silent_p.D189D	NM_152653.3	NP_689866.1	Q96LR5	UB2E2_HUMAN	ubiquitin-conjugating enzyme E2E 2	189					ISG15-protein conjugation (GO:0032020)|protein K11-linked ubiquitination (GO:0070979)|protein K48-linked ubiquitination (GO:0070936)|protein K63-linked ubiquitination (GO:0070534)		ATP binding (GO:0005524)|ISG15 ligase activity (GO:0042296)|ubiquitin-protein transferase activity (GO:0004842)	p.D189D(1)		endometrium(2)|kidney(1)|large_intestine(3)|lung(2)|upper_aerodigestive_tract(2)	10						CAGAGCATGACCGGATGGCCA	0.592																																					p.D189D	GBM(85;1941 2083 9456)											.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C567T	3						.						103.0	87.0	92.0					3																	23631283		2203	4300	6503	23606287	SO:0001819	synonymous_variant	7325	exon6			AK057886	CCDS2637.1	3p24.2	2011-05-19	2011-05-19		ENSG00000182247	ENSG00000182247		"""Ubiquitin-conjugating enzymes E2"""	12478	protein-coding gene	gene with protein product		602163	"""ubiquitin-conjugating enzyme E2E 2 (homologous to yeast UBC4/5)"", ""ubiquitin-conjugating enzyme E2E 2 (UBC4/5 homolog, yeast)"""			9371400	Standard	NM_152653		Approved	UbcH8, FLJ25157	uc003ccg.2	Q96LR5	OTTHUMG00000130482	ENST00000396703.1:c.567C>T	3.37:g.23631283C>T		Somatic		Capture	Illumina HiSeq	Phase_I	23606287	NM_152653		Silent	SNP	ENST00000396703.1	37	CCDS2637.1																																																																																				0.592	UBE2E2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252881.2	NM_152653	
TOP2B	7155	broad.mit.edu	37	3	25668727	25668727	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr3:25668727C>T	ENST00000264331.4	-	16	1966	c.1967G>A	c.(1966-1968)cGc>cAc	p.R656H	TOP2B_ENST00000435706.2_Missense_Mutation_p.R651H	NM_001068.2	NP_001059.2	Q02880	TOP2B_HUMAN	topoisomerase (DNA) II beta 180kDa	656					ATP catabolic process (GO:0006200)|axonogenesis (GO:0007409)|DNA topological change (GO:0006265)|DNA unwinding involved in DNA replication (GO:0006268)|forebrain development (GO:0030900)|mitotic DNA integrity checkpoint (GO:0044774)|mitotic recombination (GO:0006312)|neuron migration (GO:0001764)|resolution of meiotic recombination intermediates (GO:0000712)|sister chromatid segregation (GO:0000819)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|DNA topoisomerase complex (ATP-hydrolyzing) (GO:0009330)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding, bending (GO:0008301)|DNA topoisomerase type II (ATP-hydrolyzing) activity (GO:0003918)|enzyme binding (GO:0019899)|histone deacetylase binding (GO:0042826)|metal ion binding (GO:0046872)|protein C-terminus binding (GO:0008022)|protein heterodimerization activity (GO:0046982)|protein kinase C binding (GO:0005080)	p.R651H(2)		breast(2)|endometrium(5)|kidney(1)|large_intestine(10)|lung(14)|ovary(1)|skin(2)|stomach(1)	36					Dactinomycin(DB00970)|Daunorubicin(DB00694)|Dexrazoxane(DB00380)|Etoposide(DB00773)	AAACAAGATGCGATGCCTTTC	0.353																																					p.R651H												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G1952A	3						.						169.0	169.0	169.0					3																	25668727		1896	4110	6006	25643731	SO:0001583	missense	7155	exon16			X68060	CCDS46776.1	3p24.2	2012-08-30	2002-08-29		ENSG00000077097	ENSG00000077097	5.99.1.3		11990	protein-coding gene	gene with protein product		126431	"""topoisomerase (DNA) II beta (180kD)"""			1309226, 1333583	Standard	NM_001068		Approved		uc003cdj.3	Q02880	OTTHUMG00000155596	ENST00000264331.4:c.1967G>A	3.37:g.25668727C>T	ENSP00000264331:p.Arg656His	Somatic		Capture	Illumina HiSeq	Phase_I	25643731	NM_001068	Q13600|Q9UMG8|Q9UQP8	Missense_Mutation	SNP	ENST00000264331.4	37		.	.	.	.	.	.	.	.	.	.	C	35	5.420360	0.96111	.	.	ENSG00000077097	ENST00000435706;ENST00000264331;ENST00000424225	T;T	0.54479	0.57;0.57	5.47	5.47	0.80525	.	0.047426	0.85682	D	0.000000	T	0.79667	0.4485	M	0.91406	3.205	0.80722	D	1	D	0.89917	1.0	D	0.76575	0.988	D	0.83665	0.0163	10	0.72032	D	0.01	-11.4448	19.6613	0.95875	0.0:1.0:0.0:0.0	.	651	Q02880-2	.	H	651;656;651	ENSP00000396704:R651H;ENSP00000264331:R656H	ENSP00000264331:R656H	R	-	2	0	TOP2B	25643731	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.702000	0.84576	2.711000	0.92665	0.650000	0.86243	CGC		0.353	TOP2B-201	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding			
TGFBR2	7048	broad.mit.edu	37	3	30715678	30715678	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr3:30715678G>A	ENST00000295754.5	+	5	1718	c.1336G>A	c.(1336-1338)Gat>Aat	p.D446N	TGFBR2_ENST00000359013.4_Missense_Mutation_p.D471N	NM_003242.5	NP_003233.4	P37173	TGFR2_HUMAN	transforming growth factor, beta receptor II (70/80kDa)	446	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.		D -> N (in LDS2). {ECO:0000269|PubMed:16251899}.		activation of protein kinase activity (GO:0032147)|aging (GO:0007568)|apoptotic process (GO:0006915)|blood vessel development (GO:0001568)|brain development (GO:0007420)|bronchus morphogenesis (GO:0060434)|cartilage development (GO:0051216)|common-partner SMAD protein phosphorylation (GO:0007182)|digestive tract development (GO:0048565)|embryo implantation (GO:0007566)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic hemopoiesis (GO:0035162)|gastrulation (GO:0007369)|heart development (GO:0007507)|in utero embryonic development (GO:0001701)|lens development in camera-type eye (GO:0002088)|lens fiber cell apoptotic process (GO:1990086)|lung lobe morphogenesis (GO:0060463)|mammary gland morphogenesis (GO:0060443)|myeloid dendritic cell differentiation (GO:0043011)|negative regulation of cardiac muscle cell proliferation (GO:0060044)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|organ regeneration (GO:0031100)|palate development (GO:0060021)|pathway-restricted SMAD protein phosphorylation (GO:0060389)|patterning of blood vessels (GO:0001569)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of angiogenesis (GO:0045766)|positive regulation of B cell tolerance induction (GO:0002663)|positive regulation of cell proliferation (GO:0008284)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of NK T cell differentiation (GO:0051138)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of skeletal muscle tissue regeneration (GO:0043415)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of T cell tolerance induction (GO:0002666)|positive regulation of tolerance induction to self antigen (GO:0002651)|protein phosphorylation (GO:0006468)|receptor-mediated endocytosis (GO:0006898)|regulation of cell proliferation (GO:0042127)|response to cholesterol (GO:0070723)|response to drug (GO:0042493)|response to estrogen (GO:0043627)|response to glucose (GO:0009749)|response to mechanical stimulus (GO:0009612)|response to nutrient (GO:0007584)|smoothened signaling pathway (GO:0007224)|trachea formation (GO:0060440)|transforming growth factor beta receptor signaling pathway (GO:0007179)|vasculogenesis (GO:0001570)|wound healing (GO:0042060)	caveola (GO:0005901)|cytosol (GO:0005829)|external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|transforming growth factor beta receptor homodimeric complex (GO:0070022)	ATP binding (GO:0005524)|glycosaminoglycan binding (GO:0005539)|metal ion binding (GO:0046872)|receptor signaling protein serine/threonine kinase activity (GO:0004702)|SMAD binding (GO:0046332)|transforming growth factor beta binding (GO:0050431)|transforming growth factor beta receptor activity, type II (GO:0005026)|transforming growth factor beta-activated receptor activity (GO:0005024)|transmembrane receptor protein serine/threonine kinase activity (GO:0004675)|type I transforming growth factor beta receptor binding (GO:0034713)|type III transforming growth factor beta receptor binding (GO:0034714)	p.D446N(2)		breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(15)|lung(10)|ovary(3)|pancreas(12)|skin(1)|stomach(5)|upper_aerodigestive_tract(2)	53						CAAGCAGACCGATGTCTACTC	0.473																																					p.D446N												.	.	2	Substitution - Missense(2)	large_intestine(1)|lung(1)	c.G1336A	3	GRCh37	CM060085|CM086981	TGFBR2	M		.						158.0	136.0	143.0					3																	30715678		2203	4300	6503	30690682	SO:0001583	missense	7048	exon5				CCDS2648.1, CCDS33727.1	3p22	2014-09-17	2002-08-29		ENSG00000163513	ENSG00000163513			11773	protein-coding gene	gene with protein product		190182	"""transforming growth factor, beta receptor II (70-80kD)"""	MFS2		1319842, 15235604	Standard	NM_001024847		Approved		uc003cen.3	P37173	OTTHUMG00000130569	ENST00000295754.5:c.1336G>A	3.37:g.30715678G>A	ENSP00000295754:p.Asp446Asn	Somatic		Capture	Illumina HiSeq	Phase_I	30690682	NM_003242	B4DTV5|Q15580|Q6DKT6|Q99474	Missense_Mutation	SNP	ENST00000295754.5	37	CCDS2648.1	.	.	.	.	.	.	.	.	.	.	G	36	5.893827	0.97074	.	.	ENSG00000163513	ENST00000295754;ENST00000359013;ENST00000439925	D;D	0.99394	-5.82;-5.82	6.02	6.02	0.97574	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	D	0.99704	0.9887	H	0.97758	4.07	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.97577	1.0108	10	0.87932	D	0	.	20.547	0.99278	0.0:0.0:1.0:0.0	.	446;471	P37173;D2JYI1	TGFR2_HUMAN;.	N	446;471;276	ENSP00000295754:D446N;ENSP00000351905:D471N	ENSP00000295754:D446N	D	+	1	0	TGFBR2	30690682	1.000000	0.71417	0.970000	0.41538	0.993000	0.82548	9.869000	0.99810	2.850000	0.98022	0.650000	0.86243	GAT		0.473	TGFBR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252994.2		
STT3B	201595	broad.mit.edu	37	3	31621412	31621412	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr3:31621412G>A	ENST00000295770.2	+	3	744	c.535G>A	c.(535-537)Ggc>Agc	p.G179S	STT3B_ENST00000453168.1_3'UTR	NM_178862.1	NP_849193.1	Q8TCJ2	STT3B_HUMAN	STT3B, subunit of the oligosaccharyltransferase complex (catalytic)	179					co-translational protein modification (GO:0043686)|ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|glycoprotein catabolic process (GO:0006516)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|response to unfolded protein (GO:0006986)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|oligosaccharyltransferase complex (GO:0008250)	dolichyl-diphosphooligosaccharide-protein glycotransferase activity (GO:0004579)	p.G179S(1)		autonomic_ganglia(1)|biliary_tract(1)|breast(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(6)|lung(3)|prostate(1)|upper_aerodigestive_tract(1)	19						AACTTTTAGCGGCCTTACATC	0.388																																					p.G179S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G535A	3						.						150.0	145.0	147.0					3																	31621412		2203	4300	6503	31596416	SO:0001583	missense	201595	exon3			AK027789	CCDS2650.1	3p24.1	2013-03-06	2013-03-06		ENSG00000163527	ENSG00000163527	2.4.99.18		30611	protein-coding gene	gene with protein product	"""source of immunodominant MHC associated peptides"", ""dolichyl-diphosphooligosaccharide protein glycotransferase"""	608605	"""STT3, subunit of the oligosaccharyltransferase complex, homolog B (S. cerevisiae)"""			12887896, 12439619	Standard	XM_006713017		Approved	SIMP, FLJ90106, STT3-B	uc011axe.2	Q8TCJ2	OTTHUMG00000130673	ENST00000295770.2:c.535G>A	3.37:g.31621412G>A	ENSP00000295770:p.Gly179Ser	Somatic		Capture	Illumina HiSeq	Phase_I	31596416	NM_178862	Q96JZ4|Q96KY7	Missense_Mutation	SNP	ENST00000295770.2	37	CCDS2650.1	.	.	.	.	.	.	.	.	.	.	G	23.6	4.434705	0.83885	.	.	ENSG00000163527	ENST00000295770	.	.	.	5.73	5.73	0.89815	.	0.000000	0.85682	D	0.000000	T	0.73628	0.3611	L	0.52206	1.635	0.80722	D	1	D	0.89917	1.0	D	0.73380	0.98	T	0.65307	-0.6200	9	0.12766	T	0.61	-8.3834	19.9019	0.96988	0.0:0.0:1.0:0.0	.	179	Q8TCJ2	STT3B_HUMAN	S	179	.	ENSP00000295770:G179S	G	+	1	0	STT3B	31596416	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.869000	0.99810	2.698000	0.92095	0.591000	0.81541	GGC		0.388	STT3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253166.2	NM_178862	
CNOT10	25904	broad.mit.edu	37	3	32815000	32815000	+	Missense_Mutation	SNP	C	C	G			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	G	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr3:32815000C>G	ENST00000328834.5	+	19	2448	c.2132C>G	c.(2131-2133)gCa>gGa	p.A711G	CNOT10_ENST00000331889.6_Missense_Mutation_p.A684G|CNOT10_ENST00000454516.2_Missense_Mutation_p.A771G	NM_015442.2	NP_056257.1	Q9H9A5	CNO10_HUMAN	CCR4-NOT transcription complex, subunit 10	711					gene expression (GO:0010467)|gene silencing by RNA (GO:0031047)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|regulation of transcription, DNA-templated (GO:0006355)|regulation of translation (GO:0006417)|RNA metabolic process (GO:0016070)|transcription, DNA-templated (GO:0006351)	CCR4-NOT complex (GO:0030014)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)		p.A711G(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(5)|prostate(1)|skin(3)	23						CTGCTCCCTGCAGTGAAAACA	0.463																																					p.A711G												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C2132G	3						.						151.0	153.0	153.0					3																	32815000		2203	4300	6503	32790004	SO:0001583	missense	25904	exon19			BC002928	CCDS2655.1, CCDS58821.1, CCDS58822.1	3p23	2013-01-10			ENSG00000182973	ENSG00000182973		"""Tetratricopeptide (TTC) repeat domain containing"""	23817	protein-coding gene	gene with protein product							Standard	NR_046352		Approved	FLJ12890, FLJ13165	uc011axj.2	Q9H9A5	OTTHUMG00000130748	ENST00000328834.5:c.2132C>G	3.37:g.32815000C>G	ENSP00000330060:p.Ala711Gly	Somatic		Capture	Illumina HiSeq	Phase_I	32790004	NM_015442	B7Z7L1|F8WAF2|Q9BU30|Q9H5J7|Q9H8X1|Q9H9W0|Q9HAH3|Q9UFJ2	Missense_Mutation	SNP	ENST00000328834.5	37	CCDS2655.1	.	.	.	.	.	.	.	.	.	.	C	14.80	2.644600	0.47258	.	.	ENSG00000182973	ENST00000331889;ENST00000328834;ENST00000454516	T;T;T	0.30448	1.53;1.53;1.53	5.92	5.92	0.95590	.	0.720535	0.14873	N	0.293403	T	0.21550	0.0519	N	0.08118	0	0.80722	D	1	B;B;B;B	0.17038	0.02;0.006;0.006;0.003	B;B;B;B	0.18871	0.023;0.014;0.014;0.006	T	0.13202	-1.0518	10	0.26408	T	0.33	-1.0518	20.3167	0.98654	0.0:1.0:0.0:0.0	.	771;684;710;711	F8WAF2;Q9H9A5-3;Q9H9A5-2;Q9H9A5	.;.;.;CNOTA_HUMAN	G	684;711;771	ENSP00000329376:A684G;ENSP00000330060:A711G;ENSP00000399862:A771G	ENSP00000330060:A711G	A	+	2	0	CNOT10	32790004	0.880000	0.30214	0.218000	0.23776	0.997000	0.91878	4.928000	0.63447	2.809000	0.96659	0.557000	0.71058	GCA		0.463	CNOT10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253248.2	NM_015442	
TMPPE	643853	broad.mit.edu	37	3	33134757	33134757	+	Missense_Mutation	SNP	G	G	A	rs372764570		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr3:33134757G>A	ENST00000342462.4	-	2	1121	c.931C>T	c.(931-933)Cgg>Tgg	p.R311W	GLB1_ENST00000445488.2_Intron|GLB1_ENST00000307377.8_Intron|GLB1_ENST00000399402.3_Intron|GLB1_ENST00000307363.5_Intron|TMPPE_ENST00000416695.2_Missense_Mutation_p.R174W	NM_001039770.2	NP_001034859.2	Q6ZT21	TMPPE_HUMAN	transmembrane protein with metallophosphoesterase domain	311						integral component of membrane (GO:0016021)	hydrolase activity (GO:0016787)|metal ion binding (GO:0046872)	p.R311W(1)		breast(1)|large_intestine(5)|lung(6)|prostate(1)	13						CGTTGGGCCCGTGTGGCGGAA	0.532																																					p.R174W												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C520T	3						.	G	,TRP/ARG,,,TRP/ARG	0,4406		0,0,2203	111.0	101.0	104.0		,931,,,520	-2.2	0.0	3		104	1,8599	1.2+/-3.3	0,1,4299	no	intron,missense,intron,intron,missense	GLB1,TMPPE	NM_000404.2,NM_001039770.2,NM_001079811.1,NM_001135602.1,NM_001136238.1	,101,,,101	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	,possibly-damaging,,,possibly-damaging	,311/454,,,174/317	33134757	1,13005	2203	4300	6503	33109761	SO:0001583	missense	643853	exon2			AK126979	CCDS33732.1, CCDS46786.1	3p22.3	2014-02-12	2009-02-24		ENSG00000188167	ENSG00000188167			33865	protein-coding gene	gene with protein product							Standard	NM_001039770		Approved	FLJ45032	uc003cfk.2	Q6ZT21	OTTHUMG00000155779	ENST00000342462.4:c.931C>T	3.37:g.33134757G>A	ENSP00000343398:p.Arg311Trp	Somatic		Capture	Illumina HiSeq	Phase_I	33109761	NM_001136238	B2RNG5|Q6ZRG1	Missense_Mutation	SNP	ENST00000342462.4	37	CCDS33732.1	.	.	.	.	.	.	.	.	.	.	G	8.594	0.885277	0.17540	0.0	1.16E-4	ENSG00000188167	ENST00000416695;ENST00000342462	.	.	.	5.66	-2.16	0.07080	Metallophosphoesterase domain (1);	0.546832	0.16589	N	0.207859	T	0.43875	0.1267	L	0.56199	1.76	0.09310	N	1	P	0.46327	0.876	P	0.47376	0.545	T	0.49735	-0.8908	9	0.72032	D	0.01	-0.2286	14.5974	0.68417	0.0855:0.5116:0.4029:0.0	.	311	Q6ZT21	TMPPE_HUMAN	W	174;311	.	ENSP00000343398:R311W	R	-	1	2	TMPPE	33109761	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.389000	0.07342	-0.858000	0.04110	-0.929000	0.02709	CGG		0.532	TMPPE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341566.1	NM_001039770	
DCLK3	85443	broad.mit.edu	37	3	36779289	36779289	+	Missense_Mutation	SNP	G	G	A	rs181512442		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr3:36779289G>A	ENST00000416516.2	-	2	1352	c.862C>T	c.(862-864)Cgc>Tgc	p.R288C		NM_033403.1	NP_208382.1	Q9C098	DCLK3_HUMAN	doublecortin-like kinase 3	288						cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)	p.R288C(1)		breast(3)|endometrium(3)|kidney(2)|large_intestine(11)|lung(20)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	48						CGGGTCCTGCGGAGCTTCTCA	0.572													G|||	1	0.000199681	0.0	0.0	5008	,	,		18905	0.001		0.0	False		,,,				2504	0.0				p.R288C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C862T	3						.	G	CYS/ARG	0,3802		0,0,1901	103.0	107.0	106.0		862	2.7	0.0	3		106	1,8241		0,1,4120	no	missense	DCLK3	NM_033403.1	180	0,1,6021	AA,AG,GG		0.0121,0.0,0.0083	benign	288/649	36779289	1,12043	1901	4121	6022	36754293	SO:0001583	missense	85443	exon2			AB051552	CCDS43064.1	3p22.3	2007-04-02	2007-04-02	2007-04-02	ENSG00000163673	ENSG00000163673			19005	protein-coding gene	gene with protein product		613167	"""doublecortin and CaM kinase-like 3"""	DCAMKL3		11214970, 16869982	Standard	NM_033403		Approved	KIAA1765, DCDC3C	uc003cgi.2	Q9C098	OTTHUMG00000155805	ENST00000416516.2:c.862C>T	3.37:g.36779289G>A	ENSP00000394484:p.Arg288Cys	Somatic		Capture	Illumina HiSeq	Phase_I	36754293	NM_033403		Missense_Mutation	SNP	ENST00000416516.2	37	CCDS43064.1	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	G	4.475	0.088074	0.08583	0.0	1.21E-4	ENSG00000163673	ENST00000416516	T	0.68624	-0.34	4.48	2.66	0.31614	.	.	.	.	.	T	0.45518	0.1346	N	0.14661	0.345	0.09310	N	1	B	0.30361	0.277	B	0.10450	0.005	T	0.32295	-0.9912	9	0.66056	D	0.02	.	9.1531	0.36976	0.1619:0.0:0.8381:0.0	.	288	Q9C098	DCLK3_HUMAN	C	288	ENSP00000394484:R288C	ENSP00000394484:R288C	R	-	1	0	DCLK3	36754293	0.004000	0.15560	0.004000	0.12327	0.041000	0.13682	1.008000	0.29872	0.450000	0.26774	0.655000	0.94253	CGC		0.572	DCLK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341727.1	XM_047355	
ITGA9	3680	broad.mit.edu	37	3	37845355	37845355	+	Silent	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr3:37845355C>T	ENST00000264741.5	+	27	3187	c.2931C>T	c.(2929-2931)taC>taT	p.Y977Y	AC093415.2_ENST00000450990.1_RNA|AC093415.2_ENST00000420870.1_RNA|AC093415.2_ENST00000445429.1_RNA|AC093415.2_ENST00000438136.1_RNA	NM_002207.2	NP_002198.2	Q13797	ITA9_HUMAN	integrin, alpha 9	977					axon guidance (GO:0007411)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|integrin-mediated signaling pathway (GO:0007229)|neutrophil chemotaxis (GO:0030593)|wound healing (GO:0042060)	basal plasma membrane (GO:0009925)|integrin alpha9-beta1 complex (GO:0034679)|integrin complex (GO:0008305)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)	p.Y977Y(1)		breast(3)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(9)|lung(17)|pancreas(1)|prostate(2)|skin(6)|stomach(1)|urinary_tract(1)	44				KIRC - Kidney renal clear cell carcinoma(284;0.165)|Kidney(284;0.197)		CCCGTGGCTACGTCGTGGGGT	0.517																																					p.Y977Y												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C2931T	3						.						184.0	141.0	156.0					3																	37845355		2203	4300	6503	37820359	SO:0001819	synonymous_variant	3680	exon27			L24158	CCDS2669.1	3p21.3	2010-03-23			ENSG00000144668	ENSG00000144668		"""Integrins"""	6145	protein-coding gene	gene with protein product	"""integrin, alpha 4-like"""	603963				8245132, 8290272	Standard	NM_002207		Approved	RLC, ITGA4L, ALPHA-RLC	uc003chd.3	Q13797	OTTHUMG00000130815	ENST00000264741.5:c.2931C>T	3.37:g.37845355C>T		Somatic		Capture	Illumina HiSeq	Phase_I	37820359	NM_002207	Q14638	Silent	SNP	ENST00000264741.5	37	CCDS2669.1																																																																																				0.517	ITGA9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253361.1	NM_002207	
VILL	50853	broad.mit.edu	37	3	38043990	38043990	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr3:38043990C>T	ENST00000283713.6	+	14	1849	c.1583C>T	c.(1582-1584)gCc>gTc	p.A528V	VILL_ENST00000383759.2_Missense_Mutation_p.A528V|VILL_ENST00000465644.1_Missense_Mutation_p.A246V			O15195	VILL_HUMAN	villin-like	528					actin filament capping (GO:0051693)|cytoskeleton organization (GO:0007010)	actin cytoskeleton (GO:0015629)	structural constituent of cytoskeleton (GO:0005200)	p.A528V(1)		cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(5)|liver(1)|lung(7)|ovary(1)|pancreas(1)|prostate(3)|stomach(3)|urinary_tract(2)	28				KIRC - Kidney renal clear cell carcinoma(284;0.0525)|Kidney(284;0.0661)		GAGGTGCCAGCCCGTGCCTCA	0.572																																					p.A528V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1583T	3						.						169.0	123.0	139.0					3																	38043990		2203	4300	6503	38018994	SO:0001583	missense	50853	exon13				CCDS2670.2	3p21	2004-07-28			ENSG00000136059	ENSG00000136059			30906	protein-coding gene	gene with protein product						9179494	Standard	XM_005265191		Approved		uc003chl.3	O15195	OTTHUMG00000130814	ENST00000283713.6:c.1583C>T	3.37:g.38043990C>T	ENSP00000283713:p.Ala528Val	Somatic		Capture	Illumina HiSeq	Phase_I	38018994	NM_015873	A8MZP1|Q9BT80|Q9BWH7	Missense_Mutation	SNP	ENST00000283713.6	37	CCDS2670.2	.	.	.	.	.	.	.	.	.	.	C	16.82	3.229741	0.58777	.	.	ENSG00000136059	ENST00000283713;ENST00000383759;ENST00000356246;ENST00000465644	T;T;T	0.55413	0.52;0.52;0.52	5.18	5.18	0.71444	Gelsolin domain (1);	0.097903	0.64402	D	0.000002	T	0.65059	0.2655	L	0.59912	1.85	0.51482	D	0.999921	P	0.45474	0.859	P	0.54706	0.759	T	0.61950	-0.6957	10	0.37606	T	0.19	-32.9819	18.6667	0.91492	0.0:1.0:0.0:0.0	.	528	O15195	VILL_HUMAN	V	528;528;514;246	ENSP00000283713:A528V;ENSP00000373266:A528V;ENSP00000422096:A246V	ENSP00000283713:A528V	A	+	2	0	VILL	38018994	1.000000	0.71417	1.000000	0.80357	0.072000	0.16883	5.983000	0.70540	2.594000	0.87642	0.561000	0.74099	GCC		0.572	VILL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253360.3	NM_015873	
DLEC1	9940	broad.mit.edu	37	3	38127738	38127738	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr3:38127738C>T	ENST00000308059.6	+	9	1463	c.1442C>T	c.(1441-1443)cCg>cTg	p.P481L	DLEC1_ENST00000452631.2_Missense_Mutation_p.P481L|DLEC1_ENST00000346219.3_Missense_Mutation_p.P481L|DLEC1_ENST00000469151.1_3'UTR					deleted in lung and esophageal cancer 1									p.P481L(2)		NS(1)|breast(3)|central_nervous_system(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(14)|ovary(3)|pancreas(3)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)	51				KIRC - Kidney renal clear cell carcinoma(284;0.0664)|Kidney(284;0.0827)		ACAGTGTCACCGGTGTTGGAC	0.493																																					p.P481L												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.C1442T	3						.						194.0	191.0	192.0					3																	38127738		2028	4182	6210	38102742	SO:0001583	missense	9940	exon9			AB020522	CCDS2672.2	3p21.3	2014-07-31			ENSG00000008226	ENSG00000008226			2899	protein-coding gene	gene with protein product	"""cilia and flagella associated protein 81"""	604050				10213508	Standard	XM_005265630		Approved	DLC1, CFAP81	uc003chp.1	Q9Y238	OTTHUMG00000131085	ENST00000308059.6:c.1442C>T	3.37:g.38127738C>T	ENSP00000308597:p.Pro481Leu	Somatic		Capture	Illumina HiSeq	Phase_I	38102742	NM_007337		Missense_Mutation	SNP	ENST00000308059.6	37	CCDS2672.2	.	.	.	.	.	.	.	.	.	.	C	9.893	1.204793	0.22205	.	.	ENSG00000008226	ENST00000308059;ENST00000346219;ENST00000452631	T;T;T	0.04917	3.54;3.53;3.76	4.8	1.88	0.25563	.	0.328107	0.30374	N	0.009761	T	0.06962	0.0177	M	0.71581	2.175	0.09310	N	1	P;P;P;P	0.48998	0.863;0.918;0.604;0.918	B;B;B;B	0.40256	0.324;0.241;0.114;0.241	T	0.30357	-0.9981	10	0.38643	T	0.18	-3.7282	3.6983	0.08372	0.1978:0.4446:0.2749:0.0826	.	481;481;481;481	A1L305;F8W6T4;Q9Y238-3;Q9Y238	.;.;.;DLEC1_HUMAN	L	481	ENSP00000308597:P481L;ENSP00000315914:P481L;ENSP00000410427:P481L	ENSP00000308597:P481L	P	+	2	0	DLEC1	38102742	0.000000	0.05858	0.012000	0.15200	0.837000	0.47467	-0.450000	0.06803	0.177000	0.19895	0.557000	0.71058	CCG		0.493	DLEC1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253745.3	NM_007337	
SCN10A	6336	broad.mit.edu	37	3	38743435	38743435	+	Missense_Mutation	SNP	C	C	T	rs202040659		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr3:38743435C>T	ENST00000449082.2	-	26	4551	c.4552G>A	c.(4552-4554)Gtc>Atc	p.V1518I		NM_006514.2	NP_006505.2	Q9Y5Y9	SCNAA_HUMAN	sodium channel, voltage-gated, type X, alpha subunit	1518					AV node cell to bundle of His cell communication (GO:0086067)|bundle of His cell to Purkinje myocyte communication (GO:0086069)|membrane depolarization during action potential (GO:0086010)|neuronal action potential (GO:0019228)|regulation of atrial cardiac muscle cell membrane depolarization (GO:0060371)|regulation of cardiac muscle contraction (GO:0055117)|regulation of heart rate (GO:0002027)|regulation of ion transmembrane transport (GO:0034765)|sensory perception (GO:0007600)|sensory perception of pain (GO:0019233)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	C-fiber (GO:0044299)|extracellular vesicular exosome (GO:0070062)|voltage-gated sodium channel complex (GO:0001518)	voltage-gated sodium channel activity (GO:0005248)	p.V1518I(1)		NS(5)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(14)|kidney(5)|large_intestine(33)|lung(54)|ovary(5)|pancreas(1)|prostate(5)|skin(13)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(1)	150				KIRC - Kidney renal clear cell carcinoma(284;0.0769)|Kidney(284;0.0945)	Benzocaine(DB01086)|Bupivacaine(DB00297)|Chloroprocaine(DB01161)|Cinchocaine(DB00527)|Cocaine(DB00907)|Dyclonine(DB00645)|Hexylcaine(DB00473)|Lacosamide(DB06218)|Levobupivacaine(DB01002)|Lidocaine(DB00281)|Mepivacaine(DB00961)|Orphenadrine(DB01173)|Oxybuprocaine(DB00892)|Procaine(DB00721)|Proparacaine(DB00807)|Ropivacaine(DB00296)|Valproic Acid(DB00313)	CCTGTGAAGACGGCCACAAAG	0.448													C|||	1	0.000199681	0.0008	0.0	5008	,	,		21255	0.0		0.0	False		,,,				2504	0.0				p.V1518I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G4552A	3						.	C	ILE/VAL	4,4402	8.1+/-20.4	0,4,2199	163.0	139.0	147.0		4552	3.8	1.0	3		147	0,8600		0,0,4300	yes	missense	SCN10A	NM_006514.2	29	0,4,6499	TT,TC,CC		0.0,0.0908,0.0308	benign	1518/1957	38743435	4,13002	2203	4300	6503	38718439	SO:0001583	missense	6336	exon26			AF117907	CCDS33736.1	3p22.2	2012-02-26	2007-01-23		ENSG00000185313	ENSG00000185313		"""Sodium channels"", ""Voltage-gated ion channels / Sodium channels"""	10582	protein-coding gene	gene with protein product		604427	"""sodium channel, voltage-gated, type X, alpha polypeptide"""			9839820, 10198179, 16382098	Standard	NM_006514		Approved	Nav1.8, hPN3, SNS, PN3	uc003ciq.3	Q9Y5Y9	OTTHUMG00000048245	ENST00000449082.2:c.4552G>A	3.37:g.38743435C>T	ENSP00000390600:p.Val1518Ile	Somatic		Capture	Illumina HiSeq	Phase_I	38718439	NM_006514	A6NDQ1	Missense_Mutation	SNP	ENST00000449082.2	37	CCDS33736.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	C	0.889	-0.726012	0.03158	9.08E-4	0.0	ENSG00000185313	ENST00000449082	D	0.98060	-4.69	4.71	3.84	0.44239	Ion transport (1);	0.155796	0.47093	D	0.000258	D	0.85388	0.5685	N	0.01352	-0.895	0.26347	N	0.977261	P	0.47910	0.902	B	0.36567	0.228	D	0.85282	0.1062	10	0.02654	T	1	.	5.5909	0.17301	0.0:0.6629:0.0:0.3371	.	1518	Q9Y5Y9	SCNAA_HUMAN	I	1518	ENSP00000390600:V1518I	ENSP00000390600:V1518I	V	-	1	0	SCN10A	38718439	0.001000	0.12720	0.975000	0.42487	0.936000	0.57629	-0.072000	0.11486	1.211000	0.43351	-0.226000	0.12346	GTC		0.448	SCN10A-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109745.3	NM_006514	
SCN10A	6336	broad.mit.edu	37	3	38781051	38781051	+	Silent	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr3:38781051G>A	ENST00000449082.2	-	14	2234	c.2235C>T	c.(2233-2235)ggC>ggT	p.G745G		NM_006514.2	NP_006505.2	Q9Y5Y9	SCNAA_HUMAN	sodium channel, voltage-gated, type X, alpha subunit	745					AV node cell to bundle of His cell communication (GO:0086067)|bundle of His cell to Purkinje myocyte communication (GO:0086069)|membrane depolarization during action potential (GO:0086010)|neuronal action potential (GO:0019228)|regulation of atrial cardiac muscle cell membrane depolarization (GO:0060371)|regulation of cardiac muscle contraction (GO:0055117)|regulation of heart rate (GO:0002027)|regulation of ion transmembrane transport (GO:0034765)|sensory perception (GO:0007600)|sensory perception of pain (GO:0019233)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	C-fiber (GO:0044299)|extracellular vesicular exosome (GO:0070062)|voltage-gated sodium channel complex (GO:0001518)	voltage-gated sodium channel activity (GO:0005248)	p.G745G(1)		NS(5)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(14)|kidney(5)|large_intestine(33)|lung(54)|ovary(5)|pancreas(1)|prostate(5)|skin(13)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(1)	150				KIRC - Kidney renal clear cell carcinoma(284;0.0769)|Kidney(284;0.0945)	Benzocaine(DB01086)|Bupivacaine(DB00297)|Chloroprocaine(DB01161)|Cinchocaine(DB00527)|Cocaine(DB00907)|Dyclonine(DB00645)|Hexylcaine(DB00473)|Lacosamide(DB06218)|Levobupivacaine(DB01002)|Lidocaine(DB00281)|Mepivacaine(DB00961)|Orphenadrine(DB01173)|Oxybuprocaine(DB00892)|Procaine(DB00721)|Proparacaine(DB00807)|Ropivacaine(DB00296)|Valproic Acid(DB00313)	TCTTGGCCACGCCCAGCTCTA	0.488																																					p.G745G												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C2235T	3						.						67.0	61.0	63.0					3																	38781051		2203	4300	6503	38756055	SO:0001819	synonymous_variant	6336	exon14			AF117907	CCDS33736.1	3p22.2	2012-02-26	2007-01-23		ENSG00000185313	ENSG00000185313		"""Sodium channels"", ""Voltage-gated ion channels / Sodium channels"""	10582	protein-coding gene	gene with protein product		604427	"""sodium channel, voltage-gated, type X, alpha polypeptide"""			9839820, 10198179, 16382098	Standard	NM_006514		Approved	Nav1.8, hPN3, SNS, PN3	uc003ciq.3	Q9Y5Y9	OTTHUMG00000048245	ENST00000449082.2:c.2235C>T	3.37:g.38781051G>A		Somatic		Capture	Illumina HiSeq	Phase_I	38756055	NM_006514	A6NDQ1	Silent	SNP	ENST00000449082.2	37	CCDS33736.1																																																																																				0.488	SCN10A-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109745.3	NM_006514	
SCN11A	11280	broad.mit.edu	37	3	38888499	38888499	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr3:38888499C>T	ENST00000302328.3	-	26	5260	c.5062G>A	c.(5062-5064)Gcc>Acc	p.A1688T	SCN11A_ENST00000450244.1_Missense_Mutation_p.A1688T|SCN11A_ENST00000456224.3_Missense_Mutation_p.A1650T	NM_014139.2	NP_054858.2	Q9UI33	SCNBA_HUMAN	sodium channel, voltage-gated, type XI, alpha subunit	1688					cell death (GO:0008219)|membrane depolarization during action potential (GO:0086010)|neuronal action potential (GO:0019228)|regulation of sensory perception of pain (GO:0051930)|response to drug (GO:0042493)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	C-fiber (GO:0044299)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)|voltage-gated sodium channel complex (GO:0001518)	voltage-gated sodium channel activity (GO:0005248)	p.A1688T(2)		NS(3)|biliary_tract(1)|breast(4)|cervix(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(29)|lung(29)|ovary(3)|pancreas(2)|prostate(12)|skin(14)|upper_aerodigestive_tract(5)|urinary_tract(3)	119				Kidney(284;0.00202)|KIRC - Kidney renal clear cell carcinoma(284;0.00226)	Cocaine(DB00907)|Valproic Acid(DB00313)|Zonisamide(DB00909)	GCGGTGAAGGCGAAAAGAATA	0.453																																					p.A1688T												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G5062A	3						.						111.0	112.0	112.0					3																	38888499		2203	4300	6503	38863503	SO:0001583	missense	11280	exon26			AF126739	CCDS33737.1	3p22.2	2012-02-26	2007-01-23		ENSG00000168356	ENSG00000168356		"""Sodium channels"", ""Voltage-gated ion channels / Sodium channels"""	10583	protein-coding gene	gene with protein product		604385	"""sodium channel, voltage-gated, type XI, alpha polypeptide"", ""sodium channel, voltage-gated, type XII, alpha"""	SCN12A		10444332, 16382098	Standard	NM_014139		Approved	Nav1.9, NaN, SNS-2	uc021wvy.1	Q9UI33	OTTHUMG00000048246	ENST00000302328.3:c.5062G>A	3.37:g.38888499C>T	ENSP00000307599:p.Ala1688Thr	Somatic		Capture	Illumina HiSeq	Phase_I	38863503	NM_014139	A6NN05|C9JD48|C9JR31|Q68K15|Q8NDX3|Q9UHE0|Q9UHM0	Missense_Mutation	SNP	ENST00000302328.3	37	CCDS33737.1	.	.	.	.	.	.	.	.	.	.	C	20.6	4.024565	0.75390	.	.	ENSG00000168356	ENST00000302328;ENST00000450244;ENST00000456224	D;D;D	0.98221	-4.8;-4.8;-4.73	5.22	5.22	0.72569	.	0.000000	0.85682	D	0.000000	D	0.98614	0.9536	M	0.89534	3.04	0.50313	D	0.999868	D	0.62365	0.991	P	0.49665	0.618	D	0.99857	1.1078	10	0.87932	D	0	.	18.7766	0.91913	0.0:1.0:0.0:0.0	.	1688	Q9UI33	SCNBA_HUMAN	T	1688;1688;1650	ENSP00000307599:A1688T;ENSP00000400945:A1688T;ENSP00000416757:A1650T	ENSP00000307599:A1688T	A	-	1	0	SCN11A	38863503	1.000000	0.71417	0.419000	0.26584	0.574000	0.36063	7.770000	0.85390	2.427000	0.82271	0.650000	0.86243	GCC		0.453	SCN11A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109746.4	NM_014139	
XIRP1	165904	broad.mit.edu	37	3	39227495	39227495	+	Missense_Mutation	SNP	C	C	T	rs142860074	byFrequency	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr3:39227495C>T	ENST00000340369.3	-	2	3670	c.3442G>A	c.(3442-3444)Gtg>Atg	p.V1148M	XIRP1_ENST00000396251.1_Intron|XIRP1_ENST00000421646.1_Intron	NM_194293.2	NP_919269.2	Q702N8	XIRP1_HUMAN	xin actin-binding repeat containing 1	1148					cardiac muscle cell development (GO:0055013)|negative regulation of cell proliferation (GO:0008285)|regulation of membrane potential (GO:0042391)|sarcomere organization (GO:0045214)	fascia adherens (GO:0005916)	poly(A) RNA binding (GO:0044822)	p.V1148M(1)		breast(4)|central_nervous_system(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(14)|lung(22)|ovary(4)|pancreas(1)|prostate(2)|skin(6)	71				KIRC - Kidney renal clear cell carcinoma(284;0.0517)|Kidney(284;0.065)		AAGGTCCTCACGGGATGAGCG	0.617																																					p.V1148M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G3442A	3						.	C	,MET/VAL	1,4405	2.1+/-5.4	0,1,2202	59.0	60.0	60.0		,3442	1.6	0.0	3	dbSNP_134	60	7,8593	5.7+/-21.5	0,7,4293	yes	intron,missense	XIRP1	NM_001198621.1,NM_194293.2	,21	0,8,6495	TT,TC,CC		0.0814,0.0227,0.0615	,possibly-damaging	,1148/1844	39227495	8,12998	2203	4300	6503	39202499	SO:0001583	missense	165904	exon2			AW755250	CCDS2683.1, CCDS56245.1	3p21.33	2008-02-05	2007-06-27	2007-06-27	ENSG00000168334	ENSG00000168334			14301	protein-coding gene	gene with protein product		609777	"""cardiomyopathy associated 1"""	CMYA1		12203715, 15454575	Standard	NM_001198621		Approved	DKFZp451D042, Xin	uc003cjk.2	Q702N8	OTTHUMG00000131297	ENST00000340369.3:c.3442G>A	3.37:g.39227495C>T	ENSP00000343140:p.Val1148Met	Somatic		Capture	Illumina HiSeq	Phase_I	39202499	NM_194293	A0JP25|A4QPE2|Q68DF2|Q6ZTR3|Q702N9|Q8IVN7|Q8N1N3|Q8N904|Q8TCG7	Missense_Mutation	SNP	ENST00000340369.3	37	CCDS2683.1	.	.	.	.	.	.	.	.	.	.	C	5.679	0.309769	0.10733	2.27E-4	8.14E-4	ENSG00000168334	ENST00000340369	T	0.06142	3.34	4.39	1.58	0.23477	.	0.713130	0.12138	U	0.496126	T	0.05686	0.0149	L	0.43152	1.355	0.09310	N	1	B	0.28208	0.203	B	0.14578	0.011	T	0.34054	-0.9844	10	0.45353	T	0.12	.	6.8454	0.23984	0.0:0.6999:0.0:0.3001	.	1148	Q702N8	XIRP1_HUMAN	M	1148	ENSP00000343140:V1148M	ENSP00000343140:V1148M	V	-	1	0	XIRP1	39202499	0.840000	0.29493	0.025000	0.17156	0.219000	0.24729	1.440000	0.35024	0.227000	0.20999	0.561000	0.74099	GTG		0.617	XIRP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254065.1	XM_093522	
XIRP1	165904	broad.mit.edu	37	3	39229229	39229229	+	Nonsense_Mutation	SNP	G	G	A	rs146353398		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr3:39229229G>A	ENST00000340369.3	-	2	1936	c.1708C>T	c.(1708-1710)Cga>Tga	p.R570*	XIRP1_ENST00000396251.1_Nonsense_Mutation_p.R570*|XIRP1_ENST00000421646.1_Intron	NM_194293.2	NP_919269.2	Q702N8	XIRP1_HUMAN	xin actin-binding repeat containing 1	570	Interaction with CTNNB1. {ECO:0000250}.				cardiac muscle cell development (GO:0055013)|negative regulation of cell proliferation (GO:0008285)|regulation of membrane potential (GO:0042391)|sarcomere organization (GO:0045214)	fascia adherens (GO:0005916)	poly(A) RNA binding (GO:0044822)	p.R570*(1)		breast(4)|central_nervous_system(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(14)|lung(22)|ovary(4)|pancreas(1)|prostate(2)|skin(6)	71				KIRC - Kidney renal clear cell carcinoma(284;0.0517)|Kidney(284;0.065)		TCTTTCTGTCGTTCCTGCTGC	0.602																																					p.R570X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.C1708T	3						.	G	stop/ARG,stop/ARG	2,4404	4.2+/-10.8	0,2,2201	56.0	52.0	53.0		1708,1708	0.4	0.5	3	dbSNP_134	53	0,8600		0,0,4300	yes	stop-gained,stop-gained	XIRP1	NM_001198621.1,NM_194293.2	,	0,2,6501	AA,AG,GG		0.0,0.0454,0.0154	,	570/1122,570/1844	39229229	2,13004	2203	4300	6503	39204233	SO:0001587	stop_gained	165904	exon2			AW755250	CCDS2683.1, CCDS56245.1	3p21.33	2008-02-05	2007-06-27	2007-06-27	ENSG00000168334	ENSG00000168334			14301	protein-coding gene	gene with protein product		609777	"""cardiomyopathy associated 1"""	CMYA1		12203715, 15454575	Standard	NM_001198621		Approved	DKFZp451D042, Xin	uc003cjk.2	Q702N8	OTTHUMG00000131297	ENST00000340369.3:c.1708C>T	3.37:g.39229229G>A	ENSP00000343140:p.Arg570*	Somatic		Capture	Illumina HiSeq	Phase_I	39204233	NM_194293	A0JP25|A4QPE2|Q68DF2|Q6ZTR3|Q702N9|Q8IVN7|Q8N1N3|Q8N904|Q8TCG7	Nonsense_Mutation	SNP	ENST00000340369.3	37	CCDS2683.1	.	.	.	.	.	.	.	.	.	.	G	24.2	4.509467	0.85282	4.54E-4	0.0	ENSG00000168334	ENST00000396251;ENST00000340369	.	.	.	4.85	0.442	0.16582	.	0.365565	0.25711	N	0.028810	.	.	.	.	.	.	0.09310	N	0.999999	.	.	.	.	.	.	.	.	.	.	0.09338	T	0.73	.	9.3883	0.38356	0.0:0.1255:0.5053:0.3692	.	.	.	.	X	570	.	ENSP00000343140:R570X	R	-	1	2	XIRP1	39204233	0.908000	0.30866	0.465000	0.27155	0.105000	0.19272	1.599000	0.36751	0.157000	0.19338	-0.181000	0.13052	CGA		0.602	XIRP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254065.1	XM_093522	
ENTPD3	956	broad.mit.edu	37	3	40468994	40468994	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr3:40468994G>A	ENST00000301825.3	+	11	1703	c.1585G>A	c.(1585-1587)Gac>Aac	p.D529N	ENTPD3_ENST00000456402.1_Missense_Mutation_p.D529N|ENTPD3-AS1_ENST00000439293.1_RNA|ENTPD3-AS1_ENST00000452768.1_RNA|ENTPD3-AS1_ENST00000425156.1_RNA	NM_001248.2	NP_001239.2	O75355	ENTP3_HUMAN	ectonucleoside triphosphate diphosphohydrolase 3	529					nucleoside diphosphate catabolic process (GO:0009134)|nucleoside triphosphate catabolic process (GO:0009143)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|nucleoside-diphosphatase activity (GO:0017110)|nucleoside-triphosphatase activity (GO:0017111)	p.D529N(1)		endometrium(1)|kidney(3)|large_intestine(5)|lung(4)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	18				KIRC - Kidney renal clear cell carcinoma(284;0.0605)|Kidney(284;0.0758)		AGTGGATTCTGACTGAGCCTT	0.537																																					p.D529N												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1585A	3						.						84.0	79.0	81.0					3																	40468994		2203	4300	6503	40443998	SO:0001583	missense	956	exon11			AF039917	CCDS2691.1, CCDS74919.1	3p21.3	2004-02-26			ENSG00000168032	ENSG00000168032			3365	protein-coding gene	gene with protein product		603161		CD39L3		9676430	Standard	XM_005265605		Approved	NTPDase-3, HB6	uc003ckd.4	O75355	OTTHUMG00000131390	ENST00000301825.3:c.1585G>A	3.37:g.40468994G>A	ENSP00000301825:p.Asp529Asn	Somatic		Capture	Illumina HiSeq	Phase_I	40443998	NM_001248	B2R8D0|G5E9N0|O60495|Q8N6K2	Missense_Mutation	SNP	ENST00000301825.3	37	CCDS2691.1	.	.	.	.	.	.	.	.	.	.	G	13.39	2.222863	0.39300	.	.	ENSG00000168032	ENST00000301825;ENST00000456402	T;T	0.10860	2.83;2.83	4.94	4.94	0.65067	.	0.476289	0.19266	N	0.118539	T	0.07593	0.0191	N	0.08118	0	0.80722	D	1	B	0.14438	0.01	B	0.16289	0.015	T	0.31052	-0.9957	10	0.62326	D	0.03	.	16.4845	0.84181	0.0:0.0:1.0:0.0	.	529	O75355	ENTP3_HUMAN	N	529	ENSP00000301825:D529N;ENSP00000401565:D529N	ENSP00000301825:D529N	D	+	1	0	ENTPD3	40443998	0.963000	0.33076	0.940000	0.37924	0.052000	0.14988	3.990000	0.56965	2.687000	0.91594	0.655000	0.94253	GAC		0.537	ENTPD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254179.2	NM_001248	
ZNF619	285267	broad.mit.edu	37	3	40528746	40528746	+	Missense_Mutation	SNP	C	C	T	rs377170323		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr3:40528746C>T	ENST00000314686.5	+	6	1102	c.697C>T	c.(697-699)Cgg>Tgg	p.R233W	ZNF619_ENST00000522736.1_Missense_Mutation_p.R240W|ZNF619_ENST00000447116.2_Missense_Mutation_p.R289W|ZNF619_ENST00000520737.1_3'UTR|ZNF619_ENST00000456778.1_Missense_Mutation_p.R205W|ZNF619_ENST00000521353.1_Missense_Mutation_p.R289W|ZNF619_ENST00000432264.2_Missense_Mutation_p.R249W|ZNF619_ENST00000429348.2_Missense_Mutation_p.R249W			Q8N2I2	ZN619_HUMAN	zinc finger protein 619	233					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.R233W(1)		breast(1)|cervix(1)|endometrium(2)|large_intestine(7)|lung(6)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	21				KIRC - Kidney renal clear cell carcinoma(284;0.0525)|Kidney(284;0.0661)		AAAACTGTCACGGCATCAGAA	0.433																																					p.R205W												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C613T	3						.	C	TRP/ARG,TRP/ARG,TRP/ARG	0,4406		0,0,2203	61.0	63.0	62.0		865,613,745	0.8	0.5	3		62	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense,missense	ZNF619	NM_001145082.2,NM_001145083.1,NM_001145093.2	101,101,101	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	benign,benign,benign	289/617,205/533,249/577	40528746	1,13005	2203	4300	6503	40503750	SO:0001583	missense	285267	exon4			AK075245	CCDS46801.1, CCDS46802.1, CCDS46803.1	3p21.33	2013-01-08			ENSG00000177873	ENSG00000177873		"""Zinc fingers, C2H2-type"", ""-"""	26910	protein-coding gene	gene with protein product							Standard	NM_001145083		Approved	FLJ90764	uc011azb.2	Q8N2I2	OTTHUMG00000131391	ENST00000314686.5:c.697C>T	3.37:g.40528746C>T	ENSP00000322529:p.Arg233Trp	Somatic		Capture	Illumina HiSeq	Phase_I	40503750	NM_001145083	B4E271|C9JRN5|D4PHA2|E9PCD9	Missense_Mutation	SNP	ENST00000314686.5	37		.	.	.	.	.	.	.	.	.	.	C	6.483	0.457379	0.12342	0.0	1.16E-4	ENSG00000177873	ENST00000314686;ENST00000447116;ENST00000429348;ENST00000456778;ENST00000522736;ENST00000521353;ENST00000432264	T;T;T;T;T;T;T	0.26660	1.72;1.72;1.72;1.72;1.72;1.72;1.72	2.75	0.842	0.18927	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.25606	0.0623	M	0.83774	2.66	0.09310	N	1	B;B;B;B;B;B	0.28512	0.017;0.003;0.003;0.214;0.003;0.019	B;B;B;B;B;B	0.15052	0.002;0.0;0.0;0.012;0.0;0.001	T	0.22800	-1.0206	9	0.36615	T	0.2	.	4.1304	0.10146	0.184:0.5675:0.0:0.2485	.	205;249;289;191;240;233	B4E271;C9JRN5;E9PCD9;B7Z9B3;Q17RW3;Q8N2I2	.;.;.;.;.;ZN619_HUMAN	W	233;289;249;205;240;289;249	ENSP00000322529:R233W;ENSP00000411132:R289W;ENSP00000398024:R249W;ENSP00000397232:R205W;ENSP00000428004:R240W;ENSP00000430705:R289W;ENSP00000388710:R249W	ENSP00000322529:R233W	R	+	1	2	ZNF619	40503750	0.000000	0.05858	0.493000	0.27502	0.971000	0.66376	-1.741000	0.01837	0.084000	0.17077	-1.119000	0.02030	CGG		0.433	ZNF619-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000254180.2	NM_173656	
ZNF621	285268	broad.mit.edu	37	3	40574507	40574507	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr3:40574507C>T	ENST00000339296.5	+	5	1698	c.1246C>T	c.(1246-1248)Cgt>Tgt	p.R416C	ZNF621_ENST00000310898.1_Intron|ZNF621_ENST00000403205.2_Missense_Mutation_p.R416C|ZNF621_ENST00000490457.1_Intron|ZNF621_ENST00000431278.1_Missense_Mutation_p.R305C	NM_198484.3	NP_940886.1	Q6ZSS3	ZN621_HUMAN	zinc finger protein 621	416					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.R416C(1)		endometrium(1)|kidney(2)|large_intestine(6)|lung(8)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)	21				KIRC - Kidney renal clear cell carcinoma(284;0.0515)|Kidney(284;0.0648)		ccaaatagtgcgtgtcttcca	0.478																																					p.R416C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1246T	3						.						83.0	71.0	75.0					3																	40574507		1953	3681	5634	40549511	SO:0001583	missense	285268	exon5			AK127181	CCDS2693.1, CCDS74920.1	3p21.33	2013-01-08			ENSG00000172888	ENSG00000172888		"""Zinc fingers, C2H2-type"", ""-"""	24787	protein-coding gene	gene with protein product							Standard	XM_005265079		Approved	FLJ45246	uc003ckm.2	Q6ZSS3	OTTHUMG00000131389	ENST00000339296.5:c.1246C>T	3.37:g.40574507C>T	ENSP00000340841:p.Arg416Cys	Somatic		Capture	Illumina HiSeq	Phase_I	40549511	NM_001098414	Q14DC7|Q8TE91	Missense_Mutation	SNP	ENST00000339296.5	37	CCDS2693.1	.	.	.	.	.	.	.	.	.	.	c	12.86	2.063880	0.36373	.	.	ENSG00000172888	ENST00000403205;ENST00000339296;ENST00000431278	T;T;T	0.08896	3.24;3.24;3.04	3.83	2.01	0.26516	.	1.121610	0.07008	N	0.824679	T	0.05593	0.0147	N	0.19112	0.55	0.09310	N	0.999999	B;P	0.50819	0.009;0.939	B;B	0.40329	0.002;0.326	T	0.31861	-0.9928	10	0.52906	T	0.07	.	3.4515	0.07499	0.202:0.5869:0.0:0.2111	.	305;416	C9JZC2;Q6ZSS3	.;ZN621_HUMAN	C	416;416;305	ENSP00000386051:R416C;ENSP00000340841:R416C;ENSP00000413236:R305C	ENSP00000340841:R416C	R	+	1	0	ZNF621	40549511	0.000000	0.05858	0.000000	0.03702	0.158000	0.22134	-1.762000	0.01803	0.571000	0.29365	0.650000	0.86243	CGT		0.478	ZNF621-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254178.2	NM_198484	
ULK4	54986	broad.mit.edu	37	3	41973481	41973481	+	Silent	SNP	A	A	G			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr3:41973481A>G	ENST00000301831.4	-	5	858	c.396T>C	c.(394-396)ccT>ccC	p.P132P	ULK4_ENST00000420927.1_Silent_p.P132P	NM_017886.2	NP_060356.2	Q96C45	ULK4_HUMAN	unc-51 like kinase 4	132	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cilium morphogenesis (GO:0060271)|epithelial cilium movement (GO:0003351)|microtubule cytoskeleton organization (GO:0000226)|regulation of JNK cascade (GO:0046328)|regulation of MAPK cascade (GO:0043408)|regulation of neuron migration (GO:2001222)|regulation of neuron projection development (GO:0010975)|regulation of p38MAPK cascade (GO:1900744)|regulation of protein kinase C signaling (GO:0090036)|ventricular system development (GO:0021591)		ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)	p.P132P(2)		breast(2)|cervix(1)|large_intestine(6)|lung(7)|prostate(5)|skin(1)	22				KIRC - Kidney renal clear cell carcinoma(284;0.214)		TCAGTGTGCCAGGCCCTTCCA	0.363																																					p.P132P												.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.T396C	3						.						82.0	75.0	77.0					3																	41973481		1812	4075	5887	41948485	SO:0001819	synonymous_variant	54986	exon5			AK000581	CCDS43071.1	3p22.1	2013-07-02	2013-07-02		ENSG00000168038	ENSG00000168038			15784	protein-coding gene	gene with protein product			"""unc-51-like kinase 4 (C. elegans)"""			12477932	Standard	NM_017886		Approved	FLJ20574, REC01035, FAM7C1	uc003ckv.4	Q96C45	OTTHUMG00000156210	ENST00000301831.4:c.396T>C	3.37:g.41973481A>G		Somatic		Capture	Illumina HiSeq	Phase_I	41948485	NM_017886	A6NF15|Q8IW79|Q9NWV6|Q9UF96	Silent	SNP	ENST00000301831.4	37	CCDS43071.1																																																																																				0.363	ULK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343490.1	XM_929989	
TRAK1	22906	broad.mit.edu	37	3	42229597	42229597	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr3:42229597G>A	ENST00000327628.5	+	5	941	c.541G>A	c.(541-543)Gct>Act	p.A181T	TRAK1_ENST00000341421.3_Missense_Mutation_p.A123T|TRAK1_ENST00000487159.1_3'UTR|TRAK1_ENST00000396175.1_Missense_Mutation_p.A123T|TRAK1_ENST00000449246.1_Missense_Mutation_p.A107T	NM_001042646.2	NP_001036111.1	Q9UPV9	TRAK1_HUMAN	trafficking protein, kinesin binding 1	181	HAP1 N-terminal.				endosome to lysosome transport (GO:0008333)|protein O-linked glycosylation (GO:0006493)|protein targeting (GO:0006605)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	cytoplasm (GO:0005737)|early endosome (GO:0005769)|mitochondrion (GO:0005739)|nucleus (GO:0005634)		p.A123T(2)		central_nervous_system(2)|endometrium(1)|kidney(2)|large_intestine(8)|lung(6)|ovary(1)|upper_aerodigestive_tract(2)	22						CTACACCAGCGCTGCGGAGGA	0.572																																					p.A181T	GBM(44;195 884 22595 31865 41850)											.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G541A	3						.						165.0	160.0	161.0					3																	42229597		2203	4300	6503	42204601	SO:0001583	missense	22906	exon5				CCDS2695.1, CCDS43072.1, CCDS58826.1, CCDS74922.1	3p22.1	2012-03-05			ENSG00000182606	ENSG00000182606			29947	protein-coding gene	gene with protein product	"""OGT(O Glc NAc transferase) interacting protein 106 KDa"", ""O-linked N-acetylglucosamine transferase interacting protein 106"", ""milton homolog 1 (Drosophila)"""	608112				10470851, 12435728, 16380713, 20230862	Standard	NM_014965		Approved	OIP106, KIAA1042, MILT1	uc003cky.4	Q9UPV9	OTTHUMG00000131795	ENST00000327628.5:c.541G>A	3.37:g.42229597G>A	ENSP00000328998:p.Ala181Thr	Somatic		Capture	Illumina HiSeq	Phase_I	42204601	NM_001042646	E9PDS2|J3KNT7|Q63HR0|Q659B5|Q96B69	Missense_Mutation	SNP	ENST00000327628.5	37	CCDS43072.1	.	.	.	.	.	.	.	.	.	.	G	24.2	4.509827	0.85282	.	.	ENSG00000182606	ENST00000327628;ENST00000543338;ENST00000449246;ENST00000396175;ENST00000341421	T;T;D;D	0.91894	2.22;2.22;-2.93;-2.93	5.35	5.35	0.76521	.	0.125481	0.52532	D	0.000078	D	0.91078	0.7192	N	0.12831	0.26	0.58432	D	0.999998	D;D;D;D;D;D	0.71674	0.99;0.989;0.994;0.996;0.998;0.993	P;P;P;P;D;P	0.65573	0.663;0.736;0.828;0.666;0.936;0.856	D	0.89710	0.3911	10	0.22109	T	0.4	.	18.1317	0.89604	0.0:0.0:1.0:0.0	.	107;123;181;123;107;181	B7Z218;C9JC32;B7Z347;Q9UPV9-2;E9PDS2;Q9UPV9	.;.;.;.;.;TRAK1_HUMAN	T	181;181;107;123;123	ENSP00000328998:A181T;ENSP00000410717:A107T;ENSP00000379478:A123T;ENSP00000340702:A123T	ENSP00000328998:A181T	A	+	1	0	TRAK1	42204601	1.000000	0.71417	0.340000	0.25575	0.927000	0.56198	7.994000	0.88315	2.510000	0.84645	0.638000	0.83543	GCT		0.572	TRAK1-004	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343413.1	NM_014965	
SEC22C	9117	broad.mit.edu	37	3	42610409	42610409	+	Silent	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr3:42610409G>A	ENST00000264454.3	-	2	273	c.130C>T	c.(130-132)Ctg>Ttg	p.L44L	SEC22C_ENST00000423701.2_Silent_p.L44L|SEC22C_ENST00000536332.1_5'UTR|SEC22C_ENST00000417572.1_Silent_p.L44L|SEC22C_ENST00000493107.1_5'UTR|SEC22C_ENST00000273156.7_Silent_p.L44L			Q9BRL7	SC22C_HUMAN	SEC22 vesicle trafficking protein homolog C (S. cerevisiae)	44	Longin. {ECO:0000255|PROSITE- ProRule:PRU00231}.				ER to Golgi vesicle-mediated transport (GO:0006888)|protein transport (GO:0015031)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)		p.L44L(1)		endometrium(1)|large_intestine(2)	3				KIRC - Kidney renal clear cell carcinoma(284;0.222)		TACTGGGCCAGTCGCAAGGCT	0.438																																					p.L44L												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C130T	3						.						62.0	68.0	66.0					3																	42610409		2203	4300	6503	42585413	SO:0001819	synonymous_variant	9117	exon2			AF039568	CCDS2699.1, CCDS2700.1, CCDS56246.1	3p24.3-p22.1	2006-04-25	2006-04-25	2006-04-25	ENSG00000093183	ENSG00000093183			16828	protein-coding gene	gene with protein product		604028	"""SEC22 vesicle trafficking protein-like 3 (S. cerevisiae)"""	SEC22L3		9501016, 11001058	Standard	NM_004206		Approved	MGC13261, MGC5373	uc003clj.3	Q9BRL7	OTTHUMG00000131797	ENST00000264454.3:c.130C>T	3.37:g.42610409G>A		Somatic		Capture	Illumina HiSeq	Phase_I	42585413	NM_004206	O95152|Q68CX3|Q6UW18	Silent	SNP	ENST00000264454.3	37	CCDS2700.1																																																																																				0.438	SEC22C-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254734.1	NM_004206	
KLHL40	131377	broad.mit.edu	37	3	42732452	42732452	+	Missense_Mutation	SNP	C	C	T	rs139268932	byFrequency	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr3:42732452C>T	ENST00000287777.4	+	5	1809	c.1709C>T	c.(1708-1710)aCg>aTg	p.T570M		NM_152393.2	NP_689606.2	Q2TBA0	KLH40_HUMAN	kelch-like family member 40	570					multicellular organismal development (GO:0007275)	cytoplasm (GO:0005737)		p.T570M(1)									ACACTGGAGACGGAGTCTGGA	0.607													C|||	2	0.000399361	0.0008	0.0014	5008	,	,		18710	0.0		0.0	False		,,,				2504	0.0				p.T570M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1709T	3						.	C	MET/THR	1,4405	2.1+/-5.4	0,1,2202	83.0	69.0	73.0		1709	3.8	1.0	3	dbSNP_134	73	1,8599	1.2+/-3.3	0,1,4299	yes	missense	KBTBD5	NM_152393.2	81	0,2,6501	TT,TC,CC		0.0116,0.0227,0.0154	possibly-damaging	570/622	42732452	2,13004	2203	4300	6503	42707456	SO:0001583	missense	131377	exon5			AK056577	CCDS2703.1	3p21.33	2013-07-30	2013-02-22	2013-01-08	ENSG00000157119	ENSG00000157119		"""Kelch-like"", ""BTB/POZ domain containing"""	30372	protein-coding gene	gene with protein product	"""sarcosynapsin"", ""nemaline myopathy type 8"""	615340	"""kelch repeat and BTB (POZ) domain containing 5"", ""kelch-like 40 (Drosophila)"""	KBTBD5		23746549	Standard	NM_152393		Approved	SRYP, NEM8	uc003clv.1	Q2TBA0	OTTHUMG00000133045	ENST00000287777.4:c.1709C>T	3.37:g.42732452C>T	ENSP00000287777:p.Thr570Met	Somatic		Capture	Illumina HiSeq	Phase_I	42707456	NM_152393	Q86SI1|Q96MR2	Missense_Mutation	SNP	ENST00000287777.4	37	CCDS2703.1	1	4.578754578754579E-4	0	0.0	1	0.0027624309392265192	0	0.0	0	0.0	C	11.86	1.763414	0.31228	2.27E-4	1.16E-4	ENSG00000157119	ENST00000287777;ENST00000452129	T	0.72394	-0.65	3.77	3.77	0.43336	Kelch-type beta propeller (1);	0.540527	0.17966	U	0.156009	T	0.52141	0.1716	N	0.14661	0.345	0.27269	N	0.958412	P	0.40250	0.709	B	0.37239	0.244	T	0.52411	-0.8579	10	0.56958	D	0.05	.	11.2702	0.49133	0.1829:0.8171:0.0:0.0	.	570	Q2TBA0	KBTB5_HUMAN	M	570;315	ENSP00000287777:T570M	ENSP00000287777:T570M	T	+	2	0	KBTBD5	42707456	0.763000	0.28462	0.953000	0.39169	0.497000	0.33675	1.369000	0.34227	1.802000	0.52723	0.305000	0.20034	ACG		0.607	KLHL40-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256651.1	NM_152393	
CCR9	10803	broad.mit.edu	37	3	45942966	45942966	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr3:45942966T>C	ENST00000357632.2	+	3	866	c.686T>C	c.(685-687)gTc>gCc	p.V229A	CCR9_ENST00000422395.1_3'UTR|LZTFL1_ENST00000536047.1_Intron|Y_RNA_ENST00000364765.1_RNA|CCR9_ENST00000395963.2_Missense_Mutation_p.V217A|LZTFL1_ENST00000539217.1_Intron|CCR9_ENST00000355983.2_Missense_Mutation_p.V217A	NM_001256369.1|NM_031200.2	NP_001243298.1|NP_112477.1	P51686	CCR9_HUMAN	chemokine (C-C motif) receptor 9	229					cellular defense response (GO:0006968)|chemokine-mediated signaling pathway (GO:0070098)|chemotaxis (GO:0006935)|G-protein coupled receptor signaling pathway (GO:0007186)|immune response (GO:0006955)|positive regulation of cytosolic calcium ion concentration (GO:0007204)	cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	C-C chemokine receptor activity (GO:0016493)|chemokine receptor activity (GO:0004950)	p.V229A(1)		breast(1)|endometrium(4)|large_intestine(8)|lung(2)|ovary(2)|prostate(2)|skin(1)	20				BRCA - Breast invasive adenocarcinoma(193;0.00118)|KIRC - Kidney renal clear cell carcinoma(197;0.0182)|Kidney(197;0.0214)		CCCTTCGTGGTCATGGCTTGC	0.498																																					p.V217A												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T650C	3						.						185.0	160.0	169.0					3																	45942966		2203	4300	6503	45917970	SO:0001583	missense	10803	exon2			AJ132337	CCDS2732.1, CCDS2733.1	3p21.31	2012-09-20			ENSG00000173585	ENSG00000173585		"""GPCR / Class A : Chemokine receptors : C-C motif"", ""CD molecules"""	1610	protein-coding gene	gene with protein product		604738		GPR28		10229797	Standard	NM_006641		Approved	GPR-9-6, CDw199	uc003coz.2	P51686	OTTHUMG00000133450	ENST00000357632.2:c.686T>C	3.37:g.45942966T>C	ENSP00000350256:p.Val229Ala	Somatic		Capture	Illumina HiSeq	Phase_I	45917970	NM_006641	Q4VBM3|Q549E0|Q9UQQ6	Missense_Mutation	SNP	ENST00000357632.2	37	CCDS2732.1	.	.	.	.	.	.	.	.	.	.	T	16.49	3.136896	0.56936	.	.	ENSG00000173585	ENST00000357632;ENST00000395963;ENST00000355983	T;T;T	0.40756	1.02;1.02;1.02	4.96	4.96	0.65561	GPCR, rhodopsin-like superfamily (1);	0.318069	0.28700	N	0.014428	T	0.45696	0.1355	L	0.54965	1.715	0.54753	D	0.999983	B	0.29766	0.256	B	0.38056	0.264	T	0.46345	-0.9198	10	0.51188	T	0.08	.	14.6699	0.68937	0.0:0.0:0.0:1.0	.	229	P51686	CCR9_HUMAN	A	229;217;217	ENSP00000350256:V229A;ENSP00000379292:V217A;ENSP00000348260:V217A	ENSP00000348260:V217A	V	+	2	0	CCR9	45917970	1.000000	0.71417	1.000000	0.80357	0.620000	0.37586	8.037000	0.88933	1.858000	0.53909	0.460000	0.39030	GTC		0.498	CCR9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257323.2		
ALS2CL	259173	broad.mit.edu	37	3	46717821	46717821	+	Silent	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr3:46717821G>A	ENST00000318962.4	-	19	2183	c.2100C>T	c.(2098-2100)taC>taT	p.Y700Y	ALS2CL_ENST00000415953.1_Silent_p.Y700Y|ALS2CL_ENST00000383742.3_Silent_p.Y47Y	NM_147129.3	NP_667340.2	Q60I27	AL2CL_HUMAN	ALS2 C-terminal like	700					endosome organization (GO:0007032)|protein localization (GO:0008104)	cytoplasmic membrane-bounded vesicle (GO:0016023)	GTPase activator activity (GO:0005096)|identical protein binding (GO:0042802)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)	p.Y700Y(1)		NS(1)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|liver(1)|lung(7)|skin(3)|stomach(2)	29				BRCA - Breast invasive adenocarcinoma(193;0.000726)|KIRC - Kidney renal clear cell carcinoma(197;0.0171)|Kidney(197;0.0202)		CGACACCTGCGTAGGTAGCCT	0.632																																					p.Y700Y												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C2100T	3						.						84.0	80.0	81.0					3																	46717821		2203	4300	6503	46692825	SO:0001819	synonymous_variant	259173	exon19			AK074118	CCDS2743.1, CCDS43080.1	3p21.31	2008-01-30			ENSG00000178038	ENSG00000178038			20605	protein-coding gene	gene with protein product		612402				15388334, 8889548, 17239822	Standard	NM_147129		Approved	FLJ36525, RN49018, DKFZp686I0110	uc003cqb.2	Q60I27	OTTHUMG00000128673	ENST00000318962.4:c.2100C>T	3.37:g.46717821G>A		Somatic		Capture	Illumina HiSeq	Phase_I	46692825	NM_001190707	Q32MA1|Q6AI56|Q6ZNC5|Q6ZNC7|Q6ZTL4|Q86YD2|Q8N9U1|Q8NAL7	Silent	SNP	ENST00000318962.4	37	CCDS2743.1																																																																																				0.632	ALS2CL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250567.3	NM_147129	
ALS2CL	259173	broad.mit.edu	37	3	46727067	46727067	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr3:46727067G>A	ENST00000318962.4	-	7	817	c.734C>T	c.(733-735)cCg>cTg	p.P245L	ALS2CL_ENST00000415953.1_Missense_Mutation_p.P245L	NM_147129.3	NP_667340.2	Q60I27	AL2CL_HUMAN	ALS2 C-terminal like	245					endosome organization (GO:0007032)|protein localization (GO:0008104)	cytoplasmic membrane-bounded vesicle (GO:0016023)	GTPase activator activity (GO:0005096)|identical protein binding (GO:0042802)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)	p.P245L(1)		NS(1)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|liver(1)|lung(7)|skin(3)|stomach(2)	29				BRCA - Breast invasive adenocarcinoma(193;0.000726)|KIRC - Kidney renal clear cell carcinoma(197;0.0171)|Kidney(197;0.0202)		AGCCCGCAACGGTGCGACCGT	0.612																																					p.P245L												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C734T	3						.						121.0	93.0	102.0					3																	46727067		2203	4300	6503	46702071	SO:0001583	missense	259173	exon7			AK074118	CCDS2743.1, CCDS43080.1	3p21.31	2008-01-30			ENSG00000178038	ENSG00000178038			20605	protein-coding gene	gene with protein product		612402				15388334, 8889548, 17239822	Standard	NM_147129		Approved	FLJ36525, RN49018, DKFZp686I0110	uc003cqb.2	Q60I27	OTTHUMG00000128673	ENST00000318962.4:c.734C>T	3.37:g.46727067G>A	ENSP00000313670:p.Pro245Leu	Somatic		Capture	Illumina HiSeq	Phase_I	46702071	NM_001190707	Q32MA1|Q6AI56|Q6ZNC5|Q6ZNC7|Q6ZTL4|Q86YD2|Q8N9U1|Q8NAL7	Missense_Mutation	SNP	ENST00000318962.4	37	CCDS2743.1	.	.	.	.	.	.	.	.	.	.	G	5.188	0.220155	0.09863	.	.	ENSG00000178038	ENST00000318962;ENST00000415953	T;T	0.54675	0.56;0.56	5.17	3.4	0.38934	.	0.335418	0.25546	N	0.029923	T	0.40619	0.1124	L	0.42245	1.32	0.30335	N	0.786275	B	0.20671	0.047	B	0.12156	0.007	T	0.36163	-0.9759	10	0.37606	T	0.19	.	7.7544	0.28915	0.1859:0.0:0.8141:0.0	.	245	Q60I27	AL2CL_HUMAN	L	245	ENSP00000313670:P245L;ENSP00000413223:P245L	ENSP00000313670:P245L	P	-	2	0	ALS2CL	46702071	0.979000	0.34478	0.031000	0.17742	0.001000	0.01503	2.804000	0.47931	0.789000	0.33779	-0.251000	0.11542	CCG		0.612	ALS2CL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250567.3	NM_147129	
NBEAL2	23218	broad.mit.edu	37	3	47042540	47042540	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr3:47042540C>T	ENST00000450053.3	+	28	4534	c.4355C>T	c.(4354-4356)tCg>tTg	p.S1452L	NBEAL2_ENST00000383740.2_5'UTR|NBEAL2_ENST00000292309.5_Missense_Mutation_p.S1268L	NM_015175.2	NP_055990.1	Q6ZNJ1	NBEL2_HUMAN	neurobeachin-like 2	1452					blood coagulation (GO:0007596)|megakaryocyte development (GO:0035855)|platelet alpha granule organization (GO:0070889)|platelet formation (GO:0030220)	endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)		p.S829L(1)|p.S1452L(1)		NS(1)|breast(1)|central_nervous_system(3)|cervix(2)|endometrium(8)|kidney(5)|large_intestine(9)|lung(9)|ovary(4)|pancreas(1)|prostate(3)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	51		Acute lymphoblastic leukemia(5;0.0534)		BRCA - Breast invasive adenocarcinoma(193;0.0012)|KIRC - Kidney renal clear cell carcinoma(197;0.00575)|Kidney(197;0.00656)		GTGCTGTTCTCGGTGACGTGG	0.632																																					p.S1452L												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.C4355T	3						.						74.0	89.0	84.0					3																	47042540		2132	4235	6367	47017544	SO:0001583	missense	23218	exon28			AB011112	CCDS46817.1	3p21.31	2014-09-17			ENSG00000160796	ENSG00000160796		"""WD repeat domain containing"""	31928	protein-coding gene	gene with protein product		614169					Standard	NM_015175		Approved	KIAA0540	uc003cqp.3	Q6ZNJ1	OTTHUMG00000156497	ENST00000450053.3:c.4355C>T	3.37:g.47042540C>T	ENSP00000415034:p.Ser1452Leu	Somatic		Capture	Illumina HiSeq	Phase_I	47017544	NM_015175	O60288|Q6P994|Q6UX91|Q8NAC9	Missense_Mutation	SNP	ENST00000450053.3	37	CCDS46817.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	13.87|13.87	2.366204|2.366204	0.41902|0.41902	.|.	.|.	ENSG00000160796|ENSG00000160796	ENST00000416683|ENST00000292309;ENST00000450053	.|T;T	.|0.56103	.|0.52;0.48	5.26|5.26	4.33|4.33	0.51752|0.51752	.|.	.|0.220835	.|0.39834	.|N	.|0.001245	T|T	0.36717|0.36717	0.0977|0.0977	L|L	0.43152|0.43152	1.355|1.355	0.80722|0.80722	D|D	1|1	.|B	.|0.33379	.|0.41	.|B	.|0.23150	.|0.044	T|T	0.14172|0.14172	-1.0482|-1.0482	5|10	.|0.11794	.|T	.|0.64	.|.	10.522|10.522	0.44924|0.44924	0.0:0.8972:0.0:0.1028|0.0:0.8972:0.0:0.1028	.|.	.|1452	.|Q6ZNJ1	.|NBEL2_HUMAN	W|L	740|1268;1452	.|ENSP00000292309:S1268L;ENSP00000415034:S1452L	.|ENSP00000292309:S1268L	R|S	+|+	1|2	2|0	NBEAL2|NBEAL2	47017544|47017544	0.992000|0.992000	0.36948|0.36948	0.843000|0.843000	0.33291|0.33291	0.725000|0.725000	0.41563|0.41563	3.037000|3.037000	0.49775|0.49775	1.316000|1.316000	0.45131|0.45131	0.655000|0.655000	0.94253|0.94253	CGG|TCG		0.632	NBEAL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344363.3	XM_291064	
KLHL18	23276	broad.mit.edu	37	3	47361205	47361205	+	Silent	SNP	T	T	C			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr3:47361205T>C	ENST00000232766.5	+	2	212	c.192T>C	c.(190-192)caT>caC	p.H64H	KLHL18_ENST00000455924.2_Intron	NM_025010.4	NP_079286.2	O94889	KLH18_HUMAN	kelch-like family member 18	64								p.H64H(1)		endometrium(2)|kidney(1)|large_intestine(7)|lung(6)|ovary(1)|prostate(2)|upper_aerodigestive_tract(2)	21		Acute lymphoblastic leukemia(5;0.164)		BRCA - Breast invasive adenocarcinoma(193;0.000292)|KIRC - Kidney renal clear cell carcinoma(197;0.00645)|Kidney(197;0.00741)		CGTATTTCCATGCTATGTTTA	0.453																																					p.H64H												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.T192C	3						.						223.0	194.0	204.0					3																	47361205		2203	4300	6503	47336209	SO:0001819	synonymous_variant	23276	exon2			AB018338	CCDS33749.1	3p21	2013-01-30	2013-01-30		ENSG00000114648	ENSG00000114648		"""Kelch-like"", ""BTB/POZ domain containing"""	29120	protein-coding gene	gene with protein product			"""kelch-like 18 (Drosophila)"""			9872452	Standard	NM_025010		Approved	KIAA0795, FLJ13703	uc003crd.3	O94889	OTTHUMG00000156522	ENST00000232766.5:c.192T>C	3.37:g.47361205T>C		Somatic		Capture	Illumina HiSeq	Phase_I	47336209	NM_025010	A8K612|Q7Z3E8|Q8N125	Silent	SNP	ENST00000232766.5	37	CCDS33749.1																																																																																				0.453	KLHL18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344493.1	NM_025010	
PTPN23	25930	broad.mit.edu	37	3	47450484	47450484	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr3:47450484C>T	ENST00000265562.4	+	16	1626	c.1549C>T	c.(1549-1551)Cgt>Tgt	p.R517C	PTPN23_ENST00000431726.1_Missense_Mutation_p.R391C	NM_015466.2	NP_056281.1	Q9H3S7	PTN23_HUMAN	protein tyrosine phosphatase, non-receptor type 23	517					cilium morphogenesis (GO:0060271)|negative regulation of epithelial cell migration (GO:0010633)|peptidyl-tyrosine dephosphorylation (GO:0035335)|positive regulation of adherens junction organization (GO:1903393)|positive regulation of early endosome to late endosome transport (GO:2000643)|positive regulation of homophilic cell adhesion (GO:1903387)|protein transport (GO:0015031)|ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway (GO:0043162)	ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|early endosome (GO:0005769)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	protein kinase binding (GO:0019901)|protein tyrosine phosphatase activity (GO:0004725)	p.R517C(1)		breast(3)|central_nervous_system(1)|large_intestine(5)|lung(7)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)	23				BRCA - Breast invasive adenocarcinoma(193;0.000271)|KIRC - Kidney renal clear cell carcinoma(197;0.00558)|Kidney(197;0.00632)		TGAGCTGCACCGTGCCATGAA	0.647																																					p.R517C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1549T	3						.						116.0	105.0	109.0					3																	47450484		2203	4300	6503	47425488	SO:0001583	missense	25930	exon16			AB025194	CCDS2754.1	3p21.3	2011-06-09			ENSG00000076201	ENSG00000076201		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"""	14406	protein-coding gene	gene with protein product		606584				11095967	Standard	NM_015466		Approved	DKFZP564F0923, KIAA1471, HD-PTP	uc003crf.1	Q9H3S7	OTTHUMG00000133520	ENST00000265562.4:c.1549C>T	3.37:g.47450484C>T	ENSP00000265562:p.Arg517Cys	Somatic		Capture	Illumina HiSeq	Phase_I	47425488	NM_015466	A8K0D7|Q7KZF8|Q8N6Z5|Q9BSR5|Q9P257|Q9UG03|Q9UMZ4	Missense_Mutation	SNP	ENST00000265562.4	37	CCDS2754.1	.	.	.	.	.	.	.	.	.	.	C	18.78	3.697568	0.68386	.	.	ENSG00000076201	ENST00000456408;ENST00000265562	T	0.33654	1.4	4.29	4.29	0.51040	.	0.069301	0.56097	D	0.000025	T	0.49932	0.1586	L	0.50333	1.59	0.58432	D	0.999998	D;D	0.89917	0.996;1.0	D;D	0.74348	0.983;0.981	T	0.50625	-0.8806	10	0.72032	D	0.01	-15.319	9.5982	0.39587	0.3313:0.6687:0.0:0.0	.	391;517	B4DST5;Q9H3S7	.;PTN23_HUMAN	C	482;517	ENSP00000265562:R517C	ENSP00000265562:R517C	R	+	1	0	PTPN23	47425488	1.000000	0.71417	0.994000	0.49952	0.994000	0.84299	2.352000	0.44080	2.220000	0.72140	0.557000	0.71058	CGT		0.647	PTPN23-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257492.2	NM_015466	
SMARCC1	6599	broad.mit.edu	37	3	47727560	47727560	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr3:47727560G>A	ENST00000254480.5	-	14	1483	c.1364C>T	c.(1363-1365)gCa>gTa	p.A455V	SMARCC1_ENST00000425518.1_5'UTR	NM_003074.3	NP_003065.3	Q92922	SMRC1_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily c, member 1	455	SWIRM. {ECO:0000255|PROSITE- ProRule:PRU00247}.				ATP-dependent chromatin remodeling (GO:0043044)|chromatin remodeling (GO:0006338)|insulin receptor signaling pathway (GO:0008286)|nervous system development (GO:0007399)|nucleosome disassembly (GO:0006337)|organ morphogenesis (GO:0009887)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nBAF complex (GO:0071565)|npBAF complex (GO:0071564)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|protein complex (GO:0043234)|SWI/SNF complex (GO:0016514)|XY body (GO:0001741)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|protein N-terminus binding (GO:0047485)|transcription coactivator activity (GO:0003713)	p.A455V(1)		breast(1)|endometrium(5)|kidney(2)|large_intestine(3)|lung(15)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	33				BRCA - Breast invasive adenocarcinoma(193;7.47e-05)|KIRC - Kidney renal clear cell carcinoma(197;0.00862)|Kidney(197;0.01)		AAACCATGATGCATAACTAGG	0.428																																					p.A455V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1364T	3						.						207.0	177.0	187.0					3																	47727560		2203	4300	6503	47702564	SO:0001583	missense	6599	exon14			U66615	CCDS2758.1	3p21.31	2008-05-15			ENSG00000173473	ENSG00000173473			11104	protein-coding gene	gene with protein product		601732				8804307	Standard	NM_003074		Approved	BAF155, SRG3, Rsc8, CRACC1	uc003crq.2	Q92922	OTTHUMG00000133519	ENST00000254480.5:c.1364C>T	3.37:g.47727560G>A	ENSP00000254480:p.Ala455Val	Somatic		Capture	Illumina HiSeq	Phase_I	47702564	NM_003074	Q17RS0|Q6P172|Q8IWH2	Missense_Mutation	SNP	ENST00000254480.5	37	CCDS2758.1	.	.	.	.	.	.	.	.	.	.	G	32	5.154309	0.94686	.	.	ENSG00000173473	ENST00000254480	T	0.51817	0.69	5.85	5.85	0.93711	Winged helix-turn-helix transcription repressor DNA-binding (1);Homeodomain-like (1);SWIRM (2);	0.095598	0.64402	D	0.000001	T	0.76047	0.3933	M	0.92459	3.31	0.58432	D	0.999995	D	0.59767	0.986	D	0.65323	0.934	T	0.81468	-0.0919	10	0.87932	D	0	-22.3458	18.8021	0.92022	0.0:0.0:1.0:0.0	.	455	Q92922	SMRC1_HUMAN	V	455	ENSP00000254480:A455V	ENSP00000254480:A455V	A	-	2	0	SMARCC1	47702564	1.000000	0.71417	0.998000	0.56505	0.953000	0.61014	5.295000	0.65692	2.779000	0.95612	0.638000	0.83543	GCA		0.428	SMARCC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257491.1		
NME6	10201	broad.mit.edu	37	3	48336668	48336668	+	Silent	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr3:48336668C>T	ENST00000452211.1	-	6	528	c.291G>A	c.(289-291)acG>acA	p.T97T	NME6_ENST00000444069.1_5'UTR|NME6_ENST00000435684.1_Missense_Mutation_p.R84H|NME6_ENST00000426723.1_Intron|NME6_ENST00000442597.1_Silent_p.T97T|NME6_ENST00000426689.2_Silent_p.T97T|NME6_ENST00000447314.1_Silent_p.T52T|NME6_ENST00000421967.1_Silent_p.T105T|ZNF589_ENST00000412564.1_Intron|NME6_ENST00000450160.1_Missense_Mutation_p.R84H|NME6_ENST00000415644.1_Intron|NME6_ENST00000415053.1_Silent_p.T97T|NME6_ENST00000451657.1_Missense_Mutation_p.R84H			O75414	NDK6_HUMAN	NME/NM23 nucleoside diphosphate kinase 6	97					apoptotic process (GO:0006915)|CTP biosynthetic process (GO:0006241)|GTP biosynthetic process (GO:0006183)|negative regulation of cell growth (GO:0030308)|negative regulation of mitosis (GO:0045839)|UTP biosynthetic process (GO:0006228)	mitochondrion (GO:0005739)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|nucleoside diphosphate kinase activity (GO:0004550)	p.T105T(1)		breast(1)|large_intestine(5)	6				BRCA - Breast invasive adenocarcinoma(193;0.00029)|KIRC - Kidney renal clear cell carcinoma(197;0.00544)|Kidney(197;0.00609)		GTCCCATGAGCGTCCTCCAGA	0.567																																					p.T105T												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G315A	3						.						70.0	61.0	64.0					3																	48336668		2203	4300	6503	48311672	SO:0001819	synonymous_variant	10201	exon5			AF051941	CCDS2763.1	3p21.31	2012-05-18	2012-05-18		ENSG00000172113	ENSG00000172113			20567	protein-coding gene	gene with protein product		608294	"""non-metastatic cells 6, protein expressed in (nucleoside-diphosphate kinase)"""			10453732, 19852809	Standard	NM_005793		Approved	NM23-H6, IPIA-ALPHA	uc003cso.3	O75414	OTTHUMG00000133531	ENST00000452211.1:c.291G>A	3.37:g.48336668C>T		Somatic		Capture	Illumina HiSeq	Phase_I	48311672	NM_005793	B4DGW7|B4DM99|Q53HM5|Q96E73|Q9BQ63	Silent	SNP	ENST00000452211.1	37		.	.	.	.	.	.	.	.	.	.	C	11.55	1.670877	0.29693	.	.	ENSG00000172113	ENST00000450160;ENST00000451657;ENST00000435684	.	.	.	4.91	-9.83	0.00482	.	.	.	.	.	T	0.32675	0.0837	.	.	.	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.35919	-0.9769	7	0.59425	D	0.04	-3.4242	12.1613	0.54105	0.0:0.541:0.3009:0.1581	.	84	O75414-3	.	H	84	.	ENSP00000393261:R84H	R	-	2	0	NME6	48311672	0.000000	0.05858	0.160000	0.22671	0.612000	0.37316	-4.004000	0.00315	-2.347000	0.00620	-0.302000	0.09304	CGC		0.567	NME6-005	NOVEL	alternative_5_UTR|not_organism_supported|basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000346107.1	NM_005793	
PLXNB1	5364	broad.mit.edu	37	3	48465623	48465623	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr3:48465623C>T	ENST00000358536.4	-	3	667	c.398G>A	c.(397-399)cGg>cAg	p.R133Q	PLXNB1_ENST00000296440.6_Missense_Mutation_p.R133Q|PLXNB1_ENST00000358459.4_Missense_Mutation_p.R133Q|PLXNB1_ENST00000448774.2_Intron|PLXNB1_ENST00000456774.1_Missense_Mutation_p.R133Q	NM_002673.4	NP_002664.2	O43157	PLXB1_HUMAN	plexin B1	133	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				axon guidance (GO:0007411)|cell migration (GO:0016477)|intracellular signal transduction (GO:0035556)|negative regulation of cell adhesion (GO:0007162)|negative regulation of osteoblast proliferation (GO:0033689)|neuron projection morphogenesis (GO:0048812)|ossification involved in bone maturation (GO:0043931)|positive regulation of axonogenesis (GO:0050772)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of cell shape (GO:0008360)|regulation of cytoskeleton organization (GO:0051493)|semaphorin-plexin signaling pathway (GO:0071526)|semaphorin-plexin signaling pathway involved in bone trabecula morphogenesis (GO:1900220)|signal transduction (GO:0007165)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)|plasma membrane (GO:0005886)|semaphorin receptor complex (GO:0002116)	GTPase activating protein binding (GO:0032794)|receptor activity (GO:0004872)|semaphorin receptor activity (GO:0017154)|semaphorin receptor binding (GO:0030215)|transmembrane signaling receptor activity (GO:0004888)	p.R133Q(1)		NS(1)|breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(6)|lung(10)|ovary(3)|pancreas(2)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	47				BRCA - Breast invasive adenocarcinoma(193;0.000292)|KIRC - Kidney renal clear cell carcinoma(197;0.00549)|Kidney(197;0.00619)		CCGCTCTGGCCGCAGCAGCAG	0.692																																					p.R133Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G398A	3						.						10.0	13.0	12.0					3																	48465623		2197	4283	6480	48440627	SO:0001583	missense	5364	exon3			X87904	CCDS2765.1	3p21.31	2008-07-18			ENSG00000164050	ENSG00000164050		"""Plexins"""	9103	protein-coding gene	gene with protein product		601053		PLXN5		8570614, 11035813	Standard	XM_005265234		Approved	SEP, KIAA0407	uc003csw.2	O43157	OTTHUMG00000133527	ENST00000358536.4:c.398G>A	3.37:g.48465623C>T	ENSP00000351338:p.Arg133Gln	Somatic		Capture	Illumina HiSeq	Phase_I	48440627	NM_002673	A6H8Y2|Q6NY20|Q9UIV7|Q9UJ92|Q9UJ93	Missense_Mutation	SNP	ENST00000358536.4	37	CCDS2765.1	.	.	.	.	.	.	.	.	.	.	C	11.38	1.623172	0.28889	.	.	ENSG00000164050	ENST00000296440;ENST00000358459;ENST00000358536;ENST00000456774	T;T;T;T	0.10382	2.88;2.88;2.88;2.88	4.14	3.26	0.37387	WD40/YVTN repeat-like-containing domain (1);Semaphorin/CD100 antigen (4);	0.280434	0.30483	N	0.009534	T	0.06781	0.0173	L	0.28458	0.855	0.80722	D	1	B;B	0.30281	0.02;0.275	B;B	0.15484	0.003;0.013	T	0.37150	-0.9718	10	0.18710	T	0.47	.	10.6988	0.45915	0.0:0.9057:0.0:0.0943	.	133;133	O43157;O43157-2	PLXB1_HUMAN;.	Q	133	ENSP00000296440:R133Q;ENSP00000351242:R133Q;ENSP00000351338:R133Q;ENSP00000414199:R133Q	ENSP00000296440:R133Q	R	-	2	0	PLXNB1	48440627	0.991000	0.36638	0.998000	0.56505	0.942000	0.58702	3.459000	0.53021	0.720000	0.32209	0.655000	0.94253	CGG		0.692	PLXNB1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344454.1	NM_002673	
CELSR3	1951	broad.mit.edu	37	3	48697085	48697085	+	Missense_Mutation	SNP	G	G	A	rs531319649		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr3:48697085G>A	ENST00000164024.4	-	1	3263	c.2983C>T	c.(2983-2985)Cgg>Tgg	p.R995W	CELSR3_ENST00000544264.1_Missense_Mutation_p.R995W	NM_001407.2	NP_001398.2	Q9NYQ7	CELR3_HUMAN	cadherin, EGF LAG seven-pass G-type receptor 3	995	Cadherin 7. {ECO:0000255|PROSITE- ProRule:PRU00043}.				axonal fasciculation (GO:0007413)|cilium assembly (GO:0042384)|G-protein coupled receptor signaling pathway (GO:0007186)|homophilic cell adhesion (GO:0007156)|neuron migration (GO:0001764)|neuropeptide signaling pathway (GO:0007218)|regulation of protein localization (GO:0032880)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)	p.R995W(1)		NS(1)|biliary_tract(1)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(23)|ovary(9)|prostate(6)|skin(7)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(5)	83				BRCA - Breast invasive adenocarcinoma(193;0.000292)|KIRC - Kidney renal clear cell carcinoma(197;0.00549)|Kidney(197;0.00619)		TACTGGACCCGGCCATTGGCA	0.557													G|||	1	0.000199681	0.0	0.0	5008	,	,		22664	0.0		0.0	False		,,,				2504	0.001				p.R995W												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C2983T	3						.						59.0	59.0	59.0					3																	48697085		2203	4300	6503	48672089	SO:0001583	missense	1951	exon1			AF231023	CCDS2775.1	3p21.31	2014-08-08	2013-02-18		ENSG00000008300	ENSG00000008300		"""Cadherins / Major cadherins"", ""-"", ""GPCR / Class B : Orphans"""	3230	protein-coding gene	gene with protein product	"""flamingo homolog 1 (Drosophila)"""	604264	"""cadherin EGF LAG seven-pass G-type receptor 3, flamingo (Drosophila) homolog"""	EGFL1		9693030	Standard	NM_001407		Approved	MEGF2, HFMI1, FMI1, CDHF11	uc003cuf.1	Q9NYQ7	OTTHUMG00000133544	ENST00000164024.4:c.2983C>T	3.37:g.48697085G>A	ENSP00000164024:p.Arg995Trp	Somatic		Capture	Illumina HiSeq	Phase_I	48672089	NM_001407	O75092	Missense_Mutation	SNP	ENST00000164024.4	37	CCDS2775.1	.	.	.	.	.	.	.	.	.	.	G	14.90	2.673140	0.47781	.	.	ENSG00000008300	ENST00000164024;ENST00000544264	T;T	0.55234	0.53;0.53	5.78	3.95	0.45737	Cadherin (4);Cadherin-like (1);	.	.	.	.	T	0.75466	0.3853	M	0.86573	2.825	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.999	T	0.80039	-0.1549	9	0.87932	D	0	.	14.6413	0.68726	0.0:0.0:0.504:0.496	.	995;1065	Q9NYQ7;Q5Y190	CELR3_HUMAN;.	W	995	ENSP00000164024:R995W;ENSP00000445694:R995W	ENSP00000164024:R995W	R	-	1	2	CELSR3	48672089	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	2.136000	0.42121	0.752000	0.32923	0.561000	0.74099	CGG		0.557	CELSR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257523.1	NM_001407	
USP19	10869	broad.mit.edu	37	3	49148412	49148412	+	Silent	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr3:49148412C>T	ENST00000398888.2	-	22	3525	c.3207G>A	c.(3205-3207)cgG>cgA	p.R1069R	USP19_ENST00000417901.1_Silent_p.R1172R|USP19_ENST00000453664.1_Silent_p.R1160R|USP19_ENST00000398892.3_Silent_p.R1109R|USP19_ENST00000434032.2_Silent_p.R1170R|USP19_ENST00000398898.2_Silent_p.R1109R|USP19_ENST00000398896.1_Silent_p.R877R	NM_006677.2	NP_006668.1	O94966	UBP19_HUMAN	ubiquitin specific peptidase 19	1069	USP.				ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|negative regulation of skeletal muscle tissue development (GO:0048642)|positive regulation of cell cycle process (GO:0090068)|protein deubiquitination (GO:0016579)|regulation of cellular response to hypoxia (GO:1900037)|regulation of protein stability (GO:0031647)|response to endoplasmic reticulum stress (GO:0034976)|skeletal muscle atrophy (GO:0014732)	cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	metal ion binding (GO:0046872)|ubiquitin-specific protease activity (GO:0004843)	p.R1157R(1)		NS(1)|breast(3)|endometrium(5)|kidney(2)|large_intestine(10)|lung(5)|ovary(4)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	38				BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|Kidney(197;0.00219)|KIRC - Kidney renal clear cell carcinoma(197;0.00245)		GCACCTCAGGCCGTGTGAAGA	0.617																																					p.R1160R												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G3480A	3						.						53.0	61.0	58.0					3																	49148412		2000	4160	6160	49123416	SO:0001819	synonymous_variant	10869	exon23			AB020698	CCDS43090.1, CCDS56254.1, CCDS56255.1, CCDS56256.1	3p21.31	2005-10-13	2005-08-08		ENSG00000172046	ENSG00000172046		"""Zinc fingers, MYND-type"", ""Ubiquitin-specific peptidases"""	12617	protein-coding gene	gene with protein product		614471	"""ubiquitin specific protease 19"""			12838346	Standard	NM_001199160		Approved	KIAA0891, ZMYND9	uc011bch.2	O94966	OTTHUMG00000133611	ENST00000398888.2:c.3207G>A	3.37:g.49148412C>T		Somatic		Capture	Illumina HiSeq	Phase_I	49123416	NM_001199162	A5PKX8|A6H8U2|B4DGT3|B4DTZ0|E7EN22|E7ETS0|E9PEG8|Q3KQW4|Q641Q9|Q6NZY8|Q86XV9	Silent	SNP	ENST00000398888.2	37	CCDS43090.1																																																																																				0.617	USP19-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000257721.1	NM_006677	
USP19	10869	broad.mit.edu	37	3	49152447	49152447	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr3:49152447C>T	ENST00000398888.2	-	13	2135	c.1817G>A	c.(1816-1818)cGc>cAc	p.R606H	USP19_ENST00000488993.1_5'Flank|USP19_ENST00000417901.1_Missense_Mutation_p.R709H|USP19_ENST00000453664.1_Missense_Mutation_p.R697H|USP19_ENST00000398892.3_Missense_Mutation_p.R646H|USP19_ENST00000434032.2_Missense_Mutation_p.R707H|USP19_ENST00000398898.2_Missense_Mutation_p.R646H|USP19_ENST00000398896.1_Missense_Mutation_p.R414H	NM_006677.2	NP_006668.1	O94966	UBP19_HUMAN	ubiquitin specific peptidase 19	606	USP.				ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|negative regulation of skeletal muscle tissue development (GO:0048642)|positive regulation of cell cycle process (GO:0090068)|protein deubiquitination (GO:0016579)|regulation of cellular response to hypoxia (GO:1900037)|regulation of protein stability (GO:0031647)|response to endoplasmic reticulum stress (GO:0034976)|skeletal muscle atrophy (GO:0014732)	cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	metal ion binding (GO:0046872)|ubiquitin-specific protease activity (GO:0004843)	p.R694H(1)		NS(1)|breast(3)|endometrium(5)|kidney(2)|large_intestine(10)|lung(5)|ovary(4)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	38				BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|Kidney(197;0.00219)|KIRC - Kidney renal clear cell carcinoma(197;0.00245)		GTTCTGAATGCGATTCAGGTC	0.567																																					p.R697H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2090A	3						.						102.0	103.0	102.0					3																	49152447		2110	4236	6346	49127451	SO:0001583	missense	10869	exon14			AB020698	CCDS43090.1, CCDS56254.1, CCDS56255.1, CCDS56256.1	3p21.31	2005-10-13	2005-08-08		ENSG00000172046	ENSG00000172046		"""Zinc fingers, MYND-type"", ""Ubiquitin-specific peptidases"""	12617	protein-coding gene	gene with protein product		614471	"""ubiquitin specific protease 19"""			12838346	Standard	NM_001199160		Approved	KIAA0891, ZMYND9	uc011bch.2	O94966	OTTHUMG00000133611	ENST00000398888.2:c.1817G>A	3.37:g.49152447C>T	ENSP00000381863:p.Arg606His	Somatic		Capture	Illumina HiSeq	Phase_I	49127451	NM_001199162	A5PKX8|A6H8U2|B4DGT3|B4DTZ0|E7EN22|E7ETS0|E9PEG8|Q3KQW4|Q641Q9|Q6NZY8|Q86XV9	Missense_Mutation	SNP	ENST00000398888.2	37	CCDS43090.1	.	.	.	.	.	.	.	.	.	.	C	21.8	4.198373	0.79015	.	.	ENSG00000172046	ENST00000398896;ENST00000398898;ENST00000417901;ENST00000453664;ENST00000398892;ENST00000398888;ENST00000434032	T;T;T;T;T;T;T	0.34667	1.35;1.35;1.35;1.35;1.35;1.35;1.35	5.6	5.6	0.85130	Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (2);	0.000000	0.85682	D	0.000000	T	0.67841	0.2936	M	0.87381	2.88	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.91635	0.999;0.999;0.999;0.996;0.999	T	0.73206	-0.4056	10	0.87932	D	0	-14.47	19.6152	0.95630	0.0:1.0:0.0:0.0	.	707;697;606;646;414	E9PEG8;E7EN22;O94966;B5MEG5;E7ESU0	.;.;UBP19_HUMAN;.;.	H	414;646;709;697;646;606;707	ENSP00000381870:R414H;ENSP00000381872:R646H;ENSP00000395260:R709H;ENSP00000400090:R697H;ENSP00000381867:R646H;ENSP00000381863:R606H;ENSP00000401197:R707H	ENSP00000381863:R606H	R	-	2	0	USP19	49127451	1.000000	0.71417	0.988000	0.46212	0.983000	0.72400	5.914000	0.69964	2.628000	0.89032	0.655000	0.94253	CGC		0.567	USP19-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000257721.1	NM_006677	
USP4	7375	broad.mit.edu	37	3	49349075	49349075	+	Silent	SNP	C	C	T	rs143637177		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr3:49349075C>T	ENST00000265560.4	-	7	754	c.708G>A	c.(706-708)gcG>gcA	p.A236A	USP4_ENST00000351842.4_Intron|USP4_ENST00000488520.1_5'UTR	NM_003363.3	NP_003354.2	Q13107	UBP4_HUMAN	ubiquitin specific peptidase 4 (proto-oncogene)	236					negative regulation of protein ubiquitination (GO:0031397)|protein deubiquitination (GO:0016579)|protein localization to cell surface (GO:0034394)|regulation of protein stability (GO:0031647)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|lysosome (GO:0005764)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	adenosine receptor binding (GO:0031685)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)	p.A236A(2)		breast(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(5)|liver(1)|lung(10)|ovary(3)|prostate(1)|skin(2)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	33		Ovarian(412;0.00308)|Myeloproliferative disorder(1037;0.0255)|Hepatocellular(537;0.121)		OV - Ovarian serous cystadenocarcinoma(275;4.74e-26)|Kidney(197;2.22e-07)|KIRC - Kidney renal clear cell carcinoma(197;5.14e-06)|BRCA - Breast invasive adenocarcinoma(193;9.46e-05)		TTCTGCTAGGCGCAGTGCTTG	0.438																																					p.A236A												.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.G708A	3						.	C	,	1,4405	2.1+/-5.4	0,1,2202	121.0	117.0	119.0		708,	-2.9	1.0	3	dbSNP_134	119	0,8600		0,0,4300	no	coding-synonymous,intron	USP4	NM_003363.3,NM_199443.2	,	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	,	236/964,	49349075	1,13005	2203	4300	6503	49324079	SO:0001819	synonymous_variant	7375	exon7			U20657	CCDS2793.1, CCDS2794.1, CCDS58832.1	3p21.3	2005-10-11	2005-08-08		ENSG00000114316	ENSG00000114316		"""Ubiquitin-specific peptidases"""	12627	protein-coding gene	gene with protein product		603486	"""ubiquitin specific protease 4 (proto-oncogene)"""	UNP		12838346, 9464533	Standard	NM_199443		Approved	Unph	uc003cwq.2	Q13107	OTTHUMG00000156825	ENST00000265560.4:c.708G>A	3.37:g.49349075C>T		Somatic		Capture	Illumina HiSeq	Phase_I	49324079	NM_003363	A8K6Y0|C9IY91|O43452|O43453|Q08AK8	Silent	SNP	ENST00000265560.4	37	CCDS2793.1																																																																																				0.438	USP4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346069.1	NM_199443	
RHOA	387	broad.mit.edu	37	3	49413009	49413009	+	Missense_Mutation	SNP	C	C	T	rs11552758		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr3:49413009C>T	ENST00000418115.1	-	2	398	c.14G>A	c.(13-15)cGg>cAg	p.R5Q	RHOA_ENST00000422781.1_Missense_Mutation_p.R5Q|RHOA_ENST00000454011.2_Missense_Mutation_p.R5Q	NM_001664.2	NP_001655.1	P61586	RHOA_HUMAN	ras homolog family member A	5					actin cytoskeleton organization (GO:0030036)|androgen receptor signaling pathway (GO:0030521)|apical junction assembly (GO:0043297)|apolipoprotein A-I-mediated signaling pathway (GO:0038027)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell-matrix adhesion (GO:0007160)|cerebral cortex cell migration (GO:0021795)|cleavage furrow formation (GO:0036089)|forebrain radial glial cell differentiation (GO:0021861)|negative chemotaxis (GO:0050919)|negative regulation of axonogenesis (GO:0050771)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of intracellular steroid hormone receptor signaling pathway (GO:0033144)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of neuron differentiation (GO:0045665)|neurotrophin TRK receptor signaling pathway (GO:0048011)|ossification involved in bone maturation (GO:0043931)|phosphatidylinositol-mediated signaling (GO:0048015)|platelet activation (GO:0030168)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of axonogenesis (GO:0050772)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell growth (GO:0030307)|positive regulation of cell migration (GO:0030335)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of cytokinesis (GO:0032467)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of NF-kappaB import into nucleus (GO:0042346)|positive regulation of podosome assembly (GO:0071803)|positive regulation of smooth muscle contraction (GO:0045987)|positive regulation of stress fiber assembly (GO:0051496)|positive regulation of translation (GO:0045727)|positive regulation of vasoconstriction (GO:0045907)|regulation of axonogenesis (GO:0050770)|regulation of calcium ion transport (GO:0051924)|regulation of cell migration (GO:0030334)|regulation of dendrite development (GO:0050773)|regulation of neural precursor cell proliferation (GO:2000177)|regulation of osteoblast proliferation (GO:0033688)|regulation of small GTPase mediated signal transduction (GO:0051056)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to amino acid (GO:0043200)|response to drug (GO:0042493)|response to ethanol (GO:0045471)|response to glucocorticoid (GO:0051384)|response to glucose (GO:0009749)|response to hypoxia (GO:0001666)|response to mechanical stimulus (GO:0009612)|Rho protein signal transduction (GO:0007266)|skeletal muscle tissue development (GO:0007519)|small GTPase mediated signal transduction (GO:0007264)|spindle assembly involved in mitosis (GO:0090307)|stress fiber assembly (GO:0043149)|stress-activated protein kinase signaling cascade (GO:0031098)|substantia nigra development (GO:0021762)|trabecula morphogenesis (GO:0061383)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	apical junction complex (GO:0043296)|axon (GO:0030424)|cell cortex (GO:0005938)|cell junction (GO:0030054)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)	GDP binding (GO:0019003)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|myosin binding (GO:0017022)	p.R5Q(1)		cervix(1)|kidney(1)|large_intestine(5)|lung(1)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	12				BRCA - Breast invasive adenocarcinoma(193;8.58e-05)|Kidney(197;0.0023)|KIRC - Kidney renal clear cell carcinoma(197;0.00258)		CAGTTTCTTCCGGATGGCAGC	0.473																																					p.R5Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G14A	3						.						106.0	97.0	100.0					3																	49413009		2203	4300	6503	49388013	SO:0001583	missense	387	exon2			BC001360	CCDS2795.1	3p21.3	2012-02-27	2012-02-27	2004-03-23	ENSG00000067560	ENSG00000067560			667	protein-coding gene	gene with protein product		165390	"""ras homolog gene family, member A"""	ARH12, ARHA		9605859	Standard	NM_001664		Approved	RhoA, Rho12, RHOH12	uc003cwu.3	P61586	OTTHUMG00000156838	ENST00000418115.1:c.14G>A	3.37:g.49413009C>T	ENSP00000400175:p.Arg5Gln	Somatic		Capture	Illumina HiSeq	Phase_I	49388013	NM_001664	P06749|Q53HM4|Q5U024|Q9UDJ0|Q9UEJ4	Missense_Mutation	SNP	ENST00000418115.1	37	CCDS2795.1	.	.	.	.	.	.	.	.	.	.	C	33	5.291209	0.95546	.	.	ENSG00000067560	ENST00000418115;ENST00000454011;ENST00000422781;ENST00000445425;ENST00000431929	T;T;T;T;T	0.70399	-0.3;1.78;-0.33;-0.48;2.14	5.89	5.89	0.94794	Small GTP-binding protein domain (1);	0.000000	0.64402	D	0.000001	T	0.65943	0.2740	L	0.38175	1.15	0.80722	D	1	B	0.18166	0.026	B	0.20184	0.028	T	0.61926	-0.6962	10	0.87932	D	0	.	18.8947	0.92419	0.0:1.0:0.0:0.0	.	5	P61586	RHOA_HUMAN	Q	5	ENSP00000400175:R5Q;ENSP00000394483:R5Q;ENSP00000413587:R5Q;ENSP00000408402:R5Q;ENSP00000400747:R5Q	ENSP00000400175:R5Q	R	-	2	0	RHOA	49388013	1.000000	0.71417	0.999000	0.59377	0.896000	0.52359	7.652000	0.83633	2.809000	0.96659	0.558000	0.71614	CGG		0.473	RHOA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346157.3	NM_001664	
TCTA	6988	broad.mit.edu	37	3	49452264	49452264	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr3:49452264C>T	ENST00000273590.3	+	3	502	c.281C>T	c.(280-282)gCa>gTa	p.A94V	AMT_ENST00000476226.1_5'Flank|RHOA_ENST00000422781.1_5'Flank|RHOA_ENST00000418115.1_5'Flank|TCTA_ENST00000493381.1_3'UTR|RHOA_ENST00000454011.2_5'Flank|RHOA_ENST00000265538.3_5'Flank	NM_022171.2	NP_071503.1	P57738	TCTA_HUMAN	T-cell leukemia translocation altered	94						integral component of membrane (GO:0016021)		p.A94V(1)		large_intestine(4)|lung(1)	5				BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|Kidney(197;0.00218)|KIRC - Kidney renal clear cell carcinoma(197;0.00244)		GAAATGGCAGCAAACGAACCT	0.517																																					p.A94V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C281T	3						.						108.0	94.0	99.0					3																	49452264		2203	4300	6503	49427268	SO:0001583	missense	6988	exon3				CCDS2796.1	3p21	2012-02-27	2012-02-27		ENSG00000145022	ENSG00000145022			11692	protein-coding gene	gene with protein product		600690	"""T-cell leukemia translocation altered gene"""			7728759	Standard	NM_022171		Approved		uc003cwv.4	P57738	OTTHUMG00000156846	ENST00000273590.3:c.281C>T	3.37:g.49452264C>T	ENSP00000273590:p.Ala94Val	Somatic		Capture	Illumina HiSeq	Phase_I	49427268	NM_022171	B2R4I4|Q6I9U4|Q9BSB0	Missense_Mutation	SNP	ENST00000273590.3	37	CCDS2796.1	.	.	.	.	.	.	.	.	.	.	C	15.49	2.849619	0.51270	.	.	ENSG00000145022	ENST00000273590	.	.	.	4.11	3.15	0.36227	.	0.000000	0.64402	D	0.000002	T	0.37265	0.0997	L	0.27053	0.805	0.34535	D	0.709649	B	0.18013	0.025	B	0.21917	0.037	T	0.50767	-0.8789	9	0.66056	D	0.02	-1.2934	8.5087	0.33204	0.2311:0.7689:0.0:0.0	.	94	P57738	TCTA_HUMAN	V	94	.	ENSP00000273590:A94V	A	+	2	0	TCTA	49427268	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	1.363000	0.34159	2.289000	0.77006	0.462000	0.41574	GCA		0.517	TCTA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346210.1	NM_022171	
AMT	275	broad.mit.edu	37	3	49455006	49455006	+	Silent	SNP	G	G	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr3:49455006G>T	ENST00000273588.3	-	9	1481	c.1179C>A	c.(1177-1179)ccC>ccA	p.P393P	AMT_ENST00000476226.1_5'UTR|AMT_ENST00000546031.1_Silent_p.P296P|AMT_ENST00000458307.2_Silent_p.P349P|AMT_ENST00000395338.2_Intron|AMT_ENST00000538581.1_Silent_p.P337P	NM_000481.3	NP_000472.2	P48728	GCST_HUMAN	aminomethyltransferase	393					glycine catabolic process (GO:0006546)	mitochondrion (GO:0005739)	aminomethyltransferase activity (GO:0004047)|transaminase activity (GO:0008483)	p.P393P(1)		endometrium(1)|kidney(1)|large_intestine(1)|lung(1)|ovary(1)|skin(1)	6				BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|Kidney(197;0.00218)|KIRC - Kidney renal clear cell carcinoma(197;0.00244)	Tetrahydrofolic acid(DB00116)	TGGGCACAAAGGGCATCTTGC	0.562																																					p.P393P												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1179A	3						.						107.0	99.0	102.0					3																	49455006		2203	4300	6503	49430010	SO:0001819	synonymous_variant	275	exon9			D13811	CCDS2797.1, CCDS54583.1, CCDS54584.1, CCDS54585.1	3p21.2-p21.1	2014-09-17	2006-05-22		ENSG00000145020	ENSG00000145020	2.1.2.10		473	protein-coding gene	gene with protein product	"""glycine cleavage system protein T"""	238310	"""aminomethyltransferase (glycine cleavage system protein T)"""			1993704, 8188235	Standard	NM_000481		Approved	GCST, NKH	uc003cww.3	P48728	OTTHUMG00000156847	ENST00000273588.3:c.1179C>A	3.37:g.49455006G>T		Somatic		Capture	Illumina HiSeq	Phase_I	49430010	NM_000481	A8K3I5|B4DE61|B4DJQ0|E9PBG1|Q96IG6	Silent	SNP	ENST00000273588.3	37	CCDS2797.1																																																																																				0.562	AMT-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346216.2	NM_000481	
DAG1	1605	broad.mit.edu	37	3	49568496	49568496	+	Silent	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr3:49568496G>A	ENST00000539901.1	+	3	1110	c.552G>A	c.(550-552)gcG>gcA	p.A184A	DAG1_ENST00000308775.2_Silent_p.A184A|DAG1_ENST00000538711.1_Silent_p.A184A|DAG1_ENST00000515359.2_Silent_p.A184A|DAG1_ENST00000541308.1_Silent_p.A184A|DAG1_ENST00000545947.1_Silent_p.A184A	NM_001177644.2	NP_001171115	Q14118	DAG1_HUMAN	dystroglycan 1 (dystrophin-associated glycoprotein 1)	184	O-glycosylated at one site.|Required for laminin recognition.				basement membrane organization (GO:0071711)|branching involved in salivary gland morphogenesis (GO:0060445)|calcium-dependent cell-matrix adhesion (GO:0016340)|commissural neuron axon guidance (GO:0071679)|cytoskeletal anchoring at plasma membrane (GO:0007016)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|extracellular matrix organization (GO:0030198)|membrane protein ectodomain proteolysis (GO:0006509)|microtubule anchoring (GO:0034453)|modulation by virus of host morphology or physiology (GO:0019048)|morphogenesis of an epithelial sheet (GO:0002011)|myelination in peripheral nervous system (GO:0022011)|negative regulation of cell migration (GO:0030336)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of protein kinase B signaling (GO:0051898)|nerve maturation (GO:0021682)|NLS-bearing protein import into nucleus (GO:0006607)|response to peptide hormone (GO:0043434)	basement membrane (GO:0005604)|basolateral plasma membrane (GO:0016323)|cell outer membrane (GO:0009279)|cell-cell adherens junction (GO:0005913)|contractile ring (GO:0070938)|costamere (GO:0043034)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|dystroglycan complex (GO:0016011)|dystrophin-associated glycoprotein complex (GO:0016010)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|lamellipodium (GO:0030027)|membrane raft (GO:0045121)|node of Ranvier (GO:0033268)|nucleoplasm (GO:0005654)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|sarcolemma (GO:0042383)	actin binding (GO:0003779)|alpha-actinin binding (GO:0051393)|calcium ion binding (GO:0005509)|laminin-1 binding (GO:0043237)|SH2 domain binding (GO:0042169)|structural constituent of muscle (GO:0008307)|tubulin binding (GO:0015631)|vinculin binding (GO:0017166)|virus receptor activity (GO:0001618)	p.A184A(1)		NS(1)|autonomic_ganglia(2)|breast(2)|endometrium(1)|large_intestine(8)|lung(5)|ovary(2)|prostate(1)|skin(1)	23				BRCA - Breast invasive adenocarcinoma(193;5.13e-05)|Kidney(197;0.00241)|KIRC - Kidney renal clear cell carcinoma(197;0.00258)		CCTGTGCTGCGGATGAACCTG	0.552																																					p.A184A												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G552A	3						.						76.0	72.0	73.0					3																	49568496		2203	4300	6503	49543500	SO:0001819	synonymous_variant	1605	exon3			L19711	CCDS2799.1	3p21	2014-09-17			ENSG00000173402	ENSG00000173402			2666	protein-coding gene	gene with protein product	"""alpha-dystroglycan"", ""dystrophin-associated glycoprotein-1"", ""beta-dystroglycan"""	128239				7774920, 1741056	Standard	NM_001177643		Approved	A3a, 156DAG, AGRNR, DAG	uc021wyd.1	Q14118	OTTHUMG00000156869	ENST00000539901.1:c.552G>A	3.37:g.49568496G>A		Somatic		Capture	Illumina HiSeq	Phase_I	49543500	NM_004393	A8K6M7|Q969J9	Silent	SNP	ENST00000539901.1	37	CCDS2799.1																																																																																				0.552	DAG1-203	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346326.1		
BSN	8927	broad.mit.edu	37	3	49690023	49690023	+	Missense_Mutation	SNP	C	C	T	rs374765989	byFrequency	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr3:49690023C>T	ENST00000296452.4	+	5	3148	c.3034C>T	c.(3034-3036)Cgc>Tgc	p.R1012C		NM_003458.3	NP_003449.2	Q9UPA5	BSN_HUMAN	bassoon presynaptic cytomatrix protein	1012					synaptic transmission (GO:0007268)	axon (GO:0030424)|cell junction (GO:0030054)|dendrite (GO:0030425)|neuron projection terminus (GO:0044306)|nucleus (GO:0005634)|presynaptic cytoskeletal matrix assembled at active zones (GO:0048788)	metal ion binding (GO:0046872)	p.R1012C(1)		breast(8)|central_nervous_system(2)|cervix(2)|endometrium(16)|kidney(3)|large_intestine(17)|lung(37)|ovary(7)|pancreas(1)|prostate(4)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	106				BRCA - Breast invasive adenocarcinoma(193;6.66e-05)|KIRC - Kidney renal clear cell carcinoma(197;0.0032)|Kidney(197;0.00336)		CAGCCCCAGCCGCAGGCAGCG	0.647													C|||	2	0.000399361	0.0	0.0	5008	,	,		18510	0.001		0.0	False		,,,				2504	0.001				p.R1012C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C3034T	3						.	C	CYS/ARG	0,4406		0,0,2203	29.0	30.0	30.0		3034	5.2	1.0	3		30	1,8595		0,1,4297	no	missense	BSN	NM_003458.3	180	0,1,6500	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging	1012/3927	49690023	1,13001	2203	4298	6501	49665027	SO:0001583	missense	8927	exon5			AF052224	CCDS2800.1	3p21	2013-01-07	2013-01-07		ENSG00000164061	ENSG00000164061			1117	protein-coding gene	gene with protein product	"""zinc finger protein 231"", ""neuronal double zinc finger protein"""	604020	"""bassoon (presynaptic cytomatrix protein)"""	ZNF231		9806829, 10329005	Standard	NM_003458		Approved		uc003cxe.4	Q9UPA5	OTTHUMG00000133750	ENST00000296452.4:c.3034C>T	3.37:g.49690023C>T	ENSP00000296452:p.Arg1012Cys	Somatic		Capture	Illumina HiSeq	Phase_I	49665027	NM_003458	O43161|Q7LGH3	Missense_Mutation	SNP	ENST00000296452.4	37	CCDS2800.1	.	.	.	.	.	.	.	.	.	.	C	13.80	2.344588	0.41498	0.0	1.16E-4	ENSG00000164061	ENST00000296452	T	0.23950	1.88	5.17	5.17	0.71159	.	0.058475	0.64402	N	0.000002	T	0.48696	0.1514	M	0.64997	1.995	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.48714	-0.9011	10	0.72032	D	0.01	.	15.0845	0.72142	0.1422:0.8578:0.0:0.0	.	1012	Q9UPA5	BSN_HUMAN	C	1012	ENSP00000296452:R1012C	ENSP00000296452:R1012C	R	+	1	0	BSN	49665027	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	3.277000	0.51654	2.413000	0.81919	0.561000	0.74099	CGC		0.647	BSN-001	KNOWN	NMD_exception|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000258164.1	NM_003458	
RNF123	63891	broad.mit.edu	37	3	49738946	49738946	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr3:49738946G>A	ENST00000327697.6	+	16	1444	c.1300G>A	c.(1300-1302)Gtc>Atc	p.V434I	RNF123_ENST00000432042.1_Missense_Mutation_p.V288I	NM_022064.3	NP_071347.2	Q5XPI4	RN123_HUMAN	ring finger protein 123	434					protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)	ligase activity (GO:0016874)|zinc ion binding (GO:0008270)	p.V434I(1)		NS(1)|breast(4)|cervix(2)|endometrium(4)|kidney(4)|large_intestine(6)|lung(11)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	38				BRCA - Breast invasive adenocarcinoma(193;4.71e-05)|Kidney(197;0.00227)|KIRC - Kidney renal clear cell carcinoma(197;0.00255)		CCGCTCCGTCGTCTTCTTTTA	0.632											OREG0015570	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.V434I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1300A	3						.						52.0	56.0	54.0					3																	49738946		2203	4300	6503	49713950	SO:0001583	missense	63891	exon16			AK022627	CCDS33758.1	3p24.3	2008-02-05			ENSG00000164068	ENSG00000164068		"""RING-type (C3HC4) zinc fingers"""	21148	protein-coding gene	gene with protein product		614472					Standard	NM_022064		Approved	FLJ12565	uc003cxh.4	Q5XPI4	OTTHUMG00000156891	ENST00000327697.6:c.1300G>A	3.37:g.49738946G>A	ENSP00000328287:p.Val434Ile	Somatic	964	Capture	Illumina HiSeq	Phase_I	49713950	NM_022064	A1L4Q3|A6NLS5|Q5I022|Q6PFW4|Q71RH0|Q8IW18|Q9H0M8|Q9H5L8|Q9H9T2	Missense_Mutation	SNP	ENST00000327697.6	37	CCDS33758.1	.	.	.	.	.	.	.	.	.	.	G	13.13	2.145438	0.37825	.	.	ENSG00000164068	ENST00000327697;ENST00000389066;ENST00000432042	T;T	0.75821	-0.67;-0.97	5.71	4.84	0.62591	.	0.063441	0.64402	N	0.000009	T	0.60274	0.2256	N	0.24115	0.695	0.80722	D	1	B;B	0.15930	0.015;0.004	B;B	0.08055	0.003;0.003	T	0.54357	-0.8306	10	0.22706	T	0.39	-33.9587	13.5769	0.61879	0.0741:0.0:0.9259:0.0	.	288;434	C9J266;Q5XPI4	.;RN123_HUMAN	I	434;434;288	ENSP00000328287:V434I;ENSP00000392443:V288I	ENSP00000328287:V434I	V	+	1	0	RNF123	49713950	1.000000	0.71417	0.865000	0.33974	0.367000	0.29736	7.329000	0.79170	1.423000	0.47198	0.561000	0.74099	GTC		0.632	RNF123-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346475.2	NM_022064	
TRAIP	10293	broad.mit.edu	37	3	49869404	49869404	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr3:49869404G>A	ENST00000331456.2	-	11	1095	c.982C>T	c.(982-984)Cgg>Tgg	p.R328W	TRAIP_ENST00000469027.1_Missense_Mutation_p.R173W	NM_005879.2	NP_005870.2	Q9BWF2	TRAIP_HUMAN	TRAF interacting protein	328	Interaction with CYLD.				apoptotic process (GO:0006915)|cell proliferation (GO:0008283)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ligase activity (GO:0016874)|receptor signaling protein activity (GO:0005057)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.R328W(1)		breast(1)|endometrium(3)|kidney(2)|large_intestine(2)|liver(2)|lung(9)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	24				BRCA - Breast invasive adenocarcinoma(193;4.71e-05)|KIRC - Kidney renal clear cell carcinoma(197;0.00558)|Kidney(197;0.00632)		CTGGAGGGCCGGGCTGGGGGA	0.552																																					p.R328W												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C982T	3						.						80.0	87.0	84.0					3																	49869404		2203	4300	6503	49844408	SO:0001583	missense	10293	exon11			BC019283	CCDS2806.1	3p21.31	2013-01-09			ENSG00000183763	ENSG00000183763		"""RING-type (C3HC4) zinc fingers"""	30764	protein-coding gene	gene with protein product	"""ring finger protein 206"""	605958				9104814	Standard	NM_005879		Approved	TRIP, RNF206	uc003cxs.1	Q9BWF2	OTTHUMG00000158269	ENST00000331456.2:c.982C>T	3.37:g.49869404G>A	ENSP00000328203:p.Arg328Trp	Somatic		Capture	Illumina HiSeq	Phase_I	49844408	NM_005879	B5BU84|B5BUL3|O00467	Missense_Mutation	SNP	ENST00000331456.2	37	CCDS2806.1	.	.	.	.	.	.	.	.	.	.	G	16.99	3.274688	0.59649	.	.	ENSG00000183763	ENST00000331456;ENST00000469027	T	0.46451	0.87	5.83	4.96	0.65561	.	0.693602	0.14928	N	0.290270	T	0.35189	0.0923	L	0.29908	0.895	0.20638	N	0.99988	B;D	0.61080	0.01;0.989	B;B	0.43123	0.003;0.409	T	0.18178	-1.0345	10	0.66056	D	0.02	-12.2055	13.2069	0.59803	0.0731:0.0:0.9269:0.0	.	328;328	A8K807;Q9BWF2	.;TRAIP_HUMAN	W	328;173	ENSP00000420085:R173W	ENSP00000328203:R328W	R	-	1	2	TRAIP	49844408	0.358000	0.24947	0.552000	0.28243	0.363000	0.29612	4.186000	0.58337	1.488000	0.48433	-0.136000	0.14681	CGG		0.552	TRAIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350518.1	NM_005879	
HYAL1	3373	broad.mit.edu	37	3	50338046	50338046	+	Silent	SNP	C	C	T	rs587680396		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr3:50338046C>T	ENST00000266031.4	-	3	1791	c.1176G>A	c.(1174-1176)acG>acA	p.T392T	NAT6_ENST00000417393.1_5'Flank|HYAL3_ENST00000336307.1_5'Flank|HYAL1_ENST00000320295.8_Silent_p.T392T|HYAL1_ENST00000395143.2_Silent_p.T362T|HYAL3_ENST00000359051.3_5'Flank|HYAL3_ENST00000450982.1_5'Flank|HYAL3_ENST00000513170.1_5'Flank|HYAL3_ENST00000415204.1_5'Flank|HYAL1_ENST00000457214.2_Silent_p.T210T|NAT6_ENST00000443842.1_5'Flank|HYAL1_ENST00000447605.2_Silent_p.T133T|NAT6_ENST00000354862.4_5'Flank|HYAL1_ENST00000395144.2_Silent_p.T392T|NAT6_ENST00000443094.2_5'Flank			Q12794	HYAL1_HUMAN	hyaluronoglucosaminidase 1	392	EGF-like.				carbohydrate metabolic process (GO:0005975)|cartilage development (GO:0051216)|cellular response to fibroblast growth factor stimulus (GO:0044344)|cellular response to interleukin-1 (GO:0071347)|cellular response to pH (GO:0071467)|cellular response to platelet-derived growth factor stimulus (GO:0036120)|cellular response to tumor necrosis factor (GO:0071356)|cellular response to UV-B (GO:0071493)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|embryonic skeletal joint morphogenesis (GO:0060272)|glycosaminoglycan metabolic process (GO:0030203)|hyaluronan biosynthetic process (GO:0030213)|hyaluronan catabolic process (GO:0030214)|hyaluronan metabolic process (GO:0030212)|inflammatory response (GO:0006954)|negative regulation of cell growth (GO:0030308)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell growth (GO:0030307)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of growth (GO:0045927)|positive regulation of hyaluranon cable assembly (GO:1900106)|response to antibiotic (GO:0046677)|response to reactive oxygen species (GO:0000302)|response to virus (GO:0009615)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|hyaluranon cable (GO:0036117)|lysosomal lumen (GO:0043202)|lysosome (GO:0005764)	hyaluronan synthase activity (GO:0050501)|hyalurononglucosaminidase activity (GO:0004415)|transcription factor binding (GO:0008134)	p.T392T(1)		cervix(1)|endometrium(2)|large_intestine(1)|lung(6)|prostate(1)	11				BRCA - Breast invasive adenocarcinoma(193;0.000272)|KIRC - Kidney renal clear cell carcinoma(197;0.00544)|Kidney(197;0.00607)		CACCACCAGGCGTGAGCTGGA	0.637													C|||	1	0.000199681	0.0	0.0	5008	,	,		18033	0.001		0.0	False		,,,				2504	0.0				p.T392T												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G1176A	3						.						61.0	65.0	64.0					3																	50338046		2203	4300	6503	50313050	SO:0001819	synonymous_variant	3373	exon6			U90094	CCDS2816.1, CCDS2817.1, CCDS46832.1, CCDS46833.1	3p21.31	2014-07-17			ENSG00000114378	ENSG00000114378	3.2.1.35		5320	protein-coding gene	gene with protein product		607071				9223416, 9409739	Standard	NM_153281		Approved	LUCA1, HYAL-1, FUS2, NAT6	uc003czp.4	Q12794	OTTHUMG00000156941	ENST00000266031.4:c.1176G>A	3.37:g.50338046C>T		Somatic		Capture	Illumina HiSeq	Phase_I	50313050	NM_153281	Q6FH23|Q6PIZ6|Q7KYU2|Q7LE34|Q8NFK5|Q8NFK6|Q8NFK7|Q8NFK8|Q8NFK9|Q93013|Q9UKD5|Q9UNI8	Silent	SNP	ENST00000266031.4	37	CCDS2816.1																																																																																				0.637	HYAL1-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346703.1		
RRP9	9136	broad.mit.edu	37	3	51970353	51970353	+	Missense_Mutation	SNP	G	G	A	rs143989805	byFrequency	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr3:51970353G>A	ENST00000232888.6	-	8	728	c.655C>T	c.(655-657)Cgc>Tgc	p.R219C		NM_004704.3	NP_004695.1	O43818	U3IP2_HUMAN	ribosomal RNA processing 9, small subunit (SSU) processome component, homolog (yeast)	219					rRNA processing (GO:0006364)	nucleus (GO:0005634)|small nuclear ribonucleoprotein complex (GO:0030532)|small nucleolar ribonucleoprotein complex (GO:0005732)	poly(A) RNA binding (GO:0044822)	p.R219C(1)		breast(3)|endometrium(1)|kidney(1)|large_intestine(7)|liver(1)|lung(6)|ovary(1)|skin(1)	21				BRCA - Breast invasive adenocarcinoma(193;8.04e-05)|Kidney(197;0.000553)|KIRC - Kidney renal clear cell carcinoma(197;0.000724)		AGCTTGCTGCGGTCACCAGAG	0.597													G|||	2	0.000399361	0.0	0.0	5008	,	,		17347	0.002		0.0	False		,,,				2504	0.0				p.R219C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C655T	3						.	G	CYS/ARG	3,4403	6.2+/-15.9	0,3,2200	114.0	113.0	113.0		655	1.1	1.0	3	dbSNP_134	113	0,8600		0,0,4300	yes	missense	RRP9	NM_004704.3	180	0,3,6500	AA,AG,GG		0.0,0.0681,0.0231	probably-damaging	219/476	51970353	3,13003	2203	4300	6503	51945393	SO:0001583	missense	9136	exon8			AJ001340	CCDS2837.1	3p21.31	2013-01-10	2008-02-26	2006-10-24	ENSG00000114767	ENSG00000114767		"""WD repeat domain containing"""	16829	protein-coding gene	gene with protein product			"""RNA, U3 small nucleolar interacting protein 2"""	RNU3IP2		9418896, 12032086	Standard	NM_004704		Approved	U3-55K	uc003dbw.2	O43818	OTTHUMG00000156930	ENST00000232888.6:c.655C>T	3.37:g.51970353G>A	ENSP00000232888:p.Arg219Cys	Somatic		Capture	Illumina HiSeq	Phase_I	51945393	NM_004704	B2R996|Q8IZ30	Missense_Mutation	SNP	ENST00000232888.6	37	CCDS2837.1	2	9.157509157509158E-4	0	0.0	0	0.0	2	0.0034965034965034965	0	0.0	G	16.49	3.138393	0.56936	6.81E-4	0.0	ENSG00000114767	ENST00000232888	T	0.63096	-0.02	5.3	1.06	0.20224	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.363284	0.32244	N	0.006368	T	0.61464	0.2349	L	0.48642	1.525	0.47584	D	0.99946	D	0.65815	0.995	P	0.59703	0.862	T	0.56842	-0.7912	10	0.38643	T	0.18	-19.4272	4.0487	0.09785	0.2868:0.0:0.3765:0.3367	.	219	O43818	U3IP2_HUMAN	C	219	ENSP00000232888:R219C	ENSP00000232888:R219C	R	-	1	0	RRP9	51945393	0.064000	0.20934	0.999000	0.59377	0.875000	0.50365	0.214000	0.17541	0.257000	0.21650	-0.137000	0.14449	CGC		0.597	RRP9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346637.1	NM_004704	
DNAH1	25981	broad.mit.edu	37	3	52383097	52383097	+	Splice_Site	SNP	A	A	G			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr3:52383097A>G	ENST00000420323.2	+	13	2561	c.2300A>G	c.(2299-2301)aAa>aGa	p.K767R		NM_015512.4	NP_056327	Q9P2D7	DYH1_HUMAN	dynein, axonemal, heavy chain 1	767	Stem. {ECO:0000250}.				cilium movement (GO:0003341)|cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|response to mechanical stimulus (GO:0009612)	axonemal dynein complex (GO:0005858)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)	p.K767R(1)		cervix(2)|endometrium(18)|kidney(6)|large_intestine(3)|lung(31)|prostate(1)|urinary_tract(1)	62				BRCA - Breast invasive adenocarcinoma(193;2.02e-05)|OV - Ovarian serous cystadenocarcinoma(275;0.000207)|Kidney(197;0.0022)|KIRC - Kidney renal clear cell carcinoma(197;0.00245)		TCCTTTCTCAAGTGCGTACGT	0.587																																					p.K767R												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A2300G	3						.						118.0	121.0	120.0					3																	52383097		2194	4275	6469	52358137	SO:0001630	splice_region_variant	25981	exon13			U61738	CCDS46842.1	3p21-p14	2008-02-05	2006-09-04		ENSG00000114841	ENSG00000114841		"""Axonemal dyneins"""	2940	protein-coding gene	gene with protein product		603332	"""dynein, axonemal, heavy polypeptide 1"""			8812413, 9256245	Standard	NM_015512		Approved	XLHSRF-1, DNAHC1, HDHC7, HL-11, HL11	uc011bef.2	Q9P2D7	OTTHUMG00000158378	ENST00000420323.2:c.2300+1A>G	3.37:g.52383097A>G		Somatic		Capture	Illumina HiSeq	Phase_I	52358137	NM_015512	B0I1R6|O00436|O15435|O95491|Q6ZU48|Q86YK7|Q8TEJ4|Q92863|Q9H8E6|Q9UFW6|Q9Y4Z7	Missense_Mutation	SNP	ENST00000420323.2	37	CCDS46842.1	.	.	.	.	.	.	.	.	.	.	A	11.81	1.748281	0.30955	.	.	ENSG00000114841	ENST00000420323	T	0.24908	1.83	5.24	3.88	0.44766	.	0.150136	0.30584	N	0.009320	T	0.17238	0.0414	L	0.33245	0.995	0.40975	D	0.984738	B;B	0.13594	0.002;0.008	B;B	0.17722	0.003;0.019	T	0.07214	-1.0784	10	0.18710	T	0.47	.	9.1059	0.36698	0.8421:0.0:0.1579:0.0	.	767;767	C9JXH6;Q9P2D7-3	.;.	R	767	ENSP00000401514:K767R	ENSP00000401514:K767R	K	+	2	0	DNAH1	52358137	0.998000	0.40836	1.000000	0.80357	0.667000	0.39255	0.903000	0.28475	1.987000	0.57996	0.533000	0.62120	AAA		0.587	DNAH1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350816.1	NM_015512	Missense_Mutation
SEMA3G	56920	broad.mit.edu	37	3	52473987	52473987	+	Missense_Mutation	SNP	C	C	T	rs139945135		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr3:52473987C>T	ENST00000231721.2	-	11	1270	c.1271G>A	c.(1270-1272)cGc>cAc	p.R424H		NM_020163.1	NP_064548.1	Q9NS98	SEM3G_HUMAN	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3G	424	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				multicellular organismal development (GO:0007275)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	receptor activity (GO:0004872)	p.R424H(1)		kidney(1)|large_intestine(5)|lung(8)|ovary(2)|prostate(1)|skin(1)	18				BRCA - Breast invasive adenocarcinoma(193;1.69e-05)|Kidney(197;0.00173)|KIRC - Kidney renal clear cell carcinoma(197;0.00196)|OV - Ovarian serous cystadenocarcinoma(275;0.0333)		AAGGACAGGGCGGCCATGTCG	0.627																																					p.R424H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1271A	3						.	C	HIS/ARG	0,4406		0,0,2203	79.0	82.0	81.0		1271	5.1	1.0	3	dbSNP_134	81	1,8599	1.2+/-3.3	0,1,4299	no	missense	SEMA3G	NM_020163.1	29	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging	424/783	52473987	1,13005	2203	4300	6503	52449027	SO:0001583	missense	56920	exon11				CCDS2856.1	3p21.1	2013-01-11			ENSG00000010319	ENSG00000010319		"""Semaphorins"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	30400	protein-coding gene	gene with protein product						11214971	Standard	XM_005265327		Approved	FLJ00014, sem2	uc003dea.1	Q9NS98	OTTHUMG00000158570	ENST00000231721.2:c.1271G>A	3.37:g.52473987C>T	ENSP00000231721:p.Arg424His	Somatic		Capture	Illumina HiSeq	Phase_I	52449027	NM_020163	Q7L9D9|Q9H7Q3	Missense_Mutation	SNP	ENST00000231721.2	37	CCDS2856.1	.	.	.	.	.	.	.	.	.	.	C	21.9	4.220179	0.79464	0.0	1.16E-4	ENSG00000010319	ENST00000231721	T	0.12255	2.7	5.13	5.13	0.70059	WD40/YVTN repeat-like-containing domain (1);Semaphorin/CD100 antigen (4);	0.197097	0.44688	D	0.000431	T	0.41789	0.1174	M	0.80616	2.505	0.43080	D	0.994735	D	0.89917	1.0	D	0.73380	0.98	T	0.36744	-0.9735	10	0.62326	D	0.03	.	18.7621	0.91856	0.0:1.0:0.0:0.0	.	424	Q9NS98	SEM3G_HUMAN	H	424	ENSP00000231721:R424H	ENSP00000231721:R424H	R	-	2	0	SEMA3G	52449027	0.872000	0.30054	1.000000	0.80357	0.684000	0.39900	1.568000	0.36418	2.672000	0.90937	0.561000	0.74099	CGC		0.627	SEMA3G-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351354.1	NM_020163	
SEMA3G	56920	broad.mit.edu	37	3	52474084	52474084	+	Missense_Mutation	SNP	G	G	A	rs140387468		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr3:52474084G>A	ENST00000231721.2	-	11	1173	c.1174C>T	c.(1174-1176)Cgg>Tgg	p.R392W		NM_020163.1	NP_064548.1	Q9NS98	SEM3G_HUMAN	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3G	392	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				multicellular organismal development (GO:0007275)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	receptor activity (GO:0004872)	p.R392W(1)		kidney(1)|large_intestine(5)|lung(8)|ovary(2)|prostate(1)|skin(1)	18				BRCA - Breast invasive adenocarcinoma(193;1.69e-05)|Kidney(197;0.00173)|KIRC - Kidney renal clear cell carcinoma(197;0.00196)|OV - Ovarian serous cystadenocarcinoma(275;0.0333)		CCAAAAGGCCGTCCTGGCTGT	0.632																																					p.R392W												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1174T	3						.	G	TRP/ARG	0,4406		0,0,2203	73.0	68.0	70.0		1174	4.3	0.9	3	dbSNP_134	70	1,8599	1.2+/-3.3	0,1,4299	no	missense	SEMA3G	NM_020163.1	101	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging	392/783	52474084	1,13005	2203	4300	6503	52449124	SO:0001583	missense	56920	exon11				CCDS2856.1	3p21.1	2013-01-11			ENSG00000010319	ENSG00000010319		"""Semaphorins"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	30400	protein-coding gene	gene with protein product						11214971	Standard	XM_005265327		Approved	FLJ00014, sem2	uc003dea.1	Q9NS98	OTTHUMG00000158570	ENST00000231721.2:c.1174C>T	3.37:g.52474084G>A	ENSP00000231721:p.Arg392Trp	Somatic		Capture	Illumina HiSeq	Phase_I	52449124	NM_020163	Q7L9D9|Q9H7Q3	Missense_Mutation	SNP	ENST00000231721.2	37	CCDS2856.1	.	.	.	.	.	.	.	.	.	.	G	15.98	2.991775	0.54041	0.0	1.16E-4	ENSG00000010319	ENST00000231721	T	0.33216	1.42	5.13	4.26	0.50523	WD40/YVTN repeat-like-containing domain (1);Semaphorin/CD100 antigen (4);	0.067898	0.56097	D	0.000032	T	0.49389	0.1554	M	0.65975	2.015	0.46874	D	0.999237	D	0.89917	1.0	D	0.81914	0.995	T	0.50145	-0.8862	10	0.66056	D	0.02	.	8.5656	0.33538	0.0783:0.0:0.7709:0.1508	.	392	Q9NS98	SEM3G_HUMAN	W	392	ENSP00000231721:R392W	ENSP00000231721:R392W	R	-	1	2	SEMA3G	52449124	0.271000	0.24162	0.896000	0.35187	0.442000	0.32017	2.046000	0.41260	1.402000	0.46780	0.561000	0.74099	CGG		0.632	SEMA3G-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351354.1	NM_020163	
SEMA3G	56920	broad.mit.edu	37	3	52475291	52475291	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr3:52475291G>A	ENST00000231721.2	-	7	801	c.802C>T	c.(802-804)Cgc>Tgc	p.R268C		NM_020163.1	NP_064548.1	Q9NS98	SEM3G_HUMAN	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3G	268	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				multicellular organismal development (GO:0007275)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	receptor activity (GO:0004872)	p.R268C(1)		kidney(1)|large_intestine(5)|lung(8)|ovary(2)|prostate(1)|skin(1)	18				BRCA - Breast invasive adenocarcinoma(193;1.69e-05)|Kidney(197;0.00173)|KIRC - Kidney renal clear cell carcinoma(197;0.00196)|OV - Ovarian serous cystadenocarcinoma(275;0.0333)		ACGCAGACGCGGCCCACGCGG	0.607																																					p.R268C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C802T	3						.						61.0	48.0	52.0					3																	52475291		2203	4300	6503	52450331	SO:0001583	missense	56920	exon7				CCDS2856.1	3p21.1	2013-01-11			ENSG00000010319	ENSG00000010319		"""Semaphorins"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	30400	protein-coding gene	gene with protein product						11214971	Standard	XM_005265327		Approved	FLJ00014, sem2	uc003dea.1	Q9NS98	OTTHUMG00000158570	ENST00000231721.2:c.802C>T	3.37:g.52475291G>A	ENSP00000231721:p.Arg268Cys	Somatic		Capture	Illumina HiSeq	Phase_I	52450331	NM_020163	Q7L9D9|Q9H7Q3	Missense_Mutation	SNP	ENST00000231721.2	37	CCDS2856.1	.	.	.	.	.	.	.	.	.	.	G	17.95	3.513848	0.64522	.	.	ENSG00000010319	ENST00000231721	T	0.49720	0.77	4.56	4.56	0.56223	WD40/YVTN repeat-like-containing domain (1);Semaphorin/CD100 antigen (4);	0.064498	0.64402	D	0.000006	T	0.78629	0.4313	H	0.96239	3.79	0.58432	D	0.999999	D	0.89917	1.0	D	0.97110	1.0	D	0.86216	0.1628	10	0.87932	D	0	.	16.4876	0.84189	0.0:0.0:1.0:0.0	.	268	Q9NS98	SEM3G_HUMAN	C	268	ENSP00000231721:R268C	ENSP00000231721:R268C	R	-	1	0	SEMA3G	52450331	0.291000	0.24352	0.983000	0.44433	0.372000	0.29890	2.498000	0.45363	2.390000	0.81377	0.561000	0.74099	CGC		0.607	SEMA3G-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351354.1	NM_020163	
STAB1	23166	broad.mit.edu	37	3	52548456	52548456	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr3:52548456C>T	ENST00000321725.6	+	34	3698	c.3622C>T	c.(3622-3624)Cgc>Tgc	p.R1208C		NM_015136.2	NP_055951.2	Q9NY15	STAB1_HUMAN	stabilin 1	1208	FAS1 4. {ECO:0000255|PROSITE- ProRule:PRU00082, ECO:0000305}.				cell adhesion (GO:0007155)|cell-cell signaling (GO:0007267)|defense response to bacterium (GO:0042742)|inflammatory response (GO:0006954)|negative regulation of angiogenesis (GO:0016525)|oxidation-reduction process (GO:0055114)|receptor-mediated endocytosis (GO:0006898)	endocytic vesicle membrane (GO:0030666)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	hyaluronic acid binding (GO:0005540)|low-density lipoprotein particle binding (GO:0030169)|low-density lipoprotein receptor activity (GO:0005041)|protein disulfide oxidoreductase activity (GO:0015035)|scavenger receptor activity (GO:0005044)	p.R1208C(1)		breast(4)|central_nervous_system(3)|endometrium(7)|kidney(2)|large_intestine(13)|liver(1)|lung(27)|ovary(1)|pancreas(1)|prostate(4)|skin(6)|upper_aerodigestive_tract(4)|urinary_tract(3)	76				BRCA - Breast invasive adenocarcinoma(193;1.73e-05)|Kidney(197;0.00182)|KIRC - Kidney renal clear cell carcinoma(197;0.00205)|OV - Ovarian serous cystadenocarcinoma(275;0.0482)		GGGTGGACACCGCAACTCCCT	0.642																																					p.R1208C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C3622T	3						.						71.0	74.0	73.0					3																	52548456		2203	4300	6503	52523496	SO:0001583	missense	23166	exon34			AJ275213	CCDS33768.1	3p21.31	2008-07-18			ENSG00000010327	ENSG00000010327			18628	protein-coding gene	gene with protein product	"""MS-1 antigen"", ""fasciclin egf-like, laminin-type egf-like, and link domain-containing scavenger receptor-1"", ""common lymphatic endothelial and vascular endothelial receptor-1"""	608560				11829752, 12077138	Standard	XM_005264973		Approved	KIAA0246, STAB-1, FEEL-1, CLEVER-1, FELE-1, FEX1	uc003dej.3	Q9NY15	OTTHUMG00000158574	ENST00000321725.6:c.3622C>T	3.37:g.52548456C>T	ENSP00000312946:p.Arg1208Cys	Somatic		Capture	Illumina HiSeq	Phase_I	52523496	NM_015136	A7E297|Q8IUH0|Q8IUH1|Q93072	Missense_Mutation	SNP	ENST00000321725.6	37	CCDS33768.1	.	.	.	.	.	.	.	.	.	.	C	20.5	3.997558	0.74818	.	.	ENSG00000010327	ENST00000321725	D	0.90444	-2.67	5.55	4.62	0.57501	FAS1 domain (5);	0.229461	0.35555	N	0.003136	D	0.93641	0.7969	M	0.69823	2.125	0.50039	D	0.999841	D	0.89917	1.0	D	0.71414	0.973	D	0.92783	0.6242	10	0.48119	T	0.1	.	10.8756	0.46909	0.2655:0.7345:0.0:0.0	.	1208	Q9NY15	STAB1_HUMAN	C	1208	ENSP00000312946:R1208C	ENSP00000312946:R1208C	R	+	1	0	STAB1	52523496	1.000000	0.71417	1.000000	0.80357	0.822000	0.46500	2.965000	0.49200	2.627000	0.88993	0.561000	0.74099	CGC		0.642	STAB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351380.2	NM_015136	
PRKCD	5580	broad.mit.edu	37	3	53223108	53223108	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr3:53223108A>G	ENST00000394729.2	+	16	1917	c.1589A>G	c.(1588-1590)gAc>gGc	p.D530G	PRKCD_ENST00000330452.3_Missense_Mutation_p.D530G	NM_212539.1	NP_997704.1	Q05655	KPCD_HUMAN	protein kinase C, delta	530	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of phospholipase C activity (GO:0007202)|apoptotic process (GO:0006915)|B cell proliferation (GO:0042100)|blood coagulation (GO:0007596)|cell cycle (GO:0007049)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular senescence (GO:0090398)|cytokine-mediated signaling pathway (GO:0019221)|defense response to bacterium (GO:0042742)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|gene expression (GO:0010467)|immunoglobulin mediated immune response (GO:0016064)|innate immune response (GO:0045087)|interferon-gamma-mediated signaling pathway (GO:0060333)|interleukin-10 production (GO:0032613)|interleukin-12 production (GO:0032615)|intrinsic apoptotic signaling pathway in response to oxidative stress (GO:0008631)|mRNA metabolic process (GO:0016071)|negative regulation of actin filament polymerization (GO:0030837)|negative regulation of filopodium assembly (GO:0051490)|negative regulation of glial cell apoptotic process (GO:0034351)|negative regulation of inflammatory response (GO:0050728)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of peptidyl-tyrosine phosphorylation (GO:0050732)|negative regulation of platelet aggregation (GO:0090331)|negative regulation of protein binding (GO:0032091)|neurotrophin TRK receptor signaling pathway (GO:0048011)|neutrophil activation (GO:0042119)|peptidyl-threonine phosphorylation (GO:0018107)|platelet activation (GO:0030168)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of ceramide biosynthetic process (GO:2000304)|positive regulation of glucosylceramide catabolic process (GO:2000753)|positive regulation of phospholipid scramblase activity (GO:1900163)|positive regulation of protein dephosphorylation (GO:0035307)|positive regulation of response to DNA damage stimulus (GO:2001022)|positive regulation of sphingomyelin catabolic process (GO:2000755)|positive regulation of superoxide anion generation (GO:0032930)|protein phosphorylation (GO:0006468)|protein stabilization (GO:0050821)|regulation of receptor activity (GO:0010469)|RNA metabolic process (GO:0016070)|signal transduction (GO:0007165)|termination of signal transduction (GO:0023021)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|nuclear matrix (GO:0016363)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium-independent protein kinase C activity (GO:0004699)|enzyme activator activity (GO:0008047)|enzyme binding (GO:0019899)|insulin receptor substrate binding (GO:0043560)|metal ion binding (GO:0046872)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein kinase C activity (GO:0004697)|protein serine/threonine kinase activity (GO:0004674)	p.D530G(2)		breast(1)|central_nervous_system(4)|endometrium(3)|kidney(1)|large_intestine(3)|lung(8)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	26		Ovarian(412;0.0728)		OV - Ovarian serous cystadenocarcinoma(275;3.58e-08)|BRCA - Breast invasive adenocarcinoma(193;0.000142)|Kidney(197;0.00153)|KIRC - Kidney renal clear cell carcinoma(197;0.00173)	Ingenol Mebutate(DB05013)|Tamoxifen(DB00675)	TTCTCTGTGGACTGGTGGTCT	0.592																																					p.D530G												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.A1589G	3						.						99.0	102.0	101.0					3																	53223108		2203	4300	6503	53198148	SO:0001583	missense	5580	exon17				CCDS2870.1	3p21.31	2009-07-10			ENSG00000163932	ENSG00000163932	2.7.11.1		9399	protein-coding gene	gene with protein product		176977				8188219	Standard	NM_006254		Approved		uc003dgm.3	Q05655	OTTHUMG00000133659	ENST00000394729.2:c.1589A>G	3.37:g.53223108A>G	ENSP00000378217:p.Asp530Gly	Somatic		Capture	Illumina HiSeq	Phase_I	53198148	NM_006254	B0KZ81|B2R834|Q15144|Q86XJ6	Missense_Mutation	SNP	ENST00000394729.2	37	CCDS2870.1	.	.	.	.	.	.	.	.	.	.	A	28.6	4.933523	0.92458	.	.	ENSG00000163932	ENST00000394729;ENST00000330452	T;T	0.73575	-0.76;-0.76	5.48	5.48	0.80851	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	D	0.91791	0.7403	H	0.98980	4.39	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.94775	0.7948	10	0.87932	D	0	.	14.6756	0.68978	1.0:0.0:0.0:0.0	.	530	Q05655	KPCD_HUMAN	G	530	ENSP00000378217:D530G;ENSP00000331602:D530G	ENSP00000331602:D530G	D	+	2	0	PRKCD	53198148	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.136000	0.94489	2.297000	0.77311	0.533000	0.62120	GAC		0.592	PRKCD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257818.1		
TKT	7086	broad.mit.edu	37	3	53276233	53276233	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr3:53276233C>T	ENST00000462138.1	-	2	221	c.133G>A	c.(133-135)Gca>Aca	p.A45T	TKT_ENST00000296289.6_5'UTR|TKT_ENST00000423525.2_Missense_Mutation_p.A45T|TKT_ENST00000423516.1_Missense_Mutation_p.A45T			P29401	TKT_HUMAN	transketolase	45					carbohydrate metabolic process (GO:0005975)|energy reserve metabolic process (GO:0006112)|glyceraldehyde-3-phosphate biosynthetic process (GO:0046166)|pentose-phosphate shunt (GO:0006098)|pentose-phosphate shunt, non-oxidative branch (GO:0009052)|regulation of growth (GO:0040008)|small molecule metabolic process (GO:0044281)|xylulose biosynthetic process (GO:0005999)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|peroxisome (GO:0005777)|vesicle (GO:0031982)	cofactor binding (GO:0048037)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|transketolase activity (GO:0004802)	p.A45T(1)		endometrium(5)|large_intestine(4)|lung(4)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	17		Prostate(884;0.0959)		BRCA - Breast invasive adenocarcinoma(193;0.000159)|OV - Ovarian serous cystadenocarcinoma(275;0.000314)|Kidney(197;0.00178)|KIRC - Kidney renal clear cell carcinoma(197;0.00201)		ATGATCTCTGCGGCGCTGCAG	0.582																																					p.A45T	Colon(133;1506 2347 35238 42177)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G133A	3						.						115.0	111.0	113.0					3																	53276233		2203	4300	6503	53251273	SO:0001583	missense	7086	exon2				CCDS2871.1, CCDS58834.1	3p14.3	2008-07-31	2008-07-31		ENSG00000163931	ENSG00000163931	2.2.1.1		11834	protein-coding gene	gene with protein product	"""Wernicke-Korsakoff syndrome"""	606781				1567394	Standard	NM_001064		Approved		uc011beq.2	P29401	OTTHUMG00000158192	ENST00000462138.1:c.133G>A	3.37:g.53276233C>T	ENSP00000417773:p.Ala45Thr	Somatic		Capture	Illumina HiSeq	Phase_I	53251273	NM_001135055	A8K089|B4DE31|E7EPA7|Q8TBA3|Q96HH3	Missense_Mutation	SNP	ENST00000462138.1	37	CCDS2871.1	.	.	.	.	.	.	.	.	.	.	C	16.65	3.182180	0.57800	.	.	ENSG00000163931	ENST00000462138;ENST00000423525;ENST00000423516	T;T;T	0.29917	1.55;1.55;1.55	5.75	5.75	0.90469	Transketolase, N-terminal (1);	0.049305	0.85682	D	0.000000	T	0.60534	0.2276	M	0.81802	2.56	0.80722	D	1	D;D;D	0.89917	0.997;0.977;1.0	P;P;D	0.70016	0.729;0.68;0.967	T	0.63274	-0.6674	10	0.72032	D	0.01	-12.4769	19.9501	0.97195	0.0:1.0:0.0:0.0	.	45;45;45	E7EPA7;B3KSI4;P29401	.;.;TKT_HUMAN	T	45	ENSP00000417773:A45T;ENSP00000405455:A45T;ENSP00000391481:A45T	ENSP00000391481:A45T	A	-	1	0	TKT	53251273	1.000000	0.71417	0.186000	0.23195	0.970000	0.65996	6.026000	0.70873	2.732000	0.93576	0.655000	0.94253	GCA		0.582	TKT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350356.1		
CACNA1D	776	broad.mit.edu	37	3	53700473	53700473	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr3:53700473G>T	ENST00000350061.5	+	7	1538	c.1027G>T	c.(1027-1029)Ggc>Tgc	p.G343C	CACNA1D_ENST00000288139.4_Missense_Mutation_p.G343C|CACNA1D_ENST00000422281.2_Missense_Mutation_p.G343C	NM_001128840.1	NP_001122312.1	Q01668	CAC1D_HUMAN	calcium channel, voltage-dependent, L type, alpha 1D subunit	343					adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|axon guidance (GO:0007411)|calcium ion import (GO:0070509)|calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|energy reserve metabolic process (GO:0006112)|membrane depolarization during action potential (GO:0086010)|membrane depolarization during cardiac muscle cell action potential (GO:0086012)|membrane repolarization during SA node cell action potential (GO:0086052)|positive regulation of calcium ion transport (GO:0051928)|regulation of atrial cardiac muscle cell membrane repolarization (GO:0060372)|regulation of heart rate by cardiac conduction (GO:0086091)|regulation of insulin secretion (GO:0050796)|regulation of potassium ion transmembrane transport (GO:1901379)|regulation of potassium ion transmembrane transporter activity (GO:1901016)|sensory perception of sound (GO:0007605)|small molecule metabolic process (GO:0044281)	plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)|Z disc (GO:0030018)	alpha-actinin binding (GO:0051393)|ankyrin binding (GO:0030506)|high voltage-gated calcium channel activity (GO:0008331)|metal ion binding (GO:0046872)|voltage-gated calcium channel activity (GO:0005245)|voltage-gated calcium channel activity involved in cardiac muscle cell action potential (GO:0086007)|voltage-gated calcium channel activity involved SA node cell action potential (GO:0086059)	p.G343C(1)		breast(3)|central_nervous_system(9)|cervix(2)|endometrium(11)|kidney(7)|large_intestine(13)|liver(1)|lung(29)|ovary(6)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	90				BRCA - Breast invasive adenocarcinoma(193;0.00029)|KIRC - Kidney renal clear cell carcinoma(284;0.0145)|Kidney(284;0.0175)|OV - Ovarian serous cystadenocarcinoma(275;0.0613)	Amlodipine(DB00381)|Cinnarizine(DB00568)|Clevidipine(DB04920)|Dronedarone(DB04855)|Felodipine(DB01023)|Isradipine(DB00270)|Nicardipine(DB00622)|Nifedipine(DB01115)|Nilvadipine(DB06712)|Nimodipine(DB00393)|Nisoldipine(DB00401)|Nitrendipine(DB01054)|Spironolactone(DB00421)|Verapamil(DB00661)	CCCGAACGGAGGCATCACCAA	0.537																																					p.G343C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1027T	3						.						202.0	199.0	200.0					3																	53700473		2203	4300	6503	53675513	SO:0001583	missense	776	exon7			AB209171	CCDS2872.1, CCDS46848.1, CCDS46849.1	3p14.3	2012-03-07			ENSG00000157388	ENSG00000157388		"""Calcium channel subunits"", ""Voltage-gated ion channels / Calcium channels"""	1391	protein-coding gene	gene with protein product		114206		CCHL1A2, CACNL1A2		1664412	Standard	NM_000720		Approved	Cav1.3, CACH3, CACN4	uc003dgu.5	Q01668	OTTHUMG00000158278	ENST00000350061.5:c.1027G>T	3.37:g.53700473G>T	ENSP00000288133:p.Gly343Cys	Somatic		Capture	Illumina HiSeq	Phase_I	53675513	NM_001128839	B0FYA3|Q13916|Q13931|Q71UT1|Q9UDC3	De_novo_Start_OutOfFrame	SNP	ENST00000350061.5	37	CCDS46848.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	27.4|27.4	4.826844|4.826844	0.90955|0.90955	.|.	.|.	ENSG00000157388|ENSG00000157388	ENST00000481085|ENST00000350061;ENST00000288139;ENST00000422281;ENST00000481478	.|D;D;D;D	.|0.97850	.|-4.57;-4.57;-4.57;-4.53	5.15|5.15	5.15|5.15	0.70609|0.70609	.|Ion transport (1);	.|0.000000	.|0.85682	.|D	.|0.000000	D|D	0.99414|0.99414	0.9793|0.9793	H|H	0.99444|0.99444	4.57|4.57	0.80722|0.80722	D|D	1|1	.|D;D;D	.|0.89917	.|1.0;1.0;1.0	.|D;D;D	.|0.97110	.|1.0;1.0;1.0	D|D	0.98066|0.98066	1.0396|1.0396	5|10	.|0.87932	.|D	.|0	.|.	18.8081|18.8081	0.92047|0.92047	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|343;343;343	.|B0FYA3;Q01668;Q01668-2	.|.;CAC1D_HUMAN;.	D|C	28|343;343;343;16	.|ENSP00000288133:G343C;ENSP00000288139:G343C;ENSP00000409174:G343C;ENSP00000418014:G16C	.|ENSP00000288139:G343C	E|G	+|+	3|1	2|0	CACNA1D|CACNA1D	53675513|53675513	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.895000|0.895000	0.52256|0.52256	9.601000|9.601000	0.98297|0.98297	2.676000|2.676000	0.91093|0.91093	0.561000|0.561000	0.74099|0.74099	GAG|GGC		0.537	CACNA1D-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350557.1	NM_000720	
FLNB	2317	broad.mit.edu	37	3	58135897	58135897	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr3:58135897C>T	ENST00000295956.4	+	38	6475	c.6310C>T	c.(6310-6312)Cgg>Tgg	p.R2104W	FLNB_ENST00000348383.5_Intron|FLNB_ENST00000357272.4_Missense_Mutation_p.R2104W|FLNB_ENST00000490882.1_Missense_Mutation_p.R2135W|FLNB_ENST00000429972.2_Missense_Mutation_p.R2093W|FLNB_ENST00000493452.1_Missense_Mutation_p.R1911W|FLNB_ENST00000419752.2_Missense_Mutation_p.R1924W|FLNB_ENST00000358537.3_Missense_Mutation_p.R2080W	NM_001457.3	NP_001448.2	O75369	FLNB_HUMAN	filamin B, beta	2104	Interaction with FLNA 1.|Interaction with the cytoplasmic tail of GP1BA.				actin cytoskeleton organization (GO:0030036)|cell differentiation (GO:0030154)|cytokine-mediated signaling pathway (GO:0019221)|cytoskeletal anchoring at plasma membrane (GO:0007016)|signal transduction (GO:0007165)|skeletal muscle tissue development (GO:0007519)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|stress fiber (GO:0001725)	actin binding (GO:0003779)|identical protein binding (GO:0042802)|poly(A) RNA binding (GO:0044822)	p.R2104W(1)		NS(1)|breast(13)|central_nervous_system(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(23)|liver(2)|lung(38)|ovary(6)|prostate(3)|skin(8)|upper_aerodigestive_tract(3)|urinary_tract(5)	120				BRCA - Breast invasive adenocarcinoma(55;0.000335)|KIRC - Kidney renal clear cell carcinoma(284;0.0726)|Kidney(284;0.0898)		CCGCACCAGTCGGGCCCCGTC	0.607																																					p.R2135W												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C6403T	3						.						102.0	112.0	108.0					3																	58135897		2203	4300	6503	58110937	SO:0001583	missense	2317	exon39			AF043045	CCDS2885.1, CCDS54599.1, CCDS54600.1, CCDS54601.1	3p14.3	2011-02-11	2009-07-23		ENSG00000136068	ENSG00000136068			3755	protein-coding gene	gene with protein product	"""actin binding protein 278"""	603381	"""filamin B, beta (actin binding protein 278)"", ""Larsen syndrome 1 (autosomal dominant)"""	FLN1L, LRS1		8327473, 10449914, 14991055, 16801345	Standard	NM_001457		Approved	TAP, TABP, ABP-278, FH1	uc010hne.2	O75369	OTTHUMG00000159158	ENST00000295956.4:c.6310C>T	3.37:g.58135897C>T	ENSP00000295956:p.Arg2104Trp	Somatic		Capture	Illumina HiSeq	Phase_I	58110937	NM_001164317	B2ZZ83|B2ZZ84|B2ZZ85|C9JKE6|C9JMC4|Q13706|Q59EC2|Q60FE7|Q6MZJ1|Q8WXS9|Q8WXT0|Q8WXT1|Q8WXT2|Q8WXT3|Q9NRB5|Q9NT26|Q9UEV9	Missense_Mutation	SNP	ENST00000295956.4	37	CCDS2885.1	.	.	.	.	.	.	.	.	.	.	C	20.7	4.034971	0.75617	.	.	ENSG00000136068	ENST00000295956;ENST00000490882;ENST00000358537;ENST00000429972;ENST00000357272;ENST00000493452;ENST00000419752	D;D;D;D;D;D;D	0.86627	-2.07;-2.08;-2.08;-2.08;-2.15;-1.83;-1.83	6.17	6.17	0.99709	Immunoglobulin E-set (1);	0.113900	0.64402	D	0.000008	D	0.92469	0.7609	M	0.70275	2.135	0.48452	D	0.99965	D;D;D;D;D;D	0.89917	0.999;1.0;1.0;1.0;0.999;0.999	D;D;D;D;D;D	0.74674	0.958;0.984;0.975;0.938;0.975;0.975	D	0.92396	0.5925	10	0.72032	D	0.01	.	14.1492	0.65370	0.2615:0.7385:0.0:0.0	.	2080;2135;1911;1924;2093;2104	O75369-2;B2ZZ83;E7EN95;O75369-7;Q60FE7;O75369	.;.;.;.;.;FLNB_HUMAN	W	2104;2135;2080;2093;2104;1911;1924	ENSP00000295956:R2104W;ENSP00000420213:R2135W;ENSP00000351339:R2080W;ENSP00000415599:R2093W;ENSP00000349819:R2104W;ENSP00000418510:R1911W;ENSP00000414532:R1924W	ENSP00000295956:R2104W	R	+	1	2	FLNB	58110937	0.999000	0.42202	0.996000	0.52242	0.692000	0.40212	0.903000	0.28475	2.941000	0.99782	0.655000	0.94253	CGG		0.607	FLNB-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000353569.1	NM_001457	
CADPS	8618	broad.mit.edu	37	3	62570893	62570893	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr3:62570893C>T	ENST00000383710.4	-	8	1893	c.1544G>A	c.(1543-1545)cGa>cAa	p.R515Q	CADPS_ENST00000283269.9_Missense_Mutation_p.R515Q|CADPS_ENST00000357948.3_Missense_Mutation_p.R515Q	NM_003716.3	NP_003707.2	Q9ULU8	CAPS1_HUMAN	Ca++-dependent secretion activator	515					catecholamine secretion (GO:0050432)|exocytosis (GO:0006887)|protein transport (GO:0015031)|synaptic vesicle priming (GO:0016082)|vesicle organization (GO:0016050)	cell junction (GO:0030054)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|membrane (GO:0016020)|synapse (GO:0045202)	lipid binding (GO:0008289)|metal ion binding (GO:0046872)|protein kinase binding (GO:0019901)	p.R515Q(2)		breast(3)|central_nervous_system(2)|endometrium(6)|kidney(6)|large_intestine(24)|lung(38)|ovary(4)|prostate(3)|skin(3)|stomach(1)|urinary_tract(2)	92		Lung SC(41;0.0452)		BRCA - Breast invasive adenocarcinoma(55;5.98e-05)|KIRC - Kidney renal clear cell carcinoma(15;0.0246)|Kidney(15;0.0334)		CTTATCCATTCGGACAGCAAG	0.448																																					p.R515Q												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G1544A	3						.						196.0	184.0	188.0					3																	62570893		2203	4300	6503	62545933	SO:0001583	missense	8618	exon8			U36448	CCDS2898.1, CCDS2899.1, CCDS46858.1	3p21.1	2013-01-10	2008-08-28		ENSG00000163618	ENSG00000163618		"""Pleckstrin homology (PH) domain containing"""	1426	protein-coding gene	gene with protein product		604667				1516133	Standard	NM_183393		Approved	CAPS, KIAA1121, CAPS1	uc003dll.2	Q9ULU8	OTTHUMG00000158651	ENST00000383710.4:c.1544G>A	3.37:g.62570893C>T	ENSP00000373215:p.Arg515Gln	Somatic		Capture	Illumina HiSeq	Phase_I	62545933	NM_183393	A6NF60|Q13339|Q6GQQ6|Q8N2Z5|Q8N3M7|Q8NFR0|Q96BC2	Missense_Mutation	SNP	ENST00000383710.4	37	CCDS46858.1	.	.	.	.	.	.	.	.	.	.	C	33	5.238302	0.95240	.	.	ENSG00000163618	ENST00000383709;ENST00000383710;ENST00000357948;ENST00000283269;ENST00000542833	T;T;T	0.54675	0.58;0.56;0.58	6.04	5.17	0.71159	.	0.000000	0.85682	D	0.000000	T	0.71484	0.3345	M	0.69358	2.11	0.80722	D	1	D;D;D;D	0.89917	1.0;0.974;0.999;1.0	D;B;D;D	0.72625	0.976;0.288;0.978;0.967	T	0.75575	-0.3270	10	0.87932	D	0	.	17.4261	0.87526	0.0:0.8755:0.1245:0.0	.	515;515;515;515	Q9ULU8-2;Q9ULU8-3;Q9ULU8;Q9ULU8-4	.;.;CAPS1_HUMAN;.	Q	515;515;515;515;10	ENSP00000373215:R515Q;ENSP00000350632:R515Q;ENSP00000283269:R515Q	ENSP00000283269:R515Q	R	-	2	0	CADPS	62545933	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	7.818000	0.86416	1.556000	0.49512	0.563000	0.77884	CGA		0.448	CADPS-013	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351951.5	NM_003716, NM_183393, NM_183394	
MAGI1	9223	broad.mit.edu	37	3	65416493	65416493	+	Missense_Mutation	SNP	C	C	T	rs375653415		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr3:65416493C>T	ENST00000497477.2	-	11	1426	c.1427G>A	c.(1426-1428)cGg>cAg	p.R476Q	MAGI1_ENST00000483466.1_Missense_Mutation_p.R476Q|MAGI1_ENST00000402939.2_Missense_Mutation_p.R476Q|MAGI1_ENST00000470990.1_5'UTR|MAGI1_ENST00000330909.8_Missense_Mutation_p.R476Q			Q96QZ7	MAGI1_HUMAN	membrane associated guanylate kinase, WW and PDZ domain containing 1	476	PDZ 2. {ECO:0000255|PROSITE- ProRule:PRU00143}.				cell adhesion (GO:0007155)|cell surface receptor signaling pathway (GO:0007166)|neuron death (GO:0070997)|protein complex assembly (GO:0006461)	cell junction (GO:0030054)|cell projection (GO:0042995)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	alpha-actinin binding (GO:0051393)|ATP binding (GO:0005524)|protein C-terminus binding (GO:0008022)	p.R476Q(4)		breast(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|liver(1)|lung(21)|pancreas(1)|skin(5)	51		Lung NSC(201;0.0016)		BRCA - Breast invasive adenocarcinoma(55;0.00138)|KIRC - Kidney renal clear cell carcinoma(15;0.0988)|Kidney(15;0.133)		ACTGCTTTTCCGCAGCTTTGT	0.463																																					p.R476Q												.	.	4	Substitution - Missense(4)	large_intestine(2)|haematopoietic_and_lymphoid_tissue(2)	c.G1427A	3						.	C	GLN/ARG,GLN/ARG,GLN/ARG	0,4406		0,0,2203	143.0	124.0	130.0		1427,1427,1427	5.7	1.0	3		130	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense,missense	MAGI1	NM_001033057.1,NM_004742.2,NM_015520.1	43,43,43	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	benign,benign,benign	476/1463,476/1257,476/1288	65416493	1,13005	2203	4300	6503	65391533	SO:0001583	missense	9223	exon11			AB010894	CCDS33780.1, CCDS33781.1, CCDS2904.1	3p14.1	2009-10-06	2005-05-10	2005-05-10	ENSG00000151276	ENSG00000151276			946	protein-coding gene	gene with protein product		602625	"""BAI1-associated protein 1"""	BAIAP1		9647739, 9225980	Standard	XM_005265563		Approved	BAP1, MAGI-1, TNRC19, AIP3, WWP3	uc003dmn.3	Q96QZ7	OTTHUMG00000157554	ENST00000497477.2:c.1427G>A	3.37:g.65416493C>T	ENSP00000424369:p.Arg476Gln	Somatic		Capture	Illumina HiSeq	Phase_I	65391533	NM_015520	A8K188|O00309|O43863|O75085|Q96QZ8|Q96QZ9	Missense_Mutation	SNP	ENST00000497477.2	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	17.65|17.65	3.441532|3.441532	0.63067|0.63067	0.0|0.0	1.16E-4|1.16E-4	ENSG00000151276|ENSG00000151276	ENST00000460329|ENST00000402939;ENST00000330909;ENST00000422949;ENST00000463103;ENST00000483466;ENST00000497477;ENST00000472257	.|T;T;T;T;T;T	.|0.26067	.|1.76;1.76;1.76;1.76;1.76;1.76	5.73|5.73	5.73|5.73	0.89815|0.89815	.|.	.|0.097054	.|0.64402	.|N	.|0.000002	T|T	0.20210|0.20210	0.0486|0.0486	N|N	0.03050|0.03050	-0.425|-0.425	0.49798|0.49798	D|D	0.999825|0.999825	.|D;D;P;B;B	.|0.61697	.|0.957;0.99;0.886;0.081;0.181	.|P;P;B;B;B	.|0.52710	.|0.481;0.707;0.272;0.07;0.044	T|T	0.25745|0.25745	-1.0123|-1.0123	5|10	.|0.14656	.|T	.|0.56	-20.4479|-20.4479	19.914|19.914	0.97034|0.97034	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|476;476;476;476;476	.|Q96QZ7-6;Q96QZ7-4;Q96QZ7-3;Q96QZ7-2;Q96QZ7-5	.|.;.;.;.;.	R|Q	357|476;476;372;351;476;476;262	.|ENSP00000385450:R476Q;ENSP00000331157:R476Q;ENSP00000418177:R351Q;ENSP00000420323:R476Q;ENSP00000424369:R476Q;ENSP00000420796:R262Q	.|ENSP00000331157:R476Q	G|R	-|-	1|2	0|0	MAGI1|MAGI1	65391533|65391533	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.997000|0.997000	0.91878|0.91878	3.492000|3.492000	0.53259|0.53259	2.712000|2.712000	0.92718|0.92718	0.557000|0.557000	0.71058|0.71058	GGA|CGG		0.463	MAGI1-007	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000349132.2	NM_004742	
SLC25A26	115286	broad.mit.edu	37	3	66420958	66420958	+	Silent	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr3:66420958C>T	ENST00000413054.1	+	7	449	c.375C>T	c.(373-375)ggC>ggT	p.G125G	SLC25A26_ENST00000354883.6_Silent_p.G213G|SLC25A26_ENST00000484768.1_3'UTR|SLC25A26_ENST00000536651.1_3'UTR|SLC25A26_ENST00000336733.6_Silent_p.G125G			Q70HW3	SAMC_HUMAN	solute carrier family 25 (S-adenosylmethionine carrier), member 26	213					S-adenosyl-L-methionine transmembrane transport (GO:1901962)|S-adenosyl-L-methionine transport (GO:0015805)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	S-adenosyl-L-methionine transmembrane transporter activity (GO:0000095)	p.G213G(1)		endometrium(1)|large_intestine(1)|lung(2)|pancreas(1)|stomach(2)|urinary_tract(1)	8		Lung NSC(201;0.00774)		BRCA - Breast invasive adenocarcinoma(55;0.00046)|KIRC - Kidney renal clear cell carcinoma(15;0.0515)|Kidney(15;0.0648)		CACAGGCTGGCTCCAGCACTG	0.552																																					p.G150G												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C450T	3						.						105.0	92.0	97.0					3																	66420958		2203	4300	6503	66503648	SO:0001819	synonymous_variant	115286	exon8			AJ580932	CCDS54604.1, CCDS2905.2	3p14.2	2013-05-22	2012-03-29		ENSG00000144741	ENSG00000144741		"""Solute carriers"""	20661	protein-coding gene	gene with protein product		611037	"""solute carrier family 25 (mitochondrial carrier; phosphate carrier), member 26"""			14674884	Standard	NM_173471		Approved		uc011bfq.2	Q70HW3	OTTHUMG00000149917	ENST00000413054.1:c.375C>T	3.37:g.66420958C>T		Somatic		Capture	Illumina HiSeq	Phase_I	66503648	NM_173471	A8K758|B3KRZ7|Q7Z786|Q96E68	Silent	SNP	ENST00000413054.1	37		.	.	.	.	.	.	.	.	.	.	C	8.010	0.757222	0.15846	.	.	ENSG00000144741	ENST00000413054	.	.	.	5.74	-11.5	0.00074	.	.	.	.	.	T	0.39655	0.1086	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.47182	-0.9137	4	.	.	.	-12.2262	4.8088	0.13333	0.0846:0.3986:0.2576:0.2592	.	.	.	.	V	150	.	.	A	+	2	0	SLC25A26	66503648	0.368000	0.25031	0.182000	0.23118	0.171000	0.22731	-0.710000	0.05024	-2.115000	0.00831	-0.258000	0.10820	GCT		0.552	SLC25A26-002	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000313895.2	NM_173471	
LRIG1	26018	broad.mit.edu	37	3	66434606	66434606	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr3:66434606T>C	ENST00000273261.3	-	14	2404	c.1880A>G	c.(1879-1881)aAc>aGc	p.N627S	LRIG1_ENST00000496559.2_5'UTR|LRIG1_ENST00000383703.3_Missense_Mutation_p.N651S|SLC25A26_ENST00000536651.1_Intron	NM_015541.2	NP_056356.2	Q96JA1	LRIG1_HUMAN	leucine-rich repeats and immunoglobulin-like domains 1	627	Ig-like C2-type 2.				innervation (GO:0060384)|otolith morphogenesis (GO:0032474)|sensory perception of sound (GO:0007605)	integral component of membrane (GO:0016021)		p.N627S(1)		NS(2)|breast(2)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(7)|lung(12)|ovary(3)|prostate(1)|skin(4)|stomach(4)|urinary_tract(1)	42		Lung NSC(201;0.0101)		BRCA - Breast invasive adenocarcinoma(55;0.00047)		AATCTGAGGGTTTGGGTGACC	0.567																																					p.N627S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A1880G	3						.						164.0	156.0	158.0					3																	66434606		2203	4300	6503	66517296	SO:0001583	missense	26018	exon14			AB050468	CCDS33783.1	3p14	2013-01-14			ENSG00000144749	ENSG00000144749		"""Immunoglobulin superfamily / I-set domain containing"""	17360	protein-coding gene	gene with protein product	"""ortholog of mouse integral membrane glycoprotein LIG-1"", ""leucine-rich repeat protein LRIG1"""	608868				11414704, 12234026	Standard	NM_015541		Approved	LIG-1, DKFZP586O1624, LIG1	uc003dmx.3	Q96JA1	OTTHUMG00000158727	ENST00000273261.3:c.1880A>G	3.37:g.66434606T>C	ENSP00000273261:p.Asn627Ser	Somatic		Capture	Illumina HiSeq	Phase_I	66517296	NM_015541	Q6IQ51|Q96CF9|Q9BYB8|Q9UFI4	Missense_Mutation	SNP	ENST00000273261.3	37	CCDS33783.1	.	.	.	.	.	.	.	.	.	.	T	3.245	-0.154430	0.06544	.	.	ENSG00000144749	ENST00000273261;ENST00000383703;ENST00000383702	T;T	0.66280	-0.2;-0.2	6.17	3.83	0.44106	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.209130	0.49305	N	0.000159	T	0.31979	0.0814	N	0.04162	-0.26	0.34542	D	0.710411	B;B;B	0.14438	0.01;0.006;0.006	B;B;B	0.20577	0.03;0.03;0.017	T	0.27468	-1.0073	10	0.07030	T	0.85	.	6.3828	0.21544	0.0:0.1478:0.2364:0.6158	.	651;627;627	Q96JA1-2;Q5XWD3;Q96JA1	.;.;LRIG1_HUMAN	S	627;651;530	ENSP00000273261:N627S;ENSP00000373208:N651S	ENSP00000273261:N627S	N	-	2	0	LRIG1	66517296	0.981000	0.34729	0.933000	0.37362	0.301000	0.27625	4.148000	0.58085	0.582000	0.29556	-0.250000	0.11733	AAC		0.567	LRIG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351930.1	NM_015541	
KBTBD8	84541	broad.mit.edu	37	3	67053715	67053715	+	Silent	SNP	C	C	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr3:67053715C>A	ENST00000417314.2	+	3	373	c.324C>A	c.(322-324)gcC>gcA	p.A108A	KBTBD8_ENST00000460576.1_Intron|KBTBD8_ENST00000469661.1_Intron|KBTBD8_ENST00000295568.4_Silent_p.A82A			Q8NFY9	KBTB8_HUMAN	kelch repeat and BTB (POZ) domain containing 8	108	BTB. {ECO:0000255|PROSITE- ProRule:PRU00037}.					cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)		p.A82A(1)		breast(1)|endometrium(1)|kidney(4)|large_intestine(7)|lung(4)|ovary(2)|prostate(1)	20		Lung NSC(201;0.0765)		BRCA - Breast invasive adenocarcinoma(55;6.02e-06)|KIRC - Kidney renal clear cell carcinoma(39;0.105)|Kidney(39;0.125)		TGAACTATGCCTACACTTCCA	0.418																																					p.A108A												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C324A	3						.						192.0	182.0	186.0					3																	67053715		2203	4300	6503	67136405	SO:0001819	synonymous_variant	84541	exon3			AF385438	CCDS2906.1, CCDS2906.2	3p14	2013-01-08			ENSG00000163376	ENSG00000163376		"""BTB/POZ domain containing"""	30691	protein-coding gene	gene with protein product	"""T-cell activation kelch repeat protein"""					11347906	Standard	NM_032505		Approved	TA-KRP, KIAA1842	uc003dmy.3	Q8NFY9	OTTHUMG00000158779	ENST00000417314.2:c.324C>A	3.37:g.67053715C>A		Somatic		Capture	Illumina HiSeq	Phase_I	67136405	NM_032505	B4DTW6|Q96JI5	Silent	SNP	ENST00000417314.2	37	CCDS2906.2																																																																																				0.418	KBTBD8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352189.1	NM_032505	
FAM19A1	407738	broad.mit.edu	37	3	68466451	68466451	+	Missense_Mutation	SNP	T	T	G			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr3:68466451T>G	ENST00000478136.1	+	3	630	c.140T>G	c.(139-141)aTa>aGa	p.I47R	FAM19A1_ENST00000496687.1_Missense_Mutation_p.I47R|FAM19A1_ENST00000491017.1_3'UTR	NM_213609.3	NP_998774.2	Q7Z5A9	F19A1_HUMAN	family with sequence similarity 19 (chemokine (C-C motif)-like), member A1	47						endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)		p.I47R(1)		central_nervous_system(1)|endometrium(1)|kidney(1)|lung(3)|ovary(1)	7		Lung NSC(201;0.0117)		BRCA - Breast invasive adenocarcinoma(55;7.7e-05)|Epithelial(33;0.000937)|KIRC - Kidney renal clear cell carcinoma(39;0.0579)|Kidney(39;0.0743)		TGTGAAGTGATAGCAGCACAC	0.478																																					p.I47R												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T140G	3						.						108.0	105.0	106.0					3																	68466451		1967	4146	6113	68549141	SO:0001583	missense	407738	exon3			AY325114	CCDS54606.1	3p14.1	2005-01-20			ENSG00000183662	ENSG00000183662			21587	protein-coding gene	gene with protein product						15028294	Standard	NM_213609		Approved	TAFA-1	uc003dnd.3	Q7Z5A9	OTTHUMG00000158745	ENST00000478136.1:c.140T>G	3.37:g.68466451T>G	ENSP00000418575:p.Ile47Arg	Somatic		Capture	Illumina HiSeq	Phase_I	68549141	NM_213609	A8K0V3|Q8TCL8	Missense_Mutation	SNP	ENST00000478136.1	37	CCDS54606.1	.	.	.	.	.	.	.	.	.	.	T	28.1	4.887940	0.91814	.	.	ENSG00000183662	ENST00000478136;ENST00000496687	.	.	.	5.66	5.66	0.87406	.	0.000000	0.85682	D	0.000000	T	0.75700	0.3885	L	0.54323	1.7	0.80722	D	1	D	0.69078	0.997	D	0.81914	0.995	T	0.78011	-0.2371	9	0.87932	D	0	.	16.1823	0.81920	0.0:0.0:0.0:1.0	.	47	Q7Z5A9	F19A1_HUMAN	R	47	.	ENSP00000418575:I47R	I	+	2	0	FAM19A1	68549141	1.000000	0.71417	0.953000	0.39169	0.981000	0.71138	7.993000	0.88291	2.274000	0.75844	0.477000	0.44152	ATA		0.478	FAM19A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352004.1	NM_213609	
CNTN3	5067	broad.mit.edu	37	3	74418355	74418355	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr3:74418355G>A	ENST00000263665.6	-	7	958	c.931C>T	c.(931-933)Cgt>Tgt	p.R311C		NM_020872.1	NP_065923.1	Q9P232	CNTN3_HUMAN	contactin 3 (plasmacytoma associated)	311	Ig-like C2-type 3.				cell adhesion (GO:0007155)|nervous system development (GO:0007399)	anchored component of membrane (GO:0031225)|plasma membrane (GO:0005886)		p.R311C(1)		NS(2)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(14)|lung(39)|ovary(1)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	83		Lung NSC(201;0.138)|Lung SC(41;0.21)		Epithelial(33;0.00212)|BRCA - Breast invasive adenocarcinoma(55;0.00258)|LUSC - Lung squamous cell carcinoma(21;0.00461)|Lung(16;0.01)		TAAGTGAGACGCCCTCTGGCA	0.413																																					p.R311C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C931T	3						.						72.0	68.0	70.0					3																	74418355		2203	4299	6502	74501045	SO:0001583	missense	5067	exon7			AB040929	CCDS33790.1	3p12.3	2013-02-11			ENSG00000113805	ENSG00000113805		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	2173	protein-coding gene	gene with protein product		601325		PANG		8661054, 8586965	Standard	XM_005264757		Approved	BIG-1	uc003dpm.1	Q9P232	OTTHUMG00000158813	ENST00000263665.6:c.931C>T	3.37:g.74418355G>A	ENSP00000263665:p.Arg311Cys	Somatic		Capture	Illumina HiSeq	Phase_I	74501045	NM_020872	B9EK50|Q9H039	Missense_Mutation	SNP	ENST00000263665.6	37	CCDS33790.1	.	.	.	.	.	.	.	.	.	.	G	18.96	3.734565	0.69189	.	.	ENSG00000113805	ENST00000263665	D	0.96232	-3.95	5.25	5.25	0.73442	Immunoglobulin-like (1);	0.000000	0.85682	D	0.000000	D	0.97885	0.9305	M	0.77616	2.38	0.51767	D	0.999936	D	0.89917	1.0	D	0.64877	0.93	D	0.98528	1.0626	10	0.66056	D	0.02	.	18.8669	0.92296	0.0:0.0:1.0:0.0	.	311	Q9P232	CNTN3_HUMAN	C	311	ENSP00000263665:R311C	ENSP00000263665:R311C	R	-	1	0	CNTN3	74501045	0.126000	0.22350	0.990000	0.47175	0.980000	0.70556	1.490000	0.35573	2.437000	0.82529	0.591000	0.81541	CGT		0.413	CNTN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352306.1	NM_020872	
CNTN3	5067	broad.mit.edu	37	3	74474039	74474039	+	Silent	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr3:74474039G>A	ENST00000263665.6	-	4	438	c.411C>T	c.(409-411)ggC>ggT	p.G137G		NM_020872.1	NP_065923.1	Q9P232	CNTN3_HUMAN	contactin 3 (plasmacytoma associated)	137	Ig-like C2-type 2.				cell adhesion (GO:0007155)|nervous system development (GO:0007399)	anchored component of membrane (GO:0031225)|plasma membrane (GO:0005886)		p.G137G(1)		NS(2)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(14)|lung(39)|ovary(1)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	83		Lung NSC(201;0.138)|Lung SC(41;0.21)		Epithelial(33;0.00212)|BRCA - Breast invasive adenocarcinoma(55;0.00258)|LUSC - Lung squamous cell carcinoma(21;0.00461)|Lung(16;0.01)		CAACTCCCTGGCCTTCACGCA	0.418																																					p.G137G												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C411T	3						.						84.0	75.0	78.0					3																	74474039		2203	4300	6503	74556729	SO:0001819	synonymous_variant	5067	exon4			AB040929	CCDS33790.1	3p12.3	2013-02-11			ENSG00000113805	ENSG00000113805		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	2173	protein-coding gene	gene with protein product		601325		PANG		8661054, 8586965	Standard	XM_005264757		Approved	BIG-1	uc003dpm.1	Q9P232	OTTHUMG00000158813	ENST00000263665.6:c.411C>T	3.37:g.74474039G>A		Somatic		Capture	Illumina HiSeq	Phase_I	74556729	NM_020872	B9EK50|Q9H039	Silent	SNP	ENST00000263665.6	37	CCDS33790.1																																																																																				0.418	CNTN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352306.1	NM_020872	
EPHA6	285220	broad.mit.edu	37	3	97185299	97185299	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr3:97185299A>G	ENST00000514100.1	+	4	285	c.43A>G	c.(43-45)Aat>Gat	p.N15D	EPHA6_ENST00000442602.2_Intron|EPHA6_ENST00000389672.5_Intron|EPHA6_ENST00000502694.1_Missense_Mutation_p.N15D	NM_001278300.1	NP_001265229.1	Q9UF33	EPHA6_HUMAN	EPH receptor A6	0						integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ephrin receptor activity (GO:0005003)	p.N15D(1)		NS(1)|breast(1)|central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(6)|liver(2)|lung(60)|ovary(3)|skin(11)|stomach(5)|upper_aerodigestive_tract(2)	101						gtactggcttaatgaaaagtg	0.423																																					p.N15D												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A43G	3						.						114.0	108.0	110.0					3																	97185299		1851	4097	5948	98667989	SO:0001583	missense	285220	exon5			AK092565	CCDS46876.1, CCDS54616.1, CCDS63697.1	3q12.1	2013-02-11	2004-10-28		ENSG00000080224	ENSG00000080224		"""EPH receptors"", ""Sterile alpha motif (SAM) domain containing"", ""Fibronectin type III domain containing"""	19296	protein-coding gene	gene with protein product		600066				12471243	Standard	NM_001080448		Approved	FLJ35246	uc010how.1	Q9UF33	OTTHUMG00000159208	ENST00000514100.1:c.43A>G	3.37:g.97185299A>G	ENSP00000421711:p.Asn15Asp	Somatic		Capture	Illumina HiSeq	Phase_I	98667989	NM_173655	D6RAL5	Missense_Mutation	SNP	ENST00000514100.1	37		.	.	.	.	.	.	.	.	.	.	A	9.331	1.060445	0.19987	.	.	ENSG00000080224	ENST00000514100;ENST00000502694	D;T	0.82167	-1.58;-1.33	3.58	2.43	0.29744	.	.	.	.	.	T	0.67439	0.2893	N	0.14661	0.345	0.09310	N	0.999999	B;B	0.06786	0.0;0.001	B;B	0.04013	0.001;0.001	T	0.58126	-0.7691	9	0.62326	D	0.03	.	5.5896	0.17293	0.8754:0.0:0.1246:0.0	.	15;15	Q9UF33-2;D6RAL5	.;.	D	15	ENSP00000421711:N15D;ENSP00000423950:N15D	ENSP00000423950:N15D	N	+	1	0	EPHA6	98667989	0.002000	0.14202	0.021000	0.16686	0.048000	0.14542	0.923000	0.28757	0.742000	0.32697	0.491000	0.48974	AAT		0.423	EPHA6-007	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000359997.1	NM_001080448	
KIAA0226	9711	broad.mit.edu	37	3	197420648	197420648	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr3:197420648C>T	ENST00000296343.5	-	11	1723	c.1724G>A	c.(1723-1725)cGt>cAt	p.R575H	KIAA0226_ENST00000273582.5_Missense_Mutation_p.R530H|KIAA0226_ENST00000389665.5_Missense_Mutation_p.R575H	NM_014687.1	NP_055502.1	Q92622	RUBIC_HUMAN	KIAA0226	575	Ser-rich.				autophagy (GO:0006914)|cell death (GO:0008219)|endocytosis (GO:0006897)|negative regulation of autophagy (GO:0010507)|negative regulation of endocytosis (GO:0045806)	early endosome (GO:0005769)|late endosome (GO:0005770)|lysosome (GO:0005764)		p.R575H(1)|p.R530H(1)|p.R423H(1)		NS(2)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|lung(13)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	31	all_cancers(143;8.26e-10)|Ovarian(172;0.0418)|Breast(254;0.0976)		Epithelial(36;2.19e-23)|all cancers(36;1.39e-21)|OV - Ovarian serous cystadenocarcinoma(49;1.21e-18)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(93;0.0446)		TGCCGAATCACGTGAGCTGAA	0.443																																					p.R575H	Esophageal Squamous(3;167 355 3763 15924)											.	.	3	Substitution - Missense(3)	large_intestine(3)	c.G1724A	3						.						83.0	85.0	85.0					3																	197420648		1958	4165	6123	198905045	SO:0001583	missense	9711	exon11			D86979	CCDS43195.1, CCDS46987.1	3q29	2011-08-09			ENSG00000145016	ENSG00000145016			28991	protein-coding gene	gene with protein product	"""RUN domain and cysteine-rich domain containing, Beclin 1-interacting protein"""	613516				9039502, 19270693, 20826435	Standard	XM_005269374		Approved	rubicon, rundataxin	uc003fyc.2	Q92622	OTTHUMG00000155452	ENST00000296343.5:c.1724G>A	3.37:g.197420648C>T	ENSP00000296343:p.Arg575His	Somatic		Capture	Illumina HiSeq	Phase_I	198905045	NM_014687	Q96CK5	Missense_Mutation	SNP	ENST00000296343.5	37	CCDS43195.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	11.32|11.32	1.605168|1.605168	0.28623|0.28623	.|.	.|.	ENSG00000145016|ENSG00000145016	ENST00000273582;ENST00000296343;ENST00000389665|ENST00000415452	.|.	.|.	.|.	5.64|5.64	4.77|4.77	0.60923|0.60923	.|.	0.133360|.	0.53938|.	D|.	0.000057|.	T|T	0.24509|0.24509	0.0594|0.0594	N|N	0.03608|0.03608	-0.345|-0.345	0.35197|0.35197	D|D	0.773901|0.773901	B;B;B|.	0.16166|.	0.016;0.009;0.009|.	B;B;B|.	0.13407|.	0.009;0.006;0.003|.	T|T	0.32107|0.32107	-0.9919|-0.9919	9|5	0.25751|.	T|.	0.34|.	.|.	8.7418|8.7418	0.34562|0.34562	0.0:0.7612:0.0:0.2388|0.0:0.7612:0.0:0.2388	.|.	575;530;575|.	Q92622-3;Q92622-2;Q92622|.	.;.;RUBIC_HUMAN|.	H|M	530;575;575|334	.|.	ENSP00000273582:R530H|.	R|V	-|-	2|1	0|0	KIAA0226|KIAA0226	198905045|198905045	0.050000|0.050000	0.20438|0.20438	0.988000|0.988000	0.46212|0.46212	0.544000|0.544000	0.35116|0.35116	0.322000|0.322000	0.19576|0.19576	1.384000|1.384000	0.46424|0.46424	0.655000|0.655000	0.94253|0.94253	CGT|GTG		0.443	KIAA0226-011	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000340184.1	XM_032901	
WDR17	116966	broad.mit.edu	37	4	177071291	177071292	+	Frame_Shift_Ins	INS	-	-	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	-	-	-	A	-	-	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr4:177071291_177071292insA	ENST00000280190.4	+	16	2373_2374	c.2217_2218insA	c.(2218-2220)aaafs	p.K740fs	WDR17_ENST00000508596.1_Frame_Shift_Ins_p.K716fs|WDR17_ENST00000507824.2_Frame_Shift_Ins_p.K723fs|WDR17_ENST00000393643.2_Frame_Shift_Ins_p.K716fs			Q8IZU2	WDR17_HUMAN	WD repeat domain 17	740								p.L742fs*15(1)		breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(18)|lung(46)|ovary(2)|pancreas(1)|prostate(3)|skin(5)|stomach(1)|upper_aerodigestive_tract(6)|urinary_tract(1)	92		Breast(14;0.00015)|Melanoma(52;0.00886)|Prostate(90;0.00996)|Renal(120;0.0183)|all_hematologic(60;0.107)|all_neural(102;0.164)		all cancers(43;2.21e-20)|Epithelial(43;9.71e-18)|OV - Ovarian serous cystadenocarcinoma(60;2.38e-09)|GBM - Glioblastoma multiforme(59;0.000295)|STAD - Stomach adenocarcinoma(60;0.000703)|LUSC - Lung squamous cell carcinoma(193;0.0232)		ATTCTCAAGTGAAAAAACTAAG	0.332																																					p.V739fs												.	.	1	Insertion - Frameshift(1)	large_intestine(1)	c.2217_2218insA	4						.																																			177308286	SO:0001589	frameshift_variant	116966	exon16			AF492460	CCDS3825.1, CCDS43284.1, CCDS43284.2	4q34	2013-01-09			ENSG00000150627	ENSG00000150627		"""WD repeat domain containing"""	16661	protein-coding gene	gene with protein product		609005				12401215	Standard	NM_170710		Approved		uc003iuj.3	Q8IZU2	OTTHUMG00000160791	ENST00000280190.4:c.2223dupA	4.37:g.177071297_177071297dupA	ENSP00000280190:p.Lys740fs	Somatic		Capture	Illumina HiSeq	Phase_I	177308285	NM_170710	E7EQX0|Q0QD35	Frame_Shift_Ins	INS	ENST00000280190.4	37	CCDS3825.1																																																																																				0.332	WDR17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362334.2		
ADH1C	126	broad.mit.edu	37	4	100264146	100264146	+	RNA	SNP	A	A	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr4:100264146A>T	ENST00000510055.1	-	0	808				ADH1C_ENST00000515683.1_RNA			P00326	ADH1G_HUMAN	alcohol dehydrogenase 1C (class I), gamma polypeptide						ethanol oxidation (GO:0006069)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)	alcohol dehydrogenase (NAD) activity (GO:0004022)|zinc ion binding (GO:0008270)								OV - Ovarian serous cystadenocarcinoma(123;1.08e-07)	Ethanol(DB00898)|Fomepizole(DB01213)	GCTGCTTTACAGCCCATAACA	0.468																																					p.C212S												.	.	0			c.T634A	4						.						255.0	257.0	256.0					4																	100264146		2203	4300	6503	100483169			126	exon6			M12272		4q23	2010-03-16			ENSG00000248144	ENSG00000248144	1.1.1.1	"""Alcohol dehydrogenases"""	251	protein-coding gene	gene with protein product		103730		ADH3		3006456	Standard	NM_000669		Approved		uc031sgp.1	P00326	OTTHUMG00000161422		4.37:g.100264146A>T		Somatic		Capture	Illumina HiSeq	Phase_I	100483169	NM_000669	Q4PJ18|Q5WRV0|Q6LBW4|Q6NWV0|Q6NZA7	Missense_Mutation	SNP	ENST00000510055.1	37																																																																																					0.468	ADH1C-004	KNOWN	mRNA_end_NF|basic	processed_transcript	polymorphic_pseudogene	OTTHUMT00000365189.2	NM_000669	
GSTCD	79807	broad.mit.edu	37	4	106640422	106640422	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr4:106640422C>T	ENST00000515279.1	+	3	852	c.632C>T	c.(631-633)cCc>cTc	p.P211L	GSTCD_ENST00000360505.5_Missense_Mutation_p.P211L|GSTCD_ENST00000394730.3_Missense_Mutation_p.P124L|GSTCD_ENST00000394728.3_Missense_Mutation_p.P211L|GSTCD_ENST00000507281.1_Missense_Mutation_p.P124L|GSTCD_ENST00000515255.1_Intron			Q8NEC7	GSTCD_HUMAN	glutathione S-transferase, C-terminal domain containing	211	GST C-terminal.					extracellular vesicular exosome (GO:0070062)		p.P124L(1)		breast(2)|central_nervous_system(1)|endometrium(2)|large_intestine(5)|lung(2)|ovary(1)|skin(1)	14		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;3.15e-07)|READ - Rectum adenocarcinoma(30;0.139)		GTTGGGCCTCCCCTTACTAAG	0.473																																					p.P124L												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C371T	4						.						106.0	113.0	110.0					4																	106640422		2203	4300	6503	106859871	SO:0001583	missense	79807	exon3			BC032942	CCDS3672.2, CCDS43257.1	4q24	2008-02-05	2006-05-09		ENSG00000138780	ENSG00000138780			25806	protein-coding gene	gene with protein product		615912	"""Glutathione S-transferase, C-terminal domain containing"""			12477932	Standard	NM_001031720		Approved	FLJ13273	uc003hxz.4	Q8NEC7	OTTHUMG00000131211	ENST00000515279.1:c.632C>T	4.37:g.106640422C>T	ENSP00000422354:p.Pro211Leu	Somatic		Capture	Illumina HiSeq	Phase_I	106859871	NM_024751	A8K8J0|A8MVD3|H9KV97|Q9H8S3	Missense_Mutation	SNP	ENST00000515279.1	37	CCDS43257.1	.	.	.	.	.	.	.	.	.	.	C	10.86	1.470823	0.26423	.	.	ENSG00000138780	ENST00000394730;ENST00000507281;ENST00000515279;ENST00000360505;ENST00000394728	.	.	.	4.1	3.22	0.36961	Glutathione S-transferase, C-terminal-like (1);Glutathione S-transferase/chloride channel, C-terminal (1);	1.353330	0.04966	N	0.463014	T	0.35480	0.0933	L	0.40543	1.245	0.09310	N	1	B;B	0.23249	0.082;0.007	B;B	0.25140	0.058;0.003	T	0.32188	-0.9916	9	0.52906	T	0.07	1.9465	3.8819	0.09082	0.1699:0.5688:0.1652:0.0961	.	124;211	D6R9W2;Q8NEC7	.;GSTCD_HUMAN	L	124;124;211;211;211	.	ENSP00000353695:P211L	P	+	2	0	GSTCD	106859871	0.002000	0.14202	0.001000	0.08648	0.004000	0.04260	1.441000	0.35035	1.245000	0.43885	0.650000	0.86243	CCC		0.473	GSTCD-006	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363981.1	NM_024751	
SGMS2	166929	broad.mit.edu	37	4	108824419	108824419	+	Missense_Mutation	SNP	C	C	T	rs201568395		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr4:108824419C>T	ENST00000394684.4	+	5	1161	c.604C>T	c.(604-606)Cgg>Tgg	p.R202W	RP11-286E11.1_ENST00000499098.1_RNA|SGMS2_ENST00000394686.3_Missense_Mutation_p.R202W|RP11-286E11.1_ENST00000513071.1_RNA|SGMS2_ENST00000359079.4_Missense_Mutation_p.R202W	NM_001136258.1	NP_001129730.1	Q8NHU3	SMS2_HUMAN	sphingomyelin synthase 2	202					small molecule metabolic process (GO:0044281)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)|sphingomyelin biosynthetic process (GO:0006686)	Golgi apparatus (GO:0005794)|integral component of cell outer membrane (GO:0045203)|integral component of Golgi membrane (GO:0030173)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ceramide cholinephosphotransferase activity (GO:0047493)|kinase activity (GO:0016301)|sphingomyelin synthase activity (GO:0033188)	p.R202W(1)		central_nervous_system(1)|endometrium(2)|large_intestine(8)|liver(2)|lung(6)|prostate(1)	20				OV - Ovarian serous cystadenocarcinoma(123;2.95e-05)		AAAAGTTCAACGGATTCTACG	0.418													C|||	1	0.000199681	0.0	0.0014	5008	,	,		17372	0.0		0.0	False		,,,				2504	0.0				p.R202W												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C604T	4						.						207.0	197.0	201.0					4																	108824419		2203	4300	6503	109043868	SO:0001583	missense	166929	exon4			BC041369	CCDS3677.1	4q25	2008-02-05			ENSG00000164023	ENSG00000164023	2.7.8.27		28395	protein-coding gene	gene with protein product		611574				14685263	Standard	NM_152621		Approved	MGC26963, SMS2	uc003hyl.4	Q8NHU3	OTTHUMG00000131811	ENST00000394684.4:c.604C>T	4.37:g.108824419C>T	ENSP00000378176:p.Arg202Trp	Somatic		Capture	Illumina HiSeq	Phase_I	109043868	NM_001136257	A8K2S9|B2RA61	Missense_Mutation	SNP	ENST00000394684.4	37	CCDS3677.1	0	0.0	0	0.0	0	0.0	0	0.0	0	0.0	C	15.30	2.792177	0.50102	.	.	ENSG00000164023	ENST00000394684;ENST00000503862;ENST00000359079;ENST00000394686	T;T;T	0.52983	0.64;0.64;0.64	5.47	4.61	0.57282	.	0.000000	0.85682	D	0.000000	T	0.62792	0.2457	M	0.90425	3.115	0.80722	D	1	P	0.49635	0.926	P	0.48063	0.565	T	0.72323	-0.4328	10	0.72032	D	0.01	-19.0514	13.3985	0.60868	0.4064:0.5936:0.0:0.0	.	202	Q8NHU3	SMS2_HUMAN	W	202;29;202;202	ENSP00000378176:R202W;ENSP00000351981:R202W;ENSP00000378178:R202W	ENSP00000351981:R202W	R	+	1	2	SGMS2	109043868	1.000000	0.71417	0.916000	0.36221	0.405000	0.30901	2.781000	0.47750	1.279000	0.44446	0.655000	0.94253	CGG		0.418	SGMS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254752.1	NM_152621	
CYP2U1	113612	broad.mit.edu	37	4	108866751	108866751	+	Silent	SNP	C	C	T	rs373823906		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr4:108866751C>T	ENST00000332884.6	+	2	1391	c.1116C>T	c.(1114-1116)ccC>ccT	p.P372P	RP11-286E11.1_ENST00000513071.1_RNA|CYP2U1_ENST00000508453.1_Silent_p.P163P	NM_183075.2	NP_898898.1	Q7Z449	CP2U1_HUMAN	cytochrome P450, family 2, subfamily U, polypeptide 1	372					arachidonic acid metabolic process (GO:0019369)|cell death (GO:0008219)|omega-hydroxylase P450 pathway (GO:0097267)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	aromatase activity (GO:0070330)|heme binding (GO:0020037)|iron ion binding (GO:0005506)	p.P372P(2)		breast(1)|large_intestine(2)|lung(4)|skin(2)|urinary_tract(1)	10		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;0.000128)		CGCTGAACCCCGATGTACAAG	0.403																																					p.P372P												.	.	2	Substitution - coding silent(2)	large_intestine(1)|lung(1)	c.C1116T	4						.	T		1,4405		0,1,2202	134.0	131.0	132.0		1116	-11.7	0.0	4		132	0,8600		0,0,4300	no	coding-synonymous	CYP2U1	NM_183075.2		0,1,6502	TT,TC,CC		0.0,0.0227,0.0077		372/545	108866751	1,13005	2203	4300	6503	109086200	SO:0001819	synonymous_variant	113612	exon2			BC012027	CCDS34047.1	4q25	2012-11-23			ENSG00000155016	ENSG00000155016		"""Cytochrome P450s"""	20582	protein-coding gene	gene with protein product	"""spastic paraplegia 49"""	610670				14975754, 14660610	Standard	XM_005262717		Approved	SPG49	uc003hyp.3	Q7Z449	OTTHUMG00000161084	ENST00000332884.6:c.1116C>T	4.37:g.108866751C>T		Somatic		Capture	Illumina HiSeq	Phase_I	109086200	NM_183075	B2RMV7|Q96EQ6	Silent	SNP	ENST00000332884.6	37	CCDS34047.1																																																																																				0.403	CYP2U1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363691.2	NM_183075	
ALPK1	80216	broad.mit.edu	37	4	113348783	113348783	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr4:113348783G>A	ENST00000458497.1	+	9	1036	c.757G>A	c.(757-759)Gat>Aat	p.D253N	ALPK1_ENST00000504176.2_Missense_Mutation_p.D175N|ALPK1_ENST00000177648.9_Missense_Mutation_p.D253N	NM_001102406.1|NM_025144.3	NP_001095876.1|NP_079420.3	Q96QP1	ALPK1_HUMAN	alpha-kinase 1	253							ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)	p.D253N(1)		NS(1)|breast(1)|cervix(1)|endometrium(8)|kidney(2)|large_intestine(11)|lung(20)|ovary(6)|prostate(2)|urinary_tract(1)	53		Ovarian(17;0.0446)|Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;0.00325)		GAGCAAGAACGATTATGAAAA	0.393																																					p.D253N												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G757A	4						.						102.0	99.0	100.0					4																	113348783		2203	4300	6503	113568232	SO:0001583	missense	80216	exon9			AY044164	CCDS3697.1, CCDS58923.1	4q26	2008-02-05			ENSG00000073331	ENSG00000073331			20917	protein-coding gene	gene with protein product	"""lymphocyte alpha-kinase"""	607347				10021370, 10819331	Standard	NM_025144		Approved	Lak, FLJ22670, KIAA1527	uc003ian.4	Q96QP1	OTTHUMG00000132911	ENST00000458497.1:c.757G>A	4.37:g.113348783G>A	ENSP00000398048:p.Asp253Asn	Somatic		Capture	Illumina HiSeq	Phase_I	113568232	NM_025144	B4E3G1|F5H138|Q68CI9|Q6P9F9|Q6ZNK4|Q9P201	Missense_Mutation	SNP	ENST00000458497.1	37	CCDS3697.1	.	.	.	.	.	.	.	.	.	.	G	29.9	5.045460	0.93685	.	.	ENSG00000073331	ENST00000458497;ENST00000177648;ENST00000504176	T;T;T	0.31247	1.5;1.5;1.5	5.28	5.28	0.74379	.	0.000000	0.85682	D	0.000000	T	0.59636	0.2208	M	0.77820	2.39	0.53688	D	0.999978	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;0.999;0.999	T	0.64441	-0.6407	10	0.87932	D	0	-26.3778	18.9142	0.92498	0.0:0.0:1.0:0.0	.	175;175;253	F5H138;B4E3G1;Q96QP1	.;.;ALPK1_HUMAN	N	253;253;175	ENSP00000398048:D253N;ENSP00000177648:D253N;ENSP00000426044:D175N	ENSP00000177648:D253N	D	+	1	0	ALPK1	113568232	1.000000	0.71417	0.929000	0.37066	0.739000	0.42172	8.564000	0.90726	2.462000	0.83206	0.563000	0.77884	GAT		0.393	ALPK1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256421.2	NM_025144	
ANK2	287	broad.mit.edu	37	4	114213658	114213658	+	Silent	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr4:114213658C>T	ENST00000357077.4	+	21	2417	c.2364C>T	c.(2362-2364)aaC>aaT	p.N788N	ANK2_ENST00000264366.6_Silent_p.N788N|ANK2_ENST00000506722.1_Silent_p.N767N|ANK2_ENST00000509550.1_5'Flank|ANK2_ENST00000394537.3_Silent_p.N788N	NM_001148.4	NP_001139.3	Q01484	ANK2_HUMAN	ankyrin 2, neuronal	788					atrial cardiac muscle cell action potential (GO:0086014)|atrial cardiac muscle cell to AV node cell communication (GO:0086066)|atrial septum development (GO:0003283)|axon guidance (GO:0007411)|cardiac muscle contraction (GO:0060048)|cellular calcium ion homeostasis (GO:0006874)|cellular protein localization (GO:0034613)|membrane depolarization during SA node cell action potential (GO:0086046)|paranodal junction assembly (GO:0030913)|positive regulation of calcium ion transmembrane transporter activity (GO:1901021)|positive regulation of calcium ion transport (GO:0051928)|positive regulation of cation channel activity (GO:2001259)|positive regulation of gene expression (GO:0010628)|positive regulation of potassium ion transmembrane transporter activity (GO:1901018)|positive regulation of potassium ion transport (GO:0043268)|protein localization to cell surface (GO:0034394)|protein localization to endoplasmic reticulum (GO:0070972)|protein localization to M-band (GO:0036309)|protein localization to organelle (GO:0033365)|protein localization to plasma membrane (GO:0072659)|protein localization to T-tubule (GO:0036371)|protein stabilization (GO:0050821)|protein targeting to plasma membrane (GO:0072661)|regulation of calcium ion transmembrane transporter activity (GO:1901019)|regulation of calcium ion transport (GO:0051924)|regulation of cardiac muscle cell contraction (GO:0086004)|regulation of cardiac muscle cell membrane potential (GO:0086036)|regulation of cardiac muscle contraction (GO:0055117)|regulation of cardiac muscle contraction by calcium ion signaling (GO:0010882)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of heart rate (GO:0002027)|regulation of heart rate by cardiac conduction (GO:0086091)|regulation of protein stability (GO:0031647)|regulation of release of sequestered calcium ion into cytosol (GO:0051279)|regulation of ventricular cardiac muscle cell membrane repolarization (GO:0060307)|response to methylmercury (GO:0051597)|SA node cell action potential (GO:0086015)|SA node cell to atrial cardiac muscle cell communication (GO:0086070)|sarcoplasmic reticulum calcium ion transport (GO:0070296)|T-tubule organization (GO:0033292)|ventricular cardiac muscle cell action potential (GO:0086005)	A band (GO:0031672)|basolateral plasma membrane (GO:0016323)|costamere (GO:0043034)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|integral component of plasma membrane (GO:0005887)|intercalated disc (GO:0014704)|intracellular (GO:0005622)|M band (GO:0031430)|membrane raft (GO:0045121)|neuron projection (GO:0043005)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|Z disc (GO:0030018)	ATPase binding (GO:0051117)|enzyme binding (GO:0019899)|ion channel binding (GO:0044325)|potassium channel regulator activity (GO:0015459)|protein binding, bridging (GO:0030674)|protein kinase binding (GO:0019901)|spectrin binding (GO:0030507)|structural constituent of cytoskeleton (GO:0005200)	p.N788N(1)		NS(1)|biliary_tract(1)|breast(9)|central_nervous_system(10)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(54)|liver(2)|lung(112)|ovary(8)|pancreas(1)|prostate(7)|skin(11)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(10)	248		Ovarian(17;0.0448)|Hepatocellular(203;0.218)		OV - Ovarian serous cystadenocarcinoma(123;4.92e-05)		CCAAGCCCAACGCCACCACTG	0.597																																					p.N788N												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C2364T	4						.						51.0	37.0	42.0					4																	114213658		2203	4300	6503	114433107	SO:0001819	synonymous_variant	287	exon21			M37123	CCDS3702.1, CCDS43261.1, CCDS54796.1	4q25-q26	2014-09-17	2003-03-12		ENSG00000145362	ENSG00000145362		"""Ankyrin repeat domain containing"""	493	protein-coding gene	gene with protein product		106410	"""long (electrocardiographic) QT syndrome 4"""	LQT4		7485162, 12571597	Standard	NM_001148		Approved		uc003ibe.4	Q01484	OTTHUMG00000132912	ENST00000357077.4:c.2364C>T	4.37:g.114213658C>T		Somatic		Capture	Illumina HiSeq	Phase_I	114433107	NM_020977	Q01485|Q08AC7|Q08AC8|Q7Z3L5	Silent	SNP	ENST00000357077.4	37	CCDS3702.1																																																																																				0.597	ANK2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256422.2	NM_001148	
ARSJ	79642	broad.mit.edu	37	4	114823912	114823912	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr4:114823912T>C	ENST00000315366.7	-	2	2184	c.1318A>G	c.(1318-1320)Atc>Gtc	p.I440V	ARSJ_ENST00000541197.1_Missense_Mutation_p.I440V	NM_024590.3	NP_078866.3	Q5FYB0	ARSJ_HUMAN	arylsulfatase family, member J	440					cellular protein metabolic process (GO:0044267)|glycosphingolipid metabolic process (GO:0006687)|post-translational protein modification (GO:0043687)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)	arylsulfatase activity (GO:0004065)|metal ion binding (GO:0046872)	p.I440V(1)		endometrium(1)|large_intestine(5)|lung(7)|ovary(2)|prostate(3)|skin(2)|urinary_tract(1)	21		Ovarian(17;0.0035)|Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;0.00194)		GTGTTCCAGATCCCATAGCCT	0.507																																					p.I440V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A1318G	4						.						94.0	94.0	94.0					4																	114823912		1939	4147	6086	115043361	SO:0001583	missense	79642	exon2				CCDS43264.1	4q26	2013-02-14	2006-03-07		ENSG00000180801	ENSG00000180801		"""Arylsulfatase family"""	26286	protein-coding gene	gene with protein product		610010	"""arylsulfatase J"""			12975309, 16174644	Standard	NM_024590		Approved	FLJ23548	uc003ibq.1	Q5FYB0	OTTHUMG00000161067	ENST00000315366.7:c.1318A>G	4.37:g.114823912T>C	ENSP00000320219:p.Ile440Val	Somatic		Capture	Illumina HiSeq	Phase_I	115043361	NM_024590	A2RUG0|B7ZM45|Q1HA39|Q5FWE4|Q6UWT9	Missense_Mutation	SNP	ENST00000315366.7	37	CCDS43264.1	.	.	.	.	.	.	.	.	.	.	T	9.374	1.071375	0.20147	.	.	ENSG00000180801	ENST00000315366;ENST00000541197	D;D	0.93712	-3.27;-3.27	5.54	5.54	0.83059	Alkaline phosphatase-like, alpha/beta/alpha (1);Sulfatase (1);Alkaline-phosphatase-like, core domain (1);	1.544500	0.04759	N	0.425919	D	0.91660	0.7364	L	0.35644	1.08	0.33833	D	0.63051	B;B	0.31655	0.334;0.22	B;B	0.36092	0.217;0.163	T	0.77930	-0.2403	10	0.13470	T	0.59	.	15.6762	0.77326	0.0:0.0:0.0:1.0	.	440;440	Q1HA39;Q5FYB0	.;ARSJ_HUMAN	V	440	ENSP00000320219:I440V;ENSP00000438836:I440V	ENSP00000320219:I440V	I	-	1	0	ARSJ	115043361	0.936000	0.31750	1.000000	0.80357	0.984000	0.73092	1.394000	0.34509	2.102000	0.63906	0.533000	0.62120	ATC		0.507	ARSJ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363650.1	NM_024590	
IL2	3558	broad.mit.edu	37	4	123377577	123377577	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr4:123377577G>T	ENST00000226730.4	-	1	303	c.19C>A	c.(19-21)Ctg>Atg	p.L7M		NM_000586.3	NP_000577.2	P60568	IL2_HUMAN	interleukin 2	7					cell adhesion (GO:0007155)|cell-cell signaling (GO:0007267)|extrinsic apoptotic signaling pathway in absence of ligand (GO:0097192)|immune response (GO:0006955)|natural killer cell activation (GO:0030101)|negative regulation of apoptotic process (GO:0043066)|negative regulation of B cell apoptotic process (GO:0002903)|negative regulation of heart contraction (GO:0045822)|negative regulation of inflammatory response (GO:0050728)|negative regulation of lymphocyte proliferation (GO:0050672)|negative regulation of protein phosphorylation (GO:0001933)|positive regulation of activated T cell proliferation (GO:0042104)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of cell growth (GO:0030307)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of dendritic spine development (GO:0060999)|positive regulation of immunoglobulin secretion (GO:0051024)|positive regulation of inflammatory response (GO:0050729)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interleukin-17 production (GO:0032740)|positive regulation of isotype switching to IgG isotypes (GO:0048304)|positive regulation of regulatory T cell differentiation (GO:0045591)|positive regulation of tissue remodeling (GO:0034105)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tyrosine phosphorylation of Stat5 protein (GO:0042523)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|regulation of T cell homeostatic proliferation (GO:0046013)|T cell differentiation (GO:0030217)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	carbohydrate binding (GO:0030246)|cytokine activity (GO:0005125)|glycosphingolipid binding (GO:0043208)|growth factor activity (GO:0008083)|interleukin-2 receptor binding (GO:0005134)|kinase activator activity (GO:0019209)	p.L7M(1)		endometrium(2)|large_intestine(4)|lung(6)|skin(1)	13				LUSC - Lung squamous cell carcinoma(721;0.185)	Pseudoephedrine(DB00852)	ATGCAAGACAGGAGTTGCATC	0.418			T	TNFRSF17	intestinal T-cell lymphoma																																p.L7M			Dom	yes		4	4q26-q27	3558	interleukin 2		L	.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C19A	4						.						136.0	127.0	130.0					4																	123377577		2203	4300	6503	123597027	SO:0001583	missense	3558	exon1			U25676	CCDS3726.1	4q26-q27	2011-07-14			ENSG00000109471	ENSG00000109471		"""Interleukins and interleukin receptors"""	6001	protein-coding gene	gene with protein product	"""T cell growth factor"""	147680				3260003	Standard	NM_000586		Approved	IL-2, TCGF	uc003ier.3	P60568	OTTHUMG00000133075	ENST00000226730.4:c.19C>A	4.37:g.123377577G>T	ENSP00000226730:p.Leu7Met	Somatic		Capture	Illumina HiSeq	Phase_I	123597027	NM_000586	P01585	Missense_Mutation	SNP	ENST00000226730.4	37	CCDS3726.1	.	.	.	.	.	.	.	.	.	.	G	15.06	2.719896	0.48728	.	.	ENSG00000109471	ENST00000226730	.	.	.	6.17	-4.17	0.03857	.	0.513538	0.16488	N	0.212258	T	0.51856	0.1699	M	0.67397	2.05	0.09310	N	1	D	0.69078	0.997	D	0.69824	0.966	T	0.46925	-0.9156	9	0.72032	D	0.01	-0.6414	7.176	0.25744	0.3191:0.2569:0.424:0.0	.	7	P60568	IL2_HUMAN	M	7	.	ENSP00000226730:L7M	L	-	1	2	IL2	123597027	0.373000	0.25073	0.004000	0.12327	0.971000	0.66376	0.040000	0.13905	-0.644000	0.05465	-0.302000	0.09304	CTG		0.418	IL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256715.2		
FAT4	79633	broad.mit.edu	37	4	126329914	126329914	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr4:126329914C>T	ENST00000394329.3	+	4	5898	c.5885C>T	c.(5884-5886)aCt>aTt	p.T1962I	FAT4_ENST00000335110.5_Missense_Mutation_p.T260I	NM_024582.4	NP_078858.4	Q6V0I7	FAT4_HUMAN	FAT atypical cadherin 4	1962	Cadherin 19. {ECO:0000255|PROSITE- ProRule:PRU00043}.				branching involved in ureteric bud morphogenesis (GO:0001658)|cerebral cortex development (GO:0021987)|digestive tract development (GO:0048565)|heart morphogenesis (GO:0003007)|heterophilic cell-cell adhesion (GO:0007157)|hippo signaling (GO:0035329)|homophilic cell adhesion (GO:0007156)|inner ear receptor stereocilium organization (GO:0060122)|neurogenesis (GO:0022008)|ossification involved in bone maturation (GO:0043931)|plasma membrane organization (GO:0007009)|regulation of metanephric nephron tubule epithelial cell differentiation (GO:0072307)	apical part of cell (GO:0045177)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.T1962I(2)		NS(6)|autonomic_ganglia(1)|breast(4)|central_nervous_system(3)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(3)|kidney(10)|large_intestine(93)|liver(3)|lung(120)|ovary(9)|pancreas(2)|prostate(21)|skin(31)|stomach(1)|upper_aerodigestive_tract(12)|urinary_tract(6)	355						GTGGGATCTACTGTTCTTGTG	0.274																																					p.T1962I												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.C5885T	4						.						128.0	131.0	130.0					4																	126329914		2203	4300	6503	126549364	SO:0001583	missense	79633	exon4			AY356402	CCDS3732.3	4q28.1	2013-05-31	2013-05-31		ENSG00000196159	ENSG00000196159		"""Cadherins / Cadherin-related"""	23109	protein-coding gene	gene with protein product	"""cadherin-related family member 11"""	612411	"""FAT tumor suppressor homolog 4 (Drosophila)"""			15003449	Standard	NM_024582		Approved	CDHF14, FAT-J, CDHR11	uc003ifj.4	Q6V0I7	OTTHUMG00000133100	ENST00000394329.3:c.5885C>T	4.37:g.126329914C>T	ENSP00000377862:p.Thr1962Ile	Somatic		Capture	Illumina HiSeq	Phase_I	126549364	NM_024582	A8K5Z6|B5MDG4|Q3LIA6|Q8TCK7|Q9H5T6	Missense_Mutation	SNP	ENST00000394329.3	37	CCDS3732.3	.	.	.	.	.	.	.	.	.	.	C	16.23	3.064096	0.55432	.	.	ENSG00000196159	ENST00000394329;ENST00000335110	T;T	0.02446	4.29;4.29	5.23	4.33	0.51752	Cadherin (3);Cadherin-like (1);	0.215721	0.22630	U	0.057594	T	0.05044	0.0135	L	0.38175	1.15	0.32731	N	0.508984	P;P	0.42161	0.552;0.772	B;P	0.46299	0.199;0.511	T	0.28554	-1.0040	10	0.35671	T	0.21	.	15.255	0.73579	0.0:0.8594:0.1406:0.0	.	260;1962	Q6V0I7-2;Q6V0I7	.;FAT4_HUMAN	I	1962;260	ENSP00000377862:T1962I;ENSP00000335169:T260I	ENSP00000335169:T260I	T	+	2	0	FAT4	126549364	0.852000	0.29690	1.000000	0.80357	0.986000	0.74619	2.504000	0.45416	2.438000	0.82558	0.655000	0.94253	ACT		0.274	FAT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256765.2	NM_024582	
FAT4	79633	broad.mit.edu	37	4	126369946	126369946	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr4:126369946C>A	ENST00000394329.3	+	9	7788	c.7775C>A	c.(7774-7776)tCc>tAc	p.S2592Y	FAT4_ENST00000335110.5_Missense_Mutation_p.S890Y	NM_024582.4	NP_078858.4	Q6V0I7	FAT4_HUMAN	FAT atypical cadherin 4	2592	Cadherin 25. {ECO:0000255|PROSITE- ProRule:PRU00043}.				branching involved in ureteric bud morphogenesis (GO:0001658)|cerebral cortex development (GO:0021987)|digestive tract development (GO:0048565)|heart morphogenesis (GO:0003007)|heterophilic cell-cell adhesion (GO:0007157)|hippo signaling (GO:0035329)|homophilic cell adhesion (GO:0007156)|inner ear receptor stereocilium organization (GO:0060122)|neurogenesis (GO:0022008)|ossification involved in bone maturation (GO:0043931)|plasma membrane organization (GO:0007009)|regulation of metanephric nephron tubule epithelial cell differentiation (GO:0072307)	apical part of cell (GO:0045177)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.S2592Y(2)		NS(6)|autonomic_ganglia(1)|breast(4)|central_nervous_system(3)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(3)|kidney(10)|large_intestine(93)|liver(3)|lung(120)|ovary(9)|pancreas(2)|prostate(21)|skin(31)|stomach(1)|upper_aerodigestive_tract(12)|urinary_tract(6)	355						ATCACAGGATCCTCTTTAAGA	0.423																																					p.S2592Y												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.C7775A	4						.						55.0	52.0	53.0					4																	126369946		2203	4299	6502	126589396	SO:0001583	missense	79633	exon9			AY356402	CCDS3732.3	4q28.1	2013-05-31	2013-05-31		ENSG00000196159	ENSG00000196159		"""Cadherins / Cadherin-related"""	23109	protein-coding gene	gene with protein product	"""cadherin-related family member 11"""	612411	"""FAT tumor suppressor homolog 4 (Drosophila)"""			15003449	Standard	NM_024582		Approved	CDHF14, FAT-J, CDHR11	uc003ifj.4	Q6V0I7	OTTHUMG00000133100	ENST00000394329.3:c.7775C>A	4.37:g.126369946C>A	ENSP00000377862:p.Ser2592Tyr	Somatic		Capture	Illumina HiSeq	Phase_I	126589396	NM_024582	A8K5Z6|B5MDG4|Q3LIA6|Q8TCK7|Q9H5T6	Missense_Mutation	SNP	ENST00000394329.3	37	CCDS3732.3	.	.	.	.	.	.	.	.	.	.	C	13.25	2.180276	0.38511	.	.	ENSG00000196159	ENST00000394329;ENST00000335110	T;T	0.53423	0.62;0.62	5.83	4.99	0.66335	Cadherin (4);Cadherin-like (1);	0.000000	0.34362	U	0.004032	T	0.56381	0.1981	M	0.64404	1.975	0.58432	D	0.999999	P;D;D	0.60160	0.731;0.987;0.984	P;D;P	0.63488	0.549;0.915;0.809	T	0.59434	-0.7455	10	0.02654	T	1	.	11.7131	0.51637	0.0:0.8596:0.0:0.1404	.	890;2592;2592	Q6V0I7-2;Q6V0I7;Q6V0I7-3	.;FAT4_HUMAN;.	Y	2592;890	ENSP00000377862:S2592Y;ENSP00000335169:S890Y	ENSP00000335169:S890Y	S	+	2	0	FAT4	126589396	0.998000	0.40836	0.237000	0.24090	0.016000	0.09150	4.833000	0.62766	1.470000	0.48102	0.650000	0.86243	TCC		0.423	FAT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256765.2	NM_024582	
FAT4	79633	broad.mit.edu	37	4	126372370	126372370	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr4:126372370A>G	ENST00000394329.3	+	9	10212	c.10199A>G	c.(10198-10200)gAc>gGc	p.D3400G	FAT4_ENST00000335110.5_Missense_Mutation_p.D1698G	NM_024582.4	NP_078858.4	Q6V0I7	FAT4_HUMAN	FAT atypical cadherin 4	3400	Cadherin 32. {ECO:0000255|PROSITE- ProRule:PRU00043}.				branching involved in ureteric bud morphogenesis (GO:0001658)|cerebral cortex development (GO:0021987)|digestive tract development (GO:0048565)|heart morphogenesis (GO:0003007)|heterophilic cell-cell adhesion (GO:0007157)|hippo signaling (GO:0035329)|homophilic cell adhesion (GO:0007156)|inner ear receptor stereocilium organization (GO:0060122)|neurogenesis (GO:0022008)|ossification involved in bone maturation (GO:0043931)|plasma membrane organization (GO:0007009)|regulation of metanephric nephron tubule epithelial cell differentiation (GO:0072307)	apical part of cell (GO:0045177)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.D3400G(2)		NS(6)|autonomic_ganglia(1)|breast(4)|central_nervous_system(3)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(3)|kidney(10)|large_intestine(93)|liver(3)|lung(120)|ovary(9)|pancreas(2)|prostate(21)|skin(31)|stomach(1)|upper_aerodigestive_tract(12)|urinary_tract(6)	355						GATGCAAATGACCCACCCATT	0.453																																					p.D3400G												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.A10199G	4						.						187.0	177.0	180.0					4																	126372370		2203	4300	6503	126591820	SO:0001583	missense	79633	exon9			AY356402	CCDS3732.3	4q28.1	2013-05-31	2013-05-31		ENSG00000196159	ENSG00000196159		"""Cadherins / Cadherin-related"""	23109	protein-coding gene	gene with protein product	"""cadherin-related family member 11"""	612411	"""FAT tumor suppressor homolog 4 (Drosophila)"""			15003449	Standard	NM_024582		Approved	CDHF14, FAT-J, CDHR11	uc003ifj.4	Q6V0I7	OTTHUMG00000133100	ENST00000394329.3:c.10199A>G	4.37:g.126372370A>G	ENSP00000377862:p.Asp3400Gly	Somatic		Capture	Illumina HiSeq	Phase_I	126591820	NM_024582	A8K5Z6|B5MDG4|Q3LIA6|Q8TCK7|Q9H5T6	Missense_Mutation	SNP	ENST00000394329.3	37	CCDS3732.3	.	.	.	.	.	.	.	.	.	.	A	18.66	3.672380	0.67928	.	.	ENSG00000196159	ENST00000394329;ENST00000335110	T;T	0.71698	-0.59;-0.59	5.14	5.14	0.70334	Cadherin (3);Cadherin-like (1);	0.000000	0.35585	U	0.003110	D	0.90222	0.6943	H	0.98333	4.205	0.80722	D	1	D;D;D	0.89917	1.0;0.996;0.998	D;D;D	0.87578	0.998;0.977;0.995	D	0.93939	0.7221	10	0.87932	D	0	.	14.9857	0.71345	1.0:0.0:0.0:0.0	.	1698;3400;3400	Q6V0I7-2;Q6V0I7;Q6V0I7-3	.;FAT4_HUMAN;.	G	3400;1698	ENSP00000377862:D3400G;ENSP00000335169:D1698G	ENSP00000335169:D1698G	D	+	2	0	FAT4	126591820	1.000000	0.71417	1.000000	0.80357	0.921000	0.55340	9.149000	0.94659	1.939000	0.56221	0.459000	0.35465	GAC		0.453	FAT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256765.2	NM_024582	
SCLT1	132320	broad.mit.edu	37	4	129964613	129964613	+	Silent	SNP	A	A	G			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr4:129964613A>G	ENST00000281142.5	-	4	674	c.171T>C	c.(169-171)gcT>gcC	p.A57A	SCLT1_ENST00000503215.1_Silent_p.A34A|SCLT1_ENST00000503401.1_Silent_p.A34A|SCLT1_ENST00000506368.1_Silent_p.A57A|SCLT1_ENST00000511426.1_Silent_p.A57A|SCLT1_ENST00000434680.1_Silent_p.A57A|SCLT1_ENST00000439369.2_Silent_p.A57A	NM_144643.2	NP_653244.2	Q96NL6	SCLT1_HUMAN	sodium channel and clathrin linker 1	57					cilium assembly (GO:0042384)|clustering of voltage-gated sodium channels (GO:0045162)	centriole (GO:0005814)|centrosome (GO:0005813)|ciliary transition fiber (GO:0097539)|clathrin complex (GO:0071439)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|microtubule cytoskeleton (GO:0015630)	sodium channel regulator activity (GO:0017080)	p.A57A(1)		central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(9)|lung(10)|ovary(3)|prostate(1)|skin(1)|stomach(1)	29						TAACAAGAGGAGCTAAAAAGC	0.264																																					p.A57A												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.T171C	4						.						36.0	37.0	37.0					4																	129964613		2203	4289	6492	130184063	SO:0001819	synonymous_variant	132320	exon4			AK055217	CCDS3740.1	4q28.2	2008-05-02			ENSG00000151466	ENSG00000151466			26406	protein-coding gene	gene with protein product		611399				15797711	Standard	XM_005262732		Approved	hCAP-1A, FLJ30655	uc003igp.2	Q96NL6	OTTHUMG00000133346	ENST00000281142.5:c.171T>C	4.37:g.129964613A>G		Somatic		Capture	Illumina HiSeq	Phase_I	130184063	NM_144643	A4QN04|Q0VAH2|Q6P2M4	Silent	SNP	ENST00000281142.5	37	CCDS3740.1																																																																																				0.264	SCLT1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257176.2	NM_144643	
PCDH10	57575	broad.mit.edu	37	4	134075509	134075509	+	Silent	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr4:134075509C>T	ENST00000264360.5	+	2	3505	c.2679C>T	c.(2677-2679)cgC>cgT	p.R893R		NM_032961.1	NP_116586.1	Q9P2E7	PCD10_HUMAN	protocadherin 10	893					homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.R893R(1)		NS(2)|breast(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(30)|liver(1)|lung(72)|ovary(2)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(6)|urinary_tract(2)	136				LUSC - Lung squamous cell carcinoma(193;0.227)		ACAGACCTCGCCGAGTTAACA	0.358																																					p.R893R												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C2679T	4						.						82.0	79.0	80.0					4																	134075509		2203	4300	6503	134294959	SO:0001819	synonymous_variant	57575	exon2			AB037821	CCDS34063.1, CCDS75192.1	4q28.3	2010-01-26				ENSG00000138650		"""Cadherins / Protocadherins : Non-clustered"""	13404	protein-coding gene	gene with protein product		608286				10835267	Standard	NM_020815		Approved	OL-PCDH, KIAA1400	uc003iha.3	Q9P2E7		ENST00000264360.5:c.2679C>T	4.37:g.134075509C>T		Somatic		Capture	Illumina HiSeq	Phase_I	134294959	NM_032961	Q4W5F6|Q96SF0	Silent	SNP	ENST00000264360.5	37	CCDS34063.1																																																																																				0.358	PCDH10-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000364457.2	NM_032961	
PCDH18	54510	broad.mit.edu	37	4	138442805	138442805	+	Missense_Mutation	SNP	T	T	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr4:138442805T>A	ENST00000344876.4	-	4	3172	c.2786A>T	c.(2785-2787)gAc>gTc	p.D929V	PCDH18_ENST00000510305.1_Missense_Mutation_p.D140V|PCDH18_ENST00000507846.1_Missense_Mutation_p.D708V|PCDH18_ENST00000511115.1_Missense_Mutation_p.D109V|PCDH18_ENST00000412923.2_Missense_Mutation_p.D928V	NM_019035.3	NP_061908.1	Q9HCL0	PCD18_HUMAN	protocadherin 18	929	Interaction with DAB1. {ECO:0000250}.				brain development (GO:0007420)|homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.D929V(1)		NS(1)|breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(27)|lung(21)|ovary(2)|pancreas(4)|prostate(3)|skin(12)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	86	all_hematologic(180;0.24)					CCAGCACTGGTCAGAGTGTCC	0.493																																					p.D929V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A2786T	4						.						131.0	131.0	131.0					4																	138442805		2203	4300	6503	138662255	SO:0001583	missense	54510	exon4			AL137471	CCDS34064.1, CCDS75193.1	4q28.3	2010-01-26			ENSG00000189184	ENSG00000189184		"""Cadherins / Protocadherins : Non-clustered"""	14268	protein-coding gene	gene with protein product		608287				10835267, 11549318	Standard	XM_005263070		Approved	KIAA1562, PCDH68L	uc003ihe.4	Q9HCL0	OTTHUMG00000161348	ENST00000344876.4:c.2786A>T	4.37:g.138442805T>A	ENSP00000355082:p.Asp929Val	Somatic		Capture	Illumina HiSeq	Phase_I	138662255	NM_019035	A8K7K3|B7ZKT1|Q52LS2	Missense_Mutation	SNP	ENST00000344876.4	37	CCDS34064.1	.	.	.	.	.	.	.	.	.	.	T	20.9	4.073769	0.76415	.	.	ENSG00000189184	ENST00000344876;ENST00000412923;ENST00000507846;ENST00000510305;ENST00000511115	D;D;D;T;T	0.83992	-1.74;-1.73;-1.79;-0.55;-0.51	5.55	5.55	0.83447	.	0.000000	0.45867	D	0.000337	D	0.91835	0.7416	M	0.84948	2.725	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	1.0;0.998;0.997;0.997	D	0.93126	0.6529	10	0.87932	D	0	.	15.7075	0.77594	0.0:0.0:0.0:1.0	.	109;708;928;929	B4DLR6;D6RIG4;Q9HCL0-2;Q9HCL0	.;.;.;PCD18_HUMAN	V	929;928;708;140;109	ENSP00000355082:D929V;ENSP00000390688:D928V;ENSP00000425903:D708V;ENSP00000424269:D140V;ENSP00000425647:D109V	ENSP00000355082:D929V	D	-	2	0	PCDH18	138662255	1.000000	0.71417	0.996000	0.52242	0.964000	0.63967	7.489000	0.81451	2.117000	0.64856	0.533000	0.62120	GAC		0.493	PCDH18-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000364614.1	NM_019035	
NAA15	80155	broad.mit.edu	37	4	140283020	140283020	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr4:140283020C>A	ENST00000296543.5	+	14	2005	c.1682C>A	c.(1681-1683)gCt>gAt	p.A561D	NAA15_ENST00000398947.1_Missense_Mutation_p.A561D	NM_057175.3	NP_476516.1	Q9BXJ9	NAA15_HUMAN	N(alpha)-acetyltransferase 15, NatA auxiliary subunit	561	Interaction with HYPK.				angiogenesis (GO:0001525)|cell differentiation (GO:0030154)|N-terminal protein amino acid acetylation (GO:0006474)|negative regulation of apoptotic process (GO:0043066)|positive regulation of transcription, DNA-templated (GO:0045893)|protein stabilization (GO:0050821)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|membrane (GO:0016020)|NatA complex (GO:0031415)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	N-acetyltransferase activity (GO:0008080)|poly(A) RNA binding (GO:0044822)|ribosome binding (GO:0043022)	p.A561D(1)		NS(1)|endometrium(3)|large_intestine(7)|liver(2)|lung(8)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	29						GCAAGAATTGCTATAGAGATC	0.368																																					p.A561D												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1682A	4						.						119.0	111.0	114.0					4																	140283020		1847	4084	5931	140502470	SO:0001583	missense	80155	exon14			AY039242	CCDS43270.1	4q31.1	2010-01-14	2010-01-14	2010-01-14	ENSG00000164134	ENSG00000164134		"""N(alpha)-acetyltransferase subunits"""	30782	protein-coding gene	gene with protein product		608000	"""NMDA receptor regulated 1"""	NARG1		12140756, 11478804, 19660095	Standard	XM_005263236		Approved	TBDN100, NATH, FLJ13340	uc003ihu.1	Q9BXJ9	OTTHUMG00000137363	ENST00000296543.5:c.1682C>A	4.37:g.140283020C>A	ENSP00000296543:p.Ala561Asp	Somatic		Capture	Illumina HiSeq	Phase_I	140502470	NM_057175	D3DNY6|Q52LG9|Q8IWH4|Q8NEV2|Q9H8P6	Missense_Mutation	SNP	ENST00000296543.5	37	CCDS43270.1	.	.	.	.	.	.	.	.	.	.	C	32	5.177586	0.94846	.	.	ENSG00000164134	ENST00000296543;ENST00000544077;ENST00000398947	T;T	0.61980	0.06;0.06	5.73	5.73	0.89815	.	0.000000	0.85682	D	0.000000	D	0.85048	0.5608	M	0.92880	3.355	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.87271	0.2286	10	0.66056	D	0.02	-9.8998	20.27	0.98469	0.0:1.0:0.0:0.0	.	561	Q9BXJ9	NAA15_HUMAN	D	561;435;561	ENSP00000296543:A561D;ENSP00000381920:A561D	ENSP00000296543:A561D	A	+	2	0	NAA15	140502470	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.445000	0.80570	2.854000	0.98071	0.655000	0.94253	GCT		0.368	NAA15-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000267839.2	NM_057175	
MAML3	55534	broad.mit.edu	37	4	140640663	140640663	+	Silent	SNP	T	T	C			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr4:140640663T>C	ENST00000509479.2	-	5	4087	c.3231A>G	c.(3229-3231)ccA>ccG	p.P1077P	MGST2_ENST00000515137.1_Intron	NM_018717.4	NP_061187			mastermind-like 3 (Drosophila)									p.P1077P(1)		breast(1)|endometrium(7)|kidney(2)|large_intestine(1)|lung(9)|ovary(1)|prostate(2)|urinary_tract(2)	25	all_hematologic(180;0.162)					TCTGGCTGCTTGGAGCAAAGC	0.627																																					p.P1073P												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.A3219G	4						.						37.0	42.0	40.0					4																	140640663		2191	4293	6484	140860113	SO:0001819	synonymous_variant	55534	exon6			AB058719	CCDS54805.1	4q31.1	2014-08-12	2003-09-24		ENSG00000196782	ENSG00000196782			16272	protein-coding gene	gene with protein product	"""mastermind (drosophila)-like 3"""	608991	"""trinucleotide repeat containing 3"""	TNRC3		12370315, 12386158	Standard	NM_018717		Approved	KIAA1816, MAM2, CAGH3, GDN	uc021xsg.1	Q96JK9	OTTHUMG00000161441	ENST00000509479.2:c.3231A>G	4.37:g.140640663T>C		Somatic		Capture	Illumina HiSeq	Phase_I	140860113	NM_018717		Silent	SNP	ENST00000509479.2	37	CCDS54805.1																																																																																				0.627	MAML3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364934.2		
CC2D2A	57545	broad.mit.edu	37	4	15504503	15504503	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr4:15504503G>A	ENST00000503292.1	+	7	575	c.395G>A	c.(394-396)cGa>cAa	p.R132Q	CC2D2A_ENST00000513811.1_3'UTR|CC2D2A_ENST00000413206.1_Missense_Mutation_p.R132Q|CC2D2A_ENST00000389652.5_Missense_Mutation_p.R83Q|CC2D2A_ENST00000424120.1_Missense_Mutation_p.R132Q	NM_001080522.2	NP_001073991.2	Q9P2K1	C2D2A_HUMAN	coiled-coil and C2 domain containing 2A	132					cilium assembly (GO:0042384)|cilium morphogenesis (GO:0060271)|smoothened signaling pathway (GO:0007224)	ciliary transition zone (GO:0035869)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|TCTN-B9D complex (GO:0036038)		p.R83Q(1)		NS(1)|breast(2)|central_nervous_system(1)|endometrium(6)|kidney(1)|large_intestine(8)|lung(5)|ovary(1)|pancreas(2)|prostate(2)|skin(1)|urinary_tract(2)	32						AGACGCTTACGAAGTCCCAGT	0.418																																					p.R132Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G395A	4						.						50.0	51.0	51.0					4																	15504503		1861	4109	5970	15113601	SO:0001583	missense	57545	exon7			AB037766, EU450799	CCDS47026.1, CCDS47027.1, CCDS47027.2, CCDS54744.1	4p15.33	2014-09-17	2007-10-19		ENSG00000048342	ENSG00000048342			29253	protein-coding gene	gene with protein product	"""Meckel syndrome, type 6"""	612013				10718198, 18513680	Standard	NM_001080522		Approved	KIAA1345, MKS6, JBTS9	uc010idv.2	Q9P2K1	OTTHUMG00000160255	ENST00000503292.1:c.395G>A	4.37:g.15504503G>A	ENSP00000421809:p.Arg132Gln	Somatic		Capture	Illumina HiSeq	Phase_I	15113601	NM_001080522	A6ND97|B3FW08|D6RB72|E7EP21|E9PEV5|Q3SYP3|Q9H8A7	Missense_Mutation	SNP	ENST00000503292.1	37	CCDS47026.1	.	.	.	.	.	.	.	.	.	.	G	8.904	0.957083	0.18507	.	.	ENSG00000048342	ENST00000424120;ENST00000413206;ENST00000426932;ENST00000510333;ENST00000512702;ENST00000503292;ENST00000389652	T;T;T;T;T	0.20463	2.07;2.07;2.07;2.07;2.07	5.84	-5.14	0.02875	.	0.991148	0.08198	N	0.982759	T	0.08537	0.0212	N	0.20685	0.6	0.09310	N	1	B;B;B	0.24132	0.005;0.003;0.098	B;B;B	0.14578	0.001;0.001;0.011	T	0.36890	-0.9729	10	0.15952	T	0.53	.	2.7583	0.05299	0.4425:0.2886:0.1624:0.1065	.	132;83;132	Q9P2K1;Q9P2K1-2;C9JKY6	C2D2A_HUMAN;.;.	Q	132;132;83;83;132;132;83	ENSP00000403465:R132Q;ENSP00000398391:R132Q;ENSP00000422875:R132Q;ENSP00000421809:R132Q;ENSP00000374303:R83Q	ENSP00000374303:R83Q	R	+	2	0	CC2D2A	15113601	0.000000	0.05858	0.036000	0.18154	0.643000	0.38383	-0.378000	0.07446	-0.727000	0.04888	0.655000	0.94253	CGA		0.418	CC2D2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359906.2	NM_001080522	
ZNF827	152485	broad.mit.edu	37	4	146824038	146824038	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr4:146824038G>A	ENST00000508784.1	-	2	600	c.373C>T	c.(373-375)Cgg>Tgg	p.R125W	ZNF827_ENST00000513320.1_Intron|ZNF827_ENST00000379448.4_Missense_Mutation_p.R125W			Q17R98	ZN827_HUMAN	zinc finger protein 827	125					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.R125W(2)		NS(1)|breast(2)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(13)|lung(18)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	48	all_hematologic(180;0.151)					TCCAGCAGCCGCCTCAAATTG	0.577																																					p.R125W												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.C373T	4						.						40.0	40.0	40.0					4																	146824038		2203	4300	6503	147043488	SO:0001583	missense	152485	exon2			AK091130	CCDS34072.1	4q31.22	2013-01-08			ENSG00000151612	ENSG00000151612		"""Zinc fingers, C2H2-type"""	27193	protein-coding gene	gene with protein product						12477932	Standard	NM_178835		Approved		uc003ikm.3	Q17R98	OTTHUMG00000161362	ENST00000508784.1:c.373C>T	4.37:g.146824038G>A	ENSP00000421863:p.Arg125Trp	Somatic		Capture	Illumina HiSeq	Phase_I	147043488	NM_178835	B7ZL52|Q7Z4S7|Q8N279	Missense_Mutation	SNP	ENST00000508784.1	37		.	.	.	.	.	.	.	.	.	.	G	16.44	3.123750	0.56613	.	.	ENSG00000151612	ENST00000508784;ENST00000379448;ENST00000281318	T;T	0.20069	2.1;2.15	5.84	0.224	0.15297	.	0.000000	0.85682	D	0.000000	T	0.14184	0.0343	L	0.27053	0.805	0.44221	D	0.997055	B;B	0.15719	0.008;0.014	B;B	0.11329	0.003;0.006	T	0.10064	-1.0646	10	0.87932	D	0	-19.0858	11.3794	0.49748	0.0603:0.0:0.5132:0.4265	.	125;125	Q17R98;Q17R98-2	ZN827_HUMAN;.	W	125;125;124	ENSP00000421863:R125W;ENSP00000368761:R125W	ENSP00000281318:R124W	R	-	1	2	ZNF827	147043488	1.000000	0.71417	0.999000	0.59377	0.909000	0.53808	2.915000	0.48805	0.065000	0.16485	-0.258000	0.10820	CGG		0.577	ZNF827-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000364654.2	NM_178835	
FBXW7	55294	broad.mit.edu	37	4	153249384	153249384	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr4:153249384C>T	ENST00000281708.4	-	9	2623	c.1394G>A	c.(1393-1395)cGt>cAt	p.R465H	FBXW7_ENST00000603548.1_Missense_Mutation_p.R465H|FBXW7_ENST00000603841.1_Missense_Mutation_p.R465H|FBXW7_ENST00000296555.5_Missense_Mutation_p.R347H|FBXW7_ENST00000263981.5_Missense_Mutation_p.R385H|FBXW7_ENST00000393956.3_Missense_Mutation_p.R289H	NM_033632.3	NP_361014.1	Q969H0	FBXW7_HUMAN	F-box and WD repeat domain containing 7, E3 ubiquitin protein ligase	465			R -> C (in a acute lymphoblastic leukemia cell line). {ECO:0000269|PubMed:11565033}.|R -> H (in a colorectal cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		cellular response to DNA damage stimulus (GO:0006974)|cellular response to UV (GO:0034644)|lipid homeostasis (GO:0055088)|lung development (GO:0030324)|negative regulation of DNA endoreduplication (GO:0032876)|negative regulation of hepatocyte proliferation (GO:2000346)|negative regulation of Notch signaling pathway (GO:0045746)|negative regulation of SREBP signaling pathway (GO:2000639)|negative regulation of triglyceride biosynthetic process (GO:0010868)|Notch signaling pathway (GO:0007219)|positive regulation of epidermal growth factor-activated receptor activity (GO:0045741)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway (GO:1903378)|positive regulation of proteasomal protein catabolic process (GO:1901800)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of ubiquitin-protein transferase activity (GO:0051443)|protein stabilization (GO:0050821)|protein ubiquitination (GO:0016567)|regulation of cell cycle G1/S phase transition (GO:1902806)|regulation of lipid storage (GO:0010883)|regulation of protein localization (GO:0032880)|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031146)|sister chromatid cohesion (GO:0007062)|vasculature development (GO:0001944)|vasculogenesis (GO:0001570)|viral process (GO:0016032)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|Parkin-FBXW7-Cul1 ubiquitin ligase complex (GO:1990452)|protein complex (GO:0043234)|SCF ubiquitin ligase complex (GO:0019005)	cyclin binding (GO:0030332)|identical protein binding (GO:0042802)|protein binding, bridging (GO:0030674)|sequence-specific DNA binding transcription factor activity (GO:0003700)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activator activity (GO:0097027)	p.R465H(69)|p.R385H(16)|p.R226H(16)|p.R465L(4)|p.R347H(4)|p.R465Y(2)|p.?(1)|p.R385L(1)|p.R226L(1)		NS(1)|biliary_tract(8)|bone(1)|breast(5)|central_nervous_system(6)|cervix(2)|endometrium(36)|haematopoietic_and_lymphoid_tissue(159)|kidney(6)|large_intestine(155)|lung(31)|ovary(10)|pancreas(3)|prostate(2)|skin(6)|stomach(16)|upper_aerodigestive_tract(9)|urinary_tract(6)	462	all_hematologic(180;0.093)	Acute lymphoblastic leukemia(8;0.000629)|all_hematologic(8;0.067)				ATGCATACAACGCACAGTGGA	0.408			"""Mis, N, D, F"""		"""colorectal, endometrial, T-ALL"""																																p.R385H			Rec	yes		4	4q31.3	55294	"""F-box and WD-40 domain protein 7 (archipelago homolog, Drosophila)"""		"""E, L"""	FBXW7,large_intestine,NS,Substitution - Missense,0 	.	114	Substitution - Missense(113)|Unknown(1)	haematopoietic_and_lymphoid_tissue(40)|large_intestine(39)|endometrium(24)|lung(5)|ovary(4)|cervix(1)|biliary_tract(1)	c.G1154A	4						.						253.0	218.0	230.0					4																	153249384		2203	4300	6503	153468834	SO:0001583	missense	55294	exon8			AF411971	CCDS3777.1, CCDS3778.1, CCDS34078.1, CCDS64082.1	4q31.23	2013-01-09	2012-02-23					"""F-boxes / WD-40 domains"", ""WD repeat domain containing"""	16712	protein-coding gene	gene with protein product	"""archipelago homolog (Drosophila)"""	606278	"""F-box and WD-40 domain protein 7 (archipelago homolog, Drosophila)"", ""F-box and WD repeat domain containing 7"""			10531037, 11425854	Standard	NM_018315		Approved	AGO, FLJ11071, SEL-10, SEL10, FBW7, FBX30, CDC4, FBXW6	uc003ims.3	Q969H0		ENST00000281708.4:c.1394G>A	4.37:g.153249384C>T	ENSP00000281708:p.Arg465His	Somatic		Capture	Illumina HiSeq	Phase_I	153468834	NM_018315	B7ZLP9|Q68DR0|Q96A16|Q96LE0|Q96RI2|Q9NUX6	Missense_Mutation	SNP	ENST00000281708.4	37	CCDS3777.1	.	.	.	.	.	.	.	.	.	.	C	32	5.178201	0.94846	.	.	ENSG00000109670	ENST00000281708;ENST00000296555;ENST00000263981;ENST00000393956	T;T;T;T	0.42513	0.97;0.97;0.97;0.97	6.05	6.05	0.98169	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.000000	0.85682	D	0.000000	T	0.63827	0.2544	L	0.56124	1.755	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	1.0;0.999;1.0;1.0	T	0.62469	-0.6848	10	0.87932	D	0	-17.2313	20.6013	0.99457	0.0:1.0:0.0:0.0	.	289;465;347;385	B7Z2C8;Q969H0;Q969H0-4;Q969H0-2	.;FBXW7_HUMAN;.;.	H	465;347;385;289	ENSP00000281708:R465H;ENSP00000296555:R347H;ENSP00000263981:R385H;ENSP00000377528:R289H	ENSP00000263981:R385H	R	-	2	0	FBXW7	153468834	1.000000	0.71417	0.960000	0.40013	0.996000	0.88848	7.818000	0.86416	2.878000	0.98634	0.650000	0.86243	CGT		0.408	FBXW7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000469956.1		
MND1	84057	broad.mit.edu	37	4	154318377	154318377	+	Nonsense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr4:154318377C>T	ENST00000504860.1	+	5	356	c.313C>T	c.(313-315)Cga>Tga	p.R105*	MND1_ENST00000240488.3_Nonsense_Mutation_p.R120*					meiotic nuclear divisions 1 homolog (S. cerevisiae)									p.R120*(1)		large_intestine(2)|lung(1)	3	all_hematologic(180;0.093)					GCAGGAAGAGCGAACCAGGCT	0.343																																					p.R120X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.C358T	4						.						64.0	63.0	63.0					4																	154318377		2203	4300	6503	154537827	SO:0001587	stop_gained	84057	exon6			AY028916	CCDS3782.1, CCDS75202.1	4q31.3	2008-02-05			ENSG00000121211	ENSG00000121211			24839	protein-coding gene	gene with protein product		611422				11940665	Standard	NM_032117		Approved	GAJ	uc003ink.2	Q9BWT6	OTTHUMG00000161523	ENST00000504860.1:c.313C>T	4.37:g.154318377C>T	ENSP00000422933:p.Arg105*	Somatic		Capture	Illumina HiSeq	Phase_I	154537827	NM_032117		Nonsense_Mutation	SNP	ENST00000504860.1	37		.	.	.	.	.	.	.	.	.	.	C	15.93	2.977043	0.53720	.	.	ENSG00000121211	ENST00000240488;ENST00000504860	.	.	.	5.44	3.65	0.41850	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-11.7315	12.2214	0.54435	0.3101:0.6899:0.0:0.0	.	.	.	.	X	120;105	.	ENSP00000240488:R120X	R	+	1	2	MND1	154537827	0.994000	0.37717	0.787000	0.31911	0.545000	0.35147	1.615000	0.36922	0.703000	0.31848	0.555000	0.69702	CGA		0.343	MND1-002	PUTATIVE	alternative_5_UTR|basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000365195.1	NM_032117	
DCHS2	54798	broad.mit.edu	37	4	155156525	155156525	+	Silent	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr4:155156525G>A	ENST00000357232.4	-	25	7913	c.7914C>T	c.(7912-7914)ggC>ggT	p.G2638G		NM_017639.3	NP_060109.2	Q6V1P9	PCD23_HUMAN	dachsous cadherin-related 2	2638					homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.G2638G(1)		NS(1)|breast(2)|central_nervous_system(1)|cervix(3)|endometrium(8)|kidney(5)|large_intestine(54)|lung(63)|ovary(4)|pancreas(1)|prostate(14)|skin(12)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	176	all_hematologic(180;0.208)	Renal(120;0.0854)		LUSC - Lung squamous cell carcinoma(193;0.107)		CAGAACAGTGGCCACTGGAGT	0.468																																					p.G2638G												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C7914T	4						.						106.0	103.0	104.0					4																	155156525		2203	4300	6503	155375975	SO:0001819	synonymous_variant	54798	exon25			BC140919	CCDS3785.1, CCDS47150.1	4q32.1	2014-06-04	2013-10-04	2004-09-03		ENSG00000197410		"""Cadherins / Cadherin-related"""	23111	protein-coding gene	gene with protein product	"""cadherin-related family member 7"""	612486	"""cadherin-like 27"", ""dachsous 2 (Drosophila)"""	CDH27, PCDH23		15003449	Standard	NM_017639		Approved	CDHJ, FLJ20047, PCDHJ, CDHR7	uc003inw.2	Q6V1P9		ENST00000357232.4:c.7914C>T	4.37:g.155156525G>A		Somatic		Capture	Illumina HiSeq	Phase_I	155375975	NM_017639	B2RU14|E9PC11|Q4W5P9|Q6ZS61|Q9NXU8	Silent	SNP	ENST00000357232.4	37	CCDS3785.1																																																																																				0.468	DCHS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365281.2	NM_001142552	
DCHS2	54798	broad.mit.edu	37	4	155180787	155180787	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr4:155180787C>A	ENST00000357232.4	-	20	5333	c.5334G>T	c.(5332-5334)caG>caT	p.Q1778H		NM_017639.3	NP_060109.2	Q6V1P9	PCD23_HUMAN	dachsous cadherin-related 2	1778	Cadherin 15. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.Q1778H(1)		NS(1)|breast(2)|central_nervous_system(1)|cervix(3)|endometrium(8)|kidney(5)|large_intestine(54)|lung(63)|ovary(4)|pancreas(1)|prostate(14)|skin(12)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	176	all_hematologic(180;0.208)	Renal(120;0.0854)		LUSC - Lung squamous cell carcinoma(193;0.107)		CATTCTCATCCTGTATCAAGA	0.393																																					p.Q1778H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G5334T	4						.						197.0	175.0	182.0					4																	155180787		2203	4300	6503	155400237	SO:0001583	missense	54798	exon20			BC140919	CCDS3785.1, CCDS47150.1	4q32.1	2014-06-04	2013-10-04	2004-09-03		ENSG00000197410		"""Cadherins / Cadherin-related"""	23111	protein-coding gene	gene with protein product	"""cadherin-related family member 7"""	612486	"""cadherin-like 27"", ""dachsous 2 (Drosophila)"""	CDH27, PCDH23		15003449	Standard	NM_017639		Approved	CDHJ, FLJ20047, PCDHJ, CDHR7	uc003inw.2	Q6V1P9		ENST00000357232.4:c.5334G>T	4.37:g.155180787C>A	ENSP00000349768:p.Gln1778His	Somatic		Capture	Illumina HiSeq	Phase_I	155400237	NM_017639	B2RU14|E9PC11|Q4W5P9|Q6ZS61|Q9NXU8	Missense_Mutation	SNP	ENST00000357232.4	37	CCDS3785.1	.	.	.	.	.	.	.	.	.	.	C	15.81	2.944207	0.53079	.	.	ENSG00000197410	ENST00000357232	T	0.38401	1.14	5.52	2.02	0.26589	Cadherin (3);Cadherin conserved site (1);Cadherin-like (1);	0.167278	0.41500	D	0.000874	T	0.50480	0.1618	M	0.76574	2.34	0.80722	D	1	D	0.67145	0.996	D	0.64042	0.921	T	0.45804	-0.9236	10	0.44086	T	0.13	.	6.8096	0.23796	0.0:0.241:0.0:0.759	.	1778	Q6V1P9	PCD23_HUMAN	H	1778	ENSP00000349768:Q1778H	ENSP00000349768:Q1778H	Q	-	3	2	DCHS2	155400237	1.000000	0.71417	0.606000	0.28943	0.746000	0.42486	0.719000	0.25881	0.670000	0.31165	0.655000	0.94253	CAG		0.393	DCHS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365281.2	NM_001142552	
DCHS2	54798	broad.mit.edu	37	4	155250756	155250756	+	Silent	SNP	C	C	T	rs375851945		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr4:155250756C>T	ENST00000357232.4	-	11	2471	c.2472G>A	c.(2470-2472)gcG>gcA	p.A824A	DCHS2_ENST00000339452.1_Silent_p.A1279A	NM_017639.3	NP_060109.2	Q6V1P9	PCD23_HUMAN	dachsous cadherin-related 2	824	Cadherin 6. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.A824A(1)		NS(1)|breast(2)|central_nervous_system(1)|cervix(3)|endometrium(8)|kidney(5)|large_intestine(54)|lung(63)|ovary(4)|pancreas(1)|prostate(14)|skin(12)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	176	all_hematologic(180;0.208)	Renal(120;0.0854)		LUSC - Lung squamous cell carcinoma(193;0.107)		AGACGTAAACCGCCATGGTGG	0.537																																					p.A1279A												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G3837A	4						.	C	,	0,4406		0,0,2203	87.0	72.0	77.0		3837,2472	2.0	0.0	4		77	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous	DCHS2	NM_001142552.1,NM_017639.3	,	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	,	1279/1370,824/2917	155250756	1,13005	2203	4300	6503	155470206	SO:0001819	synonymous_variant	54798	exon6			BC140919	CCDS3785.1, CCDS47150.1	4q32.1	2014-06-04	2013-10-04	2004-09-03		ENSG00000197410		"""Cadherins / Cadherin-related"""	23111	protein-coding gene	gene with protein product	"""cadherin-related family member 7"""	612486	"""cadherin-like 27"", ""dachsous 2 (Drosophila)"""	CDH27, PCDH23		15003449	Standard	NM_017639		Approved	CDHJ, FLJ20047, PCDHJ, CDHR7	uc003inw.2	Q6V1P9		ENST00000357232.4:c.2472G>A	4.37:g.155250756C>T		Somatic		Capture	Illumina HiSeq	Phase_I	155470206	NM_001142552	B2RU14|E9PC11|Q4W5P9|Q6ZS61|Q9NXU8	Silent	SNP	ENST00000357232.4	37	CCDS3785.1																																																																																				0.537	DCHS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365281.2	NM_001142552	
GUCY1A3	2982	broad.mit.edu	37	4	156643241	156643241	+	Nonsense_Mutation	SNP	A	A	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr4:156643241A>T	ENST00000296518.7	+	9	1977	c.1768A>T	c.(1768-1770)Aaa>Taa	p.K590*	GUCY1A3_ENST00000511108.1_Nonsense_Mutation_p.K590*|GUCY1A3_ENST00000455639.2_Nonsense_Mutation_p.K590*|GUCY1A3_ENST00000393832.3_Nonsense_Mutation_p.K332*|GUCY1A3_ENST00000513574.1_Nonsense_Mutation_p.K590*|GUCY1A3_ENST00000506455.1_Nonsense_Mutation_p.K590*|GUCY1A3_ENST00000511507.1_Nonsense_Mutation_p.K590*			Q02108	GCYA3_HUMAN	guanylate cyclase 1, soluble, alpha 3	590	Guanylate cyclase. {ECO:0000255|PROSITE- ProRule:PRU00099}.				blood circulation (GO:0008015)|blood coagulation (GO:0007596)|nitric oxide mediated signal transduction (GO:0007263)|positive regulation of cGMP biosynthetic process (GO:0030828)|regulation of blood pressure (GO:0008217)|relaxation of vascular smooth muscle (GO:0060087)|response to defense-related host nitric oxide production (GO:0052565)	guanylate cyclase complex, soluble (GO:0008074)	GTP binding (GO:0005525)|guanylate cyclase activity (GO:0004383)|heme binding (GO:0020037)|receptor activity (GO:0004872)	p.K590*(1)		central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(25)|liver(2)|lung(19)|ovary(1)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	64	all_hematologic(180;0.24)	Renal(120;0.0854)		COAD - Colon adenocarcinoma(41;0.17)		CGTTGGAGTTAAAATGCCCCG	0.418																																					p.K590X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.A1768T	4						.						256.0	245.0	248.0					4																	156643241		2203	4300	6503	156862691	SO:0001587	stop_gained	2982	exon9				CCDS34085.1, CCDS54812.1	4q31.3-q33	2008-03-18				ENSG00000164116	4.6.1.2		4685	protein-coding gene	gene with protein product		139396		GUC1A3		1352257	Standard	NM_001130687		Approved	GC-SA3	uc003iow.3	Q02108		ENST00000296518.7:c.1768A>T	4.37:g.156643241A>T	ENSP00000296518:p.Lys590*	Somatic		Capture	Illumina HiSeq	Phase_I	156862691	NM_001130682	D3DP19|D6RDW3|O43843|Q8TAH3	Nonsense_Mutation	SNP	ENST00000296518.7	37	CCDS34085.1	.	.	.	.	.	.	.	.	.	.	A	42	9.809263	0.99270	.	.	ENSG00000164116	ENST00000506455;ENST00000511108;ENST00000511507;ENST00000455639;ENST00000393832;ENST00000296518;ENST00000513574	.	.	.	5.82	5.82	0.92795	.	0.000000	0.64402	D	0.000003	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	16.1776	0.81862	1.0:0.0:0.0:0.0	.	.	.	.	X	590;590;590;590;332;590;590	.	ENSP00000296518:K590X	K	+	1	0	GUCY1A3	156862691	1.000000	0.71417	0.989000	0.46669	0.922000	0.55478	9.339000	0.96797	2.222000	0.72286	0.477000	0.44152	AAA		0.418	GUCY1A3-010	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365786.2		
NPY5R	4889	broad.mit.edu	37	4	164272572	164272572	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr4:164272572C>T	ENST00000515560.1	+	4	2669	c.1147C>T	c.(1147-1149)Cca>Tca	p.P383S	NPY5R_ENST00000506953.1_Missense_Mutation_p.P383S|NPY5R_ENST00000338566.3_Missense_Mutation_p.P383S			Q15761	NPY5R_HUMAN	neuropeptide Y receptor Y5	383					cardiac left ventricle morphogenesis (GO:0003214)|eating behavior (GO:0042755)|G-protein coupled receptor signaling pathway (GO:0007186)|generation of ovulation cycle rhythm (GO:0060112)|negative regulation of apoptotic process (GO:0043066)|negative regulation of glutamate secretion (GO:0014050)|negative regulation of synaptic transmission, GABAergic (GO:0032229)|neuropeptide signaling pathway (GO:0007218)|outflow tract morphogenesis (GO:0003151)|positive regulation of acute inflammatory response (GO:0002675)|positive regulation of smooth muscle cell proliferation (GO:0048661)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	neuropeptide Y receptor activity (GO:0004983)|pancreatic polypeptide receptor activity (GO:0001602)|peptide YY receptor activity (GO:0001601)	p.P383S(1)		NS(2)|biliary_tract(1)|breast(1)|endometrium(3)|large_intestine(4)|lung(26)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	42	all_hematologic(180;0.166)	Prostate(90;0.109)				TAGTTGGATGCCACTACACCT	0.338																																					p.P383S	Melanoma(139;1287 1774 9781 19750 25599)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1147T	4						.						157.0	148.0	151.0					4																	164272572		2203	4300	6503	164492022	SO:0001583	missense	4889	exon4			BC042416	CCDS3804.1	4q31-q32	2012-08-08				ENSG00000164129		"""GPCR / Class A : Neuropeptide receptors : Y"""	7958	protein-coding gene	gene with protein product		602001				8700207, 9417917	Standard	NM_006174		Approved	NPYR5	uc003iqn.3	Q15761		ENST00000515560.1:c.1147C>T	4.37:g.164272572C>T	ENSP00000423917:p.Pro383Ser	Somatic		Capture	Illumina HiSeq	Phase_I	164492022	NM_006174	Q6GTR7|Q92916	Missense_Mutation	SNP	ENST00000515560.1	37	CCDS3804.1	.	.	.	.	.	.	.	.	.	.	C	18.95	3.731448	0.69189	.	.	ENSG00000164129	ENST00000338566;ENST00000515560;ENST00000506953	T;T;T	0.80304	-1.36;-1.36;-1.36	4.9	4.9	0.64082	GPCR, rhodopsin-like superfamily (1);	0.000000	0.56097	D	0.000031	D	0.92512	0.7622	M	0.93507	3.425	0.58432	D	0.999998	D	0.89917	1.0	D	0.97110	1.0	D	0.94451	0.7667	10	0.87932	D	0	.	18.4497	0.90699	0.0:1.0:0.0:0.0	.	383	Q15761	NPY5R_HUMAN	S	383	ENSP00000339377:P383S;ENSP00000423917:P383S;ENSP00000423474:P383S	ENSP00000339377:P383S	P	+	1	0	NPY5R	164492022	1.000000	0.71417	0.999000	0.59377	0.838000	0.47535	6.828000	0.75308	2.428000	0.82296	0.460000	0.39030	CCA		0.338	NPY5R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364633.1	NM_006174	
FGFR3	2261	broad.mit.edu	37	4	1808053	1808053	+	Splice_Site	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr4:1808053G>A	ENST00000260795.2	+	14	2131	c.2029G>A	c.(2029-2031)Gtc>Atc	p.V677I	FGFR3_ENST00000440486.2_Splice_Site_p.V677I|FGFR3_ENST00000481110.2_Intron|FGFR3_ENST00000412135.2_Splice_Site_p.V565I|FGFR3_ENST00000340107.4_Splice_Site_p.V679I|FGFR3_ENST00000352904.1_Splice_Site_p.V565I			P22607	FGFR3_HUMAN	fibroblast growth factor receptor 3	677	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				alveolar secondary septum development (GO:0061144)|axonogenesis involved in innervation (GO:0060385)|bone maturation (GO:0070977)|bone mineralization (GO:0030282)|bone morphogenesis (GO:0060349)|cell-cell signaling (GO:0007267)|central nervous system myelination (GO:0022010)|chondrocyte differentiation (GO:0002062)|chondrocyte proliferation (GO:0035988)|cochlea development (GO:0090102)|digestive tract morphogenesis (GO:0048546)|endochondral bone growth (GO:0003416)|endochondral ossification (GO:0001958)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial cell fate commitment (GO:0072148)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor apoptotic signaling pathway (GO:1902178)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|inner ear receptor cell differentiation (GO:0060113)|insulin receptor signaling pathway (GO:0008286)|JAK-STAT cascade (GO:0007259)|lens fiber cell development (GO:0070307)|lens morphogenesis in camera-type eye (GO:0002089)|MAPK cascade (GO:0000165)|morphogenesis of an epithelium (GO:0002009)|negative regulation of astrocyte differentiation (GO:0048712)|negative regulation of developmental growth (GO:0048640)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of mitosis (GO:0045839)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of cell differentiation (GO:0045597)|positive regulation of cell proliferation (GO:0008284)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of MAPKKK cascade by fibroblast growth factor receptor signaling pathway (GO:0090080)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phospholipase activity (GO:0010518)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of tyrosine phosphorylation of Stat1 protein (GO:0042511)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|protein autophosphorylation (GO:0046777)|response to axon injury (GO:0048678)|skeletal system development (GO:0001501)|somatic stem cell maintenance (GO:0035019)|substantia nigra development (GO:0021762)	cell surface (GO:0009986)|cytoplasmic side of plasma membrane (GO:0009898)|cytoplasmic vesicle (GO:0031410)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|lysosome (GO:0005764)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|fibroblast growth factor binding (GO:0017134)|fibroblast growth factor-activated receptor activity (GO:0005007)|protein tyrosine kinase activity (GO:0004713)	p.V677I(1)		NS(1)|central_nervous_system(5)|cervix(6)|endometrium(2)|haematopoietic_and_lymphoid_tissue(40)|kidney(1)|large_intestine(5)|lung(9)|ovary(1)|pancreas(2)|prostate(9)|skin(339)|soft_tissue(4)|testis(2)|upper_aerodigestive_tract(58)|urinary_tract(2607)	3091		Breast(71;0.212)|all_epithelial(65;0.241)	all cancers(2;0.000145)|OV - Ovarian serous cystadenocarcinoma(23;0.0019)|Epithelial(3;0.00221)|GBM - Glioblastoma multiforme(2;0.234)		Palifermin(DB00039)|Pazopanib(DB06589)|Ponatinib(DB08901)	CCAGAGTGACGTGTACGTGTC	0.662		1	"""Mis, T"""	"""IGH@, ETV6"""	"""bladder, MM, T-cell lymphoma"""		"""Hypochondroplasia, Thanatophoric dysplasia"""		Saethre-Chotzen syndrome;Muenke syndrome																												p.V679I			Dom	yes		4	4p16.3	2261	fibroblast growth factor receptor 3	yes	"""L, E"""	.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2035A	4						.						51.0	46.0	48.0					4																	1808053		2203	4300	6503	1777851	SO:0001630	splice_region_variant	2261	exon15	Familial Cancer Database	Acrocephalosyndactyly type III;Muenke Nonsyndromic Coronal Craniosynostosis, FGFR3-related Craniosynostosis	M64347	CCDS3353.1, CCDS3354.1, CCDS54706.1	4p16.3	2013-01-11	2008-08-01		ENSG00000068078	ENSG00000068078		"""CD molecules"", ""Immunoglobulin superfamily / I-set domain containing"""	3690	protein-coding gene	gene with protein product		134934	"""achondroplasia, thanatophoric dwarfism"""	ACH		1847508	Standard	NM_000142		Approved	CEK2, JTK4, CD333	uc003gdu.2	P22607	OTTHUMG00000121148	ENST00000260795.2:c.2030+1G>A	4.37:g.1808053G>A		Somatic		Capture	Illumina HiSeq	Phase_I	1777851	NM_001163213	D3DVP9|D3DVQ0|Q14308|Q16294|Q16608|Q59FL9	Missense_Mutation	SNP	ENST00000260795.2	37	CCDS3353.1	.	.	.	.	.	.	.	.	.	.	g	20.9	4.068034	0.76301	.	.	ENSG00000068078	ENST00000340107;ENST00000440486;ENST00000412135;ENST00000260795;ENST00000352904	D;D;D;D;D	0.87256	-2.23;-2.23;-2.23;-2.23;-2.23	4.49	4.49	0.54785	Serine-threonine/tyrosine-protein kinase (2);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	.	.	.	.	D	0.89812	0.6823	L	0.35487	1.065	0.80722	D	1	D;D;D	0.76494	0.997;0.998;0.999	P;D;D	0.69824	0.872;0.966;0.943	D	0.91174	0.4971	9	0.62326	D	0.03	.	17.5412	0.87848	0.0:0.0:1.0:0.0	.	679;565;677	P22607-2;P22607-3;P22607	.;.;FGFR3_HUMAN	I	679;677;565;677;565	ENSP00000339824:V679I;ENSP00000414914:V677I;ENSP00000412903:V565I;ENSP00000260795:V677I;ENSP00000231803:V565I	ENSP00000260795:V677I	V	+	1	0	FGFR3	1777851	1.000000	0.71417	0.998000	0.56505	0.717000	0.41224	9.492000	0.97957	2.206000	0.71126	0.561000	0.74099	GTC		0.662	FGFR3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000241632.2	NM_000142	Missense_Mutation
CEP44	80817	broad.mit.edu	37	4	175225483	175225483	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr4:175225483G>T	ENST00000503780.1	+	6	884	c.470G>T	c.(469-471)gGc>gTc	p.G157V	CEP44_ENST00000457424.2_Missense_Mutation_p.G157V|CEP44_ENST00000296519.4_Missense_Mutation_p.G157V|CEP44_ENST00000426172.1_Missense_Mutation_p.G157V	NM_001040157.2	NP_001035247.1	Q9C0F1	CEP44_HUMAN	centrosomal protein 44kDa	157						centrosome (GO:0005813)|cytoplasm (GO:0005737)|midbody (GO:0030496)|spindle pole (GO:0000922)		p.G157V(1)		endometrium(2)|large_intestine(4)|lung(5)|stomach(1)	12						GAGGCTGTTGGCGTTGATATC	0.353																																					p.G157V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G470T	4						.						70.0	73.0	72.0					4																	175225483		2203	4300	6503	175462058	SO:0001583	missense	80817	exon6			AB051499	CCDS34106.1, CCDS47163.1	4q34	2014-02-20	2011-05-06	2011-05-06	ENSG00000164118	ENSG00000164118			29356	protein-coding gene	gene with protein product			"""KIAA1712"""	KIAA1712		21399614	Standard	NM_001040157		Approved		uc010iro.2	Q9C0F1	OTTHUMG00000160752	ENST00000503780.1:c.470G>T	4.37:g.175225483G>T	ENSP00000423153:p.Gly157Val	Somatic		Capture	Illumina HiSeq	Phase_I	175462058	NM_001040157	A8K8W9|A8MW11|B3KT53|D3DP42|Q8IXZ4	Missense_Mutation	SNP	ENST00000503780.1	37	CCDS34106.1	.	.	.	.	.	.	.	.	.	.	G	0.009	-1.818554	0.00595	.	.	ENSG00000164118	ENST00000503780;ENST00000457424;ENST00000515299;ENST00000426172;ENST00000296519	T;T;T;T;T	0.42900	0.99;0.96;1.0;0.96;0.99	5.01	3.14	0.36123	.	0.501450	0.21368	N	0.075694	T	0.35828	0.0945	L	0.36672	1.1	0.09310	N	0.99999	D;B	0.53462	0.96;0.297	P;B	0.52217	0.693;0.117	T	0.12708	-1.0537	10	0.16896	T	0.51	.	5.7791	0.18295	0.151:0.0:0.6736:0.1754	.	157;157	Q9C0F1-2;Q9C0F1	.;CEP44_HUMAN	V	157	ENSP00000423153:G157V;ENSP00000389427:G157V;ENSP00000421128:G157V;ENSP00000408221:G157V;ENSP00000296519:G157V	ENSP00000296519:G157V	G	+	2	0	CEP44	175462058	0.022000	0.18835	0.982000	0.44146	0.020000	0.10135	1.323000	0.33701	2.470000	0.83445	0.462000	0.41574	GGC		0.353	CEP44-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362109.2	NM_030633	
AGA	175	broad.mit.edu	37	4	178355642	178355642	+	Splice_Site	SNP	G	G	A	rs572348048		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr4:178355642G>A	ENST00000264595.2	-	7	827	c.700C>T	c.(700-702)Cgt>Tgt	p.R234C	AGA_ENST00000506853.1_5'UTR	NM_000027.3|NM_001171988.1	NP_000018.2|NP_001165459.1	P20933	ASPG_HUMAN	aspartylglucosaminidase	234	Substrate binding.				protein deglycosylation (GO:0006517)|protein maturation (GO:0051604)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)	N4-(beta-N-acetylglucosaminyl)-L-asparaginase activity (GO:0003948)|peptidase activity (GO:0008233)	p.R234C(1)		endometrium(1)|kidney(2)|large_intestine(6)|lung(5)|skin(2)	16		all_lung(41;1.27e-09)|Lung NSC(41;1.1e-08)|Breast(14;6.27e-05)|Melanoma(52;0.00102)|Renal(120;0.00988)|Prostate(90;0.00996)|all_hematologic(60;0.014)|Hepatocellular(41;0.148)|all_neural(102;0.164)|Colorectal(36;0.245)		all cancers(43;1.37e-22)|Epithelial(43;3.86e-20)|OV - Ovarian serous cystadenocarcinoma(60;3.8e-11)|Colorectal(24;6.98e-05)|GBM - Glioblastoma multiforme(59;0.000362)|COAD - Colon adenocarcinoma(29;0.000462)|STAD - Stomach adenocarcinoma(60;0.0029)|LUSC - Lung squamous cell carcinoma(193;0.0328)|READ - Rectum adenocarcinoma(43;0.163)		TCTCCTACACGGCTTTGAGAG	0.473													G|||	1	0.000199681	0.0008	0.0	5008	,	,		16243	0.0		0.0	False		,,,				2504	0.0				p.R234C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C700T	4						.						89.0	83.0	85.0					4																	178355642		2203	4300	6503	178592636	SO:0001630	splice_region_variant	175	exon7			X55330	CCDS3829.1	4q34.3	2014-06-23			ENSG00000038002	ENSG00000038002	3.5.1.26		318	protein-coding gene	gene with protein product	"""glycosylasparaginase"", ""N(4)-(beta-N-acetylglucosaminyl)-L-asparaginase"""	613228					Standard	NM_000027		Approved	ASRG	uc003iuu.2	P20933	OTTHUMG00000160723	ENST00000264595.2:c.699-1C>T	4.37:g.178355642G>A		Somatic		Capture	Illumina HiSeq	Phase_I	178592636	NM_000027	B2R7H2|D3DP47|Q4W5Q2|Q6FHN6|Q9UCK6|Q9UCK7|Q9UCK8	Missense_Mutation	SNP	ENST00000264595.2	37	CCDS3829.1	.	.	.	.	.	.	.	.	.	.	G	18.69	3.677085	0.68042	.	.	ENSG00000038002	ENST00000264595	D	0.95724	-3.79	5.57	5.57	0.84162	.	0.000000	0.85682	D	0.000000	D	0.98779	0.9589	H	0.98089	4.145	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.99490	1.0950	10	0.87932	D	0	-17.7857	19.1554	0.93507	0.0:0.0:1.0:0.0	.	234	P20933	ASPG_HUMAN	C	234	ENSP00000264595:R234C	ENSP00000264595:R234C	R	-	1	0	AGA	178592636	1.000000	0.71417	0.619000	0.29118	0.083000	0.17756	9.214000	0.95140	2.637000	0.89404	0.650000	0.86243	CGT		0.473	AGA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361916.1	NM_000027	Missense_Mutation
TENM3	55714	broad.mit.edu	37	4	183714058	183714058	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr4:183714058C>T	ENST00000511685.1	+	26	6356	c.6233C>T	c.(6232-6234)aCg>aTg	p.T2078M	TENM3_ENST00000406950.2_Missense_Mutation_p.T2078M			Q9P273	TEN3_HUMAN	teneurin transmembrane protein 3	2078					camera-type eye morphogenesis (GO:0048593)|homophilic cell adhesion (GO:0007156)|positive regulation of neuron projection development (GO:0010976)|self proteolysis (GO:0097264)|signal transduction (GO:0007165)	cell projection (GO:0042995)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)	p.T2078M(1)									ATGACCTATACGAAGCACTTT	0.378																																					p.T2078M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C6233T	4						.						45.0	44.0	45.0					4																	183714058		1861	4100	5961	183951052	SO:0001583	missense	55714	exon25			AF195420	CCDS47165.1	4q35	2012-10-02	2012-10-02	2012-10-02	ENSG00000218336	ENSG00000218336			29944	protein-coding gene	gene with protein product		610083	"""odz, odd Oz/ten-m homolog 3 (Drosophila)"""	ODZ3		10331952, 10625539	Standard	NM_001080477		Approved	Ten-M3, KIAA1455	uc003ivd.1	Q9P273	OTTHUMG00000160682	ENST00000511685.1:c.6233C>T	4.37:g.183714058C>T	ENSP00000424226:p.Thr2078Met	Somatic		Capture	Illumina HiSeq	Phase_I	183951052	NM_001080477	Q5XUL9|Q96SY2|Q9NV77|Q9NVW1|Q9NZJ2	Missense_Mutation	SNP	ENST00000511685.1	37	CCDS47165.1	.	.	.	.	.	.	.	.	.	.	C	16.91	3.253606	0.59212	.	.	ENSG00000218336	ENST00000511685;ENST00000406950	D;D	0.88354	-2.37;-2.37	4.79	4.79	0.61399	.	.	.	.	.	D	0.94162	0.8127	M	0.74258	2.255	0.80722	D	1	D	0.89917	1.0	D	0.78314	0.991	D	0.94814	0.7981	9	0.87932	D	0	.	18.0329	0.89290	0.0:1.0:0.0:0.0	.	2078	Q9P273	TEN3_HUMAN	M	2078	ENSP00000424226:T2078M;ENSP00000385276:T2078M	ENSP00000385276:T2078M	T	+	2	0	ODZ3	183951052	1.000000	0.71417	0.899000	0.35326	0.619000	0.37552	7.625000	0.83145	2.476000	0.83614	0.563000	0.77884	ACG		0.378	TENM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361734.1		
FAT1	2195	broad.mit.edu	37	4	187524362	187524362	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr4:187524362C>T	ENST00000441802.2	-	19	11527	c.11318G>A	c.(11317-11319)cGc>cAc	p.R3773H		NM_005245.3	NP_005236.2	Q14517	FAT1_HUMAN	FAT atypical cadherin 1	3773					actin filament organization (GO:0007015)|anatomical structure morphogenesis (GO:0009653)|cell adhesion (GO:0007155)|cell migration (GO:0016477)|cell-cell signaling (GO:0007267)|establishment or maintenance of cell polarity (GO:0007163)|homophilic cell adhesion (GO:0007156)|single organismal cell-cell adhesion (GO:0016337)	cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|lamellipodium (GO:0030027)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.R3773H(1)		NS(1)|breast(3)|central_nervous_system(3)|endometrium(38)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(33)|lung(88)|ovary(13)|pancreas(2)|prostate(16)|skin(2)|upper_aerodigestive_tract(11)|urinary_tract(4)	228						CCTGTGGTGGCGGGGAGTCAC	0.522										HNSCC(5;0.00058)																											p.R3773H	Colon(197;1040 2055 4143 4984 49344)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G11318A	4						.						47.0	48.0	47.0					4																	187524362		2040	4190	6230	187761356	SO:0001583	missense	2195	exon19			X87241	CCDS47177.1	4q35.2	2013-05-31	2013-05-31	2008-10-30	ENSG00000083857	ENSG00000083857		"""Cadherins / Cadherin-related"""	3595	protein-coding gene	gene with protein product	"""cadherin-related family member 8"""	600976	"""FAT tumor suppressor (Drosophila) homolog"", ""FAT tumor suppressor homolog 1 (Drosophila)"""	FAT		8586420	Standard	XM_005262834		Approved	CDHF7, CDHR8	uc003izf.3	Q14517	OTTHUMG00000160320	ENST00000441802.2:c.11318G>A	4.37:g.187524362C>T	ENSP00000406229:p.Arg3773His	Somatic		Capture	Illumina HiSeq	Phase_I	187761356	NM_005245		Missense_Mutation	SNP	ENST00000441802.2	37	CCDS47177.1	.	.	.	.	.	.	.	.	.	.	C	12.61	1.988563	0.35036	.	.	ENSG00000083857	ENST00000441802;ENST00000260147	T	0.51574	0.7	4.2	3.35	0.38373	.	0.060123	0.64402	N	0.000003	T	0.42877	0.1222	M	0.72118	2.19	0.58432	D	0.999998	B	0.31193	0.312	B	0.22601	0.04	T	0.45308	-0.9270	10	0.56958	D	0.05	.	9.5721	0.39433	0.0:0.8279:0.0:0.1721	.	3773	Q14517	FAT1_HUMAN	H	3773;3775	ENSP00000406229:R3773H	ENSP00000260147:R3775H	R	-	2	0	FAT1	187761356	0.998000	0.40836	0.971000	0.41717	0.432000	0.31715	3.895000	0.56258	1.119000	0.41883	0.557000	0.71058	CGC		0.522	FAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360209.3	NM_005245	
WHSC1	7468	broad.mit.edu	37	4	1962776	1962776	+	Silent	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr4:1962776C>T	ENST00000382895.3	+	20	3701	c.3270C>T	c.(3268-3270)aaC>aaT	p.N1090N	WHSC1_ENST00000508803.1_Silent_p.N1090N|WHSC1_ENST00000382891.5_Silent_p.N1090N|WHSC1_ENST00000382892.2_Silent_p.N1090N|WHSC1_ENST00000382888.3_Silent_p.N438N|WHSC1_ENST00000482415.2_3'UTR	NM_133330.2	NP_579877.1	O96028	NSD2_HUMAN	Wolf-Hirschhorn syndrome candidate 1	1090	SET. {ECO:0000255|PROSITE- ProRule:PRU00190}.				anatomical structure morphogenesis (GO:0009653)|atrial septum primum morphogenesis (GO:0003289)|atrial septum secundum morphogenesis (GO:0003290)|bone development (GO:0060348)|membranous septum morphogenesis (GO:0003149)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|nuclear membrane (GO:0031965)|nucleolus (GO:0005730)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|zinc ion binding (GO:0008270)	p.N1090N(1)		breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(10)|lung(14)|ovary(4)|pancreas(1)|prostate(3)|skin(4)|urinary_tract(3)	48		all_epithelial(65;1.34e-05)	OV - Ovarian serous cystadenocarcinoma(23;0.00606)	STAD - Stomach adenocarcinoma(129;0.232)		AATTTGTTAACGAGTACGTTG	0.507			T	IGH@	MM																																p.N1090N			Dom	yes		4	4p16.3	7468	Wolf-Hirschhorn syndrome candidate 1(MMSET)		L	.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C3270T	4						.						266.0	218.0	234.0					4																	1962776		2203	4300	6503	1932574	SO:0001819	synonymous_variant	7468	exon19			AF083386	CCDS3356.1, CCDS33940.1, CCDS46999.1	4p16.3	2013-05-20			ENSG00000109685	ENSG00000109685		"""Zinc fingers, PHD-type"""	12766	protein-coding gene	gene with protein product		602952				9618163, 9787135	Standard	NM_133334		Approved	MMSET, NSD2	uc003gdz.4	O96028	OTTHUMG00000121147	ENST00000382895.3:c.3270C>T	4.37:g.1962776C>T		Somatic		Capture	Illumina HiSeq	Phase_I	1932574	NM_133331	A2A2T2|A2A2T3|A2A2T4|A7MCZ1|D3DVQ2|O96031|Q4VBY8|Q672J1|Q6IS00|Q86V01|Q9BZB4|Q9UI92|Q9UPR2	Silent	SNP	ENST00000382895.3	37	CCDS33940.1																																																																																				0.507	WHSC1-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366269.2	NM_133330	
HTT	3064	broad.mit.edu	37	4	3240237	3240237	+	Silent	SNP	C	C	T	rs374515950		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr4:3240237C>T	ENST00000355072.5	+	65	9100	c.8955C>T	c.(8953-8955)gaC>gaT	p.D2985D		NM_002111.6	NP_002102	P42858	HD_HUMAN	huntingtin	2985					anterior/posterior pattern specification (GO:0009952)|axon cargo transport (GO:0008088)|cell aging (GO:0007569)|citrulline metabolic process (GO:0000052)|determination of adult lifespan (GO:0008340)|dopamine receptor signaling pathway (GO:0007212)|endoplasmic reticulum organization (GO:0007029)|endosomal transport (GO:0016197)|ER to Golgi vesicle-mediated transport (GO:0006888)|establishment of mitotic spindle orientation (GO:0000132)|Golgi organization (GO:0007030)|grooming behavior (GO:0007625)|hormone metabolic process (GO:0042445)|insulin secretion (GO:0030073)|iron ion homeostasis (GO:0055072)|L-glutamate import (GO:0051938)|lactate biosynthetic process from pyruvate (GO:0019244)|locomotory behavior (GO:0007626)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of neuron apoptotic process (GO:0043524)|neural plate formation (GO:0021990)|neuron apoptotic process (GO:0051402)|neuron development (GO:0048666)|olfactory lobe development (GO:0021988)|organ development (GO:0048513)|paraxial mesoderm formation (GO:0048341)|positive regulation of inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0031587)|protein import into nucleus (GO:0006606)|quinolinate biosynthetic process (GO:0019805)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane potential (GO:0051881)|regulation of protein phosphatase type 2A activity (GO:0034047)|regulation of synaptic plasticity (GO:0048167)|response to calcium ion (GO:0051592)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)|social behavior (GO:0035176)|spermatogenesis (GO:0007283)|striatum development (GO:0021756)|urea cycle (GO:0000050)|vesicle transport along microtubule (GO:0047496)|visual learning (GO:0008542)	autophagic vacuole (GO:0005776)|axon (GO:0030424)|cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|inclusion body (GO:0016234)|late endosome (GO:0005770)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|protein complex (GO:0043234)	beta-tubulin binding (GO:0048487)|diazepam binding (GO:0050809)|dynactin binding (GO:0034452)|dynein intermediate chain binding (GO:0045505)|identical protein binding (GO:0042802)|ion channel binding (GO:0044325)|p53 binding (GO:0002039)|transcription factor binding (GO:0008134)	p.D2985D(1)		breast(1)|cervix(2)|endometrium(14)|kidney(5)|large_intestine(23)|lung(28)|ovary(4)|prostate(2)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	87		all_epithelial(65;0.18)		UCEC - Uterine corpus endometrioid carcinoma (64;0.187)		AGTTTCTAGACGACTTCTTCC	0.562																																					p.D2985D												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C8955T	4						.	C		1,3983		0,1,1991	62.0	69.0	67.0		8955	-9.6	0.2	4		67	0,8334		0,0,4167	no	coding-synonymous	HTT	NM_002111.6		0,1,6158	TT,TC,CC		0.0,0.0251,0.0081		2985/3143	3240237	1,12317	1992	4167	6159	3210035	SO:0001819	synonymous_variant	3064	exon65			L12392	CCDS43206.1	4p16.3	2014-09-17	2007-12-04	2007-12-04	ENSG00000197386	ENSG00000197386		"""Endogenous ligands"""	4851	protein-coding gene	gene with protein product		613004	"""huntingtin (Huntington disease)"""	HD		8458085	Standard	NM_002111		Approved	IT15	uc021xkv.1	P42858	OTTHUMG00000159916	ENST00000355072.5:c.8955C>T	4.37:g.3240237C>T		Somatic		Capture	Illumina HiSeq	Phase_I	3210035	NM_002111	Q9UQB7	Silent	SNP	ENST00000355072.5	37	CCDS43206.1																																																																																				0.562	HTT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358234.2	NM_002111	
RGS12	6002	broad.mit.edu	37	4	3318586	3318586	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr4:3318586T>C	ENST00000344733.5	+	2	1593	c.689T>C	c.(688-690)aTg>aCg	p.M230T	RGS12_ENST00000336727.3_Missense_Mutation_p.M230T|RGS12_ENST00000543385.1_Missense_Mutation_p.M230T|RGS12_ENST00000382788.3_Missense_Mutation_p.M230T	NM_198229.2	NP_937872.1	O14924	RGS12_HUMAN	regulator of G-protein signaling 12	230	PID. {ECO:0000255|PROSITE- ProRule:PRU00148}.				positive regulation of GTPase activity (GO:0043547)|regulation of catalytic activity (GO:0050790)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|termination of G-protein coupled receptor signaling pathway (GO:0038032)|transcription, DNA-templated (GO:0006351)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	GTPase activator activity (GO:0005096)|GTPase regulator activity (GO:0030695)|receptor signaling protein activity (GO:0005057)	p.M230T(1)		autonomic_ganglia(1)|breast(4)|endometrium(3)|kidney(2)|large_intestine(9)|lung(16)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	43				UCEC - Uterine corpus endometrioid carcinoma (64;0.168)		AACGTGGCGATGATCGTGGGC	0.493																																					p.M230T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T689C	4						.						81.0	75.0	77.0					4																	3318586		2203	4300	6503	3288384	SO:0001583	missense	6002	exon2			AF035152	CCDS3366.1, CCDS3367.1, CCDS3368.1	4p16.3	2008-02-05	2007-08-14		ENSG00000159788	ENSG00000159788		"""Regulators of G-protein signaling"""	9994	protein-coding gene	gene with protein product		602512	"""regulator of G-protein signalling 12"""			9651375	Standard	NM_198229		Approved		uc003ggw.3	O14924	OTTHUMG00000090277	ENST00000344733.5:c.689T>C	4.37:g.3318586T>C	ENSP00000339381:p.Met230Thr	Somatic		Capture	Illumina HiSeq	Phase_I	3288384	NM_002926	B1AQ30|B1AQ31|B1AQ32|B7Z764|E7EMN9|O14922|O14923|O43510|O75338|Q147X0|Q8WX95	Missense_Mutation	SNP	ENST00000344733.5	37	CCDS3366.1	.	.	.	.	.	.	.	.	.	.	T	12.74	2.027658	0.35797	.	.	ENSG00000159788	ENST00000543385;ENST00000344733;ENST00000336727;ENST00000382788	T;T;T;T	0.14022	2.54;2.54;2.54;2.54	4.54	4.54	0.55810	Phosphotyrosine interaction domain (2);Pleckstrin homology-type (1);	0.000000	0.85682	D	0.000000	T	0.29684	0.0741	L	0.58302	1.8	0.80722	D	1	P;D;D	0.69078	0.568;0.995;0.997	B;P;D	0.64321	0.147;0.829;0.924	T	0.01541	-1.1329	10	0.44086	T	0.13	-37.9993	13.0609	0.59005	0.0:0.0:0.0:1.0	.	230;230;230	Q8WX97;O14924;O14924-4	.;RGS12_HUMAN;.	T	230	ENSP00000440566:M230T;ENSP00000339381:M230T;ENSP00000338509:M230T;ENSP00000372238:M230T	ENSP00000338509:M230T	M	+	2	0	RGS12	3288384	1.000000	0.71417	0.998000	0.56505	0.052000	0.14988	7.744000	0.85034	1.684000	0.51022	0.402000	0.26972	ATG		0.493	RGS12-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000206602.1	NM_002926	
CRMP1	1400	broad.mit.edu	37	4	5857906	5857906	+	Missense_Mutation	SNP	C	C	T	rs386671024		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr4:5857906C>T	ENST00000397890.2	-	4	656	c.442G>A	c.(442-444)Gtt>Att	p.V148I	CRMP1_ENST00000512574.1_Missense_Mutation_p.V146I|CRMP1_ENST00000324989.7_Missense_Mutation_p.V262I|CRMP1_ENST00000511535.1_5'UTR	NM_001313.3	NP_001304.1	Q14194	DPYL1_HUMAN	collapsin response mediator protein 1	148					axon guidance (GO:0007411)|nervous system development (GO:0007399)|nucleobase-containing compound metabolic process (GO:0006139)|pyrimidine nucleobase catabolic process (GO:0006208)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|dendrite (GO:0030425)|neuronal cell body (GO:0043025)	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amides (GO:0016812)	p.V262I(1)		NS(1)|cervix(2)|endometrium(4)|large_intestine(10)|lung(11)|ovary(2)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	36				Colorectal(103;0.0721)		TCCTCCCGAACGCCATCGTAC	0.527																																					p.V148I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G442A	4						.						109.0	93.0	99.0					4																	5857906		2203	4300	6503	5908807	SO:0001583	missense	1400	exon4			D78012	CCDS33950.1, CCDS43207.1, CCDS75102.1	4p16.1	2008-05-15			ENSG00000072832	ENSG00000072832			2365	protein-coding gene	gene with protein product		602462				8973361	Standard	XM_005247940		Approved	DRP-1, DPYSL1	uc003gis.3	Q14194	OTTHUMG00000125489	ENST00000397890.2:c.442G>A	4.37:g.5857906C>T	ENSP00000380987:p.Val148Ile	Somatic		Capture	Illumina HiSeq	Phase_I	5908807	NM_001313	A0EJG6|Q13024|Q4W5F1|Q96TC8	Missense_Mutation	SNP	ENST00000397890.2	37	CCDS43207.1	.	.	.	.	.	.	.	.	.	.	c	11.80	1.747692	0.30955	.	.	ENSG00000072832	ENST00000324989;ENST00000397890;ENST00000534845;ENST00000512574	D;D;D	0.88046	-2.33;-2.33;-2.33	3.09	2.1	0.27182	Amidohydrolase 1 (1);Metal-dependent hydrolase, composite domain (1);	0.248007	0.33382	N	0.004966	T	0.75148	0.3810	N	0.25992	0.78	0.36987	D	0.894587	B;B;B;B	0.12013	0.0;0.005;0.0;0.0	B;B;B;B	0.17098	0.007;0.017;0.004;0.007	T	0.70230	-0.4929	10	0.33940	T	0.23	-13.9845	5.6222	0.17463	0.0:0.7478:0.0:0.2522	.	262;146;148;85	A0EJG6;E9PD68;Q14194;B3KT07	.;.;DPYL1_HUMAN;.	I	262;148;148;146	ENSP00000321606:V262I;ENSP00000380987:V148I;ENSP00000425742:V146I	ENSP00000321606:V262I	V	-	1	0	CRMP1	5908807	0.410000	0.25376	0.983000	0.44433	0.995000	0.86356	0.911000	0.28584	1.577000	0.49804	0.537000	0.68136	GTT		0.527	CRMP1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358871.1	NM_001313	
WFS1	7466	broad.mit.edu	37	4	6290749	6290749	+	Silent	SNP	G	G	A	rs200831572		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr4:6290749G>A	ENST00000226760.1	+	4	521	c.351G>A	c.(349-351)acG>acA	p.T117T	WFS1_ENST00000503569.1_Silent_p.T117T	NM_001145853.1|NM_006005.3	NP_001139325.1|NP_005996.2	O76024	WFS1_HUMAN	Wolfram syndrome 1 (wolframin)	117					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|calcium ion homeostasis (GO:0055074)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum calcium ion homeostasis (GO:0032469)|endoplasmic reticulum unfolded protein response (GO:0030968)|ER overload response (GO:0006983)|ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|glucose homeostasis (GO:0042593)|kidney development (GO:0001822)|negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway (GO:1902236)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of programmed cell death (GO:0043069)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of type B pancreatic cell apoptotic process (GO:2000675)|neurological system process (GO:0050877)|olfactory behavior (GO:0042048)|polyubiquitinated misfolded protein transport (GO:0070845)|positive regulation of calcium ion transport (GO:0051928)|positive regulation of growth (GO:0045927)|positive regulation of protein metabolic process (GO:0051247)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of proteolysis (GO:0045862)|protein maturation by protein folding (GO:0022417)|protein stabilization (GO:0050821)|renal water homeostasis (GO:0003091)|response to endoplasmic reticulum stress (GO:0034976)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of endoplasmic reticulum membrane (GO:0030176)	activating transcription factor binding (GO:0033613)|ATPase binding (GO:0051117)|transporter activity (GO:0005215)|ubiquitin protein ligase binding (GO:0031625)	p.T117T(1)		central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(6)|prostate(2)|skin(1)|stomach(1)|urinary_tract(1)	21				Colorectal(103;0.0512)		CCGGCGACACGGATGAAGAAC	0.652																																					p.T117T												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G351A	4						.						65.0	47.0	53.0					4																	6290749		2201	4299	6500	6341650	SO:0001819	synonymous_variant	7466	exon4			AF084481	CCDS3386.1	4p16.1	2014-06-18			ENSG00000109501	ENSG00000109501			12762	protein-coding gene	gene with protein product		606201		DFNA6, DFNA14, DFNA38		7987399, 9771706	Standard	NM_006005		Approved	DIDMOAD, WFS	uc003gix.3	O76024	OTTHUMG00000090431	ENST00000226760.1:c.351G>A	4.37:g.6290749G>A		Somatic		Capture	Illumina HiSeq	Phase_I	6341650	NM_001145853	B2R797|D3DVT1|Q8N6I3|Q9UNW6	Silent	SNP	ENST00000226760.1	37	CCDS3386.1																																																																																				0.652	WFS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206863.1		
WFS1	7466	broad.mit.edu	37	4	6293666	6293666	+	Silent	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr4:6293666C>T	ENST00000226760.1	+	6	824	c.654C>T	c.(652-654)ccC>ccT	p.P218P	WFS1_ENST00000503569.1_Silent_p.P218P	NM_001145853.1|NM_006005.3	NP_001139325.1|NP_005996.2	O76024	WFS1_HUMAN	Wolfram syndrome 1 (wolframin)	218					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|calcium ion homeostasis (GO:0055074)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum calcium ion homeostasis (GO:0032469)|endoplasmic reticulum unfolded protein response (GO:0030968)|ER overload response (GO:0006983)|ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|glucose homeostasis (GO:0042593)|kidney development (GO:0001822)|negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway (GO:1902236)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of programmed cell death (GO:0043069)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of type B pancreatic cell apoptotic process (GO:2000675)|neurological system process (GO:0050877)|olfactory behavior (GO:0042048)|polyubiquitinated misfolded protein transport (GO:0070845)|positive regulation of calcium ion transport (GO:0051928)|positive regulation of growth (GO:0045927)|positive regulation of protein metabolic process (GO:0051247)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of proteolysis (GO:0045862)|protein maturation by protein folding (GO:0022417)|protein stabilization (GO:0050821)|renal water homeostasis (GO:0003091)|response to endoplasmic reticulum stress (GO:0034976)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of endoplasmic reticulum membrane (GO:0030176)	activating transcription factor binding (GO:0033613)|ATPase binding (GO:0051117)|transporter activity (GO:0005215)|ubiquitin protein ligase binding (GO:0031625)	p.P218P(1)		central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(6)|prostate(2)|skin(1)|stomach(1)|urinary_tract(1)	21				Colorectal(103;0.0512)		AGCCAGGCCCCGTGCCCAAGT	0.652																																					p.P218P												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C654T	4						.						39.0	36.0	37.0					4																	6293666		2198	4298	6496	6344567	SO:0001819	synonymous_variant	7466	exon6			AF084481	CCDS3386.1	4p16.1	2014-06-18			ENSG00000109501	ENSG00000109501			12762	protein-coding gene	gene with protein product		606201		DFNA6, DFNA14, DFNA38		7987399, 9771706	Standard	NM_006005		Approved	DIDMOAD, WFS	uc003gix.3	O76024	OTTHUMG00000090431	ENST00000226760.1:c.654C>T	4.37:g.6293666C>T		Somatic		Capture	Illumina HiSeq	Phase_I	6344567	NM_001145853	B2R797|D3DVT1|Q8N6I3|Q9UNW6	Silent	SNP	ENST00000226760.1	37	CCDS3386.1	.	.	.	.	.	.	.	.	.	.	C	2.004	-0.428656	0.04701	.	.	ENSG00000109501	ENST00000506362	D	0.91894	-2.93	4.37	-8.75	0.00834	.	0.123185	0.56097	D	0.000033	D	0.89501	0.6733	.	.	.	0.42644	D	0.993426	.	.	.	.	.	.	D	0.84463	0.0595	7	0.45353	T	0.12	-18.6769	7.7201	0.28727	0.3911:0.4618:0.0:0.1471	.	.	.	.	L	84	ENSP00000424103:P84L	ENSP00000424103:P84L	P	+	2	0	WFS1	6344567	0.000000	0.05858	0.634000	0.29324	0.203000	0.24098	-5.357000	0.00128	-2.063000	0.00890	-0.415000	0.06103	CCG		0.652	WFS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206863.1		
MAN2B2	23324	broad.mit.edu	37	4	6588823	6588823	+	Silent	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr4:6588823G>A	ENST00000285599.3	+	4	528	c.492G>A	c.(490-492)gcG>gcA	p.A164A	MAN2B2_ENST00000504248.1_Silent_p.A164A	NM_015274.1	NP_056089.1	Q9Y2E5	MA2B2_HUMAN	mannosidase, alpha, class 2B, member 2	164					mannose metabolic process (GO:0006013)	extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)	alpha-mannosidase activity (GO:0004559)|carbohydrate binding (GO:0030246)|zinc ion binding (GO:0008270)	p.A164A(1)		breast(2)|cervix(2)|endometrium(4)|kidney(1)|large_intestine(3)|lung(9)|ovary(4)|prostate(2)|skin(2)|urinary_tract(1)	30						CCCTATTTGCGCTGGCGGGCT	0.632																																					p.A164A												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G492A	4						.						54.0	52.0	53.0					4																	6588823		2203	4300	6503	6639724	SO:0001819	synonymous_variant	23324	exon4			BC033307	CCDS33951.1	4p16.2	2005-11-09			ENSG00000013288	ENSG00000013288			29623	protein-coding gene	gene with protein product	"""core-specific lysosomal alpha-1,6-Mannosidase"""					10231032, 16115860	Standard	XR_241647		Approved	KIAA0935	uc003gjf.1	Q9Y2E5	OTTHUMG00000160073	ENST00000285599.3:c.492G>A	4.37:g.6588823G>A		Somatic		Capture	Illumina HiSeq	Phase_I	6639724	NM_015274	Q66MP2|Q86T67	Silent	SNP	ENST00000285599.3	37	CCDS33951.1	.	.	.	.	.	.	.	.	.	.	G	7.707	0.694379	0.15039	.	.	ENSG00000013288	ENST00000505907	.	.	.	4.09	-1.97	0.07503	.	.	.	.	.	T	0.41743	0.1172	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.29731	-1.0002	4	.	.	.	-26.4129	2.8761	0.05631	0.3369:0.3148:0.2605:0.0877	.	.	.	.	H	163	.	.	R	+	2	0	MAN2B2	6639724	0.976000	0.34144	0.932000	0.37286	0.441000	0.31987	0.045000	0.14013	-0.319000	0.08652	-0.236000	0.12185	CGC		0.632	MAN2B2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359106.2	NM_015274	
SLIT2	9353	broad.mit.edu	37	4	20525513	20525513	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr4:20525513G>A	ENST00000504154.1	+	13	1513	c.1261G>A	c.(1261-1263)Gcc>Acc	p.A421T	SLIT2_ENST00000503837.1_Missense_Mutation_p.A425T|SLIT2_ENST00000273739.5_Missense_Mutation_p.A425T|SLIT2_ENST00000503823.1_Missense_Mutation_p.A421T	NM_004787.1	NP_004778.1	O94813	SLIT2_HUMAN	slit homolog 2 (Drosophila)	421					apoptotic process involved in luteolysis (GO:0061364)|axon extension involved in axon guidance (GO:0048846)|axon guidance (GO:0007411)|branching morphogenesis of an epithelial tube (GO:0048754)|cell migration involved in sprouting angiogenesis (GO:0002042)|cellular response to heparin (GO:0071504)|cellular response to hormone stimulus (GO:0032870)|chemorepulsion involved in postnatal olfactory bulb interneuron migration (GO:0021836)|corticospinal neuron axon guidance through spinal cord (GO:0021972)|dorsal/ventral axon guidance (GO:0033563)|in utero embryonic development (GO:0001701)|induction of negative chemotaxis (GO:0050929)|mammary duct terminal end bud growth (GO:0060763)|metanephros development (GO:0001656)|motor neuron axon guidance (GO:0008045)|negative chemotaxis (GO:0050919)|negative regulation of actin filament polymerization (GO:0030837)|negative regulation of axon extension (GO:0030517)|negative regulation of catalytic activity (GO:0043086)|negative regulation of cell growth (GO:0030308)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cellular response to growth factor stimulus (GO:0090288)|negative regulation of chemokine-mediated signaling pathway (GO:0070100)|negative regulation of endothelial cell migration (GO:0010596)|negative regulation of gene expression (GO:0010629)|negative regulation of lamellipodium assembly (GO:0010593)|negative regulation of leukocyte chemotaxis (GO:0002689)|negative regulation of monocyte chemotaxis (GO:0090027)|negative regulation of mononuclear cell migration (GO:0071676)|negative regulation of neutrophil chemotaxis (GO:0090024)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of retinal ganglion cell axon guidance (GO:0090260)|negative regulation of small GTPase mediated signal transduction (GO:0051058)|negative regulation of smooth muscle cell chemotaxis (GO:0071672)|negative regulation of smooth muscle cell migration (GO:0014912)|negative regulation of vascular permeability (GO:0043116)|positive regulation of apoptotic process (GO:0043065)|positive regulation of axonogenesis (GO:0050772)|response to cortisol (GO:0051414)|retinal ganglion cell axon guidance (GO:0031290)|Roundabout signaling pathway (GO:0035385)|single organismal cell-cell adhesion (GO:0016337)|ureteric bud development (GO:0001657)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|chemorepellent activity (GO:0045499)|GTPase inhibitor activity (GO:0005095)|heparin binding (GO:0008201)|identical protein binding (GO:0042802)|laminin-1 binding (GO:0043237)|protein homodimerization activity (GO:0042803)|proteoglycan binding (GO:0043394)|Roundabout binding (GO:0048495)	p.A421T(1)		NS(1)|breast(4)|central_nervous_system(4)|cervix(1)|endometrium(5)|kidney(7)|large_intestine(17)|lung(60)|ovary(3)|pancreas(1)|prostate(2)|skin(10)|upper_aerodigestive_tract(1)	116						ACCTCTTCGGGCCATTCAAAC	0.418																																					p.A421T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1261A	4						.						159.0	149.0	152.0					4																	20525513		2203	4300	6503	20134611	SO:0001583	missense	9353	exon13			AF055585	CCDS3426.1, CCDS75110.1, CCDS75111.1	4p15.2	2008-08-01	2001-11-28		ENSG00000145147	ENSG00000145147			11086	protein-coding gene	gene with protein product		603746	"""slit (Drosophila) homolog 2"""	SLIL3		9813312, 18269211	Standard	XM_005248211		Approved	Slit-2	uc003gpr.1	O94813	OTTHUMG00000128551	ENST00000504154.1:c.1261G>A	4.37:g.20525513G>A	ENSP00000422591:p.Ala421Thr	Somatic		Capture	Illumina HiSeq	Phase_I	20134611	NM_004787	B7ZLR5|O95710|Q17RU3|Q9Y5Q7	Missense_Mutation	SNP	ENST00000504154.1	37	CCDS3426.1	.	.	.	.	.	.	.	.	.	.	G	22.8	4.335082	0.81801	.	.	ENSG00000145147	ENST00000503823;ENST00000504154;ENST00000273739;ENST00000382173;ENST00000503837	T;T;T;T	0.59224	0.28;0.28;0.28;0.28	5.3	5.3	0.74995	.	0.000000	0.85682	D	0.000000	T	0.55832	0.1945	N	0.17564	0.495	0.80722	D	1	P;P	0.49696	0.927;0.864	P;P	0.51453	0.67;0.509	T	0.62053	-0.6935	10	0.66056	D	0.02	.	19.3213	0.94240	0.0:0.0:1.0:0.0	.	421;421	O94813-3;O94813	.;SLIT2_HUMAN	T	421;421;425;425;425	ENSP00000427548:A421T;ENSP00000422591:A421T;ENSP00000273739:A425T;ENSP00000422261:A425T	ENSP00000273739:A425T	A	+	1	0	SLIT2	20134611	1.000000	0.71417	1.000000	0.80357	0.839000	0.47603	4.352000	0.59404	2.635000	0.89317	0.650000	0.86243	GCC		0.418	SLIT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250396.2		
SLIT2	9353	broad.mit.edu	37	4	20535200	20535200	+	Missense_Mutation	SNP	T	T	G			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr4:20535200T>G	ENST00000504154.1	+	18	1946	c.1694T>G	c.(1693-1695)tTt>tGt	p.F565C	SLIT2_ENST00000503837.1_Missense_Mutation_p.F561C|SLIT2_ENST00000273739.5_Missense_Mutation_p.F569C|SLIT2_ENST00000503823.1_Missense_Mutation_p.F557C	NM_004787.1	NP_004778.1	O94813	SLIT2_HUMAN	slit homolog 2 (Drosophila)	565					apoptotic process involved in luteolysis (GO:0061364)|axon extension involved in axon guidance (GO:0048846)|axon guidance (GO:0007411)|branching morphogenesis of an epithelial tube (GO:0048754)|cell migration involved in sprouting angiogenesis (GO:0002042)|cellular response to heparin (GO:0071504)|cellular response to hormone stimulus (GO:0032870)|chemorepulsion involved in postnatal olfactory bulb interneuron migration (GO:0021836)|corticospinal neuron axon guidance through spinal cord (GO:0021972)|dorsal/ventral axon guidance (GO:0033563)|in utero embryonic development (GO:0001701)|induction of negative chemotaxis (GO:0050929)|mammary duct terminal end bud growth (GO:0060763)|metanephros development (GO:0001656)|motor neuron axon guidance (GO:0008045)|negative chemotaxis (GO:0050919)|negative regulation of actin filament polymerization (GO:0030837)|negative regulation of axon extension (GO:0030517)|negative regulation of catalytic activity (GO:0043086)|negative regulation of cell growth (GO:0030308)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cellular response to growth factor stimulus (GO:0090288)|negative regulation of chemokine-mediated signaling pathway (GO:0070100)|negative regulation of endothelial cell migration (GO:0010596)|negative regulation of gene expression (GO:0010629)|negative regulation of lamellipodium assembly (GO:0010593)|negative regulation of leukocyte chemotaxis (GO:0002689)|negative regulation of monocyte chemotaxis (GO:0090027)|negative regulation of mononuclear cell migration (GO:0071676)|negative regulation of neutrophil chemotaxis (GO:0090024)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of retinal ganglion cell axon guidance (GO:0090260)|negative regulation of small GTPase mediated signal transduction (GO:0051058)|negative regulation of smooth muscle cell chemotaxis (GO:0071672)|negative regulation of smooth muscle cell migration (GO:0014912)|negative regulation of vascular permeability (GO:0043116)|positive regulation of apoptotic process (GO:0043065)|positive regulation of axonogenesis (GO:0050772)|response to cortisol (GO:0051414)|retinal ganglion cell axon guidance (GO:0031290)|Roundabout signaling pathway (GO:0035385)|single organismal cell-cell adhesion (GO:0016337)|ureteric bud development (GO:0001657)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|chemorepellent activity (GO:0045499)|GTPase inhibitor activity (GO:0005095)|heparin binding (GO:0008201)|identical protein binding (GO:0042802)|laminin-1 binding (GO:0043237)|protein homodimerization activity (GO:0042803)|proteoglycan binding (GO:0043394)|Roundabout binding (GO:0048495)	p.F565C(1)		NS(1)|breast(4)|central_nervous_system(4)|cervix(1)|endometrium(5)|kidney(7)|large_intestine(17)|lung(60)|ovary(3)|pancreas(1)|prostate(2)|skin(10)|upper_aerodigestive_tract(1)	116						TTTAGAAACTTTAGCAACAAT	0.313																																					p.F565C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T1694G	4						.						63.0	65.0	64.0					4																	20535200		2203	4300	6503	20144298	SO:0001583	missense	9353	exon18			AF055585	CCDS3426.1, CCDS75110.1, CCDS75111.1	4p15.2	2008-08-01	2001-11-28		ENSG00000145147	ENSG00000145147			11086	protein-coding gene	gene with protein product		603746	"""slit (Drosophila) homolog 2"""	SLIL3		9813312, 18269211	Standard	XM_005248211		Approved	Slit-2	uc003gpr.1	O94813	OTTHUMG00000128551	ENST00000504154.1:c.1694T>G	4.37:g.20535200T>G	ENSP00000422591:p.Phe565Cys	Somatic		Capture	Illumina HiSeq	Phase_I	20144298	NM_004787	B7ZLR5|O95710|Q17RU3|Q9Y5Q7	Missense_Mutation	SNP	ENST00000504154.1	37	CCDS3426.1	.	.	.	.	.	.	.	.	.	.	T	22.0	4.231060	0.79688	.	.	ENSG00000145147	ENST00000503823;ENST00000504154;ENST00000273739;ENST00000382173;ENST00000503837	T;T;T;T	0.58358	0.34;0.34;0.34;0.34	5.5	5.5	0.81552	.	0.116668	0.64402	D	0.000011	T	0.58032	0.2094	L	0.27053	0.805	0.43798	D	0.996345	D;D	0.58620	0.979;0.983	P;P	0.59948	0.789;0.866	T	0.63152	-0.6701	10	0.87932	D	0	.	15.6063	0.76676	0.0:0.0:0.0:1.0	.	557;565	O94813-3;O94813	.;SLIT2_HUMAN	C	557;565;569;561;561	ENSP00000427548:F557C;ENSP00000422591:F565C;ENSP00000273739:F569C;ENSP00000422261:F561C	ENSP00000273739:F569C	F	+	2	0	SLIT2	20144298	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	7.942000	0.87708	2.098000	0.63641	0.533000	0.62120	TTT		0.313	SLIT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250396.2		
PPARGC1A	10891	broad.mit.edu	37	4	23833222	23833222	+	Silent	SNP	A	A	G			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr4:23833222A>G	ENST00000264867.2	-	3	506	c.387T>C	c.(385-387)ccT>ccC	p.P129P	PPARGC1A_ENST00000509702.1_5'UTR	NM_013261.3	NP_037393.1	Q9UBK2	PRGC1_HUMAN	peroxisome proliferator-activated receptor gamma, coactivator 1 alpha	129					androgen metabolic process (GO:0008209)|androgen receptor signaling pathway (GO:0030521)|brown fat cell differentiation (GO:0050873)|cellular glucose homeostasis (GO:0001678)|cellular respiration (GO:0045333)|cellular response to fatty acid (GO:0071398)|cellular response to hypoxia (GO:0071456)|cellular response to nitrite (GO:0071250)|cellular response to oxidative stress (GO:0034599)|cellular response to thyroid hormone stimulus (GO:0097067)|cellular response to tumor necrosis factor (GO:0071356)|circadian regulation of gene expression (GO:0032922)|digestion (GO:0007586)|fatty acid oxidation (GO:0019395)|flavone metabolic process (GO:0051552)|galactose metabolic process (GO:0006012)|gluconeogenesis (GO:0006094)|mitochondrion organization (GO:0007005)|mRNA processing (GO:0006397)|negative regulation of glycolytic process (GO:0045820)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of neuron death (GO:1901215)|negative regulation of receptor activity (GO:2000272)|positive regulation of ATP biosynthetic process (GO:2001171)|positive regulation of cellular respiration (GO:1901857)|positive regulation of energy homeostasis (GO:2000507)|positive regulation of fatty acid oxidation (GO:0046321)|positive regulation of gluconeogenesis (GO:0045722)|positive regulation of histone acetylation (GO:0035066)|positive regulation of mitochondrial DNA metabolic process (GO:1901860)|positive regulation of mitochondrion organization (GO:0010822)|positive regulation of muscle tissue development (GO:1901863)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of smooth muscle cell proliferation (GO:0048661)|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 stabilization (GO:0050821)|regulation of circadian rhythm (GO:0042752)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|regulation of transcription, DNA-templated (GO:0006355)|respiratory electron transport chain (GO:0022904)|response to cold (GO:0009409)|response to epinephrine (GO:0071871)|response to leucine (GO:0043201)|response to muscle activity (GO:0014850)|response to norepinephrine (GO:0071873)|response to starvation (GO:0042594)|response to statin (GO:0036273)|RNA splicing (GO:0008380)|temperature homeostasis (GO:0001659)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cytosol (GO:0005829)|DNA-directed RNA polymerase II, core complex (GO:0005665)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	androgen receptor binding (GO:0050681)|chromatin DNA binding (GO:0031490)|DNA binding (GO:0003677)|ligand-dependent nuclear receptor binding (GO:0016922)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|nucleotide binding (GO:0000166)|RNA binding (GO:0003723)|RNA polymerase II transcription cofactor activity (GO:0001104)|sequence-specific DNA binding (GO:0043565)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|ubiquitin protein ligase binding (GO:0031625)	p.P129P(1)		central_nervous_system(1)|endometrium(7)|kidney(3)|large_intestine(7)|liver(1)|lung(24)|ovary(3)|skin(5)	51		Breast(46;0.0503)				GGGTGCCGTCAGGCATGGAGG	0.552																																					p.P129P	Esophageal Squamous(29;694 744 13796 34866 44181)											.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.T387C	4						.						292.0	233.0	253.0					4																	23833222		2203	4300	6503	23442320	SO:0001819	synonymous_variant	10891	exon3			AF106698	CCDS3429.1	4p15.1	2013-02-12	2006-10-17	2004-02-04	ENSG00000109819	ENSG00000109819		"""RNA binding motif (RRM) containing"""	9237	protein-coding gene	gene with protein product		604517	"""peroxisome proliferative activated receptor, gamma, coactivator 1"", ""peroxisome proliferative activated receptor, gamma, coactivator 1, alpha"""	PPARGC1		10585775	Standard	NM_013261		Approved	PGC1, PGC1A	uc003gqs.3	Q9UBK2	OTTHUMG00000097747	ENST00000264867.2:c.387T>C	4.37:g.23833222A>G		Somatic		Capture	Illumina HiSeq	Phase_I	23442320	NM_013261	B7Z406|G8DM16|I3RTT5|I3RTT6|I3RTT7|I3RTT8|I3RTT9|Q3LIG1|Q4W5M7|Q9UN32	Silent	SNP	ENST00000264867.2	37	CCDS3429.1																																																																																				0.552	PPARGC1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214976.1	NM_013261	
COX7B2	170712	broad.mit.edu	37	4	46737005	46737005	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr4:46737005G>T	ENST00000396533.1	-	4	455	c.205C>A	c.(205-207)Cct>Act	p.P69T	COX7B2_ENST00000355591.3_Missense_Mutation_p.P69T|COX7B2_ENST00000543208.1_Missense_Mutation_p.P68T|COX7B2_ENST00000302930.5_Missense_Mutation_p.P69T			Q8TF08	CX7B2_HUMAN	cytochrome c oxidase subunit VIIb2	69						integral component of membrane (GO:0016021)|mitochondrial respiratory chain (GO:0005746)	cytochrome-c oxidase activity (GO:0004129)	p.P68T(1)		large_intestine(1)|lung(4)	5						CTGCCAACAGGGGATAGGTTC	0.413																																					p.P69T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C205A	4						.						120.0	108.0	112.0					4																	46737005		2203	4300	6503	46431762	SO:0001583	missense	170712	exon3			AF125109	CCDS3472.2	4p12	2011-07-04			ENSG00000170516	ENSG00000170516		"""Mitochondrial respiratory chain complex / Complex IV"""	24381	protein-coding gene	gene with protein product		609811				15623157	Standard	NM_130902		Approved		uc003gxf.3	Q8TF08	OTTHUMG00000099423	ENST00000396533.1:c.205C>A	4.37:g.46737005G>T	ENSP00000379784:p.Pro69Thr	Somatic		Capture	Illumina HiSeq	Phase_I	46431762	NM_130902	Q32Q40	Missense_Mutation	SNP	ENST00000396533.1	37	CCDS3472.2	.	.	.	.	.	.	.	.	.	.	G	17.20	3.329206	0.60743	.	.	ENSG00000170516	ENST00000355591;ENST00000396533;ENST00000302930;ENST00000543208	T;T;T;T	0.65549	-0.16;-0.16;-0.16;-0.16	4.57	3.73	0.42828	Cytochrome C oxidase, subunit VIIB, domain (2);	0.057250	0.64402	D	0.000001	T	0.72724	0.3496	.	.	.	0.34097	D	0.661437	D	0.63880	0.993	D	0.64595	0.927	T	0.80294	-0.1443	9	0.59425	D	0.04	-17.8679	8.5104	0.33213	0.1027:0.0:0.8973:0.0	.	69	Q8TF08	CX7B2_HUMAN	T	69;69;69;68	ENSP00000347799:P69T;ENSP00000379784:P69T;ENSP00000305964:P69T;ENSP00000437439:P68T	ENSP00000305964:P69T	P	-	1	0	COX7B2	46431762	1.000000	0.71417	1.000000	0.80357	0.970000	0.65996	4.603000	0.61105	1.535000	0.49220	0.585000	0.79938	CCT		0.413	COX7B2-002	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000313899.1	NM_130902	
TXK	7294	broad.mit.edu	37	4	48069667	48069667	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr4:48069667G>A	ENST00000264316.4	-	15	1656	c.1571C>T	c.(1570-1572)gCg>gTg	p.A524V	TXK_ENST00000507351.1_Missense_Mutation_p.A179V	NM_003328.2	NP_003319.2	P42681	TXK_HUMAN	TXK tyrosine kinase	524	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of phospholipase C activity (GO:0007202)|adaptive immune response (GO:0002250)|cytokine production (GO:0001816)|interferon-gamma production (GO:0032609)|interleukin-4 production (GO:0032633)|NK T cell differentiation (GO:0001865)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interferon-gamma-mediated signaling pathway (GO:0060335)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|T cell receptor signaling pathway (GO:0050852)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|RNA polymerase II regulatory region DNA binding (GO:0001012)	p.A524V(1)		breast(2)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(11)|prostate(2)	25						CCAGGTTTCCGCAATCTCTGT	0.488																																					p.A524V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1571T	4						.						118.0	123.0	122.0					4																	48069667		2203	4300	6503	47764424	SO:0001583	missense	7294	exon15			L27071	CCDS3480.1	4p12	2013-02-14	2003-04-01		ENSG00000074966	ENSG00000074966	2.7.10.1	"""SH2 domain containing"""	12434	protein-coding gene	gene with protein product		600058	"""PTK4 protein tyrosine kinase 4"""	PTK4		7951233, 7528718	Standard	NM_003328		Approved	TKL, PSCTK5, BTKL, RLK	uc003gxx.4	P42681	OTTHUMG00000102065	ENST00000264316.4:c.1571C>T	4.37:g.48069667G>A	ENSP00000264316:p.Ala524Val	Somatic		Capture	Illumina HiSeq	Phase_I	47764424	NM_003328	Q14220	Missense_Mutation	SNP	ENST00000264316.4	37	CCDS3480.1	.	.	.	.	.	.	.	.	.	.	G	1.970	-0.436694	0.04636	.	.	ENSG00000074966	ENST00000264316;ENST00000507351	T;T	0.74421	-0.84;-0.83	4.95	4.95	0.65309	Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.154302	0.42821	D	0.000650	T	0.48607	0.1509	N	0.05441	-0.05	0.35991	D	0.836725	B;B	0.31949	0.158;0.348	B;B	0.09377	0.002;0.004	T	0.59862	-0.7374	10	0.62326	D	0.03	.	7.9169	0.29822	0.1387:0.0:0.8613:0.0	.	211;524	B4DTB5;P42681	.;TXK_HUMAN	V	524;179	ENSP00000264316:A524V;ENSP00000423481:A179V	ENSP00000264316:A524V	A	-	2	0	TXK	47764424	0.974000	0.33945	0.941000	0.38009	0.040000	0.13550	3.303000	0.51858	2.733000	0.93635	0.561000	0.74099	GCG		0.488	TXK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219869.7	NM_003328	
FRYL	285527	broad.mit.edu	37	4	48542543	48542543	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr4:48542543C>T	ENST00000503238.1	-	43	6121	c.6122G>A	c.(6121-6123)cGa>cAa	p.R2041Q	FRYL_ENST00000358350.4_Missense_Mutation_p.R2041Q|FRYL_ENST00000264319.7_5'UTR|FRYL_ENST00000537810.1_Missense_Mutation_p.R2041Q|FRYL_ENST00000507873.2_5'UTR			O94915	FRYL_HUMAN	FRY-like	2041					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)			p.R2041Q(1)		breast(2)|central_nervous_system(2)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(21)|lung(38)|ovary(1)|pancreas(1)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	91						AATCTTCTCTCGACTCTCTGA	0.378																																					p.R2041Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G6122A	4						.						105.0	95.0	98.0					4																	48542543		1845	4087	5932	48237300	SO:0001583	missense	285527	exon46			AL833170	CCDS43227.1	4p12	2011-08-03	2006-11-17	2005-11-24	ENSG00000075539	ENSG00000075539			29127	protein-coding gene	gene with protein product			"""KIAA0826"", ""furry homolog-like (Drosophila)"""	KIAA0826		10048485	Standard	NM_015030		Approved	DKFZp686E205	uc003gyh.1	O94915	OTTHUMG00000160608	ENST00000503238.1:c.6122G>A	4.37:g.48542543C>T	ENSP00000426064:p.Arg2041Gln	Somatic		Capture	Illumina HiSeq	Phase_I	48237300	NM_015030	O95640|Q8WTZ5|Q9NT40	Missense_Mutation	SNP	ENST00000503238.1	37	CCDS43227.1	.	.	.	.	.	.	.	.	.	.	C	20.4	3.976084	0.74360	.	.	ENSG00000075539	ENST00000503238;ENST00000358350;ENST00000537810	T;T;T	0.32023	1.47;1.47;1.47	6.16	6.16	0.99307	Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.56292	0.1975	M	0.67397	2.05	0.80722	D	1	D;D;D	0.76494	0.999;0.999;0.997	D;D;D	0.80764	0.994;0.971;0.913	T	0.35919	-0.9769	10	0.29301	T	0.29	.	20.8598	0.99761	0.0:1.0:0.0:0.0	.	871;2041;2041	Q6ZR29;O94915;F5GX82	.;FRYL_HUMAN;.	Q	2041	ENSP00000426064:R2041Q;ENSP00000351113:R2041Q;ENSP00000441114:R2041Q	ENSP00000351113:R2041Q	R	-	2	0	FRYL	48237300	1.000000	0.71417	1.000000	0.80357	0.065000	0.16274	7.750000	0.85110	2.937000	0.99478	0.650000	0.86243	CGA		0.378	FRYL-011	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000369265.2		
PDGFRA	5156	broad.mit.edu	37	4	55155225	55155225	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr4:55155225T>C	ENST00000257290.5	+	21	3155	c.2824T>C	c.(2824-2826)Tcc>Ccc	p.S942P	FIP1L1_ENST00000507166.1_Missense_Mutation_p.S702P	NM_006206.4	NP_006197.1	P16234	PGFRA_HUMAN	platelet-derived growth factor receptor, alpha polypeptide	942	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				adrenal gland development (GO:0030325)|cardiac myofibril assembly (GO:0055003)|cell activation (GO:0001775)|cell chemotaxis (GO:0060326)|cellular response to amino acid stimulus (GO:0071230)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic skeletal system morphogenesis (GO:0048704)|epidermal growth factor receptor signaling pathway (GO:0007173)|estrogen metabolic process (GO:0008210)|extracellular matrix organization (GO:0030198)|face morphogenesis (GO:0060325)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|hematopoietic progenitor cell differentiation (GO:0002244)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|Leydig cell differentiation (GO:0033327)|lung development (GO:0030324)|luteinization (GO:0001553)|male genitalia development (GO:0030539)|metanephric glomerular capillary formation (GO:0072277)|negative regulation of platelet activation (GO:0010544)|neurotrophin TRK receptor signaling pathway (GO:0048011)|odontogenesis of dentin-containing tooth (GO:0042475)|palate development (GO:0060021)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|platelet aggregation (GO:0070527)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|platelet-derived growth factor receptor-alpha signaling pathway (GO:0035790)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell proliferation by VEGF-activated platelet derived growth factor receptor signaling pathway (GO:0038091)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of DNA replication (GO:0045740)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of fibroblast proliferation (GO:0048146)|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)|protein autophosphorylation (GO:0046777)|regulation of actin cytoskeleton reorganization (GO:2000249)|regulation of chemotaxis (GO:0050920)|regulation of mesenchymal stem cell differentiation (GO:2000739)|retina vasculature development in camera-type eye (GO:0061298)|signal transduction involved in regulation of gene expression (GO:0023019)|viral process (GO:0016032)|wound healing (GO:0042060)	cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|intrinsic component of plasma membrane (GO:0031226)|membrane (GO:0016020)|microvillus (GO:0005902)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|platelet-derived growth factor alpha-receptor activity (GO:0005018)|platelet-derived growth factor binding (GO:0048407)|platelet-derived growth factor receptor binding (GO:0005161)|protein homodimerization activity (GO:0042803)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|vascular endothelial growth factor binding (GO:0038085)|vascular endothelial growth factor-activated receptor activity (GO:0005021)	p.S942P(1)		NS(1)|autonomic_ganglia(1)|bone(1)|breast(4)|central_nervous_system(17)|cervix(1)|endometrium(4)|eye(1)|gastrointestinal_tract_(site_indeterminate)(1)|haematopoietic_and_lymphoid_tissue(22)|kidney(6)|large_intestine(26)|liver(4)|lung(48)|ovary(4)|prostate(6)|skin(11)|small_intestine(49)|soft_tissue(727)|stomach(32)|urinary_tract(1)	967	all_cancers(7;0.000425)|all_lung(4;0.000343)|Lung NSC(11;0.000467)|all_epithelial(27;0.0131)|all_neural(26;0.0209)|Glioma(25;0.08)		GBM - Glioblastoma multiforme(1;4.18e-71)|all cancers(1;4.76e-45)|LUSC - Lung squamous cell carcinoma(32;0.00256)		Becaplermin(DB00102)|Imatinib(DB00619)|Pazopanib(DB06589)|Ponatinib(DB08901)|Regorafenib(DB08896)|Sunitinib(DB01268)	GAAGAGACCCTCCTTTTACCA	0.512			"""Mis, O, T"""	FIP1L1	"""GIST, idiopathic hypereosinophilic syndrome, paediatric GBM"""				Gastrointestinal Stromal Tumors, Sporadic Multiple Primary;Familial Intestinal Neurofibromatosis	TSP Lung(21;0.16)																											p.S942P	Pancreas(151;208 1913 7310 23853 37092)		Dom	yes		4	4q11-q13	5156	"""platelet-derived growth factor, alpha-receptor"""		"""L, M, O"""	.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T2824C	4						.						173.0	163.0	167.0					4																	55155225		2203	4300	6503	54849982	SO:0001583	missense	5156	exon21	Familial Cancer Database	Sporadic Multiple GIST;Familial Intestinal Stromal Tumors, NF3B, subset of Familial GIST,	D50001	CCDS3495.1	4q12	2014-09-17			ENSG00000134853	ENSG00000134853		"""CD molecules"", ""Immunoglobulin superfamily / I-set domain containing"""	8803	protein-coding gene	gene with protein product		173490					Standard	NM_006206		Approved	CD140a, PDGFR2	uc003han.4	P16234	OTTHUMG00000128699	ENST00000257290.5:c.2824T>C	4.37:g.55155225T>C	ENSP00000257290:p.Ser942Pro	Somatic		Capture	Illumina HiSeq	Phase_I	54849982	NM_006206	B2RE69|E9PBH0|Q6P4H5|Q96KZ7|Q9UD28	Missense_Mutation	SNP	ENST00000257290.5	37	CCDS3495.1	.	.	.	.	.	.	.	.	.	.	T	17.25	3.341147	0.60963	.	.	ENSG00000145216;ENSG00000134853	ENST00000507166;ENST00000257290	D;D	0.90732	-2.72;-2.72	6.07	6.07	0.98685	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.000000	0.31922	U	0.006854	D	0.93562	0.7945	L	0.55743	1.74	0.80722	D	1	D	0.89917	1.0	D	0.74023	0.982	D	0.92050	0.5647	10	0.27785	T	0.31	.	16.3021	0.82825	0.0:0.0:0.0:1.0	.	942	P16234	PGFRA_HUMAN	P	702;942	ENSP00000423325:S702P;ENSP00000257290:S942P	ENSP00000423325:S702P	S	+	1	0	FIP1L1;PDGFRA	54849982	0.999000	0.42202	1.000000	0.80357	0.974000	0.67602	4.077000	0.57598	2.326000	0.78906	0.533000	0.62120	TCC		0.512	PDGFRA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250598.2	NM_006206	
SRD5A3	79644	broad.mit.edu	37	4	56230247	56230247	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr4:56230247A>G	ENST00000264228.4	+	3	599	c.371A>G	c.(370-372)gAg>gGg	p.E124G	SRD5A3-AS1_ENST00000596312.1_RNA|SRD5A3-AS1_ENST00000609700.1_RNA|SRD5A3-AS1_ENST00000609573.1_RNA|SRD5A3-AS1_ENST00000609580.1_RNA|SRD5A3-AS1_ENST00000595103.1_RNA|SRD5A3-AS1_ENST00000609487.1_RNA|SRD5A3-AS1_ENST00000596289.1_RNA|SRD5A3-AS1_ENST00000608086.1_RNA|SRD5A3-AS1_ENST00000608265.1_RNA|SRD5A3-AS1_ENST00000609051.1_RNA|SRD5A3-AS1_ENST00000608558.1_RNA|SRD5A3_ENST00000514398.1_3'UTR|SRD5A3-AS1_ENST00000595734.1_RNA|SRD5A3-AS1_ENST00000598906.1_RNA|SRD5A3-AS1_ENST00000609500.1_RNA|SRD5A3-AS1_ENST00000510637.1_RNA|SRD5A3-AS1_ENST00000433175.2_RNA	NM_024592.4	NP_078868.1	Q9H8P0	PORED_HUMAN	steroid 5 alpha-reductase 3	124					androgen biosynthetic process (GO:0006702)|cellular protein metabolic process (GO:0044267)|dolichol metabolic process (GO:0019348)|dolichol-linked oligosaccharide biosynthetic process (GO:0006488)|dolichyl diphosphate biosynthetic process (GO:0006489)|polyprenol catabolic process (GO:0016095)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	3-oxo-5-alpha-steroid 4-dehydrogenase activity (GO:0003865)|cholestenone 5-alpha-reductase activity (GO:0047751)|oxidoreductase activity, acting on the CH-CH group of donors, NAD or NADP as acceptor (GO:0016628)	p.E124G(1)		cervix(1)|large_intestine(3)|lung(6)|prostate(1)|skin(1)	12	all_cancers(7;0.0308)|all_lung(4;0.00195)|Lung NSC(11;0.00431)|all_epithelial(27;0.0425)|Glioma(25;0.08)|all_neural(26;0.101)		Epithelial(7;0.0179)		Spironolactone(DB00421)	GTAGGAGGGGAGCTGGCACTG	0.438																																					p.E124G												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A371G	4						.						218.0	200.0	206.0					4																	56230247		2203	4300	6503	55925004	SO:0001583	missense	79644	exon3			AK023414	CCDS3498.1	4q12	2009-07-21			ENSG00000128039	ENSG00000128039			25812	protein-coding gene	gene with protein product		611715				17986282	Standard	NM_024592		Approved	FLJ13352, SRD5A2L, SRD5A2L1	uc003hau.3	Q9H8P0	OTTHUMG00000128733	ENST00000264228.4:c.371A>G	4.37:g.56230247A>G	ENSP00000264228:p.Glu124Gly	Somatic		Capture	Illumina HiSeq	Phase_I	55925004	NM_024592	Q4W5Q6	Missense_Mutation	SNP	ENST00000264228.4	37	CCDS3498.1	.	.	.	.	.	.	.	.	.	.	A	12.05	1.822442	0.32237	.	.	ENSG00000128039	ENST00000264228	T	0.38560	1.13	5.48	5.48	0.80851	.	0.450957	0.24132	N	0.041251	T	0.40595	0.1123	M	0.63428	1.95	0.54753	D	0.999989	B	0.02656	0.0	B	0.01281	0.0	T	0.22173	-1.0224	10	0.23891	T	0.37	-23.5158	13.3131	0.60390	1.0:0.0:0.0:0.0	.	124	Q9H8P0	PORED_HUMAN	G	124	ENSP00000264228:E124G	ENSP00000264228:E124G	E	+	2	0	SRD5A3	55925004	0.996000	0.38824	0.984000	0.44739	0.051000	0.14879	1.069000	0.30641	2.084000	0.62774	0.459000	0.35465	GAG		0.438	SRD5A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250644.2	NM_024592	
CLOCK	9575	broad.mit.edu	37	4	56345063	56345063	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr4:56345063A>G	ENST00000309964.4	-	5	425	c.175T>C	c.(175-177)Tcc>Ccc	p.S59P	CLOCK_ENST00000513440.1_Missense_Mutation_p.S59P|CLOCK_ENST00000506923.1_5'UTR|CLOCK_ENST00000381322.1_Missense_Mutation_p.S59P	NM_004898.3	NP_004889.1	O15516	CLOCK_HUMAN	clock circadian regulator	59	bHLH. {ECO:0000255|PROSITE- ProRule:PRU00981}.				cellular response to ionizing radiation (GO:0071479)|chromatin organization (GO:0006325)|circadian regulation of gene expression (GO:0032922)|circadian rhythm (GO:0007623)|DNA damage checkpoint (GO:0000077)|histone acetylation (GO:0016573)|negative regulation of glucocorticoid receptor signaling pathway (GO:2000323)|negative regulation of transcription, DNA-templated (GO:0045892)|photoperiodism (GO:0009648)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|regulation of hair cycle (GO:0042634)|regulation of insulin secretion (GO:0050796)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|regulation of type B pancreatic cell development (GO:2000074)|response to redox state (GO:0051775)|signal transduction (GO:0007165)|spermatogenesis (GO:0007283)	chromatoid body (GO:0033391)|chromosome (GO:0005694)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	chromatin DNA binding (GO:0031490)|core promoter binding (GO:0001047)|DNA binding (GO:0003677)|E-box binding (GO:0070888)|histone acetyltransferase activity (GO:0004402)|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 (GO:0000982)|RNA polymerase II transcription factor binding transcription factor activity involved in positive regulation of transcription (GO:0001190)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)	p.S59P(1)		breast(1)|central_nervous_system(3)|cervix(1)|endometrium(4)|kidney(5)|large_intestine(9)|lung(8)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	38	Lung NSC(11;0.00335)|Glioma(25;0.08)|all_epithelial(27;0.0992)|all_neural(26;0.101)		LUSC - Lung squamous cell carcinoma(4;1.62e-07)|Lung(4;1.34e-06)|Epithelial(7;0.0107)			ggaagcatggatcccagttct	0.299																																					p.S59P												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T175C	4						.						61.0	61.0	61.0					4																	56345063		2202	4299	6501	56039820	SO:0001583	missense	9575	exon6			AF011568	CCDS3500.1	4q12	2012-12-07	2012-12-07		ENSG00000134852	ENSG00000134852		"""Chromatin-modifying enzymes / K-acetyltransferases"", ""Basic helix-loop-helix proteins"""	2082	protein-coding gene	gene with protein product		601851	"""clock (mouse) homolog"", ""clock homolog (mouse)"""			10198158	Standard	NM_001267843		Approved	KIAA0334, KAT13D, bHLHe8	uc003hba.2	O15516	OTTHUMG00000102141	ENST00000309964.4:c.175T>C	4.37:g.56345063A>G	ENSP00000308741:p.Ser59Pro	Somatic		Capture	Illumina HiSeq	Phase_I	56039820	NM_004898	A0AV01|A2I2N9|O14516|Q9UIT8	Missense_Mutation	SNP	ENST00000309964.4	37	CCDS3500.1	.	.	.	.	.	.	.	.	.	.	A	27.7	4.855202	0.91355	.	.	ENSG00000134852	ENST00000309964;ENST00000381322;ENST00000513440	D;D;D	0.98120	-4.73;-4.73;-4.73	6.07	6.07	0.98685	Helix-loop-helix DNA-binding (5);	0.153499	0.64402	D	0.000012	D	0.98257	0.9423	M	0.71036	2.16	0.58432	D	0.99999	P	0.52842	0.956	P	0.59825	0.864	D	0.99174	1.0865	10	0.87932	D	0	.	16.6406	0.85098	1.0:0.0:0.0:0.0	.	59	O15516	CLOCK_HUMAN	P	59	ENSP00000308741:S59P;ENSP00000370723:S59P;ENSP00000426983:S59P	ENSP00000308741:S59P	S	-	1	0	CLOCK	56039820	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.995000	0.70631	2.326000	0.78906	0.533000	0.62120	TCC		0.299	CLOCK-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361993.2	NM_004898	
KIAA1211	57482	broad.mit.edu	37	4	57181042	57181042	+	Silent	SNP	C	C	T	rs543789864		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr4:57181042C>T	ENST00000504228.1	+	6	1479	c.1374C>T	c.(1372-1374)gcC>gcT	p.A458A	KIAA1211_ENST00000541073.1_Silent_p.A451A|KIAA1211_ENST00000264229.6_Silent_p.A458A			Q6ZU35	K1211_HUMAN	KIAA1211	458	Glu-rich.							p.A458A(1)		endometrium(7)|large_intestine(10)|lung(39)|ovary(2)|prostate(3)|skin(3)|stomach(1)	65	Glioma(25;0.08)|all_neural(26;0.101)					ACCCAGAGGCCGAGCGGCGAA	0.607																																					p.A458A												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1374T	4						.						26.0	35.0	32.0					4																	57181042		1999	4170	6169	56875799	SO:0001819	synonymous_variant	57482	exon8			AB033037	CCDS43230.1	4q12	2012-08-03			ENSG00000109265	ENSG00000109265			29219	protein-coding gene	gene with protein product						10574462, 11230166	Standard	NM_020722		Approved		uc003hbk.2	Q6ZU35	OTTHUMG00000160749	ENST00000504228.1:c.1374C>T	4.37:g.57181042C>T		Somatic		Capture	Illumina HiSeq	Phase_I	56875799	NM_020722	Q9NTE2|Q9NTP8|Q9ULK9	Silent	SNP	ENST00000504228.1	37	CCDS43230.1																																																																																				0.607	KIAA1211-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362097.2	NM_020722	
AASDH	132949	broad.mit.edu	37	4	57219643	57219643	+	Silent	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr4:57219643C>T	ENST00000205214.6	-	9	1683	c.1503G>A	c.(1501-1503)ctG>ctA	p.L501L	AASDH_ENST00000513376.1_Silent_p.L401L|AASDH_ENST00000510762.1_5'Flank|AASDH_ENST00000602986.1_Silent_p.L348L|AASDH_ENST00000434343.2_Silent_p.L16L|AASDH_ENST00000451613.1_Silent_p.L501L|AASDH_ENST00000502617.1_Silent_p.L501L	NM_181806.2	NP_861522.2	Q4L235	ACSF4_HUMAN	aminoadipate-semialdehyde dehydrogenase	501					fatty acid metabolic process (GO:0006631)		acid-thiol ligase activity (GO:0016878)|ATP binding (GO:0005524)	p.L501L(1)		endometrium(2)|kidney(2)|large_intestine(8)|lung(17)|ovary(4)|prostate(3)|skin(2)|stomach(1)|urinary_tract(1)	40	Glioma(25;0.08)|all_neural(26;0.101)	all_hematologic(202;0.0017)				GATATTTCTGCAGTTCTTTAA	0.358																																					p.L501L												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G1503A	4						.						85.0	85.0	85.0					4																	57219643		2203	4300	6503	56914400	SO:0001819	synonymous_variant	132949	exon9			AF516672	CCDS3504.1, CCDS68705.1, CCDS68706.1, CCDS75126.1, CCDS75127.1	4q12	2010-12-14			ENSG00000157426	ENSG00000157426	1.2.1.31	"""Acyl-CoA synthetase family"""	23993	protein-coding gene	gene with protein product	"""acyl-CoA synthetase family member 4"""	614365				15865210, 12712191, 17762044	Standard	XM_005265721		Approved	NRPS998, LYS2, ACSF4	uc003hbn.3	Q4L235	OTTHUMG00000128841	ENST00000205214.6:c.1503G>A	4.37:g.57219643C>T		Somatic		Capture	Illumina HiSeq	Phase_I	56914400	NM_181806	A5D8V3|A5PL22|Q63HK2|Q63HR7|Q6IPP8|Q6TFZ6|Q7Z5Y3|Q96BW4|Q9P064	Silent	SNP	ENST00000205214.6	37	CCDS3504.1																																																																																				0.358	AASDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250780.1	NM_181806	
GNRHR	2798	broad.mit.edu	37	4	68610310	68610310	+	Missense_Mutation	SNP	G	G	A	rs200026876		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr4:68610310G>A	ENST00000226413.4	-	2	742	c.718C>T	c.(718-720)Cgg>Tgg	p.R240W	SNORA62_ENST00000365504.1_RNA|GNRHR_ENST00000420975.2_Missense_Mutation_p.T197M|UBA6-AS1_ENST00000500538.2_RNA|UBA6-AS1_ENST00000502758.1_RNA	NM_000406.2	NP_000397.1	P30968	GNRHR_HUMAN	gonadotropin-releasing hormone receptor	240					cellular response to gonadotropin-releasing hormone (GO:0097211)|G-protein coupled receptor signaling pathway (GO:0007186)|multicellular organismal development (GO:0007275)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	gonadotropin-releasing hormone receptor activity (GO:0004968)	p.R240W(1)		endometrium(2)|large_intestine(4)|liver(1)|lung(4)|ovary(1)|urinary_tract(1)	13					Abarelix(DB00106)|Buserelin(DB06719)|Cetrorelix(DB00050)|Danazol(DB01406)|Degarelix(DB06699)|Gonadorelin(DB00644)|Goserelin(DB00014)|Leuprolide(DB00007)|Nafarelin(DB00666)	TGAAGGACCCGTGTCAGGGTG	0.423																																					p.R240W												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C718T	4						.						90.0	93.0	92.0					4																	68610310		2203	4300	6503	68292905	SO:0001583	missense	2798	exon2				CCDS3517.1, CCDS47064.1	4q21.2	2012-08-08			ENSG00000109163	ENSG00000109163		"""GPCR / Class A : Gonadotropin-releasing hormone receptors"""	4421	protein-coding gene	gene with protein product		138850		GRHR		8386108	Standard	NM_000406		Approved	LHRHR	uc003hdn.3	P30968	OTTHUMG00000129302	ENST00000226413.4:c.718C>T	4.37:g.68610310G>A	ENSP00000226413:p.Arg240Trp	Somatic		Capture	Illumina HiSeq	Phase_I	68292905	NM_000406	O75793|Q14D13|Q92644	Missense_Mutation	SNP	ENST00000226413.4	37	CCDS3517.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	15.15|15.15	2.747166|2.747166	0.49257|0.49257	.|.	.|.	ENSG00000109163|ENSG00000109163	ENST00000226413|ENST00000420975	T|T	0.44881|0.80653	0.91|-1.4	5.31|5.31	4.45|4.45	0.53987|0.53987	GPCR, rhodopsin-like superfamily (1);|.	0.901823|.	0.09383|.	N|.	0.809718|.	T|T	0.80529|0.80529	0.4640|0.4640	.|.	.|.	.|.	0.09310|0.09310	N|N	0.999997|0.999997	D|P	0.61697|0.51791	0.99|0.948	P|P	0.54210|0.50270	0.745|0.636	T|T	0.69617|0.69617	-0.5097|-0.5097	9|8	0.87932|0.33940	D|T	0|0.23	-0.1702|-0.1702	11.2753|11.2753	0.49163|0.49163	0.0:0.0:0.8036:0.1964|0.0:0.0:0.8036:0.1964	.|.	240|197	P30968|P30968-2	GNRHR_HUMAN|.	W|M	240|197	ENSP00000226413:R240W|ENSP00000397561:T197M	ENSP00000226413:R240W|ENSP00000397561:T197M	R|T	-|-	1|2	2|0	GNRHR|GNRHR	68292905|68292905	0.917000|0.917000	0.31117|0.31117	0.864000|0.864000	0.33941|0.33941	0.686000|0.686000	0.39977|0.39977	2.229000|2.229000	0.42990|0.42990	1.350000|1.350000	0.45770|0.45770	0.643000|0.643000	0.83706|0.83706	CGG|ACG		0.423	GNRHR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251432.2		
YTHDC1	91746	broad.mit.edu	37	4	69202893	69202893	+	Silent	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr4:69202893C>T	ENST00000344157.4	-	4	1070	c.735G>A	c.(733-735)gaG>gaA	p.E245E	YTHDC1_ENST00000355665.3_Silent_p.E245E|YTHDC1_ENST00000579690.1_Silent_p.E245E	NM_001031732.2	NP_001026902.1	Q96MU7	YTDC1_HUMAN	YTH domain containing 1	245	Glu-rich.				mRNA splice site selection (GO:0006376)	nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)	p.E245E(1)		NS(1)|breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(10)|lung(7)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)	30						cttcttcttcctcctcctcct	0.468																																					p.E245E												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G735A	4						.						170.0	118.0	135.0					4																	69202893		2203	4300	6503	68885488	SO:0001819	synonymous_variant	91746	exon4			AK098515	CCDS3522.2, CCDS33992.1	4q13.3	2009-01-14			ENSG00000083896	ENSG00000083896			30626	protein-coding gene	gene with protein product						12368078, 10564280	Standard	XM_005265706		Approved	YT521, KIAA1966, YT521-B	uc003hdx.3	Q96MU7	OTTHUMG00000129306	ENST00000344157.4:c.735G>A	4.37:g.69202893C>T		Somatic		Capture	Illumina HiSeq	Phase_I	68885488	NM_001031732	Q4W5Q3|Q7Z622|Q8TF35	Silent	SNP	ENST00000344157.4	37	CCDS33992.1																																																																																				0.468	YTHDC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251437.1	NM_133370	
UGT2A1	10941	broad.mit.edu	37	4	70512815	70512815	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr4:70512815C>T	ENST00000503640.1	-	1	603	c.548G>A	c.(547-549)tGt>tAt	p.C183Y	UGT2A1_ENST00000514019.1_Missense_Mutation_p.C183Y|UGT2A1_ENST00000512704.1_Missense_Mutation_p.C183Y|UGT2A1_ENST00000286604.4_Missense_Mutation_p.C183Y	NM_006798.3	NP_006789.2	Q9Y4X1	UD2A1_HUMAN	UDP glucuronosyltransferase 2 family, polypeptide A1, complex locus	183					cellular glucuronidation (GO:0052695)|detection of chemical stimulus (GO:0009593)|metabolic process (GO:0008152)|sensory perception of smell (GO:0007608)	integral component of membrane (GO:0016021)	glucuronosyltransferase activity (GO:0015020)	p.C183Y(1)		NS(1)|central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(8)|lung(11)|ovary(2)|prostate(1)|skin(2)	30						TACCTTCCCACAGTGCTTTTC	0.413																																					p.C183Y												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G548A	4						.						94.0	81.0	85.0					4																	70512815		2203	4299	6502	70547404	SO:0001583	missense	10941	exon1			AJ006054	CCDS3529.1, CCDS58901.1, CCDS58902.1	4q13	2013-03-28	2010-12-02					"""UDP glucuronosyltransferases"""	12542	protein-coding gene	gene with protein product		604716	"""UDP glycosyltransferase 2 family, polypeptide A1"", ""UDP glucuronosyltransferase 2 family, polypeptide A1"""			10359671	Standard	NM_001252274		Approved		uc011caq.2	Q9Y4X1	OTTHUMG00000184942	ENST00000503640.1:c.548G>A	4.37:g.70512815C>T	ENSP00000424478:p.Cys183Tyr	Somatic		Capture	Illumina HiSeq	Phase_I	70547404	NM_006798	B4E2F4|D3GER1|D3GER2|E9PDM7|J3KNA3	Missense_Mutation	SNP	ENST00000503640.1	37	CCDS3529.1	.	.	.	.	.	.	.	.	.	.	C	17.75	3.466636	0.63625	.	.	ENSG00000173610	ENST00000503640;ENST00000512704;ENST00000514019;ENST00000286604	T;T;T;T	0.60920	0.15;0.15;0.15;0.29	5.78	5.78	0.91487	.	0.000000	0.85682	D	0.000000	T	0.75295	0.3830	M	0.66439	2.03	.	.	.	D;D;D;D	0.89917	0.999;0.997;1.0;1.0	D;D;D;D	0.91635	0.999;0.969;0.999;0.999	T	0.76222	-0.3038	9	0.66056	D	0.02	.	17.4952	0.87715	0.0:1.0:0.0:0.0	.	183;183;183;183	E9PDM7;B4E2F4;D6RFW5;Q9Y4X1	.;.;.;UD2A1_HUMAN	Y	183	ENSP00000424478:C183Y;ENSP00000421432:C183Y;ENSP00000425497:C183Y;ENSP00000286604:C183Y	ENSP00000286604:C183Y	C	-	2	0	UGT2A1	70547404	1.000000	0.71417	1.000000	0.80357	0.914000	0.54420	5.284000	0.65627	2.744000	0.94065	0.591000	0.81541	TGT		0.413	UGT2A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251554.3	NM_006798	
RUFY3	22902	broad.mit.edu	37	4	71588315	71588315	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr4:71588315G>A	ENST00000226328.4	+	1	588	c.25G>A	c.(25-27)Gat>Aat	p.D9N	RUFY3_ENST00000536664.1_5'Flank|RUFY3_ENST00000381006.3_Missense_Mutation_p.D9N|RUFY3_ENST00000417478.2_Intron	NM_014961.3	NP_055776.1	Q7L099	RUFY3_HUMAN	RUN and FYVE domain containing 3	9					negative regulation of axonogenesis (GO:0050771)	filopodium (GO:0030175)|growth cone (GO:0030426)		p.D9N(1)		endometrium(1)|kidney(3)|large_intestine(4)|lung(6)|prostate(1)|stomach(1)	16		all_hematologic(202;0.248)	Lung(101;0.235)			GCCTCCGACCGATATGCCAAC	0.502																																					p.D9N												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G25A	4						.						179.0	151.0	161.0					4																	71588315		2203	4300	6503	71807179	SO:0001583	missense	22902	exon1			AF112221	CCDS3547.1, CCDS34001.1, CCDS47068.1, CCDS75138.1	4q13.3	2009-05-29			ENSG00000018189	ENSG00000018189		"""Zinc fingers, FYVE domain containing"""	30285	protein-coding gene	gene with protein product	"""single axon-related 1"""	611194				17439943	Standard	NM_001130709		Approved	RIPx, KIAA0871, Singar1	uc003hfr.3	Q7L099	OTTHUMG00000129910	ENST00000226328.4:c.25G>A	4.37:g.71588315G>A	ENSP00000226328:p.Asp9Asn	Somatic		Capture	Illumina HiSeq	Phase_I	71807179	NM_014961	B3KM25|B4DYW7|D9N163|O94948|Q9UI00	Missense_Mutation	SNP	ENST00000226328.4	37	CCDS3547.1	.	.	.	.	.	.	.	.	.	.	G	22.5	4.296097	0.81025	.	.	ENSG00000018189	ENST00000381006;ENST00000226328	T;T	0.13307	2.98;2.6	5.64	5.64	0.86602	.	0.231673	0.41823	D	0.000819	T	0.12646	0.0307	N	0.08118	0	0.80722	D	1	D;P	0.54047	0.964;0.688	P;B	0.47075	0.536;0.055	T	0.11616	-1.0580	10	0.56958	D	0.05	-7.6337	19.7133	0.96105	0.0:0.0:1.0:0.0	.	9;9	Q7L099-3;Q7L099	.;RUFY3_HUMAN	N	9	ENSP00000370394:D9N;ENSP00000226328:D9N	ENSP00000226328:D9N	D	+	1	0	RUFY3	71807179	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	9.476000	0.97823	2.659000	0.90383	0.650000	0.86243	GAT		0.502	RUFY3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000252161.2	NM_014961	
SEPT11	55752	broad.mit.edu	37	4	77941690	77941690	+	Nonsense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr4:77941690C>T	ENST00000264893.6	+	7	1021	c.820C>T	c.(820-822)Cga>Tga	p.R274*	SEPT11_ENST00000541121.1_Nonsense_Mutation_p.R284*|SEPT11_ENST00000512575.1_Intron|SEPT11_ENST00000502584.1_Nonsense_Mutation_p.R274*|SEPT11_ENST00000510515.1_Nonsense_Mutation_p.R284*|SEPT11_ENST00000505788.1_Nonsense_Mutation_p.R274*	NM_018243.2	NP_060713.1	Q9NVA2	SEP11_HUMAN	septin 11	274	Septin-type G.				cell cycle (GO:0007049)|cell division (GO:0051301)|protein heterooligomerization (GO:0051291)	cell junction (GO:0030054)|cell projection (GO:0042995)|extracellular vesicular exosome (GO:0070062)|septin complex (GO:0031105)|stress fiber (GO:0001725)|synapse (GO:0045202)	GTP binding (GO:0005525)	p.R274*(1)		endometrium(2)|kidney(3)|large_intestine(3)|lung(1)|skin(1)|stomach(1)	11						TGTGAAACTTCGAGAGATGCT	0.473																																					p.R274X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.C820T	4						.						95.0	90.0	92.0					4																	77941690		2203	4300	6503	78160714	SO:0001587	stop_gained	55752	exon7			AK001711	CCDS34018.1	4q21.1	2013-01-21			ENSG00000138758	ENSG00000138758		"""Septins"""	25589	protein-coding gene	gene with protein product		612887				14999297, 15140406	Standard	NM_018243		Approved	FLJ10849	uc003hkj.3	Q9NVA2	OTTHUMG00000160854	ENST00000264893.6:c.820C>T	4.37:g.77941690C>T	ENSP00000264893:p.Arg274*	Somatic		Capture	Illumina HiSeq	Phase_I	78160714	NM_018243	B7Z7Z6|E9KL32|Q4W5G1|Q7L4N1|Q96SP1|Q9UFY9	Nonsense_Mutation	SNP	ENST00000264893.6	37	CCDS34018.1	.	.	.	.	.	.	.	.	.	.	C	39	7.837056	0.98516	.	.	ENSG00000138758	ENST00000264893;ENST00000502584;ENST00000510641;ENST00000505788;ENST00000510515;ENST00000541121	.	.	.	5.23	4.38	0.52667	.	0.091745	0.45867	D	0.000337	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	13.1321	0.59389	0.2896:0.7104:0.0:0.0	.	.	.	.	X	274;274;266;274;284;284	.	ENSP00000264893:R274X	R	+	1	2	SEPT11	78160714	0.586000	0.26782	0.837000	0.33122	0.988000	0.76386	1.200000	0.32247	1.172000	0.42781	0.591000	0.81541	CGA		0.473	SEPT11-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000362676.1	NM_018243	
CNOT6L	246175	broad.mit.edu	37	4	78652648	78652648	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr4:78652648G>A	ENST00000504123.1	-	9	1047	c.917C>T	c.(916-918)gCg>gTg	p.A306V	CNOT6L_ENST00000264903.4_Missense_Mutation_p.A306V			Q96LI5	CNO6L_HUMAN	CCR4-NOT transcription complex, subunit 6-like	306	Nuclease domain.				gene expression (GO:0010467)|gene silencing by RNA (GO:0031047)|mRNA destabilization (GO:0061157)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cytoplasmic mRNA processing body assembly (GO:0010606)|regulation of transcription, DNA-templated (GO:0006355)|regulation of translation (GO:0006417)|RNA metabolic process (GO:0016070)|transcription, DNA-templated (GO:0006351)	CCR4-NOT complex (GO:0030014)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|poly(A)-specific ribonuclease activity (GO:0004535)	p.A306V(1)		kidney(1)|large_intestine(1)|lung(6)|urinary_tract(1)	9						ATTAGCCATCGCCACTTGGTT	0.368																																					p.A306V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C917T	4						.						98.0	97.0	97.0					4																	78652648		2139	4282	6421	78871672	SO:0001583	missense	246175	exon9			AL133112	CCDS68731.1	4q13.3	2014-06-17				ENSG00000138767			18042	protein-coding gene	gene with protein product							Standard	NM_144571		Approved	DKFZp434K098, Ccr4b	uc003hks.3	Q96LI5		ENST00000504123.1:c.917C>T	4.37:g.78652648G>A	ENSP00000424896:p.Ala306Val	Somatic		Capture	Illumina HiSeq	Phase_I	78871672	NM_144571	Q9UF92	Missense_Mutation	SNP	ENST00000504123.1	37		.	.	.	.	.	.	.	.	.	.	G	34	5.335352	0.95758	.	.	ENSG00000138767	ENST00000504123;ENST00000264903;ENST00000512485;ENST00000505983	D;D;D;D	0.95205	-3.64;-3.64;-3.64;-3.64	5.76	5.76	0.90799	Endonuclease/exonuclease/phosphatase (2);	0.000000	0.85682	D	0.000000	D	0.97241	0.9098	M	0.76002	2.32	0.80722	D	1	D;D	0.89917	1.0;0.993	D;D	0.91635	0.999;0.944	D	0.97403	0.9997	10	0.87932	D	0	-3.5689	19.9699	0.97282	0.0:0.0:1.0:0.0	.	279;306	Q96LI5-2;Q96LI5	.;CNO6L_HUMAN	V	306;306;313;81	ENSP00000424896:A306V;ENSP00000264903:A306V;ENSP00000425571:A313V;ENSP00000426320:A81V	ENSP00000264903:A306V	A	-	2	0	CNOT6L	78871672	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	9.869000	0.99810	2.730000	0.93505	0.591000	0.81541	GCG		0.368	CNOT6L-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000362515.1		
FRAS1	80144	broad.mit.edu	37	4	79461921	79461921	+	Silent	SNP	G	G	A	rs376389151		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr4:79461921G>A	ENST00000264895.6	+	74	12122	c.11682G>A	c.(11680-11682)gcG>gcA	p.A3894A		NM_025074.6	NP_079350.5	Q86XX4	FRAS1_HUMAN	Fraser extracellular matrix complex subunit 1	3890					cell communication (GO:0007154)|embryonic limb morphogenesis (GO:0030326)|metanephros morphogenesis (GO:0003338)|morphogenesis of an epithelium (GO:0002009)|palate development (GO:0060021)|protein transport (GO:0015031)|skin development (GO:0043588)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|sublamina densa (GO:0061618)	metal ion binding (GO:0046872)	p.A3894A(1)		breast(2)|central_nervous_system(2)|cervix(2)|endometrium(14)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(5)|lung(54)|prostate(7)|skin(2)|urinary_tract(4)	103						AAGAGTTGGCGGTAGCTGCGT	0.488																																					p.A3894A												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G11682A	4						.	G		2,4046		0,2,2022	49.0	55.0	53.0		11682	-2.0	0.0	4		53	1,8379		0,1,4189	no	coding-synonymous	FRAS1	NM_025074.6		0,3,6211	AA,AG,GG		0.0119,0.0494,0.0241		3894/4013	79461921	3,12425	2024	4190	6214	79680945	SO:0001819	synonymous_variant	80144	exon74			AB040933	CCDS54772.1	4q21.21	2014-06-25	2014-06-25		ENSG00000138759	ENSG00000138759			19185	protein-coding gene	gene with protein product		607830	"""Fraser syndrome 1"""			12766769, 3118036	Standard	NM_025074		Approved	FLJ22031, FLJ14927, KIAA1500	uc003hlb.2	Q86XX4	OTTHUMG00000160856	ENST00000264895.6:c.11682G>A	4.37:g.79461921G>A		Somatic		Capture	Illumina HiSeq	Phase_I	79680945	NM_025074	A2RRR8|Q86UZ4|Q8N3U9|Q8NAU7|Q96JW7|Q9H6N9|Q9P228	Silent	SNP	ENST00000264895.6	37	CCDS54771.1	.	.	.	.	.	.	.	.	.	.	G	0.019	-1.459986	0.01062	4.94E-4	1.19E-4	ENSG00000138759	ENST00000512123	.	.	.	6.16	-2.04	0.07343	.	.	.	.	.	T	0.32466	0.0830	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.36792	-0.9733	4	.	.	.	.	9.5674	0.39407	0.0:0.3149:0.4999:0.1852	.	.	.	.	S	2123	.	.	G	+	1	0	FRAS1	79680945	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	-1.902000	0.01596	-0.229000	0.09854	0.650000	0.86243	GGT		0.488	FRAS1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding			
BMP2K	55589	broad.mit.edu	37	4	79832589	79832589	+	Missense_Mutation	SNP	C	C	T	rs370861712		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr4:79832589C>T	ENST00000335016.5	+	16	3054	c.2888C>T	c.(2887-2889)aCg>aTg	p.T963M	PAQR3_ENST00000295462.3_Intron	NM_198892.1	NP_942595.1	Q9NSY1	BMP2K_HUMAN	BMP2 inducible kinase	963					regulation of bone mineralization (GO:0030500)	nucleus (GO:0005634)	ATP binding (GO:0005524)|phosphatase regulator activity (GO:0019208)|protein serine/threonine kinase activity (GO:0004674)	p.T963M(1)		NS(1)|breast(1)|endometrium(4)|large_intestine(2)|lung(3)|prostate(1)|urinary_tract(1)	13						GATGAAATAACGGGGAGCCAG	0.473													C|||	1	0.000199681	0.0008	0.0	5008	,	,		20763	0.0		0.0	False		,,,				2504	0.0				p.T963M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C2888T	4						.	C	MET/THR	2,3784		0,2,1891	60.0	57.0	58.0		2888	5.4	1.0	4		58	0,8216		0,0,4108	no	missense	BMP2K	NM_198892.1	81	0,2,5999	TT,TC,CC		0.0,0.0528,0.0167	probably-damaging	963/1162	79832589	2,12000	1893	4108	6001	80051613	SO:0001583	missense	55589	exon16			AB015331	CCDS34019.1, CCDS47083.1	4q21.21	2008-05-15			ENSG00000138756	ENSG00000138756			18041	protein-coding gene	gene with protein product							Standard	NM_017593		Approved	DKFZp434K0614, BIKe	uc003hlk.3	Q9NSY1	OTTHUMG00000160900	ENST00000335016.5:c.2888C>T	4.37:g.79832589C>T	ENSP00000334836:p.Thr963Met	Somatic		Capture	Illumina HiSeq	Phase_I	80051613	NM_198892	O94791|Q4W5H2|Q8IYF2|Q8N2G7|Q8NHG9|Q9NTG8	Missense_Mutation	SNP	ENST00000335016.5	37	CCDS47083.1	.	.	.	.	.	.	.	.	.	.	C	11.79	1.744393	0.30865	5.28E-4	0.0	ENSG00000138756	ENST00000335016	T	0.74526	-0.85	5.41	5.41	0.78517	.	0.491893	0.18079	N	0.152346	D	0.82742	0.5103	L	0.57536	1.79	0.80722	D	1	D	0.76494	0.999	P	0.57720	0.826	D	0.84158	0.0427	10	0.87932	D	0	-9.8261	19.1973	0.93695	0.0:1.0:0.0:0.0	.	963	Q9NSY1	BMP2K_HUMAN	M	963	ENSP00000334836:T963M	ENSP00000334836:T963M	T	+	2	0	BMP2K	80051613	0.786000	0.28738	0.978000	0.43139	0.556000	0.35491	3.212000	0.51145	2.538000	0.85594	0.484000	0.47621	ACG		0.473	BMP2K-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_017593	
ARHGAP24	83478	broad.mit.edu	37	4	86643084	86643084	+	Missense_Mutation	SNP	A	A	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr4:86643084A>T	ENST00000395184.1	+	3	693	c.227A>T	c.(226-228)aAt>aTt	p.N76I	ARHGAP24_ENST00000506421.1_3'UTR|MIR4451_ENST00000580577.1_RNA|ARHGAP24_ENST00000503995.1_Missense_Mutation_p.N76I	NM_001025616.2	NP_001020787.2	Q8N264	RHG24_HUMAN	Rho GTPase activating protein 24	76	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				activation of Rac GTPase activity (GO:0032863)|angiogenesis (GO:0001525)|cell differentiation (GO:0030154)|negative regulation of Rac protein signal transduction (GO:0035021)|negative regulation of ruffle assembly (GO:1900028)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|wound healing, spreading of epidermal cells (GO:0035313)	cell projection (GO:0042995)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|focal adhesion (GO:0005925)	Rac GTPase activator activity (GO:0030675)	p.N76I(1)		breast(3)|cervix(1)|endometrium(3)|large_intestine(4)|lung(10)|skin(1)|stomach(1)|urinary_tract(1)	24		Hepatocellular(203;0.114)|all_hematologic(202;0.21)|Acute lymphoblastic leukemia(40;0.242)		OV - Ovarian serous cystadenocarcinoma(123;0.000571)		CATCCCTGCAATGAAGAGAAC	0.368																																					p.N76I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A227T	4						.						143.0	141.0	142.0					4																	86643084		2203	4300	6503	86862108	SO:0001583	missense	83478	exon3			AK091196	CCDS3611.1, CCDS34025.1, CCDS43246.1	4q22.1	2013-01-10			ENSG00000138639	ENSG00000138639		"""Rho GTPase activating proteins"", ""Pleckstrin homology (PH) domain containing"""	25361	protein-coding gene	gene with protein product		610586				11230166, 15254788	Standard	NM_001042669		Approved	DKFZP564B1162, FLJ33877, FilGAP	uc003hpk.3	Q8N264	OTTHUMG00000130427	ENST00000395184.1:c.227A>T	4.37:g.86643084A>T	ENSP00000378611:p.Asn76Ile	Somatic		Capture	Illumina HiSeq	Phase_I	86862108	NM_001025616	Q4KMG1|Q6ZNV3|Q86TI5|Q86WE4|Q9H0T6	Missense_Mutation	SNP	ENST00000395184.1	37	CCDS34025.1	.	.	.	.	.	.	.	.	.	.	A	15.92	2.976571	0.53720	.	.	ENSG00000138639	ENST00000395184;ENST00000503995	T;T	0.76316	-1.01;-1.01	4.97	4.97	0.65823	Pleckstrin homology-type (1);Pleckstrin homology domain (3);	0.108412	0.64402	D	0.000009	D	0.83658	0.5302	L	0.58510	1.815	0.80722	D	1	P;B;D	0.61080	0.898;0.123;0.989	P;B;P	0.61328	0.887;0.123;0.775	D	0.84531	0.0633	10	0.51188	T	0.08	.	13.9319	0.64001	1.0:0.0:0.0:0.0	.	76;76;221	Q8N264;Q8N264-4;Q8N264-5	RHG24_HUMAN;.;.	I	76	ENSP00000378611:N76I;ENSP00000423206:N76I	ENSP00000378611:N76I	N	+	2	0	ARHGAP24	86862108	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	3.227000	0.51262	1.998000	0.58463	0.528000	0.53228	AAT		0.368	ARHGAP24-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252815.2	NM_031305	
PKD2	5311	broad.mit.edu	37	4	88986571	88986571	+	Missense_Mutation	SNP	G	G	A	rs529945469	byFrequency	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr4:88986571G>A	ENST00000508588.1	+	6	813	c.418G>A	c.(418-420)Gtg>Atg	p.V140M	PKD2_ENST00000511337.1_3'UTR|PKD2_ENST00000237596.2_Missense_Mutation_p.V722M|PKD2_ENST00000502363.1_Missense_Mutation_p.V140M			Q9BZL6	KPCD2_HUMAN	polycystic kidney disease 2 (autosomal dominant)	392					angiogenesis (GO:0001525)|cell adhesion (GO:0007155)|cell death (GO:0008219)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|endothelial tube morphogenesis (GO:0061154)|intracellular signal transduction (GO:0035556)|peptidyl-serine phosphorylation (GO:0018105)|positive regulation of angiogenesis (GO:0045766)|positive regulation of blood vessel endothelial cell migration (GO:0043536)|positive regulation of cell adhesion (GO:0045785)|positive regulation of CREB transcription factor activity (GO:0032793)|positive regulation of DNA biosynthetic process (GO:2000573)|positive regulation of endothelial cell chemotaxis (GO:2001028)|positive regulation of endothelial cell chemotaxis by VEGF-activated vascular endothelial growth factor receptor signaling pathway (GO:0038033)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of fibroblast growth factor receptor signaling pathway (GO:0045743)|positive regulation of histone deacetylase activity (GO:1901727)|positive regulation of interleukin-2 production (GO:0032743)|positive regulation of interleukin-8 production (GO:0032757)|positive regulation of intracellular signal transduction (GO:1902533)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of T cell receptor signaling pathway (GO:0050862)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030949)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|T cell receptor signaling pathway (GO:0050852)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|protein kinase C activity (GO:0004697)|protein serine/threonine kinase activity (GO:0004674)	p.V722M(1)		breast(1)|endometrium(4)|kidney(1)|large_intestine(8)|liver(2)|lung(15)|skin(4)|upper_aerodigestive_tract(1)	36		Hepatocellular(203;0.114)|Acute lymphoblastic leukemia(40;0.221)		OV - Ovarian serous cystadenocarcinoma(123;9.98e-10)|COAD - Colon adenocarcinoma(81;0.0237)		AAAAAATACCGTGGATGACAT	0.398																																					p.V722M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2164A	4						.						102.0	107.0	105.0					4																	88986571		2203	4300	6503	89205595	SO:0001583	missense	5311	exon11			U50928	CCDS3627.1	4q22.1	2014-01-28			ENSG00000118762	ENSG00000118762		"""Voltage-gated ion channels / Transient receptor potential cation channels"", ""EF-hand domain containing"""	9009	protein-coding gene	gene with protein product	"""transient receptor potential cation channel, subfamily P, member 2"""	173910				8298643	Standard	NM_000297		Approved	PKD4, PC2, Pc-2, TRPP2	uc003hre.3	Q13563	OTTHUMG00000160982	ENST00000508588.1:c.418G>A	4.37:g.88986571G>A	ENSP00000427131:p.Val140Met	Somatic		Capture	Illumina HiSeq	Phase_I	89205595	NM_000297	Q8TB08|Q9P0T6|Q9Y3X8	Missense_Mutation	SNP	ENST00000508588.1	37		.	.	.	.	.	.	.	.	.	.	G	15.44	2.832987	0.50951	.	.	ENSG00000118762	ENST00000237596;ENST00000508588;ENST00000502363	T;T;T	0.55234	0.53;0.53;0.53	5.65	4.81	0.61882	EF-hand-like domain (1);	0.064559	0.64402	D	0.000008	T	0.61540	0.2355	L	0.49126	1.545	0.54753	D	0.999984	D	0.71674	0.998	P	0.56865	0.808	T	0.63980	-0.6514	10	0.54805	T	0.06	-19.8062	14.4246	0.67207	0.0706:0.0:0.9294:0.0	.	722	Q13563	PKD2_HUMAN	M	722;140;140	ENSP00000237596:V722M;ENSP00000427131:V140M;ENSP00000425289:V140M	ENSP00000237596:V722M	V	+	1	0	PKD2	89205595	1.000000	0.71417	0.528000	0.27938	0.133000	0.20885	6.070000	0.71220	1.399000	0.46721	0.655000	0.94253	GTG		0.398	PKD2-002	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000363253.2	NM_000297	
PKD2	5311	broad.mit.edu	37	4	88989152	88989152	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr4:88989152G>A	ENST00000508588.1	+	8	1110	c.715G>A	c.(715-717)Gga>Aga	p.G239R	PKD2_ENST00000511337.1_3'UTR|PKD2_ENST00000237596.2_Missense_Mutation_p.G821R|PKD2_ENST00000502363.1_Missense_Mutation_p.G239R			Q9BZL6	KPCD2_HUMAN	polycystic kidney disease 2 (autosomal dominant)	0					angiogenesis (GO:0001525)|cell adhesion (GO:0007155)|cell death (GO:0008219)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|endothelial tube morphogenesis (GO:0061154)|intracellular signal transduction (GO:0035556)|peptidyl-serine phosphorylation (GO:0018105)|positive regulation of angiogenesis (GO:0045766)|positive regulation of blood vessel endothelial cell migration (GO:0043536)|positive regulation of cell adhesion (GO:0045785)|positive regulation of CREB transcription factor activity (GO:0032793)|positive regulation of DNA biosynthetic process (GO:2000573)|positive regulation of endothelial cell chemotaxis (GO:2001028)|positive regulation of endothelial cell chemotaxis by VEGF-activated vascular endothelial growth factor receptor signaling pathway (GO:0038033)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of fibroblast growth factor receptor signaling pathway (GO:0045743)|positive regulation of histone deacetylase activity (GO:1901727)|positive regulation of interleukin-2 production (GO:0032743)|positive regulation of interleukin-8 production (GO:0032757)|positive regulation of intracellular signal transduction (GO:1902533)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of T cell receptor signaling pathway (GO:0050862)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030949)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|T cell receptor signaling pathway (GO:0050852)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|protein kinase C activity (GO:0004697)|protein serine/threonine kinase activity (GO:0004674)	p.G821R(1)		breast(1)|endometrium(4)|kidney(1)|large_intestine(8)|liver(2)|lung(15)|skin(4)|upper_aerodigestive_tract(1)	36		Hepatocellular(203;0.114)|Acute lymphoblastic leukemia(40;0.221)		OV - Ovarian serous cystadenocarcinoma(123;9.98e-10)|COAD - Colon adenocarcinoma(81;0.0237)		TGAAGATAGCGGACATAGCTC	0.473																																					p.G821R												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2461A	4						.						153.0	137.0	143.0					4																	88989152		2203	4300	6503	89208176	SO:0001583	missense	5311	exon13			U50928	CCDS3627.1	4q22.1	2014-01-28			ENSG00000118762	ENSG00000118762		"""Voltage-gated ion channels / Transient receptor potential cation channels"", ""EF-hand domain containing"""	9009	protein-coding gene	gene with protein product	"""transient receptor potential cation channel, subfamily P, member 2"""	173910				8298643	Standard	NM_000297		Approved	PKD4, PC2, Pc-2, TRPP2	uc003hre.3	Q13563	OTTHUMG00000160982	ENST00000508588.1:c.715G>A	4.37:g.88989152G>A	ENSP00000427131:p.Gly239Arg	Somatic		Capture	Illumina HiSeq	Phase_I	89208176	NM_000297	Q8TB08|Q9P0T6|Q9Y3X8	Missense_Mutation	SNP	ENST00000508588.1	37		.	.	.	.	.	.	.	.	.	.	G	19.33	3.807348	0.70797	.	.	ENSG00000118762	ENST00000237596;ENST00000508588;ENST00000502363	T;D;D	0.92858	-0.47;-3.12;-3.12	5.38	5.38	0.77491	.	0.000000	0.85682	D	0.000000	D	0.95655	0.8587	M	0.68593	2.085	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.95093	0.8223	10	0.49607	T	0.09	-20.6562	19.4972	0.95079	0.0:0.0:1.0:0.0	.	821	Q13563	PKD2_HUMAN	R	821;239;239	ENSP00000237596:G821R;ENSP00000427131:G239R;ENSP00000425289:G239R	ENSP00000237596:G821R	G	+	1	0	PKD2	89208176	1.000000	0.71417	1.000000	0.80357	0.298000	0.27526	7.285000	0.78660	2.668000	0.90789	0.563000	0.77884	GGA		0.473	PKD2-002	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000363253.2	NM_000297	
GRID2	2895	broad.mit.edu	37	4	94690558	94690558	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr4:94690558C>T	ENST00000282020.4	+	15	2816	c.2558C>T	c.(2557-2559)aCg>aTg	p.T853M	GRID2_ENST00000510992.1_Missense_Mutation_p.T758M	NM_001510.2	NP_001501.2	O43424	GRID2_HUMAN	glutamate receptor, ionotropic, delta 2	853					cellular protein localization (GO:0034613)|cerebellar granule cell differentiation (GO:0021707)|glutamate receptor signaling pathway (GO:0007215)|heterophilic cell-cell adhesion (GO:0007157)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|prepulse inhibition (GO:0060134)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of neuron apoptotic process (GO:0043523)|regulation of neuron projection development (GO:0010975)|synaptic transmission, glutamatergic (GO:0035249)|transport (GO:0006810)	cell junction (GO:0030054)|dendrite (GO:0030425)|dendritic spine (GO:0043197)|integral component of plasma membrane (GO:0005887)|ionotropic glutamate receptor complex (GO:0008328)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|synapse (GO:0045202)	extracellular-glutamate-gated ion channel activity (GO:0005234)|glutamate receptor activity (GO:0008066)|ionotropic glutamate receptor activity (GO:0004970)|PDZ domain binding (GO:0030165)|scaffold protein binding (GO:0097110)	p.T853M(1)		NS(2)|breast(2)|central_nervous_system(1)|endometrium(6)|kidney(4)|large_intestine(18)|lung(45)|ovary(3)|prostate(6)|skin(9)|upper_aerodigestive_tract(3)|urinary_tract(1)	100		Hepatocellular(203;0.114)|all_hematologic(202;0.177)		OV - Ovarian serous cystadenocarcinoma(123;3.22e-06)|LUSC - Lung squamous cell carcinoma(81;0.185)|Lung(65;0.191)		ATGCTGGAGACGTGGTGGAAC	0.488																																					p.T853M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C2558T	4						.						89.0	96.0	93.0					4																	94690558		2203	4300	6503	94909581	SO:0001583	missense	2895	exon15			AF009014	CCDS3637.1, CCDS68758.1	4q22	2012-08-29			ENSG00000152208	ENSG00000152208		"""Ligand-gated ion channels / Glutamate receptors, ionotropic"", ""Glutamate receptors"""	4576	protein-coding gene	gene with protein product		602368				9465309	Standard	NM_001510		Approved	GluD2, GluR-delta-2	uc011cdt.2	O43424	OTTHUMG00000130975	ENST00000282020.4:c.2558C>T	4.37:g.94690558C>T	ENSP00000282020:p.Thr853Met	Somatic		Capture	Illumina HiSeq	Phase_I	94909581	NM_001510	E9PH24|Q4KKU8|Q4KKU9|Q4KKV0|Q59FZ1	Missense_Mutation	SNP	ENST00000282020.4	37	CCDS3637.1	.	.	.	.	.	.	.	.	.	.	C	14.67	2.606068	0.46527	.	.	ENSG00000152208	ENST00000282020;ENST00000510992	T;T	0.13307	2.66;2.6	5.18	5.18	0.71444	.	0.050970	0.85682	D	0.000000	T	0.12646	0.0307	N	0.08118	0	0.58432	D	0.999991	D;D	0.61080	0.989;0.989	P;P	0.48488	0.579;0.579	T	0.16660	-1.0395	10	0.56958	D	0.05	.	18.7248	0.91710	0.0:1.0:0.0:0.0	.	758;853	E9PH24;O43424	.;GRID2_HUMAN	M	853;758	ENSP00000282020:T853M;ENSP00000421257:T758M	ENSP00000282020:T853M	T	+	2	0	GRID2	94909581	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.882000	0.69714	2.420000	0.82092	0.655000	0.94253	ACG		0.488	GRID2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253588.2		
FAT1	2195	broad.mit.edu	37	4	187630303	187630303	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr4:187630303G>A	ENST00000441802.2	-	2	888	c.679C>T	c.(679-681)Cgt>Tgt	p.R227C		NM_005245.3	NP_005236.2	Q14517	FAT1_HUMAN	FAT atypical cadherin 1	227	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				actin filament organization (GO:0007015)|anatomical structure morphogenesis (GO:0009653)|cell adhesion (GO:0007155)|cell migration (GO:0016477)|cell-cell signaling (GO:0007267)|establishment or maintenance of cell polarity (GO:0007163)|homophilic cell adhesion (GO:0007156)|single organismal cell-cell adhesion (GO:0016337)	cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|lamellipodium (GO:0030027)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.R227C(1)		NS(1)|breast(3)|central_nervous_system(3)|endometrium(38)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(33)|lung(88)|ovary(13)|pancreas(2)|prostate(16)|skin(2)|upper_aerodigestive_tract(11)|urinary_tract(4)	228						TTCATGCCACGGTCCGCAGCG	0.493										HNSCC(5;0.00058)																											p.R227C	Colon(197;1040 2055 4143 4984 49344)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C679T	4						.						114.0	114.0	114.0					4																	187630303		2167	4282	6449	187867297	SO:0001583	missense	2195	exon2			X87241	CCDS47177.1	4q35.2	2013-05-31	2013-05-31	2008-10-30	ENSG00000083857	ENSG00000083857		"""Cadherins / Cadherin-related"""	3595	protein-coding gene	gene with protein product	"""cadherin-related family member 8"""	600976	"""FAT tumor suppressor (Drosophila) homolog"", ""FAT tumor suppressor homolog 1 (Drosophila)"""	FAT		8586420	Standard	XM_005262834		Approved	CDHF7, CDHR8	uc003izf.3	Q14517	OTTHUMG00000160320	ENST00000441802.2:c.679C>T	4.37:g.187630303G>A	ENSP00000406229:p.Arg227Cys	Somatic		Capture	Illumina HiSeq	Phase_I	187867297	NM_005245		Missense_Mutation	SNP	ENST00000441802.2	37	CCDS47177.1	.	.	.	.	.	.	.	.	.	.	G	17.54	3.414287	0.62511	.	.	ENSG00000083857	ENST00000441802;ENST00000260147;ENST00000509647	T;T	0.53206	0.63;0.63	5.2	5.2	0.72013	Cadherin (4);Cadherin-like (1);	0.000000	0.85682	D	0.000000	T	0.70902	0.3277	M	0.77712	2.385	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.73760	-0.3881	10	0.66056	D	0.02	.	18.5053	0.90894	0.0:0.0:1.0:0.0	.	227	Q14517	FAT1_HUMAN	C	227	ENSP00000406229:R227C;ENSP00000423736:R227C	ENSP00000260147:R227C	R	-	1	0	FAT1	187867297	1.000000	0.71417	0.999000	0.59377	0.933000	0.57130	5.166000	0.64965	2.704000	0.92352	0.591000	0.81541	CGT		0.493	FAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360209.3	NM_005245	
PJA2	9867	broad.mit.edu	37	5	108691616	108691616	+	Splice_Site	SNP	C	C	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr5:108691616C>A	ENST00000361189.2	-	7	2003	c.1764G>T	c.(1762-1764)gaG>gaT	p.E588D	PJA2_ENST00000361557.3_Splice_Site_p.E588D	NM_014819.4	NP_055634.3	O43164	PJA2_HUMAN	praja ring finger 2, E3 ubiquitin protein ligase	588	Interaction with PRKAR1A, PRKAR2A and PRKAR2B.				long-term memory (GO:0007616)|protein ubiquitination (GO:0016567)|regulation of protein kinase A signaling (GO:0010738)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	ligase activity (GO:0016874)|protein kinase A catalytic subunit binding (GO:0034236)|protein kinase A regulatory subunit binding (GO:0034237)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.E588D(1)		endometrium(2)|kidney(2)|large_intestine(5)|lung(8)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	21		all_cancers(142;4.4e-06)|all_epithelial(76;8.17e-08)|Prostate(80;0.00676)|Lung NSC(167;0.0436)|Ovarian(225;0.0443)|all_lung(232;0.053)|Colorectal(57;0.0946)|Breast(839;0.151)		OV - Ovarian serous cystadenocarcinoma(64;3.46e-10)|Epithelial(69;6.02e-09)|COAD - Colon adenocarcinoma(37;0.224)		ATGAACATACCTCCATAGCCT	0.388																																					p.E588D												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1764T	5						.						113.0	112.0	113.0					5																	108691616		2202	4300	6502	108719515	SO:0001630	splice_region_variant	9867	exon7			AB007898	CCDS4099.1	5q22.1	2013-01-09	2012-02-23	2003-06-05	ENSG00000198961	ENSG00000198961		"""RING-type (C3HC4) zinc fingers"""	17481	protein-coding gene	gene with protein product			"""ring finger protein 131"", ""praja ring finger 2"""	RNF131			Standard	NM_014819		Approved	KIAA0438, Neurodap1	uc003kos.4	O43164	OTTHUMG00000128750	ENST00000361189.2:c.1764+1G>T	5.37:g.108691616C>A		Somatic		Capture	Illumina HiSeq	Phase_I	108719515	NM_014819	A8K6U4|D3DSZ5|Q68D49|Q8N1G5	Missense_Mutation	SNP	ENST00000361189.2	37	CCDS4099.1	.	.	.	.	.	.	.	.	.	.	C	33	5.280103	0.95489	.	.	ENSG00000198961	ENST00000361189;ENST00000361557	T;T	0.13089	2.62;2.62	5.34	5.34	0.76211	.	0.000000	0.64402	D	0.000001	T	0.28566	0.0707	L	0.32530	0.975	0.53688	D	0.999975	D	0.76494	0.999	D	0.85130	0.997	T	0.00690	-1.1608	9	.	.	.	-16.5444	19.2339	0.93850	0.0:1.0:0.0:0.0	.	588	O43164	PJA2_HUMAN	D	588	ENSP00000354775:E588D;ENSP00000355284:E588D	.	E	-	3	2	PJA2	108719515	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	5.913000	0.69957	2.775000	0.95449	0.650000	0.86243	GAG		0.388	PJA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250663.1	NM_014819	Missense_Mutation
CTNND2	1501	broad.mit.edu	37	5	11082866	11082866	+	Silent	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr5:11082866G>A	ENST00000304623.8	-	16	2919	c.2730C>T	c.(2728-2730)tgC>tgT	p.C910C	CTNND2_ENST00000359640.2_Silent_p.C852C|CTNND2_ENST00000495388.2_5'UTR|CTNND2_ENST00000458100.2_Silent_p.C477C|CTNND2_ENST00000511377.1_Silent_p.C819C|CTNND2_ENST00000503622.1_Silent_p.C573C	NM_001332.2	NP_001323.1	Q9UQB3	CTND2_HUMAN	catenin (cadherin-associated protein), delta 2	910					cell adhesion (GO:0007155)|learning (GO:0007612)|morphogenesis of a branching structure (GO:0001763)|multicellular organismal development (GO:0007275)|regulation of synaptic plasticity (GO:0048167)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|transcription, DNA-templated (GO:0006351)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|nucleus (GO:0005634)		p.C910C(1)		NS(1)|autonomic_ganglia(1)|breast(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(29)|liver(1)|lung(71)|ovary(4)|pancreas(2)|prostate(1)|skin(5)|upper_aerodigestive_tract(4)|urinary_tract(2)	136						TGGCCACCGCGCACACCACAC	0.527																																					p.C910C												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C2730T	5						.						126.0	110.0	116.0					5																	11082866		2203	4300	6503	11135866	SO:0001819	synonymous_variant	1501	exon16			U52828	CCDS3881.1, CCDS75227.1, CCDS75228.1	5p15.2	2013-02-14	2012-08-15		ENSG00000169862	ENSG00000169862		"""Armadillo repeat containing"""	2516	protein-coding gene	gene with protein product	"""neural plakophilin-related arm-repeat protein"""	604275	"""catenin (cadherin-associated protein), delta 2 (neural plakophilin-related arm-repeat protein)"""			9342840, 9223106	Standard	XM_005248251		Approved	NPRAP, GT24	uc003jfa.1	Q9UQB3	OTTHUMG00000090511	ENST00000304623.8:c.2730C>T	5.37:g.11082866G>A		Somatic		Capture	Illumina HiSeq	Phase_I	11135866	NM_001332	B0FTZ7|O00379|O15390|O43206|O43840|Q13589|Q9UM66|Q9UPM3	Silent	SNP	ENST00000304623.8	37	CCDS3881.1	.	.	.	.	.	.	.	.	.	.	G	10.46	1.355572	0.24598	.	.	ENSG00000169862	ENST00000538638	.	.	.	5.04	-4.39	0.03611	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.4712	0.75441	0.8735:0.0:0.1265:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	CTNND2	11135866	0.003000	0.15002	0.793000	0.32043	0.958000	0.62258	-0.963000	0.03837	-0.659000	0.05359	-0.253000	0.11424	.		0.527	CTNND2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206999.1	NM_001332	
MAN2A1	4124	broad.mit.edu	37	5	109106146	109106146	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr5:109106146G>A	ENST00000261483.4	+	7	2152	c.1100G>A	c.(1099-1101)tGc>tAc	p.C367Y		NM_002372.2	NP_002363.2	Q16706	MA2A1_HUMAN	mannosidase, alpha, class 2A, member 1	367					cellular protein metabolic process (GO:0044267)|in utero embryonic development (GO:0001701)|liver development (GO:0001889)|lung alveolus development (GO:0048286)|mannose metabolic process (GO:0006013)|mitochondrion organization (GO:0007005)|N-glycan processing (GO:0006491)|positive regulation of neurogenesis (GO:0050769)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|respiratory gaseous exchange (GO:0007585)|retina morphogenesis in camera-type eye (GO:0060042)|vacuole organization (GO:0007033)	cis-Golgi network (GO:0005801)|extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	carbohydrate binding (GO:0030246)|hydrolase activity, hydrolyzing N-glycosyl compounds (GO:0016799)|mannosyl-oligosaccharide 1,3-1,6-alpha-mannosidase activity (GO:0004572)|zinc ion binding (GO:0008270)	p.C367Y(1)		breast(2)|central_nervous_system(2)|endometrium(7)|kidney(2)|large_intestine(13)|lung(20)|ovary(3)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	55		all_cancers(142;8.66e-07)|all_epithelial(76;7.73e-09)|Prostate(80;0.000303)|Lung NSC(167;0.0186)|all_lung(232;0.0241)|Ovarian(225;0.0444)|Colorectal(57;0.0959)|Breast(839;0.244)		OV - Ovarian serous cystadenocarcinoma(64;2.17e-10)|Epithelial(69;1.37e-09)|COAD - Colon adenocarcinoma(37;0.141)		CCTAAAATATGCTGCCAGTTT	0.438																																					p.C367Y												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1100A	5						.						120.0	111.0	114.0					5																	109106146		2202	4300	6502	109134045	SO:0001583	missense	4124	exon7				CCDS34209.1	5q21.3	2013-09-20			ENSG00000112893	ENSG00000112893	3.2.1.114		6824	protein-coding gene	gene with protein product	"""golgi integral membrane protein 7"""	154582		MANA2		1757461, 15004235	Standard	NM_002372		Approved	GOLIM7	uc003kou.1	Q16706	OTTHUMG00000162834	ENST00000261483.4:c.1100G>A	5.37:g.109106146G>A	ENSP00000261483:p.Cys367Tyr	Somatic		Capture	Illumina HiSeq	Phase_I	109134045	NM_002372	Q16767	Missense_Mutation	SNP	ENST00000261483.4	37	CCDS34209.1	.	.	.	.	.	.	.	.	.	.	G	25.7	4.668195	0.88348	.	.	ENSG00000112893	ENST00000261483	T	0.74526	-0.85	5.75	5.75	0.90469	Glycoside hydrolase/deacetylase, beta/alpha-barrel (1);Glycoside hydrolase, family 38, core (2);	0.000000	0.85682	D	0.000000	D	0.89181	0.6642	M	0.88842	2.985	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.90399	0.4401	10	0.87932	D	0	-16.9617	19.942	0.97168	0.0:0.0:1.0:0.0	.	367	Q16706	MA2A1_HUMAN	Y	367	ENSP00000261483:C367Y	ENSP00000261483:C367Y	C	+	2	0	MAN2A1	109134045	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.832000	0.99423	2.700000	0.92200	0.563000	0.77884	TGC		0.438	MAN2A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370680.1		
APC	324	broad.mit.edu	37	5	112173917	112173917	+	Nonsense_Mutation	SNP	C	C	T	rs121913333		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr5:112173917C>T	ENST00000457016.1	+	16	3006	c.2626C>T	c.(2626-2628)Cga>Tga	p.R876*	CTC-554D6.1_ENST00000520401.1_Intron|APC_ENST00000508376.2_Nonsense_Mutation_p.R876*|APC_ENST00000257430.4_Nonsense_Mutation_p.R876*			P25054	APC_HUMAN	adenomatous polyposis coli	876	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.R876*(38)|p.S874_R876>*(1)|p.?(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)		TTCTTCAAAGCGAGGTTTGCA	0.463		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.R858X	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,NS,Substitution - Nonsense,0 	.	40	Substitution - Nonsense(38)|Unknown(1)|Complex - deletion inframe(1)	large_intestine(37)|lung(1)|breast(1)|skin(1)	c.C2572T	5	GRCh37	CM942020	APC	M	rs121913333	.						70.0	72.0	71.0					5																	112173917		2202	4300	6502	112201816	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.2626C>T	5.37:g.112173917C>T	ENSP00000413133:p.Arg876*	Somatic		Capture	Illumina HiSeq	Phase_I	112201816	NM_001127511	D3DT03|Q15162|Q15163|Q93042	Nonsense_Mutation	SNP	ENST00000457016.1	37	CCDS4107.1	.	.	.	.	.	.	.	.	.	.	C	37	6.588996	0.97688	.	.	ENSG00000134982	ENST00000457016;ENST00000507379;ENST00000257430;ENST00000508376;ENST00000512211	.	.	.	5.92	4.09	0.47781	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-11.2738	14.8639	0.70401	0.3912:0.6088:0.0:0.0	.	.	.	.	X	876;858;876;876;876	.	ENSP00000257430:R876X	R	+	1	2	APC	112201816	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	1.385000	0.34408	0.785000	0.33685	0.557000	0.71058	CGA		0.463	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038	
APC	324	broad.mit.edu	37	5	112175639	112175639	+	Nonsense_Mutation	SNP	C	C	T	rs121913332		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr5:112175639C>T	ENST00000457016.1	+	16	4728	c.4348C>T	c.(4348-4350)Cga>Tga	p.R1450*	CTC-554D6.1_ENST00000520401.1_Intron|APC_ENST00000508376.2_Nonsense_Mutation_p.R1450*|APC_ENST00000257430.4_Nonsense_Mutation_p.R1450*			P25054	APC_HUMAN	adenomatous polyposis coli	1450	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.R1450*(153)|p.?(1)|p.P1424fs*19(1)|p.K1192fs*3(1)|p.R1450fs*22(1)|p.S1436fs*22(1)|p.R1450fs*5(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)		TCAAACCAAGCGAGAAGTACC	0.478	R1450*(LS123_LARGE_INTESTINE)|R1450*(MKN74_STOMACH)|R1450*(SW1417_LARGE_INTESTINE)|R1450*(SW837_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.R1432X	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,rectum,Substitution - Nonsense,0 	.	159	Substitution - Nonsense(153)|Deletion - Frameshift(4)|Unknown(1)|Insertion - Frameshift(1)	large_intestine(136)|stomach(13)|soft_tissue(4)|small_intestine(3)|endometrium(1)|skin(1)|pancreas(1)	c.C4294T	5	GRCh37	CM930030	APC	M	rs121913332	.						102.0	90.0	94.0					5																	112175639		2202	4300	6502	112203538	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.4348C>T	5.37:g.112175639C>T	ENSP00000413133:p.Arg1450*	Somatic		Capture	Illumina HiSeq	Phase_I	112203538	NM_001127511	D3DT03|Q15162|Q15163|Q93042	Nonsense_Mutation	SNP	ENST00000457016.1	37	CCDS4107.1	.	.	.	.	.	.	.	.	.	.	C	41	8.651223	0.98901	.	.	ENSG00000134982	ENST00000457016;ENST00000257430;ENST00000508376	.	.	.	6.17	4.2	0.49525	.	0.600559	0.18052	N	0.153248	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-1.0649	14.037	0.64651	0.426:0.574:0.0:0.0	.	.	.	.	X	1450	.	.	R	+	1	2	APC	112203538	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	3.171000	0.50824	1.564000	0.49628	0.655000	0.94253	CGA		0.478	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038	
MCC	4163	broad.mit.edu	37	5	112384920	112384920	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr5:112384920G>A	ENST00000302475.4	-	14	2518	c.1955C>T	c.(1954-1956)aCg>aTg	p.T652M	MCC_ENST00000514701.3_5'UTR|MCC_ENST00000515367.2_Missense_Mutation_p.T589M|MCC_ENST00000408903.3_Missense_Mutation_p.T842M	NM_002387.2	NP_002378	P23508	CRCM_HUMAN	mutated in colorectal cancers	652					negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of epithelial cell migration (GO:0010633)|negative regulation of epithelial cell proliferation (GO:0050680)|signal transduction (GO:0007165)|Wnt signaling pathway (GO:0016055)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)	p.T652M(1)|p.T842M(1)		endometrium(4)|kidney(3)|large_intestine(15)|liver(2)|lung(8)|ovary(2)|pancreas(1)|prostate(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	42		all_cancers(142;5.89e-08)|all_epithelial(76;3.57e-11)|all_lung(232;0.000605)|Lung NSC(810;0.000697)|Colorectal(10;0.00146)|Prostate(80;0.00174)|Ovarian(225;0.0175)|Breast(839;0.198)		OV - Ovarian serous cystadenocarcinoma(64;2.04e-54)|Epithelial(69;9.69e-49)|all cancers(49;6.25e-44)|COAD - Colon adenocarcinoma(37;0.0432)|Colorectal(14;0.0766)		GGCCTCCCGCGTGCTCAGCTT	0.602																																					p.T842M												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.C2525T	5						.						50.0	38.0	42.0					5																	112384920		2202	4300	6502	112412819	SO:0001583	missense	4163	exon16				CCDS4111.1, CCDS43351.1	5q21-q22	2013-01-10			ENSG00000171444	ENSG00000171444		"""EF-hand domain containing"""	6935	protein-coding gene	gene with protein product		159350				1848370	Standard	NM_002387		Approved		uc003kql.4	P23508	OTTHUMG00000128804	ENST00000302475.4:c.1955C>T	5.37:g.112384920G>A	ENSP00000305617:p.Thr652Met	Somatic		Capture	Illumina HiSeq	Phase_I	112412819	NM_001085377	D3DT05|Q6ZR04	Missense_Mutation	SNP	ENST00000302475.4	37	CCDS4111.1	.	.	.	.	.	.	.	.	.	.	G	15.69	2.907541	0.52333	.	.	ENSG00000171444	ENST00000302475;ENST00000515367;ENST00000408903	T;T;T	0.36157	2.41;2.41;1.27	4.87	4.87	0.63330	.	0.067143	0.64402	D	0.000016	T	0.40347	0.1113	N	0.19112	0.55	0.48975	D	0.999735	P;D;D	0.76494	0.861;0.99;0.999	B;P;P	0.58928	0.295;0.799;0.848	T	0.36286	-0.9754	10	0.56958	D	0.05	-20.8539	14.4924	0.67660	0.0:0.1476:0.8524:0.0	.	652;842;652	B7Z6G0;P23508-2;P23508	.;.;CRCM_HUMAN	M	652;589;842	ENSP00000305617:T652M;ENSP00000421615:T589M;ENSP00000386227:T842M	ENSP00000305617:T652M	T	-	2	0	MCC	112412819	1.000000	0.71417	0.997000	0.53966	0.985000	0.73830	4.632000	0.61311	2.239000	0.73571	0.462000	0.41574	ACG		0.602	MCC-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000250736.3	NM_001085377	
YTHDC2	64848	broad.mit.edu	37	5	112860778	112860778	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr5:112860778G>A	ENST00000161863.4	+	3	592	c.379G>A	c.(379-381)Gtt>Att	p.V127I	YTHDC2_ENST00000515883.1_Missense_Mutation_p.V127I	NM_022828.3	NP_073739.3	Q9H6S0	YTDC2_HUMAN	YTH domain containing 2	127					ATP catabolic process (GO:0006200)|positive regulation by host of viral genome replication (GO:0044829)|response to interleukin-1 (GO:0070555)|response to tumor necrosis factor (GO:0034612)	endoplasmic reticulum (GO:0005783)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|poly(A) RNA binding (GO:0044822)|RNA polymerase binding (GO:0070063)|RNA-dependent ATPase activity (GO:0008186)	p.V127I(1)		NS(2)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(6)|large_intestine(13)|lung(10)|pancreas(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	43		all_cancers(142;7.69e-05)|all_epithelial(76;6.42e-07)|Colorectal(10;0.00278)|Prostate(80;0.00955)|Ovarian(225;0.0444)|Lung NSC(810;0.143)|all_lung(232;0.163)|Breast(839;0.244)		OV - Ovarian serous cystadenocarcinoma(64;7.2e-08)|Epithelial(69;8.83e-08)|all cancers(49;6.9e-06)|COAD - Colon adenocarcinoma(37;0.0458)|Colorectal(14;0.0594)		AAAACATGCTGTTAGGAGCCT	0.378																																					p.V127I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G379A	5						.						113.0	108.0	110.0					5																	112860778		2202	4300	6502	112888677	SO:0001583	missense	64848	exon3			AK000915	CCDS4113.1	5q22.3	2008-02-05			ENSG00000047188	ENSG00000047188			24721	protein-coding gene	gene with protein product						12477932	Standard	NM_022828		Approved	FLJ2194, FLJ10053, DKFZp564A186	uc003kqn.3	Q9H6S0	OTTHUMG00000128837	ENST00000161863.4:c.379G>A	5.37:g.112860778G>A	ENSP00000161863:p.Val127Ile	Somatic		Capture	Illumina HiSeq	Phase_I	112888677	NM_022828	B2RP66	Missense_Mutation	SNP	ENST00000161863.4	37	CCDS4113.1	.	.	.	.	.	.	.	.	.	.	G	8.824	0.938350	0.18206	.	.	ENSG00000047188	ENST00000161863;ENST00000515883;ENST00000514720;ENST00000511372	T;T	0.06294	4.33;3.32	5.74	4.87	0.63330	.	0.295951	0.33161	N	0.005212	T	0.02970	0.0088	N	0.04959	-0.14	0.38485	D	0.947827	B	0.02656	0.0	B	0.04013	0.001	T	0.40646	-0.9552	10	0.07325	T	0.83	.	11.4808	0.50324	0.1367:0.0:0.8633:0.0	.	127	Q9H6S0	YTDC2_HUMAN	I	127;127;67;37	ENSP00000161863:V127I;ENSP00000423101:V127I	ENSP00000161863:V127I	V	+	1	0	YTHDC2	112888677	0.977000	0.34250	1.000000	0.80357	0.999000	0.98932	1.032000	0.30178	2.703000	0.92315	0.655000	0.94253	GTT		0.378	YTHDC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250776.2	NM_022828	
LVRN	206338	broad.mit.edu	37	5	115350146	115350146	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr5:115350146C>T	ENST00000357872.4	+	16	2496	c.2372C>T	c.(2371-2373)gCg>gTg	p.A791V	AQPEP_ENST00000515454.1_3'UTR	NM_173800.4	NP_776161.3	Q6Q4G3	AMPQ_HUMAN		791						integral component of membrane (GO:0016021)	metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)	p.A791V(1)									TTTGTAACTGCGTGTTGGTTG	0.363																																					p.A791V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C2372T	5						.						116.0	111.0	113.0					5																	115350146		2202	4300	6502	115378045	SO:0001583	missense	206338	exon16																														ENST00000357872.4:c.2372C>T	5.37:g.115350146C>T	ENSP00000350541:p.Ala791Val	Somatic		Capture	Illumina HiSeq	Phase_I	115378045	NM_173800	A8K6J0|C9JGD2|Q32MR1|Q4G0I9|Q4G0V2|Q86XA3|Q8NBZ2	Missense_Mutation	SNP	ENST00000357872.4	37	CCDS4124.1	.	.	.	.	.	.	.	.	.	.	C	9.164	1.019345	0.19355	.	.	ENSG00000172901	ENST00000357872;ENST00000379578	T	0.09723	2.95	5.55	1.81	0.25067	.	0.178454	0.37348	N	0.002135	T	0.12646	0.0307	M	0.82132	2.575	0.09310	N	0.999999	P	0.36249	0.545	B	0.29942	0.109	T	0.13415	-1.0510	10	0.62326	D	0.03	.	8.1834	0.31324	0.0:0.6749:0.0:0.3251	.	791	Q6Q4G3	AMPQ_HUMAN	V	791;780	ENSP00000350541:A791V	ENSP00000350541:A791V	A	+	2	0	AC010282.1	115378045	0.862000	0.29867	0.046000	0.18839	0.448000	0.32197	1.506000	0.35747	0.315000	0.23110	-0.964000	0.02622	GCG		0.363	AQPEP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250852.1		
PRR16	51334	broad.mit.edu	37	5	120022338	120022338	+	Silent	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr5:120022338G>A	ENST00000407149.2	+	2	1058	c.849G>A	c.(847-849)gtG>gtA	p.V283V	PRR16_ENST00000379551.2_Silent_p.V260V|PRR16_ENST00000446965.1_Silent_p.V213V|PRR16_ENST00000505123.1_Silent_p.V213V			Q569H4	LARGN_HUMAN	proline rich 16	283	Pro-rich.				positive regulation of cell size (GO:0045793)|positive regulation of translation (GO:0045727)			p.V260V(1)		endometrium(2)|kidney(2)|large_intestine(5)|lung(12)|ovary(1)|pancreas(2)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	28		all_cancers(142;0.0464)|Prostate(80;0.00446)	KIRC - Kidney renal clear cell carcinoma(527;0.159)|Kidney(363;0.221)	OV - Ovarian serous cystadenocarcinoma(64;0.000126)|Epithelial(69;0.000331)|all cancers(49;0.00169)		CTGCAACTGTGCCTCCTCCCA	0.468																																					p.V260V												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G780A	5						.						59.0	61.0	60.0					5																	120022338		2203	4300	6503	120050237	SO:0001819	synonymous_variant	51334	exon3			AF242769	CCDS4127.1, CCDS75290.1	5q23.1	2006-08-22			ENSG00000184838	ENSG00000184838			29654	protein-coding gene	gene with protein product		615931				15971941	Standard	XM_005272010		Approved	DSC54	uc003ksp.3	Q569H4	OTTHUMG00000128903	ENST00000407149.2:c.849G>A	5.37:g.120022338G>A		Somatic		Capture	Illumina HiSeq	Phase_I	120050237	NM_016644	D3DSZ0|Q8IXY1|Q9NYI5	Silent	SNP	ENST00000407149.2	37																																																																																					0.468	PRR16-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000371059.1	NM_016644	
MEGF10	84466	broad.mit.edu	37	5	126771097	126771097	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr5:126771097A>G	ENST00000274473.6	+	17	2287	c.2020A>G	c.(2020-2022)Acc>Gcc	p.T674A	MEGF10_ENST00000503335.2_Missense_Mutation_p.T674A	NM_032446.2	NP_115822.1	Q96KG7	MEG10_HUMAN	multiple EGF-like-domains 10	674	EGF-like 12. {ECO:0000255|PROSITE- ProRule:PRU00076}.|Necessary for interaction with AP2M1, self-assembly and formation of the irregular, mosaic-like adhesion pattern.				homotypic cell-cell adhesion (GO:0034109)|muscle cell development (GO:0055001)|recognition of apoptotic cell (GO:0043654)|regulation of muscle cell differentiation (GO:0051147)|regulation of skeletal muscle tissue development (GO:0048641)|skeletal muscle satellite cell activation (GO:0014719)|skeletal muscle satellite cell differentiation (GO:0014816)|skeletal muscle satellite cell proliferation (GO:0014841)	cell projection (GO:0042995)|integral component of membrane (GO:0016021)|phagocytic cup (GO:0001891)		p.T674A(1)		breast(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(10)|lung(28)|ovary(4)|prostate(2)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	68		Prostate(80;0.165)	KIRC - Kidney renal clear cell carcinoma(527;0.0268)|Kidney(363;0.0488)	OV - Ovarian serous cystadenocarcinoma(64;0.0657)|Epithelial(69;0.123)		AGGAATTTGTACCTGCACCAA	0.473																																					p.T674A												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A2020G	5						.						107.0	90.0	96.0					5																	126771097		2203	4300	6503	126798996	SO:0001583	missense	84466	exon17			AK021631	CCDS4142.1	5q33	2008-02-05			ENSG00000145794	ENSG00000145794			29634	protein-coding gene	gene with protein product		612453				11347906	Standard	NM_032446		Approved	KIAA1780	uc003kui.4	Q96KG7	OTTHUMG00000128984	ENST00000274473.6:c.2020A>G	5.37:g.126771097A>G	ENSP00000274473:p.Thr674Ala	Somatic		Capture	Illumina HiSeq	Phase_I	126798996	NM_032446	Q68DE5|Q8WUL3	Missense_Mutation	SNP	ENST00000274473.6	37	CCDS4142.1	.	.	.	.	.	.	.	.	.	.	A	13.20	2.165893	0.38217	.	.	ENSG00000145794	ENST00000503335;ENST00000274473	T;T	0.48836	0.8;0.8	6.04	3.48	0.39840	Epidermal growth factor-like (1);Epidermal growth factor-like, type 3 (1);	0.229124	0.35615	N	0.003097	T	0.23289	0.0563	N	0.12961	0.28	0.40065	D	0.975945	B	0.02656	0.0	B	0.04013	0.001	T	0.06516	-1.0822	10	0.15499	T	0.54	-21.2228	3.7836	0.08690	0.6614:0.1382:0.0685:0.1318	.	674	Q96KG7	MEG10_HUMAN	A	674	ENSP00000423354:T674A;ENSP00000274473:T674A	ENSP00000274473:T674A	T	+	1	0	MEGF10	126798996	0.862000	0.29867	1.000000	0.80357	0.990000	0.78478	1.692000	0.37731	1.066000	0.40716	0.460000	0.39030	ACC		0.473	MEGF10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250973.2	NM_032446	
TERT	7015	broad.mit.edu	37	5	1278780	1278780	+	Silent	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr5:1278780G>A	ENST00000310581.5	-	6	2319	c.2262C>T	c.(2260-2262)caC>caT	p.H754H	TERT_ENST00000296820.5_Silent_p.H754H|TERT_ENST00000334602.6_Silent_p.H754H|TERT_ENST00000508104.2_Silent_p.H754H	NM_001193376.1|NM_198253.2	NP_001180305.1|NP_937983.2	O14746	TERT_HUMAN	telomerase reverse transcriptase	754	Reverse transcriptase. {ECO:0000255|PROSITE-ProRule:PRU00405}.				DNA strand elongation (GO:0022616)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|replicative senescence (GO:0090399)|telomere formation via telomerase (GO:0032203)|telomere maintenance (GO:0000723)|telomere maintenance via telomerase (GO:0007004)	chromosome, telomeric region (GO:0000781)|cytoplasm (GO:0005737)|nuclear telomere cap complex (GO:0000783)|nucleoplasm (GO:0005654)|telomerase holoenzyme complex (GO:0005697)	metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|telomerase activity (GO:0003720)|telomeric DNA binding (GO:0042162)|telomeric RNA binding (GO:0070034)|telomeric template RNA reverse transcriptase activity (GO:0003721)	p.H742H(1)|p.H754H(1)		NS(1)|breast(1)|central_nervous_system(3)|endometrium(2)|kidney(4)|large_intestine(3)|lung(22)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)	41	all_cancers(3;3.17e-16)|Lung NSC(6;8.55e-15)|all_lung(6;7.2e-14)|all_epithelial(6;1.87e-10)		Epithelial(17;0.00105)|all cancers(22;0.00178)|OV - Ovarian serous cystadenocarcinoma(19;0.00239)|Lung(60;0.185)		Zidovudine(DB00495)	CCTTGCGGACGTGCCCATGGG	0.572									TERT Mutation-Associated Haematological Disorders;Pulmonary Fibrosis, Idiopathic;Congenital Dyskeratosis																												p.H754H												.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.C2262T	5						.						434.0	348.0	377.0					5																	1278780		2203	4300	6503	1331780	SO:0001819	synonymous_variant	7015	exon6	Familial Cancer Database	;Hamman-Rich syndrome, Fibrocystic Pulmonary Dysplasia;Zinsser-Engman-Cole syndrome, Dyskeratosis Congenita	AF015950	CCDS3861.2, CCDS54831.1	5p15.33	2014-09-17			ENSG00000164362	ENSG00000164362			11730	protein-coding gene	gene with protein product		187270				9252327	Standard	NM_198253		Approved	TRT, TP2, TCS1, hEST2, EST2	uc003jcb.1	O14746	OTTHUMG00000090357	ENST00000310581.5:c.2262C>T	5.37:g.1278780G>A		Somatic		Capture	Illumina HiSeq	Phase_I	1331780	NM_198253	O14783|Q2XS35|Q8N6C3|Q8NG38|Q8NG46	Missense_Mutation	SNP	ENST00000310581.5	37	CCDS3861.2																																																																																				0.572	TERT-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000206729.2		
ACSL6	23305	broad.mit.edu	37	5	131310506	131310506	+	Intron	SNP	G	G	A	rs532058565		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr5:131310506G>A	ENST00000379240.1	-	11	1147				ACSL6_ENST00000543479.1_Missense_Mutation_p.A313V|ACSL6_ENST00000296869.4_Missense_Mutation_p.A338V|ACSL6_ENST00000379244.1_Missense_Mutation_p.A313V|ACSL6_ENST00000544770.1_Intron|ACSL6_ENST00000379249.3_Missense_Mutation_p.A313V|ACSL6_ENST00000379272.2_Intron|ACSL6_ENST00000431707.1_Intron|ACSL6_ENST00000379264.2_Intron|ACSL6_ENST00000379246.1_Intron|ACSL6_ENST00000357096.1_Intron|ACSL6_ENST00000379255.1_Intron			Q9UKU0	ACSL6_HUMAN	acyl-CoA synthetase long-chain family member 6						acyl-CoA metabolic process (GO:0006637)|cellular lipid metabolic process (GO:0044255)|cellular response to insulin stimulus (GO:0032869)|fatty acid transport (GO:0015908)|long-chain fatty acid metabolic process (GO:0001676)|long-chain fatty-acyl-CoA biosynthetic process (GO:0035338)|neuroblast proliferation (GO:0007405)|neuron development (GO:0048666)|phospholipid biosynthetic process (GO:0008654)|positive regulation of neuron projection development (GO:0010976)|positive regulation of plasma membrane long-chain fatty acid transport (GO:0010747)|positive regulation of triglyceride biosynthetic process (GO:0010867)|response to gravity (GO:0009629)|response to hypoxia (GO:0001666)|response to nutrient (GO:0007584)|response to steroid hormone (GO:0048545)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrial outer membrane (GO:0005741)|nucleus (GO:0005634)|peroxisome (GO:0005777)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|enzyme binding (GO:0019899)|long-chain fatty acid-CoA ligase activity (GO:0004467)|protein homodimerization activity (GO:0042803)	p.A338V(1)		NS(1)|breast(1)|endometrium(2)|kidney(4)|large_intestine(8)|lung(12)|ovary(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	35		all_cancers(142;0.107)|Breast(839;0.198)|Lung NSC(810;0.216)|all_lung(232;0.248)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			GTGCACATCCGCACAAGTGGG	0.522													G|||	1	0.000199681	0.0	0.0014	5008	,	,		21690	0.0		0.0	False		,,,				2504	0.0				p.A338V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1013T	5						.						62.0	57.0	59.0					5																	131310506		2203	4300	6503	131338405	SO:0001627	intron_variant	23305	exon11			AB020644	CCDS34228.1, CCDS34229.1, CCDS56381.1, CCDS56382.1, CCDS56383.1	5q31	2008-02-05	2004-02-19	2004-02-20	ENSG00000164398	ENSG00000164398		"""Acyl-CoA synthetase family"""	16496	protein-coding gene	gene with protein product		604443	"""fatty-acid-Coenzyme A ligase, long-chain 6"""	FACL6		10502316, 10548543	Standard	NM_015256		Approved	KIAA0837, ACS2, LACS5, LACS2	uc003kvy.2	Q9UKU0	OTTHUMG00000150692	ENST00000379240.1:c.993+79C>T	5.37:g.131310506G>A		Somatic		Capture	Illumina HiSeq	Phase_I	131338405	NM_015256	J3KPG3|O94924|O95829|Q108M9|Q108N0|Q4G191|Q86TN7	Missense_Mutation	SNP	ENST00000379240.1	37		.	.	.	.	.	.	.	.	.	.	G	15.10	2.731951	0.48939	.	.	ENSG00000164398	ENST00000379249;ENST00000296869;ENST00000379244;ENST00000543479;ENST00000434099	T;T;T;T;T	0.11063	2.81;2.81;2.81;2.81;2.81	5.16	3.12	0.35913	.	0.203031	0.51477	D	0.000088	T	0.08358	0.0208	N	0.19112	0.55	0.80722	D	1	B;B;B	0.18461	0.011;0.028;0.023	B;B;B	0.26202	0.021;0.067;0.04	T	0.17715	-1.0360	10	0.56958	D	0.05	.	11.452	0.50158	0.0:0.0:0.3786:0.6214	.	313;303;338	Q9UKU0-3;B4DFW3;Q9UKU0-8	.;.;.	V	313;338;313;313;278	ENSP00000368551:A313V;ENSP00000296869:A338V;ENSP00000368546:A313V;ENSP00000442124:A313V;ENSP00000397507:A278V	ENSP00000296869:A338V	A	-	2	0	ACSL6	131338405	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	4.061000	0.57485	1.147000	0.42369	0.555000	0.69702	GCG		0.522	ACSL6-004	NOVEL	basic|appris_candidate_longest|exp_conf	protein_coding	protein_coding	OTTHUMT00000132622.1	NM_015256	
CDKL3	51265	broad.mit.edu	37	5	133642368	133642368	+	Missense_Mutation	SNP	G	G	A	rs550312225	byFrequency	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr5:133642368G>A	ENST00000265334.4	-	10	1508	c.1390C>T	c.(1390-1392)Cgc>Tgc	p.R464C	CDKL3_ENST00000609383.1_Intron|CDKL3_ENST00000435240.2_Missense_Mutation_p.R169C|CDKL3_ENST00000536186.1_Missense_Mutation_p.R169C|CDKL3_ENST00000521118.1_Missense_Mutation_p.R464C|CDKL3_ENST00000523054.1_Missense_Mutation_p.R275C|CTD-2410N18.4_ENST00000518409.1_RNA|CDKL3_ENST00000609654.1_Missense_Mutation_p.R275C	NM_001113575.1	NP_001107047.1	Q8IVW4	CDKL3_HUMAN	cyclin-dependent kinase-like 3	464					cellular protein modification process (GO:0006464)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)|protein kinase activity (GO:0004672)	p.R464C(2)		breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(3)|prostate(3)	11			KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			GAAGAAGTGCGTCTCTTTTTT	0.333													G|||	2	0.000399361	0.0	0.0014	5008	,	,		17516	0.0		0.001	False		,,,				2504	0.0				p.R464C												.	.	2	Substitution - Missense(2)	large_intestine(1)|endometrium(1)	c.C1390T	5						.						100.0	89.0	92.0					5																	133642368		1568	3582	5150	133670267	SO:0001583	missense	51265	exon10			AF130372	CCDS47264.1, CCDS47265.1, CCDS75303.1	5q31.1	2014-09-09			ENSG00000006837	ENSG00000006837	2.7.11.22	"""Cyclin-dependent kinases"""	15483	protein-coding gene	gene with protein product	"""serine-threonine protein kinase NKIAMRE"""	608459				10463609	Standard	NM_016508		Approved	NKIAMRE	uc003kzf.4	Q8IVW4	OTTHUMG00000186341	ENST00000265334.4:c.1390C>T	5.37:g.133642368G>A	ENSP00000265334:p.Arg464Cys	Somatic		Capture	Illumina HiSeq	Phase_I	133670267	NM_001113575	D3DQA0|D3DQA1|Q9P114	Missense_Mutation	SNP	ENST00000265334.4	37	CCDS47264.1	.	.	.	.	.	.	.	.	.	.	G	12.83	2.056848	0.36277	.	.	ENSG00000006837	ENST00000536186;ENST00000435240;ENST00000265334;ENST00000523054;ENST00000521118	T;T;T;T;T	0.76968	0.29;0.27;-1.0;-1.01;-1.06	5.28	3.1	0.35709	.	0.215024	0.32134	N	0.006532	T	0.77267	0.4105	L	0.32530	0.975	0.80722	D	1	D;B;B;B;D	0.89917	1.0;0.055;0.032;0.004;0.998	D;B;B;B;P	0.63703	0.917;0.011;0.02;0.003;0.609	T	0.76926	-0.2778	10	0.87932	D	0	-34.7746	6.4981	0.22153	0.1228:0.0:0.7115:0.1657	.	275;169;169;275;464	B4DX41;B4DRK6;B4DGS2;B7Z2C5;Q8IVW4	.;.;.;.;CDKL3_HUMAN	C	169;169;464;275;464	ENSP00000441545:R169C;ENSP00000399807:R169C;ENSP00000265334:R464C;ENSP00000428500:R275C;ENSP00000428689:R464C	ENSP00000265334:R464C	R	-	1	0	CDKL3	133670267	0.443000	0.25641	0.966000	0.40874	0.047000	0.14425	0.617000	0.24359	1.112000	0.41740	0.462000	0.41574	CGC		0.333	CDKL3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000377697.1	NM_001113575	
HSPA9	3313	broad.mit.edu	37	5	137902719	137902719	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr5:137902719G>A	ENST00000297185.3	-	8	975	c.850C>T	c.(850-852)Cgg>Tgg	p.R284W	HSPA9_ENST00000501917.2_5'Flank	NM_004134.6	NP_004125.3	P38646	GRP75_HUMAN	heat shock 70kDa protein 9 (mortalin)	284					cellular protein metabolic process (GO:0044267)|negative regulation of apoptotic process (GO:0043066)|protein export from nucleus (GO:0006611)|protein folding (GO:0006457)|protein targeting to mitochondrion (GO:0006626)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)|unfolded protein binding (GO:0051082)	p.R284W(1)		breast(2)|endometrium(1)|kidney(4)|large_intestine(8)|lung(12)|upper_aerodigestive_tract(1)	28			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00325)			ACAATGTGCCGTAGCAAGGCC	0.413																																					p.R284W												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C850T	5						.						148.0	154.0	152.0					5																	137902719		2203	4300	6503	137930618	SO:0001583	missense	3313	exon8			L11066	CCDS4208.1	5q31.1	2011-09-02	2006-10-31	2006-10-31	ENSG00000113013	ENSG00000113013		"""Heat shock proteins / HSP70"""	5244	protein-coding gene	gene with protein product		600548	"""heat shock 70kDa protein 9B (mortalin-2)"""	HSPA9B		7684501	Standard	NM_004134		Approved	GRP75, PBP74, mot-2, mthsp75	uc003ldf.3	P38646	OTTHUMG00000129206	ENST00000297185.3:c.850C>T	5.37:g.137902719G>A	ENSP00000297185:p.Arg284Trp	Somatic		Capture	Illumina HiSeq	Phase_I	137930618	NM_004134	B2RCM1|P30036|P31932|Q1HB43|Q53H23|Q6GU03|Q9BWB7|Q9UC56	Missense_Mutation	SNP	ENST00000297185.3	37	CCDS4208.1	.	.	.	.	.	.	.	.	.	.	G	16.30	3.085032	0.55861	.	.	ENSG00000113013	ENST00000297185;ENST00000541333;ENST00000540484	T	0.32023	1.47	5.2	5.2	0.72013	.	0.615022	0.17560	N	0.169854	T	0.49389	0.1554	M	0.92367	3.3	0.38909	D	0.95749	B;B	0.13145	0.001;0.007	B;B	0.11329	0.005;0.006	T	0.58956	-0.7544	10	0.87932	D	0	0.3905	18.7029	0.91627	0.0:0.0:1.0:0.0	.	215;284	B7Z1V7;P38646	.;GRP75_HUMAN	W	284;237;270	ENSP00000297185:R284W	ENSP00000297185:R284W	R	-	1	2	HSPA9	137930618	0.994000	0.37717	0.994000	0.49952	0.992000	0.81027	4.108000	0.57817	2.566000	0.86566	0.655000	0.94253	CGG		0.413	HSPA9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251285.1	NM_004134	
CTNNA1	1495	broad.mit.edu	37	5	138266583	138266583	+	Nonsense_Mutation	SNP	G	G	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr5:138266583G>T	ENST00000302763.7	+	16	2347	c.2257G>T	c.(2257-2259)Gga>Tga	p.G753*	CTNNA1_ENST00000355078.5_Nonsense_Mutation_p.G650*|CTNNA1_ENST00000540387.1_Nonsense_Mutation_p.G383*|CTNNA1_ENST00000518825.1_Nonsense_Mutation_p.G753*	NM_001903.2	NP_001894.2	P35221	CTNA1_HUMAN	catenin (cadherin-associated protein), alpha 1, 102kDa	753					adherens junction organization (GO:0034332)|aging (GO:0007568)|apical junction assembly (GO:0043297)|axon regeneration (GO:0031103)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|cellular protein localization (GO:0034613)|cellular response to indole-3-methanol (GO:0071681)|epithelial cell-cell adhesion (GO:0090136)|establishment or maintenance of cell polarity (GO:0007163)|gap junction assembly (GO:0016264)|male gonad development (GO:0008584)|muscle cell differentiation (GO:0042692)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell motility (GO:2000146)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|negative regulation of integrin-mediated signaling pathway (GO:2001045)|negative regulation of neuroblast proliferation (GO:0007406)|odontogenesis of dentin-containing tooth (GO:0042475)|ovarian follicle development (GO:0001541)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of smoothened signaling pathway (GO:0045880)|protein heterooligomerization (GO:0051291)|response to estrogen (GO:0043627)	acrosomal vesicle (GO:0001669)|actin cytoskeleton (GO:0015629)|catenin complex (GO:0016342)|cell-cell junction (GO:0005911)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|intercalated disc (GO:0014704)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|zonula adherens (GO:0005915)	beta-catenin binding (GO:0008013)|cadherin binding (GO:0045296)|gamma-catenin binding (GO:0045295)|poly(A) RNA binding (GO:0044822)|structural molecule activity (GO:0005198)|vinculin binding (GO:0017166)	p.G753*(1)		NS(1)|breast(7)|cervix(2)|endometrium(4)|kidney(6)|large_intestine(16)|lung(9)|oesophagus(2)|ovary(3)|prostate(1)|upper_aerodigestive_tract(1)	52			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00325)			TGCTGAGGCAGGATCCAGGAT	0.512																																					p.G753X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.G2257T	5						.						81.0	81.0	81.0					5																	138266583		2203	4300	6503	138294482	SO:0001587	stop_gained	1495	exon16			D13866	CCDS34243.1, CCDS75315.1	5q31.2	2008-02-05	2002-08-29			ENSG00000044115			2509	protein-coding gene	gene with protein product		116805	"""catenin (cadherin-associated protein), alpha 1 (102kD)"""			1924379	Standard	XM_005271898		Approved	CAP102	uc003ldh.3	P35221		ENST00000302763.7:c.2257G>T	5.37:g.138266583G>T	ENSP00000304669:p.Gly753*	Somatic		Capture	Illumina HiSeq	Phase_I	138294482	NM_001903	Q12795|Q8N1C0	Nonsense_Mutation	SNP	ENST00000302763.7	37	CCDS34243.1	.	.	.	.	.	.	.	.	.	.	G	38	7.141802	0.98092	.	.	ENSG00000044115	ENST00000355078;ENST00000302763;ENST00000537034;ENST00000541863;ENST00000518825;ENST00000540387;ENST00000520520	.	.	.	5.43	5.43	0.79202	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	-16.203	19.0128	0.92881	0.0:0.0:1.0:0.0	.	.	.	.	X	650;753;753;738;753;383;28	.	ENSP00000304669:G753X	G	+	1	0	CTNNA1	138294482	1.000000	0.71417	0.990000	0.47175	0.987000	0.75469	9.635000	0.98437	2.825000	0.97269	0.655000	0.94253	GGA		0.512	CTNNA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373868.1	NM_001903	
CXXC5	51523	broad.mit.edu	37	5	139060342	139060342	+	Silent	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr5:139060342G>A	ENST00000302517.3	+	2	948	c.234G>A	c.(232-234)ccG>ccA	p.P78P	CXXC5_ENST00000511048.1_Silent_p.P78P	NM_016463.7	NP_057547.5	Q7LFL8	CXXC5_HUMAN	CXXC finger protein 5	78					positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nucleolus (GO:0005730)	DNA binding (GO:0003677)|signal transducer activity (GO:0004871)|zinc ion binding (GO:0008270)	p.P78P(1)		central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(7)|upper_aerodigestive_tract(1)	12			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GCTCCCGCCCGCTCTCCCACT	0.637																																					p.P78P												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G234A	5						.						60.0	76.0	71.0					5																	139060342		2088	4211	6299	139040526	SO:0001819	synonymous_variant	51523	exon2			AK024338	CCDS43370.1	5q31.3	2014-02-18	2011-12-01						26943	protein-coding gene	gene with protein product	"""retinoid-inducible nuclear factor"", ""WT1-induced Inhibitor of Dishevelled"""	612752				11042152, 19001364, 19182210, 20220130	Standard	NM_016463		Approved	HSPC195, RINF, WID	uc010jfg.1	Q7LFL8		ENST00000302517.3:c.234G>A	5.37:g.139060342G>A		Somatic		Capture	Illumina HiSeq	Phase_I	139040526	NM_016463	B3KND0|C8CBA8|Q8TB79|Q9NV51|Q9P0S8	Silent	SNP	ENST00000302517.3	37	CCDS43370.1																																																																																				0.637	CXXC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372744.1	NM_016463	
NRG2	9542	broad.mit.edu	37	5	139267060	139267060	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr5:139267060G>A	ENST00000361474.1	-	2	961	c.737C>T	c.(736-738)aCg>aTg	p.T246M	NRG2_ENST00000340391.3_Missense_Mutation_p.T43M|NRG2_ENST00000289422.7_Missense_Mutation_p.T246M|NRG2_ENST00000394770.1_Missense_Mutation_p.T246M|NRG2_ENST00000358522.3_Missense_Mutation_p.T246M|NRG2_ENST00000289409.4_Missense_Mutation_p.T246M|NRG2_ENST00000545385.1_Missense_Mutation_p.T246M|NRG2_ENST00000541337.1_Missense_Mutation_p.T246M|NRG2_ENST00000518130.1_5'UTR	NM_004883.2	NP_004874.1	O14511	NRG2_HUMAN	neuregulin 2	246	Ig-like C2-type.				embryo development (GO:0009790)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|signal transduction (GO:0007165)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	receptor binding (GO:0005102)	p.T154M(2)|p.T246M(2)		breast(2)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(5)|ovary(1)|pancreas(2)|prostate(1)|skin(1)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(1)	25			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CACCTGTCCCGTCTGGCTCTT	0.582																																					p.T246M												.	.	4	Substitution - Missense(4)	large_intestine(4)	c.C737T	5						.						96.0	81.0	86.0					5																	139267060		2203	4300	6503	139247244	SO:0001583	missense	9542	exon2				CCDS4217.1, CCDS54910.1	5q23-q33	2013-01-11			ENSG00000158458	ENSG00000158458		"""Immunoglobulin superfamily / I-set domain containing"""	7998	protein-coding gene	gene with protein product	"""neural- and thymus-derived activator for ErbB kinases"", ""divergent of neuregulin-1"""	603818				9168114, 9168115	Standard	NM_004883		Approved	Don-1, NTAK, HRG2	uc003lev.2	O14511	OTTHUMG00000129241	ENST00000361474.1:c.737C>T	5.37:g.139267060G>A	ENSP00000354910:p.Thr246Met	Somatic		Capture	Illumina HiSeq	Phase_I	139247244	NM_013981		Missense_Mutation	SNP	ENST00000361474.1	37	CCDS4217.1	.	.	.	.	.	.	.	.	.	.	G	17.85	3.491233	0.64074	.	.	ENSG00000158458	ENST00000541337;ENST00000289422;ENST00000361474;ENST00000446269;ENST00000545385;ENST00000394770;ENST00000340391;ENST00000289409;ENST00000358522;ENST00000544729;ENST00000378238	T;T;T;T;T;T;T;T;T	0.68624	-0.34;-0.34;-0.34;-0.34;-0.34;-0.34;-0.34;-0.34;-0.34	5.29	4.36	0.52297	Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.349244	0.26616	N	0.023382	T	0.66327	0.2778	M	0.68317	2.08	0.37234	D	0.905809	P;P;P;P	0.47253	0.868;0.725;0.868;0.892	B;B;B;P	0.45232	0.294;0.37;0.294;0.474	T	0.74269	-0.3720	10	0.59425	D	0.04	-8.1125	10.3883	0.44154	0.0:0.0:0.7124:0.2876	.	246;246;246;246	O14511-2;O14511;O14511-4;O14511-3	.;NRG2_HUMAN;.;.	M	246;246;246;246;246;246;43;246;246;154;246	ENSP00000444235:T246M;ENSP00000289422:T246M;ENSP00000354910:T246M;ENSP00000438753:T246M;ENSP00000378251:T246M;ENSP00000342660:T43M;ENSP00000289409:T246M;ENSP00000351323:T246M;ENSP00000367483:T246M	ENSP00000289409:T246M	T	-	2	0	NRG2	139247244	0.990000	0.36364	0.969000	0.41365	0.991000	0.79684	2.167000	0.42415	2.473000	0.83533	0.462000	0.41574	ACG		0.582	NRG2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000251340.1	NM_013982	
SLC35A4	113829	broad.mit.edu	37	5	139946949	139946949	+	Silent	SNP	C	C	T	rs150614957		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr5:139946949C>T	ENST00000514199.1	+	2	1881	c.195C>T	c.(193-195)tgC>tgT	p.C65C	APBB3_ENST00000507279.1_Intron|APBB3_ENST00000357560.4_5'Flank|SLC35A4_ENST00000323146.3_Silent_p.C65C|APBB3_ENST00000508496.2_5'Flank			Q96G79	S35A4_HUMAN	solute carrier family 35, member A4	65	Leu-rich.					Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	sugar:proton symporter activity (GO:0005351)	p.C65C(1)		endometrium(4)|kidney(2)|large_intestine(3)|lung(4)	13			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TACTGTTATGCGCCTTCTCCC	0.652													.|||	1	0.000199681	0.0	0.0	5008	,	,		20809	0.001		0.0	False		,,,				2504	0.0				p.C65C												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C195T	5						.						63.0	55.0	57.0					5																	139946949		2203	4299	6502	139927133	SO:0001819	synonymous_variant	113829	exon3			AJ420598	CCDS4231.1	5q31.3	2013-05-22			ENSG00000176087	ENSG00000176087		"""Solute carriers"""	20753	protein-coding gene	gene with protein product							Standard	NM_080670		Approved		uc003lgg.1	Q96G79	OTTHUMG00000129495	ENST00000514199.1:c.195C>T	5.37:g.139946949C>T		Somatic		Capture	Illumina HiSeq	Phase_I	139927133	NM_080670	A8K013	Silent	SNP	ENST00000514199.1	37	CCDS4231.1																																																																																				0.652	SLC35A4-004	PUTATIVE	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372815.1	NM_080670	
PCDHA8	56140	broad.mit.edu	37	5	140222666	140222666	+	Missense_Mutation	SNP	C	C	T	rs564409198		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr5:140222666C>T	ENST00000531613.1	+	1	1760	c.1760C>T	c.(1759-1761)gCg>gTg	p.A587V	PCDHA5_ENST00000529859.1_Intron|PCDHA7_ENST00000525929.1_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA8_ENST00000378123.3_Missense_Mutation_p.A587V|PCDHA6_ENST00000529310.1_Intron|PCDHA6_ENST00000527624.1_Intron	NM_018911.2	NP_061734.1	Q9Y5H6	PCDA8_HUMAN	protocadherin alpha 8	587	Cadherin 6. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)	p.A587V(2)		NS(2)|breast(3)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(10)|lung(31)|ovary(2)|prostate(2)|skin(4)|stomach(2)|upper_aerodigestive_tract(6)	78			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TCTGTGGGCGCGGGCCACGTG	0.677																																					p.A587V												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.C1760T	5						.						59.0	62.0	61.0					5																	140222666		2196	4264	6460	140202850	SO:0001583	missense	56140	exon1			AF152486	CCDS54919.1	5q31	2010-11-26				ENSG00000204962		"""Cadherins / Protocadherins : Clustered"""	8674	other	complex locus constituent	"""KIAA0345-like 6"""	606314				10380929	Standard	NM_018911		Approved			Q9Y5H6		ENST00000531613.1:c.1760C>T	5.37:g.140222666C>T	ENSP00000434655:p.Ala587Val	Somatic		Capture	Illumina HiSeq	Phase_I	140202850	NM_031856	B9EGT7|O75281	Missense_Mutation	SNP	ENST00000531613.1	37	CCDS54919.1	.	.	.	.	.	.	.	.	.	.	C	7.599	0.672322	0.14776	.	.	ENSG00000204962	ENST00000531613;ENST00000378123	T;T	0.18960	2.18;2.18	3.71	1.84	0.25277	Cadherin (2);Cadherin-like (1);	0.221904	0.22057	U	0.065239	T	0.10723	0.0262	N	0.17345	0.48	0.22017	N	0.999415	B;B	0.15141	0.01;0.012	B;B	0.12837	0.008;0.008	T	0.23084	-1.0198	10	0.36615	T	0.2	.	5.3007	0.15776	0.1599:0.6369:0.0:0.2032	.	587;587	Q9Y5H6;Q9Y5H6-2	PCDA8_HUMAN;.	V	587	ENSP00000434655:A587V;ENSP00000367363:A587V	ENSP00000367363:A587V	A	+	2	0	PCDHA8	140202850	0.000000	0.05858	0.040000	0.18447	0.002000	0.02628	-0.241000	0.08940	0.174000	0.19809	-1.231000	0.01572	GCG		0.677	PCDHA8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372830.2	NM_018911	
PCDHB7	56129	broad.mit.edu	37	5	140553577	140553577	+	Silent	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr5:140553577C>T	ENST00000231137.3	+	1	1335	c.1161C>T	c.(1159-1161)gaC>gaT	p.D387D		NM_018940.2	NP_061763.1	Q9Y5E2	PCDB7_HUMAN	protocadherin beta 7	387	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.D387D(1)		NS(2)|breast(2)|central_nervous_system(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(20)|lung(54)|ovary(5)|prostate(7)|skin(7)|upper_aerodigestive_tract(4)|urinary_tract(1)	119			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			CCATCCAGGACGATGTCCCCT	0.473																																					p.D387D												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1161T	5						.						73.0	74.0	73.0					5																	140553577		2203	4300	6503	140533761	SO:0001819	synonymous_variant	56129	exon1			AF152500	CCDS4249.1	5q31	2010-01-26			ENSG00000113212	ENSG00000113212		"""Cadherins / Protocadherins : Clustered"""	8692	other	protocadherin		606333				10380929	Standard	NM_018940		Approved	PCDH-BETA7	uc003lit.3	Q9Y5E2	OTTHUMG00000129608	ENST00000231137.3:c.1161C>T	5.37:g.140553577C>T		Somatic		Capture	Illumina HiSeq	Phase_I	140533761	NM_018940	A1L3Y8	Silent	SNP	ENST00000231137.3	37	CCDS4249.1																																																																																				0.473	PCDHB7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251803.2	NM_018940	
PCDHB16	57717	broad.mit.edu	37	5	140562651	140562651	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr5:140562651A>G	ENST00000361016.2	+	1	1672	c.517A>G	c.(517-519)Agc>Ggc	p.S173G		NM_020957.1	NP_066008.1	Q9NRJ7	PCDBG_HUMAN	protocadherin beta 16	173	Cadherin 2. {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.S173G(1)		breast(1)|endometrium(10)|kidney(3)|large_intestine(14)|lung(29)|ovary(5)|pancreas(2)|prostate(3)|skin(1)|urinary_tract(1)	69			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			CTATAAAATCAGCCCAAGCTC	0.443																																					p.S173G												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A517G	5						.						43.0	46.0	45.0					5																	140562651		2201	4297	6498	140542835	SO:0001583	missense	57717	exon1			AF217757	CCDS4251.1	5q31	2014-04-11			ENSG00000196963			"""Cadherins / Protocadherins : Clustered"""	14546	other	protocadherin	"""cadherin ME1"", ""protocadherin-3x"", ""PCDHbeta 16"""	606345				11230163, 11322959	Standard	NM_020957		Approved	PCDHB8a, PCDH3X, KIAA1621, PCDH-BETA16, ME1	uc003liv.3	Q9NRJ7	OTTHUMG00000188325	ENST00000361016.2:c.517A>G	5.37:g.140562651A>G	ENSP00000354293:p.Ser173Gly	Somatic		Capture	Illumina HiSeq	Phase_I	140542835	NM_020957	B3KPK5|Q8IYD5|Q96SE9|Q9HCF1	Missense_Mutation	SNP	ENST00000361016.2	37	CCDS4251.1	.	.	.	.	.	.	.	.	.	.	A	6.551	0.469980	0.12461	.	.	ENSG00000196963	ENST00000361016	T	0.54071	0.59	4.69	3.46	0.39613	Cadherin (4);Cadherin-like (1);	0.000000	0.40908	D	0.000982	T	0.52240	0.1722	M	0.76002	2.32	0.09310	N	1	B	0.20368	0.044	B	0.26693	0.072	T	0.54377	-0.8303	10	0.72032	D	0.01	.	9.6546	0.39919	0.7238:0.0:0.0:0.2762	.	173	Q9NRJ7	PCDBG_HUMAN	G	173	ENSP00000354293:S173G	ENSP00000354293:S173G	S	+	1	0	PCDHB16	140542835	0.000000	0.05858	0.014000	0.15608	0.141000	0.21300	0.964000	0.29306	1.737000	0.51674	0.533000	0.62120	AGC		0.443	PCDHB16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251800.1	NM_020957	
PCDHB16	57717	broad.mit.edu	37	5	140568307	140568307	+	IGR	SNP	T	T	C	rs17844523		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr5:140568307T>C	ENST00000361016.2	+	0	4814					NM_020957.1	NP_066008.1	Q9NRJ7	PCDBG_HUMAN	protocadherin beta 16						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)			breast(1)|endometrium(10)|kidney(3)|large_intestine(14)|lung(29)|ovary(5)|pancreas(2)|prostate(3)|skin(1)|urinary_tract(1)	69			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			ACATCGGCAGTGTCAGCGCCA	0.652																																					p.V472A												.	.	0			c.T1415C	5						.						94.0	106.0	102.0					5																	140568307		2203	4296	6499	140548491	SO:0001628	intergenic_variant	56127	exon1			AF217757	CCDS4251.1	5q31	2014-04-11			ENSG00000196963			"""Cadherins / Protocadherins : Clustered"""	14546	other	protocadherin	"""cadherin ME1"", ""protocadherin-3x"", ""PCDHbeta 16"""	606345				11230163, 11322959	Standard	NM_020957		Approved	PCDHB8a, PCDH3X, KIAA1621, PCDH-BETA16, ME1	uc003liv.3	Q9NRJ7	OTTHUMG00000188325		5.37:g.140568307T>C		Somatic		Capture	Illumina HiSeq	Phase_I	140548491	NM_019119	B3KPK5|Q8IYD5|Q96SE9|Q9HCF1	Silent	SNP	ENST00000361016.2	37	CCDS4251.1																																																																																				0.652	PCDHB16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251800.1	NM_020957	
PCDHGA2	56113	broad.mit.edu	37	5	140720504	140720504	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr5:140720504G>A	ENST00000394576.2	+	1	1966	c.1966G>A	c.(1966-1968)Gcc>Acc	p.A656T	PCDHGA1_ENST00000517417.1_Intron	NM_018915.2	NP_061738.1	Q9Y5H1	PCDG2_HUMAN	protocadherin gamma subfamily A, 2	656	Cadherin 6. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.A656T(1)		breast(3)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(20)|lung(32)|ovary(1)|prostate(4)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	77			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CCCTCTCTCCGCCACTGTCAC	0.701																																					p.A656T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1966A	5						.						34.0	41.0	39.0					5																	140720504		2200	4295	6495	140700688	SO:0001583	missense	56113	exon1			AF152508	CCDS47289.1	5q31	2011-03-28			ENSG00000081853	ENSG00000081853		"""Cadherins / Protocadherins : Clustered"""	8700	other	protocadherin		606289				10380929	Standard	NM_018915		Approved	PCDH-GAMMA-A2		Q9Y5H1	OTTHUMG00000163679	ENST00000394576.2:c.1966G>A	5.37:g.140720504G>A	ENSP00000378077:p.Ala656Thr	Somatic		Capture	Illumina HiSeq	Phase_I	140700688	NM_032009	Q52LL6|Q9Y5D5	Missense_Mutation	SNP	ENST00000394576.2	37	CCDS47289.1	.	.	.	.	.	.	.	.	.	.	.	11.41	1.630332	0.28978	.	.	ENSG00000081853	ENST00000394576	T	0.51071	0.72	5.14	4.27	0.50696	Cadherin (4);Cadherin-like (1);	0.000000	0.41097	U	0.000956	T	0.42291	0.1196	L	0.39326	1.205	0.28900	N	0.893339	P;P	0.45594	0.709;0.862	B;B	0.41466	0.261;0.358	T	0.44205	-0.9343	10	0.56958	D	0.05	.	15.2028	0.73153	0.0:0.0:0.8582:0.1418	.	656;656	Q9Y5H1-2;Q9Y5H1	.;PCDG2_HUMAN	T	656	ENSP00000378077:A656T	ENSP00000378077:A656T	A	+	1	0	PCDHGA2	140700688	0.417000	0.25432	0.783000	0.31826	0.012000	0.07955	1.220000	0.32491	1.310000	0.45006	0.485000	0.47835	GCC		0.701	PCDHGA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374738.1	NM_018915	
FCHSD1	89848	broad.mit.edu	37	5	141021127	141021127	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr5:141021127G>A	ENST00000435817.2	-	20	2061	c.2011C>T	c.(2011-2013)Cgt>Tgt	p.R671C	FCHSD1_ENST00000522126.1_3'UTR|FCHSD1_ENST00000523856.1_5'UTR|FCHSD1_ENST00000522783.1_3'UTR	NM_033449.2	NP_258260.1	Q86WN1	FCSD1_HUMAN	FCH and double SH3 domains 1	671	Pro-rich.							p.R671C(1)	FCHSD1/BRAF(2)	central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(8)|lung(5)|ovary(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	24			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GGTGGTGGACGCATCTGTAGG	0.582																																					p.R671C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C2011T	5						.						52.0	62.0	59.0					5																	141021127		1961	4136	6097	141001311	SO:0001583	missense	89848	exon20			AK027281	CCDS47295.1	5q31.3	2008-02-05			ENSG00000197948	ENSG00000197948			25463	protein-coding gene	gene with protein product						11214971, 15067381	Standard	NM_033449		Approved	FLJ00007	uc003llk.3	Q86WN1	OTTHUMG00000163762	ENST00000435817.2:c.2011C>T	5.37:g.141021127G>A	ENSP00000399259:p.Arg671Cys	Somatic		Capture	Illumina HiSeq	Phase_I	141001311	NM_033449	Q6UX75|Q86Y77|Q9NXX8	Missense_Mutation	SNP	ENST00000435817.2	37	CCDS47295.1	.	.	.	.	.	.	.	.	.	.	G	17.64	3.438965	0.63067	.	.	ENSG00000197948	ENST00000435817	T	0.28895	1.59	5.25	5.25	0.73442	.	0.068186	0.64402	D	0.000012	T	0.44307	0.1287	L	0.32530	0.975	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.79108	0.992;0.982	T	0.24440	-1.0160	10	0.59425	D	0.04	-13.2361	14.5305	0.67923	0.0:0.0:1.0:0.0	.	351;671	Q86WN1-2;Q86WN1	.;FCSD1_HUMAN	C	671	ENSP00000399259:R671C	ENSP00000399259:R671C	R	-	1	0	FCHSD1	141001311	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	3.309000	0.51903	2.885000	0.99019	0.655000	0.94253	CGT		0.582	FCHSD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375282.2	NM_033449	
ARAP3	64411	broad.mit.edu	37	5	141041285	141041285	+	Missense_Mutation	SNP	G	G	A	rs150284423		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr5:141041285G>A	ENST00000239440.4	-	21	3150	c.3085C>T	c.(3085-3087)Cgc>Tgc	p.R1029C	ARAP3_ENST00000513878.1_Missense_Mutation_p.R691C|ARAP3_ENST00000512390.1_5'UTR|ARAP3_ENST00000508305.1_Missense_Mutation_p.R860C	NM_022481.5	NP_071926.4	Q8WWN8	ARAP3_HUMAN	ArfGAP with RhoGAP domain, ankyrin repeat and PH domain 3	1029	Rho-GAP. {ECO:0000255|PROSITE- ProRule:PRU00172}.				cytoskeleton organization (GO:0007010)|negative regulation of cell migration (GO:0030336)|negative regulation of Rac protein signal transduction (GO:0035021)|negative regulation of Rho protein signal transduction (GO:0035024)|regulation of ARF GTPase activity (GO:0032312)|regulation of cell shape (GO:0008360)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	ARF GTPase activator activity (GO:0008060)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|phosphatidylinositol-3,4-bisphosphate binding (GO:0043325)|Rho GTPase activator activity (GO:0005100)|zinc ion binding (GO:0008270)	p.R1029C(1)		NS(1)|breast(7)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(13)|lung(14)|ovary(1)|prostate(2)|skin(4)|stomach(1)	53						GCCAGTGTGCGGCGGTTGACC	0.552													G|||	1	0.000199681	0.0008	0.0	5008	,	,		16342	0.0		0.0	False		,,,				2504	0.0				p.R1029C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C3085T	5						.	G	CYS/ARG	5,4401	9.9+/-24.2	0,5,2198	92.0	97.0	95.0		3085	3.4	1.0	5	dbSNP_134	95	0,8600		0,0,4300	yes	missense	ARAP3	NM_022481.5	180	0,5,6498	AA,AG,GG		0.0,0.1135,0.0384	probably-damaging	1029/1545	141041285	5,13001	2203	4300	6503	141021469	SO:0001583	missense	64411	exon21			AJ310567	CCDS4266.1	5q31.3	2013-01-11	2008-09-22	2008-09-22	ENSG00000120318	ENSG00000120318		"""ADP-ribosylation factor GTPase activating proteins"", ""Sterile alpha motif (SAM) domain containing"", ""Pleckstrin homology (PH) domain containing"", ""Ankyrin repeat domain containing"""	24097	protein-coding gene	gene with protein product		606647	"""centaurin, delta 3"""	CENTD3		11804589, 12015138	Standard	XM_005268497		Approved	FLJ21065, DRAG1	uc003llm.3	Q8WWN8	OTTHUMG00000129610	ENST00000239440.4:c.3085C>T	5.37:g.141041285G>A	ENSP00000239440:p.Arg1029Cys	Somatic		Capture	Illumina HiSeq	Phase_I	141021469	NM_022481	B4DIT1|D3DQE3	Missense_Mutation	SNP	ENST00000239440.4	37	CCDS4266.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	G	21.4	4.144989	0.77888	0.001135	0.0	ENSG00000120318	ENST00000508305;ENST00000239440;ENST00000513878	T;T;T	0.19806	2.12;2.12;2.12	5.33	3.39	0.38822	Rho GTPase-activating protein domain (4);Rho GTPase activation protein (1);	0.296295	0.27618	N	0.018577	T	0.27629	0.0679	L	0.28192	0.835	0.45502	D	0.998466	D;D;D	0.89917	0.999;0.999;1.0	D;P;D	0.67725	0.953;0.899;0.939	T	0.03017	-1.1082	10	0.66056	D	0.02	.	8.2156	0.31509	0.0:0.1223:0.4636:0.4141	.	691;860;1029	B4DIT1;G5E9Y3;Q8WWN8	.;.;ARAP3_HUMAN	C	860;1029;691	ENSP00000421826:R860C;ENSP00000239440:R1029C;ENSP00000421468:R691C	ENSP00000239440:R1029C	R	-	1	0	ARAP3	141021469	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	2.290000	0.43531	1.459000	0.47892	0.655000	0.94253	CGC		0.552	ARAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251805.1	NM_022481	
JAKMIP2	9832	broad.mit.edu	37	5	147040853	147040853	+	Silent	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr5:147040853C>T	ENST00000265272.5	-	3	752	c.285G>A	c.(283-285)caG>caA	p.Q95Q	JAKMIP2_ENST00000507386.1_Silent_p.Q95Q|JAKMIP2_ENST00000333010.6_Silent_p.Q53Q	NM_001270941.1|NM_014790.4	NP_001257870.1|NP_055605.2	Q96AA8	JKIP2_HUMAN	janus kinase and microtubule interacting protein 2	95						Golgi apparatus (GO:0005794)		p.Q95Q(1)		NS(1)|autonomic_ganglia(1)|breast(3)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(22)|lung(18)|ovary(3)|pancreas(1)|prostate(4)|skin(3)|upper_aerodigestive_tract(2)	64			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CCTGCTCGTGCTGCTTGATAA	0.552																																					p.Q95Q												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G285A	5						.						196.0	180.0	185.0					5																	147040853		2203	4300	6503	147021046	SO:0001819	synonymous_variant	9832	exon3			AB011127	CCDS4285.1, CCDS59495.1, CCDS64284.1, CCDS75352.1	5q32	2009-08-13	2009-08-13		ENSG00000176049	ENSG00000176049			29067	protein-coding gene	gene with protein product		611197				9628581	Standard	NM_001270941		Approved	JAMIP2, KIAA0555	uc010jgo.2	Q96AA8	OTTHUMG00000129731	ENST00000265272.5:c.285G>A	5.37:g.147040853C>T		Somatic		Capture	Illumina HiSeq	Phase_I	147021046	NM_014790	A4ZZA7|A8K5G5|B4DSG0|G5E9Y0|O60302|Q548S1	Silent	SNP	ENST00000265272.5	37	CCDS4285.1																																																																																				0.552	JAKMIP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251941.1	NM_014790	
SH3TC2	79628	broad.mit.edu	37	5	148384346	148384346	+	Silent	SNP	C	C	T	rs144873879	byFrequency	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr5:148384346C>T	ENST00000515425.1	-	17	3896	c.3795G>A	c.(3793-3795)ctG>ctA	p.L1265L	SH3TC2_ENST00000502274.1_Silent_p.L127L|SH3TC2_ENST00000538184.1_3'UTR|SH3TC2_ENST00000512049.1_Silent_p.L1258L	NM_024577.3	NP_078853.2	Q8TF17	S3TC2_HUMAN	SH3 domain and tetratricopeptide repeats 2	1265					cell death (GO:0008219)|peripheral nervous system myelin maintenance (GO:0032287)|regulation of ERBB signaling pathway (GO:1901184)|regulation of intracellular protein transport (GO:0033157)	cytoplasmic vesicle (GO:0031410)|plasma membrane (GO:0005886)|recycling endosome (GO:0055037)		p.L1265L(1)		breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(12)|ovary(3)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	39			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TGCTGTGCCACAGGGGGCTCT	0.627																																					p.L1265L												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G3795A	5						.						45.0	42.0	43.0					5																	148384346		2203	4300	6503	148364539	SO:0001819	synonymous_variant	79628	exon17			AK127248	CCDS4293.1	5q32	2014-09-17			ENSG00000169247	ENSG00000169247		"""Tetratricopeptide (TTC) repeat domain containing"""	29427	protein-coding gene	gene with protein product		608206				14574644	Standard	NM_024577		Approved	KIAA1985, CMT4C	uc003lpu.3	Q8TF17	OTTHUMG00000129930	ENST00000515425.1:c.3795G>A	5.37:g.148384346C>T		Somatic		Capture	Illumina HiSeq	Phase_I	148364539	NM_024577	B3KWE5|Q14CC0|Q14CF5|Q9H8I5	Silent	SNP	ENST00000515425.1	37	CCDS4293.1																																																																																				0.627	SH3TC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252186.2	NM_024577	
FAT2	2196	broad.mit.edu	37	5	150922979	150922979	+	Missense_Mutation	SNP	G	G	A	rs560174924	byFrequency	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr5:150922979G>A	ENST00000261800.5	-	9	7721	c.7709C>T	c.(7708-7710)aCg>aTg	p.T2570M		NM_001447.2	NP_001438.1	Q9NYQ8	FAT2_HUMAN	FAT atypical cadherin 2	2570	Cadherin 22. {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.T2570M(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)			GATCTTCACCGTGCAGAAGGC	0.463													G|||	2	0.000399361	0.0008	0.0014	5008	,	,		20024	0.0		0.0	False		,,,				2504	0.0				p.T2570M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C7709T	5						.						162.0	165.0	164.0					5																	150922979		2203	4300	6503	150903172	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.7709C>T	5.37:g.150922979G>A	ENSP00000261800:p.Thr2570Met	Somatic		Capture	Illumina HiSeq	Phase_I	150903172	NM_001447	O75091|Q9NSR7	Missense_Mutation	SNP	ENST00000261800.5	37	CCDS4317.1	.	.	.	.	.	.	.	.	.	.	G	14.24	2.474991	0.43942	.	.	ENSG00000086570	ENST00000261800	T	0.57107	0.42	5.36	4.49	0.54785	Cadherin (4);Cadherin-like (1);	0.184421	0.37857	N	0.001909	T	0.67449	0.2894	M	0.74389	2.26	0.44899	D	0.997915	D	0.71674	0.998	D	0.65323	0.934	T	0.68784	-0.5317	10	0.51188	T	0.08	.	10.066	0.42303	0.1525:0.0:0.8475:0.0	.	2570	Q9NYQ8	FAT2_HUMAN	M	2570	ENSP00000261800:T2570M	ENSP00000261800:T2570M	T	-	2	0	FAT2	150903172	1.000000	0.71417	0.825000	0.32803	0.956000	0.61745	5.474000	0.66781	1.261000	0.44149	0.462000	0.41574	ACG		0.463	FAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252434.1	NM_001447	
NMUR2	56923	broad.mit.edu	37	5	151771837	151771837	+	Missense_Mutation	SNP	A	A	G	rs554719017		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr5:151771837A>G	ENST00000255262.3	-	4	1328	c.1163T>C	c.(1162-1164)aTg>aCg	p.M388T		NM_020167.4	NP_064552.3	Q9GZQ4	NMUR2_HUMAN	neuromedin U receptor 2	388			M -> V (in dbSNP:rs4958531).		activation of phospholipase A2 activity by calcium-mediated signaling (GO:0043006)|arachidonic acid secretion (GO:0050482)|calcium ion transport (GO:0006816)|calcium-mediated signaling (GO:0019722)|cell-cell signaling (GO:0007267)|central nervous system development (GO:0007417)|chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|feeding behavior (GO:0007631)|grooming behavior (GO:0007625)|inositol phosphate-mediated signaling (GO:0048016)|neuropeptide signaling pathway (GO:0007218)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|reduction of food intake in response to dietary excess (GO:0002023)|regulation of smooth muscle contraction (GO:0006940)|response to pain (GO:0048265)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|GTP binding (GO:0005525)|intracellular calcium activated chloride channel activity (GO:0005229)|neuromedin U binding (GO:0042924)|neuromedin U receptor activity (GO:0001607)	p.M388T(1)		breast(1)|endometrium(1)|kidney(2)|large_intestine(12)|liver(1)|lung(15)|ovary(3)|pancreas(1)|prostate(4)|skin(3)|upper_aerodigestive_tract(1)	44		Medulloblastoma(196;0.091)|all_hematologic(541;0.103)	Kidney(363;0.000106)|KIRC - Kidney renal clear cell carcinoma(527;0.000672)			AGAGTTGTGCATGGATGACTG	0.483																																					p.M388T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T1163C	5						.						172.0	168.0	169.0					5																	151771837		2203	4300	6503	151752030	SO:0001583	missense	56923	exon4			AF242874	CCDS4321.1	5q33.1	2012-08-08		2004-05-28	ENSG00000132911	ENSG00000132911		"""GPCR / Class A : Neuromedin U receptors"""	16454	protein-coding gene	gene with protein product		605108		NMU2R		8940772, 10894543	Standard	NM_020167		Approved		uc003luv.2	Q9GZQ4	OTTHUMG00000130131	ENST00000255262.3:c.1163T>C	5.37:g.151771837A>G	ENSP00000255262:p.Met388Thr	Somatic		Capture	Illumina HiSeq	Phase_I	151752030	NM_020167	Q7LC54|Q96AM5|Q9NRA6	Missense_Mutation	SNP	ENST00000255262.3	37	CCDS4321.1	.	.	.	.	.	.	.	.	.	.	A	5.825	0.336394	0.11013	.	.	ENSG00000132911	ENST00000255262	T	0.68624	-0.34	4.37	0.425	0.16473	.	3.685620	0.00763	N	0.001145	T	0.41926	0.1180	N	0.02011	-0.69	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.33343	-0.9872	10	0.32370	T	0.25	-2.2138	8.3262	0.32158	0.749:0.0:0.251:0.0	.	388	Q9GZQ4	NMUR2_HUMAN	T	388	ENSP00000255262:M388T	ENSP00000255262:M388T	M	-	2	0	NMUR2	151752030	0.105000	0.21958	0.000000	0.03702	0.000000	0.00434	1.251000	0.32862	-0.013000	0.14199	-0.456000	0.05471	ATG		0.483	NMUR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252439.1	NM_020167	
FAM134B	54463	broad.mit.edu	37	5	16572168	16572168	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr5:16572168C>T	ENST00000306320.9	-	2	450	c.364G>A	c.(364-366)Gtc>Atc	p.V122I		NM_001034850.2	NP_001030022.1	Q9H6L5	F134B_HUMAN	family with sequence similarity 134, member B	122					sensory perception of pain (GO:0019233)	cis-Golgi network (GO:0005801)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)		p.V122I(1)		breast(1)|kidney(1)|large_intestine(4)|lung(5)|ovary(2)|prostate(2)|skin(1)	16						AGTATCATGACGGAAATCAGG	0.328																																					p.V122I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G364A	5						.						96.0	91.0	92.0					5																	16572168		1874	4106	5980	16625168	SO:0001583	missense	54463	exon2			BC053326	CCDS43304.1, CCDS43305.1	5p15.1	2014-09-17			ENSG00000154153	ENSG00000154153			25964	protein-coding gene	gene with protein product		613114				19838196, 24327336	Standard	NM_001034850		Approved	FLJ20152	uc003jfs.3	Q9H6L5	OTTHUMG00000161788	ENST00000306320.9:c.364G>A	5.37:g.16572168C>T	ENSP00000304642:p.Val122Ile	Somatic		Capture	Illumina HiSeq	Phase_I	16625168	NM_001034850	Q69YN8|Q9H6K6|Q9H764|Q9NXM8	Missense_Mutation	SNP	ENST00000306320.9	37	CCDS43304.1	.	.	.	.	.	.	.	.	.	.	C	2.667	-0.278403	0.05679	.	.	ENSG00000154153	ENST00000306320	T	0.40225	1.04	4.93	0.844	0.18943	.	0.655088	0.14476	N	0.317264	T	0.12347	0.0300	N	0.02960	-0.455	0.20074	N	0.999939	B	0.16603	0.018	B	0.14578	0.011	T	0.26744	-1.0094	10	0.05833	T	0.94	-6.4199	1.8158	0.03100	0.1464:0.4311:0.2424:0.1801	.	122	Q9H6L5	F134B_HUMAN	I	122	ENSP00000304642:V122I	ENSP00000304642:V122I	V	-	1	0	FAM134B	16625168	0.423000	0.25482	0.022000	0.16811	0.648000	0.38561	0.555000	0.23422	0.230000	0.21059	-0.145000	0.13849	GTC		0.328	FAM134B-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000366090.1	NM_001034850	
ITK	3702	broad.mit.edu	37	5	156670725	156670725	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr5:156670725A>G	ENST00000422843.3	+	12	1305	c.1153A>G	c.(1153-1155)Aag>Gag	p.K385E	ITK_ENST00000519749.1_3'UTR	NM_005546.3	NP_005537.3	Q08881	ITK_HUMAN	IL2-inducible T-cell kinase	385	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of phospholipase C activity (GO:0007202)|adaptive immune response (GO:0002250)|cellular defense response (GO:0006968)|cytokine production (GO:0001816)|Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|interferon-gamma production (GO:0032609)|interleukin-4 production (GO:0032633)|intracellular signal transduction (GO:0035556)|NK T cell differentiation (GO:0001865)|peptidyl-tyrosine phosphorylation (GO:0018108)|signal transduction (GO:0007165)|T cell activation (GO:0042110)|T cell receptor signaling pathway (GO:0050852)	cell-cell junction (GO:0005911)|cytosol (GO:0005829)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)	p.K385E(1)		breast(4)|central_nervous_system(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(14)|lung(25)|ovary(8)|prostate(2)|skin(7)|stomach(2)|upper_aerodigestive_tract(1)	70	Renal(175;0.00212)	Medulloblastoma(196;0.0354)|all_neural(177;0.1)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)		Pazopanib(DB06589)	CTGGCTCAACAAGGACAAGGT	0.498			T	SYK	peripheral T-cell lymphoma																																p.K385E	Esophageal Squamous(70;1378 1469 8785 19883)		Dom	yes		5	5q31-q32	3702	IL2-inducible T-cell kinase		L	.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A1153G	5						.						182.0	176.0	178.0					5																	156670725		2203	4300	6503	156603303	SO:0001583	missense	3702	exon12			D13720	CCDS4336.1	5q31-q32	2014-09-17			ENSG00000113263	ENSG00000113263		"""Pleckstrin homology (PH) domain containing"", ""SH2 domain containing"""	6171	protein-coding gene	gene with protein product		186973				8364206	Standard	NM_005546		Approved	EMT, PSCTK2, LYK	uc003lwo.1	Q08881	OTTHUMG00000130245	ENST00000422843.3:c.1153A>G	5.37:g.156670725A>G	ENSP00000398655:p.Lys385Glu	Somatic		Capture	Illumina HiSeq	Phase_I	156603303	NM_005546	B2R752|Q32ML7	Missense_Mutation	SNP	ENST00000422843.3	37	CCDS4336.1	.	.	.	.	.	.	.	.	.	.	A	16.02	3.003289	0.54254	.	.	ENSG00000113263	ENST00000422843	T	0.62364	0.03	5.79	5.79	0.91817	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.281183	0.45606	D	0.000347	T	0.47488	0.1448	N	0.21282	0.65	0.39036	D	0.960039	B	0.20671	0.047	B	0.19148	0.024	T	0.47222	-0.9134	10	0.39692	T	0.17	.	11.3732	0.49713	0.8489:0.151:0.0:0.0	.	385	Q08881	ITK_HUMAN	E	385	ENSP00000398655:K385E	ENSP00000398655:K385E	K	+	1	0	ITK	156603303	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	2.575000	0.46025	2.208000	0.71279	0.533000	0.62120	AAG		0.498	ITK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252569.2		
SH3PXD2B	285590	broad.mit.edu	37	5	171773199	171773199	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr5:171773199C>T	ENST00000311601.5	-	12	1299	c.1129G>A	c.(1129-1131)Gcc>Acc	p.A377T	SH3PXD2B_ENST00000519643.1_Missense_Mutation_p.A377T	NM_001017995.2	NP_001017995.1	A1X283	SPD2B_HUMAN	SH3 and PX domains 2B	377	SH3 3. {ECO:0000255|PROSITE- ProRule:PRU00192}.				adipose tissue development (GO:0060612)|bone development (GO:0060348)|cell differentiation (GO:0030154)|extracellular matrix disassembly (GO:0022617)|eye development (GO:0001654)|heart development (GO:0007507)|podosome assembly (GO:0071800)|positive regulation of fat cell differentiation (GO:0045600)|protein localization to membrane (GO:0072657)|skeletal system development (GO:0001501)|superoxide metabolic process (GO:0006801)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|podosome (GO:0002102)	phosphatidylinositol-3,5-bisphosphate binding (GO:0080025)|phosphatidylinositol-3-phosphate binding (GO:0032266)|phosphatidylinositol-4-phosphate binding (GO:0070273)|phosphatidylinositol-5-phosphate binding (GO:0010314)|SH2 domain binding (GO:0042169)	p.A377T(2)		NS(1)|breast(1)|endometrium(1)|kidney(3)|large_intestine(9)|lung(12)|ovary(3)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	36	Renal(175;0.000159)|Lung NSC(126;0.011)|all_lung(126;0.0175)	Medulloblastoma(196;0.0207)|all_neural(177;0.0625)	Kidney(164;7.24e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000516)			TGGAATTCGGCGATGGTGTAA	0.582																																					p.A377T												.	.	2	Substitution - Missense(2)	large_intestine(1)|lung(1)	c.G1129A	5						.						268.0	241.0	250.0					5																	171773199		2203	4300	6503	171705804	SO:0001583	missense	285590	exon12			AK095834	CCDS34291.1	5q35.2	2008-02-05	2006-02-13	2006-02-13	ENSG00000174705	ENSG00000174705			29242	protein-coding gene	gene with protein product		613293	"""KIAA1295"""	KIAA1295		10718198	Standard	NM_001017995		Approved	FLJ20831	uc003mbr.3	A1X283	OTTHUMG00000163280	ENST00000311601.5:c.1129G>A	5.37:g.171773199C>T	ENSP00000309714:p.Ala377Thr	Somatic		Capture	Illumina HiSeq	Phase_I	171705804	NM_001017995	B6F0V2|Q9P2Q1	Missense_Mutation	SNP	ENST00000311601.5	37	CCDS34291.1	.	.	.	.	.	.	.	.	.	.	C	29.9	5.044051	0.93685	.	.	ENSG00000174705	ENST00000519643;ENST00000311601	T;T	0.64085	-0.08;0.8	5.31	5.31	0.75309	Src homology-3 domain (4);	0.000000	0.85682	D	0.000000	T	0.78578	0.4305	M	0.69823	2.125	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	T	0.80899	-0.1176	10	0.87932	D	0	-20.6308	16.4653	0.84077	0.0:1.0:0.0:0.0	.	377	A1X283	SPD2B_HUMAN	T	377	ENSP00000430890:A377T;ENSP00000309714:A377T	ENSP00000309714:A377T	A	-	1	0	SH3PXD2B	171705804	1.000000	0.71417	0.438000	0.26821	0.810000	0.45777	7.416000	0.80143	2.490000	0.84030	0.455000	0.32223	GCC		0.582	SH3PXD2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372449.1	NM_017963	
HK3	3101	broad.mit.edu	37	5	176315478	176315478	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr5:176315478C>T	ENST00000292432.5	-	10	1250	c.1159G>A	c.(1159-1161)Gtc>Atc	p.V387I		NM_002115.2	NP_002106.2	P52790	HXK3_HUMAN	hexokinase 3 (white cell)	387	Hexokinase type-2 1.|Regulatory.				carbohydrate metabolic process (GO:0005975)|carbohydrate phosphorylation (GO:0046835)|cellular glucose homeostasis (GO:0001678)|glucose 6-phosphate metabolic process (GO:0051156)|glucose transport (GO:0015758)|glycolytic process (GO:0006096)|hexose metabolic process (GO:0019318)|hexose transport (GO:0008645)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	cytosol (GO:0005829)|mitochondrion (GO:0005739)|protein complex (GO:0043234)	ATP binding (GO:0005524)|fructokinase activity (GO:0008865)|glucokinase activity (GO:0004340)|hexokinase activity (GO:0004396)|hormone binding (GO:0042562)|mannokinase activity (GO:0019158)	p.V387I(1)		breast(2)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(21)|ovary(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	47	all_cancers(89;0.000104)|Renal(175;0.000269)|Lung NSC(126;0.00696)|all_lung(126;0.0115)	Medulloblastoma(196;0.00498)|all_neural(177;0.0138)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			GCCGCACAGACGTGCTGCACA	0.657																																					p.V387I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1159A	5						.						21.0	20.0	20.0					5																	176315478		2154	4233	6387	176248084	SO:0001583	missense	3101	exon10				CCDS4407.1	5q35.2	2008-02-05			ENSG00000160883	ENSG00000160883	2.7.1.1		4925	protein-coding gene	gene with protein product		142570				8812439	Standard	NM_002115		Approved		uc003mfa.3	P52790	OTTHUMG00000130855	ENST00000292432.5:c.1159G>A	5.37:g.176315478C>T	ENSP00000292432:p.Val387Ile	Somatic		Capture	Illumina HiSeq	Phase_I	176248084	NM_002115	Q8N1E7	Missense_Mutation	SNP	ENST00000292432.5	37	CCDS4407.1	.	.	.	.	.	.	.	.	.	.	C	12.23	1.874645	0.33069	.	.	ENSG00000160883	ENST00000292432	D	0.98164	-4.76	5.14	4.23	0.50019	Hexokinase, C-terminal (1);	0.140594	0.32785	N	0.005653	D	0.95149	0.8428	L	0.37507	1.11	0.30937	N	0.726202	P	0.48407	0.91	B	0.42462	0.388	D	0.92575	0.6069	10	0.24483	T	0.36	.	8.5801	0.33623	0.0:0.7576:0.1571:0.0854	.	387	P52790	HXK3_HUMAN	I	387	ENSP00000292432:V387I	ENSP00000292432:V387I	V	-	1	0	HK3	176248084	0.889000	0.30405	0.049000	0.19019	0.048000	0.14542	1.748000	0.38308	1.088000	0.41272	0.561000	0.74099	GTC		0.657	HK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253428.1		
SLC34A1	6569	broad.mit.edu	37	5	176813546	176813546	+	Missense_Mutation	SNP	G	G	A	rs570463028	byFrequency	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr5:176813546G>A	ENST00000324417.5	+	5	602	c.511G>A	c.(511-513)Gtc>Atc	p.V171I	SLC34A1_ENST00000512593.1_Missense_Mutation_p.V171I	NM_003052.4	NP_003043.3	Q06495	NPT2A_HUMAN	solute carrier family 34 (type II sodium/phosphate contransporter), member 1	171					arsenate ion transmembrane transport (GO:1901684)|bone remodeling (GO:0046849)|cellular response to metal ion (GO:0071248)|cellular response to parathyroid hormone stimulus (GO:0071374)|cellular response to staurosporine (GO:0072734)|dentinogenesis (GO:0097187)|gentamycin metabolic process (GO:1901128)|glycoprotein metabolic process (GO:0009100)|indole metabolic process (GO:0042431)|ion transport (GO:0006811)|kidney development (GO:0001822)|ossification (GO:0001503)|phosphate ion homeostasis (GO:0055062)|phosphate ion transport (GO:0006817)|positive regulation of membrane potential (GO:0045838)|positive regulation of phosphate transmembrane transport (GO:2000187)|positive regulation of sodium-dependent phosphate transport (GO:2000120)|protein homooligomerization (GO:0051260)|response to cadmium ion (GO:0046686)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to growth hormone (GO:0060416)|response to lead ion (GO:0010288)|response to magnesium ion (GO:0032026)|response to mercury ion (GO:0046689)|response to potassium ion (GO:0035864)|response to thyroid hormone (GO:0097066)|response to vitamin A (GO:0033189)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)|tricarboxylic acid metabolic process (GO:0072350)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|brush border membrane (GO:0031526)|cell surface (GO:0009986)|endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|membrane-bounded vesicle (GO:0031988)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	sodium-dependent phosphate transmembrane transporter activity (GO:0015321)|symporter activity (GO:0015293)	p.V171I(1)		breast(1)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(5)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	24	all_cancers(89;2.04e-05)|Renal(175;0.000269)|Lung NSC(126;0.000832)|all_lung(126;0.00152)	all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			ATCCATCATCGTCAGCATGGT	0.637													G|||	2	0.000399361	0.0	0.0	5008	,	,		20531	0.0		0.0	False		,,,				2504	0.002				p.V171I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G511A	5						.						75.0	72.0	73.0					5																	176813546		2203	4300	6503	176746152	SO:0001583	missense	6569	exon5			L13258	CCDS4418.1, CCDS54953.1	5q35.3	2013-07-17	2013-07-17		ENSG00000131183	ENSG00000131183		"""Solute carriers"""	11019	protein-coding gene	gene with protein product	"""sodium/phosphate co-transporter"", ""solute carrier family 17 (sodium phosphate), member 2"", ""Na+-phosphate cotransporter type II"""	182309	"""solute carrier family 34 (sodium phosphate), member 1"""	NPT2, SLC17A2		8327470, 8693007	Standard	NM_003052		Approved	NAPI-3, NPTIIa, SLC11	uc003mgk.4	Q06495	OTTHUMG00000130857	ENST00000324417.5:c.511G>A	5.37:g.176813546G>A	ENSP00000321424:p.Val171Ile	Somatic		Capture	Illumina HiSeq	Phase_I	176746152	NM_001167579	B4DPE3	Missense_Mutation	SNP	ENST00000324417.5	37	CCDS4418.1	.	.	.	.	.	.	.	.	.	.	G	33	5.224222	0.95139	.	.	ENSG00000131183	ENST00000512593;ENST00000324417	D;D	0.86497	-2.13;-2.13	5.76	5.76	0.90799	.	0.000000	0.85682	D	0.000000	D	0.89876	0.6842	L	0.37750	1.13	0.58432	D	0.999999	D	0.65815	0.995	P	0.60949	0.881	D	0.89244	0.3586	10	0.46703	T	0.11	-19.7164	19.9772	0.97314	0.0:0.0:1.0:0.0	.	171	Q06495	NPT2A_HUMAN	I	171	ENSP00000423022:V171I;ENSP00000321424:V171I	ENSP00000321424:V171I	V	+	1	0	SLC34A1	176746152	1.000000	0.71417	0.990000	0.47175	0.892000	0.51952	8.002000	0.88514	2.724000	0.93272	0.563000	0.77884	GTC		0.637	SLC34A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253431.1	NM_003052	
B4GALT7	11285	broad.mit.edu	37	5	177035584	177035584	+	Silent	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr5:177035584C>T	ENST00000029410.5	+	4	795	c.684C>T	c.(682-684)gaC>gaT	p.D228D	RP11-1277A3.1_ENST00000499900.2_RNA	NM_007255.2	NP_009186.1	Q9UBV7	B4GT7_HUMAN	xylosylprotein beta 1,4-galactosyltransferase, polypeptide 7	228	N-acetyl-D-glucosamine binding. {ECO:0000250}.				carbohydrate metabolic process (GO:0005975)|cellular protein modification process (GO:0006464)|chondroitin sulfate metabolic process (GO:0030204)|extracellular fibril organization (GO:0043206)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan metabolic process (GO:0030203)|negative regulation of fibroblast proliferation (GO:0048147)|protein N-linked glycosylation (GO:0006487)|proteoglycan metabolic process (GO:0006029)|small molecule metabolic process (GO:0044281)	Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	beta-N-acetylglucosaminylglycopeptide beta-1,4-galactosyltransferase activity (GO:0003831)|galactosyltransferase activity (GO:0008378)|manganese ion binding (GO:0030145)|xylosylprotein 4-beta-galactosyltransferase activity (GO:0046525)	p.D228D(1)		endometrium(2)|large_intestine(1)|lung(1)|pancreas(1)|skin(1)|urinary_tract(1)	7	all_cancers(89;0.00033)|Renal(175;0.000269)|Lung NSC(126;0.00161)|all_lung(126;0.00286)	all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			GCCGCGAGGACGACGAGTTCT	0.652																																					p.D228D												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C684T	5						.						46.0	52.0	50.0					5																	177035584		2203	4300	6503	176968190	SO:0001819	synonymous_variant	11285	exon4			AB028600	CCDS4429.1	5q35.1-q35.3	2013-02-19	2012-07-18		ENSG00000027847	ENSG00000027847		"""Beta 4-glycosyltransferases"""	930	protein-coding gene	gene with protein product	"""galactosyltransferase I"""	604327				10438455, 10473568	Standard	NM_007255		Approved	XGALT-1, beta4Gal-T7	uc003mhy.3	Q9UBV7	OTTHUMG00000130851	ENST00000029410.5:c.684C>T	5.37:g.177035584C>T		Somatic		Capture	Illumina HiSeq	Phase_I	176968190	NM_007255	B3KN39|Q9UHN2	Silent	SNP	ENST00000029410.5	37	CCDS4429.1																																																																																				0.652	B4GALT7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253421.1	NM_007255	
BTNL8	79908	broad.mit.edu	37	5	180338370	180338370	+	Silent	SNP	G	G	A	rs386695827|rs148878394	byFrequency	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr5:180338370G>A	ENST00000340184.4	+	3	635	c.429G>A	c.(427-429)acG>acA	p.T143T	BTNL8_ENST00000511704.1_Silent_p.T27T|BTNL8_ENST00000505126.1_5'UTR|BTNL8_ENST00000533815.2_5'UTR|BTNL8_ENST00000231229.4_Silent_p.T143T|Y_RNA_ENST00000410920.1_RNA|BTNL8_ENST00000400707.3_Silent_p.T18T|BTNL8_ENST00000508408.1_Silent_p.T143T	NM_001040462.2	NP_001035552.1	Q6UX41	BTNL8_HUMAN	butyrophilin-like 8	143	Ig-like V-type 2.		T -> A (in dbSNP:rs2276995). {ECO:0000269|PubMed:15489334}.		immune system process (GO:0002376)	integral component of membrane (GO:0016021)		p.T143T(1)		breast(1)|endometrium(4)|kidney(2)|large_intestine(4)|lung(12)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	28	all_cancers(89;3.37e-05)|all_epithelial(37;3.77e-06)|Renal(175;0.000159)|Lung NSC(126;0.00211)|all_lung(126;0.00371)|Breast(19;0.114)	all_cancers(40;0.0801)|Medulloblastoma(196;0.0392)|all_neural(177;0.0529)|all_hematologic(541;0.191)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			TTTCCATCACGGGATATGTTG	0.527													G|||	11	0.00219649	0.0076	0.0014	5008	,	,		20284	0.0		0.0	False		,,,				2504	0.0				p.T27T												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G81A	5						.	G	,,,,,	30,4376	25.3+/-52.1	2,26,2175	244.0	268.0	260.0		429,81,429,54,,429	-0.2	0.0	5	dbSNP_134	260	0,8592		0,0,4296	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,utr-5,coding-synonymous	BTNL8	NM_001040462.2,NM_001159707.1,NM_001159708.1,NM_001159709.1,NM_001159710.1,NM_024850.2	,,,,,	2,26,6471	AA,AG,GG		0.0,0.6809,0.2308	,,,,,	143/501,27/385,143/341,18/376,,143/348	180338370	30,12968	2203	4296	6499	180270976	SO:0001819	synonymous_variant	79908	exon2			AK025111	CCDS4459.1, CCDS43413.1, CCDS54956.1, CCDS54957.1, CCDS54958.1, CCDS54959.1	5q35.3	2014-01-14			ENSG00000113303	ENSG00000113303		"""Immunoglobulin superfamily / V-set domain containing"", ""Butyrophilins"""	26131	protein-coding gene	gene with protein product		615606				12975309	Standard	NM_024850		Approved	FLJ21458, BTN9.2	uc003mmp.3	Q6UX41	OTTHUMG00000130932	ENST00000340184.4:c.429G>A	5.37:g.180338370G>A		Somatic		Capture	Illumina HiSeq	Phase_I	180270976	NM_001159707	A4QMZ8|A6NEX6|B7Z409|B7Z5B1|E9PEF6|E9PG07|F2Z2B2|F8W712|Q9H730	Silent	SNP	ENST00000340184.4	37	CCDS43413.1																																																																																				0.527	BTNL8-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000368440.1	NM_024850	
SDHA	6389	broad.mit.edu	37	5	224547	224547	+	Nonsense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr5:224547C>T	ENST00000264932.6	+	3	338	c.223C>T	c.(223-225)Cga>Tga	p.R75*	SDHA_ENST00000510361.1_Nonsense_Mutation_p.R75*|SDHA_ENST00000504309.1_Nonsense_Mutation_p.R75*	NM_004168.2	NP_004159.2	P31040	SDHA_HUMAN	succinate dehydrogenase complex, subunit A, flavoprotein (Fp)	75					cellular metabolic process (GO:0044237)|nervous system development (GO:0007399)|oxidation-reduction process (GO:0055114)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)|succinate metabolic process (GO:0006105)|tricarboxylic acid cycle (GO:0006099)	mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex II (GO:0005749)|mitochondrion (GO:0005739)	flavin adenine dinucleotide binding (GO:0050660)|succinate dehydrogenase (ubiquinone) activity (GO:0008177)	p.R75*(1)		NS(1)|breast(1)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(6)|liver(2)|lung(16)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	40			Epithelial(17;0.0159)|all cancers(22;0.0236)|OV - Ovarian serous cystadenocarcinoma(19;0.0674)|Lung(60;0.113)		Succinic acid(DB00139)	GGCAGGCTTGCGAGCTGCATT	0.478									Familial Paragangliomas																												p.R75X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.C223T	5						.						121.0	124.0	123.0					5																	224547		2203	4300	6503	277547	SO:0001587	stop_gained	6389	exon3	Familial Cancer Database	Hereditary Glomus Tumors, Familial Paragangliomas, Hereditary Paragangliomas, type 1-3: PGL1, PGL2, PGL3, incl. Familial Carotid Body Paraganglioma and Sensorineural Hearing Loss	BC001380	CCDS3853.1	5p15	2014-09-17			ENSG00000073578	ENSG00000073578		"""Mitochondrial respiratory chain complex / Complex II"""	10680	protein-coding gene	gene with protein product		600857		SDH2		7798181	Standard	XM_005248329		Approved	FP, SDHF	uc003jao.4	P31040	OTTHUMG00000090275	ENST00000264932.6:c.223C>T	5.37:g.224547C>T	ENSP00000264932:p.Arg75*	Somatic		Capture	Illumina HiSeq	Phase_I	277547	NM_004168	A8K5J6|B4DJ60|E9PBJ5|Q16395|Q59GW8|Q8IW48|Q9UMY5	Nonsense_Mutation	SNP	ENST00000264932.6	37	CCDS3853.1	.	.	.	.	.	.	.	.	.	.	c	34	5.380890	0.95945	.	.	ENSG00000073578	ENST00000264932;ENST00000327872;ENST00000504309;ENST00000510361	.	.	.	5.56	4.67	0.58626	.	0.000000	0.64402	U	0.000002	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	13.7272	0.62765	0.1554:0.8446:0.0:0.0	.	.	.	.	X	75	.	ENSP00000264932:R75X	R	+	1	2	SDHA	277547	1.000000	0.71417	1.000000	0.80357	0.859000	0.49053	2.106000	0.41835	1.457000	0.47850	0.539000	0.68188	CGA		0.478	SDHA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206599.1	NM_004168	
SLC9A3	6550	broad.mit.edu	37	5	476160	476160	+	Silent	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr5:476160C>T	ENST00000264938.3	-	14	2124	c.2115G>A	c.(2113-2115)gcG>gcA	p.A705A	CTD-2228K2.7_ENST00000606319.1_RNA|CTD-2228K2.7_ENST00000607005.1_RNA|CTD-2228K2.7_ENST00000607286.1_RNA|SLC9A3_ENST00000514375.1_Silent_p.A696A|CTD-2228K2.7_ENST00000606288.1_RNA|CTD-2228K2.5_ENST00000342584.3_5'Flank	NM_004174.2	NP_004165.2	P48764	SL9A3_HUMAN	solute carrier family 9, subfamily A (NHE3, cation proton antiporter 3), member 3	705					ion transport (GO:0006811)|regulation of pH (GO:0006885)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|brush border (GO:0005903)|brush border membrane (GO:0031526)|cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	PDZ domain binding (GO:0030165)|sodium:proton antiporter activity (GO:0015385)	p.A705A(1)		NS(2)|biliary_tract(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(4)|liver(2)|lung(16)|prostate(3)|skin(2)|urinary_tract(1)	37			Epithelial(17;0.000529)|OV - Ovarian serous cystadenocarcinoma(19;0.00153)|all cancers(22;0.00186)|Lung(60;0.0863)			TGAAATTCTGCGCAGGGCTCT	0.642																																					p.A705A												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G2115A	5						.						26.0	29.0	28.0					5																	476160		2203	4300	6503	529160	SO:0001819	synonymous_variant	6550	exon14				CCDS3855.1, CCDS64116.1	5p15.3	2013-05-22	2012-03-22		ENSG00000066230	ENSG00000066230		"""Solute carriers"""	11073	protein-coding gene	gene with protein product		182307	"""solute carrier family 9 (sodium/hydrogen exchanger), isoform 3"", ""solute carrier family 9 (sodium/hydrogen exchanger), member 3"""	NHE3		8096830	Standard	NM_004174		Approved		uc003jbe.2	P48764	OTTHUMG00000090315	ENST00000264938.3:c.2115G>A	5.37:g.476160C>T		Somatic		Capture	Illumina HiSeq	Phase_I	529160	NM_004174	B7ZKR2|E9PF67|Q3MIW3	Silent	SNP	ENST00000264938.3	37	CCDS3855.1																																																																																				0.642	SLC9A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206677.2	NM_004174	
ICE1	23379	broad.mit.edu	37	5	5460617	5460617	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr5:5460617G>T	ENST00000296564.7	+	13	1392	c.1170G>T	c.(1168-1170)gaG>gaT	p.E390D		NM_015325.2	NP_056140.1	Q9Y2F5	ICE1_HUMAN		390					positive regulation of intracellular protein transport (GO:0090316)|positive regulation of protein complex assembly (GO:0031334)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|snRNA transcription from RNA polymerase II promoter (GO:0042795)|snRNA transcription from RNA polymerase III promoter (GO:0042796)	Cajal body (GO:0015030)|histone locus body (GO:0035363)|transcription elongation factor complex (GO:0008023)|transcriptionally active chromatin (GO:0035327)	protein homodimerization activity (GO:0042803)	p.E390D(1)		breast(2)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(14)|ovary(1)|prostate(4)|upper_aerodigestive_tract(1)	35						ATTCTGCTGAGTGTGTTTCAG	0.368																																					p.E390D												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1170T	5						.						36.0	35.0	35.0					5																	5460617		1826	4088	5914	5513617	SO:0001583	missense	23379	exon13																														ENST00000296564.7:c.1170G>T	5.37:g.5460617G>T	ENSP00000296564:p.Glu390Asp	Somatic		Capture	Illumina HiSeq	Phase_I	5513617	NM_015325	Q68DE1|Q6ZT40|Q7L587|Q7Z3A9|Q9NTH9	Missense_Mutation	SNP	ENST00000296564.7	37	CCDS47187.1	.	.	.	.	.	.	.	.	.	.	g	15.68	2.904167	0.52333	.	.	ENSG00000164151	ENST00000296564	T	0.44482	0.92	4.68	-4.63	0.03359	.	0.877805	0.09786	U	0.755981	T	0.24509	0.0594	L	0.27053	0.805	0.09310	N	1	B	0.21225	0.053	B	0.20767	0.031	T	0.26538	-1.0100	10	0.62326	D	0.03	-9.8105	5.5228	0.16941	0.4596:0.2545:0.2859:0.0	.	390	Q9Y2F5	K0947_HUMAN	D	390	ENSP00000296564:E390D	ENSP00000296564:E390D	E	+	3	2	KIAA0947	5513617	0.000000	0.05858	0.000000	0.03702	0.215000	0.24574	-0.855000	0.04295	-0.812000	0.04363	0.298000	0.19748	GAG		0.368	KIAA0947-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365575.1		
PAPD7	11044	broad.mit.edu	37	5	6746494	6746494	+	Silent	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr5:6746494C>T	ENST00000230859.6	+	7	792	c.663C>T	c.(661-663)agC>agT	p.S221S		NM_001171805.1|NM_001171806.1|NM_006999.4	NP_001165276.1|NP_001165277.1|NP_008930.1	Q5XG87	PAPD7_HUMAN	PAP associated domain containing 7	451					double-strand break repair (GO:0006302)|mitotic chromosome condensation (GO:0007076)|response to drug (GO:0042493)|sister chromatid cohesion (GO:0007062)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|DNA-directed DNA polymerase activity (GO:0003887)|metal ion binding (GO:0046872)|polynucleotide adenylyltransferase activity (GO:0004652)|SMC family protein binding (GO:0043221)	p.S221S(1)		cervix(1)|endometrium(2)|large_intestine(8)|lung(10)|ovary(2)|pancreas(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	27						CCATGACCAGCGGGTACAGAC	0.527																																					p.S221S	NSCLC(7;212 333 5667 23379 46547)											.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C663T	5						.						90.0	94.0	93.0					5																	6746494		2203	4300	6503	6799494	SO:0001819	synonymous_variant	11044	exon7			AF089896	CCDS3871.1	5p15	2010-11-18	2010-01-19	2010-01-19	ENSG00000112941	ENSG00000112941			16705	protein-coding gene	gene with protein product	"""topoisomerase-related function protein 4-1"", ""polymerase (DNA-directed) sigma"", ""DNA polymerase kappa"", ""TUTase5"""	605198	"""polymerase (DNA directed) sigma"""	POLS		10066793, 10926539	Standard	NM_006999		Approved	POLK, TRF4, LAK-1, TRF4-1	uc003jdx.1	Q5XG87	OTTHUMG00000090457	ENST00000230859.6:c.663C>T	5.37:g.6746494C>T		Somatic		Capture	Illumina HiSeq	Phase_I	6799494	NM_001171805	A8K1E2|M1JCE6|O43289|Q17RZ1|Q9Y6C1	Silent	SNP	ENST00000230859.6	37	CCDS3871.1																																																																																				0.527	PAPD7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206904.1	NM_006999	
CDH12	1010	broad.mit.edu	37	5	21802329	21802329	+	Silent	SNP	G	G	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr5:21802329G>T	ENST00000382254.1	-	10	2289	c.1203C>A	c.(1201-1203)acC>acA	p.T401T	CDH12_ENST00000522262.1_Silent_p.T361T|CDH12_ENST00000521384.1_5'UTR|CDH12_ENST00000504376.2_Silent_p.T401T	NM_004061.3	NP_004052.2	P55289	CAD12_HUMAN	cadherin 12, type 2 (N-cadherin 2)	401	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				adherens junction organization (GO:0034332)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.T401T(1)		NS(2)|breast(2)|cervix(1)|endometrium(6)|kidney(4)|large_intestine(19)|lung(75)|ovary(2)|prostate(3)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	120						CGCCAATGATGGTCCCTACCG	0.478										HNSCC(59;0.17)																											p.T401T												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1203A	5						.						99.0	75.0	83.0					5																	21802329		2203	4300	6503	21838086	SO:0001819	synonymous_variant	1010	exon10			L33477	CCDS3890.1	5p14.3	2010-01-26			ENSG00000154162	ENSG00000154162		"""Cadherins / Major cadherins"""	1751	protein-coding gene	gene with protein product		600562				7731968	Standard	NM_004061		Approved	Br-cadherin, CDHB	uc003jgk.2	P55289	OTTHUMG00000090591	ENST00000382254.1:c.1203C>A	5.37:g.21802329G>T		Somatic		Capture	Illumina HiSeq	Phase_I	21838086	NM_004061	B2RBT1|B7Z2U6|Q86UD2	Silent	SNP	ENST00000382254.1	37	CCDS3890.1																																																																																				0.478	CDH12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207139.1	NM_004061	
PRDM9	56979	broad.mit.edu	37	5	23526569	23526569	+	Nonsense_Mutation	SNP	G	G	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr5:23526569G>T	ENST00000296682.3	+	11	1554	c.1372G>T	c.(1372-1374)Gaa>Taa	p.E458*		NM_020227.2	NP_064612.2	Q9NQV7	PRDM9_HUMAN	PR domain containing 9	458					meiotic gene conversion (GO:0006311)|positive regulation of meiosis I (GO:0060903)|positive regulation of reciprocal meiotic recombination (GO:0010845)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	chromosome (GO:0005694)|nucleoplasm (GO:0005654)	histone methyltransferase activity (H3-K4 specific) (GO:0042800)|metal ion binding (GO:0046872)|recombination hotspot binding (GO:0010844)|sequence-specific DNA binding (GO:0043565)	p.E458*(2)		NS(1)|breast(1)|central_nervous_system(3)|endometrium(15)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(27)|lung(87)|ovary(6)|pancreas(2)|prostate(4)|skin(10)|upper_aerodigestive_tract(11)	172						AGAGATCAAAGAAAGGTCCAA	0.483										HNSCC(3;0.000094)																											p.E458X												.	.	2	Substitution - Nonsense(2)	large_intestine(1)|lung(1)	c.G1372T	5						.						45.0	47.0	46.0					5																	23526569		2203	4300	6503	23562326	SO:0001587	stop_gained	56979	exon11			AF275816	CCDS43307.1	5p14.2	2014-06-03			ENSG00000164256	ENSG00000164256		"""-"", ""Zinc fingers, C2H2-type"""	13994	protein-coding gene	gene with protein product	"""PR-domain containing protein 9"""	609760	"""minisatellite binding protein 3, 115kDa"", ""minisatellite binding protein 3 (115kD)"""	MSBP3		10668202, 2062643, 24634223	Standard	NM_020227		Approved	PFM6, ZNF899	uc003jgo.3	Q9NQV7	OTTHUMG00000161918	ENST00000296682.3:c.1372G>T	5.37:g.23526569G>T	ENSP00000296682:p.Glu458*	Somatic		Capture	Illumina HiSeq	Phase_I	23562326	NM_020227	B4DX22|Q27Q50	Nonsense_Mutation	SNP	ENST00000296682.3	37	CCDS43307.1	.	.	.	.	.	.	.	.	.	.	G	22.6	4.312366	0.81358	.	.	ENSG00000164256	ENST00000296682;ENST00000253473	.	.	.	2.58	-1.97	0.07503	.	1.405680	0.04985	N	0.466386	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.07175	T	0.84	1.8182	4.2772	0.10815	0.3656:0.1739:0.4605:0.0	.	.	.	.	X	458;252	.	ENSP00000253473:E252X	E	+	1	0	PRDM9	23562326	0.000000	0.05858	0.000000	0.03702	0.169000	0.22640	-0.843000	0.04350	-0.531000	0.06340	0.400000	0.26472	GAA		0.483	PRDM9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366375.1	NM_020227	
CDH10	1008	broad.mit.edu	37	5	24498606	24498606	+	Silent	SNP	G	G	A	rs139927244	byFrequency	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr5:24498606G>A	ENST00000264463.4	-	9	1923	c.1416C>T	c.(1414-1416)cgC>cgT	p.R472R	CDH10_ENST00000502921.1_5'UTR	NM_006727.3	NP_006718.2	Q9Y6N8	CAD10_HUMAN	cadherin 10, type 2 (T2-cadherin)	472	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				adherens junction organization (GO:0034332)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|homophilic cell adhesion (GO:0007156)|single organismal cell-cell adhesion (GO:0016337)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.R472R(1)		NS(1)|breast(8)|central_nervous_system(2)|cervix(1)|endometrium(9)|kidney(2)|large_intestine(29)|lung(111)|ovary(6)|pancreas(6)|skin(4)|stomach(2)|upper_aerodigestive_tract(4)	185				STAD - Stomach adenocarcinoma(35;0.0556)		AAACAGCCACGCGTGTTGTCT	0.393										HNSCC(23;0.051)																											p.R472R												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1416T	5						.	G		0,4406		0,0,2203	82.0	82.0	82.0		1416	-11.1	0.4	5	dbSNP_134	82	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	CDH10	NM_006727.3		0,2,6501	AA,AG,GG		0.0233,0.0,0.0154		472/789	24498606	2,13004	2203	4300	6503	24534363	SO:0001819	synonymous_variant	1008	exon9			AF039747	CCDS3892.1	5p14.2	2010-01-26			ENSG00000040731	ENSG00000040731		"""Cadherins / Major cadherins"""	1749	protein-coding gene	gene with protein product		604555				2059658	Standard	NM_006727		Approved		uc003jgr.2	Q9Y6N8	OTTHUMG00000090667	ENST00000264463.4:c.1416C>T	5.37:g.24498606G>A		Somatic		Capture	Illumina HiSeq	Phase_I	24534363	NM_006727	Q9ULB3	Silent	SNP	ENST00000264463.4	37	CCDS3892.1																																																																																				0.393	CDH10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207345.2	NM_006727	
DROSHA	29102	broad.mit.edu	37	5	31511212	31511212	+	Silent	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr5:31511212G>A	ENST00000511367.2	-	8	1606	c.1362C>T	c.(1360-1362)agC>agT	p.S454S	DROSHA_ENST00000513349.1_Silent_p.S417S|DROSHA_ENST00000442743.1_Silent_p.S417S|DROSHA_ENST00000344624.3_Silent_p.S454S	NM_013235.4	NP_037367.3	Q9NRR4	RNC_HUMAN	drosha, ribonuclease type III	454					defense response to Gram-negative bacterium (GO:0050829)|defense response to Gram-positive bacterium (GO:0050830)|gene expression (GO:0010467)|miRNA metabolic process (GO:0010586)|pre-miRNA processing (GO:0031054)|primary miRNA processing (GO:0031053)|ribosome biogenesis (GO:0042254)|RNA phosphodiester bond hydrolysis (GO:0090501)|RNA phosphodiester bond hydrolysis, endonucleolytic (GO:0090502)|rRNA catabolic process (GO:0016075)	nucleoplasm (GO:0005654)	lipopolysaccharide binding (GO:0001530)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|ribonuclease III activity (GO:0004525)	p.S454S(1)		breast(4)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(19)|lung(33)|ovary(2)|skin(1)	66						TTTCTTGCCTGCTCCCCAACT	0.458																																					p.S454S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1362T	5						.						118.0	113.0	114.0					5																	31511212		1963	4152	6115	31546969	SO:0001819	synonymous_variant	29102	exon8			AF116910	CCDS47194.1, CCDS47195.1	5q11.2	2010-11-17	2010-10-28	2010-10-28	ENSG00000113360	ENSG00000113360	3.1.26.3		17904	protein-coding gene	gene with protein product	"""drosha, ribonuclease type III"", ""drosha, double-stranded RNA-specific endoribonuclease"""	608828	"""ribonuclease type III, nuclear"""	RNASEN		10713462, 10948199	Standard	NM_013235		Approved	RNASE3L, Etohi2, HSA242976, RN3	uc003jhg.2	Q9NRR4	OTTHUMG00000161976	ENST00000511367.2:c.1362C>T	5.37:g.31511212G>A		Somatic		Capture	Illumina HiSeq	Phase_I	31546969	NM_013235	E7EMP9|Q7Z5V2|Q86YH0|Q9NW73|Q9Y2V9|Q9Y4Y0	Silent	SNP	ENST00000511367.2	37	CCDS47195.1	.	.	.	.	.	.	.	.	.	.	G	11.30	1.597808	0.28445	.	.	ENSG00000113360	ENST00000512076	.	.	.	6.16	2.18	0.27775	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-6.7394	2.2989	0.04157	0.2545:0.2902:0.3549:0.1003	.	.	.	.	X	216	.	.	Q	-	1	0	DROSHA	31546969	0.998000	0.40836	0.998000	0.56505	0.989000	0.77384	0.602000	0.24134	0.428000	0.26173	0.650000	0.86243	CAG		0.458	DROSHA-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366561.3	NM_013235	
DROSHA	29102	broad.mit.edu	37	5	31526817	31526817	+	Nonsense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr5:31526817G>A	ENST00000511367.2	-	4	467	c.223C>T	c.(223-225)Cga>Tga	p.R75*	DROSHA_ENST00000513349.1_Nonsense_Mutation_p.R75*|DROSHA_ENST00000504361.1_5'Flank|DROSHA_ENST00000442743.1_Nonsense_Mutation_p.R75*|DROSHA_ENST00000344624.3_Nonsense_Mutation_p.R75*	NM_013235.4	NP_037367.3	Q9NRR4	RNC_HUMAN	drosha, ribonuclease type III	75	Pro-rich.				defense response to Gram-negative bacterium (GO:0050829)|defense response to Gram-positive bacterium (GO:0050830)|gene expression (GO:0010467)|miRNA metabolic process (GO:0010586)|pre-miRNA processing (GO:0031054)|primary miRNA processing (GO:0031053)|ribosome biogenesis (GO:0042254)|RNA phosphodiester bond hydrolysis (GO:0090501)|RNA phosphodiester bond hydrolysis, endonucleolytic (GO:0090502)|rRNA catabolic process (GO:0016075)	nucleoplasm (GO:0005654)	lipopolysaccharide binding (GO:0001530)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|ribonuclease III activity (GO:0004525)	p.R75*(1)		breast(4)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(19)|lung(33)|ovary(2)|skin(1)	66						AAGTCTGGTCGTGGAGGGAGA	0.582																																					p.R75X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.C223T	5						.						35.0	41.0	39.0					5																	31526817		1947	4135	6082	31562574	SO:0001587	stop_gained	29102	exon4			AF116910	CCDS47194.1, CCDS47195.1	5q11.2	2010-11-17	2010-10-28	2010-10-28	ENSG00000113360	ENSG00000113360	3.1.26.3		17904	protein-coding gene	gene with protein product	"""drosha, ribonuclease type III"", ""drosha, double-stranded RNA-specific endoribonuclease"""	608828	"""ribonuclease type III, nuclear"""	RNASEN		10713462, 10948199	Standard	NM_013235		Approved	RNASE3L, Etohi2, HSA242976, RN3	uc003jhg.2	Q9NRR4	OTTHUMG00000161976	ENST00000511367.2:c.223C>T	5.37:g.31526817G>A	ENSP00000425979:p.Arg75*	Somatic		Capture	Illumina HiSeq	Phase_I	31562574	NM_013235	E7EMP9|Q7Z5V2|Q86YH0|Q9NW73|Q9Y2V9|Q9Y4Y0	Nonsense_Mutation	SNP	ENST00000511367.2	37	CCDS47195.1	.	.	.	.	.	.	.	.	.	.	G	21.4	4.146887	0.77888	.	.	ENSG00000113360	ENST00000511367;ENST00000344624;ENST00000442743;ENST00000513349;ENST00000265075;ENST00000382188;ENST00000507438	.	.	.	5.04	0.42	0.16444	.	0.084265	0.44902	D	0.000419	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-9.2136	14.8567	0.70344	0.0:0.0:0.3568:0.6432	.	.	.	.	X	75;75;75;75;68;68;75	.	ENSP00000265075:R68X	R	-	1	2	DROSHA	31562574	0.862000	0.29867	0.980000	0.43619	0.994000	0.84299	1.327000	0.33746	0.135000	0.18707	0.563000	0.77884	CGA		0.582	DROSHA-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366561.3	NM_013235	
PDZD2	23037	broad.mit.edu	37	5	32074084	32074084	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr5:32074084C>T	ENST00000438447.1	+	18	3260	c.2872C>T	c.(2872-2874)Cgc>Tgc	p.R958C	PDZD2_ENST00000282493.3_Missense_Mutation_p.R958C			O15018	PDZD2_HUMAN	PDZ domain containing 2	958					cell adhesion (GO:0007155)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|nucleus (GO:0005634)		p.R958C(1)		NS(2)|breast(4)|central_nervous_system(5)|cervix(2)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(31)|lung(58)|ovary(6)|prostate(2)|skin(8)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	148						CCCTCTCCTCCGCCAGAGGAA	0.612																																					p.R958C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C2872T	5						.						59.0	63.0	62.0					5																	32074084		2203	4300	6503	32109841	SO:0001583	missense	23037	exon17			AB002298	CCDS34137.1	5p14.1	2008-02-05	2006-01-24	2006-01-24		ENSG00000133401			18486	protein-coding gene	gene with protein product		610697	"""PDZ domain containing 3"""	PDZK3		9205841	Standard	XM_005248271		Approved	KIAA0300	uc003jhm.3	O15018		ENST00000438447.1:c.2872C>T	5.37:g.32074084C>T	ENSP00000402033:p.Arg958Cys	Somatic		Capture	Illumina HiSeq	Phase_I	32109841	NM_178140	Q9BXD4	Missense_Mutation	SNP	ENST00000438447.1	37	CCDS34137.1	.	.	.	.	.	.	.	.	.	.	C	23.3	4.394815	0.83011	.	.	ENSG00000133401	ENST00000438447;ENST00000382161;ENST00000282493	T;T	0.14766	2.48;2.48	5.78	4.88	0.63580	.	0.000000	0.50627	D	0.000119	T	0.27559	0.0677	L	0.36672	1.1	0.58432	D	0.999999	P;D	0.89917	0.943;1.0	B;D	0.91635	0.209;0.999	T	0.00628	-1.1637	10	0.87932	D	0	.	14.0264	0.64588	0.1512:0.8488:0.0:0.0	.	784;958	B4E3P2;O15018	.;PDZD2_HUMAN	C	958;760;958	ENSP00000402033:R958C;ENSP00000282493:R958C	ENSP00000282493:R958C	R	+	1	0	PDZD2	32109841	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	1.970000	0.40520	2.724000	0.93272	0.563000	0.77884	CGC		0.612	PDZD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366608.1		
PDZD2	23037	broad.mit.edu	37	5	32090758	32090758	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr5:32090758G>A	ENST00000438447.1	+	20	7592	c.7204G>A	c.(7204-7206)Gaa>Aaa	p.E2402K	PDZD2_ENST00000282493.3_Missense_Mutation_p.E2402K			O15018	PDZD2_HUMAN	PDZ domain containing 2	2402					cell adhesion (GO:0007155)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|nucleus (GO:0005634)		p.E2402K(2)		NS(2)|breast(4)|central_nervous_system(5)|cervix(2)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(31)|lung(58)|ovary(6)|prostate(2)|skin(8)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	148						TTCCTGCAGCGAAAACCAAAG	0.597																																					p.E2402K												.	.	2	Substitution - Missense(2)	large_intestine(1)|skin(1)	c.G7204A	5						.						56.0	58.0	58.0					5																	32090758		2203	4300	6503	32126515	SO:0001583	missense	23037	exon19			AB002298	CCDS34137.1	5p14.1	2008-02-05	2006-01-24	2006-01-24		ENSG00000133401			18486	protein-coding gene	gene with protein product		610697	"""PDZ domain containing 3"""	PDZK3		9205841	Standard	XM_005248271		Approved	KIAA0300	uc003jhm.3	O15018		ENST00000438447.1:c.7204G>A	5.37:g.32090758G>A	ENSP00000402033:p.Glu2402Lys	Somatic		Capture	Illumina HiSeq	Phase_I	32126515	NM_178140	Q9BXD4	Missense_Mutation	SNP	ENST00000438447.1	37	CCDS34137.1	.	.	.	.	.	.	.	.	.	.	G	28.9	4.959099	0.92726	.	.	ENSG00000133401	ENST00000438447;ENST00000382161;ENST00000282493	T;T	0.12039	2.72;2.72	5.15	5.15	0.70609	.	0.000000	0.52532	D	0.000065	T	0.34629	0.0904	M	0.65975	2.015	0.44469	D	0.997407	D	0.76494	0.999	D	0.70716	0.97	T	0.01966	-1.1238	10	0.35671	T	0.21	.	16.1187	0.81325	0.0:0.0:1.0:0.0	.	2402	O15018	PDZD2_HUMAN	K	2402;2203;2402	ENSP00000402033:E2402K;ENSP00000282493:E2402K	ENSP00000282493:E2402K	E	+	1	0	PDZD2	32126515	1.000000	0.71417	0.990000	0.47175	0.933000	0.57130	6.351000	0.73022	2.381000	0.81170	0.561000	0.74099	GAA		0.597	PDZD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366608.1		
NPR3	4883	broad.mit.edu	37	5	32739001	32739001	+	Silent	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr5:32739001C>T	ENST00000265074.8	+	3	1267	c.924C>T	c.(922-924)caC>caT	p.H308H	NPR3_ENST00000434067.2_Silent_p.H92H|NPR3_ENST00000415685.2_Silent_p.H92H|NPR3_ENST00000415167.2_Silent_p.H308H	NM_000908.3|NM_001204375.1	NP_000899.1|NP_001191304.1	P17342	ANPRC_HUMAN	natriuretic peptide receptor 3	308					adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|negative regulation of adenylate cyclase activity (GO:0007194)|negative regulation of smooth muscle cell proliferation (GO:0048662)|osteoclast proliferation (GO:0002158)|pancreatic juice secretion (GO:0030157)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|positive regulation of nitric-oxide synthase activity (GO:0051000)|positive regulation of urine volume (GO:0035810)|regulation of blood pressure (GO:0008217)|regulation of osteoblast proliferation (GO:0033688)|skeletal system development (GO:0001501)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	G-protein coupled peptide receptor activity (GO:0008528)|hormone binding (GO:0042562)|natriuretic peptide receptor activity (GO:0016941)|peptide hormone binding (GO:0017046)	p.H308H(1)		autonomic_ganglia(1)|central_nervous_system(1)|endometrium(2)|large_intestine(5)|lung(12)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	24					Nesiritide(DB04899)	GAGACAAACACGACTTTGAAG	0.428																																					p.H308H												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C924T	5						.						133.0	127.0	129.0					5																	32739001		1886	4121	6007	32774758	SO:0001819	synonymous_variant	4883	exon3				CCDS47196.1, CCDS56356.1, CCDS56357.1	5p13.3	2014-03-03	2014-03-03		ENSG00000113389	ENSG00000113389			7945	protein-coding gene	gene with protein product	"""guanylate cyclase C"""	108962	"""chromosome 5 open reading frame 23"", ""atrionatriuretic peptide receptor C"", ""natriuretic peptide receptor C/guanylate cyclase C (atrionatriuretic peptide receptor C)"", ""natriuretic peptide receptor C"""	NPRC, ANPRC, C5orf23		2162522, 1979052	Standard	NM_000908		Approved	GUCY2B, FLJ14054	uc003jhv.3	P17342	OTTHUMG00000150316	ENST00000265074.8:c.924C>T	5.37:g.32739001C>T		Somatic		Capture	Illumina HiSeq	Phase_I	32774758	NM_000908	A2RRD1|B4DT84|E7EPG9	Silent	SNP	ENST00000265074.8	37	CCDS56357.1																																																																																				0.428	NPR3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000317550.3	NM_000908	
SLC1A3	6507	broad.mit.edu	37	5	36680546	36680546	+	Missense_Mutation	SNP	G	G	A	rs199787096		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr5:36680546G>A	ENST00000265113.4	+	8	1620	c.1144G>A	c.(1144-1146)Gtg>Atg	p.V382M	CTD-2353F22.1_ENST00000510740.1_RNA|SLC1A3_ENST00000381918.3_Missense_Mutation_p.V382M	NM_004172.4	NP_004163.3	P43003	EAA1_HUMAN	solute carrier family 1 (glial high affinity glutamate transporter), member 3	382					auditory behavior (GO:0031223)|cell morphogenesis involved in neuron differentiation (GO:0048667)|cranial nerve development (GO:0021545)|D-aspartate import (GO:0070779)|gamma-aminobutyric acid biosynthetic process (GO:0009449)|glutamate biosynthetic process (GO:0006537)|ion transport (GO:0006811)|L-glutamate import (GO:0051938)|neuromuscular process controlling balance (GO:0050885)|neurotransmitter uptake (GO:0001504)|positive regulation of synaptic transmission (GO:0050806)|response to antibiotic (GO:0046677)|response to drug (GO:0042493)|response to light stimulus (GO:0009416)|response to wounding (GO:0009611)|sensory perception of sound (GO:0007605)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	cell projection (GO:0042995)|cell surface (GO:0009986)|fibril (GO:0043205)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	glutamate binding (GO:0016595)|high-affinity glutamate transmembrane transporter activity (GO:0005314)|L-glutamate transmembrane transporter activity (GO:0005313)|sodium:dicarboxylate symporter activity (GO:0017153)	p.V382M(1)		breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(8)|liver(1)|lung(23)|skin(1)	41	all_lung(31;0.000245)		Epithelial(62;0.0444)|Lung(74;0.111)|all cancers(62;0.128)|COAD - Colon adenocarcinoma(61;0.14)|Colorectal(62;0.202)			GAACAATGGCGTGGACAAGCG	0.527													G|||	1	0.000199681	0.0	0.0	5008	,	,		20568	0.001		0.0	False		,,,				2504	0.0				p.V382M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1144A	5						.	G	MET/VAL,MET/VAL	0,4406		0,0,2203	106.0	87.0	93.0		1144,1144	5.8	1.0	5		93	2,8598	2.2+/-6.3	0,2,4298	no	missense,missense	SLC1A3	NM_001166695.1,NM_004172.4	21,21	0,2,6501	AA,AG,GG		0.0233,0.0,0.0154	probably-damaging,probably-damaging	382/498,382/543	36680546	2,13004	2203	4300	6503	36716303	SO:0001583	missense	6507	exon7				CCDS3919.1, CCDS54844.1	5p13	2013-05-22			ENSG00000079215	ENSG00000079215		"""Solute carriers"""	10941	protein-coding gene	gene with protein product	"""glutamate transporter variant EAAT1ex9skip"""	600111				7521911, 7698014	Standard	NM_004172		Approved	EAAT1, GLAST, EA6	uc003jkj.4	P43003	OTTHUMG00000090793	ENST00000265113.4:c.1144G>A	5.37:g.36680546G>A	ENSP00000265113:p.Val382Met	Somatic		Capture	Illumina HiSeq	Phase_I	36716303	NM_001166695	B2R5T3|Q4JCQ8	Missense_Mutation	SNP	ENST00000265113.4	37	CCDS3919.1	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	G	27.9	4.869227	0.91587	0.0	2.33E-4	ENSG00000079215	ENST00000265113;ENST00000427100;ENST00000381918	T;T	0.66995	-0.24;-0.24	5.8	5.8	0.92144	.	0.059356	0.64402	D	0.000002	D	0.87892	0.6292	H	0.95470	3.675	0.58432	D	0.99999	D;D	0.65815	0.995;0.995	D;D	0.70716	0.914;0.97	D	0.90670	0.4597	10	0.87932	D	0	-27.3266	20.0609	0.97674	0.0:0.0:1.0:0.0	.	382;382	Q4JCQ8;P43003	.;EAA1_HUMAN	M	382;330;382	ENSP00000265113:V382M;ENSP00000371343:V382M	ENSP00000265113:V382M	V	+	1	0	SLC1A3	36716303	1.000000	0.71417	1.000000	0.80357	0.964000	0.63967	5.768000	0.68858	2.755000	0.94549	0.655000	0.94253	GTG		0.527	SLC1A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207579.2	NM_004172	
NIPBL	25836	broad.mit.edu	37	5	37000958	37000958	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr5:37000958G>T	ENST00000282516.8	+	13	4041	c.3542G>T	c.(3541-3543)aGg>aTg	p.R1181M	NIPBL_ENST00000448238.2_Missense_Mutation_p.R1181M	NM_015384.4|NM_133433.3	NP_056199.2|NP_597677.2	Q6KC79	NIPBL_HUMAN	Nipped-B homolog (Drosophila)	1181					brain development (GO:0007420)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to X-ray (GO:0071481)|cognition (GO:0050890)|developmental growth (GO:0048589)|ear morphogenesis (GO:0042471)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic forelimb morphogenesis (GO:0035115)|embryonic viscerocranium morphogenesis (GO:0048703)|external genitalia morphogenesis (GO:0035261)|eye morphogenesis (GO:0048592)|face morphogenesis (GO:0060325)|fat cell differentiation (GO:0045444)|forelimb morphogenesis (GO:0035136)|gall bladder development (GO:0061010)|heart morphogenesis (GO:0003007)|maintenance of mitotic sister chromatid cohesion (GO:0034088)|metanephros development (GO:0001656)|mitotic cell cycle (GO:0000278)|mitotic sister chromatid cohesion (GO:0007064)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|outflow tract morphogenesis (GO:0003151)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of multicellular organism growth (GO:0040018)|positive regulation of ossification (GO:0045778)|regulation of developmental growth (GO:0048638)|regulation of embryonic development (GO:0045995)|regulation of hair cycle (GO:0042634)|sensory perception of sound (GO:0007605)|stem cell maintenance (GO:0019827)|uterus morphogenesis (GO:0061038)	extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|SMC loading complex (GO:0032116)	chromatin binding (GO:0003682)|chromo shadow domain binding (GO:0070087)|histone deacetylase binding (GO:0042826)|protein C-terminus binding (GO:0008022)|protein N-terminus binding (GO:0047485)	p.R1181M(2)		autonomic_ganglia(1)|breast(4)|endometrium(9)|kidney(22)|large_intestine(21)|liver(1)|lung(47)|ovary(7)|pancreas(1)|prostate(1)|skin(7)|upper_aerodigestive_tract(3)|urinary_tract(4)	128	all_lung(31;0.000447)|Hepatocellular(1;0.108)		Epithelial(62;0.072)|COAD - Colon adenocarcinoma(61;0.14)|all cancers(62;0.191)|Colorectal(62;0.202)			CAGAAGAAAAGGAAAGCATAT	0.299																																					p.R1181M												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G3542T	5						.						77.0	78.0	78.0					5																	37000958		2202	4296	6498	37036715	SO:0001583	missense	25836	exon13			AB019494	CCDS3920.1, CCDS47198.1	5p13.2	2009-08-28			ENSG00000164190	ENSG00000164190			28862	protein-coding gene	gene with protein product	"""sister chromatid cohesion 2 homolog (yeast)"""	608667				15146186, 15146185	Standard	NM_133433		Approved	IDN3, DKFZp434L1319, FLJ11203, FLJ12597, FLJ13354, FLJ13648, Scc2	uc003jkl.4	Q6KC79	OTTHUMG00000090795	ENST00000282516.8:c.3542G>T	5.37:g.37000958G>T	ENSP00000282516:p.Arg1181Met	Somatic		Capture	Illumina HiSeq	Phase_I	37036715	NM_015384	Q6KCD6|Q6N080|Q6ZT92|Q7Z2E6|Q8N4M5|Q9Y6Y3|Q9Y6Y4	Missense_Mutation	SNP	ENST00000282516.8	37	CCDS3920.1	.	.	.	.	.	.	.	.	.	.	G	20.4	3.984410	0.74474	.	.	ENSG00000164190	ENST00000282516;ENST00000448238	D;D	0.93659	-3.26;-3.26	5.91	5.91	0.95273	.	0.000000	0.85682	D	0.000000	D	0.95853	0.8650	L	0.59436	1.845	0.58432	D	0.999995	D;D	0.76494	0.989;0.999	P;D	0.66847	0.85;0.947	D	0.94789	0.7960	10	0.42905	T	0.14	.	19.8989	0.96978	0.0:0.0:1.0:0.0	.	1181;1181	Q6KC79;Q6KC79-2	NIPBL_HUMAN;.	M	1181	ENSP00000282516:R1181M;ENSP00000406266:R1181M	ENSP00000282516:R1181M	R	+	2	0	NIPBL	37036715	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	6.380000	0.73158	2.791000	0.96007	0.650000	0.86243	AGG		0.299	NIPBL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207582.1	NM_015384	
RICTOR	253260	broad.mit.edu	37	5	38975693	38975693	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr5:38975693C>A	ENST00000357387.3	-	10	865	c.835G>T	c.(835-837)Gca>Tca	p.A279S	RICTOR_ENST00000296782.5_Missense_Mutation_p.A279S	NM_152756.3	NP_689969.2			RPTOR independent companion of MTOR, complex 2									p.A279S(1)		NS(1)|breast(4)|central_nervous_system(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(14)|lung(33)|ovary(3)|prostate(3)|skin(5)	75	all_lung(31;0.000396)					AGAAATCGTGCTTCTCTGTCT	0.403																																					p.A279S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G835T	5						.						87.0	85.0	86.0					5																	38975693		2203	4300	6503	39011450	SO:0001583	missense	253260	exon10				CCDS34148.1, CCDS68861.1	5p13.1	2009-07-09			ENSG00000164327	ENSG00000164327			28611	protein-coding gene	gene with protein product	"""rapamycin-insensitive companion of mTOR"", ""pianissimo"""	609022				12477932	Standard	XM_005248278		Approved	MGC39830, AVO3, PIA, KIAA1999	uc003jlp.2	Q6R327	OTTHUMG00000162037	ENST00000357387.3:c.835G>T	5.37:g.38975693C>A	ENSP00000349959:p.Ala279Ser	Somatic		Capture	Illumina HiSeq	Phase_I	39011450	NM_152756		Missense_Mutation	SNP	ENST00000357387.3	37	CCDS34148.1	.	.	.	.	.	.	.	.	.	.	C	14.69	2.609961	0.46527	.	.	ENSG00000164327	ENST00000357387;ENST00000296782	T;T	0.47177	0.85;0.85	5.93	5.93	0.95920	Armadillo-type fold (1);	0.048468	0.85682	D	0.000000	T	0.66567	0.2802	L	0.54323	1.7	0.58432	D	0.999998	B;B;D	0.61697	0.041;0.029;0.99	B;B;D	0.73380	0.027;0.009;0.98	T	0.66404	-0.5932	10	0.87932	D	0	-17.1507	19.3277	0.94268	0.0:1.0:0.0:0.0	.	279;279;279	E7ETT0;Q6R327;Q6R327-3	.;RICTR_HUMAN;.	S	279	ENSP00000349959:A279S;ENSP00000296782:A279S	ENSP00000296782:A279S	A	-	1	0	RICTOR	39011450	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	5.139000	0.64801	2.812000	0.96745	0.555000	0.69702	GCA		0.403	RICTOR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366985.1	NM_152756	
MAP3K1	4214	broad.mit.edu	37	5	56170877	56170877	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr5:56170877G>A	ENST00000399503.3	+	10	1705	c.1705G>A	c.(1705-1707)Gtt>Att	p.V569I		NM_005921.1	NP_005912.1	Q13233	M3K1_HUMAN	mitogen-activated protein kinase kinase kinase 1, E3 ubiquitin protein ligase	569					activation of MAPKK activity (GO:0000186)|apoptotic mitochondrial changes (GO:0008637)|cellular response to mechanical stimulus (GO:0071260)|epithelial cell morphogenesis (GO:0003382)|eyelid development in camera-type eye (GO:0061029)|Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|positive regulation of actin filament polymerization (GO:0030838)|protein phosphorylation (GO:0006468)|regulation of cell migration (GO:0030334)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|transforming growth factor beta receptor signaling pathway (GO:0007179)|wound healing (GO:0042060)	cytosol (GO:0005829)	ATP binding (GO:0005524)|JUN kinase kinase activity (GO:0008545)|MAP kinase kinase kinase activity (GO:0004709)|protein kinase activity (GO:0004672)|protein kinase binding (GO:0019901)|zinc ion binding (GO:0008270)	p.V406I(1)		NS(1)|breast(19)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(8)|lung(11)|ovary(1)|skin(3)|urinary_tract(1)	57		Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223)		OV - Ovarian serous cystadenocarcinoma(10;6.08e-40)		AATGGAACTCGTTGGCTGCTT	0.443																																					p.V569I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1705A	5						.						163.0	154.0	157.0					5																	56170877		1879	4125	6004	56206634	SO:0001583	missense	4214	exon10			U29671, AF042838	CCDS43318.1	5q11.2	2012-02-23	2012-02-23		ENSG00000095015	ENSG00000095015		"""Mitogen-activated protein kinase cascade / Kinase kinase kinases"""	6848	protein-coding gene	gene with protein product		600982	"""mitogen-activated protein kinase kinase kinase 1"""	MEKK1		8597633	Standard	NM_005921		Approved	MEKK, MAPKKK1	uc003jqw.4	Q13233	OTTHUMG00000059486	ENST00000399503.3:c.1705G>A	5.37:g.56170877G>A	ENSP00000382423:p.Val569Ile	Somatic		Capture	Illumina HiSeq	Phase_I	56206634	NM_005921		Missense_Mutation	SNP	ENST00000399503.3	37	CCDS43318.1	.	.	.	.	.	.	.	.	.	.	G	30	5.050910	0.93740	.	.	ENSG00000095015	ENST00000399503	T	0.70516	-0.49	5.89	5.89	0.94794	.	0.000000	0.64402	D	0.000001	D	0.83248	0.5213	M	0.61703	1.905	0.58432	D	0.999999	D	0.76494	0.999	D	0.71184	0.972	D	0.83463	0.0055	10	0.72032	D	0.01	.	20.2576	0.98430	0.0:0.0:1.0:0.0	.	569	Q13233	M3K1_HUMAN	I	569	ENSP00000382423:V569I	ENSP00000382423:V569I	V	+	1	0	MAP3K1	56206634	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	8.441000	0.90313	2.783000	0.95769	0.655000	0.94253	GTT		0.443	MAP3K1-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000132309.2	XM_042066	
MAP3K1	4214	broad.mit.edu	37	5	56180651	56180651	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr5:56180651C>T	ENST00000399503.3	+	16	3980	c.3980C>T	c.(3979-3981)gCa>gTa	p.A1327V		NM_005921.1	NP_005912.1	Q13233	M3K1_HUMAN	mitogen-activated protein kinase kinase kinase 1, E3 ubiquitin protein ligase	1327	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of MAPKK activity (GO:0000186)|apoptotic mitochondrial changes (GO:0008637)|cellular response to mechanical stimulus (GO:0071260)|epithelial cell morphogenesis (GO:0003382)|eyelid development in camera-type eye (GO:0061029)|Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|positive regulation of actin filament polymerization (GO:0030838)|protein phosphorylation (GO:0006468)|regulation of cell migration (GO:0030334)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|transforming growth factor beta receptor signaling pathway (GO:0007179)|wound healing (GO:0042060)	cytosol (GO:0005829)	ATP binding (GO:0005524)|JUN kinase kinase activity (GO:0008545)|MAP kinase kinase kinase activity (GO:0004709)|protein kinase activity (GO:0004672)|protein kinase binding (GO:0019901)|zinc ion binding (GO:0008270)			NS(1)|breast(19)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(8)|lung(11)|ovary(1)|skin(3)|urinary_tract(1)	57		Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223)		OV - Ovarian serous cystadenocarcinoma(10;6.08e-40)		GAATGGATGGCAGGTATGTTA	0.318																																					p.A1327V												.	.	0			c.C3980T	5						.						94.0	86.0	88.0					5																	56180651		1868	4103	5971	56216408	SO:0001583	missense	4214	exon16			U29671, AF042838	CCDS43318.1	5q11.2	2012-02-23	2012-02-23		ENSG00000095015	ENSG00000095015		"""Mitogen-activated protein kinase cascade / Kinase kinase kinases"""	6848	protein-coding gene	gene with protein product		600982	"""mitogen-activated protein kinase kinase kinase 1"""	MEKK1		8597633	Standard	NM_005921		Approved	MEKK, MAPKKK1	uc003jqw.4	Q13233	OTTHUMG00000059486	ENST00000399503.3:c.3980C>T	5.37:g.56180651C>T	ENSP00000382423:p.Ala1327Val	Somatic		Capture	Illumina HiSeq	Phase_I	56216408	NM_005921		Missense_Mutation	SNP	ENST00000399503.3	37	CCDS43318.1	.	.	.	.	.	.	.	.	.	.	C	30	5.050516	0.93740	.	.	ENSG00000095015	ENST00000399503	T	0.25749	1.78	5.51	5.51	0.81932	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.48223	0.1488	L	0.49640	1.575	0.80722	D	1	D	0.71674	0.998	D	0.80764	0.994	T	0.40683	-0.9550	10	0.62326	D	0.03	.	19.4853	0.95026	0.0:1.0:0.0:0.0	.	1327	Q13233	M3K1_HUMAN	V	1327	ENSP00000382423:A1327V	ENSP00000382423:A1327V	A	+	2	0	MAP3K1	56216408	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	6.799000	0.75160	2.596000	0.87737	0.644000	0.83932	GCA		0.318	MAP3K1-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000132309.2	XM_042066	
KIF2A	3796	broad.mit.edu	37	5	61645900	61645900	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr5:61645900G>A	ENST00000401507.3	+	4	598	c.287G>A	c.(286-288)cGg>cAg	p.R96Q	KIF2A_ENST00000506857.1_Missense_Mutation_p.R69Q|KIF2A_ENST00000509663.2_Intron|KIF2A_ENST00000407818.3_Missense_Mutation_p.R96Q|KIF2A_ENST00000381103.2_Missense_Mutation_p.R76Q	NM_001243953.1|NM_004520.4	NP_001230882.1|NP_004511.2	O00139	KIF2A_HUMAN	kinesin heavy chain member 2A	96	Globular. {ECO:0000255}.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|ATP catabolic process (GO:0006200)|blood coagulation (GO:0007596)|cell differentiation (GO:0030154)|metabolic process (GO:0008152)|microtubule depolymerization (GO:0007019)|microtubule-based movement (GO:0007018)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic spindle organization (GO:0007052)|nervous system development (GO:0007399)	centrosome (GO:0005813)|cytosol (GO:0005829)|kinesin complex (GO:0005871)|membrane (GO:0016020)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|motor activity (GO:0003774)	p.R96Q(1)|p.R69Q(1)		NS(1)|endometrium(3)|kidney(3)|large_intestine(3)|lung(3)|ovary(1)|skin(1)	15		Lung NSC(810;8.94e-06)|Prostate(74;0.0132)|Ovarian(174;0.051)|Breast(144;0.077)		Lung(70;0.14)		TAGAATCGACGGACTGTAGCT	0.318																																					p.R96Q												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G287A	5						.						47.0	45.0	45.0					5																	61645900		2202	4295	6497	61681657	SO:0001583	missense	3796	exon4			BC031828	CCDS3980.2, CCDS47216.1, CCDS58949.1	5q12-q13	2008-02-05	2006-09-26	2006-09-26	ENSG00000068796	ENSG00000068796		"""Kinesins"""	6318	protein-coding gene	gene with protein product		602591	"""kinesin heavy chain member 2"""	KIF2		9177777	Standard	NM_001098511		Approved	HK2	uc003jsz.4	O00139	OTTHUMG00000097755	ENST00000401507.3:c.287G>A	5.37:g.61645900G>A	ENSP00000385622:p.Arg96Gln	Somatic		Capture	Illumina HiSeq	Phase_I	61681657	NM_001098511	A5YM42|A5YM54|B4DY54|D3DW97|E9PB70|Q7Z5I3|Q8N5Q7	Missense_Mutation	SNP	ENST00000401507.3	37	CCDS3980.2	.	.	.	.	.	.	.	.	.	.	G	28.3	4.910420	0.92107	.	.	ENSG00000068796	ENST00000401507;ENST00000381103;ENST00000514082;ENST00000407818;ENST00000512541;ENST00000506857	T;T;T;T;T;T	0.73789	-0.61;-0.62;1.86;-0.78;0.81;-0.66	5.87	5.87	0.94306	.	0.051970	0.85682	D	0.000000	T	0.79879	0.4522	L	0.45228	1.405	0.80722	D	1	P;D;B;D	0.65815	0.496;0.995;0.176;0.99	B;P;B;P	0.59357	0.034;0.856;0.013;0.478	T	0.73202	-0.4057	10	0.18710	T	0.47	.	20.206	0.98277	0.0:0.0:1.0:0.0	.	96;96;96;76	B4DM85;O00139-4;O00139;E9PB70	.;.;KIF2A_HUMAN;.	Q	96;76;96;96;69;69	ENSP00000385622:R96Q;ENSP00000370493:R76Q;ENSP00000423542:R96Q;ENSP00000385000:R96Q;ENSP00000425411:R69Q;ENSP00000423772:R69Q	ENSP00000370493:R76Q	R	+	2	0	KIF2A	61681657	1.000000	0.71417	1.000000	0.80357	0.883000	0.51084	8.801000	0.91905	2.785000	0.95823	0.655000	0.94253	CGG		0.318	KIF2A-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317989.1	NM_004520	
FOXD1	2297	broad.mit.edu	37	5	72744053	72744053	+	Silent	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr5:72744053C>T	ENST00000499003.3	-	1	299	c.135G>A	c.(133-135)cgG>cgA	p.R45R	FOXD1_ENST00000513595.1_5'Flank|RP11-79P5.2_ENST00000514661.1_lincRNA	NM_004472.2	NP_004463.1	Q16676	FOXD1_HUMAN	forkhead box D1	45					axon guidance (GO:0007411)|dichotomous subdivision of terminal units involved in ureteric bud branching (GO:0060678)|metanephric capsule development (GO:0072213)|metanephric capsule specification (GO:0072267)|metanephric nephron development (GO:0072210)|negative regulation of transcription, DNA-templated (GO:0045892)|nephrogenic mesenchyme development (GO:0072076)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of gene expression (GO:0010628)|positive regulation of kidney development (GO:0090184)	nucleus (GO:0005634)	DNA binding (GO:0003677)|DNA binding, bending (GO:0008301)|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)			endometrium(1)|kidney(1)|lung(2)	4		Lung NSC(167;0.00327)|Ovarian(174;0.0175)|Prostate(461;0.151)		OV - Ovarian serous cystadenocarcinoma(47;1.07e-54)		ggacagccagccggggcccgc	0.716																																					p.R45R												.	.	0			c.G135A	5						.						20.0	19.0	20.0					5																	72744053		1528	3425	4953	72779809	SO:0001819	synonymous_variant	2297	exon1			U59831	CCDS75259.1	5q13.2	2014-06-04			ENSG00000251493	ENSG00000251493		"""Forkhead boxes"""	3802	protein-coding gene	gene with protein product		601091		FKHL8		7957066, 8825632	Standard	NM_004472		Approved	FREAC4	uc003kcp.3	Q16676	OTTHUMG00000162495	ENST00000499003.3:c.135G>A	5.37:g.72744053C>T		Somatic		Capture	Illumina HiSeq	Phase_I	72779809	NM_004472	Q12949	Silent	SNP	ENST00000499003.3	37																																																																																					0.716	FOXD1-001	KNOWN	sequence_error|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000369154.2	NM_004472	
AP3B1	8546	broad.mit.edu	37	5	77330247	77330247	+	Silent	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr5:77330247G>A	ENST00000255194.6	-	24	3007	c.2832C>T	c.(2830-2832)tcC>tcT	p.S944S	AP3B1_ENST00000523204.1_5'UTR|AP3B1_ENST00000519295.1_Silent_p.S895S	NM_001271769.1	NP_001258698.1	O00203	AP3B1_HUMAN	adaptor-related protein complex 3, beta 1 subunit	944					anterograde axon cargo transport (GO:0008089)|anterograde synaptic vesicle transport (GO:0048490)|antigen processing and presentation, exogenous lipid antigen via MHC class Ib (GO:0048007)|blood coagulation (GO:0007596)|intracellular protein transport (GO:0006886)|melanosome organization (GO:0032438)|positive regulation of NK T cell differentiation (GO:0051138)|protein targeting to lysosome (GO:0006622)	AP-3 adaptor complex (GO:0030123)|cytoplasmic vesicle (GO:0031410)|Golgi apparatus (GO:0005794)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)	GTP-dependent protein binding (GO:0030742)|protein phosphatase binding (GO:0019903)	p.S944S(1)		breast(5)|central_nervous_system(2)|cervix(1)|endometrium(3)|large_intestine(12)|lung(12)|prostate(1)|skin(2)|urinary_tract(1)	39		all_lung(232;0.000397)|Lung NSC(167;0.00106)|Ovarian(174;0.0105)|Prostate(461;0.215)		OV - Ovarian serous cystadenocarcinoma(54;8.23e-47)|Epithelial(54;2.74e-41)|all cancers(79;4.8e-36)		AAACTGTAATGGATCCCTCAG	0.348									Hermansky-Pudlak syndrome																												p.S944S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C2832T	5						.						77.0	81.0	79.0					5																	77330247		2203	4300	6503	77366003	SO:0001819	synonymous_variant	8546	exon24	Familial Cancer Database	HPS, HPS1-8	U81504	CCDS4041.1, CCDS64186.1	5q14.1	2014-09-17			ENSG00000132842	ENSG00000132842			566	protein-coding gene	gene with protein product		603401				9182526, 9151686	Standard	NM_003664		Approved	ADTB3A, HPS2	uc003kfj.4	O00203	OTTHUMG00000106919	ENST00000255194.6:c.2832C>T	5.37:g.77330247G>A		Somatic		Capture	Illumina HiSeq	Phase_I	77366003	NM_003664	E5RJ68|O00580|Q7Z393|Q9HD66	Silent	SNP	ENST00000255194.6	37	CCDS4041.1	.	.	.	.	.	.	.	.	.	.	G	10.05	1.243189	0.22796	.	.	ENSG00000132842	ENST00000522901	.	.	.	6.05	4.26	0.50523	.	.	.	.	.	T	0.60881	0.2303	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.59198	-0.7499	4	.	.	.	-8.2216	10.4252	0.44373	0.2409:0.0:0.7591:0.0	.	.	.	.	L	44	.	.	P	-	2	0	AP3B1	77366003	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	0.496000	0.22499	1.561000	0.49584	0.650000	0.86243	CCA		0.348	AP3B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000225548.2		
AP3B1	8546	broad.mit.edu	37	5	77477331	77477331	+	Splice_Site	SNP	C	C	T	rs146871001	byFrequency	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr5:77477331C>T	ENST00000255194.6	-	8	1117	c.942G>A	c.(940-942)gcG>gcA	p.A314A	AP3B1_ENST00000519295.1_Splice_Site_p.A265A	NM_001271769.1	NP_001258698.1	O00203	AP3B1_HUMAN	adaptor-related protein complex 3, beta 1 subunit	314					anterograde axon cargo transport (GO:0008089)|anterograde synaptic vesicle transport (GO:0048490)|antigen processing and presentation, exogenous lipid antigen via MHC class Ib (GO:0048007)|blood coagulation (GO:0007596)|intracellular protein transport (GO:0006886)|melanosome organization (GO:0032438)|positive regulation of NK T cell differentiation (GO:0051138)|protein targeting to lysosome (GO:0006622)	AP-3 adaptor complex (GO:0030123)|cytoplasmic vesicle (GO:0031410)|Golgi apparatus (GO:0005794)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)	GTP-dependent protein binding (GO:0030742)|protein phosphatase binding (GO:0019903)	p.A314A(1)		breast(5)|central_nervous_system(2)|cervix(1)|endometrium(3)|large_intestine(12)|lung(12)|prostate(1)|skin(2)|urinary_tract(1)	39		all_lung(232;0.000397)|Lung NSC(167;0.00106)|Ovarian(174;0.0105)|Prostate(461;0.215)		OV - Ovarian serous cystadenocarcinoma(54;8.23e-47)|Epithelial(54;2.74e-41)|all cancers(79;4.8e-36)		TTTAACATACCGCAGCATTCC	0.338									Hermansky-Pudlak syndrome				C|||	10	0.00199681	0.0008	0.0058	5008	,	,		18648	0.005		0.0	False		,,,				2504	0.0				p.A314A												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G942A	5						.	C		0,4406		0,0,2203	78.0	78.0	78.0		942	4.2	1.0	5	dbSNP_134	78	3,8597	2.2+/-6.3	0,3,4297	yes	coding-synonymous-near-splice	AP3B1	NM_003664.3		0,3,6500	TT,TC,CC		0.0349,0.0,0.0231		314/1095	77477331	3,13003	2203	4300	6503	77513087	SO:0001630	splice_region_variant	8546	exon8	Familial Cancer Database	HPS, HPS1-8	U81504	CCDS4041.1, CCDS64186.1	5q14.1	2014-09-17			ENSG00000132842	ENSG00000132842			566	protein-coding gene	gene with protein product		603401				9182526, 9151686	Standard	NM_003664		Approved	ADTB3A, HPS2	uc003kfj.4	O00203	OTTHUMG00000106919	ENST00000255194.6:c.942+1G>A	5.37:g.77477331C>T		Somatic		Capture	Illumina HiSeq	Phase_I	77513087	NM_003664	E5RJ68|O00580|Q7Z393|Q9HD66	Silent	SNP	ENST00000255194.6	37	CCDS4041.1																																																																																				0.338	AP3B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000225548.2		Silent
SCAMP1	9522	broad.mit.edu	37	5	77712399	77712399	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr5:77712399G>A	ENST00000538629.1	+	4	426	c.269G>A	c.(268-270)cGc>cAc	p.R90H	SCAMP1_ENST00000339292.4_3'UTR	NM_004866.4	NP_004857.4	O15126	SCAM1_HUMAN	secretory carrier membrane protein 1	90					endocytosis (GO:0006897)|exocytosis (GO:0006887)|post-Golgi vesicle-mediated transport (GO:0006892)|protein transport (GO:0015031)	clathrin-coated vesicle (GO:0030136)|integral component of membrane (GO:0016021)|recycling endosome membrane (GO:0055038)|synaptic vesicle membrane (GO:0030672)|trans-Golgi network (GO:0005802)|zymogen granule membrane (GO:0042589)							all_lung(232;0.000397)|Lung NSC(167;0.00105)|Ovarian(174;0.0105)|Prostate(461;0.214)		OV - Ovarian serous cystadenocarcinoma(54;1.9e-46)|Epithelial(54;9.4e-43)|all cancers(79;1.12e-37)		CTTCTTAAGCGCCAGGAAGAA	0.348																																					p.R90H												.	.	0			c.G269A	5						.						46.0	42.0	44.0					5																	77712399		1831	4081	5912	77748155	SO:0001583	missense	9522	exon4			AF038966	CCDS75264.1	5q14.1	2013-02-21			ENSG00000085365	ENSG00000085365		"""Secretory carrier membrane proteins"""	10563	protein-coding gene	gene with protein product		606911				9378760	Standard	NM_004866		Approved	SCAMP37	uc003kfl.3	O15126	OTTHUMG00000162479	ENST00000538629.1:c.269G>A	5.37:g.77712399G>A	ENSP00000475496:p.Arg90His	Somatic		Capture	Illumina HiSeq	Phase_I	77748155	NM_004866	O43587|Q6FG23|Q96BX1|Q96QK5	Missense_Mutation	SNP	ENST00000538629.1	37																																																																																					0.348	SCAMP1-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_004866	
HOMER1	9456	broad.mit.edu	37	5	78752771	78752771	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr5:78752771G>A	ENST00000334082.6	-	2	1518	c.76C>T	c.(76-78)Ccc>Tcc	p.P26S	HOMER1_ENST00000508576.1_Missense_Mutation_p.P26S|HOMER1_ENST00000282260.6_Missense_Mutation_p.P26S|HOMER1_ENST00000535690.1_Intron	NM_004272.3	NP_004263.1	Q86YM7	HOME1_HUMAN	homer homolog 1 (Drosophila)	26	WH1. {ECO:0000255|PROSITE- ProRule:PRU00410}.				behavioral response to cocaine (GO:0048148)|chemical homeostasis within a tissue (GO:0048875)|circadian rhythm (GO:0007623)|phospholipase C-activating G-protein coupled glutamate receptor signaling pathway (GO:0007206)|positive regulation of calcium ion transport (GO:0051928)|positive regulation of signal transduction (GO:0009967)|protein localization to synapse (GO:0035418)|regulation of calcium ion import (GO:0090279)|regulation of cation channel activity (GO:2001257)|regulation of store-operated calcium entry (GO:2001256)|response to calcium ion (GO:0051592)|response to nicotine (GO:0035094)|skeletal muscle contraction (GO:0003009)|skeletal muscle fiber development (GO:0048741)|synaptic transmission (GO:0007268)	apical part of cell (GO:0045177)|axon (GO:0030424)|cell junction (GO:0030054)|costamere (GO:0043034)|dendritic shaft (GO:0043198)|integral component of plasma membrane (GO:0005887)|neuronal cell body (GO:0043025)|neuronal postsynaptic density (GO:0097481)|postsynaptic membrane (GO:0045211)|Z disc (GO:0030018)	ion channel binding (GO:0044325)|signaling adaptor activity (GO:0035591)	p.P26S(1)		endometrium(2)|kidney(1)|large_intestine(5)|lung(3)|prostate(2)|skin(1)	14		Lung NSC(167;0.00131)|all_lung(232;0.00151)|Ovarian(174;0.0261)|Prostate(461;0.191)		OV - Ovarian serous cystadenocarcinoma(54;1.87e-44)|Epithelial(54;7.07e-41)|all cancers(79;5.5e-36)		TTGCTGGTGGGTACCCAGTTC	0.423																																					p.P26S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C76T	5						.						242.0	228.0	233.0					5																	78752771		1908	4127	6035	78788527	SO:0001583	missense	9456	exon2			BC015502	CCDS43335.1, CCDS64188.1, CCDS64189.1	5q14.2	2008-02-05			ENSG00000152413	ENSG00000152413			17512	protein-coding gene	gene with protein product		604798				9808459, 9808458	Standard	NM_004272		Approved	Ves-1, SYN47, HOMER-1B	uc003kfy.4	Q86YM7	OTTHUMG00000134278	ENST00000334082.6:c.76C>T	5.37:g.78752771G>A	ENSP00000334382:p.Pro26Ser	Somatic		Capture	Illumina HiSeq	Phase_I	78788527	NM_004272	B2R688|O96003|Q86YM5	Missense_Mutation	SNP	ENST00000334082.6	37	CCDS43335.1	.	.	.	.	.	.	.	.	.	.	G	28.9	4.959665	0.92791	.	.	ENSG00000152413	ENST00000334082;ENST00000508576;ENST00000282260	D;D;D	0.98666	-5.06;-5.06;-5.06	5.72	5.72	0.89469	EVH1 (3);Pleckstrin homology-type (1);	0.000000	0.85682	D	0.000000	D	0.99390	0.9785	M	0.92317	3.295	0.80722	D	1	P;D;D	0.89917	0.757;1.0;1.0	P;D;D	0.97110	0.619;0.999;1.0	D	0.98863	1.0763	10	0.87932	D	0	-2.1103	19.879	0.96888	0.0:0.0:1.0:0.0	.	26;26;26	Q86YM7-2;Q86YM7-3;Q86YM7	.;.;HOME1_HUMAN	S	26	ENSP00000334382:P26S;ENSP00000426651:P26S;ENSP00000282260:P26S	ENSP00000282260:P26S	P	-	1	0	HOMER1	78788527	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.869000	0.99810	2.695000	0.91970	0.655000	0.94253	CCC		0.423	HOMER1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258856.1	NM_004272	
CMYA5	202333	broad.mit.edu	37	5	79030606	79030606	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr5:79030606G>T	ENST00000446378.2	+	2	6049	c.6018G>T	c.(6016-6018)gaG>gaT	p.E2006D		NM_153610.3	NP_705838.3	Q8N3K9	CMYA5_HUMAN	cardiomyopathy associated 5	2006					negative regulation of calcineurin-NFAT signaling cascade (GO:0070885)|negative regulation of protein phosphatase type 2B activity (GO:0032513)|regulation of skeletal muscle adaptation (GO:0014733)	costamere (GO:0043034)		p.E2006D(1)		NS(2)|breast(4)|central_nervous_system(1)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(4)|kidney(4)|large_intestine(37)|lung(34)|ovary(6)|pancreas(2)|prostate(5)|skin(5)|stomach(11)|upper_aerodigestive_tract(3)|urinary_tract(1)	128		Lung NSC(167;0.00296)|all_lung(232;0.00327)|Ovarian(174;0.0262)		OV - Ovarian serous cystadenocarcinoma(54;9.85e-46)|Epithelial(54;3.38e-40)|all cancers(79;3.43e-35)		ACATAGCAGAGGGGAAGGAGA	0.403																																					p.E2006D												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G6018T	5						.						60.0	58.0	59.0					5																	79030606		1851	4092	5943	79066362	SO:0001583	missense	202333	exon2			AW755254, AL831986	CCDS47238.1	5q14.1	2013-02-11			ENSG00000164309	ENSG00000164309		"""Tripartite motif containing / Tripartite motif containing"", ""A-kinase anchor proteins"", ""Fibronectin type III domain containing"""	14305	protein-coding gene	gene with protein product	"""genethonin-3"", ""tripartite motif-containing 76"""	612193	"""chromosome 5 open reading frame 10"""	C5orf10		14688250	Standard	NM_153610		Approved	myospryn, SPRYD2, DKFZp451G223, TRIM76	uc003kgc.3	Q8N3K9	OTTHUMG00000162548	ENST00000446378.2:c.6018G>T	5.37:g.79030606G>T	ENSP00000394770:p.Glu2006Asp	Somatic		Capture	Illumina HiSeq	Phase_I	79066362	NM_153610	A0PJB7|Q05CT4|Q2NKX1|Q2T9G9|Q69YQ8|Q69YQ9|Q6P517|Q6P5U3|Q7Z4I1|Q86T34|Q86T49|Q8N3S4|Q8N3S7|Q8NAG8|Q9UK88	Missense_Mutation	SNP	ENST00000446378.2	37	CCDS47238.1	.	.	.	.	.	.	.	.	.	.	G	14.04	2.416782	0.42918	.	.	ENSG00000164309	ENST00000446378	T	0.54675	0.56	5.76	1.61	0.23674	.	0.200780	0.24999	N	0.033931	T	0.35008	0.0917	L	0.29908	0.895	0.09310	N	1	P	0.46987	0.888	B	0.42163	0.378	T	0.14699	-1.0463	10	0.40728	T	0.16	.	4.8577	0.13568	0.2711:0.0:0.5792:0.1497	.	2006	Q8N3K9	CMYA5_HUMAN	D	2006	ENSP00000394770:E2006D	ENSP00000394770:E2006D	E	+	3	2	CMYA5	79066362	0.051000	0.20477	0.080000	0.20451	0.005000	0.04900	0.145000	0.16157	0.704000	0.31869	0.505000	0.49811	GAG		0.403	CMYA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369497.1	NM_153610	
THBS4	7060	broad.mit.edu	37	5	79372746	79372746	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr5:79372746C>T	ENST00000350881.2	+	16	2151	c.1961C>T	c.(1960-1962)aCc>aTc	p.T654I	CTD-2201I18.1_ENST00000503007.1_RNA|THBS4_ENST00000511733.1_Missense_Mutation_p.T563I|CTD-2201I18.1_ENST00000514042.1_RNA	NM_003248.4	NP_003239.2	P35443	TSP4_HUMAN	thrombospondin 4	654					behavioral response to pain (GO:0048266)|endothelial cell-cell adhesion (GO:0071603)|myoblast migration (GO:0051451)|negative regulation of angiogenesis (GO:0016525)|positive regulation of cell division (GO:0051781)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of neutrophil chemotaxis (GO:0090023)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|regulation of tissue remodeling (GO:0034103)|response to endoplasmic reticulum stress (GO:0034976)|response to unfolded protein (GO:0006986)|tissue remodeling (GO:0048771)	basement membrane (GO:0005604)|endoplasmic reticulum (GO:0005783)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|sarcoplasmic reticulum (GO:0016529)	calcium ion binding (GO:0005509)|heparin binding (GO:0008201)|integrin binding (GO:0005178)	p.T654I(1)		breast(1)|endometrium(4)|kidney(2)|large_intestine(9)|lung(14)|ovary(1)|stomach(3)	34		Lung NSC(167;0.00328)|all_lung(232;0.00355)|Ovarian(174;0.0261)		OV - Ovarian serous cystadenocarcinoma(54;6.3e-45)|Epithelial(54;1.77e-39)|all cancers(79;3.2e-34)		CAGCTGGACACCGATAAGGAT	0.562																																					p.T654I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1961T	5						.						208.0	193.0	198.0					5																	79372746		2203	4300	6503	79408502	SO:0001583	missense	7060	exon16				CCDS4049.1	5q13	2008-05-15			ENSG00000113296	ENSG00000113296			11788	protein-coding gene	gene with protein product		600715				7852353	Standard	NM_003248		Approved		uc021yaw.1	P35443	OTTHUMG00000108173	ENST00000350881.2:c.1961C>T	5.37:g.79372746C>T	ENSP00000339730:p.Thr654Ile	Somatic		Capture	Illumina HiSeq	Phase_I	79408502	NM_003248	B2R909|Q86TG2	Missense_Mutation	SNP	ENST00000350881.2	37	CCDS4049.1	.	.	.	.	.	.	.	.	.	.	C	27.3	4.818028	0.90790	.	.	ENSG00000113296	ENST00000350881;ENST00000511733	D;D	0.98567	-5.0;-5.0	5.22	5.22	0.72569	.	0.048114	0.85682	D	0.000000	D	0.98760	0.9583	M	0.76574	2.34	0.80722	D	1	D	0.71674	0.998	D	0.69824	0.966	D	0.98572	1.0646	10	0.39692	T	0.17	-18.3442	19.3435	0.94355	0.0:1.0:0.0:0.0	.	654	P35443	TSP4_HUMAN	I	654;563	ENSP00000339730:T654I;ENSP00000422298:T563I	ENSP00000339730:T654I	T	+	2	0	THBS4	79408502	1.000000	0.71417	0.974000	0.42286	0.994000	0.84299	5.817000	0.69229	2.866000	0.98385	0.650000	0.86243	ACC		0.562	THBS4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226977.1		
FAM151B	167555	broad.mit.edu	37	5	79815570	79815570	+	Missense_Mutation	SNP	C	C	T	rs527461710		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr5:79815570C>T	ENST00000282226.4	+	4	531	c.376C>T	c.(376-378)Cgt>Tgt	p.R126C	FAM151B_ENST00000511718.1_3'UTR	NM_205548.2	NP_991111.2	Q6UXP7	F151B_HUMAN	family with sequence similarity 151, member B	126								p.R126C(1)		breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(1)|ovary(1)	7		Lung NSC(167;0.0427)|all_lung(232;0.0464)|Ovarian(174;0.113)		OV - Ovarian serous cystadenocarcinoma(54;8.21e-47)|Epithelial(54;8.3e-42)|all cancers(79;1.97e-36)		GCATCTGAAGCGTCCTGTATG	0.378																																					p.R126C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C376T	5						.						119.0	103.0	108.0					5																	79815570		2203	4300	6503	79851326	SO:0001583	missense	167555	exon4				CCDS4051.1	5q14.1	2007-12-18	2007-12-18		ENSG00000152380	ENSG00000152380			33716	protein-coding gene	gene with protein product							Standard	NM_205548		Approved	UNQ9217	uc003kgv.2	Q6UXP7	OTTHUMG00000131303	ENST00000282226.4:c.376C>T	5.37:g.79815570C>T	ENSP00000282226:p.Arg126Cys	Somatic		Capture	Illumina HiSeq	Phase_I	79851326	NM_205548	A2RRE4	Missense_Mutation	SNP	ENST00000282226.4	37	CCDS4051.1	.	.	.	.	.	.	.	.	.	.	c	10.70	1.425398	0.25639	.	.	ENSG00000152380	ENST00000282226	T	0.12774	2.65	5.76	3.05	0.35203	.	0.420046	0.27650	N	0.018424	T	0.12561	0.0305	L	0.48642	1.525	0.22521	N	0.999029	B	0.24368	0.102	B	0.20767	0.031	T	0.17319	-1.0373	10	0.37606	T	0.19	-11.6253	10.5561	0.45118	0.0:0.7935:0.0:0.2065	.	126	Q6UXP7	F151B_HUMAN	C	126	ENSP00000282226:R126C	ENSP00000282226:R126C	R	+	1	0	FAM151B	79851326	0.989000	0.36119	0.027000	0.17364	0.955000	0.61496	1.624000	0.37018	0.366000	0.24427	-0.170000	0.13304	CGT		0.378	FAM151B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254072.1	NM_205548	
VCAN	1462	broad.mit.edu	37	5	82833364	82833364	+	Silent	SNP	A	A	G			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr5:82833364A>G	ENST00000265077.3	+	8	5107	c.4542A>G	c.(4540-4542)acA>acG	p.T1514T	VCAN_ENST00000502527.2_Intron|VCAN_ENST00000342785.4_Intron|VCAN_ENST00000513016.1_3'UTR|VCAN-AS1_ENST00000512090.1_RNA|VCAN_ENST00000343200.5_Silent_p.T527T|VCAN_ENST00000512590.2_Intron	NM_004385.4	NP_004376.2	P13611	CSPG2_HUMAN	versican	1514	GAG-beta.				carbohydrate metabolic process (GO:0005975)|cell adhesion (GO:0007155)|cell recognition (GO:0008037)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|extracellular matrix organization (GO:0030198)|glial cell migration (GO:0008347)|glycosaminoglycan metabolic process (GO:0030203)|heart development (GO:0007507)|multicellular organismal development (GO:0007275)|osteoblast differentiation (GO:0001649)|small molecule metabolic process (GO:0044281)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi lumen (GO:0005796)|intracellular membrane-bounded organelle (GO:0043231)|lysosomal lumen (GO:0043202)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)|glycosaminoglycan binding (GO:0005539)|hyaluronic acid binding (GO:0005540)	p.T1514T(1)		NS(2)|biliary_tract(1)|breast(3)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(52)|lung(64)|ovary(8)|pancreas(3)|prostate(13)|skin(14)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(5)	190		Lung NSC(167;0.0216)|all_lung(232;0.0251)|Ovarian(174;0.142)		OV - Ovarian serous cystadenocarcinoma(54;2.47e-41)|Epithelial(54;2.51e-34)|all cancers(79;5.19e-29)	Hyaluronan(DB08818)	AAAGTGGAACAGCCAAAAAAG	0.448																																					p.T527T												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.A1581G	5						.						71.0	70.0	70.0					5																	82833364		2203	4300	6503	82869120	SO:0001819	synonymous_variant	1462	exon7			X15998	CCDS4060.1, CCDS47242.1, CCDS54875.1, CCDS54876.1	5q14.2-q14.3	2013-05-07	2007-02-15	2007-02-15	ENSG00000038427	ENSG00000038427		"""Immunoglobulin superfamily / V-set domain containing"", ""Proteoglycans / Extracellular Matrix : Hyalectans"""	2464	protein-coding gene	gene with protein product	"""versican proteoglycan"""	118661	"""chondroitin sulfate proteoglycan 2"""	CSPG2		1478664, 21063030	Standard	NM_004385		Approved	PG-M	uc003kii.3	P13611	OTTHUMG00000131321	ENST00000265077.3:c.4542A>G	5.37:g.82833364A>G		Somatic		Capture	Illumina HiSeq	Phase_I	82869120	NM_001164097	P20754|Q13010|Q13189|Q15123|Q9UCL9|Q9UNW5	Silent	SNP	ENST00000265077.3	37	CCDS4060.1																																																																																				0.448	VCAN-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000254092.3	NM_004385	
GPR98	84059	broad.mit.edu	37	5	89975443	89975443	+	Missense_Mutation	SNP	C	C	T	rs367621359		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr5:89975443C>T	ENST00000405460.2	+	26	5617	c.5521C>T	c.(5521-5523)Cgt>Tgt	p.R1841C		NM_032119.3	NP_115495.3	Q8WXG9	GPR98_HUMAN	G protein-coupled receptor 98	1841					detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|G-protein coupled receptor signaling pathway (GO:0007186)|inner ear receptor stereocilium organization (GO:0060122)|maintenance of organ identity (GO:0048496)|nervous system development (GO:0007399)|neurological system process (GO:0050877)|neuropeptide signaling pathway (GO:0007218)|photoreceptor cell maintenance (GO:0045494)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|single organismal cell-cell adhesion (GO:0016337)|visual perception (GO:0007601)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|stereocilia ankle link complex (GO:0002142)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)	p.R1841C(1)		NS(4)|breast(7)|central_nervous_system(6)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(3)|kidney(18)|large_intestine(46)|liver(2)|lung(80)|ovary(12)|pancreas(5)|prostate(1)|skin(50)|stomach(7)|upper_aerodigestive_tract(8)|urinary_tract(6)	269		all_cancers(142;1.05e-09)|all_epithelial(76;1.81e-12)|all_lung(232;5.41e-06)|Lung NSC(167;1.72e-05)|Ovarian(174;0.00948)|Colorectal(57;0.133)|Breast(839;0.192)		OV - Ovarian serous cystadenocarcinoma(54;7.01e-30)|Epithelial(54;6.79e-25)|all cancers(79;1.88e-20)		TATTCACAAACGTGGTAAGCA	0.383																																					p.R1841C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C5521T	5						.	C	CYS/ARG	1,3755		0,1,1877	168.0	157.0	160.0		5521	6.0	0.1	5		160	0,8228		0,0,4114	no	missense	GPR98	NM_032119.3	180	0,1,5991	TT,TC,CC		0.0,0.0266,0.0083	probably-damaging	1841/6307	89975443	1,11983	1878	4114	5992	90011199	SO:0001583	missense	84059	exon26			AB014586	CCDS47246.1	5q13	2014-08-08	2006-05-26	2006-05-26	ENSG00000164199	ENSG00000164199		"""-"", ""GPCR / Class B : Orphans"""	17416	protein-coding gene	gene with protein product		602851	"""monogenic, audiogenic seizure susceptibility 1 homolog (mouse)"""	USH2C, MASS1		10976914, 14740321	Standard	NM_032119		Approved	DKFZp761P0710, KIAA0686, FEB4, VLGR1b	uc003kju.3	Q8WXG9	OTTHUMG00000162668	ENST00000405460.2:c.5521C>T	5.37:g.89975443C>T	ENSP00000384582:p.Arg1841Cys	Somatic		Capture	Illumina HiSeq	Phase_I	90011199	NM_032119	O75171|Q8TF58|Q9H0X5|Q9UL61	De_novo_Start_OutOfFrame	SNP	ENST00000405460.2	37	CCDS47246.1	.	.	.	.	.	.	.	.	.	.	C	12.67	2.008155	0.35415	2.66E-4	0.0	ENSG00000164199	ENST00000405460;ENST00000296619;ENST00000399043	T	0.27557	1.66	6.04	6.04	0.98038	.	0.834106	0.11619	N	0.545951	T	0.38188	0.1031	L	0.44542	1.39	0.80722	D	1	D	0.61697	0.99	P	0.48571	0.582	T	0.10847	-1.0612	10	0.72032	D	0.01	.	15.3129	0.74048	0.1398:0.8602:0.0:0.0	.	1841	Q8WXG9	GPR98_HUMAN	C	1841	ENSP00000384582:R1841C	ENSP00000296619:R1841C	R	+	1	0	GPR98	90011199	0.002000	0.14202	0.055000	0.19348	0.776000	0.43924	1.624000	0.37018	2.873000	0.98535	0.561000	0.74099	CGT		0.383	GPR98-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369993.2	NM_032119	
GPR98	84059	broad.mit.edu	37	5	90059269	90059269	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr5:90059269A>G	ENST00000405460.2	+	59	12364	c.12268A>G	c.(12268-12270)Acc>Gcc	p.T4090A		NM_032119.3	NP_115495.3	Q8WXG9	GPR98_HUMAN	G protein-coupled receptor 98	4090	Calx-beta 27. {ECO:0000255}.				detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|G-protein coupled receptor signaling pathway (GO:0007186)|inner ear receptor stereocilium organization (GO:0060122)|maintenance of organ identity (GO:0048496)|nervous system development (GO:0007399)|neurological system process (GO:0050877)|neuropeptide signaling pathway (GO:0007218)|photoreceptor cell maintenance (GO:0045494)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|single organismal cell-cell adhesion (GO:0016337)|visual perception (GO:0007601)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|stereocilia ankle link complex (GO:0002142)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)	p.T4090A(1)		NS(4)|breast(7)|central_nervous_system(6)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(3)|kidney(18)|large_intestine(46)|liver(2)|lung(80)|ovary(12)|pancreas(5)|prostate(1)|skin(50)|stomach(7)|upper_aerodigestive_tract(8)|urinary_tract(6)	269		all_cancers(142;1.05e-09)|all_epithelial(76;1.81e-12)|all_lung(232;5.41e-06)|Lung NSC(167;1.72e-05)|Ovarian(174;0.00948)|Colorectal(57;0.133)|Breast(839;0.192)		OV - Ovarian serous cystadenocarcinoma(54;7.01e-30)|Epithelial(54;6.79e-25)|all cancers(79;1.88e-20)		TTTGAATGGGACCCTTCATTT	0.418																																					p.T4090A												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A12268G	5						.						66.0	64.0	65.0					5																	90059269		1856	4101	5957	90095025	SO:0001583	missense	84059	exon59			AB014586	CCDS47246.1	5q13	2014-08-08	2006-05-26	2006-05-26	ENSG00000164199	ENSG00000164199		"""-"", ""GPCR / Class B : Orphans"""	17416	protein-coding gene	gene with protein product		602851	"""monogenic, audiogenic seizure susceptibility 1 homolog (mouse)"""	USH2C, MASS1		10976914, 14740321	Standard	NM_032119		Approved	DKFZp761P0710, KIAA0686, FEB4, VLGR1b	uc003kju.3	Q8WXG9	OTTHUMG00000162668	ENST00000405460.2:c.12268A>G	5.37:g.90059269A>G	ENSP00000384582:p.Thr4090Ala	Somatic		Capture	Illumina HiSeq	Phase_I	90095025	NM_032119	O75171|Q8TF58|Q9H0X5|Q9UL61	Missense_Mutation	SNP	ENST00000405460.2	37	CCDS47246.1	.	.	.	.	.	.	.	.	.	.	A	15.98	2.992588	0.54041	.	.	ENSG00000164199	ENST00000405460;ENST00000296619	T	0.33654	1.4	5.21	5.21	0.72293	Na-Ca exchanger/integrin-beta4 (2);	0.045633	0.85682	D	0.000000	T	0.58524	0.2128	M	0.80982	2.52	0.80722	D	1	D	0.71674	0.998	D	0.67725	0.953	T	0.58137	-0.7689	10	0.17832	T	0.49	.	15.3698	0.74554	1.0:0.0:0.0:0.0	.	4090	Q8WXG9	GPR98_HUMAN	A	4090	ENSP00000384582:T4090A	ENSP00000296619:T4090A	T	+	1	0	GPR98	90095025	1.000000	0.71417	0.896000	0.35187	0.671000	0.39405	7.662000	0.83803	2.094000	0.63399	0.460000	0.39030	ACC		0.418	GPR98-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369993.2	NM_032119	
SYNPO	11346	broad.mit.edu	37	5	150029070	150029070	+	Frame_Shift_Del	DEL	G	G	-	rs144297430		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	-	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr5:150029070delG	ENST00000394243.1	+	3	2339	c.1965delG	c.(1963-1965)cagfs	p.Q655fs	SYNPO_ENST00000519664.1_Frame_Shift_Del_p.Q411fs|SYNPO_ENST00000307662.4_Frame_Shift_Del_p.Q411fs|SYNPO_ENST00000522122.1_Frame_Shift_Del_p.Q655fs	NM_001166208.1	NP_001159680.1	Q8N3V7	SYNPO_HUMAN	synaptopodin	655					positive regulation of actin filament bundle assembly (GO:0032233)|regulation of stress fiber assembly (GO:0051492)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|dendritic spine (GO:0043197)|postsynaptic membrane (GO:0045211)|stress fiber (GO:0001725)|tight junction (GO:0005923)	actin binding (GO:0003779)	p.E413fs*2(1)		NS(1)|cervix(1)|endometrium(3)|large_intestine(6)|lung(4)|prostate(1)|urinary_tract(2)	18		Medulloblastoma(196;0.134)|all_hematologic(541;0.224)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			AGAGGGACCAGGGGGAGGTAG	0.642																																					p.Q655fs												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.1965delG	5						.						19.0	21.0	20.0					5																	150029070		2203	4298	6501	150009263	SO:0001589	frameshift_variant	11346	exon3			AF499137	CCDS4308.1, CCDS54937.1, CCDS54938.1	5q33.1	2008-02-05			ENSG00000171992	ENSG00000171992			30672	protein-coding gene	gene with protein product		608155				9314539, 10470851	Standard	NM_007286		Approved	KIAA1029	uc003lsn.3	Q8N3V7	OTTHUMG00000130078	ENST00000394243.1:c.1965delG	5.37:g.150029070delG	ENSP00000377789:p.Gln655fs	Somatic		Capture	Illumina HiSeq	Phase_I	150009263	NM_001166208	A5PKZ8|D3DQG8|O15271|Q9UPX1	Frame_Shift_Del	DEL	ENST00000394243.1	37	CCDS54937.1																																																																																				0.642	SYNPO-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000252371.1	NM_007286	
TRIM41	90933	broad.mit.edu	37	5	180661483	180661483	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr5:180661483G>A	ENST00000315073.5	+	6	2311	c.1601G>A	c.(1600-1602)cGc>cAc	p.R534H	TRIM41_ENST00000351937.5_Intron|TRIM41_ENST00000510072.1_3'UTR	NM_033549.4	NP_291027.3	Q8WV44	TRI41_HUMAN	tripartite motif containing 41	534	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.				protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)	ligase activity (GO:0016874)|zinc ion binding (GO:0008270)	p.R534H(1)		NS(1)|endometrium(4)|kidney(2)|large_intestine(7)|lung(3)|prostate(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	26	all_cancers(89;9.17e-06)|all_epithelial(37;1.19e-06)|Renal(175;0.000159)|Lung NSC(126;0.00354)|all_lung(126;0.00609)|Breast(19;0.0684)	all_cancers(40;0.000209)|Medulloblastoma(196;0.0133)|all_neural(177;0.0199)|all_lung(500;0.0221)|all_hematologic(541;0.0433)|Lung NSC(249;0.132)|Ovarian(839;0.238)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			CACCATCGCCGCCGCCGGCTC	0.667																																					p.R534H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1601A	5						.						26.0	29.0	28.0					5																	180661483		2201	4297	6498	180594089	SO:0001583	missense	90933	exon6			AF258579	CCDS4465.1, CCDS4466.1	5q35.3	2013-01-09	2011-01-25		ENSG00000146063	ENSG00000146063		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	19013	protein-coding gene	gene with protein product	"""RING-finger protein that interacts with C kinase"""	610530	"""tripartite motif-containing 41"""			16022281	Standard	NM_033549		Approved	MGC1127, RINCK	uc003mne.2	Q8WV44	OTTHUMG00000130965	ENST00000315073.5:c.1601G>A	5.37:g.180661483G>A	ENSP00000320869:p.Arg534His	Somatic		Capture	Illumina HiSeq	Phase_I	180594089	NM_033549	B3KNJ6|D3DWR9|Q5BKT0|Q7L484|Q96Q10|Q9BSL8	Missense_Mutation	SNP	ENST00000315073.5	37	CCDS4466.1	.	.	.	.	.	.	.	.	.	.	G	13.30	2.195884	0.38806	.	.	ENSG00000146063	ENST00000315073;ENST00000438174	T	0.53857	0.6	4.86	3.98	0.46160	Concanavalin A-like lectin/glucanase (1);B30.2/SPRY domain (1);SPla/RYanodine receptor SPRY (1);	0.000000	0.52532	D	0.000063	T	0.42944	0.1225	L	0.42245	1.32	0.28259	N	0.92492	B	0.15141	0.012	B	0.11329	0.006	T	0.43814	-0.9368	10	0.62326	D	0.03	.	8.9083	0.35537	0.1016:0.0:0.8984:0.0	.	534	Q8WV44	TRI41_HUMAN	H	534;219	ENSP00000320869:R534H	ENSP00000320869:R534H	R	+	2	0	TRIM41	180594089	1.000000	0.71417	1.000000	0.80357	0.436000	0.31835	5.468000	0.66743	1.287000	0.44583	0.298000	0.19748	CGC		0.667	TRIM41-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253574.3	NM_201627	
PREP	5550	broad.mit.edu	37	6	105729686	105729686	+	Silent	SNP	G	G	A	rs141753924	byFrequency	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr6:105729686G>A	ENST00000369110.3	-	14	1965	c.1773C>T	c.(1771-1773)atC>atT	p.I591I	RP3-355L5.4_ENST00000452363.1_RNA	NM_002726.4	NP_002717.3	P48147	PPCE_HUMAN	prolyl endopeptidase	591					proteolysis (GO:0006508)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	serine-type endopeptidase activity (GO:0004252)|serine-type exopeptidase activity (GO:0070008)|serine-type peptidase activity (GO:0008236)	p.I591I(1)		breast(1)|endometrium(2)|large_intestine(7)|lung(12)|ovary(3)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	29		all_cancers(87;0.000128)|Acute lymphoblastic leukemia(125;1.9e-08)|all_hematologic(75;9.25e-07)|all_epithelial(87;0.0344)|Lung NSC(302;0.191)|Colorectal(196;0.202)			Oxytocin(DB00107)	AAGCATGGCCGATGGTATATT	0.418																																					p.I591I												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1773T	6						.	G		0,4406		0,0,2203	121.0	104.0	110.0		1773	-11.4	0.0	6	dbSNP_134	110	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	PREP	NM_002726.4		0,2,6501	AA,AG,GG		0.0233,0.0,0.0154		591/711	105729686	2,13004	2203	4300	6503	105836379	SO:0001819	synonymous_variant	5550	exon14				CCDS5053.1	6q22	2008-02-05			ENSG00000085377	ENSG00000085377	3.4.21.26		9358	protein-coding gene	gene with protein product		600400				7959018	Standard	NM_002726		Approved		uc003prc.3	P48147	OTTHUMG00000015297	ENST00000369110.3:c.1773C>T	6.37:g.105729686G>A		Somatic		Capture	Illumina HiSeq	Phase_I	105836379	NM_002726	Q8N6D4	Silent	SNP	ENST00000369110.3	37	CCDS5053.1																																																																																				0.418	PREP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041658.1		
MAK	4117	broad.mit.edu	37	6	10802142	10802142	+	Nonsense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr6:10802142G>A	ENST00000313243.2	-	8	1196	c.814C>T	c.(814-816)Cga>Tga	p.R272*	MAK_ENST00000538030.1_Nonsense_Mutation_p.R272*|MAK_ENST00000536370.1_Nonsense_Mutation_p.R272*|MAK_ENST00000354489.2_Nonsense_Mutation_p.R272*|RP11-637O19.3_ENST00000480294.1_Intron|MAK_ENST00000474039.1_Nonsense_Mutation_p.R272*|SYCP2L_ENST00000543878.1_Intron			P20794	MAK_HUMAN	male germ cell-associated kinase	272	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.		R -> P (in a breast infiltrating ductal carcinoma sample; somatic mutation). {ECO:0000269|PubMed:17344846}.		cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|photoreceptor cell maintenance (GO:0045494)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of transcription, DNA-templated (GO:0006355)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|midbody (GO:0030496)|mitotic spindle (GO:0072686)|nucleus (GO:0005634)|photoreceptor inner segment (GO:0001917)|photoreceptor outer segment (GO:0001750)	ATP binding (GO:0005524)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)|protein kinase activity (GO:0004672)|transcription coactivator activity (GO:0003713)	p.R272*(1)		breast(2)|endometrium(2)|kidney(2)|large_intestine(6)|lung(8)|prostate(1)|skin(1)	22	Breast(50;0.107)|Ovarian(93;0.107)	all_hematologic(90;0.117)				GCTGTCGGTCGTTTCTTTGGA	0.393											OREG0017187	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.R272X												MAK,breast,NS,Substitution - Missense,+1 	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.C814T	6						.						111.0	106.0	108.0					6																	10802142		2203	4300	6503	10910128	SO:0001587	stop_gained	4117	exon7				CCDS4516.1, CCDS75398.1, CCDS75399.1	6p24.2	2014-01-28			ENSG00000111837	ENSG00000111837			6816	protein-coding gene	gene with protein product		154235				16951154	Standard	NM_005906		Approved	dJ417M14.2, RP62	uc021ylk.1	P20794	OTTHUMG00000014247	ENST00000313243.2:c.814C>T	6.37:g.10802142G>A	ENSP00000313021:p.Arg272*	Somatic	667	Capture	Illumina HiSeq	Phase_I	10910128	NM_005906	F1T0K6|G1FL29|Q547D0|Q9NUH7	Nonsense_Mutation	SNP	ENST00000313243.2	37	CCDS4516.1	.	.	.	.	.	.	.	.	.	.	G	38	7.099084	0.98063	.	.	ENSG00000111837	ENST00000313243;ENST00000354489;ENST00000538030;ENST00000536370	.	.	.	5.42	5.42	0.78866	.	0.058165	0.64402	D	0.000003	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	15.3246	0.74150	0.0:0.0:0.8518:0.1482	.	.	.	.	X	272	.	ENSP00000313021:R272X	R	-	1	2	MAK	10910128	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	5.423000	0.66458	2.691000	0.91804	0.655000	0.94253	CGA		0.393	MAK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039841.1	NM_005906	
BEND3	57673	broad.mit.edu	37	6	107391251	107391251	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr6:107391251G>A	ENST00000369042.1	-	4	1334	c.1144C>T	c.(1144-1146)Cgg>Tgg	p.R382W	BEND3_ENST00000429433.2_Missense_Mutation_p.R382W			Q5T5X7	BEND3_HUMAN	BEN domain containing 3	382								p.R382W(1)		central_nervous_system(1)|cervix(2)|endometrium(3)|large_intestine(7)|lung(10)|ovary(4)|prostate(3)	30						GTGCTGCTCCGGTCAAGAGAC	0.632																																					p.R382W												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1144T	6						.						70.0	68.0	69.0					6																	107391251		2203	4300	6503	107497944	SO:0001583	missense	57673	exon5			AB046773	CCDS34507.1	6q21	2012-11-22	2008-10-03	2008-10-03	ENSG00000178409	ENSG00000178409		"""BEN domain containing"""	23040	protein-coding gene	gene with protein product			"""KIAA1553"""	KIAA1553			Standard	NM_001080450		Approved		uc003prs.2	Q5T5X7	OTTHUMG00000015308	ENST00000369042.1:c.1144C>T	6.37:g.107391251G>A	ENSP00000358038:p.Arg382Trp	Somatic		Capture	Illumina HiSeq	Phase_I	107497944	NM_001080450	A2RRH2|Q9HCL9	Missense_Mutation	SNP	ENST00000369042.1	37	CCDS34507.1	.	.	.	.	.	.	.	.	.	.	G	15.23	2.771656	0.49680	.	.	ENSG00000178409	ENST00000369042;ENST00000429433	.	.	.	5.32	4.44	0.53790	.	0.202799	0.41823	D	0.000816	T	0.51466	0.1676	L	0.27053	0.805	0.43435	D	0.995607	D	0.89917	1.0	D	0.66979	0.948	T	0.59674	-0.7410	9	0.62326	D	0.03	-0.5387	12.1298	0.53936	0.0:0.0:0.5275:0.4725	.	382	Q5T5X7	BEND3_HUMAN	W	382	.	ENSP00000358038:R382W	R	-	1	2	BEND3	107497944	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	2.527000	0.45615	1.439000	0.47511	0.561000	0.74099	CGG		0.632	BEND3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041686.1	NM_020913	
METTL24	728464	broad.mit.edu	37	6	110644068	110644068	+	Missense_Mutation	SNP	C	C	T	rs545654177		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr6:110644068C>T	ENST00000338882.4	-	2	325	c.326G>A	c.(325-327)cGg>cAg	p.R109Q	METTL24_ENST00000490043.1_5'UTR	NM_001123364.1	NP_001116836.1	Q5JXM2	MET24_HUMAN	methyltransferase like 24	109						extracellular region (GO:0005576)	methyltransferase activity (GO:0008168)	p.R109Q(1)									TATATGCCACCGGGGACCCTG	0.522													C|||	1	0.000199681	0.0	0.0	5008	,	,		20164	0.0		0.0	False		,,,				2504	0.001				p.R109Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G326A	6						.						55.0	53.0	54.0					6																	110644068		1568	3582	5150	110750761	SO:0001583	missense	728464	exon2				CCDS43489.1	6q21	2012-03-08	2012-02-21	2012-02-21	ENSG00000053328	ENSG00000053328			21566	protein-coding gene	gene with protein product			"""chromosome 6 open reading frame 186"""	C6orf186			Standard	NM_001123364		Approved	dJ71D21.2	uc010kdu.1	Q5JXM2	OTTHUMG00000015359	ENST00000338882.4:c.326G>A	6.37:g.110644068C>T	ENSP00000344071:p.Arg109Gln	Somatic		Capture	Illumina HiSeq	Phase_I	110750761	NM_001123364	Q6ZSU5	Missense_Mutation	SNP	ENST00000338882.4	37	CCDS43489.1	.	.	.	.	.	.	.	.	.	.	C	18.48	3.633530	0.67015	.	.	ENSG00000053328	ENST00000338882	T	0.52057	0.68	5.45	5.45	0.79879	.	0.000000	0.85682	D	0.000000	T	0.59459	0.2195	M	0.65498	2.005	0.53005	D	0.999964	D	0.89917	1.0	D	0.76575	0.988	T	0.60801	-0.7191	10	0.52906	T	0.07	-22.4033	14.7961	0.69878	0.0:1.0:0.0:0.0	.	109	Q5JXM2	CF186_HUMAN	Q	109	ENSP00000344071:R109Q	ENSP00000344071:R109Q	R	-	2	0	C6orf186	110750761	1.000000	0.71417	1.000000	0.80357	0.142000	0.21351	4.903000	0.63272	2.563000	0.86464	0.650000	0.86243	CGG		0.522	METTL24-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000041794.1	NM_001123364	
CDK19	23097	broad.mit.edu	37	6	110988759	110988759	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr6:110988759G>A	ENST00000368911.3	-	4	513	c.334C>T	c.(334-336)Cgt>Tgt	p.R112C	CDK19_ENST00000323817.3_Missense_Mutation_p.R52C	NM_015076.3	NP_055891.1	Q9BWU1	CDK19_HUMAN	cyclin-dependent kinase 19	112	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.						ATP binding (GO:0005524)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)	p.R112C(1)		breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(5)|lung(9)|ovary(2)|prostate(2)|skin(1)	22						TTTGATGCACGGTGAAACTTA	0.308																																					p.R112C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C334T	6						.						65.0	65.0	65.0					6																	110988759		2203	4300	6503	111095452	SO:0001583	missense	23097	exon4			AL122055	CCDS5085.1, CCDS75503.1	6q21	2011-10-25	2009-12-16	2009-12-16	ENSG00000155111	ENSG00000155111		"""Cyclin-dependent kinases"""	19338	protein-coding gene	gene with protein product		614720	"""cyclin-dependent kinase (CDC2-like) 11"", ""cell division cycle 2-like 6 (CDK8-like)"""	CDK11, CDC2L6		10470851, 19884882	Standard	XM_005266871		Approved	KIAA1028, bA346C16.3	uc003puh.1	Q9BWU1	OTTHUMG00000015365	ENST00000368911.3:c.334C>T	6.37:g.110988759G>A	ENSP00000357907:p.Arg112Cys	Somatic		Capture	Illumina HiSeq	Phase_I	111095452	NM_015076	Q5JQZ7|Q5JR00|Q8TC78|Q9UPX2	Missense_Mutation	SNP	ENST00000368911.3	37	CCDS5085.1	.	.	.	.	.	.	.	.	.	.	G	19.06	3.753562	0.69648	.	.	ENSG00000155111	ENST00000368911;ENST00000323817;ENST00000392576;ENST00000457688	T;T;T	0.46063	0.88;0.88;0.88	5.27	5.27	0.74061	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.051474	0.85682	D	0.000000	T	0.54532	0.1864	M	0.65677	2.01	0.80722	D	1	D	0.89917	1.0	D	0.77004	0.989	T	0.58962	-0.7543	10	0.87932	D	0	-19.3429	13.8731	0.63631	0.0:0.0:0.8474:0.1526	.	112	Q9BWU1	CDK19_HUMAN	C	112;52;51;52	ENSP00000357907:R112C;ENSP00000317665:R52C;ENSP00000415621:R52C	ENSP00000317665:R52C	R	-	1	0	CDK19	111095452	1.000000	0.71417	0.999000	0.59377	0.998000	0.95712	5.147000	0.64851	2.487000	0.83934	0.551000	0.68910	CGT		0.308	CDK19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041804.1	NM_015076	
TRAF3IP2	10758	broad.mit.edu	37	6	111913040	111913040	+	Missense_Mutation	SNP	G	G	A	rs376682410		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr6:111913040G>A	ENST00000340026.6	-	3	871	c.277C>T	c.(277-279)Cgc>Tgc	p.R93C	TRAF3IP2-AS1_ENST00000532353.1_RNA|TRAF3IP2_ENST00000359831.4_Missense_Mutation_p.R84C|TRAF3IP2_ENST00000392556.4_5'UTR|TRAF3IP2_ENST00000368761.5_Missense_Mutation_p.R84C			O43734	CIKS_HUMAN	TRAF3 interacting protein 2	93	Mediates interaction with TRAF6.				B cell apoptotic process (GO:0001783)|humoral immune response (GO:0006959)|immunoglobulin secretion (GO:0048305)|intracellular signal transduction (GO:0035556)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)			p.R93C(1)		central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(3)|lung(5)|ovary(2)|prostate(1)|urinary_tract(1)	18		all_cancers(87;7.87e-06)|Acute lymphoblastic leukemia(125;3.61e-09)|all_hematologic(75;2.63e-07)|all_epithelial(87;0.0024)|Colorectal(196;0.021)		OV - Ovarian serous cystadenocarcinoma(136;0.033)|all cancers(137;0.0412)|Epithelial(106;0.0732)		ACTTGAGTGCGCAGGCAGGTG	0.557																																					p.R84C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C250T	6						.	G	CYS/ARG,CYS/ARG	0,4406		0,0,2203	70.0	72.0	71.0		250,250	4.2	0.7	6		71	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	TRAF3IP2	NM_147686.2,NM_001164281.1	180,180	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	benign,benign	84/566,84/565	111913040	1,13005	2203	4300	6503	112019733	SO:0001583	missense	10758	exon2			AF136405	CCDS5093.1, CCDS55049.1, CCDS55050.1	6q21	2008-09-05	2002-06-20	2005-04-13	ENSG00000056972	ENSG00000056972			1343	protein-coding gene	gene with protein product		607043	"""chromosome 6 open reading frame 5"", ""chromosome 6 open reading frame 2"""	C6orf4, C6orf5, C6orf6, C6orf2		10962033, 10962024	Standard	NR_028338		Approved	DKFZP586G0522, ACT1, CIKS	uc003pvf.4	O43734	OTTHUMG00000015379	ENST00000340026.6:c.277C>T	6.37:g.111913040G>A	ENSP00000345984:p.Arg93Cys	Somatic		Capture	Illumina HiSeq	Phase_I	112019733	NM_147686	B2RAY9|E1P555|Q5R3A3|Q7Z6Q1|Q7Z6Q2|Q7Z6Q3|Q9H5W2|Q9H6Y3|Q9NS14|Q9UG72	Missense_Mutation	SNP	ENST00000340026.6	37		.	.	.	.	.	.	.	.	.	.	G	12.60	1.985764	0.35036	0.0	1.16E-4	ENSG00000056972	ENST00000392555;ENST00000368761;ENST00000340026;ENST00000359831	T;T;T	0.50548	0.77;0.76;0.74	5.91	4.16	0.48862	.	0.000000	0.64402	D	0.000005	T	0.29190	0.0726	M	0.66939	2.045	0.80722	D	1	B;B;B	0.17268	0.012;0.021;0.002	B;B;B	0.15870	0.006;0.014;0.0	T	0.26258	-1.0108	10	0.87932	D	0	-22.4043	9.2352	0.37461	0.1654:0.0:0.8346:0.0	.	93;84;84	O43734;O43734-2;Q7Z6Q1	CIKS_HUMAN;.;.	C	93;84;93;84	ENSP00000357750:R84C;ENSP00000345984:R93C;ENSP00000352889:R84C	ENSP00000345984:R93C	R	-	1	0	TRAF3IP2	112019733	0.008000	0.16893	0.686000	0.30086	0.757000	0.42996	0.835000	0.27531	0.859000	0.35456	-0.263000	0.10527	CGC		0.557	TRAF3IP2-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000041841.2		
CEP85L	387119	broad.mit.edu	37	6	118887261	118887261	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr6:118887261G>A	ENST00000368491.3	-	3	1072	c.451C>T	c.(451-453)Cgg>Tgg	p.R151W	CEP85L_ENST00000368488.5_Missense_Mutation_p.R154W|CEP85L_ENST00000472713.1_5'UTR|CEP85L_ENST00000360290.3_Missense_Mutation_p.R49W|CEP85L_ENST00000392500.3_Missense_Mutation_p.R154W|CEP85L_ENST00000419517.2_Missense_Mutation_p.R151W	NM_001042475.2	NP_001035940.1	Q5SZL2	CE85L_HUMAN	centrosomal protein 85kDa-like	151						centrosome (GO:0005813)|cytoplasm (GO:0005737)		p.R151W(1)									CGAAGTGGCCGGAAGTCCTTC	0.502																																					p.R151W												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C451T	6						.						147.0	128.0	135.0					6																	118887261		2203	4300	6503	118993954	SO:0001583	missense	387119	exon3			AF308284	CCDS5119.2, CCDS43498.1, CCDS55052.1	6q22.31	2011-11-25	2011-11-25	2011-11-25	ENSG00000111860	ENSG00000111860			21638	protein-coding gene	gene with protein product			"""chromosome 6 open reading frame 204"""	C6orf204			Standard	NM_206921		Approved	NY-BR-15, bA57K17.2	uc003pya.2	Q5SZL2	OTTHUMG00000015465	ENST00000368491.3:c.451C>T	6.37:g.118887261G>A	ENSP00000357477:p.Arg151Trp	Somatic		Capture	Illumina HiSeq	Phase_I	118993954	NM_206921	A1A4E1|A2A3P2|A2IDE5|F8W6J2|G3V0H3|Q2TAM2|Q5T323|Q7Z5K7|Q9H289	Missense_Mutation	SNP	ENST00000368491.3	37	CCDS43498.1	.	.	.	.	.	.	.	.	.	.	G	17.39	3.377591	0.61735	.	.	ENSG00000111860	ENST00000368491;ENST00000368488;ENST00000434604;ENST00000392500;ENST00000360290;ENST00000419517	T;T;T;T;T;T	0.35421	1.92;1.92;2.16;1.78;1.31;1.77	5.86	1.73	0.24493	.	0.131349	0.50627	D	0.000119	T	0.32734	0.0839	L	0.27053	0.805	0.30709	N	0.749441	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;0.999	D;D;D;D;D	0.72625	0.974;0.978;0.978;0.965;0.965	T	0.42916	-0.9423	10	0.87932	D	0	-12.789	16.7407	0.85458	0.0:0.0:0.2874:0.7126	.	49;154;151;154;151	B4DYT2;Q5SZL2-2;G3V0H3;F8W6J2;Q5SZL2	.;.;.;.;CF204_HUMAN	W	151;154;154;154;49;151	ENSP00000357477:R151W;ENSP00000357474:R154W;ENSP00000392131:R154W;ENSP00000376288:R154W;ENSP00000353434:R49W;ENSP00000393317:R151W	ENSP00000353434:R49W	R	-	1	2	C6orf204	118993954	1.000000	0.71417	0.992000	0.48379	0.997000	0.91878	1.712000	0.37940	0.313000	0.23062	0.655000	0.94253	CGG		0.502	CEP85L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041996.2	NM_001042475	
MAN1A1	4121	broad.mit.edu	37	6	119510998	119510998	+	Silent	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr6:119510998G>A	ENST00000368468.3	-	10	1818	c.1377C>T	c.(1375-1377)atC>atT	p.I459I		NM_005907.3	NP_005898.2	P33908	MA1A1_HUMAN	mannosidase, alpha, class 1A, member 1	459					cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	calcium ion binding (GO:0005509)|mannosidase activity (GO:0015923)|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity (GO:0004571)	p.I459I(2)		central_nervous_system(1)|endometrium(2)|large_intestine(6)|lung(8)|ovary(2)|prostate(2)|skin(3)	24		all_epithelial(87;0.173)		OV - Ovarian serous cystadenocarcinoma(136;0.0612)|GBM - Glioblastoma multiforme(226;0.0702)|all cancers(137;0.115)		TCCACTCTGCGATATAAGTTA	0.498																																					p.I459I	Ovarian(136;8 1825 12608 33541 47587)											.	.	2	Substitution - coding silent(2)	large_intestine(1)|prostate(1)	c.C1377T	6						.						73.0	68.0	70.0					6																	119510998		2203	4300	6503	119552697	SO:0001819	synonymous_variant	4121	exon10			AK025599	CCDS5122.1	6q22	2008-08-29			ENSG00000111885	ENSG00000111885	3.2.1.113		6821	protein-coding gene	gene with protein product		604344				8223597	Standard	NM_005907		Approved		uc003pym.2	P33908	OTTHUMG00000015472	ENST00000368468.3:c.1377C>T	6.37:g.119510998G>A		Somatic		Capture	Illumina HiSeq	Phase_I	119552697	NM_005907	E7EU32|Q6P052|Q9NU44|Q9UJI3	Silent	SNP	ENST00000368468.3	37	CCDS5122.1																																																																																				0.498	MAN1A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042015.1	NM_005907	
PTPRK	5796	broad.mit.edu	37	6	128561245	128561245	+	Nonsense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr6:128561245G>A	ENST00000368215.3	-	5	627	c.628C>T	c.(628-630)Caa>Taa	p.Q210*	PTPRK_ENST00000368213.5_Nonsense_Mutation_p.Q210*|PTPRK_ENST00000368207.3_Nonsense_Mutation_p.Q210*|PTPRK_ENST00000524481.1_5'UTR|PTPRK_ENST00000368226.4_Nonsense_Mutation_p.Q210*|PTPRK_ENST00000368227.3_Nonsense_Mutation_p.Q210*|PTPRK_ENST00000368210.3_Nonsense_Mutation_p.Q210*|PTPRK_ENST00000532331.1_Nonsense_Mutation_p.Q210*			Q15262	PTPRK_HUMAN	protein tyrosine phosphatase, receptor type, K	210	Ig-like C2-type.				cell adhesion (GO:0007155)|cell migration (GO:0016477)|cellular response to reactive oxygen species (GO:0034614)|cellular response to UV (GO:0034644)|focal adhesion assembly (GO:0048041)|negative regulation of cell cycle (GO:0045786)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of keratinocyte proliferation (GO:0010839)|negative regulation of transcription, DNA-templated (GO:0045892)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|protein localization to cell surface (GO:0034394)|signal transduction (GO:0007165)|transforming growth factor beta receptor signaling pathway (GO:0007179)	axon (GO:0030424)|cell surface (GO:0009986)|cell-cell junction (GO:0005911)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|leading edge membrane (GO:0031256)|neuronal cell body (GO:0043025)|photoreceptor outer segment (GO:0001750)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|protein kinase binding (GO:0019901)|protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)	p.Q210*(1)	PTPRK/RSPO3(10)	autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(14)|lung(24)|ovary(3)|pancreas(1)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(1)	72				all cancers(137;0.0118)|GBM - Glioblastoma multiforme(226;0.0372)|OV - Ovarian serous cystadenocarcinoma(136;0.24)		GTAGCGTTTTGCCCTGCATTC	0.423																																					p.Q210X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.C628T	6						.						141.0	114.0	123.0					6																	128561245		2203	4300	6503	128602938	SO:0001587	stop_gained	5796	exon5			L77886	CCDS5137.1, CCDS47473.1, CCDS75517.1	6q22.2-q22.3	2013-02-11			ENSG00000152894	ENSG00000152894		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	9674	protein-coding gene	gene with protein product		602545				9047348, 8663237	Standard	NM_002844		Approved	R-PTP-kappa	uc010kfc.3	Q15262	OTTHUMG00000015536	ENST00000368215.3:c.628C>T	6.37:g.128561245G>A	ENSP00000357198:p.Gln210*	Somatic		Capture	Illumina HiSeq	Phase_I	128602938	NM_002844	B2RTQ8|B7ZMG0|Q14763|Q5TG10|Q5TG11	Nonsense_Mutation	SNP	ENST00000368215.3	37		.	.	.	.	.	.	.	.	.	.	G	38	6.839953	0.97877	.	.	ENSG00000152894	ENST00000368226;ENST00000368227;ENST00000532331;ENST00000368213;ENST00000368210;ENST00000368215;ENST00000368207;ENST00000427676	.	.	.	5.96	5.96	0.96718	.	0.142686	0.48286	D	0.000192	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.72032	D	0.01	.	20.4014	0.98996	0.0:0.0:1.0:0.0	.	.	.	.	X	210;210;210;210;210;210;210;67	.	ENSP00000357190:Q210X	Q	-	1	0	PTPRK	128602938	1.000000	0.71417	1.000000	0.80357	0.634000	0.38068	9.745000	0.98856	2.819000	0.97034	0.585000	0.79938	CAA		0.423	PTPRK-005	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000042163.1		
TAAR9	134860	broad.mit.edu	37	6	132859536	132859536	+	RNA	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr6:132859536C>T	ENST00000434551.1	+	0	108					NM_175057.3	NP_778227.3	Q96RI9	TAAR9_HUMAN	trace amine associated receptor 9 (gene/pseudogene)						G-protein coupled receptor signaling pathway (GO:0007186)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|trace-amine receptor activity (GO:0001594)	p.Y36Y(1)				Breast(56;0.112)			OV - Ovarian serous cystadenocarcinoma(155;0.0042)|GBM - Glioblastoma multiforme(226;0.00816)		CTATCCTCTACGCCGTCCTTG	0.478																																					p.Y36Y	Colon(10;433 445 15992 45047 47213)											.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C108T	6						.						123.0	119.0	120.0					6																	132859536		2031	4220	6251	132901229			134860	exon1			AF380189	CCDS75520.1	6q23.2	2013-10-02	2010-03-12	2005-02-24	ENSG00000237110	ENSG00000237110		"""GPCR / Class A : Trace amine associated receptors"""	20977	protein-coding gene	gene with protein product		608282	"""trace amine receptor 3"", ""trace amine associated receptor 9"""	TRAR3		15718104	Standard	NM_175057		Approved	TA3, TAR3	uc011eci.2	Q96RI9	OTTHUMG00000015578		6.37:g.132859536C>T		Somatic		Capture	Illumina HiSeq	Phase_I	132901229	NM_175057		Silent	SNP	ENST00000434551.1	37																																																																																					0.478	TAAR9-001	KNOWN	mRNA_end_NF|cds_end_NF|basic	polymorphic_pseudogene	polymorphic_pseudogene	OTTHUMT00000042254.2	NM_175057	
MYB	4602	broad.mit.edu	37	6	135516913	135516913	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr6:135516913G>A	ENST00000367814.4	+	9	1162	c.976G>A	c.(976-978)Ggg>Agg	p.G326R	MYB_ENST00000534044.1_Missense_Mutation_p.G326R|MYB_ENST00000341911.5_Missense_Mutation_p.G326R|MYB_ENST00000525369.1_Intron|MYB-AS1_ENST00000455534.1_RNA|MYB_ENST00000534121.1_Missense_Mutation_p.G326R|MYB_ENST00000527615.1_Missense_Mutation_p.G326R|MYB_ENST00000528774.1_Missense_Mutation_p.G323R|MYB_ENST00000531845.1_3'UTR|MYB_ENST00000442647.2_Missense_Mutation_p.G323R|MYB_ENST00000316528.8_Missense_Mutation_p.G326R|MYB_ENST00000533624.1_Missense_Mutation_p.G291R	NM_001161659.1|NM_005375.2	NP_001155131.1|NP_005366.2	P10242	MYB_HUMAN	v-myb avian myeloblastosis viral oncogene homolog	326	Transcription activation domain (PubMed:2189102). {ECO:0000269|PubMed:2189102}.				B cell differentiation (GO:0030183)|blood coagulation (GO:0007596)|calcium ion transport (GO:0006816)|chromatin remodeling (GO:0006338)|embryonic digestive tract development (GO:0048566)|G1/S transition of mitotic cell cycle (GO:0000082)|homeostasis of number of cells (GO:0048872)|in utero embryonic development (GO:0001701)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of histone H3-K4 methylation (GO:0051571)|positive regulation of histone H3-K9 methylation (GO:0051574)|positive regulation of T-helper cell differentiation (GO:0045624)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|thymus development (GO:0048538)	nuclear matrix (GO:0016363)	chromatin binding (GO:0003682)|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)	p.G326R(2)		breast(4)|endometrium(1)|kidney(2)|large_intestine(3)|lung(13)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	28	all_epithelial(2;0.109)|Breast(56;0.158)|Colorectal(23;0.221)	Lung NSC(302;3.08e-05)|Ovarian(999;0.208)		OV - Ovarian serous cystadenocarcinoma(155;0.0079)|GBM - Glioblastoma multiforme(68;0.0117)		CAGCTACCCCGGGTGGCACAG	0.527			T	NFIB	adenoid cystic carcinoma																																p.G291R			Dom	yes		6	6q22-23	4602	v-myb myeloblastosis viral oncogene homolog		E	.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G871A	6						.						138.0	122.0	128.0					6																	135516913		2203	4300	6503	135558606	SO:0001583	missense	4602	exon8				CCDS5174.1, CCDS47481.1, CCDS47482.1, CCDS55058.1, CCDS55059.1, CCDS55060.1, CCDS55061.1, CCDS55062.1	6q22-q23	2013-07-09	2013-07-09		ENSG00000118513	ENSG00000118513			7545	protein-coding gene	gene with protein product		189990				17599807	Standard	NM_001130172		Approved	c-myb	uc003qfh.3	P10242	OTTHUMG00000015629	ENST00000367814.4:c.976G>A	6.37:g.135516913G>A	ENSP00000356788:p.Gly326Arg	Somatic		Capture	Illumina HiSeq	Phase_I	135558606	NM_001161660	E9PI07|E9PLZ5|E9PNA4|E9PNL6|E9PRS2|P78391|P78392|P78525|P78526|Q14023|Q14024|Q708E4|Q708E7|Q9UE83	Missense_Mutation	SNP	ENST00000367814.4	37	CCDS5174.1	.	.	.	.	.	.	.	.	.	.	G	16.88	3.245459	0.59103	.	.	ENSG00000118513	ENST00000341911;ENST00000442647;ENST00000316528;ENST00000237302;ENST00000367814;ENST00000527615;ENST00000528774;ENST00000534121;ENST00000534044;ENST00000533624	T;T;T;T;T;T;T;T;T	0.31769	2.7;2.23;2.23;2.24;1.48;2.69;2.63;1.91;2.15	5.7	5.7	0.88788	.	0.240078	0.50627	D	0.000101	T	0.27205	0.0667	N	0.19112	0.55	0.50632	D	0.999884	D;D;D;D;D;D;P;D	0.89917	0.977;0.977;0.976;0.993;0.984;1.0;0.947;0.982	P;P;P;P;P;P;B;P	0.61940	0.636;0.515;0.619;0.668;0.491;0.896;0.336;0.618	T	0.08351	-1.0726	10	0.72032	D	0.01	-11.1447	13.0801	0.59109	0.0732:0.0:0.9268:0.0	.	291;326;323;323;326;326;326;326	E9PI07;E9PLZ5;P10242-2;E9PNL6;E9PNA4;P10242-4;P10242;Q708E1	.;.;.;.;.;.;MYB_HUMAN;.	R	326;323;326;326;326;326;323;326;326;291	ENSP00000339992:G326R;ENSP00000410825:G323R;ENSP00000326328:G326R;ENSP00000356788:G326R;ENSP00000433227:G326R;ENSP00000434723:G323R;ENSP00000432851:G326R;ENSP00000435055:G326R;ENSP00000436605:G291R	ENSP00000237302:G326R	G	+	1	0	MYB	135558606	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.164000	0.58190	2.692000	0.91855	0.467000	0.42956	GGG		0.527	MYB-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000042347.4		
PHACTR2	9749	broad.mit.edu	37	6	144081724	144081724	+	Missense_Mutation	SNP	A	A	C			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr6:144081724A>C	ENST00000427704.2	+	5	738	c.608A>C	c.(607-609)cAg>cCg	p.Q203P	PHACTR2_ENST00000440869.2_Missense_Mutation_p.Q214P|PHACTR2_ENST00000305766.6_Intron|PHACTR2_ENST00000367582.3_Intron|PHACTR2_ENST00000367584.4_Intron	NM_001100166.1|NM_014721.2	NP_001093636.1|NP_055536.2	O75167	PHAR2_HUMAN	phosphatase and actin regulator 2	203							protein phosphatase inhibitor activity (GO:0004864)	p.Q214P(1)		NS(3)|breast(1)|cervix(1)|endometrium(3)|large_intestine(4)|lung(13)|ovary(2)|prostate(1)|upper_aerodigestive_tract(2)	30				OV - Ovarian serous cystadenocarcinoma(155;1.58e-05)|GBM - Glioblastoma multiforme(68;0.0386)		CCTGGTAAGCAGGCCCCCGTC	0.582																																					p.Q214P	Pancreas(12;292 433 7358 48260 52635)|Ovarian(20;501 618 3485 36581 49208)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A641C	6						.						48.0	54.0	52.0					6																	144081724		1855	4092	5947	144123417	SO:0001583	missense	9749	exon5			AB014580	CCDS43512.1, CCDS47492.1, CCDS47493.1, CCDS47494.1	6q24.1	2013-01-24	2004-05-20	2004-05-20	ENSG00000112419	ENSG00000112419		"""Phosphatase and actin regulators"""	20956	protein-coding gene	gene with protein product		608724	"""chromosome 6 open reading frame 56"""	C6orf56		9734811, 15107502	Standard	NM_001100164		Approved	KIAA0680	uc010khi.3	O75167	OTTHUMG00000015732	ENST00000427704.2:c.608A>C	6.37:g.144081724A>C	ENSP00000391763:p.Gln203Pro	Somatic		Capture	Illumina HiSeq	Phase_I	144123417	NM_001100164	A6NKP5|A7MCZ5|A8MZC0|B2RWP7|B4DN76|B4DPB5|B4DTH7|Q5TFA0|Q68DM2	Missense_Mutation	SNP	ENST00000427704.2	37	CCDS47492.1	.	.	.	.	.	.	.	.	.	.	A	22.2	4.263244	0.80358	.	.	ENSG00000112419	ENST00000427704;ENST00000440869	T;T	0.25579	1.8;1.79	6.08	6.08	0.98989	.	0.806950	0.11952	N	0.513635	T	0.38026	0.1025	L	0.56769	1.78	0.80722	D	1	D;D	0.76494	0.999;0.998	D;D	0.80764	0.994;0.986	T	0.01889	-1.1253	10	0.32370	T	0.25	.	15.2149	0.73258	1.0:0.0:0.0:0.0	.	214;203	O75167-4;O75167	.;PHAR2_HUMAN	P	203;214	ENSP00000391763:Q203P;ENSP00000417038:Q214P	ENSP00000391763:Q203P	Q	+	2	0	PHACTR2	144123417	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	5.701000	0.68325	2.333000	0.79357	0.533000	0.62120	CAG		0.582	PHACTR2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000042528.2	NM_014721	
UTRN	7402	broad.mit.edu	37	6	145160380	145160380	+	Silent	SNP	G	G	A	rs116654180		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr6:145160380G>A	ENST00000367545.3	+	71	10137	c.10137G>A	c.(10135-10137)tcG>tcA	p.S3379S	UTRN_ENST00000367526.4_Silent_p.S934S	NM_007124.2	NP_009055.2	P46939	UTRO_HUMAN	utrophin	3379					aging (GO:0007568)|muscle cell differentiation (GO:0042692)|muscle contraction (GO:0006936)|muscle organ development (GO:0007517)|neuron projection morphogenesis (GO:0048812)|positive regulation of cell-matrix adhesion (GO:0001954)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of neuron projection development (GO:0010976)|regulation of cellular response to growth factor stimulus (GO:0090287)|regulation of sodium ion transmembrane transporter activity (GO:2000649)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|dystrophin-associated glycoprotein complex (GO:0016010)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|filopodium membrane (GO:0031527)|membrane (GO:0016020)|membrane raft (GO:0045121)|myofibril (GO:0030016)|neuromuscular junction (GO:0031594)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|protein complex (GO:0043234)|sarcolemma (GO:0042383)	actin binding (GO:0003779)|calcium ion binding (GO:0005509)|integrin binding (GO:0005178)|protein kinase binding (GO:0019901)|vinculin binding (GO:0017166)|zinc ion binding (GO:0008270)	p.S3379S(1)		NS(1)|autonomic_ganglia(1)|breast(7)|central_nervous_system(1)|cervix(2)|endometrium(21)|kidney(10)|large_intestine(29)|lung(56)|ovary(5)|pancreas(1)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	148		Ovarian(120;0.218)		OV - Ovarian serous cystadenocarcinoma(155;5.72e-07)|GBM - Glioblastoma multiforme(68;4.9e-05)|Colorectal(48;0.213)		TGAGCTACTCGCTTGATCCAG	0.532																																					p.S3379S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G10137A	6						.						113.0	101.0	105.0					6																	145160380		2203	4300	6503	145202073	SO:0001819	synonymous_variant	7402	exon71			AK023675	CCDS34547.1	6q24	2008-02-05	2006-12-13		ENSG00000152818	ENSG00000152818			12635	protein-coding gene	gene with protein product		128240	"""utrophin (homologous to dystrophin)"""	DMDL		1426262	Standard	NM_007124		Approved	DRP, DRP1	uc003qkt.3	P46939	OTTHUMG00000015746	ENST00000367545.3:c.10137G>A	6.37:g.145160380G>A		Somatic		Capture	Illumina HiSeq	Phase_I	145202073	NM_007124	Q5SYY1|Q5SZ57|Q9UJ40	Silent	SNP	ENST00000367545.3	37	CCDS34547.1																																																																																				0.532	UTRN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042551.1		
SASH1	23328	broad.mit.edu	37	6	148808782	148808782	+	Silent	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr6:148808782G>A	ENST00000367467.3	+	8	1135	c.660G>A	c.(658-660)tcG>tcA	p.S220S		NM_015278.3	NP_056093.3	O94885	SASH1_HUMAN	SAM and SH3 domain containing 1	220					positive regulation of angiogenesis (GO:0045766)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of lipopolysaccharide-mediated signaling pathway (GO:0031666)|positive regulation of NIK/NF-kappaB signaling (GO:1901224)|positive regulation of p38MAPK cascade (GO:1900745)|protein polyubiquitination (GO:0000209)|regulation of protein autoubiquitination (GO:1902498)|regulation of protein K63-linked ubiquitination (GO:1900044)	membrane (GO:0016020)|protein complex (GO:0043234)	mitogen-activated protein kinase kinase kinase binding (GO:0031435)|protein C-terminus binding (GO:0008022)|protein complex scaffold (GO:0032947)|protein kinase binding (GO:0019901)	p.S220S(1)		breast(4)|central_nervous_system(1)|endometrium(9)|kidney(1)|large_intestine(11)|lung(20)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	52		Ovarian(120;0.0169)		OV - Ovarian serous cystadenocarcinoma(155;5.63e-11)|GBM - Glioblastoma multiforme(68;0.0701)		ACCGGCAGTCGGCTGCCCTGG	0.493																																					p.S220S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G660A	6						.						99.0	106.0	104.0					6																	148808782		2203	4300	6503	148850475	SO:0001819	synonymous_variant	23328	exon8			AB018333	CCDS5212.1	6q24.3	2013-01-10			ENSG00000111961	ENSG00000111961		"""SAM and SH3 domain containing"", ""Sterile alpha motif (SAM) domain containing"""	19182	protein-coding gene	gene with protein product		607955				9872452, 12771949	Standard	NM_015278		Approved	KIAA0790, dJ323M4.1, SH3D6A	uc003qme.1	O94885	OTTHUMG00000015773	ENST00000367467.3:c.660G>A	6.37:g.148808782G>A		Somatic		Capture	Illumina HiSeq	Phase_I	148850475	NM_015278	Q5TGN5|Q8TAI0|Q9H7R7	Silent	SNP	ENST00000367467.3	37	CCDS5212.1																																																																																				0.493	SASH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042619.1	NM_015278	
C6orf211	79624	broad.mit.edu	37	6	151779639	151779639	+	Nonsense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr6:151779639G>A	ENST00000367294.3	+	3	583	c.324G>A	c.(322-324)tgG>tgA	p.W108*	C6orf211_ENST00000545879.1_5'UTR|C6orf211_ENST00000483931.1_3'UTR	NM_024573.1	NP_078849.1	Q9H993	CF211_HUMAN	chromosome 6 open reading frame 211	108								p.W108*(1)		breast(1)|cervix(1)|endometrium(1)|large_intestine(5)|lung(7)	15			BRCA - Breast invasive adenocarcinoma(37;0.183)	OV - Ovarian serous cystadenocarcinoma(155;5.27e-11)		AATCAAGATGGTTCTACTCAC	0.343																																					p.W108X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.G324A	6						.						107.0	106.0	106.0					6																	151779639		2203	4299	6502	151821332	SO:0001587	stop_gained	79624	exon3			AJ420548	CCDS5233.1, CCDS69224.1	6q25.1	2013-01-07			ENSG00000146476	ENSG00000146476			17872	protein-coding gene	gene with protein product							Standard	NM_001286562		Approved	FLJ12910	uc003qok.1	Q9H993	OTTHUMG00000015838	ENST00000367294.3:c.324G>A	6.37:g.151779639G>A	ENSP00000356263:p.Trp108*	Somatic		Capture	Illumina HiSeq	Phase_I	151821332	NM_024573	Q96FC6|Q9UFY5	Nonsense_Mutation	SNP	ENST00000367294.3	37	CCDS5233.1	.	.	.	.	.	.	.	.	.	.	G	39	7.488457	0.98316	.	.	ENSG00000146476	ENST00000367294	.	.	.	5.69	5.69	0.88448	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	19.8155	0.96566	0.0:0.0:1.0:0.0	.	.	.	.	X	108	.	ENSP00000356263:W108X	W	+	3	0	C6orf211	151821332	1.000000	0.71417	0.999000	0.59377	0.930000	0.56654	9.869000	0.99810	2.691000	0.91804	0.563000	0.77884	TGG		0.343	C6orf211-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042724.1	NM_024573	
TULP4	56995	broad.mit.edu	37	6	158735122	158735122	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr6:158735122G>A	ENST00000367097.3	+	1	1431	c.74G>A	c.(73-75)cGt>cAt	p.R25H	RP11-732M18.3_ENST00000432358.1_lincRNA|TULP4_ENST00000367094.2_Missense_Mutation_p.R25H	NM_020245.4	NP_064630.2	Q9NRJ4	TULP4_HUMAN	tubby like protein 4	25					intracellular signal transduction (GO:0035556)|protein ubiquitination (GO:0016567)|regulation of transcription, DNA-templated (GO:0006355)|response to nutrient (GO:0007584)	cytoplasm (GO:0005737)	sequence-specific DNA binding transcription factor activity (GO:0003700)	p.R25H(1)		endometrium(7)|kidney(2)|large_intestine(15)|lung(17)|ovary(1)|pancreas(1)|prostate(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	49		Breast(66;0.000781)|Ovarian(120;0.0308)|Lung SC(201;0.164)|Prostate(117;0.171)		OV - Ovarian serous cystadenocarcinoma(65;1.64e-18)|BRCA - Breast invasive adenocarcinoma(81;2.67e-05)		TGGAAGGGGCGTGTCCCCAAG	0.547																																					p.R25H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G74A	6						.						93.0	82.0	85.0					6																	158735122		2203	4300	6503	158655110	SO:0001583	missense	56995	exon1				CCDS34561.1, CCDS34562.1	6q25-q26	2013-01-10			ENSG00000130338	ENSG00000130338		"""WD repeat domain containing"""	15530	protein-coding gene	gene with protein product						11595174	Standard	NM_020245		Approved	TUSP, KIAA1397	uc003qrf.3	Q9NRJ4	OTTHUMG00000015910	ENST00000367097.3:c.74G>A	6.37:g.158735122G>A	ENSP00000356064:p.Arg25His	Somatic		Capture	Illumina HiSeq	Phase_I	158655110	NM_001007466	Q5T3M2|Q5T3M3|Q9HD22|Q9P2F0	Missense_Mutation	SNP	ENST00000367097.3	37	CCDS34561.1	.	.	.	.	.	.	.	.	.	.	G	31	5.058304	0.93846	.	.	ENSG00000130338	ENST00000367097;ENST00000367094	T;T	0.03301	3.98;3.98	5.76	5.76	0.90799	WD40 repeat-like-containing domain (1);	0.000000	0.85682	D	0.000000	T	0.04861	0.0131	N	0.08118	0	0.80722	D	1	D;D;D	0.89917	0.998;1.0;1.0	P;D;D	0.78314	0.905;0.985;0.991	T	0.61392	-0.7072	10	0.56958	D	0.05	-20.5941	19.9766	0.97312	0.0:0.0:1.0:0.0	.	25;25;25	B4E202;Q9NRJ4-2;Q9NRJ4	.;.;TULP4_HUMAN	H	25	ENSP00000356064:R25H;ENSP00000356061:R25H	ENSP00000356061:R25H	R	+	2	0	TULP4	158655110	1.000000	0.71417	0.923000	0.36655	0.919000	0.55068	9.751000	0.98889	2.739000	0.93911	0.555000	0.69702	CGT		0.547	TULP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042869.1	NM_020245	
IGF2R	3482	broad.mit.edu	37	6	160517488	160517488	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr6:160517488G>A	ENST00000356956.1	+	45	6821	c.6673G>A	c.(6673-6675)Gtg>Atg	p.V2225M	RP11-288H12.3_ENST00000569097.1_RNA|IGF2R_ENST00000475584.1_3'UTR	NM_000876.2	NP_000867	P11717	MPRI_HUMAN	insulin-like growth factor 2 receptor	2225					insulin-like growth factor receptor signaling pathway (GO:0048009)|liver development (GO:0001889)|organ regeneration (GO:0031100)|positive regulation of apoptotic process (GO:0043065)|post-embryonic development (GO:0009791)|receptor-mediated endocytosis (GO:0006898)|response to retinoic acid (GO:0032526)|signal transduction (GO:0007165)|spermatogenesis (GO:0007283)	cell surface (GO:0009986)|clathrin coat (GO:0030118)|endocytic vesicle (GO:0030139)|endosome (GO:0005768)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|late endosome (GO:0005770)|lysosome (GO:0005764)|membrane (GO:0016020)|nuclear envelope lumen (GO:0005641)|perinuclear region of cytoplasm (GO:0048471)|trans-Golgi network transport vesicle (GO:0030140)	G-protein coupled receptor activity (GO:0004930)|glycoprotein binding (GO:0001948)|identical protein binding (GO:0042802)|insulin-like growth factor-activated receptor activity (GO:0005010)|mannose binding (GO:0005537)|phosphoprotein binding (GO:0051219)|receptor activity (GO:0004872)|retinoic acid binding (GO:0001972)|transporter activity (GO:0005215)	p.V2225M(1)		breast(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(27)|lung(31)|ovary(3)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	95		Breast(66;0.000777)|Ovarian(120;0.0305)		OV - Ovarian serous cystadenocarcinoma(65;2.45e-17)|BRCA - Breast invasive adenocarcinoma(81;1.09e-05)	Mecasermin(DB01277)	TCTCGATGTCGTGTTTGCCTC	0.512																																					p.V2225M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G6673A	6						.						302.0	217.0	246.0					6																	160517488		2203	4300	6503	160437478	SO:0001583	missense	3482	exon45			J03528	CCDS5273.1	6q25.3	2014-09-16			ENSG00000197081	ENSG00000197081		"""CD molecules"""	5467	protein-coding gene	gene with protein product	"""cation-independent mannose-6 phosphate receptor"""	147280					Standard	NM_000876		Approved	CD222, MPRI, MPR1, CIMPR, M6P-R	uc003qta.3	P11717	OTTHUMG00000015945	ENST00000356956.1:c.6673G>A	6.37:g.160517488G>A	ENSP00000349437:p.Val2225Met	Somatic		Capture	Illumina HiSeq	Phase_I	160437478	NM_000876	Q7Z7G9|Q96PT5	Missense_Mutation	SNP	ENST00000356956.1	37	CCDS5273.1	.	.	.	.	.	.	.	.	.	.	G	16.44	3.123640	0.56613	.	.	ENSG00000197081	ENST00000356956	T	0.04083	3.71	5.69	5.69	0.88448	Mannose-6-phosphate receptor, binding (1);	0.232974	0.43579	D	0.000554	T	0.09774	0.0240	M	0.79123	2.44	0.43439	D	0.995613	D	0.61697	0.99	P	0.55011	0.766	T	0.01405	-1.1363	10	0.44086	T	0.13	-28.1939	13.4845	0.61357	0.0806:0.0:0.9194:0.0	.	2225	P11717	MPRI_HUMAN	M	2225	ENSP00000349437:V2225M	ENSP00000349437:V2225M	V	+	1	0	IGF2R	160437478	1.000000	0.71417	0.996000	0.52242	0.642000	0.38348	3.377000	0.52425	2.677000	0.91161	0.655000	0.94253	GTG		0.512	IGF2R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042931.1	NM_000876	
SLC22A1	6580	broad.mit.edu	37	6	160551194	160551194	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr6:160551194C>T	ENST00000366963.4	+	2	617	c.470C>T	c.(469-471)gCg>gTg	p.A157V	SLC22A1_ENST00000457470.2_Missense_Mutation_p.A157V|SLC22A1_ENST00000324965.4_Missense_Mutation_p.A157V	NM_003057.2|NM_153187.1	NP_003048.1|NP_694857.1	O15245	S22A1_HUMAN	solute carrier family 22 (organic cation transporter), member 1	157					dopamine transport (GO:0015872)|drug transmembrane transport (GO:0006855)|epinephrine transport (GO:0048241)|establishment or maintenance of transmembrane electrochemical gradient (GO:0010248)|norepinephrine transport (GO:0015874)|organic cation transport (GO:0015695)|protein homooligomerization (GO:0051260)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	acetylcholine transmembrane transporter activity (GO:0005277)|dopamine transmembrane transporter activity (GO:0005329)|norepinephrine transmembrane transporter activity (GO:0005333)|organic cation transmembrane transporter activity (GO:0015101)|quaternary ammonium group transmembrane transporter activity (GO:0015651)|secondary active organic cation transmembrane transporter activity (GO:0008513)	p.A157V(1)	SLC22A1/CUTA(2)	breast(1)|endometrium(3)|large_intestine(3)|lung(13)|upper_aerodigestive_tract(1)	21		Breast(66;0.000776)|Ovarian(120;0.00556)		OV - Ovarian serous cystadenocarcinoma(65;2.73e-17)|BRCA - Breast invasive adenocarcinoma(81;1.1e-06)	Acebutolol(DB01193)|Acepromazine(DB01614)|Aciclovir(DB00787)|Amantadine(DB00915)|Amiloride(DB00594)|Aminohippurate(DB00345)|Caspofungin(DB00520)|Chlorphenamine(DB01114)|Chlorpromazine(DB00477)|Choline(DB00122)|Cimetidine(DB00501)|Cladribine(DB00242)|Clonidine(DB00575)|Codeine(DB00318)|Cytarabine(DB00987)|Desipramine(DB01151)|Dinoprostone(DB00917)|Diphenhydramine(DB01075)|Disopyramide(DB00280)|Dopamine(DB00988)|Epinephrine(DB00668)|Estradiol(DB00783)|Estropipate(DB04574)|Ganciclovir(DB01004)|Gentian Violet(DB00406)|Guanidine(DB00536)|Histamine Phosphate(DB00667)|Imatinib(DB00619)|Imipramine(DB00458)|Indinavir(DB00224)|Lamivudine(DB00709)|Latanoprost(DB00654)|Metformin(DB00331)|Midazolam(DB00683)|Nelfinavir(DB00220)|Nicotine(DB00184)|Norepinephrine(DB00368)|Oxaliplatin(DB00526)|Pancuronium(DB01337)|Phenformin(DB00914)|Phenoxybenzamine(DB00925)|Pipotiazine(DB01621)|Pramipexole(DB00413)|Prazosin(DB00457)|Probenecid(DB01032)|Procainamide(DB01035)|Progesterone(DB00396)|Quinidine(DB00908)|Quinine(DB00468)|Ranitidine(DB00863)|Reserpine(DB00206)|Rocuronium(DB00728)|Saquinavir(DB01232)|Spermine(DB00127)|Testosterone(DB00624)|Thiamine(DB00152)|Thioproperazine(DB01622)|Thiothixene(DB01623)|Tubocurarine(DB01199)|Vecuronium(DB01339)|Verapamil(DB00661)	TGTTTGAATGCGGGCTTCTTG	0.507																																					p.A157V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C470T	6						.						259.0	225.0	237.0					6																	160551194		2203	4300	6503	160471184	SO:0001583	missense	6580	exon2			U77086	CCDS5274.1, CCDS5275.1	6q25.3	2013-05-22			ENSG00000175003	ENSG00000175003		"""Solute carriers"""	10963	protein-coding gene	gene with protein product		602607				9605850	Standard	NM_003057		Approved	OCT1	uc003qtc.3	O15245	OTTHUMG00000015947	ENST00000366963.4:c.470C>T	6.37:g.160551194C>T	ENSP00000355930:p.Ala157Val	Somatic		Capture	Illumina HiSeq	Phase_I	160471184	NM_003057	A6NFF3|A8K1H2|C9JSU6|O15395|Q9NQD4	Missense_Mutation	SNP	ENST00000366963.4	37	CCDS5274.1	.	.	.	.	.	.	.	.	.	.	c	0.005	-2.143335	0.00332	.	.	ENSG00000175003	ENST00000366963;ENST00000324965;ENST00000457470	T;T;T	0.70516	-0.49;-0.49;-0.49	3.56	-0.312	0.12758	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.905329	0.09242	N	0.829017	T	0.17959	0.0431	N	0.05031	-0.125	0.09310	N	1	B;B	0.06786	0.001;0.0	B;B	0.06405	0.002;0.001	T	0.35724	-0.9777	10	0.02654	T	1	.	8.6555	0.34060	0.0:0.3996:0.0:0.6004	.	157;157	O15245-2;O15245	.;S22A1_HUMAN	V	157	ENSP00000355930:A157V;ENSP00000318103:A157V;ENSP00000409557:A157V	ENSP00000318103:A157V	A	+	2	0	SLC22A1	160471184	0.965000	0.33210	0.513000	0.27749	0.003000	0.03518	1.855000	0.39378	0.061000	0.16311	-0.370000	0.07254	GCG		0.507	SLC22A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042938.2		
MAP3K4	4216	broad.mit.edu	37	6	161470128	161470128	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr6:161470128G>A	ENST00000392142.4	+	3	972	c.824G>A	c.(823-825)cGg>cAg	p.R275Q	MAP3K4_ENST00000366920.2_Missense_Mutation_p.R275Q|MAP3K4_ENST00000348824.7_Missense_Mutation_p.R275Q|MAP3K4_ENST00000366919.2_Missense_Mutation_p.R275Q	NM_005922.2	NP_005913	Q9Y6R4	M3K4_HUMAN	mitogen-activated protein kinase kinase kinase 4	275					activation of MAPKK activity (GO:0000186)|chorionic trophoblast cell differentiation (GO:0060718)|intracellular signal transduction (GO:0035556)|male germ-line sex determination (GO:0019100)|MAPK cascade (GO:0000165)|placenta development (GO:0001890)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of p38MAPK cascade (GO:1900745)|regulation of gene expression (GO:0010468)|response to UV-C (GO:0010225)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|MAP kinase kinase kinase activity (GO:0004709)|metal ion binding (GO:0046872)	p.R275Q(4)		breast(6)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(20)|lung(28)|ovary(3)|skin(2)|stomach(1)	77		Breast(66;0.000776)|Ovarian(120;0.0367)|Prostate(117;0.0771)		OV - Ovarian serous cystadenocarcinoma(65;1.85e-18)|BRCA - Breast invasive adenocarcinoma(81;3.04e-05)		CATGCAGGACGGACAATTAAC	0.433																																					p.R275Q												.	.	4	Substitution - Missense(4)	large_intestine(4)	c.G824A	6						.						64.0	65.0	65.0					6																	161470128		2203	4300	6503	161390118	SO:0001583	missense	4216	exon3			AF002715	CCDS34565.1, CCDS34566.1, CCDS75544.1	6q26	2012-10-02			ENSG00000085511	ENSG00000085511		"""Mitogen-activated protein kinase cascade / Kinase kinase kinases"""	6856	protein-coding gene	gene with protein product		602425		MEKK4		9305639	Standard	XM_005266988		Approved	MTK1, MAPKKK4, KIAA0213	uc003qtn.3	Q9Y6R4	OTTHUMG00000015968	ENST00000392142.4:c.824G>A	6.37:g.161470128G>A	ENSP00000375986:p.Arg275Gln	Somatic		Capture	Illumina HiSeq	Phase_I	161390118	NM_006724	A6H8W0|B7ZLD3|B9EG75|Q5VTT8|Q5VTT9|Q92612|Q9H408	Missense_Mutation	SNP	ENST00000392142.4	37	CCDS34565.1	.	.	.	.	.	.	.	.	.	.	G	36	5.608994	0.96637	.	.	ENSG00000085511	ENST00000366919;ENST00000392142;ENST00000540111;ENST00000366920;ENST00000348824	T;T;T;T	0.34667	1.35;1.35;1.35;1.35	6.14	6.14	0.99180	.	0.000000	0.85682	D	0.000000	T	0.58906	0.2155	M	0.76328	2.33	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.85130	0.997;0.996	T	0.59059	-0.7525	10	0.87932	D	0	-34.585	20.819	0.99723	0.0:0.0:1.0:0.0	.	275;275	Q9Y6R4-2;Q9Y6R4	.;M3K4_HUMAN	Q	275	ENSP00000355886:R275Q;ENSP00000375986:R275Q;ENSP00000355887:R275Q;ENSP00000297332:R275Q	ENSP00000297332:R275Q	R	+	2	0	MAP3K4	161390118	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	9.432000	0.97498	2.927000	0.99377	0.637000	0.83480	CGG		0.433	MAP3K4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000042988.3		
RNASET2	8635	broad.mit.edu	37	6	167352449	167352449	+	Missense_Mutation	SNP	G	G	A	rs117003826		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr6:167352449G>A	ENST00000508775.1	-	6	899	c.380C>T	c.(379-381)gCg>gTg	p.A127V	RNASET2_ENST00000496851.2_5'UTR|RNASET2_ENST00000366855.6_Missense_Mutation_p.A89V|RNASET2_ENST00000476238.2_Missense_Mutation_p.A127V|RP11-514O12.4_ENST00000507747.1_Missense_Mutation_p.R108C	NM_003730.4	NP_003721.2	O00584	RNT2_HUMAN	ribonuclease T2	127					RNA catabolic process (GO:0006401)|RNA phosphodiester bond hydrolysis (GO:0090501)	endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)	ribonuclease activity (GO:0004540)|ribonuclease T2 activity (GO:0033897)|RNA binding (GO:0003723)	p.A127V(2)		large_intestine(4)|lung(4)	8		Breast(66;1.53e-05)|Ovarian(120;0.0606)		OV - Ovarian serous cystadenocarcinoma(33;1.53e-19)|BRCA - Breast invasive adenocarcinoma(81;5.01e-06)|GBM - Glioblastoma multiforme(31;0.00665)		GGAGTTGAGCGCATCCACCTG	0.562													G|||	1	0.000199681	0.0	0.0	5008	,	,		20671	0.001		0.0	False		,,,				2504	0.0				p.A127V												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.C380T	6						.						104.0	93.0	96.0					6																	167352449		2203	4300	6503	167272439	SO:0001583	missense	8635	exon6			AJ419866	CCDS5295.1	6q27	2014-05-20			ENSG00000026297	ENSG00000026297			21686	protein-coding gene	gene with protein product		612944				9192857	Standard	NM_003730		Approved	RNASE6PL, FLJ10907, bA514O12.3	uc003qve.3	O00584	OTTHUMG00000016009	ENST00000508775.1:c.380C>T	6.37:g.167352449G>A	ENSP00000426455:p.Ala127Val	Somatic		Capture	Illumina HiSeq	Phase_I	167272439	NM_003730	B2RDA7|E1P5C3|Q5T8Q0|Q8TCU2|Q9BZ46|Q9BZ47	Missense_Mutation	SNP	ENST00000508775.1	37	CCDS5295.1	1|1	4.578754578754579E-4|4.578754578754579E-4	0|0	0.0|0.0	0|0	0.0|0.0	1|1	0.0017482517482517483|0.0017482517482517483	0|0	0.0|0.0	G|G	11.60|11.60	1.687294|1.687294	0.29962|0.29962	.|.	.|.	ENSG00000026297|ENSG00000249141;ENSG00000026297	ENST00000366855;ENST00000508775;ENST00000428859;ENST00000476238;ENST00000478180;ENST00000425007|ENST00000507747;ENST00000310843	T;T;T;T|.	0.65364|.	-0.12;-0.15;-0.15;-0.15|.	5.23|5.23	1.43|1.43	0.22495|0.22495	.|.	0.563808|.	0.19430|.	N|.	0.114468|.	T|T	0.15305|0.15305	0.0369|0.0369	N|N	0.20845|0.20845	0.615|0.615	0.09310|0.09310	N|N	1|1	P;P|D	0.44260|0.67145	0.83;0.713|0.996	B;B|P	0.42738|0.55965	0.396;0.077|0.788	T|T	0.03910|0.03910	-1.0993|-1.0993	10|8	0.38643|0.36615	T|T	0.18|0.2	-17.2616|-17.2616	4.2673|4.2673	0.10769|0.10769	0.3622:0.1637:0.4741:0.0|0.3622:0.1637:0.4741:0.0	.|.	177;127|15	C9JIU8;O00584|Q5TCT2	.;RNT2_HUMAN|.	V|C	89;127;177;127;127;136|108;112	ENSP00000424947:A89V;ENSP00000426455:A127V;ENSP00000422846:A127V;ENSP00000426059:A127V|.	ENSP00000424947:A89V|ENSP00000308991:R112C	A|R	-|-	2|1	0|0	RNASET2|RNASET2;RP11-514O12.4	167272439|167272439	0.083000|0.083000	0.21467|0.21467	0.001000|0.001000	0.08648|0.08648	0.085000|0.085000	0.17905|0.17905	0.302000|0.302000	0.19192|0.19192	0.309000|0.309000	0.22966|0.22966	0.462000|0.462000	0.41574|0.41574	GCG|CGC		0.562	RNASET2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043089.2	NM_003730	
SMOC2	64094	broad.mit.edu	37	6	168999659	168999659	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr6:168999659C>T	ENST00000356284.2	+	8	1019	c.799C>T	c.(799-801)Cgc>Tgc	p.R267C	SMOC2_ENST00000354536.5_Missense_Mutation_p.R278C	NM_001166412.1	NP_001159884.1	Q9H3U7	SMOC2_HUMAN	SPARC related modular calcium binding 2	267	Thyroglobulin type-1 2. {ECO:0000255|PROSITE-ProRule:PRU00500}.				extracellular matrix organization (GO:0030198)|positive regulation of cell-substrate adhesion (GO:0010811)|signal transduction (GO:0007165)	basement membrane (GO:0005604)|interstitial matrix (GO:0005614)	calcium ion binding (GO:0005509)|heparin binding (GO:0008201)	p.R278C(1)		NS(1)|autonomic_ganglia(1)|breast(2)|endometrium(1)|kidney(1)|large_intestine(6)|lung(12)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	32		Breast(66;0.000141)|Esophageal squamous(34;0.222)|Ovarian(120;0.231)		OV - Ovarian serous cystadenocarcinoma(33;1.31e-19)|BRCA - Breast invasive adenocarcinoma(81;3.06e-06)|GBM - Glioblastoma multiforme(31;0.00109)		GGACACGGGGCGCCCCATTCC	0.652																																					p.R267C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C799T	6						.						47.0	41.0	43.0					6																	168999659		2203	4296	6499	168741584	SO:0001583	missense	64094	exon8			AB014730	CCDS5307.1, CCDS55076.1	6q27	2013-01-10			ENSG00000112562	ENSG00000112562		"""EF-hand domain containing"""	20323	protein-coding gene	gene with protein product		607223				12031507	Standard	NM_022138		Approved	SMAP2	uc003qwr.2	Q9H3U7	OTTHUMG00000016050	ENST00000356284.2:c.799C>T	6.37:g.168999659C>T	ENSP00000348630:p.Arg267Cys	Somatic		Capture	Illumina HiSeq	Phase_I	168741584	NM_001166412	B3KPS7|Q4G169|Q5TAT7|Q5TAT8|Q86VV9|Q96SF3|Q9H1L3|Q9H1L4|Q9H3U0|Q9H4F7|Q9HCV2	Missense_Mutation	SNP	ENST00000356284.2	37	CCDS55076.1	.	.	.	.	.	.	.	.	.	.	C	20.7	4.036795	0.75617	.	.	ENSG00000112562	ENST00000356284;ENST00000354536;ENST00000366793	T;T	0.64803	-0.12;-0.12	4.89	4.89	0.63831	Thyroglobulin type-1 (4);EF-hand-like domain (1);	0.150274	0.43579	D	0.000554	T	0.78336	0.4267	M	0.86953	2.85	0.58432	D	0.999998	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.998	T	0.80509	-0.1351	10	0.45353	T	0.12	-13.6591	17.1175	0.86694	0.0:1.0:0.0:0.0	.	267;278	Q9H3U7;Q9H3U7-2	SMOC2_HUMAN;.	C	267;278;267	ENSP00000348630:R267C;ENSP00000346537:R278C	ENSP00000346537:R278C	R	+	1	0	SMOC2	168741584	0.999000	0.42202	0.943000	0.38184	0.683000	0.39861	4.164000	0.58190	2.268000	0.75426	0.386000	0.25728	CGC		0.652	SMOC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043201.1		
DUSP22	56940	broad.mit.edu	37	6	348125	348125	+	Missense_Mutation	SNP	G	G	A	rs138056339	byFrequency	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr6:348125G>A	ENST00000344450.5	+	6	729	c.286G>A	c.(286-288)Gtg>Atg	p.V96M	DUSP22_ENST00000605035.1_5'UTR|DUSP22_ENST00000603453.1_5'UTR|DUSP22_ENST00000605315.1_5'UTR|DUSP22_ENST00000419235.2_Missense_Mutation_p.V96M|DUSP22_ENST00000604971.1_5'UTR|DUSP22_ENST00000605863.1_5'UTR	NM_020185.3	NP_064570.1	Q9NRW4	DUS22_HUMAN	dual specificity phosphatase 22	96	Tyrosine-protein phosphatase.				apoptotic process (GO:0006915)|cell proliferation (GO:0008283)|inactivation of MAPK activity (GO:0000188)|multicellular organismal development (GO:0007275)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of JNK cascade (GO:0046330)|protein dephosphorylation (GO:0006470)|regulation of cell proliferation (GO:0042127)|transforming growth factor beta receptor signaling pathway (GO:0007179)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)	p.V96M(1)		central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(16)|ovary(1)|skin(2)	26	all_hematologic(77;0.228)	Breast(5;0.0249)|all_hematologic(90;0.0489)		OV - Ovarian serous cystadenocarcinoma(45;0.0277)|BRCA - Breast invasive adenocarcinoma(62;0.0669)		CTCCAGGAGCGTGACACTGGT	0.612																																					p.V96M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G286A	6						.	G	MET/VAL	2,4404	2.1+/-5.4	0,2,2201	175.0	163.0	167.0		286	5.8	1.0	6	dbSNP_134	167	2,8598	2.2+/-6.3	0,2,4298	yes	missense	DUSP22	NM_020185.3	21	0,4,6499	AA,AG,GG		0.0233,0.0454,0.0308	probably-damaging	96/185	348125	4,13002	2203	4300	6503	293125	SO:0001583	missense	56940	exon6			AF165519	CCDS4468.1, CCDS69035.1	6p25.3	2013-09-19			ENSG00000112679	ENSG00000112679		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Atypical dual specificity phosphatases"""	16077	protein-coding gene	gene with protein product						9205128, 11717427	Standard	NM_001286555		Approved	MKPX, JSP1, JKAP, VHX	uc003msx.3	Q9NRW4	OTTHUMG00000014113	ENST00000344450.5:c.286G>A	6.37:g.348125G>A	ENSP00000345281:p.Val96Met	Somatic		Capture	Illumina HiSeq	Phase_I	293125	NM_020185	B4DK56|Q59GW2|Q5VWR2|Q96AR1	Missense_Mutation	SNP	ENST00000344450.5	37	CCDS4468.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	35|35	5.413586|5.413586	0.96072|0.96072	4.54E-4|4.54E-4	2.33E-4|2.33E-4	ENSG00000112679|ENSG00000112679	ENST00000419235|ENST00000344450	.|T	.|0.61040	.|0.14	5.82|5.82	5.82|5.82	0.92795|0.92795	.|Dual specificity phosphatase, catalytic domain (1);Protein-tyrosine/Dual-specificity phosphatase (1);Dual specificity phosphatase, subgroup, catalytic domain (2);	.|0.000000	.|0.64402	.|D	.|0.000001	D|D	0.82834|0.82834	0.5123|0.5123	H|H	0.96208|0.96208	3.785|3.785	0.80722|0.80722	D|D	1|1	.|D;D;D	.|0.89917	.|1.0;1.0;1.0	.|D;D;D	.|0.73380	.|0.98;0.972;0.961	D|D	0.87323|0.87323	0.2319|0.2319	5|10	.|0.72032	.|D	.|0.01	.|.	20.0852|20.0852	0.97797|0.97797	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|96;53;96	.|Q9NRW4-2;B3KSA8;Q9NRW4	.|.;.;DUS22_HUMAN	H|M	33|96	.|ENSP00000345281:V96M	.|ENSP00000345281:V96M	R|V	+|+	2|1	0|0	DUSP22|DUSP22	293125|293125	1.000000|1.000000	0.71417|0.71417	0.987000|0.987000	0.45799|0.45799	0.967000|0.967000	0.64934|0.64934	7.947000|7.947000	0.87758|0.87758	2.752000|2.752000	0.94435|0.94435	0.655000|0.655000	0.94253|0.94253	CGT|GTG		0.612	DUSP22-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000039621.1	NM_020185	
EXOC2	55770	broad.mit.edu	37	6	549246	549246	+	Missense_Mutation	SNP	G	G	A	rs373080488		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr6:549246G>A	ENST00000230449.4	-	22	2302	c.2167C>T	c.(2167-2169)Cgt>Tgt	p.R723C	EXOC2_ENST00000448181.3_Missense_Mutation_p.R318C	NM_018303.5	NP_060773.3	Q96KP1	EXOC2_HUMAN	exocyst complex component 2	723					cellular protein metabolic process (GO:0044267)|exocytosis (GO:0006887)|Golgi to plasma membrane transport (GO:0006893)|membrane organization (GO:0061024)|protein transport (GO:0015031)	exocyst (GO:0000145)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|plasma membrane (GO:0005886)		p.R723C(1)		breast(4)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(9)|liver(1)|lung(16)|ovary(4)|pancreas(1)|prostate(2)	46	Ovarian(93;0.0733)	Breast(5;0.0014)|all_lung(73;0.0697)|all_hematologic(90;0.0897)		OV - Ovarian serous cystadenocarcinoma(45;0.0507)|BRCA - Breast invasive adenocarcinoma(62;0.14)		AAGGTGTGACGTTCTAGATAG	0.383																																					p.R723C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C2167T	6						.	G	CYS/ARG	1,4405	2.1+/-5.4	0,1,2202	183.0	173.0	176.0		2167	5.4	1.0	6		176	0,8600		0,0,4300	no	missense	EXOC2	NM_018303.4	180	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	probably-damaging	723/925	549246	1,13005	2203	4300	6503	494246	SO:0001583	missense	55770	exon22			AJ420556	CCDS34327.1	6p25.3	2013-01-22	2005-11-01	2005-11-01	ENSG00000112685	ENSG00000112685			24968	protein-coding gene	gene with protein product		615329	"""SEC5-like 1 (S. cerevisiae)"""	SEC5L1		12575951, 12459492	Standard	NM_018303		Approved	FLJ11026, Sec5p	uc003mtd.4	Q96KP1	OTTHUMG00000137437	ENST00000230449.4:c.2167C>T	6.37:g.549246G>A	ENSP00000230449:p.Arg723Cys	Somatic		Capture	Illumina HiSeq	Phase_I	494246	NM_018303	B2RBE6|Q5JPC8|Q96AN6|Q9NUZ8|Q9UJM7	Missense_Mutation	SNP	ENST00000230449.4	37	CCDS34327.1	.	.	.	.	.	.	.	.	.	.	G	20.9	4.071379	0.76301	2.27E-4	0.0	ENSG00000112685	ENST00000230449;ENST00000448181	T	0.47528	0.84	5.41	5.41	0.78517	.	0.000000	0.85682	D	0.000000	T	0.57651	0.2068	M	0.66939	2.045	0.80722	D	1	D	0.89917	1.0	P	0.58721	0.844	T	0.60224	-0.7305	10	0.56958	D	0.05	1.0973	19.1915	0.93669	0.0:0.0:1.0:0.0	.	723	Q96KP1	EXOC2_HUMAN	C	723;318	ENSP00000230449:R723C	ENSP00000230449:R723C	R	-	1	0	EXOC2	494246	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	4.412000	0.59787	2.515000	0.84797	0.655000	0.94253	CGT		0.383	EXOC2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039627.1	NM_018303	
TUBB2B	347733	broad.mit.edu	37	6	3225820	3225820	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr6:3225820C>T	ENST00000259818.7	-	4	694	c.503G>A	c.(502-504)aGc>aAc	p.S168N	TUBB2B_ENST00000473006.1_5'UTR	NM_178012.4	NP_821080.1	Q9BVA1	TBB2B_HUMAN	tubulin, beta 2B class IIb	168					'de novo' posttranslational protein folding (GO:0051084)|cellular protein metabolic process (GO:0044267)|microtubule-based process (GO:0007017)|neuron migration (GO:0001764)|protein folding (GO:0006457)|protein polymerization (GO:0051258)	cytoplasm (GO:0005737)|microtubule (GO:0005874)|nucleus (GO:0005634)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|structural constituent of cytoskeleton (GO:0005200)	p.S168N(1)		kidney(2)|large_intestine(5)|lung(1)|prostate(1)|skin(1)	10	Ovarian(93;0.0386)	all_hematologic(90;0.108)				GGGCATGACGCTGAAGGTGTT	0.612																																					p.S168N												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G503A	6						.						22.0	25.0	24.0					6																	3225820		1921	3854	5775	3170819	SO:0001583	missense	347733	exon4			BC001352	CCDS4485.1	6p25.2	2011-10-10	2011-10-10		ENSG00000137285	ENSG00000137285		"""Tubulins"""	30829	protein-coding gene	gene with protein product	"""class IIb beta-tubulin"""	612850	"""tubulin, beta 2B"""			8619474, 9110174	Standard	NM_178012		Approved	MGC8685, DKFZp566F223, bA506K6.1	uc003mvg.3	Q9BVA1	OTTHUMG00000014143	ENST00000259818.7:c.503G>A	6.37:g.3225820C>T	ENSP00000259818:p.Ser168Asn	Somatic		Capture	Illumina HiSeq	Phase_I	3170819	NM_178012	A8K068	Missense_Mutation	SNP	ENST00000259818.7	37	CCDS4485.1	.	.	.	.	.	.	.	.	.	.	C	17.90	3.503125	0.64298	.	.	ENSG00000137285	ENST00000259818	T	0.72505	-0.66	5.21	5.21	0.72293	Tubulin/FtsZ, GTPase domain (4);	0.000000	0.85682	D	0.000000	D	0.89347	0.6689	H	0.97707	4.06	0.80722	D	1	D;D;B	0.71674	0.998;0.998;0.004	D;D;B	0.91635	0.999;0.999;0.067	D	0.93089	0.6498	10	0.87932	D	0	.	18.7626	0.91858	0.0:1.0:0.0:0.0	.	168;168;168	Q8IZ29;Q8IWP6;Q9BVA1	.;.;TBB2B_HUMAN	N	168	ENSP00000259818:S168N	ENSP00000259818:S168N	S	-	2	0	TUBB2B	3170819	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.651000	0.83577	2.420000	0.82092	0.514000	0.50259	AGC		0.612	TUBB2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039680.2	NM_178012	
CDYL	9425	broad.mit.edu	37	6	4935881	4935881	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr6:4935881G>A	ENST00000328908.5	+	5	1117	c.986G>A	c.(985-987)cGt>cAt	p.R329H	CDYL_ENST00000472453.1_3'UTR|CDYL_ENST00000397588.3_Missense_Mutation_p.R275H|CDYL_ENST00000343762.5_Missense_Mutation_p.R143H|CDYL_ENST00000449732.2_Missense_Mutation_p.R143H			Q9Y232	CDYL1_HUMAN	chromodomain protein, Y-like	329					regulation of transcription, DNA-templated (GO:0006355)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	histone acetyltransferase activity (GO:0004402)|methylated histone binding (GO:0035064)|transcription corepressor activity (GO:0003714)	p.R329H(1)		breast(2)|kidney(2)|large_intestine(9)|lung(13)|skin(1)|stomach(2)|urinary_tract(1)	30	Ovarian(93;0.11)	all_hematologic(90;0.0901)|Lung NSC(90;0.244)		OV - Ovarian serous cystadenocarcinoma(45;0.182)		AAGCGATTGCGTTTCAGCGTG	0.453																																					p.R143H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G428A	6						.						127.0	120.0	122.0					6																	4935881		2203	4300	6503	4880880	SO:0001583	missense	9425	exon3			AF081258	CCDS4491.2, CCDS47364.1	6p25.1	2010-05-04	2003-09-12		ENSG00000153046	ENSG00000153046			1811	protein-coding gene	gene with protein product	"""CDY-like, autosomal"", ""testis-specific chromodomain Y-like protein"""	603778	"""chromodomain protein, Y chromosome-like"""			10192397	Standard	NM_001143970		Approved	DKFZP586C1622, CDYL1	uc003mwj.3	Q9Y232	OTTHUMG00000014170	ENST00000328908.5:c.986G>A	6.37:g.4935881G>A	ENSP00000330512:p.Arg329His	Somatic		Capture	Illumina HiSeq	Phase_I	4880880	NM_001143970	A8K6D6|B4DLG4|Q0VDG7|Q32NC5|Q5VX99|Q6P7T5|Q9BWZ2|Q9Y424	Missense_Mutation	SNP	ENST00000328908.5	37		.	.	.	.	.	.	.	.	.	.	G	19.94	3.919315	0.73098	.	.	ENSG00000153046	ENST00000328908;ENST00000440139;ENST00000397588;ENST00000449732;ENST00000343762	T;T;T;T	0.60040	0.59;0.22;0.28;0.28	6.07	6.07	0.98685	.	0.000000	0.85682	D	0.000000	T	0.35480	0.0933	L	0.29908	0.895	0.80722	D	1	B;B	0.25169	0.119;0.05	B;B	0.27262	0.078;0.028	T	0.16364	-1.0405	9	.	.	.	.	19.6321	0.95713	0.0:0.0:1.0:0.0	.	275;329	Q9Y232-2;Q9Y232	.;CDYL1_HUMAN	H	329;55;275;143;143	ENSP00000330512:R329H;ENSP00000380718:R275H;ENSP00000394076:R143H;ENSP00000340908:R143H	.	R	+	2	0	CDYL	4880880	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	9.640000	0.98453	2.884000	0.98904	0.655000	0.94253	CGT		0.453	CDYL-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000039736.1	NM_004824	
TRIM38	10475	broad.mit.edu	37	6	25966902	25966902	+	Missense_Mutation	SNP	A	A	C	rs186435630		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr6:25966902A>C	ENST00000357085.3	+	3	628	c.152A>C	c.(151-153)cAa>cCa	p.Q51P	TRIM38_ENST00000349458.3_Missense_Mutation_p.Q51P	NM_006355.3	NP_006346.1	O00635	TRI38_HUMAN	tripartite motif containing 38	51					negative regulation of defense response to virus (GO:0050687)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of viral entry into host cell (GO:0046598)|positive regulation of viral genome replication (GO:0045070)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein K48-linked ubiquitination (GO:0070936)|regulation of interferon-beta production (GO:0032648)|signal transduction (GO:0007165)	intracellular (GO:0005622)	signal transducer activity (GO:0004871)|zinc ion binding (GO:0008270)	p.Q51P(1)		breast(3)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(5)|lung(8)|upper_aerodigestive_tract(2)	23						AGCCAAAAGCAACTGAGGCAG	0.507																																					p.Q51P												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A152C	6						.						85.0	82.0	83.0					6																	25966902		2203	4300	6503	26074881	SO:0001583	missense	10475	exon3			U90547	CCDS4568.1	6p21.3	2011-04-20	2011-01-25	2002-06-07	ENSG00000112343	ENSG00000112343		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	10059	protein-coding gene	gene with protein product			"""ring finger protein 15"", ""tripartite motif-containing 38"""	RNF15			Standard	XR_241880		Approved	RORET	uc003nfm.4	O00635	OTTHUMG00000014414	ENST00000357085.3:c.152A>C	6.37:g.25966902A>C	ENSP00000349596:p.Gln51Pro	Somatic		Capture	Illumina HiSeq	Phase_I	26074881	NM_006355	B2R862	Missense_Mutation	SNP	ENST00000357085.3	37	CCDS4568.1	.	.	.	.	.	.	.	.	.	.	a	8.974	0.973688	0.18736	.	.	ENSG00000112343	ENST00000540262;ENST00000349458;ENST00000357085	T;T;T	0.08896	3.04;3.04;3.04	2.82	-3.42	0.04825	Zinc finger, RING/FYVE/PHD-type (1);Zinc finger, RING-type (2);Zinc finger, C3HC4 RING-type (1);	3.059360	0.00974	N	0.003284	T	0.04048	0.0113	L	0.60455	1.87	0.09310	N	1	P;P	0.37176	0.586;0.586	P;P	0.45377	0.478;0.478	T	0.20806	-1.0264	10	0.41790	T	0.15	.	1.7083	0.02887	0.4454:0.2998:0.1073:0.1474	.	51;51	B2R862;O00635	.;TRI38_HUMAN	P	51	ENSP00000443976:Q51P;ENSP00000230099:Q51P;ENSP00000349596:Q51P	ENSP00000230099:Q51P	Q	+	2	0	TRIM38	26074881	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.877000	0.04197	-1.220000	0.02594	-1.463000	0.01021	CAA		0.507	TRIM38-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040076.2		
TRIM38	10475	broad.mit.edu	37	6	25983838	25983838	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr6:25983838T>C	ENST00000357085.3	+	8	1797	c.1321T>C	c.(1321-1323)Tcc>Ccc	p.S441P	TRIM38_ENST00000349458.3_Missense_Mutation_p.S441P|U91328.21_ENST00000608931.1_RNA	NM_006355.3	NP_006346.1	O00635	TRI38_HUMAN	tripartite motif containing 38	441	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.				negative regulation of defense response to virus (GO:0050687)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of viral entry into host cell (GO:0046598)|positive regulation of viral genome replication (GO:0045070)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein K48-linked ubiquitination (GO:0070936)|regulation of interferon-beta production (GO:0032648)|signal transduction (GO:0007165)	intracellular (GO:0005622)	signal transducer activity (GO:0004871)|zinc ion binding (GO:0008270)	p.S441P(1)		breast(3)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(5)|lung(8)|upper_aerodigestive_tract(2)	23						CCCGAAGGCTTCCTTCTCTGA	0.483																																					p.S441P												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T1321C	6						.						73.0	72.0	72.0					6																	25983838		2203	4300	6503	26091817	SO:0001583	missense	10475	exon8			U90547	CCDS4568.1	6p21.3	2011-04-20	2011-01-25	2002-06-07	ENSG00000112343	ENSG00000112343		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	10059	protein-coding gene	gene with protein product			"""ring finger protein 15"", ""tripartite motif-containing 38"""	RNF15			Standard	XR_241880		Approved	RORET	uc003nfm.4	O00635	OTTHUMG00000014414	ENST00000357085.3:c.1321T>C	6.37:g.25983838T>C	ENSP00000349596:p.Ser441Pro	Somatic		Capture	Illumina HiSeq	Phase_I	26091817	NM_006355	B2R862	Missense_Mutation	SNP	ENST00000357085.3	37	CCDS4568.1	.	.	.	.	.	.	.	.	.	.	t	15.59	2.879042	0.51801	.	.	ENSG00000112343	ENST00000540262;ENST00000349458;ENST00000357085	T;T;T	0.70399	-0.48;-0.48;-0.48	4.25	-0.918	0.10482	Concanavalin A-like lectin/glucanase (1);SPla/RYanodine receptor subgroup (1);Butyrophylin-like (1);B30.2/SPRY domain (1);SPla/RYanodine receptor SPRY (1);	0.300620	0.24433	N	0.038576	T	0.34193	0.0889	L	0.50333	1.59	0.25473	N	0.987806	B;B	0.28208	0.203;0.203	B;B	0.32583	0.148;0.148	T	0.26224	-1.0109	10	0.22109	T	0.4	.	1.4637	0.02401	0.2906:0.0874:0.1503:0.4717	.	441;441	B2R862;O00635	.;TRI38_HUMAN	P	441	ENSP00000443976:S441P;ENSP00000230099:S441P;ENSP00000349596:S441P	ENSP00000230099:S441P	S	+	1	0	TRIM38	26091817	0.002000	0.14202	0.830000	0.32933	0.914000	0.54420	-0.119000	0.10676	-0.143000	0.11334	0.533000	0.62120	TCC		0.483	TRIM38-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040076.2		
HIST1H1A	3024	broad.mit.edu	37	6	26017597	26017597	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr6:26017597C>A	ENST00000244573.3	-	1	443	c.364G>T	c.(364-366)Ggc>Tgc	p.G122C		NM_005325.3	NP_005316.1	Q02539	H11_HUMAN	histone cluster 1, H1a	122					nucleosome assembly (GO:0006334)|spermatogenesis (GO:0007283)	nuclear chromatin (GO:0000790)|nuclear euchromatin (GO:0005719)|nucleosome (GO:0000786)	chromatin DNA binding (GO:0031490)	p.G122C(1)		cervix(1)|endometrium(4)|kidney(1)|large_intestine(3)|ovary(3)|prostate(1)	13						TTTGAGGCGCCGGGCTTGGTT	0.537																																					p.G122C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G364T	6						.						84.0	92.0	89.0					6																	26017597		2203	4300	6503	26125576	SO:0001583	missense	3024	exon1			AF531299	CCDS4569.1	6p22.1	2012-11-16	2006-10-11	2003-02-21	ENSG00000124610	ENSG00000124610		"""Histones / Replication-dependent"""	4715	protein-coding gene	gene with protein product		142709	"""H1 histone family, member 1"", ""histone 1, H1a"""	H1F1		2759094, 12408966	Standard	NM_005325		Approved	H1.1, H1a	uc003nfo.3	Q02539	OTTHUMG00000016413	ENST00000244573.3:c.364G>T	6.37:g.26017597C>A	ENSP00000244573:p.Gly122Cys	Somatic		Capture	Illumina HiSeq	Phase_I	26125576	NM_005325	Q3MJ34	Missense_Mutation	SNP	ENST00000244573.3	37	CCDS4569.1	.	.	.	.	.	.	.	.	.	.	N	7.010	0.556670	0.13436	.	.	ENSG00000124610	ENST00000244573	T	0.04049	3.72	4.31	1.92	0.25849	.	1.591480	0.03632	N	0.238127	T	0.01061	0.0035	N	0.08118	0	0.20563	N	0.999889	P	0.41673	0.759	B	0.38921	0.285	T	0.41840	-0.9486	10	0.87932	D	0	-12.7522	5.9549	0.19267	0.0:0.2244:0.0:0.7756	.	122	Q02539	H11_HUMAN	C	122	ENSP00000244573:G122C	ENSP00000244573:G122C	G	-	1	0	HIST1H1A	26125576	0.006000	0.16342	0.002000	0.10522	0.001000	0.01503	-0.007000	0.12810	0.283000	0.22279	-0.320000	0.08662	GGC		0.537	HIST1H1A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043884.1	NM_005325	
HIST1H2BD	3017	broad.mit.edu	37	6	26158515	26158515	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr6:26158515G>A	ENST00000289316.2	+	1	142	c.118G>A	c.(118-120)Gtg>Atg	p.V40M	HIST1H2BD_ENST00000377777.4_Missense_Mutation_p.V40M	NM_138720.2	NP_619790.1	P58876	H2B1D_HUMAN	histone cluster 1, H2bd	40					chromatin organization (GO:0006325)	extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|nucleosome (GO:0000786)|nucleus (GO:0005634)	DNA binding (GO:0003677)	p.V40M(1)		breast(2)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(2)|lung(6)|ovary(2)|pancreas(1)|prostate(1)|skin(1)	24						GAGCTATTCAGTGTATGTGTA	0.552																																					p.V40M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G118A	6						.						198.0	183.0	188.0					6																	26158515		2203	4300	6503	26266494	SO:0001583	missense	3017	exon1			M60751	CCDS4587.1	6p22.1	2011-01-27	2006-10-11	2003-02-14	ENSG00000158373	ENSG00000158373		"""Histones / Replication-dependent"""	4747	protein-coding gene	gene with protein product		602799	"""H2B histone family, member B"", ""histone 1, H2bd"""	H2BFB		1916825, 12408966	Standard	NM_021063		Approved	H2B/b	uc003ngr.3	P58876	OTTHUMG00000014426	ENST00000289316.2:c.118G>A	6.37:g.26158515G>A	ENSP00000289316:p.Val40Met	Somatic		Capture	Illumina HiSeq	Phase_I	26266494	NM_021063		Missense_Mutation	SNP	ENST00000289316.2	37	CCDS4587.1	.	.	.	.	.	.	.	.	.	.	.	12.94	2.087414	0.36855	.	.	ENSG00000158373	ENST00000377777;ENST00000289316	T;T	0.24723	1.84;1.84	5.19	4.31	0.51392	Histone-fold (2);Histone core (1);	0.225081	0.22973	N	0.053413	T	0.11623	0.0283	L	0.54323	1.7	0.33670	D	0.610817	B	0.12630	0.006	B	0.20577	0.03	T	0.05225	-1.0898	10	0.32370	T	0.25	.	8.1937	0.31383	0.2174:0.0:0.7826:0.0	.	40	P58876	H2B1D_HUMAN	M	40	ENSP00000367008:V40M;ENSP00000289316:V40M	ENSP00000289316:V40M	V	+	1	0	HIST1H2BD	26266494	0.996000	0.38824	0.679000	0.29978	0.379000	0.30106	3.066000	0.50002	2.820000	0.97059	0.650000	0.86243	GTG		0.552	HIST1H2BD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040088.1	NM_021063	
HIST1H3G	8355	broad.mit.edu	37	6	26271298	26271298	+	Silent	SNP	A	A	G			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr6:26271298A>G	ENST00000305910.3	-	1	314	c.315T>C	c.(313-315)ttT>ttC	p.F105F	HIST1H2BI_ENST00000377733.2_5'Flank	NM_003534.2	NP_003525.1	P68431	H31_HUMAN	histone cluster 1, H3g	105					blood coagulation (GO:0007596)|chromatin organization (GO:0006325)|DNA replication-dependent nucleosome assembly (GO:0006335)|regulation of gene silencing (GO:0060968)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nuclear chromosome (GO:0000228)|nucleoplasm (GO:0005654)|nucleosome (GO:0000786)|nucleus (GO:0005634)|protein complex (GO:0043234)	DNA binding (GO:0003677)	p.F105F(1)		breast(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(4)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	12						TGGTATCCTCAAAGAGCCCCA	0.572																																					p.F105F												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.T315C	6						.						90.0	92.0	91.0					6																	26271298		2203	4300	6503	26379277	SO:0001819	synonymous_variant	8355	exon1			Z80785	CCDS4602.1	6p22.1	2011-07-22	2006-10-11	2003-03-14	ENSG00000256018			"""Histones / Replication-dependent"""	4772	protein-coding gene	gene with protein product		602815	"""H3 histone family, member H"", ""histone 1, H3g"""	H3FH		9119399, 12408966	Standard	NM_003534		Approved	H3/h	uc003nhi.3	P68431	OTTHUMG00000014436	ENST00000305910.3:c.315T>C	6.37:g.26271298A>G		Somatic		Capture	Illumina HiSeq	Phase_I	26379277	NM_003534	A0PJT7|A5PLR1|P02295|P02296|P16106|Q6ISV8|Q6NWP8|Q6NWP9|Q6NXU4|Q71DJ3|Q93081	Silent	SNP	ENST00000305910.3	37	CCDS4602.1																																																																																				0.572	HIST1H3G-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040099.2	NM_003534	
BTN3A2	11118	broad.mit.edu	37	6	26374575	26374575	+	Missense_Mutation	SNP	G	G	A	rs376441641		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr6:26374575G>A	ENST00000356386.2	+	9	1173	c.985G>A	c.(985-987)Gat>Aat	p.D329N	BTN3A2_ENST00000396934.3_Missense_Mutation_p.D306N|BTN3A2_ENST00000377708.2_Missense_Mutation_p.D329N|BTN3A2_ENST00000527422.1_Missense_Mutation_p.D329N|BTN3A2_ENST00000508906.2_Missense_Mutation_p.D287N|BTN3A2_ENST00000396948.1_Missense_Mutation_p.D329N	NM_001197246.2|NM_001197247.1|NM_007047.3	NP_001184175.1|NP_001184176.1|NP_008978.2	P78410	BT3A2_HUMAN	butyrophilin, subfamily 3, member A2	329					interferon-gamma secretion (GO:0072643)|T cell mediated immunity (GO:0002456)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)		p.D329N(1)		central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(5)	10						GTCTTCGTCCGATACCAATAA	0.478													G|||	1	0.000199681	0.0	0.0	5008	,	,		15896	0.0		0.0	False		,,,				2504	0.001				p.D287N												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G859A	6						.	G	ASN/ASP,ASN/ASP,ASN/ASP,ASN/ASP,ASN/ASP	0,4406		0,0,2203	204.0	169.0	181.0		985,985,916,859,985	-0.6	0.0	6		181	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense,missense,missense,missense	BTN3A2	NM_001197246.1,NM_001197247.1,NM_001197248.1,NM_001197249.1,NM_007047.3	23,23,23,23,23	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging	329/335,329/335,306/312,287/293,329/335	26374575	1,13005	2203	4300	6503	26482554	SO:0001583	missense	11118	exon8			U90546	CCDS4605.1, CCDS56399.1, CCDS56400.1	6p22.1	2014-01-14			ENSG00000186470	ENSG00000186470		"""Immunoglobulin superfamily / V-set domain containing"", ""Butyrophilins"""	1139	protein-coding gene	gene with protein product		613594				9149941	Standard	NM_007047		Approved	BTN3.2	uc010jqi.2	P78410	OTTHUMG00000014450	ENST00000356386.2:c.985G>A	6.37:g.26374575G>A	ENSP00000348751:p.Asp329Asn	Somatic		Capture	Illumina HiSeq	Phase_I	26482554	NM_001197249	B4DRT7|B4E103|F5H791|F8W6E0|O00477|O15338|O75658|Q76PA0|Q9BU81|Q9NR44	Missense_Mutation	SNP	ENST00000356386.2	37	CCDS4605.1	.	.	.	.	.	.	.	.	.	.	g	6.635	0.485540	0.12641	0.0	1.16E-4	ENSG00000186470	ENST00000527422;ENST00000356386;ENST00000396934;ENST00000377708;ENST00000396948;ENST00000508906	T;T;T;T;T;T	0.03889	3.92;3.92;3.77;3.92;3.92;4.34	0.814	-0.55	0.11825	.	.	.	.	.	T	0.00695	0.0023	N	0.08118	0	0.09310	N	1	B;B	0.20368	0.044;0.026	B;B	0.04013	0.001;0.0	T	0.46884	-0.9159	9	0.48119	T	0.1	.	3.6026	0.08030	0.0:0.0:0.4376:0.5624	.	306;329	F8W6E0;P78410	.;BT3A2_HUMAN	N	329;329;306;329;329;287	ENSP00000432138:D329N;ENSP00000348751:D329N;ENSP00000380140:D306N;ENSP00000366937:D329N;ENSP00000380152:D329N;ENSP00000442687:D287N	ENSP00000348751:D329N	D	+	1	0	BTN3A2	26482554	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.341000	0.07811	-0.214000	0.10078	-0.718000	0.03613	GAT		0.478	BTN3A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040113.2		
PGBD1	84547	broad.mit.edu	37	6	28268873	28268873	+	Silent	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr6:28268873C>T	ENST00000405948.2	+	7	1662	c.1242C>T	c.(1240-1242)agC>agT	p.S414S	PGBD1_ENST00000259883.3_Silent_p.S414S	NM_001184743.1|NM_032507.3	NP_001171672.1|NP_115896.1	Q96JS3	PGBD1_HUMAN	piggyBac transposable element derived 1	414						membrane (GO:0016020)|nucleus (GO:0005634)	scavenger receptor activity (GO:0005044)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.S414S(1)		endometrium(2)|kidney(2)|large_intestine(7)|lung(16)|ovary(4)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(2)	41						ATCTCAAGAGCGAAAAGTTGA	0.348																																					p.S414S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1242T	6						.						71.0	77.0	75.0					6																	28268873		2198	4298	6496	28376852	SO:0001819	synonymous_variant	84547	exon7			D88259	CCDS4648.1	6p22.1	2013-01-09			ENSG00000137338	ENSG00000137338		"""-"""	19398	protein-coding gene	gene with protein product							Standard	NM_001184743		Approved	HUCEP-4, dJ874C20.4, SCAND4	uc003nkz.3	Q96JS3	OTTHUMG00000014520	ENST00000405948.2:c.1242C>T	6.37:g.28268873C>T		Somatic		Capture	Illumina HiSeq	Phase_I	28376852	NM_001184743	Q53F43|Q6NTF5|Q8WWS4	Silent	SNP	ENST00000405948.2	37	CCDS4648.1																																																																																				0.348	PGBD1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040188.2		
C2	717	broad.mit.edu	37	6	31895931	31895931	+	Silent	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr6:31895931G>A	ENST00000299367.5	+	2	522	c.246G>A	c.(244-246)gcG>gcA	p.A82A	CFB_ENST00000556679.1_Silent_p.A82A|CFB_ENST00000456570.1_Silent_p.A82A|C2_ENST00000469372.1_Intron|CFB_ENST00000477310.1_Silent_p.A82A|C2_ENST00000418949.2_Silent_p.A82A|C2_ENST00000452323.2_Intron|C2_ENST00000442278.2_Intron	NM_000063.4	NP_000054.2	P06681	CO2_HUMAN	complement component 2	82	Sushi 1. {ECO:0000255|PROSITE- ProRule:PRU00302}.				complement activation (GO:0006956)|complement activation, classical pathway (GO:0006958)|innate immune response (GO:0045087)|positive regulation of apoptotic cell clearance (GO:2000427)|regulation of complement activation (GO:0030449)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	metal ion binding (GO:0046872)|serine-type endopeptidase activity (GO:0004252)	p.A82A(1)		haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(12)|ovary(1)|skin(2)|urinary_tract(2)	27		Ovarian(999;0.00965)		LUAD - Lung adenocarcinoma(999;0.247)		TGTCTAAGGCGGTCTGCAAAC	0.617																																					p.A82A												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G246A	6						.																																			32003910	SO:0001819	synonymous_variant	717	exon2				CCDS4728.1, CCDS54991.1, CCDS56416.1, CCDS75427.1, CCDS75428.1	6p21.3	2014-09-17			ENSG00000166278	ENSG00000166278		"""Complement system"""	1248	protein-coding gene	gene with protein product		613927					Standard	NM_001145903		Approved		uc011hbs.1	P06681	OTTHUMG00000031190	ENST00000299367.5:c.246G>A	6.37:g.31895931G>A		Somatic		Capture	Illumina HiSeq	Phase_I	32003910	NM_000063	B4DPF3|B4DV20|E9PFN7|O19694|Q13904	Silent	SNP	ENST00000299367.5	37	CCDS4728.1																																																																																				0.617	C2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076379.9		
DAXX	1616	broad.mit.edu	37	6	33286559	33286559	+	Silent	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr6:33286559G>A	ENST00000374542.5	-	8	2388	c.2184C>T	c.(2182-2184)tgC>tgT	p.C728C	DAXX_ENST00000266000.6_Silent_p.C728C|DAXX_ENST00000477162.1_5'Flank|ZBTB22_ENST00000418724.1_5'Flank|DAXX_ENST00000414083.2_Silent_p.C653C|ZBTB22_ENST00000431845.2_5'Flank	NM_001141969.1|NM_001141970.1|NM_001350.4	NP_001135441.1|NP_001135442.1|NP_001341.1	Q9UER7	DAXX_HUMAN	death-domain associated protein	728	Interaction with SPOP.				activation of JUN kinase activity (GO:0007257)|androgen receptor signaling pathway (GO:0030521)|apoptotic process (GO:0006915)|chromatin remodeling (GO:0006338)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|mitotic cytokinesis (GO:0000281)|negative regulation of transcription, DNA-templated (GO:0045892)|nucleosome assembly (GO:0006334)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of neuron death (GO:1901216)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of protein phosphorylation (GO:0001934)|regulation of protein ubiquitination (GO:0031396)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	chromosome, centromeric region (GO:0000775)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|heterochromatin (GO:0000792)|nucleus (GO:0005634)|PML body (GO:0016605)|SWI/SNF superfamily-type complex (GO:0070603)	androgen receptor binding (GO:0050681)|enzyme binding (GO:0019899)|heat shock protein binding (GO:0031072)|histone binding (GO:0042393)|p53 binding (GO:0002039)|protein homodimerization activity (GO:0042803)|protein kinase activator activity (GO:0030295)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|receptor signaling protein activity (GO:0005057)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)|ubiquitin protein ligase binding (GO:0031625)	p.C728C(1)		breast(1)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(5)|large_intestine(2)|lung(7)|ovary(3)|pancreas(18)|prostate(3)|skin(4)|upper_aerodigestive_tract(4)|urinary_tract(1)	55						CTTCTGGATCGCATTGTGTGG	0.473			"""Mis, F, N"""		Pancreatic neuroendocrine tumors. Paediatric GBM																																p.C740C			Rec	yes		6	6p21.3	1616	death-domain associated protein		E	.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C2220T	6						.						104.0	90.0	94.0					6																	33286559		2203	4300	6503	33394537	SO:0001819	synonymous_variant	1616	exon8			AF006041	CCDS4776.1, CCDS59008.1	6p21.3	2008-08-29	2008-08-29			ENSG00000204209			2681	protein-coding gene	gene with protein product		603186	"""death-associated protein 6"""			9407001, 9215629	Standard	NM_001141970		Approved	DAP6	uc011dre.2	Q9UER7		ENST00000374542.5:c.2184C>T	6.37:g.33286559G>A		Somatic		Capture	Illumina HiSeq	Phase_I	33394537	NM_001141970	B4E1I3|F5H082|O14747|O15141|O15208|Q5STK9|Q9BWI3	Silent	SNP	ENST00000374542.5	37	CCDS4776.1																																																																																				0.473	DAXX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076403.1		
ZNF76	7629	broad.mit.edu	37	6	35258057	35258057	+	Silent	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr6:35258057C>T	ENST00000373953.3	+	6	713	c.447C>T	c.(445-447)agC>agT	p.S149S	ZNF76_ENST00000339411.5_Silent_p.S149S|ZNF76_ENST00000440666.2_Silent_p.S123S	NM_003427.3	NP_003418.2	P36508	ZNF76_HUMAN	zinc finger protein 76	149					regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription from RNA polymerase III promoter (GO:0006359)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.S149S(1)		breast(1)|cervix(1)|kidney(1)|large_intestine(4)|lung(5)|ovary(1)|prostate(1)|skin(1)|stomach(1)	16						TTCATGACAGCCAGATTCCCC	0.532																																					p.S149S	Esophageal Squamous(52;92 1039 20612 23956 34676)											.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C447T	6						.						205.0	194.0	198.0					6																	35258057		2203	4300	6503	35366035	SO:0001819	synonymous_variant	7629	exon6			M91592	CCDS4801.1, CCDS75435.1	6p21.31	2013-01-08	2011-02-25		ENSG00000065029	ENSG00000065029		"""Zinc fingers, C2H2-type"""	13149	protein-coding gene	gene with protein product		194549	"""zinc finger protein 76 (expressed in testis)"""	D6S229E		1427894	Standard	XM_005249364		Approved	Zfp523, ZNF523	uc003oki.1	P36508	OTTHUMG00000014564	ENST00000373953.3:c.447C>T	6.37:g.35258057C>T		Somatic		Capture	Illumina HiSeq	Phase_I	35366035	NM_003427	Q9BQB2	Silent	SNP	ENST00000373953.3	37	CCDS4801.1																																																																																				0.532	ZNF76-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040279.2	NM_003427	
ZNF76	7629	broad.mit.edu	37	6	35260380	35260380	+	Silent	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr6:35260380C>T	ENST00000373953.3	+	10	1247	c.981C>T	c.(979-981)acC>acT	p.T327T	ZNF76_ENST00000339411.5_Silent_p.T327T|ZNF76_ENST00000440666.2_Silent_p.T301T	NM_003427.3	NP_003418.2	P36508	ZNF76_HUMAN	zinc finger protein 76	327					regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription from RNA polymerase III promoter (GO:0006359)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.T327T(1)		breast(1)|cervix(1)|kidney(1)|large_intestine(4)|lung(5)|ovary(1)|prostate(1)|skin(1)|stomach(1)	16						AACGCTTCACCGAGTACTCGA	0.627																																					p.T327T	Esophageal Squamous(52;92 1039 20612 23956 34676)											.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C981T	6						.						88.0	66.0	73.0					6																	35260380		2203	4300	6503	35368358	SO:0001819	synonymous_variant	7629	exon10			M91592	CCDS4801.1, CCDS75435.1	6p21.31	2013-01-08	2011-02-25		ENSG00000065029	ENSG00000065029		"""Zinc fingers, C2H2-type"""	13149	protein-coding gene	gene with protein product		194549	"""zinc finger protein 76 (expressed in testis)"""	D6S229E		1427894	Standard	XM_005249364		Approved	Zfp523, ZNF523	uc003oki.1	P36508	OTTHUMG00000014564	ENST00000373953.3:c.981C>T	6.37:g.35260380C>T		Somatic		Capture	Illumina HiSeq	Phase_I	35368358	NM_003427	Q9BQB2	Silent	SNP	ENST00000373953.3	37	CCDS4801.1																																																																																				0.627	ZNF76-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040279.2	NM_003427	
TEAD3	7005	broad.mit.edu	37	6	35444120	35444120	+	Nonsense_Mutation	SNP	C	C	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr6:35444120C>A	ENST00000402886.3	-	7	658	c.505G>T	c.(505-507)Gag>Tag	p.E169*	TEAD3_ENST00000338863.7_Nonsense_Mutation_p.E229*			Q99594	TEAD3_HUMAN	TEA domain family member 3	229	Pro-rich.				female pregnancy (GO:0007565)|gene expression (GO:0010467)|hippo signaling (GO:0035329)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription initiation from RNA polymerase II promoter (GO:0006367)	nucleoplasm (GO:0005654)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|RNA polymerase II transcription factor binding (GO:0001085)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.E229*(1)		central_nervous_system(1)|large_intestine(1)|lung(5)|ovary(1)|prostate(1)|urinary_tract(1)	10						GCTGAATACTCCAGGAGCCGC	0.642																																					p.E229X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.G685T	6						.						33.0	42.0	39.0					6																	35444120		2004	4177	6181	35552098	SO:0001587	stop_gained	7005	exon9			X94439	CCDS47414.1	6p21.2	2008-07-28			ENSG00000007866	ENSG00000007866			11716	protein-coding gene	gene with protein product		603170		TEAD5		9889009, 9148898	Standard	NM_003214		Approved	TEF-5, ETFR-1	uc003oku.4	Q99594	OTTHUMG00000014571	ENST00000402886.3:c.505G>T	6.37:g.35444120C>A	ENSP00000384577:p.Glu169*	Somatic		Capture	Illumina HiSeq	Phase_I	35552098	NM_003214	O95910|Q5BJG7|Q8N6Y4	Nonsense_Mutation	SNP	ENST00000402886.3	37		.	.	.	.	.	.	.	.	.	.	C	19.46	3.832669	0.71258	.	.	ENSG00000007866	ENST00000338863;ENST00000402886;ENST00000373905;ENST00000433586	.	.	.	4.94	4.94	0.65067	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.66056	D	0.02	-29.9588	17.3306	0.87262	0.0:1.0:0.0:0.0	.	.	.	.	X	229;169;245;140	.	ENSP00000345772:E229X	E	-	1	0	TEAD3	35552098	1.000000	0.71417	0.852000	0.33557	0.711000	0.40976	7.577000	0.82486	2.571000	0.86741	0.561000	0.74099	GAG		0.642	TEAD3-005	NOVEL	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000316961.2		
LHFPL5	222662	broad.mit.edu	37	6	35773652	35773652	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr6:35773652G>A	ENST00000373853.1	+	1	583	c.205G>A	c.(205-207)Gtg>Atg	p.V69M	LHFPL5_ENST00000360215.1_Missense_Mutation_p.V69M			Q8TAF8	TMHS_HUMAN	lipoma HMGIC fusion partner-like 5	69					auditory receptor cell stereocilium organization (GO:0060088)|detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|ion transport (GO:0006811)	apical plasma membrane (GO:0016324)|integral component of membrane (GO:0016021)|stereocilium bundle tip (GO:0032426)		p.V69M(1)		endometrium(4)|large_intestine(4)|lung(7)|prostate(2)|skin(2)|urinary_tract(1)	20						CTCCTACTGCGTGGGTAACGT	0.587																																					p.V69M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G205A	6						.						232.0	212.0	219.0					6																	35773652		2203	4300	6503	35881630	SO:0001583	missense	222662	exon1			BC028630	CCDS4812.1	6p21.31	2014-01-28				ENSG00000197753			21253	protein-coding gene	gene with protein product		609427	"""deafness, autosomal recessive 67"""	DFNB67		16459341	Standard	NM_182548		Approved	MGC33835, dJ510O8.8, Tmhs	uc003olg.1	Q8TAF8		ENST00000373853.1:c.205G>A	6.37:g.35773652G>A	ENSP00000362960:p.Val69Met	Somatic		Capture	Illumina HiSeq	Phase_I	35881630	NM_182548	B3KX66	Missense_Mutation	SNP	ENST00000373853.1	37	CCDS4812.1	.	.	.	.	.	.	.	.	.	.	g	23.0	4.368478	0.82463	.	.	ENSG00000197753	ENST00000373853;ENST00000360215	T;T	0.72505	-0.66;-0.66	5.57	4.69	0.59074	.	0.052718	0.64402	D	0.000001	T	0.49218	0.1544	L	0.50333	1.59	0.41048	D	0.98528	D	0.53462	0.96	B	0.44108	0.441	T	0.54207	-0.8328	10	0.30078	T	0.28	-24.4614	5.3237	0.15895	0.2741:0.0:0.7259:0.0	.	69	Q8TAF8	TMHS_HUMAN	M	69	ENSP00000362960:V69M;ENSP00000353346:V69M	ENSP00000353346:V69M	V	+	1	0	LHFPL5	35881630	1.000000	0.71417	1.000000	0.80357	0.896000	0.52359	4.394000	0.59671	2.640000	0.89533	0.537000	0.68136	GTG		0.587	LHFPL5-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040323.1	NM_182548	
SLC26A8	116369	broad.mit.edu	37	6	35923016	35923016	+	Silent	SNP	C	C	T	rs115593646	byFrequency	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr6:35923016C>T	ENST00000490799.1	-	17	2498	c.2145G>A	c.(2143-2145)gcG>gcA	p.A715A	SLC26A8_ENST00000355574.2_Silent_p.A715A|SLC26A8_ENST00000394602.2_Silent_p.A610A	NM_052961.3	NP_443193.1			solute carrier family 26 (anion exchanger), member 8									p.A715A(1)		breast(1)|central_nervous_system(1)|cervix(2)|endometrium(2)|kidney(4)|large_intestine(6)|lung(16)|ovary(3)|prostate(6)|skin(3)|upper_aerodigestive_tract(2)	46						GCAGTAGAGACGCATCTGAGT	0.498													c|||	7	0.00139776	0.0	0.0101	5008	,	,		20927	0.0		0.0	False		,,,				2504	0.0				p.A715A												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G2145A	6						.						155.0	144.0	148.0					6																	35923016		2203	4300	6503	36030994	SO:0001819	synonymous_variant	116369	exon17			AF331522	CCDS4813.1, CCDS4814.1	6p21	2013-07-18	2013-07-18		ENSG00000112053	ENSG00000112053		"""Solute carriers"""	14468	protein-coding gene	gene with protein product		608480	"""solute carrier family 26, member 8"""			11834742, 11829495	Standard	NM_001193476		Approved		uc003olm.3	Q96RN1	OTTHUMG00000014586	ENST00000490799.1:c.2145G>A	6.37:g.35923016C>T		Somatic		Capture	Illumina HiSeq	Phase_I	36030994	NM_052961		Silent	SNP	ENST00000490799.1	37	CCDS4813.1																																																																																				0.498	SLC26A8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040325.2		
TBC1D22B	55633	broad.mit.edu	37	6	37284924	37284924	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr6:37284924T>C	ENST00000373491.3	+	12	1477	c.1331T>C	c.(1330-1332)gTg>gCg	p.V444A		NM_017772.2	NP_060242.2	Q9NU19	TB22B_HUMAN	TBC1 domain family, member 22B	444							Rab GTPase activator activity (GO:0005097)	p.V444A(1)		breast(1)|endometrium(1)|large_intestine(2)|lung(10)|prostate(1)	15			OV - Ovarian serous cystadenocarcinoma(102;0.241)			CATCTCTACGTGTGTGCAGCC	0.483																																					p.V444A												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T1331C	6						.						111.0	91.0	98.0					6																	37284924		2202	4299	6501	37392902	SO:0001583	missense	55633	exon12			AK096340	CCDS4832.1	6p21.2	2005-01-05	2005-01-05	2005-01-05	ENSG00000065491	ENSG00000065491			21602	protein-coding gene	gene with protein product			"""chromosome 6 open reading frame 197"""	C6orf197			Standard	NM_017772		Approved	FLJ20337, dJ744I24.2	uc003onn.3	Q9NU19	OTTHUMG00000014619	ENST00000373491.3:c.1331T>C	6.37:g.37284924T>C	ENSP00000362590:p.Val444Ala	Somatic		Capture	Illumina HiSeq	Phase_I	37392902	NM_017772	A8KA28|Q32MQ8|Q5VUK9|Q6P4C3|Q7Z6P7|Q9BPV6|Q9BUT5|Q9NXB6	Missense_Mutation	SNP	ENST00000373491.3	37	CCDS4832.1	.	.	.	.	.	.	.	.	.	.	T	16.83	3.231262	0.58777	.	.	ENSG00000065491	ENST00000373491	T	0.29655	1.56	5.75	5.75	0.90469	Rab-GAP/TBC domain (3);	0.000000	0.85682	D	0.000000	T	0.57562	0.2062	M	0.91872	3.25	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	T	0.69117	-0.5230	10	0.87932	D	0	.	15.0342	0.71731	0.0:0.0:0.0:1.0	.	444;444	A8KA28;Q9NU19	.;TB22B_HUMAN	A	444	ENSP00000362590:V444A	ENSP00000362590:V444A	V	+	2	0	TBC1D22B	37392902	1.000000	0.71417	0.984000	0.44739	0.003000	0.03518	7.642000	0.83385	2.181000	0.69327	0.455000	0.32223	GTG		0.483	TBC1D22B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040402.1	NM_017772	
DNAH8	1769	broad.mit.edu	37	6	38885713	38885713	+	Missense_Mutation	SNP	A	A	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr6:38885713A>T	ENST00000359357.3	+	68	9924	c.9670A>T	c.(9670-9672)Aca>Tca	p.T3224S	DNAH8_ENST00000449981.2_Missense_Mutation_p.T3441S|DNAH8_ENST00000441566.1_Missense_Mutation_p.T3188S			Q96JB1	DYH8_HUMAN	dynein, axonemal, heavy chain 8	3224	Stalk. {ECO:0000250}.				cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)	p.T3224S(2)		NS(7)|breast(9)|central_nervous_system(4)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(3)|kidney(16)|large_intestine(44)|liver(4)|lung(101)|ovary(7)|pancreas(2)|prostate(8)|skin(28)|stomach(4)|upper_aerodigestive_tract(6)|urinary_tract(4)	260						GATGAGTGCAACAGGATTCCT	0.328																																					p.T3224S												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.A9670T	6						.						55.0	60.0	58.0					6																	38885713		2203	4300	6503	38993691	SO:0001583	missense	1769	exon68			Z83806	CCDS75447.1	6p21.2	2012-04-19	2006-09-04		ENSG00000124721	ENSG00000124721		"""Axonemal dyneins"""	2952	protein-coding gene	gene with protein product		603337	"""dynein, axonemal, heavy polypeptide 8"""			9373155	Standard	NM_001206927		Approved	hdhc9	uc021yzh.1	Q96JB1	OTTHUMG00000016253	ENST00000359357.3:c.9670A>T	6.37:g.38885713A>T	ENSP00000352312:p.Thr3224Ser	Somatic		Capture	Illumina HiSeq	Phase_I	38993691	NM_001371	O00438|Q5JYI2|Q5T2M3|Q5T2M4|Q5TG00|Q9UEM4	Missense_Mutation	SNP	ENST00000359357.3	37		.	.	.	.	.	.	.	.	.	.	A	4.794	0.147577	0.09134	.	.	ENSG00000124721	ENST00000449981;ENST00000327475;ENST00000359357;ENST00000441566	T;T;T	0.51574	0.7;0.7;0.7	5.82	1.94	0.25998	Dynein heavy chain, coiled coil stalk (1);	0.346876	0.29980	N	0.010702	T	0.03564	0.0102	N	0.01209	-0.955	0.19945	N	0.999941	B	0.02656	0.0	B	0.06405	0.002	T	0.39396	-0.9616	10	0.07030	T	0.85	.	1.9795	0.03423	0.5423:0.1741:0.1671:0.1165	.	3224	Q96JB1	DYH8_HUMAN	S	3429;3429;3224;3188	ENSP00000333363:T3429S;ENSP00000352312:T3224S;ENSP00000402294:T3188S	ENSP00000333363:T3429S	T	+	1	0	DNAH8	38993691	0.001000	0.12720	0.962000	0.40283	0.984000	0.73092	0.092000	0.15066	1.025000	0.39708	0.528000	0.53228	ACA		0.328	DNAH8-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000043574.1	NM_001206927	
DAAM2	23500	broad.mit.edu	37	6	39866712	39866712	+	Splice_Site	SNP	T	T	C			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr6:39866712T>C	ENST00000398904.2	+	22	2860	c.2678T>C	c.(2677-2679)gTg>gCg	p.V893A	RP11-61I13.3_ENST00000420293.1_RNA|RP11-61I13.3_ENST00000606829.1_RNA|DAAM2_ENST00000538976.1_Splice_Site_p.V893A|RP11-61I13.3_ENST00000430595.1_RNA|DAAM2_ENST00000274867.4_Splice_Site_p.V893A|RP11-61I13.3_ENST00000437947.1_RNA			Q86T65	DAAM2_HUMAN	dishevelled associated activator of morphogenesis 2	893	FH2. {ECO:0000255|PROSITE- ProRule:PRU00774}.				actin cytoskeleton organization (GO:0030036)|determination of left/right symmetry (GO:0007368)			p.V893A(1)		NS(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(9)|lung(18)|ovary(2)|prostate(4)|skin(2)|upper_aerodigestive_tract(5)	49	Ovarian(28;0.0355)|Colorectal(47;0.196)					GCGGTGGAGGTGGTGAGTACC	0.562																																					p.V893A												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T2678C	6						.						86.0	104.0	98.0					6																	39866712		2075	4220	6295	39974690	SO:0001630	splice_region_variant	23500	exon22			AB002379	CCDS54999.1, CCDS56426.1	6p21.1	2008-07-30			ENSG00000146122	ENSG00000146122			18143	protein-coding gene	gene with protein product		606627				11779461, 12632087	Standard	NM_015345		Approved	KIAA0381	uc003oow.3	Q86T65	OTTHUMG00000014653	ENST00000398904.2:c.2679+1T>C	6.37:g.39866712T>C		Somatic		Capture	Illumina HiSeq	Phase_I	39974690	NM_015345	G5EA45|Q5T4T8|Q5T4U0|Q9NQI5|Q9Y4G0	Missense_Mutation	SNP	ENST00000398904.2	37	CCDS56426.1	.	.	.	.	.	.	.	.	.	.	T	9.350	1.065233	0.20067	.	.	ENSG00000146122	ENST00000274867;ENST00000398904;ENST00000538976	T;T;T	0.15952	2.38;2.38;2.38	5.35	2.89	0.33648	Actin-binding FH2/DRF autoregulatory (1);Actin-binding FH2 (3);	0.702636	0.13745	N	0.365672	T	0.02610	0.0079	N	0.16130	0.375	0.80722	D	1	B;B	0.20988	0.019;0.05	B;B	0.24701	0.032;0.055	T	0.38200	-0.9672	10	0.16420	T	0.52	.	3.6066	0.08045	0.1612:0.1715:0.0:0.6673	.	893;893	G5EA45;Q86T65	.;DAAM2_HUMAN	A	893	ENSP00000274867:V893A;ENSP00000381876:V893A;ENSP00000437808:V893A	ENSP00000274867:V893A	V	+	2	0	DAAM2	39974690	1.000000	0.71417	1.000000	0.80357	0.946000	0.59487	0.754000	0.26390	0.443000	0.26582	0.533000	0.62120	GTG		0.562	DAAM2-003	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000280648.1		Missense_Mutation
FRS3	10817	broad.mit.edu	37	6	41738516	41738516	+	Missense_Mutation	SNP	T	T	G			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr6:41738516T>G	ENST00000373018.3	-	7	1571	c.1320A>C	c.(1318-1320)caA>caC	p.Q440H	FRS3_ENST00000259748.2_Missense_Mutation_p.Q440H	NM_006653.3	NP_006644.1	O43559	FRS3_HUMAN	fibroblast growth factor receptor substrate 3	440					fibroblast growth factor receptor signaling pathway (GO:0008543)|signal transduction (GO:0007165)	plasma membrane (GO:0005886)	fibroblast growth factor receptor binding (GO:0005104)	p.Q440H(1)		breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(4)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	14	Ovarian(28;0.0355)|Colorectal(47;0.121)		Epithelial(12;8.38e-05)|STAD - Stomach adenocarcinoma(11;0.000204)|Colorectal(64;0.00062)|COAD - Colon adenocarcinoma(64;0.00152)			GCATGGGGGCTTGGGGGCTCG	0.647																																					p.Q440H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A1320C	6						.						42.0	51.0	48.0					6																	41738516		2203	4299	6502	41846494	SO:0001583	missense	10817	exon7			AF036718	CCDS4860.1	6p21.1	2010-08-05			ENSG00000137218	ENSG00000137218			16970	protein-coding gene	gene with protein product		607744				8761293, 9660748	Standard	NM_006653		Approved	SNT-2, FRS2beta, FRS2B	uc003orc.1	O43559	OTTHUMG00000014686	ENST00000373018.3:c.1320A>C	6.37:g.41738516T>G	ENSP00000362109:p.Gln440His	Somatic		Capture	Illumina HiSeq	Phase_I	41846494	NM_006653	Q5T3D5	Missense_Mutation	SNP	ENST00000373018.3	37	CCDS4860.1	.	.	.	.	.	.	.	.	.	.	T	9.475	1.096521	0.20552	.	.	ENSG00000137218	ENST00000373018;ENST00000259748	T;T	0.22945	1.93;1.93	5.33	-9.04	0.00734	.	2.991180	0.00674	N	0.000640	T	0.02083	0.0065	N	0.08118	0	0.09310	N	1	B	0.30709	0.291	B	0.24541	0.054	T	0.20472	-1.0274	10	0.13108	T	0.6	0.1934	2.5941	0.04849	0.2281:0.3736:0.2576:0.1407	.	440	O43559	FRS3_HUMAN	H	440	ENSP00000362109:Q440H;ENSP00000259748:Q440H	ENSP00000259748:Q440H	Q	-	3	2	FRS3	41846494	0.000000	0.05858	0.000000	0.03702	0.927000	0.56198	-0.923000	0.04000	-1.005000	0.03417	-0.250000	0.11733	CAA		0.647	FRS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040532.2	NM_006653	
CUL7	9820	broad.mit.edu	37	6	43018059	43018059	+	Silent	SNP	A	A	G			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr6:43018059A>G	ENST00000265348.3	-	5	1396	c.1311T>C	c.(1309-1311)atT>atC	p.I437I	CUL7_ENST00000478630.1_5'Flank|CUL7_ENST00000535468.1_Silent_p.I521I			Q14999	CUL7_HUMAN	cullin 7	437	Interaction with TP53.				activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|epithelial to mesenchymal transition (GO:0001837)|Golgi organization (GO:0007030)|microtubule cytoskeleton organization (GO:0000226)|mitotic cytokinesis (GO:0000281)|placenta development (GO:0001890)|positive regulation of dendrite morphogenesis (GO:0050775)|protein ubiquitination (GO:0016567)|proteolysis (GO:0006508)|regulation of mitosis (GO:0007088)|ubiquitin-dependent protein catabolic process (GO:0006511)|vasculogenesis (GO:0001570)|viral process (GO:0016032)	3M complex (GO:1990393)|anaphase-promoting complex (GO:0005680)|centrosome (GO:0005813)|Cul7-RING ubiquitin ligase complex (GO:0031467)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)		p.I437I(1)		breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(8)|liver(1)|lung(11)|ovary(3)|prostate(2)|skin(3)|stomach(1)|urinary_tract(1)	49			all cancers(41;0.00231)|Colorectal(64;0.00237)|COAD - Colon adenocarcinoma(64;0.00473)|OV - Ovarian serous cystadenocarcinoma(102;0.0442)|KIRC - Kidney renal clear cell carcinoma(15;0.133)|Kidney(15;0.188)			CCATGTCCTCAATGTCTTCCT	0.542																																					p.I437I												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.T1311C	6						.						198.0	167.0	178.0					6																	43018059		2203	4300	6503	43126037	SO:0001819	synonymous_variant	9820	exon5			BC033647	CCDS4881.1, CCDS55003.1	6p21.1	2011-05-24	2004-03-22	2004-03-22	ENSG00000044090	ENSG00000044090			21024	protein-coding gene	gene with protein product		609577	"""KIAA0076"""	KIAA0076		12481031, 12904573	Standard	NM_014780		Approved	dJ20C7.5	uc011dvb.2	Q14999	OTTHUMG00000014718	ENST00000265348.3:c.1311T>C	6.37:g.43018059A>G		Somatic		Capture	Illumina HiSeq	Phase_I	43126037	NM_014780	B4DYZ0|F5H0L1|Q5T654	Silent	SNP	ENST00000265348.3	37	CCDS4881.1																																																																																				0.542	CUL7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040575.1	NM_014780	
SRF	6722	broad.mit.edu	37	6	43143699	43143699	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr6:43143699A>G	ENST00000265354.4	+	3	1394	c.1036A>G	c.(1036-1038)Atg>Gtg	p.M346V	SRF_ENST00000457278.2_Missense_Mutation_p.M142V	NM_003131.2	NP_003122.1	P11831	SRF_HUMAN	serum response factor (c-fos serum response element-binding transcription factor)	346					angiogenesis involved in wound healing (GO:0060055)|associative learning (GO:0008306)|cardiac myofibril assembly (GO:0055003)|cardiac vascular smooth muscle cell differentiation (GO:0060947)|cell migration involved in sprouting angiogenesis (GO:0002042)|cell-matrix adhesion (GO:0007160)|cellular response to glucose stimulus (GO:0071333)|cellular senescence (GO:0090398)|contractile actin filament bundle assembly (GO:0030038)|developmental growth (GO:0048589)|dorsal aorta morphogenesis (GO:0035912)|epithelial cell-cell adhesion (GO:0090136)|epithelial structure maintenance (GO:0010669)|erythrocyte development (GO:0048821)|eyelid development in camera-type eye (GO:0061029)|heart development (GO:0007507)|heart looping (GO:0001947)|heart trabecula formation (GO:0060347)|hematopoietic stem cell differentiation (GO:0060218)|hippocampus development (GO:0021766)|long term synaptic depression (GO:0060292)|long-term memory (GO:0007616)|megakaryocyte development (GO:0035855)|mesoderm formation (GO:0001707)|morphogenesis of an epithelial sheet (GO:0002011)|mRNA transcription from RNA polymerase II promoter (GO:0042789)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of beta-amyloid clearance (GO:1900222)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|neuron development (GO:0048666)|neuron migration (GO:0001764)|neuron projection development (GO:0031175)|patterning of blood vessels (GO:0001569)|platelet activation (GO:0030168)|platelet formation (GO:0030220)|positive regulation of cell differentiation (GO:0045597)|positive regulation of filopodium assembly (GO:0051491)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of smooth muscle contraction (GO:0045987)|positive regulation of transcription by glucose (GO:0046016)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase II promoter involved in myocardial precursor cell differentiation (GO:0003257)|positive regulation of transcription initiation from RNA polymerase II promoter (GO:0060261)|positive regulation of transcription via serum response element binding (GO:0010735)|positive thymic T cell selection (GO:0045059)|primitive streak formation (GO:0090009)|regulation of cell adhesion (GO:0030155)|regulation of smooth muscle cell differentiation (GO:0051150)|regulation of water loss via skin (GO:0033561)|response to cytokine (GO:0034097)|response to hormone (GO:0009725)|response to hypoxia (GO:0001666)|response to toxic substance (GO:0009636)|sarcomere organization (GO:0045214)|skin morphogenesis (GO:0043589)|stress fiber assembly (GO:0043149)|tangential migration from the subventricular zone to the olfactory bulb (GO:0022028)|tight junction assembly (GO:0070830)|transcription from RNA polymerase II promoter (GO:0006366)|trophectodermal cell differentiation (GO:0001829)	cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)	chromatin DNA binding (GO:0031490)|protein homodimerization activity (GO:0042803)|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)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|RNA polymerase II transcription factor binding transcription factor activity (GO:0001076)|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)|serum response element binding (GO:0010736)|transcription factor binding (GO:0008134)	p.M346V(1)		breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(3)|lung(2)|ovary(1)	12			Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.011)|OV - Ovarian serous cystadenocarcinoma(102;0.0423)			CTTCACCCTCATGCCTGGTGA	0.572																																					p.M346V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A1036G	6						.						47.0	44.0	45.0					6																	43143699		2203	4300	6503	43251677	SO:0001583	missense	6722	exon3			J03161	CCDS4889.1	6p	2008-02-05			ENSG00000112658	ENSG00000112658			11291	protein-coding gene	gene with protein product		600589				3203386	Standard	NM_003131		Approved	MCM1	uc003oui.3	P11831	OTTHUMG00000014722	ENST00000265354.4:c.1036A>G	6.37:g.43143699A>G	ENSP00000265354:p.Met346Val	Somatic		Capture	Illumina HiSeq	Phase_I	43251677	NM_003131	Q5T648	Missense_Mutation	SNP	ENST00000265354.4	37	CCDS4889.1	.	.	.	.	.	.	.	.	.	.	A	18.43	3.621408	0.66787	.	.	ENSG00000112658	ENST00000265354;ENST00000457278	D	0.83914	-1.78	5.09	5.09	0.68999	.	0.000000	0.85682	D	0.000000	D	0.83968	0.5369	L	0.50333	1.59	0.58432	D	0.999995	P	0.49447	0.924	P	0.60682	0.878	D	0.84875	0.0827	10	0.46703	T	0.11	-3.8603	14.8525	0.70309	1.0:0.0:0.0:0.0	.	346	P11831	SRF_HUMAN	V	346;142	ENSP00000265354:M346V	ENSP00000265354:M346V	M	+	1	0	SRF	43251677	1.000000	0.71417	1.000000	0.80357	0.547000	0.35210	8.880000	0.92407	1.913000	0.55393	0.459000	0.35465	ATG		0.572	SRF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040581.1	NM_003131	
YIPF3	25844	broad.mit.edu	37	6	43483725	43483725	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr6:43483725C>T	ENST00000372422.2	-	2	372	c.190G>A	c.(190-192)Gct>Act	p.A64T	POLR1C_ENST00000372389.3_5'Flank|POLR1C_ENST00000304004.3_5'Flank|YIPF3_ENST00000506469.1_Missense_Mutation_p.A70T|POLR1C_ENST00000372344.2_5'Flank	NM_015388.3	NP_056203.2	Q9GZM5	YIPF3_HUMAN	Yip1 domain family, member 3	64					cell differentiation (GO:0030154)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|plasma membrane (GO:0005886)|transport vesicle (GO:0030133)		p.A64T(1)		large_intestine(2)|lung(4)|pancreas(1)|prostate(1)|skin(1)	9	all_cancers(18;3.79e-05)|Lung NSC(15;0.00217)|all_lung(25;0.00536)		Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.00736)|OV - Ovarian serous cystadenocarcinoma(102;0.0711)			GCTGCATCAGCGTCTACTTCT	0.557																																					p.A64T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G190A	6						.						89.0	82.0	84.0					6																	43483725		2203	4300	6503	43591703	SO:0001583	missense	25844	exon2			AK000946	CCDS4899.1	6p21.1	2009-10-06	2005-07-04	2005-07-04	ENSG00000137207	ENSG00000137207		"""Yip1 domain family"""	21023	protein-coding gene	gene with protein product		609775	"""chromosome 6 open reading frame 109"""	C6orf109			Standard	NM_015388		Approved	DKFZp566C243, KLIP1, dJ337H4.3, FinGER3	uc003ovl.2	Q9GZM5	OTTHUMG00000014738	ENST00000372422.2:c.190G>A	6.37:g.43483725C>T	ENSP00000361499:p.Ala64Thr	Somatic		Capture	Illumina HiSeq	Phase_I	43591703	NM_015388	Q5JTD2|Q6FI85|Q8NI57|Q9NWE3|Q9Y3U9	Missense_Mutation	SNP	ENST00000372422.2	37	CCDS4899.1	.	.	.	.	.	.	.	.	.	.	C	22.8	4.340093	0.81911	.	.	ENSG00000137207	ENST00000372422;ENST00000504851;ENST00000506469;ENST00000503972;ENST00000511831	T;T;T	0.46451	0.87;0.87;0.88	5.7	5.7	0.88788	.	0.113012	0.64402	D	0.000013	T	0.16811	0.0404	L	0.29908	0.895	0.46011	D	0.998813	P;B;B	0.38020	0.615;0.306;0.306	B;B;B	0.31337	0.128;0.089;0.089	T	0.04796	-1.0926	10	0.14656	T	0.56	.	18.009	0.89217	0.0:1.0:0.0:0.0	.	64;70;64	D6RED8;E7EQR8;Q9GZM5	.;.;YIPF3_HUMAN	T	64;64;70;64;29	ENSP00000361499:A64T;ENSP00000425494:A70T;ENSP00000421461:A64T	ENSP00000259737:A64T	A	-	1	0	YIPF3	43591703	0.994000	0.37717	0.989000	0.46669	0.976000	0.68499	3.071000	0.50041	2.687000	0.91594	0.460000	0.39030	GCT		0.557	YIPF3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040639.2	NM_015388	
XPO5	57510	broad.mit.edu	37	6	43501741	43501741	+	Silent	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr6:43501741G>A	ENST00000265351.7	-	21	2556	c.2346C>T	c.(2344-2346)acC>acT	p.T782T		NM_020750.2	NP_065801.1	Q9HAV4	XPO5_HUMAN	exportin 5	782					gene expression (GO:0010467)|gene silencing by RNA (GO:0031047)|protein export from nucleus (GO:0006611)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|protein transporter activity (GO:0008565)|RNA binding (GO:0003723)|tRNA binding (GO:0000049)	p.T782T(1)		NS(1)|breast(2)|central_nervous_system(1)|endometrium(2)|kidney(8)|large_intestine(4)|lung(10)|ovary(1)|skin(3)|stomach(1)|urinary_tract(1)	34	all_cancers(18;2.08e-05)|Lung NSC(15;0.000907)|all_lung(25;0.00243)		all cancers(41;0.000321)|Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|OV - Ovarian serous cystadenocarcinoma(102;0.0524)			ATGTATTGTGGGTTCTGAAAG	0.408																																					p.T782T												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C2346T	6						.						125.0	119.0	121.0					6																	43501741		1847	4097	5944	43609719	SO:0001819	synonymous_variant	57510	exon21			AB033117	CCDS47430.1	6p21.1	2011-04-13			ENSG00000124571	ENSG00000124571		"""Exportins"""	17675	protein-coding gene	gene with protein product		607845				11777942, 12426392	Standard	NM_020750		Approved	KIAA1291	uc003ovp.3	Q9HAV4	OTTHUMG00000014742	ENST00000265351.7:c.2346C>T	6.37:g.43501741G>A		Somatic		Capture	Illumina HiSeq	Phase_I	43609719	NM_020750	Q5JTE6|Q96G48|Q96HN3|Q9BWM6|Q9BZV5|Q9H9M4|Q9NT89|Q9NW39|Q9ULC9	Silent	SNP	ENST00000265351.7	37	CCDS47430.1																																																																																				0.408	XPO5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040657.2	NM_020750	
TFAP2B	7021	broad.mit.edu	37	6	50791468	50791468	+	Missense_Mutation	SNP	G	G	C			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	C	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr6:50791468G>C	ENST00000393655.3	+	2	599	c.430G>C	c.(430-432)Gtc>Ctc	p.V144L	TFAP2B_ENST00000263046.4_Missense_Mutation_p.V153L|TFAP2B_ENST00000489228.1_3'UTR	NM_003221.3	NP_003212.2	Q92481	AP2B_HUMAN	transcription factor AP-2 beta (activating enhancer binding protein 2 beta)	144					aorta morphogenesis (GO:0035909)|calcium ion homeostasis (GO:0055074)|cellular ammonia homeostasis (GO:0097275)|cellular creatinine homeostasis (GO:0097276)|cellular urea homeostasis (GO:0097277)|collecting duct development (GO:0072044)|distal tubule development (GO:0072017)|ductus arteriosus closure (GO:0097070)|fat cell differentiation (GO:0045444)|forelimb morphogenesis (GO:0035136)|glucose homeostasis (GO:0042593)|glucose metabolic process (GO:0006006)|hindlimb morphogenesis (GO:0035137)|kidney development (GO:0001822)|magnesium ion homeostasis (GO:0010960)|metanephric nephron development (GO:0072210)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|phosphate ion homeostasis (GO:0055062)|positive regulation of cell proliferation (GO:0008284)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of urine volume (GO:0035810)|potassium ion homeostasis (GO:0055075)|regulation of BMP signaling pathway (GO:0030510)|regulation of cell differentiation (GO:0045595)|regulation of insulin secretion (GO:0050796)|regulation of transcription, DNA-templated (GO:0006355)|renal water homeostasis (GO:0003091)|response to drug (GO:0042493)|response to lithium ion (GO:0010226)|retina layer formation (GO:0010842)|skin development (GO:0043588)|sodium ion homeostasis (GO:0055078)|sympathetic nervous system development (GO:0048485)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|cysteine-type endopeptidase inhibitor activity involved in apoptotic process (GO:0043027)|DNA binding (GO:0003677)|enhancer sequence-specific DNA binding (GO:0001158)|protein dimerization activity (GO:0046983)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|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 core promoter sequence-specific DNA binding transcription factor activity (GO:0000983)|RNA polymerase II transcription coactivator activity (GO:0001105)|RNA polymerase II transcription corepressor activity (GO:0001106)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)	p.V144I(2)|p.V144L(1)		NS(1)|breast(2)|endometrium(6)|kidney(1)|large_intestine(11)|lung(16)|prostate(2)|upper_aerodigestive_tract(1)	40	Lung NSC(77;0.156)					CTACCACTCGGTCCGCCGGCC	0.716																																					p.V144L	Pancreas(116;1373 2332 5475 10752)											.	.	3	Substitution - Missense(3)	lung(2)|large_intestine(1)	c.G430C	6						.						9.0	11.0	10.0					6																	50791468		2179	4283	6462	50899427	SO:0001583	missense	7021	exon2			X95694	CCDS4934.2	6p12	2008-02-05	2001-11-28		ENSG00000008196	ENSG00000008196			11743	protein-coding gene	gene with protein product		601601	"""transcription factor AP-2 beta (activating enhancer-binding protein 2 beta)"""			7555706, 8661133	Standard	NM_003221		Approved	AP2-B	uc003pag.3	Q92481	OTTHUMG00000014836	ENST00000393655.3:c.430G>C	6.37:g.50791468G>C	ENSP00000377265:p.Val144Leu	Somatic		Capture	Illumina HiSeq	Phase_I	50899427	NM_003221	Q5JYX6|Q9NQ63|Q9NU99|Q9UJI7|Q9Y214|Q9Y3K3	Missense_Mutation	SNP	ENST00000393655.3	37	CCDS4934.2	.	.	.	.	.	.	.	.	.	.	G	29.4	5.004293	0.93287	.	.	ENSG00000008196	ENST00000393655;ENST00000344788;ENST00000263046	D;T;D	0.97378	-4.36;-1.15;-4.36	5.43	5.43	0.79202	.	0.000000	0.85682	D	0.000000	D	0.93884	0.8043	L	0.54323	1.7	0.80722	D	1	P	0.42692	0.787	B	0.38056	0.264	D	0.93413	0.6770	10	0.29301	T	0.29	-8.0845	19.2485	0.93913	0.0:0.0:1.0:0.0	.	144	Q92481	AP2B_HUMAN	L	144;142;153	ENSP00000377265:V144L;ENSP00000342252:V142L;ENSP00000263046:V153L	ENSP00000263046:V153L	V	+	1	0	TFAP2B	50899427	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.505000	0.97989	2.558000	0.86282	0.563000	0.77884	GTC		0.716	TFAP2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040886.3	NM_003221	
PKHD1	5314	broad.mit.edu	37	6	51875135	51875135	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr6:51875135A>G	ENST00000371117.3	-	35	5998	c.5723T>C	c.(5722-5724)aTa>aCa	p.I1908T	PKHD1_ENST00000340994.4_Missense_Mutation_p.I1908T	NM_138694.3	NP_619639.3	P08F94	PKHD1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)	1908					cellular calcium ion homeostasis (GO:0006874)|cilium assembly (GO:0042384)|homeostatic process (GO:0042592)|kidney development (GO:0001822)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cellular component movement (GO:0051271)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of protein kinase B signaling (GO:0051898)|positive regulation of cell proliferation (GO:0008284)|regulation of centrosome duplication (GO:0010824)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of TOR signaling (GO:0032006)|single organismal cell-cell adhesion (GO:0016337)	anchored component of external side of plasma membrane (GO:0031362)|apical plasma membrane (GO:0016324)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|mitotic spindle (GO:0072686)|perinuclear region of cytoplasm (GO:0048471)|primary cilium (GO:0072372)	receptor activity (GO:0004872)	p.I1908T(1)		NS(1)|autonomic_ganglia(1)|breast(8)|central_nervous_system(5)|cervix(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(59)|lung(139)|ovary(16)|prostate(8)|skin(20)|soft_tissue(1)|stomach(2)|upper_aerodigestive_tract(7)|urinary_tract(5)	304	Lung NSC(77;0.0605)					GCGTTTCCGTATCTCAGTAAT	0.383																																					p.I1908T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T5723C	6	GRCh37	CM054806	PKHD1	M		.						139.0	123.0	128.0					6																	51875135		2203	4300	6503	51983094	SO:0001583	missense	5314	exon35			AF480064	CCDS4935.1, CCDS4936.1	6p21.2-p12	2012-11-26	2003-04-16		ENSG00000170927	ENSG00000170927			9016	protein-coding gene	gene with protein product	"""tigmin"", ""polyductin"", ""fibrocystin"""	606702	"""TIG multiple domains 1"""	TIGM1		9503014	Standard	NM_138694		Approved	ARPKD, FCYT	uc003pah.1	P08F94	OTTHUMG00000014841	ENST00000371117.3:c.5723T>C	6.37:g.51875135A>G	ENSP00000360158:p.Ile1908Thr	Somatic		Capture	Illumina HiSeq	Phase_I	51983094	NM_170724	Q5VUA2|Q5VUA3|Q5VWV1|Q86Z26|Q8TCZ9	Missense_Mutation	SNP	ENST00000371117.3	37	CCDS4935.1	.	.	.	.	.	.	.	.	.	.	A	12.72	2.022726	0.35701	.	.	ENSG00000170927	ENST00000371117;ENST00000340994;ENST00000393616	D;D	0.88124	-2.14;-2.34	5.53	5.53	0.82687	.	0.000000	0.85682	D	0.000000	D	0.85630	0.5741	L	0.34521	1.04	0.39009	D	0.959517	D;D	0.76494	0.997;0.999	D;D	0.85130	0.981;0.997	D	0.83588	0.0121	10	0.15952	T	0.53	.	15.6556	0.77133	1.0:0.0:0.0:0.0	.	1908;1908	P08F94-2;P08F94	.;PKHD1_HUMAN	T	1908	ENSP00000360158:I1908T;ENSP00000341097:I1908T	ENSP00000341097:I1908T	I	-	2	0	PKHD1	51983094	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	7.135000	0.77276	2.099000	0.63709	0.455000	0.32223	ATA		0.383	PKHD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040893.1	NM_138694	
PAQR8	85315	broad.mit.edu	37	6	52268178	52268178	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr6:52268178G>A	ENST00000442253.2	+	2	341	c.167G>A	c.(166-168)cGc>cAc	p.R56H	PAQR8_ENST00000360726.3_Missense_Mutation_p.R56H	NM_133367.4	NP_588608.1	Q8TEZ7	MPRB_HUMAN	progestin and adipoQ receptor family member VIII	56					multicellular organismal development (GO:0007275)|oogenesis (GO:0048477)|response to steroid hormone (GO:0048545)|steroid hormone mediated signaling pathway (GO:0043401)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	steroid binding (GO:0005496)|steroid hormone receptor activity (GO:0003707)	p.R56H(1)		endometrium(1)|kidney(2)|large_intestine(1)|lung(9)|ovary(1)|skin(1)|urinary_tract(2)	17	Lung NSC(77;0.0875)					ACCGGCTACCGCCCCACGGGG	0.602																																					p.R56H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G167A	6						.						57.0	61.0	59.0					6																	52268178		2203	4300	6503	52376137	SO:0001583	missense	85315	exon2			AF347029	CCDS4941.1	6p12	2012-08-10	2005-05-20	2005-05-20	ENSG00000170915	ENSG00000170915			15708	protein-coding gene	gene with protein product		607780	"""chromosome 6 open reading frame 33"""	C6orf33		11676489, 12574519	Standard	NM_133367		Approved	LMPB1, MPRB	uc003pao.4	Q8TEZ7	OTTHUMG00000014846	ENST00000442253.2:c.167G>A	6.37:g.52268178G>A	ENSP00000406197:p.Arg56His	Somatic		Capture	Illumina HiSeq	Phase_I	52376137	NM_133367	B2RCF6|Q86WL0|Q8N6D3|Q9HD02	Missense_Mutation	SNP	ENST00000442253.2	37	CCDS4941.1	.	.	.	.	.	.	.	.	.	.	G	29.3	4.995145	0.93167	.	.	ENSG00000170915	ENST00000512121;ENST00000442253;ENST00000360726	T;T;T	0.73152	-0.72;0.32;0.32	5.3	5.3	0.74995	.	0.000000	0.85682	D	0.000000	D	0.85137	0.5628	M	0.89478	3.035	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.87883	0.2679	10	0.87932	D	0	-20.4393	17.9429	0.89030	0.0:0.0:1.0:0.0	.	56	Q8TEZ7	MPRB_HUMAN	H	56	ENSP00000427161:R56H;ENSP00000406197:R56H;ENSP00000353953:R56H	ENSP00000353953:R56H	R	+	2	0	PAQR8	52376137	1.000000	0.71417	0.999000	0.59377	0.926000	0.56050	9.869000	0.99810	2.485000	0.83878	0.655000	0.94253	CGC		0.602	PAQR8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040903.2	NM_133367	
ICK	22858	broad.mit.edu	37	6	52905990	52905990	+	Silent	SNP	G	G	A	rs376439891		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr6:52905990G>A	ENST00000350082.5	-	2	391	c.45C>T	c.(43-45)taC>taT	p.Y15Y	ICK_ENST00000356971.3_Silent_p.Y15Y	NM_014920.3	NP_055735.1	Q9UPZ9	ICK_HUMAN	intestinal cell (MAK-like) kinase	15	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159, ECO:0000305}.				intracellular signal transduction (GO:0035556)|multicellular organismal development (GO:0007275)|protein phosphorylation (GO:0006468)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)|magnesium ion binding (GO:0000287)|protein serine/threonine kinase activity (GO:0004674)	p.Y15Y(1)		breast(1)|central_nervous_system(2)|endometrium(4)|kidney(2)|large_intestine(6)|lung(10)|ovary(1)|prostate(1)|skin(3)|stomach(1)	31	Lung NSC(77;0.103)					GGACGGAACCGTAGGTTCCAT	0.493																																					p.Y15Y												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C45T	6						.	G	,	0,4406		0,0,2203	155.0	145.0	148.0		45,45	-12.3	0.0	6		148	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous	ICK	NM_014920.3,NM_016513.4	,	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	,	15/633,15/633	52905990	1,13005	2203	4300	6503	53013949	SO:0001819	synonymous_variant	22858	exon3			AB023153	CCDS4949.1	6p12.3-p11.2	2008-02-05			ENSG00000112144	ENSG00000112144			21219	protein-coding gene	gene with protein product		612325				12103360	Standard	NM_014920		Approved	MRK, LCK2, KIAA0936, MGC46090	uc003pbi.2	Q9UPZ9	OTTHUMG00000014870	ENST00000350082.5:c.45C>T	6.37:g.52905990G>A		Somatic		Capture	Illumina HiSeq	Phase_I	53013949	NM_016513	A7MD41|O75985|Q5THL2|Q8IYH8|Q9BX17|Q9NYX3	Silent	SNP	ENST00000350082.5	37	CCDS4949.1																																																																																				0.493	ICK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040952.1	NM_016513	
HMGCLL1	54511	broad.mit.edu	37	6	55304272	55304272	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr6:55304272T>C	ENST00000398661.2	-	9	1102	c.971A>G	c.(970-972)gAg>gGg	p.E324G	HMGCLL1_ENST00000370850.2_Missense_Mutation_p.E191G|HMGCLL1_ENST00000308161.4_Missense_Mutation_p.E262G|HMGCLL1_ENST00000508459.1_Missense_Mutation_p.E128G|HMGCLL1_ENST00000507223.1_5'UTR|HMGCLL1_ENST00000274901.4_Missense_Mutation_p.E294G	NM_019036.2	NP_061909.2	Q8TB92	HMGC2_HUMAN	3-hydroxymethyl-3-methylglutaryl-CoA lyase-like 1	324					ketone body biosynthetic process (GO:0046951)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)	hydroxymethylglutaryl-CoA lyase activity (GO:0004419)|metal ion binding (GO:0046872)	p.E324G(1)		breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(8)|ovary(1)|pancreas(1)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	31	Lung NSC(77;0.0875)		LUSC - Lung squamous cell carcinoma(124;0.23)			TATCAAATCCTCAGTGGCTAC	0.423																																					p.E324G	Ovarian(35;840 893 7837 15538 42887)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A971G	6						.						97.0	92.0	94.0					6																	55304272		1861	4101	5962	55412231	SO:0001583	missense	54511	exon9			AK055075	CCDS43474.1, CCDS43475.1, CCDS75472.1, CCDS75473.1	6p12.1	2010-04-30	2010-04-30		ENSG00000146151	ENSG00000146151			21359	protein-coding gene	gene with protein product			"""3-hydroxymethyl-3-methylglutaryl-Coenzyme A lyase-like 1"""			8619474, 9110174	Standard	NM_001042406		Approved	DKFZP434G1411, bA418P12.1	uc003pcn.3	Q8TB92	OTTHUMG00000014902	ENST00000398661.2:c.971A>G	6.37:g.55304272T>C	ENSP00000381654:p.Glu324Gly	Somatic		Capture	Illumina HiSeq	Phase_I	55412231	NM_019036	B1AQ42|B3KNV0|B7Z1S7|F8W793|Q6ZSA9	Missense_Mutation	SNP	ENST00000398661.2	37	CCDS43475.1	.	.	.	.	.	.	.	.	.	.	t	28.0	4.886037	0.91814	.	.	ENSG00000146151	ENST00000274901;ENST00000398661;ENST00000370850;ENST00000508459;ENST00000308161	D;D;D;D;D	0.98889	-5.21;-5.21;-5.21;-5.17;-5.21	5.82	5.82	0.92795	Aldolase-type TIM barrel (1);Pyruvate carboxyltransferase (2);	0.049621	0.85682	D	0.000000	D	0.99569	0.9845	H	0.98849	4.35	0.80722	D	1	D;D;D;D;D	0.89917	0.998;1.0;1.0;1.0;1.0	D;D;D;D;D	0.97110	0.991;1.0;0.993;0.999;1.0	D	0.97662	1.0161	10	0.87932	D	0	-18.3907	16.1811	0.81903	0.0:0.0:0.0:1.0	.	128;191;262;294;324	B7Z4D4;B7Z212;F8W793;Q8TB92-2;Q8TB92	.;.;.;.;HMGC2_HUMAN	G	294;324;191;128;262	ENSP00000274901:E294G;ENSP00000381654:E324G;ENSP00000359887:E191G;ENSP00000424309:E128G;ENSP00000309737:E262G	ENSP00000274901:E294G	E	-	2	0	HMGCLL1	55412231	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	6.240000	0.72363	2.223000	0.72356	0.446000	0.29264	GAG		0.423	HMGCLL1-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000360290.1	XM_166383	
DST	667	broad.mit.edu	37	6	56480761	56480761	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr6:56480761C>T	ENST00000370765.6	-	24	7611	c.7504G>A	c.(7504-7506)Gaa>Aaa	p.E2502K	DST_ENST00000370754.5_Intron|DST_ENST00000421834.2_Intron|DST_ENST00000361203.3_Intron|DST_ENST00000312431.6_Intron|DST_ENST00000370769.4_Intron|DST_ENST00000446842.2_Intron|DST_ENST00000244364.6_Intron|DST_ENST00000370788.2_Intron	NM_001723.5	NP_001714.1	Q03001	DYST_HUMAN	dystonin	1798					axonogenesis (GO:0007409)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell motility (GO:0048870)|cytoplasmic microtubule organization (GO:0031122)|cytoskeleton organization (GO:0007010)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)|integrin-mediated signaling pathway (GO:0007229)|intermediate filament cytoskeleton organization (GO:0045104)|maintenance of cell polarity (GO:0030011)|microtubule cytoskeleton organization (GO:0000226)|regulation of microtubule polymerization or depolymerization (GO:0031110)|response to wounding (GO:0009611)|retrograde axon cargo transport (GO:0008090)	actin cytoskeleton (GO:0015629)|axon (GO:0030424)|basal plasma membrane (GO:0009925)|basement membrane (GO:0005604)|cell leading edge (GO:0031252)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|hemidesmosome (GO:0030056)|integral component of membrane (GO:0016021)|intermediate filament (GO:0005882)|intermediate filament cytoskeleton (GO:0045111)|microtubule cytoskeleton (GO:0015630)|microtubule plus-end (GO:0035371)|neurofilament cytoskeleton (GO:0060053)|nucleus (GO:0005634)|Z disc (GO:0030018)	calcium ion binding (GO:0005509)|integrin binding (GO:0005178)|microtubule plus-end binding (GO:0051010)|protein C-terminus binding (GO:0008022)|protein homodimerization activity (GO:0042803)	p.E2502K(2)		NS(1)|breast(5)|central_nervous_system(8)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(22)|lung(43)|ovary(7)|prostate(1)|skin(4)|upper_aerodigestive_tract(3)	105	Lung NSC(77;0.103)		LUSC - Lung squamous cell carcinoma(124;0.0485)|Lung(124;0.0956)			TGCAAAGCTTCGGCCACCCGG	0.493																																					p.E2502K												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G7504A	6						.						74.0	80.0	78.0					6																	56480761		2203	4300	6503	56588720	SO:0001583	missense	667	exon24			M22942, M69225	CCDS4959.1, CCDS47443.1, CCDS75474.1	6p12.1	2013-01-10	2004-06-25	2004-07-01	ENSG00000151914	ENSG00000151914		"""EF-hand domain containing"""	1090	protein-coding gene	gene with protein product		113810	"""bullous pemphigoid antigen 1, 230/240kDa"""	BPAG1		2461961, 2276744	Standard	NM_001144770		Approved	BP240, KIAA0728, FLJ21489, FLJ13425, FLJ32235, FLJ30627, CATX-15, BPA, MACF2	uc021zba.2	Q03001	OTTHUMG00000014913	ENST00000370765.6:c.7504G>A	6.37:g.56480761C>T	ENSP00000359801:p.Glu2502Lys	Somatic		Capture	Illumina HiSeq	Phase_I	56588720	NM_001723	B7Z3H1|O94833|Q12825|Q13266|Q13267|Q13775|Q5TBT0|Q5TBT2|Q5TF23|Q5TF24|Q8N1T8|Q8N8J3|Q8WXK8|Q8WXK9|Q96AK9|Q96DQ5|Q96J76|Q96QT5|Q9H555|Q9UGD7|Q9UGD8|Q9UN10	Missense_Mutation	SNP	ENST00000370765.6	37	CCDS4959.1	.	.	.	.	.	.	.	.	.	.	C	16.39	3.109428	0.56398	.	.	ENSG00000151914	ENST00000370765	T	0.79554	-1.28	5.94	5.94	0.96194	.	.	.	.	.	D	0.86335	0.5908	.	.	.	0.27888	N	0.939445	D	0.69078	0.997	P	0.56648	0.803	D	0.86746	0.1957	7	0.72032	D	0.01	.	20.3593	0.98849	0.0:1.0:0.0:0.0	.	2502	Q03001-3	.	K	2502	ENSP00000359801:E2502K	ENSP00000359801:E2502K	E	-	1	0	DST	56588720	0.999000	0.42202	0.923000	0.36655	0.123000	0.20343	4.014000	0.57145	2.822000	0.97130	0.557000	0.71058	GAA		0.493	DST-010	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000041027.2	NM_001723	
LMBRD1	55788	broad.mit.edu	37	6	70423652	70423652	+	Missense_Mutation	SNP	C	C	T	rs140874824		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr6:70423652C>T	ENST00000370577.3	-	9	1029	c.800G>A	c.(799-801)cGc>cAc	p.R267H	LMBRD1_ENST00000370570.1_Missense_Mutation_p.R194H	NM_018368.3	NP_060838.3	Q9NUN5	LMBD1_HUMAN	LMBR1 domain containing 1	267					cobalamin metabolic process (GO:0009235)|insulin receptor internalization (GO:0038016)|negative regulation of glucose import (GO:0046325)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of protein kinase B signaling (GO:0051898)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	clathrin-coated endocytic vesicle (GO:0045334)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|plasma membrane (GO:0005886)	cobalamin binding (GO:0031419)	p.R267H(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(7)|lung(11)|ovary(2)|upper_aerodigestive_tract(1)	31						TTTTAAGGCGCGTTTATCCCT	0.373																																					p.R267H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G800A	6						.	C	HIS/ARG	0,4406		0,0,2203	108.0	104.0	105.0		800	3.8	0.9	6	dbSNP_134	105	1,8599	1.2+/-3.3	0,1,4299	no	missense	LMBRD1	NM_018368.3	29	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	benign	267/541	70423652	1,13005	2203	4300	6503	70480373	SO:0001583	missense	55788	exon9			AF113224	CCDS4969.1	6q13	2011-05-12	2005-07-25	2005-07-25	ENSG00000168216	ENSG00000168216			23038	protein-coding gene	gene with protein product		612625	"""chromosome 6 open reading frame 209"""	C6orf209		19136951	Standard	NM_018368		Approved	FLJ11240, bA810I22.1, cblF	uc003pfa.3	Q9NUN5	OTTHUMG00000014985	ENST00000370577.3:c.800G>A	6.37:g.70423652C>T	ENSP00000359609:p.Arg267His	Somatic		Capture	Illumina HiSeq	Phase_I	70480373	NM_018368	A8K204|E1P531|Q5VUN6|Q86Y70|Q96FW4|Q9BY56|Q9NZD6	Missense_Mutation	SNP	ENST00000370577.3	37	CCDS4969.1	.	.	.	.	.	.	.	.	.	.	C	13.45	2.240749	0.39598	0.0	1.16E-4	ENSG00000168216	ENST00000370577;ENST00000370570	T;T	0.27557	1.67;1.66	5.63	3.84	0.44239	.	0.171896	0.52532	D	0.000076	T	0.13500	0.0327	L	0.49513	1.565	0.42720	D	0.99367	B	0.30236	0.274	B	0.23275	0.045	T	0.06552	-1.0820	10	0.62326	D	0.03	-8.5204	9.5676	0.39409	0.0:0.7874:0.0:0.2126	.	267	Q9NUN5	LMBD1_HUMAN	H	267;194	ENSP00000359609:R267H;ENSP00000359602:R194H	ENSP00000359602:R194H	R	-	2	0	LMBRD1	70480373	0.699000	0.27786	0.942000	0.38095	0.667000	0.39255	1.137000	0.31479	1.522000	0.49001	0.591000	0.81541	CGC		0.373	LMBRD1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041124.1	NM_018368	
RIMS1	22999	broad.mit.edu	37	6	72806830	72806830	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr6:72806830C>T	ENST00000521978.1	+	3	424	c.424C>T	c.(424-426)Cgc>Tgc	p.R142C	RIMS1_ENST00000491071.2_Missense_Mutation_p.R142C|RIMS1_ENST00000522291.1_Missense_Mutation_p.R142C|RIMS1_ENST00000264839.7_Missense_Mutation_p.R142C|RIMS1_ENST00000348717.5_Missense_Mutation_p.R142C|RIMS1_ENST00000517960.1_Missense_Mutation_p.R142C|RIMS1_ENST00000518273.1_Missense_Mutation_p.R142C|RIMS1_ENST00000520567.1_Missense_Mutation_p.R142C	NM_014989.5	NP_055804.2	Q86UR5	RIMS1_HUMAN	regulating synaptic membrane exocytosis 1	142	RabBD. {ECO:0000255|PROSITE- ProRule:PRU00234}.				calcium ion-dependent exocytosis (GO:0017156)|calcium ion-dependent exocytosis of neurotransmitter (GO:0048791)|glutamate secretion (GO:0014047)|intracellular protein transport (GO:0006886)|membrane fusion (GO:0061025)|neurotransmitter secretion (GO:0007269)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of gene expression (GO:0010628)|positive regulation of inhibitory postsynaptic membrane potential (GO:0097151)|protein complex assembly (GO:0006461)|regulated secretory pathway (GO:0045055)|regulation of catalytic activity (GO:0050790)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of neurotransmitter secretion (GO:0046928)|response to stimulus (GO:0050896)|secretion (GO:0046903)|synaptic transmission (GO:0007268)|synaptic vesicle exocytosis (GO:0016079)|visual perception (GO:0007601)	cell junction (GO:0030054)|plasma membrane (GO:0005886)|presynaptic active zone (GO:0048786)|presynaptic membrane (GO:0042734)	metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|Rab GTPase binding (GO:0017137)|small GTPase regulator activity (GO:0005083)	p.R142C(1)		NS(1)|breast(2)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(25)|liver(4)|lung(35)|ovary(9)|pancreas(3)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	102		all_epithelial(107;0.179)|all_hematologic(105;0.212)				GTTCTGTGCGCGCTGCGGAGG	0.483																																					p.R142C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C424T	6						.						82.0	85.0	84.0					6																	72806830		2086	4230	6316	72863551	SO:0001583	missense	22999	exon3			AB002338	CCDS47449.1, CCDS55029.1, CCDS55030.1, CCDS55031.1, CCDS55032.1, CCDS55033.1	6q12-q13	2008-10-16	2002-06-12	2002-06-14	ENSG00000079841	ENSG00000079841			17282	protein-coding gene	gene with protein product	"""Rab3-interacting molecule"""	606629	"""RAB3 interacting protein 2"""	RAB3IP2, CORD7		9205841, 11438518	Standard	NM_001168407		Approved	RIM, KIAA0340, RIM1	uc003pga.4	Q86UR5	OTTHUMG00000015009	ENST00000521978.1:c.424C>T	6.37:g.72806830C>T	ENSP00000428417:p.Arg142Cys	Somatic		Capture	Illumina HiSeq	Phase_I	72863551	NM_014989	A7MBN6|B7Z2M0|B7Z2Q9|B7Z3S3|B7Z6S2|E7EX08|E9PCB7|E9PCZ1|E9PF48|E9PHF5|E9PHR1|O15048|Q5JY21|Q5JY25|Q5SZK1|Q8TDY9|Q8TDZ5|Q9HBA1|Q9HBA2|Q9HBA3|Q9HBA4|Q9HBA5|Q9HBA6	Missense_Mutation	SNP	ENST00000521978.1	37	CCDS47449.1	.	.	.	.	.	.	.	.	.	.	C	19.98	3.926228	0.73327	.	.	ENSG00000079841	ENST00000491071;ENST00000350827;ENST00000352008;ENST00000348717;ENST00000349908;ENST00000346609;ENST00000264839;ENST00000517960;ENST00000518273;ENST00000520567;ENST00000522291;ENST00000521978	T;T;T;T;T;T;T;T	0.78003	-1.14;-1.14;-1.14;-1.14;-1.14;-1.14;-1.14;-1.14	5.81	3.81	0.43845	Zinc finger, RING/FYVE/PHD-type (1);Rab-binding domain (1);Zinc finger, FYVE-related (1);Zinc finger, FYVE/PHD-type (1);	0.000000	0.64402	D	0.000014	D	0.87241	0.6128	M	0.86953	2.85	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.90380	0.4387	10	0.87932	D	0	-11.8199	16.1824	0.81920	0.3188:0.6812:0.0:0.0	.	142	Q86UR5	RIMS1_HUMAN	C	142	ENSP00000430101:R142C;ENSP00000275037:R142C;ENSP00000264839:R142C;ENSP00000429959:R142C;ENSP00000430408:R142C;ENSP00000430502:R142C;ENSP00000430932:R142C;ENSP00000428417:R142C	ENSP00000264839:R142C	R	+	1	0	RIMS1	72863551	0.998000	0.40836	0.887000	0.34795	0.811000	0.45836	3.887000	0.56197	1.408000	0.46895	0.655000	0.94253	CGC		0.483	RIMS1-011	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374968.1		
HTR1B	3351	broad.mit.edu	37	6	78172741	78172741	+	Missense_Mutation	SNP	G	G	A	rs200726002		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr6:78172741G>A	ENST00000369947.2	-	1	749	c.380C>T	c.(379-381)tCg>tTg	p.S127L		NM_000863.1	NP_000854.1	P28222	5HT1B_HUMAN	5-hydroxytryptamine (serotonin) receptor 1B, G protein-coupled	127	Agonist binding.				adenylate cyclase-inhibiting serotonin receptor signaling pathway (GO:0007198)|bone remodeling (GO:0046849)|cellular response to alkaloid (GO:0071312)|cellular response to drug (GO:0035690)|cellular response to temperature stimulus (GO:0071502)|drinking behavior (GO:0042756)|G-protein coupled receptor internalization (GO:0002031)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|negative regulation of cAMP biosynthetic process (GO:0030818)|negative regulation of serotonin secretion (GO:0014063)|negative regulation of synaptic transmission, GABAergic (GO:0032229)|negative regulation of synaptic transmission, glutamatergic (GO:0051967)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|regulation of behavior (GO:0050795)|regulation of dopamine secretion (GO:0014059)|response to cocaine (GO:0042220)|response to ethanol (GO:0045471)|response to mineralocorticoid (GO:0051385)|synaptic transmission (GO:0007268)|vasoconstriction (GO:0042310)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	drug binding (GO:0008144)|serotonin binding (GO:0051378)|serotonin receptor activity (GO:0004993)	p.S127L(1)		NS(1)|breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(9)|prostate(2)|upper_aerodigestive_tract(2)	25		all_cancers(76;0.0867)|Acute lymphoblastic leukemia(125;0.00119)|all_hematologic(105;0.0332)		BRCA - Breast invasive adenocarcinoma(397;0.205)	Almotriptan(DB00918)|Amitriptyline(DB00321)|Amoxapine(DB00543)|Apomorphine(DB00714)|Aripiprazole(DB01238)|Asenapine(DB06216)|Bopindolol(DB08807)|Bromocriptine(DB01200)|Cabergoline(DB00248)|Clozapine(DB00363)|Dihydroergotamine(DB00320)|Eletriptan(DB00216)|Ergoloid mesylate(DB01049)|Ergotamine(DB00696)|Frovatriptan(DB00998)|Ketamine(DB01221)|Lisuride(DB00589)|Loxapine(DB00408)|Methysergide(DB00247)|Naratriptan(DB00952)|Olanzapine(DB00334)|Ondansetron(DB00904)|Penbutolol(DB01359)|Pergolide(DB01186)|Pindolol(DB00960)|Pramipexole(DB00413)|Propranolol(DB00571)|Quetiapine(DB01224)|Rizatriptan(DB00953)|Ropinirole(DB00268)|Sumatriptan(DB00669)|Yohimbine(DB01392)|Ziprasidone(DB00246)|Zolmitriptan(DB00315)	GATGTCCGACGACAGCCAGAA	0.597													G|||	1	0.000199681	0.0	0.0	5008	,	,		17311	0.001		0.0	False		,,,				2504	0.0				p.S127L												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C380T	6						.	G	LEU/SER	0,4406		0,0,2203	97.0	74.0	82.0		380	5.3	1.0	6		82	1,8599	1.2+/-3.3	0,1,4299	no	missense	HTR1B	NM_000863.1	145	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	possibly-damaging	127/391	78172741	1,13005	2203	4300	6503	78229460	SO:0001583	missense	3351	exon1			BC069065	CCDS4986.1	6q13	2012-08-08	2012-02-03		ENSG00000135312	ENSG00000135312		"""5-HT (serotonin) receptors"", ""GPCR / Class A : 5-HT (serotonin) receptors, GPCR only"""	5287	protein-coding gene	gene with protein product		182131	"""5-hydroxytryptamine (serotonin) receptor 1B"""			1348246, 11247661	Standard	NM_000863		Approved	S12, 5-HT1B, HTR1D2, 5-HT1DB	uc003pil.1	P28222	OTTHUMG00000015066	ENST00000369947.2:c.380C>T	6.37:g.78172741G>A	ENSP00000358963:p.Ser127Leu	Somatic		Capture	Illumina HiSeq	Phase_I	78229460	NM_000863	Q4VAY7	Missense_Mutation	SNP	ENST00000369947.2	37	CCDS4986.1	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	G	16.13	3.037266	0.54896	0.0	1.16E-4	ENSG00000135312	ENST00000369947	T	0.18810	2.19	5.27	5.27	0.74061	GPCR, rhodopsin-like superfamily (1);	0.000000	0.85682	D	0.000000	T	0.17619	0.0423	M	0.81341	2.54	0.80722	D	1	B	0.33266	0.404	B	0.27796	0.083	T	0.02588	-1.1137	9	.	.	.	.	18.0523	0.89353	0.0:0.0:1.0:0.0	.	127	P28222	5HT1B_HUMAN	L	127	ENSP00000358963:S127L	.	S	-	2	0	HTR1B	78229460	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	6.361000	0.73070	2.746000	0.94184	0.561000	0.74099	TCG		0.597	HTR1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041292.1	NM_000863	
IBTK	25998	broad.mit.edu	37	6	82881217	82881217	+	Silent	SNP	A	A	G			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr6:82881217A>G	ENST00000306270.7	-	29	4536	c.3987T>C	c.(3985-3987)ccT>ccC	p.P1329P	IBTK_ENST00000503631.1_Silent_p.P1128P|IBTK_ENST00000510291.1_Silent_p.P1314P	NM_015525.2	NP_056340.2	Q9P2D0	IBTK_HUMAN	inhibitor of Bruton agammaglobulinemia tyrosine kinase	1329					negative regulation of protein phosphorylation (GO:0001933)|negative regulation of protein tyrosine kinase activity (GO:0061099)|release of sequestered calcium ion into cytosol (GO:0051209)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	protein kinase binding (GO:0019901)|protein tyrosine kinase inhibitor activity (GO:0030292)	p.P1329P(1)		central_nervous_system(2)|endometrium(9)|kidney(3)|large_intestine(10)|lung(19)|ovary(3)|pancreas(1)|prostate(2)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	54		all_cancers(76;3.38e-06)|Acute lymphoblastic leukemia(125;3.41e-06)|all_hematologic(105;0.000865)|all_epithelial(107;0.0037)		BRCA - Breast invasive adenocarcinoma(397;0.0901)		caaactcttcagggttgccaa	0.418																																					p.P1329P												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.T3987C	6						.						84.0	69.0	74.0					6																	82881217		2203	4300	6503	82937936	SO:0001819	synonymous_variant	25998	exon29			AF235049	CCDS34490.1, CCDS75486.1	6q14.3	2013-01-10	2003-10-06	2003-10-08	ENSG00000005700	ENSG00000005700		"""BTB/POZ domain containing"", ""Ankyrin repeat domain containing"""	17853	protein-coding gene	gene with protein product		606457	"""Bruton agammaglobulinemia tyrosine kinase inhibitor"""	BTKI		11577348	Standard	XM_006715453		Approved	DKFZP564B116, BTBD26	uc003pjl.1	Q9P2D0	OTTHUMG00000015102	ENST00000306270.7:c.3987T>C	6.37:g.82881217A>G		Somatic		Capture	Illumina HiSeq	Phase_I	82937936	NM_015525	Q2QKU2|Q2QKU3|Q2QKU4|Q5TFD7|Q5TFD9|Q8IUQ9|Q8IUY7|Q8TAI4|Q9HBI8|Q9Y3T8	Silent	SNP	ENST00000306270.7	37	CCDS34490.1																																																																																				0.418	IBTK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041337.2	NM_015525	
DOPEY1	23033	broad.mit.edu	37	6	83869550	83869550	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr6:83869550C>T	ENST00000349129.2	+	37	7093	c.6833C>T	c.(6832-6834)aCg>aTg	p.T2278M	DOPEY1_ENST00000369739.3_Missense_Mutation_p.T2269M|DOPEY1_ENST00000484282.1_3'UTR|DOPEY1_ENST00000237163.5_Missense_Mutation_p.T2162M	NM_015018.3	NP_055833.2	Q5JWR5	DOP1_HUMAN	dopey family member 1	2278					protein transport (GO:0015031)			p.T2278M(1)		breast(4)|central_nervous_system(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|lung(16)|ovary(5)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)	67		all_cancers(76;2.29e-06)|Acute lymphoblastic leukemia(125;3.41e-06)|all_hematologic(105;0.000865)|all_epithelial(107;0.00203)		BRCA - Breast invasive adenocarcinoma(397;0.053)		CTGGAGACAACGTACACAGGA	0.488																																					p.T2278M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C6833T	6						.						76.0	78.0	77.0					6																	83869550		2203	4300	6503	83926269	SO:0001583	missense	23033	exon37			AK027030	CCDS4996.1, CCDS64467.1	6q15	2013-03-05	2006-02-02	2006-02-02	ENSG00000083097	ENSG00000083097			21194	protein-coding gene	gene with protein product			"""KIAA1117"""	KIAA1117		16301316, 16303751, 10931277	Standard	NM_015018		Approved	dJ202D23.2	uc011dyy.2	Q5JWR5	OTTHUMG00000016365	ENST00000349129.2:c.6833C>T	6.37:g.83869550C>T	ENSP00000195654:p.Thr2278Met	Somatic		Capture	Illumina HiSeq	Phase_I	83926269	NM_015018	Q86XV1|Q9H5J5|Q9NSL4|Q9UPN5|Q9Y414	Missense_Mutation	SNP	ENST00000349129.2	37	CCDS4996.1	.	.	.	.	.	.	.	.	.	.	C	18.53	3.643694	0.67244	.	.	ENSG00000083097	ENST00000349129;ENST00000237163;ENST00000369739	T;T	0.46819	0.86;0.86	5.63	5.63	0.86233	.	0.093327	0.64402	D	0.000001	T	0.55000	0.1893	L	0.43152	1.355	0.80722	D	1	D;D;D	0.89917	0.982;1.0;1.0	P;D;D	0.81914	0.628;0.995;0.995	T	0.46359	-0.9197	10	0.34782	T	0.22	.	19.6748	0.95926	0.0:1.0:0.0:0.0	.	2169;2269;2278	E1P545;B2RWN9;Q5JWR5	.;.;DOP1_HUMAN	M	2278;2162;2162	ENSP00000195654:T2278M;ENSP00000237163:T2162M	ENSP00000237163:T2162M	T	+	2	0	DOPEY1	83926269	1.000000	0.71417	1.000000	0.80357	0.293000	0.27360	7.456000	0.80751	2.653000	0.90120	0.655000	0.94253	ACG		0.488	DOPEY1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043785.2	NM_015018	
MDN1	23195	broad.mit.edu	37	6	90371809	90371809	+	Silent	SNP	A	A	G			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr6:90371809A>G	ENST00000369393.3	-	87	14677	c.14562T>C	c.(14560-14562)gaT>gaC	p.D4854D	MDN1_ENST00000428876.1_Silent_p.D4854D			Q9NU22	MDN1_HUMAN	MDN1, midasin homolog (yeast)	4854					ATP catabolic process (GO:0006200)|protein complex assembly (GO:0006461)	cytoplasm (GO:0005737)|intermediate filament cytoskeleton (GO:0045111)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|unfolded protein binding (GO:0051082)	p.D4854D(1)		NS(1)|breast(13)|central_nervous_system(2)|cervix(3)|endometrium(22)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(52)|liver(1)|lung(83)|ovary(10)|pancreas(1)|prostate(10)|skin(6)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	218		all_cancers(76;1.47e-06)|Acute lymphoblastic leukemia(125;2.23e-10)|Prostate(29;5.55e-10)|all_hematologic(105;2.42e-06)|all_epithelial(107;0.00246)		BRCA - Breast invasive adenocarcinoma(108;0.0193)		TCATTACCTCATCTATTTGTT	0.393																																					p.D4854D												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.T14562C	6						.						383.0	331.0	349.0					6																	90371809		2203	4299	6502	90428530	SO:0001819	synonymous_variant	23195	exon87			AF503925	CCDS5024.1	6q15	2014-01-28			ENSG00000112159	ENSG00000112159			18302	protein-coding gene	gene with protein product						9205841, 12102729	Standard	XM_005248699		Approved	KIAA0301	uc003pnn.1	Q9NU22	OTTHUMG00000015213	ENST00000369393.3:c.14562T>C	6.37:g.90371809A>G		Somatic		Capture	Illumina HiSeq	Phase_I	90428530	NM_014611	O15019|Q5T794	Silent	SNP	ENST00000369393.3	37	CCDS5024.1																																																																																				0.393	MDN1-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041514.2		
CASP8AP2	9994	broad.mit.edu	37	6	90573531	90573531	+	RNA	SNP	A	A	G			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr6:90573531A>G	ENST00000551025.1	+	0	3540									caspase 8 associated protein 2											NS(1)|endometrium(7)|kidney(6)|large_intestine(12)|lung(21)|ovary(2)|urinary_tract(2)	51		all_cancers(76;3.64e-09)|Prostate(29;1.16e-10)|Acute lymphoblastic leukemia(125;1.45e-10)|all_hematologic(105;7.74e-07)|all_epithelial(107;4.69e-05)|Lung NSC(302;0.238)		BRCA - Breast invasive adenocarcinoma(108;0.0953)		GAATGAAACAAACCATTAATA	0.403																																					p.Q701Q	Colon(187;1656 2025 17045 31481 39901)											.	.	0			c.A2103G	6						.						52.0	48.0	50.0					6																	90573531		1892	4117	6009	90630252			9994	exon7			AB037736		6q15	2012-04-19	2008-10-30		ENSG00000118412	ENSG00000118412			1510	protein-coding gene	gene with protein product	"""FLICE-associated huge protein"""	606880	"""CASP8 associated protein 2"""			10235259, 17245429, 17003126	Standard	NM_001137668		Approved	FLASH, CED-4, RIP25, FLJ11208, KIAA1315	uc011dzz.2	Q9UKL3	OTTHUMG00000015212		6.37:g.90573531A>G		Somatic		Capture	Illumina HiSeq	Phase_I	90630252	NM_001137667		Silent	SNP	ENST00000551025.1	37																																																																																					0.403	CASP8AP2-202	KNOWN	basic	processed_transcript	processed_transcript		NM_001137667	
GJA10	84694	broad.mit.edu	37	6	90604650	90604650	+	Missense_Mutation	SNP	C	C	T	rs540684772		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr6:90604650C>T	ENST00000369352.1	+	1	463	c.463C>T	c.(463-465)Cgt>Tgt	p.R155C		NM_032602.1	NP_115991.1	P57773	CXA9_HUMAN	gap junction protein, alpha 10, 62kDa	155					cell communication (GO:0007154)	connexon complex (GO:0005922)|integral component of membrane (GO:0016021)		p.R155C(1)		breast(2)|endometrium(2)|kidney(1)|large_intestine(10)|lung(17)|ovary(1)|skin(3)|urinary_tract(1)	37		all_cancers(76;5.71e-06)|Acute lymphoblastic leukemia(125;2.23e-10)|Prostate(29;5.55e-10)|all_hematologic(105;2.42e-06)|all_epithelial(107;0.00527)		BRCA - Breast invasive adenocarcinoma(108;0.0915)		ATGTCTGCTGCGTACTTATGT	0.438													C|||	1	0.000199681	0.0	0.0	5008	,	,		20829	0.0		0.0	False		,,,				2504	0.001				p.R155C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C463T	6						.						129.0	124.0	126.0					6																	90604650		2203	4300	6503	90661371	SO:0001583	missense	84694	exon1			AF296766	CCDS5025.1	6q15-q16	2008-02-05			ENSG00000135355	ENSG00000135355		"""Ion channels / Gap junction proteins (connexins)"""	16995	protein-coding gene	gene with protein product	"""connexin 62"""	611924					Standard	NM_032602		Approved	CX62	uc011eaa.2	Q969M2	OTTHUMG00000015210	ENST00000369352.1:c.463C>T	6.37:g.90604650C>T	ENSP00000358358:p.Arg155Cys	Somatic		Capture	Illumina HiSeq	Phase_I	90661371	NM_032602	B2R722|B3KVQ2|Q5TA63|Q96KG0	Missense_Mutation	SNP	ENST00000369352.1	37	CCDS5025.1	.	.	.	.	.	.	.	.	.	.	C	13.71	2.318294	0.40996	.	.	ENSG00000135355	ENST00000369352	D	0.97906	-4.6	4.91	3.08	0.35506	.	0.117649	0.64402	D	0.000011	D	0.88858	0.6551	L	0.34521	1.04	0.58432	D	0.999993	P	0.37500	0.597	B	0.28385	0.089	D	0.86321	0.1692	10	0.35671	T	0.21	.	6.884	0.24189	0.1427:0.7066:0.0:0.1507	.	155	Q969M2	CXA10_HUMAN	C	155	ENSP00000358358:R155C	ENSP00000358358:R155C	R	+	1	0	GJA10	90661371	0.999000	0.42202	0.989000	0.46669	0.996000	0.88848	1.174000	0.31932	0.635000	0.30488	0.563000	0.77884	CGT		0.438	GJA10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041505.1	NM_032602	
GPR63	81491	broad.mit.edu	37	6	97246967	97246967	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr6:97246967G>A	ENST00000229955.3	-	2	986	c.641C>T	c.(640-642)gCc>gTc	p.A214V	GPR63_ENST00000417980.1_Missense_Mutation_p.A214V	NM_001143957.2|NM_030784.3	NP_001137429.1|NP_110411.1	Q9BZJ6	GPR63_HUMAN	G protein-coupled receptor 63	214						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	G-protein coupled receptor activity (GO:0004930)	p.A214V(1)		kidney(1)|large_intestine(5)|lung(13)|ovary(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	25		all_cancers(76;6.89e-05)|Acute lymphoblastic leukemia(125;7.02e-10)|all_hematologic(75;1.23e-06)|all_epithelial(107;0.0618)|Colorectal(196;0.0721)		BRCA - Breast invasive adenocarcinoma(108;0.0912)		GTTTCCTACGGCTAAAGGAAA	0.458																																					p.A214V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C641T	6						.						74.0	75.0	74.0					6																	97246967		2203	4300	6503	97353688	SO:0001583	missense	81491	exon3			AF317654	CCDS5036.1	6q16.1-q16.3	2012-08-21			ENSG00000112218	ENSG00000112218		"""GPCR / Class A : Orphans"""	13302	protein-coding gene	gene with protein product		606915					Standard	NM_030784		Approved	PSP24(beta), PSP24B	uc003pou.3	Q9BZJ6	OTTHUMG00000015245	ENST00000229955.3:c.641C>T	6.37:g.97246967G>A	ENSP00000229955:p.Ala214Val	Somatic		Capture	Illumina HiSeq	Phase_I	97353688	NM_001143957	Q9UJH3	Missense_Mutation	SNP	ENST00000229955.3	37	CCDS5036.1	.	.	.	.	.	.	.	.	.	.	G	10.79	1.448637	0.26074	.	.	ENSG00000112218	ENST00000536583;ENST00000417980;ENST00000229955;ENST00000369268	T;T;T	0.36340	1.26;1.26;1.26	5.3	4.43	0.53597	GPCR, rhodopsin-like superfamily (1);	0.138562	0.47093	D	0.000257	T	0.09335	0.0230	N	0.05259	-0.085	0.48135	D	0.999596	B	0.13594	0.008	B	0.20955	0.032	T	0.07102	-1.0790	10	0.29301	T	0.29	-1.9713	14.4008	0.67044	0.0718:0.0:0.9282:0.0	.	214	Q9BZJ6	GPR63_HUMAN	V	238;214;214;214	ENSP00000393170:A214V;ENSP00000229955:A214V;ENSP00000358273:A214V	ENSP00000229955:A214V	A	-	2	0	GPR63	97353688	1.000000	0.71417	0.812000	0.32479	0.679000	0.39708	9.420000	0.97426	1.378000	0.46305	0.650000	0.86243	GCC		0.458	GPR63-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041566.2		
AKAP12	9590	broad.mit.edu	37	6	151673000	151673000	+	Frame_Shift_Del	DEL	C	C	-			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	-	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr6:151673000delC	ENST00000253332.1	+	3	3663	c.3474delC	c.(3472-3474)atcfs	p.I1158fs	AKAP12_ENST00000402676.2_Frame_Shift_Del_p.I1158fs|AKAP12_ENST00000359755.5_Frame_Shift_Del_p.I1053fs|AKAP12_ENST00000354675.6_Frame_Shift_Del_p.I1060fs			Q02952	AKA12_HUMAN	A kinase (PRKA) anchor protein 12	1158					G-protein coupled receptor signaling pathway (GO:0007186)|positive regulation of cAMP biosynthetic process (GO:0030819)|positive regulation of protein kinase A signaling (GO:0010739)|protein targeting (GO:0006605)|regulation of protein kinase C signaling (GO:0090036)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|focal adhesion (GO:0005925)	adenylate cyclase binding (GO:0008179)|protein kinase A binding (GO:0051018)	p.P1160fs*18(1)		breast(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(22)|lung(22)|ovary(2)|pancreas(1)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	68		Ovarian(120;0.125)	BRCA - Breast invasive adenocarcinoma(37;0.175)	OV - Ovarian serous cystadenocarcinoma(155;2.98e-11)		AACAGGCTATCCCCCCTGACT	0.527																																					p.I1158fs	Melanoma(141;1616 1805 10049 24534 51979)											.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.3474delC	6						.						104.0	103.0	104.0					6																	151673000		2203	4300	6503	151714693	SO:0001589	frameshift_variant	9590	exon4			U81607	CCDS5229.1, CCDS5230.1	6q24-q25	2011-07-01	2008-08-29		ENSG00000131016	ENSG00000131016		"""A-kinase anchor proteins"""	370	protein-coding gene	gene with protein product	"""gravin"", ""Src-Suppressed C Kinase Substrate"""	604698	"""A kinase (PRKA) anchor protein (gravin) 12"""			9000000	Standard	NM_144497		Approved	AKAP250, SSeCKS	uc011eep.2	Q02952	OTTHUMG00000015833	ENST00000253332.1:c.3474delC	6.37:g.151673000delC	ENSP00000253332:p.Ile1158fs	Somatic		Capture	Illumina HiSeq	Phase_I	151714693	NM_005100	O00310|O00498|Q4LE68|Q5SZ80|Q5TGN1|Q68D82|Q99970	Frame_Shift_Del	DEL	ENST00000253332.1	37	CCDS5229.1																																																																																				0.527	AKAP12-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000042712.1		
SMOC2	64094	broad.mit.edu	37	6	169053754	169053754	+	Silent	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr6:169053754G>A	ENST00000356284.2	+	11	1351	c.1131G>A	c.(1129-1131)agG>agA	p.R377R	SMOC2_ENST00000354536.5_Silent_p.R388R	NM_001166412.1	NP_001159884.1	Q9H3U7	SMOC2_HUMAN	SPARC related modular calcium binding 2	377	EF-hand 1. {ECO:0000255|PROSITE- ProRule:PRU00448}.				extracellular matrix organization (GO:0030198)|positive regulation of cell-substrate adhesion (GO:0010811)|signal transduction (GO:0007165)	basement membrane (GO:0005604)|interstitial matrix (GO:0005614)	calcium ion binding (GO:0005509)|heparin binding (GO:0008201)	p.R388R(1)		NS(1)|autonomic_ganglia(1)|breast(2)|endometrium(1)|kidney(1)|large_intestine(6)|lung(12)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	32		Breast(66;0.000141)|Esophageal squamous(34;0.222)|Ovarian(120;0.231)		OV - Ovarian serous cystadenocarcinoma(33;1.31e-19)|BRCA - Breast invasive adenocarcinoma(81;3.06e-06)|GBM - Glioblastoma multiforme(31;0.00109)		CCTTCAAGAGGTTCCTTCGCA	0.428																																					p.R377R												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G1131A	6						.						88.0	89.0	89.0					6																	169053754		2203	4300	6503	168795679	SO:0001819	synonymous_variant	64094	exon11			AB014730	CCDS5307.1, CCDS55076.1	6q27	2013-01-10			ENSG00000112562	ENSG00000112562		"""EF-hand domain containing"""	20323	protein-coding gene	gene with protein product		607223				12031507	Standard	NM_022138		Approved	SMAP2	uc003qwr.2	Q9H3U7	OTTHUMG00000016050	ENST00000356284.2:c.1131G>A	6.37:g.169053754G>A		Somatic		Capture	Illumina HiSeq	Phase_I	168795679	NM_001166412	B3KPS7|Q4G169|Q5TAT7|Q5TAT8|Q86VV9|Q96SF3|Q9H1L3|Q9H1L4|Q9H3U0|Q9H4F7|Q9HCV2	Silent	SNP	ENST00000356284.2	37	CCDS55076.1																																																																																				0.428	SMOC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043201.1		
ZAN	7455	broad.mit.edu	37	7	100358106	100358106	+	RNA	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr7:100358106C>T	ENST00000348028.3	+	0	3954				ZAN_ENST00000546292.1_RNA|ZAN_ENST00000349350.6_RNA|ZAN_ENST00000427578.1_RNA|ZAN_ENST00000449052.1_RNA|ZAN_ENST00000542585.1_RNA|ZAN_ENST00000546213.1_RNA|ZAN_ENST00000421100.1_RNA|ZAN_ENST00000443370.1_RNA|ZAN_ENST00000538115.1_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.F1263F(1)		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)			AGACGGAGTTCGGTTTGCGGG	0.587																																					p.F1263F												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C3789T	7						.						98.0	109.0	105.0					7																	100358106		2161	4245	6406	100196042			7455	exon19			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.100358106C>T		Somatic		Capture	Illumina HiSeq	Phase_I	100196042	NM_173059	A0FKC8|D6W5W4|O00218|Q96L85|Q96L86|Q96L87|Q96L88|Q96L89|Q96L90|Q9BXN9|Q9BZ83|Q9BZ84|Q9BZ85|Q9BZ86|Q9BZ87|Q9BZ88	Silent	SNP	ENST00000348028.3	37																																																																																					0.587	ZAN-006	KNOWN	basic	polymorphic_pseudogene	polymorphic_pseudogene	OTTHUMT00000347214.1	NM_003386	
NAPEPLD	222236	broad.mit.edu	37	7	102768975	102768975	+	Nonsense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr7:102768975C>T	ENST00000417955.1	-	2	403	c.249G>A	c.(247-249)tgG>tgA	p.W83*	NAPEPLD_ENST00000427257.1_Nonsense_Mutation_p.W83*|NAPEPLD_ENST00000455523.2_Nonsense_Mutation_p.W156*|NAPEPLD_ENST00000465647.1_Nonsense_Mutation_p.W83*|NAPEPLD_ENST00000341533.4_Nonsense_Mutation_p.W83*			Q6IQ20	NAPEP_HUMAN	N-acyl phosphatidylethanolamine phospholipase D	83					phospholipid catabolic process (GO:0009395)	extracellular vesicular exosome (GO:0070062)|photoreceptor outer segment membrane (GO:0042622)	N-acylphosphatidylethanolamine-specific phospholipase D activity (GO:0070290)|zinc ion binding (GO:0008270)	p.W83*(1)		endometrium(2)|large_intestine(5)|lung(6)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	17						CCATTATCAGCCATCTGAGAA	0.388																																					p.W83X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.G249A	7						.						129.0	120.0	123.0					7																	102768975		2203	4300	6503	102556211	SO:0001587	stop_gained	222236	exon2			BC037350, AY357337	CCDS5729.1	7q22.1	2014-03-14			ENSG00000161048	ENSG00000161048	3.1.4.54		21683	protein-coding gene	gene with protein product	"""chromosome 7 open reading frame 18, N-acyl-phosphatidylethanolamine-hydrolyzing phospholipase D"""	612334				14634025, 15820312, 18067139	Standard	NM_198990		Approved	FMP30, C7orf18, NAPE-PLD	uc003vbd.2	Q6IQ20	OTTHUMG00000157204	ENST00000417955.1:c.249G>A	7.37:g.102768975C>T	ENSP00000407112:p.Trp83*	Somatic		Capture	Illumina HiSeq	Phase_I	102556211	NM_198990	Q5CZ87|Q769K1	Nonsense_Mutation	SNP	ENST00000417955.1	37	CCDS5729.1	.	.	.	.	.	.	.	.	.	.	C	26.3	4.727150	0.89390	.	.	ENSG00000161048	ENST00000341533;ENST00000417955;ENST00000465647;ENST00000427257;ENST00000455523;ENST00000418294	.	.	.	6.16	6.16	0.99307	.	0.218205	0.51477	D	0.000087	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-53.7803	20.8598	0.99761	0.0:1.0:0.0:0.0	.	.	.	.	X	83;83;83;83;156;83	.	ENSP00000340093:W83X	W	-	3	0	NAPEPLD	102556211	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	3.213000	0.51153	2.937000	0.99478	0.650000	0.86243	TGG		0.388	NAPEPLD-002	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347904.1	NM_198990	
LRRN3	54674	broad.mit.edu	37	7	110764264	110764264	+	Missense_Mutation	SNP	G	G	C			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	C	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr7:110764264G>C	ENST00000422987.3	+	2	2267	c.1436G>C	c.(1435-1437)gGa>gCa	p.G479A	IMMP2L_ENST00000437687.1_Intron|LRRN3_ENST00000308478.5_Missense_Mutation_p.G479A|IMMP2L_ENST00000450877.1_Intron|IMMP2L_ENST00000331762.3_Intron|LRRN3_ENST00000451085.1_Missense_Mutation_p.G479A|IMMP2L_ENST00000447215.1_Intron|IMMP2L_ENST00000415362.1_Intron|IMMP2L_ENST00000405709.2_Intron|IMMP2L_ENST00000489381.1_Intron|IMMP2L_ENST00000452895.1_Intron	NM_018334.4	NP_060804.3	Q9H3W5	LRRN3_HUMAN	leucine rich repeat neuronal 3	479	Ig-like C2-type.				positive regulation of protein phosphorylation (GO:0001934)	clathrin adaptor complex (GO:0030131)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.G479A(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(15)|lung(20)|ovary(2)|pancreas(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	55				UCEC - Uterine corpus endometrioid carcinoma (4;0.245)|LUSC - Lung squamous cell carcinoma(290;0.0715)|Lung(3;0.0864)|STAD - Stomach adenocarcinoma(3;0.125)		CATTCTGAGGGAACACTAGAT	0.418																																					p.G479A												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1436C	7						.						73.0	74.0	73.0					7																	110764264		2203	4300	6503	110551500	SO:0001583	missense	54674	exon2			AB060967	CCDS5754.1	7q31.1	2013-02-11			ENSG00000173114	ENSG00000173114		"""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	17200	protein-coding gene	gene with protein product	"""fibronectin type III, immunoglobulin and leucine rich repeat domains 5"""					11549284	Standard	NM_001099660		Approved	NLRR3, FLJ11129, FIGLER5	uc003vfs.4	Q9H3W5	OTTHUMG00000155039	ENST00000422987.3:c.1436G>C	7.37:g.110764264G>C	ENSP00000412417:p.Gly479Ala	Somatic		Capture	Illumina HiSeq	Phase_I	110551500	NM_018334	O43377|Q6I9V8|Q8IYQ6	Missense_Mutation	SNP	ENST00000422987.3	37	CCDS5754.1	.	.	.	.	.	.	.	.	.	.	G	16.84	3.234037	0.58886	.	.	ENSG00000173114	ENST00000308478;ENST00000451085;ENST00000422987	T;T;T	0.64803	-0.12;-0.12;-0.12	6.17	6.17	0.99709	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.64402	D	0.000007	D	0.84433	0.5471	M	0.90759	3.145	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.85504	0.1193	10	0.66056	D	0.02	.	20.8794	0.99867	0.0:0.0:1.0:0.0	.	479	Q9H3W5	LRRN3_HUMAN	A	479	ENSP00000312001:G479A;ENSP00000397312:G479A;ENSP00000412417:G479A	ENSP00000312001:G479A	G	+	2	0	LRRN3	110551500	1.000000	0.71417	1.000000	0.80357	0.550000	0.35303	9.869000	0.99810	2.941000	0.99782	0.655000	0.94253	GGA		0.418	LRRN3-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338171.2	NM_018334	
FEZF1	389549	broad.mit.edu	37	7	121944301	121944301	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr7:121944301G>T	ENST00000442488.2	-	1	258	c.191C>A	c.(190-192)tCt>tAt	p.S64Y	FEZF1-AS1_ENST00000428449.1_RNA|FEZF1-AS1_ENST00000424404.1_RNA|FEZF1-AS1_ENST00000437317.1_RNA|FEZF1_ENST00000427185.2_Missense_Mutation_p.S64Y|FEZF1_ENST00000331178.4_Missense_Mutation_p.S64Y	NM_001024613.2|NM_001160264.1	NP_001019784.2|NP_001153736.1	A0PJY2	FEZF1_HUMAN	FEZ family zinc finger 1	64					axon guidance (GO:0007411)|forebrain anterior/posterior pattern specification (GO:0021797)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuron migration (GO:0001764)|olfactory bulb development (GO:0021772)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)	p.S64Y(1)		breast(1)|large_intestine(3)|lung(18)|ovary(2)|prostate(1)	25						GAGATGCAGAGAGTGCTTGGG	0.632																																					p.S64Y												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C191A	7						.						112.0	102.0	105.0					7																	121944301		2203	4300	6503	121731537	SO:0001583	missense	389549	exon1			AY726588	CCDS34741.1, CCDS34741.2, CCDS55157.1	7q31.32	2013-01-08	2006-08-15	2006-08-15	ENSG00000128610	ENSG00000128610		"""Zinc fingers, C2H2-type"""	22788	protein-coding gene	gene with protein product		613301	"""zinc finger protein 312B"""	ZNF312B			Standard	NM_001024613		Approved		uc003vkd.3	A0PJY2	OTTHUMG00000157091	ENST00000442488.2:c.191C>A	7.37:g.121944301G>T	ENSP00000411145:p.Ser64Tyr	Somatic		Capture	Illumina HiSeq	Phase_I	121731537	NM_001024613	A0PJY3|A4D0W3|B4DUP9|B7ZM98	Missense_Mutation	SNP	ENST00000442488.2	37	CCDS34741.2	.	.	.	.	.	.	.	.	.	.	G	17.17	3.319979	0.60634	.	.	ENSG00000128610	ENST00000442488;ENST00000331178;ENST00000427185	T;T;T	0.07021	3.24;3.38;3.23	4.65	4.65	0.58169	.	0.345945	0.34628	N	0.003812	T	0.07234	0.0183	N	0.14661	0.345	0.38043	D	0.935517	P;P	0.49447	0.79;0.924	B;B	0.41813	0.143;0.367	T	0.37572	-0.9700	10	0.49607	T	0.09	-1.2616	18.0697	0.89402	0.0:0.0:1.0:0.0	.	64;64	A0PJY2;A0PJY2-2	FEZF1_HUMAN;.	Y	64	ENSP00000411145:S64Y;ENSP00000332777:S64Y;ENSP00000392727:S64Y	ENSP00000332777:S64Y	S	-	2	0	FEZF1	121731537	0.997000	0.39634	1.000000	0.80357	0.998000	0.95712	3.777000	0.55364	2.560000	0.86352	0.555000	0.69702	TCT		0.632	FEZF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347410.1	NM_001024613	
ZNF800	168850	broad.mit.edu	37	7	127014059	127014059	+	Missense_Mutation	SNP	G	G	A	rs148414799		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr7:127014059G>A	ENST00000393313.1	-	5	1922	c.1331C>T	c.(1330-1332)cCg>cTg	p.P444L	ZNF800_ENST00000393312.1_Missense_Mutation_p.P444L|ZNF800_ENST00000265827.3_Missense_Mutation_p.P444L|ZNF800_ENST00000485577.1_5'Flank			Q2TB10	ZN800_HUMAN	zinc finger protein 800	444					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.P444L(2)		breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(6)|lung(8)|ovary(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	32						CTGTGCTGCCGGTGTGTTCTT	0.408																																					p.P444L												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.C1331T	7						.						82.0	84.0	83.0					7																	127014059		2203	4300	6503	126801295	SO:0001583	missense	168850	exon5			AF218032	CCDS5795.1	7q31.33	2008-05-02			ENSG00000048405	ENSG00000048405		"""Zinc fingers, C2H2-type"""	27267	protein-coding gene	gene with protein product						12477932	Standard	NM_176814		Approved		uc003vly.1	Q2TB10	OTTHUMG00000023456	ENST00000393313.1:c.1331C>T	7.37:g.127014059G>A	ENSP00000376989:p.Pro444Leu	Somatic		Capture	Illumina HiSeq	Phase_I	126801295	NM_176814	Q9HBN0	Missense_Mutation	SNP	ENST00000393313.1	37	CCDS5795.1	.	.	.	.	.	.	.	.	.	.	G	7.748	0.702775	0.15172	.	.	ENSG00000048405	ENST00000393313;ENST00000265827;ENST00000393312	T;T;T	0.15139	2.45;2.45;2.45	5.84	4.96	0.65561	.	0.171581	0.51477	N	0.000087	T	0.09202	0.0227	N	0.08118	0	0.34499	D	0.705807	B;B	0.12630	0.006;0.006	B;B	0.06405	0.002;0.002	T	0.18209	-1.0344	8	.	.	.	-11.3167	13.9527	0.64129	0.0727:0.0:0.9272:0.0	.	347;444	B7Z4V7;Q2TB10	.;ZN800_HUMAN	L	444	ENSP00000376989:P444L;ENSP00000265827:P444L;ENSP00000376988:P444L	.	P	-	2	0	ZNF800	126801295	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.508000	0.60441	1.463000	0.47967	0.591000	0.81541	CCG		0.408	ZNF800-002	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000141823.1	NM_176814	
TNPO3	23534	broad.mit.edu	37	7	128622359	128622359	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr7:128622359C>T	ENST00000265388.5	-	14	1945	c.1802G>A	c.(1801-1803)aGc>aAc	p.S601N	TNPO3_ENST00000471234.1_Missense_Mutation_p.S537N|TNPO3_ENST00000393245.1_Missense_Mutation_p.S635N|TNPO3_ENST00000471166.1_Missense_Mutation_p.S635N|TNPO3_ENST00000482320.1_Missense_Mutation_p.S535N			Q9Y5L0	TNPO3_HUMAN	transportin 3	601					splicing factor protein import into nucleus (GO:0035048)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	receptor activity (GO:0004872)	p.S635N(1)|p.S601N(1)		central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(2)|lung(7)|ovary(2)|prostate(2)|skin(3)	22						TATGCCATTGCTGGGCTCTTG	0.438																																					p.S601N	Pancreas(147;583 2585 39696 52331)											.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G1802A	7						.						125.0	110.0	115.0					7																	128622359		2203	4300	6503	128409595	SO:0001583	missense	23534	exon14			AF145029	CCDS5809.1, CCDS55162.1	7q32.2	2014-02-03			ENSG00000064419	ENSG00000064419		"""Importins"""	17103	protein-coding gene	gene with protein product	"""importin 12"""	610032	"""limb girdle muscular dystrophy 1F (autosomal dominant)"""	LGMD1F		10366588, 10713112, 23543484, 23667635	Standard	NM_012470		Approved	TRN-SR, MTR10A, TRN-SR2, IPO12	uc003vol.2	Q9Y5L0	OTTHUMG00000158409	ENST00000265388.5:c.1802G>A	7.37:g.128622359C>T	ENSP00000265388:p.Ser601Asn	Somatic		Capture	Illumina HiSeq	Phase_I	128409595	NM_012470	A4D1K9|C9IZM0|Q6NUM1|Q96G71|Q96GU9|Q9Y3R2	Missense_Mutation	SNP	ENST00000265388.5	37	CCDS5809.1	.	.	.	.	.	.	.	.	.	.	C	9.171	1.021167	0.19433	.	.	ENSG00000064419	ENST00000393245;ENST00000265388;ENST00000482320;ENST00000471234;ENST00000471166	T	0.67345	-0.26	5.8	4.01	0.46588	Armadillo-type fold (1);	0.269079	0.48767	N	0.000166	T	0.41096	0.1144	N	0.08118	0	0.36357	D	0.860472	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.04013	0.0;0.0;0.001;0.001	T	0.31223	-0.9951	10	0.15066	T	0.55	.	8.6026	0.33754	0.0:0.8265:0.0:0.1735	.	537;635;601;601	C9IZM0;C9J7E5;Q9Y5L0-3;Q9Y5L0	.;.;.;TNPO3_HUMAN	N	635;601;535;537;635	ENSP00000418646:S537N	ENSP00000265388:S601N	S	-	2	0	TNPO3	128409595	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	3.118000	0.50414	0.816000	0.34421	0.650000	0.86243	AGC		0.438	TNPO3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350929.1	NM_012470	
SMO	6608	broad.mit.edu	37	7	128852088	128852088	+	Silent	SNP	A	A	C			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr7:128852088A>C	ENST00000249373.3	+	12	2440	c.2160A>C	c.(2158-2160)ggA>ggC	p.G720G	RP11-286H14.8_ENST00000466717.1_RNA	NM_005631.4	NP_005622.1	Q99835	SMO_HUMAN	smoothened, frizzled class receptor	720					adenohypophysis development (GO:0021984)|anterior/posterior pattern specification (GO:0009952)|atrial septum morphogenesis (GO:0060413)|axon extension involved in axon guidance (GO:0048846)|canonical Wnt signaling pathway (GO:0060070)|cardioblast differentiation (GO:0010002)|cell fate specification (GO:0001708)|cellular response to cholesterol (GO:0071397)|central nervous system neuron differentiation (GO:0021953)|cerebellar cortex morphogenesis (GO:0021696)|ciliary receptor clustering involved in smoothened signaling pathway (GO:0060830)|detection of cell density by contact stimulus involved in contact inhibition (GO:0060248)|determination of left/right asymmetry in lateral mesoderm (GO:0003140)|determination of left/right symmetry (GO:0007368)|dorsal/ventral neural tube patterning (GO:0021904)|embryonic camera-type eye development (GO:0031076)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic neurocranium morphogenesis (GO:0048702)|embryonic viscerocranium morphogenesis (GO:0048703)|epithelial-mesenchymal cell signaling (GO:0060684)|exocrine pancreas development (GO:0031017)|facial nerve development (GO:0021561)|floor plate formation (GO:0021508)|forebrain morphogenesis (GO:0048853)|gonad development (GO:0008406)|hair follicle morphogenesis (GO:0031069)|heart looping (GO:0001947)|heart morphogenesis (GO:0003007)|in utero embryonic development (GO:0001701)|mammary gland epithelial cell differentiation (GO:0060644)|mesenchymal to epithelial transition involved in metanephric renal vesicle formation (GO:0072285)|midgut development (GO:0007494)|multicellular organism growth (GO:0035264)|muscle cell fate commitment (GO:0042693)|myoblast migration (GO:0051451)|negative regulation of apoptotic process (GO:0043066)|negative regulation of DNA binding (GO:0043392)|negative regulation of epithelial cell differentiation (GO:0030857)|negative regulation of gene expression (GO:0010629)|negative regulation of hair follicle development (GO:0051799)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural crest cell migration (GO:0001755)|neuron fate commitment (GO:0048663)|neuron projection regeneration (GO:0031102)|odontogenesis of dentin-containing tooth (GO:0042475)|osteoblast differentiation (GO:0001649)|otolith morphogenesis (GO:0032474)|pancreas morphogenesis (GO:0061113)|positive regulation of branching involved in ureteric bud morphogenesis (GO:0090190)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of gene expression (GO:0010628)|positive regulation of hh target transcription factor activity (GO:0007228)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of protein import into nucleus (GO:0042307)|positive regulation of smoothened signaling pathway (GO:0045880)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein localization to nucleus (GO:0034504)|protein stabilization (GO:0050821)|regulation of heart morphogenesis (GO:2000826)|regulation of stem cell maintenance (GO:2000036)|renal system development (GO:0072001)|semicircular canal morphogenesis (GO:0048752)|skeletal muscle fiber development (GO:0048741)|smoothened signaling pathway (GO:0007224)|smoothened signaling pathway involved in regulation of cerebellar granule cell precursor cell proliferation (GO:0021938)|smoothened signaling pathway involved in ventral spinal cord patterning (GO:0021910)|somite development (GO:0061053)|spermatogenesis (GO:0007283)|thalamus development (GO:0021794)|type B pancreatic cell development (GO:0003323)|vasculogenesis (GO:0001570)|ventral midline determination (GO:0007371)	ciliary membrane (GO:0060170)|cilium (GO:0005929)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|primary cilium (GO:0072372)	drug binding (GO:0008144)|G-protein coupled receptor activity (GO:0004930)|patched binding (GO:0005113)|PDZ domain binding (GO:0030165)|Wnt-activated receptor activity (GO:0042813)|Wnt-protein binding (GO:0017147)	p.G720G(1)		biliary_tract(1)|central_nervous_system(5)|endometrium(1)|kidney(4)|large_intestine(14)|liver(1)|lung(11)|pancreas(2)|prostate(1)|skin(20)|upper_aerodigestive_tract(3)|urinary_tract(1)	64					Fluocinonide(DB01047)|Vismodegib(DB08828)	GTGCCTGGGGAGCTGGGGACT	0.672			Mis		skin basal cell																																p.G720G			Dom	yes		7	7q31-q32	6608	smoothened homolog (Drosophila)		E	.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.A2160C	7						.						25.0	21.0	22.0					7																	128852088		2198	4296	6494	128639324	SO:0001819	synonymous_variant	6608	exon12			U84401	CCDS5811.1	7q32.1	2014-01-29	2014-01-29	2003-01-17	ENSG00000128602	ENSG00000128602		"""GPCR / Class F : Frizzled receptors"""	11119	protein-coding gene	gene with protein product	"""frizzled family member 11"""	601500	"""smoothened (Drosophila) homolog"", ""smoothened homolog (Drosophila)"", ""smoothened, seven transmembrane spanning receptor"", ""smoothened, frizzled family receptor"""	SMOH		9628830	Standard	NM_005631		Approved	FZD11	uc003vor.3	Q99835	OTTHUMG00000158421	ENST00000249373.3:c.2160A>C	7.37:g.128852088A>C		Somatic		Capture	Illumina HiSeq	Phase_I	128639324	NM_005631	A4D1K5	Silent	SNP	ENST00000249373.3	37	CCDS5811.1																																																																																				0.672	SMO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350986.1	NM_005631	
STRIP2	57464	broad.mit.edu	37	7	129122719	129122719	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr7:129122719C>T	ENST00000249344.2	+	20	2126	c.2086C>T	c.(2086-2088)Cgg>Tgg	p.R696W	STRIP2_ENST00000435494.2_Missense_Mutation_p.R696W|RNU1-72P_ENST00000362976.1_RNA	NM_020704.2	NP_065755.1	Q9ULQ0	STRP2_HUMAN	striatin interacting protein 2	696					cell migration (GO:0016477)|cytoskeleton organization (GO:0007010)|regulation of cell shape (GO:0008360)	cytoplasm (GO:0005737)		p.R696W(1)									AATCTTAAAGCGGGCCCTCAA	0.448																																					p.R696W												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C2086T	7						.						89.0	90.0	90.0					7																	129122719		2203	4300	6503	128909955	SO:0001583	missense	57464	exon20			AB032996	CCDS34752.1, CCDS47709.1	7q32.3	2012-11-05	2012-11-05	2012-11-05	ENSG00000128578	ENSG00000128578			22209	protein-coding gene	gene with protein product	"""FAR11 factor arrest 11 homolog B (yeast)"""		"""family with sequence similarity 40, member B"""	FAM40B		22782902, 22298706, 18782753	Standard	NM_020704		Approved	KIAA1170, FAR11B	uc011koy.2	Q9ULQ0	OTTHUMG00000157695	ENST00000249344.2:c.2086C>T	7.37:g.129122719C>T	ENSP00000249344:p.Arg696Trp	Somatic		Capture	Illumina HiSeq	Phase_I	128909955	NM_020704	Q8WUZ4	Missense_Mutation	SNP	ENST00000249344.2	37	CCDS34752.1	.	.	.	.	.	.	.	.	.	.	C	21.1	4.104131	0.76983	.	.	ENSG00000128578	ENST00000249344;ENST00000435494	T;T	0.55052	0.54;0.56	5.32	4.42	0.53409	.	0.000000	0.85682	D	0.000000	T	0.76905	0.4053	M	0.90145	3.09	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.998;1.0	T	0.82596	-0.0379	10	0.87932	D	0	-21.6836	14.3986	0.67027	0.1569:0.8431:0.0:0.0	.	696;696	Q9ULQ0;Q9ULQ0-2	FA40B_HUMAN;.	W	696	ENSP00000249344:R696W;ENSP00000392393:R696W	ENSP00000249344:R696W	R	+	1	2	FAM40B	128909955	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	2.088000	0.41663	1.341000	0.45600	0.655000	0.94253	CGG		0.448	STRIP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349418.1	NM_001134336	
KLF14	136259	broad.mit.edu	37	7	130418117	130418117	+	Silent	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr7:130418117C>T	ENST00000310992.4	-	1	771	c.744G>A	c.(742-744)acG>acA	p.T248T		NM_138693.2	NP_619638.2	Q8TD94	KLF14_HUMAN	Kruppel-like factor 14	248					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.T248T(1)		large_intestine(3)|lung(1)|skin(1)|upper_aerodigestive_tract(1)	6	Melanoma(18;0.0435)					CGCCCGTGTGCGTCCTGTAGT	0.647																																					p.T248T												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G744A	7						.						50.0	48.0	49.0					7																	130418117		2203	4300	6503	130068657	SO:0001819	synonymous_variant	136259	exon1			AF490374	CCDS5825.1	7q32.3	2014-05-06			ENSG00000174595	ENSG00000266265		"""Kruppel-like transcription factors"", ""Zinc fingers, C2H2-type"""	23025	protein-coding gene	gene with protein product		609393				17480121	Standard	NM_138693		Approved	BTEB5	uc003vqk.2	Q8TD94	OTTHUMG00000188298	ENST00000310992.4:c.744G>A	7.37:g.130418117C>T		Somatic		Capture	Illumina HiSeq	Phase_I	130068657	NM_138693	Q19A42|Q19A43	Silent	SNP	ENST00000310992.4	37	CCDS5825.1																																																																																				0.647	KLF14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338013.1	NM_138693	
LRGUK	136332	broad.mit.edu	37	7	133812236	133812236	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr7:133812236A>G	ENST00000285928.2	+	1	185	c.116A>G	c.(115-117)cAg>cGg	p.Q39R	LRGUK_ENST00000473068.1_3'UTR	NM_144648.1	NP_653249.1	Q96M69	LRGUK_HUMAN	leucine-rich repeats and guanylate kinase domain containing	39						cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|kinase activity (GO:0016301)	p.Q39R(1)		breast(1)|endometrium(2)|kidney(2)|large_intestine(12)|lung(23)|ovary(1)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	49						AAAGAGCGTCAGCCTTGCTGG	0.577																																					p.Q39R												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A116G	7						.						96.0	94.0	95.0					7																	133812236		2203	4300	6503	133462776	SO:0001583	missense	136332	exon1			AK057348	CCDS5830.1	7q33	2006-10-27			ENSG00000155530	ENSG00000155530			21964	protein-coding gene	gene with protein product							Standard	NM_144648		Approved	FLJ32786	uc003vrm.1	Q96M69	OTTHUMG00000155320	ENST00000285928.2:c.116A>G	7.37:g.133812236A>G	ENSP00000285928:p.Gln39Arg	Somatic		Capture	Illumina HiSeq	Phase_I	133462776	NM_144648	Q2M3I1	Missense_Mutation	SNP	ENST00000285928.2	37	CCDS5830.1	.	.	.	.	.	.	.	.	.	.	A	9.840	1.190668	0.21954	.	.	ENSG00000155530	ENST00000285928	T	0.35605	1.3	3.8	-0.378	0.12497	.	1.002150	0.08047	N	0.996076	T	0.30198	0.0757	L	0.57536	1.79	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.39800	-0.9596	10	0.66056	D	0.02	0.8499	2.2903	0.04136	0.4372:0.0:0.2755:0.2873	.	39	Q96M69	LRGUK_HUMAN	R	39	ENSP00000285928:Q39R	ENSP00000285928:Q39R	Q	+	2	0	LRGUK	133462776	0.000000	0.05858	0.000000	0.03702	0.013000	0.08279	-0.136000	0.10405	-0.059000	0.13154	0.529000	0.55759	CAG		0.577	LRGUK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339442.1	NM_144648	
SLC13A4	26266	broad.mit.edu	37	7	135366342	135366342	+	Missense_Mutation	SNP	G	G	A	rs148837419		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr7:135366342G>A	ENST00000354042.4	-	16	2539	c.1850C>T	c.(1849-1851)gCg>gTg	p.A617V	SLC13A4_ENST00000491630.1_5'UTR|C7orf73_ENST00000422968.1_Intron	NM_012450.2	NP_036582.2	Q9UKG4	S13A4_HUMAN	solute carrier family 13 (sodium/sulfate symporter), member 4	617					sodium ion transmembrane transport (GO:0035725)|sulfate transport (GO:0008272)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	sodium:sulfate symporter activity (GO:0015382)	p.A617V(1)		breast(1)|central_nervous_system(2)|endometrium(3)|kidney(2)|large_intestine(6)|lung(7)|skin(1)|upper_aerodigestive_tract(2)	24						GCTGACCCTCGCCCATGCTGG	0.542																																					p.A617V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1850T	7						.	A	VAL/ALA	1,4405	2.1+/-5.4	0,1,2202	187.0	142.0	157.0		1850	3.3	0.8	7	dbSNP_134	157	0,8600		0,0,4300	no	missense	SLC13A4	NM_012450.2	64	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	benign	617/627	135366342	1,13005	2203	4300	6503	135016882	SO:0001583	missense	26266	exon16			AF169301	CCDS5840.1	7q33	2013-07-18	2013-07-18		ENSG00000164707	ENSG00000164707		"""Solute carriers"""	15827	protein-coding gene	gene with protein product	"""sulphate transporter 1"""	604309	"""solute carrier family 13 (sodium/sulphate symporters), member 4"""			10535998	Standard	NM_012450		Approved	SUT-1, SUT1	uc003vta.3	Q9UKG4	OTTHUMG00000155539	ENST00000354042.4:c.1850C>T	7.37:g.135366342G>A	ENSP00000297282:p.Ala617Val	Somatic		Capture	Illumina HiSeq	Phase_I	135016882	NM_012450	A4D1Q4|Q8N631	Missense_Mutation	SNP	ENST00000354042.4	37	CCDS5840.1	.	.	.	.	.	.	.	.	.	.	g	14.15	2.448981	0.43531	2.27E-4	0.0	ENSG00000164707	ENST00000354042	T	0.74002	-0.8	5.11	3.33	0.38152	.	0.115340	0.64402	N	0.000019	T	0.67011	0.2848	M	0.79475	2.455	0.58432	D	0.999999	P;B	0.39831	0.69;0.209	B;B	0.23018	0.043;0.027	T	0.69079	-0.5240	10	0.72032	D	0.01	.	9.835	0.40965	0.1662:0.0:0.8338:0.0	.	486;617	Q59HF0;Q9UKG4	.;S13A4_HUMAN	V	617	ENSP00000297282:A617V	ENSP00000297282:A617V	A	-	2	0	SLC13A4	135016882	1.000000	0.71417	0.796000	0.32109	0.369000	0.29798	6.582000	0.74049	0.767000	0.33267	-0.226000	0.12346	GCG		0.542	SLC13A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340558.1	NM_012450	
PTN	5764	broad.mit.edu	37	7	136938300	136938300	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr7:136938300C>T	ENST00000348225.2	-	3	627	c.200G>A	c.(199-201)cGg>cAg	p.R67Q	PTN_ENST00000393083.2_Missense_Mutation_p.R67Q	NM_002825.5	NP_002816.1	P21246	PTN_HUMAN	pleiotrophin	67					bone mineralization (GO:0030282)|learning (GO:0007612)|negative regulation of catalytic activity (GO:0043086)|nervous system development (GO:0007399)|positive regulation of cell division (GO:0051781)|positive regulation of cell proliferation (GO:0008284)|transmembrane receptor protein tyrosine phosphatase signaling pathway (GO:0007185)	endoplasmic reticulum (GO:0005783)|extracellular space (GO:0005615)	heparin binding (GO:0008201)|protein phosphatase inhibitor activity (GO:0004864)	p.R67Q(1)		NS(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(10)|pancreas(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	23						AGTGCCCTCCCGTGTGCCCAG	0.522																																					p.R67Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G200A	7						.						109.0	91.0	97.0					7																	136938300		2203	4300	6503	136588840	SO:0001583	missense	5764	exon3			M57399	CCDS5844.1	7q33	2014-01-30	2008-07-31		ENSG00000105894	ENSG00000105894		"""Endogenous ligands"""	9630	protein-coding gene	gene with protein product	"""heparin binding growth factor 8"""	162095	"""neurite growth-promoting factor 1"""	NEGF1		1457401, 1768439	Standard	NM_002825		Approved	HBNF, HBGF8	uc003vtq.2	P21246	OTTHUMG00000155709	ENST00000348225.2:c.200G>A	7.37:g.136938300C>T	ENSP00000341170:p.Arg67Gln	Somatic		Capture	Illumina HiSeq	Phase_I	136588840	NM_002825	Q5U0B0|Q6ICQ5|Q9UCC6	Missense_Mutation	SNP	ENST00000348225.2	37	CCDS5844.1	.	.	.	.	.	.	.	.	.	.	C	33	5.215873	0.95104	.	.	ENSG00000105894	ENST00000348225;ENST00000393083	.	.	.	5.65	4.77	0.60923	Midkine heparin-binding growth factor, N-terminal (3);Midkine heparin-binding growth factor, conserved site (1);Midkine heparin-binding growth factor, disulphide-rich domain (1);	0.000000	0.85682	D	0.000000	T	0.77116	0.4083	M	0.66297	2.02	0.52099	D	0.999941	D;D	0.89917	1.0;1.0	D;D	0.85130	0.968;0.997	T	0.79962	-0.1582	9	0.87932	D	0	-21.0225	14.5889	0.68347	0.0:0.93:0.0:0.07	.	67;67	C9JR52;P21246	.;PTN_HUMAN	Q	67	.	ENSP00000341170:R67Q	R	-	2	0	PTN	136588840	1.000000	0.71417	1.000000	0.80357	0.750000	0.42670	7.613000	0.82986	1.391000	0.46566	0.585000	0.79938	CGG		0.522	PTN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341339.1	NM_002825	
KIAA1549	57670	broad.mit.edu	37	7	138552736	138552736	+	Silent	SNP	G	G	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr7:138552736G>T	ENST00000422774.1	-	15	4962	c.4914C>A	c.(4912-4914)gcC>gcA	p.A1638A	KIAA1549_ENST00000242365.4_Silent_p.A1588A|KIAA1549_ENST00000440172.1_Silent_p.A1638A			Q9HCM3	K1549_HUMAN	KIAA1549	1638						integral component of membrane (GO:0016021)		p.A1588A(2)|p.A1638A(1)	KIAA1549/BRAF(703)	large_intestine(4)|pancreas(1)|upper_aerodigestive_tract(2)	7						ATCCGATGTAGGCTGAGTTGT	0.627			O	BRAF	pilocytic astrocytoma																																p.A1638A	NSCLC(119;1534 1718 44213 46230 50068)		Dom	yes		7	7q34	57670	KIAA1549		O	.	.	3	Substitution - coding silent(3)	large_intestine(3)	c.C4914A	7						.						53.0	60.0	58.0					7																	138552736		2038	4175	6213	138203276	SO:0001819	synonymous_variant	57670	exon15				CCDS47723.1, CCDS47723.2, CCDS56513.1	7q34	2009-10-09			ENSG00000122778	ENSG00000122778			22219	protein-coding gene	gene with protein product		613344					Standard	NM_020910		Approved		uc011kql.2	Q9HCM3	OTTHUMG00000157214	ENST00000422774.1:c.4914C>A	7.37:g.138552736G>T		Somatic		Capture	Illumina HiSeq	Phase_I	138203276	NM_001164665	B6HY55|B6HY56|B6HY58|B6HY60|B6HY61|B6HY62|B6HY63|B6HY64|B6HY65|B6HY66|Q5BJD6|Q8IY15|Q9H0M3	Silent	SNP	ENST00000422774.1	37	CCDS56513.1																																																																																				0.627	KIAA1549-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000348092.1		
KIAA1549	57670	broad.mit.edu	37	7	138602453	138602453	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr7:138602453G>A	ENST00000422774.1	-	2	1967	c.1919C>T	c.(1918-1920)tCg>tTg	p.S640L	KIAA1549_ENST00000242365.4_Missense_Mutation_p.S590L|KIAA1549_ENST00000440172.1_Missense_Mutation_p.S640L			Q9HCM3	K1549_HUMAN	KIAA1549	640	Ser-rich.					integral component of membrane (GO:0016021)		p.S590L(1)|p.S640L(1)	KIAA1549/BRAF(703)	large_intestine(4)|pancreas(1)|upper_aerodigestive_tract(2)	7						TTCCGAAGGCGAAGAGATGGA	0.493			O	BRAF	pilocytic astrocytoma																																p.S640L	NSCLC(119;1534 1718 44213 46230 50068)		Dom	yes		7	7q34	57670	KIAA1549		O	.	.	2	Substitution - Missense(2)	large_intestine(2)	c.C1919T	7						.						28.0	32.0	31.0					7																	138602453		1932	4134	6066	138252993	SO:0001583	missense	57670	exon2				CCDS47723.1, CCDS47723.2, CCDS56513.1	7q34	2009-10-09			ENSG00000122778	ENSG00000122778			22219	protein-coding gene	gene with protein product		613344					Standard	NM_020910		Approved		uc011kql.2	Q9HCM3	OTTHUMG00000157214	ENST00000422774.1:c.1919C>T	7.37:g.138602453G>A	ENSP00000416040:p.Ser640Leu	Somatic		Capture	Illumina HiSeq	Phase_I	138252993	NM_001164665	B6HY55|B6HY56|B6HY58|B6HY60|B6HY61|B6HY62|B6HY63|B6HY64|B6HY65|B6HY66|Q5BJD6|Q8IY15|Q9H0M3	Missense_Mutation	SNP	ENST00000422774.1	37	CCDS56513.1	.	.	.	.	.	.	.	.	.	.	G	3.400	-0.122384	0.06795	.	.	ENSG00000122778	ENST00000440172;ENST00000242365;ENST00000422774	T;T;T	0.22134	1.97;1.98;1.97	4.25	1.47	0.22746	.	0.942262	0.08691	N	0.907886	T	0.09512	0.0234	N	0.11560	0.145	0.09310	N	1	B;B	0.14012	0.005;0.009	B;B	0.06405	0.001;0.002	T	0.40997	-0.9533	10	0.10377	T	0.69	.	6.1735	0.20431	0.449:0.0:0.551:0.0	.	640;640	Q9HCM3;Q9HCM3-2	K1549_HUMAN;.	L	640;590;640	ENSP00000406661:S640L;ENSP00000242365:S590L;ENSP00000416040:S640L	ENSP00000242365:S590L	S	-	2	0	KIAA1549	138252993	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	0.711000	0.25764	0.119000	0.18210	0.591000	0.81541	TCG		0.493	KIAA1549-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000348092.1		
KIAA1549	57670	broad.mit.edu	37	7	138603258	138603258	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr7:138603258C>T	ENST00000422774.1	-	2	1162	c.1114G>A	c.(1114-1116)Gct>Act	p.A372T	KIAA1549_ENST00000242365.4_Missense_Mutation_p.A322T|KIAA1549_ENST00000440172.1_Missense_Mutation_p.A372T			Q9HCM3	K1549_HUMAN	KIAA1549	372						integral component of membrane (GO:0016021)		p.A303T(1)|p.A322T(1)|p.A372T(1)	KIAA1549/BRAF(703)	large_intestine(4)|pancreas(1)|upper_aerodigestive_tract(2)	7						GTTGGTGAAGCAGAGGACGCA	0.507			O	BRAF	pilocytic astrocytoma																																p.A372T	NSCLC(119;1534 1718 44213 46230 50068)		Dom	yes		7	7q34	57670	KIAA1549		O	.	.	3	Substitution - Missense(3)	large_intestine(3)	c.G1114A	7						.						142.0	149.0	146.0					7																	138603258		2122	4235	6357	138253798	SO:0001583	missense	57670	exon2				CCDS47723.1, CCDS47723.2, CCDS56513.1	7q34	2009-10-09			ENSG00000122778	ENSG00000122778			22219	protein-coding gene	gene with protein product		613344					Standard	NM_020910		Approved		uc011kql.2	Q9HCM3	OTTHUMG00000157214	ENST00000422774.1:c.1114G>A	7.37:g.138603258C>T	ENSP00000416040:p.Ala372Thr	Somatic		Capture	Illumina HiSeq	Phase_I	138253798	NM_001164665	B6HY55|B6HY56|B6HY58|B6HY60|B6HY61|B6HY62|B6HY63|B6HY64|B6HY65|B6HY66|Q5BJD6|Q8IY15|Q9H0M3	Missense_Mutation	SNP	ENST00000422774.1	37	CCDS56513.1	.	.	.	.	.	.	.	.	.	.	C	0.706	-0.789066	0.02884	.	.	ENSG00000122778	ENST00000440172;ENST00000242365;ENST00000422774	T;T;T	0.22743	1.94;1.95;1.94	4.84	-9.69	0.00524	.	0.698070	0.13013	N	0.420662	T	0.09423	0.0232	N	0.14661	0.345	0.09310	N	1	B;B	0.06786	0.001;0.001	B;B	0.08055	0.001;0.003	T	0.17107	-1.0380	10	0.31617	T	0.26	.	13.5129	0.61524	0.0:0.5756:0.2845:0.1398	.	372;372	Q9HCM3;Q9HCM3-2	K1549_HUMAN;.	T	372;322;372	ENSP00000406661:A372T;ENSP00000242365:A322T;ENSP00000416040:A372T	ENSP00000242365:A322T	A	-	1	0	KIAA1549	138253798	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.346000	0.02634	-2.633000	0.00433	-0.355000	0.07637	GCT		0.507	KIAA1549-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000348092.1		
TAS2R4	50832	broad.mit.edu	37	7	141478773	141478773	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr7:141478773C>T	ENST00000247881.2	+	1	532	c.485C>T	c.(484-486)aCg>aTg	p.T162M	SSBP1_ENST00000465582.1_Intron	NM_016944.1	NP_058640.1	Q9NYW5	TA2R4_HUMAN	taste receptor, type 2, member 4	162					detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)|respiratory gaseous exchange (GO:0007585)|sensory perception of taste (GO:0050909)|signal transduction (GO:0007165)	cilium (GO:0005929)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	bitter taste receptor activity (GO:0033038)|taste receptor activity (GO:0008527)	p.T162M(1)		endometrium(1)|large_intestine(4)|lung(2)	7	Melanoma(164;0.0171)			BRCA - Breast invasive adenocarcinoma(188;0.196)		CTTGTGACTACGAGAAATAAC	0.448																																					p.T162M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C485T	7						.						264.0	252.0	256.0					7																	141478773		2203	4300	6503	141125242	SO:0001583	missense	50832	exon1			AF227131	CCDS5868.1	7q31.3-q32	2012-08-22			ENSG00000127364	ENSG00000127364		"""Taste receptors / Type 2"", ""GPCR / Unclassified : Taste receptors"""	14911	protein-coding gene	gene with protein product		604869				10761934, 10761935	Standard	NM_016944		Approved	T2R4	uc003vwq.1	Q9NYW5	OTTHUMG00000157634	ENST00000247881.2:c.485C>T	7.37:g.141478773C>T	ENSP00000247881:p.Thr162Met	Somatic		Capture	Illumina HiSeq	Phase_I	141125242	NM_016944	Q645W5|Q75MV8	Missense_Mutation	SNP	ENST00000247881.2	37	CCDS5868.1	.	.	.	.	.	.	.	.	.	.	c	2.578	-0.297967	0.05532	.	.	ENSG00000127364	ENST00000247881	T	0.37752	1.18	5.31	-4.66	0.03329	.	2.144230	0.01480	N	0.016640	T	0.24084	0.0583	L	0.36672	1.1	0.09310	N	1	B	0.15141	0.012	B	0.18263	0.021	T	0.07347	-1.0777	10	0.34782	T	0.22	.	1.0435	0.01564	0.4279:0.1961:0.1612:0.2148	.	162	Q9NYW5	TA2R4_HUMAN	M	162	ENSP00000247881:T162M	ENSP00000247881:T162M	T	+	2	0	TAS2R4	141125242	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	-0.734000	0.04893	-1.035000	0.03291	-1.099000	0.02127	ACG		0.448	TAS2R4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349285.1		
TRPV5	56302	broad.mit.edu	37	7	142627463	142627463	+	Silent	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr7:142627463G>A	ENST00000265310.1	-	2	555	c.207C>T	c.(205-207)acC>acT	p.T69T	TRPV5_ENST00000442623.1_Silent_p.T69T	NM_019841.4	NP_062815.2	Q9NQA5	TRPV5_HUMAN	transient receptor potential cation channel, subfamily V, member 5	69					calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|calcium ion transport into cytosol (GO:0060402)|ion transmembrane transport (GO:0034220)|protein tetramerization (GO:0051262)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)	p.T69T(1)		NS(1)|breast(2)|central_nervous_system(3)|endometrium(2)|kidney(1)|large_intestine(14)|lung(32)|ovary(3)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(3)	67	Melanoma(164;0.059)					GAACGTCACAGGTGCAGTCCA	0.498																																					p.T69T												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C207T	7						.						171.0	140.0	151.0					7																	142627463		2203	4300	6503	142337585	SO:0001819	synonymous_variant	56302	exon2			AJ271207	CCDS5875.1	7q34	2013-01-10	2002-01-29	2002-02-01	ENSG00000127412	ENSG00000127412		"""Voltage-gated ion channels / Transient receptor potential cation channels"", ""Ankyrin repeat domain containing"""	3145	protein-coding gene	gene with protein product		606679	"""epithelial calcium channel 1"""	ECAC1		10944439, 10945469, 16382100	Standard	NM_019841		Approved	CaT2	uc003wby.1	Q9NQA5	OTTHUMG00000157157	ENST00000265310.1:c.207C>T	7.37:g.142627463G>A		Somatic		Capture	Illumina HiSeq	Phase_I	142337585	NM_019841	A4D2H7|E9PBZ6|Q8N4C1|Q8NDW5|Q8NDX7|Q8NDX8|Q96PM6	Silent	SNP	ENST00000265310.1	37	CCDS5875.1																																																																																				0.498	TRPV5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347660.1	NM_019841	
EPHA1	2041	broad.mit.edu	37	7	143097002	143097002	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr7:143097002C>T	ENST00000275815.3	-	4	663	c.577G>A	c.(577-579)Gcc>Acc	p.A193T		NM_005232.4	NP_005223.4	P21709	EPHA1_HUMAN	EPH receptor A1	193	Cys-rich.|Eph LBD. {ECO:0000255|PROSITE- ProRule:PRU00883}.				activation of Rho GTPase activity (GO:0032862)|angiogenesis (GO:0001525)|cell surface receptor signaling pathway (GO:0007166)|negative regulation of cell migration (GO:0030336)|negative regulation of protein kinase activity (GO:0006469)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell-matrix adhesion (GO:0001954)|positive regulation of stress fiber assembly (GO:0051496)|protein autophosphorylation (GO:0046777)|regulation of Rac GTPase activity (GO:0032314)|substrate adhesion-dependent cell spreading (GO:0034446)	integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein kinase binding (GO:0019901)|transmembrane-ephrin receptor activity (GO:0005005)	p.A193T(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(11)|lung(21)|ovary(4)|skin(1)|stomach(1)|urinary_tract(3)	51	Melanoma(164;0.205)	Myeloproliferative disorder(862;0.0255)				GACACCAGGGCCACACAGGCA	0.642																																					p.A193T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G577A	7						.						34.0	33.0	33.0					7																	143097002		2203	4297	6500	142807124	SO:0001583	missense	2041	exon4			M18391	CCDS5884.1	7q32-q36	2013-02-11	2004-10-28		ENSG00000146904	ENSG00000146904	2.7.10.1	"""EPH receptors"", ""Sterile alpha motif (SAM) domain containing"", ""Fibronectin type III domain containing"""	3385	protein-coding gene	gene with protein product		179610	"""EphA1"""	EPHT, EPHT1		9267020	Standard	NM_005232		Approved	EPH	uc003wcz.3	P21709	OTTHUMG00000155894	ENST00000275815.3:c.577G>A	7.37:g.143097002C>T	ENSP00000275815:p.Ala193Thr	Somatic		Capture	Illumina HiSeq	Phase_I	142807124	NM_005232	A1L3V3|B5A966|B5A967|Q15405	Missense_Mutation	SNP	ENST00000275815.3	37	CCDS5884.1	.	.	.	.	.	.	.	.	.	.	C	20.3	3.972336	0.74246	.	.	ENSG00000146904	ENST00000275815	T	0.06768	3.26	4.79	4.79	0.61399	Tyrosine-protein kinase, receptor class V, conserved site (1);Ephrin receptor, ligand binding (2);Galactose-binding domain-like (1);	0.000000	0.56097	D	0.000029	T	0.19725	0.0474	M	0.87328	2.875	0.46849	D	0.999228	B	0.20780	0.048	B	0.25140	0.058	T	0.07309	-1.0779	10	0.87932	D	0	.	18.0282	0.89275	0.0:1.0:0.0:0.0	.	193	P21709	EPHA1_HUMAN	T	193	ENSP00000275815:A193T	ENSP00000275815:A193T	A	-	1	0	EPHA1	142807124	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.771000	0.62318	2.469000	0.83416	0.655000	0.94253	GCC		0.642	EPHA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342154.1		
ARHGEF35	445328	broad.mit.edu	37	7	143885468	143885468	+	Silent	SNP	A	A	G			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr7:143885468A>G	ENST00000378115.2	-	2	138	c.9T>C	c.(7-9)gcT>gcC	p.A3A	ARHGEF35_ENST00000543357.1_Silent_p.A3A	NM_001003702.2	NP_001003702.2	A5YM69	ARG35_HUMAN	Rho guanine nucleotide exchange factor (GEF) 35	3								p.A3A(1)		kidney(1)|large_intestine(1)|lung(3)|stomach(1)	6						GGGCCTCCTCAGCCTCCATCA	0.498																																					p.A3A												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.T9C	7						.						48.0	46.0	47.0					7																	143885468		1910	3410	5320	143516401	SO:0001819	synonymous_variant	445328	exon2			AK125680	CCDS34770.1	7q35	2012-07-24	2010-04-13	2010-04-13	ENSG00000213214	ENSG00000213214		"""Rho guanine nucleotide exchange factors"""	33846	protein-coding gene	gene with protein product			"""Rho guanine nucleotide exchange factor (GEF) 5-like"""	ARHGEF5L			Standard	NM_001003702		Approved	FLJ43692, CTAGE4	uc003wdz.2	A5YM69	OTTHUMG00000158010	ENST00000378115.2:c.9T>C	7.37:g.143885468A>G		Somatic		Capture	Illumina HiSeq	Phase_I	143516401	NM_001003702	Q6ZUI2	Silent	SNP	ENST00000378115.2	37	CCDS34770.1																																																																																				0.498	ARHGEF35-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349997.1	NM_001003702	
CNTNAP2	26047	broad.mit.edu	37	7	146741036	146741036	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr7:146741036G>A	ENST00000361727.3	+	4	956	c.440G>A	c.(439-441)cGg>cAg	p.R147Q		NM_014141.5	NP_054860.1	Q9UHC6	CNTP2_HUMAN	contactin associated protein-like 2	147	F5/8 type C. {ECO:0000255|PROSITE- ProRule:PRU00081}.				adult behavior (GO:0030534)|brain development (GO:0007420)|cell adhesion (GO:0007155)|cellular protein localization (GO:0034613)|cerebral cortex development (GO:0021987)|clustering of voltage-gated potassium channels (GO:0045163)|learning (GO:0007612)|limbic system development (GO:0021761)|neuron projection development (GO:0031175)|neuron recognition (GO:0008038)|protein localization to juxtaparanode region of axon (GO:0071205)|social behavior (GO:0035176)|striatum development (GO:0021756)|superior temporal gyrus development (GO:0071109)|thalamus development (GO:0021794)|transmission of nerve impulse (GO:0019226)|vocalization behavior (GO:0071625)	axolemma (GO:0030673)|axon (GO:0030424)|cell surface (GO:0009986)|dendrite (GO:0030425)|early endosome (GO:0005769)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|juxtaparanode region of axon (GO:0044224)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|perikaryon (GO:0043204)|voltage-gated potassium channel complex (GO:0008076)	enzyme binding (GO:0019899)	p.R147Q(1)		NS(3)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(21)|lung(105)|ovary(9)|pancreas(2)|prostate(5)|skin(7)|stomach(3)|upper_aerodigestive_tract(6)|urinary_tract(3)	188	Melanoma(164;0.153)	all_cancers(3;3.51e-10)|all_epithelial(3;1.4e-05)|Myeloproliferative disorder(3;0.00452)|Lung NSC(3;0.0067)|all_lung(3;0.00794)	OV - Ovarian serous cystadenocarcinoma(82;0.0319)			GGTGTGGTCCGGCACGAATTA	0.428										HNSCC(39;0.1)																											p.R147Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G440A	7						.						165.0	142.0	150.0					7																	146741036		2203	4300	6503	146371969	SO:0001583	missense	26047	exon4			AF193613	CCDS5889.1	7q35	2008-02-04			ENSG00000174469	ENSG00000174469			13830	protein-coding gene	gene with protein product		604569				10624965, 10048485	Standard	NM_014141		Approved	Caspr2, KIAA0868, NRXN4	uc003weu.2	Q9UHC6	OTTHUMG00000152743	ENST00000361727.3:c.440G>A	7.37:g.146741036G>A	ENSP00000354778:p.Arg147Gln	Somatic		Capture	Illumina HiSeq	Phase_I	146371969	NM_014141	D3DWG2|Q14DG2|Q52LV1|Q5H9Q7|Q9UQ12	Missense_Mutation	SNP	ENST00000361727.3	37	CCDS5889.1	.	.	.	.	.	.	.	.	.	.	G	12.23	1.876659	0.33162	.	.	ENSG00000174469	ENST00000361727	D	0.98178	-4.77	5.37	5.37	0.77165	Coagulation factor 5/8 C-terminal type domain (3);Galactose-binding domain-like (1);	0.000000	0.51477	D	0.000099	D	0.92450	0.7603	N	0.13043	0.29	0.80722	D	1	P	0.42456	0.78	B	0.28849	0.095	D	0.91985	0.5598	10	0.22706	T	0.39	.	11.2079	0.48780	0.0849:0.0:0.9151:0.0	.	147	Q9UHC6	CNTP2_HUMAN	Q	147	ENSP00000354778:R147Q	ENSP00000354778:R147Q	R	+	2	0	CNTNAP2	146371969	0.998000	0.40836	0.844000	0.33320	0.084000	0.17831	3.136000	0.50554	2.512000	0.84698	0.462000	0.41574	CGG		0.428	CNTNAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327668.1		
EZH2	2146	broad.mit.edu	37	7	148514988	148514988	+	Silent	SNP	A	A	G			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr7:148514988A>G	ENST00000460911.1	-	10	1294	c.1206T>C	c.(1204-1206)gaT>gaC	p.D402D	EZH2_ENST00000350995.2_Silent_p.D363D|EZH2_ENST00000478654.1_Silent_p.D393D|EZH2_ENST00000483967.1_Silent_p.D393D|EZH2_ENST00000476773.1_Silent_p.D393D|EZH2_ENST00000320356.2_Silent_p.D407D|EZH2_ENST00000541220.1_Silent_p.D393D			Q15910	EZH2_HUMAN	enhancer of zeste 2 polycomb repressive complex 2 subunit	402	Interaction with CDYL.				cellular response to hydrogen peroxide (GO:0070301)|cerebellar cortex development (GO:0021695)|chromatin organization (GO:0006325)|DNA methylation (GO:0006306)|G1 to G0 transition (GO:0070314)|histone H3-K27 methylation (GO:0070734)|negative regulation of epidermal cell differentiation (GO:0045605)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of gene expression, epigenetic (GO:0045814)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|negative regulation of striated muscle cell differentiation (GO:0051154)|negative regulation of transcription elongation from RNA polymerase II promoter (GO:0034244)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|positive regulation of Ras GTPase activity (GO:0032320)|protein localization to chromatin (GO:0071168)|regulation of cell proliferation (GO:0042127)|regulation of circadian rhythm (GO:0042752)|regulation of gliogenesis (GO:0014013)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|ESC/E(Z) complex (GO:0035098)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|pronucleus (GO:0045120)	chromatin binding (GO:0003682)|chromatin DNA binding (GO:0031490)|core promoter binding (GO:0001047)|DNA binding (GO:0003677)|histone methyltransferase activity (GO:0042054)|histone methyltransferase activity (H3-K27 specific) (GO:0046976)|RNA binding (GO:0003723)|sequence-specific DNA binding (GO:0043565)	p.D407D(1)|p.D363D(1)		breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(313)|kidney(3)|large_intestine(8)|liver(1)|lung(23)|parathyroid(2)|skin(3)|upper_aerodigestive_tract(3)	359	Melanoma(164;0.15)		OV - Ovarian serous cystadenocarcinoma(82;0.00239)			TCGAAGTTTCATCTTTCTTCT	0.408			Mis		DLBCL																																p.D363D			Rec?	yes		7	7q35-q36	2146	enhancer of zeste homolog 2		L	.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.T1089C	7						.						273.0	212.0	233.0					7																	148514988		2203	4300	6503	148145921	SO:0001819	synonymous_variant	2146	exon9				CCDS5891.1, CCDS5892.1, CCDS56516.1, CCDS56517.1, CCDS56518.1	7q35-q36	2014-09-17	2014-05-28		ENSG00000106462	ENSG00000106462		"""Chromatin-modifying enzymes / K-methyltransferases"""	3527	protein-coding gene	gene with protein product		601573	"""enhancer of zeste (Drosophila) homolog 2"", ""enhancer of zeste homolog 2 (Drosophila)"""			8954776, 17172412	Standard	NM_152998		Approved	EZH1, ENX-1, KMT6, KMT6A	uc003wfb.2	Q15910	OTTHUMG00000158973	ENST00000460911.1:c.1206T>C	7.37:g.148514988A>G		Somatic		Capture	Illumina HiSeq	Phase_I	148145921	NM_152998	B2RAQ1|B3KS30|B7Z1D6|B7Z7L6|Q15755|Q75MG3|Q92857|Q96FI6	Silent	SNP	ENST00000460911.1	37	CCDS56516.1																																																																																				0.408	EZH2-008	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000352744.1	NM_004456	
ZNF786	136051	broad.mit.edu	37	7	148769184	148769184	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr7:148769184G>A	ENST00000491431.1	-	4	744	c.680C>T	c.(679-681)aCg>aTg	p.T227M	ZNF786_ENST00000451334.3_Missense_Mutation_p.T190M|ZNF786_ENST00000316286.9_Missense_Mutation_p.T141M	NM_152411.3	NP_689624.2	Q8N393	ZN786_HUMAN	zinc finger protein 786	227					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.T226M(1)		breast(4)|cervix(1)|kidney(1)|large_intestine(3)|lung(10)|prostate(2)|skin(2)|soft_tissue(1)|urinary_tract(2)	26	Melanoma(164;0.15)		OV - Ovarian serous cystadenocarcinoma(82;0.00463)			CGGCATCTGCGTCTCCGCCCT	0.592																																					p.T227M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C680T	7						.						29.0	35.0	33.0					7																	148769184		2096	4216	6312	148400117	SO:0001583	missense	136051	exon4			AK095701, AL834510	CCDS47738.1	7q36.1	2013-01-08			ENSG00000197362	ENSG00000197362		"""Zinc fingers, C2H2-type"", ""-"""	21806	protein-coding gene	gene with protein product							Standard	NM_152411		Approved	DKFZp762I137	uc003wfh.2	Q8N393	OTTHUMG00000158975	ENST00000491431.1:c.680C>T	7.37:g.148769184G>A	ENSP00000417470:p.Thr227Met	Somatic		Capture	Illumina HiSeq	Phase_I	148400117	NM_152411	A1A568|B4DMI1	Missense_Mutation	SNP	ENST00000491431.1	37	CCDS47738.1	.	.	.	.	.	.	.	.	.	.	G	9.598	1.127910	0.20959	.	.	ENSG00000197362	ENST00000316286;ENST00000538412;ENST00000491431;ENST00000451334	T;T;T	0.08370	3.1;3.22;3.14	4.31	1.08	0.20341	.	2.276800	0.02185	N	0.060792	T	0.04543	0.0124	N	0.08118	0	0.09310	N	1	P	0.51240	0.943	B	0.37047	0.24	T	0.23691	-1.0181	10	0.87932	D	0	0.6087	4.7154	0.12893	0.2156:0.0:0.6187:0.1657	.	227	Q8N393	ZN786_HUMAN	M	141;141;227;190	ENSP00000313516:T141M;ENSP00000417470:T227M;ENSP00000404984:T190M	ENSP00000313516:T141M	T	-	2	0	ZNF786	148400117	0.008000	0.16893	0.000000	0.03702	0.001000	0.01503	1.890000	0.39728	0.380000	0.24823	-0.291000	0.09656	ACG		0.592	ZNF786-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352751.1	NM_152411	
ZNF425	155054	broad.mit.edu	37	7	148801589	148801589	+	Silent	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr7:148801589G>A	ENST00000378061.2	-	4	1506	c.1374C>T	c.(1372-1374)cgC>cgT	p.R458R		NM_001001661.2	NP_001001661.1	Q6IV72	ZN425_HUMAN	zinc finger protein 425	458					negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.R458R(1)		breast(6)|endometrium(4)|kidney(3)|large_intestine(11)|lung(20)|ovary(3)|skin(2)|upper_aerodigestive_tract(1)	50	Melanoma(164;0.15)		OV - Ovarian serous cystadenocarcinoma(82;0.00463)			GCTGGTGGGCGCGCATGGCGT	0.662																																					p.R458R												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1374T	7						.						33.0	34.0	34.0					7																	148801589		2203	4300	6503	148432522	SO:0001819	synonymous_variant	155054	exon4			AK056498	CCDS34773.1	7q36.1	2013-01-08			ENSG00000204947	ENSG00000204947		"""Zinc fingers, C2H2-type"", ""-"""	20690	protein-coding gene	gene with protein product							Standard	NM_001001661		Approved		uc003wfj.3	Q6IV72	OTTHUMG00000158971	ENST00000378061.2:c.1374C>T	7.37:g.148801589G>A		Somatic		Capture	Illumina HiSeq	Phase_I	148432522	NM_001001661	B3KPM1|Q08AG3	Silent	SNP	ENST00000378061.2	37	CCDS34773.1																																																																																				0.662	ZNF425-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352726.1	XM_088140	
ZNF746	155061	broad.mit.edu	37	7	149191149	149191149	+	Silent	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr7:149191149G>A	ENST00000340622.3	-	3	617	c.337C>T	c.(337-339)Ctg>Ttg	p.L113L	ZNF746_ENST00000461958.2_Silent_p.L113L|ZNF746_ENST00000458143.2_Silent_p.L113L			Q6NUN9	ZN746_HUMAN	zinc finger protein 746	113	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of neuron death (GO:1901216)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)	p.L113L(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(5)|large_intestine(4)|lung(11)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	34	Melanoma(164;0.165)		OV - Ovarian serous cystadenocarcinoma(82;0.00358)			CAGTCCTCCAGCTTGCCCCAC	0.562																																					p.L113L												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C337T	7						.						189.0	162.0	171.0					7																	149191149		2203	4300	6503	148822082	SO:0001819	synonymous_variant	155061	exon3			AK055975	CCDS5897.1, CCDS55180.1	7q36.1	2013-01-08			ENSG00000181220	ENSG00000181220		"""Zinc fingers, C2H2-type"", ""-"""	21948	protein-coding gene	gene with protein product		613914					Standard	NM_152557		Approved	FLJ31413	uc010lpi.2	Q6NUN9	OTTHUMG00000158972	ENST00000340622.3:c.337C>T	7.37:g.149191149G>A		Somatic		Capture	Illumina HiSeq	Phase_I	148822082	NM_001163474	A8K6Z9|Q6ZRF9	Silent	SNP	ENST00000340622.3	37	CCDS5897.1																																																																																				0.562	ZNF746-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000352730.1	NM_152557	
KRBA1	84626	broad.mit.edu	37	7	149427638	149427638	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr7:149427638A>G	ENST00000485033.2	+	13	1943	c.1943A>G	c.(1942-1944)tAc>tGc	p.Y648C	KRBA1_ENST00000319551.8_Missense_Mutation_p.Y648C|KRBA1_ENST00000255992.10_Missense_Mutation_p.Y708C|KRBA1_ENST00000479560.1_3'UTR			A5PL33	KRBA1_HUMAN	KRAB-A domain containing 1	709	Pro-rich.							p.Y708C(1)		breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(17)|ovary(1)|prostate(1)	27	Melanoma(164;0.165)|Ovarian(565;0.177)		OV - Ovarian serous cystadenocarcinoma(82;0.00625)			GAGCCCAGGTACTGCAGCGGC	0.657																																					p.T709A												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A2125G	7						.						27.0	30.0	29.0					7																	149427638		1927	4121	6048	149058571	SO:0001583	missense	84626	exon15			AB058765	CCDS75674.1	7q36	2014-02-12	2006-08-15		ENSG00000133619	ENSG00000133619		"""-"""	22228	protein-coding gene	gene with protein product			"""KRAB A domain containing 1"""				Standard	NM_001290187		Approved	KIAA1862	uc003wfz.3	A5PL33	OTTHUMG00000157886	ENST00000485033.2:c.1943A>G	7.37:g.149427638A>G	ENSP00000420112:p.Tyr648Cys	Somatic		Capture	Illumina HiSeq	Phase_I	149058571	NM_032534	A7E2F5|E7ENE9|Q8N4X0|Q96JG5	Missense_Mutation	SNP	ENST00000485033.2	37		.	.	.	.	.	.	.	.	.	.	A	12.70	2.015837	0.35606	.	.	ENSG00000133619	ENST00000255992;ENST00000319551;ENST00000485033	T;T;T	0.30714	1.52;1.52;1.52	4.5	-4.35	0.03656	.	2.127480	0.01941	N	0.041860	T	0.24699	0.0599	.	.	.	0.09310	N	1	P;P	0.42010	0.768;0.768	B;B	0.41036	0.346;0.346	T	0.28933	-1.0028	9	0.51188	T	0.08	7.0E-4	5.6753	0.17745	0.2908:0.3089:0.4002:0.0	.	648;709	E7ENE9;A5PL33	.;KRBA1_HUMAN	C	708;648;648	ENSP00000255992:Y708C;ENSP00000317165:Y648C;ENSP00000420112:Y648C	ENSP00000255992:Y708C	Y	+	2	0	KRBA1	149058571	0.000000	0.05858	0.000000	0.03702	0.026000	0.11368	-0.651000	0.05372	-1.079000	0.03113	-0.376000	0.06991	TAC		0.657	KRBA1-004	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000349841.3	NM_032534	
SSPO	23145	broad.mit.edu	37	7	149475969	149475969	+	RNA	SNP	A	A	G			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr7:149475969A>G	ENST00000378016.2	+	0	935							A2VEC9	SSPO_HUMAN	SCO-spondin						cell adhesion (GO:0007155)	extracellular space (GO:0005615)	peptidase inhibitor activity (GO:0030414)					Melanoma(164;0.165)|Ovarian(565;0.177)		OV - Ovarian serous cystadenocarcinoma(82;0.00625)			ATCTCTGTGGACCACGAGCTC	0.632																																					p.D312G												.	.	0			c.A935G	7						.						106.0	120.0	116.0					7																	149475969		2075	4208	6283	149106902			23145	exon7			AK093431		7q36.1	2013-08-07	2013-08-06		ENSG00000197558	ENSG00000197558			21998	protein-coding gene	gene with protein product	"""subcommissural organ spondin"", ""SCO protein, thrombospondin domain containing"""		"""SCO-spondin homolog (Bos taurus)"""			8743952, 11008217	Standard	NM_198455		Approved	SCO-spondin, KIAA0543, FLJ36112	uc010lpk.3	A2VEC9	OTTHUMG00000157884		7.37:g.149475969A>G		Somatic		Capture	Illumina HiSeq	Phase_I	149106902	NM_198455	Q76B61	Missense_Mutation	SNP	ENST00000378016.2	37																																																																																					0.632	SSPO-202	KNOWN	basic	processed_transcript	processed_transcript			
GIMAP8	155038	broad.mit.edu	37	7	150163814	150163814	+	Missense_Mutation	SNP	G	G	A	rs143529569		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr7:150163814G>A	ENST00000307271.3	+	2	602	c.28G>A	c.(28-30)Gaa>Aaa	p.E10K		NM_175571.2	NP_783161.1	Q8ND71	GIMA8_HUMAN	GTPase, IMAP family member 8	10	AIG1-type G 1.					cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	GTP binding (GO:0005525)	p.E10K(2)		breast(3)|central_nervous_system(3)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(11)|lung(26)|ovary(2)|skin(7)|stomach(1)|urinary_tract(1)	62			OV - Ovarian serous cystadenocarcinoma(82;0.0218)	UCEC - Uterine corpus endometrioid carcinoma (81;0.17)		CCAGATGTCCGAACTGCGGCT	0.507																																					p.E10K												.	.	2	Substitution - Missense(2)	large_intestine(1)|skin(1)	c.G28A	7						.						48.0	51.0	50.0					7																	150163814		2203	4300	6503	149794747	SO:0001583	missense	155038	exon2			AL834361	CCDS34777.1	7q36.1	2014-04-04			ENSG00000171115	ENSG00000171115		"""GTPases, IMAP"""	21792	protein-coding gene	gene with protein product	"""immune-associated nucleotide-binding protein 9"""					15474311	Standard	XM_005249951		Approved	DKFZp667I133, hIAN6, IAN9	uc003whj.3	Q8ND71	OTTHUMG00000158327	ENST00000307271.3:c.28G>A	7.37:g.150163814G>A	ENSP00000305107:p.Glu10Lys	Somatic		Capture	Illumina HiSeq	Phase_I	149794747	NM_175571		Missense_Mutation	SNP	ENST00000307271.3	37	CCDS34777.1	.	.	.	.	.	.	.	.	.	.	G	16.98	3.271644	0.59649	.	.	ENSG00000171115	ENST00000307271	T	0.61274	0.12	4.48	-5.23	0.02798	.	1.488750	0.04286	N	0.344696	T	0.49541	0.1563	L	0.50847	1.595	0.09310	N	1	D	0.67145	0.996	P	0.49683	0.619	T	0.50676	-0.8800	10	0.18710	T	0.47	.	1.8855	0.03237	0.3116:0.3671:0.1974:0.1239	.	10	Q8ND71	GIMA8_HUMAN	K	10	ENSP00000305107:E10K	ENSP00000305107:E10K	E	+	1	0	GIMAP8	149794747	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	0.230000	0.17852	-1.051000	0.03226	-0.844000	0.03045	GAA		0.507	GIMAP8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350701.1	NM_175571	
AGAP3	116988	broad.mit.edu	37	7	150831565	150831565	+	Nonsense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr7:150831565C>T	ENST00000463381.1	+	11	1217	c.721C>T	c.(721-723)Cga>Tga	p.R241*	AGAP3_ENST00000397238.2_Nonsense_Mutation_p.R469*	NM_001281300.1	NP_001268229.1	Q96P47	AGAP3_HUMAN	ArfGAP with GTPase domain, ankyrin repeat and PH domain 3	520	Small GTPase-like.				cellular response to reactive oxygen species (GO:0034614)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein import into nucleus, translocation (GO:0000060)|regulation of ARF GTPase activity (GO:0032312)|small GTPase mediated signal transduction (GO:0007264)	cell periphery (GO:0071944)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	ARF GTPase activator activity (GO:0008060)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|zinc ion binding (GO:0008270)	p.R469*(1)		central_nervous_system(2)|endometrium(3)|kidney(3)|large_intestine(3)|liver(2)|lung(9)|ovary(2)|prostate(3)|urinary_tract(1)	28						GCGCCTGCCCCGAGCCACACC	0.667																																					p.R469X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.C1405T	7						.						17.0	24.0	21.0					7																	150831565		2004	4178	6182	150462498	SO:0001587	stop_gained	116988	exon11			AF413079	CCDS43681.1, CCDS55185.1, CCDS64802.1	7q36.1	2013-01-11	2008-09-22	2008-09-22	ENSG00000133612	ENSG00000133612		"""ADP-ribosylation factor GTPase activating proteins"", ""Pleckstrin homology (PH) domain containing"", ""Ankyrin repeat domain containing"""	16923	protein-coding gene	gene with protein product			"""centaurin, gamma 3"""	CENTG3			Standard	NM_001042535		Approved		uc003wjg.1	Q96P47	OTTHUMG00000158724	ENST00000463381.1:c.721C>T	7.37:g.150831565C>T	ENSP00000418016:p.Arg241*	Somatic		Capture	Illumina HiSeq	Phase_I	150462498	NM_031946	B3KNZ8|E9PAL8|Q59EN0|Q96RK3	Nonsense_Mutation	SNP	ENST00000463381.1	37		.	.	.	.	.	.	.	.	.	.	C	42	9.469326	0.99180	.	.	ENSG00000133612	ENST00000463381;ENST00000397232;ENST00000397238;ENST00000335355	.	.	.	4.4	3.5	0.40072	.	0.000000	0.56097	D	0.000022	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	11.7296	0.51728	0.3366:0.6634:0.0:0.0	.	.	.	.	X	241;25;469;433	.	ENSP00000334157:R433X	R	+	1	2	AGAP3	150462498	0.031000	0.19500	1.000000	0.80357	0.995000	0.86356	0.210000	0.17455	1.165000	0.42670	0.655000	0.94253	CGA		0.667	AGAP3-002	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000351909.2	NM_031946	
NUB1	51667	broad.mit.edu	37	7	151065005	151065005	+	Missense_Mutation	SNP	G	G	A	rs373576077		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr7:151065005G>A	ENST00000355851.4	+	10	1123	c.1046G>A	c.(1045-1047)cGa>cAa	p.R349Q	NUB1_ENST00000413040.2_Missense_Mutation_p.R373Q|NUB1_ENST00000568733.1_Missense_Mutation_p.R373Q|NUB1_ENST00000566856.1_Missense_Mutation_p.R349Q	NM_001243351.1	NP_001230280.1	Q9Y5A7	NUB1_HUMAN	negative regulator of ubiquitin-like proteins 1	349					positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|protein ubiquitination (GO:0016567)|response to interferon-gamma (GO:0034341)|response to tumor necrosis factor (GO:0034612)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)		p.R349Q(2)		endometrium(1)|large_intestine(7)|lung(3)	11			OV - Ovarian serous cystadenocarcinoma(82;0.00569)	UCEC - Uterine corpus endometrioid carcinoma (81;0.172)		CAAGGGATCCGAAACTATCAC	0.323											OREG0018452	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.R349Q												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G1046A	7						.	G	GLN/ARG	1,3659		0,1,1829	64.0	59.0	61.0		1046	3.8	0.8	7		61	0,8182		0,0,4091	no	missense	NUB1	NM_016118.4	43	0,1,5920	AA,AG,GG		0.0,0.0273,0.0084	benign	349/602	151065005	1,11841	1830	4091	5921	150695938	SO:0001583	missense	51667	exon10			AF300717	CCDS47751.1, CCDS47751.2, CCDS59089.1	7q36	2006-07-27			ENSG00000013374	ENSG00000013374			17623	protein-coding gene	gene with protein product	"""NEDD8 ultimate buster-1"""	607981				10508479, 11259415	Standard	NM_001243351		Approved	BS4, NYREN18	uc003wjx.3	Q9Y5A7	OTTHUMG00000157365	ENST00000355851.4:c.1046G>A	7.37:g.151065005G>A	ENSP00000348110:p.Arg349Gln	Somatic	1737	Capture	Illumina HiSeq	Phase_I	150695938	NM_016118	O95422|Q75MR9|Q8IX22|Q9BXR2	Missense_Mutation	SNP	ENST00000355851.4	37		.	.	.	.	.	.	.	.	.	.	G	7.323	0.617344	0.14129	2.73E-4	0.0	ENSG00000013374	ENST00000413040;ENST00000355851	T	0.62788	0.0	5.63	3.77	0.43336	UBA-like (1);	0.252750	0.34156	N	0.004213	T	0.46151	0.1378	L	0.36672	1.1	0.21445	N	0.99968	B;B	0.20988	0.03;0.05	B;B	0.09377	0.002;0.004	T	0.30592	-0.9973	10	0.33940	T	0.23	-9.2092	5.9963	0.19495	0.0727:0.1347:0.6531:0.1395	.	349;349	Q9Y5A7;Q9Y5A7-2	NUB1_HUMAN;.	Q	349	ENSP00000348110:R349Q	ENSP00000348110:R349Q	R	+	2	0	NUB1	150695938	1.000000	0.71417	0.776000	0.31678	0.247000	0.25773	4.126000	0.57937	0.684000	0.31448	0.655000	0.94253	CGA		0.323	NUB1-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_016118	
NUB1	51667	broad.mit.edu	37	7	151074175	151074175	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr7:151074175C>T	ENST00000355851.4	+	15	1789	c.1712C>T	c.(1711-1713)gCc>gTc	p.A571V	WDR86_ENST00000463000.1_5'UTR|NUB1_ENST00000413040.2_Missense_Mutation_p.A581V|NUB1_ENST00000568733.1_Missense_Mutation_p.A595V|NUB1_ENST00000566856.1_Missense_Mutation_p.A557V	NM_001243351.1	NP_001230280.1	Q9Y5A7	NUB1_HUMAN	negative regulator of ubiquitin-like proteins 1	571	NEDD8-binding 2.				positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|protein ubiquitination (GO:0016567)|response to interferon-gamma (GO:0034341)|response to tumor necrosis factor (GO:0034612)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)		p.A557V(1)		endometrium(1)|large_intestine(7)|lung(3)	11			OV - Ovarian serous cystadenocarcinoma(82;0.00569)	UCEC - Uterine corpus endometrioid carcinoma (81;0.172)		GAGACAGAGGCCGTCAATGAG	0.433																																					p.A557V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1670T	7						.						65.0	64.0	64.0					7																	151074175		1904	4125	6029	150705108	SO:0001583	missense	51667	exon15			AF300717	CCDS47751.1, CCDS47751.2, CCDS59089.1	7q36	2006-07-27			ENSG00000013374	ENSG00000013374			17623	protein-coding gene	gene with protein product	"""NEDD8 ultimate buster-1"""	607981				10508479, 11259415	Standard	NM_001243351		Approved	BS4, NYREN18	uc003wjx.3	Q9Y5A7	OTTHUMG00000157365	ENST00000355851.4:c.1712C>T	7.37:g.151074175C>T	ENSP00000348110:p.Ala571Val	Somatic		Capture	Illumina HiSeq	Phase_I	150705108	NM_016118	O95422|Q75MR9|Q8IX22|Q9BXR2	Missense_Mutation	SNP	ENST00000355851.4	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	16.64|16.64	3.178434|3.178434	0.57692|0.57692	.|.	.|.	ENSG00000013374|ENSG00000013374	ENST00000413040;ENST00000355851|ENST00000460712	T|.	0.49720|.	0.77|.	5.76|5.76	5.76|5.76	0.90799|0.90799	.|.	0.125717|.	0.56097|.	D|.	0.000030|.	T|T	0.77287|0.77287	0.4108|0.4108	M|M	0.75615|0.75615	2.305|2.305	0.47778|0.47778	D|D	0.999512|0.999512	B;P|.	0.37061|.	0.445;0.58|.	B;B|.	0.36335|.	0.111;0.222|.	T|T	0.75972|0.75972	-0.3129|-0.3129	10|5	0.20519|.	T|.	0.43|.	-24.5407|-24.5407	18.9386|18.9386	0.92597|0.92597	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	571;557|.	Q9Y5A7;Q9Y5A7-2|.	NUB1_HUMAN;.|.	V|S	557;571|158	ENSP00000348110:A571V|.	ENSP00000348110:A571V|.	A|P	+|+	2|1	0|0	NUB1|NUB1	150705108|150705108	0.965000|0.965000	0.33210|0.33210	0.969000|0.969000	0.41365|0.41365	0.899000|0.899000	0.52679|0.52679	2.117000|2.117000	0.41939|0.41939	2.720000|2.720000	0.93068|0.93068	0.591000|0.591000	0.81541|0.81541	GCC|CCG		0.433	NUB1-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_016118	
LMBR1	64327	broad.mit.edu	37	7	156629550	156629550	+	Silent	SNP	G	G	A	rs143018746		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr7:156629550G>A	ENST00000353442.5	-	2	332	c.96C>T	c.(94-96)taC>taT	p.Y32Y	LMBR1_ENST00000540390.1_Intron|LMBR1_ENST00000354505.4_Silent_p.Y32Y	NM_022458.3	NP_071903.2	Q8WVP7	LMBR1_HUMAN	limb development membrane protein 1	32					embryonic digit morphogenesis (GO:0042733)	integral component of membrane (GO:0016021)		p.Y32Y(1)		breast(1)|endometrium(4)|kidney(1)|large_intestine(2)|lung(9)|skin(1)	18	Ovarian(565;0.218)	all_hematologic(28;0.0592)	OV - Ovarian serous cystadenocarcinoma(82;0.00231)	UCEC - Uterine corpus endometrioid carcinoma (81;0.208)		AGGAAACAACGTAGAGAATGG	0.323																																					p.Y32Y												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C96T	7						.						107.0	94.0	98.0					7																	156629550		2196	4299	6495	156322311	SO:0001819	synonymous_variant	64327	exon2			AF107454	CCDS5945.1	7q36.3	2013-08-05	2013-08-05	2005-07-25	ENSG00000105983	ENSG00000105983			13243	protein-coding gene	gene with protein product		605522	"""chromosome 7 open reading frame 2"", ""limb region 1 homolog (mouse)"""	C7orf2		10329000, 11090342	Standard	NM_022458		Approved	ACHP, FLJ11665, ZRS	uc003wmw.4	Q8WVP7	OTTHUMG00000151510	ENST00000353442.5:c.96C>T	7.37:g.156629550G>A		Somatic		Capture	Illumina HiSeq	Phase_I	156322311	NM_022458	A4D242|Q8N3E3|Q96QZ5|Q9H5N0|Q9HAG9|Q9UDN5|Q9Y6U2	De_novo_Start_InFrame	SNP	ENST00000353442.5	37	CCDS5945.1																																																																																				0.323	LMBR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347939.3	NM_022458	
NCAPG2	54892	broad.mit.edu	37	7	158457250	158457250	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr7:158457250C>T	ENST00000409423.1	-	15	1844	c.1672G>A	c.(1672-1674)Gcc>Acc	p.A558T	NCAPG2_ENST00000541468.1_Missense_Mutation_p.A59T|NCAPG2_ENST00000356309.3_Missense_Mutation_p.A558T|NCAPG2_ENST00000409339.3_Missense_Mutation_p.A558T|NCAPG2_ENST00000449727.2_Missense_Mutation_p.A558T|NCAPG2_ENST00000275830.10_Missense_Mutation_p.A350T	NM_001281932.1	NP_001268861.1	Q86XI2	CNDG2_HUMAN	non-SMC condensin II complex, subunit G2	558					chromosome condensation (GO:0030261)|inner cell mass cell proliferation (GO:0001833)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)	membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	methylated histone binding (GO:0035064)	p.A558T(1)		NS(1)|breast(1)|endometrium(5)|kidney(5)|large_intestine(7)|liver(1)|lung(15)|ovary(1)|pancreas(1)|prostate(1)|skin(1)	39	Ovarian(565;0.152)	all_cancers(7;3.44e-11)|all_epithelial(9;3.05e-05)|all_hematologic(28;0.014)	OV - Ovarian serous cystadenocarcinoma(82;0.00174)	UCEC - Uterine corpus endometrioid carcinoma (81;0.187)|STAD - Stomach adenocarcinoma(7;0.18)		TGTTCGTGGGCGTACTGATAG	0.512																																					p.A558T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1672A	7						.						107.0	110.0	109.0					7																	158457250		2103	4253	6356	158150011	SO:0001583	missense	54892	exon14			BC043404	CCDS43686.1, CCDS64816.1	7q36.3	2006-09-04	2006-09-04	2006-09-04	ENSG00000146918	ENSG00000146918			21904	protein-coding gene	gene with protein product		608532	"""leucine zipper protein 5"""	LUZP5		14532007	Standard	NM_001281933		Approved	FLJ20311, MTB, CAP-G2, hCAP-G2	uc003wnv.1	Q86XI2	OTTHUMG00000151438	ENST00000409423.1:c.1672G>A	7.37:g.158457250C>T	ENSP00000386569:p.Ala558Thr	Somatic		Capture	Illumina HiSeq	Phase_I	158150011	NM_017760	A4D228|Q7Z3J9|Q8WUG8|Q9BRX6|Q9H8S2|Q9H9K6	Missense_Mutation	SNP	ENST00000409423.1	37	CCDS43686.1	.	.	.	.	.	.	.	.	.	.	C	25.1	4.598613	0.87055	.	.	ENSG00000146918	ENST00000541468;ENST00000356309;ENST00000409423;ENST00000275830;ENST00000409339;ENST00000545393;ENST00000449727	T;T;T;T;T;T	0.39997	1.05;1.11;1.11;1.15;1.1;1.1	5.6	5.6	0.85130	.	0.000000	0.85682	D	0.000000	T	0.68100	0.2964	M	0.78801	2.425	0.58432	D	0.999994	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.91635	0.999;0.992;0.996;0.998	T	0.68804	-0.5312	10	0.56958	D	0.05	-18.9395	19.9663	0.97271	0.0:1.0:0.0:0.0	.	558;59;350;558	Q86XI2-2;B4DHE5;E7EUH9;Q86XI2	.;.;.;CNDG2_HUMAN	T	59;558;558;350;558;59;558	ENSP00000442337:A59T;ENSP00000348657:A558T;ENSP00000386569:A558T;ENSP00000275830:A350T;ENSP00000387007:A558T;ENSP00000388326:A558T	ENSP00000275830:A350T	A	-	1	0	NCAPG2	158150011	1.000000	0.71417	0.211000	0.23655	0.666000	0.39218	4.560000	0.60802	2.780000	0.95670	0.655000	0.94253	GCC		0.512	NCAPG2-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327111.1	NM_017760	
NCAPG2	54892	broad.mit.edu	37	7	158457405	158457405	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr7:158457405C>T	ENST00000409423.1	-	15	1689	c.1517G>A	c.(1516-1518)cGt>cAt	p.R506H	NCAPG2_ENST00000541468.1_Missense_Mutation_p.R7H|NCAPG2_ENST00000356309.3_Missense_Mutation_p.R506H|NCAPG2_ENST00000409339.3_Missense_Mutation_p.R506H|NCAPG2_ENST00000449727.2_Missense_Mutation_p.R506H|NCAPG2_ENST00000275830.10_Missense_Mutation_p.R298H	NM_001281932.1	NP_001268861.1	Q86XI2	CNDG2_HUMAN	non-SMC condensin II complex, subunit G2	506					chromosome condensation (GO:0030261)|inner cell mass cell proliferation (GO:0001833)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)	membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	methylated histone binding (GO:0035064)	p.R506H(1)		NS(1)|breast(1)|endometrium(5)|kidney(5)|large_intestine(7)|liver(1)|lung(15)|ovary(1)|pancreas(1)|prostate(1)|skin(1)	39	Ovarian(565;0.152)	all_cancers(7;3.44e-11)|all_epithelial(9;3.05e-05)|all_hematologic(28;0.014)	OV - Ovarian serous cystadenocarcinoma(82;0.00174)	UCEC - Uterine corpus endometrioid carcinoma (81;0.187)|STAD - Stomach adenocarcinoma(7;0.18)		AGTTTCCAGACGAACCAGAAT	0.488																																					p.R506H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1517A	7						.						62.0	66.0	65.0					7																	158457405		2031	4201	6232	158150166	SO:0001583	missense	54892	exon14			BC043404	CCDS43686.1, CCDS64816.1	7q36.3	2006-09-04	2006-09-04	2006-09-04	ENSG00000146918	ENSG00000146918			21904	protein-coding gene	gene with protein product		608532	"""leucine zipper protein 5"""	LUZP5		14532007	Standard	NM_001281933		Approved	FLJ20311, MTB, CAP-G2, hCAP-G2	uc003wnv.1	Q86XI2	OTTHUMG00000151438	ENST00000409423.1:c.1517G>A	7.37:g.158457405C>T	ENSP00000386569:p.Arg506His	Somatic		Capture	Illumina HiSeq	Phase_I	158150166	NM_017760	A4D228|Q7Z3J9|Q8WUG8|Q9BRX6|Q9H8S2|Q9H9K6	Missense_Mutation	SNP	ENST00000409423.1	37	CCDS43686.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	35|35	5.513997|5.513997	0.96402|0.96402	.|.	.|.	ENSG00000146918|ENSG00000146918	ENST00000541468;ENST00000356309;ENST00000409423;ENST00000275830;ENST00000409339;ENST00000545393;ENST00000449727|ENST00000441982	T;T;T;T;T;T|.	0.41758|.	0.99;1.44;1.44;1.48;1.44;1.44|.	5.81|5.81	5.81|5.81	0.92471|0.92471	Armadillo-type fold (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	D|D	0.83022|0.83022	0.5164|0.5164	M|M	0.83603|0.83603	2.65|2.65	0.80722|0.80722	D|D	1|1	D;D;D;D|.	0.89917|.	1.0;1.0;1.0;1.0|.	D;D;D;D|.	0.97110|.	1.0;0.998;0.997;0.999|.	T|T	0.82653|0.82653	-0.0351|-0.0351	10|5	0.87932|.	D|.	0|.	-22.4663|-22.4663	20.4375|20.4375	0.99097|0.99097	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	506;7;298;506|.	Q86XI2-2;B4DHE5;E7EUH9;Q86XI2|.	.;.;.;CNDG2_HUMAN|.	H|I	7;506;506;298;506;7;506|308	ENSP00000442337:R7H;ENSP00000348657:R506H;ENSP00000386569:R506H;ENSP00000275830:R298H;ENSP00000387007:R506H;ENSP00000388326:R506H|.	ENSP00000275830:R298H|.	R|V	-|-	2|1	0|0	NCAPG2|NCAPG2	158150166|158150166	1.000000|1.000000	0.71417|0.71417	0.935000|0.935000	0.37517|0.37517	0.947000|0.947000	0.59692|0.59692	7.618000|7.618000	0.83043|0.83043	2.906000|2.906000	0.99361|0.99361	0.655000|0.655000	0.94253|0.94253	CGT|GTC		0.488	NCAPG2-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327111.1	NM_017760	
PDGFA	5154	broad.mit.edu	37	7	540801	540801	+	Missense_Mutation	SNP	C	C	T	rs145010817		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr7:540801C>T	ENST00000354513.5	-	5	924	c.532G>A	c.(532-534)Gcc>Acc	p.A178T	PDGFA_ENST00000402802.3_Missense_Mutation_p.A178T	NM_002607.5	NP_002598.4	P04085	PDGFA_HUMAN	platelet-derived growth factor alpha polypeptide	178					actin cytoskeleton organization (GO:0030036)|angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cell activation (GO:0001775)|cell projection assembly (GO:0030031)|cell-cell signaling (GO:0007267)|embryo development (GO:0009790)|epidermal growth factor receptor signaling pathway (GO:0007173)|extracellular matrix organization (GO:0030198)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|hair follicle development (GO:0001942)|innate immune response (GO:0045087)|inner ear development (GO:0048839)|lung alveolus development (GO:0048286)|negative chemotaxis (GO:0050919)|negative regulation of phosphatidylinositol biosynthetic process (GO:0010512)|negative regulation of platelet activation (GO:0010544)|neurotrophin TRK receptor signaling pathway (GO:0048011)|organ morphogenesis (GO:0009887)|phosphatidylinositol-mediated signaling (GO:0048015)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of DNA replication (GO:0045740)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of metanephric mesenchymal cell migration by platelet-derived growth factor receptor-beta signaling pathway (GO:0035793)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein autophosphorylation (GO:0031954)|positive regulation of protein kinase B signaling (GO:0051897)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of branching involved in salivary gland morphogenesis by epithelial-mesenchymal signaling (GO:0060683)|regulation of peptidyl-tyrosine phosphorylation (GO:0050730)|regulation of smooth muscle cell migration (GO:0014910)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to hypoxia (GO:0001666)|response to inorganic substance (GO:0010035)|response to retinoic acid (GO:0032526)|response to wounding (GO:0009611)|skin development (GO:0043588)|transforming growth factor beta receptor signaling pathway (GO:0007179)|wound healing (GO:0042060)	cell surface (GO:0009986)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi membrane (GO:0000139)|microvillus (GO:0005902)|platelet alpha granule lumen (GO:0031093)	collagen binding (GO:0005518)|growth factor activity (GO:0008083)|platelet-derived growth factor binding (GO:0048407)|platelet-derived growth factor receptor binding (GO:0005161)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)	p.A178T(1)		central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(8)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	16		Ovarian(82;0.0112)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0178)|Epithelial(4;1.1e-17)|OV - Ovarian serous cystadenocarcinoma(56;1.7e-17)|all cancers(6;4.89e-15)		GTCGCGCAGGCGCACTCCAAA	0.557																																					p.A178T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G532A	7						.	T	THR/ALA,THR/ALA	0,4406		0,0,2203	264.0	244.0	251.0		532,532	0.4	0.0	7	dbSNP_134	251	5,8587	4.3+/-15.6	0,5,4291	no	missense,missense	PDGFA	NM_002607.5,NM_033023.4	58,58	0,5,6494	TT,TC,CC		0.0582,0.0,0.0385	benign,benign	178/212,178/197	540801	5,12993	2203	4296	6499	507327	SO:0001583	missense	5154	exon5				CCDS34578.1, CCDS47524.1	7p22	2008-07-18			ENSG00000197461	ENSG00000197461			8799	protein-coding gene	gene with protein product	"""PDGF A-chain"", ""platelet-derived growth factor alpha chain"""	173430				1505216, 2536956	Standard	NM_002607		Approved	PDGF1, PDGF-A	uc003sir.3	P04085	OTTHUMG00000151412	ENST00000354513.5:c.532G>A	7.37:g.540801C>T	ENSP00000346508:p.Ala178Thr	Somatic		Capture	Illumina HiSeq	Phase_I	507327	NM_002607	B5BU73	Missense_Mutation	SNP	ENST00000354513.5	37	CCDS34578.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	c|c	0.210|0.210	-1.037158|-1.037158	0.02013|0.02013	0.0|0.0	5.82E-4|5.82E-4	ENSG00000197461|ENSG00000197461	ENST00000402802;ENST00000354513|ENST00000400761	T;T|.	0.41758|.	0.99;0.99|.	4.98|4.98	0.443|0.443	0.16587|0.16587	Platelet-derived growth factor (PDGF) (3);|.	0.478547|.	0.24020|.	N|.	0.042281|.	T|T	0.21103|0.21103	0.0508|0.0508	N|N	0.15975|0.15975	0.35|0.35	0.27412|0.27412	N|N	0.954534|0.954534	P;B;B|.	0.35033|.	0.481;0.003;0.002|.	B;B;B|.	0.20384|.	0.029;0.005;0.005|.	T|T	0.30001|0.30001	-0.9993|-0.9993	10|5	0.23302|.	T|.	0.38|.	-4.6998|-4.6998	8.8029|8.8029	0.34920|0.34920	0.0:0.2377:0.0:0.7623|0.0:0.2377:0.0:0.7623	.|.	192;178;178|.	Q32M96;P04085-2;P04085|.	.;.;PDGFA_HUMAN|.	T|H	178|184	ENSP00000383889:A178T;ENSP00000346508:A178T|.	ENSP00000346508:A178T|.	A|R	-|-	1|2	0|0	PDGFA|PDGFA	507327|507327	0.001000|0.001000	0.12720|0.12720	0.043000|0.043000	0.18650|0.18650	0.124000|0.124000	0.20399|0.20399	-0.335000|-0.335000	0.07873|0.07873	-0.151000|-0.151000	0.11176|0.11176	-0.726000|-0.726000	0.03593|0.03593	GCC|CGC		0.557	PDGFA-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000322534.1		
SNX8	29886	broad.mit.edu	37	7	2290469	2290469	+	IGR	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr7:2290469C>T	ENST00000222990.3	-	0	4727				NUDT1_ENST00000356714.1_Missense_Mutation_p.R102C|NUDT1_ENST00000397049.1_Missense_Mutation_p.R125C|NUDT1_ENST00000397048.1_Missense_Mutation_p.R125C|NUDT1_ENST00000397046.1_Missense_Mutation_p.R102C|NUDT1_ENST00000343985.4_Missense_Mutation_p.R125C|NUDT1_ENST00000487426.1_3'UTR|NUDT1_ENST00000339737.2_Missense_Mutation_p.R102C	NM_013321.2	NP_037453.1	Q9Y5X2	SNX8_HUMAN	sorting nexin 8						early endosome to Golgi transport (GO:0034498)|intracellular protein transport (GO:0006886)	early endosome membrane (GO:0031901)	identical protein binding (GO:0042802)|phosphatidylinositol binding (GO:0035091)	p.R125C(1)		breast(2)|endometrium(5)|kidney(1)|large_intestine(3)|lung(8)|ovary(2)|prostate(2)|skin(3)	26		Ovarian(82;0.11)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0853)|OV - Ovarian serous cystadenocarcinoma(56;3.79e-14)		TACAGAAATGCGCCCATGCTG	0.532																																					p.R125C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C373T	7						.						173.0	183.0	179.0					7																	2290469		2203	4300	6503	2256995	SO:0001628	intergenic_variant	4521	exon5			AF121858	CCDS5331.1	7p22.3	2010-08-05			ENSG00000106266	ENSG00000106266		"""Sorting nexins"""	14972	protein-coding gene	gene with protein product		614905					Standard	NM_013321		Approved	Mvp1	uc003slw.3	Q9Y5X2	OTTHUMG00000151512		7.37:g.2290469C>T		Somatic		Capture	Illumina HiSeq	Phase_I	2256995	NM_198949	A4D207|Q96I67	Missense_Mutation	SNP	ENST00000222990.3	37	CCDS5331.1	.	.	.	.	.	.	.	.	.	.	C	7.899	0.733949	0.15574	.	.	ENSG00000106268	ENST00000356714;ENST00000397049;ENST00000397046;ENST00000397048;ENST00000343985;ENST00000339737	T;T;T;T;T;T	0.08282	3.11;3.11;3.11;3.11;3.11;3.11	5.22	3.41	0.39046	NUDIX hydrolase domain (3);NUDIX hydrolase domain-like (1);	0.154583	0.53938	D	0.000058	T	0.14141	0.0342	M	0.83012	2.62	0.80722	D	1	B	0.26902	0.163	B	0.28709	0.093	T	0.02098	-1.1214	10	0.54805	T	0.06	-19.557	10.3919	0.44175	0.0:0.7859:0.0:0.2141	.	143	P36639	8ODP_HUMAN	C	102;125;102;125;125;102	ENSP00000349148:R102C;ENSP00000380242:R125C;ENSP00000380239:R102C;ENSP00000380241:R125C;ENSP00000339503:R125C;ENSP00000343439:R102C	ENSP00000343439:R102C	R	+	1	0	NUDT1	2256995	0.999000	0.42202	0.985000	0.45067	0.024000	0.10985	0.841000	0.27613	1.204000	0.43247	-0.448000	0.05591	CGC		0.532	SNX8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322949.2		
AMZ1	155185	broad.mit.edu	37	7	2740161	2740161	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr7:2740161G>A	ENST00000312371.4	+	2	444	c.76G>A	c.(76-78)Gca>Aca	p.A26T	AMZ1_ENST00000407112.1_Missense_Mutation_p.A26T	NM_133463.1	NP_597720.1	Q400G9	AMZ1_HUMAN	archaelysin family metallopeptidase 1	26							metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)	p.A26T(1)		breast(2)|kidney(1)|large_intestine(4)|lung(8)|skin(1)	16		Ovarian(82;0.0779)		OV - Ovarian serous cystadenocarcinoma(56;5.03e-14)		CTCCACTGACGCAGCCCTGCA	0.667																																					p.A26T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G76A	7						.						102.0	108.0	106.0					7																	2740161		2203	4300	6503	2706687	SO:0001583	missense	155185	exon2			AB075830	CCDS34589.1, CCDS64582.1	7p22.3	2008-01-17			ENSG00000174945	ENSG00000174945			22231	protein-coding gene	gene with protein product	"""archaemetzincin-1"""	615168				15972818	Standard	NM_133463		Approved	KIAA1950	uc003smr.1	Q400G9	OTTHUMG00000152111	ENST00000312371.4:c.76G>A	7.37:g.2740161G>A	ENSP00000308149:p.Ala26Thr	Somatic		Capture	Illumina HiSeq	Phase_I	2706687	NM_133463	B3KRS0|Q8TF51	Missense_Mutation	SNP	ENST00000312371.4	37	CCDS34589.1	.	.	.	.	.	.	.	.	.	.	G	8.931	0.963565	0.18583	.	.	ENSG00000174945	ENST00000312371;ENST00000407112	T;T	0.31510	1.96;1.49	4.24	-1.64	0.08318	.	0.887885	0.09591	N	0.781532	T	0.13798	0.0334	N	0.08118	0	0.09310	N	1	B;B	0.34181	0.44;0.013	B;B	0.19148	0.024;0.002	T	0.08310	-1.0728	10	0.45353	T	0.12	-4.1793	13.1227	0.59336	0.0997:0.7429:0.1574:0.0	.	26;26	B3KRS0;Q400G9	.;AMZ1_HUMAN	T	26	ENSP00000308149:A26T;ENSP00000386020:A26T	ENSP00000308149:A26T	A	+	1	0	AMZ1	2706687	0.000000	0.05858	0.000000	0.03702	0.351000	0.29236	-0.545000	0.06069	-0.376000	0.07943	-0.311000	0.09066	GCA		0.667	AMZ1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325244.1	NM_133463	
SDK1	221935	broad.mit.edu	37	7	4153028	4153028	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr7:4153028C>T	ENST00000404826.2	+	24	3681	c.3542C>T	c.(3541-3543)aCg>aTg	p.T1181M	SDK1_ENST00000389531.3_Missense_Mutation_p.T1181M	NM_152744.3	NP_689957.3	Q7Z5N4	SDK1_HUMAN	sidekick cell adhesion molecule 1	1181	Fibronectin type-III 6. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell adhesion (GO:0007155)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)		p.T1181M(3)		NS(1)|breast(6)|central_nervous_system(3)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(42)|lung(55)|ovary(4)|pancreas(1)|prostate(4)|skin(6)|upper_aerodigestive_tract(4)|urinary_tract(4)	153		all_cancers(1;0.127)|Ovarian(82;0.0177)|Myeloproliferative disorder(862;0.194)		UCEC - Uterine corpus endometrioid carcinoma (126;0.121)|OV - Ovarian serous cystadenocarcinoma(56;9.65e-15)		ACCAGCGTCACGGTCCGTACT	0.647																																					p.T1181M												.	.	3	Substitution - Missense(3)	large_intestine(3)	c.C3542T	7						.						101.0	107.0	105.0					7																	4153028		2203	4300	6503	4119554	SO:0001583	missense	221935	exon24			AK074077	CCDS34590.1	7p22.3	2013-02-11	2011-12-09		ENSG00000146555	ENSG00000146555		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	19307	protein-coding gene	gene with protein product		607216	"""sidekick homolog 1 (chicken)"", ""sidekick homolog 1, cell adhesion molecule (chicken)"""			12230981, 17307840, 15213259	Standard	NM_001079653		Approved	FLJ31425	uc003smx.3	Q7Z5N4	OTTHUMG00000151733	ENST00000404826.2:c.3542C>T	7.37:g.4153028C>T	ENSP00000385899:p.Thr1181Met	Somatic		Capture	Illumina HiSeq	Phase_I	4119554	NM_152744	Q8TEN9|Q8TEP5|Q96N44	Missense_Mutation	SNP	ENST00000404826.2	37	CCDS34590.1	.	.	.	.	.	.	.	.	.	.	C	16.63	3.177758	0.57692	.	.	ENSG00000146555	ENST00000404826;ENST00000389531	T;T	0.59638	0.25;0.25	4.92	4.04	0.47022	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.339119	0.27976	N	0.017099	T	0.75882	0.3910	M	0.87971	2.92	0.44181	D	0.996997	D;D	0.89917	0.999;1.0	P;D	0.67103	0.891;0.949	T	0.79412	-0.1814	10	0.87932	D	0	.	10.8848	0.46960	0.0:0.7979:0.1297:0.0724	.	1181;1181	F8W6X9;Q7Z5N4	.;SDK1_HUMAN	M	1181	ENSP00000385899:T1181M;ENSP00000374182:T1181M	ENSP00000374182:T1181M	T	+	2	0	SDK1	4119554	1.000000	0.71417	0.607000	0.28956	0.505000	0.33919	4.552000	0.60747	1.213000	0.43380	-0.126000	0.14955	ACG		0.647	SDK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323702.1	NM_152744	
SDK1	221935	broad.mit.edu	37	7	4185416	4185416	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr7:4185416G>A	ENST00000404826.2	+	29	4430	c.4291G>A	c.(4291-4293)Ggc>Agc	p.G1431S	SDK1_ENST00000389531.3_Missense_Mutation_p.G1431S	NM_152744.3	NP_689957.3	Q7Z5N4	SDK1_HUMAN	sidekick cell adhesion molecule 1	1431	Fibronectin type-III 8. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell adhesion (GO:0007155)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)		p.G1431S(1)		NS(1)|breast(6)|central_nervous_system(3)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(42)|lung(55)|ovary(4)|pancreas(1)|prostate(4)|skin(6)|upper_aerodigestive_tract(4)|urinary_tract(4)	153		all_cancers(1;0.127)|Ovarian(82;0.0177)|Myeloproliferative disorder(862;0.194)		UCEC - Uterine corpus endometrioid carcinoma (126;0.121)|OV - Ovarian serous cystadenocarcinoma(56;9.65e-15)		CGTGGAGGTCGGCGCCACAGT	0.662																																					p.G1431S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G4291A	7						.						62.0	57.0	59.0					7																	4185416		2203	4299	6502	4151942	SO:0001583	missense	221935	exon29			AK074077	CCDS34590.1	7p22.3	2013-02-11	2011-12-09		ENSG00000146555	ENSG00000146555		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	19307	protein-coding gene	gene with protein product		607216	"""sidekick homolog 1 (chicken)"", ""sidekick homolog 1, cell adhesion molecule (chicken)"""			12230981, 17307840, 15213259	Standard	NM_001079653		Approved	FLJ31425	uc003smx.3	Q7Z5N4	OTTHUMG00000151733	ENST00000404826.2:c.4291G>A	7.37:g.4185416G>A	ENSP00000385899:p.Gly1431Ser	Somatic		Capture	Illumina HiSeq	Phase_I	4151942	NM_152744	Q8TEN9|Q8TEP5|Q96N44	Missense_Mutation	SNP	ENST00000404826.2	37	CCDS34590.1	.	.	.	.	.	.	.	.	.	.	G	3.003	-0.205640	0.06180	.	.	ENSG00000146555	ENST00000404826;ENST00000389531	T;T	0.54479	0.57;0.57	4.96	4.96	0.65561	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.000000	0.64402	D	0.000001	T	0.47764	0.1463	N	0.10629	0.01	0.44956	D	0.997976	P;D	0.89917	0.941;1.0	B;D	0.97110	0.358;1.0	T	0.40270	-0.9572	10	0.13470	T	0.59	.	10.7984	0.46474	0.0865:0.0:0.9135:0.0	.	1431;1431	F8W6X9;Q7Z5N4	.;SDK1_HUMAN	S	1431	ENSP00000385899:G1431S;ENSP00000374182:G1431S	ENSP00000374182:G1431S	G	+	1	0	SDK1	4151942	1.000000	0.71417	0.997000	0.53966	0.791000	0.44710	3.278000	0.51662	2.296000	0.77279	0.462000	0.41574	GGC		0.662	SDK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323702.1	NM_152744	
MMD2	221938	broad.mit.edu	37	7	4949627	4949627	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr7:4949627C>T	ENST00000404774.3	-	6	688	c.494G>A	c.(493-495)cGt>cAt	p.R165H	MMD2_ENST00000401401.3_Intron|MMD2_ENST00000406755.1_Intron	NM_001100600.1	NP_001094070.1	Q8IY49	PAQRA_HUMAN	monocyte to macrophage differentiation-associated 2	165						Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)		p.R165H(1)		central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(11)	14		Ovarian(82;0.0175)		UCEC - Uterine corpus endometrioid carcinoma (126;0.097)|OV - Ovarian serous cystadenocarcinoma(56;3.4e-14)		TGCCTCCCCACGAAGAAACTG	0.572																																					p.R165H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G494A	7						.						88.0	92.0	91.0					7																	4949627		2000	4181	6181	4916153	SO:0001583	missense	221938	exon6			BC037881	CCDS47529.1, CCDS47530.1, CCDS59047.1	7p22	2004-06-23			ENSG00000136297	ENSG00000136297			30133	protein-coding gene	gene with protein product		614581				12477932	Standard	NM_198403		Approved	PAQR10	uc003sno.4	Q8IY49	OTTHUMG00000151844	ENST00000404774.3:c.494G>A	7.37:g.4949627C>T	ENSP00000384690:p.Arg165His	Somatic		Capture	Illumina HiSeq	Phase_I	4916153	NM_001100600	B5MBW4|Q6NVU5|Q6TCH0	Missense_Mutation	SNP	ENST00000404774.3	37	CCDS47529.1	.	.	.	.	.	.	.	.	.	.	C	8.120	0.780738	0.16120	.	.	ENSG00000136297	ENST00000404774	.	.	.	4.05	-8.09	0.01090	.	8.371250	0.00465	N	0.000109	T	0.15565	0.0375	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.11867	-1.0570	9	0.38643	T	0.18	.	3.2801	0.06912	0.0947:0.1692:0.4772:0.259	.	165	Q8IY49	PAQRA_HUMAN	H	165	.	ENSP00000384690:R165H	R	-	2	0	MMD2	4916153	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.832000	0.00743	-2.150000	0.00796	-1.328000	0.01277	CGT		0.572	MMD2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324136.1	NM_198403	
RBAK-RBAKDN	100533952	broad.mit.edu	37	7	5112728	5112728	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr7:5112728G>T	ENST00000407184.1	+	8	877	c.611G>T	c.(610-612)gGg>gTg	p.G204V	RBAKDN_ENST00000498308.1_lincRNA|RBAK-RBAKDN_ENST00000396904.2_3'UTR					RBAK-RBAKDN readthrough																		GGGGAACATGGGGCTTTCCCT	0.652																																					.												.	.	0			.	7						.						36.0	38.0	37.0					7																	5112728		2203	4300	6503	5079254	SO:0001583	missense	389458	.				CCDS56463.1	7p22.1	2013-05-20				ENSG00000272968			42971	other	readthrough							Standard	NM_001204513		Approved				OTTHUMG00000186010	ENST00000407184.1:c.611G>T	7.37:g.5112728G>T	ENSP00000385560:p.Gly204Val	Somatic		Capture	Illumina HiSeq	Phase_I	5079254	.		Missense_Mutation	SNP	ENST00000407184.1	37		.	.	.	.	.	.	.	.	.	.	G	11.19	1.566176	0.27915	.	.	ENSG00000146587	ENST00000407184	T	0.01369	4.97	3.37	2.46	0.29980	.	.	.	.	.	T	0.05502	0.0145	.	.	.	.	.	.	D	0.76494	0.999	D	0.71656	0.974	T	0.12319	-1.0552	7	0.87932	D	0	.	6.8524	0.24022	0.143:0.0:0.857:0.0	.	72	A6NC62	YG007_HUMAN	V	204	ENSP00000385560:G204V	ENSP00000385560:G204V	G	+	2	0	RBAK	5079254	0.000000	0.05858	0.004000	0.12327	0.036000	0.12997	-0.233000	0.09041	0.685000	0.31468	0.563000	0.77884	GGG		0.652	RBAK-RBAKDN-001	KNOWN	basic|appris_principal|readthrough_transcript	protein_coding	protein_coding	OTTHUMT00000472007.1		
TNRC18	84629	broad.mit.edu	37	7	5402371	5402371	+	Silent	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr7:5402371C>T	ENST00000430969.1	-	12	4653	c.4305G>A	c.(4303-4305)ggG>ggA	p.G1435G	TNRC18_ENST00000399537.4_Silent_p.G1435G	NM_001080495.2	NP_001073964.2	O15417	TNC18_HUMAN	trinucleotide repeat containing 18	1435							chromatin binding (GO:0003682)	p.G490G(1)|p.G1435G(1)		central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(8)	11		Ovarian(82;0.142)		UCEC - Uterine corpus endometrioid carcinoma (126;0.195)|OV - Ovarian serous cystadenocarcinoma(56;5.32e-15)		CCACCACGGGCCCATCCAGCA	0.672																																					p.G1435G												.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.G4305A	7						.						18.0	23.0	22.0					7																	5402371		1993	4151	6144	5368897	SO:0001819	synonymous_variant	84629	exon12			U80753	CCDS47534.1	7p22.1	2012-04-17			ENSG00000182095	ENSG00000182095		"""Trinucleotide (CAG) repeat containing"""	11962	protein-coding gene	gene with protein product						9225980	Standard	NM_001080495		Approved	CAGL79, TNRC18A, KIAA1856	uc003soi.4	O15417	OTTHUMG00000151831	ENST00000430969.1:c.4305G>A	7.37:g.5402371C>T		Somatic		Capture	Illumina HiSeq	Phase_I	5368897	NM_001080495	A8MX41|Q96JH1|Q96K91	Silent	SNP	ENST00000430969.1	37	CCDS47534.1																																																																																				0.672	TNRC18-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding			
PMS2	5395	broad.mit.edu	37	7	6018236	6018236	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr7:6018236C>T	ENST00000265849.7	-	13	2371	c.2266G>A	c.(2266-2268)Gat>Aat	p.D756N	PMS2_ENST00000382321.4_Missense_Mutation_p.D355N|PMS2_ENST00000406569.3_Intron|PMS2_ENST00000441476.2_Missense_Mutation_p.D650N	NM_000535.5	NP_000526	P54278	PMS2_HUMAN	PMS2 postmeiotic segregation increased 2 (S. cerevisiae)	756					ATP catabolic process (GO:0006200)|mismatch repair (GO:0006298)|response to drug (GO:0042493)|somatic hypermutation of immunoglobulin genes (GO:0016446)|somatic recombination of immunoglobulin gene segments (GO:0016447)	cytoplasm (GO:0005737)|microtubule cytoskeleton (GO:0015630)|MutLalpha complex (GO:0032389)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|DNA binding (GO:0003677)|endonuclease activity (GO:0004519)|single base insertion or deletion binding (GO:0032138)	p.D756N(1)		breast(2)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(6)|kidney(2)|large_intestine(11)|lung(13)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	46		Ovarian(82;0.0694)		UCEC - Uterine corpus endometrioid carcinoma (126;0.101)|OV - Ovarian serous cystadenocarcinoma(56;4.39e-15)		CCATTTTCATCGATAACAAAA	0.423			"""Mis, N, F"""			"""colorectal, endometrial, ovarian, medulloblastoma, glioma"""		Direct reversal of damage;Mismatch excision repair (MMR)	Turcot syndrome;Lynch syndrome;Constitutional Mismatch Repair Deficiency Syndrome																												p.D756N		yes	Rec		"""Hereditary non-polyposis colorectal cancer, Turcot syndrome"""	7	7p22	5395	PMS2 postmeiotic segregation increased 2 (S. cerevisiae)		E	.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2266A	7						.						87.0	71.0	76.0					7																	6018236		2194	4284	6478	5984762	SO:0001583	missense	5395	exon13	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Hereditary Non-Polyposis Colorectal Cancer, HNPCC, Lynch syndromes 1 and 2 (= Cancer Family Syndrome), Hereditary Mismatch Repair Deficiency syndrome, HMRDS;Mismatch Repair Cancer syndrome, MMRCS, Childhood Cancer Syndrome, CCS, Biallelic Mismatch Repair Gene Mutations Associated Early Onset Cancer, Lynch syndrome type III		CCDS5343.1	7p22.1	2014-09-17	2001-11-28		ENSG00000122512	ENSG00000122512			9122	protein-coding gene	gene with protein product		600259	"""postmeiotic segregation increased (S. cerevisiae) 2"""	PMSL2		8072530	Standard	NM_000535		Approved	H_DJ0042M02.9, HNPCC4	uc003spl.3	P54278	OTTHUMG00000023135	ENST00000265849.7:c.2266G>A	7.37:g.6018236C>T	ENSP00000265849:p.Asp756Asn	Somatic		Capture	Illumina HiSeq	Phase_I	5984762	NM_000535	B2R610|Q52LH6|Q5FBW9|Q5FBX1|Q5FBX2|Q75MR2	Missense_Mutation	SNP	ENST00000265849.7	37	CCDS5343.1	.	.	.	.	.	.	.	.	.	.	C	14.69	2.610661	0.46527	.	.	ENSG00000122512	ENST00000265849;ENST00000382322;ENST00000382321;ENST00000441476	T;T;T	0.75704	-0.96;-0.96;-0.96	5.73	3.93	0.45458	MutL, C-terminal, dimerisation (2);	0.184892	0.44688	N	0.000426	T	0.77136	0.4086	L	0.39467	1.215	0.54753	D	0.999981	B;B;D	0.89917	0.027;0.024;1.0	B;B;D	0.97110	0.009;0.021;1.0	T	0.71461	-0.4586	10	0.21540	T	0.41	-12.9681	8.9849	0.35988	0.0:0.7512:0.0:0.2488	.	355;756;650	P54278-2;P54278;C9J167	.;PMS2_HUMAN;.	N	756;709;355;650	ENSP00000265849:D756N;ENSP00000371758:D355N;ENSP00000392843:D650N	ENSP00000265849:D756N	D	-	1	0	PMS2	5984762	0.994000	0.37717	0.024000	0.17045	0.643000	0.38383	2.867000	0.48428	0.772000	0.33382	0.555000	0.69702	GAT		0.423	PMS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207353.3	NM_000535	
PMS2	5395	broad.mit.edu	37	7	6038813	6038813	+	Nonsense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr7:6038813G>A	ENST00000265849.7	-	6	736	c.631C>T	c.(631-633)Cga>Tga	p.R211*	PMS2_ENST00000406569.3_Nonsense_Mutation_p.R211*|PMS2_ENST00000469652.1_Intron|PMS2_ENST00000382321.4_Nonsense_Mutation_p.R211*|PMS2_ENST00000441476.2_Nonsense_Mutation_p.R105*	NM_000535.5	NP_000526	P54278	PMS2_HUMAN	PMS2 postmeiotic segregation increased 2 (S. cerevisiae)	211					ATP catabolic process (GO:0006200)|mismatch repair (GO:0006298)|response to drug (GO:0042493)|somatic hypermutation of immunoglobulin genes (GO:0016446)|somatic recombination of immunoglobulin gene segments (GO:0016447)	cytoplasm (GO:0005737)|microtubule cytoskeleton (GO:0015630)|MutLalpha complex (GO:0032389)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|DNA binding (GO:0003677)|endonuclease activity (GO:0004519)|single base insertion or deletion binding (GO:0032138)	p.R211*(1)		breast(2)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(6)|kidney(2)|large_intestine(11)|lung(13)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	46		Ovarian(82;0.0694)		UCEC - Uterine corpus endometrioid carcinoma (126;0.101)|OV - Ovarian serous cystadenocarcinoma(56;4.39e-15)		ACAGGCTGTCGTTTTCCTTGT	0.483			"""Mis, N, F"""			"""colorectal, endometrial, ovarian, medulloblastoma, glioma"""		Direct reversal of damage;Mismatch excision repair (MMR)	Turcot syndrome;Lynch syndrome;Constitutional Mismatch Repair Deficiency Syndrome																												p.R211X		yes	Rec		"""Hereditary non-polyposis colorectal cancer, Turcot syndrome"""	7	7p22	5395	PMS2 postmeiotic segregation increased 2 (S. cerevisiae)		E	.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.C631T	7						.						167.0	151.0	157.0					7																	6038813		2203	4300	6503	6005339	SO:0001587	stop_gained	5395	exon6	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Hereditary Non-Polyposis Colorectal Cancer, HNPCC, Lynch syndromes 1 and 2 (= Cancer Family Syndrome), Hereditary Mismatch Repair Deficiency syndrome, HMRDS;Mismatch Repair Cancer syndrome, MMRCS, Childhood Cancer Syndrome, CCS, Biallelic Mismatch Repair Gene Mutations Associated Early Onset Cancer, Lynch syndrome type III		CCDS5343.1	7p22.1	2014-09-17	2001-11-28		ENSG00000122512	ENSG00000122512			9122	protein-coding gene	gene with protein product		600259	"""postmeiotic segregation increased (S. cerevisiae) 2"""	PMSL2		8072530	Standard	NM_000535		Approved	H_DJ0042M02.9, HNPCC4	uc003spl.3	P54278	OTTHUMG00000023135	ENST00000265849.7:c.631C>T	7.37:g.6038813G>A	ENSP00000265849:p.Arg211*	Somatic		Capture	Illumina HiSeq	Phase_I	6005339	NM_000535	B2R610|Q52LH6|Q5FBW9|Q5FBX1|Q5FBX2|Q75MR2	Nonsense_Mutation	SNP	ENST00000265849.7	37	CCDS5343.1	.	.	.	.	.	.	.	.	.	.	G	38	6.747181	0.97809	.	.	ENSG00000122512	ENST00000265849;ENST00000382322;ENST00000382321;ENST00000441476;ENST00000406569	.	.	.	5.65	3.78	0.43462	.	0.066363	0.56097	D	0.000023	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.13108	T	0.6	-11.4747	13.7455	0.62872	0.0:0.0:0.4256:0.5744	.	.	.	.	X	211;164;211;105;211	.	ENSP00000265849:R211X	R	-	1	2	PMS2	6005339	1.000000	0.71417	0.680000	0.29994	0.997000	0.91878	2.492000	0.45311	0.689000	0.31550	0.591000	0.81541	CGA		0.483	PMS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207353.3	NM_000535	
MIOS	54468	broad.mit.edu	37	7	7634699	7634699	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr7:7634699A>G	ENST00000340080.4	+	10	2553	c.2132A>G	c.(2131-2133)cAt>cGt	p.H711R	MIOS_ENST00000405785.1_Missense_Mutation_p.H711R	NM_019005.3	NP_061878.3	Q9NXC5	MIO_HUMAN	missing oocyte, meiosis regulator, homolog (Drosophila)	711						lysosomal membrane (GO:0005765)		p.H711R(1)		breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(15)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	32						AGGTTTTGGCATAAACGAGCT	0.353																																					p.H711R												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A2132G	7						.						115.0	110.0	111.0					7																	7634699		1824	4085	5909	7601224	SO:0001583	missense	54468	exon10				CCDS43554.1	7p21.3	2011-09-12			ENSG00000164654	ENSG00000164654			21905	protein-coding gene	gene with protein product	"""WD repeat-containing protein mio"""	615359				14973288	Standard	NM_019005		Approved	FLJ20323	uc003srf.3	Q9NXC5	OTTHUMG00000152440	ENST00000340080.4:c.2132A>G	7.37:g.7634699A>G	ENSP00000339881:p.His711Arg	Somatic		Capture	Illumina HiSeq	Phase_I	7601224	NM_019005	B2RTV6|O75216|Q7L551|Q9H092	Missense_Mutation	SNP	ENST00000340080.4	37	CCDS43554.1	.	.	.	.	.	.	.	.	.	.	A	16.32	3.090523	0.55968	.	.	ENSG00000164654	ENST00000340080;ENST00000405785	T;T	0.42131	0.98;0.98	5.58	5.58	0.84498	.	0.000000	0.85682	D	0.000000	T	0.40670	0.1126	L	0.50333	1.59	0.80722	D	1	B;B	0.22003	0.063;0.063	B;B	0.30251	0.113;0.113	T	0.22661	-1.0210	10	0.14656	T	0.56	-14.1421	16.0634	0.80856	1.0:0.0:0.0:0.0	.	711;711	B4DGE7;Q9NXC5	.;MIO_HUMAN	R	711	ENSP00000339881:H711R;ENSP00000384088:H711R	ENSP00000339881:H711R	H	+	2	0	MIOS	7601224	1.000000	0.71417	1.000000	0.80357	0.955000	0.61496	8.903000	0.92573	2.255000	0.74692	0.533000	0.62120	CAT		0.353	MIOS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326218.1	NM_019005	
ANKMY2	57037	broad.mit.edu	37	7	16666737	16666737	+	Nonsense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr7:16666737G>A	ENST00000306999.2	-	3	442	c.199C>T	c.(199-201)Cga>Tga	p.R67*	ANKMY2_ENST00000421746.1_5'UTR	NM_020319.2	NP_064715.1	Q8IV38	ANKY2_HUMAN	ankyrin repeat and MYND domain containing 2	67						cilium (GO:0005929)	metal ion binding (GO:0046872)	p.R67*(1)		central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(6)|lung(8)|ovary(1)|prostate(1)|urinary_tract(1)	23	Lung NSC(10;0.103)|all_lung(11;0.204)			UCEC - Uterine corpus endometrioid carcinoma (126;0.195)		GCTCCATGTCGCAGTAGTAAT	0.343																																					p.R67X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.C199T	7						.						97.0	84.0	88.0					7																	16666737		2203	4300	6503	16633262	SO:0001587	stop_gained	57037	exon3			AK001740	CCDS5361.1	7p21	2013-01-10			ENSG00000106524	ENSG00000106524		"""Zinc fingers, MYND-type"", ""Ankyrin repeat domain containing"""	25370	protein-coding gene	gene with protein product						12477932	Standard	NM_020319		Approved	DKFZP564O043, ZMYND20	uc003sti.3	Q8IV38	OTTHUMG00000090806	ENST00000306999.2:c.199C>T	7.37:g.16666737G>A	ENSP00000303570:p.Arg67*	Somatic		Capture	Illumina HiSeq	Phase_I	16633262	NM_020319	A4D124|Q659G1|Q96BL3	Nonsense_Mutation	SNP	ENST00000306999.2	37	CCDS5361.1	.	.	.	.	.	.	.	.	.	.	G	27.4	4.828507	0.90955	.	.	ENSG00000106524	ENST00000306999	.	.	.	5.73	2.84	0.33178	.	0.066526	0.64402	D	0.000006	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.07990	T	0.79	-0.181	11.5216	0.50553	0.0:0.1149:0.5279:0.3571	.	.	.	.	X	67	.	ENSP00000303570:R67X	R	-	1	2	ANKMY2	16633262	1.000000	0.71417	0.426000	0.26672	0.860000	0.49131	3.644000	0.54381	0.307000	0.22880	-0.158000	0.13435	CGA		0.343	ANKMY2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207600.2	NM_020319	
PRPS1L1	221823	broad.mit.edu	37	7	18067214	18067214	+	Silent	SNP	G	G	A	rs368138725		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr7:18067214G>A	ENST00000506618.2	-	1	272	c.192C>T	c.(190-192)aaC>aaT	p.N64N		NM_175886.2	NP_787082	P21108	PRPS3_HUMAN	phosphoribosyl pyrophosphate synthetase 1-like 1	64					5-phosphoribose 1-diphosphate biosynthetic process (GO:0006015)|nucleotide biosynthetic process (GO:0009165)|ribonucleoside monophosphate biosynthetic process (GO:0009156)		ATP binding (GO:0005524)|kinase activity (GO:0016301)|magnesium ion binding (GO:0000287)|protein homodimerization activity (GO:0042803)|ribose phosphate diphosphokinase activity (GO:0004749)	p.N64N(2)		endometrium(1)|kidney(1)|large_intestine(3)|lung(9)|ovary(1)|prostate(3)	18	Lung NSC(10;0.0385)|all_lung(11;0.0736)					TTAGACTGTCGTTGATTTCGC	0.478																																					p.N64N												.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.C192T	7						.	G		0,4406		0,0,2203	355.0	348.0	350.0		192	-0.3	1.0	7		350	3,8597	3.0+/-9.4	0,3,4297	no	coding-synonymous	PRPS1L1	NM_175886.2		0,3,6500	AA,AG,GG		0.0349,0.0,0.0231		64/319	18067214	3,13003	2203	4300	6503	18033739	SO:0001819	synonymous_variant	221823	exon1			M57423	CCDS47552.1	7p21.1	2010-12-10			ENSG00000229937	ENSG00000229937			9463	protein-coding gene	gene with protein product		611566		PRPSL		2168892	Standard	NM_175886		Approved	PRPS3	uc003stz.3	P21108	OTTHUMG00000152742	ENST00000506618.2:c.192C>T	7.37:g.18067214G>A		Somatic		Capture	Illumina HiSeq	Phase_I	18033739	NM_175886	Q6P5P6	Silent	SNP	ENST00000506618.2	37	CCDS47552.1																																																																																				0.478	PRPS1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327667.1	NM_175886	
FERD3L	222894	broad.mit.edu	37	7	19184785	19184785	+	Silent	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr7:19184785G>A	ENST00000275461.3	-	1	259	c.201C>T	c.(199-201)tgC>tgT	p.C67C	AC003986.5_ENST00000452700.1_RNA	NM_152898.2	NP_690862.1	Q96RJ6	FER3L_HUMAN	Fer3-like bHLH transcription factor	67	Poly-Glu.				cell development (GO:0048468)|floor plate development (GO:0033504)|negative regulation of transcription, DNA-templated (GO:0045892)|regulation of neurogenesis (GO:0050767)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)	p.C67C(1)		breast(1)|endometrium(4)|large_intestine(8)|lung(16)|ovary(1)|prostate(2)|skin(1)|urinary_tract(2)	35						ggtccacttcgcactcctctt	0.632																																					p.C67C												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C201T	7						.						63.0	42.0	49.0					7																	19184785		2203	4300	6503	19151310	SO:0001819	synonymous_variant	222894	exon1			AF369897	CCDS5368.1	7p21.3	2013-10-17	2013-10-17		ENSG00000146618	ENSG00000146618		"""Basic helix-loop-helix proteins"""	16660	protein-coding gene	gene with protein product			"""Fer3-like (Drosophila)"""			11472856, 12217327	Standard	NM_152898		Approved	NATO3, N-TWIST, bHLHa31	uc003suo.1	Q96RJ6	OTTHUMG00000090823	ENST00000275461.3:c.201C>T	7.37:g.19184785G>A		Somatic		Capture	Illumina HiSeq	Phase_I	19151310	NM_152898	Q495K0	Silent	SNP	ENST00000275461.3	37	CCDS5368.1																																																																																				0.632	FERD3L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207627.1		
DFNA5	1687	broad.mit.edu	37	7	24756913	24756913	+	Silent	SNP	G	G	A	rs370243045		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr7:24756913G>A	ENST00000342947.3	-	5	1082	c.657C>T	c.(655-657)taC>taT	p.Y219Y	DFNA5_ENST00000545231.1_Silent_p.Y55Y|DFNA5_ENST00000419307.1_Silent_p.Y55Y|DFNA5_ENST00000409775.3_Silent_p.Y219Y|DFNA5_ENST00000409970.1_Silent_p.Y55Y|DFNA5_ENST00000559637.1_5'UTR	NM_004403.2	NP_004394.1	O60443	DFNA5_HUMAN	deafness, autosomal dominant 5	219					apoptotic process (GO:0006915)|inner ear receptor cell differentiation (GO:0060113)|negative regulation of cell proliferation (GO:0008285)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|sensory perception of sound (GO:0007605)	cytoplasm (GO:0005737)		p.Y219Y(1)		endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(6)|ovary(1)|prostate(3)|stomach(1)	19						CAATGACACCGTAGGCAATGG	0.587																																					p.Y219Y	GBM(78;184 1250 20134 20900 23600)											.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C657T	7						.	G	,,	1,4405	2.1+/-5.4	0,1,2202	153.0	110.0	125.0		657,165,657	-4.1	0.0	7		125	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous,coding-synonymous	DFNA5	NM_001127453.1,NM_001127454.1,NM_004403.2	,,	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	,,	219/497,55/333,219/497	24756913	1,13005	2203	4300	6503	24723438	SO:0001819	synonymous_variant	1687	exon5			AF007790	CCDS5389.1, CCDS47563.1	7p15	2011-07-01			ENSG00000105928	ENSG00000105928			2810	protein-coding gene	gene with protein product		608798				8589696, 9450185	Standard	NM_004403		Approved	ICERE-1	uc010kus.1	O60443	OTTHUMG00000023237	ENST00000342947.3:c.657C>T	7.37:g.24756913G>A		Somatic		Capture	Illumina HiSeq	Phase_I	24723438	NM_001127453	A4D156|B2RAX9|B3KT05|O14590|Q08AQ8|Q9UBV3	Silent	SNP	ENST00000342947.3	37	CCDS5389.1	.	.	.	.	.	.	.	.	.	.	G	3.507	-0.100521	0.06967	2.27E-4	0.0	ENSG00000105928	ENST00000415480;ENST00000446822	.	.	.	5.7	-4.06	0.03986	.	.	.	.	.	T	0.59418	0.2192	.	.	.	0.36333	D	0.859011	.	.	.	.	.	.	T	0.60870	-0.7177	4	.	.	.	-8.0654	15.581	0.76439	0.757:0.0:0.243:0.0	.	.	.	.	M	8;44	.	.	T	-	2	0	DFNA5	24723438	0.000000	0.05858	0.023000	0.16930	0.616000	0.37450	-1.087000	0.03383	-1.355000	0.02186	-1.578000	0.00866	ACG		0.587	DFNA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214060.2	NM_004403	
NFE2L3	9603	broad.mit.edu	37	7	26225319	26225319	+	Silent	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr7:26225319C>T	ENST00000056233.3	+	4	2260	c.2001C>T	c.(1999-2001)acC>acT	p.T667T		NM_004289.6	NP_004280.5	Q9Y4A8	NF2L3_HUMAN	nuclear factor, erythroid 2-like 3	667					transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)	p.T667T(1)		breast(2)|endometrium(1)|kidney(2)|large_intestine(4)|lung(5)|ovary(1)|prostate(2)|skin(5)|urinary_tract(7)	29						TCCAGTGTACCCATGATGGAA	0.418																																					p.T667T												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C2001T	7						.						80.0	80.0	80.0					7																	26225319		2203	4298	6501	26191844	SO:0001819	synonymous_variant	9603	exon4			AB010812	CCDS5396.1	7p15.2	2013-08-23	2013-08-23		ENSG00000050344	ENSG00000050344		"""basic leucine zipper proteins"""	7783	protein-coding gene	gene with protein product		604135	"""nuclear factor (erythroid-derived 2)-like 3"""			10037736	Standard	NM_004289		Approved	Nrf3	uc003sxq.3	Q9Y4A8	OTTHUMG00000023882	ENST00000056233.3:c.2001C>T	7.37:g.26225319C>T		Somatic		Capture	Illumina HiSeq	Phase_I	26191844	NM_004289	Q6NUS0|Q7Z498|Q86UJ4|Q86VR5|Q9UQA4	Silent	SNP	ENST00000056233.3	37	CCDS5396.1																																																																																				0.418	NFE2L3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214088.1		
CRHR2	1395	broad.mit.edu	37	7	30695267	30695267	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr7:30695267C>T	ENST00000471646.1	-	10	1399	c.982G>A	c.(982-984)Gtc>Atc	p.V328I	CRHR2_ENST00000348438.4_Missense_Mutation_p.V355I|CRHR2_ENST00000506074.2_Missense_Mutation_p.V328I|CRHR2_ENST00000341843.4_Missense_Mutation_p.V314I	NM_001202482.1|NM_001202483.1|NM_001883.4	NP_001189411.1|NP_001189412.1|NP_001874.2	Q13324	CRFR2_HUMAN	corticotropin releasing hormone receptor 2	328					adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|negative regulation of angiogenesis (GO:0016525)|negative regulation of cAMP-mediated signaling (GO:0043951)|positive regulation of cAMP-mediated signaling (GO:0043950)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	corticotrophin-releasing factor receptor activity (GO:0015056)	p.V328I(1)		breast(2)|kidney(2)|large_intestine(7)|lung(10)|ovary(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	28						CCGGGATTGACGAAGAAGAGC	0.602																																					p.V328I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G982A	7						.						163.0	157.0	159.0					7																	30695267		2203	4300	6503	30661792	SO:0001583	missense	1395	exon10				CCDS5429.1, CCDS56477.1, CCDS56478.1, CCDS75576.1	7p21-p15	2012-08-10			ENSG00000106113	ENSG00000106113		"""GPCR / Class B : Corticotropin-releasing factor receptors"""	2358	protein-coding gene	gene with protein product		602034				8536644	Standard	NM_001883		Approved	CRF2, CRF-RB, HM-CRF	uc003tbp.3	Q13324	OTTHUMG00000023218	ENST00000471646.1:c.982G>A	7.37:g.30695267C>T	ENSP00000418722:p.Val328Ile	Somatic		Capture	Illumina HiSeq	Phase_I	30661792	NM_001883	B2R967|B3SXS6|B3SXS7|B3SXS8|B3SXT0|F8WA81|O43461|Q4QRJ4|Q99431	Missense_Mutation	SNP	ENST00000471646.1	37	CCDS5429.1	.	.	.	.	.	.	.	.	.	.	C	14.34	2.505001	0.44558	.	.	ENSG00000106113	ENST00000471646;ENST00000348438;ENST00000341843;ENST00000506074	T;T;T;T	0.36699	1.24;1.24;1.24;1.24	5.11	2.3	0.28687	GPCR, family 2-like (1);	0.058371	0.64402	N	0.000002	T	0.26557	0.0649	L	0.37630	1.12	0.54753	D	0.999984	B;B;B;B;B	0.23937	0.006;0.012;0.094;0.017;0.006	B;B;B;B;B	0.23716	0.037;0.034;0.048;0.03;0.037	T	0.04708	-1.0932	10	0.39692	T	0.17	.	9.2532	0.37568	0.0:0.7552:0.0:0.2448	.	327;328;355;314;328	B3SXT0;B3SXS6;Q13324-2;Q13324-3;Q13324	.;.;.;.;CRFR2_HUMAN	I	328;355;314;328	ENSP00000418722:V328I;ENSP00000340943:V355I;ENSP00000344304:V314I;ENSP00000426498:V328I	ENSP00000344304:V314I	V	-	1	0	CRHR2	30661792	0.995000	0.38212	0.996000	0.52242	0.400000	0.30750	3.327000	0.52045	0.261000	0.21753	-0.224000	0.12420	GTC		0.602	CRHR2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250448.3		
STARD3NL	83930	broad.mit.edu	37	7	38254028	38254028	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr7:38254028A>G	ENST00000009041.7	+	3	553	c.296A>G	c.(295-297)gAt>gGt	p.D99G	STARD3NL_ENST00000544203.1_Missense_Mutation_p.D92G|STARD3NL_ENST00000396013.1_Missense_Mutation_p.D99G|STARD3NL_ENST00000434197.1_Missense_Mutation_p.D99G	NM_032016.3	NP_114405.1	O95772	MENTO_HUMAN	STARD3 N-terminal like	99	MENTAL. {ECO:0000255|PROSITE- ProRule:PRU00770}.					endosome (GO:0005768)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)		p.D99V(1)|p.D99G(1)		endometrium(2)|large_intestine(2)|lung(4)|ovary(1)|skin(1)	10						TCATATTTTGATATATTTGTA	0.333																																					p.D99G												.	.	2	Substitution - Missense(2)	large_intestine(1)|endometrium(1)	c.A296G	7						.						136.0	142.0	140.0					7																	38254028		2203	4300	6503	38220553	SO:0001583	missense	83930	exon3			AJ492267	CCDS5455.1	7p14-p13	2003-02-06			ENSG00000010270	ENSG00000010270			19169	protein-coding gene	gene with protein product		611759				12393907	Standard	NM_032016		Approved	MENTHO, MGC3251	uc003tfr.3	O95772	OTTHUMG00000023659	ENST00000009041.7:c.296A>G	7.37:g.38254028A>G	ENSP00000009041:p.Asp99Gly	Somatic		Capture	Illumina HiSeq	Phase_I	38220553	NM_032016	A4D1X0	Missense_Mutation	SNP	ENST00000009041.7	37	CCDS5455.1	.	.	.	.	.	.	.	.	.	.	A	24.1	4.491427	0.84962	.	.	ENSG00000010270	ENST00000009041;ENST00000544203;ENST00000434197;ENST00000396013;ENST00000440144;ENST00000453225;ENST00000429075	T;T;T;T;T;T;T	0.64260	-0.09;-0.09;-0.09;-0.09;-0.09;-0.09;-0.09	5.52	5.52	0.82312	MENTAL domain (2);	0.000000	0.85682	D	0.000000	T	0.82047	0.4952	M	0.89414	3.03	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.85757	0.1347	10	0.87932	D	0	-18.7273	14.6458	0.68759	1.0:0.0:0.0:0.0	.	99;99	C9JKL2;O95772	.;MENTO_HUMAN	G	99;92;99;99;99;99;99	ENSP00000009041:D99G;ENSP00000439436:D92G;ENSP00000394000:D99G;ENSP00000379334:D99G;ENSP00000411933:D99G;ENSP00000395455:D99G;ENSP00000402028:D99G	ENSP00000009041:D99G	D	+	2	0	STARD3NL	38220553	1.000000	0.71417	1.000000	0.80357	0.959000	0.62525	8.424000	0.90267	2.100000	0.63781	0.523000	0.50628	GAT		0.333	STARD3NL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226929.2		
INHBA	3624	broad.mit.edu	37	7	41729345	41729345	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr7:41729345T>C	ENST00000242208.4	-	3	1430	c.1184A>G	c.(1183-1185)aAg>aGg	p.K395R	INHBA_ENST00000464515.1_5'UTR|AC005027.3_ENST00000416150.1_RNA|INHBA_ENST00000442711.1_Missense_Mutation_p.K395R	NM_002192.2	NP_002183.1	P08476	INHBA_HUMAN	inhibin, beta A	395					activin receptor signaling pathway (GO:0032924)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell surface receptor signaling pathway (GO:0007166)|cell-cell signaling (GO:0007267)|cellular response to cholesterol (GO:0071397)|cellular response to follicle-stimulating hormone stimulus (GO:0071372)|defense response (GO:0006952)|endodermal cell differentiation (GO:0035987)|erythrocyte differentiation (GO:0030218)|extrinsic apoptotic signaling pathway (GO:0097191)|eyelid development in camera-type eye (GO:0061029)|G1/S transition of mitotic cell cycle (GO:0000082)|growth (GO:0040007)|hair follicle development (GO:0001942)|hematopoietic progenitor cell differentiation (GO:0002244)|hemoglobin biosynthetic process (GO:0042541)|male gonad development (GO:0008584)|mesodermal cell differentiation (GO:0048333)|negative regulation of B cell differentiation (GO:0045578)|negative regulation of cell cycle (GO:0045786)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of follicle-stimulating hormone secretion (GO:0046882)|negative regulation of interferon-gamma biosynthetic process (GO:0045077)|negative regulation of macrophage differentiation (GO:0045650)|negative regulation of phosphorylation (GO:0042326)|nervous system development (GO:0007399)|odontogenesis (GO:0042476)|ovarian follicle development (GO:0001541)|palate development (GO:0060021)|positive regulation of cellular protein metabolic process (GO:0032270)|positive regulation of erythrocyte differentiation (GO:0045648)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)|positive regulation of follicle-stimulating hormone secretion (GO:0046881)|positive regulation of ovulation (GO:0060279)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|progesterone secretion (GO:0042701)|regulation of follicle-stimulating hormone secretion (GO:0046880)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to drug (GO:0042493)	activin A complex (GO:0043509)|extracellular region (GO:0005576)|inhibin A complex (GO:0043512)	cytokine activity (GO:0005125)|growth factor activity (GO:0008083)|hormone activity (GO:0005179)|identical protein binding (GO:0042802)|peptide hormone binding (GO:0017046)|type II activin receptor binding (GO:0070699)	p.K395R(1)		biliary_tract(1)|breast(2)|endometrium(2)|kidney(1)|large_intestine(15)|lung(26)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	55						GGGTCTCAGCTTGGTGGGCAC	0.507										TSP Lung(11;0.080)																											p.K395R												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A1184G	7						.						137.0	115.0	122.0					7																	41729345		2203	4300	6503	41695870	SO:0001583	missense	3624	exon3				CCDS5464.1	7p15-p13	2014-01-30	2007-07-30		ENSG00000122641	ENSG00000122641		"""Endogenous ligands"""	6066	protein-coding gene	gene with protein product		147290	"""inhibin, beta A (activin A, activin AB alpha polypeptide)"""			3345731	Standard	NM_002192		Approved		uc003thr.3	P08476	OTTHUMG00000023574	ENST00000242208.4:c.1184A>G	7.37:g.41729345T>C	ENSP00000242208:p.Lys395Arg	Somatic		Capture	Illumina HiSeq	Phase_I	41695870	NM_002192	Q14599	Missense_Mutation	SNP	ENST00000242208.4	37	CCDS5464.1	.	.	.	.	.	.	.	.	.	.	.	12.89	2.074845	0.36566	.	.	ENSG00000122641	ENST00000242208;ENST00000442711	T;T	0.64260	-0.09;-0.09	5.86	5.86	0.93980	Transforming growth factor-beta, C-terminal (3);	0.099081	0.64402	D	0.000002	T	0.48114	0.1482	N	0.17345	0.48	0.52501	D	0.999952	B	0.31968	0.349	B	0.30716	0.119	T	0.48258	-0.9051	10	0.39692	T	0.17	-26.6365	16.2449	0.82437	0.0:0.0:0.0:1.0	.	395	P08476	INHBA_HUMAN	R	395	ENSP00000242208:K395R;ENSP00000397197:K395R	ENSP00000242208:K395R	K	-	2	0	INHBA	41695870	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.392000	0.52537	2.241000	0.73720	0.482000	0.46254	AAG		0.507	INHBA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250793.1		
MRPL32	64983	broad.mit.edu	37	7	42974676	42974676	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr7:42974676C>T	ENST00000223324.2	+	2	440	c.253C>T	c.(253-255)Cgc>Tgc	p.R85C	PSMA2_ENST00000223321.4_5'Flank|PSMA2_ENST00000445517.1_5'Flank|PSMA2_ENST00000442788.1_5'Flank|MRPL32_ENST00000496564.1_3'UTR|PSMA2_ENST00000538645.1_5'Flank	NM_031903.2	NP_114109.1	Q9BYC8	RM32_HUMAN	mitochondrial ribosomal protein L32	85					translation (GO:0006412)	large ribosomal subunit (GO:0015934)|mitochondrial ribosome (GO:0005761)	poly(A) RNA binding (GO:0044822)|structural constituent of ribosome (GO:0003735)	p.R85C(1)		endometrium(1)|kidney(1)|large_intestine(2)|lung(6)	10						CAAAAATAGACGCACCATTGA	0.428																																					p.R85C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C253T	7						.						100.0	92.0	95.0					7																	42974676		2203	4300	6503	42941201	SO:0001583	missense	64983	exon2			AB051343	CCDS5468.1	7p14	2012-09-13			ENSG00000106591	ENSG00000106591		"""Mitochondrial ribosomal proteins / large subunits"""	14035	protein-coding gene	gene with protein product		611839				11543634	Standard	NM_031903		Approved	HSPC283, L32mt, MRP-L32, bMRP-59b	uc003tia.3	Q9BYC8	OTTHUMG00000155180	ENST00000223324.2:c.253C>T	7.37:g.42974676C>T	ENSP00000223324:p.Arg85Cys	Somatic		Capture	Illumina HiSeq	Phase_I	42941201	NM_031903	Q96Q68|Q9P098	Missense_Mutation	SNP	ENST00000223324.2	37	CCDS5468.1	.	.	.	.	.	.	.	.	.	.	C	15.97	2.988964	0.53934	.	.	ENSG00000106591	ENST00000223324	.	.	.	5.35	5.35	0.76521	.	0.000000	0.85682	D	0.000000	T	0.63414	0.2509	M	0.85197	2.74	0.80722	D	1	D	0.54047	0.964	B	0.42798	0.398	T	0.70601	-0.4827	9	0.48119	T	0.1	-2.9047	13.9972	0.64409	0.1512:0.8487:0.0:0.0	.	85	Q9BYC8	RM32_HUMAN	C	85	.	ENSP00000223324:R85C	R	+	1	0	MRPL32	42941201	1.000000	0.71417	0.995000	0.50966	0.988000	0.76386	3.914000	0.56401	2.500000	0.84329	0.650000	0.86243	CGC		0.428	MRPL32-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338669.1	NM_031903	
DBNL	28988	broad.mit.edu	37	7	44100497	44100497	+	Silent	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr7:44100497C>T	ENST00000448521.1	+	13	1373	c.1275C>T	c.(1273-1275)taC>taT	p.Y425Y	DBNL_ENST00000494774.1_Silent_p.Y426Y|DBNL_ENST00000452943.1_Silent_p.Y401Y|DBNL_ENST00000490734.2_Silent_p.Y331Y|DBNL_ENST00000440166.1_Silent_p.Y322Y|DBNL_ENST00000468694.1_Silent_p.Y434Y|DBNL_ENST00000456905.1_Silent_p.Y377Y|DBNL_ENST00000497184.1_3'UTR	NM_001014436.2	NP_001014436.1	Q9UJU6	DBNL_HUMAN	drebrin-like	425	SH3. {ECO:0000255|PROSITE- ProRule:PRU00192}.				activation of JUN kinase activity (GO:0007257)|apoptotic process (GO:0006915)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|endocytosis (GO:0006897)|immune system process (GO:0002376)|neuron projection morphogenesis (GO:0048812)|podosome assembly (GO:0071800)|Rac protein signal transduction (GO:0016601)|synapse assembly (GO:0007416)	cell cortex (GO:0005938)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|dendrite (GO:0030425)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|podosome (GO:0002102)|postsynaptic density (GO:0014069)|ruffle (GO:0001726)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|enzyme activator activity (GO:0008047)	p.Y426Y(1)		breast(1)|large_intestine(3)|lung(5)|ovary(1)|skin(1)|stomach(1)	12						CTGCCAACTACGTGGAGCTCA	0.572																																					p.Y426Y	NSCLC(68;573 1327 18604 34760 37992)											.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1278T	7						.						131.0	103.0	112.0					7																	44100497		2203	4300	6503	44067022	SO:0001819	synonymous_variant	28988	exon13			AF151364	CCDS34622.1, CCDS34623.1, CCDS47579.1, CCDS64633.1, CCDS64634.1	7p13	2004-07-22			ENSG00000136279	ENSG00000136279			2696	protein-coding gene	gene with protein product		610106				10087302	Standard	NM_014063		Approved	SH3P7, HIP-55	uc003tjq.4	Q9UJU6	OTTHUMG00000155350	ENST00000448521.1:c.1275C>T	7.37:g.44100497C>T		Somatic		Capture	Illumina HiSeq	Phase_I	44067022	NM_014063	A4D2I9|B4DEM2|C9J7P1|P84070|Q6IAI8|Q96F30|Q96K74|Q9HBN8|Q9NR72	Silent	SNP	ENST00000448521.1	37	CCDS34623.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	9.690|9.690	1.151524|1.151524	0.21371|0.21371	.|.	.|.	ENSG00000136279|ENSG00000136279	ENST00000432854|ENST00000452661	.|.	.|.	.|.	5.4|5.4	-6.83|-6.83	0.01693|0.01693	.|.	.|.	.|.	.|.	.|.	T|T	0.63260|0.63260	0.2496|0.2496	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.66810|0.66810	-0.5829|-0.5829	4|4	.|.	.|.	.|.	-21.5864|-21.5864	16.458|16.458	0.84029|0.84029	0.0:0.3521:0.0:0.6479|0.0:0.3521:0.0:0.6479	.|.	.|.	.|.	.|.	C|M	354|133	.|.	.|.	R|T	+|+	1|2	0|0	DBNL|DBNL	44067022|44067022	0.275000|0.275000	0.24201|0.24201	0.762000|0.762000	0.31397|0.31397	0.987000|0.987000	0.75469|0.75469	-0.230000|-0.230000	0.09083|0.09083	-1.421000|-1.421000	0.02007|0.02007	-0.266000|-0.266000	0.10368|0.10368	CGT|ACG		0.572	DBNL-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000339572.2	NM_014063	
DDX56	54606	broad.mit.edu	37	7	44612026	44612026	+	Missense_Mutation	SNP	G	G	A	rs62459150		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr7:44612026G>A	ENST00000258772.5	-	5	671	c.565C>T	c.(565-567)Cgg>Tgg	p.R189W	DDX56_ENST00000431640.1_Missense_Mutation_p.R189W|DDX56_ENST00000485367.1_5'UTR	NM_001257189.1|NM_019082.3	NP_001244118.1|NP_061955.1	Q9NY93	DDX56_HUMAN	DEAD (Asp-Glu-Ala-Asp) box helicase 56	189	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				ATP catabolic process (GO:0006200)|rRNA processing (GO:0006364)	membrane (GO:0016020)|nucleolus (GO:0005730)	ATP binding (GO:0005524)|ATP-dependent RNA helicase activity (GO:0004004)|poly(A) RNA binding (GO:0044822)	p.R189W(1)		breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(5)|lung(5)|upper_aerodigestive_tract(1)	16						TGGTAAATCCGGGGCAAGTGA	0.493													G|||	1	0.000199681	0.0008	0.0	5008	,	,		20625	0.0		0.0	False		,,,				2504	0.0				p.R189W												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C565T	7						.	G	TRP/ARG	3,4403		0,3,2200	65.0	64.0	65.0		565	4.2	1.0	7	dbSNP_129	65	0,8600		0,0,4300	yes	missense	DDX56	NM_019082.2	101	0,3,6500	AA,AG,GG		0.0,0.0681,0.0231	probably-damaging	189/548	44612026	3,13003	2203	4300	6503	44578551	SO:0001583	missense	54606	exon5			AJ131712	CCDS5492.1, CCDS59053.1	7p13	2012-02-23	2012-02-23		ENSG00000136271	ENSG00000136271		"""DEAD-boxes"""	18193	protein-coding gene	gene with protein product	"""nucleolar helicase of 61 kDa"""	608023	"""DEAD (Asp-Glu-Ala-Asp) box polypeptide 56"""			10749921	Standard	NM_019082		Approved	NOH61	uc003tlg.4	Q9NY93	OTTHUMG00000129211	ENST00000258772.5:c.565C>T	7.37:g.44612026G>A	ENSP00000258772:p.Arg189Trp	Somatic		Capture	Illumina HiSeq	Phase_I	44578551	NM_019082	A4D2K9|C9JV95|Q6IAE2|Q9H9I8	Missense_Mutation	SNP	ENST00000258772.5	37	CCDS5492.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	.	21.6	4.178472	0.78564	6.81E-4	0.0	ENSG00000136271	ENST00000258772;ENST00000431640	T;T	0.16324	2.35;2.35	6.07	4.22	0.49857	DEAD-like helicase (2);DNA/RNA helicase, DEAD/DEAH box type, N-terminal (1);	0.054851	0.64402	D	0.000001	T	0.38480	0.1042	M	0.70842	2.15	0.41381	D	0.987556	D;D	0.89917	0.999;1.0	D;D	0.66979	0.948;0.948	T	0.23511	-1.0186	10	0.87932	D	0	-23.4188	12.482	0.55850	0.0:0.0:0.5773:0.4227	rs62459150	189;189	C9JV95;Q9NY93	.;DDX56_HUMAN	W	189	ENSP00000258772:R189W;ENSP00000393488:R189W	ENSP00000258772:R189W	R	-	1	2	DDX56	44578551	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	2.884000	0.48562	0.846000	0.35142	0.655000	0.94253	CGG		0.493	DDX56-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251291.1	NM_019082	
OGDH	4967	broad.mit.edu	37	7	44736044	44736044	+	Silent	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr7:44736044C>T	ENST00000222673.5	+	14	1830	c.1788C>T	c.(1786-1788)gaC>gaT	p.D596D	OGDH_ENST00000449767.1_Silent_p.D592D|OGDH_ENST00000447398.1_Silent_p.D607D|OGDH_ENST00000439616.2_Silent_p.D446D|OGDH_ENST00000543843.1_Silent_p.D547D|OGDH_ENST00000444676.1_Silent_p.D611D	NM_002541.3	NP_002532.2	Q02218	ODO1_HUMAN	oxoglutarate (alpha-ketoglutarate) dehydrogenase (lipoamide)	596					2-oxoglutarate metabolic process (GO:0006103)|cellular metabolic process (GO:0044237)|cellular nitrogen compound metabolic process (GO:0034641)|cerebellar cortex development (GO:0021695)|generation of precursor metabolites and energy (GO:0006091)|glycolytic process (GO:0006096)|hippocampus development (GO:0021766)|lysine catabolic process (GO:0006554)|NADH metabolic process (GO:0006734)|olfactory bulb mitral cell layer development (GO:0061034)|pyramidal neuron development (GO:0021860)|small molecule metabolic process (GO:0044281)|striatum development (GO:0021756)|succinyl-CoA metabolic process (GO:0006104)|tangential migration from the subventricular zone to the olfactory bulb (GO:0022028)|thalamus development (GO:0021794)|tricarboxylic acid cycle (GO:0006099)	mitochondrial matrix (GO:0005759)|mitochondrial membrane (GO:0031966)|mitochondrion (GO:0005739)|oxoglutarate dehydrogenase complex (GO:0045252)	metal ion binding (GO:0046872)|oxoglutarate dehydrogenase (NAD+) activity (GO:0034602)|oxoglutarate dehydrogenase (succinyl-transferring) activity (GO:0004591)|thiamine pyrophosphate binding (GO:0030976)	p.D596D(1)		breast(2)|endometrium(5)|kidney(2)|large_intestine(6)|lung(13)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(4)	36					Valproic Acid(DB00313)	TCACCCTGGACGGGCAGCCCA	0.527																																					p.D596D												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1788T	7						.						82.0	75.0	77.0					7																	44736044		2203	4300	6503	44702569	SO:0001819	synonymous_variant	4967	exon14			D10523	CCDS34627.1, CCDS47580.1, CCDS55107.1	7p13-p11.2	2010-11-23			ENSG00000105953	ENSG00000105953	1.2.4.2		8124	protein-coding gene	gene with protein product		613022				8020988, 1542694	Standard	NM_002541		Approved	E1k	uc003tln.3	Q02218	OTTHUMG00000155304	ENST00000222673.5:c.1788C>T	7.37:g.44736044C>T		Somatic		Capture	Illumina HiSeq	Phase_I	44702569	NM_002541	B4E2U9|D3DVL0|E9PBM1|Q96DD3|Q9UDX0	Silent	SNP	ENST00000222673.5	37	CCDS34627.1																																																																																				0.527	OGDH-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000339391.1		
ZMIZ2	83637	broad.mit.edu	37	7	44805021	44805021	+	Silent	SNP	G	G	A	rs373008599		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr7:44805021G>A	ENST00000309315.4	+	16	2208	c.2085G>A	c.(2083-2085)ccG>ccA	p.P695P	ZMIZ2_ENST00000413916.1_Silent_p.P637P|ZMIZ2_ENST00000433667.1_Silent_p.P663P|ZMIZ2_ENST00000265346.7_Silent_p.P669P|ZMIZ2_ENST00000441627.1_Silent_p.P695P	NM_031449.3	NP_113637.3	Q8NF64	ZMIZ2_HUMAN	zinc finger, MIZ-type containing 2	695					positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	mitochondrion (GO:0005739)|nuclear replication fork (GO:0043596)|nucleus (GO:0005634)	ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|zinc ion binding (GO:0008270)	p.P695P(1)		breast(3)|endometrium(2)|kidney(3)|large_intestine(6)|lung(10)|ovary(6)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	35						AGGAGGAGCCGGATGGGCCAG	0.667																																					p.P669P	NSCLC(20;604 852 1948 16908 50522)											.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G2007A	7						.	G	,	0,4238		0,0,2119	32.0	35.0	34.0		2085,2007	-10.3	0.1	7		34	1,8473		0,1,4236	no	coding-synonymous,coding-synonymous	ZMIZ2	NM_031449.3,NM_174929.2	,	0,1,6355	AA,AG,GG		0.0118,0.0,0.0079	,	695/921,669/895	44805021	1,12711	2119	4237	6356	44771546	SO:0001819	synonymous_variant	83637	exon14			AK090415	CCDS43576.1, CCDS43577.1, CCDS75591.1	7p13	2009-11-06			ENSG00000122515	ENSG00000122515		"""Zinc fingers, MIZ-type"""	22229	protein-coding gene	gene with protein product		611196					Standard	XM_005249866		Approved	KIAA1886, hZIMP7, ZIMP7, DKFZp761I2123, NET27	uc003tlr.3	Q8NF64	OTTHUMG00000155817	ENST00000309315.4:c.2085G>A	7.37:g.44805021G>A		Somatic		Capture	Illumina HiSeq	Phase_I	44771546	NM_174929	A4D2K7|D3DVL1|O94790|Q0VGB4|Q659A8|Q6JKL5|Q8WTX8|Q96Q01|Q9BQH7	Silent	SNP	ENST00000309315.4	37	CCDS43576.1																																																																																				0.667	ZMIZ2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341790.1	NM_031449	
COBL	23242	broad.mit.edu	37	7	51203960	51203960	+	Silent	SNP	C	C	T	rs201927430		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr7:51203960C>T	ENST00000265136.7	-	6	1017	c.852G>A	c.(850-852)tcG>tcA	p.S284S	COBL_ENST00000395540.2_Silent_p.S284S|COBL_ENST00000441453.1_Silent_p.S284S|COBL_ENST00000395542.2_Silent_p.S309S	NM_015198.3	NP_056013.2	O75128	COBL_HUMAN	cordon-bleu WH2 repeat protein	284					actin filament network formation (GO:0051639)|actin filament polymerization (GO:0030041)|collateral sprouting in absence of injury (GO:0048669)|digestive tract development (GO:0048565)|embryonic axis specification (GO:0000578)|floor plate development (GO:0033504)|liver development (GO:0001889)|neural tube closure (GO:0001843)|notochord development (GO:0030903)|positive regulation of dendrite development (GO:1900006)|somite specification (GO:0001757)	actin filament (GO:0005884)|axon (GO:0030424)|axonal growth cone (GO:0044295)|cell cortex (GO:0005938)|dendrite (GO:0030425)|dendritic growth cone (GO:0044294)|neuronal cell body (GO:0043025)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	actin monomer binding (GO:0003785)	p.S284S(1)		NS(2)|autonomic_ganglia(1)|central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(10)|lung(26)|ovary(3)|prostate(4)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	65	Glioma(55;0.08)					TGCTGCCCAGCGAGAGGGATG	0.577																																					p.S284S	NSCLC(189;2119 2138 12223 30818 34679)											.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G852A	7						.						64.0	57.0	60.0					7																	51203960		2203	4300	6503	51171454	SO:0001819	synonymous_variant	23242	exon6			AB014533	CCDS34637.1, CCDS75601.1, CCDS75602.1	7p12.2-p12.1	2012-12-07	2012-12-07		ENSG00000106078	ENSG00000106078			22199	protein-coding gene	gene with protein product		610317	"""cordon-bleu homolog (mouse)"""				Standard	NM_015198		Approved	KIAA0633	uc003tpr.4	O75128	OTTHUMG00000155999	ENST00000265136.7:c.852G>A	7.37:g.51203960C>T		Somatic		Capture	Illumina HiSeq	Phase_I	51171454	NM_015198	A4D257|A7E2B0|B7ZLW9|B9EGF8|Q2T9J3|Q504Y4|Q86XA7|Q8N304|Q8TCM1	Silent	SNP	ENST00000265136.7	37	CCDS34637.1	.	.	.	.	.	.	.	.	.	.	C	4.547	0.101545	0.08731	.	.	ENSG00000106078	ENST00000452534	.	.	.	5.55	-11.1	0.00147	.	.	.	.	.	T	0.42177	0.1191	.	.	.	0.53005	D	0.999964	.	.	.	.	.	.	T	0.65446	-0.6166	4	.	.	.	.	5.7385	0.18079	0.1585:0.0665:0.4029:0.372	.	.	.	.	T	203	.	.	A	-	1	0	COBL	51171454	0.000000	0.05858	0.000000	0.03702	0.550000	0.35303	-3.611000	0.00415	-5.658000	0.00011	-2.295000	0.00263	GCT		0.577	COBL-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000342682.1	NM_015198	
EGFR	1956	broad.mit.edu	37	7	55223573	55223573	+	Missense_Mutation	SNP	G	G	A	rs552062864		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr7:55223573G>A	ENST00000275493.2	+	8	1117	c.940G>A	c.(940-942)Gac>Aac	p.D314N	EGFR_ENST00000454757.2_Missense_Mutation_p.D261N|EGFR_ENST00000442591.1_Missense_Mutation_p.D314N|EGFR_ENST00000420316.2_Missense_Mutation_p.D314N|EGFR_ENST00000344576.2_Missense_Mutation_p.D314N|EGFR_ENST00000342916.3_Missense_Mutation_p.D314N|EGFR_ENST00000455089.1_Missense_Mutation_p.D269N	NM_005228.3	NP_005219.2	P00533	EGFR_HUMAN	epidermal growth factor receptor	314					activation of phospholipase A2 activity by calcium-mediated signaling (GO:0043006)|activation of phospholipase C activity (GO:0007202)|alkanesulfonate metabolic process (GO:0019694)|astrocyte activation (GO:0048143)|axon guidance (GO:0007411)|cell proliferation (GO:0008283)|cell surface receptor signaling pathway (GO:0007166)|cellular response to amino acid stimulus (GO:0071230)|cellular response to dexamethasone stimulus (GO:0071549)|cellular response to drug (GO:0035690)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to estradiol stimulus (GO:0071392)|cellular response to mechanical stimulus (GO:0071260)|cerebral cortex cell migration (GO:0021795)|circadian rhythm (GO:0007623)|digestive tract morphogenesis (GO:0048546)|diterpenoid metabolic process (GO:0016101)|embryonic placenta development (GO:0001892)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|hair follicle development (GO:0001942)|hydrogen peroxide metabolic process (GO:0042743)|innate immune response (GO:0045087)|learning or memory (GO:0007611)|liver development (GO:0001889)|lung development (GO:0030324)|magnesium ion homeostasis (GO:0010960)|MAPK cascade (GO:0000165)|morphogenesis of an epithelial fold (GO:0060571)|negative regulation of apoptotic process (GO:0043066)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of mitotic cell cycle (GO:0045930)|negative regulation of protein catabolic process (GO:0042177)|neurotrophin TRK receptor signaling pathway (GO:0048011)|ossification (GO:0001503)|ovulation cycle (GO:0042698)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|polysaccharide metabolic process (GO:0005976)|positive regulation of catenin import into nucleus (GO:0035413)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle (GO:0031659)|positive regulation of DNA repair (GO:0045739)|positive regulation of DNA replication (GO:0045740)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of inflammatory response (GO:0050729)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of phosphorylation (GO:0042327)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of superoxide anion generation (GO:0032930)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of vasoconstriction (GO:0045907)|positive regulation of vasodilation (GO:0045909)|protein autophosphorylation (GO:0046777)|protein insertion into membrane (GO:0051205)|regulation of nitric-oxide synthase activity (GO:0050999)|regulation of peptidyl-tyrosine phosphorylation (GO:0050730)|response to calcium ion (GO:0051592)|response to cobalamin (GO:0033590)|response to hydroxyisoflavone (GO:0033594)|response to osmotic stress (GO:0006970)|response to oxidative stress (GO:0006979)|response to stress (GO:0006950)|response to UV-A (GO:0070141)|salivary gland morphogenesis (GO:0007435)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|tongue development (GO:0043586)|translation (GO:0006412)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|endosome membrane (GO:0010008)|extracellular space (GO:0005615)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|membrane raft (GO:0045121)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|Shc-EGFR complex (GO:0070435)	actin filament binding (GO:0051015)|ATP binding (GO:0005524)|chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|enzyme binding (GO:0019899)|epidermal growth factor-activated receptor activity (GO:0005006)|identical protein binding (GO:0042802)|MAP kinase kinase kinase activity (GO:0004709)|protein heterodimerization activity (GO:0046982)|protein phosphatase binding (GO:0019903)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|transmembrane signaling receptor activity (GO:0004888)|ubiquitin protein ligase binding (GO:0031625)	p.D314N(2)		NS(2)|adrenal_gland(5)|biliary_tract(8)|bone(3)|breast(18)|central_nervous_system(106)|endometrium(26)|eye(3)|haematopoietic_and_lymphoid_tissue(9)|kidney(11)|large_intestine(85)|liver(2)|lung(13575)|oesophagus(21)|ovary(38)|pancreas(3)|peritoneum(11)|pleura(2)|prostate(35)|salivary_gland(11)|skin(9)|small_intestine(1)|soft_tissue(4)|stomach(41)|thymus(2)|thyroid(14)|upper_aerodigestive_tract(59)|urinary_tract(6)	14110	all_cancers(1;1.57e-46)|all_epithelial(1;5.62e-37)|Lung NSC(1;9.29e-25)|all_lung(1;4.39e-23)|Esophageal squamous(2;7.55e-08)|Breast(14;0.0318)		GBM - Glioblastoma multiforme(1;0)|all cancers(1;2.19e-314)|Lung(13;4.65e-05)|LUSC - Lung squamous cell carcinoma(13;0.000168)|STAD - Stomach adenocarcinoma(5;0.00164)|Epithelial(13;0.0607)		Afatinib(DB08916)|Cetuximab(DB00002)|Erlotinib(DB00530)|Gefitinib(DB00317)|Lapatinib(DB01259)|Lidocaine(DB00281)|Panitumumab(DB01269)|Trastuzumab(DB00072)|Vandetanib(DB05294)	CTGTGGGGCCGACAGCTATGA	0.597		8	"""A, O, Mis"""		"""glioma, NSCLC"""	NSCLC			Lung Cancer, Familial Clustering of	TCGA GBM(3;<1E-08)|TSP Lung(4;<1E-08)			G|||	1	0.000199681	0.0008	0.0	5008	,	,		14401	0.0		0.0	False		,,,				2504	0.0				p.D314N		yes	Dom	yes	Familial lung cancer	7	7p12.3-p12.1	1956	"""epidermal growth factor receptor (erythroblastic leukemia viral (v-erb-b) oncogene homolog, avian)"""		"""E, O"""	.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G940A	7						.						52.0	49.0	50.0					7																	55223573		2203	4300	6503	55191067	SO:0001583	missense	1956	exon8	Familial Cancer Database	incl. Hereditary Lung cancer, Hereditary Non-Small Cell Lung cancer		CCDS5514.1, CCDS5515.1, CCDS5516.1, CCDS47587.1	7p12	2014-09-17	2010-06-25		ENSG00000146648	ENSG00000146648			3236	protein-coding gene	gene with protein product	"""erythroblastic leukemia viral (v-erb-b) oncogene homolog (avian)"""	131550	"""epidermal growth factor receptor (avian erythroblastic leukemia viral (v-erb-b) oncogene homolog)"""	ERBB		1505215	Standard	NM_201282		Approved	ERBB1	uc003tqk.3	P00533	OTTHUMG00000023661	ENST00000275493.2:c.940G>A	7.37:g.55223573G>A	ENSP00000275493:p.Asp314Asn	Somatic		Capture	Illumina HiSeq	Phase_I	55191067	NM_201282	O00688|O00732|P06268|Q14225|Q68GS5|Q92795|Q9BZS2|Q9GZX1|Q9H2C9|Q9H3C9|Q9UMD7|Q9UMD8|Q9UMG5	Missense_Mutation	SNP	ENST00000275493.2	37	CCDS5514.1	.	.	.	.	.	.	.	.	.	.	G	6.182	0.401776	0.11696	.	.	ENSG00000146648	ENST00000455089;ENST00000342916;ENST00000395504;ENST00000344576;ENST00000420316;ENST00000275493;ENST00000442591;ENST00000454757;ENST00000533450	T;T;T;T;T;T;T	0.62105	0.05;0.05;0.05;0.05;0.05;0.05;0.05	5.64	5.64	0.86602	Growth factor, receptor (1);Furin-like cysteine-rich domain (1);	0.139334	0.64402	D	0.000004	T	0.44222	0.1283	N	0.11818	0.18	0.47245	D	0.999364	B;B;B;B;B	0.15719	0.002;0.001;0.014;0.004;0.011	B;B;B;B;B	0.14023	0.003;0.01;0.008;0.002;0.003	T	0.39440	-0.9614	10	0.08837	T	0.75	.	18.2675	0.90056	0.0:0.0:1.0:0.0	.	269;314;314;314;314	Q504U8;P00533;P00533-3;P00533-4;P00533-2	.;EGFR_HUMAN;.;.;.	N	269;314;184;314;314;314;314;261;108	ENSP00000415559:D269N;ENSP00000342376:D314N;ENSP00000345973:D314N;ENSP00000413843:D314N;ENSP00000275493:D314N;ENSP00000410031:D314N;ENSP00000395243:D261N	ENSP00000275493:D314N	D	+	1	0	EGFR	55191067	1.000000	0.71417	0.964000	0.40570	0.144000	0.21451	5.098000	0.64548	2.655000	0.90218	0.655000	0.94253	GAC		0.597	EGFR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251456.2	NM_005228	
VOPP1	81552	broad.mit.edu	37	7	55540719	55540719	+	Silent	SNP	C	C	T	rs11238366		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr7:55540719C>T	ENST00000285279.5	-	5	548	c.348G>A	c.(346-348)ccG>ccA	p.P116P	VOPP1_ENST00000418904.1_Silent_p.P99P|VOPP1_ENST00000428097.1_Silent_p.P49P|VOPP1_ENST00000454227.1_Silent_p.P53P|VOPP1_ENST00000453256.1_Silent_p.P49P|VOPP1_ENST00000545390.1_Silent_p.P113P|VOPP1_ENST00000428648.1_Silent_p.P49P|VOPP1_ENST00000433959.1_Silent_p.P107P|VOPP1_ENST00000427700.1_Silent_p.P114P	NM_001284282.1|NM_030796.3	NP_001271211.1|NP_110423.3	Q96AW1	VOPP1_HUMAN	vesicular, overexpressed in cancer, prosurvival protein 1	116	Pro-rich.				regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)	cytoplasmic vesicle membrane (GO:0030659)|endosome (GO:0005768)|integral component of organelle membrane (GO:0031301)	signal transducer activity (GO:0004871)	p.A79T(1)		endometrium(1)|lung(4)	5						TGTAATAGGGCGGCCCCGGCT	0.607																																					p.P116P												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G348A	7						.	C		0,3804		0,0,1902	34.0	39.0	38.0		348	0.9	0.9	7	dbSNP_120	38	1,8203		0,1,4101	no	coding-synonymous	VOPP1	NM_030796.3		0,1,6003	TT,TC,CC		0.0122,0.0,0.0083		116/173	55540719	1,12007	1902	4102	6004	55508213	SO:0001819	synonymous_variant	81552	exon5				CCDS47588.1, CCDS64654.1, CCDS64656.1	7p11.2	2010-06-22			ENSG00000154978	ENSG00000154978			34518	protein-coding gene	gene with protein product	"""Glioblastoma-amplified secreted protein"", ""EGFR-coamplified and overexpressed protein"""	611915				15735698	Standard	NM_030796		Approved	ECop, GASP, FLJ20532, DKFZp564K0822	uc003tqs.3	Q96AW1	OTTHUMG00000156124	ENST00000285279.5:c.348G>A	7.37:g.55540719C>T		Somatic		Capture	Illumina HiSeq	Phase_I	55508213	NM_030796	B0AZU1|B2RAT4|B3KS72|C9JWR3|Q6FIE3|Q8NBN8|Q96RE5|Q9H0W4	Missense_Mutation	SNP	ENST00000285279.5	37	CCDS47588.1																																																																																				0.607	VOPP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343074.1	NM_030796	
SUMF2	25870	broad.mit.edu	37	7	56142408	56142408	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr7:56142408G>A	ENST00000413756.1	+	5	537	c.514G>A	c.(514-516)Gcc>Acc	p.A172T	SUMF2_ENST00000275607.9_Missense_Mutation_p.A84T|SUMF2_ENST00000342190.6_Missense_Mutation_p.A191T|SUMF2_ENST00000437307.2_Intron|SUMF2_ENST00000395435.2_Intron|SUMF2_ENST00000434526.2_Missense_Mutation_p.A191T|SUMF2_ENST00000395436.2_Missense_Mutation_p.A176T			Q8NBJ7	SUMF2_HUMAN	sulfatase modifying factor 2	172					cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)	endoplasmic reticulum lumen (GO:0005788)	metal ion binding (GO:0046872)	p.A172T(1)		breast(2)|endometrium(2)|large_intestine(1)|lung(6)|ovary(2)|skin(1)	14	Breast(14;0.214)		Lung(13;0.00024)|LUSC - Lung squamous cell carcinoma(13;0.00099)			GTGGGAGTTTGCCGCCCGAGG	0.567											OREG0018081	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.A176T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G526A	7						.						80.0	82.0	82.0					7																	56142408		2203	4300	6503	56109902	SO:0001583	missense	25870	exon4			AK075477	CCDS5524.2, CCDS43588.2, CCDS43589.2, CCDS47589.1, CCDS55111.1	7q11.1	2004-04-30			ENSG00000129103	ENSG00000129103			20415	protein-coding gene	gene with protein product		607940				12757706	Standard	NM_015411		Approved	DKFZp566I1024	uc003trv.3	Q8NBJ7	OTTHUMG00000129373	ENST00000413756.1:c.514G>A	7.37:g.56142408G>A	ENSP00000406445:p.Ala172Thr	Somatic	1013	Capture	Illumina HiSeq	Phase_I	56109902	NM_001042469	B4DU41|B4DWQ0|Q14DW5|Q53ZE3|Q96BH2|Q9BRN3|Q9BWI1|Q9Y405	Missense_Mutation	SNP	ENST00000413756.1	37		.	.	.	.	.	.	.	.	.	.	G	36	5.758556	0.96898	.	.	ENSG00000129103	ENST00000395436;ENST00000434526;ENST00000275607;ENST00000413952;ENST00000342190;ENST00000413756;ENST00000451338	D;D;D;D;D;D;D	0.98947	-5.26;-5.26;-5.26;-5.26;-5.26;-5.26;-5.26	5.53	5.53	0.82687	C-type lectin fold (1);Formylglycine-generating sulphatase enzyme domain (2);	0.000000	0.85682	D	0.000000	D	0.99554	0.9840	H	0.98388	4.22	0.80722	D	1	D;D;D	0.89917	1.0;1.0;0.999	D;D;D	0.97110	1.0;1.0;0.924	D	0.97933	1.0321	10	0.72032	D	0.01	-11.665	18.8414	0.92186	0.0:0.0:1.0:0.0	.	176;172;191	A8MXB9;Q8NBJ7;F8WA42	.;SUMF2_HUMAN;.	T	176;191;84;194;191;172;189	ENSP00000378824:A176T;ENSP00000400922:A191T;ENSP00000275607:A84T;ENSP00000414434:A194T;ENSP00000341938:A191T;ENSP00000406445:A172T;ENSP00000410796:A189T	ENSP00000275607:A84T	A	+	1	0	SUMF2	56109902	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.603000	0.98315	2.777000	0.95525	0.591000	0.81541	GCC		0.567	SUMF2-013	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000341457.2	NM_015411	
ZNF92	168374	broad.mit.edu	37	7	64863783	64863783	+	Silent	SNP	T	T	C			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr7:64863783T>C	ENST00000328747.7	+	4	955	c.756T>C	c.(754-756)acT>acC	p.T252T	ZNF92_ENST00000431504.1_Silent_p.T176T|ZNF92_ENST00000357512.2_Silent_p.T220T|ZNF92_ENST00000450302.2_Silent_p.T183T	NM_152626.2	NP_689839.1	Q03936	ZNF92_HUMAN	zinc finger protein 92	252					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)	p.T252T(1)		breast(2)|endometrium(1)|large_intestine(3)|lung(4)|pancreas(1)|skin(1)|stomach(1)	13		Lung NSC(55;0.159)				TAATTCATACTGGAGAGAAAC	0.348																																					p.T252T												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.T756C	7						.						37.0	40.0	39.0					7																	64863783		2139	4250	6389	64501218	SO:0001819	synonymous_variant	168374	exon4			M61872	CCDS34646.1, CCDS47596.1, CCDS75608.1, CCDS75609.1	7q11.21	2013-01-08	2006-05-12		ENSG00000146757	ENSG00000146757		"""Zinc fingers, C2H2-type"", ""-"""	13168	protein-coding gene	gene with protein product		603974	"""zinc finger protein 92 (HTF12)"""			8467795	Standard	NM_001287533		Approved	HPF12, TF12	uc003ttz.3	Q03936	OTTHUMG00000156557	ENST00000328747.7:c.756T>C	7.37:g.64863783T>C		Somatic		Capture	Illumina HiSeq	Phase_I	64501218	NM_152626	A6NNF9|Q8N492|Q8NB35	Silent	SNP	ENST00000328747.7	37	CCDS34646.1																																																																																				0.348	ZNF92-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000344589.2	NM_152626	
SEMA3C	10512	broad.mit.edu	37	7	80418628	80418628	+	Missense_Mutation	SNP	C	C	T	rs367759300		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr7:80418628C>T	ENST00000265361.3	-	12	1909	c.1348G>A	c.(1348-1350)Gga>Aga	p.G450R	SEMA3C_ENST00000419255.2_Missense_Mutation_p.G450R|SEMA3C_ENST00000544525.1_Missense_Mutation_p.G468R	NM_006379.3	NP_006370.1	Q99985	SEM3C_HUMAN	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3C	450	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				axon guidance (GO:0007411)|blood vessel remodeling (GO:0001974)|cardiac right ventricle morphogenesis (GO:0003215)|dichotomous subdivision of terminal units involved in salivary gland branching (GO:0060666)|immune response (GO:0006955)|limb bud formation (GO:0060174)|neural crest cell migration (GO:0001755)|neural tube development (GO:0021915)|outflow tract morphogenesis (GO:0003151)|post-embryonic development (GO:0009791)|pulmonary myocardium development (GO:0003350)|response to drug (GO:0042493)|somitogenesis (GO:0001756)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	receptor activity (GO:0004872)	p.G450*(1)|p.G450R(1)		NS(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(17)|ovary(1)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	34						TTACCTGTTCCGAGAAACAGG	0.393																																					p.G450R												.	.	2	Substitution - Nonsense(1)|Substitution - Missense(1)	large_intestine(1)|lung(1)	c.G1348A	7						.	C	ARG/GLY	1,4405	2.1+/-5.4	0,1,2202	136.0	127.0	130.0		1348	5.7	0.6	7		130	0,8600		0,0,4300	no	missense	SEMA3C	NM_006379.3	125	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	probably-damaging	450/752	80418628	1,13005	2203	4300	6503	80256564	SO:0001583	missense	10512	exon12			AB000220	CCDS5596.1	7q21-q31	2013-01-11			ENSG00000075223	ENSG00000075223		"""Semaphorins"", ""Immunoglobulin superfamily / I-set domain containing"""	10725	protein-coding gene	gene with protein product		602645		SEMAE		7748561, 9168980	Standard	NM_006379		Approved	SemE	uc003uhj.3	Q99985	OTTHUMG00000023447	ENST00000265361.3:c.1348G>A	7.37:g.80418628C>T	ENSP00000265361:p.Gly450Arg	Somatic		Capture	Illumina HiSeq	Phase_I	80256564	NM_006379	B4DRL8	Missense_Mutation	SNP	ENST00000265361.3	37	CCDS5596.1	.	.	.	.	.	.	.	.	.	.	C	24.0	4.483655	0.84854	2.27E-4	0.0	ENSG00000075223	ENST00000265361;ENST00000419255;ENST00000544525	T;T;T	0.32753	1.44;1.44;1.44	5.74	5.74	0.90152	WD40/YVTN repeat-like-containing domain (1);Semaphorin/CD100 antigen (4);	0.000000	0.85682	D	0.000000	T	0.68485	0.3006	M	0.93678	3.445	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.76658	-0.2878	10	0.87932	D	0	.	19.9145	0.97053	0.0:1.0:0.0:0.0	.	468;450	F5H1Z7;Q99985	.;SEM3C_HUMAN	R	450;450;468	ENSP00000265361:G450R;ENSP00000411193:G450R;ENSP00000445649:G468R	ENSP00000265361:G450R	G	-	1	0	SEMA3C	80256564	1.000000	0.71417	0.649000	0.29536	0.518000	0.34316	7.818000	0.86416	2.707000	0.92482	0.557000	0.71058	GGA		0.393	SEMA3C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253279.1	NM_006379	
PCLO	27445	broad.mit.edu	37	7	82451893	82451893	+	Silent	SNP	G	G	A	rs138863699		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr7:82451893G>A	ENST00000333891.9	-	20	15046	c.14709C>T	c.(14707-14709)agC>agT	p.S4903S	PCLO_ENST00000426442.2_5'UTR|PCLO_ENST00000423517.2_Silent_p.S4903S	NM_033026.5	NP_149015.2			piccolo presynaptic cytomatrix protein									p.S4903S(1)		breast(3)|central_nervous_system(3)|cervix(5)|endometrium(19)|haematopoietic_and_lymphoid_tissue(3)|kidney(19)|large_intestine(35)|lung(145)|ovary(7)|prostate(4)|upper_aerodigestive_tract(14)|urinary_tract(2)	259						TCTGAGTGACGCTGGTTTTGC	0.502													G|||	1	0.000199681	0.0	0.0	5008	,	,		17024	0.0		0.001	False		,,,				2504	0.0				p.S4903S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C14709T	7						.	G	,	0,4168		0,0,2084	204.0	214.0	211.0		14709,14709	1.5	1.0	7	dbSNP_134	211	1,8419		0,1,4209	no	coding-synonymous,coding-synonymous	PCLO	NM_014510.2,NM_033026.5	,	0,1,6293	AA,AG,GG		0.0119,0.0,0.0079	,	4903/4936,4903/5143	82451893	1,12587	2084	4210	6294	82289829	SO:0001819	synonymous_variant	27445	exon20			AB011131	CCDS47630.1, CCDS47631.1	7q11.23-q21.3	2013-01-07	2013-01-07		ENSG00000186472	ENSG00000186472			13406	protein-coding gene	gene with protein product	"""aczonin"""	604918	"""piccolo (presynaptic cytomatrix protein)"""			8900486, 9628581	Standard	NM_014510		Approved	KIAA0559, DKFZp779G1236, ACZ	uc003uhx.2	Q9Y6V0	OTTHUMG00000154853	ENST00000333891.9:c.14709C>T	7.37:g.82451893G>A		Somatic		Capture	Illumina HiSeq	Phase_I	82289829	NM_033026		Silent	SNP	ENST00000333891.9	37	CCDS47630.1																																																																																				0.502	PCLO-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337368.5	NM_014510	
PCLO	27445	broad.mit.edu	37	7	82470819	82470819	+	Missense_Mutation	SNP	C	C	T	rs369280378		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr7:82470819C>T	ENST00000333891.9	-	14	14390	c.14053G>A	c.(14053-14055)Gat>Aat	p.D4685N	PCLO_ENST00000426442.2_5'UTR|PCLO_ENST00000423517.2_Missense_Mutation_p.D4685N	NM_033026.5	NP_149015.2			piccolo presynaptic cytomatrix protein									p.D4685N(1)		breast(3)|central_nervous_system(3)|cervix(5)|endometrium(19)|haematopoietic_and_lymphoid_tissue(3)|kidney(19)|large_intestine(35)|lung(145)|ovary(7)|prostate(4)|upper_aerodigestive_tract(14)|urinary_tract(2)	259						TTTGTTCCATCGGTAGGCTGT	0.308																																					p.D4685N												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G14053A	7						.	C	ASN/ASP,ASN/ASP	1,3601		0,1,1800	52.0	51.0	51.0		14053,14053	5.5	1.0	7		51	1,8129		0,1,4064	no	missense,missense	PCLO	NM_014510.2,NM_033026.5	23,23	0,2,5864	TT,TC,CC		0.0123,0.0278,0.017	probably-damaging,probably-damaging	4685/4936,4685/5143	82470819	2,11730	1801	4065	5866	82308755	SO:0001583	missense	27445	exon14			AB011131	CCDS47630.1, CCDS47631.1	7q11.23-q21.3	2013-01-07	2013-01-07		ENSG00000186472	ENSG00000186472			13406	protein-coding gene	gene with protein product	"""aczonin"""	604918	"""piccolo (presynaptic cytomatrix protein)"""			8900486, 9628581	Standard	NM_014510		Approved	KIAA0559, DKFZp779G1236, ACZ	uc003uhx.2	Q9Y6V0	OTTHUMG00000154853	ENST00000333891.9:c.14053G>A	7.37:g.82470819C>T	ENSP00000334319:p.Asp4685Asn	Somatic		Capture	Illumina HiSeq	Phase_I	82308755	NM_033026		Missense_Mutation	SNP	ENST00000333891.9	37	CCDS47630.1	.	.	.	.	.	.	.	.	.	.	C	15.95	2.982709	0.53827	2.78E-4	1.23E-4	ENSG00000186472	ENST00000333891;ENST00000423517;ENST00000380195	T;T	0.16597	2.33;2.34	5.48	5.48	0.80851	.	.	.	.	.	T	0.27900	0.0687	N	0.22421	0.69	0.80722	D	1	D;D;P;P	0.76494	0.999;0.999;0.709;0.76	P;P;B;B	0.60345	0.873;0.873;0.085;0.054	T	0.03728	-1.1009	9	0.87932	D	0	.	19.364	0.94454	0.0:1.0:0.0:0.0	.	4685;4685;115;182	Q9Y6V0-5;Q9Y6V0-6;Q9Y6V0-3;Q32P40	.;.;.;.	N	4685;4685;181	ENSP00000334319:D4685N;ENSP00000388393:D4685N	ENSP00000334319:D4685N	D	-	1	0	PCLO	82308755	1.000000	0.71417	1.000000	0.80357	0.750000	0.42670	6.939000	0.75911	2.547000	0.85894	0.655000	0.94253	GAT		0.308	PCLO-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337368.5	NM_014510	
PCLO	27445	broad.mit.edu	37	7	82580448	82580448	+	Silent	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr7:82580448C>T	ENST00000333891.9	-	6	9793	c.9456G>A	c.(9454-9456)acG>acA	p.T3152T	PCLO_ENST00000437081.1_5'Flank|PCLO_ENST00000423517.2_Silent_p.T3152T	NM_033026.5	NP_149015.2			piccolo presynaptic cytomatrix protein									p.T3152T(3)|p.T3083T(2)		breast(3)|central_nervous_system(3)|cervix(5)|endometrium(19)|haematopoietic_and_lymphoid_tissue(3)|kidney(19)|large_intestine(35)|lung(145)|ovary(7)|prostate(4)|upper_aerodigestive_tract(14)|urinary_tract(2)	259						CTGCAATGTCCGTTTCAGATG	0.428																																					p.T3152T												.	.	5	Substitution - coding silent(5)	kidney(3)|large_intestine(2)	c.G9456A	7						.						57.0	54.0	55.0					7																	82580448		1945	4172	6117	82418384	SO:0001819	synonymous_variant	27445	exon6			AB011131	CCDS47630.1, CCDS47631.1	7q11.23-q21.3	2013-01-07	2013-01-07		ENSG00000186472	ENSG00000186472			13406	protein-coding gene	gene with protein product	"""aczonin"""	604918	"""piccolo (presynaptic cytomatrix protein)"""			8900486, 9628581	Standard	NM_014510		Approved	KIAA0559, DKFZp779G1236, ACZ	uc003uhx.2	Q9Y6V0	OTTHUMG00000154853	ENST00000333891.9:c.9456G>A	7.37:g.82580448C>T		Somatic		Capture	Illumina HiSeq	Phase_I	82418384	NM_033026		Silent	SNP	ENST00000333891.9	37	CCDS47630.1																																																																																				0.428	PCLO-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337368.5	NM_014510	
DMTF1	9988	broad.mit.edu	37	7	86811589	86811589	+	Silent	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr7:86811589G>A	ENST00000394703.5	+	12	1319	c.756G>A	c.(754-756)gcG>gcA	p.A252A	DMTF1_ENST00000411766.2_3'UTR|DMTF1_ENST00000413276.2_Silent_p.A252A|DMTF1_ENST00000432937.2_Silent_p.A164A|DMTF1_ENST00000331242.7_Silent_p.A252A|DMTF1_ENST00000414194.2_5'UTR	NM_021145.3	NP_066968.3	Q9Y222	DMTF1_HUMAN	cyclin D binding myb-like transcription factor 1	252	Interaction with CCND1, CCND2 and CCND3. {ECO:0000250}.|Myb-like 1. {ECO:0000255|PROSITE- ProRule:PRU00133}.|Required for DNA-binding. {ECO:0000250}.				cell cycle (GO:0007049)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.A252A(1)		central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(4)|ovary(1)	16	Esophageal squamous(14;0.0058)					TAGGGGCGGCGCTAGGAAGAA	0.458																																					p.A252A												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G756A	7						.						144.0	131.0	135.0					7																	86811589		2203	4300	6503	86649525	SO:0001819	synonymous_variant	9988	exon10			AF084530	CCDS5601.1, CCDS47633.1	7q21	2014-06-25			ENSG00000135164	ENSG00000135164			14603	protein-coding gene	gene with protein product	"""cyclin D-binding Myb-like protein"""	608491				10095122, 24958102	Standard	NR_024549		Approved	DMP1, DMTF, hDMP1, MRUL	uc003uih.3	Q9Y222	OTTHUMG00000154135	ENST00000394703.5:c.756G>A	7.37:g.86811589G>A		Somatic		Capture	Illumina HiSeq	Phase_I	86649525	NM_001142327	B2RBE1|B4DJS5|Q05C48|Q59G79|Q6IS13|Q969T2|Q9H2Z2|Q9H2Z3	Silent	SNP	ENST00000394703.5	37	CCDS5601.1																																																																																				0.458	DMTF1-002	KNOWN	alternative_5_UTR|non_canonical_TEC|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334025.5	NM_021145	
RUNDC3B	154661	broad.mit.edu	37	7	87370826	87370826	+	Missense_Mutation	SNP	A	A	C			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr7:87370826A>C	ENST00000338056.3	+	7	1022	c.611A>C	c.(610-612)aAg>aCg	p.K204T	RUNDC3B_ENST00000493037.1_Missense_Mutation_p.K187T|RUNDC3B_ENST00000496000.1_3'UTR|RUNDC3B_ENST00000394654.3_Missense_Mutation_p.K187T	NM_001134405.1|NM_138290.2	NP_001127877.1|NP_612147.1	Q96NL0	RUN3B_HUMAN	RUN domain containing 3B	204	RUN. {ECO:0000255|PROSITE- ProRule:PRU00178}.							p.K204T(1)		breast(2)|endometrium(3)|kidney(2)|large_intestine(7)|lung(8)|ovary(1)|prostate(1)|skin(2)	26	Esophageal squamous(14;0.00164)					TTCTGCCTAAAGGGAGAGGGG	0.303																																					p.K187T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A560C	7						.						62.0	61.0	61.0					7																	87370826		2203	4298	6501	87208762	SO:0001583	missense	154661	exon6				CCDS5609.1, CCDS47635.1, CCDS47636.1	7q21.12	2009-01-14			ENSG00000105784	ENSG00000105784			30286	protein-coding gene	gene with protein product						12645870	Standard	NM_138290		Approved	RPIP9, RPIB9	uc003ujb.3	Q96NL0	OTTHUMG00000131035	ENST00000338056.3:c.611A>C	7.37:g.87370826A>C	ENSP00000337732:p.Lys204Thr	Somatic		Capture	Illumina HiSeq	Phase_I	87208762	NM_001134405	B4DFD0|E9PBR4|Q8IWW5|Q8NB55|Q8TBG7	Missense_Mutation	SNP	ENST00000338056.3	37	CCDS5609.1	.	.	.	.	.	.	.	.	.	.	A	20.8	4.057190	0.76074	.	.	ENSG00000105784	ENST00000338056;ENST00000493037;ENST00000394654	T;T;T	0.28069	1.63;1.63;1.63	5.16	5.16	0.70880	RUN (3);	0.000000	0.85682	D	0.000000	T	0.61362	0.2341	M	0.89414	3.03	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;0.999;0.999;0.988	D;D;D;D;D	0.87578	0.998;0.998;0.994;0.994;0.919	T	0.68853	-0.5299	10	0.59425	D	0.04	-11.8876	13.9767	0.64277	1.0:0.0:0.0:0.0	.	187;187;109;187;204	E9PBR4;B4DFD0;Q96NL0-2;Q96NL0-4;Q96NL0	.;.;.;.;RUN3B_HUMAN	T	204;187;187	ENSP00000337732:K204T;ENSP00000420394:K187T;ENSP00000378149:K187T	ENSP00000337732:K204T	K	+	2	0	RUNDC3B	87208762	1.000000	0.71417	0.998000	0.56505	0.986000	0.74619	7.489000	0.81451	1.929000	0.55896	0.533000	0.62120	AAG		0.303	RUNDC3B-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000253679.1	NM_138290	
STEAP1	26872	broad.mit.edu	37	7	89790423	89790423	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr7:89790423A>G	ENST00000297205.2	+	3	589	c.389A>G	c.(388-390)tAc>tGc	p.Y130C	STEAP2-AS1_ENST00000478318.2_RNA	NM_012449.2	NP_036581.1	Q9UHE8	STEA1_HUMAN	six transmembrane epithelial antigen of the prostate 1	130	Ferric oxidoreductase.				ion transport (GO:0006811)|iron ion homeostasis (GO:0055072)|transmembrane transport (GO:0055085)	cell-cell junction (GO:0005911)|endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	channel activity (GO:0015267)|metal ion binding (GO:0046872)|oxidoreductase activity (GO:0016491)|transporter activity (GO:0005215)	p.Y130C(1)		kidney(2)|large_intestine(3)|lung(6)|skin(2)|upper_aerodigestive_tract(1)	14	all_hematologic(106;0.112)					GCATTGGTTTACCTGCCAGGT	0.388																																					p.Y130C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A389G	7						.						107.0	103.0	104.0					7																	89790423		2203	4300	6503	89628359	SO:0001583	missense	26872	exon3			AF186249	CCDS5614.1	7q21	2011-08-31	2005-02-21	2005-02-24	ENSG00000164647	ENSG00000164647		"""Serine peptidases / Serine peptidases"""	11378	protein-coding gene	gene with protein product		604415	"""six transmembrane epithelial antigen of the prostate"""	STEAP			Standard	NM_012449		Approved	PRSS24	uc003ujx.3	Q9UHE8	OTTHUMG00000023006	ENST00000297205.2:c.389A>G	7.37:g.89790423A>G	ENSP00000297205:p.Tyr130Cys	Somatic		Capture	Illumina HiSeq	Phase_I	89628359	NM_012449	A4D1E0|O95034	Missense_Mutation	SNP	ENST00000297205.2	37	CCDS5614.1	.	.	.	.	.	.	.	.	.	.	A	19.21	3.783704	0.70222	.	.	ENSG00000164647	ENST00000297205	D	0.91577	-2.87	5.17	5.17	0.71159	Flavoprotein transmembrane component (1);	0.000000	0.64402	D	0.000006	D	0.94850	0.8336	M	0.74467	2.265	0.49798	D	0.99982	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.95422	0.8508	10	0.87932	D	0	-11.8321	15.1745	0.72901	1.0:0.0:0.0:0.0	.	130;130	B4E221;Q9UHE8	.;STEA1_HUMAN	C	130	ENSP00000297205:Y130C	ENSP00000297205:Y130C	Y	+	2	0	STEAP1	89628359	1.000000	0.71417	1.000000	0.80357	0.966000	0.64601	8.396000	0.90190	2.160000	0.67779	0.533000	0.62120	TAC		0.388	STEAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059327.3	NM_012449	
CFAP69	79846	broad.mit.edu	37	7	89874766	89874766	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr7:89874766G>A	ENST00000389297.4	+	1	279	c.28G>A	c.(28-30)Gcc>Acc	p.A10T	C7orf63_ENST00000463311.1_3'UTR|C7orf63_ENST00000316089.8_Missense_Mutation_p.A10T|C7orf63_ENST00000497910.1_Missense_Mutation_p.A10T	NM_001039706.2|NM_001160138.1	NP_001034795.2|NP_001153610.1	A5D8W1	CG063_HUMAN		10								p.A10T(2)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(12)|lung(14)|ovary(1)|prostate(3)	37						CGGGGCGACCGCCGAGGCCCA	0.657																																					p.A10T												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G28A	7						.						65.0	73.0	70.0					7																	89874766		1917	4124	6041	89712702	SO:0001583	missense	79846	exon1																														ENST00000389297.4:c.28G>A	7.37:g.89874766G>A	ENSP00000373948:p.Ala10Thr	Somatic		Capture	Illumina HiSeq	Phase_I	89712702	NM_001160138	A3KMP9|B4DYW6|B4DZP7|B9EIM7|Q6V705|Q8IY89|Q9H7C2	Missense_Mutation	SNP	ENST00000389297.4	37	CCDS43613.2	.	.	.	.	.	.	.	.	.	.	G	19.39	3.819241	0.71028	.	.	ENSG00000105792	ENST00000389297;ENST00000316089;ENST00000497910	T;T;T	0.16743	2.32;2.32;2.32	4.44	3.56	0.40772	.	.	.	.	.	T	0.11750	0.0286	L	0.31294	0.92	0.18873	N	0.999985	B;B;B	0.26041	0.01;0.01;0.14	B;B;B	0.15484	0.005;0.005;0.013	T	0.20009	-1.0288	9	0.33141	T	0.24	-0.0018	8.5044	0.33179	0.107:0.0:0.893:0.0	.	10;10;10	A5D8W1-5;A5D8W1;A5D8W1-4	.;CG063_HUMAN;.	T	10	ENSP00000373948:A10T;ENSP00000321753:A10T;ENSP00000419549:A10T	ENSP00000321753:A10T	A	+	1	0	C7orf63	89712702	0.022000	0.18835	0.078000	0.20375	0.016000	0.09150	0.411000	0.21115	1.211000	0.43351	0.655000	0.94253	GCC		0.657	C7orf63-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000139891.4		
ANKIB1	54467	broad.mit.edu	37	7	91936936	91936936	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr7:91936936A>G	ENST00000265742.3	+	3	828	c.452A>G	c.(451-453)tAt>tGt	p.Y151C		NM_019004.1	NP_061877.1	Q9P2G1	AKIB1_HUMAN	ankyrin repeat and IBR domain containing 1	151							zinc ion binding (GO:0008270)	p.Y151C(1)		cervix(1)|endometrium(7)|kidney(3)|large_intestine(10)|lung(19)|skin(1)	41	all_cancers(62;2.06e-09)|all_epithelial(64;9.24e-09)|Breast(17;0.0034)|all_lung(186;0.0509)|Lung NSC(181;0.0692)		STAD - Stomach adenocarcinoma(171;6.16e-05)|all cancers(6;0.00183)|Lung(22;0.123)|LUSC - Lung squamous cell carcinoma(200;0.225)			CCCTTGCACTATGCTGCTGCC	0.363																																					p.Y151C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A452G	7						.						50.0	46.0	47.0					7																	91936936		1867	4091	5958	91774872	SO:0001583	missense	54467	exon3			AB037807	CCDS47639.1	7q21.3	2013-01-10			ENSG00000001629	ENSG00000001629		"""Ankyrin repeat domain containing"""	22215	protein-coding gene	gene with protein product							Standard	NM_019004		Approved	DKFZP434A0225, KIAA1386	uc003ulw.2	Q9P2G1	OTTHUMG00000155859	ENST00000265742.3:c.452A>G	7.37:g.91936936A>G	ENSP00000265742:p.Tyr151Cys	Somatic		Capture	Illumina HiSeq	Phase_I	91774872	NM_019004	Q6GMS4|Q6P3S9|Q9NTD7|Q9NW49	Missense_Mutation	SNP	ENST00000265742.3	37	CCDS47639.1	.	.	.	.	.	.	.	.	.	.	A	22.2	4.262340	0.80358	.	.	ENSG00000001629	ENST00000265742	T	0.64991	-0.13	5.8	5.8	0.92144	Ankyrin repeat-containing domain (4);	0.000000	0.85682	D	0.000000	T	0.77003	0.4067	M	0.62723	1.935	0.58432	D	0.999999	D	0.89917	1.0	D	0.74023	0.982	T	0.79342	-0.1843	10	0.87932	D	0	.	16.1506	0.81618	1.0:0.0:0.0:0.0	.	151	Q9P2G1	AKIB1_HUMAN	C	151	ENSP00000265742:Y151C	ENSP00000265742:Y151C	Y	+	2	0	ANKIB1	91774872	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.962000	0.93254	2.206000	0.71126	0.528000	0.53228	TAT		0.363	ANKIB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342018.1		
SAMD9	54809	broad.mit.edu	37	7	92731748	92731748	+	Silent	SNP	A	A	G			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr7:92731748A>G	ENST00000379958.2	-	3	3932	c.3663T>C	c.(3661-3663)aaT>aaC	p.N1221N		NM_001193307.1|NM_017654.3	NP_001180236.1|NP_060124.2	Q5K651	SAMD9_HUMAN	sterile alpha motif domain containing 9	1221						cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)		p.N1221N(1)		NS(1)|breast(4)|central_nervous_system(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(20)|lung(32)|ovary(4)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(2)	88	all_cancers(62;5.71e-11)|all_epithelial(64;3.25e-10)|Breast(17;0.000675)|Lung NSC(181;0.0969)|all_lung(186;0.125)		STAD - Stomach adenocarcinoma(171;0.000302)			TAGATAGCTCATTTTTATTAT	0.323																																					p.N1221N												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.T3663C	7						.						68.0	75.0	72.0					7																	92731748		2203	4298	6501	92569684	SO:0001819	synonymous_variant	54809	exon2			AB095925	CCDS34680.1	7q21.2	2013-01-10	2004-07-15	2004-07-16	ENSG00000205413	ENSG00000205413		"""Sterile alpha motif (SAM) domain containing"""	1348	protein-coding gene	gene with protein product		610456	"""chromosome 7 open reading frame 5"""	C7orf5			Standard	NM_017654		Approved	KIAA2004, FLJ20073	uc003umg.3	Q5K651	OTTHUMG00000155809	ENST00000379958.2:c.3663T>C	7.37:g.92731748A>G		Somatic		Capture	Illumina HiSeq	Phase_I	92569684	NM_001193307	A2RU68|Q5K649|Q6P080|Q75N21|Q8IVG6|Q9NXS8	Silent	SNP	ENST00000379958.2	37	CCDS34680.1																																																																																				0.323	SAMD9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341761.1	NM_017654	
TFPI2	7980	broad.mit.edu	37	7	93519504	93519504	+	Silent	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr7:93519504G>A	ENST00000222543.5	-	2	528	c.216C>T	c.(214-216)aaC>aaT	p.N72N	AC002076.10_ENST00000435257.1_RNA|GNGT1_ENST00000455502.1_Intron|TFPI2_ENST00000545378.1_Silent_p.N72N	NM_001271003.1|NM_001271004.1|NM_006528.3	NP_001257932.1|NP_001257933.1|NP_006519.1	P48307	TFPI2_HUMAN	tissue factor pathway inhibitor 2	72	BPTI/Kunitz inhibitor 1. {ECO:0000255|PROSITE-ProRule:PRU00031}.				blood coagulation (GO:0007596)	nucleus (GO:0005634)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)|serine-type endopeptidase inhibitor activity (GO:0004867)	p.N72N(1)		endometrium(1)|large_intestine(5)|lung(5)|pancreas(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	14	all_cancers(62;4.45e-10)|all_epithelial(64;2.92e-09)|Lung NSC(181;0.218)		STAD - Stomach adenocarcinoma(171;0.000967)			AATTGTTGGCGTTGCCCTCGC	0.617																																					p.N72N												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C216T	7						.						37.0	39.0	38.0					7																	93519504		2203	4300	6503	93357440	SO:0001819	synonymous_variant	7980	exon2			L27624	CCDS5632.1	7q	2008-07-18			ENSG00000105825	ENSG00000105825			11761	protein-coding gene	gene with protein product		600033				7896752, 8945635	Standard	NM_006528		Approved	PP5, TFPI-2, REF1	uc003umy.2	P48307	OTTHUMG00000022963	ENST00000222543.5:c.216C>T	7.37:g.93519504G>A		Somatic		Capture	Illumina HiSeq	Phase_I	93357440	NM_006528	Q66ME8|Q8NAK6|Q9UC86	Silent	SNP	ENST00000222543.5	37	CCDS5632.1																																																																																				0.617	TFPI2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254720.2	NM_006528	
PPP1R9A	55607	broad.mit.edu	37	7	94540145	94540145	+	Silent	SNP	T	T	G			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr7:94540145T>G	ENST00000433881.1	+	2	1252	c.720T>G	c.(718-720)tcT>tcG	p.S240S	PPP1R9A_ENST00000424654.1_Silent_p.S240S|PPP1R9A_ENST00000456331.2_Silent_p.S240S|PPP1R9A_ENST00000433360.1_Silent_p.S240S|PPP1R9A_ENST00000289495.5_Silent_p.S240S|PPP1R9A_ENST00000340694.4_Silent_p.S240S			Q9ULJ8	NEB1_HUMAN	protein phosphatase 1, regulatory subunit 9A	240					actin filament organization (GO:0007015)|calcium-mediated signaling (GO:0019722)|neuron projection development (GO:0031175)	cell junction (GO:0030054)|cortical actin cytoskeleton (GO:0030864)|dendritic spine (GO:0043197)|filopodium (GO:0030175)|growth cone (GO:0030426)|synapse (GO:0045202)		p.S240S(1)		breast(3)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(11)|liver(2)|lung(22)|ovary(2)|prostate(1)|skin(4)|upper_aerodigestive_tract(8)|urinary_tract(5)	71	all_cancers(62;9.12e-11)|all_epithelial(64;4.34e-09)		STAD - Stomach adenocarcinoma(171;0.0031)			ATTTACCATCTGTTACTGTTA	0.418										HNSCC(28;0.073)																											p.S240S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.T720G	7						.						81.0	74.0	76.0					7																	94540145		2203	4300	6503	94378081	SO:0001819	synonymous_variant	55607	exon1			AB033048	CCDS34683.1, CCDS55127.1, CCDS55128.1	7q21.3	2013-01-10	2011-10-04		ENSG00000158528	ENSG00000158528		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"", ""Sterile alpha motif (SAM) domain containing"""	14946	protein-coding gene	gene with protein product		602468	"""protein phosphatase 1, regulatory (inhibitor) subunit 9A"""			10574462	Standard	NM_001166160		Approved	Neurabin-I, KIAA1222, FLJ20068	uc010lfj.3	Q9ULJ8	OTTHUMG00000155566	ENST00000433881.1:c.720T>G	7.37:g.94540145T>G		Somatic		Capture	Illumina HiSeq	Phase_I	94378081	NM_001166163	A1L494|B2RWQ1|E9PCA0|E9PCK6|E9PDX1|F8W7J9|O76059|Q9NXT2	Silent	SNP	ENST00000433881.1	37	CCDS34683.1																																																																																				0.418	PPP1R9A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340662.1	NM_001166160	
TECPR1	25851	broad.mit.edu	37	7	97851727	97851727	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr7:97851727C>T	ENST00000447648.2	-	22	3334	c.3035G>A	c.(3034-3036)cGg>cAg	p.R1012Q	TECPR1_ENST00000479975.1_5'UTR|TECPR1_ENST00000379795.3_Missense_Mutation_p.R1014Q			Q7Z6L1	TCPR1_HUMAN	tectonin beta-propeller repeat containing 1	1012					autophagic vacuole fusion (GO:0000046)|autophagy (GO:0006914)	autophagic vacuole membrane (GO:0000421)|cytoplasmic vesicle (GO:0031410)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)	phosphatidylinositol-3-phosphate binding (GO:0032266)	p.R1013Q(1)		central_nervous_system(2)|endometrium(8)|kidney(1)|large_intestine(1)|lung(9)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	26						CACGGATCCCCGGTAGAAGGC	0.667																																					p.R1012Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G3035A	7						.						18.0	24.0	22.0					7																	97851727		2059	4188	6247	97689663	SO:0001583	missense	25851	exon22				CCDS47648.1	7q21.3	2009-01-30			ENSG00000205356	ENSG00000205356			22214	protein-coding gene	gene with protein product		614781					Standard	NM_015395		Approved	DKFZP434B0335, FLJ23419, FLJ90593, KIAA1358	uc003upg.4	Q7Z6L1	OTTHUMG00000154273	ENST00000447648.2:c.3035G>A	7.37:g.97851727C>T	ENSP00000404923:p.Arg1012Gln	Somatic		Capture	Illumina HiSeq	Phase_I	97689663	NM_015395	A8KAD1|B3KPZ1|C9J024|F5GX57|Q96EB0|Q9P2I9|Q9UFR6	Missense_Mutation	SNP	ENST00000447648.2	37	CCDS47648.1	.	.	.	.	.	.	.	.	.	.	C	34	5.403778	0.96051	.	.	ENSG00000205356	ENST00000447648;ENST00000379795	T;T	0.80123	-1.34;-1.34	4.7	4.7	0.59300	.	0.061927	0.64402	D	0.000010	D	0.89269	0.6667	M	0.75264	2.295	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.90654	0.4585	10	0.87932	D	0	-44.072	16.8055	0.85626	0.0:1.0:0.0:0.0	.	1012	Q7Z6L1	TCPR1_HUMAN	Q	1012;1014	ENSP00000404923:R1012Q;ENSP00000369121:R1014Q	ENSP00000369121:R1014Q	R	-	2	0	TECPR1	97689663	1.000000	0.71417	0.994000	0.49952	0.641000	0.38312	7.624000	0.83124	2.443000	0.82685	0.655000	0.94253	CGG		0.667	TECPR1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000334661.1	NM_015395	
BAIAP2L1	55971	broad.mit.edu	37	7	97984375	97984375	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr7:97984375A>G	ENST00000005260.8	-	3	408	c.193T>C	c.(193-195)Tcc>Ccc	p.S65P	BAIAP2L1_ENST00000462558.1_5'UTR	NM_018842.4	NP_061330.2	Q9UHR4	BI2L1_HUMAN	BAI1-associated protein 2-like 1	65	IMD. {ECO:0000255|PROSITE- ProRule:PRU00668}.				filopodium assembly (GO:0046847)|positive regulation of actin cytoskeleton reorganization (GO:2000251)|positive regulation of actin filament polymerization (GO:0030838)|response to bacterium (GO:0009617)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	proline-rich region binding (GO:0070064)	p.S65P(1)		NS(1)|breast(1)|cervix(1)|endometrium(3)|large_intestine(7)|lung(8)|ovary(1)|prostate(1)	23	all_cancers(62;4.34e-10)|all_epithelial(64;5e-10)|Esophageal squamous(72;0.00918)|Lung NSC(181;0.0113)|all_lung(186;0.0126)		STAD - Stomach adenocarcinoma(171;0.215)			GACACGGGGGACCCAGTGGCA	0.512																																					p.S65P												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T193C	7						.						110.0	91.0	97.0					7																	97984375		2203	4300	6503	97822311	SO:0001583	missense	55971	exon3			AF119666	CCDS34687.1	7q22.1	2012-10-04			ENSG00000006453	ENSG00000006453			21649	protein-coding gene	gene with protein product		611877					Standard	NM_018842		Approved	IRTKS	uc003upj.3	Q9UHR4	OTTHUMG00000165117	ENST00000005260.8:c.193T>C	7.37:g.97984375A>G	ENSP00000005260:p.Ser65Pro	Somatic		Capture	Illumina HiSeq	Phase_I	97822311	NM_018842	A4D268|Q75L21|Q75L22|Q96CV4|Q9H5F5|Q9Y2M8	Missense_Mutation	SNP	ENST00000005260.8	37	CCDS34687.1	.	.	.	.	.	.	.	.	.	.	A	26.5	4.745329	0.89663	.	.	ENSG00000006453	ENST00000005260	T	0.34275	1.37	5.83	5.83	0.93111	IRSp53/MIM homology domain (IMD) (3);	0.000000	0.85682	D	0.000000	T	0.63450	0.2512	M	0.84433	2.695	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.69139	-0.5224	10	0.72032	D	0.01	-12.7917	12.64	0.56705	1.0:0.0:0.0:0.0	.	65	Q9UHR4	BI2L1_HUMAN	P	65	ENSP00000005260:S65P	ENSP00000005260:S65P	S	-	1	0	AC093799.1	97822311	1.000000	0.71417	1.000000	0.80357	0.918000	0.54935	6.568000	0.73987	2.241000	0.73720	0.524000	0.50904	TCC		0.512	BAIAP2L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334681.1	NM_018842	
NPTX2	4885	broad.mit.edu	37	7	98257719	98257719	+	Silent	SNP	C	C	T	rs374536975	byFrequency	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr7:98257719C>T	ENST00000265634.3	+	5	1239	c.1074C>T	c.(1072-1074)acC>acT	p.T358T		NM_002523.2	NP_002514.1	P47972	NPTX2_HUMAN	neuronal pentraxin II	358	Pentaxin.				synaptic transmission (GO:0007268)	extracellular region (GO:0005576)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)	p.T358T(1)		breast(1)|central_nervous_system(2)|endometrium(1)|large_intestine(5)|lung(5)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	18	all_cancers(62;2.28e-09)|all_epithelial(64;4.86e-10)|Esophageal squamous(72;0.00918)|Lung NSC(181;0.0128)|all_lung(186;0.0142)		STAD - Stomach adenocarcinoma(171;0.215)			CCCAGGACACCGTGGGGGGTA	0.567													C|||	2	0.000399361	0.0015	0.0	5008	,	,		19517	0.0		0.0	False		,,,				2504	0.0				p.T358T												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1074T	7						.	C		3,4403	6.2+/-15.9	0,3,2200	43.0	36.0	38.0		1074	-11.9	0.0	7		38	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	NPTX2	NM_002523.2		0,4,6499	TT,TC,CC		0.0116,0.0681,0.0308		358/432	98257719	4,13002	2203	4300	6503	98095655	SO:0001819	synonymous_variant	4885	exon5				CCDS5657.1	7q21.3-q22.1	2008-04-30			ENSG00000106236	ENSG00000106236			7953	protein-coding gene	gene with protein product	"""apexin"""	600750				8530029	Standard	NM_002523		Approved		uc003upl.2	P47972	OTTHUMG00000154369	ENST00000265634.3:c.1074C>T	7.37:g.98257719C>T		Somatic		Capture	Illumina HiSeq	Phase_I	98095655	NM_002523	A4D267|Q86XV7|Q96G70	Silent	SNP	ENST00000265634.3	37	CCDS5657.1																																																																																				0.567	NPTX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334982.1	NM_002523	
TRRAP	8295	broad.mit.edu	37	7	98545942	98545942	+	Silent	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr7:98545942G>A	ENST00000359863.4	+	33	4835	c.4626G>A	c.(4624-4626)acG>acA	p.T1542T	TRRAP_ENST00000446306.3_Silent_p.T1523T|TRRAP_ENST00000355540.3_Silent_p.T1524T	NM_001244580.1	NP_001231509.1	Q9Y4A5	TRRAP_HUMAN	transformation/transcription domain-associated protein	1542					chromatin organization (GO:0006325)|histone acetylation (GO:0016573)|histone deubiquitination (GO:0016578)|histone H2A acetylation (GO:0043968)|histone H4 acetylation (GO:0043967)|mitotic cell cycle checkpoint (GO:0007093)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	NuA4 histone acetyltransferase complex (GO:0035267)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PCAF complex (GO:0000125)|STAGA complex (GO:0030914)|Swr1 complex (GO:0000812)|transcription factor TFTC complex (GO:0033276)	phosphotransferase activity, alcohol group as acceptor (GO:0016773)|transcription coactivator activity (GO:0003713)|transcription cofactor activity (GO:0003712)	p.T1542T(1)|p.T1524T(1)		NS(3)|breast(1)|central_nervous_system(10)|endometrium(16)|kidney(7)|large_intestine(36)|liver(1)|lung(54)|ovary(10)|pancreas(1)|prostate(8)|skin(16)|stomach(5)|upper_aerodigestive_tract(6)|urinary_tract(2)	176	all_cancers(62;6.96e-09)|all_epithelial(64;4.86e-09)|Lung NSC(181;0.01)|all_lung(186;0.016)|Esophageal squamous(72;0.0274)		STAD - Stomach adenocarcinoma(171;0.215)			TCATGAAAACGGAGCGGGCGA	0.493																																					p.T1524T												.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.G4572A	7						.						85.0	78.0	81.0					7																	98545942		2203	4300	6503	98383878	SO:0001819	synonymous_variant	8295	exon32			AF076974	CCDS5659.1, CCDS59066.1	7q21.2-q22.1	2010-06-22			ENSG00000196367	ENSG00000196367			12347	protein-coding gene	gene with protein product		603015				9708738, 9885574	Standard	NM_003496		Approved	TR-AP, PAF400, Tra1	uc003upp.3	Q9Y4A5	OTTHUMG00000150403	ENST00000359863.4:c.4626G>A	7.37:g.98545942G>A		Somatic		Capture	Illumina HiSeq	Phase_I	98383878	NM_003496	A4D265|O75218|Q9Y631|Q9Y6H4	Silent	SNP	ENST00000359863.4	37	CCDS59066.1	.	.	.	.	.	.	.	.	.	.	G	2.858	-0.236846	0.05944	.	.	ENSG00000196367	ENST00000456197	.	.	.	5.74	-4.76	0.03229	.	.	.	.	.	T	0.38427	0.1040	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.39901	-0.9591	4	.	.	.	.	2.38	0.04352	0.3646:0.2154:0.3156:0.1044	.	.	.	.	Q	1264	.	.	R	+	2	0	TRRAP	98383878	0.002000	0.14202	0.922000	0.36590	0.265000	0.26407	-1.225000	0.02956	-0.601000	0.05783	-0.367000	0.07326	CGG		0.493	TRRAP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000317978.1	NM_003496	
TRRAP	8295	broad.mit.edu	37	7	98591250	98591250	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr7:98591250C>T	ENST00000359863.4	+	65	10104	c.9895C>T	c.(9895-9897)Cgc>Tgc	p.R3299C	TRRAP_ENST00000446306.3_Missense_Mutation_p.R3288C|TRRAP_ENST00000355540.3_Missense_Mutation_p.R3270C	NM_001244580.1	NP_001231509.1	Q9Y4A5	TRRAP_HUMAN	transformation/transcription domain-associated protein	3299					chromatin organization (GO:0006325)|histone acetylation (GO:0016573)|histone deubiquitination (GO:0016578)|histone H2A acetylation (GO:0043968)|histone H4 acetylation (GO:0043967)|mitotic cell cycle checkpoint (GO:0007093)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	NuA4 histone acetyltransferase complex (GO:0035267)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PCAF complex (GO:0000125)|STAGA complex (GO:0030914)|Swr1 complex (GO:0000812)|transcription factor TFTC complex (GO:0033276)	phosphotransferase activity, alcohol group as acceptor (GO:0016773)|transcription coactivator activity (GO:0003713)|transcription cofactor activity (GO:0003712)	p.R3299C(1)|p.R3270C(1)		NS(3)|breast(1)|central_nervous_system(10)|endometrium(16)|kidney(7)|large_intestine(36)|liver(1)|lung(54)|ovary(10)|pancreas(1)|prostate(8)|skin(16)|stomach(5)|upper_aerodigestive_tract(6)|urinary_tract(2)	176	all_cancers(62;6.96e-09)|all_epithelial(64;4.86e-09)|Lung NSC(181;0.01)|all_lung(186;0.016)|Esophageal squamous(72;0.0274)		STAD - Stomach adenocarcinoma(171;0.215)			ACCCATGTGGCGCTGCAGCCG	0.547																																					p.R3270C												TRRAP,large_intestine,NS,Substitution - Missense,-1 	.	2	Substitution - Missense(2)	large_intestine(2)	c.C9808T	7						.						162.0	129.0	140.0					7																	98591250		2203	4300	6503	98429186	SO:0001583	missense	8295	exon64			AF076974	CCDS5659.1, CCDS59066.1	7q21.2-q22.1	2010-06-22			ENSG00000196367	ENSG00000196367			12347	protein-coding gene	gene with protein product		603015				9708738, 9885574	Standard	NM_003496		Approved	TR-AP, PAF400, Tra1	uc003upp.3	Q9Y4A5	OTTHUMG00000150403	ENST00000359863.4:c.9895C>T	7.37:g.98591250C>T	ENSP00000352925:p.Arg3299Cys	Somatic		Capture	Illumina HiSeq	Phase_I	98429186	NM_003496	A4D265|O75218|Q9Y631|Q9Y6H4	Missense_Mutation	SNP	ENST00000359863.4	37	CCDS59066.1	.	.	.	.	.	.	.	.	.	.	C	21.4	4.145197	0.77888	.	.	ENSG00000196367	ENST00000359863;ENST00000355540;ENST00000446306	T;T	0.03212	4.01;4.01	5.41	4.52	0.55395	.	0.055185	0.64402	N	0.000002	T	0.13114	0.0318	M	0.68952	2.095	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.80764	0.994;0.965;0.981	T	0.01416	-1.1360	10	0.39692	T	0.17	.	8.5942	0.33705	0.2483:0.6765:0.0:0.0753	.	3270;3027;3299	Q9Y4A5-2;Q59FH1;Q9Y4A5	.;.;TRRAP_HUMAN	C	3299;3270;3287	ENSP00000352925:R3299C;ENSP00000347733:R3270C	ENSP00000347733:R3270C	R	+	1	0	TRRAP	98429186	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	3.889000	0.56212	1.405000	0.46838	0.650000	0.86243	CGC		0.547	TRRAP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000317978.1	NM_003496	
ARPC1B	10095	broad.mit.edu	37	7	98985795	98985795	+	Silent	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr7:98985795C>T	ENST00000451682.1	+	6	612	c.303C>T	c.(301-303)tgC>tgT	p.C101C	ARPC1B_ENST00000474880.1_3'UTR|ARPC1B_ENST00000252725.5_Silent_p.C101C			O15143	ARC1B_HUMAN	actin related protein 2/3 complex, subunit 1B, 41kDa	101					Arp2/3 complex-mediated actin nucleation (GO:0034314)|cellular component movement (GO:0006928)	actin cytoskeleton (GO:0015629)|Arp2/3 protein complex (GO:0005885)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)	structural constituent of cytoskeleton (GO:0005200)	p.C101C(1)		central_nervous_system(1)|endometrium(2)|large_intestine(5)|liver(2)|lung(1)	11	all_cancers(62;3.49e-09)|all_epithelial(64;2.57e-10)|Lung NSC(181;0.0053)|all_lung(186;0.00895)|Esophageal squamous(72;0.0166)		STAD - Stomach adenocarcinoma(171;0.215)			CTGCCCGCTGCGTGCGCTGGG	0.617																																					p.C101C												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C303T	7						.						59.0	56.0	57.0					7																	98985795		2203	4300	6503	98823731	SO:0001819	synonymous_variant	10095	exon4			AF006084	CCDS5661.1	7q22.1	2013-03-14	2002-08-29		ENSG00000130429	ENSG00000130429		"""Actin related protein 2/3 complex subunits"", ""WD repeat domain containing"""	704	protein-coding gene	gene with protein product	"""ARP2/3 protein complex subunit p41"", ""actin related protein 2/3 complex, subunit 1A (41 kD)"""	604223	"""actin related protein 2/3 complex, subunit 1B (41 kD)"""			9230079, 9359840	Standard	NM_005720		Approved	ARC41, p40-ARC, p41-ARC	uc003upz.3	O15143	OTTHUMG00000154552	ENST00000451682.1:c.303C>T	7.37:g.98985795C>T		Somatic		Capture	Illumina HiSeq	Phase_I	98823731	NM_005720	Q9BU00	Silent	SNP	ENST00000451682.1	37	CCDS5661.1																																																																																				0.617	ARPC1B-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335894.1	NM_005720	
COPS6	10980	broad.mit.edu	37	7	99688711	99688711	+	Silent	SNP	G	G	A	rs377111966		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr7:99688711G>A	ENST00000303904.3	+	7	622	c.585G>A	c.(583-585)gcG>gcA	p.A195A	MIR93_ENST00000385024.1_RNA|MIR25_ENST00000384816.1_RNA|COPS6_ENST00000418625.1_Silent_p.A194A|MIR106B_ENST00000385301.1_RNA	NM_006833.4	NP_006824.2	Q7L5N1	CSN6_HUMAN	COP9 signalosome subunit 6	195					cullin deneddylation (GO:0010388)|viral process (GO:0016032)	COP9 signalosome (GO:0008180)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)		p.A195A(1)		breast(1)|endometrium(3)|large_intestine(4)|lung(2)|prostate(1)|stomach(1)	12	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)		STAD - Stomach adenocarcinoma(171;0.129)			CAGAGGAAGCGGAACGCATTG	0.537																																					p.A195A												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G585A	7						.	G		1,4405	2.1+/-5.4	0,1,2202	138.0	114.0	123.0		585	-8.1	0.7	7		123	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	COPS6	NM_006833.4		0,2,6501	AA,AG,GG		0.0116,0.0227,0.0154		195/328	99688711	2,13004	2203	4300	6503	99526647	SO:0001819	synonymous_variant	10980	exon7			BC002520	CCDS5682.1	7q22.1	2013-03-14	2013-03-14		ENSG00000168090	ENSG00000168090			21749	protein-coding gene	gene with protein product	"""COP9 subunit 6 (MOV34 homolog, 34 kD)"""	614729	"""COP9 constitutive photomorphogenic homolog subunit 6 (Arabidopsis)"""			12477932	Standard	NM_006833		Approved	MOV34-34KD, CSN6	uc003usu.3	Q7L5N1	OTTHUMG00000154632	ENST00000303904.3:c.585G>A	7.37:g.99688711G>A		Somatic		Capture	Illumina HiSeq	Phase_I	99526647	NM_006833	A4D2A3|O15387	Silent	SNP	ENST00000303904.3	37	CCDS5682.1																																																																																				0.537	COPS6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000336412.3	NM_006833	
GAL3ST4	79690	broad.mit.edu	37	7	99757694	99757694	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr7:99757694G>A	ENST00000360039.4	-	4	1710	c.1318C>T	c.(1318-1320)Cgg>Tgg	p.R440W	GAL3ST4_ENST00000411994.1_3'UTR|C7orf43_ENST00000457641.1_5'Flank|GAL3ST4_ENST00000413800.1_Missense_Mutation_p.R440W|C7orf43_ENST00000498638.1_5'Flank|C7orf43_ENST00000316937.3_5'Flank|GAL3ST4_ENST00000426974.2_Missense_Mutation_p.R378W|GAL3ST4_ENST00000423751.1_3'UTR|C7orf43_ENST00000419841.1_5'Flank	NM_024637.4	NP_078913.3	Q96RP7	G3ST4_HUMAN	galactose-3-O-sulfotransferase 4	440					cell-cell signaling (GO:0007267)|glycoprotein metabolic process (GO:0009100)|oligosaccharide metabolic process (GO:0009311)|proteoglycan biosynthetic process (GO:0030166)|sulfur compound metabolic process (GO:0006790)	extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	3'-phosphoadenosine 5'-phosphosulfate binding (GO:0050656)|galactose 3-O-sulfotransferase activity (GO:0050694)|galactosylceramide sulfotransferase activity (GO:0001733)|proteoglycan sulfotransferase activity (GO:0050698)	p.R440W(1)		cervix(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(8)|ovary(5)|prostate(1)|upper_aerodigestive_tract(1)	26	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)					AATCCACTCCGAAGTATATAG	0.552																																					p.R440W												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1318T	7						.						91.0	79.0	83.0					7																	99757694		2203	4300	6503	99595630	SO:0001583	missense	79690	exon4			AF316113	CCDS5688.1	7q22.1	2007-04-02			ENSG00000197093	ENSG00000197093		"""Sulfotransferases, membrane-bound"""	24145	protein-coding gene	gene with protein product		608235				11333265	Standard	NM_024637		Approved	FLJ12116	uc003utu.3	Q96RP7	OTTHUMG00000154885	ENST00000360039.4:c.1318C>T	7.37:g.99757694G>A	ENSP00000353142:p.Arg440Trp	Somatic		Capture	Illumina HiSeq	Phase_I	99595630	NM_024637	A4D2A8|B4DWL8|D6W5U5|Q8N3P7|Q8WZ17|Q96E33|Q9HA78	Missense_Mutation	SNP	ENST00000360039.4	37	CCDS5688.1	.	.	.	.	.	.	.	.	.	.	G	16.60	3.167893	0.57476	.	.	ENSG00000197093	ENST00000413800;ENST00000360039;ENST00000426974	T;T;T	0.16073	2.37;2.37;2.37	5.92	4.97	0.65823	.	0.473238	0.19393	U	0.115369	T	0.36220	0.0959	M	0.72894	2.215	0.09310	N	1	D;D	0.89917	1.0;0.998	D;P	0.63033	0.91;0.817	T	0.14671	-1.0464	10	0.87932	D	0	-5.7265	10.6119	0.45427	0.0:0.0:0.7646:0.2354	.	378;440	B4DWL8;Q96RP7	.;G3ST4_HUMAN	W	440;440;378	ENSP00000400451:R440W;ENSP00000353142:R440W;ENSP00000398304:R378W	ENSP00000353142:R440W	R	-	1	2	GAL3ST4	99595630	0.522000	0.26266	0.997000	0.53966	0.749000	0.42624	3.265000	0.51561	2.813000	0.96785	0.561000	0.74099	CGG		0.552	GAL3ST4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337495.2	NM_024637	
GAL3ST4	79690	broad.mit.edu	37	7	99758106	99758106	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr7:99758106C>T	ENST00000360039.4	-	4	1298	c.906G>A	c.(904-906)atG>atA	p.M302I	GAL3ST4_ENST00000411994.1_Nonsense_Mutation_p.W201*|C7orf43_ENST00000457641.1_5'Flank|GAL3ST4_ENST00000413800.1_Missense_Mutation_p.M302I|C7orf43_ENST00000316937.3_5'Flank|GAL3ST4_ENST00000426974.2_Missense_Mutation_p.M240I|GAL3ST4_ENST00000423751.1_Nonsense_Mutation_p.W201*|C7orf43_ENST00000419841.1_5'Flank	NM_024637.4	NP_078913.3	Q96RP7	G3ST4_HUMAN	galactose-3-O-sulfotransferase 4	302					cell-cell signaling (GO:0007267)|glycoprotein metabolic process (GO:0009100)|oligosaccharide metabolic process (GO:0009311)|proteoglycan biosynthetic process (GO:0030166)|sulfur compound metabolic process (GO:0006790)	extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	3'-phosphoadenosine 5'-phosphosulfate binding (GO:0050656)|galactose 3-O-sulfotransferase activity (GO:0050694)|galactosylceramide sulfotransferase activity (GO:0001733)|proteoglycan sulfotransferase activity (GO:0050698)	p.M302I(1)		cervix(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(8)|ovary(5)|prostate(1)|upper_aerodigestive_tract(1)	26	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)					ACTCAGCCACCATGACCAGGT	0.552																																					p.M302I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G906A	7						.						101.0	93.0	96.0					7																	99758106		2203	4300	6503	99596042	SO:0001583	missense	79690	exon4			AF316113	CCDS5688.1	7q22.1	2007-04-02			ENSG00000197093	ENSG00000197093		"""Sulfotransferases, membrane-bound"""	24145	protein-coding gene	gene with protein product		608235				11333265	Standard	NM_024637		Approved	FLJ12116	uc003utu.3	Q96RP7	OTTHUMG00000154885	ENST00000360039.4:c.906G>A	7.37:g.99758106C>T	ENSP00000353142:p.Met302Ile	Somatic		Capture	Illumina HiSeq	Phase_I	99596042	NM_024637	A4D2A8|B4DWL8|D6W5U5|Q8N3P7|Q8WZ17|Q96E33|Q9HA78	Missense_Mutation	SNP	ENST00000360039.4	37	CCDS5688.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	23.5|23.5	4.428642|4.428642	0.83667|0.83667	.|.	.|.	ENSG00000197093|ENSG00000197093	ENST00000413800;ENST00000360039;ENST00000426974|ENST00000423751;ENST00000411994	T;T;T|.	0.13778|.	2.56;2.56;2.56|.	4.82|4.82	4.82|4.82	0.62117|0.62117	.|.	0.094421|.	0.42420|.	U|.	0.000718|.	T|.	0.48409|.	0.1498|.	L|L	0.46741|0.46741	1.465|1.465	0.32700|0.32700	N|N	0.513012|0.513012	B;B|.	0.26002|.	0.139;0.008|.	B;B|.	0.25405|.	0.06;0.015|.	T|.	0.58907|.	-0.7553|.	10|.	0.45353|0.45353	T|T	0.12|0.12	-4.5418|-4.5418	8.9291|8.9291	0.35659|0.35659	0.0:0.9006:0.0:0.0994|0.0:0.9006:0.0:0.0994	.|.	240;302|.	B4DWL8;Q96RP7|.	.;G3ST4_HUMAN|.	I|X	302;302;240|201	ENSP00000400451:M302I;ENSP00000353142:M302I;ENSP00000398304:M240I|.	ENSP00000353142:M302I|ENSP00000414733:W201X	M|W	-|-	3|2	0|0	GAL3ST4|GAL3ST4	99596042|99596042	0.435000|0.435000	0.25577|0.25577	1.000000|1.000000	0.80357|0.80357	0.993000|0.993000	0.82548|0.82548	-0.037000|-0.037000	0.12164|0.12164	2.518000|2.518000	0.84900|0.84900	0.511000|0.511000	0.50034|0.50034	ATG|TGG		0.552	GAL3ST4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337495.2	NM_024637	
MIR182	406958	broad.mit.edu	37	7	129410228	129410228	+	RNA	SNP	G	G	A	rs77586312	byFrequency	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr7:129410228G>A	ENST00000385255.1	-	0	104					NR_029614.1				microRNA 182																		ACAGGGTGCCGGCTGAGTCCT	0.617													G|||	25	0.00499201	0.0174	0.0029	5008	,	,		18856	0.0		0.0	False		,,,				2504	0.0				.												.	.	0			.	7						.	G		37,3099		0,37,1531	38.0	41.0	40.0			-2.3	0.0	7	dbSNP_131	40	0,7164		0,0,3582	no	intergenic				0,37,5113	AA,AG,GG		0.0,1.1798,0.3592			129410228	37,10263	1568	3582	5150	129197464			406958	.					7q32.2	2011-09-12		2008-12-18	ENSG00000207990	ENSG00000207990		"""ncRNAs / Micro RNAs"""	31553	non-coding RNA	RNA, micro		611607		MIRN182			Standard	NR_029614		Approved	hsa-mir-182	uc011kpb.1				7.37:g.129410228G>A		Somatic		Capture	Illumina HiSeq	Phase_I	129197464	.		RNA	SNP	ENST00000385255.1	37																																																																																					0.617	MIR182-201	KNOWN	basic	miRNA	miRNA		NR_029614	
ZNF767P	79970	broad.mit.edu	37	7	149317031	149317031	+	RNA	SNP	A	A	G			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr7:149317031A>G	ENST00000463567.1	-	0	583					NR_027788.1		Q75MW2	ZN767_HUMAN										p.L141P(1)		central_nervous_system(1)|endometrium(2)|large_intestine(1)|lung(1)	5	Melanoma(164;0.165)|Ovarian(565;0.177)		OV - Ovarian serous cystadenocarcinoma(82;0.00434)			TGGGGTCCACAGGAACATCTG	0.572																																					.												.	.	1	Substitution - Missense(1)	large_intestine(1)	.	7						.						60.0	60.0	60.0					7																	149317031		2203	4300	6503	148947964			79970	.																															7.37:g.149317031A>G		Somatic		Capture	Illumina HiSeq	Phase_I	148947964	.	D3DWG6|Q86WY4|Q9H9J3	Missense_Mutation	SNP	ENST00000463567.1	37																																																																																					0.572	ZNF767-001	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000352753.2		
ESYT2	57488	broad.mit.edu	37	7	158531716	158531716	+	Silent	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr7:158531716G>A	ENST00000251527.5	-	18	2411	c.2346C>T	c.(2344-2346)tgC>tgT	p.C782C	ESYT2_ENST00000435514.2_Silent_p.C217C	NM_020728.2	NP_065779.1	A0FGR8	ESYT2_HUMAN	extended synaptotagmin-like protein 2	810					endocytosis (GO:0006897)|lipid transport (GO:0006869)	extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|integral component of plasma membrane (GO:0005887)|intrinsic component of endoplasmic reticulum membrane (GO:0031227)|membrane (GO:0016020)|organelle membrane contact site (GO:0044232)	calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)|identical protein binding (GO:0042802)|phosphatidylcholine binding (GO:0031210)|phosphatidylethanolamine binding (GO:0008429)|phosphatidylinositol binding (GO:0035091)	p.C782C(1)		breast(1)|central_nervous_system(2)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(7)|lung(16)|prostate(2)	32						GCCCCCACCTGCAGGCATGCA	0.597																																					p.C782C												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C2346T	7						.						96.0	83.0	88.0					7																	158531716		2203	4300	6503	158224477	SO:0001819	synonymous_variant	57488	exon18			AB033054	CCDS34791.1	7q36.3	2014-07-02	2009-06-23	2009-06-23	ENSG00000117868	ENSG00000117868		"""Synaptotagmins"""	22211	protein-coding gene	gene with protein product			"""family with sequence similarity 62 (C2 domain containing), member B"""	FAM62B		17672888	Standard	NM_020728		Approved	KIAA1228, CHR2SYT	uc003wob.1	A0FGR8	OTTHUMG00000151436	ENST00000251527.5:c.2346C>T	7.37:g.158531716G>A		Somatic		Capture	Illumina HiSeq	Phase_I	158224477	NM_020728	A4D229|Q69YJ2|Q6UKI4|Q6ZTU0|Q6ZVU1|Q9BQS0|Q9NW47|Q9ULJ2	Silent	SNP	ENST00000251527.5	37	CCDS34791.1	.	.	.	.	.	.	.	.	.	.	G	12.72	2.022229	0.35701	.	.	ENSG00000117868	ENST00000377650	.	.	.	4.71	3.81	0.43845	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	-2.5799	9.4582	0.38767	0.1713:0.0:0.8286:0.0	.	.	.	.	X	217	.	ENSP00000366878:Q217X	Q	-	1	0	ESYT2	158224477	1.000000	0.71417	1.000000	0.80357	0.762000	0.43233	5.132000	0.64758	2.318000	0.78349	0.462000	0.41574	CAG		0.597	ESYT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322647.1	NM_020728	
VPS13B	157680	broad.mit.edu	37	8	100454693	100454693	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr8:100454693T>C	ENST00000358544.2	+	23	3386	c.3275T>C	c.(3274-3276)gTa>gCa	p.V1092A	VPS13B_ENST00000357162.2_Missense_Mutation_p.V1092A|VPS13B_ENST00000395996.1_Missense_Mutation_p.V1092A	NM_017890.4	NP_060360.3	Q7Z7G8	VP13B_HUMAN	vacuolar protein sorting 13 homolog B (yeast)	1092					protein transport (GO:0015031)			p.V1092A(1)		NS(1)|autonomic_ganglia(1)|breast(6)|central_nervous_system(4)|cervix(3)|endometrium(11)|haematopoietic_and_lymphoid_tissue(4)|kidney(10)|large_intestine(37)|lung(78)|ovary(8)|pancreas(3)|prostate(5)|skin(9)|upper_aerodigestive_tract(4)|urinary_tract(9)	193	Breast(36;3.73e-07)		OV - Ovarian serous cystadenocarcinoma(57;0.00636)			AGTACAATTGTATCTGGTGAC	0.383																																					p.V1092A	Colon(161;2205 2542 7338 31318)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T3275C	8						.						169.0	158.0	162.0					8																	100454693		2203	4300	6503	100523869	SO:0001583	missense	157680	exon23			AJ608772	CCDS6280.1, CCDS6281.1, CCDS6283.1, CCDS47903.1	8q22-q23	2014-09-17	2006-12-19	2005-04-08	ENSG00000132549	ENSG00000132549			2183	protein-coding gene	gene with protein product		607817	"""Cohen syndrome 1"""	CHS1, COH1		7920642, 15498460	Standard	NM_181661		Approved		uc003yiv.4	Q7Z7G8	OTTHUMG00000140383	ENST00000358544.2:c.3275T>C	8.37:g.100454693T>C	ENSP00000351346:p.Val1092Ala	Somatic		Capture	Illumina HiSeq	Phase_I	100523869	NM_152564	C9JD30|Q709C6|Q709C7|Q7Z7G4|Q7Z7G5|Q7Z7G6|Q7Z7G7|Q8NB77|Q9NWV1|Q9Y4E7	Missense_Mutation	SNP	ENST00000358544.2	37	CCDS6280.1	.	.	.	.	.	.	.	.	.	.	T	17.09	3.300006	0.60195	.	.	ENSG00000132549	ENST00000357162;ENST00000358544;ENST00000395996	T;T;T	0.44083	0.93;0.93;0.93	5.71	5.71	0.89125	.	0.138860	0.47455	D	0.000240	T	0.48040	0.1478	N	0.24115	0.695	0.40377	D	0.979407	P;D;P;P	0.60160	0.952;0.987;0.893;0.783	P;P;B;B	0.60117	0.736;0.869;0.446;0.363	T	0.51872	-0.8650	10	0.54805	T	0.06	.	15.9886	0.80183	0.0:0.0:0.0:1.0	.	1091;1092;1092;1092	Q7Z7G8-6;Q7Z7G8-2;Q7Z7G8;Q7Z7G8-3	.;.;VP13B_HUMAN;.	A	1092	ENSP00000349685:V1092A;ENSP00000351346:V1092A;ENSP00000379318:V1092A	ENSP00000349685:V1092A	V	+	2	0	VPS13B	100523869	1.000000	0.71417	0.998000	0.56505	0.952000	0.60782	7.419000	0.80179	2.178000	0.69098	0.482000	0.46254	GTA		0.383	VPS13B-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000277138.1	NM_184042	
VPS13B	157680	broad.mit.edu	37	8	100829831	100829831	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr8:100829831G>A	ENST00000358544.2	+	45	8347	c.8236G>A	c.(8236-8238)Gtt>Att	p.V2746I	VPS13B_ENST00000357162.2_Missense_Mutation_p.V2721I|VPS13B_ENST00000395996.1_3'UTR	NM_017890.4	NP_060360.3	Q7Z7G8	VP13B_HUMAN	vacuolar protein sorting 13 homolog B (yeast)	2746					protein transport (GO:0015031)			p.V2746I(1)		NS(1)|autonomic_ganglia(1)|breast(6)|central_nervous_system(4)|cervix(3)|endometrium(11)|haematopoietic_and_lymphoid_tissue(4)|kidney(10)|large_intestine(37)|lung(78)|ovary(8)|pancreas(3)|prostate(5)|skin(9)|upper_aerodigestive_tract(4)|urinary_tract(9)	193	Breast(36;3.73e-07)		OV - Ovarian serous cystadenocarcinoma(57;0.00636)			ACTAAAAGTCGTTCAGCATTA	0.373																																					p.V2721I	Colon(161;2205 2542 7338 31318)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G8161A	8						.						93.0	91.0	91.0					8																	100829831		2203	4300	6503	100899007	SO:0001583	missense	157680	exon45			AJ608772	CCDS6280.1, CCDS6281.1, CCDS6283.1, CCDS47903.1	8q22-q23	2014-09-17	2006-12-19	2005-04-08	ENSG00000132549	ENSG00000132549			2183	protein-coding gene	gene with protein product		607817	"""Cohen syndrome 1"""	CHS1, COH1		7920642, 15498460	Standard	NM_181661		Approved		uc003yiv.4	Q7Z7G8	OTTHUMG00000140383	ENST00000358544.2:c.8236G>A	8.37:g.100829831G>A	ENSP00000351346:p.Val2746Ile	Somatic		Capture	Illumina HiSeq	Phase_I	100899007	NM_152564	C9JD30|Q709C6|Q709C7|Q7Z7G4|Q7Z7G5|Q7Z7G6|Q7Z7G7|Q8NB77|Q9NWV1|Q9Y4E7	Missense_Mutation	SNP	ENST00000358544.2	37	CCDS6280.1	.	.	.	.	.	.	.	.	.	.	G	21.0	4.088527	0.76756	.	.	ENSG00000132549	ENST00000357162;ENST00000358544	T;T	0.70986	-0.53;-0.53	5.6	5.6	0.85130	.	0.148919	0.44097	D	0.000496	T	0.74898	0.3777	L	0.29908	0.895	0.80722	D	1	D;D	0.76494	0.999;0.998	D;P	0.68353	0.957;0.766	T	0.66508	-0.5906	10	0.10111	T	0.7	.	19.9742	0.97299	0.0:0.0:1.0:0.0	.	2721;2746	Q7Z7G8-2;Q7Z7G8	.;VP13B_HUMAN	I	2721;2746	ENSP00000349685:V2721I;ENSP00000351346:V2746I	ENSP00000349685:V2721I	V	+	1	0	VPS13B	100899007	1.000000	0.71417	0.988000	0.46212	0.969000	0.65631	7.162000	0.77515	2.792000	0.96026	0.650000	0.86243	GTT		0.373	VPS13B-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000277138.1	NM_184042	
RGS22	26166	broad.mit.edu	37	8	101052208	101052208	+	Silent	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr8:101052208G>A	ENST00000360863.6	-	13	2240	c.2046C>T	c.(2044-2046)tgC>tgT	p.C682C	RGS22_ENST00000523437.1_Silent_p.C670C|RGS22_ENST00000523287.1_Silent_p.C501C	NM_015668.3	NP_056483.3	Q8NE09	RGS22_HUMAN	regulator of G-protein signaling 22	682					positive regulation of GTPase activity (GO:0043547)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	GTPase activator activity (GO:0005096)	p.C682C(1)	RGS22/SYCP1(2)	breast(3)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(9)|lung(33)|ovary(3)|prostate(2)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	68			Epithelial(11;6.71e-08)|all cancers(13;4.19e-06)|OV - Ovarian serous cystadenocarcinoma(57;0.000469)|STAD - Stomach adenocarcinoma(118;0.169)			CTGAATGCTCGCAGAATTTAG	0.313																																					p.C682C												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C2046T	8						.						47.0	41.0	43.0					8																	101052208		1801	4063	5864	101121384	SO:0001819	synonymous_variant	26166	exon13			AY009106	CCDS43758.1, CCDS69521.1, CCDS75775.1	8q22.2	2014-01-21	2007-08-14		ENSG00000132554	ENSG00000132554		"""Regulators of G-protein signaling"""	24499	protein-coding gene	gene with protein product		615650	"""regulator of G-protein signalling 22"""				Standard	XM_005250856		Approved	DKFZP434I092, PRTD-NY2, CT145	uc003yjb.1	Q8NE09	OTTHUMG00000164802	ENST00000360863.6:c.2046C>T	8.37:g.101052208G>A		Somatic		Capture	Illumina HiSeq	Phase_I	101121384	NM_015668	A8K944|Q569L2|Q86Y71|Q9BYZ4|Q9UFN6	Silent	SNP	ENST00000360863.6	37	CCDS43758.1																																																																																				0.313	RGS22-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000380365.1	NM_015668	
ABRA	137735	broad.mit.edu	37	8	107782176	107782176	+	Silent	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr8:107782176C>T	ENST00000311955.3	-	1	297	c.243G>A	c.(241-243)tcG>tcA	p.S81S		NM_139166.4	NP_631905.1			actin-binding Rho activating protein									p.S81S(1)		breast(1)|kidney(4)|large_intestine(7)|lung(11)|ovary(2)|prostate(2)	27			OV - Ovarian serous cystadenocarcinoma(57;3.83e-09)			GGCGGGGTGGCGACTTTGGGG	0.552																																					p.S81S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G243A	8						.						98.0	98.0	98.0					8																	107782176		2203	4300	6503	107851352	SO:0001819	synonymous_variant	137735	exon1			AF503617	CCDS6305.1	8q23.1	2012-02-06			ENSG00000174429	ENSG00000174429			30655	protein-coding gene	gene with protein product	"""striated muscle activator of Rho-dependent signaling"""	609747				11983702	Standard	NM_139166		Approved	STARS	uc003ymm.4	Q8N0Z2	OTTHUMG00000164809	ENST00000311955.3:c.243G>A	8.37:g.107782176C>T		Somatic		Capture	Illumina HiSeq	Phase_I	107851352	NM_139166		Silent	SNP	ENST00000311955.3	37	CCDS6305.1																																																																																				0.552	ABRA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380416.1	NM_139166	
KCNV1	27012	broad.mit.edu	37	8	110984616	110984616	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr8:110984616T>C	ENST00000524391.1	-	3	1894	c.862A>G	c.(862-864)Atc>Gtc	p.I288V	RP11-696P8.2_ENST00000530667.1_RNA|KCNV1_ENST00000297404.1_Missense_Mutation_p.I288V			Q6PIU1	KCNV1_HUMAN	potassium channel, subfamily V, member 1	288					potassium ion transport (GO:0006813)|protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|ion channel inhibitor activity (GO:0008200)|potassium channel regulator activity (GO:0015459)	p.I288V(1)		breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(20)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	37	all_neural(195;0.219)		OV - Ovarian serous cystadenocarcinoma(57;5.35e-13)			AGAAGAGTGATGTAGAAGGGC	0.577																																					p.I288V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A862G	8						.						98.0	77.0	84.0					8																	110984616		2203	4300	6503	111053792	SO:0001583	missense	27012	exon2			AF167082	CCDS6314.1	8q23.2	2011-07-05				ENSG00000164794		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	18861	protein-coding gene	gene with protein product		608164				8670833, 16382104	Standard	NM_014379		Approved	Kv8.1	uc003ynr.4	Q6PIU1		ENST00000524391.1:c.862A>G	8.37:g.110984616T>C	ENSP00000435954:p.Ile288Val	Somatic		Capture	Illumina HiSeq	Phase_I	111053792	NM_014379	Q9UHJ4	Missense_Mutation	SNP	ENST00000524391.1	37	CCDS6314.1	.	.	.	.	.	.	.	.	.	.	T	3.395	-0.123443	0.06795	.	.	ENSG00000164794	ENST00000524391;ENST00000297404;ENST00000545728	D;D	0.98345	-4.88;-4.88	5.95	5.95	0.96441	Ion transport (1);	0.117336	0.56097	D	0.000023	D	0.95056	0.8399	N	0.21097	0.63	0.41661	D	0.989185	B	0.14012	0.009	B	0.11329	0.006	D	0.93008	0.6429	10	0.18710	T	0.47	.	15.5881	0.76502	0.0:0.0:0.0:1.0	.	288	Q6PIU1	KCNV1_HUMAN	V	288;288;164	ENSP00000435954:I288V;ENSP00000297404:I288V	ENSP00000297404:I288V	I	-	1	0	KCNV1	111053792	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	3.078000	0.50096	2.272000	0.75746	0.460000	0.39030	ATC		0.577	KCNV1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385525.1	NM_014379	
TRPS1	7227	broad.mit.edu	37	8	116426316	116426316	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr8:116426316G>A	ENST00000220888.5	-	6	3940	c.3781C>T	c.(3781-3783)Cat>Tat	p.H1261Y	TRPS1_ENST00000395715.3_Missense_Mutation_p.H1274Y|TRPS1_ENST00000520276.1_Missense_Mutation_p.H1265Y|TRPS1_ENST00000519076.1_Missense_Mutation_p.H1015Y			Q9UHF7	TRPS1_HUMAN	trichorhinophalangeal syndrome I	1261	Transcriptional repressor domain. {ECO:0000250}.				chondrocyte differentiation (GO:0002062)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|NLS-bearing protein import into nucleus (GO:0006607)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|regulation of chondrocyte differentiation (GO:0032330)|regulation of histone deacetylation (GO:0031063)|skeletal system development (GO:0001501)|transcription from RNA polymerase II promoter (GO:0006366)|transmembrane receptor protein serine/threonine kinase signaling pathway (GO:0007178)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)	p.H1261Y(1)		autonomic_ganglia(1)|breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(25)|lung(58)|ovary(3)|pancreas(1)|prostate(1)|skin(6)|urinary_tract(2)	111	all_cancers(13;5.44e-23)|all_epithelial(1;2.14e-27)|Lung NSC(37;2.55e-05)|Ovarian(258;0.0219)		Epithelial(1;9.78e-37)|all cancers(1;3.14e-31)|BRCA - Breast invasive adenocarcinoma(1;2.56e-12)			CTCTGGATATGTGTTGTGAAG	0.413									Langer-Giedion syndrome																												p.H1274Y												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C3820T	8						.						183.0	170.0	174.0					8																	116426316		1906	4127	6033	116495492	SO:0001583	missense	7227	exon7	Familial Cancer Database	Trichorhinophalangeal syndrome type 2, TRPS II	AF183810	CCDS6318.2, CCDS64957.1	8q23.3	2014-06-23			ENSG00000104447	ENSG00000104447		"""GATA zinc finger domain containing"", ""Zinc fingers, C2H2-type"""	12340	protein-coding gene	gene with protein product		604386				8530105, 10615131, 10647898	Standard	NM_001282903		Approved	LGCR	uc003yny.3	Q9UHF7	OTTHUMG00000142829	ENST00000220888.5:c.3781C>T	8.37:g.116426316G>A	ENSP00000220888:p.His1261Tyr	Somatic		Capture	Illumina HiSeq	Phase_I	116495492	NM_014112	B4E1Z5|Q08AU2|Q9NWE1|Q9UHH6	Missense_Mutation	SNP	ENST00000220888.5	37		.	.	.	.	.	.	.	.	.	.	G	18.46	3.627830	0.66901	.	.	ENSG00000104447	ENST00000395715;ENST00000220888;ENST00000519076;ENST00000520276	T;T;T;T	0.72051	-0.62;-0.62;-0.62;-0.62	5.43	5.43	0.79202	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (1);	0.000000	0.85682	D	0.000000	D	0.87989	0.6317	M	0.90870	3.155	0.80722	D	1	D;D;D	0.71674	0.998;0.997;0.998	D;D;D	0.80764	0.994;0.986;0.994	D	0.90420	0.4416	10	0.87932	D	0	.	19.2461	0.93902	0.0:0.0:1.0:0.0	.	1265;1261;1274	Q9UHF7-3;Q9UHF7;Q9UHF7-2	.;TRPS1_HUMAN;.	Y	1274;1261;1015;1265	ENSP00000379065:H1274Y;ENSP00000220888:H1261Y;ENSP00000428910:H1015Y;ENSP00000428680:H1265Y	ENSP00000220888:H1261Y	H	-	1	0	TRPS1	116495492	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	9.822000	0.99363	2.525000	0.85131	0.655000	0.94253	CAT		0.413	TRPS1-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000286436.3	NM_014112	
TRPS1	7227	broad.mit.edu	37	8	116599711	116599711	+	Silent	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr8:116599711G>A	ENST00000220888.5	-	4	2337	c.2178C>T	c.(2176-2178)ggC>ggT	p.G726G	TRPS1_ENST00000395715.3_Silent_p.G739G|TRPS1_ENST00000519674.1_Silent_p.G726G|TRPS1_ENST00000520276.1_Silent_p.G730G|TRPS1_ENST00000519076.1_Silent_p.G480G			Q9UHF7	TRPS1_HUMAN	trichorhinophalangeal syndrome I	726	Mediates interaction with GLI3.				chondrocyte differentiation (GO:0002062)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|NLS-bearing protein import into nucleus (GO:0006607)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|regulation of chondrocyte differentiation (GO:0032330)|regulation of histone deacetylation (GO:0031063)|skeletal system development (GO:0001501)|transcription from RNA polymerase II promoter (GO:0006366)|transmembrane receptor protein serine/threonine kinase signaling pathway (GO:0007178)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)	p.G726G(1)		autonomic_ganglia(1)|breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(25)|lung(58)|ovary(3)|pancreas(1)|prostate(1)|skin(6)|urinary_tract(2)	111	all_cancers(13;5.44e-23)|all_epithelial(1;2.14e-27)|Lung NSC(37;2.55e-05)|Ovarian(258;0.0219)		Epithelial(1;9.78e-37)|all cancers(1;3.14e-31)|BRCA - Breast invasive adenocarcinoma(1;2.56e-12)			CGTCCTCTTCGCCGTTGGCTG	0.498									Langer-Giedion syndrome																												p.G739G												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C2217T	8						.						160.0	162.0	161.0					8																	116599711		2025	4182	6207	116668886	SO:0001819	synonymous_variant	7227	exon5	Familial Cancer Database	Trichorhinophalangeal syndrome type 2, TRPS II	AF183810	CCDS6318.2, CCDS64957.1	8q23.3	2014-06-23			ENSG00000104447	ENSG00000104447		"""GATA zinc finger domain containing"", ""Zinc fingers, C2H2-type"""	12340	protein-coding gene	gene with protein product		604386				8530105, 10615131, 10647898	Standard	NM_001282903		Approved	LGCR	uc003yny.3	Q9UHF7	OTTHUMG00000142829	ENST00000220888.5:c.2178C>T	8.37:g.116599711G>A		Somatic		Capture	Illumina HiSeq	Phase_I	116668886	NM_014112	B4E1Z5|Q08AU2|Q9NWE1|Q9UHH6	Silent	SNP	ENST00000220888.5	37																																																																																					0.498	TRPS1-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000286436.3	NM_014112	
EIF3H	8667	broad.mit.edu	37	8	117768030	117768030	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr8:117768030A>G	ENST00000276682.4	-	3	815	c.49T>C	c.(49-51)Tcc>Ccc	p.S17P	EIF3H_ENST00000521861.1_Missense_Mutation_p.S3P					eukaryotic translation initiation factor 3, subunit H									p.S3P(1)		large_intestine(2)|lung(10)|skin(1)	13	all_cancers(13;3.98e-22)|Lung NSC(37;0.000183)|Ovarian(258;0.0172)					TCCTTGCGGGACGCCATCTTT	0.607																																					p.S3P												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T7C	8						.						60.0	46.0	50.0					8																	117768030		2203	4300	6503	117837211	SO:0001583	missense	8667	exon1			U54559	CCDS6319.1	8q24.11	2007-07-27	2007-07-27	2007-07-27	ENSG00000147677	ENSG00000147677			3273	protein-coding gene	gene with protein product		603912	"""eukaryotic translation initiation factor 3, subunit 3 gamma, 40kDa"""	EIF3S3		9341143	Standard	NM_003756		Approved	eIF3-gamma, eIF3-p40, eIF3h	uc003yoa.3	O15372	OTTHUMG00000164919	ENST00000276682.4:c.49T>C	8.37:g.117768030A>G	ENSP00000276682:p.Ser17Pro	Somatic		Capture	Illumina HiSeq	Phase_I	117837211	NM_003756		Missense_Mutation	SNP	ENST00000276682.4	37		.	.	.	.	.	.	.	.	.	.	A	28.2	4.898427	0.91962	.	.	ENSG00000147677	ENST00000521861;ENST00000276682;ENST00000518995;ENST00000522453;ENST00000520813	T;T;T	0.51574	0.81;0.89;0.7	5.65	5.65	0.86999	.	0.110945	0.64402	D	0.000005	T	0.39911	0.1096	N	0.08118	0	0.48571	D	0.999679	P;P;B	0.48350	0.909;0.651;0.149	P;B;B	0.51297	0.665;0.19;0.027	T	0.48139	-0.9061	10	0.72032	D	0.01	-16.0046	13.3611	0.60657	1.0:0.0:0.0:0.0	.	3;17;3	B4DJN9;B3KS98;O15372	.;.;EIF3H_HUMAN	P	3;17;3;3;17	ENSP00000429931:S3P;ENSP00000276682:S17P;ENSP00000428669:S3P	ENSP00000276682:S17P	S	-	1	0	EIF3H	117837211	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	4.710000	0.61873	2.371000	0.80710	0.533000	0.62120	TCC		0.607	EIF3H-003	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000380913.1	NM_003756	
DLC1	10395	broad.mit.edu	37	8	13251063	13251063	+	Splice_Site	SNP	G	G	A	rs545557528		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr8:13251063G>A	ENST00000276297.4	-	4	1722	c.1313C>T	c.(1312-1314)aCg>aTg	p.T438M	DLC1_ENST00000316609.5_Splice_Site_p.T438M|DLC1_ENST00000511869.1_Splice_Site_p.T438M	NM_182643.2	NP_872584.2	Q96QB1	RHG07_HUMAN	DLC1 Rho GTPase activating protein	438					actin cytoskeleton organization (GO:0030036)|activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic process (GO:0006915)|focal adhesion assembly (GO:0048041)|forebrain development (GO:0030900)|heart morphogenesis (GO:0003007)|hindbrain morphogenesis (GO:0021575)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of Rho protein signal transduction (GO:0035024)|negative regulation of stress fiber assembly (GO:0051497)|neural tube closure (GO:0001843)|positive regulation of execution phase of apoptosis (GO:1900119)|positive regulation of protein dephosphorylation (GO:0035307)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of cell shape (GO:0008360)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	caveola (GO:0005901)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|nucleus (GO:0005634)	lipid binding (GO:0008289)|Rho GTPase activator activity (GO:0005100)|SH2 domain binding (GO:0042169)	p.T438M(2)		NS(2)|breast(2)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(39)|lung(32)|ovary(4)|pancreas(2)|prostate(4)|skin(2)|stomach(2)|upper_aerodigestive_tract(5)|urinary_tract(1)	110						AGAACTCACCGTAGTCTTGGG	0.398													G|||	1	0.000199681	0.0008	0.0	5008	,	,		18321	0.0		0.0	False		,,,				2504	0.0				p.T438M												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.C1313T	8						.						125.0	125.0	125.0					8																	13251063		2203	4300	6503	13295434	SO:0001630	splice_region_variant	10395	exon4			AF035119	CCDS5989.1, CCDS5990.1, CCDS5991.1, CCDS5991.2, CCDS55201.1	8p22	2014-06-20	2014-06-20		ENSG00000164741	ENSG00000164741		"""Rho GTPase activating proteins"", ""StAR-related lipid transfer (START) domain containing"""	2897	protein-coding gene	gene with protein product	"""StAR-related lipid transfer (START) domain containing 12"""	604258	"""deleted in liver cancer 1"""			9605766, 11214970	Standard	NM_182643		Approved	HP, ARHGAP7, STARD12, DLC-1, p122-RhoGAP	uc003wwm.2	Q96QB1	OTTHUMG00000090825	ENST00000276297.4:c.1314+1C>T	8.37:g.13251063G>A		Somatic		Capture	Illumina HiSeq	Phase_I	13295434	NM_182643	B4DR10|B8PTI0|E9PDZ8|E9PF76|E9PGY9|O14868|O43199|Q7Z5R8|Q86UC6|Q9C0E0|Q9H7A2	Missense_Mutation	SNP	ENST00000276297.4	37	CCDS5989.1	.	.	.	.	.	.	.	.	.	.	G	3.022	-0.201643	0.06219	.	.	ENSG00000164741	ENST00000276297;ENST00000316609;ENST00000511869	T;T;T	0.11930	3.63;2.73;2.73	4.65	-9.29	0.00653	.	2.895140	0.00843	N	0.001764	T	0.06826	0.0174	N	0.04508	-0.205	0.39482	D	0.967901	B;B;B	0.09022	0.002;0.001;0.001	B;B;B	0.06405	0.002;0.001;0.001	T	0.29882	-0.9997	10	0.35671	T	0.21	.	13.98	0.64299	0.7562:0.1159:0.1279:0.0	.	438;438;438	E9PF76;Q96QB1-3;Q96QB1	.;.;RHG07_HUMAN	M	438	ENSP00000276297:T438M;ENSP00000321034:T438M;ENSP00000425878:T438M	ENSP00000276297:T438M	T	-	2	0	DLC1	13295434	0.000000	0.05858	0.002000	0.10522	0.281000	0.26958	-1.014000	0.03641	-2.110000	0.00837	-0.766000	0.03442	ACG		0.398	DLC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000207632.2	NM_182643, NM_006094	Missense_Mutation
EXT1	2131	broad.mit.edu	37	8	118812030	118812030	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr8:118812030T>C	ENST00000378204.2	-	11	2968	c.2162A>G	c.(2161-2163)cAg>cGg	p.Q721R		NM_000127.2	NP_000118.2	Q16394	EXT1_HUMAN	exostosin glycosyltransferase 1	721					axon guidance (GO:0007411)|carbohydrate metabolic process (GO:0005975)|cellular polysaccharide biosynthetic process (GO:0033692)|embryonic skeletal joint development (GO:0072498)|endoderm development (GO:0007492)|gastrulation (GO:0007369)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan metabolic process (GO:0030203)|heparan sulfate proteoglycan biosynthetic process (GO:0015012)|heparan sulfate proteoglycan biosynthetic process, polysaccharide chain biosynthetic process (GO:0015014)|mesoderm development (GO:0007498)|olfactory bulb development (GO:0021772)|ossification (GO:0001503)|protein glycosylation (GO:0006486)|signal transduction (GO:0007165)|skeletal system development (GO:0001501)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of endoplasmic reticulum membrane (GO:0030176)|integral component of membrane (GO:0016021)	acetylglucosaminyltransferase activity (GO:0008375)|glucuronosyl-N-acetylglucosaminyl-proteoglycan 4-alpha-N-acetylglucosaminyltransferase activity (GO:0050508)|glucuronosyltransferase activity (GO:0015020)|heparan sulfate N-acetylglucosaminyltransferase activity (GO:0042328)|N-acetylglucosaminyl-proteoglycan 4-beta-glucuronosyltransferase activity (GO:0050509)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|transferase activity, transferring glycosyl groups (GO:0016757)	p.Q721R(1)		breast(1)|endometrium(7)|kidney(1)|large_intestine(12)|lung(10)|ovary(3)|prostate(1)|stomach(1)|urinary_tract(2)	38	all_cancers(13;2.36e-26)|Lung NSC(37;5.02e-07)|Ovarian(258;0.0173)		STAD - Stomach adenocarcinoma(47;0.012)			GAGCCTCATCTGAGAGTGGAT	0.547			"""Mis, N, F, S"""			"""exostoses, osteosarcoma"""			Langer-Giedion syndrome;Hereditary Multiple Exostoses																												p.Q721R		yes	Rec		Multiple Exostoses Type 1	8	8q24.11-q24.13	2131	multiple exostoses type 1 gene		M	.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A2162G	8						.						87.0	83.0	84.0					8																	118812030		2203	4300	6503	118881211	SO:0001583	missense	2131	exon11	Familial Cancer Database	Trichorhinophalangeal syndrome type 2, TRPS II;HME, Hereditary Exostoses, Multiple Osteochondromatosis, Multiple Cartilaginous Exostoses	S79639	CCDS6324.1	8q24.11	2014-09-17	2013-03-01		ENSG00000182197	ENSG00000182197	2.4.1.224, 2.4.1.225	"""Exostosin glycosyltransferase family"""	3512	protein-coding gene	gene with protein product	"""Glucuronosyl-N-acetylglucosaminyl-proteoglycan 4-alpha-N- acetylglucosaminyltransferase"", ""N-acetylglucosaminyl-proteoglycan 4-beta-glucuronosyltransferase"""	608177	"""Langer-Giedion syndrome chromosome region"", ""exostoses (multiple) 1"", ""exostosin 1"""	LGCR, LGS			Standard	NM_000127		Approved	ttv	uc003yok.1	Q16394	OTTHUMG00000059718	ENST00000378204.2:c.2162A>G	8.37:g.118812030T>C	ENSP00000367446:p.Gln721Arg	Somatic		Capture	Illumina HiSeq	Phase_I	118881211	NM_000127	B2R7V2|Q9BVI9	Missense_Mutation	SNP	ENST00000378204.2	37	CCDS6324.1	.	.	.	.	.	.	.	.	.	.	T	12.38	1.920326	0.33908	.	.	ENSG00000182197	ENST00000378204	D	0.85955	-2.05	5.96	5.96	0.96718	EXTL2, alpha-1,4-N-acetylhexosaminyltransferase (1);	0.052886	0.85682	D	0.000000	D	0.84844	0.5562	M	0.62154	1.92	0.58432	D	0.999991	B	0.27594	0.182	B	0.32533	0.147	T	0.81473	-0.0917	10	0.32370	T	0.25	-10.214	16.4484	0.83959	0.0:0.0:0.0:1.0	.	721	Q16394	EXT1_HUMAN	R	721	ENSP00000367446:Q721R	ENSP00000367446:Q721R	Q	-	2	0	EXT1	118881211	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.288000	0.72679	2.285000	0.76669	0.533000	0.62120	CAG		0.547	EXT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132768.3	NM_000127	
TG	7038	broad.mit.edu	37	8	133953756	133953756	+	Silent	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr8:133953756C>T	ENST00000220616.4	+	26	5242	c.5202C>T	c.(5200-5202)tgC>tgT	p.C1734C	TG_ENST00000377869.1_Silent_p.C1677C|TG_ENST00000542445.1_Intron	NM_003235.4	NP_003226.4	P01266	THYG_HUMAN	thyroglobulin	1734					hormone biosynthetic process (GO:0042446)|iodide transport (GO:0015705)|regulation of myelination (GO:0031641)|signal transduction (GO:0007165)|thyroid gland development (GO:0030878)|thyroid hormone generation (GO:0006590)	extracellular region (GO:0005576)|extracellular space (GO:0005615)		p.C1734C(1)		NS(1)|breast(11)|central_nervous_system(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(34)|liver(2)|lung(59)|ovary(9)|pancreas(2)|prostate(6)|skin(7)|stomach(4)|upper_aerodigestive_tract(4)|urinary_tract(8)	168	Ovarian(258;0.00438)|Acute lymphoblastic leukemia(118;0.155)	Myeloproliferative disorder(644;0.00878)|Acute lymphoblastic leukemia(644;0.0559)|Breast(495;0.0735)	BRCA - Breast invasive adenocarcinoma(115;0.000701)	KIRC - Kidney renal clear cell carcinoma(542;0.0546)		ATCTGTGTTGCGATGGCTTCG	0.537																																					p.C1734C												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C5202T	8						.						160.0	128.0	139.0					8																	133953756		2203	4300	6503	134022938	SO:0001819	synonymous_variant	7038	exon26			AU141420	CCDS34944.1	8q24	2012-10-02			ENSG00000042832	ENSG00000042832			11764	protein-coding gene	gene with protein product		188450					Standard	NM_003235		Approved	TGN, AITD3	uc003ytw.3	P01266	OTTHUMG00000164649	ENST00000220616.4:c.5202C>T	8.37:g.133953756C>T		Somatic		Capture	Illumina HiSeq	Phase_I	134022938	NM_003235	O15274|O43899|Q15593|Q15948|Q9NYR1|Q9NYR2|Q9UMZ0|Q9UNY3	Silent	SNP	ENST00000220616.4	37	CCDS34944.1																																																																																				0.537	TG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379606.1	NM_003235	
ZFAT	57623	broad.mit.edu	37	8	135612824	135612824	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr8:135612824T>C	ENST00000377838.3	-	7	2504	c.2330A>G	c.(2329-2331)tAt>tGt	p.Y777C	ZFAT_ENST00000523399.1_Missense_Mutation_p.Y715C|ZFAT_ENST00000520727.1_Missense_Mutation_p.Y765C|ZFAT_ENST00000520356.1_Missense_Mutation_p.Y765C|ZFAT_ENST00000429442.2_Missense_Mutation_p.Y765C|ZFAT-AS1_ENST00000505776.1_RNA|ZFAT_ENST00000520214.1_Missense_Mutation_p.Y765C	NM_001174157.1|NM_020863.3	NP_001167628.1|NP_065914.2	Q9P243	ZFAT_HUMAN	zinc finger and AT hook domain containing	777					hematopoietic progenitor cell differentiation (GO:0002244)|spongiotrophoblast layer development (GO:0060712)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)	p.Y765C(1)		autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(10)|kidney(9)|large_intestine(8)|lung(16)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	54	all_epithelial(106;8.26e-19)|Lung NSC(106;3.47e-07)|all_lung(105;1.39e-06)|Ovarian(258;0.0102)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0432)			GATGGAAGAATAATGACACTG	0.418																																					p.Y715C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A2144G	8						.						113.0	112.0	112.0					8																	135612824		1948	4149	6097	135682006	SO:0001583	missense	57623	exon6			BC025423	CCDS43768.1, CCDS47924.1, CCDS43768.2, CCDS55275.1, CCDS55276.1	8q24.23	2008-06-05	2008-01-25	2008-01-25	ENSG00000066827	ENSG00000066827		"""Zinc fingers, C2H2-type"""	19899	protein-coding gene	gene with protein product		610931	"""zinc finger protein 406"""	ZNF406, ZFAT1		10819331, 18329245	Standard	NM_020863		Approved	KIAA1485	uc003yup.3	Q9P243	OTTHUMG00000164321	ENST00000377838.3:c.2330A>G	8.37:g.135612824T>C	ENSP00000367069:p.Tyr777Cys	Somatic		Capture	Illumina HiSeq	Phase_I	135682006	NM_001174157	B7ZL15|E9PER3|Q3MIM5|Q6PJ01|Q75PJ6|Q75PJ7|Q75PJ9|Q86X64	Missense_Mutation	SNP	ENST00000377838.3	37	CCDS47924.1	.	.	.	.	.	.	.	.	.	.	T	22.7	4.319920	0.81469	.	.	ENSG00000066827	ENST00000520356;ENST00000520727;ENST00000429442;ENST00000377838;ENST00000520214;ENST00000318135;ENST00000523399;ENST00000398946	T;T;T;T;T;T	0.28666	1.6;1.6;1.6;1.6;1.6;1.6	5.42	5.42	0.78866	Zinc finger, C2H2-like (1);	0.000000	0.85682	D	0.000000	T	0.55289	0.1911	M	0.69823	2.125	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	1.0;1.0;0.999;1.0	T	0.59064	-0.7524	10	0.72032	D	0.01	-20.0854	14.9503	0.71067	0.0:0.0:0.0:1.0	.	715;765;765;777	E9PER3;E9PBN4;Q9P243-3;Q9P243	.;.;.;ZFAT_HUMAN	C	765;765;765;777;765;664;715;765	ENSP00000427879:Y765C;ENSP00000427831:Y765C;ENSP00000394501:Y765C;ENSP00000367069:Y777C;ENSP00000428483:Y765C;ENSP00000429091:Y715C	ENSP00000326997:Y664C	Y	-	2	0	ZFAT	135682006	1.000000	0.71417	0.983000	0.44433	0.996000	0.88848	7.997000	0.88414	2.189000	0.69895	0.533000	0.62120	TAT		0.418	ZFAT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378272.1	NM_001029939	
FAM135B	51059	broad.mit.edu	37	8	139164811	139164811	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr8:139164811G>A	ENST00000395297.1	-	13	2077	c.1907C>T	c.(1906-1908)aCc>aTc	p.T636I		NM_015912.3	NP_056996.2	Q49AJ0	F135B_HUMAN	family with sequence similarity 135, member B	636								p.T636I(2)		NS(3)|breast(9)|endometrium(21)|kidney(5)|large_intestine(28)|liver(1)|lung(135)|ovary(9)|pancreas(1)|prostate(7)|skin(9)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(1)	238	all_epithelial(106;8.29e-14)|Lung NSC(106;6.88e-06)|all_lung(105;1.44e-05)|Ovarian(258;0.00672)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0805)			CTCAGAGGGGGTGAGTTTCAA	0.468										HNSCC(54;0.14)																											p.T636I												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.C1907T	8						.						106.0	105.0	105.0					8																	139164811		1892	4123	6015	139233993	SO:0001583	missense	51059	exon13			AB196635	CCDS6375.2	8q24.23	2008-11-05			ENSG00000147724	ENSG00000147724			28029	protein-coding gene	gene with protein product						8619474, 9110174	Standard	NM_015912		Approved	C8ORFK32	uc003yuy.3	Q49AJ0	OTTHUMG00000149864	ENST00000395297.1:c.1907C>T	8.37:g.139164811G>A	ENSP00000378710:p.Thr636Ile	Somatic		Capture	Illumina HiSeq	Phase_I	139233993	NM_015912	B5MDB3|O95879|Q2WGJ7|Q3KP46	Missense_Mutation	SNP	ENST00000395297.1	37	CCDS6375.2	.	.	.	.	.	.	.	.	.	.	G	4.553	0.102690	0.08731	.	.	ENSG00000147724	ENST00000395297	T	0.14266	2.52	4.83	-7.37	0.01412	.	1.553540	0.03375	N	0.199474	T	0.03739	0.0106	N	0.02011	-0.69	0.09310	N	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.001;0.001;0.0	T	0.32188	-0.9916	10	0.27082	T	0.32	2.1644	1.7669	0.03004	0.1662:0.2349:0.3666:0.2323	.	636;636;636	Q49AJ0-3;Q49AJ0-4;Q49AJ0	.;.;F135B_HUMAN	I	636	ENSP00000378710:T636I	ENSP00000276737:T636I	T	-	2	0	FAM135B	139233993	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	-0.026000	0.12392	-1.226000	0.02574	-1.311000	0.01308	ACC		0.468	FAM135B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313590.3	NM_015912	
FAM135B	51059	broad.mit.edu	37	8	139207506	139207506	+	Missense_Mutation	SNP	G	G	T	rs375948638		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr8:139207506G>T	ENST00000395297.1	-	9	1038	c.868C>A	c.(868-870)Cta>Ata	p.L290I		NM_015912.3	NP_056996.2	Q49AJ0	F135B_HUMAN	family with sequence similarity 135, member B	290								p.L290I(2)		NS(3)|breast(9)|endometrium(21)|kidney(5)|large_intestine(28)|liver(1)|lung(135)|ovary(9)|pancreas(1)|prostate(7)|skin(9)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(1)	238	all_epithelial(106;8.29e-14)|Lung NSC(106;6.88e-06)|all_lung(105;1.44e-05)|Ovarian(258;0.00672)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0805)			ATTACCTGTAGCTCTGAGCAC	0.423										HNSCC(54;0.14)																											p.L290I												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.C868A	8						.	G	ILE/LEU	0,3734		0,0,1867	88.0	84.0	85.0		868	2.5	1.0	8		85	1,8199		0,1,4099	no	missense	FAM135B	NM_015912.3	5	0,1,5966	TT,TG,GG		0.0122,0.0,0.0084	probably-damaging	290/1407	139207506	1,11933	1867	4100	5967	139276688	SO:0001583	missense	51059	exon9			AB196635	CCDS6375.2	8q24.23	2008-11-05			ENSG00000147724	ENSG00000147724			28029	protein-coding gene	gene with protein product						8619474, 9110174	Standard	NM_015912		Approved	C8ORFK32	uc003yuy.3	Q49AJ0	OTTHUMG00000149864	ENST00000395297.1:c.868C>A	8.37:g.139207506G>T	ENSP00000378710:p.Leu290Ile	Somatic		Capture	Illumina HiSeq	Phase_I	139276688	NM_015912	B5MDB3|O95879|Q2WGJ7|Q3KP46	Missense_Mutation	SNP	ENST00000395297.1	37	CCDS6375.2	.	.	.	.	.	.	.	.	.	.	G	14.66	2.600469	0.46423	0.0	1.22E-4	ENSG00000147724	ENST00000395297	T	0.78246	-1.16	4.3	2.49	0.30216	.	0.246922	0.30575	N	0.009333	T	0.80221	0.4583	L	0.46157	1.445	0.35484	D	0.798403	D	0.63880	0.993	D	0.76071	0.987	T	0.80358	-0.1416	10	0.42905	T	0.14	-11.309	5.8178	0.18506	0.2368:0.0:0.7632:0.0	.	290	Q49AJ0	F135B_HUMAN	I	290	ENSP00000378710:L290I	ENSP00000276737:L290I	L	-	1	2	FAM135B	139276688	1.000000	0.71417	0.965000	0.40720	0.922000	0.55478	1.941000	0.40233	0.741000	0.32674	0.650000	0.86243	CTA		0.423	FAM135B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313590.3	NM_015912	
COL22A1	169044	broad.mit.edu	37	8	139833397	139833397	+	Silent	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr8:139833397G>A	ENST00000303045.6	-	7	1673	c.1227C>T	c.(1225-1227)taC>taT	p.Y409Y	COL22A1_ENST00000435777.1_Silent_p.Y409Y	NM_152888.1	NP_690848.1	Q8NFW1	COMA1_HUMAN	collagen, type XXII, alpha 1	409	Laminin G-like.				extracellular matrix organization (GO:0030198)	collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)		p.Y409Y(1)		breast(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(14)|large_intestine(29)|lung(107)|ovary(13)|pancreas(1)|prostate(3)|skin(12)|upper_aerodigestive_tract(15)|urinary_tract(4)	211	all_epithelial(106;1.55e-12)|Lung NSC(106;1.67e-05)|all_lung(105;3.39e-05)|Ovarian(258;0.00672)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0517)			GCACACTGTCGTAGAGGCGCT	0.587										HNSCC(7;0.00092)																											p.Y409Y												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1227T	8						.						171.0	121.0	138.0					8																	139833397		2203	4300	6503	139902579	SO:0001819	synonymous_variant	169044	exon7			AF406780	CCDS6376.1	8q24.3	2013-01-16			ENSG00000169436	ENSG00000169436		"""Collagens"""	22989	protein-coding gene	gene with protein product		610026					Standard	NM_152888		Approved		uc003yvd.3	Q8NFW1	OTTHUMG00000150035	ENST00000303045.6:c.1227C>T	8.37:g.139833397G>A		Somatic		Capture	Illumina HiSeq	Phase_I	139902579	NM_152888	B7ZMH0|C9K0G4|Q8IVT9	Silent	SNP	ENST00000303045.6	37	CCDS6376.1																																																																																				0.587	COL22A1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000315905.2	XM_291257	
KCNK9	51305	broad.mit.edu	37	8	140631062	140631062	+	Silent	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr8:140631062G>A	ENST00000520439.1	-	2	627	c.564C>T	c.(562-564)caC>caT	p.H188H	KCNK9_ENST00000523477.1_5'Flank|KCNK9_ENST00000303015.1_Silent_p.H188H	NM_001282534.1	NP_001269463.1	Q9NPC2	KCNK9_HUMAN	potassium channel, subfamily K, member 9	188					cochlea development (GO:0090102)|potassium ion transport (GO:0006813)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|synaptic vesicle (GO:0008021)	potassium channel activity (GO:0005267)|voltage-gated ion channel activity (GO:0005244)	p.H188H(2)		NS(1)|endometrium(9)|kidney(1)|large_intestine(9)|lung(17)|ovary(2)|prostate(3)|skin(1)	43	all_cancers(97;3.94e-14)|all_epithelial(106;4.81e-13)|Lung NSC(106;8.18e-05)|all_lung(105;0.00015)|Ovarian(258;0.00235)|Acute lymphoblastic leukemia(118;0.155)	Ovarian(118;0.134)	BRCA - Breast invasive adenocarcinoma(115;0.0855)		Doxapram(DB00561)|Halothane(DB01159)	AGTAGTAGGCGTGGAAGAAGC	0.592																																					p.H188H												.	.	2	Substitution - coding silent(2)	large_intestine(1)|kidney(1)	c.C564T	8						.						93.0	89.0	90.0					8																	140631062		2203	4300	6503	140700244	SO:0001819	synonymous_variant	51305	exon2			AF212829	CCDS6377.1	8q24.3	2012-03-07			ENSG00000169427	ENSG00000169427		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels, Two-P"""	6283	protein-coding gene	gene with protein product		605874				10734076, 16382106	Standard	NM_001282534		Approved	K2p9.1, TASK3, TASK-3	uc003yvf.1	Q9NPC2	OTTHUMG00000164186	ENST00000520439.1:c.564C>T	8.37:g.140631062G>A		Somatic		Capture	Illumina HiSeq	Phase_I	140700244	NM_016601	Q2M290|Q540F2	Silent	SNP	ENST00000520439.1	37	CCDS6377.1																																																																																				0.592	KCNK9-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378473.1	NM_016601	
SLC45A4	57210	broad.mit.edu	37	8	142229000	142229000	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr8:142229000C>T	ENST00000024061.3	-	4	893	c.586G>A	c.(586-588)Gcc>Acc	p.A196T	SLC45A4_ENST00000433583.2_Missense_Mutation_p.A189T|SLC45A4_ENST00000517878.1_Missense_Mutation_p.A247T|SLC45A4_ENST00000519067.1_Missense_Mutation_p.A196T	NM_001080431.1	NP_001073900.1	Q5BKX6	S45A4_HUMAN	solute carrier family 45, member 4						transport (GO:0006810)	integral component of membrane (GO:0016021)		p.A196T(1)		breast(1)|central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(6)|lung(9)|ovary(3)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	31	all_cancers(97;1.52e-15)|all_epithelial(106;2.92e-14)|Lung NSC(106;1.23e-05)|all_lung(105;1.75e-05)|Ovarian(258;0.01)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0493)			AGGTGCAGGGCCACGGACACC	0.672																																					p.A196T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G586A	8						.						87.0	91.0	90.0					8																	142229000		2203	4300	6503	142298182	SO:0001583	missense	57210	exon4			AB032952	CCDS34948.1, CCDS69550.1, CCDS75795.1	8q24.3	2013-05-22						"""Solute carriers"""	29196	protein-coding gene	gene with protein product							Standard	NM_001080431		Approved	KIAA1126	uc003ywd.1	Q5BKX6		ENST00000024061.3:c.586G>A	8.37:g.142229000C>T	ENSP00000024061:p.Ala196Thr	Somatic		Capture	Illumina HiSeq	Phase_I	142298182	NM_001080431	Q6ZRI2|Q9ULU3	Missense_Mutation	SNP	ENST00000024061.3	37	CCDS34948.1	.	.	.	.	.	.	.	.	.	.	C	10.54	1.378764	0.24944	.	.	ENSG00000022567	ENST00000519067;ENST00000517878;ENST00000433583;ENST00000024061;ENST00000520137	D;D;D;D;D	0.92752	-3.1;-3.1;-3.1;-3.1;-3.1	5.57	1.82	0.25136	.	1.065750	0.07066	N	0.834641	D	0.83096	0.5180	N	0.11698	0.16	0.25982	N	0.982355	B;B;B	0.15473	0.003;0.013;0.0	B;B;B	0.13407	0.007;0.009;0.002	T	0.68435	-0.5409	10	0.27082	T	0.32	-15.5587	7.0466	0.25048	0.1227:0.6814:0.0:0.1959	.	247;196;196	E7EV90;Q5BKX6-3;Q5BKX6-2	.;.;.	T	196;247;189;196;54	ENSP00000429059:A196T;ENSP00000428137:A247T;ENSP00000400799:A189T;ENSP00000024061:A196T;ENSP00000429033:A54T	ENSP00000024061:A196T	A	-	1	0	SLC45A4	142298182	0.000000	0.05858	0.971000	0.41717	0.787000	0.44495	1.005000	0.29834	0.062000	0.16340	-1.023000	0.02433	GCC		0.672	SLC45A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378571.3	XM_050325	
PSCA	8000	broad.mit.edu	37	8	143763396	143763396	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr8:143763396A>G	ENST00000301258.4	+	3	274	c.191A>G	c.(190-192)gAc>gGc	p.D64G		NM_005672.4	NP_005663.2	O43653	PSCA_HUMAN	prostate stem cell antigen	73	UPAR/Ly6.					anchored component of membrane (GO:0031225)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)		p.D64G(1)		endometrium(1)|large_intestine(1)	2	all_cancers(97;3.96e-12)|all_epithelial(106;1.19e-08)|Lung NSC(106;0.000413)|all_lung(105;0.00106)|Medulloblastoma(13;0.00276)|all_neural(13;0.00559)|Ovarian(258;0.0254)|Acute lymphoblastic leukemia(118;0.155)					TGCGTGGATGACTCACAGGAC	0.632																																					p.D64G												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A191G	8						.						43.0	49.0	47.0					8																	143763396		2183	4270	6453	143760398	SO:0001583	missense	8000	exon3			AF043498	CCDS47925.1, CCDS47925.2	8q24.2	2004-02-03				ENSG00000167653			9500	protein-coding gene	gene with protein product		602470				9465086	Standard	NM_005672		Approved		uc022bcd.1	O43653		ENST00000301258.4:c.191A>G	8.37:g.143763396A>G	ENSP00000301258:p.Asp64Gly	Somatic		Capture	Illumina HiSeq	Phase_I	143760398	NM_005672	Q6UW92	Missense_Mutation	SNP	ENST00000301258.4	37	CCDS47925.2	.	.	.	.	.	.	.	.	.	.	A	9.417	1.081996	0.20309	.	.	ENSG00000167653	ENST00000301258	.	.	.	3.11	0.69	0.18039	Ly-6 antigen / uPA receptor -like (1);CD59 antigen (1);	0.258016	0.30723	N	0.009013	T	0.25158	0.0611	L	0.38692	1.165	0.09310	N	0.999993	B	0.12630	0.006	B	0.15484	0.013	T	0.13737	-1.0498	9	0.19590	T	0.45	.	4.8738	0.13646	0.7266:0.0:0.2734:0.0	.	73	O43653	PSCA_HUMAN	G	73	.	ENSP00000301258:D73G	D	+	2	0	PSCA	143760398	0.001000	0.12720	0.000000	0.03702	0.006000	0.05464	1.100000	0.31025	0.138000	0.18790	-0.371000	0.07208	GAC		0.632	PSCA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367112.2	NM_005672	
VPS28	51160	broad.mit.edu	37	8	145650190	145650190	+	Silent	SNP	G	G	A	rs532037544		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr8:145650190G>A	ENST00000526054.1	-	6	350	c.313C>T	c.(313-315)Ctg>Ttg	p.L105L	VPS28_ENST00000526734.1_5'Flank|VPS28_ENST00000292510.4_Silent_p.L105L|VPS28_ENST00000377348.2_Silent_p.L105L|VPS28_ENST00000529182.1_Silent_p.L105L			Q9UK41	VPS28_HUMAN	vacuolar protein sorting 28 homolog (S. cerevisiae)	105	VPS28 N-terminal. {ECO:0000255|PROSITE- ProRule:PRU00645}.				endosomal transport (GO:0016197)|intracellular transport of virus (GO:0075733)|membrane organization (GO:0061024)|negative regulation of protein ubiquitination (GO:0031397)|protein transport (GO:0015031)|ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway (GO:0043162)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral protein processing (GO:0019082)|virion assembly (GO:0019068)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endosome (GO:0005768)|endosome membrane (GO:0010008)|ESCRT I complex (GO:0000813)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)		p.L105L(1)		kidney(1)|large_intestine(1)|lung(4)|prostate(1)	7	all_cancers(97;6.64e-12)|all_epithelial(106;2.89e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;1.08e-41)|Epithelial(56;8.67e-41)|all cancers(56;1.1e-35)|BRCA - Breast invasive adenocarcinoma(115;0.035)|Colorectal(110;0.055)			TCCATGGCCAGCGGGCAGTCC	0.662													G|||	1	0.000199681	0.0	0.0	5008	,	,		18409	0.001		0.0	False		,,,				2504	0.0				p.L105L												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C313T	8						.						109.0	92.0	98.0					8																	145650190		2203	4300	6503	145620998	SO:0001819	synonymous_variant	51160	exon7			AF316887	CCDS6425.1, CCDS34967.1	8q24.3	2014-08-12	2006-04-04		ENSG00000160948	ENSG00000160948			18178	protein-coding gene	gene with protein product		611952	"""vacuolar protein sorting 28 (yeast)"""				Standard	NM_183057		Approved		uc003zct.1	Q9UK41	OTTHUMG00000165209	ENST00000526054.1:c.313C>T	8.37:g.145650190G>A		Somatic		Capture	Illumina HiSeq	Phase_I	145620998	NM_183057	Q86VK0	Silent	SNP	ENST00000526054.1	37	CCDS6425.1																																																																																				0.662	VPS28-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382694.1		
CSMD1	64478	broad.mit.edu	37	8	2808661	2808661	+	Silent	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr8:2808661G>A	ENST00000520002.1	-	67	10734	c.10179C>T	c.(10177-10179)gcC>gcT	p.A3393A	CSMD1_ENST00000602557.1_Silent_p.A3393A|CSMD1_ENST00000537824.1_Silent_p.A3392A|CSMD1_ENST00000602723.1_Silent_p.A3216A|CSMD1_ENST00000400186.3_Silent_p.A3216A|CSMD1_ENST00000542608.1_Silent_p.A3215A			Q96PZ7	CSMD1_HUMAN	CUB and Sushi multiple domains 1	3393						integral component of membrane (GO:0016021)		p.A3392A(1)|p.A3121A(1)		breast(20)|large_intestine(5)	25		all_cancers(1;5.7e-41)|all_epithelial(1;2.54e-36)|Lung NSC(1;7.54e-11)|all_lung(1;3.2e-10)|Hepatocellular(1;3.78e-05)|Breast(1;0.000196)|Myeloproliferative disorder(4;0.000374)|Esophageal squamous(1;0.0157)|Ovarian(12;0.091)|Renal(68;0.144)|Colorectal(14;0.234)		all cancers(1;5.03e-41)|Epithelial(1;4.78e-31)|Lung(1;1.14e-14)|LUSC - Lung squamous cell carcinoma(1;2.34e-14)|GBM - Glioblastoma multiforme(1;4.49e-10)|Colorectal(4;1.18e-07)|OV - Ovarian serous cystadenocarcinoma(1;3.2e-07)|BRCA - Breast invasive adenocarcinoma(1;6.17e-07)|COAD - Colon adenocarcinoma(4;0.000539)|READ - Rectum adenocarcinoma(4;0.00896)|Kidney(5;0.00957)|KIRC - Kidney renal clear cell carcinoma(5;0.0689)		CCACTGGCGAGGCTTCGCTGA	0.463																																					p.L3393F												.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.C10177T	8						.						89.0	85.0	87.0					8																	2808661		1941	4139	6080	2796068	SO:0001819	synonymous_variant	64478	exon66					8p23.2	2012-04-17			ENSG00000183117	ENSG00000183117		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	14026	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 24"""	608397					Standard	NM_033225		Approved	KIAA1890, PPP1R24	uc022aqr.1	Q96PZ7	OTTHUMG00000163605	ENST00000520002.1:c.10179C>T	8.37:g.2808661G>A		Somatic		Capture	Illumina HiSeq	Phase_I	2796068	NM_033225	Q0H0J5|Q96QU9|Q96RM4	Silent	SNP	ENST00000520002.1	37		.	.	.	.	.	.	.	.	.	.	G	0.261	-0.999780	0.02128	.	.	ENSG00000183117	ENST00000335551	.	.	.	5.2	-2.95	0.05564	.	.	.	.	.	T	0.22360	0.0539	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.32929	-0.9888	4	.	.	.	.	5.745	0.18114	0.5508:0.0:0.2491:0.2001	.	.	.	.	F	2795	.	.	L	-	1	0	CSMD1	2796068	0.378000	0.25114	0.000000	0.03702	0.004000	0.04260	0.213000	0.17521	-0.247000	0.09597	-0.154000	0.13518	CTC		0.463	CSMD1-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000374500.2	NM_033225	
SGK223	157285	broad.mit.edu	37	8	8185246	8185246	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr8:8185246C>T	ENST00000520004.1	-	5	3310	c.3046G>A	c.(3046-3048)Ggc>Agc	p.G1016S	SGK223_ENST00000330777.4_Missense_Mutation_p.G1016S			Q86YV5	SG223_HUMAN		1018	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.						ATP binding (GO:0005524)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)	p.G1016S(1)|p.G1018S(1)									TAGGTGCTGCCGGGGTCCTCA	0.547																																					p.G1016S	GBM(34;731 755 10259 33573 33867)											.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G3046A	8						.						46.0	50.0	48.0					8																	8185246		2094	4228	6322	8222656	SO:0001583	missense	157285	exon4																														ENST00000520004.1:c.3046G>A	8.37:g.8185246C>T	ENSP00000428054:p.Gly1016Ser	Somatic		Capture	Illumina HiSeq	Phase_I	8222656	NM_001080826	Q8N3N5	Missense_Mutation	SNP	ENST00000520004.1	37	CCDS43706.1	.	.	.	.	.	.	.	.	.	.	C	5.236	0.228937	0.09916	.	.	ENSG00000182319	ENST00000330777;ENST00000520004	T;T	0.26957	1.7;1.7	4.82	3.88	0.44766	Protein kinase, catalytic domain (1);	0.354215	0.28736	N	0.014302	T	0.12774	0.0310	N	0.25890	0.77	0.09310	N	1	B	0.26363	0.147	B	0.15870	0.014	T	0.19289	-1.0310	10	0.12103	T	0.63	.	5.9237	0.19096	0.2496:0.6544:0.0:0.096	.	1016	Q86YV5	SG223_HUMAN	S	1016	ENSP00000330930:G1016S;ENSP00000428054:G1016S	ENSP00000330930:G1016S	G	-	1	0	AC068353.1	8222656	0.095000	0.21747	0.979000	0.43373	0.987000	0.75469	0.704000	0.25661	2.670000	0.90874	0.563000	0.77884	GGC		0.547	SGK223-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374864.1		
SGK223	157285	broad.mit.edu	37	8	8185525	8185525	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr8:8185525C>T	ENST00000520004.1	-	5	3031	c.2767G>A	c.(2767-2769)Gtg>Atg	p.V923M	SGK223_ENST00000330777.4_Missense_Mutation_p.V923M			Q86YV5	SG223_HUMAN		925							ATP binding (GO:0005524)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)	p.V925M(1)|p.V923M(1)									TGACTGGACACGCTCAGCTGG	0.677																																					p.V923M	GBM(34;731 755 10259 33573 33867)											.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G2767A	8						.						32.0	38.0	36.0					8																	8185525		1990	4153	6143	8222935	SO:0001583	missense	157285	exon4																														ENST00000520004.1:c.2767G>A	8.37:g.8185525C>T	ENSP00000428054:p.Val923Met	Somatic		Capture	Illumina HiSeq	Phase_I	8222935	NM_001080826	Q8N3N5	Missense_Mutation	SNP	ENST00000520004.1	37	CCDS43706.1	.	.	.	.	.	.	.	.	.	.	C	10.79	1.448912	0.26074	.	.	ENSG00000182319	ENST00000330777;ENST00000520004	T;T	0.58797	0.31;0.31	4.73	2.93	0.34026	.	0.311378	0.27447	N	0.019321	T	0.36580	0.0972	L	0.29908	0.895	0.31863	N	0.620674	P	0.36144	0.539	B	0.19946	0.027	T	0.43228	-0.9404	10	0.34782	T	0.22	.	9.7422	0.40424	0.0:0.7655:0.0:0.2345	.	923	Q86YV5	SG223_HUMAN	M	923	ENSP00000330930:V923M;ENSP00000428054:V923M	ENSP00000330930:V923M	V	-	1	0	AC068353.1	8222935	0.865000	0.29922	0.843000	0.33291	0.547000	0.35210	1.663000	0.37429	0.725000	0.32318	0.563000	0.77884	GTG		0.677	SGK223-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374864.1		
PPP1R3B	79660	broad.mit.edu	37	8	8998765	8998765	+	Missense_Mutation	SNP	C	C	T	rs368157445		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr8:8998765C>T	ENST00000310455.3	-	2	547	c.397G>A	c.(397-399)Gtc>Atc	p.V133I	RP11-10A14.3_ENST00000520017.1_RNA|PPP1R3B_ENST00000519699.1_Missense_Mutation_p.V133I|RP11-10A14.3_ENST00000522057.1_RNA	NM_001201329.1|NM_024607.3	NP_001188258.1|NP_078883.2	Q86XI6	PPR3B_HUMAN	protein phosphatase 1, regulatory subunit 3B	133	CBM21. {ECO:0000255|PROSITE- ProRule:PRU00491}.				glycogen metabolic process (GO:0005977)|regulation of glycogen biosynthetic process (GO:0005979)|regulation of glycogen catabolic process (GO:0005981)	glycogen granule (GO:0042587)|intracellular membrane-bounded organelle (GO:0043231)|protein phosphatase type 1 complex (GO:0000164)	protein phosphatase regulator activity (GO:0019888)	p.V133I(1)		endometrium(1)|large_intestine(3)|lung(5)|ovary(1)|prostate(1)|skin(1)	12				COAD - Colon adenocarcinoma(149;0.0717)|READ - Rectum adenocarcinoma(644;0.241)		TCAAGGCAGACGTGGTCGGCC	0.488																																					p.V133I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G397A	8						.	C	ILE/VAL,ILE/VAL	1,4405	2.1+/-5.4	0,1,2202	109.0	98.0	101.0		397,397	5.9	1.0	8		101	0,8600		0,0,4300	no	missense,missense	PPP1R3B	NM_001201329.1,NM_024607.3	29,29	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	probably-damaging,probably-damaging	133/286,133/286	8998765	1,13005	2203	4300	6503	9036175	SO:0001583	missense	79660	exon2			AK024067	CCDS5973.1	8p23.1	2012-04-17	2011-10-04		ENSG00000173281	ENSG00000173281		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	14942	protein-coding gene	gene with protein product	"""PP1 subunit R4"", ""hepatic glycogen-targeting subunit, G(L)"""	610541	"""protein phosphatase 1, regulatory (inhibitor) subunit 3B"""			11948623, 17555403	Standard	NM_024607		Approved	GL, FLJ14005, PPP1R4	uc003wsn.4	Q86XI6	OTTHUMG00000129329	ENST00000310455.3:c.397G>A	8.37:g.8998765C>T	ENSP00000308318:p.Val133Ile	Somatic		Capture	Illumina HiSeq	Phase_I	9036175	NM_024607	B3KTV3|Q9H812	Missense_Mutation	SNP	ENST00000310455.3	37	CCDS5973.1	.	.	.	.	.	.	.	.	.	.	C	32	5.160096	0.94727	2.27E-4	0.0	ENSG00000173281	ENST00000310455;ENST00000519699	T;T	0.73152	-0.72;-0.72	5.87	5.87	0.94306	Putative phosphatase regulatory subunit (2);	0.000000	0.85682	D	0.000000	D	0.85349	0.5676	M	0.80422	2.495	0.80722	D	1	D	0.76494	0.999	D	0.80764	0.994	D	0.84976	0.0885	10	0.49607	T	0.09	-44.4129	19.1829	0.93630	0.0:1.0:0.0:0.0	.	133	Q86XI6	PPR3B_HUMAN	I	133	ENSP00000308318:V133I;ENSP00000428642:V133I	ENSP00000308318:V133I	V	-	1	0	PPP1R3B	9036175	1.000000	0.71417	0.964000	0.40570	0.945000	0.59286	6.096000	0.71446	2.780000	0.95670	0.561000	0.74099	GTC		0.488	PPP1R3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251472.1	NM_024607	
MICU3	286097	broad.mit.edu	37	8	16961932	16961932	+	Silent	SNP	T	T	C			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr8:16961932T>C	ENST00000318063.5	+	10	1059	c.1017T>C	c.(1015-1017)gaT>gaC	p.D339D	MICU3_ENST00000519866.1_3'UTR	NM_181723.2	NP_859074.1	Q86XE3	MICU3_HUMAN	mitochondrial calcium uptake family, member 3	339						integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)	calcium ion binding (GO:0005509)	p.D339D(1)									TAGTAACAGATACTACACTTC	0.274																																					p.D339D												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.T1017C	8						.						65.0	67.0	66.0					8																	16961932		2203	4282	6485	17006303	SO:0001819	synonymous_variant	286097	exon10			BC032868	CCDS5999.1	8p22	2013-03-26	2013-03-26	2013-03-14	ENSG00000155970	ENSG00000155970		"""EF-hand domain containing"""	27820	protein-coding gene	gene with protein product		610633	"""EF hand domain family A2"", ""EF-hand domain family, member A2"""	EFHA2		23409044	Standard	NM_181723		Approved	DKFZp313A0139	uc003wxd.2	Q86XE3	OTTHUMG00000096965	ENST00000318063.5:c.1017T>C	8.37:g.16961932T>C		Somatic		Capture	Illumina HiSeq	Phase_I	17006303	NM_181723	Q8IYZ3	Silent	SNP	ENST00000318063.5	37	CCDS5999.1	.	.	.	.	.	.	.	.	.	.	T	9.117	1.007964	0.19199	.	.	ENSG00000155970	ENST00000519044	.	.	.	4.82	1.22	0.21188	.	.	.	.	.	T	0.55016	0.1894	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.46857	-0.9161	4	.	.	.	-8.4556	7.8966	0.29710	0.0:0.3478:0.0:0.6522	.	.	.	.	T	184	.	.	I	+	2	0	EFHA2	17006303	0.995000	0.38212	1.000000	0.80357	0.996000	0.88848	0.237000	0.17985	0.391000	0.25143	0.528000	0.53228	ATA		0.274	MICU3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214031.1	NM_181723	
BMP1	649	broad.mit.edu	37	8	22067133	22067133	+	Silent	SNP	C	C	T	rs376975956		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr8:22067133C>T	ENST00000306385.5	+	19	3421	c.2751C>T	c.(2749-2751)tgC>tgT	p.C917C	BMP1_ENST00000354870.5_3'UTR	NM_006129.4	NP_006120.1	P13497	BMP1_HUMAN	bone morphogenetic protein 1	917	CUB 5. {ECO:0000255|PROSITE- ProRule:PRU00059}.				cartilage condensation (GO:0001502)|cell differentiation (GO:0030154)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|lipoprotein metabolic process (GO:0042157)|multicellular organismal development (GO:0007275)|ossification (GO:0001503)|positive regulation of cartilage development (GO:0061036)|proteolysis (GO:0006508)|skeletal system development (GO:0001501)|small molecule metabolic process (GO:0044281)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|membrane-bounded vesicle (GO:0031988)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|peptidase activity (GO:0008233)|zinc ion binding (GO:0008270)	p.C917C(1)		breast(1)|endometrium(7)|kidney(2)|large_intestine(7)|lung(7)|ovary(2)|prostate(1)|skin(3)	30				Colorectal(74;0.00229)|COAD - Colon adenocarcinoma(73;0.0661)|READ - Rectum adenocarcinoma(644;0.11)		AGACCGACTGCGGCTATGACT	0.652																																					p.C917C												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C2751T	8						.	C		0,4406		0,0,2203	226.0	177.0	193.0		2751	-7.7	0.9	8		193	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	BMP1	NM_006129.4		0,1,6502	TT,TC,CC		0.0116,0.0,0.0077		917/987	22067133	1,13005	2203	4300	6503	22123078	SO:0001819	synonymous_variant	649	exon19				CCDS6026.1, CCDS34856.1	8p21	2013-02-06	2004-08-09		ENSG00000168487	ENSG00000168487	3.4.24.19	"""Bone morphogenetic proteins"""	1067	protein-coding gene	gene with protein product	"""procollagen C-endopeptidase"""	112264	"""procollagen C-endopeptidase"""	PCOLC		2004778	Standard	NM_006129		Approved		uc003xbg.3	P13497	OTTHUMG00000097761	ENST00000306385.5:c.2751C>T	8.37:g.22067133C>T		Somatic		Capture	Illumina HiSeq	Phase_I	22123078	NM_006129	A8K6F5|B2RN46|D3DSR0|Q13292|Q13872|Q14874|Q99421|Q99422|Q99423|Q9UL38	Silent	SNP	ENST00000306385.5	37	CCDS6026.1																																																																																				0.652	BMP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214995.2	NM_006132	
BMP1	649	broad.mit.edu	37	8	22069194	22069194	+	Nonsense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr8:22069194C>T	ENST00000306385.5	+	20	3584	c.2914C>T	c.(2914-2916)Cga>Tga	p.R972*	BMP1_ENST00000354870.5_3'UTR	NM_006129.4	NP_006120.1	P13497	BMP1_HUMAN	bone morphogenetic protein 1	972	CUB 5. {ECO:0000255|PROSITE- ProRule:PRU00059}.				cartilage condensation (GO:0001502)|cell differentiation (GO:0030154)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|lipoprotein metabolic process (GO:0042157)|multicellular organismal development (GO:0007275)|ossification (GO:0001503)|positive regulation of cartilage development (GO:0061036)|proteolysis (GO:0006508)|skeletal system development (GO:0001501)|small molecule metabolic process (GO:0044281)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|membrane-bounded vesicle (GO:0031988)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|peptidase activity (GO:0008233)|zinc ion binding (GO:0008270)	p.R972*(1)		breast(1)|endometrium(7)|kidney(2)|large_intestine(7)|lung(7)|ovary(2)|prostate(1)|skin(3)	30				Colorectal(74;0.00229)|COAD - Colon adenocarcinoma(73;0.0661)|READ - Rectum adenocarcinoma(644;0.11)		TTTCCACCTGCGATACACCAG	0.577																																					p.R972X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.C2914T	8						.						131.0	108.0	116.0					8																	22069194		2203	4300	6503	22125139	SO:0001587	stop_gained	649	exon20				CCDS6026.1, CCDS34856.1	8p21	2013-02-06	2004-08-09		ENSG00000168487	ENSG00000168487	3.4.24.19	"""Bone morphogenetic proteins"""	1067	protein-coding gene	gene with protein product	"""procollagen C-endopeptidase"""	112264	"""procollagen C-endopeptidase"""	PCOLC		2004778	Standard	NM_006129		Approved		uc003xbg.3	P13497	OTTHUMG00000097761	ENST00000306385.5:c.2914C>T	8.37:g.22069194C>T	ENSP00000305714:p.Arg972*	Somatic		Capture	Illumina HiSeq	Phase_I	22125139	NM_006129	A8K6F5|B2RN46|D3DSR0|Q13292|Q13872|Q14874|Q99421|Q99422|Q99423|Q9UL38	Nonsense_Mutation	SNP	ENST00000306385.5	37	CCDS6026.1	.	.	.	.	.	.	.	.	.	.	C	47	13.024673	0.99714	.	.	ENSG00000168487	ENST00000306385	.	.	.	4.7	4.7	0.59300	.	0.000000	0.33534	U	0.004820	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	16.5807	0.84714	0.0:1.0:0.0:0.0	.	.	.	.	X	972	.	ENSP00000305714:R972X	R	+	1	2	BMP1	22125139	1.000000	0.71417	0.999000	0.59377	0.996000	0.88848	7.631000	0.83237	2.441000	0.82636	0.655000	0.94253	CGA		0.577	BMP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214995.2	NM_006132	
NKX3-1	4824	broad.mit.edu	37	8	23539069	23539069	+	Nonsense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr8:23539069G>A	ENST00000380871.4	-	2	407	c.370C>T	c.(370-372)Cag>Tag	p.Q124*	NKX3-1_ENST00000523261.1_Nonsense_Mutation_p.Q49*	NM_006167.3	NP_006158.2	Q99801	NKX31_HUMAN	NK3 homeobox 1	124					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|androgen receptor signaling pathway (GO:0030521)|branching involved in prostate gland morphogenesis (GO:0060442)|branching morphogenesis of an epithelial tube (GO:0048754)|cellular response to drug (GO:0035690)|cellular response to hypoxia (GO:0071456)|cellular response to interleukin-1 (GO:0071347)|cellular response to steroid hormone stimulus (GO:0071383)|cellular response to tumor necrosis factor (GO:0071356)|dorsal aorta development (GO:0035907)|epithelial cell proliferation involved in salivary gland morphogenesis (GO:0060664)|heart development (GO:0007507)|male gonad development (GO:0008584)|metanephros development (GO:0001656)|mitotic cell cycle arrest (GO:0071850)|multicellular organismal development (GO:0007275)|negative regulation of cell proliferation (GO:0008285)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of estrogen receptor binding (GO:0071899)|negative regulation of gene expression (GO:0010629)|negative regulation of insulin-like growth factor receptor signaling pathway (GO:0043569)|negative regulation of mitotic cell cycle (GO:0045930)|negative regulation of transcription, DNA-templated (GO:0045892)|pharyngeal system development (GO:0060037)|positive regulation of androgen secretion (GO:2000836)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of cell death (GO:0010942)|positive regulation of cell division (GO:0051781)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of gene expression (GO:0010628)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitotic cell cycle (GO:0045931)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of response to DNA damage stimulus (GO:2001022)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein kinase B signaling (GO:0043491)|regulation of transcription, DNA-templated (GO:0006355)|response to testosterone (GO:0033574)|salivary gland development (GO:0007431)|somitogenesis (GO:0001756)|steroid hormone mediated signaling pathway (GO:0043401)	intracellular (GO:0005622)|nucleus (GO:0005634)	androgen receptor activity (GO:0004882)|core promoter binding (GO:0001047)|estrogen receptor activity (GO:0030284)|estrogen receptor binding (GO:0030331)|histone deacetylase binding (GO:0042826)|protein kinase activator activity (GO:0030295)|protein self-association (GO:0043621)|RNA polymerase II core promoter sequence-specific DNA binding transcription factor activity (GO:0000983)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|transcription regulatory region sequence-specific DNA binding (GO:0000976)	p.Q124*(1)		large_intestine(3)|lung(4)|prostate(5)|skin(2)	14		Prostate(55;0.114)		Colorectal(74;0.0146)|COAD - Colon adenocarcinoma(73;0.061)|BRCA - Breast invasive adenocarcinoma(99;0.0708)		GAGCGCTTCTGCGGCTGCTTA	0.577																																					p.Q124X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.C370T	8						.						84.0	92.0	89.0					8																	23539069		2203	4300	6503	23595014	SO:0001587	stop_gained	4824	exon2				CCDS6042.1, CCDS59095.1	8p21.2	2012-03-09	2007-07-09	2002-10-04	ENSG00000167034	ENSG00000167034		"""Homeoboxes / ANTP class : NKL subclass"""	7838	protein-coding gene	gene with protein product		602041	"""NK homeobox (Drosophila), family 3, A"", ""NK3 transcription factor related, locus 1 (Drosophila)"""	NKX3A		9226374	Standard	NM_006167		Approved	NKX3.1, BAPX2	uc011kzx.2	Q99801	OTTHUMG00000097851	ENST00000380871.4:c.370C>T	8.37:g.23539069G>A	ENSP00000370253:p.Gln124*	Somatic		Capture	Illumina HiSeq	Phase_I	23595014	NM_006167	O15465|Q9H2P4|Q9H2P5|Q9H2P6|Q9H2P7|Q9HBG0	Nonsense_Mutation	SNP	ENST00000380871.4	37	CCDS6042.1	.	.	.	.	.	.	.	.	.	.	G	23.8	4.456321	0.84317	.	.	ENSG00000167034	ENST00000380871;ENST00000300332;ENST00000523261	.	.	.	5.65	5.65	0.86999	.	0.491185	0.19481	N	0.113204	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.09084	T	0.74	.	17.2626	0.87075	0.0:0.0:1.0:0.0	.	.	.	.	X	124;80;49	.	ENSP00000300332:Q80X	Q	-	1	0	NKX3-1	23595014	0.994000	0.37717	0.953000	0.39169	0.656000	0.38851	2.863000	0.48396	2.941000	0.99782	0.655000	0.94253	CAG		0.577	NKX3-1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215141.2		
ADAM7	8756	broad.mit.edu	37	8	24344824	24344824	+	Missense_Mutation	SNP	A	A	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr8:24344824A>T	ENST00000175238.6	+	11	1168	c.1085A>T	c.(1084-1086)gAt>gTt	p.D362V	ADAM7_ENST00000520720.1_Missense_Mutation_p.D134V|ADAM7_ENST00000380789.1_Missense_Mutation_p.D362V|RP11-561E1.1_ENST00000519364.1_RNA|RP11-624C23.1_ENST00000523578.1_RNA|RP11-624C23.1_ENST00000519689.1_RNA	NM_003817.3	NP_003808.2	Q9H2U9	ADAM7_HUMAN	ADAM metallopeptidase domain 7	362	Peptidase M12B. {ECO:0000255|PROSITE- ProRule:PRU00276}.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)	p.D362V(1)		NS(1)|endometrium(5)|kidney(1)|large_intestine(17)|lung(24)|ovary(1)|skin(15)	64		Prostate(55;0.0181)		Colorectal(74;0.0199)|COAD - Colon adenocarcinoma(73;0.0754)|BRCA - Breast invasive adenocarcinoma(99;0.182)		ATGGACAGTGATGGAAGGTGA	0.483																																					p.D362V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A1085T	8						.						99.0	74.0	82.0					8																	24344824		2203	4300	6503	24400714	SO:0001583	missense	8756	exon11			AF090327	CCDS6045.1	8p21.2	2005-08-18	2005-08-18		ENSG00000069206	ENSG00000069206		"""ADAM metallopeptidase domain containing"""	214	protein-coding gene	gene with protein product		607310	"""a disintegrin and metalloproteinase domain 7"""				Standard	NM_003817		Approved	GP-83, EAPI	uc003xeb.3	Q9H2U9	OTTHUMG00000097859	ENST00000175238.6:c.1085A>T	8.37:g.24344824A>T	ENSP00000175238:p.Asp362Val	Somatic		Capture	Illumina HiSeq	Phase_I	24400714	NM_003817	A8K8X7|O75959|Q6PEJ6	Missense_Mutation	SNP	ENST00000175238.6	37	CCDS6045.1	.	.	.	.	.	.	.	.	.	.	A	4.178	0.031565	0.08101	.	.	ENSG00000069206	ENST00000175238;ENST00000380789;ENST00000520720;ENST00000335595	T;T;T	0.61859	0.07;0.07;0.07	4.93	-3.85	0.04243	Metallopeptidase, catalytic domain (1);Peptidase M12B, ADAM/reprolysin (2);	1.449900	0.03946	N	0.287643	T	0.26011	0.0634	N	0.02865	-0.47	0.29705	N	0.839866	B;B	0.30146	0.27;0.27	B;B	0.28011	0.054;0.085	T	0.04005	-1.0985	10	0.24483	T	0.36	.	1.3625	0.02194	0.4093:0.216:0.2429:0.1318	.	134;362	E5RK87;Q9H2U9	.;ADAM7_HUMAN	V	362;362;134;177	ENSP00000175238:D362V;ENSP00000370166:D362V;ENSP00000430400:D134V	ENSP00000175238:D362V	D	+	2	0	ADAM7	24400714	0.000000	0.05858	0.000000	0.03702	0.052000	0.14988	-1.733000	0.01850	-1.393000	0.02079	-0.415000	0.06103	GAT		0.483	ADAM7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215150.1	NM_003817	
BNIP3L	665	broad.mit.edu	37	8	26252748	26252748	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr8:26252748C>A	ENST00000380629.2	+	3	520	c.287C>A	c.(286-288)cCt>cAt	p.P96H	BNIP3L_ENST00000518611.1_Missense_Mutation_p.P56H|BNIP3L_ENST00000520409.1_Missense_Mutation_p.P56H|BNIP3L_ENST00000523515.1_Missense_Mutation_p.P56H	NM_004331.2	NP_004322.1	O60238	BNI3L_HUMAN	BCL2/adenovirus E1B 19kDa interacting protein 3-like	96					defense response to virus (GO:0051607)|mitochondrial outer membrane permeabilization (GO:0097345)|mitochondrial protein catabolic process (GO:0035694)|negative regulation of apoptotic process (GO:0043066)|positive regulation of apoptotic process (GO:0043065)|viral process (GO:0016032)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|intrinsic component of membrane (GO:0031224)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|nuclear envelope (GO:0005635)	identical protein binding (GO:0042802)|lamin binding (GO:0005521)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)	p.P96H(1)		large_intestine(3)|lung(1)	4		all_cancers(63;0.086)|Ovarian(32;2.61e-05)|all_epithelial(46;0.0514)|Prostate(55;0.157)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0019)|Epithelial(17;1.59e-12)|all cancers(2;3.75e-11)|OV - Ovarian serous cystadenocarcinoma(2;2.57e-08)|Colorectal(74;0.135)		TCTTCTAGCCCTTCGCCACAA	0.403																																					p.P96H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C287A	8						.						76.0	68.0	71.0					8																	26252748		2203	4300	6503	26308665	SO:0001583	missense	665	exon3			AB004788	CCDS6050.1	8p21	2014-05-13	2002-08-29		ENSG00000104765	ENSG00000104765			1085	protein-coding gene	gene with protein product		605368	"""BCL2/adenovirus E1B 19kD-interacting protein 3-like"""			9523198, 9973195	Standard	NM_004331		Approved	Nix, BNIP3a	uc003xex.1	O60238	OTTHUMG00000099433	ENST00000380629.2:c.287C>A	8.37:g.26252748C>A	ENSP00000370003:p.Pro96His	Somatic		Capture	Illumina HiSeq	Phase_I	26308665	NM_004331	B0AZS9|Q5JW63|Q8NF87	Missense_Mutation	SNP	ENST00000380629.2	37	CCDS6050.1	.	.	.	.	.	.	.	.	.	.	C	22.7	4.322803	0.81580	.	.	ENSG00000104765	ENST00000380629;ENST00000221209;ENST00000523949;ENST00000523515;ENST00000520409;ENST00000518611	.	.	.	6.07	6.07	0.98685	.	0.000000	0.85682	D	0.000000	D	0.85155	0.5632	M	0.87547	2.89	0.80722	D	1	D	0.89917	1.0	D	0.76071	0.987	D	0.84745	0.0753	9	0.49607	T	0.09	.	20.6593	0.99626	0.0:1.0:0.0:0.0	.	96	O60238	BNI3L_HUMAN	H	96;96;74;56;56;56	.	ENSP00000221209:P96H	P	+	2	0	BNIP3L	26308665	1.000000	0.71417	1.000000	0.80357	0.781000	0.44180	4.995000	0.63908	2.885000	0.99019	0.655000	0.94253	CCT		0.403	BNIP3L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216895.1	NM_004331	
DPYSL2	1808	broad.mit.edu	37	8	26484796	26484796	+	Silent	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr8:26484796C>T	ENST00000311151.5	+	6	1018	c.606C>T	c.(604-606)ggC>ggT	p.G202G	DPYSL2_ENST00000521983.1_3'UTR|DPYSL2_ENST00000521913.1_Silent_p.G166G|DPYSL2_ENST00000523027.1_Silent_p.G166G	NM_001386.5	NP_001377.1	Q16555	DPYL2_HUMAN	dihydropyrimidinase-like 2	202					axon guidance (GO:0007411)|cytoskeleton organization (GO:0007010)|endocytosis (GO:0006897)|nervous system development (GO:0007399)|nucleobase-containing compound metabolic process (GO:0006139)|olfactory bulb development (GO:0021772)|positive regulation of glutamate secretion (GO:0014049)|pyrimidine nucleobase catabolic process (GO:0006208)|regulation of neuron differentiation (GO:0045664)|response to amphetamine (GO:0001975)|response to cocaine (GO:0042220)|response to drug (GO:0042493)|signal transduction (GO:0007165)|spinal cord development (GO:0021510)|synaptic vesicle transport (GO:0048489)	axon (GO:0030424)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|dendrite (GO:0030425)|extracellular vesicular exosome (GO:0070062)|growth cone (GO:0030426)|membrane (GO:0016020)|mitochondrion (GO:0005739)|neuronal cell body (GO:0043025)|protein complex (GO:0043234)	dihydropyrimidinase activity (GO:0004157)	p.G202G(2)		breast(1)|endometrium(5)|large_intestine(8)|lung(3)|prostate(1)|skin(1)|stomach(1)	20		all_cancers(63;0.121)|Ovarian(32;2.68e-05)|all_epithelial(46;0.116)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0228)|Epithelial(17;3.33e-10)|Colorectal(74;0.183)		CAGAAAATGGCGACATCATTG	0.498																																					p.G202G												.	.	2	Substitution - coding silent(2)	large_intestine(1)|endometrium(1)	c.C606T	8						.						139.0	126.0	131.0					8																	26484796		2203	4300	6503	26540713	SO:0001819	synonymous_variant	1808	exon6			D78013	CCDS6051.1, CCDS59096.1	8p22-p21	2011-09-28			ENSG00000092964	ENSG00000092964			3014	protein-coding gene	gene with protein product		602463				8973361	Standard	NM_001197293		Approved	DRP-2, DHPRP2, CRMP2, DRP2	uc003xfa.3	Q16555	OTTHUMG00000099439	ENST00000311151.5:c.606C>T	8.37:g.26484796C>T		Somatic		Capture	Illumina HiSeq	Phase_I	26540713	NM_001386	A8K5H2|B4DR31|D3DSS7|O00424	Silent	SNP	ENST00000311151.5	37	CCDS6051.1																																																																																				0.498	DPYSL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216904.3	NM_001386	
ADRA1A	148	broad.mit.edu	37	8	26722159	26722159	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr8:26722159A>G	ENST00000519229.1	-	1	334	c.328T>C	c.(328-330)Tgc>Cgc	p.C110R	ADRA1A_ENST00000380572.3_Missense_Mutation_p.C110R|ADRA1A_ENST00000358857.5_Missense_Mutation_p.C110R|ADRA1A_ENST00000380582.3_Missense_Mutation_p.C110R|ADRA1A_ENST00000380581.2_Missense_Mutation_p.C110R|ADRA1A_ENST00000380587.1_Missense_Mutation_p.C110R|ADRA1A_ENST00000354550.4_Missense_Mutation_p.C110R|ADRA1A_ENST00000380586.1_Missense_Mutation_p.C110R|ADRA1A_ENST00000276393.4_Missense_Mutation_p.C110R|ADRA1A_ENST00000380573.3_Missense_Mutation_p.C110R			P25100	ADA1D_HUMAN	adrenoceptor alpha 1A	180					adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|adrenergic receptor signaling pathway (GO:0071875)|cell proliferation (GO:0008283)|cell-cell signaling (GO:0007267)|DNA metabolic process (GO:0006259)|G-protein coupled receptor signaling pathway (GO:0007186)|multicellular organismal development (GO:0007275)|negative regulation of the force of heart contraction involved in baroreceptor response to increased systemic arterial blood pressure (GO:0001986)|norepinephrine-epinephrine vasoconstriction involved in regulation of systemic arterial blood pressure (GO:0001994)|positive regulation of cell proliferation (GO:0008284)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	alpha1-adrenergic receptor activity (GO:0004937)	p.C110R(2)		breast(2)|endometrium(3)|kidney(1)|large_intestine(10)|lung(17)|ovary(1)|prostate(1)|skin(1)	36		all_cancers(63;0.122)|Ovarian(32;2.61e-05)|all_epithelial(46;0.118)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0228)|Epithelial(17;4.92e-10)|Colorectal(74;0.0132)|READ - Rectum adenocarcinoma(644;0.115)	Alfuzosin(DB00346)|Amitriptyline(DB00321)|Amoxapine(DB00543)|Amphetamine(DB00182)|Bromocriptine(DB01200)|Cabergoline(DB00248)|Carvedilol(DB01136)|Chlorpromazine(DB00477)|Clonidine(DB00575)|Dapiprazole(DB00298)|Desipramine(DB01151)|Doxazosin(DB00590)|Doxepin(DB01142)|Dronedarone(DB04855)|Droxidopa(DB06262)|Epinephrine(DB00668)|Ergoloid mesylate(DB01049)|Ergotamine(DB00696)|Fenoldopam(DB00800)|Imipramine(DB00458)|Labetalol(DB00598)|Maprotiline(DB00934)|Mephentermine(DB01365)|Methotrimeprazine(DB01403)|Methoxamine(DB00723)|Mianserin(DB06148)|Midodrine(DB00211)|Mirtazapine(DB00370)|Nicardipine(DB00622)|Norepinephrine(DB00368)|Nortriptyline(DB00540)|Oxymetazoline(DB00935)|Pergolide(DB01186)|Phenoxybenzamine(DB00925)|Phenylephrine(DB00388)|Prazosin(DB00457)|Promazine(DB00420)|Propiomazine(DB00777)|Quetiapine(DB01224)|Sertindole(DB06144)|Silodosin(DB06207)|Tamsulosin(DB00706)|Terazosin(DB01162)|Xylometazoline(DB06694)	GACGCGGTGCAGCACAGCACA	0.632																																					p.C110R												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.T328C	8						.						104.0	96.0	99.0					8																	26722159		2203	4300	6503	26778076	SO:0001583	missense	148	exon1			L31774	CCDS6052.1, CCDS6053.1, CCDS6054.1, CCDS34869.1	8p21.2	2012-08-08	2012-05-09		ENSG00000120907	ENSG00000120907		"""GPCR / Class A : Adrenoceptors : alpha"""	277	protein-coding gene	gene with protein product		104221	"""adrenergic, alpha-1A-, receptor"""	ADRA1C			Standard	NM_033303		Approved	ADRA1L1	uc003xfh.1	P35348	OTTHUMG00000099459	ENST00000519229.1:c.328T>C	8.37:g.26722159A>G	ENSP00000430793:p.Cys110Arg	Somatic		Capture	Illumina HiSeq	Phase_I	26778076	NM_033302	Q9NPY0	Missense_Mutation	SNP	ENST00000519229.1	37		.	.	.	.	.	.	.	.	.	.	A	19.51	3.840316	0.71488	.	.	ENSG00000120907	ENST00000380586;ENST00000380587;ENST00000380582;ENST00000380581;ENST00000519229;ENST00000354550;ENST00000276393;ENST00000380573;ENST00000380572;ENST00000358857	T;T;T;T;T;T;T;T;T;T	0.73575	-0.76;-0.76;-0.76;-0.76;-0.76;-0.76;-0.76;-0.76;-0.76;-0.76	4.83	4.83	0.62350	GPCR, rhodopsin-like superfamily (1);	0.000000	0.85682	D	0.000000	D	0.89863	0.6838	H	0.95712	3.71	0.80722	D	1	D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D	0.97110	1.0;1.0;1.0;1.0;0.999;1.0	D	0.92827	0.6277	10	0.87932	D	0	.	14.3686	0.66823	1.0:0.0:0.0:0.0	.	110;110;110;110;110;110	P35348-9;P35348-8;P35348;P35348-4;P35348-3;B0ZBD3	.;.;ADA1A_HUMAN;.;.;.	R	110	ENSP00000369960:C110R;ENSP00000369961:C110R;ENSP00000369956:C110R;ENSP00000369955:C110R;ENSP00000430793:C110R;ENSP00000346557:C110R;ENSP00000276393:C110R;ENSP00000369947:C110R;ENSP00000369946:C110R;ENSP00000351725:C110R	ENSP00000276393:C110R	C	-	1	0	ADRA1A	26778076	1.000000	0.71417	1.000000	0.80357	0.969000	0.65631	9.287000	0.95975	1.916000	0.55485	0.460000	0.39030	TGC		0.632	ADRA1A-009	PUTATIVE	not_organism_supported|basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000376207.1	NM_033303	
EPHX2	2053	broad.mit.edu	37	8	27398101	27398101	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr8:27398101C>A	ENST00000521400.1	+	15	1737	c.1307C>A	c.(1306-1308)cCc>cAc	p.P436H	EPHX2_ENST00000517536.1_Missense_Mutation_p.P253H|EPHX2_ENST00000521780.1_Missense_Mutation_p.P370H|EPHX2_ENST00000518379.1_Missense_Mutation_p.P404H|EPHX2_ENST00000380476.3_Missense_Mutation_p.P383H	NM_001979.5	NP_001970.2	P34913	HYES_HUMAN	epoxide hydrolase 2, cytoplasmic	436	Epoxide hydrolase.				arachidonic acid metabolic process (GO:0019369)|cellular calcium ion homeostasis (GO:0006874)|cholesterol homeostasis (GO:0042632)|dephosphorylation (GO:0016311)|drug metabolic process (GO:0017144)|epoxygenase P450 pathway (GO:0019373)|inflammatory response (GO:0006954)|phospholipid dephosphorylation (GO:0046839)|positive regulation of gene expression (GO:0010628)|positive regulation of vasodilation (GO:0045909)|reactive oxygen species metabolic process (GO:0072593)|regulation of blood pressure (GO:0008217)|regulation of cholesterol metabolic process (GO:0090181)|response to toxic substance (GO:0009636)|small molecule metabolic process (GO:0044281)|stilbene catabolic process (GO:0046272)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|peroxisome (GO:0005777)	10-hydroxy-9-(phosphonooxy)octadecanoate phosphatase activity (GO:0033885)|epoxide hydrolase activity (GO:0004301)|lipid phosphatase activity (GO:0042577)|magnesium ion binding (GO:0000287)|phosphatase activity (GO:0016791)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)|toxic substance binding (GO:0015643)	p.P436L(1)|p.P436H(1)		cervix(1)|endometrium(8)|kidney(1)|large_intestine(1)|lung(8)|ovary(1)|skin(5)|stomach(1)|urinary_tract(1)	27		Ovarian(32;2.61e-05)|all_epithelial(46;0.207)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0226)|Epithelial(17;1.12e-09)|Colorectal(74;0.157)		CCAGAAGAGCCCAGCCTCAGC	0.512																																					p.P436H												.	.	2	Substitution - Missense(2)	large_intestine(1)|skin(1)	c.C1307A	8						.						89.0	91.0	90.0					8																	27398101		2203	4300	6503	27454018	SO:0001583	missense	2053	exon15			L05779	CCDS6060.1, CCDS59097.1, CCDS59098.1	8p21	2010-04-23			ENSG00000120915	ENSG00000120915	3.3.2.10		3402	protein-coding gene	gene with protein product		132811					Standard	NM_001979		Approved		uc003xfu.4	P34913	OTTHUMG00000102115	ENST00000521400.1:c.1307C>A	8.37:g.27398101C>A	ENSP00000430269:p.Pro436His	Somatic		Capture	Illumina HiSeq	Phase_I	27454018	NM_001979	B2Z3B1|B3KTU8|B3KUA0|G3V134|J3KPH7|Q16764|Q9HBJ1|Q9HBJ2	Missense_Mutation	SNP	ENST00000521400.1	37	CCDS6060.1	.	.	.	.	.	.	.	.	.	.	C	19.80	3.894491	0.72639	.	.	ENSG00000120915	ENST00000521400;ENST00000517536;ENST00000521780;ENST00000380476;ENST00000415449;ENST00000518379	T;T;T;T;T	0.64438	-0.1;-0.1;-0.1;-0.1;-0.1	5.79	5.79	0.91817	Alpha/beta hydrolase fold-1 (1);	0.335703	0.36034	N	0.002833	T	0.79405	0.4440	M	0.80847	2.515	0.51012	D	0.999903	D;D	0.76494	0.999;0.999	D;D	0.74674	0.984;0.975	T	0.79193	-0.1904	10	0.44086	T	0.13	-7.454	15.524	0.75887	0.0:1.0:0.0:0.0	.	404;436	E5RFU2;P34913	.;HYES_HUMAN	H	436;253;370;383;383;404	ENSP00000430269:P436H;ENSP00000428875:P253H;ENSP00000430302:P370H;ENSP00000369843:P383H;ENSP00000427956:P404H	ENSP00000369843:P383H	P	+	2	0	EPHX2	27454018	0.444000	0.25649	0.999000	0.59377	0.838000	0.47535	2.938000	0.48987	2.729000	0.93468	0.455000	0.32223	CCC		0.512	EPHX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219954.4		
CLU	1191	broad.mit.edu	37	8	27457326	27457326	+	Missense_Mutation	SNP	C	C	T	rs146625005		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr8:27457326C>T	ENST00000316403.10	-	7	1540	c.1135G>A	c.(1135-1137)Gaa>Aaa	p.E379K	CLU_ENST00000405140.3_Missense_Mutation_p.E379K|CLU_ENST00000560366.1_Missense_Mutation_p.E431K|CLU_ENST00000523500.1_Missense_Mutation_p.E379K|CLU_ENST00000546343.1_Missense_Mutation_p.E390K			P10909	CLUS_HUMAN	clusterin	379					blood coagulation (GO:0007596)|cell morphogenesis (GO:0000902)|central nervous system myelin maintenance (GO:0032286)|chaperone-mediated protein complex assembly (GO:0051131)|chaperone-mediated protein folding (GO:0061077)|complement activation (GO:0006956)|complement activation, classical pathway (GO:0006958)|innate immune response (GO:0045087)|intrinsic apoptotic signaling pathway (GO:0097193)|lipid metabolic process (GO:0006629)|microglial cell activation (GO:0001774)|microglial cell proliferation (GO:0061518)|negative regulation of beta-amyloid formation (GO:1902430)|negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage (GO:1902230)|negative regulation of protein homooligomerization (GO:0032463)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of apoptotic process (GO:0043065)|positive regulation of beta-amyloid formation (GO:1902004)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of neurofibrillary tangle assembly (GO:1902998)|positive regulation of neuron death (GO:1901216)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of tau-protein kinase activity (GO:1902949)|positive regulation of tumor necrosis factor production (GO:0032760)|protein import (GO:0017038)|protein stabilization (GO:0050821)|regulation of beta-amyloid clearance (GO:1900221)|regulation of neuron death (GO:1901214)|regulation of neuronal signal transduction (GO:1902847)|release of cytochrome c from mitochondria (GO:0001836)|response to misfolded protein (GO:0051788)|response to virus (GO:0009615)|reverse cholesterol transport (GO:0043691)	apical dendrite (GO:0097440)|blood microparticle (GO:0072562)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrion (GO:0005739)|neurofibrillary tangle (GO:0097418)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|platelet alpha granule lumen (GO:0031093)|spherical high-density lipoprotein particle (GO:0034366)	misfolded protein binding (GO:0051787)|ubiquitin protein ligase binding (GO:0031625)	p.E431K(1)		endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(8)|ovary(2)	21		Ovarian(32;2.61e-05)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0204)|Colorectal(74;0.132)		TACTGGTCTTCGCCTTGCGTG	0.602													C|||	1	0.000199681	0.0008	0.0	5008	,	,		19404	0.0		0.0	False		,,,				2504	0.0				p.E390K												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1168A	8						.	C	LYS/GLU	4,4402	6.2+/-15.9	0,4,2199	73.0	58.0	63.0		1135	-1.3	0.0	8	dbSNP_134	63	0,8600		0,0,4300	yes	missense	CLU	NM_203339.2	56	0,4,6499	TT,TC,CC		0.0,0.0908,0.0308	benign	379/450	27457326	4,13002	2203	4300	6503	27513243	SO:0001583	missense	1191	exon7			M64722	CCDS47832.1	8p21-p12	2012-11-30	2006-02-10		ENSG00000120885	ENSG00000120885			2095	protein-coding gene	gene with protein product	"""complement lysis inhibitor"", ""sulfated glycoprotein 2"", ""testosterone-repressed prostate message 2"", ""apolipoprotein J"""	185430	"""clusterin (complement lysis inhibitor, SP-40,40, sulfated glycoprotein 2, testosterone-repressed prostate message 2, apolipoprotein J)"""	CLI, APOJ		1585460	Standard	NR_038335		Approved	SGP-2, SP-40, TRPM-2, KUB1, CLU1, CLU2	uc003xfz.2	P10909	OTTHUMG00000102114	ENST00000316403.10:c.1135G>A	8.37:g.27457326C>T	ENSP00000315130:p.Glu379Lys	Somatic		Capture	Illumina HiSeq	Phase_I	27513243	NM_001171138	B2R9Q1|B3KSE6|P11380|P11381|Q2TU75|Q5HYC1|Q7Z5B9	Missense_Mutation	SNP	ENST00000316403.10	37	CCDS47832.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	10.48|10.48	1.360840|1.360840	0.24598|0.24598	9.08E-4|9.08E-4	0.0|0.0	ENSG00000120885|ENSG00000120885	ENST00000316403;ENST00000546343;ENST00000405140;ENST00000523500;ENST00000380446;ENST00000520012|ENST00000522098	T;T;T|.	0.22743|.	1.94;1.95;1.95|.	5.62|5.62	-1.34|-1.34	0.09143|0.09143	Clusterin, C-terminal (1);|.	1.317630|.	0.05186|.	N|.	0.502222|.	T|T	0.30417|0.30417	0.0764|0.0764	L|L	0.37750|0.37750	1.13|1.13	0.09310|0.09310	N|N	1|1	B;P;P;P|.	0.51791|.	0.271;0.948;0.948;0.844|.	B;B;B;B|.	0.42771|.	0.035;0.397;0.325;0.195|.	T|T	0.30446|0.30446	-0.9978|-0.9978	10|5	0.11182|.	T|.	0.66|.	-1.8795|-1.8795	5.1021|5.1021	0.14764|0.14764	0.0:0.2278:0.3231:0.4491|0.0:0.2278:0.3231:0.4491	.|.	244;431;390;379|.	E7ETA7;P10909-2;P10909-5;P10909|.	.;.;.;CLUS_HUMAN|.	K|Q	431;390;379;379;204;244|241	ENSP00000446413:E390K;ENSP00000385419:E379K;ENSP00000429620:E379K|.	ENSP00000315130:E431K|.	E|R	-|-	1|2	0|0	CLU|CLU	27513243|27513243	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.069000|0.069000	0.16628|0.16628	-0.021000|-0.021000	0.12504|0.12504	-0.158000|-0.158000	0.11040|0.11040	-0.830000|-0.830000	0.03078|0.03078	GAA|CGA		0.602	CLU-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219953.3	NM_001831	
SCARA3	51435	broad.mit.edu	37	8	27528637	27528637	+	Silent	SNP	T	T	C			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr8:27528637T>C	ENST00000301904.3	+	6	1610	c.1590T>C	c.(1588-1590)acT>acC	p.T530T	SCARA3_ENST00000337221.4_Intron	NM_016240.2	NP_057324.2	Q6AZY7	SCAR3_HUMAN	scavenger receptor class A, member 3	530					receptor-mediated endocytosis (GO:0006898)|response to oxidative stress (GO:0006979)|UV protection (GO:0009650)	collagen trimer (GO:0005581)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	scavenger receptor activity (GO:0005044)	p.T530T(1)		breast(1)|large_intestine(3)|ovary(1)|skin(3)|upper_aerodigestive_tract(1)	9		Ovarian(32;2.61e-05)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0219)|Colorectal(74;0.148)		GCTTTGGAACTGGAGGGCCGA	0.677																																					p.T530T												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.T1590C	8						.						9.0	11.0	10.0					8																	27528637		2176	4243	6419	27584556	SO:0001819	synonymous_variant	51435	exon6			AB007829	CCDS34870.1, CCDS34871.1	8p21	2010-03-24			ENSG00000168077	ENSG00000168077			19000	protein-coding gene	gene with protein product	"""macrophage scavenger receptor-like 1"""	602728				9747040, 9580669	Standard	NM_182826		Approved	CSR1, CSR, MSLR1, APC7, MSRL1	uc003xga.1	Q6AZY7	OTTHUMG00000163898	ENST00000301904.3:c.1590T>C	8.37:g.27528637T>C		Somatic		Capture	Illumina HiSeq	Phase_I	27584556	NM_016240	Q9UM15|Q9UM16	Silent	SNP	ENST00000301904.3	37	CCDS34871.1																																																																																				0.677	SCARA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376258.2	NM_016240	
EXTL3	2137	broad.mit.edu	37	8	28608183	28608183	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr8:28608183C>T	ENST00000220562.4	+	7	3462	c.2560C>T	c.(2560-2562)Cgg>Tgg	p.R854W	EXTL3_ENST00000523149.1_Missense_Mutation_p.R470W|EXTL3_ENST00000519886.1_Intron	NM_001440.2	NP_001431.1	O43909	EXTL3_HUMAN	exostosin-like glycosyltransferase 3	854					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|heparan sulfate proteoglycan biosynthetic process (GO:0015012)|positive regulation of cell growth (GO:0030307)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|intrinsic component of endoplasmic reticulum membrane (GO:0031227)	glucuronyl-galactosyl-proteoglycan 4-alpha-N-acetylglucosaminyltransferase activity (GO:0001888)|metal ion binding (GO:0046872)	p.R854W(1)		biliary_tract(1)|endometrium(3)|kidney(2)|large_intestine(15)|lung(8)|ovary(1)|prostate(2)|skin(2)|soft_tissue(1)|urinary_tract(1)	36		Ovarian(32;0.069)		KIRC - Kidney renal clear cell carcinoma(542;0.107)|Kidney(114;0.129)|Colorectal(74;0.228)		GGTGACCTCACGGTGGACATT	0.557																																					p.R854W												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C2560T	8						.						97.0	82.0	87.0					8																	28608183		2203	4300	6503	28664102	SO:0001583	missense	2137	exon7			U76188	CCDS6070.1	8p22-p12	2013-03-01	2013-03-01		ENSG00000012232	ENSG00000012232	2.4.1.223	"""Exostosin glycosyltransferase family"""	3518	protein-coding gene	gene with protein product	"""REG receptor"", ""glucuronyl-galactosyl-proteoglycan 4-alpha-N-acetylglucosaminyltransferase"""	605744	"""exostoses (multiple)-like 3"""			9479495, 9450183, 11257457	Standard	NM_001440		Approved	botv, REGR	uc003xgz.2	O43909	OTTHUMG00000102146	ENST00000220562.4:c.2560C>T	8.37:g.28608183C>T	ENSP00000220562:p.Arg854Trp	Somatic		Capture	Illumina HiSeq	Phase_I	28664102	NM_001440	D3DST8|O00225|Q53XT3	Missense_Mutation	SNP	ENST00000220562.4	37	CCDS6070.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	16.86|16.86	3.240202|3.240202	0.58995|0.58995	.|.	.|.	ENSG00000012232|ENSG00000012232	ENST00000523149;ENST00000220562;ENST00000517738|ENST00000521473	T;T;D|.	0.86562|.	-1.2;-1.2;-2.14|.	5.49|5.49	2.55|2.55	0.30701|0.30701	EXTL2, alpha-1,4-N-acetylhexosaminyltransferase (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	D|D	0.82802|0.82802	0.5116|0.5116	M|M	0.92026|0.92026	3.265|3.265	0.80722|0.80722	D|D	1|1	D|.	0.89917|.	1.0|.	D|.	0.97110|.	1.0|.	D|D	0.85190|0.85190	0.1009|0.1009	10|5	0.72032|.	D|.	0.01|.	-25.4195|-25.4195	14.3216|14.3216	0.66489|0.66489	0.3897:0.6103:0.0:0.0|0.3897:0.6103:0.0:0.0	.|.	854|.	O43909|.	EXTL3_HUMAN|.	W|M	470;854;100|144	ENSP00000428691:R470W;ENSP00000220562:R854W;ENSP00000430652:R100W|.	ENSP00000220562:R854W|.	R|T	+|+	1|2	2|0	EXTL3|EXTL3	28664102|28664102	0.993000|0.993000	0.37304|0.37304	0.706000|0.706000	0.30403|0.30403	0.394000|0.394000	0.30568|0.30568	3.128000|3.128000	0.50492|0.50492	0.217000|0.217000	0.20800|0.20800	-0.324000|-0.324000	0.08512|0.08512	CGG|ACG		0.557	EXTL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219987.3	NM_001440	
WRN	7486	broad.mit.edu	37	8	30977906	30977906	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr8:30977906G>A	ENST00000298139.5	+	21	2845	c.2596G>A	c.(2596-2598)Gtc>Atc	p.V866I		NM_000553.4	NP_000544.2	Q14191	WRN_HUMAN	Werner syndrome, RecQ helicase-like	866	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.				aging (GO:0007568)|ATP catabolic process (GO:0006200)|base-excision repair (GO:0006284)|cell aging (GO:0007569)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to gamma radiation (GO:0071480)|cellular response to starvation (GO:0009267)|DNA duplex unwinding (GO:0032508)|DNA metabolic process (GO:0006259)|DNA recombination (GO:0006310)|DNA replication (GO:0006260)|DNA synthesis involved in DNA repair (GO:0000731)|double-strand break repair (GO:0006302)|multicellular organismal aging (GO:0010259)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|nucleolus to nucleoplasm transport (GO:0032066)|positive regulation of hydrolase activity (GO:0051345)|regulation of apoptotic process (GO:0042981)|regulation of growth rate (GO:0040009)|replication fork processing (GO:0031297)|replicative cell aging (GO:0001302)|response to oxidative stress (GO:0006979)|response to UV-C (GO:0010225)|telomere maintenance (GO:0000723)	centrosome (GO:0005813)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)	3'-5' DNA helicase activity (GO:0043138)|3'-5' exonuclease activity (GO:0008408)|ATP binding (GO:0005524)|ATP-dependent 3'-5' DNA helicase activity (GO:0043140)|ATP-dependent DNA helicase activity (GO:0004003)|ATPase activity (GO:0016887)|bubble DNA binding (GO:0000405)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)|exonuclease activity (GO:0004527)|four-way junction helicase activity (GO:0009378)|G-quadruplex DNA binding (GO:0051880)|helicase activity (GO:0004386)|magnesium ion binding (GO:0000287)|manganese ion binding (GO:0030145)|protein complex binding (GO:0032403)|protein homodimerization activity (GO:0042803)|Y-form DNA binding (GO:0000403)	p.V866I(1)		central_nervous_system(2)|endometrium(4)|kidney(4)|large_intestine(13)|lung(28)|ovary(3)|skin(3)|upper_aerodigestive_tract(3)	60		Breast(100;0.195)		KIRC - Kidney renal clear cell carcinoma(542;0.147)|Kidney(114;0.176)|Colorectal(111;0.192)		TTCTTGTCACGTCCTCTGGGC	0.378			"""Mis, N, F, S"""			"""osteosarcoma, meningioma, others"""		Genes defective in diseases associated with sensitivity to DNA damaging agents	Werner syndrome																												p.V866I	Ovarian(18;161 598 2706 14834 27543)	yes	Rec		Werner Syndrome	8	8p12-p11.2	7486	Werner syndrome (RECQL2)		"""L, E, M, O"""	.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2596A	8						.						95.0	90.0	91.0					8																	30977906		2203	4299	6502	31097448	SO:0001583	missense	7486	exon21	Familial Cancer Database	WS, Adult Progeria		CCDS6082.1	8p12	2014-09-17	2009-03-19		ENSG00000165392	ENSG00000165392			12791	protein-coding gene	gene with protein product		604611	"""Werner syndrome"""			9288107	Standard	NM_000553		Approved	RECQL2, RECQ3	uc003xio.4	Q14191	OTTHUMG00000163894	ENST00000298139.5:c.2596G>A	8.37:g.30977906G>A	ENSP00000298139:p.Val866Ile	Somatic		Capture	Illumina HiSeq	Phase_I	31097448	NM_000553	A1KYY9	Missense_Mutation	SNP	ENST00000298139.5	37	CCDS6082.1	.	.	.	.	.	.	.	.	.	.	G	6.493	0.459076	0.12342	.	.	ENSG00000165392	ENST00000298139	T	0.04654	3.58	5.76	-8.39	0.00969	Helicase, C-terminal (1);	1.334170	0.05168	N	0.499071	T	0.03220	0.0094	N	0.26092	0.79	0.09310	N	1	B;B	0.20887	0.002;0.049	B;B	0.16722	0.007;0.016	T	0.39820	-0.9595	10	0.44086	T	0.13	0.4006	5.9521	0.19253	0.1071:0.4025:0.3103:0.1801	.	276;866	Q59F09;Q14191	.;WRN_HUMAN	I	866	ENSP00000298139:V866I	ENSP00000298139:V866I	V	+	1	0	WRN	31097448	0.000000	0.05858	0.000000	0.03702	0.031000	0.12232	-1.511000	0.02260	-2.056000	0.00898	-2.086000	0.00376	GTC		0.378	WRN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376248.1		
NRG1	3084	broad.mit.edu	37	8	32611938	32611938	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr8:32611938G>A	ENST00000405005.3	+	8	749	c.749G>A	c.(748-750)tGc>tAc	p.C250Y	NRG1_ENST00000287842.3_Missense_Mutation_p.C247Y|NRG1_ENST00000287845.5_Missense_Mutation_p.C221Y|NRG1_ENST00000523079.1_Missense_Mutation_p.C247Y|NRG1_ENST00000341377.5_3'UTR|NRG1_ENST00000521670.1_Missense_Mutation_p.C250Y|NRG1_ENST00000338921.4_Missense_Mutation_p.C258Y|NRG1_ENST00000356819.4_Missense_Mutation_p.C255Y|NRG1_ENST00000539990.1_Missense_Mutation_p.C93Y|NRG1_ENST00000519301.1_Missense_Mutation_p.C200Y			Q02297	NRG1_HUMAN	neuregulin 1	250					activation of transmembrane receptor protein tyrosine kinase activity (GO:0007171)|cardiac conduction system development (GO:0003161)|cardiac muscle cell differentiation (GO:0055007)|cardiac muscle cell myoblast differentiation (GO:0060379)|cell communication (GO:0007154)|cell migration (GO:0016477)|cell morphogenesis (GO:0000902)|cell proliferation (GO:0008283)|cellular protein complex disassembly (GO:0043624)|embryo development (GO:0009790)|endocardial cell differentiation (GO:0060956)|epidermal growth factor receptor signaling pathway (GO:0007173)|ERBB signaling pathway (GO:0038127)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glial cell fate commitment (GO:0021781)|innate immune response (GO:0045087)|locomotory behavior (GO:0007626)|mammary gland development (GO:0030879)|MAPK cascade (GO:0000165)|negative regulation of cardiac muscle cell apoptotic process (GO:0010667)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|negative regulation of protein catabolic process (GO:0042177)|negative regulation of secretion (GO:0051048)|negative regulation of transcription, DNA-templated (GO:0045892)|nervous system development (GO:0007399)|neural crest cell development (GO:0014032)|neuron fate commitment (GO:0048663)|neurotransmitter receptor metabolic process (GO:0045213)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peripheral nervous system development (GO:0007422)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell growth (GO:0030307)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein tyrosine kinase activity (GO:0061098)|positive regulation of Ras protein signal transduction (GO:0046579)|positive regulation of striated muscle cell differentiation (GO:0051155)|regulation of protein heterodimerization activity (GO:0043497)|regulation of protein homodimerization activity (GO:0043496)|synapse assembly (GO:0007416)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|ventricular cardiac muscle cell differentiation (GO:0055012)|ventricular trabecula myocardium morphogenesis (GO:0003222)|wound healing (GO:0042060)	apical plasma membrane (GO:0016324)|axon (GO:0030424)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|neuromuscular junction (GO:0031594)|nucleus (GO:0005634)	cytokine activity (GO:0005125)|ErbB-3 class receptor binding (GO:0043125)|growth factor activity (GO:0008083)|protein tyrosine kinase activator activity (GO:0030296)|receptor binding (GO:0005102)|receptor tyrosine kinase binding (GO:0030971)|transcription cofactor activity (GO:0003712)|transmembrane receptor protein tyrosine kinase activator activity (GO:0030297)	p.C255Y(1)		endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(18)|ovary(1)|prostate(1)|skin(1)	39		Breast(100;0.203)		KIRC - Kidney renal clear cell carcinoma(67;0.0768)|Kidney(114;0.0943)		ACCGGCATCTGCATCGCCCTC	0.527																																					p.C247Y												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G740A	8						.						244.0	166.0	192.0					8																	32611938		2203	4300	6503	32731480	SO:0001583	missense	3084	exon8			L12261	CCDS6084.1, CCDS6085.1, CCDS6086.1, CCDS6087.1, CCDS47836.1, CCDS55218.1, CCDS55219.1, CCDS75727.1	8p21-p12	2014-06-23			ENSG00000157168	ENSG00000157168		"""Immunoglobulin superfamily / I-set domain containing"""	7997	protein-coding gene	gene with protein product		142445	"""NRG1 intronic transcript 2 (non-protein coding)"""	HGL, NRG1-IT2		1350381, 8095334	Standard	NM_013962		Approved	HRG, NDF, GGF	uc003xiu.2	Q02297	OTTHUMG00000163918	ENST00000405005.3:c.749G>A	8.37:g.32611938G>A	ENSP00000384620:p.Cys250Tyr	Somatic		Capture	Illumina HiSeq	Phase_I	32731480	NM_013957	A5YAK4|A5YAK5|A8K1L2|B7Z4Z3|E9PHH4|O14667|P98202|Q02298|Q02299|Q07110|Q07111|Q12779|Q12780|Q12781|Q12782|Q12783|Q12784|Q15491|Q7RTV9|Q7RTW0|Q7RTW1|Q7RTW2|Q8NFN1|Q8NFN2|Q8NFN3|Q9UPE3	Missense_Mutation	SNP	ENST00000405005.3	37	CCDS6085.1	.	.	.	.	.	.	.	.	.	.	G	33	5.262794	0.95399	.	.	ENSG00000157168	ENST00000518104;ENST00000519301;ENST00000523534;ENST00000523079;ENST00000338921;ENST00000356819;ENST00000287840;ENST00000287845;ENST00000287842;ENST00000405005;ENST00000521670;ENST00000518084;ENST00000522402;ENST00000519240;ENST00000539990	T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.63417	-0.04;-0.04;-0.04;-0.04;-0.04;-0.04;-0.04;-0.04;-0.04;-0.04;-0.04;-0.04;-0.04;-0.04	5.47	5.47	0.80525	Neuregulin 1-related, C-terminal (1);	0.000000	0.85682	D	0.000000	T	0.80336	0.4604	M	0.73962	2.25	0.80722	D	1	D;D;D;D;D;D;D;D;D;D;D	0.76494	0.998;0.999;0.999;0.999;0.999;0.999;0.989;0.997;0.998;0.999;0.998	D;D;D;D;D;D;P;D;D;D;D	0.87578	0.998;0.998;0.992;0.974;0.985;0.992;0.689;0.974;0.981;0.974;0.947	T	0.82149	-0.0600	10	0.87932	D	0	-9.3645	19.3324	0.94297	0.0:0.0:1.0:0.0	.	93;96;247;221;255;246;258;247;250;255;250	B7Z1E3;B7Z1D7;E9PHH4;F8W9E3;Q7RTW4;B0FYA9;Q02297-2;Q02297-7;Q02297;Q02297-6;Q02297-3	.;.;.;.;.;.;.;.;NRG1_HUMAN;.;.	Y	217;200;323;247;258;255;250;221;247;250;250;101;96;93;93	ENSP00000430053:C217Y;ENSP00000429582:C200Y;ENSP00000429067:C323Y;ENSP00000430120:C247Y;ENSP00000343395:C258Y;ENSP00000349275:C255Y;ENSP00000287840:C250Y;ENSP00000287845:C221Y;ENSP00000287842:C247Y;ENSP00000384620:C250Y;ENSP00000428828:C250Y;ENSP00000430862:C96Y;ENSP00000428411:C93Y;ENSP00000439276:C93Y	ENSP00000287840:C250Y	C	+	2	0	NRG1	32731480	1.000000	0.71417	1.000000	0.80357	0.936000	0.57629	9.869000	0.99810	2.569000	0.86673	0.650000	0.86243	TGC		0.527	NRG1-017	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000472504.1		
GPR124	25960	broad.mit.edu	37	8	37704403	37704403	+	IGR	SNP	A	A	C			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr8:37704403A>C	ENST00000412232.2	+	0	5651				BRF2_ENST00000220659.6_Missense_Mutation_p.L169V|BRF2_ENST00000520601.1_Missense_Mutation_p.L169V	NM_032777.9	NP_116166.9	Q96PE1	GP124_HUMAN	G protein-coupled receptor 124						central nervous system development (GO:0007417)|endothelial cell migration (GO:0043542)|G-protein coupled receptor signaling pathway (GO:0007186)|negative regulation of vascular endothelial growth factor signaling pathway (GO:1900747)|neuropeptide signaling pathway (GO:0007218)|positive regulation of endothelial cell migration (GO:0010595)|regulation of angiogenesis (GO:0045765)|regulation of chemotaxis (GO:0050920)|regulation of establishment of blood-brain barrier (GO:0090210)|sprouting angiogenesis (GO:0002040)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)	p.L169V(1)		central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(4)|lung(16)|ovary(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	37			BRCA - Breast invasive adenocarcinoma(5;2.75e-24)|LUSC - Lung squamous cell carcinoma(8;3.5e-10)			AGTTCTGCCAAGCACAGAGAT	0.517																																					p.L169V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T505G	8						.						237.0	239.0	238.0					8																	37704403		2203	4300	6503	37823561	SO:0001628	intergenic_variant	55290	exon3			AB040964	CCDS6097.2	8p11.22	2014-08-08			ENSG00000020181	ENSG00000020181		"""-"", ""GPCR / Class B : Orphans"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	17849	protein-coding gene	gene with protein product	"""tumor endothelial marker 5"""	606823				11559528, 12565841	Standard	NM_032777		Approved	TEM5, DKFZp434C211, DKFZp434J0911, KIAA1531, FLJ14390	uc003xkj.3	Q96PE1	OTTHUMG00000156182		8.37:g.37704403A>C		Somatic		Capture	Illumina HiSeq	Phase_I	37823561	NM_018310	A6H8W3|D3DSW4|Q8N3R1|Q8TEM3|Q96KB2|Q9P1Z7|Q9UFY4	Missense_Mutation	SNP	ENST00000412232.2	37	CCDS6097.2	.	.	.	.	.	.	.	.	.	.	A	14.93	2.683744	0.47991	.	.	ENSG00000104221	ENST00000220659;ENST00000545765;ENST00000520601	.	.	.	5.54	0.525	0.17072	.	0.243603	0.34932	N	0.003578	T	0.48132	0.1483	L	0.59436	1.845	0.80722	D	1	B	0.31599	0.33	B	0.28011	0.085	T	0.41251	-0.9519	9	0.46703	T	0.11	.	9.9587	0.41682	0.4768:0.0:0.5232:0.0	.	169	Q9HAW0	BRF2_HUMAN	V	169;146;169	.	ENSP00000220659:L169V	L	-	1	2	BRF2	37823561	0.998000	0.40836	1.000000	0.80357	0.997000	0.91878	0.383000	0.20651	0.075000	0.16796	0.454000	0.30748	TTG		0.517	GPR124-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343331.2		
GOT1L1	137362	broad.mit.edu	37	8	37794557	37794557	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr8:37794557C>T	ENST00000307599.4	-	5	637	c.538G>A	c.(538-540)Gtc>Atc	p.V180I	GOT1L1_ENST00000518826.1_5'Flank	NM_152413.2	NP_689626.2	Q8NHS2	AATC2_HUMAN	glutamic-oxaloacetic transaminase 1-like 1	180					biosynthetic process (GO:0009058)|cellular amino acid metabolic process (GO:0006520)	cytoplasm (GO:0005737)	pyridoxal phosphate binding (GO:0030170)|transaminase activity (GO:0008483)	p.V180I(3)		central_nervous_system(1)|endometrium(3)|lung(8)|ovary(1)|prostate(1)	14	Colorectal(12;0.00627)	Lung NSC(58;0.118)|all_lung(54;0.195)	LUSC - Lung squamous cell carcinoma(8;1.37e-11)			ATCACAAGGACACAGCCATGT	0.557																																					p.V180I												.	.	3	Substitution - Missense(3)	prostate(2)|large_intestine(1)	c.G538A	8						.						115.0	122.0	120.0					8																	37794557		2049	4190	6239	37913714	SO:0001583	missense	137362	exon5			BC029504	CCDS47839.1	8p12	2005-09-22			ENSG00000169154	ENSG00000169154			28487	protein-coding gene	gene with protein product						12477932	Standard	NM_152413		Approved	MGC33309	uc011lbj.1	Q8NHS2	OTTHUMG00000164027	ENST00000307599.4:c.538G>A	8.37:g.37794557C>T	ENSP00000303077:p.Val180Ile	Somatic		Capture	Illumina HiSeq	Phase_I	37913714	NM_152413	A8MWL4	Missense_Mutation	SNP	ENST00000307599.4	37	CCDS47839.1	.	.	.	.	.	.	.	.	.	.	C	4.284	0.051921	0.08291	.	.	ENSG00000169154	ENST00000307599	D	0.90620	-2.7	4.75	-8.21	0.01041	Aminotransferase, class I/classII (1);Pyridoxal phosphate-dependent transferase, major region, subdomain 1 (1);Pyridoxal phosphate-dependent transferase, major domain (1);	0.547984	0.16256	N	0.222495	T	0.75845	0.3905	N	0.16656	0.425	0.39023	D	0.959784	B	0.16396	0.017	B	0.19946	0.027	T	0.58640	-0.7601	10	0.05525	T	0.97	-3.7742	13.8319	0.63386	0.0:0.1881:0.0:0.8119	.	180	Q8NHS2	AATC2_HUMAN	I	180	ENSP00000303077:V180I	ENSP00000303077:V180I	V	-	1	0	GOT1L1	37913714	0.000000	0.05858	0.005000	0.12908	0.124000	0.20399	-1.584000	0.02114	-1.815000	0.01222	-0.263000	0.10527	GTC		0.557	GOT1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376823.1	NM_152413	
ADAM2	2515	broad.mit.edu	37	8	39646227	39646227	+	Silent	SNP	G	G	A	rs199916948		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr8:39646227G>A	ENST00000265708.4	-	8	706	c.603C>T	c.(601-603)gtC>gtT	p.V201V	ADAM2_ENST00000521880.1_Silent_p.V201V|ADAM2_ENST00000347580.4_Silent_p.V182V|ADAM2_ENST00000379853.2_Intron	NM_001464.3	NP_001455.3	Q99965	ADAM2_HUMAN	ADAM metallopeptidase domain 2	201	Peptidase M12B. {ECO:0000255|PROSITE- ProRule:PRU00276}.				adult behavior (GO:0030534)|binding of sperm to zona pellucida (GO:0007339)|cell adhesion (GO:0007155)|fusion of sperm to egg plasma membrane (GO:0007342)|multicellular organism reproduction (GO:0032504)|single fertilization (GO:0007338)|visual learning (GO:0008542)	cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	integrin binding (GO:0005178)|metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)	p.V201V(2)		haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(11)|lung(29)|ovary(3)|prostate(1)|skin(5)|urinary_tract(1)	53		all_cancers(7;2.38e-28)|all_epithelial(6;8.85e-21)|all_lung(54;1.24e-07)|Lung NSC(58;1.94e-07)|Hepatocellular(245;0.00745)|Breast(189;0.00908)|Renal(179;0.0183)|Colorectal(162;0.246)	LUSC - Lung squamous cell carcinoma(45;0.000149)	READ - Rectum adenocarcinoma(644;0.0689)|Kidney(114;0.162)		CTTTTTGAGCGACAACAGTTG	0.289													G|||	1	0.000199681	0.0	0.0	5008	,	,		13346	0.001		0.0	False		,,,				2504	0.0				p.V201V												.	.	2	Substitution - coding silent(2)	large_intestine(1)|lung(1)	c.C603T	8						.						94.0	87.0	89.0					8																	39646227		2203	4300	6503	39765384	SO:0001819	synonymous_variant	2515	exon8			U52370	CCDS34884.1, CCDS64882.1, CCDS64883.1	8p11.2	2009-03-25	2008-07-31		ENSG00000104755	ENSG00000104755		"""ADAM metallopeptidase domain containing"""	198	protein-coding gene	gene with protein product	"""cancer/testis antigen 15"""	601533	"""fertilin beta"""	FTNB		8702389, 9070941	Standard	NM_001278113		Approved	PH-30b, PH30, CT15	uc003xnj.4	Q99965	OTTHUMG00000164041	ENST00000265708.4:c.603C>T	8.37:g.39646227G>A		Somatic		Capture	Illumina HiSeq	Phase_I	39765384	NM_001464	P78326|Q9UQQ8	Silent	SNP	ENST00000265708.4	37	CCDS34884.1																																																																																				0.289	ADAM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376926.1	NM_001464	
ZMAT4	79698	broad.mit.edu	37	8	40532421	40532421	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr8:40532421G>A	ENST00000297737.6	-	5	525	c.379C>T	c.(379-381)Cgg>Tgg	p.R127W	ZMAT4_ENST00000315769.7_Intron	NM_024645.2	NP_078921.1	Q9H898	ZMAT4_HUMAN	zinc finger, matrin-type 4	127						nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)	p.R127W(2)		NS(2)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(4)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)	18	Ovarian(28;0.00724)|Colorectal(14;0.0468)	all_cancers(7;0.00936)|all_epithelial(6;3.53e-06)|all_lung(54;0.0318)|Lung NSC(58;0.0919)|Esophageal squamous(32;0.15)|Hepatocellular(245;0.152)	LUSC - Lung squamous cell carcinoma(45;0.00722)			GTGTCCATCCGTGGGGGCTTA	0.527																																					p.R127W												.	.	2	Substitution - Missense(2)	large_intestine(1)|endometrium(1)	c.C379T	8						.						120.0	121.0	121.0					8																	40532421		2203	4300	6503	40651578	SO:0001583	missense	79698	exon5			AK023904	CCDS34885.1, CCDS47848.1	8p11.21	2012-10-05	2010-09-15		ENSG00000165061	ENSG00000165061		"""Zinc fingers, matrin-type"""	25844	protein-coding gene	gene with protein product						12477932	Standard	NM_024645		Approved	FLJ13842	uc003xnr.3	Q9H898	OTTHUMG00000164049	ENST00000297737.6:c.379C>T	8.37:g.40532421G>A	ENSP00000297737:p.Arg127Trp	Somatic		Capture	Illumina HiSeq	Phase_I	40651578	NM_024645	Q8WUT8	Missense_Mutation	SNP	ENST00000297737.6	37	CCDS34885.1	.	.	.	.	.	.	.	.	.	.	G	14.33	2.504173	0.44558	.	.	ENSG00000165061	ENST00000297737;ENST00000519406	T;T	0.43294	0.95;0.95	5.94	2.84	0.33178	.	0.593171	0.18818	N	0.130308	T	0.24236	0.0587	N	0.14661	0.345	0.09310	N	0.999996	B	0.13594	0.008	B	0.04013	0.001	T	0.18147	-1.0346	10	0.62326	D	0.03	-24.1197	7.7306	0.28786	0.0833:0.0:0.5379:0.3788	.	127	Q9H898	ZMAT4_HUMAN	W	127	ENSP00000297737:R127W;ENSP00000428423:R127W	ENSP00000297737:R127W	R	-	1	2	ZMAT4	40651578	0.282000	0.24268	0.677000	0.29947	0.865000	0.49528	1.191000	0.32138	0.726000	0.32339	0.557000	0.71058	CGG		0.527	ZMAT4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376950.1	NM_024645	
AGPAT6	137964	broad.mit.edu	37	8	41476486	41476486	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr8:41476486G>T	ENST00000396987.3	+	12	2179	c.1252G>T	c.(1252-1254)Gac>Tac	p.D418Y	RP11-360L9.8_ENST00000581909.1_RNA	NM_178819.3	NP_848934.1	Q86UL3	GPAT4_HUMAN	1-acylglycerol-3-phosphate O-acyltransferase 6	418					acyl-CoA metabolic process (GO:0006637)|CDP-diacylglycerol biosynthetic process (GO:0016024)|cellular lipid metabolic process (GO:0044255)|diacylglycerol metabolic process (GO:0046339)|fatty acid metabolic process (GO:0006631)|glandular epithelial cell maturation (GO:0002071)|glycerophospholipid biosynthetic process (GO:0046474)|lactation (GO:0007595)|lipid biosynthetic process (GO:0008610)|phosphatidic acid biosynthetic process (GO:0006654)|phosphatidylcholine biosynthetic process (GO:0006656)|phospholipid metabolic process (GO:0006644)|regulation of multicellular organism growth (GO:0040014)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	glycerol-3-phosphate O-acyltransferase activity (GO:0004366)	p.D418Y(1)		endometrium(3)|kidney(2)|large_intestine(3)|lung(6)	14	Ovarian(28;0.00769)|Colorectal(14;0.0202)|Lung SC(25;0.211)	all_lung(54;0.0131)|Lung NSC(58;0.0363)|Hepatocellular(245;0.0462)|Esophageal squamous(32;0.0844)	OV - Ovarian serous cystadenocarcinoma(14;0.00126)|Colorectal(10;0.0014)|Lung(22;0.00177)|LUSC - Lung squamous cell carcinoma(45;0.00392)|COAD - Colon adenocarcinoma(11;0.0147)			AGGACTTGTGGACCTGCTGTG	0.493																																					p.D418Y												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1252T	8						.						123.0	107.0	112.0					8																	41476486		2203	4300	6503	41595643	SO:0001583	missense	137964	exon12			AF406612	CCDS6117.1	8p11.21	2013-02-05	2013-02-05			ENSG00000158669	2.3.1.15	"""1-acylglycerol-3-phosphate O-acyltransferases"""	20880	protein-coding gene	gene with protein product	"""lysophosphatidic acid acyltransferase, zeta"""	608143	"""1-acylglycerol-3-phosphate O-acyltransferase 6 (lysophosphatidic acid acyltransferase, zeta)"""			12938015	Standard	NM_178819		Approved	DKFZp586M1819, LPAAT-zeta	uc003xnz.2	Q86UL3		ENST00000396987.3:c.1252G>T	8.37:g.41476486G>T	ENSP00000380184:p.Asp418Tyr	Somatic		Capture	Illumina HiSeq	Phase_I	41595643	NM_178819	Q86V89	Missense_Mutation	SNP	ENST00000396987.3	37	CCDS6117.1	.	.	.	.	.	.	.	.	.	.	G	29.3	4.998324	0.93227	.	.	ENSG00000158669	ENST00000396987	T	0.50813	0.73	5.56	5.56	0.83823	.	0.000000	0.85682	D	0.000000	T	0.72724	0.3496	M	0.87900	2.915	0.80722	D	1	D	0.71674	0.998	D	0.64595	0.927	T	0.77943	-0.2398	10	0.87932	D	0	.	18.5095	0.90910	0.0:0.0:1.0:0.0	.	418	Q86UL3	GPAT4_HUMAN	Y	418	ENSP00000380184:D418Y	ENSP00000380184:D418Y	D	+	1	0	AGPAT6	41595643	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	9.864000	0.99589	2.579000	0.87056	0.655000	0.94253	GAC		0.493	AGPAT6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377158.1	NM_178819	
NSMAF	8439	broad.mit.edu	37	8	59535941	59535941	+	Missense_Mutation	SNP	C	C	T	rs367758314		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr8:59535941C>T	ENST00000038176.3	-	8	711	c.499G>A	c.(499-501)Gcc>Acc	p.A167T	NSMAF_ENST00000427130.2_Missense_Mutation_p.A198T|NSMAF_ENST00000519858.1_5'UTR	NM_003580.3	NP_003571.2	Q92636	FAN_HUMAN	neutral sphingomyelinase (N-SMase) activation associated factor	167					ceramide metabolic process (GO:0006672)|intracellular signal transduction (GO:0035556)|positive regulation of apoptotic process (GO:0043065)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)	receptor signaling protein activity (GO:0005057)|sphingomyelin phosphodiesterase activator activity (GO:0016230)	p.A167T(1)		autonomic_ganglia(1)|central_nervous_system(1)|endometrium(7)|kidney(3)|large_intestine(7)|lung(11)|ovary(1)|pancreas(1)|prostate(2)|skin(3)|urinary_tract(1)	38		all_lung(136;0.174)|Lung NSC(129;0.2)				CTTACCATGGCGGTTTGGTCA	0.308													C|||	1	0.000199681	0.0	0.0	5008	,	,		18724	0.0		0.0	False		,,,				2504	0.001				p.A167T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G499A	8						.	C	THR/ALA,THR/ALA	0,4406		0,0,2203	108.0	113.0	111.0		592,499	5.7	1.0	8		111	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	NSMAF	NM_001144772.1,NM_003580.3	58,58	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging,probably-damaging	198/949,167/918	59535941	1,13005	2203	4300	6503	59698495	SO:0001583	missense	8439	exon8			X96586	CCDS6173.1, CCDS47864.1	8q12-q13	2013-01-10			ENSG00000035681	ENSG00000035681		"""WD repeat domain containing"""	8017	protein-coding gene	gene with protein product		603043				8808629, 10640829	Standard	NM_003580		Approved	FAN	uc011lee.2	Q92636	OTTHUMG00000164352	ENST00000038176.3:c.499G>A	8.37:g.59535941C>T	ENSP00000038176:p.Ala167Thr	Somatic		Capture	Illumina HiSeq	Phase_I	59698495	NM_003580	B4DFB0|E9PCH0|Q8IW26	Missense_Mutation	SNP	ENST00000038176.3	37	CCDS6173.1	.	.	.	.	.	.	.	.	.	.	C	28.1	4.888590	0.91814	0.0	1.16E-4	ENSG00000035681	ENST00000038176;ENST00000427130	T;T	0.54675	0.57;0.56	5.66	5.66	0.87406	.	0.000000	0.85682	D	0.000000	T	0.75613	0.3873	M	0.80616	2.505	0.58432	D	0.999999	D;P;D	0.89917	1.0;0.895;0.99	D;B;B	0.91635	0.999;0.216;0.406	T	0.75966	-0.3131	9	.	.	.	.	19.7344	0.96195	0.0:1.0:0.0:0.0	.	198;167;167	Q92636-2;A8K9G4;Q92636	.;.;FAN_HUMAN	T	167;198	ENSP00000038176:A167T;ENSP00000411012:A198T	.	A	-	1	0	NSMAF	59698495	1.000000	0.71417	0.993000	0.49108	0.741000	0.42261	7.027000	0.76463	2.673000	0.90976	0.591000	0.81541	GCC		0.308	NSMAF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378384.1	NM_003580	
PREX2	80243	broad.mit.edu	37	8	68934286	68934286	+	Missense_Mutation	SNP	A	A	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr8:68934286A>T	ENST00000288368.4	+	4	629	c.352A>T	c.(352-354)Atc>Ttc	p.I118F	PREX2_ENST00000529398.1_3'UTR	NM_024870.2|NM_025170.4	NP_079146.2|NP_079446.3	Q70Z35	PREX2_HUMAN	phosphatidylinositol-3,4,5-trisphosphate-dependent Rac exchange factor 2	118	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.				adult locomotory behavior (GO:0008344)|dendrite morphogenesis (GO:0048813)|G-protein coupled receptor signaling pathway (GO:0007186)|intracellular signal transduction (GO:0035556)|positive regulation of Rac GTPase activity (GO:0032855)		Rac GTPase activator activity (GO:0030675)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)	p.I118F(2)		NS(6)|biliary_tract(1)|breast(4)|endometrium(11)|kidney(16)|large_intestine(25)|liver(4)|lung(57)|ovary(2)|pancreas(4)|prostate(3)|skin(42)|upper_aerodigestive_tract(1)|urinary_tract(2)	178						CAAGTTTCGTATCTATGATGA	0.299																																					p.I118F												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.A352T	8						.						102.0	100.0	101.0					8																	68934286		2202	4300	6502	69096840	SO:0001583	missense	80243	exon4			AK024079	CCDS6201.1	8q13.1	2014-06-13	2008-09-15	2008-09-15	ENSG00000046889	ENSG00000046889		"""Rho guanine nucleotide exchange factors"""	22950	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 129"""	612139	"""DEP domain containing 2"""	DEPDC2		15304342, 15304343	Standard	NM_024870		Approved	DEP.2, FLJ12987, P-REX2, PPP1R129	uc003xxv.1	Q70Z35	OTTHUMG00000164402	ENST00000288368.4:c.352A>T	8.37:g.68934286A>T	ENSP00000288368:p.Ile118Phe	Somatic		Capture	Illumina HiSeq	Phase_I	69096840	NM_025170	B4DFX0|Q32KL0|Q32KL1|Q6R7Q3|Q6R7Q4|Q9H805|Q9H961	Missense_Mutation	SNP	ENST00000288368.4	37	CCDS6201.1	.	.	.	.	.	.	.	.	.	.	A	22.0	4.226321	0.79576	.	.	ENSG00000046889	ENST00000288368;ENST00000396539;ENST00000354677	T	0.64618	-0.11	6.04	6.04	0.98038	Dbl homology (DH) domain (5);	0.116795	0.56097	D	0.000029	T	0.73737	0.3625	M	0.65677	2.01	0.80722	D	1	P;P;P	0.45011	0.848;0.605;0.713	P;P;P	0.53809	0.617;0.735;0.516	T	0.76250	-0.3028	10	0.87932	D	0	.	16.5885	0.84745	1.0:0.0:0.0:0.0	.	118;118;118	Q70Z35-2;Q70Z35;Q70Z35-3	.;PREX2_HUMAN;.	F	118	ENSP00000288368:I118F	ENSP00000288368:I118F	I	+	1	0	PREX2	69096840	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.969000	0.63735	2.317000	0.78254	0.460000	0.39030	ATC		0.299	PREX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378620.1	NM_025170	
C8orf34	116328	broad.mit.edu	37	8	69351747	69351747	+	Missense_Mutation	SNP	A	A	C			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr8:69351747A>C	ENST00000539993.1	+	2	632	c.83A>C	c.(82-84)aAg>aCg	p.K28T	C8orf34_ENST00000349492.3_3'UTR|C8orf34_ENST00000337103.4_Missense_Mutation_p.K3T|C8orf34_ENST00000518698.1_Missense_Mutation_p.K114T|C8orf34_ENST00000523686.1_Missense_Mutation_p.K28T|C8orf34_ENST00000348340.2_Missense_Mutation_p.K28T			Q49A92	CH034_HUMAN	chromosome 8 open reading frame 34	28								p.K3T(1)		NS(1)|breast(2)|endometrium(3)|kidney(2)|large_intestine(9)|lung(12)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)	36			Epithelial(68;0.0117)|OV - Ovarian serous cystadenocarcinoma(28;0.0227)|all cancers(69;0.0502)			TTAATGACCAAGTTAATAACT	0.378																																					p.K114T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A341C	8						.						75.0	72.0	73.0					8																	69351747		2203	4300	6503	69514301	SO:0001583	missense	116328	exon2			AB056652	CCDS6203.1, CCDS6203.2	8q13	2009-10-01			ENSG00000165084	ENSG00000165084			30905	protein-coding gene	gene with protein product	"""vestibule 1"""						Standard	NM_052958		Approved	vest-1, VEST1	uc010lyz.3	Q49A92	OTTHUMG00000164438	ENST00000539993.1:c.83A>C	8.37:g.69351747A>C	ENSP00000438159:p.Lys28Thr	Somatic		Capture	Illumina HiSeq	Phase_I	69514301	NM_052958	A8K5X1|G3XAM6|Q8N1X0|Q8N9M7|Q8ND19|Q96Q28	Missense_Mutation	SNP	ENST00000539993.1	37		.	.	.	.	.	.	.	.	.	.	A	24.4	4.522246	0.85600	.	.	ENSG00000165084	ENST00000518698;ENST00000539993;ENST00000523686;ENST00000348340;ENST00000337103	T;T;T;T;T	0.76839	-1.05;-1.05;-1.05;-1.05;0.05	5.72	5.72	0.89469	cAMP-dependent protein kinase, regulatory subunit, type I/II alpha/beta (1);	0.000000	0.85682	D	0.000000	D	0.86736	0.6004	M	0.67953	2.075	0.47778	D	0.999518	D;P;D	0.89917	1.0;0.873;1.0	D;B;D	0.85130	0.996;0.298;0.997	D	0.86605	0.1869	9	.	.	.	-18.0653	16.0178	0.80455	1.0:0.0:0.0:0.0	.	28;28;28	Q49A92;Q49A92-3;Q49A92-5	CH034_HUMAN;.;.	T	114;28;28;28;3	ENSP00000427820:K114T;ENSP00000438159:K28T;ENSP00000429102:K28T;ENSP00000345255:K28T;ENSP00000337174:K3T	.	K	+	2	0	C8orf34	69514301	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.915000	0.92740	2.180000	0.69256	0.528000	0.53228	AAG		0.378	C8orf34-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_052958	
SLCO5A1	81796	broad.mit.edu	37	8	70744278	70744278	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr8:70744278G>T	ENST00000260126.4	-	2	1337	c.631C>A	c.(631-633)Ctc>Atc	p.L211I	SLCO5A1_ENST00000528658.1_5'UTR|RP11-159H10.3_ENST00000501104.2_RNA|RP11-159H10.3_ENST00000533300.1_RNA|SLCO5A1_ENST00000530307.1_Missense_Mutation_p.L211I|RP11-159H10.3_ENST00000528800.2_RNA|SLCO5A1_ENST00000524945.1_Missense_Mutation_p.L211I	NM_030958.2	NP_112220.2	Q9H2Y9	SO5A1_HUMAN	solute carrier organic anion transporter family, member 5A1	211						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	transporter activity (GO:0005215)	p.L211I(1)		NS(1)|breast(2)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(11)|lung(24)|ovary(3)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	53	Breast(64;0.0654)		Epithelial(68;0.0141)|OV - Ovarian serous cystadenocarcinoma(28;0.0315)|all cancers(69;0.0594)			AAGGCGAAGAGGGCTGCCCCG	0.667																																					p.L211I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C631A	8						.						21.0	26.0	24.0					8																	70744278		2203	4299	6502	70906832	SO:0001583	missense	81796	exon2			AF205075	CCDS6205.1, CCDS55242.1, CCDS55243.1	8q13.1	2013-05-22	2003-11-25	2003-11-26	ENSG00000137571	ENSG00000137571		"""Solute carriers"""	19046	protein-coding gene	gene with protein product		613543	"""solute carrier family 21 (organic anion transporter), member 15"""	SLC21A15		12507753	Standard	NM_030958		Approved	OATPRP4, OATP-J, OATP5A1	uc003xyl.3	Q9H2Y9	OTTHUMG00000165121	ENST00000260126.4:c.631C>A	8.37:g.70744278G>T	ENSP00000260126:p.Leu211Ile	Somatic		Capture	Illumina HiSeq	Phase_I	70906832	NM_030958	A4QPC2|B2RPF7|B3KMU7|E9PKK5|G3V1C0	Missense_Mutation	SNP	ENST00000260126.4	37	CCDS6205.1	.	.	.	.	.	.	.	.	.	.	G	13.49	2.251945	0.39797	.	.	ENSG00000137571	ENST00000260126;ENST00000524945;ENST00000530307	T;T;T	0.42131	0.98;0.98;0.98	5.49	3.65	0.41850	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.066221	0.64402	D	0.000014	T	0.37100	0.0991	L	0.35644	1.08	0.35852	D	0.826825	B;B;B;B	0.32040	0.109;0.037;0.196;0.353	B;B;B;B	0.39531	0.249;0.06;0.231;0.302	T	0.40701	-0.9549	10	0.32370	T	0.25	.	11.5781	0.50875	0.0:0.253:0.6157:0.1312	.	211;211;211;211	B4DR09;E9PKK5;Q9H2Y9;G3V1C0	.;.;SO5A1_HUMAN;.	I	211	ENSP00000260126:L211I;ENSP00000434422:L211I;ENSP00000431611:L211I	ENSP00000260126:L211I	L	-	1	0	SLCO5A1	70906832	1.000000	0.71417	0.876000	0.34364	0.830000	0.47004	3.770000	0.55310	0.652000	0.30806	0.561000	0.74099	CTC		0.667	SLCO5A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381990.3	NM_030958	
MSC	9242	broad.mit.edu	37	8	72754954	72754954	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr8:72754954G>A	ENST00000325509.4	-	2	852	c.563C>T	c.(562-564)cCg>cTg	p.P188L	RP11-383H13.1_ENST00000521467.1_Intron|RP11-383H13.1_ENST00000537896.1_5'Flank|RP11-383H13.1_ENST00000524152.1_5'Flank|MSC_ENST00000518440.1_5'UTR	NM_005098.3	NP_005089.2	O60682	MUSC_HUMAN	musculin	188					branchiomeric skeletal muscle development (GO:0014707)|diaphragm development (GO:0060539)|palate development (GO:0060021)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001206)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)	p.P188L(1)		endometrium(2)|large_intestine(4)|lung(13)|pancreas(1)|prostate(4)|skin(2)	26	Breast(64;0.176)		Epithelial(68;0.137)|BRCA - Breast invasive adenocarcinoma(89;0.203)			GTCAGAGTCCGGTCTTCCCGA	0.463																																					p.P188L												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C563T	8						.						298.0	297.0	297.0					8																	72754954		1937	4134	6071	72917508	SO:0001583	missense	9242	exon2				CCDS43746.1	8q13.3	2013-06-07	2010-04-28		ENSG00000178860	ENSG00000178860		"""Basic helix-loop-helix proteins"""	7321	protein-coding gene	gene with protein product	"""activated B-cell factor-1"""	603628	"""musculin (activated B-cell factor-1)"""			9584154, 10198176	Standard	NM_005098		Approved	ABF-1, bHLHa22	uc003xyx.1	O60682	OTTHUMG00000164489	ENST00000325509.4:c.563C>T	8.37:g.72754954G>A	ENSP00000321445:p.Pro188Leu	Somatic		Capture	Illumina HiSeq	Phase_I	72917508	NM_005098	O75946|Q53XZ2|Q9BRE7	Missense_Mutation	SNP	ENST00000325509.4	37	CCDS43746.1	.	.	.	.	.	.	.	.	.	.	G	28.0	4.878521	0.91740	.	.	ENSG00000178860	ENST00000325509	D	0.97924	-4.61	4.88	4.88	0.63580	Helix-loop-helix DNA-binding (1);	0.061993	0.64402	D	0.000003	D	0.98124	0.9381	L	0.54323	1.7	0.80722	D	1	D	0.89917	1.0	D	0.67231	0.95	D	0.99364	1.0918	10	0.87932	D	0	.	18.2206	0.89901	0.0:0.0:1.0:0.0	.	188	O60682	MUSC_HUMAN	L	188	ENSP00000321445:P188L	ENSP00000321445:P188L	P	-	2	0	MSC	72917508	1.000000	0.71417	0.977000	0.42913	0.966000	0.64601	7.039000	0.76544	2.559000	0.86315	0.462000	0.41574	CCG		0.463	MSC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378974.1	NM_005098	
TRPA1	8989	broad.mit.edu	37	8	72950287	72950287	+	Silent	SNP	A	A	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr8:72950287A>T	ENST00000262209.4	-	20	2523	c.2316T>A	c.(2314-2316)acT>acA	p.T772T	RP11-383H13.1_ENST00000537896.1_Intron|RP11-383H13.1_ENST00000524152.1_Intron|RP11-383H13.1_ENST00000457356.4_Intron|TRPA1_ENST00000519720.1_5'UTR	NM_007332.2	NP_015628.2	O75762	TRPA1_HUMAN	transient receptor potential cation channel, subfamily A, member 1	772					calcium ion transmembrane transport (GO:0070588)|detection of chemical stimulus involved in sensory perception of pain (GO:0050968)|detection of mechanical stimulus involved in sensory perception of pain (GO:0050966)|ion transmembrane transport (GO:0034220)|ion transport (GO:0006811)|response to cold (GO:0009409)|response to drug (GO:0042493)|response to hydrogen peroxide (GO:0042542)|response to pain (GO:0048265)|thermoception (GO:0050955)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|stereocilium bundle (GO:0032421)	calcium channel activity (GO:0005262)|channel activity (GO:0015267)	p.T772T(2)		NS(1)|breast(2)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(26)|lung(44)|ovary(4)|prostate(6)|stomach(1)	98			Epithelial(68;0.223)		Menthol(DB00825)	AAATCATACAAGTTTTTATTA	0.259																																					p.T772T												.	.	2	Substitution - coding silent(2)	ovary(1)|large_intestine(1)	c.T2316A	8						.						22.0	23.0	23.0					8																	72950287		2188	4260	6448	73112841	SO:0001819	synonymous_variant	8989	exon20			Y10601	CCDS34908.1	8q13	2013-01-10	2003-11-20	2003-11-20	ENSG00000104321	ENSG00000104321		"""Voltage-gated ion channels / Transient receptor potential cation channels"", ""Ankyrin repeat domain containing"""	497	protein-coding gene	gene with protein product		604775	"""ankyrin-like with transmembrane domains 1"""	ANKTM1		16382100	Standard	NM_007332		Approved		uc003xza.3	O75762	OTTHUMG00000164516	ENST00000262209.4:c.2316T>A	8.37:g.72950287A>T		Somatic		Capture	Illumina HiSeq	Phase_I	73112841	NM_007332	A6NIN6	Silent	SNP	ENST00000262209.4	37	CCDS34908.1																																																																																				0.259	TRPA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379079.2	NM_007332	
TRPA1	8989	broad.mit.edu	37	8	72987577	72987577	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr8:72987577T>C	ENST00000262209.4	-	1	275	c.68A>G	c.(67-69)gAg>gGg	p.E23G		NM_007332.2	NP_015628.2	O75762	TRPA1_HUMAN	transient receptor potential cation channel, subfamily A, member 1	23					calcium ion transmembrane transport (GO:0070588)|detection of chemical stimulus involved in sensory perception of pain (GO:0050968)|detection of mechanical stimulus involved in sensory perception of pain (GO:0050966)|ion transmembrane transport (GO:0034220)|ion transport (GO:0006811)|response to cold (GO:0009409)|response to drug (GO:0042493)|response to hydrogen peroxide (GO:0042542)|response to pain (GO:0048265)|thermoception (GO:0050955)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|stereocilium bundle (GO:0032421)	calcium channel activity (GO:0005262)|channel activity (GO:0015267)	p.E23G(1)		NS(1)|breast(2)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(26)|lung(44)|ovary(4)|prostate(6)|stomach(1)	98			Epithelial(68;0.223)		Menthol(DB00825)	CGGCACATCCTCATAGACAAC	0.642																																					p.E23G												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A68G	8						.						104.0	105.0	105.0					8																	72987577		2203	4300	6503	73150131	SO:0001583	missense	8989	exon1			Y10601	CCDS34908.1	8q13	2013-01-10	2003-11-20	2003-11-20	ENSG00000104321	ENSG00000104321		"""Voltage-gated ion channels / Transient receptor potential cation channels"", ""Ankyrin repeat domain containing"""	497	protein-coding gene	gene with protein product		604775	"""ankyrin-like with transmembrane domains 1"""	ANKTM1		16382100	Standard	NM_007332		Approved		uc003xza.3	O75762	OTTHUMG00000164516	ENST00000262209.4:c.68A>G	8.37:g.72987577T>C	ENSP00000262209:p.Glu23Gly	Somatic		Capture	Illumina HiSeq	Phase_I	73150131	NM_007332	A6NIN6	Missense_Mutation	SNP	ENST00000262209.4	37	CCDS34908.1	.	.	.	.	.	.	.	.	.	.	T	9.964	1.223570	0.22457	.	.	ENSG00000104321	ENST00000262209	T	0.41065	1.01	4.58	0.826	0.18829	.	0.721411	0.13724	N	0.367158	T	0.20618	0.0496	L	0.27053	0.805	0.22591	N	0.998953	P	0.35433	0.501	B	0.27608	0.081	T	0.11108	-1.0601	10	0.23891	T	0.37	-0.0195	3.6532	0.08212	0.1685:0.1834:0.0:0.6481	.	23	O75762	TRPA1_HUMAN	G	23	ENSP00000262209:E23G	ENSP00000262209:E23G	E	-	2	0	TRPA1	73150131	0.986000	0.35501	0.091000	0.20842	0.012000	0.07955	0.839000	0.27586	0.052000	0.16007	0.482000	0.46254	GAG		0.642	TRPA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379079.2	NM_007332	
KCNB2	9312	broad.mit.edu	37	8	73848578	73848578	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr8:73848578C>T	ENST00000523207.1	+	3	1576	c.988C>T	c.(988-990)Cgg>Tgg	p.R330W		NM_004770.2	NP_004761.2	Q92953	KCNB2_HUMAN	potassium voltage-gated channel, Shab-related subfamily, member 2	330					potassium ion transport (GO:0006813)|protein homooligomerization (GO:0051260)|regulation of smooth muscle contraction (GO:0006940)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)	p.R330W(1)		NS(1)|breast(4)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(20)|liver(2)|lung(31)|ovary(2)|pancreas(3)|prostate(2)|skin(8)|upper_aerodigestive_tract(4)|urinary_tract(1)	85	Breast(64;0.137)		Epithelial(68;0.105)		Dalfampridine(DB06637)	CACCCTTAGGCGGAGTTACAA	0.493																																					p.R330W												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C988T	8						.						93.0	93.0	93.0					8																	73848578		2203	4300	6503	74011132	SO:0001583	missense	9312	exon3			U69962	CCDS6209.1	8q13.2	2012-07-05			ENSG00000182674	ENSG00000182674		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	6232	protein-coding gene	gene with protein product		607738				9612272, 16382104	Standard	NM_004770		Approved	Kv2.2	uc003xzb.3	Q92953	OTTHUMG00000164498	ENST00000523207.1:c.988C>T	8.37:g.73848578C>T	ENSP00000430846:p.Arg330Trp	Somatic		Capture	Illumina HiSeq	Phase_I	74011132	NM_004770	Q7Z7D0|Q9BXD3	Missense_Mutation	SNP	ENST00000523207.1	37	CCDS6209.1	.	.	.	.	.	.	.	.	.	.	C	18.50	3.636737	0.67130	.	.	ENSG00000182674	ENST00000523207	D	0.98585	-5.01	5.74	5.74	0.90152	Ion transport (1);	0.000000	0.41194	D	0.000932	D	0.99152	0.9707	M	0.92604	3.325	0.58432	D	0.999992	D	0.89917	1.0	D	0.81914	0.995	D	0.99297	1.0900	10	0.72032	D	0.01	.	15.5086	0.75760	0.1389:0.8611:0.0:0.0	.	330	Q92953	KCNB2_HUMAN	W	330	ENSP00000430846:R330W	ENSP00000430846:R330W	R	+	1	2	KCNB2	74011132	0.841000	0.29509	0.994000	0.49952	0.546000	0.35178	1.639000	0.37176	2.702000	0.92279	0.655000	0.94253	CGG		0.493	KCNB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378998.1	NM_004770	
SLC7A13	157724	broad.mit.edu	37	8	87226722	87226722	+	Nonsense_Mutation	SNP	T	T	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr8:87226722T>A	ENST00000297524.3	-	4	1436	c.1333A>T	c.(1333-1335)Aga>Tga	p.R445*	SLC7A13_ENST00000419776.2_3'UTR|CTD-3118D11.3_ENST00000523112.1_RNA	NM_138817.2	NP_620172.2	Q8TCU3	S7A13_HUMAN	solute carrier family 7 (anionic amino acid transporter), member 13	445						integral component of membrane (GO:0016021)	amino acid transmembrane transporter activity (GO:0015171)	p.R445*(1)		breast(3)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(4)|lung(24)|ovary(1)|pancreas(1)|prostate(1)|skin(3)	45						CAAGCCAATCTTATTTTAAAA	0.348																																					p.R445X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.A1333T	8						.						56.0	61.0	60.0					8																	87226722		2203	4300	6503	87295838	SO:0001587	stop_gained	157724	exon4			AJ417661	CCDS34917.1	8q21.3	2013-07-15	2011-07-12		ENSG00000164893	ENSG00000164893		"""Solute carriers"""	23092	protein-coding gene	gene with protein product						11907033, 11943479	Standard	XM_005250804		Approved	AGT-1, XAT2	uc003ydq.1	Q8TCU3	OTTHUMG00000163663	ENST00000297524.3:c.1333A>T	8.37:g.87226722T>A	ENSP00000297524:p.Arg445*	Somatic		Capture	Illumina HiSeq	Phase_I	87295838	NM_138817	Q05C37|Q08AH9|Q96N84	Nonsense_Mutation	SNP	ENST00000297524.3	37	CCDS34917.1	.	.	.	.	.	.	.	.	.	.	T	12.75	2.030925	0.35797	.	.	ENSG00000164893	ENST00000297524	.	.	.	4.13	-0.155	0.13395	.	0.844613	0.10208	N	0.702444	.	.	.	.	.	.	0.09310	N	1	.	.	.	.	.	.	.	.	.	.	0.19590	T	0.45	.	5.8345	0.18599	0.0:0.1058:0.4904:0.4039	.	.	.	.	X	445	.	ENSP00000297524:R445X	R	-	1	2	SLC7A13	87295838	0.001000	0.12720	0.000000	0.03702	0.068000	0.16541	1.079000	0.30766	0.195000	0.20347	0.533000	0.62120	AGA		0.348	SLC7A13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374704.1	NM_138817	
DCAF4L2	138009	broad.mit.edu	37	8	88885382	88885382	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr8:88885382A>G	ENST00000319675.3	-	1	914	c.818T>C	c.(817-819)gTg>gCg	p.V273A		NM_152418.3	NP_689631.1	Q8NA75	DC4L2_HUMAN	DDB1 and CUL4 associated factor 4-like 2	273								p.V273A(1)		breast(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(19)|liver(2)|lung(40)|ovary(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	83						CAGAGAAGTCACTGCTGAATC	0.498																																					p.V273A												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T818C	8						.						107.0	98.0	101.0					8																	88885382		2203	4300	6503	88954498	SO:0001583	missense	138009	exon1			AL833507	CCDS6245.1	8q21.3	2013-01-09	2009-07-17	2009-07-17		ENSG00000176566		"""WD repeat domain containing"""	26657	protein-coding gene	gene with protein product			"""WD repeat domain 21C"""	WDR21C		14702039	Standard	NM_152418		Approved		uc003ydz.3	Q8NA75		ENST00000319675.3:c.818T>C	8.37:g.88885382A>G	ENSP00000316496:p.Val273Ala	Somatic		Capture	Illumina HiSeq	Phase_I	88954498	NM_152418		Missense_Mutation	SNP	ENST00000319675.3	37	CCDS6245.1	.	.	.	.	.	.	.	.	.	.	A	15.85	2.955629	0.53293	.	.	ENSG00000176566	ENST00000319675	T	0.73789	-0.78	1.92	0.341	0.15991	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.115558	0.64402	D	0.000010	T	0.79621	0.4477	M	0.73962	2.25	0.33765	D	0.622314	D	0.55800	0.973	P	0.62298	0.9	T	0.80970	-0.1144	10	0.72032	D	0.01	.	5.5062	0.16856	0.7167:0.2833:0.0:0.0	.	273	Q8NA75	DC4L2_HUMAN	A	273	ENSP00000316496:V273A	ENSP00000316496:V273A	V	-	2	0	DCAF4L2	88954498	1.000000	0.71417	0.008000	0.14137	0.019000	0.09904	4.226000	0.58606	0.627000	0.30340	0.383000	0.25322	GTG		0.498	DCAF4L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375302.1	NM_152418	
TMEM55A	55529	broad.mit.edu	37	8	92020996	92020996	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr8:92020996C>T	ENST00000285419.3	-	5	828	c.514G>A	c.(514-516)Gca>Aca	p.A172T		NM_018710.2	NP_061180.1	Q8N4L2	TM55A_HUMAN	transmembrane protein 55A	172						endosome (GO:0005768)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)	hydrolase activity (GO:0016787)	p.A172T(1)		breast(1)|endometrium(2)|large_intestine(5)|lung(3)|prostate(1)|upper_aerodigestive_tract(1)	13			BRCA - Breast invasive adenocarcinoma(11;0.033)			GGGCATTTTGCCAGAGTGTTG	0.323																																					p.A172T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G514A	8						.						122.0	125.0	124.0					8																	92020996		2203	4300	6503	92090172	SO:0001583	missense	55529	exon5			BC033892	CCDS6252.1	8q21.3	2005-08-09			ENSG00000155099	ENSG00000155099			25452	protein-coding gene	gene with protein product		609864				12477932	Standard	NM_018710		Approved	DKFZp762O076	uc003yes.3	Q8N4L2	OTTHUMG00000164019	ENST00000285419.3:c.514G>A	8.37:g.92020996C>T	ENSP00000285419:p.Ala172Thr	Somatic		Capture	Illumina HiSeq	Phase_I	92090172	NM_018710	B2R9H4|Q68CU2	Missense_Mutation	SNP	ENST00000285419.3	37	CCDS6252.1	.	.	.	.	.	.	.	.	.	.	C	35	5.517232	0.96416	.	.	ENSG00000155099	ENST00000285419;ENST00000520014	.	.	.	5.91	5.91	0.95273	.	0.000000	0.85682	D	0.000000	T	0.79299	0.4422	M	0.66439	2.03	0.80722	D	1	D	0.69078	0.997	D	0.77004	0.989	T	0.79448	-0.1799	9	0.72032	D	0.01	-22.6062	19.9115	0.97026	0.0:1.0:0.0:0.0	.	172	Q8N4L2	TM55A_HUMAN	T	172;178	.	ENSP00000285419:A172T	A	-	1	0	TMEM55A	92090172	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	6.672000	0.74477	2.804000	0.96469	0.650000	0.86243	GCA		0.323	TMEM55A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376778.1	NM_018710	
KIAA1429	25962	broad.mit.edu	37	8	95539335	95539335	+	Silent	SNP	G	G	A	rs563314504	byFrequency	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr8:95539335G>A	ENST00000297591.5	-	8	1212	c.1137C>T	c.(1135-1137)atC>atT	p.I379I	KIAA1429_ENST00000421249.2_Silent_p.I379I|KIAA1429_ENST00000437199.1_Silent_p.I379I	NM_015496.4	NP_056311.2	Q69YN4	VIR_HUMAN	KIAA1429	379					mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)	p.I379I(1)		NS(1)|breast(3)|central_nervous_system(1)|endometrium(4)|kidney(5)|large_intestine(16)|lung(28)|ovary(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	66	Breast(36;3.29e-05)		BRCA - Breast invasive adenocarcinoma(8;0.00185)			CTGAGGCTTCGATTGCCCCTG	0.343													G|||	2	0.000399361	0.0	0.0029	5008	,	,		19534	0.0		0.0	False		,,,				2504	0.0				p.I379I												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1137T	8						.						145.0	149.0	147.0					8																	95539335		2203	4300	6503	95608511	SO:0001819	synonymous_variant	25962	exon8			AB037850	CCDS34923.1, CCDS47894.1	8q22.1	2008-11-25			ENSG00000164944	ENSG00000164944			24500	protein-coding gene	gene with protein product	"""functional spliceosome-associated protein 121"""					10718198	Standard	NM_015496		Approved	DKFZP434I116, fSAP121	uc003ygo.2	Q69YN4	OTTHUMG00000164426	ENST00000297591.5:c.1137C>T	8.37:g.95539335G>A		Somatic		Capture	Illumina HiSeq	Phase_I	95608511	NM_015496	Q2M1N0|Q6AHX9|Q6NT78|Q7Z6C7|Q8IXH4|Q9BTH4|Q9H9C9|Q9NWR3|Q9P2B8|Q9UFW1	Silent	SNP	ENST00000297591.5	37	CCDS34923.1																																																																																				0.343	KIAA1429-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378720.2	NM_015496	
POP1	10940	broad.mit.edu	37	8	99142440	99142440	+	Missense_Mutation	SNP	C	C	T	rs150132872		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr8:99142440C>T	ENST00000401707.2	+	5	802	c.721C>T	c.(721-723)Cgg>Tgg	p.R241W	POP1_ENST00000349693.3_Missense_Mutation_p.R241W	NM_001145860.1|NM_001145861.1	NP_001139332.1|NP_001139333.1	Q99575	POP1_HUMAN	processing of precursor 1, ribonuclease P/MRP subunit (S. cerevisiae)	241					RNA phosphodiester bond hydrolysis (GO:0090501)|RNA phosphodiester bond hydrolysis, endonucleolytic (GO:0090502)|tRNA 5'-leader removal (GO:0001682)|tRNA catabolic process (GO:0016078)	extracellular space (GO:0005615)|nucleolar ribonuclease P complex (GO:0005655)|ribonuclease MRP complex (GO:0000172)	poly(A) RNA binding (GO:0044822)|ribonuclease MRP activity (GO:0000171)|ribonuclease P activity (GO:0004526)	p.R241W(1)		autonomic_ganglia(1)|breast(3)|endometrium(4)|large_intestine(9)|lung(15)|ovary(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	36	Breast(36;1.78e-06)		OV - Ovarian serous cystadenocarcinoma(57;0.145)			CATGACGAACCGGTGCCTCCT	0.498																																					p.R241W												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C721T	8						.	C	TRP/ARG,TRP/ARG,TRP/ARG	1,4405		0,1,2202	76.0	75.0	75.0		721,721,721	4.1	0.0	8	dbSNP_134	75	0,8598		0,0,4299	yes	missense,missense,missense	POP1	NM_001145860.1,NM_001145861.1,NM_015029.2	101,101,101	0,1,6501	TT,TC,CC		0.0,0.0227,0.0077	probably-damaging,probably-damaging,probably-damaging	241/1025,241/1025,241/1025	99142440	1,13003	2203	4299	6502	99211616	SO:0001583	missense	10940	exon5			D31765	CCDS6277.1	8q22.2	2012-05-21			ENSG00000104356	ENSG00000104356			30129	protein-coding gene	gene with protein product	"""processing of precursors 1"""	602486				10199568, 8918471	Standard	NM_015029		Approved		uc011lgv.2	Q99575	OTTHUMG00000164635	ENST00000401707.2:c.721C>T	8.37:g.99142440C>T	ENSP00000385787:p.Arg241Trp	Somatic		Capture	Illumina HiSeq	Phase_I	99211616	NM_001145860	A8K5W9|Q15037	Missense_Mutation	SNP	ENST00000401707.2	37	CCDS6277.1	.	.	.	.	.	.	.	.	.	.	C	14.60	2.584060	0.46110	2.27E-4	0.0	ENSG00000104356	ENST00000401707;ENST00000349693	T;T	0.44881	0.91;0.91	5.91	4.08	0.47627	Ribonuclease P/MRP, subunit POP1 (1);	0.441265	0.23766	N	0.044766	T	0.48786	0.1519	L	0.39245	1.2	0.09310	N	1	D	0.57257	0.979	P	0.61658	0.892	T	0.32771	-0.9894	9	.	.	.	-14.9496	10.1439	0.42751	0.0:0.7926:0.1363:0.0712	.	241	Q99575	POP1_HUMAN	W	241	ENSP00000385787:R241W;ENSP00000339529:R241W	.	R	+	1	2	POP1	99211616	0.042000	0.20092	0.007000	0.13788	0.221000	0.24807	1.880000	0.39628	0.800000	0.34041	-0.140000	0.14226	CGG		0.498	POP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379470.1	NM_015029	
STK3	6788	broad.mit.edu	37	8	99779547	99779547	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr8:99779547C>T	ENST00000419617.2	-	3	300	c.160G>A	c.(160-162)Gca>Aca	p.A54T	STK3_ENST00000523601.1_Missense_Mutation_p.A82T	NM_006281.3	NP_006272.2	Q13188	STK3_HUMAN	serine/threonine kinase 3	54	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				apoptotic process (GO:0006915)|cell differentiation involved in embryonic placenta development (GO:0060706)|central nervous system development (GO:0007417)|endocardium development (GO:0003157)|hepatocyte apoptotic process (GO:0097284)|hippo signaling (GO:0035329)|intracellular signal transduction (GO:0035556)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of organ growth (GO:0046621)|neural tube formation (GO:0001841)|positive regulation of apoptotic process (GO:0043065)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|positive regulation of JNK cascade (GO:0046330)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|primitive hemopoiesis (GO:0060215)|protein phosphorylation (GO:0006468)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|protein dimerization activity (GO:0046983)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activator activity (GO:0043539)|protein serine/threonine kinase activity (GO:0004674)	p.A54T(1)		breast(2)|endometrium(2)|kidney(1)|large_intestine(4)|lung(6)|ovary(1)|upper_aerodigestive_tract(1)	17	Breast(36;2.4e-06)	Breast(495;0.106)	OV - Ovarian serous cystadenocarcinoma(57;0.0382)	KIRC - Kidney renal clear cell carcinoma(542;9.44e-06)		TGTTTAATTGCGACAACTTGA	0.323																																					p.A54T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G160A	8						.						108.0	100.0	103.0					8																	99779547		1877	4142	6019	99848723	SO:0001583	missense	6788	exon3			BC010640	CCDS47900.1, CCDS59108.1, CCDS75774.1	8q22.2	2011-05-24	2010-06-25		ENSG00000104375	ENSG00000104375			11406	protein-coding gene	gene with protein product		605030	"""serine/threonine kinase 3 (Ste20, yeast homolog)"""			8816758	Standard	NM_006281		Approved	MST2, KRS1	uc003yip.4	Q13188	OTTHUMG00000164651	ENST00000419617.2:c.160G>A	8.37:g.99779547C>T	ENSP00000390500:p.Ala54Thr	Somatic		Capture	Illumina HiSeq	Phase_I	99848723	NM_006281	A8K722|B3KYA7|Q15445|Q15801|Q96FM6	Missense_Mutation	SNP	ENST00000419617.2	37	CCDS47900.1	.	.	.	.	.	.	.	.	.	.	C	34	5.319913	0.95682	.	.	ENSG00000104375	ENST00000419617;ENST00000523601;ENST00000518165	T;T;T	0.41758	0.99;0.99;1.53	5.67	5.67	0.87782	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.77308	0.4111	H	0.95950	3.745	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.77004	0.978;0.989;0.985	D	0.84472	0.0600	10	0.87932	D	0	.	19.7782	0.96405	0.0:1.0:0.0:0.0	.	54;54;82	E5RFQ9;Q13188;B3KYA7	.;STK3_HUMAN;.	T	54;82;54	ENSP00000390500:A54T;ENSP00000429744:A82T;ENSP00000428014:A54T	ENSP00000390500:A54T	A	-	1	0	STK3	99848723	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.776000	0.85560	2.667000	0.90743	0.561000	0.74099	GCA		0.323	STK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379635.1	NM_006281	
ZNF517	340385	broad.mit.edu	37	8	146032884	146032884	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr8:146032884C>T	ENST00000531720.1	+	4	628	c.583C>T	c.(583-585)Cac>Tac	p.H195Y	ZNF517_ENST00000526178.1_Intron|ZNF517_ENST00000525105.1_Intron|ZNF517_ENST00000359971.3_Missense_Mutation_p.H195Y			Q6ZMY9	ZN517_HUMAN	zinc finger protein 517	195					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.H195Y(1)		breast(1)|endometrium(2)|large_intestine(2)|lung(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	13	all_cancers(97;1.03e-11)|all_epithelial(106;6.69e-11)|Lung NSC(106;4.08e-05)|all_lung(105;0.000125)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		Epithelial(56;5.47e-39)|OV - Ovarian serous cystadenocarcinoma(54;6.38e-39)|all cancers(56;5.47e-34)|BRCA - Breast invasive adenocarcinoma(115;0.0355)|Colorectal(110;0.055)			GCTTCTCAGGCACCAGATCAT	0.632																																					p.H195Y												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C583T	8						.						28.0	26.0	27.0					8																	146032884		2195	4297	6492	146003688	SO:0001583	missense	340385	exon5			AK096527	CCDS6434.1	8q24.3	2013-01-08				ENSG00000197363		"""Zinc fingers, C2H2-type"", ""-"""	27984	protein-coding gene	gene with protein product							Standard	NM_213605		Approved		uc003zed.1	Q6ZMY9		ENST00000531720.1:c.583C>T	8.37:g.146032884C>T	ENSP00000436103:p.His195Tyr	Somatic		Capture	Illumina HiSeq	Phase_I	146003688	NM_213605		Missense_Mutation	SNP	ENST00000531720.1	37	CCDS6434.1	.	.	.	.	.	.	.	.	.	.	C	17.53	3.412850	0.62511	.	.	ENSG00000197363	ENST00000359971;ENST00000531720	D;D	0.86769	-2.17;-2.17	2.55	2.55	0.30701	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	D	0.92195	0.7525	M	0.87328	2.875	0.31631	N	0.649061	D	0.71674	0.998	P	0.58172	0.834	D	0.91380	0.5126	9	0.62326	D	0.03	.	12.1804	0.54208	0.0:1.0:0.0:0.0	.	195	Q6ZMY9	ZN517_HUMAN	Y	195	ENSP00000353058:H195Y;ENSP00000436103:H195Y	ENSP00000353058:H195Y	H	+	1	0	ZNF517	146003688	0.964000	0.33143	0.547000	0.28179	0.592000	0.36648	4.687000	0.61708	1.419000	0.47118	0.462000	0.41574	CAC		0.632	ZNF517-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382642.1	XM_291261	
COL15A1	1306	broad.mit.edu	37	9	101785683	101785683	+	Silent	SNP	C	C	T	rs546379223		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr9:101785683C>T	ENST00000375001.3	+	14	2229	c.1806C>T	c.(1804-1806)gaC>gaT	p.D602D		NM_001855.3	NP_001846.3	P39059	COFA1_HUMAN	collagen, type XV, alpha 1	602	Nonhelical region 2 (NC2).				angiogenesis (GO:0001525)|cell adhesion (GO:0007155)|cell differentiation (GO:0030154)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|signal transduction (GO:0007165)	collagen type XV trimer (GO:0005582)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	extracellular matrix structural constituent (GO:0005201)	p.D602D(1)		NS(1)|breast(4)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(20)|liver(1)|lung(42)|ovary(6)|prostate(5)|skin(6)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	107		Acute lymphoblastic leukemia(62;0.0562)				GGGGCTCGGACGTCGGCTCTG	0.562																																					p.D602D												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1806T	9						.						59.0	57.0	58.0					9																	101785683		2203	4300	6503	100825504	SO:0001819	synonymous_variant	1306	exon14			L25286	CCDS35081.1	9q21-q22	2013-01-16			ENSG00000204291	ENSG00000204291		"""Proteoglycans / Extracellular Matrix : Collagen proteoglycans"", ""Collagens"""	2192	protein-coding gene	gene with protein product	"""collagen type XV proteoglycan"""	120325				1427836	Standard	NM_001855		Approved		uc004azb.2	P39059	OTTHUMG00000020351	ENST00000375001.3:c.1806C>T	9.37:g.101785683C>T		Somatic		Capture	Illumina HiSeq	Phase_I	100825504	NM_001855	Q5T6J4|Q9UDC5|Q9Y4W4	Silent	SNP	ENST00000375001.3	37	CCDS35081.1																																																																																				0.562	COL15A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053386.3	NM_001855	
INVS	27130	broad.mit.edu	37	9	102988438	102988438	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr9:102988438G>A	ENST00000262457.2	+	4	553	c.368G>A	c.(367-369)cGg>cAg	p.R123Q	INVS_ENST00000262456.2_Missense_Mutation_p.R123Q|INVS_ENST00000460636.2_3'UTR|INVS_ENST00000541287.1_Missense_Mutation_p.R27Q	NM_014425.3	NP_055240.2	Q9Y283	INVS_HUMAN	inversin	123					embryonic heart tube left/right pattern formation (GO:0060971)|kidney development (GO:0001822)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|pancreas development (GO:0031016)|post-embryonic development (GO:0009791)|Wnt signaling pathway (GO:0016055)	cilium (GO:0005929)|cytoplasm (GO:0005737)|membrane (GO:0016020)|microtubule (GO:0005874)|nucleus (GO:0005634)		p.R123Q(1)		breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(5)|ovary(4)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	31		Acute lymphoblastic leukemia(62;0.056)				TTGACCACCCGGCACAGGAGC	0.428																																					p.R123Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G368A	9						.						57.0	55.0	56.0					9																	102988438		2203	4300	6503	102028259	SO:0001583	missense	27130	exon4			AF039217	CCDS6746.1, CCDS6747.1	9q31	2013-01-10	2003-08-11		ENSG00000119509	ENSG00000119509		"""Ankyrin repeat domain containing"""	17870	protein-coding gene	gene with protein product	"""nephrocystin 2"""	243305	"""nephronophthisis 2 (infantile)"""	NPHP2		12872123	Standard	NM_014425		Approved		uc004bap.2	Q9Y283	OTTHUMG00000020364	ENST00000262457.2:c.368G>A	9.37:g.102988438G>A	ENSP00000262457:p.Arg123Gln	Somatic		Capture	Illumina HiSeq	Phase_I	102028259	NM_183245	A2A2Y2|Q2NKL0|Q5W0T6|Q8IVX8|Q9BRB9|Q9Y488|Q9Y498	Missense_Mutation	SNP	ENST00000262457.2	37	CCDS6746.1	.	.	.	.	.	.	.	.	.	.	G	28.0	4.879069	0.91740	.	.	ENSG00000119509	ENST00000262457;ENST00000541287;ENST00000262456	T;T;T	0.67523	-0.13;-0.27;-0.13	5.6	5.6	0.85130	Ankyrin repeat-containing domain (4);	0.000000	0.85682	D	0.000000	T	0.73729	0.3624	L	0.33293	1	0.80722	D	1	D;D;P	0.89917	0.999;1.0;0.85	D;D;B	0.74023	0.955;0.982;0.198	T	0.70371	-0.4890	10	0.30854	T	0.27	.	17.8035	0.88595	0.0:0.0:1.0:0.0	.	27;123;123	F5GZH2;Q9Y283;Q9Y283-2	.;INVS_HUMAN;.	Q	123;27;123	ENSP00000262457:R123Q;ENSP00000444454:R27Q;ENSP00000262456:R123Q	ENSP00000262456:R123Q	R	+	2	0	INVS	102028259	1.000000	0.71417	0.995000	0.50966	0.481000	0.33189	7.666000	0.83877	2.628000	0.89032	0.655000	0.94253	CGG		0.428	INVS-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053407.1	NM_014425	
MSANTD3	91283	broad.mit.edu	37	9	103204373	103204373	+	Silent	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr9:103204373G>A	ENST00000395067.2	+	2	424	c.153G>A	c.(151-153)gcG>gcA	p.A51A	MSANTD3_ENST00000374885.1_Silent_p.A51A|TMEFF1_ENST00000334943.6_5'Flank|MSANTD3-TMEFF1_ENST00000502978.1_5'Flank	NM_001198805.1|NM_001198806.1|NM_080655.2	NP_001185734.1|NP_001185735.1|NP_542386.1	Q96H12	MSD3_HUMAN	Myb/SANT-like DNA-binding domain containing 3	51	Myb-like.							p.A51A(1)		endometrium(2)|lung(2)	4						CCTGGCAGGCGCTGGCCCACG	0.483																																					p.A51A												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G153A	9						.						41.0	41.0	41.0					9																	103204373		2203	4300	6503	102244194	SO:0001819	synonymous_variant	8577	exon2			BC008993	CCDS6749.1, CCDS56579.1	9q31.1	2012-03-13	2012-03-13	2012-03-13	ENSG00000066697	ENSG00000066697			23370	protein-coding gene	gene with protein product			"""chromosome 9 open reading frame 30"""	C9orf30			Standard	NM_080655		Approved	MGC17337		Q96H12	OTTHUMG00000020365	ENST00000395067.2:c.153G>A	9.37:g.103204373G>A		Somatic		Capture	Illumina HiSeq	Phase_I	102244194	NM_080655	B2RC35|Q5T726|Q5T727|Q5T728	Silent	SNP	ENST00000395067.2	37	CCDS6749.1																																																																																				0.483	MSANTD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053410.1	NM_080655	
ABCA1	19	broad.mit.edu	37	9	107562120	107562120	+	Silent	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr9:107562120C>T	ENST00000374736.3	-	36	5317	c.4923G>A	c.(4921-4923)caG>caA	p.Q1641Q		NM_005502.3	NP_005493.2	O95477	ABCA1_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 1	1641					apolipoprotein A-I-mediated signaling pathway (GO:0038027)|cellular lipid metabolic process (GO:0044255)|cellular response to cholesterol (GO:0071397)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to retinoic acid (GO:0071300)|cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|endosomal transport (GO:0016197)|G-protein coupled receptor signaling pathway (GO:0007186)|high-density lipoprotein particle assembly (GO:0034380)|interleukin-1 beta secretion (GO:0050702)|intracellular cholesterol transport (GO:0032367)|lipoprotein metabolic process (GO:0042157)|lysosome organization (GO:0007040)|negative regulation of cholesterol storage (GO:0010887)|negative regulation of macrophage derived foam cell differentiation (GO:0010745)|peptide secretion (GO:0002790)|phagocytosis, engulfment (GO:0006911)|phospholipid efflux (GO:0033700)|phospholipid homeostasis (GO:0055091)|phospholipid translocation (GO:0045332)|platelet dense granule organization (GO:0060155)|positive regulation of cAMP biosynthetic process (GO:0030819)|positive regulation of cholesterol efflux (GO:0010875)|protein lipidation (GO:0006497)|regulation of Cdc42 protein signal transduction (GO:0032489)|response to drug (GO:0042493)|response to laminar fluid shear stress (GO:0034616)|response to low-density lipoprotein particle (GO:0055098)|response to nutrient (GO:0007584)|reverse cholesterol transport (GO:0043691)|small molecule metabolic process (GO:0044281)	endocytic vesicle (GO:0030139)|external side of plasma membrane (GO:0009897)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|perinuclear region of cytoplasm (GO:0048471)|phagocytic vesicle (GO:0045335)|plasma membrane (GO:0005886)	anion transmembrane transporter activity (GO:0008509)|apolipoprotein A-I binding (GO:0034186)|apolipoprotein A-I receptor activity (GO:0034188)|apolipoprotein binding (GO:0034185)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|ATPase binding (GO:0051117)|cholesterol binding (GO:0015485)|cholesterol transporter activity (GO:0017127)|phospholipid binding (GO:0005543)|phospholipid transporter activity (GO:0005548)|receptor binding (GO:0005102)|small GTPase binding (GO:0031267)|syntaxin binding (GO:0019905)	p.Q1641Q(1)		NS(1)|autonomic_ganglia(1)|breast(5)|central_nervous_system(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(31)|liver(1)|lung(40)|ovary(5)|pancreas(2)|prostate(4)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	115				OV - Ovarian serous cystadenocarcinoma(323;0.023)	Adenosine triphosphate(DB00171)|Glyburide(DB01016)|Probucol(DB01599)	CTGAGAGCTGCTGCTTGGTGA	0.488																																					p.Q1641Q												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G4923A	9						.						146.0	130.0	135.0					9																	107562120		2203	4300	6503	106601941	SO:0001819	synonymous_variant	19	exon36			AJ012376	CCDS6762.1	9q31	2014-03-14			ENSG00000165029	ENSG00000165029		"""ATP binding cassette transporters / subfamily A"""	29	protein-coding gene	gene with protein product	"""Tangier disease"""	600046		ABC1, HDLDT1		8088782, 10431236, 10431237, 10431238	Standard	NM_005502		Approved	TGD	uc004bcl.3	O95477	OTTHUMG00000020417	ENST00000374736.3:c.4923G>A	9.37:g.107562120C>T		Somatic		Capture	Illumina HiSeq	Phase_I	106601941	NM_005502	Q5VX33|Q96S56|Q96T85|Q9NQV4|Q9UN06|Q9UN07|Q9UN08|Q9UN09	Silent	SNP	ENST00000374736.3	37	CCDS6762.1																																																																																				0.488	ABCA1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053491.1	NM_005502	
ABCA1	19	broad.mit.edu	37	9	107645364	107645364	+	Missense_Mutation	SNP	C	C	T	rs138438101		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr9:107645364C>T	ENST00000374736.3	-	5	771	c.377G>A	c.(376-378)cGc>cAc	p.R126H	ABCA1_ENST00000374733.1_Missense_Mutation_p.R66H|ABCA1_ENST00000423487.2_Missense_Mutation_p.R126H	NM_005502.3	NP_005493.2	O95477	ABCA1_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 1	126					apolipoprotein A-I-mediated signaling pathway (GO:0038027)|cellular lipid metabolic process (GO:0044255)|cellular response to cholesterol (GO:0071397)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to retinoic acid (GO:0071300)|cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|endosomal transport (GO:0016197)|G-protein coupled receptor signaling pathway (GO:0007186)|high-density lipoprotein particle assembly (GO:0034380)|interleukin-1 beta secretion (GO:0050702)|intracellular cholesterol transport (GO:0032367)|lipoprotein metabolic process (GO:0042157)|lysosome organization (GO:0007040)|negative regulation of cholesterol storage (GO:0010887)|negative regulation of macrophage derived foam cell differentiation (GO:0010745)|peptide secretion (GO:0002790)|phagocytosis, engulfment (GO:0006911)|phospholipid efflux (GO:0033700)|phospholipid homeostasis (GO:0055091)|phospholipid translocation (GO:0045332)|platelet dense granule organization (GO:0060155)|positive regulation of cAMP biosynthetic process (GO:0030819)|positive regulation of cholesterol efflux (GO:0010875)|protein lipidation (GO:0006497)|regulation of Cdc42 protein signal transduction (GO:0032489)|response to drug (GO:0042493)|response to laminar fluid shear stress (GO:0034616)|response to low-density lipoprotein particle (GO:0055098)|response to nutrient (GO:0007584)|reverse cholesterol transport (GO:0043691)|small molecule metabolic process (GO:0044281)	endocytic vesicle (GO:0030139)|external side of plasma membrane (GO:0009897)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|perinuclear region of cytoplasm (GO:0048471)|phagocytic vesicle (GO:0045335)|plasma membrane (GO:0005886)	anion transmembrane transporter activity (GO:0008509)|apolipoprotein A-I binding (GO:0034186)|apolipoprotein A-I receptor activity (GO:0034188)|apolipoprotein binding (GO:0034185)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|ATPase binding (GO:0051117)|cholesterol binding (GO:0015485)|cholesterol transporter activity (GO:0017127)|phospholipid binding (GO:0005543)|phospholipid transporter activity (GO:0005548)|receptor binding (GO:0005102)|small GTPase binding (GO:0031267)|syntaxin binding (GO:0019905)	p.R126H(1)		NS(1)|autonomic_ganglia(1)|breast(5)|central_nervous_system(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(31)|liver(1)|lung(40)|ovary(5)|pancreas(2)|prostate(4)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	115				OV - Ovarian serous cystadenocarcinoma(323;0.023)	Adenosine triphosphate(DB00171)|Glyburide(DB01016)|Probucol(DB01599)	CAGAACTTTGCGCATGTCCTT	0.453																																					p.R126H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G377A	9						.	C	HIS/ARG	0,4406		0,0,2203	167.0	157.0	160.0		377	1.9	0.6	9	dbSNP_134	160	1,8599	1.2+/-3.3	0,1,4299	no	missense	ABCA1	NM_005502.3	29	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	benign	126/2262	107645364	1,13005	2203	4300	6503	106685185	SO:0001583	missense	19	exon5			AJ012376	CCDS6762.1	9q31	2014-03-14			ENSG00000165029	ENSG00000165029		"""ATP binding cassette transporters / subfamily A"""	29	protein-coding gene	gene with protein product	"""Tangier disease"""	600046		ABC1, HDLDT1		8088782, 10431236, 10431237, 10431238	Standard	NM_005502		Approved	TGD	uc004bcl.3	O95477	OTTHUMG00000020417	ENST00000374736.3:c.377G>A	9.37:g.107645364C>T	ENSP00000363868:p.Arg126His	Somatic		Capture	Illumina HiSeq	Phase_I	106685185	NM_005502	Q5VX33|Q96S56|Q96T85|Q9NQV4|Q9UN06|Q9UN07|Q9UN08|Q9UN09	Missense_Mutation	SNP	ENST00000374736.3	37	CCDS6762.1	.	.	.	.	.	.	.	.	.	.	C	8.006	0.756436	0.15846	0.0	1.16E-4	ENSG00000165029	ENST00000374736;ENST00000423487;ENST00000374733	D;D;D	0.95918	-3.85;-3.85;-3.85	5.49	1.88	0.25563	.	0.567931	0.21605	N	0.071891	D	0.86690	0.5993	N	0.08118	0	0.26805	N	0.969127	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.75010	-0.3468	10	0.24483	T	0.36	.	8.7159	0.34411	0.0:0.2302:0.0:0.7698	.	66;126	B1AMI1;O95477	.;ABCA1_HUMAN	H	126;126;66	ENSP00000363868:R126H;ENSP00000416623:R126H;ENSP00000363865:R66H	ENSP00000363865:R66H	R	-	2	0	ABCA1	106685185	0.361000	0.24972	0.569000	0.28460	0.859000	0.49053	1.329000	0.33770	0.132000	0.18615	-0.302000	0.09304	CGC		0.453	ABCA1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053491.1	NM_005502	
ZNF462	58499	broad.mit.edu	37	9	109687408	109687408	+	Silent	SNP	T	T	C			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr9:109687408T>C	ENST00000277225.5	+	3	1504	c.1215T>C	c.(1213-1215)gaT>gaC	p.D405D	ZNF462_ENST00000441147.2_5'Flank|ZNF462_ENST00000457913.1_Silent_p.D405D			Q96JM2	ZN462_HUMAN	zinc finger protein 462	405					chromatin organization (GO:0006325)|negative regulation of DNA binding (GO:0043392)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.D405D(1)		NS(2)|autonomic_ganglia(2)|breast(5)|central_nervous_system(4)|cervix(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(17)|large_intestine(20)|lung(32)|ovary(5)|prostate(6)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	119						GTGCTATGGATCACCAGACAT	0.418																																					p.D405D												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.T1215C	9						.						109.0	103.0	105.0					9																	109687408		2203	4300	6503	108727229	SO:0001819	synonymous_variant	58499	exon3			AB058706	CCDS35096.1	9q31.3	2008-02-05			ENSG00000148143	ENSG00000148143		"""Zinc fingers, C2H2-type"""	21684	protein-coding gene	gene with protein product							Standard	NM_021224		Approved	DKFZP762N2316, KIAA1803, Zfp462	uc004bcz.3	Q96JM2	OTTHUMG00000020438	ENST00000277225.5:c.1215T>C	9.37:g.109687408T>C		Somatic		Capture	Illumina HiSeq	Phase_I	108727229	NM_021224	Q5T0T4|Q8N408	Silent	SNP	ENST00000277225.5	37	CCDS35096.1																																																																																				0.418	ZNF462-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000053532.2	NM_021224	
CTNNAL1	8727	broad.mit.edu	37	9	111761423	111761423	+	Silent	SNP	T	T	C			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr9:111761423T>C	ENST00000325551.4	-	2	341	c.255A>G	c.(253-255)gtA>gtG	p.V85V	CTNNAL1_ENST00000374595.4_Silent_p.V85V|CTNNAL1_ENST00000325580.6_Silent_p.V85V|CTNNAL1_ENST00000374593.4_Silent_p.V85V	NM_003798.2	NP_003789.1	Q9UBT7	CTNL1_HUMAN	catenin (cadherin-associated protein), alpha-like 1	85					cell adhesion (GO:0007155)|Rho protein signal transduction (GO:0007266)	actin cytoskeleton (GO:0015629)|cytosol (GO:0005829)|plasma membrane (GO:0005886)	structural molecule activity (GO:0005198)	p.V85V(1)		cervix(1)|endometrium(2)|kidney(1)|large_intestine(9)|lung(5)|ovary(1)|prostate(4)|urinary_tract(2)	25				STAD - Stomach adenocarcinoma(157;0.0768)		TAGCTTCTCCTACTTTAACAA	0.343																																					p.V85V												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.A255G	9						.						170.0	170.0	170.0					9																	111761423		2203	4300	6503	110801244	SO:0001819	synonymous_variant	8727	exon2			AF030233	CCDS6775.1, CCDS69638.1	9q31.2	2008-07-21			ENSG00000119326	ENSG00000119326			2512	protein-coding gene	gene with protein product	"""alpha-catulin"", ""alpha2-catulin"""	604785				9806841	Standard	XM_005252291		Approved	CLLP, alpha-CATU	uc004bdo.1	Q9UBT7	OTTHUMG00000020466	ENST00000325551.4:c.255A>G	9.37:g.111761423T>C		Somatic		Capture	Illumina HiSeq	Phase_I	110801244	NM_003798	B5BU47|O76084|Q53FQ2|Q5JTQ7|Q5JTQ8|Q9Y401	Silent	SNP	ENST00000325551.4	37	CCDS6775.1																																																																																				0.343	CTNNAL1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000053577.1	NM_003798	
EPB41L4B	54566	broad.mit.edu	37	9	112017804	112017804	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr9:112017804G>A	ENST00000374566.3	-	11	1673	c.1156C>T	c.(1156-1158)Cgc>Tgc	p.R386C	EPB41L4B_ENST00000374557.4_Missense_Mutation_p.R386C	NM_019114.3	NP_061987.3	Q9H329	E41LB_HUMAN	erythrocyte membrane protein band 4.1 like 4B	386					actomyosin structure organization (GO:0031032)	apical part of cell (GO:0045177)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extrinsic component of membrane (GO:0019898)	structural constituent of cytoskeleton (GO:0005200)	p.R386C(1)		NS(2)|breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(6)|lung(14)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	39						AATCTGAAGCGAGAGCCCAGC	0.493																																					p.R386C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1156T	9						.						87.0	83.0	84.0					9																	112017804		1936	4154	6090	111057625	SO:0001583	missense	54566	exon11			AB032179	CCDS43859.1, CCDS43860.1	9q22.1-q22.3	2008-02-05			ENSG00000095203	ENSG00000095203			19818	protein-coding gene	gene with protein product		610340				10783258	Standard	NM_018424		Approved	EHM2	uc004bdz.1	Q9H329	OTTHUMG00000020470	ENST00000374566.3:c.1156C>T	9.37:g.112017804G>A	ENSP00000363694:p.Arg386Cys	Somatic		Capture	Illumina HiSeq	Phase_I	111057625	NM_018424	Q5T4G5|Q5T4G6|Q9H328|Q9P2V3	Missense_Mutation	SNP	ENST00000374566.3	37	CCDS43859.1	.	.	.	.	.	.	.	.	.	.	G	34	5.383256	0.95967	.	.	ENSG00000095203	ENST00000262536;ENST00000374566;ENST00000374557;ENST00000311609	D;D	0.88664	-2.41;-2.41	5.8	5.8	0.92144	FERM adjacent (FA) (1);	0.000000	0.40302	N	0.001126	D	0.95532	0.8548	M	0.86651	2.83	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.993;0.998	D	0.95571	0.8638	10	0.87932	D	0	.	20.0467	0.97609	0.0:0.0:1.0:0.0	.	386;386	Q9H329-2;Q9H329	.;E41LB_HUMAN	C	71;386;386;308	ENSP00000363694:R386C;ENSP00000363685:R386C	ENSP00000262536:R71C	R	-	1	0	EPB41L4B	111057625	1.000000	0.71417	0.982000	0.44146	0.990000	0.78478	9.793000	0.99091	2.749000	0.94314	0.655000	0.94253	CGC		0.493	EPB41L4B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000053592.1	NM_018424	
C9orf152	401546	broad.mit.edu	37	9	112963592	112963592	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr9:112963592G>A	ENST00000400613.4	-	2	965	c.356C>T	c.(355-357)aCg>aTg	p.T119M	C9orf152_ENST00000473442.1_Intron	NM_001012993.2	NP_001013011.2	Q5JTZ5	CI152_HUMAN	chromosome 9 open reading frame 152	119								p.T98M(1)		NS(1)|endometrium(1)|large_intestine(1)|lung(1)|skin(1)|stomach(1)	6						CTCCAGGTGCGTGTGCCATGG	0.582																																					p.T119M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C356T	9						.						94.0	86.0	89.0					9																	112963592		2203	4300	6503	112003413	SO:0001583	missense	401546	exon2			BX648620	CCDS35102.2	9q31.3	2012-04-03			ENSG00000188959	ENSG00000188959			31455	protein-coding gene	gene with protein product							Standard	NM_001012993		Approved	bA470J20.2	uc011lwk.2	Q5JTZ5	OTTHUMG00000020478	ENST00000400613.4:c.356C>T	9.37:g.112963592G>A	ENSP00000383456:p.Thr119Met	Somatic		Capture	Illumina HiSeq	Phase_I	112003413	NM_001012993	A8MWT6	Missense_Mutation	SNP	ENST00000400613.4	37	CCDS35102.2	.	.	.	.	.	.	.	.	.	.	G	14.14	2.446281	0.43429	.	.	ENSG00000188959	ENST00000400613	.	.	.	4.53	3.63	0.41609	.	0.106709	0.40728	N	0.001033	T	0.55369	0.1916	L	0.32530	0.975	0.32217	N	0.575781	D	0.89917	1.0	D	0.72338	0.977	T	0.65240	-0.6216	9	0.87932	D	0	-8.2753	12.3796	0.55299	0.0:0.0:0.8304:0.1695	.	119	Q5JTZ5	CI152_HUMAN	M	119	.	ENSP00000383456:T119M	T	-	2	0	C9orf152	112003413	0.928000	0.31464	0.952000	0.39060	0.081000	0.17604	1.319000	0.33655	1.495000	0.48549	0.655000	0.94253	ACG		0.582	C9orf152-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053602.2	NM_001012993	
SLC46A2	57864	broad.mit.edu	37	9	115648838	115648838	+	Silent	SNP	G	G	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr9:115648838G>T	ENST00000374228.4	-	3	1503	c.1272C>A	c.(1270-1272)acC>acA	p.T424T	RP11-408O19.5_ENST00000605480.1_RNA	NM_033051.3	NP_149040.3	Q9BY10	TSCOT_HUMAN	solute carrier family 46, member 2	424					negative regulation of T cell apoptotic process (GO:0070233)|regulation of T cell differentiation (GO:0045580)|T cell homeostasis (GO:0043029)|thymus development (GO:0048538)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	symporter activity (GO:0015293)	p.T424T(1)		central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(11)|pancreas(1)|skin(1)	18						TGTTGTACAAGGTGGATGTCA	0.532																																					p.T424T												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1272A	9						.						221.0	171.0	188.0					9																	115648838		2203	4300	6503	114688659	SO:0001819	synonymous_variant	57864	exon3			AF242557	CCDS6786.1	9q32	2013-05-22	2007-03-29	2007-03-29	ENSG00000119457	ENSG00000119457		"""Solute carriers"""	16055	protein-coding gene	gene with protein product		608956	"""thymic stromal co-transporter"""	TSCOT		10978518, 12826694	Standard	NM_033051		Approved	Ly110	uc004bgk.3	Q9BY10	OTTHUMG00000020513	ENST00000374228.4:c.1272C>A	9.37:g.115648838G>T		Somatic		Capture	Illumina HiSeq	Phase_I	114688659	NM_033051	B1ALK1|Q86VT0|Q96NE2	Silent	SNP	ENST00000374228.4	37	CCDS6786.1																																																																																				0.532	SLC46A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053702.1	NM_033051	
TNC	3371	broad.mit.edu	37	9	117788871	117788871	+	Silent	SNP	G	G	A	rs142272539	byFrequency	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr9:117788871G>A	ENST00000350763.4	-	26	6684	c.6273C>T	c.(6271-6273)agC>agT	p.S2091S	TNC_ENST00000537320.1_Silent_p.S1454S|TNC_ENST00000535648.1_Silent_p.S1636S|TNC_ENST00000345230.3_Silent_p.S1454S|TNC_ENST00000340094.3_Silent_p.S1727S|TNC_ENST00000423613.2_Silent_p.S1818S|TNC_ENST00000542877.1_Silent_p.S1728S|TNC_ENST00000341037.4_Silent_p.S1909S|TNC_ENST00000346706.3_Silent_p.S1545S	NM_002160.3	NP_002151.2	P24821	TENA_HUMAN	tenascin C	2091	Fibrinogen C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00739}.				bud outgrowth involved in lung branching (GO:0060447)|cell adhesion (GO:0007155)|cellular response to prostaglandin D stimulus (GO:0071799)|cellular response to retinoic acid (GO:0071300)|cellular response to vitamin D (GO:0071305)|extracellular matrix organization (GO:0030198)|mesenchymal-epithelial cell signaling involved in prostate gland development (GO:0060739)|negative regulation of cell adhesion (GO:0007162)|neuromuscular junction development (GO:0007528)|odontogenesis of dentin-containing tooth (GO:0042475)|osteoblast differentiation (GO:0001649)|peripheral nervous system axon regeneration (GO:0014012)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|prostate gland epithelium morphogenesis (GO:0060740)|response to ethanol (GO:0045471)|response to fibroblast growth factor (GO:0071774)|response to mechanical stimulus (GO:0009612)|response to wounding (GO:0009611)|wound healing (GO:0042060)	basement membrane (GO:0005604)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|focal adhesion (GO:0005925)|interstitial matrix (GO:0005614)|membrane (GO:0016020)	syndecan binding (GO:0045545)	p.S2091S(1)		NS(3)|breast(5)|central_nervous_system(4)|endometrium(8)|kidney(6)|large_intestine(32)|liver(1)|lung(39)|ovary(1)|pancreas(2)|prostate(5)|skin(5)|stomach(5)|upper_aerodigestive_tract(2)|urinary_tract(2)	120						CATCTCCCACGCTGAACTTGT	0.567													G|||	3	0.000599042	0.0	0.0014	5008	,	,		13539	0.0		0.002	False		,,,				2504	0.0				p.S2091S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C6273T	9						.	G		3,4403	6.2+/-15.9	0,3,2200	131.0	98.0	109.0		6273	-4.3	0.9	9	dbSNP_134	109	8,8592	6.4+/-24.3	0,8,4292	no	coding-synonymous	TNC	NM_002160.3		0,11,6492	AA,AG,GG		0.093,0.0681,0.0846		2091/2202	117788871	11,12995	2203	4300	6503	116828692	SO:0001819	synonymous_variant	3371	exon26				CCDS6811.1	9q33.1	2014-01-28	2008-07-31	2002-06-07	ENSG00000041982	ENSG00000041982		"""Fibrinogen C domain containing"", ""Fibronectin type III domain containing"""	5318	protein-coding gene	gene with protein product	"""hexabrachion (tenascin)"""	187380	"""hexabrachion (tenascin C, cytotactin)"", ""deafness, autosomal dominant 56"""	HXB, DFNA56		1704365, 1707164, 23936043	Standard	NM_002160		Approved	TN, MGC167029	uc004bjj.4	P24821	OTTHUMG00000021010	ENST00000350763.4:c.6273C>T	9.37:g.117788871G>A		Somatic		Capture	Illumina HiSeq	Phase_I	116828692	NM_002160	C9IYT7|C9J575|C9J6D9|C9J848|Q14583|Q15567|Q5T7S3	Silent	SNP	ENST00000350763.4	37	CCDS6811.1																																																																																				0.567	TNC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055418.2	NM_002160	
TNC	3371	broad.mit.edu	37	9	117838850	117838850	+	Silent	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr9:117838850G>A	ENST00000350763.4	-	8	3090	c.2679C>T	c.(2677-2679)ctC>ctT	p.L893L	TNC_ENST00000537320.1_Silent_p.L893L|TNC_ENST00000535648.1_Silent_p.L893L|TNC_ENST00000345230.3_Silent_p.L893L|TNC_ENST00000340094.3_Silent_p.L893L|TNC_ENST00000423613.2_Silent_p.L893L|TNC_ENST00000542877.1_Silent_p.L893L|TNC_ENST00000341037.4_Silent_p.L893L|TNC_ENST00000346706.3_Silent_p.L893L	NM_002160.3	NP_002151.2	P24821	TENA_HUMAN	tenascin C	893	Fibronectin type-III 3. {ECO:0000255|PROSITE-ProRule:PRU00316}.				bud outgrowth involved in lung branching (GO:0060447)|cell adhesion (GO:0007155)|cellular response to prostaglandin D stimulus (GO:0071799)|cellular response to retinoic acid (GO:0071300)|cellular response to vitamin D (GO:0071305)|extracellular matrix organization (GO:0030198)|mesenchymal-epithelial cell signaling involved in prostate gland development (GO:0060739)|negative regulation of cell adhesion (GO:0007162)|neuromuscular junction development (GO:0007528)|odontogenesis of dentin-containing tooth (GO:0042475)|osteoblast differentiation (GO:0001649)|peripheral nervous system axon regeneration (GO:0014012)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|prostate gland epithelium morphogenesis (GO:0060740)|response to ethanol (GO:0045471)|response to fibroblast growth factor (GO:0071774)|response to mechanical stimulus (GO:0009612)|response to wounding (GO:0009611)|wound healing (GO:0042060)	basement membrane (GO:0005604)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|focal adhesion (GO:0005925)|interstitial matrix (GO:0005614)|membrane (GO:0016020)	syndecan binding (GO:0045545)	p.L893L(1)		NS(3)|breast(5)|central_nervous_system(4)|endometrium(8)|kidney(6)|large_intestine(32)|liver(1)|lung(39)|ovary(1)|pancreas(2)|prostate(5)|skin(5)|stomach(5)|upper_aerodigestive_tract(2)|urinary_tract(2)	120						TGGGAGCATCGAGGCCTGTTT	0.458																																					p.L893L												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C2679T	9						.						222.0	204.0	210.0					9																	117838850		2203	4300	6503	116878671	SO:0001819	synonymous_variant	3371	exon8				CCDS6811.1	9q33.1	2014-01-28	2008-07-31	2002-06-07	ENSG00000041982	ENSG00000041982		"""Fibrinogen C domain containing"", ""Fibronectin type III domain containing"""	5318	protein-coding gene	gene with protein product	"""hexabrachion (tenascin)"""	187380	"""hexabrachion (tenascin C, cytotactin)"", ""deafness, autosomal dominant 56"""	HXB, DFNA56		1704365, 1707164, 23936043	Standard	NM_002160		Approved	TN, MGC167029	uc004bjj.4	P24821	OTTHUMG00000021010	ENST00000350763.4:c.2679C>T	9.37:g.117838850G>A		Somatic		Capture	Illumina HiSeq	Phase_I	116878671	NM_002160	C9IYT7|C9J575|C9J6D9|C9J848|Q14583|Q15567|Q5T7S3	Silent	SNP	ENST00000350763.4	37	CCDS6811.1																																																																																				0.458	TNC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055418.2	NM_002160	
ASTN2	23245	broad.mit.edu	37	9	119204756	119204756	+	Silent	SNP	G	G	A	rs151278272	byFrequency	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr9:119204756G>A	ENST00000313400.4	-	21	3674	c.3574C>T	c.(3574-3576)Ctg>Ttg	p.L1192L	ASTN2_ENST00000361209.2_Silent_p.L1141L|ASTN2_ENST00000341734.4_Silent_p.L244L|ASTN2_ENST00000373996.3_Silent_p.L1188L|ASTN2_ENST00000361477.3_Silent_p.L244L|ASTN2_ENST00000288520.5_Silent_p.L293L			O75129	ASTN2_HUMAN	astrotactin 2	1192					negative regulation of protein localization to cell surface (GO:2000009)	cell pole (GO:0060187)|endosome (GO:0005768)|integral component of membrane (GO:0016021)		p.L1141L(1)		breast(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(21)|lung(45)|ovary(4)|pancreas(2)|prostate(2)|skin(9)|stomach(1)|urinary_tract(1)	102						TCATCTACCAGTGGACAGGCC	0.498																																					p.L293L												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C877T	9						.						210.0	176.0	188.0					9																	119204756		2203	4300	6503	118244577	SO:0001819	synonymous_variant	23245	exon6			AF116574	CCDS6814.1, CCDS6815.1, CCDS48009.1, CCDS48009.2, CCDS55334.1	9q33	2008-02-05			ENSG00000148219	ENSG00000148219			17021	protein-coding gene	gene with protein product		612856				9734811	Standard	NM_014010		Approved	KIAA0634	uc004bjt.2	O75129	OTTHUMG00000021013	ENST00000313400.4:c.3574C>T	9.37:g.119204756G>A		Somatic		Capture	Illumina HiSeq	Phase_I	118244577	NM_198186	A2A2T7|A2A2T9|Q52LQ2|Q5JVX8|Q5JVX9|Q5JVY1|Q5VXG8|Q5VZX6|Q8N6P8|Q8WV47|Q96FL4|Q9UHW6	Silent	SNP	ENST00000313400.4	37																																																																																					0.498	ASTN2-201	KNOWN	basic	protein_coding	protein_coding		NM_014010	
TRIM32	22954	broad.mit.edu	37	9	119461145	119461145	+	Missense_Mutation	SNP	T	T	G			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr9:119461145T>G	ENST00000450136.1	+	2	1285	c.1124T>G	c.(1123-1125)gTc>gGc	p.V375G	ASTN2_ENST00000313400.4_Intron|ASTN2_ENST00000361209.2_Intron|TRIM32_ENST00000373983.2_Missense_Mutation_p.V375G|ASTN2_ENST00000373996.3_Intron|ASTN2_ENST00000361477.3_Intron	NM_001099679.1|NM_012210.3	NP_001093149.1|NP_036342.2	Q13049	TRI32_HUMAN	tripartite motif containing 32	375					fat cell differentiation (GO:0045444)|innate immune response (GO:0045087)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage (GO:1902230)|negative regulation of viral release from host cell (GO:1902187)|negative regulation of viral transcription (GO:0032897)|positive regulation of cell cycle (GO:0045787)|positive regulation of cell growth (GO:0030307)|positive regulation of cell migration (GO:0030335)|positive regulation of cell motility (GO:2000147)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of neurogenesis (GO:0050769)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of proteolysis (GO:0045862)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of type I interferon production (GO:0032481)|protein polyubiquitination (GO:0000209)|protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|regulation of type I interferon production (GO:0032479)|response to tumor necrosis factor (GO:0034612)|response to UV (GO:0009411)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|striated muscle myosin thick filament (GO:0005863)	ligase activity (GO:0016874)|myosin binding (GO:0017022)|protein self-association (GO:0043621)|RNA binding (GO:0003723)|Tat protein binding (GO:0030957)|transcription coactivator activity (GO:0003713)|translation initiation factor binding (GO:0031369)|ubiquitin binding (GO:0043130)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.V375G(1)		breast(1)|central_nervous_system(2)|endometrium(4)|kidney(3)|large_intestine(5)|liver(1)|lung(6)|prostate(1)|skin(2)|urinary_tract(1)	26						AATCTTCCAGTCAGTCTCTAC	0.502																																					p.V375G	Esophageal Squamous(92;212 1916 19711 26951)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T1124G	9						.						76.0	76.0	76.0					9																	119461145		2203	4300	6503	118500966	SO:0001583	missense	22954	exon2			U18543	CCDS6817.1	9q33.1	2014-09-17	2011-01-25		ENSG00000119401	ENSG00000119401		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	16380	protein-coding gene	gene with protein product		602290	"""limb girdle muscular dystrophy 2H (autosomal recessive)"", ""tripartite motif-containing 32"""	LGMD2H		11331580, 7778269, 16606853	Standard	NM_001099679		Approved	HT2A, TATIP, BBS11	uc004bjx.2	Q13049	OTTHUMG00000021026	ENST00000450136.1:c.1124T>G	9.37:g.119461145T>G	ENSP00000408292:p.Val375Gly	Somatic		Capture	Illumina HiSeq	Phase_I	118500966	NM_001099679	Q9NQP8	Missense_Mutation	SNP	ENST00000450136.1	37	CCDS6817.1	.	.	.	.	.	.	.	.	.	.	T	14.91	2.675038	0.47781	.	.	ENSG00000119401	ENST00000450136;ENST00000373983	T;T	0.71698	-0.59;-0.59	5.47	5.47	0.80525	Six-bladed beta-propeller, TolB-like (1);	0.000000	0.64402	D	0.000003	T	0.71239	0.3316	N	0.21194	0.64	0.80722	D	1	D	0.58268	0.982	P	0.59643	0.861	T	0.70328	-0.4902	9	.	.	.	-22.5509	15.551	0.76152	0.0:0.0:0.0:1.0	.	375	Q13049	TRI32_HUMAN	G	375	ENSP00000408292:V375G;ENSP00000363095:V375G	.	V	+	2	0	TRIM32	118500966	1.000000	0.71417	0.995000	0.50966	0.543000	0.35085	7.665000	0.83852	2.063000	0.61619	0.528000	0.53228	GTC		0.502	TRIM32-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055466.2	NM_012210	
LHX6	26468	broad.mit.edu	37	9	124979565	124979565	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr9:124979565C>T	ENST00000373755.2	-	4	485	c.377G>A	c.(376-378)cGa>cAa	p.R126Q	LHX6_ENST00000559895.1_5'UTR|LHX6_ENST00000394319.4_Missense_Mutation_p.R155Q|LHX6_ENST00000340587.3_Missense_Mutation_p.R155Q|LHX6_ENST00000373754.2_Missense_Mutation_p.R126Q|LHX6_ENST00000541397.2_Missense_Mutation_p.R144Q	NM_001242334.1	NP_001229263.1	Q9UPM6	LHX6_HUMAN	LIM homeobox 6	126	Required for interaction with LDB1. {ECO:0000250}.				cell maturation (GO:0048469)|cerebral cortex GABAergic interneuron migration (GO:0021853)|cerebral cortex radially oriented cell migration (GO:0021799)|cerebral cortex tangential migration (GO:0021800)|forebrain neuron fate commitment (GO:0021877)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)	p.R155Q(1)		endometrium(2)|kidney(1)|large_intestine(5)	8						GGTCCCGAATCGGCTGCAGGT	0.682																																					p.R155Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G464A	9						.						22.0	24.0	23.0					9																	124979565		2203	4300	6503	124019386	SO:0001583	missense	26468	exon5			AB031041	CCDS6837.2, CCDS6838.2, CCDS56583.1, CCDS56584.1, CCDS59144.1	9q33.2	2011-06-20			ENSG00000106852	ENSG00000106852		"""Homeoboxes / LIM class"""	21735	protein-coding gene	gene with protein product		608215				10393337	Standard	NM_014368		Approved	LHX6.1	uc004blx.4	Q9UPM6	OTTHUMG00000020601	ENST00000373755.2:c.377G>A	9.37:g.124979565C>T	ENSP00000362860:p.Arg126Gln	Somatic		Capture	Illumina HiSeq	Phase_I	124019386	NM_199160	A6PVQ1|A6PVQ2|A8K1B2|B7Z4D0|H0YN76|Q5T7S7|Q5T7S8|Q9NTK3|Q9UPM5	Missense_Mutation	SNP	ENST00000373755.2	37	CCDS56583.1	.	.	.	.	.	.	.	.	.	.	C	27.2	4.809360	0.90707	.	.	ENSG00000106852	ENST00000373755;ENST00000373754;ENST00000394319;ENST00000340587;ENST00000541397	D;D;D;D;D	0.87334	-2.24;-2.24;-2.24;-2.24;-2.24	5.98	5.98	0.97165	Zinc finger, LIM-type (3);	0.000000	0.85682	D	0.000000	D	0.90249	0.6951	L	0.33668	1.02	0.80722	D	1	D;P;D	0.89917	0.999;0.744;1.0	D;B;D	0.68765	0.96;0.18;0.951	D	0.89777	0.3958	10	0.49607	T	0.09	.	19.4315	0.94772	0.0:1.0:0.0:0.0	.	126;155;155	Q9UPM6;Q9UPM6-4;Q9UPM6-3	LHX6_HUMAN;.;.	Q	126;126;155;155;144	ENSP00000362860:R126Q;ENSP00000362859:R126Q;ENSP00000377854:R155Q;ENSP00000340137:R155Q;ENSP00000441464:R144Q	ENSP00000340137:R155Q	R	-	2	0	LHX6	124019386	1.000000	0.71417	1.000000	0.80357	0.187000	0.23431	6.089000	0.71384	2.838000	0.97847	0.655000	0.94253	CGA		0.682	LHX6-002	KNOWN	not_organism_supported|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000053924.2	NM_014368	
OR1N2	138882	broad.mit.edu	37	9	125315558	125315558	+	Nonsense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr9:125315558G>A	ENST00000373688.2	+	1	168	c.110G>A	c.(109-111)tGg>tAg	p.W37*		NM_001004457.1	NP_001004457.1	Q8NGR9	OR1N2_HUMAN	olfactory receptor, family 1, subfamily N, member 2	37			W -> R (in dbSNP:rs1831370). {ECO:0000269|PubMed:15489334}.			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.W37*(1)		breast(2)|large_intestine(6)|lung(10)|ovary(2)|skin(3)|stomach(3)	26						CTCTCTGAGTGGCCAGAGGAG	0.517																																					p.W37X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.G110A	9						.						111.0	101.0	104.0					9																	125315558		2203	4300	6503	124355379	SO:0001587	stop_gained	138882	exon1				CCDS35123.1	9q33.2	2013-09-20			ENSG00000171501	ENSG00000171501		"""GPCR / Class A : Olfactory receptors"""	15111	protein-coding gene	gene with protein product							Standard	NM_001004457		Approved		uc011lyx.2	Q8NGR9	OTTHUMG00000020607	ENST00000373688.2:c.110G>A	9.37:g.125315558G>A	ENSP00000362792:p.Trp37*	Somatic		Capture	Illumina HiSeq	Phase_I	124355379	NM_001004457	A3KFM2|B2RNY4|Q6IF17|Q96RA3	Nonsense_Mutation	SNP	ENST00000373688.2	37	CCDS35123.1	.	.	.	.	.	.	.	.	.	.	G	12.43	1.935980	0.34189	.	.	ENSG00000171501	ENST00000373688	.	.	.	4.31	-5.07	0.02938	.	1.300740	0.05678	N	0.589889	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.59425	D	0.04	.	3.9038	0.09174	0.2637:0.1296:0.4794:0.1273	.	.	.	.	X	37	.	ENSP00000362792:W37X	W	+	2	0	OR1N2	124355379	0.000000	0.05858	0.003000	0.11579	0.449000	0.32228	-2.920000	0.00694	-0.830000	0.04262	-0.374000	0.07098	TGG		0.517	OR1N2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053937.2		
OR5C1	392391	broad.mit.edu	37	9	125551894	125551894	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr9:125551894C>T	ENST00000373680.2	+	1	745	c.683C>T	c.(682-684)gCt>gTt	p.A228V		NM_001001923.1	NP_001001923.1	Q8NGR4	OR5C1_HUMAN	olfactory receptor, family 5, subfamily C, member 1	228						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.A228V(1)		NS(1)|endometrium(1)|large_intestine(5)|lung(6)|pancreas(1)|prostate(5)|skin(1)	20						ATCGCTGGGGCTGTGATCCAC	0.577																																					p.A228V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C683T	9						.						78.0	73.0	75.0					9																	125551894		2203	4300	6503	124591715	SO:0001583	missense	392391	exon1			AF399514	CCDS35131.1	9q34.2	2012-08-09			ENSG00000148215	ENSG00000148215		"""GPCR / Class A : Olfactory receptors"""	8331	protein-coding gene	gene with protein product				OR5C2P			Standard	NM_001001923		Approved	OR9-F, hRPK-465_F_21	uc011lzd.2	Q8NGR4	OTTHUMG00000020622	ENST00000373680.2:c.683C>T	9.37:g.125551894C>T	ENSP00000362784:p.Ala228Val	Somatic		Capture	Illumina HiSeq	Phase_I	124591715	NM_001001923	B2RN54|B9EGT0|Q96RC4	Missense_Mutation	SNP	ENST00000373680.2	37	CCDS35131.1	.	.	.	.	.	.	.	.	.	.	C	15.96	2.985926	0.53934	.	.	ENSG00000148215	ENST00000373680	T	0.00227	8.5	5.46	5.46	0.80206	GPCR, rhodopsin-like superfamily (1);	0.000000	0.36234	U	0.002710	T	0.00468	0.0015	M	0.69248	2.105	0.30780	N	0.742088	D	0.61080	0.989	P	0.57620	0.824	T	0.61093	-0.7132	10	0.72032	D	0.01	.	18.2528	0.90009	0.0:1.0:0.0:0.0	.	228	Q8NGR4	OR5C1_HUMAN	V	228	ENSP00000362784:A228V	ENSP00000362784:A228V	A	+	2	0	OR5C1	124591715	0.052000	0.20516	0.996000	0.52242	0.363000	0.29612	2.082000	0.41605	2.840000	0.97914	0.655000	0.94253	GCT		0.577	OR5C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053953.1		
NR6A1	2649	broad.mit.edu	37	9	127298312	127298312	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr9:127298312G>T	ENST00000487099.2	-	7	1081	c.924C>A	c.(922-924)ttC>ttA	p.F308L	NR6A1_ENST00000344523.4_Missense_Mutation_p.F307L|NR6A1_ENST00000416460.2_Missense_Mutation_p.F303L|NR6A1_ENST00000373584.3_Missense_Mutation_p.F304L	NM_001278546.1	NP_001265475.1	Q15406	NR6A1_HUMAN	nuclear receptor subfamily 6, group A, member 1	308					cell proliferation (GO:0008283)|gamete generation (GO:0007276)|gene expression (GO:0010467)|intracellular receptor signaling pathway (GO:0030522)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|spermatogenesis (GO:0007283)|transcription initiation from RNA polymerase II promoter (GO:0006367)	nucleoplasm (GO:0005654)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|protein homodimerization activity (GO:0042803)|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)|steroid hormone receptor activity (GO:0003707)|zinc ion binding (GO:0008270)	p.F308L(1)		NS(1)|breast(1)|cervix(1)|large_intestine(4)|lung(5)|ovary(3)|prostate(1)|skin(1)	17						AGAGCTCGCAGAAGAAAGGCA	0.522																																					p.F308L	Esophageal Squamous(192;272 2884 6208 20560)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C924A	9						.						102.0	91.0	95.0					9																	127298312		2203	4300	6503	126338133	SO:0001583	missense	2649	exon7			U64876	CCDS35137.1, CCDS55340.1, CCDS65127.1	9q33.3	2014-01-21			ENSG00000148200	ENSG00000148200		"""Nuclear hormone receptors"""	7985	protein-coding gene	gene with protein product		602778		GCNF		9134503, 8982251	Standard	NM_001489		Approved	GCNF1, RTR, CT150	uc004bor.1	Q15406	OTTHUMG00000020661	ENST00000487099.2:c.924C>A	9.37:g.127298312G>T	ENSP00000420267:p.Phe308Leu	Somatic		Capture	Illumina HiSeq	Phase_I	126338133	NM_033334	O00551|O00603|Q5T6F4|Q8NHQ0|Q92898|Q99802	Missense_Mutation	SNP	ENST00000487099.2	37	CCDS35137.1	.	.	.	.	.	.	.	.	.	.	G	19.57	3.853371	0.71719	.	.	ENSG00000148200	ENST00000487099;ENST00000373584;ENST00000416460;ENST00000344523	D;D;D;D	0.98120	-4.73;-4.73;-4.73;-4.73	5.17	5.17	0.71159	Nuclear hormone receptor, ligand-binding (2);Nuclear hormone receptor, ligand-binding, core (2);	0.147714	0.64402	D	0.000006	D	0.98086	0.9369	M	0.77486	2.375	0.80722	D	1	B;B;B	0.30664	0.006;0.289;0.021	B;P;B	0.44811	0.018;0.461;0.022	D	0.98196	1.0465	10	0.66056	D	0.02	.	18.5492	0.91057	0.0:0.0:1.0:0.0	.	304;308;303	F1DAM1;Q15406;Q15406-5	.;NR6A1_HUMAN;.	L	308;304;303;307	ENSP00000420267:F308L;ENSP00000362686:F304L;ENSP00000413701:F303L;ENSP00000341135:F307L	ENSP00000341135:F307L	F	-	3	2	NR6A1	126338133	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.761000	0.85260	2.793000	0.96121	0.563000	0.77884	TTC		0.522	NR6A1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000054043.4		
SCAI	286205	broad.mit.edu	37	9	127789184	127789184	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr9:127789184C>T	ENST00000336505.6	-	6	477	c.419G>A	c.(418-420)cGc>cAc	p.R140H	SCAI_ENST00000373549.4_Missense_Mutation_p.R163H	NM_001144877.2	NP_001138349.1	Q8N9R8	SCAI_HUMAN	suppressor of cancer cell invasion	140	Necessary to inhibit MKL1-induced SRF transcriptional activity. {ECO:0000250}.|Required for interaction with MKL1. {ECO:0000250}.				negative regulation of cell migration (GO:0030336)|negative regulation of Rho protein signal transduction (GO:0035024)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	transcription corepressor activity (GO:0003714)	p.R163H(1)		breast(2)|central_nervous_system(1)|endometrium(3)|kidney(7)|large_intestine(4)|lung(8)|ovary(2)|pancreas(1)|prostate(5)|stomach(1)|urinary_tract(1)	35						TTCCGATGTGCGTAAGCTATG	0.363																																					p.R163H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G488A	9						.						87.0	80.0	83.0					9																	127789184		1823	4075	5898	126829005	SO:0001583	missense	286205	exon7			AK093983	CCDS43877.1, CCDS48017.1	9q34.11	2009-11-06	2009-07-09	2009-07-09	ENSG00000173611	ENSG00000173611			26709	protein-coding gene	gene with protein product			"""chromosome 9 open reading frame 126"""	C9orf126			Standard	NM_173690		Approved	FLJ36664, NET40	uc004bpd.3	Q8N9R8	OTTHUMG00000020667	ENST00000336505.6:c.419G>A	9.37:g.127789184C>T	ENSP00000336756:p.Arg140His	Somatic		Capture	Illumina HiSeq	Phase_I	126829005	NM_173690	Q3SXZ1|Q3SXZ2|Q5T163|Q8N1I4	Missense_Mutation	SNP	ENST00000336505.6	37	CCDS48017.1	.	.	.	.	.	.	.	.	.	.	C	25.1	4.607794	0.87258	.	.	ENSG00000173611	ENST00000336505;ENST00000373549	T;T	0.67171	-0.25;-0.23	5.12	4.21	0.49690	.	0.160159	0.64402	D	0.000017	T	0.78214	0.4248	M	0.85710	2.77	0.58432	D	0.999999	D;D	0.65815	0.995;0.994	P;P	0.52758	0.708;0.674	T	0.83239	-0.0059	10	0.87932	D	0	-6.9813	14.9333	0.70933	0.0:0.8561:0.1439:0.0	.	140;163	Q8N9R8;Q8N9R8-2	SCAI_HUMAN;.	H	140;163	ENSP00000336756:R140H;ENSP00000362650:R163H	ENSP00000336756:R140H	R	-	2	0	SCAI	126829005	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	7.582000	0.82546	1.273000	0.44346	0.655000	0.94253	CGC		0.363	SCAI-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054055.3	NM_173690	
GAPVD1	26130	broad.mit.edu	37	9	128111712	128111712	+	Silent	SNP	C	C	T	rs374797901		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr9:128111712C>T	ENST00000495955.1	+	21	3557	c.3267C>T	c.(3265-3267)gaC>gaT	p.D1089D	GAPVD1_ENST00000312123.9_Silent_p.D1050D|GAPVD1_ENST00000265956.4_Silent_p.D1063D|GAPVD1_ENST00000394104.2_Silent_p.D1089D|GAPVD1_ENST00000394083.2_Silent_p.D1023D|GAPVD1_ENST00000297933.6_Silent_p.D1071D|GAPVD1_ENST00000394105.2_Silent_p.D1098D|GAPVD1_ENST00000470056.1_Silent_p.D1044D			Q14C86	GAPD1_HUMAN	GTPase activating protein and VPS9 domains 1	1089					endocytosis (GO:0006897)|positive regulation of GTPase activity (GO:0043547)|regulation of protein transport (GO:0051223)|regulation of small GTPase mediated signal transduction (GO:0051056)|signal transduction (GO:0007165)	cytosol (GO:0005829)|endosome (GO:0005768)|membrane (GO:0016020)	GTPase activating protein binding (GO:0032794)|GTPase activator activity (GO:0005096)|guanyl-nucleotide exchange factor activity (GO:0005085)	p.D1098D(1)		central_nervous_system(2)|endometrium(7)|kidney(4)|large_intestine(10)|lung(11)|ovary(2)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	44						CTCCCCGTGACGAAGCACTGC	0.478																																					p.D1098D												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C3294T	9						.	C		0,4406		0,0,2203	190.0	179.0	183.0		3294	-6.5	0.3	9		183	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	GAPVD1	NM_015635.2		0,1,6502	TT,TC,CC		0.0116,0.0,0.0077		1098/1488	128111712	1,13005	2203	4300	6503	127151533	SO:0001819	synonymous_variant	26130	exon20				CCDS65130.1, CCDS65131.1, CCDS65132.1	9q34.11	2008-02-05			ENSG00000165219	ENSG00000165219			23375	protein-coding gene	gene with protein product		611714					Standard	XM_005251901		Approved	DKFZP434C212, KIAA1521	uc004bpr.3	Q14C86	OTTHUMG00000020678	ENST00000495955.1:c.3267C>T	9.37:g.128111712C>T		Somatic		Capture	Illumina HiSeq	Phase_I	127151533	NM_015635	A8MYK3|B0QZ62|B0QZ63|B0QZ64|Q14C76|Q2Q1W1|Q8ND92|Q8WU86|Q96CZ4|Q9NXQ1|Q9P207|Q9Y4N0	Silent	SNP	ENST00000495955.1	37																																																																																					0.478	GAPVD1-014	KNOWN	alternative_5_UTR|basic	protein_coding	protein_coding	OTTHUMT00000355644.1		
PBX3	5090	broad.mit.edu	37	9	128692039	128692039	+	Nonsense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr9:128692039C>T	ENST00000373489.5	+	4	638	c.622C>T	c.(622-624)Cga>Tga	p.R208*	PBX3_ENST00000342287.5_Nonsense_Mutation_p.R208*|PBX3_ENST00000373487.4_Nonsense_Mutation_p.R208*|PBX3_ENST00000373483.2_Nonsense_Mutation_p.R27*|PBX3_ENST00000447726.2_Nonsense_Mutation_p.R133*|PBX3_ENST00000538998.1_3'UTR	NM_006195.5	NP_006186.1	P40426	PBX3_HUMAN	pre-B-cell leukemia homeobox 3	208					adult locomotory behavior (GO:0008344)|anterior compartment pattern formation (GO:0007387)|dorsal spinal cord development (GO:0021516)|neuron development (GO:0048666)|posterior compartment specification (GO:0007388)|regulation of respiratory gaseous exchange by neurological system process (GO:0002087)|respiratory gaseous exchange (GO:0007585)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.R208*(1)		biliary_tract(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(8)|skin(1)|upper_aerodigestive_tract(2)	24						CATCATCCATCGAAAATTTAG	0.393																																					p.R208X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.C622T	9						.						156.0	146.0	149.0					9																	128692039		2203	4300	6503	127731860	SO:0001587	stop_gained	5090	exon4				CCDS6865.1, CCDS48021.1	9q33.3	2011-06-20	2007-01-30		ENSG00000167081	ENSG00000167081		"""Homeoboxes / TALE class"""	8634	protein-coding gene	gene with protein product		176312	"""pre-B-cell leukemia transcription factor 3"""			1682799	Standard	NM_006195		Approved		uc004bqb.3	P40426	OTTHUMG00000020684	ENST00000373489.5:c.622C>T	9.37:g.128692039C>T	ENSP00000362588:p.Arg208*	Somatic		Capture	Illumina HiSeq	Phase_I	127731860	NM_006195	E9PB27|Q5JSA0|Q5JSA1|Q5VXL3|Q96PF9|Q96PG0	Nonsense_Mutation	SNP	ENST00000373489.5	37	CCDS6865.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	21.5|21.5	4.162828|4.162828	0.78226|0.78226	.|.	.|.	ENSG00000167081|ENSG00000167081	ENST00000373492;ENST00000373489;ENST00000342287;ENST00000373487;ENST00000373483;ENST00000373482;ENST00000447726;ENST00000538998|ENST00000428092	.|.	.|.	.|.	5.69|5.69	3.76|3.76	0.43208|0.43208	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	.|T	.|0.63977	.|0.2557	.|.	.|.	.|.	0.80722|0.80722	A|A	1|1	.|.	.|.	.|.	.|.	.|.	.|.	.|T	.|0.71527	.|-0.4566	.|3	0.02654|.	T|.	1|.	.|.	13.9564|13.9564	0.64152|0.64152	0.3936:0.6064:0.0:0.0|0.3936:0.6064:0.0:0.0	.|.	.|.	.|.	.|.	X|L	27;208;208;208;27;27;133;119|128	.|.	ENSP00000341990:R208X|.	R|S	+|+	1|2	2|0	PBX3|PBX3	127731860|127731860	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.997000|0.997000	0.91878|0.91878	2.963000|2.963000	0.49184|0.49184	1.392000|1.392000	0.46585|0.46585	0.555000|0.555000	0.69702|0.69702	CGA|TCG		0.393	PBX3-006	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417765.1		
ZBTB34	403341	broad.mit.edu	37	9	129643017	129643017	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr9:129643017C>A	ENST00000373452.2	+	1	1391	c.1327C>A	c.(1327-1329)Ctc>Atc	p.L443I	ZBTB34_ENST00000319119.4_Missense_Mutation_p.L447I			Q8NCN2	ZBT34_HUMAN	zinc finger and BTB domain containing 34	443					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.L447I(1)		endometrium(3)|large_intestine(2)|lung(2)|ovary(1)|prostate(3)|upper_aerodigestive_tract(1)	12						CCAAGGTACCCTCAACCAGCA	0.527																																					p.L443I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1327A	9						.						76.0	76.0	76.0					9																	129643017		2021	4190	6211	128682838	SO:0001583	missense	403341	exon2			DQ227306	CCDS48023.1	9q33.3	2013-01-08			ENSG00000177125	ENSG00000177125		"""-"", ""Zinc fingers, C2H2-type"", ""BTB/POZ domain containing"""	31446	protein-coding gene	gene with protein product		611692				16718364	Standard	NM_001099270		Approved	KIAA1993, MGC24652, ZNF918	uc004bqm.4	Q8NCN2	OTTHUMG00000020694	ENST00000373452.2:c.1327C>A	9.37:g.129643017C>A	ENSP00000362551:p.Leu443Ile	Somatic		Capture	Illumina HiSeq	Phase_I	128682838	NM_001099270	Q38IA7|Q5VYE9	Missense_Mutation	SNP	ENST00000373452.2	37	CCDS48023.1	.	.	.	.	.	.	.	.	.	.	C	22.0	4.227362	0.79576	.	.	ENSG00000177125	ENST00000319119;ENST00000373452	T;T	0.74947	-0.89;-0.89	5.88	5.88	0.94601	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);	0.000000	0.85682	D	0.000000	T	0.81597	0.4856	L	0.32530	0.975	0.80722	D	1	D	0.63880	0.993	D	0.76071	0.987	T	0.80717	-0.1258	10	0.48119	T	0.1	.	20.2279	0.98344	0.0:1.0:0.0:0.0	.	443	Q8NCN2	ZBT34_HUMAN	I	447;443	ENSP00000317534:L447I;ENSP00000362551:L443I	ENSP00000317534:L447I	L	+	1	0	ZBTB34	128682838	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.440000	0.80464	2.778000	0.95560	0.655000	0.94253	CTC		0.527	ZBTB34-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001099270	
ODF2	4957	broad.mit.edu	37	9	131256922	131256922	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr9:131256922C>T	ENST00000434106.3	+	17	2249	c.1886C>T	c.(1885-1887)gCc>gTc	p.A629V	ODF2_ENST00000351030.3_Missense_Mutation_p.A624V|ODF2_ENST00000448249.3_Missense_Mutation_p.A548V|ODF2_ENST00000393527.3_Missense_Mutation_p.A605V|ODF2_ENST00000444119.2_Missense_Mutation_p.A605V|ODF2_ENST00000546203.1_Missense_Mutation_p.A610V|ODF2_ENST00000393533.2_Missense_Mutation_p.A629V|ODF2_ENST00000372807.5_Missense_Mutation_p.A624V|ODF2_ENST00000604420.1_Missense_Mutation_p.A629V|ODF2_ENST00000372814.3_Missense_Mutation_p.A673V|ODF2_ENST00000372791.3_Missense_Mutation_p.A610V	NM_153433.1	NP_702911.1	Q5BJF6	ODFP2_HUMAN	outer dense fiber of sperm tails 2	629					G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|multicellular organismal development (GO:0007275)|regulation of cilium assembly (GO:1902017)|spermatid development (GO:0007286)	centriole (GO:0005814)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytosol (GO:0005829)|microtubule (GO:0005874)|nucleus (GO:0005634)|outer dense fiber (GO:0001520)|primary cilium (GO:0072372)	Rab GTPase binding (GO:0017137)|structural molecule activity (GO:0005198)	p.A605V(1)		autonomic_ganglia(1)|breast(7)|cervix(1)|endometrium(4)|kidney(5)|large_intestine(7)|lung(8)|ovary(1)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)	37						GACCTCACAGCCATCATATCA	0.607																																					p.A625V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1874T	9						.						69.0	64.0	66.0					9																	131256922		2203	4300	6503	130296743	SO:0001583	missense	4957	exon16			AF012549	CCDS6902.1, CCDS56585.1, CCDS56586.1, CCDS56587.1, CCDS56588.1, CCDS56589.1, CCDS56590.1	9q34	2010-04-23	2002-10-21		ENSG00000136811	ENSG00000136811			8114	protein-coding gene	gene with protein product	"""cancer/testis antigen 134"""	602015	"""outer dense fibre of sperm tails 2"""			9045620, 10072582	Standard	NM_153435		Approved	ODF84, CT134	uc004bvc.3	Q5BJF6	OTTHUMG00000020748	ENST00000434106.3:c.1886C>T	9.37:g.131256922C>T	ENSP00000403453:p.Ala629Val	Somatic		Capture	Illumina HiSeq	Phase_I	130296743	NM_153439	B1AND3|B4DRK4|B4DX73|B4DZ02|E7EWL2|F5H6J4|O14721|O60631|Q1W2J6|Q6UN26|Q7Z5I6|Q96FN2	Missense_Mutation	SNP	ENST00000434106.3	37	CCDS56588.1	.	.	.	.	.	.	.	.	.	.	C	16.21	3.057431	0.55325	.	.	ENSG00000136811	ENST00000393533;ENST00000372814;ENST00000351030;ENST00000372796;ENST00000303890;ENST00000448249;ENST00000546203;ENST00000372791	T;D;D;D;D;D;T;T	0.83673	1.43;-1.75;-1.75;-1.75;-1.75;-1.75;1.46;1.47	5.4	5.4	0.78164	.	0.267137	0.41500	D	0.000879	T	0.65595	0.2706	N	0.03608	-0.345	0.80722	D	1	B;B;B;B;B;B;B	0.22146	0.052;0.029;0.019;0.065;0.052;0.051;0.012	B;B;B;B;B;B;B	0.14023	0.007;0.009;0.007;0.01;0.007;0.009;0.009	T	0.64681	-0.6350	10	0.48119	T	0.1	-15.096	13.5456	0.61702	0.0:0.9226:0.0:0.0774	.	610;624;548;629;610;629;605	Q5BJF6-8;Q5BJF6-4;Q5BJF6-9;B4DX73;Q5BJF6-5;Q5BJF6;Q5BJF6-3	.;.;.;.;.;ODFP2_HUMAN;.	V	629;673;624;629;605;548;610;610	ENSP00000377166:A629V;ENSP00000361901:A673V;ENSP00000342581:A624V;ENSP00000361882:A629V;ENSP00000307781:A605V;ENSP00000396687:A548V;ENSP00000437579:A610V;ENSP00000361877:A610V	ENSP00000307781:A605V	A	+	2	0	ODF2	130296743	0.972000	0.33761	1.000000	0.80357	0.997000	0.91878	1.078000	0.30754	2.532000	0.85374	0.561000	0.74099	GCC		0.607	ODF2-011	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000054449.3		
SPTAN1	6709	broad.mit.edu	37	9	131346164	131346164	+	Silent	SNP	G	G	A	rs369710857		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr9:131346164G>A	ENST00000372731.4	+	16	2219	c.2109G>A	c.(2107-2109)tcG>tcA	p.S703S	SPTAN1_ENST00000358161.5_Silent_p.S703S|SPTAN1_ENST00000372739.3_Silent_p.S703S	NM_001195532.1|NM_003127.3	NP_001182461.1|NP_003118.2	Q13813	SPTN1_HUMAN	spectrin, alpha, non-erythrocytic 1	703					actin filament capping (GO:0051693)|apoptotic process (GO:0006915)|axon guidance (GO:0007411)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)	cuticular plate (GO:0032437)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|intracellular membrane-bounded organelle (GO:0043231)|lateral plasma membrane (GO:0016328)|membrane (GO:0016020)|microtubule cytoskeleton (GO:0015630)|spectrin (GO:0008091)|vesicle (GO:0031982)|Z disc (GO:0030018)	actin binding (GO:0003779)|calcium ion binding (GO:0005509)|structural constituent of cytoskeleton (GO:0005200)	p.S703S(1)		NS(2)|breast(8)|cervix(2)|endometrium(6)|kidney(4)|large_intestine(21)|liver(1)|lung(25)|ovary(5)|pancreas(1)|prostate(4)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	87						ACTTGGCTTCGGATGATTACG	0.453																																					p.S703S	NSCLC(120;833 1744 2558 35612 37579)											.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G2109A	9						.	G	,,	1,4405	2.1+/-5.4	0,1,2202	143.0	130.0	134.0		2109,2109,2109	-11.4	0.1	9		134	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous,coding-synonymous	SPTAN1	NM_001130438.2,NM_001195532.1,NM_003127.3	,,	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	,,	703/2478,703/2453,703/2473	131346164	1,13005	2203	4300	6503	130385985	SO:0001819	synonymous_variant	6709	exon16			M19725	CCDS6905.1, CCDS48036.1, CCDS75914.1	9q34.11	2013-01-10	2012-06-15		ENSG00000197694	ENSG00000197694		"""EF-hand domain containing"""	11273	protein-coding gene	gene with protein product	"""alpha-fodrin"""	182810				3336352	Standard	NM_003127		Approved		uc004bvm.4	Q13813	OTTHUMG00000020754	ENST00000372731.4:c.2109G>A	9.37:g.131346164G>A		Somatic		Capture	Illumina HiSeq	Phase_I	130385985	NM_001195532	Q13186|Q15324|Q16606|Q59EF1|Q5VXV5|Q5VXV6|Q7Z6M5|Q9P0V0	Silent	SNP	ENST00000372731.4	37	CCDS6905.1																																																																																				0.453	SPTAN1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054472.1	NM_003127	
SPTAN1	6709	broad.mit.edu	37	9	131367602	131367602	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr9:131367602C>T	ENST00000372731.4	+	31	4002	c.3892C>T	c.(3892-3894)Cgc>Tgc	p.R1298C	SPTAN1_ENST00000358161.5_Missense_Mutation_p.R1298C|SPTAN1_ENST00000372739.3_Missense_Mutation_p.R1298C	NM_001195532.1|NM_003127.3	NP_001182461.1|NP_003118.2	Q13813	SPTN1_HUMAN	spectrin, alpha, non-erythrocytic 1	1298					actin filament capping (GO:0051693)|apoptotic process (GO:0006915)|axon guidance (GO:0007411)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)	cuticular plate (GO:0032437)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|intracellular membrane-bounded organelle (GO:0043231)|lateral plasma membrane (GO:0016328)|membrane (GO:0016020)|microtubule cytoskeleton (GO:0015630)|spectrin (GO:0008091)|vesicle (GO:0031982)|Z disc (GO:0030018)	actin binding (GO:0003779)|calcium ion binding (GO:0005509)|structural constituent of cytoskeleton (GO:0005200)	p.R1298C(1)		NS(2)|breast(8)|cervix(2)|endometrium(6)|kidney(4)|large_intestine(21)|liver(1)|lung(25)|ovary(5)|pancreas(1)|prostate(4)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	87						AACAGCAGAGCGCCTGATCCA	0.532																																					p.R1278C	NSCLC(120;833 1744 2558 35612 37579)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C3832T	9						.						74.0	73.0	73.0					9																	131367602		2203	4300	6503	130407423	SO:0001583	missense	6709	exon30			M19725	CCDS6905.1, CCDS48036.1, CCDS75914.1	9q34.11	2013-01-10	2012-06-15		ENSG00000197694	ENSG00000197694		"""EF-hand domain containing"""	11273	protein-coding gene	gene with protein product	"""alpha-fodrin"""	182810				3336352	Standard	NM_003127		Approved		uc004bvm.4	Q13813	OTTHUMG00000020754	ENST00000372731.4:c.3892C>T	9.37:g.131367602C>T	ENSP00000361816:p.Arg1298Cys	Somatic		Capture	Illumina HiSeq	Phase_I	130407423	NM_001195532	Q13186|Q15324|Q16606|Q59EF1|Q5VXV5|Q5VXV6|Q7Z6M5|Q9P0V0	Missense_Mutation	SNP	ENST00000372731.4	37	CCDS6905.1	.	.	.	.	.	.	.	.	.	.	C	26.7	4.762148	0.89932	.	.	ENSG00000197694	ENST00000358161;ENST00000372731;ENST00000372739;ENST00000372719	T;T;T	0.52057	0.68;0.68;0.68	5.96	5.04	0.67666	.	0.000000	0.85682	D	0.000000	T	0.75466	0.3853	M	0.90870	3.155	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.83275	0.996;0.992;0.995	T	0.82412	-0.0470	10	0.87932	D	0	.	16.0918	0.81094	0.1387:0.8613:0.0:0.0	.	1278;1298;1298	Q13813-3;Q13813-2;Q13813	.;.;SPTA2_HUMAN	C	1298;1298;1298;1278	ENSP00000350882:R1298C;ENSP00000361816:R1298C;ENSP00000361824:R1298C	ENSP00000350882:R1298C	R	+	1	0	SPTAN1	130407423	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	6.080000	0.71299	1.466000	0.48025	0.655000	0.94253	CGC		0.532	SPTAN1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054472.1	NM_003127	
DOLK	22845	broad.mit.edu	37	9	131709240	131709240	+	Missense_Mutation	SNP	C	C	G			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr9:131709240C>G	ENST00000372586.3	-	1	658	c.343G>C	c.(343-345)Gca>Cca	p.A115P	RP11-101E3.5_ENST00000482796.1_Intron|NUP188_ENST00000372577.2_5'Flank	NM_014908.3	NP_055723.1	Q9UPQ8	DOLK_HUMAN	dolichol kinase	115					cellular protein metabolic process (GO:0044267)|dolichol-linked oligosaccharide biosynthetic process (GO:0006488)|dolichyl diphosphate biosynthetic process (GO:0006489)|dolichyl monophosphate biosynthetic process (GO:0043048)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)	endoplasmic reticulum membrane (GO:0005789)|integral component of endoplasmic reticulum membrane (GO:0030176)	dolichol kinase activity (GO:0004168)	p.A115P(1)		breast(1)|large_intestine(5)|lung(3)|ovary(1)|urinary_tract(1)	11						CCAGTGGCTGCCACCACAATG	0.577																																					p.A115P												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G343C	9						.						47.0	47.0	47.0					9																	131709240		2203	4300	6503	130749061	SO:0001583	missense	22845	exon1			AB029017	CCDS6915.1	9q34.13	2014-09-17	2007-02-09	2007-02-09	ENSG00000175283	ENSG00000175283			23406	protein-coding gene	gene with protein product	"""dolichol kinase 1"""	610746	"""transmembrane protein 15"""	TMEM15		12975309, 16923818	Standard	NM_014908		Approved	KIAA1094, DK1	uc004bwr.3	Q9UPQ8	OTTHUMG00000020765	ENST00000372586.3:c.343G>C	9.37:g.131709240C>G	ENSP00000361667:p.Ala115Pro	Somatic		Capture	Illumina HiSeq	Phase_I	130749061	NM_014908	Q5SRE6	Missense_Mutation	SNP	ENST00000372586.3	37	CCDS6915.1	.	.	.	.	.	.	.	.	.	.	C	16.58	3.164160	0.57476	.	.	ENSG00000175283	ENST00000372586;ENST00000515348	D	0.85773	-2.03	5.64	5.64	0.86602	.	0.160838	0.40302	N	0.001122	D	0.83658	0.5302	L	0.54323	1.7	0.47407	D	0.999412	B	0.28880	0.226	B	0.34138	0.176	T	0.82602	-0.0376	10	0.62326	D	0.03	-0.4933	13.6433	0.62265	0.1545:0.8455:0.0:0.0	.	115	Q9UPQ8	DOLK_HUMAN	P	115	ENSP00000361667:A115P	ENSP00000361667:A115P	A	-	1	0	DOLK	130749061	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	3.566000	0.53805	2.655000	0.90218	0.462000	0.41574	GCA		0.577	DOLK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054515.1	NM_014908	
TOR1A	1861	broad.mit.edu	37	9	132576488	132576488	+	Silent	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr9:132576488G>A	ENST00000351698.4	-	5	810	c.762C>T	c.(760-762)caC>caT	p.H254H		NM_000113.2	NP_000104.1	O14656	TOR1A_HUMAN	torsin family 1, member A (torsin A)	254	Interaction with KLC1.				ATP catabolic process (GO:0006200)|cell adhesion (GO:0007155)|chaperone mediated protein folding requiring cofactor (GO:0051085)|chaperone-mediated protein folding (GO:0061077)|chaperone-mediated protein transport (GO:0072321)|ER-associated misfolded protein catabolic process (GO:0071712)|intermediate filament cytoskeleton organization (GO:0045104)|neuron projection development (GO:0031175)|nuclear envelope organization (GO:0006998)|nuclear membrane organization (GO:0071763)|organelle organization (GO:0006996)|positive regulation of synaptic vesicle endocytosis (GO:1900244)|protein deneddylation (GO:0000338)|protein homooligomerization (GO:0051260)|protein localization to nucleus (GO:0034504)|regulation of dopamine uptake involved in synaptic transmission (GO:0051584)|regulation of protein localization to cell surface (GO:2000008)|response to oxidative stress (GO:0006979)|synaptic vesicle transport (GO:0048489)|wound healing, spreading of cells (GO:0044319)	cell junction (GO:0030054)|cytoplasmic vesicle membrane (GO:0030659)|cytoskeleton (GO:0005856)|endoplasmic reticulum lumen (GO:0005788)|extracellular vesicular exosome (GO:0070062)|extrinsic component of endoplasmic reticulum membrane (GO:0042406)|growth cone (GO:0030426)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|secretory granule (GO:0030141)|synaptic vesicle (GO:0008021)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|cytoskeletal protein binding (GO:0008092)|kinesin binding (GO:0019894)|unfolded protein binding (GO:0051082)	p.H254H(1)		central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(5)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1)	20		Ovarian(14;0.00556)				TTAAGCTGCTGTGCCAGAAGC	0.507																																					p.H254H												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C762T	9						.						81.0	78.0	79.0					9																	132576488		2203	4300	6503	131616309	SO:0001819	synonymous_variant	1861	exon5			AF007871	CCDS6930.1	9q32-q34	2008-07-21	2004-11-24	2004-11-26	ENSG00000136827	ENSG00000136827			3098	protein-coding gene	gene with protein product		605204	"""dystonia 1, torsion (autosomal dominant; torsin A)"""	DYT1		10644435	Standard	NM_000113		Approved	DQ2	uc004byl.3	O14656	OTTHUMG00000020794	ENST00000351698.4:c.762C>T	9.37:g.132576488G>A		Somatic		Capture	Illumina HiSeq	Phase_I	131616309	NM_000113	B2RB58|Q53Y64|Q96CA0	Silent	SNP	ENST00000351698.4	37	CCDS6930.1																																																																																				0.507	TOR1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054611.1	NM_000113	
ASS1	445	broad.mit.edu	37	9	133342131	133342131	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr9:133342131T>C	ENST00000372394.1	+	7	921	c.440T>C	c.(439-441)aTg>aCg	p.M147T	ASS1_ENST00000493984.2_3'UTR|ASS1_ENST00000352480.5_Missense_Mutation_p.M147T|ASS1_ENST00000372393.3_Missense_Mutation_p.M147T			P00966	ASSY_HUMAN	argininosuccinate synthase 1	147					acute-phase response (GO:0006953)|aging (GO:0007568)|arginine biosynthetic process (GO:0006526)|argininosuccinate metabolic process (GO:0000053)|aspartate metabolic process (GO:0006531)|cellular nitrogen compound metabolic process (GO:0034641)|cellular response to amine stimulus (GO:0071418)|cellular response to amino acid stimulus (GO:0071230)|cellular response to ammonium ion (GO:0071242)|cellular response to cAMP (GO:0071320)|cellular response to dexamethasone stimulus (GO:0071549)|cellular response to glucagon stimulus (GO:0071377)|cellular response to interferon-gamma (GO:0071346)|cellular response to laminar fluid shear stress (GO:0071499)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to oleic acid (GO:0071400)|cellular response to tumor necrosis factor (GO:0071356)|citrulline metabolic process (GO:0000052)|diaphragm development (GO:0060539)|kidney development (GO:0001822)|liver development (GO:0001889)|midgut development (GO:0007494)|negative regulation of leukocyte cell-cell adhesion (GO:1903038)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to growth hormone (GO:0060416)|response to mycotoxin (GO:0010046)|response to nutrient (GO:0007584)|response to zinc ion (GO:0010043)|small molecule metabolic process (GO:0044281)|urea cycle (GO:0000050)	cell body fiber (GO:0070852)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)|mitochondrial outer membrane (GO:0005741)|nucleus (GO:0005634)|perikaryon (GO:0043204)	amino acid binding (GO:0016597)|argininosuccinate synthase activity (GO:0004055)|ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)|toxic substance binding (GO:0015643)	p.M147T(1)		breast(1)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(3)|lung(4)|ovary(1)|skin(1)|urinary_tract(1)	17				OV - Ovarian serous cystadenocarcinoma(145;0.000514)	Adenosine triphosphate(DB00171)|L-Arginine(DB00125)|L-Aspartic Acid(DB00128)|L-Citrulline(DB00155)	CCCTGGAGGATGCCTGAATTC	0.602																																					p.M147T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T440C	9						.						98.0	81.0	86.0					9																	133342131		2203	4300	6503	132331952	SO:0001583	missense	445	exon7			X01630	CCDS6933.1	9q34.1	2012-10-02	2010-04-20	2006-08-24	ENSG00000130707	ENSG00000130707	6.3.4.5		758	protein-coding gene	gene with protein product		603470	"""argininosuccinate synthetase"""	ASS		3513483, 852520	Standard	NM_054012		Approved	CTLN1	uc004bzm.3	P00966	OTTHUMG00000020806	ENST00000372394.1:c.440T>C	9.37:g.133342131T>C	ENSP00000361471:p.Met147Thr	Somatic		Capture	Illumina HiSeq	Phase_I	132331952	NM_000050	Q6LDL2|Q86UZ0|Q96GT4	Missense_Mutation	SNP	ENST00000372394.1	37	CCDS6933.1	.	.	.	.	.	.	.	.	.	.	T	9.248	1.039937	0.19669	.	.	ENSG00000130707	ENST00000334909;ENST00000352480;ENST00000372394;ENST00000372393;ENST00000422569;ENST00000443588	D;D;D;D;D	0.98531	-4.98;-4.98;-4.98;-4.98;-4.98	4.79	4.79	0.61399	Rossmann-like alpha/beta/alpha sandwich fold (1);	0.055751	0.64402	U	0.000001	D	0.95658	0.8588	L	0.35487	1.065	0.44825	D	0.997839	B;B;B	0.09022	0.002;0.002;0.002	B;B;B	0.14023	0.01;0.01;0.01	D	0.93486	0.6831	10	0.52906	T	0.07	.	13.5045	0.61477	0.0:0.0:0.0:1.0	.	147;147;147	A8KAP9;Q5T6L4;P00966	.;.;ASSY_HUMAN	T	147;147;147;147;147;128	ENSP00000253004:M147T;ENSP00000361471:M147T;ENSP00000361469:M147T;ENSP00000394212:M147T;ENSP00000397785:M128T	ENSP00000361470:M147T	M	+	2	0	ASS1	132331952	1.000000	0.71417	1.000000	0.80357	0.729000	0.41735	7.271000	0.78506	1.775000	0.52247	0.379000	0.24179	ATG		0.602	ASS1-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054652.1	NM_000050	
SETX	23064	broad.mit.edu	37	9	135224714	135224714	+	Silent	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr9:135224714G>A	ENST00000224140.5	-	3	284	c.102C>T	c.(100-102)gaC>gaT	p.D34D	SETX_ENST00000393220.1_Silent_p.D34D|SETX_ENST00000372169.2_Silent_p.D34D	NM_015046.5	NP_055861.3	Q7Z333	SETX_HUMAN	senataxin	34					cell death (GO:0008219)|circadian rhythm (GO:0007623)|DNA duplex unwinding (GO:0032508)|double-strand break repair (GO:0006302)|RNA processing (GO:0006396)|termination of RNA polymerase II transcription (GO:0006369)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)	p.D34D(1)		breast(7)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(25)|liver(1)|lung(36)|ovary(2)|prostate(2)|skin(1)|stomach(4)|upper_aerodigestive_tract(1)|urinary_tract(2)	97		Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;6.82e-06)|Epithelial(140;0.000171)		AGAGGTCTTCGTCGGCTGTTT	0.468																																					p.D34D												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C102T	9						.						103.0	90.0	95.0					9																	135224714		2203	4300	6503	134214535	SO:0001819	synonymous_variant	23064	exon3			AB014525	CCDS6947.1	9q34	2014-09-17	2005-11-29	2005-11-29	ENSG00000107290	ENSG00000107290			445	protein-coding gene	gene with protein product		608465	"""amyotrophic lateral sclerosis 4"", ""spinocerebellar ataxia, recessive, non-Friedreich type 1"""	ALS4, SCAR1		9497266, 11022012	Standard	NM_015046		Approved	KIAA0625, AOA2	uc004cbk.3	Q7Z333	OTTHUMG00000020834	ENST00000224140.5:c.102C>T	9.37:g.135224714G>A		Somatic		Capture	Illumina HiSeq	Phase_I	134214535	NM_015046	A2A396|B2RPB2|B5ME16|C9JQ10|O75120|Q3KQX4|Q5JUJ1|Q68DW5|Q6AZD7|Q7Z3J6|Q8WX33|Q9H9D1|Q9NVP9	Silent	SNP	ENST00000224140.5	37	CCDS6947.1																																																																																				0.468	SETX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054774.3	NM_015046	
STKLD1	169436	broad.mit.edu	37	9	136270388	136270388	+	Missense_Mutation	SNP	C	C	T	rs143000003	byFrequency	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr9:136270388C>T	ENST00000371957.3	+	18	1993	c.1886C>T	c.(1885-1887)cCg>cTg	p.P629L	C9orf96_ENST00000371955.1_Missense_Mutation_p.P162L	NM_153710.3	NP_714921.4	Q8NE28	STKL1_HUMAN		629							ATP binding (GO:0005524)|protein kinase activity (GO:0004672)	p.P581L(1)		autonomic_ganglia(1)|central_nervous_system(3)|endometrium(1)|kidney(1)|large_intestine(5)|lung(10)|ovary(2)|stomach(2)	25				OV - Ovarian serous cystadenocarcinoma(145;1.06e-07)|Epithelial(140;1.28e-06)|all cancers(34;1.46e-05)		GAGATCCTGCCGGAGCTGGTG	0.602													C|||	4	0.000798722	0.0023	0.0014	5008	,	,		18104	0.0		0.0	False		,,,				2504	0.0				p.P629L												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1886T	9						.	C	LEU/PRO	10,4396	16.8+/-37.8	0,10,2193	44.0	41.0	42.0		1886	4.0	0.0	9	dbSNP_134	42	1,8599	1.2+/-3.3	0,1,4299	yes	missense	C9orf96	NM_153710.3	98	0,11,6492	TT,TC,CC		0.0116,0.227,0.0846	benign	629/681	136270388	11,12995	2203	4300	6503	135260209	SO:0001583	missense	169436	exon18																														ENST00000371957.3:c.1886C>T	9.37:g.136270388C>T	ENSP00000361025:p.Pro629Leu	Somatic		Capture	Illumina HiSeq	Phase_I	135260209	NM_153710	Q5T8U8|Q6ZMP6|Q6ZMQ5	Missense_Mutation	SNP	ENST00000371957.3	37	CCDS35169.1	1	4.578754578754579E-4	0	0.0	1	0.0027624309392265192	0	0.0	0	0.0	C	4.736	0.136945	0.09032	0.00227	1.16E-4	ENSG00000198870	ENST00000371957;ENST00000371955	T;T	0.46819	0.86;0.89	4.9	3.97	0.46021	Armadillo-like helical (1);Armadillo-type fold (1);	0.669254	0.14203	N	0.334558	T	0.30634	0.0771	N	0.20685	0.6	0.09310	N	0.999999	B	0.30605	0.287	B	0.15484	0.013	T	0.08229	-1.0732	10	0.31617	T	0.26	-3.4949	12.9869	0.58596	0.0:0.8358:0.1642:0.0	.	629	Q8NE28	SGK71_HUMAN	L	629;162	ENSP00000361025:P629L;ENSP00000361023:P162L	ENSP00000361023:P162L	P	+	2	0	C9orf96	135260209	0.038000	0.19896	0.038000	0.18304	0.177000	0.22998	0.920000	0.28705	1.124000	0.41980	0.561000	0.74099	CCG		0.602	C9orf96-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054855.1		
VAV2	7410	broad.mit.edu	37	9	136633692	136633692	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr9:136633692C>A	ENST00000371850.3	-	29	2492	c.2461G>T	c.(2461-2463)Gct>Tct	p.A821S	VAV2_ENST00000371851.1_Missense_Mutation_p.A811S|VAV2_ENST00000406606.3_Missense_Mutation_p.A782S	NM_001134398.1	NP_001127870.1	P52735	VAV2_HUMAN	vav 2 guanine nucleotide exchange factor	821	SH3 2. {ECO:0000255|PROSITE- ProRule:PRU00192}.				angiogenesis (GO:0001525)|apoptotic signaling pathway (GO:0097190)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell migration (GO:0016477)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|lamellipodium assembly (GO:0030032)|neurotrophin TRK receptor signaling pathway (GO:0048011)|platelet activation (GO:0030168)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|regulation of blood coagulation (GO:0030193)|regulation of gene expression (GO:0010468)|regulation of small GTPase mediated signal transduction (GO:0051056)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|plasma membrane (GO:0005886)	guanyl-nucleotide exchange factor activity (GO:0005085)|metal ion binding (GO:0046872)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)	p.A782S(1)		breast(1)|central_nervous_system(3)|endometrium(1)|kidney(3)|large_intestine(5)|lung(13)|ovary(4)|pancreas(1)|skin(2)|stomach(1)|urinary_tract(1)	35				OV - Ovarian serous cystadenocarcinoma(145;3.9e-07)|Epithelial(140;2.07e-06)|all cancers(34;9.39e-06)		CTGGCCACAGCTGTGCCGATG	0.627																																					p.A821S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2461T	9						.						73.0	62.0	66.0					9																	136633692		2203	4300	6503	135623513	SO:0001583	missense	7410	exon29				CCDS6979.1, CCDS48053.1	9q34.1	2013-02-14	2007-07-25		ENSG00000160293	ENSG00000160293		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"", ""SH2 domain containing"""	12658	protein-coding gene	gene with protein product		600428	"""vav 2 oncogene"""			7762982	Standard	NM_003371		Approved		uc004ces.3	P52735	OTTHUMG00000020882	ENST00000371850.3:c.2461G>T	9.37:g.136633692C>A	ENSP00000360916:p.Ala821Ser	Somatic		Capture	Illumina HiSeq	Phase_I	135623513	NM_001134398	A2RUM4|A8MQ12|B6ZDF5|Q5SYV3|Q5SYV4|Q5SYV5|Q6N012|Q6PIJ9|Q6Q317	Missense_Mutation	SNP	ENST00000371850.3	37	CCDS48053.1	.	.	.	.	.	.	.	.	.	.	C	27.8	4.865448	0.91511	.	.	ENSG00000160293	ENST00000371850;ENST00000371851;ENST00000406606;ENST00000325440	T;T;D	0.84070	2.08;2.08;-1.8	4.98	4.98	0.66077	Src homology-3 domain (4);	0.000000	0.85682	D	0.000000	D	0.91408	0.7289	M	0.81341	2.54	0.80722	D	1	D;D	0.89917	0.996;1.0	P;D	0.75020	0.869;0.985	D	0.92712	0.6184	10	0.87932	D	0	.	18.227	0.89921	0.0:1.0:0.0:0.0	.	821;782	P52735;P52735-3	VAV2_HUMAN;.	S	821;811;782;811	ENSP00000360916:A821S;ENSP00000360917:A811S;ENSP00000385362:A782S	ENSP00000317258:A811S	A	-	1	0	VAV2	135623513	1.000000	0.71417	0.703000	0.30354	0.544000	0.35116	7.680000	0.84062	2.297000	0.77311	0.563000	0.77884	GCT		0.627	VAV2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000054939.1		
COL5A1	1289	broad.mit.edu	37	9	137655564	137655564	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr9:137655564G>T	ENST00000371817.3	+	20	2429	c.2015G>T	c.(2014-2016)aGg>aTg	p.R672M		NM_000093.3|NM_001278074.1	NP_000084.3|NP_001265003.1	P20908	CO5A1_HUMAN	collagen, type V, alpha 1	672	Triple-helical region.				axon guidance (GO:0007411)|blood vessel development (GO:0001568)|cell adhesion (GO:0007155)|cell migration (GO:0016477)|collagen biosynthetic process (GO:0032964)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular fibril organization (GO:0043206)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|eye morphogenesis (GO:0048592)|heart morphogenesis (GO:0003007)|integrin biosynthetic process (GO:0045112)|negative regulation of endodermal cell differentiation (GO:1903225)|regulation of cellular component organization (GO:0051128)|skin development (GO:0043588)|tendon development (GO:0035989)|wound healing, spreading of epidermal cells (GO:0035313)	basement membrane (GO:0005604)|collagen type V trimer (GO:0005588)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	extracellular matrix structural constituent (GO:0005201)|heparin binding (GO:0008201)|integrin binding (GO:0005178)|metal ion binding (GO:0046872)|platelet-derived growth factor binding (GO:0048407)|proteoglycan binding (GO:0043394)	p.R672M(1)		NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(26)|liver(2)|lung(36)|ovary(4)|pancreas(4)|prostate(5)|skin(10)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(4)	115		Myeloproliferative disorder(178;0.0341)		all cancers(34;2.28e-08)|OV - Ovarian serous cystadenocarcinoma(145;6.03e-08)|Epithelial(140;6.4e-08)|GBM - Glioblastoma multiforme(294;0.131)		GTTGGGCCCAGGGGGCTGCCT	0.592																																					p.R672M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2015T	9						.						92.0	90.0	91.0					9																	137655564		2203	4300	6503	136795385	SO:0001583	missense	1289	exon20			D90279	CCDS6982.1, CCDS75932.1	9q34.2-q34.3	2014-09-17			ENSG00000130635	ENSG00000130635		"""Collagens"""	2209	protein-coding gene	gene with protein product	"""alpha 1 type V collagen"""	120215				1572660	Standard	NM_001278074		Approved		uc031tfl.1	P20908	OTTHUMG00000020891	ENST00000371817.3:c.2015G>T	9.37:g.137655564G>T	ENSP00000360882:p.Arg672Met	Somatic		Capture	Illumina HiSeq	Phase_I	136795385	NM_000093	Q15094|Q5SUX4	Missense_Mutation	SNP	ENST00000371817.3	37	CCDS6982.1	.	.	.	.	.	.	.	.	.	.	G	13.01	2.109579	0.37242	.	.	ENSG00000130635	ENST00000371817	D	0.94046	-3.34	3.9	3.9	0.45041	.	0.069023	0.52532	U	0.000066	D	0.88444	0.6438	L	0.43152	1.355	0.43014	D	0.994552	P	0.40476	0.718	B	0.36030	0.216	D	0.88666	0.3192	10	0.66056	D	0.02	.	9.2564	0.37586	0.0:0.0:0.7843:0.2157	.	672	P20908	CO5A1_HUMAN	M	672	ENSP00000360882:R672M	ENSP00000360882:R672M	R	+	2	0	COL5A1	136795385	1.000000	0.71417	1.000000	0.80357	0.898000	0.52572	7.015000	0.76387	1.904000	0.55121	0.462000	0.41574	AGG		0.592	COL5A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054954.2	NM_000093	
COL5A1	1289	broad.mit.edu	37	9	137710739	137710739	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr9:137710739G>A	ENST00000371817.3	+	56	4798	c.4384G>A	c.(4384-4386)Ggc>Agc	p.G1462S		NM_000093.3|NM_001278074.1	NP_000084.3|NP_001265003.1	P20908	CO5A1_HUMAN	collagen, type V, alpha 1	1462	Triple-helical region.				axon guidance (GO:0007411)|blood vessel development (GO:0001568)|cell adhesion (GO:0007155)|cell migration (GO:0016477)|collagen biosynthetic process (GO:0032964)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular fibril organization (GO:0043206)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|eye morphogenesis (GO:0048592)|heart morphogenesis (GO:0003007)|integrin biosynthetic process (GO:0045112)|negative regulation of endodermal cell differentiation (GO:1903225)|regulation of cellular component organization (GO:0051128)|skin development (GO:0043588)|tendon development (GO:0035989)|wound healing, spreading of epidermal cells (GO:0035313)	basement membrane (GO:0005604)|collagen type V trimer (GO:0005588)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	extracellular matrix structural constituent (GO:0005201)|heparin binding (GO:0008201)|integrin binding (GO:0005178)|metal ion binding (GO:0046872)|platelet-derived growth factor binding (GO:0048407)|proteoglycan binding (GO:0043394)	p.G1462S(1)		NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(26)|liver(2)|lung(36)|ovary(4)|pancreas(4)|prostate(5)|skin(10)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(4)	115		Myeloproliferative disorder(178;0.0341)		all cancers(34;2.28e-08)|OV - Ovarian serous cystadenocarcinoma(145;6.03e-08)|Epithelial(140;6.4e-08)|GBM - Glioblastoma multiforme(294;0.131)		CGGTCCCCCCGGCCCCATGGT	0.632																																					p.G1462S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G4384A	9						.						48.0	48.0	48.0					9																	137710739		2203	4300	6503	136850560	SO:0001583	missense	1289	exon56			D90279	CCDS6982.1, CCDS75932.1	9q34.2-q34.3	2014-09-17			ENSG00000130635	ENSG00000130635		"""Collagens"""	2209	protein-coding gene	gene with protein product	"""alpha 1 type V collagen"""	120215				1572660	Standard	NM_001278074		Approved		uc031tfl.1	P20908	OTTHUMG00000020891	ENST00000371817.3:c.4384G>A	9.37:g.137710739G>A	ENSP00000360882:p.Gly1462Ser	Somatic		Capture	Illumina HiSeq	Phase_I	136850560	NM_000093	Q15094|Q5SUX4	Missense_Mutation	SNP	ENST00000371817.3	37	CCDS6982.1	.	.	.	.	.	.	.	.	.	.	G	22.2	4.258159	0.80246	.	.	ENSG00000130635	ENST00000371817	D	0.99527	-6.09	4.69	4.69	0.59074	.	0.000000	0.85682	U	0.000000	D	0.99718	0.9891	H	0.96633	3.855	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.97089	0.9789	10	0.87932	D	0	.	17.6063	0.88039	0.0:0.0:1.0:0.0	.	1462	P20908	CO5A1_HUMAN	S	1462	ENSP00000360882:G1462S	ENSP00000360882:G1462S	G	+	1	0	COL5A1	136850560	1.000000	0.71417	0.990000	0.47175	0.827000	0.46813	9.732000	0.98816	2.150000	0.67090	0.448000	0.29417	GGC		0.632	COL5A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054954.2	NM_000093	
SEC16A	9919	broad.mit.edu	37	9	139371250	139371250	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr9:139371250G>A	ENST00000371706.3	-	1	317	c.284C>T	c.(283-285)gCa>gTa	p.A95V	SEC16A_ENST00000431893.2_Missense_Mutation_p.A95V|SEC16A_ENST00000290037.6_Missense_Mutation_p.A95V|SEC16A_ENST00000313050.7_Missense_Mutation_p.A273V			O15027	SC16A_HUMAN	SEC16 homolog A (S. cerevisiae)	95					COPII vesicle coating (GO:0048208)|endoplasmic reticulum organization (GO:0007029)|protein transport (GO:0015031)|substantia nigra development (GO:0021762)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)		p.A273V(1)		breast(1)|central_nervous_system(3)|endometrium(7)|kidney(5)|large_intestine(15)|lung(14)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51		Myeloproliferative disorder(178;0.0511)		Epithelial(140;2.9e-06)|OV - Ovarian serous cystadenocarcinoma(145;5.88e-06)		GGGCAAGGCTGCTGGGGGAGC	0.587																																					p.A273V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C818T	9						.						28.0	32.0	31.0					9																	139371250		1972	4159	6131	138491071	SO:0001583	missense	9919	exon3			AK074565	CCDS55351.1, CCDS75936.1	9q34.3	2007-06-20	2007-06-20	2007-06-20	ENSG00000148396	ENSG00000148396			29006	protein-coding gene	gene with protein product		612854	"""KIAA0310"""	KIAA0310		9205841	Standard	NM_014866		Approved	p250	uc004chx.3	O15027	OTTHUMG00000020932	ENST00000371706.3:c.284C>T	9.37:g.139371250G>A	ENSP00000360771:p.Ala95Val	Somatic		Capture	Illumina HiSeq	Phase_I	138491071	NM_014866	A1YCA4|Q4G0D7|Q5SXP0|Q5SXP1|Q8N347|Q96HP1	Missense_Mutation	SNP	ENST00000371706.3	37		.	.	.	.	.	.	.	.	.	.	G	12.07	1.828951	0.32329	.	.	ENSG00000148396	ENST00000313050;ENST00000371706;ENST00000290037;ENST00000431893	T;T;T;T	0.26373	1.78;1.74;1.74;1.74	5.19	1.18	0.20946	.	0.768215	0.11449	N	0.562979	T	0.19604	0.0471	L	0.36672	1.1	0.19575	N	0.999965	B;B;B	0.21225	0.031;0.053;0.053	B;B;B	0.20955	0.014;0.032;0.019	T	0.24119	-1.0169	10	0.35671	T	0.21	-4.7728	9.1956	0.37226	0.0:0.5022:0.3341:0.1636	.	273;95;95	F1T0I1;O15027-5;O15027-4	.;.;.	V	273;95;95;95	ENSP00000325827:A273V;ENSP00000360771:A95V;ENSP00000290037:A95V;ENSP00000387583:A95V	ENSP00000290037:A95V	A	-	2	0	SEC16A	138491071	0.792000	0.28813	0.003000	0.11579	0.042000	0.13812	1.061000	0.30542	0.017000	0.15025	0.655000	0.94253	GCA		0.587	SEC16A-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000055077.1	XM_088459	
C9orf173	441476	broad.mit.edu	37	9	140146526	140146526	+	Silent	SNP	G	G	A	rs74822962	byFrequency	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr9:140146526G>A	ENST00000412566.1	+	3	351	c.342G>A	c.(340-342)ccG>ccA	p.P114P	C9orf173_ENST00000388931.3_Silent_p.P114P			Q8N7X2	CI173_HUMAN	chromosome 9 open reading frame 173	114								p.P114P(1)		kidney(1)|large_intestine(1)|lung(5)|pancreas(1)	8						TGCCGAGCCCGTCCGTACGAG	0.672													G|||	36	0.0071885	0.0257	0.0029	5008	,	,		16156	0.0		0.0	False		,,,				2504	0.0				p.P114P												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G342A	9						.	G		64,4044		0,64,1990	40.0	50.0	47.0		342	-7.8	0.0	9	dbSNP_132	47	1,8369		0,1,4184	no	coding-synonymous	C9orf173	NM_001004353.2		0,65,6174	AA,AG,GG		0.0119,1.5579,0.5209		114/309	140146526	65,12413	2054	4185	6239	139266347	SO:0001819	synonymous_variant	441476	exon3				CCDS48065.1, CCDS59156.1, CCDS75940.1, CCDS75941.1	9q34.3	2009-10-02			ENSG00000197768	ENSG00000197768			37285	protein-coding gene	gene with protein product							Standard	NM_001256699		Approved	FLJ40246	uc004cmk.2	Q8N7X2		ENST00000412566.1:c.342G>A	9.37:g.140146526G>A		Somatic		Capture	Illumina HiSeq	Phase_I	139266347	NM_001004353	A2RU24|B7ZM72|B7ZM76|Q8NEA3	Silent	SNP	ENST00000412566.1	37	CCDS48065.1																																																																																				0.672	C9orf173-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001004353	
NOXA1	10811	broad.mit.edu	37	9	140320738	140320738	+	Silent	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr9:140320738G>A	ENST00000341349.2	+	2	396	c.216G>A	c.(214-216)gcG>gcA	p.A72A	NOXA1_ENST00000392815.2_Silent_p.A72A	NM_001256067.1|NM_006647.1	NP_001242996.1|NP_006638.1	Q86UR1	NOXA1_HUMAN	NADPH oxidase activator 1	72	Mediates interaction with RAC1.				positive regulation of catalytic activity (GO:0043085)|regulation of hydrogen peroxide metabolic process (GO:0010310)|regulation of respiratory burst (GO:0060263)|superoxide metabolic process (GO:0006801)	cytoplasm (GO:0005737)|NADPH oxidase complex (GO:0043020)	enzyme binding (GO:0019899)|Rac GTPase binding (GO:0048365)|SH3 domain binding (GO:0017124)|superoxide-generating NADPH oxidase activator activity (GO:0016176)	p.A72A(1)		cervix(1)|large_intestine(2)|lung(2)|skin(3)|upper_aerodigestive_tract(1)	9	all_cancers(76;0.0926)			OV - Ovarian serous cystadenocarcinoma(145;0.000238)|Epithelial(140;0.000982)		CCTGCATGGCGGTTGGCTTCT	0.572																																					p.A72A												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G216A	9						.						143.0	119.0	127.0					9																	140320738		2203	4300	6503	139440559	SO:0001819	synonymous_variant	10811	exon2			AF039697	CCDS7042.1, CCDS59157.1	9q34.3	2013-09-20	2002-12-09	2002-12-13	ENSG00000188747	ENSG00000188747			10668	protein-coding gene	gene with protein product		611255	"""serologically defined colon cancer antigen 31"""	SDCCAG31		9610721	Standard	NM_001256067		Approved	NY-CO-31, FLJ25475	uc004cmu.3	Q86UR1	OTTHUMG00000131781	ENST00000341349.2:c.216G>A	9.37:g.140320738G>A		Somatic		Capture	Illumina HiSeq	Phase_I	139440559	NM_006647	O60533|Q29VU9|Q29VV0|Q2TAM1|Q8IUS3	Silent	SNP	ENST00000341349.2	37	CCDS7042.1																																																																																				0.572	NOXA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254713.1		
KCNV2	169522	broad.mit.edu	37	9	2717905	2717905	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr9:2717905G>A	ENST00000382082.3	+	1	404	c.166G>A	c.(166-168)Gag>Aag	p.E56K		NM_133497.3	NP_598004.1	Q8TDN2	KCNV2_HUMAN	potassium channel, subfamily V, member 2	56					protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)	p.E56K(1)		NS(1)|breast(1)|central_nervous_system(3)|endometrium(5)|kidney(4)|large_intestine(7)|lung(9)|ovary(1)|prostate(2)|skin(2)	35				GBM - Glioblastoma multiforme(50;0.0257)		CTACTACATCGAGGAAGACGA	0.647																																					p.E56K												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G166A	9						.						151.0	120.0	130.0					9																	2717905		2203	4300	6503	2707905	SO:0001583	missense	169522	exon1			AF348983	CCDS6447.1	9p24.2	2011-07-05			ENSG00000168263	ENSG00000168263		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	19698	protein-coding gene	gene with protein product		607604				12060745, 16382104	Standard	NM_133497		Approved	Kv8.2	uc003zho.2	Q8TDN2	OTTHUMG00000019449	ENST00000382082.3:c.166G>A	9.37:g.2717905G>A	ENSP00000371514:p.Glu56Lys	Somatic		Capture	Illumina HiSeq	Phase_I	2707905	NM_133497	Q5T6X0	Missense_Mutation	SNP	ENST00000382082.3	37	CCDS6447.1	.	.	.	.	.	.	.	.	.	.	G	21.6	4.180250	0.78677	.	.	ENSG00000168263	ENST00000423608;ENST00000382082	D	0.97138	-4.26	5.35	5.35	0.76521	.	1.878680	0.02548	N	0.095285	D	0.94879	0.8345	L	0.34521	1.04	0.37858	D	0.929605	P	0.44006	0.824	B	0.29663	0.105	D	0.84536	0.0636	10	0.62326	D	0.03	.	19.0627	0.93099	0.0:0.0:1.0:0.0	.	56	Q8TDN2	KCNV2_HUMAN	K	56	ENSP00000371514:E56K	ENSP00000371514:E56K	E	+	1	0	KCNV2	2707905	1.000000	0.71417	1.000000	0.80357	0.789000	0.44602	4.892000	0.63193	2.499000	0.84300	0.467000	0.42956	GAG		0.647	KCNV2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051528.1	NM_133497	
KCNV2	169522	broad.mit.edu	37	9	2718710	2718710	+	Missense_Mutation	SNP	C	C	T	rs376858051		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr9:2718710C>T	ENST00000382082.3	+	1	1209	c.971C>T	c.(970-972)aCg>aTg	p.T324M		NM_133497.3	NP_598004.1	Q8TDN2	KCNV2_HUMAN	potassium channel, subfamily V, member 2	324					protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)	p.T324M(1)		NS(1)|breast(1)|central_nervous_system(3)|endometrium(5)|kidney(4)|large_intestine(7)|lung(9)|ovary(1)|prostate(2)|skin(2)	35				GBM - Glioblastoma multiforme(50;0.0257)		CTAGCCTCCACGCCCGACCTG	0.682																																					p.T324M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C971T	9						.						45.0	50.0	48.0					9																	2718710		2203	4299	6502	2708710	SO:0001583	missense	169522	exon1			AF348983	CCDS6447.1	9p24.2	2011-07-05			ENSG00000168263	ENSG00000168263		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	19698	protein-coding gene	gene with protein product		607604				12060745, 16382104	Standard	NM_133497		Approved	Kv8.2	uc003zho.2	Q8TDN2	OTTHUMG00000019449	ENST00000382082.3:c.971C>T	9.37:g.2718710C>T	ENSP00000371514:p.Thr324Met	Somatic		Capture	Illumina HiSeq	Phase_I	2708710	NM_133497	Q5T6X0	Missense_Mutation	SNP	ENST00000382082.3	37	CCDS6447.1	.	.	.	.	.	.	.	.	.	.	C	17.64	3.439776	0.63067	.	.	ENSG00000168263	ENST00000382082	D	0.97480	-4.4	5.22	5.22	0.72569	Ion transport (1);	0.000000	0.85682	D	0.000000	D	0.98523	0.9507	M	0.83012	2.62	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.99741	1.1015	10	0.87932	D	0	.	18.8074	0.92043	0.0:1.0:0.0:0.0	.	324	Q8TDN2	KCNV2_HUMAN	M	324	ENSP00000371514:T324M	ENSP00000371514:T324M	T	+	2	0	KCNV2	2708710	1.000000	0.71417	0.974000	0.42286	0.400000	0.30750	7.818000	0.86416	2.434000	0.82447	0.563000	0.77884	ACG		0.682	KCNV2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051528.1	NM_133497	
KCNV2	169522	broad.mit.edu	37	9	2718982	2718982	+	Silent	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr9:2718982C>T	ENST00000382082.3	+	1	1481	c.1243C>T	c.(1243-1245)Ctg>Ttg	p.L415L		NM_133497.3	NP_598004.1	Q8TDN2	KCNV2_HUMAN	potassium channel, subfamily V, member 2	415					protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)	p.L415L(1)		NS(1)|breast(1)|central_nervous_system(3)|endometrium(5)|kidney(4)|large_intestine(7)|lung(9)|ovary(1)|prostate(2)|skin(2)	35				GBM - Glioblastoma multiforme(50;0.0257)		GGGCTGCCTGCTGCTCTTCAT	0.617																																					p.L415L												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1243T	9						.						70.0	58.0	62.0					9																	2718982		2203	4300	6503	2708982	SO:0001819	synonymous_variant	169522	exon1			AF348983	CCDS6447.1	9p24.2	2011-07-05			ENSG00000168263	ENSG00000168263		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	19698	protein-coding gene	gene with protein product		607604				12060745, 16382104	Standard	NM_133497		Approved	Kv8.2	uc003zho.2	Q8TDN2	OTTHUMG00000019449	ENST00000382082.3:c.1243C>T	9.37:g.2718982C>T		Somatic		Capture	Illumina HiSeq	Phase_I	2708982	NM_133497	Q5T6X0	Silent	SNP	ENST00000382082.3	37	CCDS6447.1																																																																																				0.617	KCNV2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051528.1	NM_133497	
KIAA0020	9933	broad.mit.edu	37	9	2811476	2811476	+	Missense_Mutation	SNP	G	G	A	rs142006198		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr9:2811476G>A	ENST00000397885.2	-	15	1726	c.1520C>T	c.(1519-1521)gCg>gTg	p.A507V		NM_014878.4	NP_055693.4	Q15397	K0020_HUMAN	KIAA0020	507	PUM-HD. {ECO:0000255|PROSITE- ProRule:PRU00318}.					endoplasmic reticulum (GO:0005783)|nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)	p.A507V(1)		NS(1)|breast(2)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(7)|lung(4)|ovary(1)	21				GBM - Glioblastoma multiforme(50;0.0319)		CAACACACACGCAGACTTATC	0.527																																					p.A507V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1520T	9						.						186.0	163.0	171.0					9																	2811476		2203	4300	6503	2801476	SO:0001583	missense	9933	exon15			AL832239	CCDS6448.2	9p24.2	2012-11-29			ENSG00000080608	ENSG00000080608			29676	protein-coding gene	gene with protein product	"""penguin homolog (Drosophila)"", ""minor histocompatibility antigen HA-8"""	609960				7584026, 7584028, 21266351	Standard	NM_014878		Approved	XTP5, PEN, PUF6, hPUF-A, HA-8	uc003zhp.1	Q15397	OTTHUMG00000019450	ENST00000397885.2:c.1520C>T	9.37:g.2811476G>A	ENSP00000380982:p.Ala507Val	Somatic		Capture	Illumina HiSeq	Phase_I	2801476	NM_014878	A8K804|Q547G7|Q5SZY9|Q6IB47|Q96B27|Q96L78|Q96L79|Q96L80	Missense_Mutation	SNP	ENST00000397885.2	37	CCDS6448.2	.	.	.	.	.	.	.	.	.	.	G	6.915	0.538406	0.13250	.	.	ENSG00000080608	ENST00000397885	T	0.20069	2.1	5.97	4.13	0.48395	CPL (1);Armadillo-like helical (1);Armadillo-type fold (1);	0.643517	0.17847	N	0.159996	T	0.15392	0.0371	L	0.28115	0.83	0.09310	N	1	B;B	0.10296	0.003;0.003	B;B	0.13407	0.009;0.009	T	0.17379	-1.0371	10	0.44086	T	0.13	-4.1827	10.3074	0.43689	0.2027:0.0:0.7973:0.0	.	367;507	B2RDG4;Q15397	.;K0020_HUMAN	V	507	ENSP00000380982:A507V	ENSP00000380982:A507V	A	-	2	0	KIAA0020	2801476	0.009000	0.17119	0.162000	0.22713	0.175000	0.22909	1.771000	0.38542	0.849000	0.35215	-0.140000	0.14226	GCG		0.527	KIAA0020-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051529.3	NM_014878	
GLIS3	169792	broad.mit.edu	37	9	4118462	4118462	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr9:4118462G>T	ENST00000324333.10	-	3	744	c.551C>A	c.(550-552)gCc>gAc	p.A184D	GLIS3_ENST00000381971.3_Missense_Mutation_p.A339D	NM_152629.3	NP_689842.3	Q8NEA6	GLIS3_HUMAN	GLIS family zinc finger 3	184					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription from RNA polymerase II promoter (GO:0006366)	Golgi apparatus (GO:0005794)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|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)	p.A184D(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|large_intestine(12)|lung(4)|ovary(2)|prostate(1)|skin(1)	26		Acute lymphoblastic leukemia(2;0.00464)|Breast(48;0.148)		Lung(2;0.00163)|GBM - Glioblastoma multiforme(50;0.00301)|LUSC - Lung squamous cell carcinoma(2;0.0148)		GGACAGGTTGGCCGGCGAAGC	0.672																																					p.A184D												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C551A	9						.						36.0	32.0	33.0					9																	4118462		2203	4299	6502	4108462	SO:0001583	missense	169792	exon3			BC033899	CCDS6451.1, CCDS43784.1	9p24.2	2008-05-02	2004-07-16	2004-07-16	ENSG00000107249	ENSG00000107249		"""Zinc fingers, C2H2-type"""	28510	protein-coding gene	gene with protein product		610192	"""zinc finger protein 515"""	ZNF515		14500813	Standard	NM_152629		Approved	MGC33662	uc003zhx.1	Q8NEA6	OTTHUMG00000019463	ENST00000324333.10:c.551C>A	9.37:g.4118462G>T	ENSP00000325494:p.Ala184Asp	Somatic		Capture	Illumina HiSeq	Phase_I	4108462	NM_152629	B1AL19|Q1PHK5	Missense_Mutation	SNP	ENST00000324333.10	37	CCDS6451.1	.	.	.	.	.	.	.	.	.	.	G	16.56	3.157402	0.57259	.	.	ENSG00000107249	ENST00000324333;ENST00000381971	T;T	0.17854	2.26;2.25	5.83	5.83	0.93111	.	0.000000	0.51477	D	0.000092	T	0.34687	0.0906	M	0.79475	2.455	0.47065	D	0.999304	D;P	0.53462	0.96;0.933	P;B	0.48795	0.59;0.386	T	0.07252	-1.0782	10	0.51188	T	0.08	.	20.1124	0.97915	0.0:0.0:1.0:0.0	.	339;184	Q8NEA6-2;Q8NEA6	.;GLIS3_HUMAN	D	184;339	ENSP00000325494:A184D;ENSP00000371398:A339D	ENSP00000325494:A184D	A	-	2	0	GLIS3	4108462	1.000000	0.71417	0.962000	0.40283	0.239000	0.25481	6.750000	0.74888	2.749000	0.94314	0.655000	0.94253	GCC		0.672	GLIS3-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000051559.1	NM_152629	
KDM4C	23081	broad.mit.edu	37	9	7103868	7103868	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr9:7103868G>A	ENST00000381309.3	+	18	3173	c.2608G>A	c.(2608-2610)Gtg>Atg	p.V870M	KDM4C_ENST00000442236.2_Missense_Mutation_p.V615M|KDM4C_ENST00000536108.1_3'UTR|KDM4C_ENST00000381306.3_Missense_Mutation_p.V870M|KDM4C_ENST00000428870.2_Missense_Mutation_p.V557M	NM_015061.3	NP_055876.2	Q9H3R0	KDM4C_HUMAN	lysine (K)-specific demethylase 4C	870					histone H3-K9 demethylation (GO:0033169)|positive regulation of cell proliferation (GO:0008284)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nuclear chromatin (GO:0000790)	androgen receptor binding (GO:0050681)|dioxygenase activity (GO:0051213)|enzyme binding (GO:0019899)|histone demethylase activity (H3-K9 specific) (GO:0032454)|zinc ion binding (GO:0008270)	p.V870M(1)		breast(1)|central_nervous_system(4)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(8)|lung(14)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	43						CAACCCCAACGTGGTAAGATG	0.473																																					p.V870M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2608A	9						.						144.0	104.0	118.0					9																	7103868		2203	4300	6503	7093868	SO:0001583	missense	23081	exon18			AB018323	CCDS6471.1, CCDS55285.1, CCDS55286.1, CCDS55287.1	9p24-p23	2013-01-23	2009-04-06	2009-04-06	ENSG00000107077	ENSG00000107077		"""Chromatin-modifying enzymes / K-demethylases"", ""Tudor domain containing"""	17071	protein-coding gene	gene with protein product	"""tudor domain containing 14C"""	605469	"""jumonji domain containing 2C"""	JMJD2C		9872452, 15138608	Standard	NM_015061		Approved	GASC1, KIAA0780, TDRD14C	uc003zkh.3	Q9H3R0	OTTHUMG00000019536	ENST00000381309.3:c.2608G>A	9.37:g.7103868G>A	ENSP00000370710:p.Val870Met	Somatic		Capture	Illumina HiSeq	Phase_I	7093868	NM_015061	B4E1Y4|B7ZL46|F5H347|F5H7P0|O94877|Q2M3M0|Q5JUC9|Q5VYJ2|Q5VYJ3	Missense_Mutation	SNP	ENST00000381309.3	37	CCDS6471.1	.	.	.	.	.	.	.	.	.	.	G	4.179	0.031815	0.08101	.	.	ENSG00000107077	ENST00000381309;ENST00000381306;ENST00000442236;ENST00000428870;ENST00000420847	T;T;T;T;T	0.15952	2.47;2.38;2.71;3.46;2.74	5.91	1.72	0.24424	.	1.361170	0.04311	N	0.348923	T	0.06554	0.0168	N	0.02011	-0.69	0.09310	N	0.999993	B;B;B	0.33073	0.396;0.053;0.333	B;B;B	0.23574	0.025;0.016;0.047	T	0.22034	-1.0228	10	0.45353	T	0.12	-28.0985	5.9818	0.19411	0.1354:0.0:0.4757:0.3889	.	615;870;870	E7EV17;Q9H3R0;Q9H3R0-2	.;KDM4C_HUMAN;.	M	870;870;615;557;214	ENSP00000370710:V870M;ENSP00000370707:V870M;ENSP00000409353:V615M;ENSP00000405739:V557M;ENSP00000400127:V214M	ENSP00000370707:V870M	V	+	1	0	KDM4C	7093868	0.992000	0.36948	0.706000	0.30403	0.028000	0.11728	1.166000	0.31834	0.357000	0.24183	-0.137000	0.14449	GTG		0.473	KDM4C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051692.1	NM_015061	
NFIB	4781	broad.mit.edu	37	9	14146730	14146730	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr9:14146730A>G	ENST00000380959.3	-	6	1356	c.883T>C	c.(883-885)Tca>Cca	p.S295P	NFIB_ENST00000380924.1_Missense_Mutation_p.S43P|NFIB_ENST00000380953.1_Missense_Mutation_p.S295P|NFIB_ENST00000397575.3_Missense_Mutation_p.S295P|NFIB_ENST00000397579.2_Missense_Mutation_p.S295P|NFIB_ENST00000397581.2_Missense_Mutation_p.S295P|NFIB_ENST00000380934.4_Missense_Mutation_p.S321P|NFIB_ENST00000543693.1_Missense_Mutation_p.S43P	NM_005596.3	NP_005587.2	O00712	NFIB_HUMAN	nuclear factor I/B	295					anterior commissure morphogenesis (GO:0021960)|chondrocyte differentiation (GO:0002062)|Clara cell differentiation (GO:0060486)|commissural neuron axon guidance (GO:0071679)|DNA replication (GO:0006260)|glial cell differentiation (GO:0010001)|hindbrain development (GO:0030902)|lung ciliated cell differentiation (GO:0061141)|negative regulation of DNA binding (GO:0043392)|negative regulation of epithelial cell proliferation involved in lung morphogenesis (GO:2000795)|negative regulation of mesenchymal cell proliferation involved in lung development (GO:2000791)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|principal sensory nucleus of trigeminal nerve development (GO:0021740)|transcription from RNA polymerase II promoter (GO:0006366)|Type I pneumocyte differentiation (GO:0060509)|Type II pneumocyte differentiation (GO:0060510)	cerebellar mossy fiber (GO:0044300)|nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA binding (GO:0003677)|double-stranded DNA binding (GO:0003690)|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)|RNA polymerase II transcription corepressor activity (GO:0001106)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)	p.S295P(2)		central_nervous_system(2)|endometrium(2)|large_intestine(7)|lung(5)|skin(1)	17				GBM - Glioblastoma multiforme(50;4.4e-08)|LUAD - Lung adenocarcinoma(58;0.119)|Lung(218;0.164)		GCAGCTGGTGAACTTGGAGAG	0.403			T	"""MYB, HGMA2"""	"""adenoid cystic carcinoma, lipoma"""																																p.S321P	Esophageal Squamous(132;921 1730 14828 40753 46471)		Dom	yes		9	9p24.1	4781	nuclear factor I/B		E	.	.	2	Substitution - Missense(2)	large_intestine(2)	c.T961C	9						.						192.0	185.0	187.0					9																	14146730		2203	4300	6503	14136730	SO:0001583	missense	4781	exon6			U07810	CCDS6474.1, CCDS55291.1, CCDS55292.1, CCDS65007.1	9p24.1	2008-02-05			ENSG00000147862	ENSG00000147862			7785	protein-coding gene	gene with protein product		600728				7590749	Standard	NM_001190737		Approved	NFI-RED, NFIB2, NFIB3	uc003zlf.3	O00712	OTTHUMG00000021027	ENST00000380959.3:c.883T>C	9.37:g.14146730A>G	ENSP00000370346:p.Ser295Pro	Somatic		Capture	Illumina HiSeq	Phase_I	14136730	NM_001190738	G3V1P1|H7BYE8|O00166|Q12858|Q5VW29|Q63HM5|Q6ZNF9|Q96J45	Missense_Mutation	SNP	ENST00000380959.3	37	CCDS6474.1	.	.	.	.	.	.	.	.	.	.	A	24.5	4.536937	0.85812	.	.	ENSG00000147862	ENST00000380934;ENST00000380959;ENST00000380953;ENST00000397575;ENST00000397581;ENST00000397579;ENST00000543693;ENST00000380924	T;T;T;T;T;T;T;T	0.58797	0.31;0.31;0.31;0.31;0.31;0.31;0.31;0.31	5.54	5.54	0.83059	.	0.067665	0.64402	D	0.000007	T	0.68568	0.3015	L	0.39397	1.21	0.58432	D	0.999992	D;D;D;P	0.59357	0.985;0.982;0.985;0.902	D;P;D;B	0.72075	0.976;0.677;0.976;0.204	T	0.69650	-0.5088	10	0.52906	T	0.07	-6.5513	15.97	0.80008	1.0:0.0:0.0:0.0	.	295;295;295;43	Q5VW27;Q5VW29;O00712;G3V1P1	.;.;NFIB_HUMAN;.	P	321;295;295;295;295;295;43;43	ENSP00000370321:S321P;ENSP00000370346:S295P;ENSP00000370340:S295P;ENSP00000380705:S295P;ENSP00000380711:S295P;ENSP00000380709:S295P;ENSP00000442888:S43P;ENSP00000370311:S43P	ENSP00000370311:S43P	S	-	1	0	NFIB	14136730	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	5.963000	0.70372	2.243000	0.73865	0.533000	0.62120	TCA		0.403	NFIB-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000055468.1	NM_005596	
TTC39B	158219	broad.mit.edu	37	9	15225991	15225991	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr9:15225991C>T	ENST00000512701.2	-	3	331	c.295G>A	c.(295-297)Gca>Aca	p.A99T	TTC39B_ENST00000355694.2_Missense_Mutation_p.A33T|TTC39B_ENST00000582994.1_5'UTR|TTC39B_ENST00000507993.1_Intron|TTC39B_ENST00000380850.4_Missense_Mutation_p.A99T|TTC39B_ENST00000297615.5_Intron|TTC39B_ENST00000541445.1_Missense_Mutation_p.A33T|TTC39B_ENST00000507285.1_5'UTR			Q5VTQ0	TT39B_HUMAN	tetratricopeptide repeat domain 39B	99								p.A33T(1)		NS(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(7)|ovary(2)|prostate(1)	21						CTGCTTGTTGCCATATCTGAG	0.458																																					p.A99T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G295A	9						.						118.0	110.0	113.0					9																	15225991		2203	4300	6503	15215991	SO:0001583	missense	158219	exon3			AK091187	CCDS6477.1, CCDS6477.2, CCDS55294.1, CCDS55295.1, CCDS55296.1	9p22.2	2013-01-11	2008-06-23	2008-06-23	ENSG00000155158	ENSG00000155158		"""Tetratricopeptide (TTC) repeat domain containing"""	23704	protein-coding gene	gene with protein product		613574	"""chromosome 9 open reading frame 52"""	C9orf52			Standard	NM_001168339		Approved	FLJ33868	uc003zlr.2	Q5VTQ0	OTTHUMG00000019581	ENST00000512701.2:c.295G>A	9.37:g.15225991C>T	ENSP00000422496:p.Ala99Thr	Somatic		Capture	Illumina HiSeq	Phase_I	15215991	NM_001168340	A5PLN1|B4DQ10|B4DQX4|B4DW93|Q8IVR7|Q8IXZ6|Q8N267	Missense_Mutation	SNP	ENST00000512701.2	37	CCDS6477.2	.	.	.	.	.	.	.	.	.	.	C	29.6	5.017349	0.93404	.	.	ENSG00000155158	ENST00000380850;ENST00000355694;ENST00000512701;ENST00000541445	T;T;T;T	0.54479	1.24;1.36;1.24;0.57	4.13	4.13	0.48395	.	1.765880	0.03309	N	0.190234	T	0.47395	0.1443	L	0.36672	1.1	0.35139	D	0.768731	B;P;B;B	0.34522	0.319;0.455;0.319;0.319	B;B;B;B	0.34138	0.135;0.176;0.087;0.087	T	0.33007	-0.9885	10	0.22706	T	0.39	-7.6651	12.1923	0.54278	0.0:1.0:0.0:0.0	.	99;99;33;33	E9PAQ9;E9PE60;A5PLN1;Q5VTQ0	.;.;.;TT39B_HUMAN	T	99;33;99;33	ENSP00000370231:A99T;ENSP00000347920:A33T;ENSP00000422496:A99T;ENSP00000442880:A33T	ENSP00000347920:A33T	A	-	1	0	TTC39B	15215991	1.000000	0.71417	0.994000	0.49952	0.734000	0.41952	2.953000	0.49105	2.590000	0.87494	0.655000	0.94253	GCA		0.458	TTC39B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000051758.3	NM_152574	
SNAPC3	6619	broad.mit.edu	37	9	15423928	15423928	+	Silent	SNP	T	T	C			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr9:15423928T>C	ENST00000380821.3	+	2	512	c.336T>C	c.(334-336)ctT>ctC	p.L112L	SNAPC3_ENST00000461041.1_3'UTR	NM_001039697.1	NP_001034786.1	Q92966	SNPC3_HUMAN	small nuclear RNA activating complex, polypeptide 3, 50kDa	112					gene expression (GO:0010467)|regulation of transcription, DNA-templated (GO:0006355)|snRNA transcription (GO:0009301)|transcription from RNA polymerase II promoter (GO:0006366)|transcription from RNA polymerase III promoter (GO:0006383)	nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)	p.L112L(1)		breast(1)|endometrium(3)|large_intestine(6)|lung(2)	12				GBM - Glioblastoma multiforme(50;2.15e-06)		TGAAATGCCTTGAGGACGGTG	0.398																																					p.L112L												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.T336C	9						.						191.0	170.0	177.0					9																	15423928		2203	4300	6503	15413928	SO:0001819	synonymous_variant	6619	exon2			U71300	CCDS6478.1	9p22.3	2008-07-21	2002-08-29		ENSG00000164975	ENSG00000164975			11136	protein-coding gene	gene with protein product		602348	"""small nuclear RNA activating complex, polypeptide 3, 50kD"""			9003788	Standard	XR_428427		Approved	SNAP50, PTFbeta, MGC33124, MGC132011	uc003zlt.3	Q92966	OTTHUMG00000019583	ENST00000380821.3:c.336T>C	9.37:g.15423928T>C		Somatic		Capture	Illumina HiSeq	Phase_I	15413928	NM_001039697	D3DRI8|Q2VPI6|Q5T285	Silent	SNP	ENST00000380821.3	37	CCDS6478.1																																																																																				0.398	SNAPC3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051763.2	NM_001039697	
CCDC171	203238	broad.mit.edu	37	9	15695249	15695249	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr9:15695249C>A	ENST00000380701.3	+	11	1560	c.1232C>A	c.(1231-1233)gCc>gAc	p.A411D	CCDC171_ENST00000297641.3_Missense_Mutation_p.A411D	NM_173550.2	NP_775821.2	Q6TFL3	CC171_HUMAN	coiled-coil domain containing 171	411								p.A411D(1)									AAGCACCAGGCCTTCCTAGTA	0.368																																					p.A411D												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1232A	9						.						125.0	121.0	122.0					9																	15695249		2203	4300	6503	15685249	SO:0001583	missense	203238	exon11			AY422473	CCDS6481.1	9p22.2	2012-03-26	2012-03-26	2012-03-26	ENSG00000164989	ENSG00000164989			29828	protein-coding gene	gene with protein product	"""myosin tail domain containing protein"""		"""chromosome 9 open reading frame 93"""	C9orf93		14702039	Standard	NM_173550		Approved	FLJ39267, FLJ46740, Em:AL513423.1, bA778P13.1, bA536D16.1	uc003zmd.3	Q6TFL3	OTTHUMG00000019584	ENST00000380701.3:c.1232C>A	9.37:g.15695249C>A	ENSP00000370077:p.Ala411Asp	Somatic		Capture	Illumina HiSeq	Phase_I	15685249	NM_173550	B7ZM22|Q5SU58|Q6P1W1|Q6ZR13|Q8N1Z4|Q8N8L3|Q8TBR2	Missense_Mutation	SNP	ENST00000380701.3	37	CCDS6481.1	.	.	.	.	.	.	.	.	.	.	C	14.82	2.648321	0.47258	.	.	ENSG00000164989	ENST00000297641;ENST00000380701	T;T	0.15834	2.39;2.39	5.55	5.55	0.83447	.	0.291160	0.36665	N	0.002474	T	0.10465	0.0256	N	0.19112	0.55	0.80722	D	1	P;P;P	0.41848	0.763;0.763;0.763	B;B;B	0.41619	0.361;0.361;0.361	T	0.14839	-1.0458	10	0.22706	T	0.39	-6.6251	5.766	0.18227	0.1892:0.6938:0.0:0.117	.	411;411;411	B7ZM22;Q6TFL3-3;Q6TFL3	.;.;CI093_HUMAN	D	411	ENSP00000297641:A411D;ENSP00000370077:A411D	ENSP00000297641:A411D	A	+	2	0	C9orf93	15685249	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	2.533000	0.45667	2.610000	0.88304	0.591000	0.81541	GCC		0.368	CCDC171-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051768.4	NM_173550	
MLLT3	4300	broad.mit.edu	37	9	20413791	20413791	+	Silent	SNP	C	C	T	rs146637666		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr9:20413791C>T	ENST00000380338.4	-	5	1339	c.1053G>A	c.(1051-1053)acG>acA	p.T351T	MLLT3_ENST00000429426.2_Silent_p.T348T|MIR4473_ENST00000583731.1_RNA|MLLT3_ENST00000475957.1_5'UTR|MLLT3_ENST00000355930.6_5'UTR	NM_004529.2	NP_004520.2	P42568	AF9_HUMAN	myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 3	351					anterior/posterior pattern specification (GO:0009952)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|positive regulation of Wnt signaling pathway, planar cell polarity pathway (GO:2000096)|regulation of transcription, DNA-templated (GO:0006355)|segment specification (GO:0007379)|transcription, DNA-templated (GO:0006351)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|transcription elongation factor complex (GO:0008023)		p.T351T(1)		central_nervous_system(1)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(6)|lung(24)|ovary(1)|prostate(4)|skin(1)|urinary_tract(7)	66				GBM - Glioblastoma multiforme(3;4.35e-105)|Lung(42;3.48e-06)|LUSC - Lung squamous cell carcinoma(42;7.92e-05)		ATGGCGGTAACGTTGATTTCT	0.368			T	MLL	ALL																																p.T351T			Dom	yes		9	9p22	4300	"""myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 3 (AF9)"""		L	.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G1053A	9						.	C		1,4405	2.1+/-5.4	0,1,2202	147.0	129.0	135.0		1053	-12.2	0.0	9	dbSNP_134	135	0,8600		0,0,4300	no	coding-synonymous	MLLT3	NM_004529.2		0,1,6502	TT,TC,CC		0.0,0.0227,0.0077		351/569	20413791	1,13005	2203	4300	6503	20403791	SO:0001819	synonymous_variant	4300	exon5			L13744	CCDS6494.1	9p22	2008-02-05	2001-11-28		ENSG00000171843	ENSG00000171843			7136	protein-coding gene	gene with protein product		159558	"""myeloid/lymphoid or mixed-lineage leukemia (trithorax (Drosophila) homolog); translocated to, 3"""			8506309, 8414510	Standard	NM_001286691		Approved	AF-9, AF9, YEATS3	uc003zoe.2	P42568	OTTHUMG00000019650	ENST00000380338.4:c.1053G>A	9.37:g.20413791C>T		Somatic		Capture	Illumina HiSeq	Phase_I	20403791	NM_004529	B1AMQ2|B2R7B3|B7Z755|D3DRJ8|Q8IVB0	Silent	SNP	ENST00000380338.4	37	CCDS6494.1																																																																																				0.368	MLLT3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000051872.1	NM_004529	
TEK	7010	broad.mit.edu	37	9	27157989	27157989	+	Silent	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr9:27157989G>A	ENST00000380036.4	+	2	655	c.213G>A	c.(211-213)ccG>ccA	p.P71P	TEK_ENST00000519097.1_Intron|TEK_ENST00000406359.4_Silent_p.P71P	NM_000459.3	NP_000450	Q02763	TIE2_HUMAN	TEK tyrosine kinase, endothelial	71	Ig-like C2-type 1.				angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cell-cell signaling (GO:0007267)|cell-matrix adhesion (GO:0007160)|definitive hemopoiesis (GO:0060216)|endochondral ossification (GO:0001958)|endothelial cell proliferation (GO:0001935)|glomerulus vasculature development (GO:0072012)|heart development (GO:0007507)|heart trabecula formation (GO:0060347)|intracellular signal transduction (GO:0035556)|leukocyte migration (GO:0050900)|negative regulation of angiogenesis (GO:0016525)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of inflammatory response (GO:0050728)|organ regeneration (GO:0031100)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of actin cytoskeleton reorganization (GO:2000251)|positive regulation of angiogenesis (GO:0045766)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of focal adhesion assembly (GO:0051894)|positive regulation of intracellular signal transduction (GO:1902533)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein phosphorylation (GO:0001934)|protein autophosphorylation (GO:0046777)|protein oligomerization (GO:0051259)|regulation of endothelial cell apoptotic process (GO:2000351)|regulation of establishment or maintenance of cell polarity (GO:0032878)|regulation of vascular permeability (GO:0043114)|response to cAMP (GO:0051591)|response to estrogen (GO:0043627)|response to hypoxia (GO:0001666)|response to peptide hormone (GO:0043434)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|sprouting angiogenesis (GO:0002040)|substrate adhesion-dependent cell spreading (GO:0034446)|Tie signaling pathway (GO:0048014)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	apical plasma membrane (GO:0016324)|basal plasma membrane (GO:0009925)|basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|microvillus (GO:0005902)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein tyrosine kinase activity (GO:0004713)|receptor activity (GO:0004872)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)	p.P71P(1)		breast(3)|central_nervous_system(3)|kidney(1)|lung(2)|ovary(3)|skin(3)	15		all_neural(11;7.57e-10)|Myeloproliferative disorder(762;0.0255)		Lung(218;4.08e-05)|LUSC - Lung squamous cell carcinoma(38;0.00027)	Ponatinib(DB08901)|Regorafenib(DB08896)|Vandetanib(DB05294)	ACCAGGATCCGCTGGAAGTTA	0.483																																					p.P71P												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G213A	9						.						91.0	91.0	91.0					9																	27157989		2203	4300	6503	27147989	SO:0001819	synonymous_variant	7010	exon2			L06139	CCDS6519.1, CCDS75825.1	9p21	2013-02-11	2008-07-31		ENSG00000120156	ENSG00000120156		"""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	11724	protein-coding gene	gene with protein product		600221	"""venous malformations, multiple cutaneous and mucosal"""	VMCM		1312667, 7833915	Standard	XM_005251561		Approved	TIE2, TIE-2, VMCM1, CD202b	uc003zqi.4	Q02763	OTTHUMG00000019712	ENST00000380036.4:c.213G>A	9.37:g.27157989G>A		Somatic		Capture	Illumina HiSeq	Phase_I	27147989	NM_000459	A8K6W0|B4DH20|B4DHD3|D3DRK5|E7EWI2|Q5TCU2|Q8IV34	Silent	SNP	ENST00000380036.4	37	CCDS6519.1																																																																																				0.483	TEK-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051965.3		
B4GALT1	2683	broad.mit.edu	37	9	33113848	33113848	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr9:33113848G>A	ENST00000379731.4	-	5	1174	c.988C>T	c.(988-990)Cgc>Tgc	p.R330C	B4GALT1_ENST00000535206.1_Intron|B4GALT1_ENST00000541851.1_Missense_Mutation_p.R77C	NM_001497.3	NP_001488.2	P15291	B4GT1_HUMAN	UDP-Gal:betaGlcNAc beta 1,4- galactosyltransferase, polypeptide 1	330					acute inflammatory response (GO:0002526)|angiogenesis involved in wound healing (GO:0060055)|binding of sperm to zona pellucida (GO:0007339)|branching morphogenesis of an epithelial tube (GO:0048754)|carbohydrate metabolic process (GO:0005975)|cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|development of secondary sexual characteristics (GO:0045136)|epithelial cell development (GO:0002064)|extracellular matrix organization (GO:0030198)|galactose metabolic process (GO:0006012)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate metabolic process (GO:0042339)|lactose biosynthetic process (GO:0005989)|leukocyte migration (GO:0050900)|mammary gland development (GO:0030879)|multicellular organism reproduction (GO:0032504)|negative regulation of cell proliferation (GO:0008285)|Notch signaling pathway (GO:0007219)|oligosaccharide biosynthetic process (GO:0009312)|penetration of zona pellucida (GO:0007341)|positive regulation of apoptotic process involved in mammary gland involution (GO:0060058)|positive regulation of epithelial cell proliferation involved in wound healing (GO:0060054)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation (GO:0006487)|protein N-linked glycosylation via asparagine (GO:0018279)|regulation of acrosome reaction (GO:0060046)|regulation of cellular component movement (GO:0051270)|single fertilization (GO:0007338)|small molecule metabolic process (GO:0044281)	basolateral plasma membrane (GO:0016323)|brush border membrane (GO:0031526)|desmosome (GO:0030057)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|glycocalyx (GO:0030112)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|Golgi trans cisterna (GO:0000138)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	alpha-tubulin binding (GO:0043014)|beta-N-acetylglucosaminylglycopeptide beta-1,4-galactosyltransferase activity (GO:0003831)|beta-tubulin binding (GO:0048487)|galactosyltransferase activity (GO:0008378)|lactose synthase activity (GO:0004461)|manganese ion binding (GO:0030145)|N-acetyllactosamine synthase activity (GO:0003945)|protein homodimerization activity (GO:0042803)|UDP-galactosyltransferase activity (GO:0035250)	p.R330C(1)		endometrium(1)|large_intestine(7)|lung(4)|prostate(1)|skin(1)	14			LUSC - Lung squamous cell carcinoma(29;0.0084)	GBM - Glioblastoma multiforme(74;0.121)	N-Acetyl-D-glucosamine(DB00141)	GCATTTGGGCGAGATATAGAC	0.463																																					p.R330C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C988T	9						.						98.0	96.0	97.0					9																	33113848		2203	4300	6503	33103848	SO:0001583	missense	2683	exon5			X14085	CCDS6535.1	9p13	2013-02-19			ENSG00000086062	ENSG00000086062	2.4.1.22	"""Beta 4-glycosyltransferases"""	924	protein-coding gene	gene with protein product		137060		GGTB2		9597550	Standard	NM_001497		Approved	beta4Gal-T1	uc003zsg.2	P15291	OTTHUMG00000019764	ENST00000379731.4:c.988C>T	9.37:g.33113848G>A	ENSP00000369055:p.Arg330Cys	Somatic		Capture	Illumina HiSeq	Phase_I	33103848	NM_001497	B2R710|D3DRL2|Q12909|Q12910|Q12911|Q14456|Q14509|Q14523	Missense_Mutation	SNP	ENST00000379731.4	37	CCDS6535.1	.	.	.	.	.	.	.	.	.	.	G	22.5	4.303729	0.81136	.	.	ENSG00000086062	ENST00000379731;ENST00000541701;ENST00000541851	D;D	0.86694	-2.16;-2.16	5.93	5.03	0.67393	.	0.000000	0.85682	D	0.000000	D	0.95815	0.8638	H	0.98133	4.155	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.96520	0.9385	10	0.87932	D	0	-14.4206	13.3939	0.60838	0.0776:0.0:0.9224:0.0	.	330	P15291	B4GT1_HUMAN	C	330;287;77	ENSP00000369055:R330C;ENSP00000445037:R77C	ENSP00000369055:R330C	R	-	1	0	B4GALT1	33103848	1.000000	0.71417	1.000000	0.80357	0.902000	0.53008	5.048000	0.64238	2.826000	0.97356	0.655000	0.94253	CGC		0.463	B4GALT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052039.1	NM_001497	
AQP7	364	broad.mit.edu	37	9	33385103	33385103	+	3'UTR	SNP	G	G	A	rs541770524		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr9:33385103G>A	ENST00000537089.1	-	0	1329				AQP7_ENST00000377425.4_3'UTR			O14520	AQP7_HUMAN	aquaporin 7						excretion (GO:0007588)|generation of precursor metabolites and energy (GO:0006091)|glycerol transport (GO:0015793)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	glycerol channel activity (GO:0015254)|water channel activity (GO:0015250)	p.T310M(1)		NS(1)|large_intestine(1)|lung(7)|ovary(1)|prostate(4)|skin(2)|stomach(1)	17			LUSC - Lung squamous cell carcinoma(29;0.00788)	GBM - Glioblastoma multiforme(74;0.191)		GGGAGAGATCGTGGGTTCATG	0.562													g|||	1	0.000199681	0.0	0.0	5008	,	,		18465	0.0		0.0	False		,,,				2504	0.001				p.T310M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C929T	9						.						146.0	147.0	147.0					9																	33385103		2203	4300	6503	33375103	SO:0001624	3_prime_UTR_variant	364	exon8			AB006190	CCDS6541.1	9p13	2008-02-05			ENSG00000165269	ENSG00000165269		"""Ion channels / Aquaporins"""	640	protein-coding gene	gene with protein product		602974		AQP7L		9252401	Standard	NM_001170		Approved	AQP9, AQPap	uc003zst.3	O14520	OTTHUMG00000019773	ENST00000537089.1:c.*513C>T	9.37:g.33385103G>A		Somatic		Capture	Illumina HiSeq	Phase_I	33375103	NM_001170	Q08E94|Q5T5L9|Q8NHM3	Missense_Mutation	SNP	ENST00000537089.1	37		.	.	.	.	.	.	.	.	.	.	g	5.533	0.283273	0.10458	.	.	ENSG00000165269	ENST00000379507;ENST00000297988	D;D	0.85013	-1.93;-1.93	3.7	-7.4	0.01397	.	.	.	.	.	T	0.66896	0.2836	.	.	.	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.51188	-0.8737	8	0.23302	T	0.38	5.6088	3.6616	0.08241	0.1358:0.1181:0.4916:0.2545	.	310	O14520	AQP7_HUMAN	M	309;310	ENSP00000368821:T309M;ENSP00000297988:T310M	ENSP00000297988:T310M	T	-	2	0	AQP7	33375103	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.499000	0.00968	-2.266000	0.00687	-0.487000	0.04747	ACG		0.562	AQP7-202	KNOWN	basic	protein_coding	protein_coding		NM_001170	
AQP3	360	broad.mit.edu	37	9	33443872	33443872	+	Missense_Mutation	SNP	C	C	T	rs34942735	byFrequency	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr9:33443872C>T	ENST00000297991.4	-	2	207	c.127G>A	c.(127-129)Gtg>Atg	p.V43M	AQP3_ENST00000493581.1_5'UTR	NM_004925.4	NP_004916.1	Q92482	AQP3_HUMAN	aquaporin 3 (Gill blood group)	43			V -> M (in dbSNP:rs34942735). {ECO:0000269|Ref.7}.		excretion (GO:0007588)|odontogenesis (GO:0042476)|positive regulation of immune system process (GO:0002684)|regulation of keratinocyte differentiation (GO:0045616)|renal water absorption (GO:0070295)|response to calcium ion (GO:0051592)|response to retinoic acid (GO:0032526)|response to vitamin D (GO:0033280)|transmembrane transport (GO:0055085)|transport (GO:0006810)|urea transport (GO:0015840)|water transport (GO:0006833)	basolateral plasma membrane (GO:0016323)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	glycerol channel activity (GO:0015254)|transporter activity (GO:0005215)|water channel activity (GO:0015250)	p.V43M(1)		endometrium(2)|large_intestine(3)|lung(2)|ovary(1)	8			LUSC - Lung squamous cell carcinoma(29;0.00788)	GBM - Glioblastoma multiforme(74;0.0899)		ACCTGGGCCACGGAGCCACAG	0.597													C|||	3	0.000599042	0.0015	0.0	5008	,	,		18272	0.0		0.001	False		,,,				2504	0.0				p.V43M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G127A	9						.	C	MET/VAL	1,4405	2.1+/-5.4	0,1,2202	48.0	44.0	45.0		127	4.6	1.0	9	dbSNP_126	45	1,8599	1.2+/-3.3	0,1,4299	yes	missense	AQP3	NM_004925.4	21	0,2,6501	TT,TC,CC		0.0116,0.0227,0.0154	possibly-damaging	43/293	33443872	2,13004	2203	4300	6503	33433872	SO:0001583	missense	360	exon2				CCDS6542.1	9p13	2014-07-18	2006-02-23		ENSG00000165272	ENSG00000165272		"""Ion channels / Aquaporins"", ""Blood group antigens"""	636	protein-coding gene	gene with protein product	"""Gill blood group"""	600170	"""aquaporin 3"", ""aquaporin 3 (GIL blood group)"""			7558005	Standard	NM_004925		Approved	GIL	uc003zsx.3	Q92482	OTTHUMG00000019769	ENST00000297991.4:c.127G>A	9.37:g.33443872C>T	ENSP00000297991:p.Val43Met	Somatic		Capture	Illumina HiSeq	Phase_I	33433872	NM_004925	A8K843|B2RE16|D3DRL3|O00108|Q6FGT2|Q6FGW6	Missense_Mutation	SNP	ENST00000297991.4	37	CCDS6542.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	C	18.40	3.614792	0.66672	2.27E-4	1.16E-4	ENSG00000165272	ENST00000297991;ENST00000343952	T	0.13657	2.57	5.56	4.63	0.57726	Aquaporin-like (2);	0.177934	0.49305	D	0.000157	T	0.48132	0.1483	H	0.94734	3.575	0.53688	D	0.999973	D;D;D	0.89917	0.974;0.995;1.0	P;P;D	0.68353	0.769;0.876;0.957	T	0.63314	-0.6665	10	0.87932	D	0	.	15.8375	0.78811	0.1362:0.8638:0.0:0.0	rs34942735	43;43;43	C9JAH5;Q92482;B4E034	.;AQP3_HUMAN;.	M	43	ENSP00000297991:V43M	ENSP00000297991:V43M	V	-	1	0	AQP3	33433872	0.976000	0.34144	0.986000	0.45419	0.945000	0.59286	2.470000	0.45119	2.610000	0.88304	0.551000	0.68910	GTG		0.597	AQP3-001	KNOWN	mRNA_start_NF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052055.1	NM_004925	
UBAP2	55833	broad.mit.edu	37	9	33924247	33924247	+	Silent	SNP	C	C	T	rs561000488		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr9:33924247C>T	ENST00000379238.1	-	23	2664	c.2547G>A	c.(2545-2547)gcG>gcA	p.A849A	UBAP2_ENST00000379235.1_Silent_p.A88A|UBAP2_ENST00000449054.1_Silent_p.A849A|UBAP2_ENST00000360802.1_Silent_p.A849A|UBAP2_ENST00000379239.4_Silent_p.A582A|UBAP2_ENST00000539807.1_Silent_p.A604A					ubiquitin associated protein 2									p.A849A(1)		endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(7)|lung(13)|ovary(3)|stomach(1)	32			LUSC - Lung squamous cell carcinoma(29;0.00575)	GBM - Glioblastoma multiforme(74;0.168)		GGCTGGCAAGCGCTGTGGGTG	0.577													C|||	1	0.000199681	0.0	0.0	5008	,	,		19354	0.001		0.0	False		,,,				2504	0.0				p.A849A												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G2547A	9						.						88.0	84.0	85.0					9																	33924247		2203	4300	6503	33914247	SO:0001819	synonymous_variant	55833	exon23			AB040924	CCDS6547.1, CCDS75828.1	9p11.2	2008-02-05			ENSG00000137073	ENSG00000137073			14185	protein-coding gene	gene with protein product						8871400	Standard	NM_018449		Approved	KIAA1491, bA176F3.5, FLJ22435	uc003ztq.1	Q5T6F2	OTTHUMG00000000427	ENST00000379238.1:c.2547G>A	9.37:g.33924247C>T		Somatic		Capture	Illumina HiSeq	Phase_I	33914247	NM_018449		Silent	SNP	ENST00000379238.1	37	CCDS6547.1																																																																																				0.577	UBAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001071.1	NM_018449	
IL11RA	3590	broad.mit.edu	37	9	34658543	34658543	+	Missense_Mutation	SNP	C	C	T	rs538108515		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr9:34658543C>T	ENST00000555003.1	+	8	2029	c.673C>T	c.(673-675)Cgg>Tgg	p.R225W	IL11RA_ENST00000441545.2_Missense_Mutation_p.R225W|IL11RA_ENST00000318041.9_Missense_Mutation_p.R225W|IL11RA_ENST00000378817.4_Missense_Mutation_p.R225W|IL11RA_ENST00000602473.1_Missense_Mutation_p.R225W			Q14626	I11RA_HUMAN	interleukin 11 receptor, alpha	225	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.				developmental process (GO:0032502)|embryo implantation (GO:0007566)|head development (GO:0060322)|signal transduction (GO:0007165)	integral component of plasma membrane (GO:0005887)	cytokine receptor activity (GO:0004896)|signal transducer activity (GO:0004871)|transmembrane signaling receptor activity (GO:0004888)	p.R225W(1)		breast(1)|large_intestine(1)|ovary(1)|skin(1)	4	all_epithelial(49;0.102)		STAD - Stomach adenocarcinoma(86;0.178)	GBM - Glioblastoma multiforme(74;0.174)	Oprelvekin(DB00038)	CCAGGGCCTGCGGGTAGAGTC	0.607													C|||	1	0.000199681	0.0	0.0	5008	,	,		17854	0.0		0.0	False		,,,				2504	0.001				p.R225W												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C673T	9						.						63.0	60.0	61.0					9																	34658543		2203	4300	6503	34648543	SO:0001583	missense	3590	exon8			Z38102	CCDS6567.1	9p13	2014-05-22			ENSG00000137070	ENSG00000137070		"""Interleukins and interleukin receptors"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	5967	protein-coding gene	gene with protein product		600939				7670098	Standard	NM_001142784		Approved		uc011loq.3	Q14626	OTTHUMG00000019837	ENST00000555003.1:c.673C>T	9.37:g.34658543C>T	ENSP00000450565:p.Arg225Trp	Somatic		Capture	Illumina HiSeq	Phase_I	34648543	NM_001142784	Q16542|Q5VZ80|Q7KYJ7	Missense_Mutation	SNP	ENST00000555003.1	37	CCDS6567.1	.	.	.	.	.	.	.	.	.	.	C	18.62	3.663914	0.67700	.	.	ENSG00000137070	ENST00000555003;ENST00000441545;ENST00000553620;ENST00000378817;ENST00000318041;ENST00000555981	T;T;T;T;T;T	0.73469	1.39;1.39;0.81;1.22;1.39;-0.75	5.15	4.19	0.49359	Long hematopoietin receptor, soluble alpha chain, conserved site (1);Fibronectin, type III (3);Immunoglobulin-like fold (1);	0.859093	0.10378	N	0.681856	T	0.80909	0.4714	L	0.55990	1.75	0.24266	N	0.995268	D;D	0.89917	1.0;1.0	D;D	0.76071	0.987;0.987	T	0.67662	-0.5613	10	0.59425	D	0.04	-15.6112	5.8129	0.18475	0.193:0.7109:0.0:0.0962	.	225;225	Q5VZ79;Q14626	.;I11RA_HUMAN	W	225;225;148;225;225;225	ENSP00000450565:R225W;ENSP00000394391:R225W;ENSP00000452207:R148W;ENSP00000368094:R225W;ENSP00000326500:R225W;ENSP00000450640:R225W	ENSP00000326500:R225W	R	+	1	2	IL11RA	34648543	0.886000	0.30341	0.992000	0.48379	0.966000	0.64601	1.108000	0.31123	2.401000	0.81631	0.563000	0.77884	CGG		0.607	IL11RA-006	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410625.1	NM_001142784	
VCP	7415	broad.mit.edu	37	9	35062244	35062244	+	Silent	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr9:35062244C>T	ENST00000358901.6	-	8	1810	c.915G>A	c.(913-915)gaG>gaA	p.E305E		NM_007126.3	NP_009057.1	P55072	TERA_HUMAN	valosin containing protein	305					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|aggresome assembly (GO:0070842)|cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|endoplasmic reticulum unfolded protein response (GO:0030968)|ER to Golgi vesicle-mediated transport (GO:0006888)|ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|establishment of protein localization (GO:0045184)|positive regulation of Lys63-specific deubiquitinase activity (GO:1903007)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of protein complex assembly (GO:0031334)|positive regulation of protein K63-linked deubiquitination (GO:1903006)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein homooligomerization (GO:0051260)|protein N-linked glycosylation via asparagine (GO:0018279)|protein ubiquitination (GO:0016567)|regulation of apoptotic process (GO:0042981)|retrograde protein transport, ER to cytosol (GO:0030970)|translesion synthesis (GO:0019985)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)|Hrd1p ubiquitin ligase complex (GO:0000836)|intracellular membrane-bounded organelle (GO:0043231)|lipid particle (GO:0005811)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|proteasome complex (GO:0000502)|site of double-strand break (GO:0035861)	ADP binding (GO:0043531)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|deubiquitinase activator activity (GO:0035800)|lipid binding (GO:0008289)|poly(A) RNA binding (GO:0044822)|polyubiquitin binding (GO:0031593)|protein domain specific binding (GO:0019904)|protein phosphatase binding (GO:0019903)|ubiquitin-specific protease binding (GO:1990381)	p.E305E(1)		breast(3)|endometrium(2)|kidney(1)|large_intestine(4)|lung(10)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)	24			LUSC - Lung squamous cell carcinoma(32;0.00343)|Lung(28;0.00778)			TGGCATCTAGCTCATCAATGA	0.498																																					p.E305E												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G915A	9						.						146.0	139.0	141.0					9																	35062244		2203	4300	6503	35052244	SO:0001819	synonymous_variant	7415	exon8			AC004472	CCDS6573.1	9p13.3	2014-09-17	2011-01-25		ENSG00000165280	ENSG00000165280		"""ATPases / AAA-type"""	12666	protein-coding gene	gene with protein product		601023	"""valosin-containing protein"""			8595912, 7553851	Standard	NM_007126		Approved	IBMPFD, p97	uc003zvy.2	P55072	OTTHUMG00000019855	ENST00000358901.6:c.915G>A	9.37:g.35062244C>T		Somatic		Capture	Illumina HiSeq	Phase_I	35052244	NM_007126	B2R5T8|Q0V924|Q2TAI5|Q969G7|Q9UCD5	Silent	SNP	ENST00000358901.6	37	CCDS6573.1																																																																																				0.498	VCP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052290.1	NM_007126	
UNC13B	10497	broad.mit.edu	37	9	35398614	35398614	+	Nonsense_Mutation	SNP	G	G	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr9:35398614G>T	ENST00000378495.3	+	31	3871	c.3649G>T	c.(3649-3651)Gag>Tag	p.E1217*	UNC13B_ENST00000481299.1_3'UTR|UNC13B_ENST00000378496.4_Nonsense_Mutation_p.E1217*|UNC13B_ENST00000396787.1_Nonsense_Mutation_p.E1229*	NM_006377.3	NP_006368.3	O14795	UN13B_HUMAN	unc-13 homolog B (C. elegans)	1217					apoptotic process (GO:0006915)|excretion (GO:0007588)|innervation (GO:0060384)|intracellular signal transduction (GO:0035556)|neuromuscular junction development (GO:0007528)|positive regulation of inhibitory postsynaptic membrane potential (GO:0097151)|positive regulation of synaptic vesicle priming (GO:0010808)|regulation of short-term neuronal synaptic plasticity (GO:0048172)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|synaptic vesicle docking involved in exocytosis (GO:0016081)|synaptic vesicle priming (GO:0016082)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|neuromuscular junction (GO:0031594)|plasma membrane (GO:0005886)|presynaptic active zone (GO:0048786)|terminal bouton (GO:0043195)	diacylglycerol binding (GO:0019992)|metal ion binding (GO:0046872)|receptor activity (GO:0004872)|signal transducer activity (GO:0004871)	p.E1217*(1)		breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(16)|liver(2)|lung(17)|ovary(3)|pancreas(1)|prostate(3)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(1)	63	all_epithelial(49;0.212)		LUSC - Lung squamous cell carcinoma(32;0.00343)|Lung(28;0.00778)|STAD - Stomach adenocarcinoma(86;0.194)			GGTTCTGGATGAGCTCAGCAT	0.542																																					p.E1217X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.G3649T	9						.						137.0	129.0	132.0					9																	35398614		2203	4300	6503	35388614	SO:0001587	stop_gained	10497	exon31			AF020202	CCDS6579.1	9p13.3	2008-05-15	2003-10-17	2003-10-17	ENSG00000198722	ENSG00000198722			12566	protein-coding gene	gene with protein product		605836	"""unc-13-like (C. elegans)"""	UNC13		9607201	Standard	NM_006377		Approved	hmunc13, Unc13h2	uc003zwq.3	O14795	OTTHUMG00000019856	ENST00000378495.3:c.3649G>T	9.37:g.35398614G>T	ENSP00000367756:p.Glu1217*	Somatic		Capture	Illumina HiSeq	Phase_I	35388614	NM_006377	Q5VYM8	Nonsense_Mutation	SNP	ENST00000378495.3	37	CCDS6579.1	.	.	.	.	.	.	.	.	.	.	G	44	11.005704	0.99502	.	.	ENSG00000198722	ENST00000396787;ENST00000378495;ENST00000378496;ENST00000535471	.	.	.	5.7	5.7	0.88788	.	0.206017	0.53938	D	0.000045	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.36615	T	0.2	-25.9774	19.8236	0.96607	0.0:0.0:1.0:0.0	.	.	.	.	X	1229;1217;1217;804	.	ENSP00000367756:E1217X	E	+	1	0	UNC13B	35388614	1.000000	0.71417	1.000000	0.80357	0.969000	0.65631	4.789000	0.62446	2.695000	0.91970	0.455000	0.32223	GAG		0.542	UNC13B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000052296.1	NM_006377	
NPR2	4882	broad.mit.edu	37	9	35799675	35799675	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr9:35799675C>T	ENST00000342694.2	+	3	1189	c.934C>T	c.(934-936)Cgt>Tgt	p.R312C		NM_003995.3	NP_003986.2	P20594	ANPRB_HUMAN	natriuretic peptide receptor 2	312					bone development (GO:0060348)|cell surface receptor signaling pathway (GO:0007166)|cellular response to granulocyte macrophage colony-stimulating factor stimulus (GO:0097011)|cGMP biosynthetic process (GO:0006182)|intracellular signal transduction (GO:0035556)|negative regulation of meiotic cell cycle (GO:0051447)|negative regulation of oocyte maturation (GO:1900194)|ossification (GO:0001503)|receptor guanylyl cyclase signaling pathway (GO:0007168)|regulation of blood pressure (GO:0008217)|signal transduction (GO:0007165)|single organism reproductive process (GO:0044702)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|GTP binding (GO:0005525)|guanylate cyclase activity (GO:0004383)|hormone binding (GO:0042562)|natriuretic peptide receptor activity (GO:0016941)|peptide hormone binding (GO:0017046)|protein kinase activity (GO:0004672)|receptor activity (GO:0004872)|transmembrane signaling receptor activity (GO:0004888)	p.R312C(1)		NS(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(13)|lung(14)|ovary(2)|prostate(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	45	all_epithelial(49;0.161)		LUSC - Lung squamous cell carcinoma(32;0.00521)|Lung(28;0.00697)|STAD - Stomach adenocarcinoma(86;0.194)		Erythrityl Tetranitrate(DB01613)|Nesiritide(DB04899)	ATTCCAGAATCGTCTGCTGAT	0.507																																					p.R312C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C934T	9						.						132.0	131.0	131.0					9																	35799675		2203	4300	6503	35789675	SO:0001583	missense	4882	exon3			AJ005282	CCDS6590.1	9p21-p12	2014-03-03	2014-03-03		ENSG00000159899	ENSG00000159899			7944	protein-coding gene	gene with protein product	"""guanylate cyclase B"""	108961	"""acromesomelic dysplasia, Maroteaux type"", ""atrionatriuretic peptide receptor B"", ""natriuretic peptide receptor B"""	ANPRB, NPRB, AMDM		9634515, 15146390	Standard	XM_005251478		Approved	GUCY2B, ANPb	uc003zyd.3	P20594	OTTHUMG00000019871	ENST00000342694.2:c.934C>T	9.37:g.35799675C>T	ENSP00000341083:p.Arg312Cys	Somatic		Capture	Illumina HiSeq	Phase_I	35789675	NM_003995	B0ZBF2|B0ZBF3|D3DRP3|D3DRP4|O60871|Q4VAK7|Q5TCV2|Q8TA93|Q9UQ50	Missense_Mutation	SNP	ENST00000342694.2	37	CCDS6590.1	.	.	.	.	.	.	.	.	.	.	C	22.9	4.348699	0.82132	.	.	ENSG00000159899	ENST00000342694	D	0.84370	-1.84	5.69	5.69	0.88448	Extracellular ligand-binding receptor (1);	0.000000	0.44285	D	0.000461	T	0.76884	0.4050	N	0.19112	0.55	0.54753	D	0.999982	B;D	0.61080	0.121;0.989	B;B	0.40534	0.007;0.332	T	0.81649	-0.0837	10	0.72032	D	0.01	.	16.9713	0.86301	0.0:1.0:0.0:0.0	.	312;312	P20594-2;P20594	.;ANPRB_HUMAN	C	312	ENSP00000341083:R312C	ENSP00000341083:R312C	R	+	1	0	NPR2	35789675	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	2.861000	0.48380	2.699000	0.92147	0.655000	0.94253	CGT		0.507	NPR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052345.1		
NPR2	4882	broad.mit.edu	37	9	35810674	35810674	+	IGR	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr9:35810674G>A	ENST00000342694.2	+	0	3686				SPAG8_ENST00000396638.2_Missense_Mutation_p.R349C|SPAG8_ENST00000479751.1_5'UTR|AL133410.1_ENST00000582432.1_RNA|SPAG8_ENST00000340291.2_Missense_Mutation_p.R349C|SPAG8_ENST00000484764.1_Missense_Mutation_p.R347C|HINT2_ENST00000474908.1_5'Flank	NM_003995.3	NP_003986.2	P20594	ANPRB_HUMAN	natriuretic peptide receptor 2						bone development (GO:0060348)|cell surface receptor signaling pathway (GO:0007166)|cellular response to granulocyte macrophage colony-stimulating factor stimulus (GO:0097011)|cGMP biosynthetic process (GO:0006182)|intracellular signal transduction (GO:0035556)|negative regulation of meiotic cell cycle (GO:0051447)|negative regulation of oocyte maturation (GO:1900194)|ossification (GO:0001503)|receptor guanylyl cyclase signaling pathway (GO:0007168)|regulation of blood pressure (GO:0008217)|signal transduction (GO:0007165)|single organism reproductive process (GO:0044702)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|GTP binding (GO:0005525)|guanylate cyclase activity (GO:0004383)|hormone binding (GO:0042562)|natriuretic peptide receptor activity (GO:0016941)|peptide hormone binding (GO:0017046)|protein kinase activity (GO:0004672)|receptor activity (GO:0004872)|transmembrane signaling receptor activity (GO:0004888)	p.R349C(2)		NS(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(13)|lung(14)|ovary(2)|prostate(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	45	all_epithelial(49;0.161)		LUSC - Lung squamous cell carcinoma(32;0.00521)|Lung(28;0.00697)|STAD - Stomach adenocarcinoma(86;0.194)		Erythrityl Tetranitrate(DB01613)|Nesiritide(DB04899)	ATGGCTTCACGCTTCCCTGTG	0.527																																					p.R349C												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.C1045T	9						.						44.0	44.0	44.0					9																	35810674		2203	4300	6503	35800674	SO:0001628	intergenic_variant	26206	exon4			AJ005282	CCDS6590.1	9p21-p12	2014-03-03	2014-03-03		ENSG00000159899	ENSG00000159899			7944	protein-coding gene	gene with protein product	"""guanylate cyclase B"""	108961	"""acromesomelic dysplasia, Maroteaux type"", ""atrionatriuretic peptide receptor B"", ""natriuretic peptide receptor B"""	ANPRB, NPRB, AMDM		9634515, 15146390	Standard	XM_005251478		Approved	GUCY2B, ANPb	uc003zyd.3	P20594	OTTHUMG00000019871		9.37:g.35810674G>A		Somatic		Capture	Illumina HiSeq	Phase_I	35800674	NM_172312	B0ZBF2|B0ZBF3|D3DRP3|D3DRP4|O60871|Q4VAK7|Q5TCV2|Q8TA93|Q9UQ50	Missense_Mutation	SNP	ENST00000342694.2	37	CCDS6590.1	.	.	.	.	.	.	.	.	.	.	G	15.87	2.962090	0.53400	.	.	ENSG00000137098	ENST00000340291;ENST00000484764;ENST00000396638	T;T;T	0.47177	0.85;1.04;1.03	5.72	2.45	0.29901	.	0.000000	0.53938	D	0.000043	T	0.63177	0.2489	L	0.56769	1.78	0.43863	D	0.996461	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	T	0.66814	-0.5828	10	0.87932	D	0	-15.3699	13.8259	0.63351	0.0:0.0:0.6149:0.3851	.	349;349	E9PDV6;Q99932-2	.;.	C	349;347;349	ENSP00000340982:R349C;ENSP00000418072:R347C;ENSP00000379878:R349C	ENSP00000340982:R349C	R	-	1	0	SPAG8	35800674	0.997000	0.39634	0.991000	0.47740	0.920000	0.55202	1.410000	0.34691	0.713000	0.32060	0.655000	0.94253	CGT		0.527	NPR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052345.1		
RECK	8434	broad.mit.edu	37	9	36122920	36122920	+	Missense_Mutation	SNP	T	T	G			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr9:36122920T>G	ENST00000377966.3	+	21	3360	c.2794T>G	c.(2794-2796)Tcc>Gcc	p.S932A		NM_021111.2	NP_066934.1	O95980	RECK_HUMAN	reversion-inducing-cysteine-rich protein with kazal motifs	932					blood vessel maturation (GO:0001955)|embryo implantation (GO:0007566)|extracellular matrix organization (GO:0030198)|negative regulation of endopeptidase activity (GO:0010951)	anchored component of membrane (GO:0031225)|membrane (GO:0016020)|plasma membrane (GO:0005886)	endopeptidase inhibitor activity (GO:0004866)|metalloendopeptidase inhibitor activity (GO:0008191)|serine-type endopeptidase inhibitor activity (GO:0004867)	p.S932A(1)		cervix(1)|endometrium(7)|kidney(3)|large_intestine(6)|lung(10)|ovary(1)|pancreas(1)|skin(2)|stomach(1)	32			LUSC - Lung squamous cell carcinoma(32;0.112)|STAD - Stomach adenocarcinoma(86;0.228)			CCTCATCATTTCCCAGGTACA	0.567																																					p.S932A												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T2794G	9						.						147.0	136.0	140.0					9																	36122920		2203	4300	6503	36112920	SO:0001583	missense	8434	exon21			E13833	CCDS6597.1	9p13.3	2008-05-15			ENSG00000122707	ENSG00000122707			11345	protein-coding gene	gene with protein product		605227		ST15		9789069	Standard	NM_021111		Approved	hRECK	uc003zyv.3	O95980	OTTHUMG00000019898	ENST00000377966.3:c.2794T>G	9.37:g.36122920T>G	ENSP00000367202:p.Ser932Ala	Somatic		Capture	Illumina HiSeq	Phase_I	36112920	NM_021111	B2RNS1|Q5W0K6|Q8WX37	Missense_Mutation	SNP	ENST00000377966.3	37	CCDS6597.1	.	.	.	.	.	.	.	.	.	.	T	11.35	1.613151	0.28712	.	.	ENSG00000122707	ENST00000377966	T	0.35789	1.29	5.93	4.77	0.60923	.	0.000000	0.85682	D	0.000000	T	0.21841	0.0526	L	0.28776	0.89	0.43930	D	0.996585	B;B	0.09022	0.002;0.002	B;B	0.06405	0.002;0.002	T	0.07712	-1.0758	10	0.02654	T	1	-11.7653	10.1615	0.42855	0.0:0.0:0.1676:0.8324	.	932;932	A8K9D8;O95980	.;RECK_HUMAN	A	932	ENSP00000367202:S932A	ENSP00000367202:S932A	S	+	1	0	RECK	36112920	0.999000	0.42202	0.977000	0.42913	0.988000	0.76386	3.105000	0.50314	1.041000	0.40125	0.533000	0.62120	TCC		0.567	RECK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052409.1		
MELK	9833	broad.mit.edu	37	9	36670999	36670999	+	Missense_Mutation	SNP	C	C	T	rs200746617		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr9:36670999C>T	ENST00000298048.2	+	16	1694	c.1510C>T	c.(1510-1512)Cgc>Tgc	p.R504C	MELK_ENST00000536860.1_Missense_Mutation_p.R456C|MELK_ENST00000541717.1_Missense_Mutation_p.R463C|MELK_ENST00000543751.1_Missense_Mutation_p.R472C|MELK_ENST00000536987.1_Missense_Mutation_p.R373C|MELK_ENST00000538311.1_Missense_Mutation_p.R310C|MELK_ENST00000545008.1_Missense_Mutation_p.R433C|MELK_ENST00000536329.1_Missense_Mutation_p.R433C	NM_014791.3	NP_055606.1	Q14680	MELK_HUMAN	maternal embryonic leucine zipper kinase	504	Autoinhibitory region.				apoptotic process (GO:0006915)|cell proliferation (GO:0008283)|G2/M transition of mitotic cell cycle (GO:0000086)|hemopoiesis (GO:0030097)|intrinsic apoptotic signaling pathway in response to oxidative stress (GO:0008631)|neural precursor cell proliferation (GO:0061351)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of apoptotic process (GO:0043065)|protein autophosphorylation (GO:0046777)	cell cortex (GO:0005938)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|lipid binding (GO:0008289)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein serine/threonine kinase activity (GO:0004674)	p.R504C(2)		breast(1)|endometrium(2)|kidney(4)|large_intestine(8)|lung(6)|ovary(4)|skin(2)|upper_aerodigestive_tract(2)	29		Acute lymphoblastic leukemia(2;1.09e-08)|all_hematologic(2;8.15e-06)	STAD - Stomach adenocarcinoma(86;0.228)			TTTCAGGTGCCGCTCAGTGGA	0.488													C|||	1	0.000199681	0.0008	0.0	5008	,	,		16669	0.0		0.0	False		,,,				2504	0.0				p.R504C	Ovarian(82;980 1317 7225 14391 18624)											.	.	2	Substitution - Missense(2)	ovary(1)|large_intestine(1)	c.C1510T	9						.	C	CYS/ARG	0,4406		0,0,2203	103.0	100.0	101.0		1510	5.9	1.0	9		101	1,8599	1.2+/-3.3	0,1,4299	no	missense	MELK	NM_014791.2	180	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging	504/652	36670999	1,13005	2203	4300	6503	36660999	SO:0001583	missense	9833	exon16			D79997	CCDS6606.1, CCDS59123.1, CCDS59124.1, CCDS59125.1, CCDS59126.1, CCDS59127.1, CCDS59128.1	9p13.1	2008-02-05			ENSG00000165304	ENSG00000165304			16870	protein-coding gene	gene with protein product		607025				8724849, 9136115	Standard	NM_001256689		Approved	KIAA0175	uc003zzn.4	Q14680	OTTHUMG00000019906	ENST00000298048.2:c.1510C>T	9.37:g.36670999C>T	ENSP00000298048:p.Arg504Cys	Somatic		Capture	Illumina HiSeq	Phase_I	36660999	NM_014791	A6P3A7|A6P3A8|B1AMQ6|B7Z1E6|B7Z5M5|B7Z6Q7|B7Z6R8|B7Z6Y0|B7Z7Q1|D3DRP8|F5H0Y0|F5H2R4|F5H689|Q7L3C3	Missense_Mutation	SNP	ENST00000298048.2	37	CCDS6606.1	.	.	.	.	.	.	.	.	.	.	C	23.8	4.455826	0.84209	0.0	1.16E-4	ENSG00000165304	ENST00000298048;ENST00000538311;ENST00000536987;ENST00000545008;ENST00000536860;ENST00000536329;ENST00000541717;ENST00000543751	T;T;T;T;T;T;T;T	0.73789	-0.58;0.39;0.17;0.71;0.08;-0.78;-0.56;-0.59	5.95	5.95	0.96441	.	0.099925	0.64402	D	0.000001	D	0.85279	0.5660	M	0.63843	1.955	0.80722	D	1	D;D;D;D;D;D;D	0.89917	1.0;1.0;0.999;0.999;1.0;0.999;0.999	D;D;D;D;D;P;P	0.70716	0.97;0.97;0.921;0.921;0.911;0.886;0.886	D	0.84401	0.0560	10	0.54805	T	0.06	-9.996	20.3932	0.98965	0.0:1.0:0.0:0.0	.	424;433;456;463;433;472;504	B7Z1G6;F5H2R4;F5H0Y0;F5H689;A6P3A8;A6P3A7;Q14680	.;.;.;.;.;.;MELK_HUMAN	C	504;310;373;433;456;433;463;472	ENSP00000298048:R504C;ENSP00000438226:R310C;ENSP00000439184:R373C;ENSP00000445452:R433C;ENSP00000439792:R456C;ENSP00000443550:R433C;ENSP00000437804:R463C;ENSP00000441596:R472C	ENSP00000298048:R504C	R	+	1	0	MELK	36660999	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	3.420000	0.52735	2.824000	0.97209	0.655000	0.94253	CGC		0.488	MELK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052428.3	NM_014791	
FRMPD1	22844	broad.mit.edu	37	9	37740705	37740705	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr9:37740705C>T	ENST00000539465.1	+	15	2773	c.2180C>T	c.(2179-2181)gCt>gTt	p.A727V	FRMPD1_ENST00000541302.1_Missense_Mutation_p.A596V|FRMPD1_ENST00000536622.1_Missense_Mutation_p.A549V|RP11-613M10.9_ENST00000540557.1_Intron|FRMPD1_ENST00000377765.3_Missense_Mutation_p.A727V			Q5SYB0	FRPD1_HUMAN	FERM and PDZ domain containing 1	727						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)		p.A727V(1)		NS(3)|breast(2)|central_nervous_system(2)|endometrium(5)|kidney(4)|large_intestine(22)|lung(34)|ovary(5)|prostate(3)|skin(8)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	93				GBM - Glioblastoma multiforme(29;0.00655)		GAGAGTACAGCTTCCCGGCAA	0.652																																					p.A727V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C2180T	9						.						37.0	30.0	32.0					9																	37740705		2203	4300	6503	37730705	SO:0001583	missense	22844	exon15			AB023184	CCDS6612.1	9p13.1	2008-02-05			ENSG00000070601	ENSG00000070601			29159	protein-coding gene	gene with protein product						10231032	Standard	NM_014907		Approved	KIAA0967, FRMD2	uc004aag.1	Q5SYB0	OTTHUMG00000019927	ENST00000539465.1:c.2180C>T	9.37:g.37740705C>T	ENSP00000444411:p.Ala727Val	Somatic		Capture	Illumina HiSeq	Phase_I	37730705	NM_014907	B4DZC8|B7Z807|D3DRQ3|Q14C73|Q5HY96|Q9Y2H3	Missense_Mutation	SNP	ENST00000539465.1	37	CCDS6612.1	.	.	.	.	.	.	.	.	.	.	C	10.16	1.273475	0.23221	.	.	ENSG00000070601	ENST00000377765;ENST00000539465;ENST00000536622;ENST00000541302	T;T;T;T	0.18016	3.23;3.23;2.24;2.24	5.42	4.52	0.55395	.	0.397857	0.28317	N	0.015791	T	0.13798	0.0334	L	0.51422	1.61	0.09310	N	1	B;P	0.35077	0.22;0.483	B;B	0.27887	0.039;0.084	T	0.16129	-1.0413	10	0.24483	T	0.36	-1.477	10.4899	0.44744	0.0:0.9098:0.0:0.0902	.	596;727	B4DZC8;Q5SYB0	.;FRPD1_HUMAN	V	727;727;549;596	ENSP00000366995:A727V;ENSP00000444411:A727V;ENSP00000437762:A549V;ENSP00000444804:A596V	ENSP00000366995:A727V	A	+	2	0	FRMPD1	37730705	0.031000	0.19500	0.111000	0.21465	0.033000	0.12548	1.852000	0.39348	1.439000	0.47511	-0.140000	0.14226	GCT		0.652	FRMPD1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402969.1	NM_014907	
ALDH1B1	219	broad.mit.edu	37	9	38396960	38396960	+	Silent	SNP	C	C	T	rs535405575		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr9:38396960C>T	ENST00000377698.3	+	2	1368	c.1215C>T	c.(1213-1215)ggC>ggT	p.G405G		NM_000692.4	NP_000683.3	P30837	AL1B1_HUMAN	aldehyde dehydrogenase 1 family, member B1	405					carbohydrate metabolic process (GO:0005975)|ethanol catabolic process (GO:0006068)	intracellular membrane-bounded organelle (GO:0043231)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	aldehyde dehydrogenase (NAD) activity (GO:0004029)	p.G405G(1)		NS(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(11)|prostate(1)|skin(1)|stomach(2)|urinary_tract(2)	32				GBM - Glioblastoma multiforme(29;0.043)|Lung(182;0.115)		TCTTTGGTGGCGTGCAGGATG	0.542																																					p.G405G												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1215T	9						.						109.0	88.0	95.0					9																	38396960		2203	4300	6503	38386960	SO:0001819	synonymous_variant	219	exon2			M63967	CCDS6615.1	9p13	2008-02-05			ENSG00000137124	ENSG00000137124	1.2.1.3	"""Aldehyde dehydrogenases"""	407	protein-coding gene	gene with protein product		100670		ALDH5		2061311	Standard	NM_000692		Approved	ALDHX	uc004aay.3	P30837	OTTHUMG00000019938	ENST00000377698.3:c.1215C>T	9.37:g.38396960C>T		Somatic		Capture	Illumina HiSeq	Phase_I	38386960	NM_000692	B2R8F0|Q8WX76|Q9BV45	Silent	SNP	ENST00000377698.3	37	CCDS6615.1																																																																																				0.542	ALDH1B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052492.1		
PRKACG	5568	broad.mit.edu	37	9	71628894	71628894	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr9:71628894C>T	ENST00000377276.2	-	1	145	c.115G>A	c.(115-117)Gcc>Acc	p.A39T		NM_002732.3	NP_002723.2	P22612	KAPCG_HUMAN	protein kinase, cAMP-dependent, catalytic, gamma	39					activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|blood coagulation (GO:0007596)|carbohydrate metabolic process (GO:0005975)|cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|gluconeogenesis (GO:0006094)|glucose metabolic process (GO:0006006)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|male gonad development (GO:0008584)|neurotrophin TRK receptor signaling pathway (GO:0048011)|regulation of insulin secretion (GO:0050796)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|spermatogenesis (GO:0007283)|transmembrane transport (GO:0055085)|triglyceride catabolic process (GO:0019433)|water transport (GO:0006833)	cytosol (GO:0005829)	ATP binding (GO:0005524)|cAMP-dependent protein kinase activity (GO:0004691)	p.A39T(1)		central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(3)|ovary(1)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	22						TCCGAGCTGGCGGTGTTTTGA	0.617																																					p.A39T	Esophageal Squamous(110;2236 2623 32146)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G115A	9						.						81.0	82.0	82.0					9																	71628894		2203	4300	6503	70818714	SO:0001583	missense	5568	exon1			M34182	CCDS6625.1	9q13	2012-10-02			ENSG00000165059	ENSG00000165059	2.7.11.1		9382	protein-coding gene	gene with protein product		176893				2342480, 9598317	Standard	NM_002732		Approved	PKACg	uc004agy.3	P22612	OTTHUMG00000019974	ENST00000377276.2:c.115G>A	9.37:g.71628894C>T	ENSP00000366488:p.Ala39Thr	Somatic		Capture	Illumina HiSeq	Phase_I	70818714	NM_002732	O60850|Q5VZ02|Q86YI1	Missense_Mutation	SNP	ENST00000377276.2	37	CCDS6625.1	.	.	.	.	.	.	.	.	.	.	C	9.135	1.012334	0.19277	.	.	ENSG00000165059	ENST00000377276	T	0.07800	3.16	1.03	1.03	0.20045	Protein kinase-like domain (1);	0.764050	0.10018	U	0.726323	T	0.10380	0.0254	M	0.67700	2.07	0.24902	N	0.992095	B	0.12630	0.006	B	0.16722	0.016	T	0.31641	-0.9936	10	0.31617	T	0.26	.	7.4815	0.27408	0.0:1.0:0.0:0.0	.	39	P22612	KAPCG_HUMAN	T	39	ENSP00000366488:A39T	ENSP00000366488:A39T	A	-	1	0	PRKACG	70818714	0.001000	0.12720	0.003000	0.11579	0.003000	0.03518	-0.370000	0.07523	0.458000	0.26988	0.467000	0.42956	GCC		0.617	PRKACG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052559.1		
MAMDC2	256691	broad.mit.edu	37	9	72758539	72758539	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr9:72758539C>T	ENST00000377182.4	+	9	1825	c.1208C>T	c.(1207-1209)tCc>tTc	p.S403F	MAMDC2-AS1_ENST00000591368.1_RNA	NM_153267.4	NP_694999.3	Q7Z304	MAMC2_HUMAN	MAM domain containing 2	403	MAM 3. {ECO:0000255|PROSITE- ProRule:PRU00128}.				peptide cross-linking via chondroitin 4-sulfate glycosaminoglycan (GO:0019800)	endoplasmic reticulum (GO:0005783)|interstitial matrix (GO:0005614)|membrane (GO:0016020)	glycosaminoglycan binding (GO:0005539)	p.S403F(1)		breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(5)|pancreas(1)|upper_aerodigestive_tract(1)	14						TATGGGCCCTCCCTACCAGGA	0.428																																					p.S403F												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1208T	9						.						102.0	91.0	95.0					9																	72758539		2203	4300	6503	71948359	SO:0001583	missense	256691	exon9			BC040299	CCDS6631.1	9q21.2	2008-02-05			ENSG00000165072	ENSG00000165072			23673	protein-coding gene	gene with protein product		612879					Standard	NM_153267		Approved	MGC21981	uc004ahm.2	Q7Z304	OTTHUMG00000019990	ENST00000377182.4:c.1208C>T	9.37:g.72758539C>T	ENSP00000366387:p.Ser403Phe	Somatic		Capture	Illumina HiSeq	Phase_I	71948359	NM_153267	Q5VW47|Q8WX43|Q96BM4	Missense_Mutation	SNP	ENST00000377182.4	37	CCDS6631.1	.	.	.	.	.	.	.	.	.	.	C	11.86	1.763347	0.31228	.	.	ENSG00000165072	ENST00000377182	T	0.01998	4.51	5.91	5.91	0.95273	Concanavalin A-like lectin/glucanase (1);MAM domain (4);	0.334360	0.36703	N	0.002443	T	0.03651	0.0104	L	0.43152	1.355	0.41988	D	0.990833	B	0.17852	0.024	B	0.26614	0.071	T	0.52102	-0.8620	10	0.09843	T	0.71	-18.7437	20.2857	0.98533	0.0:1.0:0.0:0.0	.	403	Q7Z304	MAMC2_HUMAN	F	403	ENSP00000366387:S403F	ENSP00000366387:S403F	S	+	2	0	MAMDC2	71948359	0.068000	0.21057	1.000000	0.80357	0.659000	0.38960	1.033000	0.30191	2.803000	0.96430	0.650000	0.86243	TCC		0.428	MAMDC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052600.1	NM_153267	
MAMDC2	256691	broad.mit.edu	37	9	72840704	72840704	+	Silent	SNP	T	T	C			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr9:72840704T>C	ENST00000377182.4	+	13	2567	c.1950T>C	c.(1948-1950)agT>agC	p.S650S	SMC5-AS1_ENST00000594708.1_RNA	NM_153267.4	NP_694999.3	Q7Z304	MAMC2_HUMAN	MAM domain containing 2	650	MAM 4. {ECO:0000255|PROSITE- ProRule:PRU00128}.				peptide cross-linking via chondroitin 4-sulfate glycosaminoglycan (GO:0019800)	endoplasmic reticulum (GO:0005783)|interstitial matrix (GO:0005614)|membrane (GO:0016020)	glycosaminoglycan binding (GO:0005539)	p.S650S(1)		breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(5)|pancreas(1)|upper_aerodigestive_tract(1)	14						CAATAAGAAGTGATATTGCCA	0.348																																					p.S650S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.T1950C	9						.						82.0	83.0	82.0					9																	72840704		2202	4299	6501	72030524	SO:0001819	synonymous_variant	256691	exon13			BC040299	CCDS6631.1	9q21.2	2008-02-05			ENSG00000165072	ENSG00000165072			23673	protein-coding gene	gene with protein product		612879					Standard	NM_153267		Approved	MGC21981	uc004ahm.2	Q7Z304	OTTHUMG00000019990	ENST00000377182.4:c.1950T>C	9.37:g.72840704T>C		Somatic		Capture	Illumina HiSeq	Phase_I	72030524	NM_153267	Q5VW47|Q8WX43|Q96BM4	Silent	SNP	ENST00000377182.4	37	CCDS6631.1																																																																																				0.348	MAMDC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052600.1	NM_153267	
TMEM2	23670	broad.mit.edu	37	9	74305071	74305071	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr9:74305071G>A	ENST00000377044.4	-	22	4327	c.3788C>T	c.(3787-3789)aCg>aTg	p.T1263M	TMEM2_ENST00000396272.3_Missense_Mutation_p.T256M|TMEM2_ENST00000377066.5_Missense_Mutation_p.T1200M	NM_001135820.1|NM_013390.2	NP_001129292.1|NP_037522.1	Q9UHN6	TMEM2_HUMAN	transmembrane protein 2	1263					multicellular organismal development (GO:0007275)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)		p.T1263M(1)		central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(15)|liver(1)|lung(19)|ovary(2)|prostate(5)|skin(1)|stomach(1)|urinary_tract(2)	56		all_epithelial(88;4.56e-14)|Myeloproliferative disorder(762;0.0255)		GBM - Glioblastoma multiforme(74;7.45e-21)|OV - Ovarian serous cystadenocarcinoma(323;1.02e-16)		AGGAAAAACCGTTTTTTCCGT	0.493																																					p.T1263M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C3788T	9						.						151.0	133.0	139.0					9																	74305071		2203	4300	6503	73494891	SO:0001583	missense	23670	exon22				CCDS6638.1, CCDS47979.1	9q21.13	2011-07-19			ENSG00000135048	ENSG00000135048			11869	protein-coding gene	gene with protein product		605835					Standard	NM_013390		Approved		uc011lsa.1	Q9UHN6	OTTHUMG00000020000	ENST00000377044.4:c.3788C>T	9.37:g.74305071G>A	ENSP00000366243:p.Thr1263Met	Somatic		Capture	Illumina HiSeq	Phase_I	73494891	NM_013390	A6H8W9|B2RTQ6|Q5T838|Q5T839|Q5T840|Q5T841|Q8NBP6|Q9P2D5	Missense_Mutation	SNP	ENST00000377044.4	37	CCDS6638.1	.	.	.	.	.	.	.	.	.	.	T	11.52	1.662243	0.29515	.	.	ENSG00000135048	ENST00000377044;ENST00000377066;ENST00000396272	T;T;T	0.74209	-0.82;-0.75;2.43	5.98	2.46	0.29980	.	0.738777	0.14147	N	0.338272	T	0.39963	0.1098	N	0.01352	-0.895	0.09310	N	1	B;B	0.15719	0.006;0.014	B;B	0.11329	0.001;0.006	T	0.26360	-1.0105	10	0.35671	T	0.21	.	1.3155	0.02106	0.1212:0.2051:0.2512:0.4225	.	1263;1200	Q9UHN6;Q9UHN6-2	TMEM2_HUMAN;.	M	1263;1200;256	ENSP00000366243:T1263M;ENSP00000366266:T1200M;ENSP00000379569:T256M	ENSP00000366243:T1263M	T	-	2	0	TMEM2	73494891	0.000000	0.05858	0.001000	0.08648	0.045000	0.14185	0.058000	0.14301	0.171000	0.19730	-0.264000	0.10439	ACG		0.493	TMEM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052618.2	NM_013390	
TRPM6	140803	broad.mit.edu	37	9	77353353	77353353	+	Missense_Mutation	SNP	G	G	A	rs146677759		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr9:77353353G>A	ENST00000360774.1	-	36	5983	c.5746C>T	c.(5746-5748)Cgg>Tgg	p.R1916W	TRPM6_ENST00000361255.3_Missense_Mutation_p.R1911W|TRPM6_ENST00000449912.2_Missense_Mutation_p.R1911W|TRPM6_ENST00000451710.3_Missense_Mutation_p.R1920W|TRPM6_ENST00000376871.3_Missense_Mutation_p.R753W|TRPM6_ENST00000376864.4_Missense_Mutation_p.R1920W|TRPM6_ENST00000376872.3_Missense_Mutation_p.R871W	NM_017662.4	NP_060132.3	Q9BX84	TRPM6_HUMAN	transient receptor potential cation channel, subfamily M, member 6	1916	Alpha-type protein kinase. {ECO:0000255|PROSITE-ProRule:PRU00501}.				calcium ion transmembrane transport (GO:0070588)|ion transmembrane transport (GO:0034220)|response to toxic substance (GO:0009636)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium channel activity (GO:0005262)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)	p.R1916W(1)		NS(2)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(22)|liver(1)|lung(53)|ovary(1)|prostate(7)|skin(12)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	126						AGCTCTCCCCGAGTGTACTCA	0.458													G|||	1	0.000199681	0.0	0.0	5008	,	,		19446	0.001		0.0	False		,,,				2504	0.0				p.R1911W												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C5731T	9						.	G	TRP/ARG,TRP/ARG,TRP/ARG	0,4406		0,0,2203	130.0	119.0	123.0		5731,5731,5746	5.0	1.0	9	dbSNP_134	123	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense,missense	TRPM6	NM_001177310.1,NM_001177311.1,NM_017662.4	101,101,101	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging,probably-damaging,probably-damaging	1911/2018,1911/2018,1916/2023	77353353	1,13005	2203	4300	6503	76543173	SO:0001583	missense	140803	exon36			AK026281	CCDS6647.1, CCDS55318.1, CCDS55319.1	9q21.13	2011-12-14	2003-12-02		ENSG00000119121	ENSG00000119121		"""Voltage-gated ion channels / Transient receptor potential cation channels"""	17995	protein-coding gene	gene with protein product		607009	"""hypomagnesemia, secondary hypocalcemia"""	HOMG, HSH		10021370, 12032570, 16382100	Standard	NM_017662		Approved	CHAK2, FLJ22628	uc004ajk.1	Q9BX84	OTTHUMG00000020027	ENST00000360774.1:c.5746C>T	9.37:g.77353353G>A	ENSP00000354006:p.Arg1916Trp	Somatic		Capture	Illumina HiSeq	Phase_I	76543173	NM_001177310	Q6VPR8|Q6VPR9|Q6VPS0|Q6VPS1|Q6VPS2	Missense_Mutation	SNP	ENST00000360774.1	37	CCDS6647.1	.	.	.	.	.	.	.	.	.	.	G	19.80	3.894011	0.72639	0.0	1.16E-4	ENSG00000119121	ENST00000360774;ENST00000451710;ENST00000376872;ENST00000376871;ENST00000449912;ENST00000361255;ENST00000376870;ENST00000376864	T;T;T;T;T;T;T	0.07114	3.22;3.22;3.22;3.22;3.22;3.22;3.22	5.94	5.03	0.67393	MHCK/EF2 kinase (3);Protein kinase-like domain (1);	0.228383	0.45606	D	0.000354	T	0.26268	0.0641	M	0.64170	1.965	0.46874	D	0.999232	D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D	0.83275	0.978;0.996;0.996;0.994;0.955;0.989	T	0.00920	-1.1514	10	0.87932	D	0	.	13.9842	0.64324	0.0:0.0:0.724:0.276	.	463;749;867;1916;1911;1911	Q9BX84-7;Q9BX84-6;Q9BX84-5;Q9BX84;Q9BX84-3;Q9BX84-2	.;.;.;TRPM6_HUMAN;.;.	W	1916;1920;871;753;1911;1911;462;1920	ENSP00000354006:R1916W;ENSP00000407341:R1920W;ENSP00000366068:R871W;ENSP00000366067:R753W;ENSP00000396672:R1911W;ENSP00000354962:R1911W;ENSP00000366060:R1920W	ENSP00000354006:R1916W	R	-	1	2	TRPM6	76543173	0.997000	0.39634	0.980000	0.43619	0.975000	0.68041	2.515000	0.45512	1.477000	0.48234	0.561000	0.74099	CGG		0.458	TRPM6-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000052693.1	NM_017662	
VPS13A	23230	broad.mit.edu	37	9	79955337	79955337	+	Silent	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr9:79955337C>T	ENST00000360280.3	+	50	7157	c.6897C>T	c.(6895-6897)gaC>gaT	p.D2299D	VPS13A_ENST00000376636.3_Silent_p.D2260D|VPS13A_ENST00000376634.4_Silent_p.D2299D|VPS13A_ENST00000357409.5_Silent_p.D2299D	NM_033305.2	NP_150648.2	Q96RL7	VP13A_HUMAN	vacuolar protein sorting 13 homolog A (S. cerevisiae)	2299					cell death (GO:0008219)|Golgi to endosome transport (GO:0006895)|locomotory behavior (GO:0007626)|nervous system development (GO:0007399)|protein localization (GO:0008104)|protein transport (GO:0015031)|social behavior (GO:0035176)	dense core granule (GO:0031045)|intracellular (GO:0005622)		p.D2299D(2)		breast(4)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(28)|liver(1)|lung(42)|ovary(3)|pancreas(3)|prostate(3)|skin(9)|upper_aerodigestive_tract(1)|urinary_tract(1)	104						TCACTATAGACCTGAGCAGTT	0.269																																					p.D2260D												.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.C6780T	9						.						66.0	69.0	68.0					9																	79955337		2203	4297	6500	79145157	SO:0001819	synonymous_variant	23230	exon49			AB023203	CCDS6655.1, CCDS6656.1, CCDS47983.1, CCDS55321.1	9q21	2014-01-30	2006-04-04	2004-02-11	ENSG00000197969	ENSG00000197969			1908	protein-coding gene	gene with protein product	"""chorein"""	605978	"""chorea acanthocytosis"", ""vacuolar protein sorting 13A (yeast)"""	CHAC		9382101, 11381253	Standard	NM_001018038		Approved	KIAA0986	uc004akr.3	Q96RL7	OTTHUMG00000020055	ENST00000360280.3:c.6897C>T	9.37:g.79955337C>T		Somatic		Capture	Illumina HiSeq	Phase_I	79145157	NM_001018037	Q5JSX9|Q5JSY0|Q5VYR5|Q702P4|Q709D0|Q86YF8|Q96S61|Q9H995|Q9Y2J1	Silent	SNP	ENST00000360280.3	37	CCDS6655.1																																																																																				0.269	VPS13A-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000052753.2	NM_015186	
HNRNPK	3190	broad.mit.edu	37	9	86586984	86586984	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr9:86586984G>A	ENST00000376264.2	-	11	1024	c.766C>T	c.(766-768)Cgg>Tgg	p.R256W	HNRNPK_ENST00000376281.4_Missense_Mutation_p.R256W|HNRNPK_ENST00000351839.3_Missense_Mutation_p.R256W|RP11-575L7.8_ENST00000448389.1_RNA|HNRNPK_ENST00000360384.5_Missense_Mutation_p.R256W|HNRNPK_ENST00000376263.3_Missense_Mutation_p.R256W|MIR7-1_ENST00000384871.1_RNA	NM_002140.3|NM_031262.2	NP_002131.2|NP_112552.1	P61978	HNRPK_HUMAN	heterogeneous nuclear ribonucleoprotein K	256	2 X 22 AA approximate repeats.|2 X 6 AA approximate repeats.|5 X 4 AA repeats of G-X-G-G.|Interaction with ZIK1. {ECO:0000250}.|Necessary for interaction with DDX1.|RNA-binding RGG-box.				gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|positive regulation of low-density lipoprotein particle receptor biosynthetic process (GO:0045716)|positive regulation of receptor-mediated endocytosis (GO:0048260)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of lipid transport by positive regulation of transcription from RNA polymerase II promoter (GO:0072369)|regulation of low-density lipoprotein particle clearance (GO:0010988)|RNA processing (GO:0006396)|RNA splicing (GO:0008380)|signal transduction (GO:0007165)|viral process (GO:0016032)	catalytic step 2 spliceosome (GO:0071013)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|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)|single-stranded DNA binding (GO:0003697)	p.R256W(1)		endometrium(3)|kidney(2)|large_intestine(4)|lung(8)|skin(1)|stomach(1)	19						CCTCTTCCCCGCATGGGAAAT	0.502																																					p.R256W												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C766T	9						.						51.0	55.0	53.0					9																	86586984		2203	4300	6503	85776804	SO:0001583	missense	3190	exon11				CCDS6667.1, CCDS6668.1	9q21.32-q21.33	2011-10-24		2008-04-18	ENSG00000165119	ENSG00000165119			5044	protein-coding gene	gene with protein product	"""transformation upregulated nuclear protein"""	600712		HNRPK		8107114	Standard	NM_031263		Approved	CSBP, TUNP	uc004anf.4	P61978	OTTHUMG00000020107	ENST00000376264.2:c.766C>T	9.37:g.86586984G>A	ENSP00000365440:p.Arg256Trp	Somatic		Capture	Illumina HiSeq	Phase_I	85776804	NM_002140	Q07244|Q15671|Q59F98|Q5T6W4|Q60577|Q922Y7|Q96J62	Missense_Mutation	SNP	ENST00000376264.2	37	CCDS6667.1	.	.	.	.	.	.	.	.	.	.	G	14.55	2.570310	0.45798	.	.	ENSG00000165119	ENST00000376281;ENST00000376264;ENST00000376263;ENST00000376268;ENST00000351839;ENST00000435158;ENST00000360384;ENST00000376258;ENST00000457156;ENST00000376256	T;T;T;T;T	0.52983	0.68;0.64;0.68;0.64;0.64	5.31	3.44	0.39384	.	0.110459	0.64402	D	0.000010	T	0.42944	0.1225	L	0.55990	1.75	0.48185	D	0.999608	B;B;B;B;B;B;B;B	0.14012	0.001;0.002;0.002;0.002;0.009;0.001;0.0;0.005	B;B;B;B;B;B;B;B	0.04013	0.0;0.0;0.0;0.0;0.001;0.0;0.0;0.0	T	0.28964	-1.0027	10	0.38643	T	0.18	-3.4821	13.384	0.60785	0.0:0.0:0.7146:0.2854	.	232;221;256;251;256;232;256;256	B4DUQ1;Q5T6W5;Q5EC54;B4DFF1;P61978-2;P61978-3;P61978;Q6IBN1	.;.;.;.;.;.;HNRPK_HUMAN;.	W	256;256;256;256;256;221;256;251;232;187	ENSP00000365458:R256W;ENSP00000365440:R256W;ENSP00000365439:R256W;ENSP00000317788:R256W;ENSP00000353552:R256W	ENSP00000317788:R256W	R	-	1	2	HNRNPK	85776804	1.000000	0.71417	1.000000	0.80357	0.930000	0.56654	2.373000	0.44266	0.696000	0.31696	0.655000	0.94253	CGG		0.502	HNRNPK-202	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000052846.2		
DAPK1	1612	broad.mit.edu	37	9	90301507	90301507	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr9:90301507G>A	ENST00000408954.3	+	21	2601	c.2266G>A	c.(2266-2268)Gtg>Atg	p.V756M	DAPK1_ENST00000469640.2_Missense_Mutation_p.V756M|DAPK1_ENST00000358077.5_Missense_Mutation_p.V756M|DAPK1_ENST00000491893.1_Missense_Mutation_p.V756M|DAPK1_ENST00000472284.1_Missense_Mutation_p.V756M	NM_004938.2	NP_004929.2	P53355	DAPK1_HUMAN	death-associated protein kinase 1	756					apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|cellular response to interferon-gamma (GO:0071346)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|intracellular signal transduction (GO:0035556)|negative regulation of apoptotic process (GO:0043066)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|negative regulation of translation (GO:0017148)|positive regulation of apoptotic process (GO:0043065)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of apoptotic process (GO:0042981)|regulation of autophagy (GO:0010506)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)	ATP binding (GO:0005524)|calmodulin binding (GO:0005516)|calmodulin-dependent protein kinase activity (GO:0004683)|identical protein binding (GO:0042802)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)	p.V757M(1)|p.V756M(1)		breast(5)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(27)|liver(2)|lung(17)|ovary(1)|prostate(2)|skin(3)|stomach(1)	72						CTGCGAGAACGTGAGTGTGAG	0.597									Chronic Lymphocytic Leukemia, Familial Clustering of																												p.V756M												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G2266A	9						.						69.0	81.0	77.0					9																	90301507		2138	4250	6388	89491327	SO:0001583	missense	1612	exon21	Familial Cancer Database	Familial CLL	X76104	CCDS43842.1	9q34.1	2013-01-10			ENSG00000196730	ENSG00000196730		"""Ankyrin repeat domain containing"""	2674	protein-coding gene	gene with protein product		600831				8530096	Standard	XM_005251757		Approved	DAPK	uc004apd.3	P53355	OTTHUMG00000020150	ENST00000408954.3:c.2266G>A	9.37:g.90301507G>A	ENSP00000386135:p.Val756Met	Somatic		Capture	Illumina HiSeq	Phase_I	89491327	NM_004938	B7ZLD2|B7ZLE7|Q14CQ7|Q1W5W0|Q68CP8|Q6ZRZ3|Q9BTL8	Missense_Mutation	SNP	ENST00000408954.3	37	CCDS43842.1	.	.	.	.	.	.	.	.	.	.	G	26.8	4.773978	0.90108	.	.	ENSG00000196730	ENST00000358077;ENST00000472284;ENST00000469640;ENST00000408954;ENST00000491893	T;T;T;T;T	0.69040	-0.31;-0.31;-0.29;-0.31;-0.37	5.15	5.15	0.70609	.	0.000000	0.45126	D	0.000388	T	0.77798	0.4184	L	0.47716	1.5	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.79108	0.992;0.992	T	0.78104	-0.2334	10	0.54805	T	0.06	.	18.4192	0.90584	0.0:0.0:1.0:0.0	.	756;756	B7ZLE7;P53355	.;DAPK1_HUMAN	M	756	ENSP00000350785:V756M;ENSP00000417076:V756M;ENSP00000418885:V756M;ENSP00000386135:V756M;ENSP00000419026:V756M	ENSP00000350785:V756M	V	+	1	0	DAPK1	89491327	1.000000	0.71417	1.000000	0.80357	0.971000	0.66376	9.620000	0.98373	2.674000	0.91012	0.655000	0.94253	GTG		0.597	DAPK1-010	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356843.1	NM_004938	
DAPK1	1612	broad.mit.edu	37	9	90322213	90322213	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr9:90322213G>T	ENST00000408954.3	+	26	4562	c.4227G>T	c.(4225-4227)gaG>gaT	p.E1409D	DAPK1_ENST00000469640.2_Missense_Mutation_p.E1434D|DAPK1_ENST00000358077.5_Missense_Mutation_p.E1409D|DAPK1_ENST00000491893.1_Missense_Mutation_p.E1343D|DAPK1_ENST00000472284.1_Missense_Mutation_p.E1409D	NM_004938.2	NP_004929.2	P53355	DAPK1_HUMAN	death-associated protein kinase 1	1409					apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|cellular response to interferon-gamma (GO:0071346)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|intracellular signal transduction (GO:0035556)|negative regulation of apoptotic process (GO:0043066)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|negative regulation of translation (GO:0017148)|positive regulation of apoptotic process (GO:0043065)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of apoptotic process (GO:0042981)|regulation of autophagy (GO:0010506)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)	ATP binding (GO:0005524)|calmodulin binding (GO:0005516)|calmodulin-dependent protein kinase activity (GO:0004683)|identical protein binding (GO:0042802)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)	p.E1410D(1)|p.E1409D(1)		breast(5)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(27)|liver(2)|lung(17)|ovary(1)|prostate(2)|skin(3)|stomach(1)	72						ATGGCCAGGAGGCCTATGCCT	0.557									Chronic Lymphocytic Leukemia, Familial Clustering of																												p.E1409D												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G4227T	9						.						34.0	38.0	37.0					9																	90322213		1959	4146	6105	89512033	SO:0001583	missense	1612	exon26	Familial Cancer Database	Familial CLL	X76104	CCDS43842.1	9q34.1	2013-01-10			ENSG00000196730	ENSG00000196730		"""Ankyrin repeat domain containing"""	2674	protein-coding gene	gene with protein product		600831				8530096	Standard	XM_005251757		Approved	DAPK	uc004apd.3	P53355	OTTHUMG00000020150	ENST00000408954.3:c.4227G>T	9.37:g.90322213G>T	ENSP00000386135:p.Glu1409Asp	Somatic		Capture	Illumina HiSeq	Phase_I	89512033	NM_004938	B7ZLD2|B7ZLE7|Q14CQ7|Q1W5W0|Q68CP8|Q6ZRZ3|Q9BTL8	Missense_Mutation	SNP	ENST00000408954.3	37	CCDS43842.1	.	.	.	.	.	.	.	.	.	.	G	12.31	1.898435	0.33535	.	.	ENSG00000196730	ENST00000358077;ENST00000472284;ENST00000469640;ENST00000408954;ENST00000491893	T;T;T;T;T	0.68025	-0.28;-0.28;-0.3;-0.28;-0.29	5.94	-2.23	0.06930	.	0.110090	0.37053	N	0.002276	T	0.39572	0.1083	N	0.19112	0.55	0.40301	D	0.978609	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.0;0.001;0.0	T	0.02378	-1.1168	10	0.28530	T	0.3	.	3.0019	0.06016	0.4442:0.1091:0.3357:0.1109	.	1343;1409;1409	B7ZLE7;P53355-3;P53355	.;.;DAPK1_HUMAN	D	1409;1409;1434;1409;1343	ENSP00000350785:E1409D;ENSP00000417076:E1409D;ENSP00000418885:E1434D;ENSP00000386135:E1409D;ENSP00000419026:E1343D	ENSP00000350785:E1409D	E	+	3	2	DAPK1	89512033	0.505000	0.26131	0.996000	0.52242	0.981000	0.71138	-0.212000	0.09319	-0.072000	0.12864	0.563000	0.77884	GAG		0.557	DAPK1-010	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356843.1	NM_004938	
SPATA31E1	286234	broad.mit.edu	37	9	90500932	90500932	+	Nonsense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr9:90500932G>A	ENST00000325643.5	+	4	1596	c.1530G>A	c.(1528-1530)tgG>tgA	p.W510*		NM_178828.4	NP_849150.3	Q6ZUB1	S31E1_HUMAN	SPATA31 subfamily E, member 1	510					cell differentiation (GO:0030154)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)		p.W510*(1)									ctccagcctggccccagtccc	0.642																																					p.W510X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.G1530A	9						.						37.0	40.0	39.0					9																	90500932		2203	4300	6503	89690752	SO:0001587	stop_gained	286234	exon4			AK093185	CCDS6676.1	9q22.1-q22.2	2012-10-12	2012-10-12	2012-10-12	ENSG00000177992	ENSG00000177992			26672	protein-coding gene	gene with protein product			"""chromosome 9 open reading frame 79"", ""family with sequence similarity 75, member E1"""	C9orf79, FAM75E1			Standard	NM_178828		Approved	FLJ35866	uc004app.4	Q6ZUB1	OTTHUMG00000020157	ENST00000325643.5:c.1530G>A	9.37:g.90500932G>A	ENSP00000322640:p.Trp510*	Somatic		Capture	Illumina HiSeq	Phase_I	89690752	NM_178828	B2RPB1|Q5SQC9|Q8NA41|Q8ND27	Nonsense_Mutation	SNP	ENST00000325643.5	37	CCDS6676.1	.	.	.	.	.	.	.	.	.	.	g	19.74	3.883196	0.72410	.	.	ENSG00000177992	ENST00000325643;ENST00000539327	.	.	.	2.24	1.32	0.21799	.	4.412020	0.00654	N	0.000574	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.32370	T	0.25	.	4.6014	0.12356	0.194:0.0:0.806:0.0	.	.	.	.	X	510;162	.	ENSP00000322640:W510X	W	+	3	0	C9orf79	89690752	0.003000	0.15002	0.000000	0.03702	0.002000	0.02628	1.258000	0.32944	0.489000	0.27749	0.603000	0.83216	TGG		0.642	SPATA31E1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052954.2	NM_178828	
SPATA31E1	286234	broad.mit.edu	37	9	90502753	90502753	+	Silent	SNP	G	G	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr9:90502753G>T	ENST00000325643.5	+	4	3417	c.3351G>T	c.(3349-3351)ccG>ccT	p.P1117P		NM_178828.4	NP_849150.3	Q6ZUB1	S31E1_HUMAN	SPATA31 subfamily E, member 1	1117					cell differentiation (GO:0030154)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)		p.P1117P(2)									GCCGTGCCCCGGGCATCCTCC	0.647																																					p.P1117P												.	.	2	Substitution - coding silent(2)	large_intestine(1)|lung(1)	c.G3351T	9						.						36.0	40.0	39.0					9																	90502753		2203	4300	6503	89692573	SO:0001819	synonymous_variant	286234	exon4			AK093185	CCDS6676.1	9q22.1-q22.2	2012-10-12	2012-10-12	2012-10-12	ENSG00000177992	ENSG00000177992			26672	protein-coding gene	gene with protein product			"""chromosome 9 open reading frame 79"", ""family with sequence similarity 75, member E1"""	C9orf79, FAM75E1			Standard	NM_178828		Approved	FLJ35866	uc004app.4	Q6ZUB1	OTTHUMG00000020157	ENST00000325643.5:c.3351G>T	9.37:g.90502753G>T		Somatic		Capture	Illumina HiSeq	Phase_I	89692573	NM_178828	B2RPB1|Q5SQC9|Q8NA41|Q8ND27	Silent	SNP	ENST00000325643.5	37	CCDS6676.1																																																																																				0.647	SPATA31E1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052954.2	NM_178828	
CDK20	23552	broad.mit.edu	37	9	90585530	90585530	+	Silent	SNP	G	G	A	rs142841498		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr9:90585530G>A	ENST00000325303.8	-	5	821	c.516C>T	c.(514-516)ccC>ccT	p.P172P	CDK20_ENST00000605159.1_Intron|CDK20_ENST00000375883.3_Intron|CDK20_ENST00000336654.5_Intron|CDK20_ENST00000375871.4_Intron	NM_001039803.2	NP_001034892.1	Q8IZL9	CDK20_HUMAN	cyclin-dependent kinase 20	172	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cell cycle (GO:0007049)|cell division (GO:0051301)|multicellular organismal development (GO:0007275)	cilium (GO:0005929)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)	p.P172P(1)		skin(1)	1						ACAGGAGCTCGGGGGCTCGGT	0.607																																					p.P172P												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C516T	9						.	G	,,,,	1,4405		0,1,2202	41.0	39.0	40.0		516,,,,	-9.5	0.1	9	dbSNP_134	40	0,8600		0,0,4300	no	coding-synonymous,intron,intron,intron,intron	CDK20	NM_001039803.2,NM_001170639.1,NM_001170640.1,NM_012119.4,NM_178432.3	,,,,	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	,,,,	172/347,,,,	90585530	1,13005	2203	4300	6503	89775350	SO:0001819	synonymous_variant	23552	exon5			AF035013	CCDS6677.1, CCDS6678.1, CCDS35060.1, CCDS55324.1, CCDS65075.1	9q22.1	2011-11-08	2009-12-16	2009-12-16	ENSG00000156345	ENSG00000156345		"""Cyclin-dependent kinases"""	21420	protein-coding gene	gene with protein product		610076	"""cell cycle related kinase"""	CCRK		19884882	Standard	NM_178432		Approved	p42	uc004apr.3	Q8IZL9	OTTHUMG00000020161	ENST00000325303.8:c.516C>T	9.37:g.90585530G>A		Somatic		Capture	Illumina HiSeq	Phase_I	89775350	NM_001039803	A2A389|A2A390|B4DQX1|O95137|Q5EDC4|Q5VYW1|Q9BUF4	Silent	SNP	ENST00000325303.8	37	CCDS35060.1																																																																																				0.607	CDK20-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214996.1	NM_012119	
SECISBP2	79048	broad.mit.edu	37	9	91965612	91965612	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr9:91965612T>C	ENST00000375807.3	+	14	2029	c.1958T>C	c.(1957-1959)gTc>gCc	p.V653A	SECISBP2_ENST00000339901.4_Missense_Mutation_p.V580A|SECISBP2_ENST00000534113.2_Missense_Mutation_p.V585A	NM_001282688.1|NM_001282690.1|NM_024077.3	NP_001269617.1|NP_001269619.1|NP_076982.3	Q96T21	SEBP2_HUMAN	SECIS binding protein 2	653					translation (GO:0006412)	mitochondrion (GO:0005739)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	mRNA 3'-UTR binding (GO:0003730)|poly(A) RNA binding (GO:0044822)|ribonucleoprotein complex binding (GO:0043021)|selenocysteine insertion sequence binding (GO:0035368)	p.V653A(1)		breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|liver(2)|lung(11)|ovary(3)|skin(2)	32						AAAGAACTGGTCCGTTTCCAA	0.468																																					p.V653A												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T1958C	9						.						247.0	212.0	224.0					9																	91965612		2203	4300	6503	91155432	SO:0001583	missense	79048	exon14			AF380995	CCDS6683.1, CCDS65076.1, CCDS65077.1	9q22	2008-02-05			ENSG00000187742	ENSG00000187742			30972	protein-coding gene	gene with protein product		607693				11230166	Standard	XM_005252193		Approved		uc004aqj.1	Q96T21	OTTHUMG00000020182	ENST00000375807.3:c.1958T>C	9.37:g.91965612T>C	ENSP00000364965:p.Val653Ala	Somatic		Capture	Illumina HiSeq	Phase_I	91155432	NM_024077	F8W892|Q5HYY1|Q8IYC0|Q9H0A1	Missense_Mutation	SNP	ENST00000375807.3	37	CCDS6683.1	.	.	.	.	.	.	.	.	.	.	T	25.7	4.661461	0.88154	.	.	ENSG00000187742	ENST00000375807;ENST00000395669;ENST00000339901;ENST00000534113	T;T;T	0.76060	-0.97;-0.99;-0.98	4.83	4.83	0.62350	.	0.000000	0.85682	D	0.000000	D	0.85013	0.5600	M	0.75777	2.31	0.49051	D	0.99974	D;D;D	0.89917	0.997;1.0;0.999	D;D;D	0.83275	0.978;0.996;0.991	D	0.85385	0.1122	10	0.44086	T	0.13	-17.828	14.8559	0.70338	0.0:0.0:0.0:1.0	.	660;580;653	Q59H19;Q96T21-2;Q96T21	.;.;SEBP2_HUMAN	A	653;659;580;585	ENSP00000364965:V653A;ENSP00000364959:V580A;ENSP00000436650:V585A	ENSP00000364959:V580A	V	+	2	0	SECISBP2	91155432	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.519000	0.81809	2.166000	0.68216	0.454000	0.30748	GTC		0.468	SECISBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052990.3	NM_024077	
SEMA4D	10507	broad.mit.edu	37	9	91978860	91978860	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr9:91978860C>T	ENST00000420987.1	-	18	2334	c.1888G>A	c.(1888-1890)Gca>Aca	p.A630T	SEMA4D_ENST00000339861.4_Missense_Mutation_p.A630T|SEMA4D_ENST00000469653.1_5'UTR|SEMA4D_ENST00000420101.2_Missense_Mutation_p.A15T|SEMA4D_ENST00000343780.4_Missense_Mutation_p.A630T|SEMA4D_ENST00000455551.2_Missense_Mutation_p.A630T	NM_001142287.1	NP_001135759.1	Q92854	SEM4D_HUMAN	sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4D	0	Ig-like C2-type.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|immune response (GO:0006955)|leukocyte aggregation (GO:0070486)|negative regulation of alkaline phosphatase activity (GO:0010693)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell adhesion (GO:0007162)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of peptidyl-tyrosine phosphorylation (GO:0050732)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|ossification involved in bone maturation (GO:0043931)|positive regulation of cell migration (GO:0030335)|positive regulation of collateral sprouting (GO:0048672)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of cell projection organization (GO:0031344)|regulation of cell shape (GO:0008360)|regulation of dendrite morphogenesis (GO:0048814)|semaphorin-plexin signaling pathway (GO:0071526)|semaphorin-plexin signaling pathway involved in bone trabecula morphogenesis (GO:1900220)	extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)|receptor binding (GO:0005102)|semaphorin receptor binding (GO:0030215)|transmembrane signaling receptor activity (GO:0004888)	p.A15T(1)		NS(1)|endometrium(3)|kidney(2)|large_intestine(13)|lung(8)|ovary(1)|pancreas(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	34						CGAATGTCTGCAGGACCTGGG	0.597																																					p.A630T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1888A	9						.						83.0	80.0	81.0					9																	91978860		2203	4300	6503	91168680	SO:0001583	missense	10507	exon19			U60800	CCDS6685.1, CCDS47991.1	9q22-q31	2013-01-11			ENSG00000187764	ENSG00000187764		"""Semaphorins"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	10732	protein-coding gene	gene with protein product	"""M-sema G"""	601866	"""chromosome 9 open reading frame 164"""	SEMAJ, C9orf164		8876214, 8969198	Standard	NM_006378		Approved	CD100, coll-4, FLJ39737	uc004aqo.1	Q92854	OTTHUMG00000020185	ENST00000420987.1:c.1888G>A	9.37:g.91978860C>T	ENSP00000391733:p.Ala630Thr	Somatic		Capture	Illumina HiSeq	Phase_I	91168680	NM_001142287	B2RPM6|Q7Z5S4|Q8N8B0	Missense_Mutation	SNP	ENST00000420987.1	37	CCDS47991.1	.	.	.	.	.	.	.	.	.	.	C	13.14	2.146972	0.37923	.	.	ENSG00000187764	ENST00000339861;ENST00000420987;ENST00000420101;ENST00000455551;ENST00000343780	T;T;T;T	0.12672	2.66;2.66;2.66;2.66	5.05	2.93	0.34026	.	0.501320	0.18373	N	0.143192	T	0.08758	0.0217	.	.	.	0.09310	N	1	B	0.32829	0.386	B	0.28011	0.085	T	0.23154	-1.0196	9	0.39692	T	0.17	.	7.569	0.27896	0.1811:0.6857:0.0:0.1332	.	630	Q92854-2	.	T	630;630;15;630;630	ENSP00000344923:A630T;ENSP00000391733:A630T;ENSP00000411981:A630T;ENSP00000343418:A630T	ENSP00000344923:A630T	A	-	1	0	SEMA4D	91168680	0.001000	0.12720	0.250000	0.24296	0.739000	0.42172	0.407000	0.21049	1.230000	0.43646	0.462000	0.41574	GCA		0.597	SEMA4D-203	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000402418.2	NM_006378	
SEMA4D	10507	broad.mit.edu	37	9	92006198	92006198	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr9:92006198C>T	ENST00000450295.1	-	9	1531	c.755G>A	c.(754-756)cGg>cAg	p.R252Q	SEMA4D_ENST00000339861.4_Missense_Mutation_p.R252Q|SEMA4D_ENST00000356444.2_Missense_Mutation_p.R252Q|SEMA4D_ENST00000343780.4_Missense_Mutation_p.R252Q|SEMA4D_ENST00000422704.2_Missense_Mutation_p.R252Q|SEMA4D_ENST00000420987.1_Missense_Mutation_p.R252Q|SEMA4D_ENST00000455551.2_Missense_Mutation_p.R252Q|SEMA4D_ENST00000438547.2_Missense_Mutation_p.R252Q			Q92854	SEM4D_HUMAN	sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4D	252	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|immune response (GO:0006955)|leukocyte aggregation (GO:0070486)|negative regulation of alkaline phosphatase activity (GO:0010693)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell adhesion (GO:0007162)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of peptidyl-tyrosine phosphorylation (GO:0050732)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|ossification involved in bone maturation (GO:0043931)|positive regulation of cell migration (GO:0030335)|positive regulation of collateral sprouting (GO:0048672)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of cell projection organization (GO:0031344)|regulation of cell shape (GO:0008360)|regulation of dendrite morphogenesis (GO:0048814)|semaphorin-plexin signaling pathway (GO:0071526)|semaphorin-plexin signaling pathway involved in bone trabecula morphogenesis (GO:1900220)	extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)|receptor binding (GO:0005102)|semaphorin receptor binding (GO:0030215)|transmembrane signaling receptor activity (GO:0004888)	p.R252Q(2)		NS(1)|endometrium(3)|kidney(2)|large_intestine(13)|lung(8)|ovary(1)|pancreas(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	34						TCTTGCTATCCGTGGGATCAG	0.572																																					p.R252Q												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G755A	9						.						183.0	131.0	149.0					9																	92006198		2203	4300	6503	91196018	SO:0001583	missense	10507	exon11			U60800	CCDS6685.1, CCDS47991.1	9q22-q31	2013-01-11			ENSG00000187764	ENSG00000187764		"""Semaphorins"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	10732	protein-coding gene	gene with protein product	"""M-sema G"""	601866	"""chromosome 9 open reading frame 164"""	SEMAJ, C9orf164		8876214, 8969198	Standard	NM_006378		Approved	CD100, coll-4, FLJ39737	uc004aqo.1	Q92854	OTTHUMG00000020185	ENST00000450295.1:c.755G>A	9.37:g.92006198C>T	ENSP00000416523:p.Arg252Gln	Somatic		Capture	Illumina HiSeq	Phase_I	91196018	NM_001142287	B2RPM6|Q7Z5S4|Q8N8B0	Missense_Mutation	SNP	ENST00000450295.1	37	CCDS6685.1	.	.	.	.	.	.	.	.	.	.	C	25.4	4.634428	0.87660	.	.	ENSG00000187764	ENST00000339861;ENST00000420987;ENST00000455551;ENST00000343780;ENST00000450295;ENST00000438547;ENST00000356444;ENST00000422704	T;T;T;T;T;T;T;T	0.31769	1.48;1.48;1.48;1.48;1.48;1.48;1.48;1.48	5.16	5.16	0.70880	WD40/YVTN repeat-like-containing domain (1);Semaphorin/CD100 antigen (4);	0.000000	0.85682	D	0.000000	T	0.71617	0.3361	H	0.97611	4.04	0.51012	D	0.9999	D;D	0.89917	1.0;1.0	D;D	0.91635	0.998;0.999	T	0.82639	-0.0358	10	0.87932	D	0	.	18.8335	0.92151	0.0:1.0:0.0:0.0	.	252;252	Q92854-2;Q92854	.;SEM4D_HUMAN	Q	252	ENSP00000344923:R252Q;ENSP00000391733:R252Q;ENSP00000411981:R252Q;ENSP00000343418:R252Q;ENSP00000416523:R252Q;ENSP00000405102:R252Q;ENSP00000348822:R252Q;ENSP00000388768:R252Q	ENSP00000344923:R252Q	R	-	2	0	SEMA4D	91196018	0.831000	0.29352	0.011000	0.14972	0.705000	0.40729	7.226000	0.78060	2.696000	0.92011	0.555000	0.69702	CGG		0.572	SEMA4D-018	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342411.1	NM_006378	
PHF2	5253	broad.mit.edu	37	9	96422612	96422612	+	Frame_Shift_Del	DEL	A	A	-	rs76832193		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	A	A	A	-	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr9:96422612delA	ENST00000359246.4	+	12	1835	c.1468delA	c.(1468-1470)aaafs	p.K492fs	PHF2_ENST00000375376.4_Intron	NM_005392.3	NP_005383.3	O75151	PHF2_HUMAN	PHD finger protein 2	492	Lys-rich.|Pro-rich.				liver development (GO:0001889)|negative regulation of chromatin silencing at rDNA (GO:0061188)|protein demethylation (GO:0006482)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	dioxygenase activity (GO:0051213)|histone demethylase activity (H3-K9 specific) (GO:0032454)|iron ion binding (GO:0005506)|methylated histone binding (GO:0035064)|zinc ion binding (GO:0008270)	p.K492fs*6(1)		breast(1)|central_nervous_system(2)|endometrium(6)|large_intestine(9)|lung(14)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	40		Myeloproliferative disorder(762;0.0255)		OV - Ovarian serous cystadenocarcinoma(323;9.11e-28)		GAAAGTGTCCAAAAAAAAGAC	0.597																																					p.K490fs												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.1468delA	9						.						20.0	23.0	22.0					9																	96422612		2202	4299	6501	95462433	SO:0001589	frameshift_variant	5253	exon12			AF043725	CCDS35069.1	9q22	2013-01-28			ENSG00000197724	ENSG00000197724		"""Chromatin-modifying enzymes / K-demethylases"", ""Zinc fingers, PHD-type"""	8920	protein-coding gene	gene with protein product	"""jumonji C domain-containing histone demethylase 1E"", ""centromere protein 35"""	604351				10051327, 20129925	Standard	NM_005392		Approved	KIAA0662, JHDM1E, CENP-35	uc004aub.3	O75151	OTTHUMG00000020253	ENST00000359246.4:c.1468delA	9.37:g.96422612delA	ENSP00000352185:p.Lys492fs	Somatic		Capture	Illumina HiSeq	Phase_I	95462433	NM_005392	Q4VXG0|Q8N3K2|Q9Y6N4	Frame_Shift_Del	DEL	ENST00000359246.4	37	CCDS35069.1																																																																																				0.597	PHF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053162.1	NM_005392	
PHF2	5253	broad.mit.edu	37	9	96425189	96425189	+	Splice_Site	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr9:96425189G>A	ENST00000359246.4	+	13	2066	c.1699G>A	c.(1699-1701)Gcc>Acc	p.A567T	PHF2_ENST00000375376.4_Intron	NM_005392.3	NP_005383.3	O75151	PHF2_HUMAN	PHD finger protein 2	567	Lys-rich.				liver development (GO:0001889)|negative regulation of chromatin silencing at rDNA (GO:0061188)|protein demethylation (GO:0006482)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	dioxygenase activity (GO:0051213)|histone demethylase activity (H3-K9 specific) (GO:0032454)|iron ion binding (GO:0005506)|methylated histone binding (GO:0035064)|zinc ion binding (GO:0008270)	p.A567T(1)		breast(1)|central_nervous_system(2)|endometrium(6)|large_intestine(9)|lung(14)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	40		Myeloproliferative disorder(762;0.0255)		OV - Ovarian serous cystadenocarcinoma(323;9.11e-28)		TTTTTTCTAGGCCACAAAGAG	0.512																																					p.A567T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1699A	9						.						139.0	131.0	134.0					9																	96425189		2203	4300	6503	95465010	SO:0001630	splice_region_variant	5253	exon13			AF043725	CCDS35069.1	9q22	2013-01-28			ENSG00000197724	ENSG00000197724		"""Chromatin-modifying enzymes / K-demethylases"", ""Zinc fingers, PHD-type"""	8920	protein-coding gene	gene with protein product	"""jumonji C domain-containing histone demethylase 1E"", ""centromere protein 35"""	604351				10051327, 20129925	Standard	NM_005392		Approved	KIAA0662, JHDM1E, CENP-35	uc004aub.3	O75151	OTTHUMG00000020253	ENST00000359246.4:c.1699-1G>A	9.37:g.96425189G>A		Somatic		Capture	Illumina HiSeq	Phase_I	95465010	NM_005392	Q4VXG0|Q8N3K2|Q9Y6N4	Missense_Mutation	SNP	ENST00000359246.4	37	CCDS35069.1	.	.	.	.	.	.	.	.	.	.	g	11.55	1.671659	0.29693	.	.	ENSG00000197724	ENST00000359246	T	0.18338	2.22	4.07	2.76	0.32466	.	0.505471	0.20779	N	0.085828	T	0.07818	0.0196	N	0.08118	0	0.80722	D	1	P	0.43788	0.817	B	0.38500	0.275	T	0.35773	-0.9775	9	.	.	.	-11.0759	9.8595	0.41105	0.1359:0.0:0.8641:0.0	.	567	O75151	PHF2_HUMAN	T	567	ENSP00000352185:A567T	.	A	+	1	0	PHF2	95465010	1.000000	0.71417	0.982000	0.44146	0.813000	0.45954	6.666000	0.74446	0.562000	0.29204	0.298000	0.19748	GCC		0.512	PHF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053162.1	NM_005392	Missense_Mutation
PTCH1	5727	broad.mit.edu	37	9	98278975	98278975	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr9:98278975C>T	ENST00000375274.2	-	1	272	c.128G>A	c.(127-129)gGa>gAa	p.G43E	PTCH1_ENST00000468211.2_5'UTR|RP11-435O5.4_ENST00000604650.1_RNA|PTCH1_ENST00000430669.2_5'UTR|PTCH1_ENST00000437951.1_5'UTR			Q13635	PTC1_HUMAN	patched 1	0					brain development (GO:0007420)|branching involved in ureteric bud morphogenesis (GO:0001658)|cell differentiation involved in kidney development (GO:0061005)|cell proliferation involved in metanephros development (GO:0072203)|cellular response to cholesterol (GO:0071397)|dorsal/ventral pattern formation (GO:0009953)|embryonic limb morphogenesis (GO:0030326)|embryonic organ development (GO:0048568)|epidermis development (GO:0008544)|glucose homeostasis (GO:0042593)|heart morphogenesis (GO:0003007)|hindlimb morphogenesis (GO:0035137)|in utero embryonic development (GO:0001701)|keratinocyte proliferation (GO:0043616)|limb morphogenesis (GO:0035108)|mammary gland duct morphogenesis (GO:0060603)|mammary gland epithelial cell differentiation (GO:0060644)|negative regulation of cell division (GO:0051782)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of multicellular organism growth (GO:0040015)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural plate axis specification (GO:0021997)|neural tube closure (GO:0001843)|neural tube patterning (GO:0021532)|organ morphogenesis (GO:0009887)|pharyngeal system development (GO:0060037)|positive regulation of cholesterol efflux (GO:0010875)|protein processing (GO:0016485)|protein targeting to plasma membrane (GO:0072661)|regulation of mitotic cell cycle (GO:0007346)|regulation of protein localization (GO:0032880)|regulation of smoothened signaling pathway (GO:0008589)|renal system development (GO:0072001)|response to chlorate (GO:0010157)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to mechanical stimulus (GO:0009612)|response to retinoic acid (GO:0032526)|smoothened signaling pathway (GO:0007224)|smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:0060831)|somite development (GO:0061053)|spinal cord motor neuron differentiation (GO:0021522)	axonal growth cone (GO:0044295)|caveola (GO:0005901)|dendritic growth cone (GO:0044294)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|midbody (GO:0030496)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|primary cilium (GO:0072372)	cholesterol binding (GO:0015485)|cyclin binding (GO:0030332)|hedgehog family protein binding (GO:0097108)|hedgehog receptor activity (GO:0008158)|heparin binding (GO:0008201)|smoothened binding (GO:0005119)	p.G43E(1)		NS(8)|bone(33)|breast(10)|central_nervous_system(95)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(8)|kidney(2)|large_intestine(18)|lung(22)|meninges(1)|oesophagus(3)|ovary(6)|prostate(2)|skin(262)|upper_aerodigestive_tract(11)|urinary_tract(2)|vulva(1)	490		Medulloblastoma(1;7.87e-06)|all_neural(1;0.000555)|Acute lymphoblastic leukemia(62;0.136)				ttcttcttctcctcctcctcc	0.567																																					p.G43E												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G128A	9						.						137.0	135.0	136.0					9																	98278975		1852	4088	5940	97318796	SO:0001583	missense	5727	exon1			AI494442	CCDS6714.1, CCDS43851.1, CCDS47995.1, CCDS47996.1	9q22.1-q31	2014-09-17	2010-06-24	2006-09-26	ENSG00000185920	ENSG00000185920			9585	protein-coding gene	gene with protein product		601309	"""patched (Drosophila) homolog"", ""patched homolog (Drosophila)"", ""patched homolog 1 (Drosophila)"""	NBCCS, PTCH		8658145	Standard	NM_001083603		Approved	BCNS	uc004avk.4	Q13635	OTTHUMG00000020280	ENST00000375274.2:c.128G>A	9.37:g.98278975C>T	ENSP00000364423:p.Gly43Glu	Somatic		Capture	Illumina HiSeq	Phase_I	97318796	NM_001083603	A3KBI9|E9PEJ8|Q13463|Q5R1U7|Q5R1U9|Q5R1V0|Q5VZC0|Q5VZC2|Q86XG7	Missense_Mutation	SNP	ENST00000375274.2	37	CCDS47995.1	.	.	.	.	.	.	.	.	.	.	c	8.074	0.770873	0.15983	.	.	ENSG00000185920	ENST00000375274	D	0.91351	-2.83	3.11	1.06	0.20224	.	.	.	.	.	T	0.80319	0.4601	.	.	.	0.80722	D	1	B	0.02656	0.0	B	0.01281	0.0	T	0.67760	-0.5587	8	0.26408	T	0.33	.	2.8576	0.05576	0.0:0.4867:0.2844:0.229	.	43	Q13635-2	.	E	43	ENSP00000364423:G43E	ENSP00000364423:G43E	G	-	2	0	PTCH1	97318796	0.200000	0.23398	0.983000	0.44433	0.415000	0.31203	0.606000	0.24194	0.575000	0.29434	0.479000	0.44913	GGA		0.567	PTCH1-007	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000406923.1	NM_000264	
ZNF367	195828	broad.mit.edu	37	9	99160583	99160583	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr9:99160583C>T	ENST00000375256.4	-	2	730	c.434G>A	c.(433-435)cGt>cAt	p.R145H		NM_153695.3	NP_710162.1	Q7RTV3	ZN367_HUMAN	zinc finger protein 367	145					regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.R145H(1)		cervix(1)|endometrium(4)|large_intestine(3)|lung(3)|prostate(1)	12		Acute lymphoblastic leukemia(62;0.0167)				GGGCCTACCACGTCGGATTCC	0.353																																					p.R145H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G434A	9						.						122.0	122.0	122.0					9																	99160583		2203	4300	6503	98200404	SO:0001583	missense	195828	exon2			AK091289	CCDS6718.1	9q22	2008-05-02			ENSG00000165244	ENSG00000165244		"""Zinc fingers, C2H2-type"""	18320	protein-coding gene	gene with protein product		610160					Standard	NM_153695		Approved	FLJ33970	uc004awf.3	Q7RTV3	OTTHUMG00000020295	ENST00000375256.4:c.434G>A	9.37:g.99160583C>T	ENSP00000364405:p.Arg145His	Somatic		Capture	Illumina HiSeq	Phase_I	98200404	NM_153695	Q6Q7C8	Missense_Mutation	SNP	ENST00000375256.4	37	CCDS6718.1	.	.	.	.	.	.	.	.	.	.	C	34	5.392068	0.95988	.	.	ENSG00000165244	ENST00000375256	T	0.07444	3.19	5.54	5.54	0.83059	.	0.000000	0.85682	D	0.000000	T	0.28200	0.0696	M	0.64997	1.995	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.996	T	0.00062	-1.2156	10	0.34782	T	0.22	-11.8595	19.6745	0.95926	0.0:1.0:0.0:0.0	.	145;145	Q7RTV3-2;Q7RTV3	.;ZN367_HUMAN	H	145	ENSP00000364405:R145H	ENSP00000364405:R145H	R	-	2	0	ZNF367	98200404	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.194000	0.77789	2.880000	0.98712	0.650000	0.86243	CGT		0.353	ZNF367-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053266.1		
CCDC180	100499483	broad.mit.edu	37	9	100139118	100139118	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr9:100139118A>G	ENST00000357054.1	+	49	5818	c.4883A>G	c.(4882-4884)cAg>cGg	p.Q1628R	RP11-23J9.4_ENST00000534123.1_RNA|CCDC180_ENST00000395220.1_3'UTR|CCDC180_ENST00000375202.2_Missense_Mutation_p.Q1683R|CCDC180_ENST00000529487.1_Missense_Mutation_p.Q1683R			Q9P1Z9	CC180_HUMAN	coiled-coil domain containing 180	1628						extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)		p.Q1628R(1)									AAGGAGGCTCAGCGCTGGAAG	0.493																																					p.Q1683R												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A5048G	9						.						119.0	103.0	108.0					9																	100139118		2203	4300	6503	99178939	SO:0001583	missense	57653	exon37			AK123391	CCDS35077.1, CCDS35077.2	9q22.33	2013-03-08	2013-03-08	2013-03-08		ENSG00000197816			29303	protein-coding gene	gene with protein product	"""Behcet's Disease Associated Gene 1"""		"""KIAA1529"", ""chromosome 9 open reading frame 174"""	KIAA1529, C9orf174		10819331	Standard	NM_020893		Approved	DKFZp434I2420, BDAG1	uc004axg.2	Q9P1Z9	OTTHUMG00000167001	ENST00000357054.1:c.4883A>G	9.37:g.100139118A>G	ENSP00000349562:p.Gln1628Arg	Somatic		Capture	Illumina HiSeq	Phase_I	99178939	NM_020893	Q2KHR6|Q5VV25|Q68DP5|Q69YV9|Q6AHY0	Missense_Mutation	SNP	ENST00000357054.1	37		.	.	.	.	.	.	.	.	.	.	A	8.605	0.887669	0.17540	.	.	ENSG00000197816	ENST00000357054;ENST00000375202;ENST00000529487	T;T;T	0.09445	3.0;2.98;2.98	3.99	2.82	0.32997	.	0.224065	0.32401	N	0.006160	T	0.10165	0.0249	L	0.45137	1.4	0.49299	D	0.999775	B;P	0.42518	0.119;0.782	B;B	0.41764	0.14;0.366	T	0.06991	-1.0796	10	0.62326	D	0.03	-5.0475	6.4898	0.22109	0.8894:0.0:0.1106:0.0	.	1822;1628	B7ZMG3;Q9P1Z9	.;CI174_HUMAN	R	1628;1683;1683	ENSP00000349562:Q1628R;ENSP00000364348:Q1683R;ENSP00000434727:Q1683R	ENSP00000349562:Q1628R	Q	+	2	0	C9orf174	99178939	0.968000	0.33430	0.628000	0.29241	0.225000	0.24961	1.399000	0.34566	0.846000	0.35142	0.533000	0.62120	CAG		0.493	CCDC180-201	KNOWN	basic	protein_coding	protein_coding		NM_020893	
CORO2A	7464	broad.mit.edu	37	9	100894473	100894473	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr9:100894473C>A	ENST00000343933.5	-	6	1016	c.759G>T	c.(757-759)tgG>tgT	p.W253C	CORO2A_ENST00000375077.4_Missense_Mutation_p.W253C	NM_003389.3	NP_003380.3	Q92828	COR2A_HUMAN	coronin, actin binding protein, 2A	253					actin cytoskeleton organization (GO:0030036)|intracellular signal transduction (GO:0035556)	actin cytoskeleton (GO:0015629)|transcriptional repressor complex (GO:0017053)	actin filament binding (GO:0051015)	p.W253C(1)		endometrium(2)|kidney(2)|large_intestine(8)|lung(7)|ovary(1)|pancreas(1)|skin(4)|urinary_tract(1)	26		Acute lymphoblastic leukemia(62;0.0559)				TCACCTGGTCCCACAAGGCCA	0.557																																					p.W253C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G759T	9						.						94.0	77.0	83.0					9																	100894473		2203	4300	6503	99934294	SO:0001583	missense	7464	exon6			U57057	CCDS6735.1	9q22.3	2013-01-10	2001-11-28		ENSG00000106789	ENSG00000106789		"""Coronins"", ""WD repeat domain containing"""	2255	protein-coding gene	gene with protein product	"""coronin 2A"", ""coronin-like protein B"", ""WD protein IR10"", ""WD-repeat protein 2"""	602159	"""coronin, actin-binding protein, 2A"""			8985118	Standard	NM_052820		Approved	IR10, WDR2	uc004aym.3	Q92828	OTTHUMG00000020340	ENST00000343933.5:c.759G>T	9.37:g.100894473C>A	ENSP00000343746:p.Trp253Cys	Somatic		Capture	Illumina HiSeq	Phase_I	99934294	NM_003389	Q5TBR5|Q92829|Q9BWS5	Missense_Mutation	SNP	ENST00000343933.5	37	CCDS6735.1	.	.	.	.	.	.	.	.	.	.	C	20.4	3.984734	0.74474	.	.	ENSG00000106789	ENST00000343933;ENST00000375077	T;T	0.11604	2.76;2.76	4.81	3.92	0.45320	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.000000	0.85682	D	0.000000	T	0.32164	0.0820	H	0.94808	3.585	0.80722	D	1	P	0.51653	0.947	P	0.50314	0.637	T	0.50101	-0.8867	10	0.87932	D	0	-7.7185	12.3435	0.55107	0.0:0.9161:0.0:0.0839	.	253	Q92828	COR2A_HUMAN	C	253	ENSP00000343746:W253C;ENSP00000364218:W253C	ENSP00000343746:W253C	W	-	3	0	CORO2A	99934294	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	7.556000	0.82233	1.381000	0.46364	0.655000	0.94253	TGG		0.557	CORO2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053357.1	NM_003389	
PNPLA7	375775	broad.mit.edu	37	9	140416114	140416114	+	Missense_Mutation	SNP	C	C	T	rs2298171		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chr9:140416114C>T	ENST00000277531.4	-	9	1042	c.856G>A	c.(856-858)Ggc>Agc	p.G286S	PNPLA7_ENST00000406427.1_Missense_Mutation_p.G311S	NM_152286.3	NP_689499.3	Q6ZV29	PLPL7_HUMAN	patatin-like phospholipase domain containing 7	286			G -> S (in dbSNP:rs2298171).		lipid metabolic process (GO:0006629)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	lysophospholipase activity (GO:0004622)	p.G286S(1)		breast(1)|central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(9)|lung(13)|ovary(1)|prostate(1)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	40	all_cancers(76;0.126)			OV - Ovarian serous cystadenocarcinoma(145;0.000268)|Epithelial(140;0.000839)		GTGGTCAGGCCGAGGTAGTTG	0.587																																					p.G286S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G856A	9						.						170.0	137.0	148.0					9																	140416114		2203	4300	6503	139535935	SO:0001583	missense	375775	exon9			AK126267	CCDS7045.1, CCDS48070.1	9q34.3	2009-01-12	2006-06-12	2006-06-12	ENSG00000130653	ENSG00000130653		"""Patatin-like phospholipase domain containing"""	24768	protein-coding gene	gene with protein product		612122	"""chromosome 9 open reading frame 111"""	C9orf111		16799181, 12640454, 19029121	Standard	XM_005266082		Approved	FLJ43070, FLJ31318, FLJ44279, RP11-48C7.2, NTEL1, NTE-R1	uc010ncj.1	Q6ZV29	OTTHUMG00000020990	ENST00000277531.4:c.856G>A	9.37:g.140416114C>T	ENSP00000277531:p.Gly286Ser	Somatic		Capture	Illumina HiSeq	Phase_I	139535935	NM_152286	B5MDD3|Q5T364|Q658X0|Q658Y3|Q6ZTS1|Q86YU8|Q8TAY5|Q96N75|Q9H7N5	Missense_Mutation	SNP	ENST00000277531.4	37	CCDS7045.1	.	.	.	.	.	.	.	.	.	.	C	27.4	4.825539	0.90955	.	.	ENSG00000130653	ENST00000371446;ENST00000277531;ENST00000406427;ENST00000371451;ENST00000434090;ENST00000371450	T;D;D;D	0.83163	0.11;-1.66;-1.69;-1.61	4.75	4.75	0.60458	.	0.000000	0.85682	D	0.000000	D	0.91243	0.7240	M	0.83953	2.67	0.35712	D	0.816438	D;D;D	0.89917	0.999;1.0;0.998	P;D;P	0.97110	0.77;1.0;0.738	D	0.94613	0.7806	10	0.62326	D	0.03	-23.9187	15.2427	0.73482	0.0:1.0:0.0:0.0	rs2298171;rs2298171	17;311;286	E2QRF8;Q6ZV29-5;Q6ZV29	.;.;PLPL7_HUMAN	S	17;286;311;286;277;311	ENSP00000360501:G17S;ENSP00000277531:G286S;ENSP00000384610:G311S;ENSP00000400582:G277S	ENSP00000277531:G286S	G	-	1	0	PNPLA7	139535935	1.000000	0.71417	1.000000	0.80357	0.676000	0.39594	7.078000	0.76821	2.176000	0.68965	0.313000	0.20887	GGC		0.587	PNPLA7-007	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000254787.1	NM_152286	
CXorf66	347487	broad.mit.edu	37	X	139038324	139038325	+	Frame_Shift_Ins	INS	-	-	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	-	-	-	T	-	-	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chrX:139038324_139038325insT	ENST00000370540.1	-	3	839_840	c.816_817insA	c.(814-819)aaacatfs	p.H273fs		NM_001013403.2	NP_001013421.1	Q5JRM2	CX066_HUMAN	chromosome X open reading frame 66	273						integral component of membrane (GO:0016021)		p.H273fs*8(1)		breast(1)|endometrium(2)|kidney(3)|large_intestine(5)|lung(13)|skin(1)|stomach(1)	26						GCAACAAGATGTTTTTTCTTGT	0.391																																					p.H273fs												.	.	1	Insertion - Frameshift(1)	large_intestine(1)	c.817_818insA	X						.																																			138865991	SO:0001589	frameshift_variant	347487	exon3				CCDS35411.1	Xq27.1	2014-05-30			ENSG00000203933	ENSG00000203933			33743	protein-coding gene	gene with protein product	"""secreted glycoprotein, X-linked"""					24709545	Standard	NM_001013403		Approved	RP11-35F15.2, SGPX	uc004fbb.3	Q5JRM2	OTTHUMG00000022539	ENST00000370540.1:c.817dupA	X.37:g.139038330_139038330dupT	ENSP00000359571:p.His273fs	Somatic		Capture	Illumina HiSeq	Phase_I	138865990	NM_001013403		Frame_Shift_Ins	INS	ENST00000370540.1	37	CCDS35411.1																																																																																				0.391	CXorf66-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058572.1	NM_001013403	
XKRX	402415	broad.mit.edu	37	X	100177878	100177878	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chrX:100177878G>A	ENST00000372956.2	-	2	1112	c.508C>T	c.(508-510)Cgt>Tgt	p.R170C	XKRX_ENST00000468904.1_Intron|XKRX_ENST00000328526.5_Missense_Mutation_p.R183C			Q6PP77	XKR2_HUMAN	XK, Kell blood group complex subunit-related, X-linked	170						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.R183C(1)		breast(1)|central_nervous_system(1)|endometrium(3)|large_intestine(4)|lung(8)|ovary(1)|prostate(1)|skin(3)	22						TGTGACATACGTTTGTAGGCA	0.557													G|||	1	0.000264901	0.0	0.0	3775	,	,		12784	0.0		0.0	False		,,,				2504	0.001				p.R170C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C508T	X						.						171.0	137.0	149.0					X																	100177878		2203	4300	6503	100064534	SO:0001583	missense	402415	exon2			AY589511	CCDS14476.1, CCDS14476.2	Xq22	2008-02-05	2006-01-12		ENSG00000182489	ENSG00000182489			29845	protein-coding gene	gene with protein product		300684	"""X Kell blood group precursor-related, X-linked"""				Standard	NM_212559		Approved	XPLAC, XKR2	uc004egn.2	Q6PP77	OTTHUMG00000022010	ENST00000372956.2:c.508C>T	X.37:g.100177878G>A	ENSP00000362047:p.Arg170Cys	Somatic		Capture	Illumina HiSeq	Phase_I	100064534	NM_212559	B2RNN6|B4DKU2|Q5H9J6	Missense_Mutation	SNP	ENST00000372956.2	37	CCDS14476.2	.	.	.	.	.	.	.	.	.	.	G	28.3	4.907624	0.92107	.	.	ENSG00000182489	ENST00000328526;ENST00000372956	T;T	0.64438	-0.1;-0.1	5.9	5.9	0.94986	.	0.000000	0.85682	D	0.000000	T	0.78723	0.4328	M	0.69358	2.11	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.79393	-0.1822	10	0.59425	D	0.04	-6.4111	18.0826	0.89445	0.0:0.0:1.0:0.0	.	170	Q6PP77	XKR2_HUMAN	C	183;170	ENSP00000327570:R183C;ENSP00000362047:R170C	ENSP00000327570:R183C	R	-	1	0	XKRX	100064534	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.338000	0.59316	2.493000	0.84123	0.600000	0.82982	CGT		0.557	XKRX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057501.3	NM_212559	
GLRA4	441509	broad.mit.edu	37	X	102974002	102974002	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chrX:102974002G>A	ENST00000372617.4	-	7	1336	c.916C>T	c.(916-918)Cgg>Tgg	p.R306W	GLRA4_ENST00000469567.1_5'Flank	NM_001024452.2	NP_001019623.2	Q5JXX5	GLRA4_HUMAN	glycine receptor, alpha 4	306						cell junction (GO:0030054)|chloride channel complex (GO:0034707)|integral component of plasma membrane (GO:0005887)|postsynaptic membrane (GO:0045211)	chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|glycine binding (GO:0016594)|transmitter-gated ion channel activity (GO:0022824)	p.R306W(1)		cervix(1)|endometrium(2)|large_intestine(2)|lung(13)|upper_aerodigestive_tract(2)|urinary_tract(1)	21						AAAGAGGCCCGGGAGCCAGAG	0.577																																					p.R306W												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C916T	X						.						66.0	71.0	70.0					X																	102974002		2203	4298	6501	102860658	SO:0001583	missense	441509	exon7			Z93848	CCDS43980.2	Xq22.2	2012-01-16			ENSG00000188828	ENSG00000188828		"""Ligand-gated ion channels / Glycine receptors"""	31715	protein-coding gene	gene with protein product							Standard	NM_001024452		Approved		uc011mse.2	Q5JXX5	OTTHUMG00000022110	ENST00000372617.4:c.916C>T	X.37:g.102974002G>A	ENSP00000361700:p.Arg306Trp	Somatic		Capture	Illumina HiSeq	Phase_I	102860658	NM_001172285		Missense_Mutation	SNP	ENST00000372617.4	37	CCDS43980.2	.	.	.	.	.	.	.	.	.	.	G	19.92	3.916131	0.73098	.	.	ENSG00000188828	ENST00000372617	D	0.86956	-2.19	5.75	4.86	0.63082	Neurotransmitter-gated ion-channel transmembrane domain (2);	0.000000	0.85682	D	0.000000	D	0.93959	0.8066	M	0.88310	2.945	0.52501	D	0.99995	D;D	0.89917	1.0;1.0	D;D	0.83275	0.996;0.992	D	0.94509	0.7717	10	0.87932	D	0	.	12.715	0.57109	0.0:0.0:0.8304:0.1696	.	306;265	Q5JXX5;B9WSA6	GLRA4_HUMAN;.	W	306	ENSP00000361700:R306W	ENSP00000361700:R306W	R	-	1	2	GLRA4	102860658	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.089000	0.64492	1.255000	0.44051	0.600000	0.82982	CGG		0.577	GLRA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057742.2	NM_001024452	
TEX13B	56156	broad.mit.edu	37	X	107225261	107225261	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chrX:107225261C>T	ENST00000302917.1	-	2	189	c.97G>A	c.(97-99)Gag>Aag	p.E33K		NM_031273.2	NP_112563.1	Q9BXU2	TX13B_HUMAN	testis expressed 13B	33								p.E33K(1)		breast(1)|endometrium(5)|large_intestine(4)|lung(13)|ovary(1)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(1)	28						AAGTAGAACTCGGGGCCTTTC	0.572																																					p.E33K												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G97A	X						.						102.0	90.0	94.0					X																	107225261		2198	4300	6498	107111917	SO:0001583	missense	56156	exon2			AF285598	CCDS14534.1	Xq23	2008-02-05	2007-03-13		ENSG00000170925	ENSG00000170925			11736	protein-coding gene	gene with protein product		300313	"""testis expressed sequence 13B"""			11279525	Standard	NM_031273		Approved	TSGA5, TGC3B	uc004enn.1	Q9BXU2	OTTHUMG00000022174	ENST00000302917.1:c.97G>A	X.37:g.107225261C>T	ENSP00000303777:p.Glu33Lys	Somatic		Capture	Illumina HiSeq	Phase_I	107111917	NM_031273	Q5JYF6	Missense_Mutation	SNP	ENST00000302917.1	37	CCDS14534.1	.	.	.	.	.	.	.	.	.	.	C	12.42	1.932347	0.34096	.	.	ENSG00000170925	ENST00000302917	.	.	.	2.72	0.923	0.19413	.	.	.	.	.	T	0.24509	0.0594	L	0.55213	1.73	0.09310	N	1	P	0.49090	0.919	B	0.34489	0.184	T	0.17167	-1.0378	8	0.49607	T	0.09	.	4.3878	0.11325	0.0:0.654:0.0:0.346	.	33	Q9BXU2	TX13B_HUMAN	K	33	.	ENSP00000303777:E33K	E	-	1	0	TEX13B	107111917	0.008000	0.16893	0.161000	0.22692	0.061000	0.15899	-0.029000	0.12329	0.129000	0.18514	0.519000	0.50382	GAG		0.572	TEX13B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057857.1		
COL4A6	1288	broad.mit.edu	37	X	107418399	107418399	+	Silent	SNP	A	A	G			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chrX:107418399A>G	ENST00000372216.4	-	30	2980	c.2880T>C	c.(2878-2880)cgT>cgC	p.R960R	COL4A6_ENST00000545689.1_Silent_p.R959R|COL4A6_ENST00000538570.1_Silent_p.R959R|COL4A6_ENST00000334504.7_Silent_p.R959R|COL4A6_ENST00000394872.2_Silent_p.R960R	NM_001847.2	NP_001838.2	Q14031	CO4A6_HUMAN	collagen, type IV, alpha 6	960	Triple-helical region.				cell adhesion (GO:0007155)|cellular response to amino acid stimulus (GO:0071230)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)	collagen type IV trimer (GO:0005587)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)	extracellular matrix structural constituent (GO:0005201)	p.R959R(1)		breast(2)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(20)|lung(41)|ovary(7)|prostate(1)|skin(1)|stomach(1)|urinary_tract(2)	92						TTGACATTGGACGTCTTGGAC	0.552									Alport syndrome with Diffuse Leiomyomatosis																												p.R959R	Melanoma(87;1895 1945 2589 7165)											.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.T2877C	X						.						200.0	177.0	185.0					X																	107418399		2203	4300	6503	107305055	SO:0001819	synonymous_variant	1288	exon30	Familial Cancer Database		U04845	CCDS14541.1, CCDS14542.1, CCDS76008.1, CCDS76009.1, CCDS76010.1	Xq22	2014-09-17			ENSG00000197565	ENSG00000197565		"""Collagens"""	2208	protein-coding gene	gene with protein product		303631				8356449	Standard	NM_033641		Approved		uc004env.4	Q14031	OTTHUMG00000022179	ENST00000372216.4:c.2880T>C	X.37:g.107418399A>G		Somatic		Capture	Illumina HiSeq	Phase_I	107305055	NM_033641	Q12823|Q14053|Q5JYH6|Q5JYH8|Q9NQM5|Q9NTX3|Q9UJ76|Q9UMG6|Q9Y4L4	Silent	SNP	ENST00000372216.4	37	CCDS14541.1																																																																																				0.552	COL4A6-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000057875.2		
KLHL13	90293	broad.mit.edu	37	X	117043552	117043552	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chrX:117043552G>A	ENST00000262820.3	-	5	1987	c.1078C>T	c.(1078-1080)Cgc>Tgc	p.R360C	KLHL13_ENST00000371882.1_Missense_Mutation_p.R309C|KLHL13_ENST00000469946.1_Missense_Mutation_p.R309C|KLHL13_ENST00000540167.1_Missense_Mutation_p.R344C|KLHL13_ENST00000371878.1_Missense_Mutation_p.R309C|KLHL13_ENST00000541812.1_Missense_Mutation_p.R344C|KLHL13_ENST00000539496.1_Missense_Mutation_p.R363C|KLHL13_ENST00000371876.1_Missense_Mutation_p.R309C|KLHL13_ENST00000545703.1_Missense_Mutation_p.R318C	NM_033495.3	NP_277030.2	Q9P2N7	KLH13_HUMAN	kelch-like family member 13	360					cytokinesis (GO:0000910)|mitotic nuclear division (GO:0007067)|protein ubiquitination (GO:0016567)	Cul3-RING ubiquitin ligase complex (GO:0031463)		p.R360C(1)		NS(1)|breast(3)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(6)|lung(9)|prostate(2)|skin(3)|stomach(1)|urinary_tract(1)	34						TCATACATGCGCAATTCCTTA	0.498																																					p.R354C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1060T	X						.						107.0	93.0	98.0					X																	117043552		2203	4300	6503	116927580	SO:0001583	missense	90293	exon5			AB037730	CCDS14571.1, CCDS55479.1, CCDS55480.1, CCDS55481.1	Xq23-q24	2013-01-30	2013-01-30	2004-02-18	ENSG00000003096	ENSG00000003096		"""Kelch-like"", ""BTB/POZ domain containing"""	22931	protein-coding gene	gene with protein product		300655	"""BTB and kelch domain containing 2, KIAA1309"", ""kelch-like 13 (Drosophila)"""	BKLHD2, KIAA1309		10718198	Standard	NM_033495		Approved	FLJ10262	uc011mtp.2	Q9P2N7	OTTHUMG00000022252	ENST00000262820.3:c.1078C>T	X.37:g.117043552G>A	ENSP00000262820:p.Arg360Cys	Somatic		Capture	Illumina HiSeq	Phase_I	116927580	NM_001168300	B3KV78|B3KWM7|B7Z3S9|B7Z5P2|B7Z802|D3DWH6|Q6P2E3|Q96QI7|Q9UDN9	Missense_Mutation	SNP	ENST00000262820.3	37	CCDS14571.1	.	.	.	.	.	.	.	.	.	.	G	15.92	2.974696	0.53720	.	.	ENSG00000003096	ENST00000371882;ENST00000371876;ENST00000371878;ENST00000447671;ENST00000541812;ENST00000540167;ENST00000539496;ENST00000262820;ENST00000545703;ENST00000469946	T;T;T;T;T;T;T;T;T;T	0.66460	-0.21;-0.21;-0.21;-0.21;-0.21;-0.21;-0.21;-0.21;-0.21;-0.21	4.88	3.94	0.45596	Galactose oxidase, beta-propeller (1);	0.000000	0.85682	D	0.000000	T	0.73087	0.3542	L	0.43152	1.355	0.80722	D	1	D;D;D;D	0.89917	0.995;1.0;0.996;0.992	P;D;P;P	0.65874	0.862;0.939;0.862;0.731	T	0.75929	-0.3144	10	0.72032	D	0.01	.	12.8816	0.58020	0.0:0.0:0.7503:0.2497	.	344;363;354;360	Q9P2N7-3;Q9P2N7-5;Q9P2N7-4;Q9P2N7	.;.;.;KLH13_HUMAN	C	309;309;309;309;344;344;363;360;318;309	ENSP00000360949:R309C;ENSP00000360943:R309C;ENSP00000360945:R309C;ENSP00000412640:R309C;ENSP00000444450:R344C;ENSP00000441029:R344C;ENSP00000443191:R363C;ENSP00000262820:R360C;ENSP00000440707:R318C;ENSP00000419803:R309C	ENSP00000262820:R360C	R	-	1	0	KLHL13	116927580	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.243000	0.65395	2.233000	0.73108	0.594000	0.82650	CGC		0.498	KLHL13-201	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_033495	
NKRF	55922	broad.mit.edu	37	X	118724000	118724000	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chrX:118724000C>T	ENST00000371527.1	-	2	2040	c.1388G>A	c.(1387-1389)cGa>cAa	p.R463Q	NKRF_ENST00000542113.1_Missense_Mutation_p.R478Q|NKRF_ENST00000304449.5_Missense_Mutation_p.R463Q|NKRF_ENST00000487600.1_Intron	NM_001173488.1	NP_001166959.1	O15226	NKRF_HUMAN	NFKB repressing factor	463					negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)	p.R463Q(1)		breast(1)|central_nervous_system(1)|endometrium(8)|kidney(3)|large_intestine(2)|lung(9)|ovary(1)|prostate(3)|skin(1)|urinary_tract(1)	30						AACTGTCATTCGGTTAAACTG	0.433																																					p.R478Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1433A	X						.						102.0	97.0	99.0					X																	118724000		2203	4300	6503	118608028	SO:0001583	missense	55922	exon4			AJ011812	CCDS35375.1, CCDS55486.1	Xq24	2013-01-28	2008-03-26		ENSG00000186416	ENSG00000186416		"""G patch domain containing"""	19374	protein-coding gene	gene with protein product		300440	"""NF-kappaB repressing factor"""			10562553	Standard	NM_017544		Approved	ITBA4, NRF	uc022cdk.1	O15226	OTTHUMG00000022277	ENST00000371527.1:c.1388G>A	X.37:g.118724000C>T	ENSP00000360582:p.Arg463Gln	Somatic		Capture	Illumina HiSeq	Phase_I	118608028	NM_001173487	G3V1N1|Q4VC41|Q9UJ91	Missense_Mutation	SNP	ENST00000371527.1	37	CCDS35375.1	.	.	.	.	.	.	.	.	.	.	C	12.82	2.051841	0.36181	.	.	ENSG00000186416	ENST00000371527;ENST00000304449;ENST00000542113	T;T;T	0.77358	-1.09;-1.09;-1.09	5.49	4.44	0.53790	Double-stranded RNA-binding (1);Double-stranded RNA-binding-like (1);	0.155495	0.56097	D	0.000034	T	0.58278	0.2111	L	0.38175	1.15	0.34670	D	0.723608	P	0.41643	0.758	B	0.24394	0.053	T	0.70528	-0.4847	10	0.52906	T	0.07	-9.7234	6.1956	0.20548	0.0:0.7224:0.0:0.2776	.	463	O15226	NKRF_HUMAN	Q	463;463;478	ENSP00000360582:R463Q;ENSP00000304803:R463Q;ENSP00000442308:R478Q	ENSP00000304803:R463Q	R	-	2	0	NKRF	118608028	1.000000	0.71417	0.990000	0.47175	0.998000	0.95712	4.755000	0.62198	2.298000	0.77334	0.600000	0.82982	CGA		0.433	NKRF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058044.1	NM_017544	
ZBTB33	10009	broad.mit.edu	37	X	119387935	119387935	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chrX:119387935G>A	ENST00000326624.2	+	2	893	c.665G>A	c.(664-666)gGc>gAc	p.G222D	ZBTB33_ENST00000557385.1_Missense_Mutation_p.G222D	NM_006777.3	NP_006768.1	Q86T24	KAISO_HUMAN	zinc finger and BTB domain containing 33	222					intracellular signal transduction (GO:0035556)|negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|methyl-CpG binding (GO:0008327)|sequence-specific DNA binding (GO:0043565)	p.G222D(1)		breast(2)|central_nervous_system(2)|endometrium(6)|large_intestine(6)|lung(5)|ovary(2)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)	26						TCTAACCCAGGCCCTGTTGCT	0.448																																					p.G222D												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G665A	X						.						75.0	66.0	69.0					X																	119387935		2203	4300	6503	119271963	SO:0001583	missense	10009	exon2			BC042753	CCDS14596.1	Xq23	2013-01-09			ENSG00000177485	ENSG00000177485		"""-"", ""BTB/POZ domain containing"", ""Zinc fingers, C2H2-type"""	16682	protein-coding gene	gene with protein product		300329					Standard	NM_001184742		Approved	ZNF-kaiso, kaiso, WUGSC:H_DJ525N14.1, KAISO, ZNF348	uc004esn.1	Q86T24	OTTHUMG00000171159	ENST00000326624.2:c.665G>A	X.37:g.119387935G>A	ENSP00000314153:p.Gly222Asp	Somatic		Capture	Illumina HiSeq	Phase_I	119271963	NM_006777	B2R5U6|O00319|Q7Z361|Q8IVP6|Q8N3P0	Missense_Mutation	SNP	ENST00000326624.2	37	CCDS14596.1	.	.	.	.	.	.	.	.	.	.	G	0.380	-0.929425	0.02359	.	.	ENSG00000177485;ENSG00000177485;ENSG00000258974	ENST00000326624;ENST00000540105;ENST00000557385	T;T	0.09350	2.99;2.99	5.66	1.63	0.23807	.	0.609580	0.18362	N	0.143550	T	0.02848	0.0085	N	0.02539	-0.55	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.42241	-0.9463	10	0.12766	T	0.61	-0.9247	1.903	0.03271	0.2228:0.26:0.3878:0.1294	.	222	Q86T24	KAISO_HUMAN	D	222	ENSP00000314153:G222D;ENSP00000450969:G222D	ENSP00000314153:G222D	G	+	2	0	ZBTB33;AC002086.1	119271963	0.405000	0.25336	0.526000	0.27913	0.838000	0.47535	0.477000	0.22196	0.627000	0.30340	0.594000	0.82650	GGC		0.448	ZBTB33-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058085.2	NM_006777	
UTP14A	10813	broad.mit.edu	37	X	129045802	129045802	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	G	G	G	Unknown	Wildtype	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chrX:129045802G>A	ENST00000394422.3	+	6	470	c.442G>A	c.(442-444)Gtc>Atc	p.V148I	RP4-537K23.4_ENST00000432062.1_RNA|UTP14A_ENST00000371051.5_Missense_Mutation_p.V94I|UTP14A_ENST00000371042.3_5'Flank|UTP14A_ENST00000425117.2_Intron	NM_006649.3	NP_006640.2	Q9BVJ6	UT14A_HUMAN	UTP14, U3 small nucleolar ribonucleoprotein, homolog A (yeast)	148					rRNA processing (GO:0006364)	nucleus (GO:0005634)|small-subunit processome (GO:0032040)	poly(A) RNA binding (GO:0044822)	p.V148I(1)		breast(1)|endometrium(1)|kidney(2)|large_intestine(6)|liver(2)|lung(16)|ovary(3)|urinary_tract(1)	32						GGACCCTGTCGTCCTGAAGAA	0.522													g|||	1	0.000264901	0.0008	0.0	3775	,	,		12137	0.0		0.0	False		,,,				2504	0.0				p.V148I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G442A	X						.						102.0	97.0	99.0					X																	129045802		2203	4300	6503	128873483	SO:0001583	missense	10813	exon6			AF039694	CCDS14615.1, CCDS55489.1	Xq26.1	2009-01-15	2004-06-01	2004-06-01	ENSG00000156697	ENSG00000156697			10665	protein-coding gene	gene with protein product		300508	"""serologically defined colon cancer antigen 16"""	SDCCAG16		9610721, 16354793	Standard	NM_006649		Approved	NY-CO-16	uc004euz.3	Q9BVJ6	OTTHUMG00000022378	ENST00000394422.3:c.442G>A	X.37:g.129045802G>A	ENSP00000377944:p.Val148Ile	None		Capture	Illumina HiSeq	Phase_I	128873483	NM_006649	A8K7A3|A8MVQ1|B4DQ08|E9PEL7|Q5JYF1	Missense_Mutation	SNP	ENST00000394422.3	37	CCDS14615.1	.	.	.	.	.	.	.	.	.	.	G	5.130	0.209647	0.09757	.	.	ENSG00000156697	ENST00000394422;ENST00000371051	T;T	0.32988	1.43;1.43	5.43	3.68	0.42216	.	0.232409	0.44483	N	0.000459	T	0.25717	0.0626	L	0.45352	1.415	0.24440	N	0.99453	B;B	0.22800	0.061;0.075	B;B	0.17433	0.011;0.018	T	0.13045	-1.0524	10	0.36615	T	0.2	-2.353	11.6822	0.51463	0.1484:0.0:0.8516:0.0	.	94;148	F8WD00;Q9BVJ6	.;UT14A_HUMAN	I	148;94	ENSP00000377944:V148I;ENSP00000360090:V94I	ENSP00000360090:V94I	V	+	1	0	UTP14A	128873483	1.000000	0.71417	0.003000	0.11579	0.072000	0.16883	3.340000	0.52143	0.496000	0.27904	-0.465000	0.05216	GTC		0.522	UTP14A-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058221.1	NM_006649	
GPC3	2719	broad.mit.edu	37	X	132833959	132833959	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chrX:132833959T>C	ENST00000370818.3	-	4	1575	c.1130A>G	c.(1129-1131)cAt>cGt	p.H377R	GPC3_ENST00000543339.1_Missense_Mutation_p.H323R|GPC3_ENST00000394299.2_Missense_Mutation_p.H400R	NM_001164618.1|NM_004484.3	NP_001158090.1|NP_004475.1	P51654	GPC3_HUMAN	glypican 3	377					anatomical structure morphogenesis (GO:0009653)|anterior/posterior axis specification (GO:0009948)|body morphogenesis (GO:0010171)|bone mineralization (GO:0030282)|branching involved in ureteric bud morphogenesis (GO:0001658)|carbohydrate metabolic process (GO:0005975)|cell proliferation involved in metanephros development (GO:0072203)|chondroitin sulfate metabolic process (GO:0030204)|coronary vasculature development (GO:0060976)|embryonic hindlimb morphogenesis (GO:0035116)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|lung development (GO:0030324)|mesenchymal cell proliferation involved in ureteric bud development (GO:0072138)|mesonephric duct morphogenesis (GO:0072180)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of growth (GO:0045926)|negative regulation of smoothened signaling pathway (GO:0045879)|osteoclast differentiation (GO:0030316)|phototransduction, visible light (GO:0007603)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of endocytosis (GO:0045807)|positive regulation of glucose import (GO:0046326)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of smoothened signaling pathway (GO:0045880)|positive regulation of Wnt signaling pathway, planar cell polarity pathway (GO:2000096)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)	anchored component of plasma membrane (GO:0046658)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|lysosomal lumen (GO:0043202)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)	peptidyl-dipeptidase inhibitor activity (GO:0060422)	p.H377R(1)		breast(1)|endometrium(4)|kidney(3)|large_intestine(8)|lung(17)|prostate(1)|skin(2)	36	Acute lymphoblastic leukemia(192;0.000127)					ATGTTCTACATGAGCAACTTT	0.338			"""T, D, Mis, N, F, S"""			Wilms tumour			Simpson-Golabi-Behmel syndrome																												p.H361R		yes	Rec/X		Simpson-Golabi-Behmel syndrome	X	Xq26.1	2719	glypican 3		O	.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A1082G	X						.						64.0	57.0	59.0					X																	132833959		2203	4298	6501	132661625	SO:0001583	missense	2719	exon4	Familial Cancer Database	SGBS	L47125	CCDS14638.1, CCDS55496.1	Xq26	2014-09-17			ENSG00000147257	ENSG00000147257		"""Proteoglycans / Cell Surface : Glypicans"""	4451	protein-coding gene	gene with protein product	"""glypican proteoglycan 3"""	300037		SDYS		8589713, 9787072	Standard	NM_004484		Approved	OCI-5, SGBS, SGBS1, SGB, DGSX	uc010nrn.2	P51654	OTTHUMG00000022448	ENST00000370818.3:c.1130A>G	X.37:g.132833959T>C	ENSP00000359854:p.His377Arg	Somatic		Capture	Illumina HiSeq	Phase_I	132661625	NM_001164618	C9JLE3|G3V1R0|Q2L880|Q2L882	Missense_Mutation	SNP	ENST00000370818.3	37	CCDS14638.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	t|t	4.318|4.318	0.058316|0.058316	0.08339|0.08339	.|.	.|.	ENSG00000147257|ENSG00000147257	ENST00000370818;ENST00000394299;ENST00000543339|ENST00000406757	T;T;T|.	0.48522|.	0.81;0.81;0.81|.	5.29|5.29	-1.9|-1.9	0.07665|0.07665	.|.	0.622737|.	0.16754|.	N|.	0.200927|.	T|T	0.34395|0.34395	0.0896|0.0896	L|L	0.47716|0.47716	1.5|1.5	0.26488|0.26488	N|N	0.97499|0.97499	B;B;B;B|.	0.06786|.	0.0;0.0;0.0;0.001|.	B;B;B;B|.	0.11329|.	0.001;0.001;0.001;0.006|.	T|T	0.33777|0.33777	-0.9855|-0.9855	10|5	0.18276|.	T|.	0.48|.	.|.	5.2139|5.2139	0.15332|0.15332	0.1226:0.2886:0.0:0.5888|0.1226:0.2886:0.0:0.5888	.|.	361;323;400;377|.	B4DTD8;G3V1R0;C9JLE3;P51654|.	.;.;.;GPC3_HUMAN|.	R|V	377;400;323|107	ENSP00000359854:H377R;ENSP00000377836:H400R;ENSP00000444222:H323R|.	ENSP00000359854:H377R|.	H|M	-|-	2|1	0|0	GPC3|GPC3	132661625|132661625	0.904000|0.904000	0.30761|0.30761	0.976000|0.976000	0.42696|0.42696	0.822000|0.822000	0.46500|0.46500	-0.221000|-0.221000	0.09202|0.09202	-0.804000|-0.804000	0.04410|0.04410	-2.089000|-2.089000	0.00373|0.00373	CAT|ATG		0.338	GPC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058356.1	NM_004484	
HPRT1	3251	broad.mit.edu	37	X	133609219	133609219	+	Missense_Mutation	SNP	G	G	A	rs387906725		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chrX:133609219G>A	ENST00000298556.7	+	3	302	c.143G>A	c.(142-144)cGt>cAt	p.R48H	HPRT1_ENST00000462974.1_3'UTR	NM_000194.2	NP_000185.1	P00492	HPRT_HUMAN	hypoxanthine phosphoribosyltransferase 1	48			R -> H (in GOUT-HPRT; AD and DD).		adenine salvage (GO:0006168)|central nervous system neuron development (GO:0021954)|cerebral cortex neuron differentiation (GO:0021895)|cytolysis (GO:0019835)|dendrite morphogenesis (GO:0048813)|dopamine metabolic process (GO:0042417)|GMP catabolic process (GO:0046038)|GMP salvage (GO:0032263)|grooming behavior (GO:0007625)|guanine salvage (GO:0006178)|hypoxanthine metabolic process (GO:0046100)|hypoxanthine salvage (GO:0043103)|IMP metabolic process (GO:0046040)|IMP salvage (GO:0032264)|locomotory behavior (GO:0007626)|lymphocyte proliferation (GO:0046651)|nucleobase-containing small molecule metabolic process (GO:0055086)|positive regulation of dopamine metabolic process (GO:0045964)|protein homotetramerization (GO:0051289)|purine nucleobase metabolic process (GO:0006144)|purine nucleotide biosynthetic process (GO:0006164)|purine ribonucleoside salvage (GO:0006166)|purine-containing compound salvage (GO:0043101)|response to amphetamine (GO:0001975)|small molecule metabolic process (GO:0044281)|striatum development (GO:0021756)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	guanine phosphoribosyltransferase activity (GO:0052657)|hypoxanthine phosphoribosyltransferase activity (GO:0004422)|magnesium ion binding (GO:0000287)|nucleotide binding (GO:0000166)|protein homodimerization activity (GO:0042803)	p.R48H(1)		breast(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(3)	9	Acute lymphoblastic leukemia(192;0.000127)				Azathioprine(DB00993)|Mercaptopurine(DB01033)|Tioguanine(DB00352)	AGGACTGAACGTCTTGCTCGA	0.403																																					p.R48H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G143A	X	GRCh37	CM920351	HPRT1	M		.						68.0	60.0	63.0					X																	133609219		2203	4300	6503	133436885	SO:0001583	missense	3251	exon3			M26434	CCDS14641.1	Xq26.2	2012-10-02	2008-08-01		ENSG00000165704	ENSG00000165704	2.4.2.8		5157	protein-coding gene	gene with protein product	"""Lesch-Nyhan syndrome"""	308000		HPRT		12175903	Standard	NM_000194		Approved	HGPRT	uc004exl.4	P00492	OTTHUMG00000022452	ENST00000298556.7:c.143G>A	X.37:g.133609219G>A	ENSP00000298556:p.Arg48His	Somatic		Capture	Illumina HiSeq	Phase_I	133436885	NM_000194	A6NHF0|B2R8M9	Missense_Mutation	SNP	ENST00000298556.7	37	CCDS14641.1	.	.	.	.	.	.	.	.	.	.	G	25.8	4.678851	0.88542	.	.	ENSG00000165704	ENST00000298556;ENST00000370796	D	0.99864	-7.28	4.68	4.68	0.58851	Phosphoribosyltransferase (1);	0.051480	0.64402	D	0.000001	D	0.99819	0.9920	M	0.76838	2.35	0.80722	D	1	D	0.89917	1.0	D	0.71414	0.973	D	0.96459	0.9340	10	0.87932	D	0	-3.8816	16.0028	0.80308	0.0:0.0:1.0:0.0	.	48	P00492	HPRT_HUMAN	H	48	ENSP00000298556:R48H	ENSP00000298556:R48H	R	+	2	0	HPRT1	133436885	1.000000	0.71417	0.710000	0.30468	0.977000	0.68977	9.378000	0.97191	2.057000	0.61298	0.600000	0.82982	CGT		0.403	HPRT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058361.1	NM_000194	
SAGE1	55511	broad.mit.edu	37	X	134988659	134988659	+	Missense_Mutation	SNP	C	C	T	rs181135819		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chrX:134988659C>T	ENST00000370709.3	+	6	685	c.685C>T	c.(685-687)Cgt>Tgt	p.R229C	SAGE1_ENST00000537770.1_Intron|SAGE1_ENST00000324447.3_Missense_Mutation_p.R229C|SAGE1_ENST00000535938.1_Missense_Mutation_p.R229C			Q9NXZ1	SAGE1_HUMAN	sarcoma antigen 1	229						nucleus (GO:0005634)		p.R229C(2)		breast(5)|endometrium(5)|large_intestine(10)|lung(23)|ovary(3)|pancreas(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	55	Acute lymphoblastic leukemia(192;0.000127)					TCGACCACGGCGTATTAATAT	0.418													c|||	1	0.000264901	0.0008	0.0	3775	,	,		19682	0.0		0.0	False		,,,				2504	0.0				p.R229C												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.C685T	X						.						192.0	162.0	172.0					X																	134988659		2203	4300	6503	134816325	SO:0001583	missense	55511	exon7			AJ278111	CCDS14652.1	Xq26	2009-03-25			ENSG00000181433	ENSG00000181433			30369	protein-coding gene	gene with protein product	"""cancer/testis antigen 14"""	300359				10919659	Standard	NM_018666		Approved	SAGE, CT14	uc004ezh.3	Q9NXZ1	OTTHUMG00000022496	ENST00000370709.3:c.685C>T	X.37:g.134988659C>T	ENSP00000359743:p.Arg229Cys	Somatic		Capture	Illumina HiSeq	Phase_I	134816325	NM_018666	Q5JNW0	Missense_Mutation	SNP	ENST00000370709.3	37	CCDS14652.1	1	6.027727546714888E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	C	11.59	1.684607	0.29872	.	.	ENSG00000181433	ENST00000324447;ENST00000535938;ENST00000370709	T;T;T	0.34072	1.38;1.38;1.38	1.18	-0.896	0.10557	.	.	.	.	.	T	0.23054	0.0557	N	0.08118	0	0.09310	N	1	D	0.69078	0.997	P	0.51999	0.687	T	0.11518	-1.0584	9	0.51188	T	0.08	.	3.8932	0.09128	0.0:0.4601:0.0:0.5399	.	229	Q9NXZ1	SAGE1_HUMAN	C	229	ENSP00000323191:R229C;ENSP00000445959:R229C;ENSP00000359743:R229C	ENSP00000323191:R229C	R	+	1	0	SAGE1	134816325	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.545000	0.06069	-0.421000	0.07416	0.287000	0.19450	CGT		0.418	SAGE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058448.1	NM_018666	
ARHGEF6	9459	broad.mit.edu	37	X	135764963	135764963	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chrX:135764963A>G	ENST00000250617.6	-	13	2638	c.1433T>C	c.(1432-1434)cTg>cCg	p.L478P	ARHGEF6_ENST00000370622.1_Missense_Mutation_p.L324P|ARHGEF6_ENST00000535227.1_Missense_Mutation_p.L351P|ARHGEF6_ENST00000370620.1_Missense_Mutation_p.L324P	NM_004840.2	NP_004831.1	Q15052	ARHG6_HUMAN	Rac/Cdc42 guanine nucleotide exchange factor (GEF) 6	478	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|cell junction assembly (GO:0034329)|JNK cascade (GO:0007254)|lamellipodium assembly (GO:0030032)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cell-cell junction (GO:0005911)|cytosol (GO:0005829)|intracellular (GO:0005622)|lamellipodium (GO:0030027)	GTPase activator activity (GO:0005096)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)	p.L478P(1)		cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(12)|liver(1)|lung(14)|prostate(1)	38	Acute lymphoblastic leukemia(192;0.000127)					TAACATTATCAGGACATTTGA	0.363																																					p.L478P												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T1433C	X						.						124.0	107.0	112.0					X																	135764963		2203	4300	6503	135592629	SO:0001583	missense	9459	exon13			D13631	CCDS14660.1	Xq26	2013-01-10	2002-05-23		ENSG00000129675	ENSG00000129675		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	685	protein-coding gene	gene with protein product	"""Rac/Cdc42 guanine exchange factor (GEF) 6"", ""PAK-interacting exchange factor, alpha"", ""rho guanine nucleotide exchange factor 6"""	300267	"""mental retardation, X-linked 46"""	MRX46		7584048, 9659915	Standard	NM_004840		Approved	alphaPIX, Cool-2, KIAA0006, alpha-PIX, Cool2	uc004fab.3	Q15052	OTTHUMG00000022518	ENST00000250617.6:c.1433T>C	X.37:g.135764963A>G	ENSP00000250617:p.Leu478Pro	Somatic		Capture	Illumina HiSeq	Phase_I	135592629	NM_004840	A6NMW9|A8K6S7|B1AL37|Q15396|Q5JQ66|Q7Z3W1|Q86XH0	Missense_Mutation	SNP	ENST00000250617.6	37	CCDS14660.1	.	.	.	.	.	.	.	.	.	.	A	19.85	3.903147	0.72754	.	.	ENSG00000129675	ENST00000250617;ENST00000370620;ENST00000370622;ENST00000535736;ENST00000535227	T;T;T;T	0.70869	-0.52;-0.52;-0.52;-0.52	5.4	5.4	0.78164	Pleckstrin homology-type (1);Pleckstrin homology domain (3);	0.138090	0.50627	D	0.000113	D	0.86201	0.5876	M	0.88570	2.965	0.80722	D	1	D;D	0.89917	0.999;1.0	D;D	0.87578	0.992;0.998	D	0.88938	0.3378	10	0.87932	D	0	.	14.4918	0.67657	1.0:0.0:0.0:0.0	.	351;478	B7Z3C7;Q15052	.;ARHG6_HUMAN	P	478;324;324;324;351	ENSP00000250617:L478P;ENSP00000359654:L324P;ENSP00000359656:L324P;ENSP00000439483:L351P	ENSP00000250617:L478P	L	-	2	0	ARHGEF6	135592629	1.000000	0.71417	0.990000	0.47175	0.986000	0.74619	8.962000	0.93254	1.801000	0.52704	0.486000	0.48141	CTG		0.363	ARHGEF6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058511.2	NM_004840	
NHS	4810	broad.mit.edu	37	X	17746117	17746117	+	Silent	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chrX:17746117C>T	ENST00000380060.3	+	6	4166	c.3828C>T	c.(3826-3828)gaC>gaT	p.D1276D	NHS_ENST00000398097.3_Silent_p.D1120D	NM_198270.2	NP_938011.1	Q6T4R5	NHS_HUMAN	Nance-Horan syndrome (congenital cataracts and dental anomalies)	1297					cell differentiation (GO:0030154)|lens development in camera-type eye (GO:0002088)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|plasma membrane (GO:0005886)|tight junction (GO:0005923)		p.D1276D(1)		breast(5)|central_nervous_system(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(17)|liver(1)|lung(26)|ovary(2)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	71	Hepatocellular(33;0.183)					CTGGTCCAGACGAAACTCTAG	0.468																																					p.D1120D												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C3360T	X						.						71.0	69.0	69.0					X																	17746117		2203	4300	6503	17656038	SO:0001819	synonymous_variant	4810	exon7				CCDS14181.1, CCDS48087.1	Xp22.3-p21.1	2014-06-18			ENSG00000188158	ENSG00000188158			7820	protein-coding gene	gene with protein product		300457					Standard	NM_001136024		Approved		uc004cxx.3	Q6T4R5	OTTHUMG00000022799	ENST00000380060.3:c.3828C>T	X.37:g.17746117C>T		Somatic		Capture	Illumina HiSeq	Phase_I	17656038	NM_001136024	B7ZVX8|E2DH69|Q5J7Q0|Q5J7Q1|Q68DR5	Silent	SNP	ENST00000380060.3	37	CCDS14181.1																																																																																				0.468	NHS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059120.1	NM_198270	
SCML2	10389	broad.mit.edu	37	X	18265952	18265952	+	Missense_Mutation	SNP	T	T	G			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chrX:18265952T>G	ENST00000251900.4	-	12	1666	c.1507A>C	c.(1507-1509)Act>Cct	p.T503P	SCML2_ENST00000398048.3_Missense_Mutation_p.T239P	NM_006089.2	NP_006080.1	Q9UQR0	SCML2_HUMAN	sex comb on midleg-like 2 (Drosophila)	503					anatomical structure morphogenesis (GO:0009653)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|PcG protein complex (GO:0031519)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.T503P(1)		breast(4)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|lung(13)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	36	Hepatocellular(33;0.183)					TATGGTACAGTTTGCTGAGGA	0.398																																					p.T503P	Esophageal Squamous(100;1252 1965 19021 35517)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A1507C	X						.						430.0	312.0	352.0					X																	18265952		2203	4300	6503	18175873	SO:0001583	missense	10389	exon12			Y18004	CCDS14185.1	Xp22	2013-01-10	2001-11-28		ENSG00000102098	ENSG00000102098		"""Sterile alpha motif (SAM) domain containing"""	10581	protein-coding gene	gene with protein product		300208	"""sex comb on midleg (Drosophila)-like 2"""			10331946	Standard	NM_006089		Approved		uc004cyl.2	Q9UQR0	OTTHUMG00000021212	ENST00000251900.4:c.1507A>C	X.37:g.18265952T>G	ENSP00000251900:p.Thr503Pro	Somatic		Capture	Illumina HiSeq	Phase_I	18175873	NM_006089	Q5JXE6|Q86U98|Q8IWD0|Q8NDP2|Q9UGC5	Missense_Mutation	SNP	ENST00000251900.4	37	CCDS14185.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.049|0.049	-1.255898|-1.255898	0.01457|0.01457	.|.	.|.	ENSG00000102098|ENSG00000102098	ENST00000420857|ENST00000251900;ENST00000398048;ENST00000442000	.|T;T	.|0.41065	.|2.31;1.01	5.19|5.19	1.57|1.57	0.23409|0.23409	.|.	.|0.911448	.|0.09269	.|N	.|0.825389	T|T	0.10637|0.10637	0.0260|0.0260	N|N	0.00368|0.00368	-1.59|-1.59	0.09310|0.09310	N|N	1|1	.|B;B;B;B	.|0.02656	.|0.0;0.0;0.0;0.0	.|B;B;B;B	.|0.04013	.|0.0;0.0;0.0;0.001	T|T	0.23619|0.23619	-1.0183|-1.0183	5|10	.|0.27082	.|T	.|0.32	.|.	2.4197|2.4197	0.04445|0.04445	0.3611:0.0:0.2321:0.4069|0.3611:0.0:0.2321:0.4069	.|.	.|471;18;239;503	.|B4DZR9;Q5JXE7;B4DRC2;Q9UQR0	.|.;.;.;SCML2_HUMAN	N|P	18|503;239;471	.|ENSP00000251900:T503P;ENSP00000381126:T239P	.|ENSP00000251900:T503P	K|T	-|-	3|1	2|0	SCML2|SCML2	18175873|18175873	0.992000|0.992000	0.36948|0.36948	0.003000|0.003000	0.11579|0.11579	0.001000|0.001000	0.01503|0.01503	1.176000|1.176000	0.31957|0.31957	0.435000|0.435000	0.26365|0.26365	-1.346000|-1.346000	0.01242|0.01242	AAA|ACT		0.398	SCML2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055941.1	NM_006089	
PHKA2	5256	broad.mit.edu	37	X	18918808	18918808	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chrX:18918808G>A	ENST00000379942.4	-	28	3702	c.3037C>T	c.(3037-3039)Cgg>Tgg	p.R1013W		NM_000292.2	NP_000283.1	P46019	KPB2_HUMAN	phosphorylase kinase, alpha 2 (liver)	1013					carbohydrate metabolic process (GO:0005975)|cellular protein modification process (GO:0006464)|generation of precursor metabolites and energy (GO:0006091)|glucose metabolic process (GO:0006006)|glycogen catabolic process (GO:0005980)|protein phosphorylation (GO:0006468)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|phosphorylase kinase complex (GO:0005964)|plasma membrane (GO:0005886)	hydrolase activity, hydrolyzing O-glycosyl compounds (GO:0004553)|phosphorylase kinase activity (GO:0004689)	p.R1013W(1)		NS(1)|biliary_tract(1)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(8)|kidney(1)|large_intestine(12)|lung(23)|ovary(2)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	61	Hepatocellular(33;0.183)					GCACTAAACCGCCTAGTCATC	0.473																																					p.R1013W												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C3037T	X						.						168.0	120.0	137.0					X																	18918808		2203	4300	6503	18828729	SO:0001583	missense	5256	exon28				CCDS14190.1	Xp22.2-p22.1	2009-07-10			ENSG00000044446	ENSG00000044446	2.7.11.19		8926	protein-coding gene	gene with protein product		300798		PHK, PYK		2387090	Standard	NM_000292		Approved		uc004cyv.4	P46019	OTTHUMG00000021222	ENST00000379942.4:c.3037C>T	X.37:g.18918808G>A	ENSP00000369274:p.Arg1013Trp	Somatic		Capture	Illumina HiSeq	Phase_I	18828729	NM_000292	A8K1T1|Q6LAJ5|Q7Z6W0|Q96CR3|Q9UDA1	Missense_Mutation	SNP	ENST00000379942.4	37	CCDS14190.1	.	.	.	.	.	.	.	.	.	.	G	16.40	3.112154	0.56398	.	.	ENSG00000044446	ENST00000379942	D	0.91351	-2.83	5.63	4.75	0.60458	.	0.463445	0.21240	N	0.077832	D	0.89399	0.6704	M	0.74881	2.28	0.45284	D	0.998286	P	0.36086	0.536	B	0.35312	0.2	D	0.88611	0.3156	10	0.87932	D	0	-10.423	10.7301	0.46091	0.0:0.0:0.6552:0.3447	.	1013	P46019	KPB2_HUMAN	W	1013	ENSP00000369274:R1013W	ENSP00000369274:R1013W	R	-	1	2	PHKA2	18828729	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	1.967000	0.40491	1.217000	0.43442	0.513000	0.50165	CGG		0.473	PHKA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055960.1	NM_000292	
GPR64	10149	broad.mit.edu	37	X	19028880	19028880	+	Silent	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chrX:19028880G>A	ENST00000379869.3	-	17	1279	c.1116C>T	c.(1114-1116)agC>agT	p.S372S	GPR64_ENST00000354791.3_Silent_p.S356S|GPR64_ENST00000357991.3_Silent_p.S369S|GPR64_ENST00000357544.3_Silent_p.S342S|GPR64_ENST00000379876.1_Silent_p.S348S|GPR64_ENST00000379878.3_Silent_p.S356S|GPR64_ENST00000340581.3_Silent_p.S342S|GPR64_ENST00000356606.4_Silent_p.S358S|GPR64_ENST00000360279.4_Silent_p.S350S|GPR64_ENST00000379873.2_Silent_p.S372S	NM_001079858.2|NM_005756.3	NP_001073327.1|NP_005747.2	Q8IZP9	GPR64_HUMAN	G protein-coupled receptor 64	372					G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)|spermatogenesis (GO:0007283)	apical plasma membrane (GO:0016324)|cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)	G-protein coupled receptor activity (GO:0004930)	p.S369S(1)		breast(5)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(9)|lung(18)|stomach(1)|urinary_tract(1)	42	Hepatocellular(33;0.183)					CAGAAATACTGCTGGTGTTGA	0.438																																					p.S342S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1026T	X						.						148.0	112.0	124.0					X																	19028880		2203	4300	6503	18938801	SO:0001819	synonymous_variant	10149	exon15			X81892	CCDS14191.1, CCDS43921.1, CCDS43922.1, CCDS43923.1, CCDS55376.1, CCDS55377.1, CCDS55378.1, CCDS55379.1	Xp22.13	2014-08-08			ENSG00000173698	ENSG00000173698		"""-"", ""GPCR / Class B : Orphans"""	4516	protein-coding gene	gene with protein product	"""epididymal protein 6"""	300572				9739419, 9150425	Standard	NM_005756		Approved	HE6, TM7LN2, EDDM6	uc004cyx.3	Q8IZP9	OTTHUMG00000021223	ENST00000379869.3:c.1116C>T	X.37:g.19028880G>A		Somatic		Capture	Illumina HiSeq	Phase_I	18938801	NM_001184837	B1AWB3|B1AWB4|B1AWB6|B1AWB7|O00406|Q14CE0|Q8IWT2|Q8IZE4|Q8IZE5|Q8IZE6|Q8IZE7|Q8IZP3|Q8IZP4	Silent	SNP	ENST00000379869.3	37	CCDS43923.1																																																																																				0.438	GPR64-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000055970.2		
PCYT1B	9468	broad.mit.edu	37	X	24597510	24597510	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chrX:24597510G>A	ENST00000379144.2	-	6	761	c.631C>T	c.(631-633)Cgt>Tgt	p.R211C	PCYT1B_ENST00000356768.4_Missense_Mutation_p.R211C|PCYT1B_ENST00000379145.1_Missense_Mutation_p.R193C	NM_004845.4	NP_004836.2	Q9Y5K3	PCY1B_HUMAN	phosphate cytidylyltransferase 1, choline, beta	211					CDP-choline pathway (GO:0006657)|glycerophospholipid biosynthetic process (GO:0046474)|ovarian follicle development (GO:0001541)|phosphatidylcholine biosynthetic process (GO:0006656)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|endoplasmic reticulum membrane (GO:0005789)	choline-phosphate cytidylyltransferase activity (GO:0004105)	p.R211C(1)		breast(2)|kidney(1)|large_intestine(5)|lung(8)|ovary(1)	17					Choline(DB00122)	TCATAGTCACGAACAATTCTG	0.438																																					p.R193C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C577T	X						.						288.0	204.0	233.0					X																	24597510		2203	4300	6503	24507431	SO:0001583	missense	9468	exon6			AF052510	CCDS14213.1, CCDS55391.1, CCDS55392.1	Xp22	2008-02-05	2005-09-05		ENSG00000102230	ENSG00000102230	2.7.7.15		8755	protein-coding gene	gene with protein product		604926	"""phosphate cytidylyltransferase 1, choline, beta isoform"""			9593753	Standard	NM_004845		Approved	CCT-beta, CTB	uc004dbi.3	Q9Y5K3	OTTHUMG00000021270	ENST00000379144.2:c.631C>T	X.37:g.24597510G>A	ENSP00000368439:p.Arg211Cys	Somatic		Capture	Illumina HiSeq	Phase_I	24507431	NM_001163264	A8IX00|B2RCX8|B4DK10|E9PD84|O60621|Q86XC9	Missense_Mutation	SNP	ENST00000379144.2	37	CCDS14213.1	.	.	.	.	.	.	.	.	.	.	G	19.86	3.905992	0.72868	.	.	ENSG00000102230	ENST00000379145;ENST00000379144;ENST00000356768	.	.	.	5.1	5.1	0.69264	Rossmann-like alpha/beta/alpha sandwich fold (1);	0.000000	0.85682	D	0.000000	T	0.79375	0.4435	M	0.81112	2.525	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;P;P	0.64321	0.924;0.842;0.842	T	0.82888	-0.0234	9	0.87932	D	0	-28.4777	17.7567	0.88451	0.0:0.0:1.0:0.0	.	211;193;211	Q9Y5K3-2;E9PD84;Q9Y5K3	.;.;PCY1B_HUMAN	C	193;211;211	.	ENSP00000349211:R211C	R	-	1	0	PCYT1B	24507431	1.000000	0.71417	1.000000	0.80357	0.814000	0.46013	4.629000	0.61290	2.380000	0.81148	0.529000	0.55759	CGT		0.438	PCYT1B-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056103.1	NM_004845	
MAGEB18	286514	broad.mit.edu	37	X	26157695	26157695	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chrX:26157695G>A	ENST00000325250.1	+	2	780	c.593G>A	c.(592-594)gGc>gAc	p.G198D		NM_173699.3	NP_775970	Q96M61	MAGBI_HUMAN	melanoma antigen family B, 18	198	Interaction with LNX1.|MAGE. {ECO:0000255|PROSITE- ProRule:PRU00127}.					cytoplasm (GO:0005737)		p.G198D(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(5)|lung(17)|skin(2)|stomach(1)|urinary_tract(2)	33						CCCAAGACTGGCCTCCTGATG	0.448																																					p.G198D												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G593A	X						.						37.0	30.0	33.0					X																	26157695		2202	4299	6501	26067616	SO:0001583	missense	286514	exon2			AK057361	CCDS14216.1	Xp21.3	2008-02-05			ENSG00000176774	ENSG00000176774			28515	protein-coding gene	gene with protein product							Standard	NM_173699		Approved	MGC33889	uc004dbq.2	Q96M61	OTTHUMG00000021282	ENST00000325250.1:c.593G>A	X.37:g.26157695G>A	ENSP00000314543:p.Gly198Asp	Somatic		Capture	Illumina HiSeq	Phase_I	26067616	NM_173699		Missense_Mutation	SNP	ENST00000325250.1	37	CCDS14216.1	.	.	.	.	.	.	.	.	.	.	G	14.13	2.444672	0.43429	.	.	ENSG00000176774	ENST00000325250	T	0.19532	2.14	4.56	4.56	0.56223	.	0.053381	0.85682	D	0.000000	T	0.51449	0.1675	M	0.90650	3.135	0.22401	N	0.999133	D	0.89917	1.0	D	0.87578	0.998	T	0.50608	-0.8808	10	0.87932	D	0	.	11.6598	0.51339	0.0:0.0:1.0:0.0	.	198	Q96M61	MAGBI_HUMAN	D	198	ENSP00000314543:G198D	ENSP00000314543:G198D	G	+	2	0	MAGEB18	26067616	0.309000	0.24518	0.391000	0.26233	0.417000	0.31264	2.389000	0.44407	2.527000	0.85204	0.600000	0.82982	GGC		0.448	MAGEB18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056120.1	NM_173699	
TAB3	257397	broad.mit.edu	37	X	30873032	30873032	+	Nonsense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chrX:30873032C>T	ENST00000378933.1	-	3	927	c.750G>A	c.(748-750)tgG>tgA	p.W250*	TAB3_ENST00000378928.1_5'Flank|TAB3_ENST00000288422.2_Nonsense_Mutation_p.W250*|TAB3_ENST00000378932.2_Nonsense_Mutation_p.W250*|TAB3_ENST00000378930.3_Nonsense_Mutation_p.W250*|TAB3-AS2_ENST00000445240.1_RNA	NM_152787.3	NP_690000.2	Q8N5C8	TAB3_HUMAN	TGF-beta activated kinase 1/MAP3K7 binding protein 3	250	Pro-rich.				activation of MAPK activity (GO:0000187)|Fc-epsilon receptor signaling pathway (GO:0038095)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|innate immune response (GO:0045087)|JNK cascade (GO:0007254)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endosome membrane (GO:0010008)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	zinc ion binding (GO:0008270)	p.W250*(1)		NS(1)|breast(1)|endometrium(8)|kidney(1)|large_intestine(6)|lung(6)|ovary(2)|pancreas(1)|skin(1)	27						GTGAGGACTGCCACGGCGTAC	0.473																																					p.W250X	Pancreas(164;1598 1985 29022 43301 49529)											.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.G750A	X						.						73.0	63.0	66.0					X																	30873032		2202	4300	6502	30782953	SO:0001587	stop_gained	257397	exon6			AY331591	CCDS14226.1	Xp21.2	2010-02-05	2010-02-05	2010-02-05	ENSG00000157625	ENSG00000157625			30681	protein-coding gene	gene with protein product	"""TAK1 binding protein 3"""	300480	"""mitogen-activated protein kinase kinase kinase 7 interacting protein 3"""	MAP3K7IP3		14633987, 14670075	Standard	XM_005274482		Approved		uc004dcj.3	Q8N5C8	OTTHUMG00000021329	ENST00000378933.1:c.750G>A	X.37:g.30873032C>T	ENSP00000368215:p.Trp250*	Somatic		Capture	Illumina HiSeq	Phase_I	30782953	NM_152787	A6NDD9|Q6VQR0	Nonsense_Mutation	SNP	ENST00000378933.1	37	CCDS14226.1	.	.	.	.	.	.	.	.	.	.	C	38	6.714916	0.97784	.	.	ENSG00000157625	ENST00000378933;ENST00000378930;ENST00000288422;ENST00000378932	.	.	.	4.82	4.82	0.62117	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-1.395	17.3833	0.87410	0.0:1.0:0.0:0.0	.	.	.	.	X	250	.	ENSP00000288422:W250X	W	-	3	0	TAB3	30782953	1.000000	0.71417	1.000000	0.80357	0.842000	0.47809	7.042000	0.76565	2.118000	0.64928	0.538000	0.68166	TGG		0.473	TAB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056173.1	NM_152787	
SYTL5	94122	broad.mit.edu	37	X	37961665	37961665	+	Missense_Mutation	SNP	G	G	A	rs148783666		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chrX:37961665G>A	ENST00000357972.5	+	10	1679	c.1133G>A	c.(1132-1134)cGt>cAt	p.R378H	SYTL5_ENST00000456733.2_Missense_Mutation_p.R378H|TM4SF2_ENST00000465127.1_Intron|SYTL5_ENST00000297875.2_Missense_Mutation_p.R378H			Q8TDW5	SYTL5_HUMAN	synaptotagmin-like 5	378					exocytosis (GO:0006887)|intracellular protein transport (GO:0006886)	membrane (GO:0016020)	metal ion binding (GO:0046872)	p.R378H(2)		central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(9)|lung(23)|prostate(1)|skin(2)|urinary_tract(1)	44						AACACTCACCGTCTGGCAAGT	0.413													G|||	1	0.000264901	0.0008	0.0	3775	,	,		13259	0.0		0.0	False		,,,				2504	0.0				p.R378H												.	.	2	Substitution - Missense(2)	large_intestine(1)|lung(1)	c.G1133A	X						.	G	HIS/ARG,HIS/ARG,HIS/ARG	1,3832		0,1,1630,571	123.0	101.0	108.0		1133,1133,1133	5.0	1.0	X	dbSNP_134	108	0,6728		0,0,2428,1872	yes	missense,missense,missense	SYTL5	NM_001163334.1,NM_001163335.1,NM_138780.2	29,29,29	0,1,4058,2443	AA,AG,GG,G		0.0,0.0261,0.0095	benign,benign,benign	378/753,378/731,378/731	37961665	1,10560	2202	4300	6502	37846609	SO:0001583	missense	94122	exon10				CCDS14244.1, CCDS55399.1	Xp21.1	2008-02-05			ENSG00000147041	ENSG00000147041			15589	protein-coding gene	gene with protein product	"""exophilin 9"""						Standard	NM_138780		Approved		uc004ddx.3	Q8TDW5	OTTHUMG00000033176	ENST00000357972.5:c.1133G>A	X.37:g.37961665G>A	ENSP00000350657:p.Arg378His	Somatic		Capture	Illumina HiSeq	Phase_I	37846609	NM_138780	A2RRF2	Missense_Mutation	SNP	ENST00000357972.5	37	CCDS14244.1	2	0.0012055455093429777	2	0.0040650406504065045	0	0.0	0	0.0	0	0.0	G	10.58	1.390703	0.25118	2.61E-4	0.0	ENSG00000147041	ENST00000297875;ENST00000357972;ENST00000456733	T;T;T	0.21361	2.01;2.01;2.27	5.0	5.0	0.66597	.	0.432082	0.27393	N	0.019567	T	0.11495	0.0280	N	0.14661	0.345	0.09310	N	0.999998	B;B	0.06786	0.001;0.0	B;B	0.01281	0.0;0.0	T	0.11891	-1.0569	10	0.42905	T	0.14	-13.9204	6.8046	0.23770	0.1783:0.0:0.8217:0.0	.	378;378	A2RRF2;Q8TDW5	.;SYTL5_HUMAN	H	378	ENSP00000297875:R378H;ENSP00000350657:R378H;ENSP00000395220:R378H	ENSP00000297875:R378H	R	+	2	0	SYTL5	37846609	0.979000	0.34478	0.998000	0.56505	0.266000	0.26442	2.526000	0.45607	2.059000	0.61396	0.594000	0.82650	CGT		0.413	SYTL5-201	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000080883.1	NM_138780	
DUSP21	63904	broad.mit.edu	37	X	44703735	44703735	+	Silent	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chrX:44703735G>A	ENST00000339042.4	+	1	487	c.357G>A	c.(355-357)gcG>gcA	p.A119A		NM_022076.3	NP_071359.3	Q9H596	DUS21_HUMAN	dual specificity phosphatase 21	119	Sufficient for mitochondrial localization. {ECO:0000250}.|Tyrosine-protein phosphatase.				peptidyl-tyrosine dephosphorylation (GO:0035335)	cytoplasm (GO:0005737)|mitochondrial inner membrane (GO:0005743)|nucleus (GO:0005634)	MAP kinase tyrosine/serine/threonine phosphatase activity (GO:0017017)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)	p.A119A(3)		breast(1)|endometrium(3)|kidney(1)|large_intestine(3)|lung(8)|skin(3)	19						TGTGCCTTGCGTACCTCATGA	0.587																																					p.A119A												.	.	3	Substitution - coding silent(3)	lung(2)|large_intestine(1)	c.G357A	X						.						105.0	78.0	87.0					X																	44703735		2203	4300	6503	44588679	SO:0001819	synonymous_variant	63904	exon1			AF143321	CCDS14264.1	Xp11.4-p11.23	2011-06-09			ENSG00000189037	ENSG00000189037		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Atypical dual specificity phosphatases"""	20476	protein-coding gene	gene with protein product		300678				12408986	Standard	NM_022076		Approved		uc004dgd.3	Q9H596	OTTHUMG00000021401	ENST00000339042.4:c.357G>A	X.37:g.44703735G>A		Somatic		Capture	Illumina HiSeq	Phase_I	44588679	NM_022076	Q0VDA6|Q6IAJ6|Q6YDQ8	Silent	SNP	ENST00000339042.4	37	CCDS14264.1																																																																																				0.587	DUSP21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056323.1	NM_022076	
TIMP1	7076	broad.mit.edu	37	X	47444680	47444680	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chrX:47444680G>A	ENST00000218388.4	+	4	448	c.278G>A	c.(277-279)tGc>tAc	p.C93Y	SYN1_ENST00000295987.7_Intron|TIMP1_ENST00000456754.2_Missense_Mutation_p.C93Y|TIMP1_ENST00000377017.1_Missense_Mutation_p.C29Y|MIR4769_ENST00000584126.1_RNA|TIMP1_ENST00000377018.2_Missense_Mutation_p.A17T|SYN1_ENST00000340666.4_Intron	NM_003254.2	NP_003245.1	P01033	TIMP1_HUMAN	TIMP metallopeptidase inhibitor 1	93	NTR. {ECO:0000255|PROSITE- ProRule:PRU00295}.				aging (GO:0007568)|blood coagulation (GO:0007596)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of membrane protein ectodomain proteolysis (GO:0051045)|negative regulation of metalloenzyme activity (GO:0048553)|negative regulation of trophoblast cell migration (GO:1901164)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of cell proliferation (GO:0008284)|regulation of integrin-mediated signaling pathway (GO:2001044)|response to cytokine (GO:0034097)|response to peptide hormone (GO:0043434)	basement membrane (GO:0005604)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|platelet alpha granule lumen (GO:0031093)	cytokine activity (GO:0005125)|metal ion binding (GO:0046872)|metalloendopeptidase inhibitor activity (GO:0008191)	p.C93Y(1)		endometrium(1)|large_intestine(2)	3						GAGAGTGTCTGCGGATACTTC	0.597																																					p.C93Y												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G278A	X						.						52.0	47.0	49.0					X																	47444680		2203	4300	6503	47329624	SO:0001583	missense	7076	exon4				CCDS14281.1	Xp11.3-p11.23	2008-07-29	2005-08-08		ENSG00000102265	ENSG00000102265			11820	protein-coding gene	gene with protein product		305370	"""tissue inhibitor of metalloproteinase 1 (erythroid potentiating activity, collagenase inhibitor)"""	TIMP, CLGI			Standard	XM_005272645		Approved	EPO	uc004dif.3	P01033	OTTHUMG00000021447	ENST00000218388.4:c.278G>A	X.37:g.47444680G>A	ENSP00000218388:p.Cys93Tyr	Somatic		Capture	Illumina HiSeq	Phase_I	47329624	NM_003254	Q14252|Q9UCU1	Missense_Mutation	SNP	ENST00000218388.4	37	CCDS14281.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	g|g	20.9|20.9	4.073898|4.073898	0.76415|0.76415	.|.	.|.	ENSG00000102265|ENSG00000102265	ENST00000377018|ENST00000218388;ENST00000456754;ENST00000377017	.|D;D;D	.|0.99758	.|-6.65;-6.65;-6.65	4.98|4.98	4.98|4.98	0.66077|0.66077	.|Tissue inhibitor of metalloproteinases-like, OB-fold (1);Netrin domain (1);	.|0.000000	.|0.64402	.|D	.|0.000004	D|D	0.99802|0.99802	0.9915|0.9915	M|M	0.91663|0.91663	3.23|3.23	0.24634|0.24634	N|N	0.993601|0.993601	D|D	0.60160|0.89917	0.987|1.0	P|D	0.56865|0.97110	0.808|1.0	D|D	0.98325|0.98325	1.0530|1.0530	8|10	0.87932|0.87932	D|D	0|0	.|.	14.9687|14.9687	0.71217|0.71217	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	17|93	B4DJK3|P01033	.|TIMP1_HUMAN	T|Y	17|93;93;29	.|ENSP00000218388:C93Y;ENSP00000406671:C93Y;ENSP00000366216:C29Y	ENSP00000366217:A17T|ENSP00000218388:C93Y	A|C	+|+	1|2	0|0	TIMP1|TIMP1	47329624|47329624	1.000000|1.000000	0.71417|0.71417	0.996000|0.996000	0.52242|0.52242	0.992000|0.992000	0.81027|0.81027	5.602000|5.602000	0.67612|0.67612	2.209000|2.209000	0.71365|0.71365	0.579000|0.579000	0.79373|0.79373	GCG|TGC		0.597	TIMP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056423.1	NM_003254	
SSX5	6758	broad.mit.edu	37	X	48054727	48054727	+	Splice_Site	SNP	T	T	G			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chrX:48054727T>G	ENST00000376923.1	-	1	67	c.68A>C	c.(67-69)aAg>aCg	p.K23T	SSX5_ENST00000347757.1_Splice_Site_p.K23T|SSX5_ENST00000311798.1_Splice_Site_p.K23T			O60225	SSX5_HUMAN	synovial sarcoma, X breakpoint 5	23	KRAB-related. {ECO:0000255|PROSITE- ProRule:PRU00120}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	nucleic acid binding (GO:0003676)	p.K23T(1)		endometrium(3)|kidney(1)|large_intestine(6)|lung(7)|skin(1)	18						TCACCTCACCTTTTGCATCTT	0.552																																					p.K23T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A68C	X						.						187.0	145.0	159.0					X																	48054727		2203	4299	6502	47939671	SO:0001630	splice_region_variant	6758	exon2			BC016640	CCDS14288.1, CCDS14289.1	Xp11.23	2008-02-05			ENSG00000165583	ENSG00000165583			11339	protein-coding gene	gene with protein product		300327					Standard	NM_021015		Approved		uc004diz.1	O60225	OTTHUMG00000021471	ENST00000376923.1:c.69+1A>C	X.37:g.48054727T>G		Somatic		Capture	Illumina HiSeq	Phase_I	47939671	NM_175723	Q5JQ59|Q5JQ60|Q96AW3	Missense_Mutation	SNP	ENST00000376923.1	37	CCDS14289.1	.	.	.	.	.	.	.	.	.	.	N	10.85	1.467131	0.26335	.	.	ENSG00000165583	ENST00000311798;ENST00000376923;ENST00000347757	T;T;T	0.18174	2.23;5.7;5.7	1.51	0.26	0.15588	Krueppel-associated box (2);Krueppel-associated box-related (1);	0.142736	0.32563	N	0.005925	T	0.30324	0.0761	M	0.78637	2.42	0.09310	N	1	P;D	0.55800	0.955;0.973	P;D	0.63283	0.821;0.913	T	0.08472	-1.0720	10	0.46703	T	0.11	.	3.126	0.06407	0.0:0.2726:0.0:0.7274	.	23;23	O60225;O60225-2	SSX5_HUMAN;.	T	23	ENSP00000312415:K23T;ENSP00000366122:K23T;ENSP00000290558:K23T	ENSP00000312415:K23T	K	-	2	0	SSX5	47939671	0.112000	0.22096	0.013000	0.15412	0.005000	0.04900	0.706000	0.25690	0.009000	0.14813	0.143000	0.16000	AAG		0.552	SSX5-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000056466.1	NM_021015	Missense_Mutation
GATA1	2623	broad.mit.edu	37	X	48650479	48650479	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chrX:48650479C>A	ENST00000376670.3	+	3	560	c.449C>A	c.(448-450)cCt>cAt	p.P150H	GATA1_ENST00000376665.3_Missense_Mutation_p.P150H	NM_002049.3	NP_002040.1	P15976	GATA1_HUMAN	GATA binding protein 1 (globin transcription factor 1)	150					basophil differentiation (GO:0030221)|blood coagulation (GO:0007596)|cell-cell signaling (GO:0007267)|cellular response to thyroid hormone stimulus (GO:0097067)|dendritic cell differentiation (GO:0097028)|embryonic hemopoiesis (GO:0035162)|eosinophil differentiation (GO:0030222)|eosinophil fate commitment (GO:0035854)|erythrocyte development (GO:0048821)|erythrocyte differentiation (GO:0030218)|in utero embryonic development (GO:0001701)|male gonad development (GO:0008584)|megakaryocyte differentiation (GO:0030219)|negative regulation of apoptotic process (GO:0043066)|negative regulation of bone mineralization (GO:0030502)|negative regulation of cell proliferation (GO:0008285)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription regulatory region DNA binding (GO:2000678)|platelet aggregation (GO:0070527)|platelet formation (GO:0030220)|positive regulation of erythrocyte differentiation (GO:0045648)|positive regulation of osteoblast proliferation (GO:0033690)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of definitive erythrocyte differentiation (GO:0010724)|regulation of glycoprotein biosynthetic process (GO:0010559)|transcription from RNA polymerase II promoter (GO:0006366)|transcriptional activation by promoter-enhancer looping (GO:0071733)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)|transcriptional repressor complex (GO:0017053)	C2H2 zinc finger domain binding (GO:0070742)|chromatin DNA binding (GO:0031490)|DNA binding (GO:0003677)|DNA binding, bending (GO:0008301)|enhancer sequence-specific DNA binding (GO:0001158)|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)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription factor binding (GO:0001085)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region sequence-specific DNA binding (GO:0000976)|zinc ion binding (GO:0008270)	p.?(2)|p.P150H(1)		breast(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(259)|large_intestine(8)|lung(9)|prostate(1)	283						ACCCTGGGACCTGCACTGCCT	0.582			"""Mis, F"""		megakaryoblastic leukemia of Downs Syndrome																																p.P150H	Pancreas(9;429 505 11287 29617)		Dom	yes		X	Xp11.23	2623	GATA binding protein 1 (globin transcription factor 1)		L	.	.	3	Unknown(2)|Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(2)|large_intestine(1)	c.C449A	X						.						62.0	54.0	57.0					X																	48650479		2203	4300	6503	48535423	SO:0001583	missense	2623	exon3			X17254	CCDS14305.1	Xp11.23	2014-09-17	2001-11-28		ENSG00000102145	ENSG00000102145		"""GATA zinc finger domain containing"""	4170	protein-coding gene	gene with protein product	"""nuclear factor, erythroid 1"""	305371	"""GATA-binding protein 1 (globin transcription factor 1)"""	GF1		1999341	Standard	NM_002049		Approved	ERYF1, NFE1, GATA-1, NF-E1	uc004dkq.4	P15976	OTTHUMG00000021504	ENST00000376670.3:c.449C>A	X.37:g.48650479C>A	ENSP00000365858:p.Pro150His	Somatic		Capture	Illumina HiSeq	Phase_I	48535423	NM_002049	Q96GB8	Missense_Mutation	SNP	ENST00000376670.3	37	CCDS14305.1	.	.	.	.	.	.	.	.	.	.	C	10.26	1.300276	0.23650	.	.	ENSG00000102145	ENST00000376670;ENST00000376665	D;D	0.97642	-4.47;-4.26	4.6	3.72	0.42706	.	1.219290	0.05794	N	0.610843	D	0.93651	0.7972	L	0.27053	0.805	0.09310	N	1	B	0.09022	0.002	B	0.06405	0.002	D	0.85034	0.0919	10	0.28530	T	0.3	-0.3107	10.104	0.42521	0.0:0.8937:0.0:0.1063	.	150	P15976	GATA1_HUMAN	H	150	ENSP00000365858:P150H;ENSP00000365853:P150H	ENSP00000365853:P150H	P	+	2	0	GATA1	48535423	0.999000	0.42202	0.924000	0.36721	0.593000	0.36681	3.023000	0.49666	1.873000	0.54277	0.492000	0.49549	CCT		0.582	GATA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056517.1	NM_002049	
GRIPAP1	56850	broad.mit.edu	37	X	48847367	48847367	+	Silent	SNP	A	A	G			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chrX:48847367A>G	ENST00000376441.1	-	7	647	c.613T>C	c.(613-615)Ttg>Ctg	p.L205L	GRIPAP1_ENST00000376444.3_Silent_p.L160L|GRIPAP1_ENST00000473581.1_5'UTR|GRIPAP1_ENST00000376425.3_Silent_p.L205L|GRIPAP1_ENST00000376423.4_Silent_p.L152L	NM_020137.3	NP_064522.3	Q4V328	GRAP1_HUMAN	GRIP1 associated protein 1	205						blood microparticle (GO:0072562)|endosome (GO:0005768)		p.L152L(1)		breast(2)|endometrium(1)|kidney(1)|large_intestine(4)|lung(2)	10						TCCCAGAGCAATCTCTTCTCC	0.587																																					p.L205L												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.T613C	X						.						128.0	110.0	117.0					X																	48847367		2203	4300	6503	48732311	SO:0001819	synonymous_variant	56850	exon7			AB032993	CCDS35248.1	Xp11.23	2008-02-05			ENSG00000068400	ENSG00000068400			18706	protein-coding gene	gene with protein product		300408				10896157	Standard	NM_020137		Approved	GRASP-1, GRASP1, KIAA1167, MPMGp800B12492Q3, DKFZp434P0630	uc004dly.1	Q4V328	OTTHUMG00000033192	ENST00000376441.1:c.613T>C	X.37:g.48847367A>G		Somatic		Capture	Illumina HiSeq	Phase_I	48732311	NM_020137	A6NL78|Q3MJ75|Q4V327|Q4V330|Q5HYG1|Q6N046|Q96DH8|Q9NQ43|Q9ULQ3	Silent	SNP	ENST00000376441.1	37	CCDS35248.1																																																																																				0.587	GRIPAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080970.2	NM_207672	
SMC1A	8243	broad.mit.edu	37	X	53439001	53439001	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chrX:53439001G>A	ENST00000322213.4	-	6	1184	c.1057C>T	c.(1057-1059)Cgg>Tgg	p.R353W	SMC1A_ENST00000375340.6_Intron	NM_006306.2	NP_006297.2	Q14683	SMC1A_HUMAN	structural maintenance of chromosomes 1A	353					DNA repair (GO:0006281)|gene expression (GO:0010467)|meiotic nuclear division (GO:0007126)|mitotic cell cycle (GO:0000278)|mitotic cell cycle checkpoint (GO:0007093)|mitotic sister chromatid cohesion (GO:0007064)|mitotic sister chromatid segregation (GO:0000070)|mitotic spindle organization (GO:0007052)|mRNA splicing, via spliceosome (GO:0000398)|negative regulation of DNA endoreduplication (GO:0032876)|response to radiation (GO:0009314)|RNA splicing (GO:0008380)|signal transduction in response to DNA damage (GO:0042770)|sister chromatid cohesion (GO:0007062)|stem cell maintenance (GO:0019827)	chromosome (GO:0005694)|chromosome, centromeric region (GO:0000775)|cohesin core heterodimer (GO:0008280)|condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinetochore (GO:0000776)|meiotic cohesin complex (GO:0030893)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|microtubule motor activity (GO:0003777)|poly(A) RNA binding (GO:0044822)|protein heterodimerization activity (GO:0046982)	p.R353W(2)		NS(1)|breast(3)|central_nervous_system(3)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(8)|ovary(5)|upper_aerodigestive_tract(2)	49						TCTTCCATCCGTTCTTCAAAC	0.527																																					p.R353W												.	.	2	Substitution - Missense(2)	large_intestine(1)|endometrium(1)	c.C1057T	X						.						113.0	72.0	86.0					X																	53439001		2203	4300	6503	53455726	SO:0001583	missense	8243	exon6			S78271	CCDS14352.1, CCDS75985.1	Xp11.22-p11.21	2014-09-17	2006-07-06	2006-07-06	ENSG00000072501	ENSG00000072501		"""Structural maintenance of chromosomes proteins"""	11111	protein-coding gene	gene with protein product		300040	"""SMC1 (structural maintenance of chromosomes 1, yeast)-like 1"", ""SMC1 structural maintenance of chromosomes 1-like 1 (yeast)"""	SMC1L1		7757074	Standard	NM_006306		Approved	DXS423E, KIAA0178, SB1.8, Smcb	uc004dsg.3	Q14683	OTTHUMG00000021614	ENST00000322213.4:c.1057C>T	X.37:g.53439001G>A	ENSP00000323421:p.Arg353Trp	Somatic		Capture	Illumina HiSeq	Phase_I	53455726	NM_006306	O14995|Q16351|Q2M228	Missense_Mutation	SNP	ENST00000322213.4	37	CCDS14352.1	.	.	.	.	.	.	.	.	.	.	G	20.5	3.997933	0.74818	.	.	ENSG00000072501	ENST00000322213	T	0.78707	-1.2	4.73	4.73	0.59995	RecF/RecN/SMC (1);	0.000000	0.85682	D	0.000000	T	0.76962	0.4061	N	0.08118	0	0.80722	D	1	D;D	0.89917	0.996;1.0	D;D	0.72625	0.937;0.978	T	0.83107	-0.0125	10	0.87932	D	0	.	15.9382	0.79734	0.0:0.0:1.0:0.0	.	331;353	Q6MZR8;Q14683	.;SMC1A_HUMAN	W	353	ENSP00000323421:R353W	ENSP00000323421:R353W	R	-	1	2	SMC1A	53455726	1.000000	0.71417	0.996000	0.52242	0.996000	0.88848	3.585000	0.53943	2.097000	0.63578	0.600000	0.82982	CGG		0.527	SMC1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056756.2	NM_006306	
PAGE5	90737	broad.mit.edu	37	X	55247041	55247041	+	Silent	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chrX:55247041G>A	ENST00000289619.5	+	1	254	c.9G>A	c.(7-9)gcG>gcA	p.A3A	PAGE5_ENST00000374955.3_Intron|PAGE5_ENST00000374952.1_Intron	NM_130467.3	NP_569734.2	Q96GU1	PAGE5_HUMAN	P antigen family, member 5 (prostate associated)	3								p.A3A(2)		breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(3)	8						TGATGCAGGCGCCATGGGCCG	0.667																																					p.A3A												.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.G9A	X						.						33.0	24.0	27.0					X																	55247041		2202	4298	6500	55263766	SO:0001819	synonymous_variant	90737	exon1			AJ344352	CCDS14368.1, CCDS35306.1	Xp11.22	2009-08-18			ENSG00000158639	ENSG00000158639			29992	protein-coding gene	gene with protein product	"""cancer/testis antigen family 16, member 1"", ""cancer/testis antigen family 16, member 2"""					11920606, 11992404	Standard	XM_006724613		Approved	PAGE-5, CT16.1, CT16.2	uc004duk.3	Q96GU1	OTTHUMG00000021650	ENST00000289619.5:c.9G>A	X.37:g.55247041G>A		Somatic		Capture	Illumina HiSeq	Phase_I	55263766	NM_130467	Q2NL97|Q5JUL0|Q8WWL9	Silent	SNP	ENST00000289619.5	37	CCDS14368.1																																																																																				0.667	PAGE5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000056861.1	NM_130467	
DGAT2L6	347516	broad.mit.edu	37	X	69421804	69421804	+	Silent	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chrX:69421804C>T	ENST00000333026.3	+	5	637	c.537C>T	c.(535-537)gcC>gcT	p.A179A		NM_198512.1	NP_940914.1	Q6ZPD8	DG2L6_HUMAN	diacylglycerol O-acyltransferase 2-like 6	179					lipid metabolic process (GO:0006629)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	transferase activity, transferring acyl groups other than amino-acyl groups (GO:0016747)	p.A179A(1)		breast(1)|endometrium(2)|large_intestine(3)|lung(5)|ovary(1)	12						CAGGCAATGCCGTGGTTATTG	0.517													C|||	1	0.000264901	0.0	0.0014	3775	,	,		13461	0.0		0.0	False		,,,				2504	0.0				p.A179A												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C537T	X						.						107.0	89.0	95.0					X																	69421804		2203	4300	6503	69338529	SO:0001819	synonymous_variant	347516	exon5			AK129500	CCDS14397.1	Xq13.1	2008-02-05			ENSG00000184210	ENSG00000184210			23250	protein-coding gene	gene with protein product		300926				15671038	Standard	NM_198512		Approved	DC3, FLJ25989	uc004dxx.1	Q6ZPD8	OTTHUMG00000021774	ENST00000333026.3:c.537C>T	X.37:g.69421804C>T		Somatic		Capture	Illumina HiSeq	Phase_I	69338529	NM_198512	Q6IEE2	Silent	SNP	ENST00000333026.3	37	CCDS14397.1																																																																																				0.517	DGAT2L6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057067.1	NM_198512	
P2RY4	5030	broad.mit.edu	37	X	69478741	69478741	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chrX:69478741C>T	ENST00000374519.2	-	1	913	c.734G>A	c.(733-735)cGc>cAc	p.R245H		NM_002565.3	NP_002556.1	P51582	P2RY4_HUMAN	pyrimidinergic receptor P2Y, G-protein coupled, 4	245					phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|transepithelial chloride transport (GO:0030321)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|G-protein coupled purinergic nucleotide receptor activity (GO:0045028)|uridine nucleotide receptor activity (GO:0015065)|UTP-activated nucleotide receptor activity (GO:0045030)	p.R245H(1)		cervix(2)|endometrium(2)|large_intestine(8)|lung(6)	18						AGCTATGGTGCGGAGAGAGCG	0.577																																					p.R245H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G734A	X						.						69.0	59.0	62.0					X																	69478741		2203	4300	6503	69395466	SO:0001583	missense	5030	exon1			X91852	CCDS14398.1	Xq13	2012-08-08			ENSG00000186912	ENSG00000186912		"""Purinergic receptors"", ""GPCR / Class A : Purinergic receptors, P2Y"""	8542	protein-coding gene	gene with protein product		300038				8537336	Standard	NM_002565		Approved	NRU, P2Y4, UNR, P2P	uc004dxz.1	P51582	OTTHUMG00000021769	ENST00000374519.2:c.734G>A	X.37:g.69478741C>T	ENSP00000363643:p.Arg245His	Somatic		Capture	Illumina HiSeq	Phase_I	69395466	NM_002565	Q4VBB7|Q4VBB8|Q502W2|Q5JT22	Missense_Mutation	SNP	ENST00000374519.2	37	CCDS14398.1	.	.	.	.	.	.	.	.	.	.	C	7.172	0.587905	0.13812	.	.	ENSG00000186912	ENST00000374519	T	0.37058	1.22	4.43	2.66	0.31614	GPCR, rhodopsin-like superfamily (1);	0.141573	0.43110	N	0.000611	T	0.42063	0.1186	M	0.87328	2.875	0.33949	D	0.644176	B	0.23650	0.089	B	0.27715	0.082	T	0.50906	-0.8772	10	0.62326	D	0.03	.	7.2167	0.25963	0.0:0.6139:0.0:0.3861	.	245	P51582	P2RY4_HUMAN	H	245	ENSP00000363643:R245H	ENSP00000363643:R245H	R	-	2	0	P2RY4	69395466	0.966000	0.33281	0.827000	0.32855	0.015000	0.08874	0.887000	0.28254	0.355000	0.24131	0.589000	0.80489	CGC		0.577	P2RY4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057058.2	NM_002565	
ARR3	407	broad.mit.edu	37	X	69497289	69497289	+	Silent	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chrX:69497289G>A	ENST00000307959.8	+	9	570	c.519G>A	c.(517-519)ccG>ccA	p.P173P	ARR3_ENST00000374495.3_Silent_p.P173P	NM_004312.2	NP_004303.2	P36575	ARRC_HUMAN	arrestin 3, retinal (X-arrestin)	173					endocytosis (GO:0006897)|regulation of protein phosphorylation (GO:0001932)|signal transduction (GO:0007165)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|photoreceptor inner segment (GO:0001917)|photoreceptor outer segment (GO:0001750)|synapse (GO:0045202)		p.P173P(1)		endometrium(3)|kidney(1)|large_intestine(4)|lung(4)|ovary(2)|prostate(1)|skin(1)	16						TTGCACCACCGGAGGCAGGCC	0.592																																					p.P173P												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G519A	X						.						73.0	63.0	67.0					X																	69497289		2203	4300	6503	69414014	SO:0001819	synonymous_variant	407	exon9				CCDS14399.1	Xq13.1	2013-10-11			ENSG00000120500	ENSG00000120500			710	protein-coding gene	gene with protein product	"""arrestin 4"""	301770				8224247	Standard	NM_004312		Approved	ARRX	uc004dyb.2	P36575	OTTHUMG00000021768	ENST00000307959.8:c.519G>A	X.37:g.69497289G>A		Somatic		Capture	Illumina HiSeq	Phase_I	69414014	NM_004312	B5B0B9|Q5JT23|Q5JT24|Q6IBF5|Q96EN2	Silent	SNP	ENST00000307959.8	37	CCDS14399.1																																																																																				0.592	ARR3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057055.2	NM_004312	
GDPD2	54857	broad.mit.edu	37	X	69646848	69646848	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chrX:69646848G>A	ENST00000374382.3	+	8	940	c.689G>A	c.(688-690)cGa>cAa	p.R230Q	GDPD2_ENST00000538649.1_Missense_Mutation_p.R151Q|GDPD2_ENST00000453994.2_Missense_Mutation_p.R230Q|GDPD2_ENST00000536730.1_Missense_Mutation_p.R151Q|GDPD2_ENST00000472623.1_3'UTR	NM_017711.3	NP_060181.2	Q9HCC8	GDPD2_HUMAN	glycerophosphodiester phosphodiesterase domain containing 2	230	GP-PDE.				glycerol metabolic process (GO:0006071)|lipid metabolic process (GO:0006629)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	glycerophosphodiester phosphodiesterase activity (GO:0008889)|glycerophosphoinositol inositolphosphodiesterase activity (GO:0047394)|metal ion binding (GO:0046872)	p.R230Q(1)		NS(1)|breast(1)|cervix(1)|endometrium(6)|large_intestine(8)|lung(3)|ovary(2)	22	Renal(35;0.156)					GTGGGACACCGAGGGGCCCCC	0.612																																					p.R151Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G452A	X						.						47.0	42.0	44.0					X																	69646848		2203	4300	6503	69563573	SO:0001583	missense	54857	exon7			AK000214	CCDS14402.1, CCDS55437.1, CCDS55438.1	Xq13.1	2011-01-25			ENSG00000130055	ENSG00000130055			25974	protein-coding gene	gene with protein product	"""osteoblast differentiation promoting factor"""					12975309	Standard	NM_017711		Approved	OBDPF, FLJ20207, GDE3	uc011mpk.2	Q9HCC8	OTTHUMG00000021776	ENST00000374382.3:c.689G>A	X.37:g.69646848G>A	ENSP00000363503:p.Arg230Gln	Somatic		Capture	Illumina HiSeq	Phase_I	69563573	NM_001171193	B4DRH4|B4DVC9|Q9NXJ6	Missense_Mutation	SNP	ENST00000374382.3	37	CCDS14402.1	.	.	.	.	.	.	.	.	.	.	G	26.0	4.698665	0.88830	.	.	ENSG00000130055	ENST00000453994;ENST00000536730;ENST00000538649;ENST00000374382	T;T;T;T	0.54675	0.56;0.56;0.56;0.56	5.63	4.72	0.59763	PLC-like phosphodiesterase, TIM beta/alpha-barrel domain (2);	0.000000	0.64402	D	0.000005	T	0.79173	0.4401	H	0.95004	3.61	0.38493	D	0.948012	D;D;D;D	0.89917	1.0;1.0;0.995;1.0	D;D;D;D	0.91635	0.998;0.999;0.954;0.996	D	0.86176	0.1603	9	.	.	.	-6.9021	13.6702	0.62420	0.0:0.1517:0.8483:0.0	.	230;16;151;230	B4DVC9;B3KUI6;B4DRH4;Q9HCC8	.;.;.;GDPD2_HUMAN	Q	230;151;151;230	ENSP00000414019:R230Q;ENSP00000445982:R151Q;ENSP00000444601:R151Q;ENSP00000363503:R230Q	.	R	+	2	0	GDPD2	69563573	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.982000	0.63825	2.351000	0.79841	0.600000	0.82982	CGA		0.612	GDPD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057070.1	NM_017711	
TAF1	6872	broad.mit.edu	37	X	70607290	70607290	+	Silent	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chrX:70607290G>A	ENST00000373790.4	+	15	2454	c.2403G>A	c.(2401-2403)acG>acA	p.T801T	TAF1_ENST00000423759.1_Silent_p.T822T|TAF1_ENST00000449580.1_Silent_p.T801T|TAF1_ENST00000276072.3_Silent_p.T822T	NM_004606.3|NM_138923.2	NP_004597.2|NP_620278.1	P21675	TAF1_HUMAN	TAF1 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 250kDa	801	Histone acetyltransferase (HAT).				cellular response to DNA damage stimulus (GO:0006974)|DNA-templated transcription, initiation (GO:0006352)|gene expression (GO:0010467)|histone acetylation (GO:0016573)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription initiation from RNA polymerase II promoter (GO:0060261)|protein autophosphorylation (GO:0046777)|regulation of transcription involved in G2/M transition of mitotic cell cycle (GO:0000117)|RNA polymerase II transcriptional preinitiation complex assembly (GO:0051123)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	MLL1 complex (GO:0071339)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor TFIID complex (GO:0005669)	ATP binding (GO:0005524)|histone acetyltransferase activity (GO:0004402)|lysine-acetylated histone binding (GO:0070577)|p53 binding (GO:0002039)|protein serine/threonine kinase activity (GO:0004674)|sequence-specific DNA binding (GO:0043565)|TBP-class protein binding (GO:0017025)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)	p.T801T(1)		breast(13)|central_nervous_system(6)|cervix(1)|endometrium(25)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(16)|lung(34)|ovary(9)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(3)	124	Renal(35;0.156)	all_lung(315;0.000321)				GGGCCAATACGCATATTCGAG	0.493																																					p.T801T												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G2403A	X						.						97.0	86.0	90.0					X																	70607290		2203	4300	6503	70524015	SO:0001819	synonymous_variant	6872	exon15				CCDS14412.1, CCDS35325.1, CCDS69783.1	Xq13.1	2011-07-01	2002-08-29	2001-12-07	ENSG00000147133	ENSG00000147133		"""Chromatin-modifying enzymes / K-acetyltransferases"""	11535	protein-coding gene	gene with protein product		313650	"""TATA box binding protein (TBP)-associated factor, RNA polymerase II, A, 250kD"", ""dystonia 3 (with Parkinsonism)"""	TAF2A, BA2R, CCG1, CCGS, DYT3		3556424, 12928496, 17952504	Standard	XM_005262295		Approved	NSCL2, TAFII250, KAT4, DYT3/TAF1	uc004dzt.4	P21675	OTTHUMG00000022723	ENST00000373790.4:c.2403G>A	X.37:g.70607290G>A		Somatic		Capture	Illumina HiSeq	Phase_I	70524015	NM_138923	A5CVC8|A5CVC9|A5CVD0|A5CVD1|B1Q2X3|Q59FZ3|Q6IUZ1|Q70Q86|Q70Q87|Q70T00|Q70T01|Q70T02|Q70T03	Silent	SNP	ENST00000373790.4	37	CCDS35325.1																																																																																				0.493	TAF1-009	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000058995.2	NM_004606	
MAGEE2	139599	broad.mit.edu	37	X	75004797	75004797	+	Silent	SNP	G	G	A			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chrX:75004797G>A	ENST00000373359.2	-	1	282	c.90C>T	c.(88-90)aaC>aaT	p.N30N		NM_138703.4	NP_619648.1	Q8TD90	MAGE2_HUMAN	melanoma antigen family E, 2	30								p.N30N(2)		autonomic_ganglia(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(5)|lung(17)|ovary(1)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	34						ACCCGGAGGCGTTAGTAGCTT	0.577																																					p.N30N												.	.	2	Substitution - coding silent(2)	large_intestine(1)|endometrium(1)	c.C90T	X						.						41.0	33.0	36.0					X																	75004797		2203	4299	6502	74921522	SO:0001819	synonymous_variant	139599	exon1			AF490509	CCDS14431.1	Xq13	2008-02-05			ENSG00000186675	ENSG00000186675			24935	protein-coding gene	gene with protein product		300760				11454705	Standard	NM_138703		Approved	HCA3	uc004ecj.2	Q8TD90	OTTHUMG00000021870	ENST00000373359.2:c.90C>T	X.37:g.75004797G>A		Somatic		Capture	Illumina HiSeq	Phase_I	74921522	NM_138703	Q5JSI5	Silent	SNP	ENST00000373359.2	37	CCDS14431.1																																																																																				0.577	MAGEE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057288.1	NM_138703	
FAM46D	169966	broad.mit.edu	37	X	79698516	79698516	+	Missense_Mutation	SNP	A	A	C			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chrX:79698516A>C	ENST00000308293.5	+	3	717	c.478A>C	c.(478-480)Aaa>Caa	p.K160Q	FAM46D_ENST00000538312.1_Missense_Mutation_p.K160Q	NM_152630.4	NP_689843.1	Q8NEK8	FA46D_HUMAN	family with sequence similarity 46, member D	160								p.K160Q(1)		kidney(1)|large_intestine(6)|liver(3)|lung(11)|ovary(1)|upper_aerodigestive_tract(1)	23						TTTAGAACTAAAATTTGTGAG	0.373																																					p.K160Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A478C	X						.						82.0	81.0	82.0					X																	79698516		2202	4299	6501	79585172	SO:0001583	missense	169966	exon5			BX537938	CCDS14446.1	Xq21.1	2009-08-18			ENSG00000174016	ENSG00000174016			28399	protein-coding gene	gene with protein product	"""cancer/testis antigen 112"""					12477932	Standard	NM_152630		Approved	MGC26999, CT1.26, CT112	uc004edl.1	Q8NEK8	OTTHUMG00000021902	ENST00000308293.5:c.478A>C	X.37:g.79698516A>C	ENSP00000308575:p.Lys160Gln	Somatic		Capture	Illumina HiSeq	Phase_I	79585172	NM_001170574	B2R9Q6|Q7Z3F6|Q8NHU1	Missense_Mutation	SNP	ENST00000308293.5	37	CCDS14446.1	.	.	.	.	.	.	.	.	.	.	A	15.02	2.710174	0.48517	.	.	ENSG00000174016	ENST00000538312;ENST00000308293	T;T	0.35236	1.32;1.32	4.8	4.8	0.61643	Domain of unknown function DUF1693 (1);	0.056200	0.64402	D	0.000001	T	0.63177	0.2489	M	0.88704	2.975	0.53688	D	0.999973	D	0.71674	0.998	D	0.66847	0.947	T	0.71041	-0.4707	10	0.87932	D	0	-17.8212	12.2722	0.54712	1.0:0.0:0.0:0.0	.	160	Q8NEK8	FA46D_HUMAN	Q	160	ENSP00000443410:K160Q;ENSP00000308575:K160Q	ENSP00000308575:K160Q	K	+	1	0	FAM46D	79585172	1.000000	0.71417	0.987000	0.45799	0.602000	0.36980	6.884000	0.75600	1.774000	0.52232	0.481000	0.45027	AAA		0.373	FAM46D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057338.1	NM_152630	
BRWD3	254065	broad.mit.edu	37	X	79979277	79979277	+	Frame_Shift_Del	DEL	A	A	-			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	A	A	A	-	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chrX:79979277delA	ENST00000373275.4	-	16	1836	c.1620delT	c.(1618-1620)tttfs	p.F540fs	BRWD3_ENST00000473691.1_5'Flank	NM_153252.4	NP_694984	Q6RI45	BRWD3_HUMAN	bromodomain and WD repeat domain containing 3	540					cytoskeleton organization (GO:0007010)|regulation of cell shape (GO:0008360)			p.F540fs*91(1)		breast(4)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(18)|lung(39)|ovary(4)|prostate(2)|skin(3)	87						ATCCAAAACCAAAAAGCAGCA	0.363																																					p.F540fs												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.1620delT	X						.						92.0	81.0	85.0					X																	79979277		2203	4300	6503	79865933	SO:0001589	frameshift_variant	254065	exon16				CCDS14447.1	Xq21.1	2013-01-09			ENSG00000165288	ENSG00000165288		"""WD repeat domain containing"""	17342	protein-coding gene	gene with protein product		300553				15543602, 16094372	Standard	NM_153252		Approved	FLJ38568, MRX93	uc004edt.3	Q6RI45	OTTHUMG00000021908	ENST00000373275.4:c.1620delT	X.37:g.79979277delA	ENSP00000362372:p.Phe540fs	Somatic		Capture	Illumina HiSeq	Phase_I	79865933	NM_153252	C9IZ39|C9J3F3|Q2T9J6|Q5JRN1|Q6RI37|Q6RI42|Q6RI44|Q8N916	Frame_Shift_Del	DEL	ENST00000373275.4	37	CCDS14447.1																																																																																				0.363	BRWD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057344.1	NM_153252	
KLHL4	56062	broad.mit.edu	37	X	86773204	86773204	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chrX:86773204A>G	ENST00000373119.4	+	1	453	c.308A>G	c.(307-309)aAt>aGt	p.N103S	KLHL4_ENST00000373114.4_Missense_Mutation_p.N103S	NM_019117.4	NP_061990.2	Q9C0H6	KLHL4_HUMAN	kelch-like family member 4	103						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)		p.N103S(1)		NS(1)|biliary_tract(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(19)|lung(29)|ovary(2)|prostate(1)|skin(1)	67						TTTCAAGCAAATGAAGATACT	0.428																																					p.N103S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A308G	X						.						62.0	61.0	61.0					X																	86773204		2203	4300	6503	86659860	SO:0001583	missense	56062	exon1			AF284765	CCDS14456.1, CCDS14457.1	Xq21.3	2013-01-30	2013-01-30		ENSG00000102271	ENSG00000102271		"""Kelch-like"", ""BTB/POZ domain containing"""	6355	protein-coding gene	gene with protein product		300348	"""kelch (Drosophila)-like 4"", ""kelch-like 4 (Drosophila)"""			11401425	Standard	NM_019117		Approved	KIAA1687, DKELCHL, KHL4	uc004efa.2	Q9C0H6	OTTHUMG00000021946	ENST00000373119.4:c.308A>G	X.37:g.86773204A>G	ENSP00000362211:p.Asn103Ser	Somatic		Capture	Illumina HiSeq	Phase_I	86659860	NM_057162	B2RTW2|Q9Y3J5	Missense_Mutation	SNP	ENST00000373119.4	37	CCDS14457.1	.	.	.	.	.	.	.	.	.	.	A	0.384	-0.926989	0.02377	.	.	ENSG00000102271	ENST00000373119;ENST00000373114	T;T	0.73681	-0.77;-0.73	5.05	5.05	0.67936	.	1.435160	0.04259	N	0.340137	T	0.55465	0.1922	N	0.11560	0.145	0.31552	N	0.658687	B;B	0.11235	0.004;0.001	B;B	0.09377	0.001;0.004	T	0.53315	-0.8456	10	0.09084	T	0.74	.	6.8884	0.24216	0.8201:0.0:0.1799:0.0	.	103;103	Q9C0H6;Q9C0H6-2	KLHL4_HUMAN;.	S	103	ENSP00000362211:N103S;ENSP00000362206:N103S	ENSP00000362206:N103S	N	+	2	0	KLHL4	86659860	1.000000	0.71417	1.000000	0.80357	0.733000	0.41908	1.511000	0.35801	1.861000	0.53984	0.417000	0.27973	AAT		0.428	KLHL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057413.1		
CLIC2	1193	broad.mit.edu	37	X	154507219	154507219	+	Silent	SNP	G	G	A	rs367873692		TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-A01R-01A-21W-A096-10	TCGA-AA-A01R-11A-12W-A096-10	g.chrX:154507219G>A	ENST00000369449.2	-	6	935	c.717C>T	c.(715-717)taC>taT	p.Y239Y	CLIC2_ENST00000465553.1_5'Flank	NM_001289.4	NP_001280.3	O15247	CLIC2_HUMAN	chloride intracellular channel 2	239	C-terminal.|GST C-terminal.				chloride transmembrane transport (GO:1902476)|negative regulation of ryanodine-sensitive calcium-release channel activity (GO:0060315)|oxidation-reduction process (GO:0055114)|positive regulation of binding (GO:0051099)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0010880)|signal transduction (GO:0007165)|transport (GO:0006810)	chloride channel complex (GO:0034707)|cytoplasm (GO:0005737)|intracellular (GO:0005622)|nucleus (GO:0005634)	chloride channel activity (GO:0005254)|glutathione peroxidase activity (GO:0004602)|voltage-gated chloride channel activity (GO:0005247)	p.Y239Y(2)		breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(6)|ovary(1)|prostate(1)|skin(1)	18	all_cancers(53;1.86e-17)|all_epithelial(53;2.71e-11)|all_lung(58;1.84e-07)|Lung NSC(58;5.62e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)|Renal(33;0.214)					CCACATTTGCGTAAGTATTTT	0.393													G|||	2	0.000529801	0.0015	0.0	3775	,	,		13397	0.0		0.0	False		,,,				2504	0.0				p.Y239Y	Melanoma(108;581 1592 2289 21669 28822)											.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.C717T	X						.	G		1,3834		0,1,1631,571	111.0	104.0	106.0		717	-0.5	0.5	X		106	0,6728		0,0,2428,1872	no	coding-synonymous	CLIC2	NM_001289.4		0,1,4059,2443	AA,AG,GG,G		0.0,0.0261,0.0095		239/248	154507219	1,10562	2203	4300	6503	154160413	SO:0001819	synonymous_variant	1193	exon6			AJ000217	CCDS14767.1	Xq28	2012-09-26			ENSG00000155962	ENSG00000155962		"""Ion channels / Chloride channels : Intracellular"""	2063	protein-coding gene	gene with protein product		300138				9339381	Standard	NM_001289		Approved	XAP121	uc004fnf.3	O15247	OTTHUMG00000022660	ENST00000369449.2:c.717C>T	X.37:g.154507219G>A		Somatic		Capture	Illumina HiSeq	Phase_I	154160413	NM_001289	A8K9S0|O15174|Q5JT80|Q8TCE3	Silent	SNP	ENST00000369449.2	37	CCDS14767.1																																																																																				0.393	CLIC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058793.1	NM_001289	
